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Sample records for biological parameters final

  1. Biological Parameters of Impact

    Science.gov (United States)

    1965-09-01

    zone between no effect and gross injury or death . For example, the pilot who survives an aircraft crash, but who is injured or unconscious so that he...Biological effects were limited to one incidence of bradycardia (116 t36 t and three instances of premature ventricular contractions. However. subjeCtiY" I...R.F.Chandler INTRODUCTION -Investigation of the biological effects of abrupt acceleration (impact) was stimulated by the advent of technical advances

  2. Telemetry System of Biological Parameters

    Directory of Open Access Journals (Sweden)

    Jan Spisak

    2005-01-01

    Full Text Available The mobile telemetry system of biological parameters serves for reading and wireless data transfer of measured values of selected biological parameters to an outlying computer. It concerns basically long time monitoring of vital function of car pilot.The goal of this projects is to propose mobile telemetry system for reading, wireless transfer and processing of biological parameters of car pilot during physical and psychical stress. It has to be made with respect to minimal consumption, weight and maximal device mobility. This system has to eliminate signal noise, which is created by biological artifacts and disturbances during the data transfer.

  3. Freshwater Biological Traits Database (Final Report)

    Science.gov (United States)

    EPA announced the release of the final report, Freshwater Biological Traits Database. This report discusses the development of a database of freshwater biological traits. The database combines several existing traits databases into an online format. The database is also...

  4. VISUALIZATION OF BIOLOGICAL TISSUE IMPEDANCE PARAMETERS

    Directory of Open Access Journals (Sweden)

    V. I. Bankov

    2016-01-01

    Full Text Available Objective. Investigation the opportunity for measurement of biological tissue impedance to visualize its parameters.Materials and methods. Studies were undertook on the experimental facility, consists of registrating measuring cell, constructed from flat inductors system, formed in oscillatory circuit, herewith investigated biological tissue is the part of this oscillatory circuit. An excitation of oscillatory circuit fulfilled by means of exciter inductor which forms impulse complex modulated electromagnetic field (ICM EMF. The measurement process and visualizations provided by set of certificated instruments: a digital oscillograph AKTAKOM ADS-2221MV, a digital generator АКТАКОМ AWG-4150 (both with software and a gauge RLC E7-22. Comparative dynamic studies of fixed volume and weight pig’s blood, adipose tissue, muscular tissue impedance were conducted by contact versus contactless methods. Contactless method in contrast to contact method gives opportunity to obtain the real morphological visualization of biological tissue irrespective of their nature.Results. Comparison of contact and contactless methods of impedance measurement shows that the inductance to capacitance ratio X(L / X(C was equal: 17 – for muscular tissue, 4 – for blood, 1 – for adipose tissue. It demonstrates the technical correspondence of both impedance registration methods. If propose the base relevance of X (L and X (C parameters for biological tissue impedance so contactless measurement method for sure shows insulating properties of adipose tissue and high conductivity for blood and muscular tissue in fixed volume-weight parameters. Registration of biological tissue impedance complex parameters by contactless method with the help of induced ICM EMF in fixed volume of biological tissue uncovers the most important informative volumes to characterize morphofunctional condition of biological tissue namely X (L / X (C.Conclusion. Contactless method of biological

  5. Parameter estimation and model selection in computational biology.

    Directory of Open Access Journals (Sweden)

    Gabriele Lillacci

    2010-03-01

    Full Text Available A central challenge in computational modeling of biological systems is the determination of the model parameters. Typically, only a fraction of the parameters (such as kinetic rate constants are experimentally measured, while the rest are often fitted. The fitting process is usually based on experimental time course measurements of observables, which are used to assign parameter values that minimize some measure of the error between these measurements and the corresponding model prediction. The measurements, which can come from immunoblotting assays, fluorescent markers, etc., tend to be very noisy and taken at a limited number of time points. In this work we present a new approach to the problem of parameter selection of biological models. We show how one can use a dynamic recursive estimator, known as extended Kalman filter, to arrive at estimates of the model parameters. The proposed method follows. First, we use a variation of the Kalman filter that is particularly well suited to biological applications to obtain a first guess for the unknown parameters. Secondly, we employ an a posteriori identifiability test to check the reliability of the estimates. Finally, we solve an optimization problem to refine the first guess in case it should not be accurate enough. The final estimates are guaranteed to be statistically consistent with the measurements. Furthermore, we show how the same tools can be used to discriminate among alternate models of the same biological process. We demonstrate these ideas by applying our methods to two examples, namely a model of the heat shock response in E. coli, and a model of a synthetic gene regulation system. The methods presented are quite general and may be applied to a wide class of biological systems where noisy measurements are used for parameter estimation or model selection.

  6. Bayesian parameter estimation for nonlinear modelling of biological pathways

    Directory of Open Access Journals (Sweden)

    Ghasemi Omid

    2011-12-01

    Full Text Available Abstract Background The availability of temporal measurements on biological experiments has significantly promoted research areas in systems biology. To gain insight into the interaction and regulation of biological systems, mathematical frameworks such as ordinary differential equations have been widely applied to model biological pathways and interpret the temporal data. Hill equations are the preferred formats to represent the reaction rate in differential equation frameworks, due to their simple structures and their capabilities for easy fitting to saturated experimental measurements. However, Hill equations are highly nonlinearly parameterized functions, and parameters in these functions cannot be measured easily. Additionally, because of its high nonlinearity, adaptive parameter estimation algorithms developed for linear parameterized differential equations cannot be applied. Therefore, parameter estimation in nonlinearly parameterized differential equation models for biological pathways is both challenging and rewarding. In this study, we propose a Bayesian parameter estimation algorithm to estimate parameters in nonlinear mathematical models for biological pathways using time series data. Results We used the Runge-Kutta method to transform differential equations to difference equations assuming a known structure of the differential equations. This transformation allowed us to generate predictions dependent on previous states and to apply a Bayesian approach, namely, the Markov chain Monte Carlo (MCMC method. We applied this approach to the biological pathways involved in the left ventricle (LV response to myocardial infarction (MI and verified our algorithm by estimating two parameters in a Hill equation embedded in the nonlinear model. We further evaluated our estimation performance with different parameter settings and signal to noise ratios. Our results demonstrated the effectiveness of the algorithm for both linearly and nonlinearly

  7. UC Merced Center for Computational Biology Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Colvin, Michael; Watanabe, Masakatsu

    2010-11-30

    Final report for the UC Merced Center for Computational Biology. The Center for Computational Biology (CCB) was established to support multidisciplinary scientific research and academic programs in computational biology at the new University of California campus in Merced. In 2003, the growing gap between biology research and education was documented in a report from the National Academy of Sciences, Bio2010 Transforming Undergraduate Education for Future Research Biologists. We believed that a new type of biological sciences undergraduate and graduate programs that emphasized biological concepts and considered biology as an information science would have a dramatic impact in enabling the transformation of biology. UC Merced as newest UC campus and the first new U.S. research university of the 21st century was ideally suited to adopt an alternate strategy - to create a new Biological Sciences majors and graduate group that incorporated the strong computational and mathematical vision articulated in the Bio2010 report. CCB aimed to leverage this strong commitment at UC Merced to develop a new educational program based on the principle of biology as a quantitative, model-driven science. Also we expected that the center would be enable the dissemination of computational biology course materials to other university and feeder institutions, and foster research projects that exemplify a mathematical and computations-based approach to the life sciences. As this report describes, the CCB has been successful in achieving these goals, and multidisciplinary computational biology is now an integral part of UC Merced undergraduate, graduate and research programs in the life sciences. The CCB began in fall 2004 with the aid of an award from U.S. Department of Energy (DOE), under its Genomes to Life program of support for the development of research and educational infrastructure in the modern biological sciences. This report to DOE describes the research and academic programs

  8. Effect of Ceramic Scaffold Architectural Parameters on Biological Response

    Directory of Open Access Journals (Sweden)

    Maria Isabella eGariboldi

    2015-10-01

    Full Text Available Numerous studies have focused on the optimization of ceramic architectures to fulfill a variety of scaffold functional requirements and improve biological response. Conventional fabrication techniques, however, do not allow for the production of geometrically controlled, reproducible structures and often fail to allow the independent variation of individual geometric parameters. Current developments in additive manufacturing technologies suggest that 3D printing will allow a more controlled and systematic exploration of scaffold architectures. This more direct translation of design into structure requires a pipeline for design-driven optimization. A theoretical framework for systematic design and evaluation of architectural parameters on biological response is presented. Four levels of architecture are considered, namely (1 surface topography, (2 pore size and geometry, (3 porous networks and (4 macroscopic pore arrangement, including the potential for spatially varied architectures. Studies exploring the effect of various parameters within these levels are reviewed. This framework will hopefully allow uncovering of new relationships between architecture and biological response in a more systematic way, as well as inform future refinement of fabrication techniques to fulfill architectural necessities with a consideration of biological implications.

  9. Effect of Ceramic Scaffold Architectural Parameters on Biological Response.

    Science.gov (United States)

    Gariboldi, Maria Isabella; Best, Serena M

    2015-01-01

    Numerous studies have focused on the optimization of ceramic architectures to fulfill a variety of scaffold functional requirements and improve biological response. Conventional fabrication techniques, however, do not allow for the production of geometrically controlled, reproducible structures and often fail to allow the independent variation of individual geometric parameters. Current developments in additive manufacturing technologies suggest that 3D printing will allow a more controlled and systematic exploration of scaffold architectures. This more direct translation of design into structure requires a pipeline for design-driven optimization. A theoretical framework for systematic design and evaluation of architectural parameters on biological response is presented. Four levels of architecture are considered, namely (1) surface topography, (2) pore size and geometry, (3) porous networks, and (4) macroscopic pore arrangement, including the potential for spatially varied architectures. Studies exploring the effect of various parameters within these levels are reviewed. This framework will hopefully allow uncovering of new relationships between architecture and biological response in a more systematic way as well as inform future refinement of fabrication techniques to fulfill architectural necessities with a consideration of biological implications.

  10. Measuring Biological Parameters in Rivers: Relevance of the Spatial Scale

    Energy Technology Data Exchange (ETDEWEB)

    Romani, A. M.

    2009-07-01

    The analyses of biological parameters in river ecosystems have been traditionally used as indicative of water quality with the advantage over chemical or physical analyses that they integrate the effects of punctual as well as long term effects. However, analyses of biological parameters (such as biomass and metabolism) performed at different spatial scales (from the microbial communities to the whole river) inform about different key processes. At the finer scale, microbial interactions and the structure of the microbial community (biofilm microbial biomass, three dimensional structure, and relevance of polysaccharide matrix) can be detected. At the reach scale, the different stream bed substrate (sediment, rocks, and particulate organic matter accumulation) are shown to play differential and specific roles on the processing of organic and inorganic materials in the flowing water. (Author)

  11. On linear models and parameter identifiability in experimental biological systems.

    Science.gov (United States)

    Lamberton, Timothy O; Condon, Nicholas D; Stow, Jennifer L; Hamilton, Nicholas A

    2014-10-07

    A key problem in the biological sciences is to be able to reliably estimate model parameters from experimental data. This is the well-known problem of parameter identifiability. Here, methods are developed for biologists and other modelers to design optimal experiments to ensure parameter identifiability at a structural level. The main results of the paper are to provide a general methodology for extracting parameters of linear models from an experimentally measured scalar function - the transfer function - and a framework for the identifiability analysis of complex model structures using linked models. Linked models are composed by letting the output of one model become the input to another model which is then experimentally measured. The linked model framework is shown to be applicable to designing experiments to identify the measured sub-model and recover the input from the unmeasured sub-model, even in cases that the unmeasured sub-model is not identifiable. Applications for a set of common model features are demonstrated, and the results combined in an example application to a real-world experimental system. These applications emphasize the insight into answering "where to measure" and "which experimental scheme" questions provided by both the parameter extraction methodology and the linked model framework. The aim is to demonstrate the tools' usefulness in guiding experimental design to maximize parameter information obtained, based on the model structure.

  12. Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems

    Directory of Open Access Journals (Sweden)

    Banga Julio R

    2006-11-01

    Full Text Available Abstract Background We consider the problem of parameter estimation (model calibration in nonlinear dynamic models of biological systems. Due to the frequent ill-conditioning and multi-modality of many of these problems, traditional local methods usually fail (unless initialized with very good guesses of the parameter vector. In order to surmount these difficulties, global optimization (GO methods have been suggested as robust alternatives. Currently, deterministic GO methods can not solve problems of realistic size within this class in reasonable computation times. In contrast, certain types of stochastic GO methods have shown promising results, although the computational cost remains large. Rodriguez-Fernandez and coworkers have presented hybrid stochastic-deterministic GO methods which could reduce computation time by one order of magnitude while guaranteeing robustness. Our goal here was to further reduce the computational effort without loosing robustness. Results We have developed a new procedure based on the scatter search methodology for nonlinear optimization of dynamic models of arbitrary (or even unknown structure (i.e. black-box models. In this contribution, we describe and apply this novel metaheuristic, inspired by recent developments in the field of operations research, to a set of complex identification problems and we make a critical comparison with respect to the previous (above mentioned successful methods. Conclusion Robust and efficient methods for parameter estimation are of key importance in systems biology and related areas. The new metaheuristic presented in this paper aims to ensure the proper solution of these problems by adopting a global optimization approach, while keeping the computational effort under reasonable values. This new metaheuristic was applied to a set of three challenging parameter estimation problems of nonlinear dynamic biological systems, outperforming very significantly all the methods previously

  13. Measurement of the Acoustic Nonlinearity Parameter for Biological Media.

    Science.gov (United States)

    Cobb, Wesley Nelson

    In vitro measurements of the acoustic nonlinearity parameter are presented for several biological media. With these measurements it is possible to predict the distortion of a finite amplitude wave in biological tissues of current diagnostic and research interest. The measurement method is based on the finite amplitude distortion of a sine wave that is emmitted by a piston source. The growth of the second harmonic component of this wave is measured by a piston receiver which is coaxial with and has the same size as the source. The experimental measurements and theory are compared in order to determine the nonlinearity parameter. The density, sound speed, and attenuation for the medium are determined in order to make this comparison. The theory developed for this study accounts for the influence of both diffraction and attenuation on the experimental measurements. The effects of dispersion, tissue inhomogeneity and gas bubbles within the excised tissues are studied. To test the measurement method, experimental results are compared with established values for the nonlinearity parameter of distilled water, ethylene glycol and glycerol. The agreement between these values suggests that the measurement uncertainty is (+OR-) 5% for liquids and (+OR-) 10% for solid tissues. Measurements are presented for dog blood and bovine serum albumen as a function of concentration. The nonlinearity parameters for liver, kidney and spleen are reported for both human and canine tissues. The values for the fresh tissues displayed little variation (6.8 to 7.8). Measurements for fixed, normal and cirrhotic tissues indicated that the nonlinearity parameter does not depend strongly on pathology. However, the values for fixed tissues were somewhat higher than those of the fresh tissues.

  14. Translating biological parameters into clinically useful diagnostic tests.

    Science.gov (United States)

    Arfken, Cynthia L; Carney, Stuart; Boutros, Nash N

    2009-08-01

    Psychiatry has lagged behind other specialties in developing diagnostic laboratory tests for the purpose of confirming or ruling out a diagnosis. Biological research into the pathophysiology of psychiatric disorders has, however, yielded some highly replicable abnormalities that have the potential for development into clinically useful diagnostic tests. To achieve this goal, a process for systematic translation must be developed and implemented. Building on our previous work, we review a proposed process using four clearly defined steps. We conclude that biological parameters currently face challenges in their pathways to becoming diagnostic tests because of both the premature release and premature abandonment of tests. Attention to a systematic translation process aided by these principles may help to avoid these problems.

  15. The extraction of parameters from final state interactions

    CERN Document Server

    Faldt, G

    2016-01-01

    It is argued that final state enhancements in production reactions at large momentum transfers, such as pp -> K^+ Lambda p, are primarily sensitive to the position of a virtual bound state pole in the Lambda p system rather than the Lambda p scattering length and effective range. These arguments are supported by a study of the dispersion relation derived to describe such processes as a function of the cut-off energy. This shows that the position of the virtual bound state is independent of the cut-off energy.

  16. Process efficiency simulation for key process parameters in biological methanogenesis

    Directory of Open Access Journals (Sweden)

    Sébastien Bernacchi

    2014-09-01

    Full Text Available New generation biofuels are a suitable approach to produce energy carriers in an almost CO2 neutral way. A promising reaction is the conversion of CO2 and H2 to CH4. This contribution aims at elucidating a bioprocess comprised of a core reaction unit using microorganisms from the Archaea life domain, which metabolize CO2 and H2 to CH4, followed by a gas purification step. The process is simulated and analyzed thermodynamically using the Aspen Plus process simulation environment. The goal of the study was to quantify effects of process parameters on overall process efficiency using a kinetic model derived from previously published experimental results. The used empirical model links the production rate of CH4 and biomass to limiting reactant concentrations. In addition, Aspen Plus was used to improve bioprocess quantification. Impacts of pressure as well as dilution of reactant gas with up to 70% non-reactive gas on overall process efficiency was evaluated. Pressure in the reactor unit of 11 bar at 65℃ with a pressure of 21 bar for gas purification led to an overall process efficiency comprised between 66% and 70% for gaseous product and between 73% and 76% if heat of compression is considered a valuable product. The combination of 2 bar pressure in the reactor and 21 bar for purification was the most efficient combination of parameters. This result shows Aspen Plus potential for similar bioprocess development as it accounts for the energetic aspect of the entire process. In fact, the optimum for the overall process efficiency was found to differ from the optimum of the reaction unit. High efficiency of over 70% demonstrates that biological methanogenesis is a promising alternative for a chemical methanation reaction.

  17. On the modeling of internal parameters in hyperelastic biological materials

    CERN Document Server

    Giantesio, Giulia

    2016-01-01

    This paper concerns the behavior of hyperelastic energies depending on an internal parameter. First, the situation in which the internal parameter is a function of the gradient of the deformation is presented. Second, two models where the parameter describes the activation of skeletal muscle tissue are analyzed. In those models, the activation parameter depends on the strain and it is important to consider the derivative of the parameter with respect to the strain in order to capture the proper behavior of the stress.

  18. Parameter estimation method for improper fractional models and its application to molecular biological systems.

    Science.gov (United States)

    Tian, Li-Ping; Liu, Lizhi; Wu, Fang-Xiang

    2010-01-01

    Derived from biochemical principles, molecular biological systems can be described by a group of differential equations. Generally these differential equations contain fractional functions plus polynomials (which we call improper fractional model) as reaction rates. As a result, molecular biological systems are nonlinear in both parameters and states. It is well known that it is challenging to estimate parameters nonlinear in a model. However, in fractional functions both the denominator and numerator are linear in the parameters while polynomials are also linear in parameters. Based on this observation, we develop an iterative linear least squares method for estimating parameters in biological systems modeled by improper fractional functions. The basic idea is to transfer optimizing a nonlinear least squares objective function into iteratively solving a sequence of linear least squares problems. The developed method is applied to the estimation of parameters in a metabolism system. The simulation results show the superior performance of the proposed method for estimating parameters in such molecular biological systems.

  19. Biological upgrading of coal-derived synthesis gas: Final report

    Energy Technology Data Exchange (ETDEWEB)

    Barik, S.; Johnson, E.R.; Ko, C.W.; Clausen, E.C.; Gaddy, J.L.

    1986-10-01

    The technical feasibility of the biological conversion of coal synthesis gas to methane has been demonstrated in the University of Arkansas laboratories. Cultures of microorganisms have been developed which achieve total conversion in the water gas shift and methanation reactions in either mixed or pure cultures. These cultures carry out these conversions at ordinary temperatures and pressures, without sulfur toxicity. Several microorganisms have been identified as having commercial potential for producing methane. These include a mixed culture of unidentified bacteria; P. productus which produces acetate, a methane precursor; and Methanothrix sp., which produces methane from acetate. These cultures have been used in mixed reactors and immobilized cell reactors to achieve total CO and H/sub 2/ conversion in a retention time of less than two hours, quite good for a biological reactor. Preliminary economic projections indicate that a biological methanation plant with a size of 5 x 10/sup 10/ Btu/day can be economically attractive. 42 refs., 26 figs., 86 tabs.

  20. Grays River Watershed and Biological Assessment, 2006 Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    May, Christopher; Geist, David [Pacific Northwest National Laboratory

    2007-04-01

    The Grays River Watershed and Biological Assessment was funded to address degradation and loss of spawning habitat for chum salmon (Onchorhynchus keta) and fall Chinook salmon (Onchoryhnchus tshawytscha). In 1999, the National Marine Fisheries Service listed lower Columbia River chum salmon as a threatened Evolutionarily Significant Unit (ESU) under the Endangered Species Act of 1973 (ESA). The Grays River watershed is one of two remaining significant chum salmon spawning locations in this ESU. Runs of Grays River chum and Chinook salmon have declined significantly during the past century, largely because of damage to spawning habitat associated with timber harvest and agriculture in the watershed. In addition, approximately 20-25% of the then-remaining chum salmon spawning habitat was lost during a 1999 channel avulsion that destroyed an important artificial spawning channel operated by the Washington Department of Fish and Wildlife (WDFW). Although the lack of stable, high-quality spawning habitat is considered the primary physical limitation on Grays River chum salmon production today, few data are available to guide watershed management and channel restoration activities. The objectives of the Grays River Watershed and Biological Assessment project were to (1) perform a comprehensive watershed and biological analysis, including hydrologic, geomorphic, and ecological assessments; (2) develop a prioritized list of actions that protect and restore critical chum and Chinook salmon spawning habitat in the Grays River based on comprehensive geomorphic, hydrologic, and stream channel assessments; and (3) gain a better understanding of chum and Chinook salmon habitat requirements and survival within the lower Columbia River and the Grays River. The watershed-based approach to river ecosystem restoration relies on a conceptual framework that describes general relationships between natural landscape characteristics, watershed-scale habitat-forming processes, aquatic

  1. Grays River Watershed and Biological Assessment Final Report 2006.

    Energy Technology Data Exchange (ETDEWEB)

    May, Christopher W.; McGrath, Kathleen E.; Geist, David R. [Pacific Northwest National Laboratory; Abbe, Timothy; Barton, Chase [Herrera Environmental Consultants, Inc.

    2008-02-04

    The Grays River Watershed and Biological Assessment was funded to address degradation and loss of spawning habitat for chum salmon (Onchorhynchus keta) and fall Chinook salmon (Onchoryhnchus tshawytscha). In 1999, the National Marine Fisheries Service listed lower Columbia River chum salmon as a threatened Evolutionarily Significant Unit (ESU) under the Endangered Species Act of 1973 (ESA). The Grays River watershed is one of two remaining significant chum salmon spawning locations in this ESU. Runs of Grays River chum and Chinook salmon have declined significantly during the past century, largely because of damage to spawning habitat associated with timber harvest and agriculture in the watershed. In addition, approximately 20-25% of the then-remaining chum salmon spawning habitat was lost during a 1999 channel avulsion that destroyed an important artificial spawning channel operated by the Washington Department of Fish and Wildlife (WDFW). Although the lack of stable, high-quality spawning habitat is considered the primary physical limitation on Grays River chum salmon production today, few data are available to guide watershed management and channel restoration activities. The objectives of the Grays River Watershed and Biological Assessment project were to (1) perform a comprehensive watershed and biological analysis, including hydrologic, geomorphic, and ecological assessments; (2) develop a prioritized list of actions that protect and restore critical chum and Chinook salmon spawning habitat in the Grays River based on comprehensive geomorphic, hydrologic, and stream channel assessments; and (3) gain a better understanding of chum and Chinook salmon habitat requirements and survival within the lower Columbia River and the Grays River. The watershed-based approach to river ecosystem restoration relies on a conceptual framework that describes general relationships between natural landscape characteristics, watershed-scale habitat-forming processes, aquatic

  2. Grays River Watershed and Biological Assessment, 2006 Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    May, Christopher; Geist, David [Pacific Northwest National Laboratory

    2007-04-01

    The Grays River Watershed and Biological Assessment was funded to address degradation and loss of spawning habitat for chum salmon (Onchorhynchus keta) and fall Chinook salmon (Onchoryhnchus tshawytscha). In 1999, the National Marine Fisheries Service listed lower Columbia River chum salmon as a threatened Evolutionarily Significant Unit (ESU) under the Endangered Species Act of 1973 (ESA). The Grays River watershed is one of two remaining significant chum salmon spawning locations in this ESU. Runs of Grays River chum and Chinook salmon have declined significantly during the past century, largely because of damage to spawning habitat associated with timber harvest and agriculture in the watershed. In addition, approximately 20-25% of the then-remaining chum salmon spawning habitat was lost during a 1999 channel avulsion that destroyed an important artificial spawning channel operated by the Washington Department of Fish and Wildlife (WDFW). Although the lack of stable, high-quality spawning habitat is considered the primary physical limitation on Grays River chum salmon production today, few data are available to guide watershed management and channel restoration activities. The objectives of the Grays River Watershed and Biological Assessment project were to (1) perform a comprehensive watershed and biological analysis, including hydrologic, geomorphic, and ecological assessments; (2) develop a prioritized list of actions that protect and restore critical chum and Chinook salmon spawning habitat in the Grays River based on comprehensive geomorphic, hydrologic, and stream channel assessments; and (3) gain a better understanding of chum and Chinook salmon habitat requirements and survival within the lower Columbia River and the Grays River. The watershed-based approach to river ecosystem restoration relies on a conceptual framework that describes general relationships between natural landscape characteristics, watershed-scale habitat-forming processes, aquatic

  3. Grays River Watershed and Biological Assessment Final Report 2006.

    Energy Technology Data Exchange (ETDEWEB)

    May, Christopher W.; McGrath, Kathleen E.; Geist, David R. [Pacific Northwest National Laboratory; Abbe, Timothy; Barton, Chase [Herrera Environmental Consultants, Inc.

    2008-02-04

    The Grays River Watershed and Biological Assessment was funded to address degradation and loss of spawning habitat for chum salmon (Onchorhynchus keta) and fall Chinook salmon (Onchoryhnchus tshawytscha). In 1999, the National Marine Fisheries Service listed lower Columbia River chum salmon as a threatened Evolutionarily Significant Unit (ESU) under the Endangered Species Act of 1973 (ESA). The Grays River watershed is one of two remaining significant chum salmon spawning locations in this ESU. Runs of Grays River chum and Chinook salmon have declined significantly during the past century, largely because of damage to spawning habitat associated with timber harvest and agriculture in the watershed. In addition, approximately 20-25% of the then-remaining chum salmon spawning habitat was lost during a 1999 channel avulsion that destroyed an important artificial spawning channel operated by the Washington Department of Fish and Wildlife (WDFW). Although the lack of stable, high-quality spawning habitat is considered the primary physical limitation on Grays River chum salmon production today, few data are available to guide watershed management and channel restoration activities. The objectives of the Grays River Watershed and Biological Assessment project were to (1) perform a comprehensive watershed and biological analysis, including hydrologic, geomorphic, and ecological assessments; (2) develop a prioritized list of actions that protect and restore critical chum and Chinook salmon spawning habitat in the Grays River based on comprehensive geomorphic, hydrologic, and stream channel assessments; and (3) gain a better understanding of chum and Chinook salmon habitat requirements and survival within the lower Columbia River and the Grays River. The watershed-based approach to river ecosystem restoration relies on a conceptual framework that describes general relationships between natural landscape characteristics, watershed-scale habitat-forming processes, aquatic

  4. Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology (Final Report)

    Science.gov (United States)

    EPA announced the release of the final report, Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology. This report describes new approaches that are faster, less resource intensive, and more robust that can help ...

  5. Retrieving the optical parameters of biological tissues using diffuse reflectance spectroscopy and Fourier series expansions. I. theory and application.

    Science.gov (United States)

    Muñoz Morales, Aarón A; Vázquez Y Montiel, Sergio

    2012-10-01

    The determination of optical parameters of biological tissues is essential for the application of optical techniques in the diagnosis and treatment of diseases. Diffuse Reflection Spectroscopy is a widely used technique to analyze the optical characteristics of biological tissues. In this paper we show that by using diffuse reflectance spectra and a new mathematical model we can retrieve the optical parameters by applying an adjustment of the data with nonlinear least squares. In our model we represent the spectra using a Fourier series expansion finding mathematical relations between the polynomial coefficients and the optical parameters. In this first paper we use spectra generated by the Monte Carlo Multilayered Technique to simulate the propagation of photons in turbid media. Using these spectra we determine the behavior of Fourier series coefficients when varying the optical parameters of the medium under study. With this procedure we find mathematical relations between Fourier series coefficients and optical parameters. Finally, the results show that our method can retrieve the optical parameters of biological tissues with accuracy that is adequate for medical applications.

  6. FY05 LDRD Final Report, A Revolution in Biological Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Chapman, H N; Bajt, S; Balhorn, R; Barty, A; Barsky, D; Bogan, M; Chung, S; Frank, M; Hau-Riege, S; Ishii, H; London, R; Marchesini, S; Noy, A; Segelke, B; Szoke, A; Szoke, H; Trebes, J; Wootton, A; Hajdu, J; Bergh, M; Caleman, C; Huldt, G; Lejon, S; der Spoel, D v; Howells, M; He, H; Spence, J; Nugent, K; Ingerman, E

    2006-01-20

    X-ray free-electron lasers (XFELs) are currently under development and will provide a peak brightness more than 10 orders of magnitude higher than modern synchrotrons. The goal of this project was to perform the fundamental research to evaluate the possibility of harnessing these unique x-ray sources to image single biological particles and molecules at atomic resolution. Using a combination of computational modeling and experimental verification where possible, they showed that it should indeed be possible to record coherent scattering patterns from single molecules with pulses that are shorter than the timescales for the degradation of the structure due to the interaction with those pulses. They used these models to determine the effectiveness of strategies to allow imaging using longer XFEL pulses and to design validation experiments to be carried out at interim ultrafast sources. They also developed and demonstrated methods to recover three-dimensional (3D) images from coherent diffraction patterns, similar to those expected from XFELs. The images of micron-sized test objects are the highest-resolution 3D images of any noncrystalline material ever formed with x-rays. The project resulted in 14 publications in peer-reviewed journals and four records of invention.

  7. Biological production of ethanol from coal. Final report

    Energy Technology Data Exchange (ETDEWEB)

    1992-12-01

    Due to the abundant supply of coal in the United States, significant research efforts have occurred over the past 15 years concerning the conversion of coal to liquid fuels. Researchers at the University of Arkansas have concentrated on a biological approach to coal liquefaction, starting with coal-derived synthesis gas as the raw material. Synthesis gas, a mixture of CO, H{sub 2}, CO{sub 2}, CH{sub 4} and sulfur gases, is first produced using traditional gasification techniques. The CO, CO{sub 2} and H{sub 2} are then converted to ethanol using a bacterial culture of Clostridium 1jungdahlii. Ethanol is the desired product if the resultant product stream is to be used as a liquid fuel. However, under normal operating conditions, the ``wild strain`` produces acetate in favor of ethanol in conjunction with growth in a 20:1 molar ratio. Research was performed to determine the conditions necessary to maximize not only the ratio of ethanol to acetate, but also to maximize the concentration of ethanol resulting in the product stream.

  8. Verbal Final Exam in Introductory Biology Yields Gains in Student Content Knowledge and Longitudinal Performance

    Science.gov (United States)

    Luckie, Douglas B.; Rivkin, Aaron M.; Aubry, Jacob R.; Marengo, Benjamin J.; Creech, Leah R.; Sweeder, Ryan D.

    2013-01-01

    We studied gains in student learning over eight semesters in which an introductory biology course curriculum was changed to include optional verbal final exams (VFs). Students could opt to demonstrate their mastery of course material via structured oral exams with the professor. In a quantitative assessment of cell biology content knowledge,…

  9. Molecular biological enhancement of coal biodesulfurization. Final technical report

    Energy Technology Data Exchange (ETDEWEB)

    Litchfield, J.H.; Zupancic, T.J.; Kittle, J.D. Jr.; Baker, B.; Palmer, D.T.; Traunero, C.G.; Wyza, R.E.; Schweitzer, A.; Conkle, H.N. [Battelle, Columbus, OH (United States); Chakravarty, L.; Tuovinen, O.H. [Ohio State Univ., Columbus, OH (United States)

    1992-10-08

    Progress is reported in understanding Thiobacillus molecular biology, specifically in the area of vector development. At the initiation of this program, the basic elements needed for performing genetic engineering in T. ferrooxidans were either not yet developed. Improved techniques are described which will make it easier to construct and analyze the genetic structure and metabolism of recombinant T. ferrooxidans. The metabolism of the model organic sulfur compound dibenzothiophene (DBT) by certain heterotrophic bacteria was confirmed and characterized. Techniques were developed to analyze the metabolites of DBT, so that individual 4S pathway metabolites could be distinguished. These techniques are expected to be valuable when engineering organic sulfur metabolism in Thiobacillus. Strain isolation techniques were used to develop pure cultures of T. ferrooxidans seven of which were assessed as potential recombinant hosts. The mixotrophic strain T. coprinus was also characterized for potential use as an electroporation host. A family of related Thiobacillus plasmids was discovered in the seven strains of P. ferrooxidans mentioned above. One of these plasmids, pTFI91, was cloned into a pUC-based plasmid vector, allowing it to propagate in E. coli. A key portion of the cloned plasmid was sequenced. This segment, which is conserved in all of the related plasmids characterized, contains the vegetative origin of DNA replication, and fortuitously, a novel insertion sequence, designated IS3091. The sequence of the DNA origin revealed that these Thiobacillus plasmids represent a unique class of replicons not previously described. The potentially useful insertion sequence IS3091 was identified as a new member of a previously undefined family of insertion sequences which include the E. coli element IS30.

  10. Harbour porpoises (Phocoena phocoena in the North Atlantic: Biological parameters

    Directory of Open Access Journals (Sweden)

    Christina Lockyer

    2003-07-01

    Information on age-related parameters, reproduction and growth is presented and assessed by region and/or population, of which there may be 14 throughout the North Atlantic. Among age related parameters, maximum longevity recorded is 24 years; maximal rate of population growth is probably 9.4% but in the range 5-10%; mortality is highest in year 1, and 3 years; ovulation rates fall in the range 0.64 - 0.988 corpus per year, and reproductive interval is 1.01-1.57 years; pregnancy rates are generally in the range 0.74 - 0.986 per year, meaning that not all females produce a calf every year; there is seasonal breeding/mating in the period June–August; gestation lasts 10-11 months; parturition generally occurs between mid-May to mid-July; duration of lactation is uncertain, but is probably at least 8 months; size at birth is usually in the range 65-75 cm with a maximum size of about 80 cm. Sex ratio is biased to males throughout life: 1.1-1.2 males : 1.0 females in the foetal stage, and 1.1-1.7 males : 1.0 females post-natal. Growth parameters indicate an asymptotic length and weight that varies with population, but usually falls in the range 153-163 cm and 55-65 kg for females and 141-149 cm and 46-51 kg for males. Growth models used for length and weight are typically based on von Bertalanffy and Gompertz models. Length at sexual maturity also varies with population, but is usually in the range 138-147 cm for females and 127-135 cm for males. There is no information based on vertebral epiphyseal fusion to indicate age at physical maturity. Foetal growth appears normal, but there is uncertainty about the existence of embryonic diapause. Size/age at weaning are uncertain, but size may be 8 months; however, entirely independent feeding may not occur until about 10 months.

  11. Fuzzy Stochastic Petri Nets for Modeling Biological Systems with Uncertain Kinetic Parameters.

    Science.gov (United States)

    Liu, Fei; Heiner, Monika; Yang, Ming

    2016-01-01

    Stochastic Petri nets (SPNs) have been widely used to model randomness which is an inherent feature of biological systems. However, for many biological systems, some kinetic parameters may be uncertain due to incomplete, vague or missing kinetic data (often called fuzzy uncertainty), or naturally vary, e.g., between different individuals, experimental conditions, etc. (often called variability), which has prevented a wider application of SPNs that require accurate parameters. Considering the strength of fuzzy sets to deal with uncertain information, we apply a specific type of stochastic Petri nets, fuzzy stochastic Petri nets (FSPNs), to model and analyze biological systems with uncertain kinetic parameters. FSPNs combine SPNs and fuzzy sets, thereby taking into account both randomness and fuzziness of biological systems. For a biological system, SPNs model the randomness, while fuzzy sets model kinetic parameters with fuzzy uncertainty or variability by associating each parameter with a fuzzy number instead of a crisp real value. We introduce a simulation-based analysis method for FSPNs to explore the uncertainties of outputs resulting from the uncertainties associated with input parameters, which works equally well for bounded and unbounded models. We illustrate our approach using a yeast polarization model having an infinite state space, which shows the appropriateness of FSPNs in combination with simulation-based analysis for modeling and analyzing biological systems with uncertain information.

  12. Environmental parameters of the Tennessee River in Alabama. 2: Physical, chemical, and biological parameters. [biological and chemical effects of thermal pollution from nuclear power plants on water quality

    Science.gov (United States)

    Rosing, L. M.

    1976-01-01

    Physical, chemical and biological water quality data from five sites in the Tennessee River, two in Guntersville Reservoir and three in Wheeler Reservoir were correlated with climatological data for three annual cycles. Two of the annual cycles are for the years prior to the Browns Ferry Nuclear Power Plant operations and one is for the first 14 months of Plant operations. A comparison of the results of the annual cycles indicates that two distinct physical conditions in the reservoirs occur, one during the warm months when the reservoirs are at capacity and one during the colder winter months when the reservoirs have been drawn-down for water storage during the rainy months and for weed control. The wide variations of physical and chemical parameters to which the biological organisms are subjected on an annual basis control the biological organisms and their population levels. A comparison of the parameters of the site below the Power plant indicates that the heated effluent from the plant operating with two of the three reactors has not had any effect on the organisms at this site. Recommendations given include the development of prediction mathematical models (statistical analysis) for the physical and chemical parameters under specific climatological conditions which affect biological organisms. Tabulated data of chemical analysis of water and organism populations studied is given.

  13. A direct method for computing extreme value (Gumbel) parameters for gapped biological sequence alignments.

    Science.gov (United States)

    Quinn, Terrance; Sinkala, Zachariah

    2014-01-01

    We develop a general method for computing extreme value distribution (Gumbel, 1958) parameters for gapped alignments. Our approach uses mixture distribution theory to obtain associated BLOSUM matrices for gapped alignments, which in turn are used for determining significance of gapped alignment scores for pairs of biological sequences. We compare our results with parameters already obtained in the literature.

  14. Physico-Chemical and Biological Parameters of the Three Rural Ponds of Sasaram of Bihar

    Directory of Open Access Journals (Sweden)

    Jyoti Choudhary

    2014-06-01

    Full Text Available Physico chemical and biological parameters of the three rural pond of Sasaram,Bihar has been studied to see the present condition for its better utilization. The study revealed that parameters are within permissible limit for fish culture and the stocking should be done as per the productivity of the water. As per the BOD estimation the ponds falls under moderately polluted category.

  15. Bayesian parameter inference and model selection by population annealing in systems biology.

    Science.gov (United States)

    Murakami, Yohei

    2014-01-01

    Parameter inference and model selection are very important for mathematical modeling in systems biology. Bayesian statistics can be used to conduct both parameter inference and model selection. Especially, the framework named approximate Bayesian computation is often used for parameter inference and model selection in systems biology. However, Monte Carlo methods needs to be used to compute Bayesian posterior distributions. In addition, the posterior distributions of parameters are sometimes almost uniform or very similar to their prior distributions. In such cases, it is difficult to choose one specific value of parameter with high credibility as the representative value of the distribution. To overcome the problems, we introduced one of the population Monte Carlo algorithms, population annealing. Although population annealing is usually used in statistical mechanics, we showed that population annealing can be used to compute Bayesian posterior distributions in the approximate Bayesian computation framework. To deal with un-identifiability of the representative values of parameters, we proposed to run the simulations with the parameter ensemble sampled from the posterior distribution, named "posterior parameter ensemble". We showed that population annealing is an efficient and convenient algorithm to generate posterior parameter ensemble. We also showed that the simulations with the posterior parameter ensemble can, not only reproduce the data used for parameter inference, but also capture and predict the data which was not used for parameter inference. Lastly, we introduced the marginal likelihood in the approximate Bayesian computation framework for Bayesian model selection. We showed that population annealing enables us to compute the marginal likelihood in the approximate Bayesian computation framework and conduct model selection depending on the Bayes factor.

  16. Relationship between the temperature and the acoustic nonlinearity parameter in biological tissues

    Institute of Scientific and Technical Information of China (English)

    LU Ying; LIU Xiaozhou; GONG Xiufen; ZHANG Dong

    2004-01-01

    Recently with the rapid development of the high-intensity focused ultrasound (HIFU) in biomedical ultrasound, much attention has been paid to the noninvasive temperature estimation in biological tissue in order to determine the region and degree of the ultrasound-induced lesions. In ultrasound hyperthermal therapy it is highly desirable to study the real-time noninvasive monitoring of temperature distribution in biological tissue. In this paper, the relationship between the nonlinearity parameter B/A and the temperature in biological tissue is studied and compared with the theoretical model as well as the experimental results from the thermocouple. Results indicated that B/A could be used as an effective tool to monitor the temperature distribution in biological media.

  17. Monte Carlo evaluation of biological variation: Random generation of correlated non-Gaussian model parameters

    Science.gov (United States)

    Hertog, Maarten L. A. T. M.; Scheerlinck, Nico; Nicolaï, Bart M.

    2009-01-01

    When modelling the behaviour of horticultural products, demonstrating large sources of biological variation, we often run into the issue of non-Gaussian distributed model parameters. This work presents an algorithm to reproduce such correlated non-Gaussian model parameters for use with Monte Carlo simulations. The algorithm works around the problem of non-Gaussian distributions by transforming the observed non-Gaussian probability distributions using a proposed SKN-distribution function before applying the covariance decomposition algorithm to generate Gaussian random co-varying parameter sets. The proposed SKN-distribution function is based on the standard Gaussian distribution function and can exhibit different degrees of both skewness and kurtosis. This technique is demonstrated using a case study on modelling the ripening of tomato fruit evaluating the propagation of biological variation with time.

  18. A termination criterion for parameter estimation in stochastic models in systems biology.

    Science.gov (United States)

    Zimmer, Christoph; Sahle, Sven

    2015-11-01

    Parameter estimation procedures are a central aspect of modeling approaches in systems biology. They are often computationally expensive, especially when the models take stochasticity into account. Typically parameter estimation involves the iterative optimization of an objective function that describes how well the model fits some measured data with a certain set of parameter values. In order to limit the computational expenses it is therefore important to apply an adequate stopping criterion for the optimization process, so that the optimization continues at least until a reasonable fit is obtained, but not much longer. In the case of stochastic modeling, at least some parameter estimation schemes involve an objective function that is itself a random variable. This means that plain convergence tests are not a priori suitable as stopping criteria. This article suggests a termination criterion suited to optimization problems in parameter estimation arising from stochastic models in systems biology. The termination criterion is developed for optimization algorithms that involve populations of parameter sets, such as particle swarm or evolutionary algorithms. It is based on comparing the variance of the objective function over the whole population of parameter sets with the variance of repeated evaluations of the objective function at the best parameter set. The performance is demonstrated for several different algorithms. To test the termination criterion we choose polynomial test functions as well as systems biology models such as an Immigration-Death model and a bistable genetic toggle switch. The genetic toggle switch is an especially challenging test case as it shows a stochastic switching between two steady states which is qualitatively different from the model behavior in a deterministic model.

  19. Gas Transport Parameters for Landfill Final Cover Soil: Measurements and Model Modification by Dry Bulk Density

    Science.gov (United States)

    Wickramarachchi, P. N.; Kawamoto, K.; Hamamoto, S.; Nagamori, M.; Moldrup, P.; Komatsu, T.

    2011-12-01

    Landfill sites have been emerging in greenhouse warming scenarios as a significant source of atmospheric methane (CH4). Until recently, landfill management strategies have mainly addressed the problem of preventing groundwater contamination and reduction of leachate generation. Being one of the largest sources of anthropogenic CH4 emission, the final cover system should also be designed for minimizing the greenhouse gases migration into the atmosphere or the areas surrounding the landfill while securing the hydraulic performance. Compared to the intensive research efforts on hydraulic performances of landfill final cover soil, few studies about gas transport characteristics of landfill cover soils have been done. However, recent soil-gas studies implied that the effects of soil physical properties such as bulk density (i.e., compaction level), soil particle size are key parameters to understand landfill gaseous performance. The gas exchange through the final cover soils is controlled by advective and diffusive gas transport. Air permeability (ka) governs the advective gas transport while the soil-gas diffusion coefficient (Dp) governs diffusive gas transport. In this study, the effects of compaction level and particle size fraction effects on ka and Dp for landfill final cover soil was investigated. The disturbed soil samples were taken from landfill final cover in Japan. A compaction tests were performed for the soil samples with two different size fractions (content , the soil samples were repacked into soil cores (i.d. 15-cm, length 12-cm, 2120 cm3) at two different compaction levels [(MP):2700 kN/m2 and (SP):600 kN/m2]. After the compaction tests, ka and Dp were measured and then samples were saturated and subsequently drained at different soil-water matric potential of 0.98, 2.94, 9.81, 1235 kPa and with air-dried and oven-dried conditions. Results showed that measured Dp and ka values for the coarser (content. Further, compaction effort was much significant

  20. Resilience of Key Biological Parameters of the Senegalese Flat Sardinella to Overfishing and Climate Change.

    Science.gov (United States)

    Ba, Kamarel; Thiaw, Modou; Lazar, Najih; Sarr, Alassane; Brochier, Timothée; Ndiaye, Ismaïla; Faye, Alioune; Sadio, Oumar; Panfili, Jacques; Thiaw, Omar Thiom; Brehmer, Patrice

    2016-01-01

    The stock of the Senegalese flat sardinella, Sardinella maderensis, is highly exploited in Senegal, West Africa. Its growth and reproduction parameters are key biological indicators for improving fisheries management. This study reviewed these parameters using landing data from small-scale fisheries in Senegal and literature information dated back more than 25 years. Age was estimated using length-frequency data to calculate growth parameters and assess the growth performance index. With global climate change there has been an increase in the average sea surface temperature along the Senegalese coast but the length-weight parameters, sex ratio, size at first sexual maturity, period of reproduction and condition factor of S. maderensis have not changed significantly. The above parameters of S. maderensis have hardly changed, despite high exploitation and fluctuations in environmental conditions that affect the early development phases of small pelagic fish in West Africa. This lack of plasticity of the species regarding of the biological parameters studied should be considered when planning relevant fishery management plans.

  1. Two Different Bifurcation Scenarios in Neural Firing Rhythms Discovered in Biological Experiments by Adjusting Two Parameters

    Institute of Scientific and Technical Information of China (English)

    WV Xiao-Bo; MO Juan; YANG Ming-Hao; ZHENG Qiao-Hua; GU Hua-Guang; HEN Wei

    2008-01-01

    @@ Two different bifurcation scenarios, one is novel and the other is relatively simpler, in the transition procedures of neural firing patterns are studied in biological experiments on a neural pacemaker by adjusting two parameters. The experimental observations are simulated with a relevant theoretical model neuron. The deterministic non-periodic firing pattern lying within the novel bifurcation scenario is suggested to be a new case of chaos, which has not been observed in previous neurodynamical experiments.

  2. Prediction uncertainty assessment of a systems biology model requires a sample of the full probability distribution of its parameters

    NARCIS (Netherlands)

    Mourik, van S.; Braak, ter C.J.F.; Stigter, J.D.; Molenaar, J.

    2014-01-01

    Multi-parameter models in systems biology are typically ‘sloppy’: some parameters or combinations of parameters may be hard to estimate from data, whereas others are not. One might expect that parameter uncertainty automatically leads to uncertain predictions, but this is not the case. We illustrate

  3. SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology

    Directory of Open Access Journals (Sweden)

    Alexander Dörr

    2014-12-01

    Full Text Available The identification of suitable model parameters for biochemical reactions has been recognized as a quite difficult endeavor. Parameter values from literature or experiments can often not directly be combined in complex reaction systems. Nature-inspired optimization techniques can find appropriate sets of parameters that calibrate a model to experimentally obtained time series data. We present SBMLsimulator, a tool that combines the Systems Biology Simulation Core Library for dynamic simulation of biochemical models with the heuristic optimization framework EvA2. SBMLsimulator provides an intuitive graphical user interface with various options as well as a fully-featured command-line interface for large-scale and script-based model simulation and calibration. In a parameter estimation study based on a published model and artificial data we demonstrate the capability of SBMLsimulator to identify parameters. SBMLsimulator is useful for both, the interactive simulation and exploration of the parameter space and for the large-scale model calibration and estimation of uncertain parameter values.

  4. Conscious knowledge of learning: accessing learning strategies in a final year high school biology class

    Science.gov (United States)

    Conner, Lindsey; Gunstone, Richard

    2004-12-01

    This paper reports on a qualitative case study investigation of the knowledge and use of learning strategies by 16 students in a final year high school biology class to expand their conscious knowledge of learning. Students were provided with opportunities to engage in purposeful inquiry into the biological, social and ethical aspects of cancer. A constructivist approach was implemented to access prior content and procedural knowledge in various ways. Students were encouraged to develop evaluation of their learning skills independently through activities that promoted metacognition. Those students who planned and monitored their work produced essays of higher quality. The value and difficulties of promoting metacognitive approaches in this context are discussed, as well as the idea that metacognitive processes are difficult to research, because they have to be conscious in order to be identified by the learner, thereby making them accessible to the researcher.

  5. Biological basis for space-variant sensor design I: parameters of monkey and human spatial vision

    Science.gov (United States)

    Rojer, Alan S.; Schwartz, Eric L.

    1991-02-01

    Biological sensor design has long provided inspiration for sensor design in machine vision. However relatively little attention has been paid to the actual design parameters provided by biological systems as opposed to the general nature of biological vision architectures. In the present paper we will provide a review of current knowledge of primate spatial vision design parameters and will present recent experimental and modeling work from our lab which demonstrates that a numerical conformal mapping which is a refinement of our previous complex logarithmic model provides the best current summary of this feature of the primate visual system. In this paper we will review recent work from our laboratory which has characterized some of the spatial architectures of the primate visual system. In particular we will review experimental and modeling studies which indicate that: . The global spatial architecture of primate visual cortex is well summarized by a numerical conformal mapping whose simplest analytic approximation is the complex logarithm function . The columnar sub-structure of primate visual cortex can be well summarized by a model based on a band-pass filtered white noise. We will also refer to ongoing work in our lab which demonstrates that: . The joint columnar/map structure of primate visual cortex can be modeled and summarized in terms of a new algorithm the ''''proto-column'''' algorithm. This work provides a reference-point for current engineering approaches to novel architectures for

  6. [Innovation in adjuvant radiotherapy for breast cancer: new biologic parameters, a perspective for treatment tailoring].

    Science.gov (United States)

    Belkacémi, Y

    2009-01-01

    In the adjuvant setting, whole breast radiation therapy (RT) delivering 50 Gy in 5 weeks with or without a boost to the tumor bed remains the standard of care. RT indications and volume definition are generally dependant on existing prognostic factors. Except in particular cases, RT technique does not vary according to the patient or tumor biology profiles in terms of total dose, dose per fraction, fractionation, and RT duration. The challenge is to define new parameters or tumor biology profiles that will allow patient selection for more tailored RT than the 5 to 7 week standard schedules. The future issue is to define biological markers able to screen patients and tumors according to their high metastatic potential (in which the primary therapeutic challenge may not be locoregional control) and those patients that have a particular radiosensitivity to ionizing radiation for higher benefit/risk ratio. Thus, it is probable that patient profiles, tumor biology markers and gene expression profiling could provide in future an added value to conventional markers to predict patients at high-risk of local and distant recurrences who need tailored treatment or a particular sequence of adjuvant therapy.

  7. Biological optimization of simultaneous boost on intra-prostatic lesions (DILs): sensitivity to TCP parameters.

    Science.gov (United States)

    Azzeroni, R; Maggio, A; Fiorino, C; Mangili, P; Cozzarini, C; De Cobelli, F; Di Muzio, N G; Calandrino, R

    2013-11-01

    The aim of this investigation was to explore the potential of biological optimization in the case of simultaneous integrated boost on intra-prostatic dominant lesions (DIL) and evaluating the impact of TCP parameters uncertainty. Different combination of TCP parameters (TD50 and γ50 in the Poisson-like model), were considered for DILs and the prostate outside DILs (CTV) for 7 intermediate/high-risk prostate patients. The aim was to maximize TCP while constraining NTCPs below 5% for all organs at risk. TCP values were highly depending on the parameters used and ranged between 38.4% and 99.9%; the optimized median physical doses were in the range 94-116 Gy and 69-77 Gy for DIL and CTV respectively. TCP values were correlated with the overlap PTV-rectum and the minimum distance between rectum and DIL. In conclusion, biological optimization for selective dose escalation is feasible and suggests prescribed dose around 90-120 Gy to the DILs. The obtained result is critically depending on the assumptions concerning the higher radioresistence in the DILs. In case of very resistant clonogens into the DIL, it may be difficult to maximize TCP to acceptable levels without violating NTCP constraints.

  8. Population and biological parameters of selected fish species from the middle Xingu River, Amazon Basin.

    Science.gov (United States)

    Camargo, M; Giarrizzo, T; Isaac, V J

    2015-08-01

    This study estimates the main biological parameters, including growth rates, asymptotic length, mortality, consumption by biomass, biological yield, and biomass, for the most abundant fish species found on the middle Xingu River, prior to the construction of the Belo Monte Dam. The specimens collected in experimental catches were analysed with empirical equations and length-based FISAT methods. For the 63 fish species studied, high growth rates (K) and high natural mortality (M) were related to early sexual maturation and low longevity. The predominance of species with short life cycles and a reduced number of age classes, determines high rates of stock turnover, which indicates high productivity for fisheries, and a low risk of overfishing.

  9. The BIOSCI electronic newsgroup network for the biological sciences. Final report, October 1, 1992--June 30, 1996

    Energy Technology Data Exchange (ETDEWEB)

    Kristofferson, D.; Mack, D.

    1996-10-01

    This is the final report for a DOE funded project on BIOSCI Electronic Newsgroup Network for the biological sciences. A usable network for scientific discussion, major announcements, problem solving, etc. has been created.

  10. Deep silicon etch for biology MEMS fabrication: review of process parameters influence versus chip design

    Science.gov (United States)

    Magis, T.; Ballerand, S.; Bellemin Comte, A.; Pollet, Olivier

    2013-03-01

    Micro-system for biology is a growing market, especially for micro-fluidic applications (environment and health). Key part for the manufacturing of biology MEMS is the deep silicon etching by plasma to create microstructures. Usual etching process as an alternation of etching and passivation steps is a well-known method for MEMS fabrication, nowadays used in high volume production for devices like sensors and actuators. MEMS for biology applications are very different in design compared to more common micro-systems like accelerometers for instance. Indeed, their design includes on the same chip structures of very diverse size like narrow pillars, large trenches and wide cavities. This makes biology MEMS fabrication very challenging for DRIE, since each type of feature considered individually would require a specific etch process. Furthermore process parameters suited to match specifications on small size features (vertical profile, low sidewall roughness) induce issues and defects on bigger structures (undercut, micro-masking) and vice versa. Thus the process window is constrained leading to trade-offs in process development. In this paper process parameters such as source and platen powers, pressure, etching and passivation gas flows and steps duration were investigated to achieve all requirements. As well interactions between those different factors were characterized at different levels, from individual critical feature up to chip scale and to wafer scale. We will show the plasma process development and tuning to reach all these specifications. We also compared different chambers configurations of our ICP tool (source wafer distance, plasma diffusion) in order to obtain a good combination of hardware and process. With optimized etching we successfully fabricate micro-fluidic devices like micro-pumps.

  11. Estimation of light transport parameters in biological media using coherent backscattering

    Indian Academy of Sciences (India)

    S Anantha Ramakrishna; K Divakara Rao

    2000-02-01

    The suitability of using the angular peak shape of the coherent backscattered light for estimating the light transport parameters of biological media has been investigated. Milk and methylene blue doped milk were used as tissue phantoms for the measurements carried out with a He–Ne laser (632.8 nm). Results indicate that while the technique accurately estimates the transport length, it can determine the absorption coefficient only when the absorption is moderately high ( > 1 cm-1) for the long transport lengths typical of tissues. Further, the possibility of determining the anisotropy factor by estimating the single scattering contribution to the diffuse background is examined.

  12. Investigating the robustness of ion beam therapy treatment plans to uncertainties in biological treatment parameters

    CERN Document Server

    Boehlen, T T; Dosanjh, M; Ferrari, A; Fossati, P; Haberer, T; Mairani, A; Patera, V

    2012-01-01

    Uncertainties in determining clinically used relative biological effectiveness (RBE) values for ion beam therapy carry the risk of absolute and relative misestimations of RBE-weighted doses for clinical scenarios. This study assesses the consequences of hypothetical misestimations of input parameters to the RBE modelling for carbon ion treatment plans by a variational approach. The impact of the variations on resulting cell survival and RBE values is evaluated as a function of the remaining ion range. In addition, the sensitivity to misestimations in RBE modelling is compared for single fields and two opposed fields using differing optimization criteria. It is demonstrated for single treatment fields that moderate variations (up to +/-50\\%) of representative nominal input parameters for four tumours result mainly in a misestimation of the RBE-weighted dose in the planning target volume (PTV) by a constant factor and only smaller RBE-weighted dose gradients. Ensuring a more uniform radiation quality in the PTV...

  13. Function of parotid gland following irradiation and its relation to biological parameters

    Energy Technology Data Exchange (ETDEWEB)

    Sasaki, T. (Tohoku Univ., Sendai, Japan); Yamamoto, M.; Takeda, M.

    1980-09-01

    The function of the parotid gland in the mouse (synthesis and secretion of ..cap alpha..-amylase) following X irradiation was analyzed in relation to the parameters of surviving acinar cell fraction, DNA or protein content, and wet weight of the gland. Both synthesis and secretion of amylase in parotid were essentially unchanged when mice were irradiated with a dose of up to 3000 rad. When mice were irradiated and then given a proliferative stimulus of isoproterenol, latent lethal damage in the acinar cell population was expressed and resulted in cell degeneration in a dose-dependent manner. The mean value of amylase activity per gland in similarly treated parotids was, however, totally unaffected. The relationship between amylase activity per gland and the other biological parameters was analyzed by regression analysis. The results indicate that amylase activity per surviving acinar cell increased proportionately to compensate for the loss of acinar cells.

  14. A cooperative strategy for parameter estimation in large scale systems biology models

    Directory of Open Access Journals (Sweden)

    Villaverde Alejandro F

    2012-06-01

    Full Text Available Abstract Background Mathematical models play a key role in systems biology: they summarize the currently available knowledge in a way that allows to make experimentally verifiable predictions. Model calibration consists of finding the parameters that give the best fit to a set of experimental data, which entails minimizing a cost function that measures the goodness of this fit. Most mathematical models in systems biology present three characteristics which make this problem very difficult to solve: they are highly non-linear, they have a large number of parameters to be estimated, and the information content of the available experimental data is frequently scarce. Hence, there is a need for global optimization methods capable of solving this problem efficiently. Results A new approach for parameter estimation of large scale models, called Cooperative Enhanced Scatter Search (CeSS, is presented. Its key feature is the cooperation between different programs (“threads” that run in parallel in different processors. Each thread implements a state of the art metaheuristic, the enhanced Scatter Search algorithm (eSS. Cooperation, meaning information sharing between threads, modifies the systemic properties of the algorithm and allows to speed up performance. Two parameter estimation problems involving models related with the central carbon metabolism of E. coli which include different regulatory levels (metabolic and transcriptional are used as case studies. The performance and capabilities of the method are also evaluated using benchmark problems of large-scale global optimization, with excellent results. Conclusions The cooperative CeSS strategy is a general purpose technique that can be applied to any model calibration problem. Its capability has been demonstrated by calibrating two large-scale models of different characteristics, improving the performance of previously existing methods in both cases. The cooperative metaheuristic presented here

  15. A Gaussian mixture model based cost function for parameter estimation of chaotic biological systems

    Science.gov (United States)

    Shekofteh, Yasser; Jafari, Sajad; Sprott, Julien Clinton; Hashemi Golpayegani, S. Mohammad Reza; Almasganj, Farshad

    2015-02-01

    As we know, many biological systems such as neurons or the heart can exhibit chaotic behavior. Conventional methods for parameter estimation in models of these systems have some limitations caused by sensitivity to initial conditions. In this paper, a novel cost function is proposed to overcome those limitations by building a statistical model on the distribution of the real system attractor in state space. This cost function is defined by the use of a likelihood score in a Gaussian mixture model (GMM) which is fitted to the observed attractor generated by the real system. Using that learned GMM, a similarity score can be defined by the computed likelihood score of the model time series. We have applied the proposed method to the parameter estimation of two important biological systems, a neuron and a cardiac pacemaker, which show chaotic behavior. Some simulated experiments are given to verify the usefulness of the proposed approach in clean and noisy conditions. The results show the adequacy of the proposed cost function.

  16. Cueing Metacognition to Improve Researching and Essay Writing in a Final Year High School Biology Class

    Science.gov (United States)

    Conner, L. N.

    2007-03-01

    This paper reports on degrees of awareness and use of specific metacognitive strategies by 16 students in a final-year high school biology class in New Zealand. The aims of the intervention were to broaden students' thinking about bioethical issues associated with cancer and to enhance students' use of metacognition. Cues and prompts were used in this unit of work to help students use metacognitive strategies since students did not generally use metacognitive strategies spontaneously. Scaffolding was mediated through the teacher modelling, questioning, cueing or prompting students to evaluate their learning. The research reported here illustrates how teachers can cue students to be more self-directed in their learning. Three case studies illustrate how learning strategies were used differentially. Most students were aware of strategies that could help them to learn more effectively. It was found that those students who were not only aware of but also used strategies to plan, monitor and evaluate their work, produced essays of higher quality.

  17. Task-Oriented Parameter Tuning Based on Priority Condition for Biologically Inspired Robot Application

    Directory of Open Access Journals (Sweden)

    Jaesung Kwon

    2015-01-01

    Full Text Available This work gives a biologically inspired control scheme for controlling a robotic system. Novel adaptive behaviors are observed from humans or animals even in unexpected disturbances or environment changes. This is why they have neural oscillator networks in the spinal cord to yield rhythmic-motor primitives robustly under a changing task. Hence, this work focuses on rhythmic arm movements that can be accomplished in terms of employing a control approach based on an artificial neural oscillator model. The main challenge is to determine various parameters for applying a neural feedback to robotic systems with performing a desired behavior and self-maintaining the entrainment effect. Hence, this work proposes a task-oriented parameter tuning algorithm based on the simulated annealing (SA. This work also illustrates how to technically implement the proposed control scheme exploiting a virtual force and neural feedback. With parameters tuned, it is verified in simulations that a 3-DOF planar robotic arm traces a given trajectory precisely, adapting to uneven external disturbances.

  18. A New Biology for the 21st Century; Ensuring the United States Leads the Coming Biology Revolution. Final committee report

    Energy Technology Data Exchange (ETDEWEB)

    None, None

    2012-05-10

    In July, 2008, the National Institutes of Health (NIH), National Science Foundation (NSF), and Department of Energy (DOE) asked the National Research Council’s Board on Life Sciences to convene a committee to examine the current state of biological research in the United States and recommend how best to capitalize on recent technological and scientific advances that have allowed biologists to integrate biological research findings, collect and interpret vastly increased amounts of data, and predict the behavior of complex biological systems. From September 2008 through July of 2009, a committee of 16 experts from the fields of biology, engineering and computational science undertook to delineate those scientific and technological advances and come to a consensus on how the U.S. might best capitalize on them. This report, authored by the Committee on a New Biology for the 21st Century, describes the committee’s work and conclusions.

  19. Employment of the covariance matrix in parameter estimation for stochastic processes in cell biology

    Science.gov (United States)

    Preuss, R.; Dieterich, P.

    2013-08-01

    The dynamics of movements of biological cells can be described with models from correlated stochastic processes. In order to overcome problems from correlated and insufficient data in the determination of the model parameters of such processes we employ the covariance matrix of the data. Since the covariance suffers itself from statistical uncertainty it is corrected by a renormalization treatment [1]. For the example of normal and fractional Brownian motion, which allows both to access all quantities on full theoretical grounds and to generate data similar to experiment, we discuss our results and those of previous works by Gregory [2] and Sivia [3]. The presented approach has the potential to estimate the aging correlation function of observed cell paths and can be applied to more complicated models.

  20. A study on biological media of ultrasonic nonlinear parameter B/A

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jeong Koo; Jung, Hong Ryang; Lim, Cheong Hwan [Hanseo Univ, Seosan (Korea, Republic of)

    2001-06-01

    This study deals with the relationship between the magnitude of ultrasonic nonlinear parameter B/A, and sound speed of amount of fat present in biological media to measure B/A system using a wide band ultrasonic transducer. To represent this case, mixtures of egg whites and egg yolk were studied. Even though the differences in density and sound speed of the two egg components were in the range of 1%, B/A increase parabolically as a function of the fat density, which is not in agreement with the Yoshizumi et al.'s suggestion. In skim, milk that dose not contain fat, both the B/A and the sound speed increase with the solubility. It is considered that protein could affect these values.

  1. TGLF Recalibration for ITER Standard Case Parameters FY2015: Theory and Simulation Performance Target Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Candy, J. [General Atomics, San Diego, CA (United States)

    2015-12-01

    flows that fit the GYRO simulations, the parameters of the model had to be tuned to each case. A physics basis for the zonal flow model was lacking. Electron energy transport at short wavelength: A secondary issue – the high-k electron energy flux – was initially assumed to be independent of the zonal flow effect. However, detailed studies of the fluctuation spectra from recent multiscale (electron and ion scale) GYRO simulations provided a critical new insight into the role of zonal flows. The multiscale simulations suggested that advection by the zonal flows strongly suppressed electron-scale turbulence. Radial shear of the zonal E×B fluctuation could not compete with the large electron-scale linear growth rate, but the kx-mixing rate of the E×B advection could. This insight led to a preliminary new model for the way zonal flows saturate both electron- and ion-scale turbulence. It was also discovered that the strength of the zonal E×B velocity could be computed from the linear growth rate spectrum. The new saturation model (SAT1), which replaces the original model (SAT0), was fit to the multiscale GYRO simulations as well as the ion-scale GYRO simulations used to calibrate the original SAT0 model. Thus, SAT1 captures the physics of both multiscale electron transport and zonal-flow stabilization. In future work, the SAT1 model will require significant further testing and (expensive) calibration with nonlinear multiscale gyrokinetic simulations over a wider variety of plasma conditions – certainly more than the small set of scans about a single C-Mod L-mode discharge. We believe the SAT1 model holds great promise as a physics-based model of the multiscale turbulent transport in fusion devices. Correction to ITER performance predictions: Finally, the impact of the SAT1model on the ITER hybrid case is mixed. Without the electron-scale contribution to the fluxes, the Dimits shift makes a significant improvement in the predicted fusion power as

  2. TGLF Recalibration for ITER Standard Case Parameters FY2015: Theory and Simulation Performance Target Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Candy, J. [General Atomics, San Diego, CA (United States)

    2015-12-01

    flows that fit the GYRO simulations, the parameters of the model had to be tuned to each case. A physics basis for the zonal flow model was lacking. Electron energy transport at short wavelength: A secondary issue – the high-k electron energy flux – was initially assumed to be independent of the zonal flow effect. However, detailed studies of the fluctuation spectra from recent multiscale (electron and ion scale) GYRO simulations provided a critical new insight into the role of zonal flows. The multiscale simulations suggested that advection by the zonal flows strongly suppressed electron-scale turbulence. Radial shear of the zonal ExB fluctuation could not compete with the large electron-scale linear growth rate, but the kx-mixing rate of the ExB advection could. This insight led to a preliminary new model for the way zonal flows saturate both electron and ion-scale turbulence. It was also discovered that the strength of the zonal ExB velocity could be computed from the linear growth rate spectrum. The new saturation model (SAT1), which replaces the original model (SAT0), was fit to the multiscale GYRO simulations as well as the ion-scale GYRO simulations used to calibrate the original SAT0 model. Thus, SAT1 captures the physics of both multiscale electron transport and zonal-flow stabilization. In future work, it the SAT1 model will require significant further testing and (expensive) calibration with nonlinear multiscale gyrokinetic simulations over a wider variety of plasma conditions – certainly more than the small set of scans about a single C-Mod L-mode discharge. We believe the SAT1 model holds great promise as a physics-based model of the multiscale turbulent transport in fusion devices. Correction to ITER performance predictions: Finally, the impact of the SAT1model on the ITER hybrid case is mixed. Without the electron-scale contribution to the fluxes, the Dimits shift makes a significant improvement in the predicted fusion power as originally

  3. Correlations between IL6 and the main clinical and biological parameters in rheumatoid arthritis

    Directory of Open Access Journals (Sweden)

    Mihaela Chicu

    2016-09-01

    Full Text Available Introduction: Cytokines are a family of complex peptide with hormone-like activity. They are soluble proteins without enzymatic activity and serves as the main intracellular mediators. Many cytokines achieves its effects by binding to special receptors membrane, and their adjustment is via soluble receptors. Cytokines are characterized by pleiotropism, overlapping and mutual adjustment. Proinflammatory cytokine involved in major rheumatoid arthritis are TNF, IL1α, IL1β, IL8.The biological effects of IL6 overlap in large part over those of TNF. If TNF is involved in induction of apoptosis or programmed cell death, IL6 is specifically associated with angiogenic factors activation and the occurrence of neovascularity to the synovium; favors articular cartilage degradation by increasing the release of MMP, decreasing PG, recruit osteoclasts, apoptosis of osteoblasts, release of degradative enzymes and the inflammatory mediators - iNOS, COX2 - TNF, IL6, IL8.Material and methods: Based on these data we proposed and realized – for the first time in Romania – the measurement of IL6 levels and the correlation with values of DAS28 score, HAQ, ESR, CRP, Hb and the immunological parameters too. The study was conducted on a group of 80 sick diagnosed with RA in various stages of evolution, under treatment with disease-modifying medication , type Methotrexate, Arava.Conclusions: Levels of IL-6 correlate a direct manner with those of acute phase reactants ,ESR, CRP and indirect values of Hb, IgG; the clinical parameters (number of tender and swollen joints, DAS28, HAQ are not influenced by values IL6.

  4. Final Technical Report - Integrated Hydrogeophysical and Hydrogeologic Driven Parameter Upscaling for Dual-Domain Transport Modeling

    Energy Technology Data Exchange (ETDEWEB)

    Shafer, John M

    2012-11-05

    The three major components of this research were: 1. Application of minimally invasive, cost effective hydrogeophysical techniques (surface and borehole), to generate fine scale (~1m or less) 3D estimates of subsurface heterogeneity. Heterogeneity is defined as spatial variability in hydraulic conductivity and/or hydrolithologic zones. 2. Integration of the fine scale characterization of hydrogeologic parameters with the hydrogeologic facies to upscale the finer scale assessment of heterogeneity to field scale. 3. Determination of the relationship between dual-domain parameters and practical characterization data.

  5. Darwin y la imposibilidad de causas finales en la biología

    Directory of Open Access Journals (Sweden)

    Corral Cuartas Álvaro

    2009-12-01

    Full Text Available La teoría de la selección natural propuesta por Charles Darwin en su obra El Origen de las Especies no sólo colocó las bases para una explicación coherente de los hechos fundamentales de la biología (el origen común de los seres vivos, la diversidad de individuos y especies y la transmisión de características hereditarias, sino que además introduce maneras nuevas de hacer filosofía. La teoría de la selección natural hace superflua cualquier posibilidad de apelar a explicaciones de tipo finalista en la ciencia. Desde Aristóteles se conocen cuatro tipos de causa: la material, la formal, la eficiente y la final. Aunque la causa eficiente es el paradigma de explicación por excelencia de las ciencias empíricas, la causa final sigue desempeñando un papel explicativo, por cuanto parece estar arraigada en nuestra estructura humana de pensamiento y la tendencia a presentar explicaciones finalistas sigue siendo recalcitrante. Quizá por estar los seres humanos tan familiarizados con la complejidad inherente a los procesos de diseño en las artes y en la técnica, suponemos por vía de analogía que la naturaleza en su complejidad exige la presencia y acción de un diseñador inteligente. Kant en la Crítica de la facultad de juzgar hace una defensa del carácter “irrenunciable” de este modelo explicativo. Para controvertir esta opinión, me apoyaré, en recientes investigaciones de Richard Dawkins y de otros biólogos contemporáneos para mostrar con la evolución de ojos en la naturaleza que el surgimiento de órganos de alta complejidad puede ser explicado sin

  6. Machine self-teaching methods for parameter optimization. Final report, October 1984-August 1986

    Energy Technology Data Exchange (ETDEWEB)

    Dillard, R.A.

    1986-12-01

    The problem of determining near-optimum parameter-control logic is addressed for cases where a sensor or communication system is highly flexible and the logic cannot be determined analytically. A system that supports human-like learning of optimum parameters is outlined. The major subsystems are (1) a simulation system (described for a radar example), (2) a performance monitoring system, (3) the learning system, and (4) the initial knowledge used by all subsystems. The initial knowledge is expressed modularly as specifications (e.g., radar constraints, performance measures, and target characteristics), relationships (among parameters, intermediate measures, and component performance measures), and formulas. The intent of the learning system is to relieve the human from the very tedious trial-and-error process of examining performance, selecting and applying curve-fitting methods, and selecting the next trial set of parameters. A learning system to design a simple radar meeting specific performance constraints is described in detail, for experimental purposes, in generic object-based code.

  7. The final COS-B database: In-flight calibration of instrumental parameters

    Science.gov (United States)

    Strong, A. W.; Bloemen, J. B. G. M.; Buccheri, R.; Hermsen, W.; Lebrun, F.; Mayer-Hasselwander, H. A.

    1985-01-01

    A method for the determination of temporal variation of sensitivity is designed to find a set of parameters which lead to maximum consistency between the intensities derived from different observation periods. This method is briefly described and the resulting sensitivity and background variations presented.

  8. Final Report: Geoelectrical Measurement of Multi-Scale Mass Transfer Parameters

    Energy Technology Data Exchange (ETDEWEB)

    Haggerty, Roy; Day-Lewis, Fred; Singha, Kamini; Johnson, Timothy; Binley, Andrew; Lane, John

    2014-03-20

    Mass transfer affects contaminant transport and is thought to control the efficiency of aquifer remediation at a number of sites within the Department of Energy (DOE) complex. An improved understanding of mass transfer is critical to meeting the enormous scientific and engineering challenges currently facing DOE. Informed design of site remedies and long-term stewardship of radionuclide-contaminated sites will require new cost-effective laboratory and field techniques to measure the parameters controlling mass transfer spatially and across a range of scales. In this project, we sought to capitalize on the geophysical signatures of mass transfer. Previous numerical modeling and pilot-scale field experiments suggested that mass transfer produces a geoelectrical signature—a hysteretic relation between sampled (mobile-domain) fluid conductivity and bulk (mobile + immobile) conductivity—over a range of scales relevant to aquifer remediation. In this work, we investigated the geoelectrical signature of mass transfer during tracer transport in a series of controlled experiments to determine the operation of controlling parameters, and also investigated the use of complex-resistivity (CR) as a means of quantifying mass transfer parameters in situ without tracer experiments. In an add-on component to our grant, we additionally considered nuclear magnetic resonance (NMR) to help parse mobile from immobile porosities. Including the NMR component, our revised study objectives were to: 1. Develop and demonstrate geophysical approaches to measure mass-transfer parameters spatially and over a range of scales, including the combination of electrical resistivity monitoring, tracer tests, complex resistivity, nuclear magnetic resonance, and materials characterization; and 2. Provide mass-transfer estimates for improved understanding of contaminant fate and transport at DOE sites, such as uranium transport at the Hanford 300 Area. To achieve our objectives, we implemented a 3

  9. Effect of photoperiod on some biological parameters of Clarias gariepinus juvenile

    Directory of Open Access Journals (Sweden)

    Solomon S. G.

    2012-11-01

    Full Text Available Photoperiod effect on Growth parameters and cannibalism of Clarias gariepinushave been well documented in resent past, but little is known about the response of other biological parameters such as, Condition factor, Shooters composition, Body colouration and Blood glucose of this important tropical fish species to different photoperiods, therefore the present study was designed to evaluate these responses of the African catfish to 24 hours of light (00D:24L, 24 hours of darkness (24D: 00L and 12 hour light / 12 hours darkness (12D: 12L. The six weeks experiment observed significant differences (P0.05 at the end of the experiment and were Significantly lower than value obtained at the start of the experiment, Shooters composition was highest in 00D:24L (41.5% i.e. 27 of 65 leading to high mortality (13.33% due to cannibalism compared to 12D: 12L (Shooters =15.27% i.e. 11 of 72, Mortality= 4% and 24D: 00L (Shooters=5.33% i.e. 4 of 75, Mortality= 0% photoperiod. More so, 93.33% (70 of 75 of fish in the dark phase (24D: 00Lexhibited Deep shiny black body colouration, while 6.67% (5 of 75 was observed of Normal fish colouration. However the fishes in the 00D: 24L photoperiod were observed to be predominantly Lighter skin colouration, (80% i.e. 52 of 65= lighter colouration, 18.46% i.e. 12 of 65= Normal skin coloration and 1.53 i.e. 1 of 65= Deep black body colouration while 12D: 12L were of Normal skin colouration (100% Normal skin colouration, also blood glucose was observed to increase as the light hours increased (P<0.05 with 24D: 00L photoperiod having the highest blood glucose level of 5.7+0.5, while those in 12D: 12L had 4.4+0.3 and 24D: 00L had the least value of 3.9+0.1. This study therefore establishes the fact that photoperiod may have no effect on the condition factor of African catfish, while higher shooters composition is highlighted as one of the causes of increased mortality and could be reduced to a large extent with reduced light

  10. Processes and parameters involved in modeling radionuclide transport from bedded salt repositories. Final report. Technical memorandum

    Energy Technology Data Exchange (ETDEWEB)

    Evenson, D.E.; Prickett, T.A.; Showalter, P.A.

    1979-07-01

    The parameters necessary to model radionuclide transport in salt beds are identified and described. A proposed plan for disposal of the radioactive wastes generated by nuclear power plants is to store waste canisters in repository sites contained in stable salt formations approximately 600 meters below the ground surface. Among the principal radioactive wastes contained in these canisters will be radioactive isotopes of neptunium, americium, uranium, and plutonium along with many highly radioactive fission products. A concern with this form of waste disposal is the possibility of ground-water flow occurring in the salt beds and endangering water supplies and the public health. Specifically, the research investigated the processes involved in the movement of radioactive wastes from the repository site by groundwater flow. Since the radioactive waste canisters also generate heat, temperature is an important factor. Among the processes affecting movement of radioactive wastes from a repository site in a salt bed are thermal conduction, groundwater movement, ion exchange, radioactive decay, dissolution and precipitation of salt, dispersion and diffusion, adsorption, and thermomigration. In addition, structural changes in the salt beds as a result of temperature changes are important. Based upon the half-lives of the radioactive wastes, he period of concern is on the order of a million years. As a result, major geologic phenomena that could affect both the salt bed and groundwater flow in the salt beds was considered. These phenomena include items such as volcanism, faulting, erosion, glaciation, and the impact of meteorites. CDM reviewed all of the critical processes involved in regional groundwater movement of radioactive wastes and identified and described the parameters that must be included to mathematically model their behavior. In addition, CDM briefly reviewed available echniques to measure these parameters.

  11. Metropolitan Programs in Applied Biological and Agricultural Occupations; A Need and Attitude Study. Final Report.

    Science.gov (United States)

    Thomas, Hollie B.; And Others

    To establish the feasibility of implementing applied biological and agricultural occupations programs in the metropolitan area of Chicago, four populations were surveyed by means of mailed questionnaires or interest inventories to determine: (1) the employment opportunities in the applied biological and agricultural industries, (2) the interests…

  12. 2012 Gordon Research Conference on Cellular and Molecular Fungal Biology, Final Progress Report

    Energy Technology Data Exchange (ETDEWEB)

    Berman, Judith [Univ. of Minnesota, Minneapolis, MN (United States)

    2012-06-22

    The Gordon Research Conference on Cellular and Molecular Fungal Biology was held at Holderness School, Holderness New Hampshire, June 17 - 22, 2012. The 2012 Gordon Conference on Cellular and Molecular Fungal Biology (CMFB) will present the latest, cutting-edge research on the exciting and growing field of molecular and cellular aspects of fungal biology. Topics will range from yeast to filamentous fungi, from model systems to economically important organisms, and from saprophytes and commensals to pathogens of plants and animals. The CMFB conference will feature a wide range of topics including systems biology, cell biology and morphogenesis, organismal interactions, genome organisation and regulation, pathogenesis, energy metabolism, biomass production and population genomics. The Conference was well-attended with 136 participants. Gordon Research Conferences does not permit publication of meeting proceedings.

  13. The highlight of the main microbiologic parameters in buffalo milk and the final product

    Directory of Open Access Journals (Sweden)

    Aurelia Coroian

    2009-10-01

    Full Text Available Research initially envisioned the determination of microbiologic parameters in buffalo milk andthe finished product. The average for coliform bacteria was 4.96±0.47, while for the total number ofyeasts and moulds, it was 633.47±20.01. Escherichia coli was present in three samples out of the 23buffalo milk samples under analysis and presented the following values: 1.5 E.coli x 103/ml, 1.1 E.coli x103/ml, respectively 2.9 E.coli x 103/ml. In addition, the total number of germs and number of somaticcells according to two categories (milk from family exploitations and milk from an ecologic farm weredetermined. Selective isolations were conducted, of different dilutions of the pure culture on Levin agar(dilutions and incubation for 24 h at 37oC. The determination of the number of coliform bacteria wasconducted using Mac-Crady tables.

  14. The effect of muscle, cooking method and final internal temperature on quality parameters of beef roast.

    Science.gov (United States)

    Modzelewska-Kapituła, Monika; Dąbrowska, Ewa; Jankowska, Barbara; Kwiatkowska, Aleksandra; Cierach, Marek

    2012-06-01

    The aim of the study was to evaluate the influence of cooking conditions (dry air and steam) and final internal temperature (75, 85, 95°C) on the physico-chemical properties of beef infraspinatus (INF) and semimembranosus (SEM) muscles as well as their tenderness and juiciness. Cooking method and temperature influenced moisture, total collagen content in cooked meat and cooking loss, whereas muscle type affected fat, total collagen content and cooking loss. Warner-Bratzler shear force values were affected by cooking method, which also influenced juiciness of roasts. Temperature affected tenderness and juiciness, whereas muscle type influenced juiciness. The most desirable tenderness had INF heated in steam and dry air to 95°C. Processing SEM in dry air to 85 and 95°C lowered the juiciness of the roasts. There were significant correlations between physico-chemical, sensorial and image attributes, however high accuracy of prediction (r(2)>0.8) was achieved only for SEM muscle.

  15. Predicting biological parameters of estuarine benthic communities using models based on environmental data

    Directory of Open Access Journals (Sweden)

    José Souto Rosa-Filho

    2004-08-01

    Full Text Available This study aimed to predict the biological parameters (species composition, abundance, richness, diversity and evenness of benthic assemblages in southern Brazil estuaries using models based on environmental data (sediment characteristics, salinity, air and water temperature and depth. Samples were collected seasonally from five estuaries between the winter of 1996 and the summer of 1998. At each estuary, samples were taken in unpolluted areas with similar characteristics related to presence or absence of vegetation, depth and distance from the mouth. In order to obtain predictive models, two methods were used, the first one based on Multiple Discriminant Analysis (MDA, and the second based on Multiple Linear Regression (MLR. Models using MDA had better results than those based on linear regression. The best results using MLR were obtained for diversity and richness. It could be concluded that the use predictions models based on environmental data would be very useful in environmental monitoring studies in estuaries.Este trabalho objetivou predizer parâmetros da estrutura de associações macrobentônicas (composição específica, abundância, riqueza, diversidade e equitatividade em estuários do Sul do Brasil, utilizando modelos baseados em dados ambientais (características dos sedimentos, salinidade, temperaturas do ar e da água, e profundidade. As amostragens foram realizadas sazonalmente em cinco estuários entre o inverno de 1996 e o verão de 1998. Em cada estuário as amostras foram coletadas em áreas não poluídas, com características semelhantes quanto a presença ou ausência de vegetação, profundidade e distância da desenbocadura. Para a obtenção dos modelos de predição, foram utilizados dois métodos: o primeiro baseado em Análise Discriminante Múltipla (ADM e o segundo em Regressão Linear Múltipla (RLM. Os modelos baseados em ADM apresentaram resultados melhores do que os baseados em regressão linear. Os melhores

  16. High-Resolution Gene Flow Model for Assessing Environmental Impacts of Transgene Escape Based on Biological Parameters and Wind Speed.

    Science.gov (United States)

    Wang, Lei; Haccou, Patsy; Lu, Bao-Rong

    2016-01-01

    Environmental impacts caused by transgene flow from genetically engineered (GE) crops to their wild relatives mediated by pollination are longstanding biosafety concerns worldwide. Mathematical modeling provides a useful tool for estimating frequencies of pollen-mediated gene flow (PMGF) that are critical for assessing such environmental impacts. However, most PMGF models are impractical for this purpose because their parameterization requires actual data from field experiments. In addition, most of these models are usually too general and ignored the important biological characteristics of concerned plant species; and therefore cannot provide accurate prediction for PMGF frequencies. It is necessary to develop more accurate PMGF models based on biological and climatic parameters that can be easily measured in situ. Here, we present a quasi-mechanistic PMGF model that only requires the input of biological and wind speed parameters without actual data from field experiments. Validation of the quasi-mechanistic model based on five sets of published data from field experiments showed significant correlations between the model-simulated and field experimental-generated PMGF frequencies. These results suggest accurate prediction for PMGF frequencies using this model, provided that the necessary biological parameters and wind speed data are available. This model can largely facilitate the assessment and management of environmental impacts caused by transgene flow, such as determining transgene flow frequencies at a particular spatial distance, and establishing spatial isolation between a GE crop and its coexisting non-GE counterparts and wild relatives.

  17. Patient Protection and Affordable Care Act; HHS Notice of Benefit and Payment Parameters for 2017. Final rule.

    Science.gov (United States)

    2016-03-08

    This final rule sets forth payment parameters and provisions related to the risk adjustment, reinsurance, and risk corridors programs; cost-sharing parameters and cost-sharing reductions; and user fees for Federally-facilitated Exchanges. It also provides additional amendments regarding the annual open enrollment period for the individual market for the 2017 and 2018 benefit years; essential health benefits; cost sharing; qualified health plans; Exchange consumer assistance programs; network adequacy; patient safety; the Small Business Health Options Program; stand-alone dental plans; third-party payments to qualified health plans; the definitions of large employer and small employer; fair health insurance premiums; student health insurance coverage; the rate review program; the medical loss ratio program; eligibility and enrollment; exemptions and appeals; and other related topics.

  18. Filtered Rayleigh scattering diagnostic for multi-parameter thermal-fluids measurements : LDRD final report.

    Energy Technology Data Exchange (ETDEWEB)

    Beresh, Steven Jay; Grasser, Thomas W.; Kearney, Sean Patrick; Schefer, Robert W.

    2004-01-01

    Simulation-based life-cycle-engineering and the ASCI program have resulted in models of unprecedented size and fidelity. The validation of these models requires high-resolution, multi-parameter diagnostics. Within the thermal-fluids disciplines, the need for detailed, high-fidelity measurements exceeds the limits of current engineering sciences capabilities and severely tests the state of the art. The focus of this LDRD is the development and application of filtered Rayleigh scattering (FRS) for high-resolution, nonintrusive measurement of gas-phase velocity and temperature. With FRS, the flow is laser-illuminated and Rayleigh scattering from naturally occurring sources is detected through a molecular filter. The filtered transmission may be interpreted to yield point or planar measurements of three-component velocities and/or thermodynamic state. Different experimental configurations may be employed to obtain compromises between spatial resolution, time resolution, and the quantity of simultaneously measured flow variables. In this report, we present the results of a three-year LDRD-funded effort to develop FRS combustion thermometry and Aerosciences velocity measurement systems. The working principles and details of our FRS opto-electronic system are presented in detail. For combustion thermometry we present 2-D, spatially correlated FRS results from nonsooting premixed and diffusion flames and from a sooting premixed flame. The FRS-measured temperatures are accurate to within {+-}50 K (3%) in a premixed CH4-air flame and within {+-}100 K for a vortex-strained diluted CH4-air diffusion flame where the FRS technique is severely tested by large variation in scattering cross section. In the diffusion flame work, FRS has been combined with Raman imaging of the CH4 fuel molecule to correct for the local light scattering properties of the combustion gases. To our knowledge, this is the first extension of FRS to nonpremixed combustion and the first use of joint FRS

  19. A Strategic Initiative in Applied Biological Simulations 01-SI-012 Final Report for FY01 - FY03

    Energy Technology Data Exchange (ETDEWEB)

    Lau, E Y; Venclovas, C; Schwegler, E; Gygi, F; Colvin, M E; Bennion, B J; Barsky, D; Mundy, C; Lightstone, F C; Galli, G; Sawicka, D

    2004-02-16

    The goal of this Strategic Initiative in Applied Computational Biology has been to apply LLNL's expertise in computational simulation to forge a new laboratory core competency in biological simulation. By every measure, this SI has been very successful in this goal. Based on a strong publication record and large number of conference presentations and invited talks, we have built a recognized niche for LLNL in the burgeoning field of computational biology. Further, many of the projects that were previously part of this LDRD are now externally funded based on the research results and expertise developed under this SI. We have created successful collaborations with a number of outside research groups including several joint projects with the new UC Davis/LLNL Comprehensive Cancer Center. In addition to these scientific collaborations, the staff developed on this SI is involved in computational biology program development and advisory roles with other DOE laboratories and DOE Headquarters. Moreover, a number of capabilities and expertise created by this SI are finding use in LLNL programmatic applications. Finally, and most importantly, this SI project has brought to LLNL the human talent on who will be the ensuring the further success of computational biology at this laboratory.

  20. Assembly, start and operation of an activated sludge reactor for the industrial effluents treatment: physico chemical and biological parameters

    Directory of Open Access Journals (Sweden)

    Márcia Regina Assalin

    2008-05-01

    Full Text Available Although of the immense available bibliography regarding the activated sludge process, little it is found in relation to the basic procedure to be adopted to implant, to activate and to monitor a reactor of activated sludge in laboratory scales. This article describes the assembly, departure and operation of an activated sludge system, operating in continuous process, at a laboratory scale, to study effluents treatments, using as example, Kraft E1 pulp mill effluent. Factors as biodegradability of the effluent to be treated, stationary state of the reactor, conventional operation parameters as physical chemistry and biological parameters are presented.

  1. Final report for Conference Support Grant "From Computational Biophysics to Systems Biology - CBSB12"

    Energy Technology Data Exchange (ETDEWEB)

    Hansmann, Ulrich H.E.

    2012-07-02

    This report summarizes the outcome of the international workshop From Computational Biophysics to Systems Biology (CBSB12) which was held June 3-5, 2012, at the University of Tennessee Conference Center in Knoxville, TN, and supported by DOE through the Conference Support Grant 120174. The purpose of CBSB12 was to provide a forum for the interaction between a data-mining interested systems biology community and a simulation and first-principle oriented computational biophysics/biochemistry community. CBSB12 was the sixth in a series of workshops of the same name organized in recent years, and the second that has been held in the USA. As in previous years, it gave researchers from physics, biology, and computer science an opportunity to acquaint each other with current trends in computational biophysics and systems biology, to explore venues of cooperation, and to establish together a detailed understanding of cells at a molecular level. The conference grant of $10,000 was used to cover registration fees and provide travel fellowships to selected students and postdoctoral scientists. By educating graduate students and providing a forum for young scientists to perform research into the working of cells at a molecular level, the workshop adds to DOE's mission of paving the way to exploit the abilities of living systems to capture, store and utilize energy.

  2. Quantitative correlation of the in vitro biological effect with parameters of molecular complexation in mutagen-interceptor systems.

    Science.gov (United States)

    Buchelnikov, Anatoly S; Evstigneev, Maxim P

    2014-09-21

    According to the theory of interceptor-protector action a quantitative link between the physico-chemical parameters of molecular complexation and in vitro biological effect in aromatic drug-interceptor systems must exist. In the present communication such link between relative change in mutagenicity of IQ-type aromatic mutagens on addition of aromatic interceptor molecules with equilibrium hetero-association constants of mutagen-interceptor complexation has been found using the published in vitro data in bacteria cell systems.

  3. Final report on supplementary comparison COOMET.L-S10: Comparison of length standards for measuring gear parameters

    Science.gov (United States)

    Makarevich, V.

    2012-01-01

    The COOMET Project No 507/BY/10, 'Supplementary comparison of length standards for measuring gear parameters', KCDB Reference COOMET.L-S10, was organized by the COOMET Technical Committee TC 1.5 'Length and Angle'. This comparison started in September 2010 and finished in September 2011. It was piloted by the Belarusian State Institute of Metrology, BelGIM, Minsk, the Republic of Belarus, with VNIIMS (Moscow, Russia) as the other participant. The transfer standard was a gear involute master provided by BelGIM. This standard has two base circle radii of 150 mm and 60 mm, and corresponding profiles on the left and on the right. The involute profile was measured from root towards tip of the tooth. The scanning was performed in automatic mode along the mid-section of the base cylinder over the complete estimation range, with a scanning speed of 2 mm s-1. The software program GEAR PRO involute was used to determine three parameters: the total profile deviation, the profile form deviation and the profile slope deviation. Each participant performed ten measurements for each of two involute profiles with basic circle radius of 150 mm and 60 mm, respectively. The measurement result for each parameter was calculated as a mean value from the ten measurements. The comparison results demonstrate that the measured values are consistent with the stated uncertainties and that the measurement standards under comparison are equivalent. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by COOMET, according to the provisions of the CIPM Mutual Recognition Arrangement (MRA).

  4. Non-Directional Radiation Spread Modeling and Non-Invasive Estimating the Radiation Scattering and Absorption Parameters in Biological Tissue

    Directory of Open Access Journals (Sweden)

    S. Yu. Makarov

    2015-01-01

    Full Text Available The article dwells on a development of new non-invasive measurement methods of optical parameters of biological tissues, which are responsible for the scattering and absorption of monochromatic radiation. It is known from the theory of radiation transfer [1] that for strongly scattering media, to which many biological tissues pertain, such parameters are parameters of diffusion approximation, as well as a scattering coefficient and an anisotropy parameter.Based on statistical modeling the paper examines a spread of non-directional radiation from a Lambert light beam with the natural polarization that illuminates a surface of the biological tissue. Statistical modeling is based on the Monte Carlo method [2]. Thus, to have the correct energy coefficient values of Fresnel reflection and transmission in simulation of such radiation by Monte Carlo method the author uses his finding that is a function of the statistical representation for the incidence of model photons [3]. The paper describes in detail a principle of fixing the power transmitted by the non-directional radiation into biological tissue [3], and the equations of a power balance in this case.Further, the paper describes the diffusion approximation of a radiation transfer theory, often used in simulation of radiation propagation in strongly scattering media and shows its application in case of fixing the power transmitted into the tissue. Thus, to represent an uneven power distribution is used an approximating expression in conditions of fixing a total input power. The paper reveals behavior peculiarities of solution on the surface of the biological tissue inside and outside of the incident beam. It is shown that the solution in the region outside of the incident beam (especially far away from it, essentially, depends neither on the particular power distribution across the surface, being a part of the tissue, nor on the refractive index of the biological tissue. It is determined only by

  5. Effects of organic versus conventional management on chemical and biological parameters in agricultural soils

    NARCIS (Netherlands)

    Diepeningen, van A.D.; Vos, de O.J.; Korthals, G.W.; Bruggen, van A.H.C.

    2006-01-01

    A comparative study of organic and conventional arable farming systems was conducted in The Netherlands to determine the effect of management practices on chemical and biological soil properties and soil health. Soils from thirteen accredited organic farms and conventionally managed neighboring farm

  6. Third international conference on intelligent systems for molecular biology (ISMB-95): Summary. Final report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-12-31

    The specific aims of the Third International Conference on Intelligent Systems for Molecular Biology (ISMB-95) were to: convene a critical mass of researchers applying advanced computational techniques to problems in molecular biology; promote interchange of problems and solutions between computer scientists and molecular biologists; create education opportunities in this cross-disciplinary field for students and senior researchers wishing to either apply or benefit from these techniques; produce an archival proceedings as a forum for rapid dissemination of new results in a peer-reviewed manner; produce a set of tutorial materials for education and training of researchers interested in this field; maintain the momentum generated by the highly successful previous conferences in the series, and establish a regular event that will help to solidify the field; and foster the involvement of women and minorities in the field.

  7. (Genetics and molecular biology of Robertson's Mutator: A workshop series): Final report

    Energy Technology Data Exchange (ETDEWEB)

    Buckner, B.

    1988-01-01

    The objectives of the Workshop Series on the Genetics and Molecular Biology of Robertson's Mutator were to assess and consolidate interpretations of current Mutator research and to recognize and honor the outstanding contributions of Donald S. Robertson. To this end, a program of lectures, workshops, posters and opportunities for informal interaction was planned and carried out as indicated in the enclosed registration booklet. Within the context of the workshops, several topics were discussed. These discussions are summarized in abstract form.

  8. Biological processes in the water column of the South Atlantic Bight: Phytoplankton response. Final progress report

    Energy Technology Data Exchange (ETDEWEB)

    Verity, P.G.; Yoder, J.A.

    1992-03-10

    This study addressed shelf-wide processes and nearshore (coastal boundary zone) processes occurring in the southeastern. Coastal boundary zone (CBZ) US continental shelf dynamics involve studies of circulation and of biological and chemical transformations. Continental shelf processes affect the removal of material from the coastal boundary zone into areas where the material no longer interacts with or influences concentrations in the CBZ. The two arbitrarily separate components are, in fact, unified. The CBZ typically extends about 300 km along-shore and about 20 km offshore from its center off Savannah, Georgia, where most runoff occurs. The rates of biological and chemical transformations are controlled by proximity to the bottom and the amounts of fine suspended organic matter originating from rivers and salt marshes. Once material is removed from this zone, either by a long-shelf or cross-shelf advection to regions where the materials are no longer in contact with the bottom, the suite of factors governing the rates of chemical and biological transformations changes. The determination of contrasting rates in these two environments was one of the central focuses of the South Atlantic Bight program.

  9. Biological and analytical variations of 16 parameters related to coagulation screening tests and the activity of coagulation factors.

    Science.gov (United States)

    Chen, Qian; Shou, Weiling; Wu, Wei; Guo, Ye; Zhang, Yujuan; Huang, Chunmei; Cui, Wei

    2015-04-01

    To accurately estimate longitudinal changes in individuals, it is important to take into consideration the biological variability of the measurement. The few studies available on the biological variations of coagulation parameters are mostly outdated. We confirmed the published results using modern, fully automated methods. Furthermore, we added data for additional coagulation parameters. At 8:00 am, 12:00 pm, and 4:00 pm on days 1, 3, and 5, venous blood was collected from 31 healthy volunteers. A total of 16 parameters related to coagulation screening tests as well as the activity of coagulation factors were analyzed; these included prothrombin time, fibrinogen (Fbg), activated partial thromboplastin time, thrombin time, international normalized ratio, prothrombin time activity, activated partial thromboplastin time ratio, fibrin(-ogen) degradation products, as well as the activity of factor II, factor V, factor VII, factor VIII, factor IX, and factor X. All intraindividual coefficients of variation (CVI) values for the parameters of the screening tests (except Fbg) were less than 5%. Conversely, the CVI values for the activity of coagulation factors were all greater than 5%. In addition, we calculated the reference change value to determine whether a significant difference exists between two test results from the same individual.

  10. Biological Ocean Margins Program. Active Microbes Responding to Inputs from the Orinoco River Plume. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Jorge E. Corredor

    2013-01-28

    The overall goal of the proposed work is to identify the active members of the heterotrophic community involved in C and N cycling in the perimeter of the Orinoco River Plume (ORP), assess their spatial distribution, quantify their metabolic activity, and correlate these parameters to plume properties such as salinity, organic matter content and phytoplankton biomass.

  11. Assessment of disinfectants in explosive destruction system for biological agent destruction : LDRD final report FY04.

    Energy Technology Data Exchange (ETDEWEB)

    Simmons, Blake Alexander; Didlake, John E. Jr.; Bradshaw, Robert W.; Crooker, Paul J.; Buffleben, George M.

    2005-01-01

    Treatment systems that can neutralize biological agents are needed to mitigate risks from novel and legacy biohazards. Tests with Bacillus thuringiensis and Bacillus steurothemophilus spores were performed in a 190-liter, 1-112 lb TNT equivalent rated Explosive Destruction System (EDS) system to evaluate its capability to treat and destroy biological agents. Five tests were conducted using three different agents to kill the spores. The EDS was operated in steam autoclave, gas fumigation and liquid decontamination modes. The first three tests used EDS as an autoclave, which uses pressurized steam to kill the spores. Autoclaving was performed at 130-140 deg C for up to 2-hours. Tests with chlorine dioxide at 750 ppm concentration for 1 hour and 10% (vol) aqueous chlorine bleach solution for 1 hour were also performed. All tests resulted in complete neutralization of the bacterial spores based on no bacterial growth in post-treatment incubations. Explosively opening a glass container to expose the bacterial spores for treatment with steam was demonstrated and could easily be done for chlorine dioxide gas or liquid bleach.

  12. Enzymology of biological nitrogen fixation. Final report, May 1, 1987--April 30, 1996

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-05-01

    Biological nitrogen fixation is of central importance in the earth`s nitrogen economy. Fixation of nitrogen is accomplished by a variety of microorganisms, all of them procaryotic. Some operate independently and some function symbiotically or associatively with photosynthesizing plants. Biological nitrogen fixation is accomplished via the reaction: N{sub 2} + 8H{sup +} + 8e{sup {minus}} {yields} 2NH{sub 3} + H{sub 2}. This reaction requires a minimum of 16 ATP under ideal laboratory conditions, so it is obvious that the energy demand of the reaction is very high. When certain nitrogen-fixing organisms are supplied fixed nitrogen (e.g., ammonium) the organisms use the fixed nitrogen and turn off their nitrogenase system, thus conserving energy. When the fixed nitrogen is exhausted, the organism reactivates its nitrogenase. The system is turned off by dinitrogenase reductase ADP-ribosyl transferase (DRAT) and turned back on by dinitrogenase reductase-activating glycohydrolase (DRAG). The authors have investigated the details of how DRAT and DRAG are formed, how they function, and the genetics of their formation and operation.

  13. Postmarketing safety reports for human drug and biological products; electronic submission requirements. Final rule.

    Science.gov (United States)

    2014-06-10

    The Food and Drug Administration (FDA or we) is amending its postmarketing safety reporting regulations for human drug and biological products to require that persons subject to mandatory reporting requirements submit safety reports in an electronic format that FDA can process, review, and archive. FDA is taking this action to improve the Agency's systems for collecting and analyzing postmarketing safety reports. The change will help the Agency to more rapidly review postmarketing safety reports, identify emerging safety problems, and disseminate safety information in support of FDA's public health mission. In addition, the amendments will be a key element in harmonizing FDA's postmarketing safety reporting regulations with international standards for the electronic submission of safety information.

  14. Final LDRD report : development of advanced UV light emitters and biological agent detection strategies.

    Energy Technology Data Exchange (ETDEWEB)

    Figiel, Jeffrey James; Crawford, Mary Hagerott; Banas, Michael Anthony; Farrow, Darcie; Armstrong, Andrew M.; Serkland, Darwin Keith; Allerman, Andrew Alan; Schmitt, Randal L.

    2007-12-01

    We present the results of a three year LDRD project which has focused on the development of novel, compact, ultraviolet solid-state sources and fluorescence-based sensing platforms that apply such devices to the sensing of biological and nuclear materials. We describe our development of 270-280 nm AlGaN-based semiconductor UV LEDs with performance suitable for evaluation in biosensor platforms as well as our development efforts towards the realization of a 340 nm AlGaN-based laser diode technology. We further review our sensor development efforts, including evaluation of the efficacy of using modulated LED excitation and phase sensitive detection techniques for fluorescence detection of bio molecules and uranyl-containing compounds.

  15. Biological processes in the water column of the South Atlantic Bight: Zooplankton responses. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Paffenhofer, G.A.

    1992-09-25

    This study sought to determine and understand the major processes governing the abundance, distribution, composition and eventual fate of zooplankton on the southeastern shelf of the US in relation to water circulation. Over much of the shelf circulation is dominated by the Gulf Stream and/or atmospheric forcing. Most of our studies concentrated on processes on the middle and outer shelf. On the latter, pronounced biological production occurs year-round at frequent intervals and is due to Gulf Stream eddies which move by at an average frequency of one every week. These eddies are rich in nutrients which, when upwelled into the euphoric zone, lead to pronounced primary production which then triggers zooplankton production.

  16. Aquatic biology in Nederlo Creek, southwestern Wisconsin. Water-resources investigations (final)

    Energy Technology Data Exchange (ETDEWEB)

    Kammerer, P.A. Jr.; Lidwin, R.A.; Mason, J.W.; Narf, R.P.

    1982-09-01

    This report presents the results of biologic investigations made during a study of hydrology and water quality in a small drainage basin in the 'Driftless Area' of southwest Wisconsin. The aquatic community is diverse and reasonably stable with little indication of environmental disturbance. Aquatic macrophyte population (dominated by Ranunculus aquatilis L., Veronica catenata Penn., and Nasturtium officinale) varies little from spring to fall. Periphytic and planktonic algae are predominantly diatoms, with the genus Achnanthes dominating both communities. The benthic invertebrate population is dominated by Trichoptera. The trout population is low and represents only a small part of the total fish population both in biomass and numbers. The wild trout population is highly dependent on spawning success; when spawning success was poor, populations the following fall were extremely low.

  17. Final Report - Phylogenomic tools and web resources for the Systems Biology Knowledgebase

    Energy Technology Data Exchange (ETDEWEB)

    Sjolander, Kimmen [Univ. of California, Berkeley, CA (United States)

    2014-12-08

    The major advance during this last reporting period (8/15/12 to present) is our release of data on the PhyloFacts website: phylogenetic trees, multiple sequence alignments and other data for protein families are now available for download from http://phylogenomics.berkeley.edu/data/. This project as a whole aimed to develop high-throughput functional annotation systems that exploit information from protein 3D structure and evolution to provide highly precise inferences of various aspects of gene function, including molecular function, biological process, pathway association, Pfam domains, cellular localization and so on. We accomplished these aims by developing and testing different systems on a database of protein family trees: the PhyloFacts Phylogenomic Encyclopedia (at http://phylogenomics.berkeley.edu/phylofacts/ ).

  18. Final Report - Phylogenomic tools and web resources for the Systems Biology Knowledgebase

    Energy Technology Data Exchange (ETDEWEB)

    Sjolander, Kimmen

    2014-11-07

    The major advance during this last reporting period (8/15/12 to present) is our release of data on the PhyloFacts website: phylogenetic trees, multiple sequence alignments and other data for protein families are now available for download from http://phylogenomics.berkeley.edu/data/. This project as a whole aimed to develop high-throughput functional annotation systems that exploit information from protein 3D structure and evolution to provide highly precise inferences of various aspects of gene function, including molecular function, biological process, pathway association, Pfam domains, cellular localization and so on. We accomplished these aims by developing and testing different systems on a database of protein family trees: the PhyloFacts Phylogenomic Encyclopedia (at http://phylogenomics.berkeley.edu/phylofacts/ ).

  19. Structural parameters, molecular properties, and biological evaluation of some terpenes targeting Schistosoma mansoni parasite.

    Science.gov (United States)

    Mafud, Ana C; Silva, Marcos P N; Monteiro, Daniela C; Oliveira, Maria F; Resende, João G; Coelho, Mayara L; de Sousa, Damião P; Mendonça, Ronaldo Z; Pinto, Pedro L S; Freitas, Rivelilson M; Mascarenhas, Yvonne P; de Moraes, Josué

    2016-01-25

    The use of natural products has a long tradition in medicine, and they have proven to be an important source of lead compounds in the development of new drugs. Among the natural compounds, terpenoids present broad-spectrum activity against infective agents such as viruses, bacteria, fungi, protozoan and helminth parasites. In this study, we report a biological screening of 38 chemically characterized terpenes from different classes, which have a hydroxyl group connected by hydrophobic chain or an acceptor site, against the blood fluke Schistosoma mansoni, the parasite responsible for schistosomiasis mansoni. In vitro bioassays revealed that 3,7-dimethyl-1-octanol (dihydrocitronellol) (10) was the most active terpene (IC50 values of 13-52 μM) and, thus, we investigated its antischistosomal activity in greater detail. Confocal laser scanning microscopy revealed that compound 10 induced severe tegumental damage in adult schistosomes and a correlation between viability and tegumental changes was observed. Furthermore, we compared all the inactive compounds with dihydrocitronellol structurally by using shape and charge modeling. Lipophilicity (miLogP) and other molecular properties (e.g. molecular polar surface area, molecular electrostatic potential) were also calculated. From the 38 terpenes studied, compound 10 is the one with the greatest flexibility, with a sufficient apolar region by which it may interact in a hydrophobic active site. In conclusion, the integration of biological and chemical analysis indicates the potential of the terpene dihydrocitronellol as an antiparasitic agent.

  20. Optimization of struvite precipitation in synthetic biologically treated swine wastewater - Determination of the optimal process parameters

    OpenAIRE

    Capdevielle, Aurélie; Sýkorová, Eva; Biscans, Béatrice; Béline, Fabrice; Daumer, Marie-Line

    2013-01-01

    International audience; A sustainable way to recover phosphorus (P) in swine wastewater involves a preliminary step of P dissolution followed by the separation of particulate organic matter. The next two steps are firstly the precipitation of struvite crystals done by adding a crystallization reagent (magnesia) and secondly the filtration of the crystals. A design of experiments with five process parameters was set up to optimize the size of the struvite crystals in a synthetic swine wastewat...

  1. Controlled biomass removal - the key parameter to achieve enhanced biological phosphorus removal in biofilm systems

    DEFF Research Database (Denmark)

    Morgenroth, E.

    1999-01-01

    In contrast to enhanced biological phosphorus removal (EBPR) in activated sludge systems mass transfer processes have a major influence on overall phosphorus removal in biofilm reactors. Based on results from a laboratory scale sequencing batch biofilm reactor (SBBR) and from a mathematical model......) had only a minor effect on overall phosphorus removal. Soluble components fully penetrate the biofilm at certain times during the SBBR cycle as a consequence of SBBR operation with large concentration variations over the cycle time. The limiting processes for EBPR is the efficient removal...... of phosphorus rich biomass from the reactor. Biomass at the base of the biofilm that is not removed during backwashing will release accumulated phosphorus due to lysis or endogenous respiration and will not contribute to net phosphorus removal. For efficient operation of EBPR in biofilm systems regular...

  2. Temporal changes in physical, chemical and biological sediment parameters in a tropical estuary after mangrove deforestation

    Science.gov (United States)

    Ellegaard, Marianne; Nguyen, Ngoc Tuong Giang; Andersen, Thorbjørn Joest; Michelsen, Anders; Nguyen, Ngoc Lam; Doan, Nhu Hai; Kristensen, Erik; Weckström, Kaarina; Son, Tong Phuoc Hoang; Lund-Hansen, Lars Chresten

    2014-04-01

    Dated sediment cores taken near the head and mouth of a tropical estuary, Nha-Phu/Binh Cang, in south central Viet Nam were analyzed for changes over time in physical, chemical and biological proxies potentially influenced by removal of the mangrove forest lining the estuary. A time-series of satellite images was obtained, which showed that the depletion of the mangrove forest at the head of the estuary was relatively recent. Most of the area was converted into aquaculture ponds, mainly in the late 1990's. The sediment record showed a clear increase in sedimentation rate at the head of the estuary at the time of mangrove deforestation and a change in diatom assemblages in the core from the mouth of the estuary indicating an increase in the water column turbidity of the entire estuary at the time of the mangrove deforestation. The proportion of fine-grained sediment and the δ13C signal both increased with distance from the head of the estuary while the carbon content decreased. The nitrogen content and the δ15N signal were more or less constant throughout the estuary. The proportion of fine-grained material and the chemical proxies were more or less stable over time in the core from the mouth while they varied synchronously over time in the core from the head of the estuary. The sediment proxies combined show that mangrove deforestation had large effects on the estuary with regard to both the physical and chemical environment with implications for the biological functioning.

  3. Biological Decolorization of C.I. Basic Green 4 Solution by Chlorella sp.:Effect of Operational Parameters

    Institute of Scientific and Technical Information of China (English)

    Khataee A. R.; Pourhassan M.; Ayazloo M.

    2009-01-01

    In recent years, the ability of microorganisms to decolorize textile wastewater has received great attention due to the environmental persistence and toxicity of these pollutants. In this paper biological decolorization of triphenylmethane dye, C.I. Basic Green 4 (BG 4), by Chlorella species was investigated. The effect of operational parameters (temperature, pH, initial dye concentration and algal concentration) on decolorization efficiency was examined. Results indicated that the desired initial pH was 9. The stability and efficiency of the algae in long-term repetitive operations were also examined. Michaelis-Menten kinetics was employed to describe the apparent correlation between the decolorization rate and dye concentration. The optimal kinetic parameters, Vmax (specific decolorization rate) and Km (maximum specific decolorization rate) were 4.6 mg dye g cell-1 h-1and 151.0 mg L-1, respectively. Fig 10, Tab 2, Ref24

  4. Effect of the physicochemical parameters of soils on the biological availability of natural and radioactive zinc

    Science.gov (United States)

    Anisimov, V. S.; Kochetkov, I. V.; Dikarev, D. V.; Anisimova, L. N.; Korneev, Yu. N.; Frigidova, L. M.

    2016-08-01

    The relationship between the main physicochemical properties of soils and the accumulation of natural Zn and 65Zn radionuclide has been studied, and the capacity of soils to limit the mobility of the element in the soil-plant system has been assessed. The contribution of each of the selected soil state parameters to the accumulation of zinc by barley has been determined, and the soil state parameters have been ranked. It has been found that the largest contributions to the variation of the resulting parameter (65Zn accumulation coefficient, K a) are made by mobile Fe (25%), free carbonates (21%), and acid-soluble Zn (18%). The largest contributions to the Znac K a are made by free carbonates (13%) and mobile Fe (8%). The contributions of physical clay and organic carbon in soils and qualitative composition of humic substances are almost similar (4% for each). No differences in the inactivating capacity of different soils (soddy-podzolic soils, gray forest soils, and chernozems) for 65Zn are observed. This is related to the fact that the transfer of 65Zn to plants is statistically significantly controlled by the contents of free carbonates, mobile iron, and potentially plantavailable forms of stable natural Zn (carrier of 65Zn) rather than the quantitative and qualitative composition of organic matter and the degree of dispersion of mineral particles. The analysis of the Znac K a/65Zn K a ratios has shown that the share of plant-available Zn in the acid-soluble form of the metal (1 M HCl) is 0.61 on the average for the studied soils, and its share in the total Zn content in the soils is only 0.14.

  5. A biological/chemical process for reduced waste and energy consumption: caprolactam production. Final report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-05-01

    A biological/chemical process for converting cyclohexane into caprolactam was investigated: microorganisms in a bioreactor would be used to convert cyclohexane into caprolactone followed by chemical synthesis of caprolactam using ammonia. Four microorganisms were isolated from natural soil and water, that can utilize cyclohexane as a sole source of C and energy for growth. They were shown to have the correct metabolic intermediates and enzymes to convert cyclohexane into cyclohexanol, cyclohexanone, and caprolactone. Genetic techniques to create and select for caprolactone hydrolase negative-mutants were developed; those are used to convert cyclohexane into caprolactone but, because of the block, are unable to metabolize the caprolactone further. Because of a new nylon carpet reycle process and the long time frame for a totally new bioprocess, a limited study was done to evaluate whether a simplified bioprocess to convert cyclohexanol into cyclohexanone or caprolactone was feasible; growth rates and key enzyme levels were measured in a collection of microorganisms that metabolize cyclohexanol to determine if the bioactivity is high enough to support an economical cyclohexanol bioprocess. Although these microorganisms had sufficient bioactivity, they could tolerate only low levels (<1%) of cyclohexanol and thus are not suitable for developing a cost effective bioprocess because of the high cost of dilute product recovery.

  6. Biological conversion of synthesis gas. Final report, August 31, 1990--September 3, 1993

    Energy Technology Data Exchange (ETDEWEB)

    Basu, R.; Klasson, K.T.; Johnson, E.R.; Takriff, M.; Clausen, E.C.; Gaddy, J.L.

    1993-09-01

    Based upon the results of this culture screening study, Rhodospirillum rubrum is recommended for biocatalysis of the water gas shift reaction and Chlorobium thiosulfatophilum is recommended for H{sub 2}S conversion to elemental sulfur. Both bacteria require tungsten light for growth and can be co-cultured together if H{sub 2}S conversion is not complete (required concentration of at least 1 ppM), thereby presenting H{sub 2} uptake by Chlorobium thiosulfatophilum. COS degradation may be accomplished by utilizing various CO-utilizing bacteria or by indirectly converting COS to elemental sulfur after the COS first undergoes reaction to H{sub 2} in water. The second alternative is probably preferred due to the low expected concentration of COS relative to H{sub 2}S. Mass transfer and kinetic studies were carried out for the Rhodospirillum rubrum and Chlorobium thiosulfatophilum bacterial systems. Rhodospirillum rubrum is a photosynthetic anaerobic bacterium which catalyzes the biological water gas shift reaction: CO + H{sub 2}O {yields} CO{sub 2} + H{sub 2}. Chlorobium thiosulfatophilum is also a photosynthetic anaerobic bacteria, and converts H{sub 2}S and COS to elemental sulfur.

  7. Final Technical Report - Use of Systems Biology Approaches to Develop Advanced Biofuel-Synthesizing Cyanobacterial Strains

    Energy Technology Data Exchange (ETDEWEB)

    Pakrasi, Himadri [Washington Univ., St. Louis, MO (United States)

    2016-09-01

    The overall objective of this project was to use a systems biology approach to evaluate the potentials of a number of cyanobacterial strains for photobiological production of advanced biofuels and/or their chemical precursors. Cyanobacteria are oxygen evolving photosynthetic prokaryotes. Among them, certain unicellular species such as Cyanothece can also fix N2, a process that is exquisitely sensitive to oxygen. To accommodate such incompatible processes in a single cell, Cyanothece produces oxygen during the day, and creates an O2-limited intracellular environment during the night to perform O2-sensitive processes such as N2-fixation. Thus, Cyanothece cells are natural bioreactors for the storage of captured solar energy with subsequent utilization at a different time during a diurnal cycle. Our studies include the identification of a novel, fast-growing, mixotrophic, transformable cyanobacterium. This strain has been sequenced and will be made available to the community. In addition, we have developed genome-scale models for a family of cyanobacteria to assess their metabolic repertoire. Furthermore, we developed a method for rapid construction of metabolic models using multiple annotation sources and a metabolic model of a related organism. This method will allow rapid annotation and screening of potential phenotypes based on the newly available genome sequences of many organisms.

  8. Biological determinants of photobioreactor design. Final report, September 1, 1993--August 31, 1995

    Energy Technology Data Exchange (ETDEWEB)

    Palsson, B.; Brown, G.G.

    1997-04-01

    Microalgae is being considered for the capture and sequestration of CO{sub 2} from power-plant flue-gases. High productivity of microalgae is necessary to make this process cost effective compared to the conventional methods used for reducing CO{sub 2} levels in the atmosphere. This obviates the need for large-scale cultivation technologies and proper photobioreactor technology. The physical factors that influence the performance of a photoautotrophic microalgal culture are the quality and composition of light, inlet carbon dioxide concentration, nutrients, and secondary metabolites at high cell densities. In developing photobioreactor technology, balancing of biological processes to the physical rate process becomes important. The effect of various light compositions on the culture kinetics was studied. To determine the optimal composition, six wavelengths 470, 555, 560, 570, 580 and 605 nm, each supplemented with 680 nm of red light, were used to cultivate cultures. Based on the results obtained, it is concluded that a monochromatic red light of 680 nm is sufficient to obtain maximum capacity.

  9. The relationship between haematocrit and some biological parameters of the Indian shad, Tenualosa ilisha (Family Clupeidae

    Directory of Open Access Journals (Sweden)

    Jawad, L. A.

    2004-12-01

    Full Text Available Haemathological parameters have been recognised as valuable tools for the monitoring of fish health. Here we analyse the relationship between haematocrit and body length, sex and reproductive state in the Indian Shad Tenualosa ilisha. Haematocrit value showed a quadratic relationship to fish size (body length, incrementing as the fish body length increased up to 400 mm, after which it decreased. Male fish showed a higher haematocrit value than females. Haematocrit appeared to be higher in the pre-spawning period than in the spawning phase, but then increased slightly in the post-spawning period.

  10. Adaptive imaging cytometry to estimate parameters of gene networks models in systems and synthetic biology.

    Directory of Open Access Journals (Sweden)

    David A Ball

    Full Text Available The use of microfluidics in live cell imaging allows the acquisition of dense time-series from individual cells that can be perturbed through computer-controlled changes of growth medium. Systems and synthetic biologists frequently perform gene expression studies that require changes in growth conditions to characterize the stability of switches, the transfer function of a genetic device, or the oscillations of gene networks. It is rarely possible to know a priori at what times the various changes should be made, and the success of the experiment is unknown until all of the image processing is completed well after the completion of the experiment. This results in wasted time and resources, due to the need to repeat the experiment to fine-tune the imaging parameters. To overcome this limitation, we have developed an adaptive imaging platform called GenoSIGHT that processes images as they are recorded, and uses the resulting data to make real-time adjustments to experimental conditions. We have validated this closed-loop control of the experiment using galactose-inducible expression of the yellow fluorescent protein Venus in Saccharomyces cerevisiae. We show that adaptive imaging improves the reproducibility of gene expression data resulting in more accurate estimates of gene network parameters while increasing productivity ten-fold.

  11. Adaptive imaging cytometry to estimate parameters of gene networks models in systems and synthetic biology.

    Science.gov (United States)

    Ball, David A; Lux, Matthew W; Adames, Neil R; Peccoud, Jean

    2014-01-01

    The use of microfluidics in live cell imaging allows the acquisition of dense time-series from individual cells that can be perturbed through computer-controlled changes of growth medium. Systems and synthetic biologists frequently perform gene expression studies that require changes in growth conditions to characterize the stability of switches, the transfer function of a genetic device, or the oscillations of gene networks. It is rarely possible to know a priori at what times the various changes should be made, and the success of the experiment is unknown until all of the image processing is completed well after the completion of the experiment. This results in wasted time and resources, due to the need to repeat the experiment to fine-tune the imaging parameters. To overcome this limitation, we have developed an adaptive imaging platform called GenoSIGHT that processes images as they are recorded, and uses the resulting data to make real-time adjustments to experimental conditions. We have validated this closed-loop control of the experiment using galactose-inducible expression of the yellow fluorescent protein Venus in Saccharomyces cerevisiae. We show that adaptive imaging improves the reproducibility of gene expression data resulting in more accurate estimates of gene network parameters while increasing productivity ten-fold.

  12. On finding and using identifiable parameter combinations in nonlinear dynamic systems biology models and COMBOS: a novel web implementation.

    Science.gov (United States)

    Meshkat, Nicolette; Kuo, Christine Er-zhen; DiStefano, Joseph

    2014-01-01

    Parameter identifiability problems can plague biomodelers when they reach the quantification stage of development, even for relatively simple models. Structural identifiability (SI) is the primary question, usually understood as knowing which of P unknown biomodel parameters p1,…, pi,…, pP are-and which are not-quantifiable in principle from particular input-output (I-O) biodata. It is not widely appreciated that the same database also can provide quantitative information about the structurally unidentifiable (not quantifiable) subset, in the form of explicit algebraic relationships among unidentifiable pi. Importantly, this is a first step toward finding what else is needed to quantify particular unidentifiable parameters of interest from new I-O experiments. We further develop, implement and exemplify novel algorithms that address and solve the SI problem for a practical class of ordinary differential equation (ODE) systems biology models, as a user-friendly and universally-accessible web application (app)-COMBOS. Users provide the structural ODE and output measurement models in one of two standard forms to a remote server via their web browser. COMBOS provides a list of uniquely and non-uniquely SI model parameters, and-importantly-the combinations of parameters not individually SI. If non-uniquely SI, it also provides the maximum number of different solutions, with important practical implications. The behind-the-scenes symbolic differential algebra algorithms are based on computing Gröbner bases of model attributes established after some algebraic transformations, using the computer-algebra system Maxima. COMBOS was developed for facile instructional and research use as well as modeling. We use it in the classroom to illustrate SI analysis; and have simplified complex models of tumor suppressor p53 and hormone regulation, based on explicit computation of parameter combinations. It's illustrated and validated here for models of moderate complexity, with

  13. On finding and using identifiable parameter combinations in nonlinear dynamic systems biology models and COMBOS: a novel web implementation.

    Directory of Open Access Journals (Sweden)

    Nicolette Meshkat

    Full Text Available Parameter identifiability problems can plague biomodelers when they reach the quantification stage of development, even for relatively simple models. Structural identifiability (SI is the primary question, usually understood as knowing which of P unknown biomodel parameters p1,…, pi,…, pP are-and which are not-quantifiable in principle from particular input-output (I-O biodata. It is not widely appreciated that the same database also can provide quantitative information about the structurally unidentifiable (not quantifiable subset, in the form of explicit algebraic relationships among unidentifiable pi. Importantly, this is a first step toward finding what else is needed to quantify particular unidentifiable parameters of interest from new I-O experiments. We further develop, implement and exemplify novel algorithms that address and solve the SI problem for a practical class of ordinary differential equation (ODE systems biology models, as a user-friendly and universally-accessible web application (app-COMBOS. Users provide the structural ODE and output measurement models in one of two standard forms to a remote server via their web browser. COMBOS provides a list of uniquely and non-uniquely SI model parameters, and-importantly-the combinations of parameters not individually SI. If non-uniquely SI, it also provides the maximum number of different solutions, with important practical implications. The behind-the-scenes symbolic differential algebra algorithms are based on computing Gröbner bases of model attributes established after some algebraic transformations, using the computer-algebra system Maxima. COMBOS was developed for facile instructional and research use as well as modeling. We use it in the classroom to illustrate SI analysis; and have simplified complex models of tumor suppressor p53 and hormone regulation, based on explicit computation of parameter combinations. It's illustrated and validated here for models of moderate

  14. Age-related differences in the biological parameters of vertebral cancellous bone from Chinese women

    Institute of Scientific and Technical Information of China (English)

    JIANG Rui; LIU Guo-min; BAI Hao-tian; WANG Tian-bin; WU Han; JIA Yun-yan; LUO Yun-gang

    2013-01-01

    Background With aging,the human fracture risk gradually increase.This is mainly due to the corresponding changes of the biomechanical parameters of human bone presents with aging.We measured the microstructural parameters of lumbar bone from women in several age groups by micro-computed tomography and scanning electron microscopy.We observed changes in lumbar cancellous bone mineral density and in biomechanical parameters with aging to elucidate the relationship between age and risk of fracture.We provide theoretical support for human pathology,fracture risk increased with age and the individualized of each age group.Methods Thirty-two fresh L3 vertebral bodies were donated from 32 women,aged 20-59 years and were divided into four age groups:20 to 29 years (group A); 30 to 39 years (group B); 40 to 49 years (group C); and 50 to 59 years (group D).Conventional lumbar separation was performed by removing soft tissue and subsidiary structures,leaving only the vertebral body.The vertebral body was cut into halves along the median sagittal plane,maintaining the upper and lower end-plates of each half,and used for biomechanical,morphological,and density measurements.Results Comparing group A to B,the rod-like trabecular thickness (Tb.Th) decreased; the trabecular spacing (Tb.Sp) increased; the plate-like Tb.Th decreased; bone mineral density,tissue mineral density,bone volume fraction,and bone surface fraction decreased,and the elastic modulus and the ultimate stress decreased (all changes P <0.05).Similar significant (P < 0.05) trends were obtained when comparing group C to D.With aging,the collagen cross-linking capacity declined,the thickness of the collagen fibrils was variable (ranging from almost the same to loose,sparse,or disordered),and the finer collagen fibrils between the thick filaments were disorganized.Conclusions In women aged 20 to 59 years,the rod-like and plate-like Tb.Th of the vertebral body decreased,while Tb.Sp increased

  15. Parameters optimization for biological molecules patterning using 248-nm ultrafast lasers

    Science.gov (United States)

    Dinca, V.; Ranella, A.; Popescu, A.; Dinescu, M.; Farsari, M.; Fotakis, C.

    2007-12-01

    Laser-induced forward transfer has been used for the deposition of photoactive biotin in micron-scale patterns. The process uses a 500 fs pulsed KrF laser beam to transfer small amounts of a liquid solution target as micron-size droplets to a substrate placed parallel and in close proximity to it. The biomolecules remain active after the transfer; this is demonstrated through fluorescence assays. In addition to the laser parameters, those regarding the target composition and the receiving surface for the miniaturization of the transferred patterns have been studied and optimized. Droplets as small as 5 μm have been obtained by reducing the target thickness and transfer energy; by increasing the percentage of glycerol added in the biomolecules solution and by using hydrophobic surfaces as receiving substrates. The influence of the glycerol addition and the hydrophobicity of the receiving surfaces on the activity of the transferred biomolecules have also been studied.

  16. Effects of chemical and biological pesticides on plant growth parameters and rhizospheric bacterial community structure in Vigna radiata

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Sunil; Gupta, Rashi; Sharma, Shilpi, E-mail: shilpi@dbeb.iitd.ac.in

    2015-06-30

    Highlights: • Non-target effects of pesticides employing qualitative and quantitative approaches. • Qualitative shifts in resident and active bacterial community structure. • Abundance of 16S rRNA gene and transcripts were reduced significantly. • Effects of biological pesticide similar to chemical pesticides on rhizospheric bacteria. - Abstract: With increasing application of pesticides in agriculture, their non-target effects on soil microbial communities are critical to soil health maintenance. The present study aimed to evaluate the effects of chemical pesticides (chlorpyrifos and cypermethrin) and a biological pesticide (azadirachtin) on growth parameters and the rhizospheric bacterial community of Vigna radiata. Qualitative and quantitative analysis by PCR-denaturing gradient gel electrophoresis (DGGE) and q-PCR, respectively, of the 16S rRNA gene and transcript were performed to study the impact of these pesticides on the resident and active rhizospheric bacterial community. While plant parameters were not affected significantly by the pesticides, a shift in the bacterial community structure was observed with an adverse effect on the abundance of 16S rRNA gene and transcripts. Chlorpyrifos showed almost complete degradation toward the end of the experiment. These non-target impacts on soil ecosystems and the fact that the effects of the biopesticide mimic those of chemical pesticides raise serious concerns regarding their application in agriculture.

  17. DARWIN Y LA IMPOSIBILIDAD DE CAUSAS FINALES EN LA BIOLOGÍA Darwin and the Impossibility of Final Causes in Biology

    Directory of Open Access Journals (Sweden)

    ÁLVARO CORRAL CUARTAS

    Full Text Available La teoría de la selección natural propuesta por Charles Darwin en su obra El origen de las especies no solo colocó las bases para una explicación coherente de los hechos fundamentales de la biología (el origen común de los seres vivos, la diversidad de individuos y especies y la transmisión de características hereditarias, sino que además introdujo maneras nuevas de hacer filosofía. La teoría de la selección natural hace superflua cualquier posibilidad de apelar a explicaciones de tipo finalista en la ciencia. Desde Aristóteles se conocen cuatro tipos de causa: la material, la formal, la eficiente y la final. Aunque la causa eficiente es el paradigma de explicación por exce-lencia de las ciencias naturales, la causa final sigue desempeñando un papel explicativo, por cuanto parece estar arraigada en nuestra estructura humana de pensamiento y la tendencia a presentar explicaciones finalistas sigue siendo recalcitrante. Quizá por estar los seres humanos tan familiarizados con la complejidad inherente a los procesos de diseño en las artes y en la técnica y quizá por la circunstancia de que los seres humanos organizamos casi todas nuestras acciones en torno a propósitos, es decir, a la definición de unos fines para los cuales buscamos unos medios, suponemos por vía de analogía que la naturaleza en su complejidad exige la presencia y acción de un diseñador inteligente. Kant en la Crítica de la facultad de juzgar hace una defensa del carácter "irrenunciable al género humano" de este modelo explicativo. Para contro-vertir esta opinión milenaria, me apoyaré, en investigaciones recientes de Richard Dawkins y de otros biólogos contemporáneos para mostrar con la evolución de ojos en la naturaleza que el surgimiento de órganos de alta complejidad puede ser explicado sin problema con la teoría de la selección natural propuesta por Darwin en 1859.Darwin’s theory of natural selection in The Origin of Species not only laid

  18. Medium energy measurements of N-N parameters. Final technical report, April 1, 1994--September 30, 1996

    Energy Technology Data Exchange (ETDEWEB)

    Ambrose, D.; Betts, W.; Coffey, P.; Glass, G.; McDonough, J.; Riley, P.; Tang, J.L.

    1998-08-01

    This document is a final technical report describing the accomplishments of the medium/high energy nuclear physics research program at the University of Texas at Austin. The research program had four main thrusts, only one of which can be considered as measurements of N-N parameters: (1) finishing the data analyses associated with recent LAMPF and TRIUMPF N-N experiments, whose overall purpose has been the determination of the nucleon-nucleon amplitudes, both for isospin 0 and 1 at medium energies; (2) continuing work on BNL E871, a search for rare decay modes of the K{sub L}; (3) work on the RHIC-STAR project, an experiment to create and study a quark gluon plasma and nuclear matter at high energy density; (4) beginning a new AGS experiment (E896) which will search for the lowest mass state of the predicted strange di-baryons, the Ho, and other exotic states of nuclear matter through nucleus-nucleus collisions.

  19. SynTec Final Technical Report: Synthetic biology for Tailored Enzyme cocktails

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Janine [Novozymes, Inc., Davis, CA (United States); Teter, Sarah [Novozymes, Inc., Davis, CA (United States)

    2016-06-30

    Using a novel enzyme screening method inspired by synthetic biology, Novozymes developed new technology under SynTec which allows for more rapidly tailoring of enzyme cocktails. The methodology can be applied to specific feedstocks, and or coupled to address a specific hydrolytic conversion process context. Using combinatorial high throughput screening of libraries of enzyme domains, we can quickly assess which combination of catalytic modules delivers the best performance for a specific condition. To demonstrate the effectiveness of the screening process, we measured performance of the output catalytic cocktail compared to CTec3/HTec3. SynTec benchmark cocktail - blend of Cellic® CTec3 and HTec3. The test substrate was - ammonia fiber expansion pretreated corn stover (AFEX™ PCS).CTec3/HTec3 was assayed at the optimal pH and temperature, and also in the absence of any pH adjustment. The new enzyme cocktail discovered under SynTec was assayed in the absence of any pH adjustment and at the optimal temperature. Conversion is delivered by SynTec enzyme at significant dose reduction relative to CTec3/HTec3 at the controlled pH optimum, and without titrant required to maintain pH, which delivers additional cost savings relative to current state of the art process. In this 2.5 year $4M project, the team delivered an experimental cocktail that significantly outperformed CTec3/HTec3 for a specific substrate, and for specific hydrolysis conditions. As a means of comparing performance improvement delivered per research dollar spent, we note that SynTec delivered a similar performance improvement to the previous award, in a shorter time and with fewer resources than for the previously successful DOE project DECREASE, a 3.5 year, $25M project, though this project focused on a different substrate and used different hydrolysis conditions. The newly implemented technology for rapid sourcing of new cellulases and hemicellulases from nature is an example of Novozymes

  20. Sonochemical degradation of the pharmaceutical fluoxetine: Effect of parameters, organic and inorganic additives and combination with a biological system

    Energy Technology Data Exchange (ETDEWEB)

    Serna-Galvis, Efraím A.; Silva-Agredo, Javier [Grupo de Investigación en Remediación Ambiental y Biocatálisis, Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín (Colombia); Giraldo-Aguirre, Ana L. [Grupo de Diseño y Formulación de Medicamentos, Cosméticos y Afines (DYFOMECO), Facultad de Química Farmacéutica, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín (Colombia); Torres-Palma, Ricardo A., E-mail: ricardo.torres@udea.edu.co [Grupo de Investigación en Remediación Ambiental y Biocatálisis, Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín (Colombia)

    2015-08-15

    Fluoxetine (FLX), one of the most widely used antidepressants in the world, is an emergent pollutant found in natural waters that causes disrupting effects on the endocrine systems of some aquatic species. This work explores the total elimination of FLX by sonochemical treatment coupled to a biological system. The biological process acting alone was shown to be unable to remove the pollutant, even under favourable conditions of pH and temperature. However, sonochemical treatment (600 kHz) was shown to be able to remove the pharmaceutical. Several parameters were evaluated for the ultrasound application: the applied power (20–60 W), dissolved gas (air, Ar and He), pH (3–11) and initial concentration of fluoxetine (2.9–162.0 μmol L{sup −1}). Additionally, the presence of organic (1-hexanol and 2-propanol) and inorganic (Fe{sup 2+}) compounds in the water matrix and the degradation of FLX in a natural mineral water were evaluated. The sonochemical treatment readily eliminates FLX following a kinetic Langmuir. After 360 min of ultrasonic irradiation, 15% mineralization was achieved. Analysis of the biodegradability provided evidence that the sonochemical process transforms the pollutant into biodegradable substances, which can then be mineralized in a subsequent biological treatment. - Highlights: • The pharmaceutical fluoxetine was effectively eliminated upon ultrasonic action. • Ultrasonic power, dissolved gas, pH and concentration of fluoxetine were evaluated. • Fe{sup 2+}, sodium nitrate or nitric acid had a positive effect on the FLX degradation. • More hydrophobic or volatile compounds than fluoxetine diminished the efficiency. • A sonochemical-biological combined process led to the total mineralization of FLX.

  1. The biology and demographic parameters of Aedes albopictus in northern peninsular Malaysia

    Institute of Scientific and Technical Information of China (English)

    H Nur Aida; Hamady Dieng; AT Nurita; MR Che Salmah; Fumio Miake; B Norasmah

    2011-01-01

    To generate life table characteristics for the dengue vector Aedes albopictus (A.albopictus ) under uncontrolled conditions, incorporating both the aquatic and the adult stages. Methods: Ten females derived from wild pupae were allowed to fully blood-feed on restrained mice. 774 eggs were hatched in seasoned water. F1 larvae were followed for development until their F2 counterparts emerged as adults. Some population parameters were monitored (F1) or estimated (F2). Results: A. albopictus exhibited increased fecundity and egg hatch success. Immature development was quick. Immature survival was high, with lowest rate in the pupal stage. Adult emergence was about 81% and sex ratio was close to 1:1. Generational mortality (K) was about 28%. A high proportion of females completed a reproductive cycle and the obtained parity rate was predicted to lead to higher fecundity in the next generation. Conclusions: It can be concluded that natural A. albopictus populations in Penang seem largely determined by quick development in combination with low immature loss and increased oviposition.

  2. Biological Behavior of Anammox Process for Municipal Wastewater Treatment: Effect of Ammonia Removal and Other Parameters

    Directory of Open Access Journals (Sweden)

    *R. Nabizadeh

    2012-09-01

    Full Text Available Historically, nitrogen compound due to major environmental and public health problems have been considered. Anaerobic ammonium oxidation processes were proposed by many advantages such as; novelty, promising method and cost-effective. In this work, we used of anommax process for a wastewater with high C:N ratios and the main parameter likes pH; temperature, NO2/NH4 ratio and behavior of COD, ammonium and nitrite during operation time of 55 days were evaluated. High efficiency in nitrite and ammonium removal is observed at pH values between 7.5 to 8 and operation times between 9 to 23 days. Furthermorethe variation of the nitrite/ammonium ratio done dependence to pH, and a higher ratio was associated with higher pH values. And lower values of NO2/NH4 ratio have occurred with decrease of pH at third phase of anommax process. The average elimination efficiency of COD was occurred about 89.22%, but the removal efficiency of COD in anommax reactor was obtained about 49.5%. Furthermorethe removal efficiency of ammonium and nitrite were provided about 50% for each.

  3. Research overview of biological and chemical conversion methods and identification of key research areas for SERI. Final task report

    Energy Technology Data Exchange (ETDEWEB)

    Milne, T. A.; Connolly, J. S.; Inman, R. E.; Reed, T. B.; Seibert, M.

    1978-09-01

    A qualitative overview of the current and future research areas of the Biological and Chemical Conversion Branch is presented. The goals of the Branch and the general areas of Branch activities are mapped out: energy and petrochemical substitutes from biomass, thermochemical conversion, and photoconversion. Each of these three areas in some detail are discussed in some detail in a general overview. Specific parts of the three major areas which have been selected are discussed in the context of present Department of Energy sponsored research including the Fuels from Biomass and Office of Basic Energy Sciences programs, for initial SERI in-house research emphasis. Finally, the Branch research efforts planned through FY 79 are outlined.

  4. Monte Carlo simulation of parameter confidence intervals for non-linear regression analysis of biological data using Microsoft Excel.

    Science.gov (United States)

    Lambert, Ronald J W; Mytilinaios, Ioannis; Maitland, Luke; Brown, Angus M

    2012-08-01

    This study describes a method to obtain parameter confidence intervals from the fitting of non-linear functions to experimental data, using the SOLVER and Analysis ToolPaK Add-In of the Microsoft Excel spreadsheet. Previously we have shown that Excel can fit complex multiple functions to biological data, obtaining values equivalent to those returned by more specialized statistical or mathematical software. However, a disadvantage of using the Excel method was the inability to return confidence intervals for the computed parameters or the correlations between them. Using a simple Monte-Carlo procedure within the Excel spreadsheet (without recourse to programming), SOLVER can provide parameter estimates (up to 200 at a time) for multiple 'virtual' data sets, from which the required confidence intervals and correlation coefficients can be obtained. The general utility of the method is exemplified by applying it to the analysis of the growth of Listeria monocytogenes, the growth inhibition of Pseudomonas aeruginosa by chlorhexidine and the further analysis of the electrophysiological data from the compound action potential of the rodent optic nerve.

  5. Biological parameter change of myopic eyes%近视眼生物学参数的改变研究

    Institute of Scientific and Technical Information of China (English)

    张芳; 吕帆

    2008-01-01

    目的 研究近视眼各生物学参数的改变.方法 对近视患者及正视者110例(174只眼),主觉加检影验光行屈光检查,采用Humphrey测量角膜平均曲率,非接触式眼内压测量仪测量眼内压:A与B型超声诊断仪测量前房深度、晶状体厚度、玻璃体腔长度及眼轴长度;角膜测厚仪测量中央角膜厚度(CCT,centercornealthickness);光学相干生物测最仪(IOL-master)测量眼轴长度;光学相干断层扫描仪(StratusOCT)测量黄斑中心视网膜厚度;按等效球镜度数(SE,sphericalequivalent)不同分正视组(SE0.05),其余两两比较均有显著性差异(P<0.01);其余参数各组比较差异均无统计学意义.结论 随着等效球镜度数增加,近视眼前房深度一定程度增加,玻璃体腔长度、眼轴随线性增加;其余生物学参数无明显改变;玻璃体腔长度增加是引起眼轴增长和等效球镜度数增加的原因.%Objective A research of biological parameter of myopic eyes. Methods One hunderd amd ten human subjects (one hunderd and seventy-four eyes) were included in this re- search. Retinoscopy was made to measure refractive errors, corneal topographer was measured by corneal to- pography system, Tonometry was used to measure IOP, Ultrasonagraphy was applied to measure anterior cham- ber length,len thickness and vitreous length respectively,Laser interference biometer was used to measure axial length, Optical coherence tomography was used to measure retina thickness of fovea area. Based on spherical e- quivalent subjects were divided into four groups: emmetropia group(SE<-0.50D), low-myopia group(-0.50D≤ SE<-3.00D), moderate myopia group ( -3.00D≤ SE<-6.00D )and high myopia group ( SE≥-6.00D ). compare biological parameter with each other in different groups,and analysis the correlation between the spherical e- quivalent and other biological parameters.Results Refraction results in emmetropia group,low-myopi a group, moderate myopia group and high

  6. Evaluation of some biological parameters of Opuntia ficus indica. 2. Influence of seed supplemented diet on rats.

    Science.gov (United States)

    Ennouri, Monia; Fetoui, Hamadi; Bourret, Evelyne; Zeghal, Najiba; Guermazi, Fadhel; Attia, Hamadi

    2006-11-01

    The present research was undertaken to evaluate some biological parameters in rats fed with a supplemented diet with Opuntia ficus indica powder seeds. Feed intake and body weight of rats were measured every two days during nine weeks of treatment. Digestibility, feed conversion efficiency and protein efficiency ratio were determined. No difference in digestibility was noticed between the different diets. The results indicated a significant decrease in body weight of rats receiving a diet partially substituted with O. ficus indica powder seeds, probably due to a significant decrease in serum-free thyroxin (FT(4)) compared to the control group. In the treated group, a decrease of glucose concentration in blood and an increase of glycogen in liver and skeletal muscle were noticed. A significant increase in HDL-cholesterol was noted in the group receiving the supplemented diet with O. ficus indica powder seeds. These results suggest that O. ficus indica seeds can be used as a healthy food.

  7. Biological Parameters and Molecular Markers of Clone CL Brener - The Reference Organism of the Trypanosoma cruzi Genome Project

    Directory of Open Access Journals (Sweden)

    Bianca Zingales

    1997-11-01

    Full Text Available Clone CL Brener is the reference organism used in the Trypanosoma cruzi Genome Project. Some biological parameters of CL Brener were determined: (a the doubling time of epimastigote forms cultured in liver infusion-tryptose (LIT medium at 28oC is 58±13 hr; (b differentiation of epimastigotes to metacyclic trypomastigotes is obtained by incubation in LIT-20% Grace´s medium; (c trypomastigotes infect mammalian cultured cells and perform the complete intracellular cycle at 33 and 37oC; (d blood forms are highly infective to mice; (e blood forms are susceptible to nifurtimox and benznidazole. The molecular typing of CL Brener has been determined: (a isoenzymatic profiles are characteristic of zymodeme ZB; (b PCR amplification of a 24Sa ribosomal RNA sequence indicates it belongs to T. cruzi lineage 1; (c schizodeme, randomly amplified polymorphic DNA (RAPD and DNA fingerprinting analyses were performed

  8. Biologic

    CERN Document Server

    Kauffman, L H

    2002-01-01

    In this paper we explore the boundary between biology and the study of formal systems (logic). In the end, we arrive at a summary formalism, a chapter in "boundary mathematics" where there are not only containers but also extainers ><, entities open to interaction and distinguishing the space that they are not. The boundary algebra of containers and extainers is to biologic what boolean algebra is to classical logic. We show how this formalism encompasses significant parts of the logic of DNA replication, the Dirac formalism for quantum mechanics, formalisms for protein folding and the basic structure of the Temperley Lieb algebra at the foundations of topological invariants of knots and links.

  9. Estimation of biological kinetic parameters from an analysis of the BOD curve of waste waters - effects of a chemical preoxidation

    Energy Technology Data Exchange (ETDEWEB)

    Berlan, F.J.; Garcia-Araya, J.F.; Alvarez, P. [Universidad de Extremadura, Badajoz (Spain). Dept. de Ingenieria Quimica y Energetica

    1997-12-31

    Urban waste waters were treated with pure ozone or combinations of ozone, hydrogen peroxide and/or UV radiation to study the course of resulting BOD (biological oxygen demand)-time profiles and to propose a kinetic model. BOD-time profiles of chemically treated waste waters show an initial lag period that first order kinetic models cannot describe. A second order kinetic model is then proposed that satisfactorily fits experimental BOD-time profiles, except when hydrogen peroxide has been used. In these cases, BOD-time profiles present the highest lag periods observed. By applying this model, three parameters are determined: the biokinetic constant (k) which is an index of the biological removal rate; the potential amount of biodegradable matter (BOD{sub T}), and the measure of the size of inocula and microbial activities of microorganisms ({lambda}). The model was checked with experimental results of BOD-time profiles corresponding to both untreated and chemically ozonated urban waste waters. Ozonated waste waters showed the highest values of k and BOD{sub T}, which implies an improvement of waste water biodegradability after ozonation. However, values of {lambda} corrsponding to ozonated waste waters presented lower values than those of untreated waste waters. This was due to the lag period observed in the BOD-time profile, which was a consequence of a lack of micro-organism acclimation to ozonated waste waters. The effect of the ozone dose, pH and carbonates during oxonation on COD (chemical oxygen demand) and the above indicated parameters was also studies. The results suggest that ozonolysis, the direct molecular ozone way of reaction, due to its selective character, increases the biodegradability of waste water more than other chemically advancec oxidation processes based on hydroxyl radical reactions. (orig./SR)

  10. FINAL REPORT: DOE CONTRACT NUMBER FG0205ER64026 Biological Neutron Scattering: A Collaboration with the Oak Ridge Center for Structural Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)

    Trewhella, Jill [Univ. of Utah, Salt Lake City, UT (United States)

    2011-01-12

    The overarching goal of this project was to promote applications of small-angle scattering in structural molecular biology by providing model examples of cutting edge applications that demonstrate the unique capabilities and potential of the DOE national user facilities at Oak Ridge, especially the newly commissioned BioSANS. The approach taken was three-fold: (1) to engage in high impact collaborative research projects that would benefit from small-angle neutron scattering to both demonstrate the power of the technique while expanding the potential user community; (2) to provide access to scattering facilities established at the University of Utah to as broad a set of researchers as possible to increase the expertise in small-angle scattering generally; and (3) to develop new methods and tools for small-angle scattering. To these ends, three major research collaborations were pursued that resulted in a significant body of published work where neutron scattering and contrast variation played a major role. These major collaborations involved studies of protein complexes involved in (1) bacterial transcription regulation and adaptive response (a DOE/BER priority area); (2) regulation of cardiac muscle; and (3) neuronal disorders. In addition, to broaden the impact of the project, smaller collaborative efforts were supported that used either small-angle X-ray or neutron scattering. Finally, the DOE supported facilities at the University of Utah were made available to researchers on a service basis and a number of independent groups took advantage of this opportunity. In all of this work, there was an emphasis on the training of students and post docs in scattering techniques, and a set of publications (a book chapter, a review, and an encyclopedia article) were produced to guide the non-specialist potential user of scattering techniques in successful applications of the techniques. We also developed a suite of user friendly web-based computational tools currently

  11. Multivariate analysis of respiratory problems and their connection with meteorological parameters and the main biological and chemical air pollutants

    Science.gov (United States)

    Matyasovszky, István; Makra, László; Bálint, Beatrix; Guba, Zoltán; Sümeghy, Zoltán

    2011-08-01

    The aim of the study is to analyse the joint effect of biological (pollen) and chemical air pollutants, as well as meteorological variables, on the hospital admissions of respiratory problems for the Szeged region in Southern Hungary. The data set used covers a nine-year period (1999-2007) and is unique in the sense that it includes—besides the daily number of respiratory hospital admissions—not just the hourly mean concentrations of CO, PM 10, NO, NO 2, O 3 and SO 2 with meteorological variables (temperature, global solar flux, relative humidity, air pressure and wind speed), but two pollen variables ( Ambrosia and total pollen excluding Ambrosia) as well. The analysis was performed using three age categories for the pollen season of Ambrosia and the pollen-free season. Meteorological elements and air pollutants are clustered in order to define optimum environmental conditions of high patient numbers. ANOVA was then used to determine whether cluster-related mean patient numbers differ significantly. Furthermore, two novel procedures are applied here: factor analysis including a special transformation and a time-varying multivariate linear regression that makes it possible to determine the rank of importance of the influencing variables in respiratory hospital admissions, and also compute the relative importance of the parameters affecting respiratory disorders. Both techniques revealed that Ambrosia pollen is an important variable that influences hospital admissions (an increase of 10 pollen grains m -3 can imply an increase of around 24% in patient numbers). The role of chemical and meteorological parameters is also significant, but their weights vary according to the seasons and the methods. Clearer results are obtained for the pollination season of Ambrosia. Here, a 10 μg m -3 increase in O 3 implies a patient number response from -17% to +11%. Wind speed is a surprisingly important variable, where a 1 m s -1 rise may result in a hospital admission

  12. A non-homogeneous dynamic Bayesian network with sequentially coupled interaction parameters for applications in systems and synthetic biology.

    Science.gov (United States)

    Grzegorczyk, Marco; Husmeier, Dirk

    2012-07-12

    An important and challenging problem in systems biology is the inference of gene regulatory networks from short non-stationary time series of transcriptional profiles. A popular approach that has been widely applied to this end is based on dynamic Bayesian networks (DBNs), although traditional homogeneous DBNs fail to model the non-stationarity and time-varying nature of the gene regulatory processes. Various authors have therefore recently proposed combining DBNs with multiple changepoint processes to obtain time varying dynamic Bayesian networks (TV-DBNs). However, TV-DBNs are not without problems. Gene expression time series are typically short, which leaves the model over-flexible, leading to over-fitting or inflated inference uncertainty. In the present paper, we introduce a Bayesian regularization scheme that addresses this difficulty. Our approach is based on the rationale that changes in gene regulatory processes appear gradually during an organism's life cycle or in response to a changing environment, and we have integrated this notion in the prior distribution of the TV-DBN parameters. We have extensively tested our regularized TV-DBN model on synthetic data, in which we have simulated short non-homogeneous time series produced from a system subject to gradual change. We have then applied our method to real-world gene expression time series, measured during the life cycle of Drosophila melanogaster, under artificially generated constant light condition in Arabidopsis thaliana, and from a synthetically designed strain of Saccharomyces cerevisiae exposed to a changing environment.

  13. Effects of gamma radiation on the biological, physico-chemical, nutritional and antioxidant parameters of chestnuts - a review.

    Science.gov (United States)

    Antonio, Amilcar L; Carocho, Márcio; Bento, Albino; Quintana, Begoña; Luisa Botelho, M; Ferreira, Isabel C F R

    2012-09-01

    Gamma radiation has been used as a post-harvest food preservation process for many years. Chestnuts are a seasonal product consumed fresh or processed, and gamma irradiation emerged recently as a possible alternative technology for their post-harvest processing, to fulfil the requirements of international phytosanitary trade laws. After harvest and storage, several problems may occur, such as the presence of infestations and development of microorganisms, namely rotting and fungi. These diminish the quality and safety of the product, decreasing the yield along the production chain. In fruits, gamma irradiation treatment is for two main purposes: conservation (ripening delay) and insect disinfestation (phytosanitary treatment). In this review, the application of gamma irradiation to chestnuts is discussed, including production data, the irradiated species and the effects on biological (sprouting, rotting, respiration rate, insects, worms and fungi), physico-chemical (color, texture, and drying rate), nutritional (energetic value, proteins, sugars and fatty acids) and antioxidant (tocopherols, ascorbic acid, phenolics, flavonoids and antioxidant activity) parameters. These changes are the basis for detecting if the food product has been irradiated or not. The validation of standards used for detection of food irradiation, as applied to chestnuts, is also discussed.

  14. DOE Final Technical Report (2009-2016): "Research Projects for Interrogations of Biological Systems: Training for the Development of Novel Radiotracers"

    Energy Technology Data Exchange (ETDEWEB)

    Jurisson, Silvia [University of Missouri-Columbia; Lever, Susan [University of Missouri-Columbia; Robertson, J. David [University of Missouri-Columbia

    2016-10-04

    This is the final technical report for DOE grant DE-SC-0002040, which was entitled "Research Projects for Interrogations of Biological Systems: Training for the Development of Novel Radiotracers". Included are the students and postdoctoral fellows trained, the publications, dissertations, presentations, and other deliverables for this project.

  15. Impacts of biological parameterization, initial conditions, and environmental forcing on parameter sensitivity and uncertainty in a marine ecosystem model for the Bering Sea

    Science.gov (United States)

    Gibson, G. A.; Spitz, Y. H.

    2011-11-01

    We use a series of Monte Carlo experiments to explore simultaneously the sensitivity of the BEST marine ecosystem model to environmental forcing, initial conditions, and biological parameterizations. Twenty model output variables were examined for sensitivity. The true sensitivity of biological and environmental parameters becomes apparent only when each parameter is allowed to vary within its realistic range. Many biological parameters were important only to their corresponding variable, but several biological parameters, e.g., microzooplankton grazing and small phytoplankton doubling rate, were consistently very important to several output variables. Assuming realistic biological and environmental variability, the standard deviation about simulated mean mesozooplankton biomass ranged from 1 to 14 mg C m - 3 during the year. Annual primary productivity was not strongly correlated with temperature but was positively correlated with initial nitrate and light. Secondary productivity was positively correlated with primary productivity and negatively correlated with spring bloom timing. Mesozooplankton productivity was not correlated with water temperature, but a shift towards a system in which smaller zooplankton undertake a greater proportion of the secondary production as the water temperature increases appears likely. This approach to incorporating environmental variability within a sensitivity analysis could be extended to any ecosystem model to gain confidence in climate-driven ecosystem predictions.

  16. Biological test methods for the ecotoxicological characterization of wastes. Final report; Biologische Testerverfahren zur oekotoxikologischen Charakterisierung von Abfaellen. Abschlussbericht

    Energy Technology Data Exchange (ETDEWEB)

    Becker, Roland [Bundesanstalt fuer Materialforschung, Berlin (Germany); Donnevert, Gerhild [Fachhochschule Giessen-Friedberg (Germany). FB MNI; Roembke, Joerg [ECT Oekotoxikologie GmbH, Floersheim am Main (Germany)

    2007-11-15

    battery the acceptance rate varied between 74.1% (Algae test) and 92.6% (Daphnia test). Methodologically, no problems occurred but further guidance on moisture determination in the terrestrial tests as well as details concerning reference testing and data evaluation for several tests are needed. Independently which test system is considered, SOI always caused the lowest effects and WOO was most toxic, while the EC50 values of INC show an intermediate toxicity. Among the aquatic tests, daphnids and one algal species were the most sensitive ones, while plants were always more sensitive than earthworms in the solid waste samples. Based on the test results from additional tests proposals for the modification of the existing basic test battery could be made. For example, the earthworm acute test could be replaced by another soil invertebrate test with higher sensitivity. Further work performed in parallel to the ring test improves waste testing considerably (e.g. the use of artificial soil as control substrate). A comparison of the ring test results with literature data published so far revealed a good agreement. The results of this ring test support confirm that a combination of a battery of biological tests and chemical residue analysis is needed for an ecotoxicological characterization of wastes. With small modifications proposed in this report the basic test battery is considered to be well suitable for the hazard and risk assessment of wastes. Further, probably multi-variate evaluation of the ring test results will improve the identification of those tests most qualified for the ecotoxicological characterization of wastes. Finally, the experiences made in the ring test support also the proposals made in CEN guideline 14735 (2005) concerning the performance of such tests. (orig.)

  17. Impact of tissue specific parameters on the predition of the biological effectiveness for treatment planning in ion beam therapy

    Energy Technology Data Exchange (ETDEWEB)

    Gruen, Rebecca Antonia

    2014-06-03

    Treatment planning in ion beam therapy requires a reliable estimation of the relative biological effectiveness (RBE) of the irradiated tissue. For the pilot project at GSI Helmholtzzentrum fuer Schwerionenforschung GmbH and at other European ion beam therapy centers RBE prediction is based on a biophysical model, the Local Effect Model (LEM). The model version in use, LEM I, is optimized to give a reliable estimation of RBE in the target volume for carbon ion irradiation. However, systematic deviations are observed for the entrance channel of carbon ions and in general for lighter ions. Thus, the LEM has been continuously developed to improve accuracy. The recent version LEM IV has proven to better describe in-vitro cell experiments. Thus, for the clinical application of LEM IV it is of interest to analyze potential differences compared to LEM I under treatment-like conditions. The systematic analysis presented in this work is aiming at the comparison of RBE-weighted doses resulting from different approaches and model versions for protons and carbon ions. This will facilitate the assessment of consequences for clinical application and the interpretation of clinical results from different institutions. In the course of this thesis it has been shown that the RBE-weighted doses predicted on the basis of LEM IV for typical situations representing chordoma treatments differ on average by less than 10 % to those based on LEM I and thus also allow a consistent interpretation of the clinical results. At Japanese ion beam therapy centers the RBE is estimated using their clinical experience from neutron therapy in combination with in-vitro measurements for carbon ions (HIMAC approach). The methods presented in this work allow direct comparison of the HIMAC approach and the LEM and thus of the clinical results obtained at Japanese and European ion beam therapy centers. Furthermore, the sensitivity of the RBE on the model parameters was evaluated. Among all parameters the

  18. The Impact of Ozone Treatment in Dynamic Bed Parameters on Changes in Biologically Active Substances of Juniper Berries.

    Directory of Open Access Journals (Sweden)

    Agnieszka Joanna Brodowska

    Full Text Available The development of the parameters of ozone decontamination method assuring the least possible losses of biologically active substances (essential oils and polyphenols and their activity in common juniper (Juniperus communis (L. berries was studied. Ozone treatment in dynamic bed was conducted 9 times. The process was conducted under different ozone concentrations (100.0; 130.0; 160.0 g O3/m3 and times (30, 60, 90 min. After each decontamination, the microbiological profile of the juniper berries was studied, and the contaminating microflora was identified. Next to the microbiological profile, the phenolic profile, as well as antioxidant activity of extracts and essential oils were determined. The total polyphenol content (TPC, composition of essential oils, free radical-scavenging capacity, total antioxidant capacity, ferric-reducing antioxidant power (FRAP, beta-carotene bleaching test (BCB and LC-MS polyphenol analysis were carried out. The study reveals that during short ozone contact times, higher amounts of TPC, 15.47 and 12.91 mg CE/g of extract, for samples 100/30 and 130/30, respectively, were demonstrated. Whereas samples 100/60, 130/60, 100/90, and 160/90 exhibited the lowest amount of phenolics. The highest antioxidant activity was found in the methanol extract obtained from ozonated berries which exhibited the lowest IC50 in all the antioxidant assays, such as DPPH, FRAP, and BCB assays. Ozone treatment showed noteworthy potential and its usage in food manufacturing and as an alternative decontamination method should be considered.

  19. Long-term effect of partial nephrectomy on biological parameters, kidney histology, and guanidino compound levels in mice.

    Science.gov (United States)

    Al Banchaabouchi, M; Marescau, B; Van Marck, E; D'hooge, R; De Deyn, P P

    2001-12-01

    The long-term adverse consequences of early renal mass reduction in mice have not yet been investigated. The effects of partial surgical nephrectomy (NX) in 2-month-old mice on some biological parameters, on histopathologic and morphometric features of the kidney, and on urea and guanidino compound (GC) levels in plasma, urine, and brain were examined at 10 days, and 1, 2, 4, and 12 months postsurgery. Body weight, urinary volume, and plasma urea were most affected at 10 days and 12 months post-NX. NX-induced changes in the remaining renal tissue (including hypertrophy, glomerular mesangial expansion, and presence of protein casts) increased with age. As in human renal insufficiency, NX mice showed significantly higher plasma guanidinosuccinic acid (GSA) and creatinine (CTN) levels at all studied periods. The same tendency could be seen for most other plasma GCs examined, except for arginine (Arg), guanidinoacetic acid (GAA), and homoarginine (HA). As seen in human pathobiochemistry, the latter 2 compounds tended to be lower in NX mice in our follow-up study. Remarkably, and also similar to humans, NX mice excreted less GAA and more GSA than controls during the entire follow-up study. During the follow-up, excretion levels of GAA were unchanged in NX and sham-operated mice. In brain, GAA and gamma-guanidinobutyric acid (GBA) levels were always higher in NX mice with a tendency to respectively increase or decrease over time in NX as well as sham-operated mice. Although urea and GC metabolism were influenced by time post-NX and aging, the model was confirmed to display a mild stable chronic impairment of renal function. Histopathologic and morphometric changes of the kidney increased with age.

  20. The Impact of Ozone Treatment in Dynamic Bed Parameters on Changes in Biologically Active Substances of Juniper Berries.

    Science.gov (United States)

    Brodowska, Agnieszka Joanna; Śmigielski, Krzysztof; Nowak, Agnieszka; Czyżowska, Agata; Otlewska, Anna

    2015-01-01

    The development of the parameters of ozone decontamination method assuring the least possible losses of biologically active substances (essential oils and polyphenols) and their activity in common juniper (Juniperus communis (L.)) berries was studied. Ozone treatment in dynamic bed was conducted 9 times. The process was conducted under different ozone concentrations (100.0; 130.0; 160.0 g O3/m3) and times (30, 60, 90 min). After each decontamination, the microbiological profile of the juniper berries was studied, and the contaminating microflora was identified. Next to the microbiological profile, the phenolic profile, as well as antioxidant activity of extracts and essential oils were determined. The total polyphenol content (TPC), composition of essential oils, free radical-scavenging capacity, total antioxidant capacity, ferric-reducing antioxidant power (FRAP), beta-carotene bleaching test (BCB) and LC-MS polyphenol analysis were carried out. The study reveals that during short ozone contact times, higher amounts of TPC, 15.47 and 12.91 mg CE/g of extract, for samples 100/30 and 130/30, respectively, were demonstrated. Whereas samples 100/60, 130/60, 100/90, and 160/90 exhibited the lowest amount of phenolics. The highest antioxidant activity was found in the methanol extract obtained from ozonated berries which exhibited the lowest IC50 in all the antioxidant assays, such as DPPH, FRAP, and BCB assays. Ozone treatment showed noteworthy potential and its usage in food manufacturing and as an alternative decontamination method should be considered.

  1. Biological traits and Life table parameters A and B biotype of Bemisia tabaci (Genn. on cotton and rapeseed

    Directory of Open Access Journals (Sweden)

    Mohammad Amin Samih

    2014-06-01

    Full Text Available The aim of this work was to construct life table of Bemisia tabaci (Gen. A and B (silverleaf whitefly B. argentifolii Bellows and Perring biotype (Hem.: Aleyrodidae on two host plants; cotton, (Gossypium hirsutum L. and rapeseed, (Brassica napus L.. Experiments were conducted in a growth chamber under 24 ± 2ºC, 55±3% RH and 16:8 (L:D h photoperiod on caged plants of cotton G. hirsutum L. (Varamin 76 variety and rapeseed B. napus L. (global variety. The intrinsic rate of natural increase (r m, net reproductive rate (R0 and mean generation time (T for B. tabaci A biotype was 0.1010 females per female per day, 18.4075 females per female and 30.079 day (d on cotton; 0.1286, 30.6760 and 26.77 d on rapeseed; and for B biotype (B. argentifolii those above respective parameters averaged 0.1033, 27.8426 and 32.74 d on cotton and 0.1750, 40.75 and 21.27 d on rapeseed. The total survival of A and B biotype from the egg to adult on cotton was 22.08 and 22.25, respectively. The results showed significant differences between the two biotype reared on either host plant for gross reproductive rate (GRR, net reproductive rate (R0 or NRR, intrinsic rates of increase (r m, finite rate of increase (λ, doubling time (DT and mean generation times (Tc. To obtain a better understanding of the biology of these biotypes, Stable age distribution (Cx and some other aspects of life history related to their hosts were also studied. Based upon the results, both biotypes showed a greater reproduction capacity on rapeseed than on cotton. Thus, rapeseed was more suitable host than cotton for two biotypes and this was an important factor in host plant selection for optimizing the control strategies of these major pests.

  2. Geoelectrical Measurement of Multi-Scale Mass Transfer Parameters Final Report to the Subsurface Biogeochemical Research Program

    Energy Technology Data Exchange (ETDEWEB)

    Day-Lewis, Frederick; Singha, Kamini; Haggerty, Roy; Johnson, Timothy; Binley, Andrew; Lane, John

    2014-03-10

    . In this project, we sought to capitalize on the geophysical signatures of mass transfer. Previous numerical modeling and pilot-scale field experiments suggested that mass transfer produces a geoelectrical signature—a hysteretic relation between sampled (mobile-domain) fluid conductivity and bulk (mobile + immobile) conductivity—over a range of scales relevant to aquifer remediation. In this work, we investigated the geoelectrical signature of mass transfer during tracer transport in a series of controlled experiments to determine the operation of controlling parameters, and also investigated the use of complex-resistivity (CR) as a means of quantifying mass transfer parameters in situ without tracer experiments. In an add-on component to our grant, we additionally considered nuclear magnetic resonance (NMR) to help parse mobile from immobile porosities. Our study objectives were to: 1. Develop and demonstrate geophysical approaches to measure mass-transfer parameters spatially and over a range of scales, including the combination of electrical resistivity monitoring, tracer tests, complex resistivity, nuclear magnetic resonance, and materials characterization; and 2. Provide mass-transfer estimates for improved understanding of contaminant fate and transport at DOE sites, such as uranium transport at the Hanford 300 Area. To achieve our objectives, we implemented a 3-part research plan involving (1) development of computer codes and techniques to estimate mass-transfer parameters from time-lapse electrical data; (2) bench-scale experiments on synthetic materials and materials from cores from the Hanford 300 Area; and (3) field demonstration experiments at the DOE’s Hanford 300 Area.

  3. "Capping Off" the Development of Graduate Capabilities in the Final Semester Unit for Biological Science Students: Review and Recommendations

    Science.gov (United States)

    Firn, Jennifer

    2015-01-01

    Biology is the most rapidly evolving scientific field of the 21st century. Biology graduates must be able to integrate concepts and collaborate outside their discipline to solve the most pressing questions of our time, e.g. world hunger, malnutrition, climate change, infectious disease and biosecurity. University educators are attempting to…

  4. Mini-review of the geotechnical parameters of municipal solid waste: Mechanical and biological pre-treated versus raw untreated waste.

    Science.gov (United States)

    Petrovic, Igor

    2016-09-01

    The most viable option for biostabilisation of old sanitary landfills, filled with raw municipal solid waste, is the so-called bioreactor landfill. Even today, bioreactor landfills are viable options in many economically developing countries. However, in order to reduce the biodegradable component of landfilled waste, mechanical and biological treatment has become a widely accepted waste treatment technology, especially in more prosperous countries. Given that mechanical and biological treatment alters the geotechnical properties of raw waste material, the design of sanitary landfills which accepts mechanically and biologically treated waste, should be carried out with a distinct set of geotechnical parameters. However, under the assumption that 'waste is waste', some design engineers might be tempted to use geotechnical parameters of untreated raw municipal solid waste and mechanical and biological pre-treated municipal solid waste interchangeably. Therefore, to provide guidelines for use and to provide an aggregated source of this information, this mini-review provides comparisons of geotechnical parameters of mechanical and biological pre-treated waste and raw untreated waste at various decomposition stages. This comparison reveals reasonable correlations between the hydraulic conductivity values of untreated and mechanical and biological pre-treated municipal solid waste. It is recognised that particle size might have a significant influence on the hydraulic conductivity of both municipal solid waste types. However, the compression ratios and shear strengths of untreated and pre-treated municipal solid waste do not show such strong correlations. Furthermore, another emerging topic that requires appropriate attention is the recovery of resources that are embedded in old landfills. Therefore, the presented results provide a valuable tool for engineers designing landfills for mechanical and biological pre-treated waste or bioreactor landfills for untreated raw

  5. New approaches to estimation of magnetotelluric parameters. Final technical report, 1 August 1989--31 July 1991

    Energy Technology Data Exchange (ETDEWEB)

    Egbert, G.D.

    1991-12-31

    Fully efficient robust data processing procedures were developed and tested for single station and remote reference magnetotelluric (Mr) data. Substantial progress was made on development, testing and comparison of optimal procedures for single station data. A principal finding of this phase of the research was that the simplest robust procedures can be more heavily biased by noise in the (input) magnetic fields, than standard least squares estimates. To deal with this difficulty we developed a robust processing scheme which combined the regression M-estimate with coherence presorting. This hybrid approach greatly improves impedance estimates, particularly in the low signal-to-noise conditions often encountered in the ``dead band`` (0.1--0.0 hz). The methods, and the results of comparisons of various single station estimators are described in detail. Progress was made on developing methods for estimating static distortion parameters, and for testing hypotheses about the underlying dimensionality of the geological section.

  6. Computed tomography of the acoustic nonlinearity parameter B/A for biological tissues via difference frequency wave from a parametric array in reflection mode

    Institute of Scientific and Technical Information of China (English)

    WANG Huanlei; ZHU Xiaofeng; GONG Xiufen; ZHANG Dong

    2003-01-01

    Based on the finite amplitude insert-substitu- tion method, a novel technique to reconstruct the acoustic nonlinear parameter B/A tomography for biological tissues in reflection mode via the difference frequency wave generated by a parametric array is developed in this paper. An experimental system is established, and the beam pattern of the difference frequency wave is measured and compared with that excited directly from a transmitter at the same frequency. B/A tomography for several biological tissues including normal and pathological tissues, is experimentally obtained with satisfying quality. Results indicate that B/A imaging using this mode may become a novel modality in ultrasonic diagnosis.

  7. The influence of design and fuel parameters on the particle emissions from wood pellets combustion. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Wiinikka, Henrik; Gebart, Rikard [Energy Technology Centre, Piteaa (Sweden)

    2005-02-01

    Combustion of solid biomass under fixed bed conditions is a common technique to generate heat and power in both small and large scale grate furnaces (domestic boilers, stoves, district heating plants). Unfortunately, combustion of biomass will generate particle emissions containing both large fly ash particles and fine particles that consist of fly ash and soot. The large fly ash particles have been produced from fusion of non-volatile ash-forming species in burning char particle. The inorganic fine particles have been produced from nucleation of volatilised ash elements (K, Na, S, Cl and Zn). If the combustion is incomplete, soot particles are also produced from secondary reaction of tar. The particles in the fine fraction grows by coagulation and coalescence to a particle diameter around 0.1 pm. Since the smallest particles are very hard to collect in ordinary cleaning devices they contribute to the ambient air pollution. Furthermore, fine airborne particles have been correlated to adverse effects on the human health. It is therefore essential to minimize particle formation from the combustion process and thereby reduce the emissions of particulates to the ambient air. The aim with this project is to study particle emissions from small scale combustion of wood pellets and to investigate the impact of different operating, construction and fuel parameters on the amount and characteristic of the combustion generated particles. To address these issues, experiments were carried out in a 10 kW updraft fired wood pellets reactor that has been custom designed for systematic investigations of particle emissions. In the flue gas stack, particle emissions were sampled on a filter. The particle mass and number size distributions were analysed by a low pressure cascade impactor and a SMPS (Scanning Electron Mobility Particle Sizer). The results showed that the temperature and the flow pattern in the combustion zone affect the particle emissions. Increasing combustion

  8. Biological methods for increasing the biogas yield of livestock waste. Final report; Biologiske metoder til foroegelse af husdyrgoednings biogaspotentiale. Slutrapport

    Energy Technology Data Exchange (ETDEWEB)

    Mladenovska, Z.; Ahring, B.K.

    2001-01-01

    Danish full-scale biogas plants operate with manure as a primary substrate, of which cattle manure represents a significant fraction. Conversion of the lignocellulosic fibre fraction of manure was shown to be the rate-degrading step of the anaerobic digestion. The aim of this project was to investigate if the biological methods, such as bioaugmentation of the reactor with specific anaerobic, hydrolytic bacteria would improve hydrolysis of fibres and result in an increase of the methane yield of cattle manure. Results of this study showed, that there is a potential for an increase of the methane yield of manure by inoculating the fibre-containing substrate with cellulose- and alkaliphilic xylane-hydrolyzing bacterial cultures. The highest increase of methane yield in batch experiment was obtained at 37 deg. C and 68 deg. C, while the effect at 55 deg. C was poor. Direct inoculation of a mesophilic reactor with Clostridium cellulovorans (DSM 3052) was not successful. The fate of the organism, followed by 16S rRNA probing, proved that DSM 3052 was not a member of the indigenous microflora, and that the active population of DSM 3052 could not be established within the reactor. On the other hand, inoculation of a reactor with our own isolate, a new clostridial strain, Clostridium sp. SA 14, resulted in a significant increase of the methane yield from 220 ml CH{sub 4}/g VS up to 330 ml CH{sub 4}/g VS. However, during the continuous reactor operation in the period of one retention time, the effect was reduced and finally disappeared. Therefore, it would be necessary in the future to develop a new strategy for establishment of this strain within the reactor environment. Anaerobic digestion of manure was also studied in a two-step process, where manure was first hydrolyzed at 68 deg. C, and thereafter digested in a conventional methanogenic step at 55 deg. C. Investigation from batch experiment resulted in a 24%- increase in methane yield for the two-step digestion compared

  9. Final Report for NFE-07-00912: Development of Model Fuels Experimental Engine Data Base & Kinetic Modeling Parameter Sets

    Energy Technology Data Exchange (ETDEWEB)

    Bunting, Bruce G [ORNL

    2012-10-01

    The automotive and engine industries are in a period of very rapid change being driven by new emission standards, new types of after treatment, new combustion strategies, the introduction of new fuels, and drive for increased fuel economy and efficiency. The rapid pace of these changes has put more pressure on the need for modeling of engine combustion and performance, in order to shorten product design and introduction cycles. New combustion strategies include homogeneous charge compression ignition (HCCI), partial-premixed combustion compression ignition (PCCI), and dilute low temperature combustion which are being developed for lower emissions and improved fuel economy. New fuels include bio-fuels such as ethanol or bio-diesel, drop-in bio-derived fuels and those derived from new crude oil sources such as gas-to-liquids, coal-to-liquids, oil sands, oil shale, and wet natural gas. Kinetic modeling of the combustion process for these new combustion regimes and fuels is necessary in order to allow modeling and performance assessment for engine design purposes. In this research covered by this CRADA, ORNL developed and supplied experimental data related to engine performance with new fuels and new combustion strategies along with interpretation and analysis of such data and consulting to Reaction Design, Inc. (RD). RD performed additional analysis of this data in order to extract important parameters and to confirm engine and kinetic models. The data generated was generally published to make it available to the engine and automotive design communities and also to the Reaction Design Model Fuels Consortium (MFC).

  10. Development of a calibration protocol and identification of the most sensitive parameters for the particulate biofilm models used in biological wastewater treatment.

    Science.gov (United States)

    Eldyasti, Ahmed; Nakhla, George; Zhu, Jesse

    2012-05-01

    Biofilm models are valuable tools for process engineers to simulate biological wastewater treatment. In order to enhance the use of biofilm models implemented in contemporary simulation software, model calibration is both necessary and helpful. The aim of this work was to develop a calibration protocol of the particulate biofilm model with a help of the sensitivity analysis of the most important parameters in the biofilm model implemented in BioWin® and verify the predictability of the calibration protocol. A case study of a circulating fluidized bed bioreactor (CFBBR) system used for biological nutrient removal (BNR) with a fluidized bed respirometric study of the biofilm stoichiometry and kinetics was used to verify and validate the proposed calibration protocol. Applying the five stages of the biofilm calibration procedures enhanced the applicability of BioWin®, which was capable of predicting most of the performance parameters with an average percentage error (APE) of 0-20%.

  11. Parameter estimation with a novel gradient-based optimization method for biological lattice-gas cellular automaton models.

    Science.gov (United States)

    Mente, Carsten; Prade, Ina; Brusch, Lutz; Breier, Georg; Deutsch, Andreas

    2011-07-01

    Lattice-gas cellular automata (LGCAs) can serve as stochastic mathematical models for collective behavior (e.g. pattern formation) emerging in populations of interacting cells. In this paper, a two-phase optimization algorithm for global parameter estimation in LGCA models is presented. In the first phase, local minima are identified through gradient-based optimization. Algorithmic differentiation is adopted to calculate the necessary gradient information. In the second phase, for global optimization of the parameter set, a multi-level single-linkage method is used. As an example, the parameter estimation algorithm is applied to a LGCA model for early in vitro angiogenic pattern formation.

  12. Biological parameters and thermal requirements of the parasitoid Praon volucre (Hymenoptera: Braconidae) with Macrosiphum euphorbiae (Hemiptera: Aphididae) as host

    NARCIS (Netherlands)

    Conti, De B.F.; Bueno, V.H.P.; Sampaio, M.V.; Lenteren, van J.C.

    2011-01-01

    The effect of temperature on the biology of Praon volucre (Haliday, 1833) (Hymenoptera: Braconidae) in Macrosiphum euphorbiae (Thomas, 1878) (Hemiptera: Aphididae) hosts was studied and the thermal requirements of the parasitoid were determined. Experiments were carried out at 16, 19, 22, 25, and 28

  13. A Non-Homogeneous Dynamic Bayesian Network with Sequentially Coupled Interaction Parameters for Applications in Systems and Synthetic Biology

    NARCIS (Netherlands)

    Grzegorczyk, Marco; Husmeier, Dirk

    2012-01-01

    An important and challenging problem in systems biology is the inference of gene regulatory networks from short non-stationary time series of transcriptional profiles. A popular approach that has been widely applied to this end is based on dynamic Bayesian networks (DBNs), although traditional homog

  14. The relation between histological, tumor-biological and clinical parameters in deep and superficial leiomyosarcoma and leiomyoma.

    NARCIS (Netherlands)

    Pijpe, Justin; Broers, Gerben H Torn; Plaat, Boudewijn E Ch; Hundeiker, M; Otto, F; Mastik, Mirjam F; Hoekstra, Harald J; Graaf, Winette T A van der; Berg, Eva van Den; Molenaar, Willemina M

    2002-01-01

    Purpose: Leiomyosarcomas (LMS) of deep and superficial tissues were examined to identify prognostic markers explaining their different biological behaviour and to define differences between cutaneous and subcutaneous LMS. LMS and leiomyomas (LM) of the skin were compared to and consistent difference

  15. Biology and reproductive parameters of the brown lygodium moth, Neomusotima conspurcatalis--a new biological control agent of Old World climbing fern in Florida.

    Science.gov (United States)

    Boughton, Anthony J; Pemberton, Robert W

    2012-04-01

    Neomusotima conspurcatalis Warren was first released in Florida as a weed biological control agent against Old World climbing fern in 2008, and readily established large field populations. A related biocontrol agent, Austromusotima camptozonale, had previously failed to establish despite several years of releases. Life history studies were conducted to determine whether aspects of the reproductive biology of N. conspurcatalis might account for these different outcomes. At 26.5°C, development from egg to adult averaged 22.2 ± 0.1 d, with 75% of larvae emerging as adults. The sex ratio averaged 1:0.8 (♂:♀), with both sexes emerging at the same time. Female moths typically mated once, on the first night after emergence, and began oviposition the next night. Females laid half their eggs on the first night and lived an average of 10.7 ± 0.8 d. Individual females maintained in cages with a male-biased sex ratio (3♂:1♀) produced significantly more larvae over their lifetime (140 ± 6.6 larvae) than individual females maintained at a ratio of 1♂:1♀ (111 ± 9.1 larvae). Sexual selection, either through 'male-male competition' or 'female choice' was likely responsible for this result, because there were no significant differences in mating frequency, duration of ovipositional period or female longevity to otherwise explain the difference. Two-fold greater lifetime reproductive output (average 127 ± 6.3 larvae) and deposition of half this output on the first night of oviposition, likely contributed to rapid field establishment of N. conspurcatalis compared with A. camptozonale.

  16. Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach

    Directory of Open Access Journals (Sweden)

    Luan Yihui

    2009-09-01

    Full Text Available Abstract Background Many aspects of biological functions can be modeled by biological networks, such as protein interaction networks, metabolic networks, and gene coexpression networks. Studying the statistical properties of these networks in turn allows us to infer biological function. Complex statistical network models can potentially more accurately describe the networks, but it is not clear whether such complex models are better suited to find biologically meaningful subnetworks. Results Recent studies have shown that the degree distribution of the nodes is not an adequate statistic in many molecular networks. We sought to extend this statistic with 2nd and 3rd order degree correlations and developed a pseudo-likelihood approach to estimate the parameters. The approach was used to analyze the MIPS and BIOGRID yeast protein interaction networks, and two yeast coexpression networks. We showed that 2nd order degree correlation information gave better predictions of gene interactions in both protein interaction and gene coexpression networks. However, in the biologically important task of predicting functionally homogeneous modules, degree correlation information performs marginally better in the case of the MIPS and BIOGRID protein interaction networks, but worse in the case of gene coexpression networks. Conclusion Our use of dK models showed that incorporation of degree correlations could increase predictive power in some contexts, albeit sometimes marginally, but, in all contexts, the use of third-order degree correlations decreased accuracy. However, it is possible that other parameter estimation methods, such as maximum likelihood, will show the usefulness of incorporating 2nd and 3rd degree correlations in predicting functionally homogeneous modules.

  17. Evolution, selection and cognition: from "learning" to parameter setting in biology and in the study of language.

    Science.gov (United States)

    Piattelli-Palmarini, M

    1989-02-01

    Most biologists and some cognitive scientists have independently reached the conclusion that there is no such thing as learning in the traditional "instructive" sense. This is, admittedly, a somewhat extreme thesis, but I defend it here in the light of data and theories jointly extracted from biology, especially from evolutionary theory and immunology, and from modern generative grammar. I also point out that the general demise of learning is uncontroversial in the biological sciences, while a similar consensus has not yet been reached in psychology and in linguistics at large. Since many arguments presently offered in defense of learning and in defense of "general intelligence" are often based on a distorted picture of human biological evolution, I devote some sections of this paper to a critique of "adaptationism," providing also a sketch of a better evolutionary theory (one based on "exaptation"). Moreover, since certain standard arguments presented today as "knock-down" in psychology, in linguistics and in artificial intelligence are a perfect replica of those once voiced by biologists in favor of instruction and against selection, I capitalize on these errors of the past to draw some lessons for the present and for the future.

  18. Final report on LDRD project: Semiconductor surface-emitting microcavity laser spectroscopy for analysis of biological cells and microstructures

    Energy Technology Data Exchange (ETDEWEB)

    Gourley, P.L.; McDonald, A.E. [Sandia National Labs., Albuquerque, NM (United States). Nanostructure and Semiconductor Physics Dept.; Gourley, M.F. [Washington Hospital Center, DC (United States); Bellum, J. [Coherent Technologies, Boulder, CO (United States)

    1997-08-01

    This article discusses a new intracavity laser technique that uses living or fixed cells as an integral part of the laser. The cells are placed on a GaAs based semiconductor wafer comprising one half of a vertical cavity surface-emitting laser. After placement, the cells are covered with a dielectric mirror to close the laser cavity. When photo-pumped with an external laser, this hybrid laser emits coherent light images and spectra that depend sensitively on the cell size, shape, and dielectric properties. The light spectra can be used to identify different cell types and distinguish normal and abnormal cells. The laser can be used to study single cells in real time as a cell-biology lab-on-a-chip, or to study large populations of cells by scanning the pump laser at high speed. The laser is well-suited to be integrated with other micro-optical or micro-fluidic components to lead to micro-optical-mechanical systems for analysis of fluids, particulates, and biological cells.

  19. The effect of intake of water on the final values of body composition parameters in active athletes using two different bioimpedance analyzers

    Directory of Open Access Journals (Sweden)

    Petr Kutáč

    2014-06-01

    Full Text Available Background:The method of bioelectrical impedance (BIA is frequently used to estimate body composition in sports. The total body water (TBW is the basic variable that BIA measures. That implies the degree of sensitivity of BIA to the hydration of the organism, which is also demonstrated by the principles of measurement that primarily relate to the hydration of the organism. It is difficult to provide standard hydration of the organism of subjects prior to measurements when taking the measurements in the field. Objective:The objective of the study is to assess the changes in the final values of the selected body composition parameters in soccer players caused by intake of water, using two devices commonly used in the field. Methods:The research was performed in a group of 33 soccer players (mean age 20.30 ± 1.18 years. The measurements were taken using Tanita BC 418 MA (frequency 50 kHz and Nutriguard-M (frequency 100 kHz. To evaluate the effect of water intake, we took two measurements before and after the intake of 500 ml of water. The parameters measured by Tanita BC 418 MA were body weight (BW, total body water (TBW, body fat (BF, fat free mass (FFM. Nutriguard-M was used to measure total body water (TBW, intra and extracellular water (ICW and ECW, body fat (BF, fat free mass (FFM, intra and extracellular mass (BCM and ECM. The differences in the means (M1 and M2 of the monitored parameters were evaluated using the Paired Samples t-test. In statistically significant differences in the mean, the practical significance was also verified using the effect of size (Cohen's d. Results:The Tanita device showed statistically significant differences after the intake of 500 ml in parameters BW (+0.42 kg, BF (+0.39 kg, +0.53% and TBW (-0.38%. As for the Nutriguard device, statistically significant differences were found in parameters TBW (+0.77 kg, ICW (+0.83 kg, FFM (+1.05 kg, BCM (+0.79 kg and ECM/BCM (-0.01. Conclusion

  20. King has no clothes: The role of the military in responding to a terrorist chemical/biological attack. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Osterman, J.L.

    1996-06-14

    The United States has begun a program of counterproliferation in order to preempt the use of WMD by such elements, however, the ability to respond to the terrorist employment of biological/chemical weapons is absent. Given the structure, capability and technical expertise in the Federal Emergency Management Agency (FEMA) and the Federal Bureau of Investigation (FBI), the Department of Defense (DoD) will be tasked to conduct the response to such an incident. The geographical Commander in Chief (CINC) and the appointed Joint Task Force (JTF) commander will ultimately be assigned the response mission. Planning, training and coordination is required to develop a force capable of responding in a timely and coordinated manner.

  1. A Framework for Parameter Estimation and Model Selection from Experimental Data in Systems Biology Using Approximate Bayesian Computation

    Science.gov (United States)

    Liepe, Juliane; Kirk, Paul; Filippi, Sarah; Toni, Tina; Barnes, Chris P.; Stumpf, Michael P.H.

    2016-01-01

    As modeling becomes a more widespread practice in the life- and biomedical sciences, we require reliable tools to calibrate models against ever more complex and detailed data. Here we present an approximate Bayesian computation framework and software environment, ABC-SysBio, which enables parameter estimation and model selection in the Bayesian formalism using Sequential Monte-Carlo approaches. We outline the underlying rationale, discuss the computational and practical issues, and provide detailed guidance as to how the important tasks of parameter inference and model selection can be carried out in practice. Unlike other available packages, ABC-SysBio is highly suited for investigating in particular the challenging problem of fitting stochastic models to data. Although computationally expensive, the additional insights gained in the Bayesian formalism more than make up for this cost, especially in complex problems. PMID:24457334

  2. The optical diagnostics of parameters of biological tissues of human intact skin in near-infrared range

    Science.gov (United States)

    Petruk, Vasyl; Kvaternyuk, Sergii; Bolyuh, Boris; Bolyuh, Dmitry; Dronenko, Vladimir; Harasim, Damian; Annabayev, Azamat

    2016-09-01

    Melanoma skin is difficult to diagnose in the early stages of development despite its location outside. Melanoma is difficult to visually differentiate from benign melanocytic nevi. In the work we investigated parameters of human intact skin in near-infrared range for different racial and gender groups. This allows to analyze statistical differences in the coefficient of diffuse reflection and use them in the differential diagnosis of cancer by optical methods subject.

  3. LC30 effects of thiamethoxam and pirimicarb, on population parameters and biological characteristics of Macrolophus pygmaeus (Hemiptera: Miridae)

    OpenAIRE

    Shima Rahmani; Solmaz Azimi; Mona Moghadasi

    2016-01-01

    Chemical pesticides have important role in integrated pest management strategies. However, they can adversely affect on natural enemies as non-target organisms, even in sublethal concentrations. In this study, sublethal effects of two insecticides, thiamethoxam and pirimicarb, were examined on demographic parameters of an important predator, Macrolophus pygmaeus. Bioassay results indicated that LC30 of thiamethoxam and pirimicarb, applied on the third instar larvae, were 451.6 and 2013.4 mg (...

  4. Some Physical, Chemical, and Biological Parameters of Samples of Scleractinium Coral Aquaculture Skeleton Used for Reconstruction/Engineering of the Bone Tissue.

    Science.gov (United States)

    Popov, A A; Sergeeva, N S; Britaev, T A; Komlev, V S; Sviridova, I K; Kirsanova, V A; Akhmedova, S A; Dgebuadze, P Yu; Teterina, A Yu; Kuvshinova, E A; Schanskii, Ya D

    2015-08-01

    Physical and chemical (phase and chemical composition, dynamics of resorption, and strength properties), and biological (cytological compatibility and scaffold properties of the surface) properties of samples of scleractinium coral skeletons from aquacultures of three types and corresponding samples of natural coral skeletons (Pocillopora verrucosa, Acropora formosa, and Acropora nobilis) were studied. Samples of scleractinium coral aquaculture skeleton of A. nobilis, A. formosa, and P. verrucosa met the requirements (all study parameters) to materials for osteoplasty and 3D-scaffolds for engineering of bone tissue.

  5. [The analysis of climatic and biological parameters for the pest spread risk modelling of the wood nematode species Bursaphelenchus spp. and Devibursaphelenchus teratospicularis (Rhabditida: Aphelenchoidea)].

    Science.gov (United States)

    Ryss, A Y; Mokrousov, M V

    2014-01-01

    Based on the forest woody species wilt areassurvey in Nizhniy Novgorod region in August 2014, the possible factors of the pest spread risk modelling were analysed on six species of the genus Bursaphelenchus and Devibursaphelenchus teratospicularis using six parameters: plant host species, beetle vector species, average temperatures in July and January, annual precipitation. It was concluded that these parameters in the evaluated wilt spots correspond to climatic and biological data of the already published woody plants wilt records in Europe and Asia caused by the same nematode pest species. It was speculated that the annual precipitation of 600 mm and average July temperature of 25 degrees C or higher, are the critical combination that may be used to develop the predicative risk modelling in the forests' and parks' wilt monitoring.

  6. LC30 effects of thiamethoxam and pirimicarb, on population parameters and biological characteristics of Macrolophus pygmaeus (Hemiptera: Miridae

    Directory of Open Access Journals (Sweden)

    Shima Rahmani

    2016-06-01

    Full Text Available Chemical pesticides have important role in integrated pest management strategies. However, they can adversely affect on natural enemies as non-target organisms, even in sublethal concentrations. In this study, sublethal effects of two insecticides, thiamethoxam and pirimicarb, were examined on demographic parameters of an important predator, Macrolophus pygmaeus. Bioassay results indicated that LC30 of thiamethoxam and pirimicarb, applied on the third instar larvae, were 451.6 and 2013.4 mg (ai L-1, respectively. The two insecticides extended the pre-adult duration, significantly. Demographic parameters were analyzed by two-sex life table. The results showed that all of the main demographic traits (r, λ, R0 and T have been changed significantly and there are also some changes in other parameters such as age-specific survival rate (lx and life expectancy (ex. Intrinsic rate of increase in control was 0.15 but it reduced to 0.10 and 0.99 day-1 in thiamethoxam and pirimicarb treatments, respectively. Also, finite rate of increase in control, thiamethoxam and pirimicarb treatments was 1.11, 1.08 and 1.03 day-1 respectively. Reproductive rate in control showed 36.75 offspring/individual but this statistic in thiamethoxam and pirimicarb treatments was 19.62 and 18.24, respectively. Mean generation time was 22.69 days in control but it extended in both treatments and illustrated 27.79 and 31.24 days in thiamethoxam and pirimicarb treatments, respectively. Thus, obtained results in this study showed that although pirimicarb and thiamethoxam are selective insecticides, they have potential to affect on the predator, M. pygmaeus severely, and need to take care in IPM programs.

  7. Optimization of struvite precipitation in synthetic biologically treated swine wastewater--determination of the optimal process parameters.

    Science.gov (United States)

    Capdevielle, Aurélie; Sýkorová, Eva; Biscans, Béatrice; Béline, Fabrice; Daumer, Marie-Line

    2013-01-15

    A sustainable way to recover phosphorus (P) in swine wastewater involves a preliminary step of P dissolution followed by the separation of particulate organic matter. The next two steps are firstly the precipitation of struvite crystals done by adding a crystallization reagent (magnesia) and secondly the filtration of the crystals. A design of experiments with five process parameters was set up to optimize the size of the struvite crystals in a synthetic swine wastewater. More than 90% of P was recovered as large crystals of struvite in optimal conditions which were: low Mg:Ca ratio (2.25:1), the leading parameter, high N:P ratio (3:1), moderate stirring rate (between 45 and 90 rpm) and low temperature (below 20 °C).These results were obtained despite the presence of a large amount of calcium and using a cheap reactant (MgO). The composition of the precipitates was identified by Raman analysis and solid dissolution. Results showed that amorphous calcium phosphate (ACP) co-precipitated with struvite and that carbonates were incorporated with solid fractions.

  8. Free radicals in biological energy conversion: EPR studies of model systems. Final report. [Mechanism of chlorophyll participation in photosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    Tollin, G.

    1976-08-31

    Energy conversion in photosynthesis is known to proceed via light-induced one-electron transfer reactions involving chlorophyll and electron donors and acceptors. Although the chemical identities of all of the components have not as yet been elucidated, considerable evidence has been accumulated which points to quinones (Q) as primary electron acceptors in both green plants and bacterial photosynthesis. Furthermore, it has been established that the initial photoprocess leads to the formation of a chlorophyll cation radical (C./sup +/). The research described in this report has as its goal the elucidation of the molecular-electronic mechanism of chlorophyll participation in photosynthesis. The following reactions have been observed: (a) Photoproduction of C./sup +/ in solution in the absence of added electron acceptors. This is a low quantum yield reaction which proceeds via the lowest excited singlet state. Bacteriochlorophyll also undergoes this reaction, whereas pheophytin does not. (b) One-electron phototransfer between the chlorophyll lowest triplet state and quinones to yield a radical pair (C./sup +/ - Q./sup +/). This may either recombine or separate. The C./sup +/ formed upon separation is unstable and reacts with hydroxylic compounds to regenerate chlorophyll. The Q./sup -/ species partly reacts with oxidized solvent and partly disproportionates. Both bacteriochlorophyll and pheophytin are also able to react with quinones in this manner. The quenching of the chlorophyll lowest singlet state by quinones does not, however, lead to detectable radical formation. These reactions seem to provide acceptable models for certain aspects of photosynthetic energy conversion, and thus elucidation of their detailed mechanisms should lead to useful insights into the nature of the biological process.

  9. The relationship between fat content and biological parameters of bigeye tuna ( Thunnus obseus) in the Western Central Indian Ocean

    Science.gov (United States)

    Song, Liming; Shen, Zhibin; Li, Jie; Li, Dongjing; Li, Yuwei

    2016-10-01

    Comparing fat content with physiological status can throw light on the reproduction and feeding behavior of the fish. The biological data of 586 bigeye tuna were collected from the longline fishery in the waters of Western Central Indian Ocean from November, 2012 to March, 2013. The spatial or temporal distribution of the fat content, and the relationships of fat content with gender, round weight, gonadal maturity and fork length were analyzed. A generalized additive model (GAM) was used to analyze the relationships between fat content and fork length (FL), gonadosomatic index (GSI), condition factor (K), and somatic index (SI). Results showed that: 1) the fat content of bigeye tuna was in the range of 3.1%-27.1% with the average 12.8%; 2) there were no significant geographical differences of average fat content ( P > 0.05) among 1° squares in general; 3) there were no significant differences ( P > 0.05) of the fat content for different genders, months, or gonad maturity stages; 4) there was an extremely significant correlation ( P = 0.000) between fat content and FL and GSI. There was no significant correlation ( P = 0.051) between fat content and K. There was a significant correlation ( P = 0.003) between fat content and SI. The results of this study suggest that the fat content of the matured fish was relatively stable. The survey area was in a spawning region, and the survey period was the spawning season for bigeye tuna.

  10. Effects of dietary selenium and vitamin E on immune response and biological blood parameters of broilers reared under thermoneutral or heat stress conditions

    Science.gov (United States)

    Habibian, Mahmood; Ghazi, Shahab; Moeini, Mohammad Mehdi; Abdolmohammadi, Alireza

    2014-07-01

    A study was conducted using 360 broiler chickens to evaluate the effects of dietary vitamin E (0, 125 and 250 mg/kg), selenium (Se, 0, 0.5 and 1 mg/kg), or their different combinations on immune response and blood biological parameters of broilers raised under either thermoneutral (TN, 23.9 °C constant) or heat stress (HS, 23.9 to 37 °C cycling) conditions. Humoral immunity was assessed by intravenous injection of 7 % sheep red blood cell (SRBC) followed by evaluation of serum for antibody titers in primary and secondary responses. Heterophil to lymphocyte (H/L) ratio also determined as an indicator of stress. Furthermore, at the end of the experiment, birds were bled for determination of some biological parameters. There was a significant reduction in body weight and feed intake, but the feed conversion ratio increased when the birds were exposed to HS ( P 0.05), whereas feed conversion was improved significantly by 125 mg/kg vitamin E ( P high concentration of Se ( P triglycerides, total cholesterol, and LDL-cholesterol were increased but serum HDL-cholesterol decreased in HS broilers ( P < 0.05).

  11. Microbial metabolic products as measuring parameters for emission studies on bio-waste treatment plants. Final report; Mikrobielle Stoffwechselprodukte als Messparameter bei Emissionsbetrachtungen an Bioabfall-Behandlungsanlagen. Abschlussbericht

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, G.; Dott, W.; Braun, S.; Dohms, E.; Mueller, T.; Thissen, R.

    2004-07-01

    Apart from the classic microbiological methods, other methods are available which are less costly and time-consuming and which are suited for a preliminary assessment of the potential hazard in the context of screening tests. These methods were investigated, and new measuring parameters were developed which can be used for assessing the potential hazard of airborne bio-aerosols in the context of biological waste treatment. (orig.) [German] Die in diesem Forschungsprojekt erarbeiteten Daten zeigen, dass sich neben den klassischen mikrobiologischen Methoden auch andere physikalisch-chemische Verfahren eignen, um eine Expositionserfassung von luftgetragenen Bioaerosolen durchzufuehren oder diese zu charakterisieren. Es wurden Verfahren etabliert, die zeit- und kostenguenstige Alternativen zu klassischen Methoden darstellen und die im Rahmen von Voruntersuchungen oder als Screening-Tests Entscheidungshilfen bei einer Gefaehrdungsabschaetzung bieten. Die erarbeiteten Methoden bedingen einen geringeren personal- und labortechnischen Aufwand und stellen eine entscheidende Vereinfachung bestehender Untersuchungskonzepte dar. Darueber hinaus wurden neue Messparameter erarbeitet, die im Rahmen einer zuverlaessigen Gefaehrdungsabschaetzung von luftgetragenen Bioaerosolen im Rahmen der Bioabfall-Behandlung eingesetzt werden koennen. (orig.)

  12. Development of biological and chemical methods for environmental monitoring of DOE waste disposal and storage facilities. Final report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1989-04-01

    Hazardous chemicals in the environment have received ever increasing attention in recent years. In response to ongoing problems with hazardous waste management, Congress enacted the Resource Conservation and Recovery Act (RCRA) in 1976. In 1980, Congress adopted the Comprehensive Environmental Response Compensation, and Liability Act (CERCLA), commonly called Superfund to provide for emergency spill response and to clean up closed or inactive hazardous waste sites. Scientists and engineers have begun to respond to the hazardous waste challenge with research and development on treatment of waste streams as well as cleanup of polluted areas. The magnitude of the problem is just now beginning to be understood. The U.S. Environmental Protection Agency (USEPA) National Priorities List as of September 13 1985, contained 318 proposed sites and 541 final sites (USEPA, 1985). Estimates of up to 30,000 sites containing hazardous wastes (1,200 to 2,000 of which present a serious threat to public health) have been made (Public Law 96-150). In addition to the large number of sites, the costs of cleanup using available technology are phenomenal. For example, a 10-acre toxic waste site in Ohio is to be cleaned up by removing chemicals from the site and treating the contaminated groundwater. The federal government has already spent more than $7 million to remove the most hazardous wastes and the groundwater decontamination alone is expected to take at least 10 years and cost $12 million. Another example of cleanup costs comes from the State of California Commission for Economic Development which predicts a bright economic future for the state except for the potential outlay of $40 billion for hazardous waste cleanup mandated by federal and state laws.

  13. Reproductive toxicity parameters and biological monitoring in occupationally and environmentally boron-exposed persons in Bandirma, Turkey.

    Science.gov (United States)

    Duydu, Yalçın; Başaran, Nurşen; Üstündağ, Aylin; Aydin, Sevtap; Ündeğer, Ülkü; Ataman, Osman Yavuz; Aydos, Kaan; Düker, Yalçın; Ickstadt, Katja; Waltrup, Britta Schulze; Golka, Klaus; Bolt, Hermann M

    2011-06-01

    Boric acid and sodium borates have been considered as being "toxic to reproduction and development", following results of animal studies with high doses. Experimentally, a NOAEL (no observed adverse effect level) of 17.5 mg B/kg-bw/day has been identified for the (male) reproductive effects of boron in a multigeneration study of rats, and a NOAEL for the developmental effects in rats was identified at 9.6 mg B/kg-bw/day. These values are being taken as the basis of current EU safety assessments. The present study was conducted to investigate the reproductive effects of boron exposure in workers employed in boric acid production plant in Bandirma, Turkey. In order to characterize the external and internal boron exposures, boron was determined in biological samples (blood, urine, semen), in workplace air, in food, and in water sources. Unfavorable effects of boron exposure on the reproductive toxicity indicators (concentration, motility, morphology of the sperm cells and blood levels of follicle-stimulating hormone (FSH), luteinizing hormone (LH), and total testosterone) were not observed. The mean calculated daily boron exposure (DBE) of the highly exposed group was 14.45 ± 6.57 (3.32-35.62) mg/day. These human exposures represent worst-case exposure conditions to boric acid/borates in Turkey. These exposure levels are considerably lower than exposures, which have previously led to reproductive effects in experimental animals. In conclusion, this means that dose levels of boron associated with developmental and reproductive toxic effects in animals are by far not reachable for humans under conditions of normal handling and use.

  14. Final Technical Report: DOE-Biological Ocean Margins Program. Microbial Ecology of Denitrifying Bacteria in the Coastal Ocean.

    Energy Technology Data Exchange (ETDEWEB)

    Lee Kerkhof

    2013-01-01

    The focus of our research was to provide a comprehensive study of the bacterioplankton populations off the coast of New Jersey near the Rutgers University marine field station using terminal restriction fragment polymorphism analysis (TRFLP) coupled to 16S rRNA genes for large data set studies. Our three revised objectives to this study became: (1) to describe bacterioplankton population dynamics in the Mid Atlantic Bight using TRFLP analysis of 16S rRNA genes. (2) to determine whether spatial and temporal factors are driving bacterioplankton community dynamics in the MAB using monthly samping along our transect line over a 2-year period. (3) to identify dominant members of a coastal bacterioplankton population by clonal library analysis of 16S rDNA genes and sequencing of PCR product corresponding to specific TRFLP peaks in the data set. Although open ocean time-series sites have been areas of microbial research for years, relatively little was known about the population dynamics of bacterioplankton communities in the coastal ocean on kilometer spatial and seasonal temporal scales. To gain a better understanding of microbial community variability, monthly samples of bacterial biomass were collected in 1995-1996 along a 34-km transect near the Long-Term Ecosystem Observatory (LEO-15) off the New Jersey coast. Surface and bottom sampling was performed at seven stations along a transect line with depths ranging from 1 to 35m (n=178). The data revealed distinct temporal patterns among the bacterioplankton communities in the Mid-Atlantic Bight rather than grouping by sample location or depth (figure 2-next page). Principal components analysis models supported the temporal patterns. In addition, partial least squares regression modeling could not discern a significant correlation from traditional oceanographic physical and phytoplankton nutrient parameters on overall bacterial community variability patterns at LEO-15. These results suggest factors not traditionally

  15. A nose-only apparatus for airborne delivery of Mycobacterium tuberculosis to mice: calibration of biological parameters.

    Science.gov (United States)

    Louveau, Céline; Descroix, Damien; Garnier, Laurence; Delamanche, Iroudayanadin; Chavarot, Pierre; Ramisse, Françoise; Marchal, Gilles; Vergnaud, Gilles

    2005-03-01

    Mycobacterium tuberculosis is the main cause of tuberculosis and is still a public health concern worldwide. This mycobacterium is transmitted through aerosols from human beings suffering from pulmonary tuberculosis to susceptible persons. To study this natural route of infection, we designed a new nose-only aerosol apparatus--system of aerosolisation of microorganisms (SAM)--in a carefully designed biohazard facility. For safety reasons, Mycobacterium smegmatis was first used to calibrate several parameters, such as inoculum density, atmospheric conditions (i.e. hygrometry) and particle size distribution. We present evidence that our apparatus is totally adapted to airborne delivery; the particle size of generated aerosol ranges from 1 to 7 microm, which is ideal for an infection by inhalation. We found that 99% of generated particles (<7 microm) could be retained by the respiratory tract, and among these particles, 62-79% (<3.3 microm) were able to reach pulmonary compartments. The next step was to simultaneously challenge 48 mice with M. tuberculosis in a highly reproducible way. We showed that a moderate dose (4 log10 colony-forming units (CFU) per mice) of M. tuberculosis was capable of causing progressive lung pathology and death in mice 30 days post-aerosolisation. Therefore, our apparatus, once calibrated, is easy to handle, safe, and can be used with any pathogen, which is spread by aerosol.

  16. A biological/chemical process for reduced waste and energy consumption, Caprolactam production: Phase 1, Select microorganisms and demonstrate feasibility. Final report

    Energy Technology Data Exchange (ETDEWEB)

    St.Martin, E.J.

    1995-08-01

    A novel biological/chemical process for converting cyclohexane into caprolactam was investigated. Microorganisms in a bioreactor would be used to convert cyclohexane into caprolactone followed by chemical synthesis of caprolactam using ammonia. The proposed bioprocess would be more energy efficient and reduce byproducts and wastes that are generated by the current chemical process. We have been successful in isolating from natural soil and water samples two microorganisms that can utilize cyclohexane as a sole source of carbon and energy for growth. These microorganisms were shown to have the correct metabolic intermediates and enzymes to convert cyclohexane into cyclohexanol, cyclohexanone and caprolactone. Genetic techniques to create and select for caprolactone hydrolase negative-mutants are being developed. These blocked-mutants will be used to convert cyclohexane into caprolactone but, because of the block, be unable to metabolize the caprolactone further and excrete it as a final end product.

  17. Investigational new drug safety reporting requirements for human drug and biological products and safety reporting requirements for bioavailability and bioequivalence studies in humans. Final rule.

    Science.gov (United States)

    2010-09-29

    The Food and Drug Administration (FDA) is amending its regulations governing safety reporting requirements for human drug and biological products subject to an investigational new drug application (IND). The final rule codifies the agency's expectations for timely review, evaluation, and submission of relevant and useful safety information and implements internationally harmonized definitions and reporting standards. The revisions will improve the utility of IND safety reports, reduce the number of reports that do not contribute in a meaningful way to the developing safety profile of the drug, expedite FDA's review of critical safety information, better protect human subjects enrolled in clinical trials, subject bioavailability and bioequivalence studies to safety reporting requirements, promote a consistent approach to safety reporting internationally, and enable the agency to better protect and promote public health.

  18. Age at Puberty and Some Biological Parameters of Awassi and its First Crosses with Charollais and Romanov Rams

    Directory of Open Access Journals (Sweden)

    Ahmad Qasem Al-Momani

    2010-01-01

    Full Text Available The aim of this experiment was to determine the age at puberty of both ram and ewe lambs of three genotypes: Awassi (A, Charollais x Awassi (CA, and Romanov x Awassi (RA F1crosses. Twenty, six-month old lambs (10 from each sex from each genotype were used. Ram and ewe lambs were kept in separate groups from the beginning until the end of the experiment. Birth weight and weaning weight were recorded for all animals. Body weights and body condition scores were recorded at monthly intervals between 6.5 and 12 months of age. Blood samples were collected weekly from ewe lambs and fortnightly from ram lambs to monitor progesterone and testosterone profiles, respectively. Semen character- istics and scrotal circumferences (SC were evaluated fortnightly. Weight at puberty in ewe and ram lambs were not sig- nificantly different among the three genotypes and ranged around 35 kg and 42 kg, respectively. In ewe lambs, age at puberty was significantly higher (P< 0.01 in A (280±11.5 d than in RA (232±11 d and CA (255±11.5 d. Age at puber- ty of ram lambs was also significantly different (P < 0.01 among the three genotypes being higher in A (243±5 d than in CA (223±5 d and RA (226±5 d ram lambs. Semen parameters improved with age in all genotypes. The RA ram lambs had greater semen concentration and lower abnormal spermatozoa than the other two genotypes (P< 0.05. Results of the present study indicate that crossing Awassi ewes with either Charollais or Romanov sires tends to improve reproduc- tive characteristics of the Fcrossbreds through advancing age at puberty in both ram and ewe lambs.

  19. Assessment of key biological and engineering design parameters for production of Chlorella zofingiensis (Chlorophyceae) in outdoor photobioreactors.

    Science.gov (United States)

    Zemke, Peter E; Sommerfeld, Milton R; Hu, Qiang

    2013-06-01

    For the design of a large field of vertical flat plate photobioreactors (PBRs), the effect of four design parameters-initial biomass concentration, optical path length, spacing, and orientation of PBRs-on the biochemical composition and productivity of Chlorella zofingiensis was investigated. A two-stage batch process was assumed in which inoculum is generated under nitrogen-sufficient conditions, followed by accumulation of lipids and carbohydrates in nitrogen-deplete conditions. For nitrogen-deplete conditions, productivity was the most sensitive to initial biomass concentration, as it affects the light availability to individual cells in the culture. An initial areal cell concentration of 50 g m(-2) inoculated into 3.8-cm optical path PBR resulted in the maximum production of lipids (2.42 ± 0.02 g m(-2) day(-1)) and carbohydrates (3.23 ± 0.21 g m(-2) day(-1)). Productivity was less sensitive to optical path length. Optical path lengths of 4.8 and 8.4 cm resulted in similar areal productivities (biomass, carbohydrate, and lipid) that were 20 % higher than a 2.4-cm optical path length. Under nitrogen-sufficient conditions, biomass productivity was 48 % higher in PBRs facing north-south during the winter compared to east-west, but orientation had little influence on biomass productivity during the spring and summer despite large differences in insolation. An optimal spacing could not be determined based on growth alone because a tradeoff was observed in which volumetric and PBR productivity increased as space between PBRs increased, but land productivity decreased.

  20. Biological Parameters for Evaluating the Toxic Potency of Petroleum Ether Extract of Wattakaka volubilis in Wistar Female Rats

    Directory of Open Access Journals (Sweden)

    Velmani Gopal

    2014-09-01

    Full Text Available Objectives: The present study investigated the toxic properties of petroleum ether extract of Wattakaka (W. volubilis in Wistar female rats. Methods: An in vitro brine shrimp lethality bioassay was studied in A. Salina nauplii, and the lethality concentrations were assessed for petroleum ether extract of W. volubilis. A water soluble portion of the test extract was used in different concentrations from 100-1000 μg/mL of 1 mg/mL stock solution. A 24-hours incubation with a 1-mL aliquot in 50 mL of aerated sea water was considered to calculate the percentage rate of dead nauplii with test extract administration against a potassium-dichromate positive control. The acute and the sub-acute toxicities of petroleum ether extract of W. volubilis were evaluated orally by using gavage in female Wistar rats. Food and water intake, body weight, general behavioral changes and mortality of animals were noted. Toxicity or death was evaluated following the administration of petroleum ether extract for 28 consecutive days in the female rats. Serum biochemical parameters, such as alanine aminotransferase (ALT, alkaline phosphatase (ALP, bilirubin, total cholesterol, triglyceride, total protein, glucose, urea, creatinine, sodium, potassium and α-amylase levels, were measured in the toxicity evaluations. Pathological changes in isolated organs, such as the liver, kidneys, and pancreas, were also examined using hematoxylin and eosin dye fixation after the end of the test extract’s administration. Results: The results of the brine-shrimp assay indicate that the evaluated concentrations of petroleum ether extract of W. volubilis were found to be non-toxic. In the acute and the sub-acute toxicity evaluations, no significant differences were observed between the control animals and the animals treated with extract of W. volubilis. No abnormal histological changes were observed in any of the animal groups treated with petroleum ether extract of W. volubilis

  1. Requirements for Foreign and Domestic Establishment Registration and Listing for Human Drugs, Including Drugs That Are Regulated Under a Biologics License Application, and Animal Drugs. Final rule.

    Science.gov (United States)

    2016-08-31

    The Food and Drug Administration (FDA) is amending its regulations governing drug establishment registration and drug listing. These amendments reorganize, modify, and clarify current regulations concerning who must register establishments and list human drugs, human drugs that are also biological products, and animal drugs. The final rule requires electronic submission, unless waived in certain circumstances, of registration and listing information. This rulemaking pertains to finished drug products and to active pharmaceutical ingredients (APIs) alone or together with one or more other ingredients. The final rule describes how and when owners or operators of establishments at which drugs are manufactured or processed must register their establishments with FDA and list the drugs they manufacture or process. In addition, the rule makes certain changes to the National Drug Code (NDC) system. We are taking this action to improve management of drug establishment registration and drug listing requirements and make these processes more efficient and effective for industry and for us. This action also supports implementation of the electronic prescribing provisions of the Medicare Prescription Drug, Improvement, and Modernization Act of 2003 (MMA) and the availability of current drug labeling information through DailyMed, a computerized repository of drug information maintained by the National Library of Medicine.

  2. Effect of Video Triggering During Conventional Lectures on Final Grades of Dental Students in an Oral Biology Course: A Two-Year Retrospective Study.

    Science.gov (United States)

    Farooq, Imran; Al-Jandan, Badr A

    2015-12-01

    The aim of this study was to analyze the effect of the inclusion of video triggers in conventional face-to-face lectures on the final grades of dental students in an oral biology course. The study consisted of two groups of students taking the course in two academic years at a dental school in Saudi Arabia: group 1, 2013-14 (control); and group 2, 2014-15. The total sample comprised 163 students (n=163; group 1: 71 and group 2: 92). Group 1 received lectures without any videos, whereas group 2 received lectures that included two to three videos of one to five minutes in duration with triggering effect (a video was shown every 10-15 minutes into the lecture). The final examination grades of the students were accessed retrospectively, and the data were compared with a chi-square test. The results confirmed that a higher number of students who received video triggering during lectures (group 2) performed better than their counterparts who did not receive video triggers (group 1); the difference was statistically significant (p<0.05). Among the group 2 students, 26% achieved a grade of A, and 37% achieved a grade of B. In contrast, only 7% of the group 1 students obtained a grade of A, and 31% achieved a grade of B. These results suggest that video triggers may offer an advantage over conventional methods and their inclusion in lectures can be a way to enhance students' learning.

  3. Predicting the partitioning of biological compounds between room-temperature ionic liquids and water by means of the solvation-parameter model.

    Science.gov (United States)

    Padró, Juan M; Ponzinibbio, Agustín; Mesa, Leidy B Agudelo; Reta, Mario

    2011-03-01

    The partition coefficients, P(IL/w), for different probe molecules as well as for compounds of biological interest between the room-temperature ionic liquids (RTILs) 1-butyl-3-methylimidazolium hexafluorophosphate, [BMIM][PF(6)], 1-hexyl-3-methylimidazolium hexafluorophosphate, [HMIM][PF(6)], 1-octyl-3-methylimidazolium tetrafluoroborate, [OMIM][BF(4)] and water were accurately measured. [BMIM][PF(6)] and [OMIM][BF(4)] were synthesized by adapting a procedure from the literature to a simpler, single-vessel and faster methodology, with a much lesser consumption of organic solvent. We employed the solvation-parameter model to elucidate the general chemical interactions involved in RTIL/water partitioning. With this purpose, we have selected different solute descriptor parameters that measure polarity, polarizability, hydrogen-bond-donor and hydrogen-bond-acceptor interactions, and cavity formation for a set of specifically selected probe molecules (the training set). The obtained multiparametric equations were used to predict the partition coefficients for compounds not present in the training set (the test set), most being of biological interest. Partial solubility of the ionic liquid in water (and water into the ionic liquid) was taken into account to explain the obtained results. This fact has not been deeply considered up to date. Solute descriptors were obtained from the literature, when available, or else calculated through commercial software. An excellent agreement between calculated and experimental log P(IL/w) values was obtained, which demonstrated that the resulting multiparametric equations are robust and allow predicting partitioning for any organic molecule in the biphasic systems studied.

  4. The effect of the application of the biological control agent EM1 on gas exchange parameters and productivity of Pisum sativum L. infected with Fusarium oxysporum Schlecht.

    Directory of Open Access Journals (Sweden)

    Adam Okorski

    2012-12-01

    Full Text Available A pot experiment on different methods of EM 1 application was conducted in the period 2002-2004. The study was carried out under controlled growth conditions. The experimental factor was the method of EM1 application. Before application, the biological preparation EM1 was propagated as recommended by the manufacturer (Greenland. The health status of the aboveground parts of 'Ramrod' pea plants was estimated at the flowering stage. The assessment of pea leaf gas exchange parameters (An, E, Gs, and Ci was made using a LI-Cor 6400 Portable Photosynthesis System. Soil application of EM1 combined with chemical control contributed to inhibiting Fusarium wilt of pea. Foliar application of EM1 combined with chemical control increased all gas exchange rates of pea leaves. Fusarium wilt of pea insignificantly decreased all gas exchange rates of pea leaves and the number of seeds per pod. The best method of EM1 application was soil treatment combined with chemical control, which increased all yield-related morphometric parameters of pea.

  5. Direct evaluation of radiobiological parameters from clinical data in the case of ion beam therapy: an alternative approach to the relative biological effectiveness.

    Science.gov (United States)

    Cometto, A; Russo, G; Bourhaleb, F; Milian, F M; Giordanengo, S; Marchetto, F; Cirio, R; Attili, A

    2014-12-07

    The relative biological effectiveness (RBE) concept is commonly used in treatment planning for ion beam therapy. Whether models based on in vitro/in vivo RBE data can be used to predict human response to treatments is an open issue. In this work an alternative method, based on an effective radiobiological parameterization directly derived from clinical data, is presented. The method has been applied to the analysis of prostate cancer trials with protons and carbon ions.Prostate cancer trials with proton and carbon ion beams reporting 5 year-local control (LC5) and grade 2 (G2) or higher genitourinary toxicity rates (TOX) were selected from literature to test the method. Treatment simulations were performed on a representative subset of patients to produce dose and linear energy transfer distribution, which were used as explicative physical variables for the radiobiological modelling. Two models were taken into consideration: the microdosimetric kinetic model (MKM) and a linear model (LM). The radiobiological parameters of the LM and MKM were obtained by coupling them with the tumor control probability and normal tissue complication probability models to fit the LC5 and TOX data through likelihood maximization. The model ranking was based on the Akaike information criterion.Results showed large confidence intervals due to the limited variety of available treatment schedules. RBE values, such as RBE = 1.1 for protons in the treated volume, were derived as a by-product of the method, showing a consistency with current approaches. Carbon ion RBE values were also derived, showing lower values than those assumed for the original treatment planning in the target region, whereas higher values were found in the bladder. Most importantly, this work shows the possibility to infer the radiobiological parametrization for proton and carbon ion treatment directly from clinical data.

  6. Analysis of biological parameters of Boophilus microplus Canestrini, 1887 exposed to entomopathogenic nematodes Steinernema carpocapsae Santa Rosa and All strains (Steinernema: Rhabditida

    Directory of Open Access Journals (Sweden)

    Gláucia Marques Freitas-Ribeiro

    2005-11-01

    Full Text Available Engorged and partially engorged females of Boophilus microplus were exposed to 600; 3,000; 6,000 and 30,000 infective juveniles of Steinernema carpocapsae Weiser, 1955 Santa Rosa and All strains per dish, under lab conditions. Eggs weight, pre-laying period, laying period, survival period, reproductive efficiency rate, percentage of larval eclosion and lethal concentrations of 50% and 90% (CL50 and CL90 were calculated for engorged females. In the case of partially engorged females, only egg weight, survival period and CL50 and CL90 were calculated. All biological parameters of engorged or partially engorged females were altered by exposition of S. carpocapsae infective juveniles (IJs, Santa Rosa and All strains (pFêmeas ingurgitadas e parcialmente ingurgitadas de B. microplus foram expostas a 600, 3000, 6000 e 30000 juvenis infectivos de Steinernema carpocapsae Weiser, 1955 linhagens Santa Rosa e ALL por placa, sob condições de laboratório. Foram investigados para fêmeas ingurgitadas: peso da massa de ovos, período pré-postura, período de postura, tempo de sobrevivência, índice de eficiência reprodutiva, percentual de aclosão de larvas e concentrações letais 50% e 90% (CL50 e CL90. Para fêmeas parcialmente ingurgitadas somente foram observados peso da massa de ovos, tempo de sobrevivência, CL50 e CL90. Todos os parâmetros biológicos de fêmeas ingurgitadas foram e parcialmente ingurgitadas foram alterados pela exposição a juvenis infectivos de S. carpocapsae linhagens Santa Rosa e ALL (P<0,05. O aumento das resposta foi diretamente proporcional ao aumento das concentrações de juvenis infectivos por placa (P<0,05. Os resultados sugerem que nematóides entomopatogênicos podem ter papel primissor no controle de carrapatos dos bovinos.

  7. Compilation and assessment of microwave bioeffects. Final report. A selective review of the literature on biological effects of microwaves in relation to the satellite power system

    Energy Technology Data Exchange (ETDEWEB)

    Justesen, D. R.; Ragan, H. A.; Rogers, L. E.; Guy, A. W.; Hjeresen, D. L.; Hinds, W. T.

    1978-05-01

    Potential biological and ecological problems are the focus of a review of the world's scientific literature on biological effects of microwave radiation. The emphasis is on recently reported data and on the 2450-MHz continuous-wave (CW) radiation that is envisioned for a Satellite Power System (SPS).

  8. Experimental methods for screening parameters influencing the growth to product yield (Y(x/CH4 of a biological methane production (BMP process performed with Methanothermobacter marburgensis

    Directory of Open Access Journals (Sweden)

    Sébastien Bernacchi

    2014-12-01

    Full Text Available 1. Specht M, Brellochs J, Frick V, et al. (2010 Storage of renewable energy in the natural gas grid. Erdoel, Erdgas, Kohle 126: 342-345.2. Thauer RK, Kaster AK, Goenrich M, et al. (2010 Hydrogenases from methanogenic archaea, nickel, a novel cofactor, and H2 storage. Annu Rev Biochem 79: 507-536.3. Liu Y, Whitman WB (2008 Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann N Y Acad Sci 1125: 171-189.4. Kaster AK, Goenrich M, Seedorf H, et al. (2011 More than 200 genes required for methane formation from H2 and CO2 and energy conservation are present in Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus. Archaea ID 973848: 1-23.5. Seifert AH, Rittmann S, Herwig C (2014 Analysis of process related factors to increase volumetric productivity and quality of biomethane with Methanothermobacter marburgensis Appl Energ 132: 155-162.6. Bernacchi S, Weissgram M, Wukovits W, et al. (2014 Process efficiency simulation for key process parameters in biological methanogenesis. AIMS bioengineering 1: 53-71.7. Thauer RK, Kaster AK, Seedorf H, et al. (2008 Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol 6: 579-591.8. Schill N, van Gulik WM, Voisard D, et al. (1996 Continuous cultures limited by a gaseous substrate: development of a simple, unstructure mathematical model and experimental verification with Methanobacterium thermoautotrophicum. Biotechnol Bioeng 51: 645-658.9. Jud G, Schneider K, Bachofen R (1997 The role of hydrogen mass transfer for the growth kinetics of Methanobacterium thermoautotrophicum in batch and chemostat cultures. J Ind Microbiol Biotechnol 19: 246-251.10. Tsao JH, Kaneshiro SM, Yu SS, et al. (1994 Continuous culture of Methanococcus jannaschii, an extremely thermophilic methanogen. Biotechnol Bioeng 43: 258-261.11. Schill N, van Gulik WM, Voisard D, et al. (1996 Continuous cultures limited by a gaseous substrate: development of a

  9. Foldit Biology

    Science.gov (United States)

    2015-07-31

    Report 8/1/2013-7/31/2015 4. TITLE AND SUBTITLE Sa. CONTRACT NUMBER Foldit Biology NOOO 14-13-C-0221 Sb. GRANT NUMBER N/A Sc. PROGRAM ELEMENT...Include area code) Unclassified Unclassified Unclassified (206) 616-2660 Zoran Popović Foldit Biology (Task 1, 2, 3, 4) Final Report...Period Covered by the Report August 1, 2013 – July 31, 2015 Date of Report: July 31, 2015 Project Title: Foldit Biology Contract Number: N00014-13

  10. Patient Protection and Affordable Care Act; program integrity: exchange, premium stabilization programs, and market standards; amendments to the HHS notice of benefit and payment parameters for 2014. Final rule.

    Science.gov (United States)

    2013-10-30

    This final rule implements provisions of the Patient Protection and Affordable Care Act and the Health Care and Education Reconciliation Act of 2010 (collectively referred to as the Affordable Care Act). Specifically, this final rule outlines financial integrity and oversight standards with respect to Affordable Insurance Exchanges, qualified health plan (QHP) issuers in Federally-facilitated Exchanges (FFEs), and States with regard to the operation of risk adjustment and reinsurance programs. It also establishes additional standards for special enrollment periods, survey vendors that may conduct enrollee satisfaction surveys on behalf of QHP issuers, and issuer participation in an FFE, and makes certain amendments to definitions and standards related to the market reform rules. These standards, which include financial integrity provisions and protections against fraud and abuse, are consistent with Title I of the Affordable Care Act. This final rule also amends and adopts as final interim provisions set forth in the Amendments to the HHS Notice of Benefit and Payment Parameters for 2014 interim final rule, published in the Federal Register on March 11, 2013, related to risk corridors and cost-sharing reduction reconciliation.

  11. Oil pollution and the significant biological resources of Puget Sound : final report field survey from 16 July 1974 to 01 September 1976 (NODC Accession 7601556)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Biological and chemical data were collected using sediment sampler and other instruments in the PUGET Sound, which is in the Northwest coastal waters of Washington....

  12. Robust design of biological circuits: evolutionary systems biology approach.

    Science.gov (United States)

    Chen, Bor-Sen; Hsu, Chih-Yuan; Liou, Jing-Jia

    2011-01-01

    Artificial gene circuits have been proposed to be embedded into microbial cells that function as switches, timers, oscillators, and the Boolean logic gates. Building more complex systems from these basic gene circuit components is one key advance for biologic circuit design and synthetic biology. However, the behavior of bioengineered gene circuits remains unstable and uncertain. In this study, a nonlinear stochastic system is proposed to model the biological systems with intrinsic parameter fluctuations and environmental molecular noise from the cellular context in the host cell. Based on evolutionary systems biology algorithm, the design parameters of target gene circuits can evolve to specific values in order to robustly track a desired biologic function in spite of intrinsic and environmental noise. The fitness function is selected to be inversely proportional to the tracking error so that the evolutionary biological circuit can achieve the optimal tracking mimicking the evolutionary process of a gene circuit. Finally, several design examples are given in silico with the Monte Carlo simulation to illustrate the design procedure and to confirm the robust performance of the proposed design method. The result shows that the designed gene circuits can robustly track desired behaviors with minimal errors even with nontrivial intrinsic and external noise.

  13. Catalogue of methods of calculation, interpolation, smoothing, and reduction for the physical, chemical, and biological parameters of deep hydrology (CATMETH) (NODC Accession 7700442)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The document presents the methods, formulas and citations used by the BNDO to process physical, chemical, and biological data for deep hydrology including...

  14. Triple Plate Mold Final Report: Optimization of the Mold Design and Casting Parameters for a Thin U-10mo Fuel Casting

    Energy Technology Data Exchange (ETDEWEB)

    Aikin, Jr., Robert M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-01-04

    This work describes the experiments and modeling that have been performed to improve and try to optimize the simultaneous casting of three plates of U-10wt%Mo in a single coil vacuum induction melting (VIM) furnace. The plates of interest are 280 mm wide by 203 mm tall by 5 mm thick (11" x 8" x 0.2"). The initial mold design and processing parameters were supplied by Y-12. The mold and casting cavity were instrumented with a number of thermocouples, and the casting performed to determine the thermal history of the mold and casting. The resulting cast plates were radiographed and numerous defects identified. Metallography was performed to help identify the nature of the radiographically observed defects. This information was then used to validate a mold filling and solidification model of that casting. Based on the initial casting, good casting design practice, and process simulation of several design alternatives, a revised design was developed with the goal of minimizing casting defects such as porosity. The redesigned mold had a larger hot-top and had its long axis along the horizontal direction. These changes were to try to develop a strong thermal gradient conducive to good feeding and minimization of micro- and macroporosity in the cast plates. An instrumented casting was then performed with the revised mold design and a linear distributor. This design yielded cast plates with significantly less radiographically identified defects. Unfortunately, there was significant variation in plate weight and metal content in their hot-tops. Fluid flow simulations were then performed on this mold/distributor design. This helped identify the issue with this linear distributor design. Additional simulations were then performed on candidate distributor redesigns and a preferred distributor annular design was identified. This improved annular design was used to produce a third instrumented casting with favorable results. These refined designs and their radiographic

  15. Derivation of radioecological parameters from the long-term emission of iodine-129. Final report; Ableitung von radiooekologischen Parametern aus dem langfristigen Eintrag von Iod-129. Abschlussbericht

    Energy Technology Data Exchange (ETDEWEB)

    Michel, R.; Klipsch, K.; Ernst, T.; Gorny, M.; Jakob, D.; Vahlbruch, J. [Zentrum fuer Strahlenschutz und Radiooekologie (ZSR), Universitaet Hannover (Germany); Synal, H.A. [Paul Scherrer Inst., ETH Hoenggerberg, Zuerich (Switzerland); Schnabel, C. [Institut fuer Teilchenphysik, ETH Hoenggerberg, Zuerich (Switzerland)

    2004-07-01

    In this project, the distribution and behaviour of {sup 129}I and {sup 127}I in the environment and its pathways through the environment to man were comprehensively investigated in order to provide a basis for estimating the radiation exposure to man due to releases of {sup 129}I. To this end, the actual situation in Lower Saxony, Germany, was studied for exemplary regions near to and far from the coast of the North Sea. Accelerator mass spectrometry, radiochemical neutron activation analysis, ion chromatography, and ICP-MS were applied to measure the iodine isotopes, {sup 129}I and P{sup 127}I, in sea-water, air, precipitation, surface and ground waters, soils, plants, animals, foodstuffs, total diet, and human and animal thyroid glands. For air-borne iodine, the speciation as well as the particle size distribution of aerosols was determined. Soil depth profiles were investigated down to depths of 2.5 m in order to study the iodine migration as well as individual surface soil samples to allow for the determination of transfer factors of the iodine isotopes into plants. From the analytical results radioecological parameters for the long-term behaviour of {sup 129}I in the pedo- and biosphere were derived. The iodine isotopes are in severe disequilibrium in the different environmental compartments. The pre-nuclear equilibrium {sup 129}I/{sup 127}I ratio in the biosphere was determined to be 2.0 x 10{sup -13} with a geometric standard deviation of 1.39. Today, the environmental isotopic ratios in Northern Germany range from 10{sup -6} to 10{sup -10}. The highest ratios are found in North Sea water, the lowest in deep soil samples and ground water. The North Sea appears as the dominant source of air-borne iodine in Northern Germany due to the emissions of European reprocessing plants. The results are discussed with respect to their radiological relevance and in view of the general protection of the environment, i.e. air, water, soil and the biosphere. (orig.)

  16. Final Report from the Department of Kinetics of Chemical and Biological Processes, Institute of Chemical Physics of Russian Academy of Sciences

    Science.gov (United States)

    1994-01-01

    photokeratitis, senile cataract, macular degeneration and so on. In laboratory of physical-chemical basis of reception, Institute of Chemical... rehabilitating complex of vitamins according to the methods developed in the Institute improved the biophysical parameters and, hence, restored organism...forage of animals. 6. Environmental and human rehabilitation Antioxidants at Low Doses for Afforestation in Polluted Regions Burlakova E.B., Apasheva

  17. NATO Planning Guide for the Estimation of Chemical, Biological, Radiological, and Nuclear (CBRN) Casualties (AMedP-8(C)) - Parameters for Estimation of Casualties from Exposure to Specified Biological Agents. Addenda to Allied Medical Publication 8

    Science.gov (United States)

    2011-01-01

    estimating the numbers of persons developing illness or dying from anthrax, botulism, Venezuelan equine encephalitis, plague, and smallpox. Five additional...the non-contagious biological agent explanation in Section 0106.7b, following the Venezuelan equine encephalitis (VEE) assumptions and limitations...comprehensive clinical studies of tularemia available were reported in the pre- antibiotic era before inhalation was understood to be a potential route of

  18. Compilation and assessment of microwave bioeffects. Final report. A selective review of the literature on biological effects of microwaves in relation to the Satellite Power System (SPS)

    Energy Technology Data Exchange (ETDEWEB)

    Justesen, D.R.; Ragan, H.A.; Rogers, L.E.; Guy, A.W.; Hjeresen, D.L.; Hinds, W.T.; Phillips, R.D.

    1978-05-01

    One of many alternate sources of electrical energy that are being considered by the Department of Energy is a microwave-mediated Satellite Power System (SPS). Once inserted into geosynchronous orbit at an altitude of more than 40,000 kilometers, a satellite would collect then convert the sun's energy to 2450-MHz microwaves, which would be beamed to the Earth's surface, where a rectifying antenna (rectenna) would convert the microwaves to electrical current suitable for industrial and domestic use. The expanse of each rectenna (about 10 by 13 kilometers), the power density of the continuous-wave microwave beam (approx. 23 mW/cm/sup 2/ at center, with fall off to 1 mW/cm/sup 2/ or less at the periphery of the rectenna), and the possibility that 20 or more satellite systems will eventually be operating, creates two sets of interrelated problems for biological/ecological assessment. These are 1) the effects of microwave fields of higher intensity on airborne biota (including human beings in aircraft) that may traffic the area above the rectenna and 2) the effects of virtually perpetual fields of much lower intensity on all forms of life at and beyond the rectennae's zone of exclusion. In this review, the scientific literature is examined, not only for biological effects that are pertinent to assessment of SPS, but for hiatuses of knowledge that will have to be filled before SPS can be vouched for operational safety.

  19. Final Report of “Collaborative research: Fundamental science of low temperature plasma-biological material interactions” (Award# DE-SC0005105)

    Energy Technology Data Exchange (ETDEWEB)

    Oehrlein, Gottlieb S. [Univ. of Maryland, College Park, MD (United States); Seog, Joonil [Univ. of Maryland, College Park, MD (United States); Graves, David [Univ. of California, Berkeley, CA (United States); Chu, J. -W. [Univ. of California, Berkeley, CA (United States)

    2014-09-24

    Low temperature plasma (LTP) treatment of biological tissue is a promising path toward sterilization of bacteria due to its versatility and ability to operate under well-controlled and relatively mild conditions. The present collaborative research of an interdisciplinary team of investigators at University of Maryland, College Park (UMD), and University of California, Berkeley (UCB) focused on establishing our knowledge on low temperature plasma-induced chemical modifications in biomolecules that result in inactivation due to various plasma species, including ions, reactive radicals, and UV/VUV photons. The overall goals of the project were to identify the mechanisms by which low and atmospheric pressure plasma (APP) deactivates endotoxic biomolecules. Additionally, we wanted to understand how deactivation processes depend on the interaction of APP with the environment. Various low pressure plasma sources, a vacuum beam system and several atmospheric pressure plasma sources were used to accomplish these objectives. In our work we elucidated for the first time the role of ions, VUV photons and radicals in biological deactivation of model endotoxic biomolecules, both in a UHV beam system and an inductively coupled, low pressure plasma system, and established the associated atomistic modifications in biomolecules. While we showed that both ions and VUV photons can be very efficient in deactivation of biomolecules, significant etching and/or deep modification (~200 nm) were accompanied by these biological effects. One of the most important findings in this work is that the significant deactivation and surface modification can occur with minimal etching using radical species. However, if radical fluxes and corresponding etch rates are relatively high, for example, at atmospheric pressure, inactivation of endotoxic biomolecule film may require near-complete removal of the film. These findings motivated further work at atmospheric pressure using several types of low

  20. Early-warning process/control for anaerobic digestion and biological nitrogen transformation processes: Batch, semi-continuous, and/or chemostat experiments. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Hickey, R. [Science Applications International Corp., McLean, VA (United States)

    1992-09-01

    The objective of this project was to develop and test an early-warning/process control model for anaerobic sludge digestion (AD). The approach was to use batch and semi-continuously fed systems and to assemble system parameter data on a real-time basis. Specific goals were to produce a real-time early warning control model and computer code, tested for internal and external validity; to determine the minimum rate of data collection for maximum lag time to predict failure with a prescribed accuracy and confidence in the prediction; and to determine and characterize any trends in the real-time data collected in response to particular perturbations to feedstock quality. Trends in the response of trace gases carbon monoxide and hydrogen in batch experiments, were found to depend on toxicant type. For example, these trace gases respond differently for organic substances vs. heavy metals. In both batch and semi-continuously feed experiments, increased organic loading lead to proportionate increases in gas production rates as well as increases in CO and H{sub 2} concentration. An analysis of variance of gas parameters confirmed that CO was the most sensitive indicator variable by virtue of its relatively larger variance compared to the others. The other parameters evaluated including gas production, methane production, hydrogen, carbon monoxide, carbon dioxide and methane concentration. In addition, a relationship was hypothesized between gaseous CO concentration and acetate concentrations in the digester. The data from semicontinuous feed experiments were supportive.

  1. Combining Physical and Biologic Parameters to Predict Radiation-Induced Lung Toxicity in Patients With Non-Small-Cell Lung Cancer Treated With Definitive Radiation Therapy

    Energy Technology Data Exchange (ETDEWEB)

    Stenmark, Matthew H. [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Cai Xuwei [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Radiation Oncology, Shanghai Cancer Hospital, Fudan University, Shanghai (China); Shedden, Kerby [Department of Biostatistics, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Hayman, James A. [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Yuan Shuanghu [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Radiation Oncology, Shangdong Cancer Hospital, Jinan (China); Ritter, Timothy [Veterans Affairs Medical Center, Ann Arbor, Michigan (United States); Ten Haken, Randall K.; Lawrence, Theodore S. [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Kong Fengming, E-mail: fengkong@med.umich.edu [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Veterans Affairs Medical Center, Ann Arbor, Michigan (United States)

    2012-10-01

    Purpose: To investigate the plasma dynamics of 5 proinflammatory/fibrogenic cytokines, including interleukin-1beta (IL-1{beta}), IL-6, IL-8, tumor necrosis factor alpha (TNF-{alpha}), and transforming growth factor beta1 (TGF-{beta}1) to ascertain their value in predicting radiation-induced lung toxicity (RILT), both individually and in combination with physical dosimetric parameters. Methods and Materials: Treatments of patients receiving definitive conventionally fractionated radiation therapy (RT) on clinical trial for inoperable stages I-III lung cancer were prospectively evaluated. Circulating cytokine levels were measured prior to and at weeks 2 and 4 during RT. The primary endpoint was symptomatic RILT, defined as grade 2 and higher radiation pneumonitis or symptomatic pulmonary fibrosis. Minimum follow-up was 18 months. Results: Of 58 eligible patients, 10 (17.2%) patients developed RILT. Lower pretreatment IL-8 levels were significantly correlated with development of RILT, while radiation-induced elevations of TGF-ss1 were weakly correlated with RILT. Significant correlations were not found for any of the remaining 3 cytokines or for any clinical or dosimetric parameters. Using receiver operator characteristic curves for predictive risk assessment modeling, we found both individual cytokines and dosimetric parameters were poor independent predictors of RILT. However, combining IL-8, TGF-ss1, and mean lung dose into a single model yielded an improved predictive ability (P<.001) compared to either variable alone. Conclusions: Combining inflammatory cytokines with physical dosimetric factors may provide a more accurate model for RILT prediction. Future study with a larger number of cases and events is needed to validate such findings.

  2. Wetland Biomass Production: emergent aquatic management options and evaluations. A final subcontract report. [Includes a bibliography containing 686 references on Typha from biological abstracts

    Energy Technology Data Exchange (ETDEWEB)

    Pratt, D.C.; Dubbe, D.R.; Garver, E.G.; Linton, P.J.

    1984-07-01

    The high yield potential and attractive chemical composition of Typha make it a particularly viable energy crop. The Minnesota research effort has demonstrated that total annual biomass yields equivalent to 30 dry tonnes/ha (13 tons/acre) are possible in planted stands. This compares with yields of total plant material between 9 and 16 dry tonnes/ha (4 to 7 tons/acre) in a typical Minnesota corn field. At least 50% of the Typha plant is comprised of a belowground rhizome system containing 40% starch and sugar. This high level of easily fermentable carbohydrate makes rhizomes an attractive feedstock for alcohol production. The aboveground portion of the plant is largely cellulose, and although it is not easily fermentable, it can be gasified or burned. This report is organized in a manner that focuses on the evaluation of the management options task. Results from stand management research performed at the University of Minnesota during 1982 and 1983 are integrated with findings from an extensive survey of relevant emergent aquatic plant research and utilization. These results and findings are then arranged in sections dealing with key steps and issues that need to be dealt with in the development of a managed emergent aquatic bio-energy system. A brief section evaluating the current status of rhizome harvesting is also included along with an indexed bibliography of the biology, ecology, and utilization of Typha which was completed with support from this SERI subcontract. 686 references, 11 figures, 17 tables.

  3. Lead exposures and biological responses in military weapons systems: Aerosol characteristics and acute lead effects among US Army artillerymen: Final report

    Energy Technology Data Exchange (ETDEWEB)

    Bhattacharyya, M.H.; Stebbings, J.H.; Peterson, D.P.; Johnson, S.A.; Kumar, R.; Goun, B.D.; Janssen, I.; Trier, J.E.

    1993-03-01

    This study was to determine the concentration and chemical nature of lead (Pb) aerosols produced during the firing of artillery and to determine the exposures and biological responses of crew members exposed to lead aerosols during such firing. The concentrations of lead-containing aerosols at crew positions depended on wind conditions, with higher concentrations when firing into a head wind. Aerosol concentrations were highest in the muzzle blast zone. Concentrations of lead in the blood of crew members rose during the first 12 days of exposure to elevated airborne lead concentrations and then leveled off. There was no rapid decrease in blood lead concentrations after completion of firing. Small decreases in hematocrit and small increases in free erythrocyte porphyrin were correlated with increasing exposure to airborne lead. These changes were reversed by seven weeks after firing. Changes in nerve conduction velocity had borderline statistical significance to airborne lead exposure. In measuring nerve conduction velocity, differences in skin temperature must be taken into account.

  4. Mechanical Instabilities of Biological Tubes

    Science.gov (United States)

    Hannezo, Edouard; Prost, Jacques; Joanny, Jean-François

    2012-07-01

    We study theoretically the morphologies of biological tubes affected by various pathologies. When epithelial cells grow, the negative tension produced by their division provokes a buckling instability. Several shapes are investigated: varicose, dilated, sinuous, or sausagelike. They are all found in pathologies of tracheal, renal tubes, or arteries. The final shape depends crucially on the mechanical parameters of the tissues: Young’s modulus, wall-to-lumen ratio, homeostatic pressure. We argue that since tissues must be in quasistatic mechanical equilibrium, abnormal shapes convey information as to what causes the pathology. We calculate a phase diagram of tubular instabilities which could be a helpful guide for investigating the underlying genetic regulation.

  5. Effects of potential food sources on biological and demographic parameters of the predatory mites Kampimodromus aberrans, Typhlodromus pyri and Amblyseius andersoni.

    Science.gov (United States)

    Lorenzon, Mauro; Pozzebon, Alberto; Duso, Carlo

    2012-11-01

    Kampimodromus aberrans, Typhlodromus pyri and Amblyseius andersoni are generalist predatory mites important in controlling tetranychid and eriophyoid mites in European vineyards. They can persist by exploiting various non-prey foods when their main prey is absent or scarce. A comparative analysis of the effects of various prey and non-prey foods on the life history of these predators is lacking. In the laboratory, predatory mites were reared on herbivorous mites (Panonychus ulmi, Eotetranychus carpini and Colomerus vitis), a potential alternative prey (Tydeus caudatus) and two non-prey foods, i.e. the pollen of Typha latifolia and the mycelium of Grape downy mildew (GDM) Plasmopara viticola. Developmental times, survival, sex ratio and fecundity as well as life table parameters were estimated. Kampimodromus aberrans developed faster on E. carpini, C. vitis or pollen than on P. ulmi and laid more eggs on pollen than on prey. Low numbers of this predator developed on GDM infected leaves. Tydeus caudatus was not suitable as prey for any of the three predatory mites. Kampimodromus aberrans showed the highest intrinsic rate of population increase when fed on pollen. Developmental times of T. pyri on prey or pollen were similar but fecundity was higher on pollen than on P. ulmi. Typhlodromus pyri had higher intrinsic rates of population increase on C. vitis and pollen than on P. ulmi; E. carpini showed intermediate values whereas GDM resulted in the lowest r ( m ) values. Development of A. andersoni females was faster on pollen and C. vitis than on P. ulmi and GDM. Fecundity was higher on pollen and mites compared to GDM. Life table parameters of A. andersoni did not differ when predators were fed with prey or pollen while GDM led to a lower r ( m ) value. On a specific diet A. andersoni exhibited faster development and higher fecundity than T. pyri and K. aberrans. These findings improve knowledge on factors affecting the potential of predatory mites in controlling

  6. Suspension membrane reactor for biological elimination of non-degradable materials from mixed effluents. Final report; Suspensionsmembranreaktor zur biologischen Eliminierung schwer abbaubarer Stoffe aus Abwassergemischen. Abschlussbericht

    Energy Technology Data Exchange (ETDEWEB)

    Raebiger, N.; Schierenbeck, A.

    2002-07-01

    An earlier research project had shown that a combined process involving membrane filtration and a bioreactor ensure substrate-specific times of residue inside the reactor, i.e. high selective conversation at low discharge rates. The second project aimed at higher flexibility. For this purpose, a two-stage suspension membrane reactor was developed in which the filtration stage and the bioreactor were decoupled. The liquid effluents are concentrated first in a nanofiltration stage, and the permeate, which should be free of non-degradable materials, is discharged. The concentrate is treated in the biological reaction stage and recirculated into the nanofiltration stage in order to ensure complete degradation during a substrate-specific time of residue. An intermediate microfiltration stage serves to retain biomass and prevent the growth of a biofilm in the nanofiltration stage. The method was tested with the practically relevant model pollutant 4-chlorophenol and a real industrial effluent from the antifelting stage of a Bremen woollen mill (Bremer Wollkaemmerei), with a high AOX concentration. [German] Im vorhergehenden Teil des Forschungsvorhabens konnte gezeigt werden, dass durch eine kombinierte Anwendung der Membranfiltration mit einem Bioreaktor eine substratspezifische Verweilzeitverteilung im Reaktor und damit eine hohe selektive Umsatzleistung bei gleichzeitig niedrigen Ablaufwerten realisierbar ist. Um eine groessere Flexibilitaet bei dem Einsatz verschiedener Membranmodule zu realisieren, wurde in dem zweiten Abschnitt des Forschungsvorhabens eine zweistufige Anlage vom Typ des Suspensions-Membranreaktors entwickelt, bei der Filtration und Bioreaktor entkoppelt werden. Das zu reinigende Abwasser wird zunaechst in einer Nanofiltrationsstufe aufkonzentriert, das moeglichst an schwer abbaubaren Stoffen freie Permeat bildet den Ablauf der Anlage. Der Konzentratstrom wird in der nachfolgenden Reaktionsstufe biologisch behandelt und in die Nanofiltrationsstufe

  7. Biological and Physicochemical Parameters Related to the Nitrogen Cycle in the Rhizospheric Soil of Native Potato (Solanum phureja Crops of Colombia

    Directory of Open Access Journals (Sweden)

    Nathalia Flórez-Zapata

    2011-01-01

    Full Text Available Nitrogen (N plays an important role in agricultural production. This study was designed to evaluate the presence of cultivable N cycle-associated microorganisms (nitrogen-fixing bacteria—NFB, proteolytic bacteria—PR, ammonifiers—AMO, ammonium-oxidizing bacteria—AOB, nitrite-oxidizing bacteria—NOB, and denitrifiers—DEN, and their relationship with physical-chemical and agronomic soil descriptors, in Solanum phureja rhizospheric soil samples, from traditional and organic crop management farms. A cluster analysis with the physical and chemical properties of soil, allowed to identify the organic matter content as an important factor that determines the outcome of that grouping. Significant differences (<0.05 between farms were found in the abundance of this groups, but correlation analysis showed that proteolytic and nitrogen fixing bacteria were the main nitrogen associated functional groups affected by soils' physical-chemical characteristics. The amount of ammonia available is affected by the agricultural management strategy, which consequently affects the NFB abundance. Finally the results showed that PR, protease activity and soil properties related with organic matter transformation has a positive relationship with productivity, which given the high organic matter content of the Andean soils being studied, we conclude that nitrogen mineralization process has an important role in the nitrogen cycle and its bioavailability in this ecosystem.

  8. Estimation of the input parameters in the Feller neuronal model

    Science.gov (United States)

    Ditlevsen, Susanne; Lansky, Petr

    2006-06-01

    The stochastic Feller neuronal model is studied, and estimators of the model input parameters, depending on the firing regime of the process, are derived. Closed expressions for the first two moments of functionals of the first-passage time (FTP) through a constant boundary in the suprathreshold regime are derived, which are used to calculate moment estimators. In the subthreshold regime, the exponentiality of the FTP is utilized to characterize the input parameters. The methods are illustrated on simulated data. Finally, approximations of the first-passage-time moments are suggested, and biological interpretations and comparisons of the parameters in the Feller and the Ornstein-Uhlenbeck models are discussed.

  9. Responses of hematological parameters, beta-endorphin, cortisol, reactive oxygen metabolites, and biological antioxidant potential in horses participating in a traditional tournament.

    Science.gov (United States)

    Pazzola, M; Pira, E; Sedda, G; Vacca, G M; Cocco, R; Sechi, S; Bonelli, P; Nicolussi, P

    2015-04-01

    Several concerns have been raised over the health of animals used in equestrian games that have their origins in historical or religious events and are currently held in many countries. This study investigated physiological stress response and health status of horses participating in the Sartiglia, a historical horse tournament held in the city of Oristano, Italy, which is principally based on the attempts of masked horsemen at a gallop to run a sword through a hole in a suspended silver star. Blood samples were collected from 21 horses the day before the tournament (D0), during the tournament (D1), and the day after the tournament (D2). Samples were analyzed for complete blood count and biochemical, hormonal, and oxidative stress assays. Data were analyzed using the mixed effect model with sampling session as one of the fixed effects. On the whole, blood parameters evidenced an optimal health status of horses at D0. Significant dehydration and increase of circulating glucose, enzymes, cortisol, and β-endorphin were registered at D1 (P horses in similar tournaments.

  10. Intra-articular use of a medical device composed of hyaluronic acid and chondroitin sulfate (Structovial CS: effects on clinical, ultrasonographic and biological parameters

    Directory of Open Access Journals (Sweden)

    Henrotin Yves

    2012-08-01

    Full Text Available Abstract Background This pilot open noncontrolled study was designed to assess the efficacy of intra-articular injections of a solution combining hyaluronic acid (HA and chondroitin sulphate (CS in the treatment of outpatients affected by knee osteoarthrosis. Findings Thirty patients with knee OA have been included. The primary objective was to assess clinical efficacy as measured by pain and Lequesne’s index. Secondary objectives were to assess potential effect of the treatment on ultrasound parameters, safety and biomarkers of cartilage metabolism and joint inflammation. After a selection visit (V1, the study treatment was administered 3 times on a weekly basis (V2, V3, V4. Follow-up was planned 6 (V5 and 12 weeks (V6 after the first intra-articular injection. Efficacy results showed a reduction in mean pain at V3 and V6 and in functional impairment, the most marked changes being measured at the two follow-up visits (V5 and V6. Although statistical significance was not achieved due to small sample size, a clear tendency towards improvement was detectable for ultrasound assessments as well as biomarkers. Except for a mild injection site hematoma for which the drug causal relationship could not be excluded, no adverse effect of clinical relevance was recorded during the study. Conclusion Although this pilot study was performed according to an open design only, the ultrasound as well as biomarkers changes strongly suggest a non-placebo effect. These preliminary results call now for a randomized controlled study to confirm the clinical relevance of the observed results. Trial registration #ISRCTN91883031

  11. Effect of plant extracts and a disinfectant on biological parameters and pathogenicity of the fungus Beauveria bassiana (Bals. Vuill. (Ascomycota: Cordycipitaceae

    Directory of Open Access Journals (Sweden)

    C. C. Martins

    Full Text Available Abstract The fungus Beauveria bassiana is naturally found in poultry houses and causes high rates of mortality in Alphitobius diaperinus. Laboratory and field experiments have shown the potential of this fungus as an insect control agent. However, in poultry houses, bacteria as Salmonella, can be found and have been studied alternative control methods for this pathogen. Thus, this study aimed to evaluate the effect of plant extracts and a disinfectant on the fungus Beauveria bassiana (strain Unioeste 4. Conidial viability, colony-forming unit (CFU counts, vegetative growth, conidia production, insecticidal activity of the fungus and compatibility were used as parameters in the evaluation of the effect of these products on the fungus. Alcoholic and aqueous extracts of jabuticaba (Myrciaria cauliflora (Mart., guava (Psidium guajava (L., and jambolan (Syzygium cumini (L., at concentrations of 10% as well as the commercial disinfectant, Peroxitane® 1512 AL, were evaluated at the recommended concentrations (RC, 1:200 (RC, 0.5 RC and 2 RC. There was a negative influence of alcoholic and aqueous extracts of jabuticaba, guava and three dilutions of Peroxitane on the viability of conidia. The CFUs and vegetative growth of the fungus were affected only by the Peroxitane (all dilutions. For conidial production, the aqueous extract of guava had a positive effect, increasing production, while the Peroxitane at the R and RC concentrations resulted in a negative influence. The mortality of A. diaperinus, caused by the fungus after exposure to these products, was 60% for the peracetic acid at 0.5 RC, and above 80% for the extracts. Thus, the results showed that all the extracts and Peroxitane at RC 0.5 are compatible with the fungus B. bassiana Unioeste 4, however only the extracts had a low impact on inoculum potential.

  12. Biological parameters and feeding behaviour of invasive whelk Rapana venosa Valenciennes, 1846 in the south-eastern Black Sea of Turkey

    Institute of Scientific and Technical Information of China (English)

    Hacer Saglam; Ertug Düzgünes

    2014-01-01

    Objective:To determine length-weight relationships, growth type and feeding behavior of the benthic predator Rapa whelk at the coast of Camburnu, south-eastern Black Sea. Methods:Rapa whelk was monthly collected by dredge sampling on the south-eastern Black Sea at 20 m depth. The relationships between morphometric parameters of Rapa whelk were described by linear and exponential models. The allometric growth of each variable relative to shell length (SL) was calculated from the function Y=aSLb or logY=loga+blogSL. The functional regression b values were tested by t-test at the 0.05 significance level if it was significantly different from isometric growth. The total time spent on feeding either on mussel tissue or live mussels was recorded for each individual under controlled conditions in laboratory. Results:The length-weight relationships showed positive allometric growth and no inter-sex variability. Body size in the male population was significantly higher than in the individuals of the female. All characters in males and females showed a trend towards allometry rather than isometry. While the total time spent feeding increased with increasing prey size the total time that Rapana venosa spent feeding decreased with increasing Rapa whelk size. The total average feeding time needed by Rapa whelks was 160 min. But they took 310 min on live mussels in 27-28 °C in the laboratory conditions. Conclusions: Length and weight relationships, growth type, total time spent feeding of this species were explained in details for this region. It would be useful to sustainable management in the south-eastern Black Sea of Turkey. The results about the feeding behaviour of this species will contribute to the understanding of the role of this species within the ecosystem.

  13. Effect of plant extracts and a disinfectant on biological parameters and pathogenicity of the fungus Beauveria bassiana (Bals.) Vuill. (Ascomycota: Cordycipitaceae).

    Science.gov (United States)

    Martins, C C; Alves, L F A; Mamprim, A P

    2016-06-01

    The fungus Beauveria bassiana is naturally found in poultry houses and causes high rates of mortality in Alphitobius diaperinus. Laboratory and field experiments have shown the potential of this fungus as an insect control agent. However, in poultry houses, bacteria as Salmonella, can be found and have been studied alternative control methods for this pathogen. Thus, this study aimed to evaluate the effect of plant extracts and a disinfectant on the fungus Beauveria bassiana (strain Unioeste 4). Conidial viability, colony-forming unit (CFU) counts, vegetative growth, conidia production, insecticidal activity of the fungus and compatibility were used as parameters in the evaluation of the effect of these products on the fungus. Alcoholic and aqueous extracts of jabuticaba (Myrciaria cauliflora (Mart.), guava (Psidium guajava (L.)), and jambolan (Syzygium cumini (L.), at concentrations of 10% as well as the commercial disinfectant, Peroxitane® 1512 AL, were evaluated at the recommended concentrations (RC), 1:200 (RC), 0.5 RC and 2 RC. There was a negative influence of alcoholic and aqueous extracts of jabuticaba, guava and three dilutions of Peroxitane on the viability of conidia. The CFUs and vegetative growth of the fungus were affected only by the Peroxitane (all dilutions). For conidial production, the aqueous extract of guava had a positive effect, increasing production, while the Peroxitane at the R and RC concentrations resulted in a negative influence. The mortality of A. diaperinus, caused by the fungus after exposure to these products, was 60% for the peracetic acid at 0.5 RC, and above 80% for the extracts. Thus, the results showed that all the extracts and Peroxitane at RC 0.5 are compatible with the fungus B. bassiana Unioeste 4, however only the extracts had a low impact on inoculum potential.

  14. Biological upgrading of coal liquids. Final report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-02-01

    A large number of bacterial enrichments have been developed for their ability to utilize nitrogen and sulfur in coal liquids and the model compound naphtha. These bacteria include the original aerobic bacteria isolated from natural sources which utilize heteroatom compounds in the presence of rich media, aerobic nitrogen-utilizing bacteria and denitrifying bacteria. The most promising isolates include Mix M, a mixture of aerobic bacteria; ER15, a pyridine-utilizing isolate; ERI6, an aniline-utilizing isolate and a sewage sludge isolate. Culture optimization experiments have led to these bacteria being able to remove up to 40 percent of the sulfur and nitrogen in naphtha and coal liquids in batch culture. Continuous culture experiments showed that the coal liquid is too toxic to the bacteria to be fed without dilution or extraction. Thus either semi-batch operation must be employed with continuous gas sparging into a batch of liquid, or acid extracted coal liquid must be employed in continuous reactor studies with continuous liquid flow. Isolate EN-1, a chemical waste isolate, removed 27 percent of the sulfur and 19 percent of the nitrogen in fed batch experiments. Isolate ERI5 removed 28 percent of the nitrogen in coal liquid in 10 days in fed batch culture. The sewage sludge isolate removed 22.5 percent of the sulfur and 6.5 percent of the nitrogen from extracted coal liquid in continuous culture, and Mix M removed 17.5 percent of the nitrogen from medium containing extracted coal liquid. An economic evaluation has been prepared for the removal of nitrogen heteroatom compounds from Wilsonville coal liquid using acid extraction followed by fermentation. Similar technology can be developed for sulfur removal. The evaluation indicates that the nitrogen heteroatom compounds can be removed for $0.09/lb of coal liquid treated.

  15. Fishery Biology Database (AGDBS)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Basic biological data are the foundation on which all assessments of fisheries resources are built. These include parameters such as the size and age composition of...

  16. Product development of probiotics as biological drugs.

    Science.gov (United States)

    Sutton, Ann

    2008-02-01

    Elements of product and manufacturing-process design are described for product development of live biotherapeutic biological drugs. Product design uses the history and the phenotypic and genotypic characterization of the selected strain. The quality and integrity of the selected strain can be ensured by preservation in a qualified cell-bank system. Manufacturing-process design includes step-by-step description, including the necessary process-input parameters and the expected output results. The active ingredients in the biological drug are usually manufactured using aseptic processing. The manufacture of the final dosage form of live biotherapeutics requires bioburden control or aseptic manufacture, as appropriate. Specifications for live biotherapeutics must comply with regulations for licensed biological products. Evidence of stability for the duration of the shelf life, as well as stability under the recommended conditions of use, must be provided for licensure.

  17. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    DeTar, Carleton [P.I.

    2012-12-10

    This document constitutes the Final Report for award DE-FC02-06ER41446 as required by the Office of Science. It summarizes accomplishments and provides copies of scientific publications with significant contribution from this award.

  18. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Gurney, Kevin R

    2015-01-12

    This document constitutes the final report under DOE grant DE-FG-08ER64649. The organization of this document is as follows: first, I will review the original scope of the proposed research. Second, I will present the current draft of a paper nearing submission to Nature Climate Change on the initial results of this funded effort. Finally, I will present the last phase of the research under this grant which has supported a Ph.D. student. To that end, I will present the graduate student’s proposed research, a portion of which is completed and reflected in the paper nearing submission. This final work phase will be completed in the next 12 months. This final workphase will likely result in 1-2 additional publications and we consider the results (as exemplified by the current paper) high quality. The continuing results will acknowledge the funding provided by DOE grant DE-FG-08ER64649.

  19. All biology is computational biology

    Science.gov (United States)

    2017-01-01

    Here, I argue that computational thinking and techniques are so central to the quest of understanding life that today all biology is computational biology. Computational biology brings order into our understanding of life, it makes biological concepts rigorous and testable, and it provides a reference map that holds together individual insights. The next modern synthesis in biology will be driven by mathematical, statistical, and computational methods being absorbed into mainstream biological training, turning biology into a quantitative science. PMID:28278152

  20. Parameter Estimation

    DEFF Research Database (Denmark)

    Sales-Cruz, Mauricio; Heitzig, Martina; Cameron, Ian;

    2011-01-01

    of optimisation techniques coupled with dynamic solution of the underlying model. Linear and nonlinear approaches to parameter estimation are investigated. There is also the application of maximum likelihood principles in the estimation of parameters, as well as the use of orthogonal collocation to generate a set...

  1. Articulatory Parameters.

    Science.gov (United States)

    Ladefoged, Peter

    1980-01-01

    Summarizes the 16 parameters hypothesized to be necessary and sufficient for linguistic phonetic specifications. Suggests seven parameters affecting tongue shapes, three determining the positions of the lips, one controlling the position of the velum, four varying laryngeal actions, and one controlling respiratory activity. (RL)

  2. Accurate Predictions of the NMR Parameters in Organic and Biological Crystallines%有机和生物晶体固态核磁共振参数的准确预测

    Institute of Scientific and Technical Information of China (English)

    何睿; 焦艳华; 梁媛嫒; 陈灿玉

    2011-01-01

    理论计算有助于复杂的有机和生物系统光谱的鉴定.对于核磁共振光谱,固体结晶中的化学位移和四极耦合常数(QCC)受到邻近的分子和晶格的氢键和范德华作用较大的影响,从而显示出与气态单体分子不同的NMR参数.因此,在固体晶体NMR参数的理论计算中有必要将氢键和范德华作用这两个因素考虑进来.基于周期性方法,本文采用L-Ala-Gly二肽和硝基苯晶体作为模型体系来考察该方法计算NMR参数的精度.研究结果显示周期结构模型能够将分子间的氢键和范德华作用考虑进来,得到的化学位移和QCC值明显优于传统的单分子模型和超分子模型得到的结果,采用该方法计算的结果能够重现NMR实验结果.%Theoretical predictions are helpful for the spectroscopic identification of complicated organic and biological systems.For nuclear magnetic resonance (NMR) parameters,however,the chemical shift and quadrupole coupling constant (QCC) of the solid crystals are considerably affected by hydrogen bonding and van der Waals interactions from neighboring molecules and the crystal lattice leading to significant spectroscopic differences compared to isolated monomer molecules.Therefore,it is necessary to take these two factors into account for the precise predictions of chemical shifts and QCCs of solid crystals.L-alanylglycine dipeptide and nitrobenzene were selected as model crystals to demonstrate these effects.Here,the chemical shielding (CS) and QCC data were calculated based on the periodic structure model.The incorporation of intermolecular hydrogen bonding and crystal lattice effects by periodic models was found to be crucial in obtaining reliable predictions of CS and QCC values and rendering more explicit spectroscopic assignments for solid organic and biological systems.

  3. MINOR PARAMETERS NEEDED FOR INDIVIDUAL-DOSE CALCULATIONS: Final Report for Tasks 7.1, 7.2, 8.1, 8.2, 9.1, 9.2, and 9.3

    Energy Technology Data Exchange (ETDEWEB)

    Anspaugh, L. R.; Napier, Bruce A.

    2009-10-23

    This brief report documents the selection of parameters needed to support individual-dose calculations from 131I released into the environment with gaseous effluents from the Mayak Production Association.

  4. Mechanical Instabilities of Biological Tubes

    CERN Document Server

    Hannezo, Edouard; Prost, Jacques; 10.1103/PhysRevLett.109.018101

    2012-01-01

    We study theoretically the shapes of biological tubes affected by various pathologies. When epithelial cells grow at an uncontrolled rate, the negative tension produced by their division provokes a buckling instability. Several shapes are investigated : varicose, enlarged, sinusoidal or sausage-like, all of which are found in pathologies of tracheal, renal tubes or arteries. The final shape depends crucially on the mechanical parameters of the tissues : Young modulus, wall-to-lumen ratio, homeostatic pressure. We argue that since tissues must be in quasistatic mechanical equilibrium, abnormal shapes convey information as to what causes the pathology. We calculate a phase diagram of tubular instabilities which could be a helpful guide for investigating the underlying genetic regulation.

  5. Standard biological parts knowledgebase.

    Science.gov (United States)

    Galdzicki, Michal; Rodriguez, Cesar; Chandran, Deepak; Sauro, Herbert M; Gennari, John H

    2011-02-24

    We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

  6. Standard biological parts knowledgebase.

    Directory of Open Access Journals (Sweden)

    Michal Galdzicki

    Full Text Available We have created the Knowledgebase of Standard Biological Parts (SBPkb as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org. The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org. SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL, a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

  7. Final Report

    DEFF Research Database (Denmark)

    Heiselberg, Per; Brohus, Henrik; Nielsen, Peter V.

    This final report for the Hybrid Ventilation Centre at Aalborg University describes the activities and research achievement in the project period from August 2001 to August 2006. The report summarises the work performed and the results achieved with reference to articles and reports published...

  8. Estimating cellular parameters through optimization procedures: elementary principles and applications

    Directory of Open Access Journals (Sweden)

    Akatsuki eKimura

    2015-03-01

    Full Text Available Construction of quantitative models is a primary goal of quantitative biology, which aims to understand cellular and organismal phenomena in a quantitative manner. In this article, we introduce optimization procedures to search for parameters in a quantitative model that can reproduce experimental data. The aim of optimization is to minimize the sum of squared errors (SSE in a prediction or to maximize likelihood. A (local maximum of likelihood or (local minimum of the SSE can efficiently be identified using gradient approaches. Addition of a stochastic process enables us to identify the global maximum/minimum without becoming trapped in local maxima/minima. Sampling approaches take advantage of increasing computational power to test numerous sets of parameters in order to determine the optimum set. By combining Bayesian inference with gradient or sampling approaches, we can estimate both the optimum parameters and the form of the likelihood function related to the parameters. Finally, we introduce four examples of research that utilize parameter optimization to obtain biological insights from quantified data: transcriptional regulation, bacterial chemotaxis, morphogenesis, and cell cycle regulation. With practical knowledge of parameter optimization, cell and developmental biologists can develop realistic models that reproduce their observations and thus, obtain mechanistic insights into phenomena of interest.

  9. Quantitative calcaneal ultrasound parameters and bone mineral density at final height in girls treated with depot gonadotrophin-releasing hormone agonist for central precocious puberty or idiopathic short stature.

    NARCIS (Netherlands)

    Kordelaar, S. van; Noordam, C.; Otten, B.J.; Bergh, J.P.W. van den

    2003-01-01

    To evaluate the effect of gonadotrophin-releasing hormone (GnRH) agonist treatment on bone quality at final height, we studied girls with central precocious puberty (CPP) and with idiopathic short stature (ISS). A total of 25 Caucasian girls were included: group A (n=14) with idiopathic CPP (mean ag

  10. Delineating parameter unidentifiabilities in complex models

    Science.gov (United States)

    Raman, Dhruva V.; Anderson, James; Papachristodoulou, Antonis

    2017-03-01

    Scientists use mathematical modeling as a tool for understanding and predicting the properties of complex physical systems. In highly parametrized models there often exist relationships between parameters over which model predictions are identical, or nearly identical. These are known as structural or practical unidentifiabilities, respectively. They are hard to diagnose and make reliable parameter estimation from data impossible. They furthermore imply the existence of an underlying model simplification. We describe a scalable method for detecting unidentifiabilities, as well as the functional relations defining them, for generic models. This allows for model simplification, and appreciation of which parameters (or functions thereof) cannot be estimated from data. Our algorithm can identify features such as redundant mechanisms and fast time-scale subsystems, as well as the regimes in parameter space over which such approximations are valid. We base our algorithm on a quantification of regional parametric sensitivity that we call `multiscale sloppiness'. Traditionally, the link between parametric sensitivity and the conditioning of the parameter estimation problem is made locally, through the Fisher information matrix. This is valid in the regime of infinitesimal measurement uncertainty. We demonstrate the duality between multiscale sloppiness and the geometry of confidence regions surrounding parameter estimates made where measurement uncertainty is non-negligible. Further theoretical relationships are provided linking multiscale sloppiness to the likelihood-ratio test. From this, we show that a local sensitivity analysis (as typically done) is insufficient for determining the reliability of parameter estimation, even with simple (non)linear systems. Our algorithm can provide a tractable alternative. We finally apply our methods to a large-scale, benchmark systems biology model of necrosis factor (NF)-κ B , uncovering unidentifiabilities.

  11. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Stinis, Panos [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-08-07

    This is the final report for the work conducted at the University of Minnesota (during the period 12/01/12-09/18/14) by PI Panos Stinis as part of the "Collaboratory on Mathematics for Mesoscopic Modeling of Materials" (CM4). CM4 is a multi-institution DOE-funded project whose aim is to conduct basic and applied research in the emerging field of mesoscopic modeling of materials.

  12. Frontiers in mathematical biology

    CERN Document Server

    1994-01-01

    Volume 100, which is the final volume of the LNBM series serves to commemorate the acievements in two decades of this influential collection of books in mathematical biology. The contributions, by the leading mathematical biologists, survey the state of the art in the subject, and offer speculative, philosophical and critical analyses of the key issues confronting the field. The papers address fundamental issues in cell and molecular biology, organismal biology, evolutionary biology, population ecology, community and ecosystem ecology, and applied biology, plus the explicit and implicit mathematical challenges. Cross-cuttting issues involve the problem of variation among units in nonlinear systems, and the related problems of the interactions among phenomena across scales of space, time and organizational complexity.

  13. Optics of Biological Particles

    CERN Document Server

    Hoekstra, Alfons; Videen, Gorden

    2007-01-01

    This book covers the optics of single biological particles, both theory and experiment, with emphasis on Elastic Light Scattering and Fluorescence. It deals with the optics of bacteria (bio-aerosols), marine particles (selected phytoplankton communities) and red and white blood cells. Moreover, there are dedicated chapters on a general theory for scattering by a cell, and modelling and simulation of scattering by inhomogeneous biological cells. Finally, one chapter is dedicated to astro-biological signatures, discussing the possibilities for detecting non-terrestrial biological material. The volume has up-to-date discussions on new experimental and numerical techniques, and many examples of applications of these techniques in real-life systems, as used to detect and characterize e.g. biological warfare agents or human blood cells.

  14. Geolocation Technologies Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Magnoli, D E

    2003-06-02

    This paper is the final report for LL998 In Situ Sensing Subtask 7 (Geo-location) undertaken for NNSA NA-22 enabling technologies R&D for Counterproliferation Detection. A few state-of-the-art resolution parameters are presented for accelerometers, indoor and outdoor GPS (Global Positioning Satellite) systems, and INSs (Inertial Navigation Systems). New technologies are described, including one which has demonstrated the ability to track within a building to a resolution of under a foot.

  15. Parâmetros biológicos de Bemisia Tabaci (genn. biótipo B (hemiptera: aleyrodidae em genótipos de algodoeiro Biological parameters of Bemisia Tabaci B biotype on cotton genotypes

    Directory of Open Access Journals (Sweden)

    Zeneide Ribeiro Campos

    2009-01-01

    Full Text Available A mosca-branca Bemisia tabaci biótipo B é uma praga de grande importância econômica para muitas culturas em todo o mundo. No Brasil, especialmente no Estado da Bahia, essa praga causou perdas que variam entre 30% e 70% em cultura de algodão. Essa pesquisa foi desenvolvida com o objetivo de avaliar parâmetros biológicos de B. tabaci biótipo B em genótipos de algodoeiro para verificar a possível ocorrência de antibiose como mecanismo de resistência sob condições de casa de vegetação. Os genótipos estudados foram IAC-23, Coodetec 406, BRS Aroeira, Fabrika, Coodetec 407, IAC-24, Makina, IAC 20-233, Coodetec 401 e CNPA Acala I. Foram avaliados os períodos de incubação e ninfal, o desenvolvimento total e a longevidade. Dos genótipos avaliados observou-se em Coodetec 406 maior período ninfal (14,7 dias e IAC-23 a menor viabilidade de ninfas (30,7%, indicando a ocorrência de resistência do tipo antibiose contra essa mosca-branca.The silverleaf whitefly Bemisia tabaci B biotype is an important pest of many crops throughout the world. In Brazil, specifically in the Bahia State, this insect caused losses estimated to 30-70% on cotton crops. The purpose of this research was to investigate biological parameters of the silverleaf whitefly biotype B in genotype of cotton bush to verify a possible occurrence of antibiosis as resistance mechanism cotton, under greenhouse conditions. The duration of the egg and nymphal stages, and the adult longevity of B. tabaci biotype B were evaluated in the genotypes IAC-23, Coodetec 406, BRS Aroeira, Fabrika, Coodetec 407, IAC-24, Makina, IAC 20-233, Coodetec 401 and CNPA Acala I. Among those evaluated genotypes, Coodetec 406 increased the nymph stage (14.7 days and IAC-23 reduced the nymphal viability (30.7%, suggesting the occurrence of antibiosis against this whitefly.

  16. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Jarillo-Herrero, Pablo [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

    2017-02-07

    This is the final report of our research program on electronic transport experiments on Topological Insulator (TI) devices, funded by the DOE Office of Basic Energy Sciences. TIbased electronic devices are attractive as platforms for spintronic applications, and for detection of emergent properties such as Majorana excitations , electron-hole condensates , and the topological magneto-electric effect . Most theoretical proposals envision geometries consisting of a planar TI device integrated with materials of distinctly different physical phases (such as ferromagnets and superconductors). Experimental realization of physics tied to the surface states is a challenge due to the ubiquitous presence of bulk carriers in most TI compounds as well as degradation during device fabrication.

  17. Systems biology, emergence and antireductionism.

    Science.gov (United States)

    Kesić, Srdjan

    2016-09-01

    This study explores the conceptual history of systems biology and its impact on philosophical and scientific conceptions of reductionism, antireductionism and emergence. Development of systems biology at the beginning of 21st century transformed biological science. Systems biology is a new holistic approach or strategy how to research biological organisms, developed through three phases. The first phase was completed when molecular biology transformed into systems molecular biology. Prior to the second phase, convergence between applied general systems theory and nonlinear dynamics took place, hence allowing the formation of systems mathematical biology. The second phase happened when systems molecular biology and systems mathematical biology, together, were applied for analysis of biological data. Finally, after successful application in science, medicine and biotechnology, the process of the formation of modern systems biology was completed. Systems and molecular reductionist views on organisms were completely opposed to each other. Implications of systems and molecular biology on reductionist-antireductionist debate were quite different. The analysis of reductionism, antireductionism and emergence issues, in the era of systems biology, revealed the hierarchy between methodological, epistemological and ontological antireductionism. Primarily, methodological antireductionism followed from the systems biology. Only after, epistemological and ontological antireductionism could be supported.

  18. Forward and inverse modeling of near-field seismic waveforms from underground nuclear explosions for effective source functions and structure parameters. Final report, 5 September 1986-5 March 1987

    Energy Technology Data Exchange (ETDEWEB)

    Burdick, L.J.; Barker, J.S.

    1987-04-05

    It is well established that near-field records of nuclear explosions can be analyzed to obtain detailed information about the seismic source function and its dependence on yield. This information is generally formulated in terms of parametrized models for the RDP and for the test-site crustal structure. In this study, results of forward modeling studies are reviewed to obtain the source and structure parameters for Pahute Mesa. These models fit the observed near-field records well, but there is some question as to how errors in crustal structure might affect seismic-source parameters. Furthermore, there is a general need to be able to develop source-structure models in a consistent, unbiased fashion. To address these issues, a simultaneous inversion was developed for source and structure parameters. In previous reports, the authors discussed the development of the method and applied it to Pahute Mesa data. This report presents an application of an improved technique for inverting for parameters in these types of problems known as the jumping method. A second problem with analysis of near-field records from explosions is that there is some question as to whether crustal materials respond in a linear anelastic or anelastic fashion or whether they have significant nonlinear response because of the high-shear strain levels. Near-field data sets from several nuclear explosions and an earthquake are examined to address this question. It is shown that if nonlinear material response occurs it does not have a large enough effect to have a significant effect on data interpretation.

  19. Biological computation

    CERN Document Server

    Lamm, Ehud

    2011-01-01

    Introduction and Biological BackgroundBiological ComputationThe Influence of Biology on Mathematics-Historical ExamplesBiological IntroductionModels and Simulations Cellular Automata Biological BackgroundThe Game of Life General Definition of Cellular Automata One-Dimensional AutomataExamples of Cellular AutomataComparison with a Continuous Mathematical Model Computational UniversalitySelf-Replication Pseudo Code Evolutionary ComputationEvolutionary Biology and Evolutionary ComputationGenetic AlgorithmsExample ApplicationsAnalysis of the Behavior of Genetic AlgorithmsLamarckian Evolution Genet

  20. Antiprotons get biological

    CERN Multimedia

    2003-01-01

    After its final run in September, the first results of the Antiproton Cell Experiment (ACE) look very promising. It was the first experiment to take data on the biological effects of antiproton beams to evaluate the potential of antiprotons in radiation therapy.

  1. Homosexuality, biology, and ideology.

    Science.gov (United States)

    Haumann, G

    1995-01-01

    This paper critically examines the complex relationships and interdependencies between biological theories on homosexuality and sociosexual ideologies. It challenges the privileged status of biology as the ultimate authority on homosexuality. This status is based on the belief that biology is a value-free science. On the contrary, this essay shows how unacknowledged assumptions and culturally bound patterns of thinking about sexuality taint biological research. Sociosexual ideologies are defined as principles that organize the ways we express our sexualities and the way we theorize about them in biology. The following ideologies are identified: (1) sexuality-as-heterosexuality, (2) sexuality-as-reproduction, (3) sexual dualism (male vs. female), and (4) the view the homosexuality is a sexual inversion. The process by which these ideologies are incorporated into biology is two-fold: (1) as a projective act from society onto nature and (2) as a reflective act from nature back into society. It is further argued that biological knowledge of homosexuality resulting from that process can be used for diverse political interests. Finally, it is proposed that since biological theories on homosexuality are inseparable from the context of their paradigmatic origin, it is possible that new theories could be derived from new ideologies.

  2. KLINO - climatology and prognosis of climate-induced changes in hydrographic parameters of the North Sea and Baltic Sea. Final report; KLINO - Klimatologie und Prognose klimainduzierter Aenderungen hydrographischer Groessen in Nord- und Ostsee. Abschlussbericht

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-04-01

    The marine climate of the North Sea and Baltic Sea was simulated and analyzed with the aid of meteorological and oceanographic models. The KLINO project is a first step towards climate impact research as sensitivity studies of the models permit preliminary statements on the effects of potential changes of marine climate. The simulations covered several decades. The models used were: WAM for calculating the swell of the Atlantic and the two marginal seas; HAMSOM for climate-induced variations of the hydrographic parameters of the NOrth Sea and Baltic Sea; HAMSOM and REMO for interactive coupling between ocean and atmosphere; HYDROMOD for extreme and normal conditions in the offshore region. [German] Im Projekt KLINO wurde das derzeitige marine Klima (Wasserstaende und mittlerer Meeresspiegel, Seegang, Stroemungen und Schichtung) von Nord- und Ostsee in Kontrollexperimenten mit Hilfe meteorologischer und ozeanographischer Modelle simuliert und nach vollzogen. Das KLINO Projekt ist in die Arbeiten zur Klima-Regionalisierung bzw. als ein erster Schritt zur Klima-Impaktforschung einzustufen, da Sensitivitaetsstudien der Modelle bereits vorsichtige Aussagen ueber die Folgen moeglicher Aenderungen des marinen Klimas zulassen. Das WAM-Modell lieferte eine Klimatologie des Seeganges fuer den Atlantik und die beiden Randmeere. Die klimainduzierten Schwankungen der hydrographischen Parameter in Nord- und Ostsee wurden mit Hilfe des HAMSOM untersucht; eine interaktive Kopplung zwischen Ozean und Atmosphaere erfolgte mit den Regionalmodellen HAMSOM und REMO. Die Simulationen deckten hinreichend lange Zeitraeume (Dekaden) ab und wurden mit beobachteten bzw. aus meteorologischen Re-Analysen abgeleiteten Fluessen von Impuls, Waerme und Frischwasser angetrieben. Zur Initialisierung und Validierung der ozeanographischen Modelle wurden umfangreiche Beobachtungsdatensaetze fuer die Parameter Temperatur, Salzgehalt, Eis, Seegang und Oberflaechenauslenkung zusammengestellt

  3. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    David A. Benson

    2012-09-24

    This project combines outcrop-scale heterogeneity characterization, laboratory experiments, and numerical simulations. The study is designed to test whether established dispersion theory accurately predicts the behavior of solute transport through heterogeneous media and to investigate the relationship between heterogeneity and the parameters that populate these models. The dispersion theory tested by this work is based upon the fractional advection-dispersion equation (fADE) model. Unlike most dispersion studies that develop a solute transport model by fitting the solute transport breakthrough curve, this project will explore the nature of the heterogeneous media to better understand the connection between the model parameters and the aquifer heterogeneity. Our work at the Colorado School of Mines was focused on the following questions: 1) What are the effects of multi-scale geologic variability on transport of conservative and reactive solutes? 2) Can those transport effects be accounted for by classical methods, and if not, can the nonlocal fractional-order equations provide better predictions? 3) Can the fractional-order equations be parameterized through a link to some simple observable geologic features? 4) Are the classical equations of transport and reaction sufficient? 5) What is the effect of anomalous transport on chemical reaction in groundwater systems? The work is predicated on the observation that upscaled transport is defined by loss of information, or spatio-temporal averaging. This averaging tends to make the transport laws such as Fick's 2nd-order diffusion equation similar to central limit theory. The fractional-order advection-dispersion equations rely on limit theory for heavy-tailed random motion that has some diverging moments. The equations predict larger tails of a plume in space and/or time than those predicted by the classical 2nd-order advection-dispersion equation. The heavy tails are often seen in plumes at field sites.

  4. Estimación de parámetros químicos y biológicos en oxisoles con uso citrícola Estimation of chemical and biological parameters on oxisols with Citrus

    Directory of Open Access Journals (Sweden)

    Humberto C Dalurzo

    2005-12-01

    Full Text Available El objetivo de este estudio fue estimar el efecto del sistema de producción citrícola sobre algunas propiedades químicas y biológicas del suelo, a fin de obtener indicadores de calidad. Se estableció un ensayo con 2 tratamientos: selva subtropical (Sv y uso citrícola (Ci. El diseño fue en bloques completamente aleatorizados. Se tomaron muestras compuestas de 0-10 cm de profundidad. Se determinaron: pH, carbono orgánico (CO, materia orgánica particulada (MOP, fósforo asimilable (P, nitrógeno total (Nt, nitrógeno potencialmente mineralizable (NPM, actividad de la fosfatasa ácida (APA, y respiración del suelo (RES como variables de respuesta. El contenido promedio de CO fue mayor en la Sv (4,03 % respecto al Ci (2,35%. A pesar del aporte de N al Citrus, el Nt y el Npm fueron mayores en la Sv. En la MOP y sus fracciones, se hallaron diferencias significativas presentando la Sv los mayores valores. El Nt explicó el 69% de la variancia de la APA y el CO el 61%: APA = 1.775 N 153,7 (r² = 0,.69. APA = 221 CO - 230 (r² = 0.61. La disminución producida por el uso citrícola revelaría que los atributos: CO, Nt, APA, NPM, MOP y RES, serían indicadores sensibles de la calidad del suelo.Knowledge about the impact of agricultural practices on soil quality is very important to plan the use and sustainable management of productive lands. Citrus cropping has recently acquired a significant economic importance in Misiones, Argentina. It is cultivated in different types of soils sensitive to erosion, like Oxisoles. The aim of this work was to determine the effect of citrus cropping on some chemical and biological soil quality indicators. The field experiment consisted of 2 treatments: subtropical rainforest (Sv and citrus (Ci. In 0-10 cm samples the following parameters were measured: pH, organic carbon (OC, particulate organic matter (POM, total nitrogen (TN, available phosphorus (P, acid phosphatase activity (APA, respiration (RES, and

  5. Lodo de esgoto em atributos biológicos do solo e na nodulação e produção de soja Sewage sludge effects on soil biological parameters and on soybean nodulation and yield

    Directory of Open Access Journals (Sweden)

    Carla Albuquerque de Souza

    2009-10-01

    Full Text Available O objetivo deste trabalho foi avaliar os efeitos da aplicação do lodo produzido pela Companhia de Saneamento Ambiental do Distrito Federal (Caesb na nodulação e rendimento de grãos da soja e em atributos biológicos de um Latossolo Vermelho de Cerrado. O experimento foi conduzido por dois anos consecutivos em um delineamento experimental de blocos ao acaso com três repetições e nove tratamentos - um controle, quatro doses de lodo de esgoto e quatro doses de fertilizante mineral - aplicados apenas no primeiro ano de cultivo. Foram avaliados: a nodulação e a produtividade da soja, o carbono da biomassa microbiana, o carbono prontamente mineralizável e a atividade das enzimas beta-glicosidase, fosfatase ácida e arilsulfatase no solo. Nos dois anos agrícolas, o rendimento de grãos da soja foi inferior ao do tratamento com o fertilizante mineral somente na dose de 1,5 Mg ha-1 de lodo de esgoto. A aplicação do lodo de esgoto no primeiro ano de cultivo não afetou a nodulação da soja, e a aplicação de até 6 Mg ha-1 não apresentou efeito sobre o carbono da biomassa microbiana, o carbono prontamente mineralizável e a atividade das enzimas beta-glicosidase, arilsulfatase e fosfatase ácida do solo no período de dois anos.The objective of this study was to evaluate the effects of applying sewage sludge produced by the Companhia de Saneamento Ambiental do Distrito Federal (Caesb on the nodulation and yield of soybean and on the biological parameters of a Cerrado Oxisol. The experiment was done for two consecutive years in a completely randomized block design with three replicates and nine treatments - one control, four dosages of sewage sludge and four dosages of mineral fertilizer - applied only in the first year of the experiment. Soybean nodulation, grain yield, soil microbial biomass carbon, readily mineralizable carbon and activity of the beta-glucosidase, acid phosphatase and arylsulphatase enzymes were evaluated. In both years

  6. 9 CFR 112.6 - Packaging biological products.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Packaging biological products. 112.6... § 112.6 Packaging biological products. (a) Each multiple-dose final container of a biological product... equipment. (e) Final containers of biological product prepared at a licensed establishment, or imported,...

  7. [Biological weapons].

    Science.gov (United States)

    Kerwat, K; Becker, S; Wulf, H; Densow, D

    2010-08-01

    Biological weapons are weapons of mass destruction that use pathogens (bacteria, viruses) or the toxins produced by them to target living organisms or to contaminate non-living substances. In the past, biological warfare has been repeatedly used. Anthrax, plague and smallpox are regarded as the most dangerous biological weapons by various institutions. Nowadays it seems quite unlikely that biological warfare will be employed in any military campaigns. However, the possibility remains that biological weapons may be used in acts of bioterrorism. In addition all diseases caused by biological weapons may also occur naturally or as a result of a laboratory accident. Risk assessment with regard to biological danger often proves to be difficult. In this context, an early identification of a potentially dangerous situation through experts is essential to limit the degree of damage.

  8. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Webb, Robert C. [Texas A& M University; Kamon, Teruki [Texas A& M University; Toback, David [Texas A& M University; Safonov, Alexei [Texas A& M University; Dutta, Bhaskar [Texas A& M University; Dimitri, Nanopoulos [Texas A& M University; Pope, Christopher [Texas A& M University; White, James [Texas A& M University

    2013-11-18

    Overview The High Energy Physics Group at Texas A&M University is submitting this final report for our grant number DE-FG02-95ER40917. This grant has supported our wide range of research activities for over a decade. The reports contained here summarize the latest work done by our research team. Task A (Collider Physics Program): CMS & CDF Profs. T. Kamon, A. Safonov, and D. Toback co-lead the Texas A&M (TAMU) collider program focusing on CDF and CMS experiments. Task D: Particle Physics Theory Our particle physics theory task is the combined effort of Profs. B. Dutta, D. Nanopoulos, and C. Pope. Task E (Underground Physics): LUX & NEXT Profs. R. Webb and J. White(deceased) lead the Xenon-based underground research program consisting of two main thrusts: the first, participation in the LUX two-phase xenon dark matter search experiment and the second, detector R&D primarily aimed at developing future detectors for underground physics (e.g. NEXT and LZ).

  9. 鄱阳湖翘嘴鳜(Siniperca chuatsi)的生物学参数及资源量的估算%The Assessment of Biological Parameters and Stock Biomass of Siniperca chuatsi in the Poyang Lake

    Institute of Scientific and Technical Information of China (English)

    吴斌; 王庆萍; 方春林; 张燕萍; 傅培峰; 陈文静; 熊小英; 周辉明; 贺刚; 王生

    2015-01-01

    研究基于鄱阳湖渔业资源调查数据,运用软件 FiSAT II 对翘嘴鳜的生物学参数及其资源量进行了初步估算。结果显示,鄱阳湖翘嘴鳜体长范围为77-526 mm;体长和体重的关系式为 W =1.888´10-5L3.042(R2=0.951, n=577),von Bertalanffy 生长方程的各参数为:渐进体长 L∞=551.25 mm,生长系数 K =0.210,理论生长起点年龄 t0=-0.601。总死亡系数 Z=1.06/a,自然死亡系数 M=0.44/a,捕捞死亡系数 F=0.62/a,最适开捕体长为150 mm。鄱阳湖翘嘴鳜开发率 E =0.58,处于资源过度利用状态。鄱阳湖翘嘴鳜的初始资源量估算高达1.92´104 t,最大可持续产量 MSY 为4384.93 t。鄱阳湖翘嘴鳜群体中补充群体和低龄剩余群体的比例明显增加,低龄化和小型化趋势凸显,资源衰退问题突出,但生长潜力依然存在。应采取降低对鄱阳湖翘嘴鳜繁殖群体的捕捞强度、保护产卵场等积极措施来保护这一珍贵的渔业资源。%Mandarin fish (Siniperca chuatsi) is a rare and precious economic species of freshwater fish with a long standing reputation because of its fast growth, meat delicate, delicious and nutrient rich. The mature artificial propagation technology has created good conditions for Siniperca chuatsi large- scale cultivation since 1980 s. However, the wild Siniperca chuatsi population is declining due to over exploitation and environmental pollution in their habitat, which may cause the decline of genetic diversity. Mandarin fish is one of abundant species in Poyang Lake and plays an important role in the lake ecosystem. Based on Poyang Lake fishery resources investigation data, we assessed biological parameters and stock biomass of Siniperca chuatsi using FiSAT II software. The results indicated that the length of Siniperca chuatsi population ranged from 77 to 526 mm, and that the relationship between body length (mm) and body weight (g) can be expressed as W = 1.888´10-5L3.042(R2

  10. Supergranular Parameters

    Science.gov (United States)

    Udayashankar, Paniveni

    2016-07-01

    I study the complexity of supergranular cells using intensity patterns from Kodaikanal solar observatory. The chaotic and turbulent aspect of the solar supergranulation can be studied by examining the interrelationships amongst the parameters characterizing supergranular cells namely size, horizontal flow field, lifetime and physical dimensions of the cells and the fractal dimension deduced from the size data. The findings are supportive of Kolmogorov's theory of turbulence. The Data consists of visually identified supergranular cells, from which a fractal dimension 'D' for supergranulation is obtained according to the relation P α AD/2 where 'A' is the area and 'P' is the perimeter of the supergranular cells. I find a fractal dimension close to about 1.3 which is consistent with that for isobars and suggests a possible turbulent origin. The cell circularity shows a dependence on the perimeter with a peak around (1.1-1.2) x 105 m. The findings are supportive of Kolmogorov's theory of turbulence.

  11. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    David W. Mazyck; Angela Lindner; CY Wu, Rick Sheahan, Ashok Jain

    2007-06-30

    distribution of TiO2 particles on the activated carbon surface. A method for pore volume impregnation using microwave irradiation was also developed. A commercial microwave oven (800 W) was used as the microwave source. Under 2450 MHz microwave irradiation, TTIP was quickly hydrolyzed and anatase TiO2 was formed in a short time (< 20 minutes). Due to the volumetric heating and selective heating of microwave, the solvent and by-products were quickly removed which reduced energy consumption and processing time. Activated carbon and TiO{sub 2}/AC were also tested for the removal of hydrogen sulfide, which was chosen as the representative total reduced sulfur (TRS) species. The BioNuchar AC support itself was a good H{sub 2}S remover. After coating TiO{sub 2} by dry impregnation, H{sub 2}S removal efficiency of TiO{sub 2}/AC decreased compared with the virgin AC due to the change of surface pH. Under UV light irradiation, H{sub 2}S removal efficiency of TiO{sub 2}/AC composite doubled, and its sulfate conversion efficiency was higher than that of AC. The formation of sulfate is preferred since the sulfate can be removed from the composite by rising with water. A pilot-scale fluidized bed reactor was designed to test the efficiency of methanol oxidation with TiO{sub 2}/AC in the presence of UV light. TiO{sub 2}/AC was prepared using the spray desiccation method. The TiO{sub 2}/AC was pre-loaded with (1) methanol (equivalent to about 2%wt) and (2) methanol and water. When the TiO{sub 2}/AC loaded with methanol only was exposed to UV light for one hour in the reactor, most of the methanol remained in the carbon pores and, thus, was not oxidized. The TiO{sub 2}/AC loaded with methanol and water desorbed about 2/3 of the methanol from its pores during fluidization, however, only a small portion of this desorbed methanol was oxidized. A biofilter system employing biological activated carbon was developed for methanol removal. The biofilter contained a mixed packing with Westvaco Bio

  12. Multiscale Biological Materials

    DEFF Research Database (Denmark)

    Frølich, Simon

    example of biological design. We investigated the architecture of A. simplex and found that an advanced hierarchical biomineralized structure acts as the interface between soft musculature and a stiff substrate, thus securing underwater attachment. In bone, the mechanical properties of the material......, and the nanoscale response of bone in compression. Lastly, a framework for the investigation of biological design principles has been developed. The framework combines parametric modeling, multi-material 3D-printing, and direct mechanical testing to efficiently screen large parameter spaces of biological design. We......Materials formed by organisms, also known as biological materials, exhibit outstanding structural properties. The range of materials formed in nature is remarkable and their functions include support, protection, motion, sensing, storage, and maintenance of physiological homeostasis. These complex...

  13. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, Philip L.

    2012-11-11

    Our research program was aimed at elucidating the nature of proton transport in ionomer membranes by means of a combination of analytical theory and molecular modeling. There were two broad thrusts. The first of these was directed towards understanding the equilibrium structure of Nafion and related polymers at various levels of hydration. The second thrust was concerned with the transport of protons through a membrane of this type. The research on structure proceeded by building on existing work, but with the introduction of some novel techniques, among which is a hybrid Molecular Dynamics--Monte Carlo approach. This method permits rapid computations by temporarily decoupling the motion of the polar side chains from that of the perfluorinated backbone, while still retaining the essential aspects of the constraint that phase separation can only continue to a very limited degree. Competition between an elastic energy due to this constraint and the tendency to phase separation lead to the equilibrium structure, which turns out to be qualitatively different at different levels of hydration. The use of a carefully formulated dielectric function was necessary to achieve accurate results. The work on transport of protons in Nafion-like membranes also involved a combination of theory and simulation. Atomistic molecular-dynamics simulations were employed to determine some of the characteristic parameters for the diffusion of hydronium in hydrated membranes. These results were used in a theoretical model of non-linear diffusion to predict transport coefficients. Among our results was the discovery that treatment with strong electric fields may enhance the properties of the polymer membranes. Our computer simulations showed that the vigorous application of a stretching force or an electric field can modify the structure of the ionomer that lies at the heart of a polymer-electrolyte-membrane fuel cell. If these predictions are verified experimentally, then it should be

  14. Biological parameters of the burrowing crayfish, Parastacus pugnax (Poeppig, 1835, in Tiuquilemu, Bío-Bío Region, Chile Parámetros biológicos del camarón excavador, Parastacus pugnax (Poeppig, 1835en Tiuquilemu, Región del Bío-Bío, Chile

    Directory of Open Access Journals (Sweden)

    Mauricio A Ibarra

    2012-07-01

    Full Text Available In order to determine the biological parameters of the burrowing crayfish (Parastacus pugnax, we fenced in 900 m² of a humid, low-lying sector in Tiuquilemu, Bío-Bío Region, Chile. Monthly samples were taken from August 2007 to August 2008, and 3,512 specimens were caught. Records were made of their carapace length (CL, total weight (TW, sex, and number of eggs (for females. The monthly size-structures showed few juveniles between 20 and 30 mm CL in nearly all months. P. pugnax was found to carry eggs from mid-spring through late autumn; size at first maturity for females was 38.1 mm CL; and fecundity varied between three and 45 eggs per female. In terms of the global sexual proportion, males were predominant in 11 of the 12 months, although the ratio was as expected (1:1. We estimated the parameters of the growth curve using modal progression analysis, obtaining CL∞, K, and t0 values of 55.3 mm, 0.23 mm year-1, and -0.58 years, respectively. The length-weight relationship was calculated separately for males and females, and no significant differences were found between sexes. The common parameters defining the potential function of a = 0.00052 and b = 2.98 (P Para determinar parámetros biológicos del camarón excavador (Parastacus pugnax, se cercó un área de 900 m² de un sector de vega en Tiuquilemu, Región del Bío-Bío Chile. En dicho lugar se efectuaron muestreos mensuales entre agosto de 2007 y agosto de 2008. A un total de 3.512 especímenes se les registró la longitud cefalotorácica (CL, peso total (TW, sexo y en hembras se determinó el número total de huevos. Se construyeron las estructuras de longitudes mensuales con escasa representación de juveniles entre 20 y 30 mm de CL, en casi la mayoría de los meses. Se determinó que el período de incubación en P. pugnax se extiende entre mediados de primavera y finales de otoño, la longitud de primera madurez en las hembras se calculó en 38,1 mm de CL y la fecundidad vari

  15. FINAL REPORT

    Energy Technology Data Exchange (ETDEWEB)

    PETER, GARY F. [UNIVERSITY OF FLORIDA

    2014-07-16

    of biomass samples imaged with all three methods, and using common analytical software to quantify parameters from the three dimensional images. In addition to the proposed experiments, we conducted imaging studies with a novel TOF-SIMS instrument available through collaborations with the AMOLF goup led by Ron Heeren at the FOM Institute in Amersterdam, Netherlands. ToF-SIMS was used to image intact cross sections of Populus stems with high spatial resolution, chemically selectivity. ToF-SIMS images were correlated with fluorescence microscopy which allowed for more positive ion identification.

  16. Biological and Physical Inventory of the Streams within the Nez Perce Reservation; Juvenile Steelhead Survey and Factors that Affect Abundance in Selected Streams in the Lower Clearwater River Basin, Idaho, 1983-1984 Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    Kucera, Paul A.; Johnson, David B. (Nez Perce Tribe, Lapwai, ID)

    1986-08-01

    A biological and physical inventory of selected tributaries in the lower Clearwater River basin was conducted to collect information for the development of alternatives and recommendations for the enhancement of the anadromous fish resources in streams on the Nez Perce Reservation. Five streams within the Reservation were selected for study: Bedrock and Cottonwood Creeks were investigated over a two year period (1983 to 1984) and Big Canyon, Jacks and Mission Creeks were studied for one year (1983). Biological information was collected and analyzed on the density, biomass, production and outmigration of juvenile summer steelhead trout. Physical habitat information was collected on available instream cover, stream discharge, stream velocity, water temperature, bottom substrate, embeddedness and stream width and depth. The report focuses on the relationships between physical stream habitat and juvenile steelhead trout abundance.

  17. Optimal Conventional and Semi-Natural Treatments for the Upper Yakima Spring Chinook Salmon Supplementation Project; Treatment Definitions and Descriptions and Biological Specifications for Facility Design, 1995-1999 Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    Hager, Robert C. (Hatchery Operations Consulting); Costello, Ronald J. (Mobrand Biometrics, Inc., Vashon Island, WA)

    1999-10-01

    This report describes the Yakima Fisheries Project facilities (Cle Elum Hatchery and acclimation satellites) which provide the mechanism to conduct state-of-the-art research for addressing questions about spring chinook supplementation strategies. The definition, descriptions, and specifications for the Yakima spring chinook supplementation program permit evaluation of alternative fish culture techniques that should yield improved methods and procedures to produce wild-like fish with higher survival that can be used to rebuild depleted spring chinook stocks of the Columbia River Basin. The definition and description of three experimental treatments, Optimal Conventional (OCT), Semi-Natural (SNT), Limited Semi-Natural (LSNT), and the biological specifications for facilities have been completed for the upper Yakima spring chinook salmon stock of the Yakima Fisheries Project. The task was performed by the Biological Specifications Work Group (BSWG) represented by Yakama Indian Nation, Washington Department of Fish and Wildlife, National Marine Fisheries Service, and Bonneville Power Administration. The control and experimental variables of the experimental treatments (OCT, SNT, and LSNT) are described in sufficient detail to assure that the fish culture facilities will be designed and operated as a production scale laboratory to produce and test supplemented upper Yakima spring chinook salmon. Product specifications of the treatment groups are proposed to serve as the generic templates for developing greater specificity for measurements of product attributes. These product specifications will be used to monitor and evaluate treatment effects, with respect to the biological response variables (post release survival, long-term fitness, reproductive success and ecological interactions).

  18. West Hackberry Strategic Petroleum Reserve site brine disposal monitoring, Year I report. Volume V. Supporting data for estuarine hydrology, discharge plume analysis, chemical oceanography, biological oceanography, and data management. Final report

    Energy Technology Data Exchange (ETDEWEB)

    DeRouen, L.R.; Hann, R.W.; Casserly, D.M.; Giammona, C.; Lascara, V.J. (eds.)

    1983-02-01

    This project centers around the Strategic Petroleum Site (SPR) known as the West Hackberry salt dome which located in southwestern Louisiana, and which is designed to store 241 million barrels of crude oil. Oil storage caverns are formed by injecting water into salt deposits, and pumping out the resulting brine. Studies described in this report were designed as follow-on studies to three months of pre-discharge characterization work, and include data collected during the first year of brine leaching operations. The objectives were to: (1) characterize the environment in terms of physical, chemical and biological attributes; (2) determine if significant adverse changes in ecosystem productivity and stability of the biological community are occurring as a result of brine discharge; and (3) determine the magnitude of any change observed. Volume V contains appendices for the following: supporting data for estuarine hydrology and hydrography; supporting data analysis of discharge plume; supporting data for water and sediment chemistry; CTD/DO and pH profiles during biological monitoring; supporting data for nekton; and supporting data for data management.

  19. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    David W. Mazyck; Angela Lindner; CY Wu, Rick Sheahan, Ashok Jain

    2007-06-30

    distribution of TiO2 particles on the activated carbon surface. A method for pore volume impregnation using microwave irradiation was also developed. A commercial microwave oven (800 W) was used as the microwave source. Under 2450 MHz microwave irradiation, TTIP was quickly hydrolyzed and anatase TiO2 was formed in a short time (< 20 minutes). Due to the volumetric heating and selective heating of microwave, the solvent and by-products were quickly removed which reduced energy consumption and processing time. Activated carbon and TiO{sub 2}/AC were also tested for the removal of hydrogen sulfide, which was chosen as the representative total reduced sulfur (TRS) species. The BioNuchar AC support itself was a good H{sub 2}S remover. After coating TiO{sub 2} by dry impregnation, H{sub 2}S removal efficiency of TiO{sub 2}/AC decreased compared with the virgin AC due to the change of surface pH. Under UV light irradiation, H{sub 2}S removal efficiency of TiO{sub 2}/AC composite doubled, and its sulfate conversion efficiency was higher than that of AC. The formation of sulfate is preferred since the sulfate can be removed from the composite by rising with water. A pilot-scale fluidized bed reactor was designed to test the efficiency of methanol oxidation with TiO{sub 2}/AC in the presence of UV light. TiO{sub 2}/AC was prepared using the spray desiccation method. The TiO{sub 2}/AC was pre-loaded with (1) methanol (equivalent to about 2%wt) and (2) methanol and water. When the TiO{sub 2}/AC loaded with methanol only was exposed to UV light for one hour in the reactor, most of the methanol remained in the carbon pores and, thus, was not oxidized. The TiO{sub 2}/AC loaded with methanol and water desorbed about 2/3 of the methanol from its pores during fluidization, however, only a small portion of this desorbed methanol was oxidized. A biofilter system employing biological activated carbon was developed for methanol removal. The biofilter contained a mixed packing with Westvaco Bio

  20. Is synthetic biology mechanical biology?

    Science.gov (United States)

    Holm, Sune

    2015-12-01

    A widespread and influential characterization of synthetic biology emphasizes that synthetic biology is the application of engineering principles to living systems. Furthermore, there is a strong tendency to express the engineering approach to organisms in terms of what seems to be an ontological claim: organisms are machines. In the paper I investigate the ontological and heuristic significance of the machine analogy in synthetic biology. I argue that the use of the machine analogy and the aim of producing rationally designed organisms does not necessarily imply a commitment to mechanical biology. The ideal of applying engineering principles to biology is best understood as expressing recognition of the machine-unlikeness of natural organisms and the limits of human cognition. The paper suggests an interpretation of the identification of organisms with machines in synthetic biology according to which it expresses a strategy for representing, understanding, and constructing living systems that are more machine-like than natural organisms.

  1. Computational biology

    DEFF Research Database (Denmark)

    Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue

    2011-01-01

    Computation via biological devices has been the subject of close scrutiny since von Neumann’s early work some 60 years ago. In spite of the many relevant works in this field, the notion of programming biological devices seems to be, at best, ill-defined. While many devices are claimed or proved t...

  2. [Biologics in SLE].

    Science.gov (United States)

    Karonitsch, Thomas; Aringer, Martin

    2015-01-01

    Biologics have become indispensable in the last decade in the treatment of the more common rheumatic diseases. For treating systemic lupus erythematodes (SLE), B-cell depletion, albeit off-label, has been a well-accepted strategy in severe and refractory disease. Unexpectedly, however, the results of the first randomized controlled rituximab trials in SLE were negative. New trials with improved study protocols are ongoing, which should resolve this issue. In 2012, with the approval of belimumab, SLE finally entered the era of approved biological therapies. The anti-Blys/BAFF antibody belimumab showed prevention of SLE flares, glucocorticoid sparing, and significant improvement in the quality of life of SLE patients, in part by drastically reducing immune complex mediated fatigue. Positive reports on further targeting approaches give hope that additional biological agents will be available for SLE therapy soon.

  3. Biological Soft Robotics.

    Science.gov (United States)

    Feinberg, Adam W

    2015-01-01

    In nature, nanometer-scale molecular motors are used to generate force within cells for diverse processes from transcription and transport to muscle contraction. This adaptability and scalability across wide temporal, spatial, and force regimes have spurred the development of biological soft robotic systems that seek to mimic and extend these capabilities. This review describes how molecular motors are hierarchically organized into larger-scale structures in order to provide a basic understanding of how these systems work in nature and the complexity and functionality we hope to replicate in biological soft robotics. These span the subcellular scale to macroscale, and this article focuses on the integration of biological components with synthetic materials, coupled with bioinspired robotic design. Key examples include nanoscale molecular motor-powered actuators, microscale bacteria-controlled devices, and macroscale muscle-powered robots that grasp, walk, and swim. Finally, the current challenges and future opportunities in the field are addressed.

  4. Biological Oceanography

    Science.gov (United States)

    Dyhrman, Sonya

    2004-10-01

    The ocean is arguably the largest habitat on the planet, and it houses an astounding array of life, from microbes to whales. As a testament to this diversity and its importance, the discipline of biological oceanography spans studies of all levels of biological organization, from that of single genes, to organisms, to their population dynamics. Biological oceanography also includes studies on how organisms interact with, and contribute to, essential global processes. Students of biological oceanography are often as comfortable looking at satellite images as they are electron micrographs. This diversity of perspective begins the textbook Biological Oceanography, with cover graphics including a Coastal Zone Color Scanner image representing chlorophyll concentration, an electron micrograph of a dinoflagellate, and a photograph of a copepod. These images instantly capture the reader's attention and illustrate some of the different scales on which budding oceanographers are required to think. Having taught a core graduate course in biological oceanography for many years, Charlie Miller has used his lecture notes as the genesis for this book. The text covers the subject of biological oceanography in a manner that is targeted to introductory graduate students, but it would also be appropriate for advanced undergraduates.

  5. Quantum Biology

    Directory of Open Access Journals (Sweden)

    Alessandro Sergi

    2009-06-01

    Full Text Available A critical assessment of the recent developmentsof molecular biology is presented.The thesis that they do not lead to a conceptualunderstanding of life and biological systems is defended.Maturana and Varela's concept of autopoiesis is briefly sketchedand its logical circularity avoided by postulatingthe existence of underlying living processes,entailing amplification from the microscopic to the macroscopic scale,with increasing complexity in the passage from one scale to the other.Following such a line of thought, the currently accepted model of condensed matter, which is based on electrostatics and short-ranged forces,is criticized. It is suggested that the correct interpretationof quantum dispersion forces (van der Waals, hydrogen bonding, and so onas quantum coherence effects hints at the necessity of includinglong-ranged forces (or mechanisms for them incondensed matter theories of biological processes.Some quantum effects in biology are reviewedand quantum mechanics is acknowledged as conceptually important to biology since withoutit most (if not all of the biological structuresand signalling processes would not even exist. Moreover, it is suggested that long-rangequantum coherent dynamics, including electron polarization,may be invoked to explain signal amplificationprocess in biological systems in general.

  6. Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models

    OpenAIRE

    Baker Syed; Poskar C; Junker Björn

    2011-01-01

    Abstract In systems biology, experimentally measured parameters are not always available, necessitating the use of computationally based parameter estimation. In order to rely on estimated parameters, it is critical to first determine which parameters can be estimated for a given model and measurement set. This is done with parameter identifiability analysis. A kinetic model of the sucrose accumulation in the sugar cane culm tissue developed by Rohwer et al. was taken as a test case model. Wh...

  7. Established and emerging biological activity markers of inflammatory bowel disease

    DEFF Research Database (Denmark)

    Nielsen, O H; Vainer, B; Madsen, S M;

    2000-01-01

    Assessment of disease activity in inflammatory bowel disease (IBD), i.e., ulcerative colitis (UC) and Crohn's disease (CD), is done using clinical parameters and various biological disease markers. Ideally, a disease marker must: be able to identify individuals at risk of a given disorder......, be disease specific, mirror the disease activity and, finally, be easily applicable for routine clinical purposes. However, no such disease markers have yet been identified for IBD. In this article, classical disease markers including erythrocyte sedimentation rate, acute phase proteins (especially...

  8. Parameters affecting HS emissions removal and re-circulating water quality in a pilot-scale sequential biological treatment system at a wastewater lift station in Brownsville, Texas, USA.

    Science.gov (United States)

    Karre, Anand K; Bairu, Pavan; Jones, Kim D; Paca, Jan

    2012-01-01

    In this study, a pilot-scale sequential biological treatment system combining a biotrickling filter and biofilter was used to optimize the removal of variable emission H(2)S loadings ranging from 30 to 120 g m(-3) h(-1)at a wastewater lift station in Brownsville, Texas USA. The biotrickling filter recycle water pH remained between 2.0 to 3.0 during the four months of unit operation and the overall removal efficiency for H(2)S was >99%. The biotrickling filter removal efficiency was 70 ± 8%, with an elimination capacity of 10 to 80 g m(-3) h(-1) while the biofilter elimination capacity ranged from 10 to 40 g m(-3) h(-1). The sequential treatment system was operated initially at an Empty Bed Residence Time (EBRT) of 120 s (50 s for the biotrickling filter and 70 s for biofilter) for two months and then at an EBRT of 60 s (25 s for biotrickling filter and 35s for biofilter) for the remainder of the operating period; remarkably, there was only a slight decrease in removal efficiency at 60 s EBRT. In order to qualitatively evaluate the changes in recycle water quality in the system on the performance of the unit in precipitating sulfur species, the equilibrium chemical model, Visual MINTEQ was employed. The model predicted speciation results based on the feed water quality and sulfur loadings, and also forecast some iron-sulfur complexes which have potential to form some complex precipitates. This research demonstrated that low pH re-circulating water quality in the biological treatment of H(2)S was possible without compromising the high removal efficiency, and that an improved understanding of the recycle water chemistry of the trickling unit of a sequential treatment system could be useful in the overall optimization of the process.

  9. Biological couplings: Function, characteristics and implementation mode

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Through rigorous natural selection, biological organisms have evolved exceptional functions highly adaptable to their living environments. Biological organisms can achieve a variety of biological functions efficiently by using the synergic actions of two or more different parts of the body, or the coupling effects of multiple factors, and demonstrate optimal adaptations to the living environment. In this paper, the function, characteristics and types of biological couplings are analyzed, the implementation mechanism and mode of biological coupling functions are revealed from the bionic viewpoint. Finally, the technological prospects of the bionic implementation of biological coupling function are predicted.

  10. Study on changes of characteristic parameters of biological tissues impedance spectroscopy in vitro within 5 to 360 min after excision at the frequency range from 1Hz to 1MHz.

    Science.gov (United States)

    Xin, Lin; Xiuzhen, Dong; Feng, Fu

    2005-01-01

    We constructed an impedance spectroscopy measurement system based on frequency response analyzer. Using four-terminal method, we measured impedance spectroscopy of rabbit different tissues in vitro within 5 to 360 minutes after excision at the frequency range from 1Hz to 1MHz. According to the measurement results, we analyzed the changes of characteristic parameters (Ro, Rinfin, fc and alpha) of different tissues in the time course. The results show that the Cole-Cole model characteristic parameters change notably in the time course. The value of Ro change great especially. For kidney, liver, spleen and heart, the value of Ro reached 700%, 125%, 170% and 200% respectively at the 6 hour after excision. The change of alpha is less than 30% for all tissues. The changes of fc are various remarkably for different tissues, for liver, kidney and heart, the value of fc decreased continually and the decrement reached 60%, 19%, 33% respectively at the end of the measurement. For muscle (longitudinal, transverse) and heart, the value of fc decreased firstly and then began to increase and reached 145% > 155% > 125% at 6 hour after excision. The results of our reaching show the measurement time plays a remarkable effect on the impedance spectroscopy measurement of tissue in vitro. We hypothesized that the dispersion observed in the impedance spectroscopy measurement in vitro between different researchers was partly due to the effect of measurement time.

  11. Loop Quantum Theory Applied to Biology and Nonlinear Whole Biology

    CERN Document Server

    Chang, Yi-Fang

    2008-01-01

    The loop quantum theory, which constitutes a very small discontinuous space, as new method is applied to biology. The model of protein folding and lungs is proposed. In the model, some known results are used, and four approximate conclusions are obtained: their structures are quantized, their space regions are finite, various singularities correspond to folding and crossed points, and different types of catastrophe exist. Further, based on the inseparability and correlativity of the biological systems, the nonlinear whole biology is proposed, and four basic hypotheses are formed. It may unify reductionism and holism, structuralism and functionalism. Finally, the medical meaning of the theory is discussed briefly.

  12. Biological preconcentrator

    Science.gov (United States)

    Manginell, Ronald P.; Bunker, Bruce C.; Huber, Dale L.

    2008-09-09

    A biological preconcentrator comprises a stimulus-responsive active film on a stimulus-producing microfabricated platform. The active film can comprise a thermally switchable polymer film that can be used to selectively absorb and desorb proteins from a protein mixture. The biological microfabricated platform can comprise a thin membrane suspended on a substrate with an integral resistive heater and/or thermoelectric cooler for thermal switching of the active polymer film disposed on the membrane. The active polymer film can comprise hydrogel-like polymers, such as poly(ethylene oxide) or poly(n-isopropylacrylamide), that are tethered to the membrane. The biological preconcentrator can be fabricated with semiconductor materials and technologies.

  13. Aristotle's biopolitics: a defense of biological teleology against biological nihilism.

    Science.gov (United States)

    Arnhart, L

    1988-02-01

    Modern Darwinian biology seems to promote nihilism, for it seems to teach that there is no rationally discoverable standard in nature for giving meaning to life. The purpose of this article is to argue for a revival of Aristotle's biological teleology as a reasonable alternative to biological nihilism. The article begins with Edward Wilson's vain struggle against nihilism. Then it is argued that a teleological understanding of nature is assumed in the practice of medicine, as illustrated by one case from Oliver Sacks' neurological practice. The article then considers the importance of biological teleology for Aristotle's moral and political philosophy, and attention is given to some points of agreement and disagreement with contemporary sociobiologists. The main part of the article is then devoted to a defense of Aristotle's biology against the five objections that might be made by a Darwinian biologist. Finally, the article illustrates the practical implications of this issue for bioethics by considering the recent work of Engelhardt.

  14. Biology Notes.

    Science.gov (United States)

    School Science Review, 1981

    1981-01-01

    Outlines a variety of laboratory procedures, techniques, and materials including construction of a survey frame for field biology, a simple tidal system, isolation and applications of plant protoplasts, tropisms, teaching lung structure, and a key to statistical methods for biologists. (DS)

  15. (Biological dosimetry)

    Energy Technology Data Exchange (ETDEWEB)

    Preston, R.J.

    1990-12-17

    The traveler attended the 1st International Conference on Biological Dosimetry in Madrid, Spain. This conference was organized to provide information to a general audience of biologists, physicists, radiotherapists, industrial hygiene personnel and individuals from related fields on the current ability of cytogenetic analysis to provide estimates of radiation dose in cases of occupational or environmental exposure. There is a growing interest in Spain in biological dosimetry because of the increased use of radiation sources for medical and occupational uses, and with this the anticipated and actual increase in numbers of overexposure. The traveler delivered the introductory lecture on Biological Dosimetry: Mechanistic Concepts'' that was intended to provide a framework by which the more applied lectures could be interpreted in a mechanistic way. A second component of the trip was to provide advice with regard to several recent cases of overexposure that had been or were being assessed by the Radiopathology and Radiotherapy Department of the Hospital General Gregorio Maranon'' in Madrid. The traveler had provided information on several of these, and had analyzed cells from some exposed or purportedly exposed individuals. The members of the biological dosimetry group were referred to individuals at REACTS at Oak Ridge Associated Universities for advice on follow-up treatment.

  16. Marine Biology

    Science.gov (United States)

    Dewees, Christopher M.; Hooper, Jon K.

    1976-01-01

    A variety of informational material for a course in marine biology or oceanology at the secondary level is presented. Among the topics discussed are: food webs and pyramids, planktonic blooms, marine life, plankton nets, food chains, phytoplankton, zooplankton, larval plankton and filter feeders. (BT)

  17. Scaffolded biology.

    Science.gov (United States)

    Minelli, Alessandro

    2016-09-01

    Descriptions and interpretations of the natural world are dominated by dichotomies such as organism vs. environment, nature vs. nurture, genetic vs. epigenetic, but in the last couple of decades strong dissatisfaction with those partitions has been repeatedly voiced and a number of alternative perspectives have been suggested, from perspectives such as Dawkins' extended phenotype, Turner's extended organism, Oyama's Developmental Systems Theory and Odling-Smee's niche construction theory. Last in time is the description of biological phenomena in terms of hybrids between an organism (scaffolded system) and a living or non-living scaffold, forming unit systems to study processes such as reproduction and development. As scaffold, eventually, we can define any resource used by the biological system, especially in development and reproduction, without incorporating it as happens in the case of resources fueling metabolism. Addressing biological systems as functionally scaffolded systems may help pointing to functional relationships that can impart temporal marking to the developmental process and thus explain its irreversibility; revisiting the boundary between development and metabolism and also regeneration phenomena, by suggesting a conceptual framework within which to investigate phenomena of regular hypermorphic regeneration such as characteristic of deer antlers; fixing a periodization of development in terms of the times at which a scaffolding relationship begins or is terminated; and promoting plant galls to legitimate study objects of developmental biology.

  18. Biology Notes.

    Science.gov (United States)

    School Science Review, 1984

    1984-01-01

    Presents information on the teaching of nutrition (including new information relating to many current O-level syllabi) and part 16 of a reading list for A- and S-level biology. Also includes a note on using earthworms as a source of material for teaching meiosis. (JN)

  19. Parámetros químicos y biológicos como indicadores de calidad del suelo en diferentes manejos Chemical and biological parameters as indicators of soil quality under different managements

    Directory of Open Access Journals (Sweden)

    Laura Ferreras

    2009-06-01

    Full Text Available El objetivo del trabajo fue evaluar la sensibilidad de una serie de parámetros químicos y bioquímicos en suelos representativos de la Región Pampeana bajo diferentes manejos con la finalidad de: i establecer los parámetros que reflejen de manera más sensible y tempranamente el grado de degradación o recuperación; ii comparar la información generada de las parcelas bajo cultivo con el mismo tipo de suelo no perturbado, considerado como referencia (T. En ensayos con diferentes manejos localizados en las EEA INTA Oliveros, Marcos Juárez y Rafaela se evaluó: Carbono orgánico total (COT, carbono asociado a la fracción fina (COff, carbono asociado a la fracción gruesa (COfg, carbono de la biomasa microbiana (CBM, actividad respiratoria microbiana (ARM y actividad de las enzimas fosfatasa ácida (Pasa, deshidrogenasa (Dasa y ureasa (Uasa. Se calculó el cociente metabólico microbiano (qCO2, a través de la relación entre ARM y el CBM, como así también las relaciones entre actividades de las enzimas y CBM en función del COT. Para cada sitio, el suelo bajo cultivo presentó en la mayoría de las variables analizadas valores inferiores con respecto a T (pThe aim of the work was to assess the sensitivity of chemical and biochemical parameters in representative soils of the Pampa Region under different managements with the purpose of i establishing the soil parameters that may have a role as early and sensitive indicators of soil ecological stress and restoration; and ii comparing the results from cropped plots with the same undisturbed soil type, considered as reference (T. The experiment was carried out on experimental plots under different soil managements at the INTA Experimental Stations at Oliveros, Marcos Juárez and Rafaela. Total organic carbon (COT, organic carbon associated with the fine fraction (COff and organic carbon associated with the coarse fraction (COfg, microbial biomass carbon (CBM, soil microbial respiration (ARM

  20. 妊娠期女性血细胞主要参数生物参考区间建立的初步探讨%Preliminary investigation on the establishment of biological reference intervals about the main parameters of blood cells among pregnant women

    Institute of Scientific and Technical Information of China (English)

    葛雅芳; 沈云岳; 唐振华

    2014-01-01

    目的:建立本实验室妊娠期女性血细胞主要参数的生物参考区间。方法选取331例正常足月分娩的孕妇,追溯其孕期检查记录,用 SAS 8.1软件对孕期间进行的2次血细胞常规检测结果进行统计分析,获得参考区间。结果比较妊娠早期和妊娠晚期的各项血常规检验结果,差异具有统计学意义(P 均<0.05)。参考区间分析显示血小板(PLT)、单核细胞百分比(M %)和嗜碱性粒细胞百分比(B %)检验结果均在现行参考区间内,故继续沿用原有参考区间;血细胞比容(HCT)和嗜酸性粒细胞百分比(E %)检验结果,经验证可合并参考区间;而红细胞计数(RBC)、血红蛋白(Hb)、白细胞计数(WBC)、中性粒细胞百分比(N %)及淋巴细胞百分比(L%)需分组建立不同的参考区间。结论新建的生物参考区间更符合孕期的生理变化,能更好的指导临床诊断和治疗。%Objective To establish the biological reference intervals about the main parameters of blood cells among pregnant women in our laboratory.Methods A total of 331 pregnant women who had normal and term delivery were enrolled.According to their medical records,their 2 reports of pregnancy routine blood cell tests were obtained. The results were analyzed statistically,and the biological reference intervals were calculated by SAS 8.1 software. Results There was statistical significance in all parameters of pregnancy routine blood cell tests between the first and third trimesters (P <0.05).The results of biological reference intervals showed that the 2 sets of data about platelet (PLT),monocyte percentage (M%)and basophilic granulocyte percentage (B %)were all within current biological reference intervals,then the current biological reference intervals could be used for pregnancy.The 2 sets of data about hematocrit (HCT)and eosinophile granulocyte percentage (E %)could be combined to

  1. Solvent effect on absorption and fluorescence spectra of three biologically active carboxamides (C1, C2 and C3). Estimation of ground and excited state dipole moment from solvatochromic method using solvent polarity parameters.

    Science.gov (United States)

    Patil, N R; Melavanki, R M; Kapatkar, S B; Ayachit, N H; Saravanan, J

    2011-05-01

    The absorption and fluorescence spectra of three Carboxamides namely (E)-2-(4-Chlorobenzylideneamino)-N-(2-chlorophenyl)-4,5,6,7-tetrahydrobenzo[b]thiophene-3-carboxamide (C(1)), (E)-N-(3-Chlorophenyl)-2-(3, 4-dimethoxybenzylideneamino)-4,5,6,7-tetrahydrobenzo[b]thiophene-3-carboxamide (C(2)) and (E)-N-(3-Chlorophenyl)-2-(3,4,5-trimethoxybenzylideneamino)-4,5,6,7-tetrahydrobenzo[b]thiophene-3-carboxamide (C(3)) have been recorded at room temperature in solvents of different polarities using dielectric constant (ε) and refractive index (n). Experimental ground (μ(g)) and excited (μ(e)) state dipole moments are estimated by means of solvatochromic shift method and also the excited dipole moments are estimated in combination with ground state dipole moments. It was estimated that dipole moments of the excited state were higher than those of the ground state of all three molecules. Further, the changes in dipole moment (Δμ) were calculated both from solvatochromic shift method and on the basis of microscopic empirical solvent polarity parameter (E(N)(T)) and the values are compared.

  2. Comportamento de Biomphalaria glabrata (Say, 1818 como critério de toxicidade em ensaios biológicos com moluscicidas Behavior of Biomphalaria glabrata (Say, 1818 as a parameter of toxicity in biological assays with molluscicides

    Directory of Open Access Journals (Sweden)

    Otávio S. Pieri

    1981-06-01

    parameters in toxicity determinations of molluscicides was assessed through the development of a method based on W.H.O. standard procedures of bioassying molluscicides and involving behavioural records by time-lapse cinematogrphy. B. glabrata adults (5 7/8 ± 1/8 whorls were subjected to different sublethal doses of copper sulfate during 24 hours and then transferred to deionized distilled water for recovery; from those records it was possible to compute: (a frequency of climbs to surface, (b frequency of crawlings out of water and (c proportion of snails on the upper, middle and botton thirds of the test containers. The Litchfield-Wilcoxon test was employed in determining a reference value (called "concentration of behavioural effect of 50%" of CBE50 in relation to each parameter. The indices thus obtained - (a 0,010, (b 0,006 and (c 0,029 ppm of copper - showed the freasibility of systematic uses of behavioural criteria of toxicity and also proved capable of detecting toxic effects of the product under concentrations much lower than those obtained from conventional lethality determinations. The data also showed an effect/log dose lienar relationship for all the parameters considered and revealed changes in snail activity as a consequence of the daily light cycle. Although the clarification of the ethological aspects involved in the control of schistosome hsot snails depends on the analysis of the relationships between the snail and its natural habitat, laboratory studies, carried out with accurate measuremente of the parameters related to protective modes of behaviour, can be of great value as well.

  3. Comparative Fluorescence Resonance Energy-Transfer Study in Pluronic Triblock Copolymer Micelle and Niosome Composed of Biological Component Cholesterol: An Investigation of Effect of Cholesterol and Sucrose on the FRET Parameters.

    Science.gov (United States)

    Roy, Arpita; Kundu, Niloy; Banik, Debasis; Sarkar, Nilmoni

    2016-01-14

    The formation of pluronic triblock copolymer (F127)-cholesterol-based niosome and its interaction with sugar (sucrose) molecules have been investigated. The morphology of F127-cholesterol -based niosome in the presence of sucrose has been successfully demonstrated using dynamic light scattering (DLS) and transmission electron microscopic (TEM) techniques. The DLS profiles and TEM images clearly suggest that the size of the niosome aggregates increases significantly in the presence of sucrose. In addition to structural characterization, a detailed comparative fluorescence resonance energy transfer (FRET) study has been carried out in these F127-containing aggregates, involving coumarin 153 (C153) as donor (D) and rhodamine 6G (R6G) as an acceptor (A) to monitor the dynamic heterogeneity of the systems. Besides, time-resolved anisotropy and fluorescence correlation spectroscopy measurements have been carried out to monitor the rotational and lateral diffusion motion in these F127-cholesterol-based aggregates using C153 and R6G, respectively. During the course of FRET study, we have observed multiple time constants of FRET inside the F127-cholesterol-based niosomes in contrast with the F127 micelle. This corresponds to the presence of more than one preferential donor-acceptor (D-A) distance in niosomes than in F127 micelle. FRET has also been successfully used to probe the effect of sucrose on the morphology of F127-cholesterol-based niosome. In the presence of sucrose, the time constant of FRET further increases as the D-A distances increase in sucrose-decorated niosome. Finally, the excitation-wavelength-dependent FRET studies have indicated that as the excitation of donor molecules varies from 408 to 440 nm the contribution of the faster rise component of the acceptor enhances considerably, which clearly establishes the dynamics heterogeneity of both systems. Our findings also indicate that FRET is completely intravesicular in nature in these block copolymer

  4. Continuous Vigilance - Evaluating Preparedness for a Biological Event

    Directory of Open Access Journals (Sweden)

    Bruria eAdini

    2014-04-01

    Full Text Available Objective: Effective response to biological events necessitates ongoing evaluation of preparedness. This study was a bilateral German-Israeli collaboration aimed at developing an evaluation tool for assessing preparedness of medical facilities for biological events.Methods: Measurable parameters were identified through a literature review for inclusion in the evaluation tool and disseminated to 228 content experts in 2 modified Delphi cycles. Focus groups were conducted to identify psychosocial needs of the medical teams. Table top and functional exercises were implemented to review applicability of the tool. Results: 117 experts from Germany and Israel participated in the modified Delphi. Out of 188 parameters that were identified, 183 achieved a consensus of >75% of the content experts. Following comments recommended in the Delphi cycles, and feedback from focus groups and hospital exercises, the final tool consisted of 172 parameters. Median level of importance of each parameter was calculated based on ranking recommended in the Delphi process. Computerized web-based software was developed to calculate scores of preparedness for biological events.Conclusions: Ongoing evaluation means, such as the tool developed in the study, can facilitate the need for a valid and reliable mechanism that may be widely adopted and implemented as quality assurance measures. The tool is based on measurable parameters and indicators that can effectively present strengths and weaknesses in managing a response to a public health threat, and accordingly, steps can be implemented to improve readiness. Adoption of such a tool is an important component of assuring public health and effective emergency management.Contact person regarding the evaluation tool: adinib@bgu.ac.ilLink to the computerized tool: http://www.be-prep.com/us

  5. Parâmetros biológicos e tabela de vida de Tetranychus urticae (Acari: Tetranychidae em cultivares de mamão Biological parameters and life table of Tetranychus urticae (Acari: Tetranychidae at papaya cultivars

    Directory of Open Access Journals (Sweden)

    Larissa Bernardino Moro

    2012-03-01

    immature stage, longevity and fecundity of adults and viability of these stages. The cultivars of papaya, "Tainung 01", "Calimosa", "Sunrise" and "Golden" are adequate hosts for T. urticae. The recorded viability above 90% was not influenced by the different cultivars during all the development phases. There was not statistic difference among the cultivars in the parameters: pre-ovopositional period, and egg viability. Mites assayed in "Tainung 01" cultivar showed a shorter duration of the egg, larva, protonymph and egg-adult. At life table parameters and fertility, presented smaller Ro, r m and λ, and larger Td. "Sunrise" is the cultivar most adequate for T. urticae development, considering that mites assayed in this cultivar showed a larger production of eggs per female, longer female longevity, and higher reproduction rate (larger Ro, r m and λ and smaller Td.

  6. Mesoscopic biology

    Indian Academy of Sciences (India)

    G V Shivashankar

    2002-02-01

    In this paper we present a qualitative outlook of mesoscopic biology where the typical length scale is of the order of nanometers and the energy scales comparable to thermal energy. Novel biomolecular machines, governed by coded information at the level of DNA and proteins, operate at these length scales in biological systems. In recent years advances in technology have led to the study of some of the design principles of these machines; in particular at the level of an individual molecule. For example, the forces that operate in molecular interactions, the stochasticity involved in these interactions and their spatio-temporal dynamics are beginning to be explored. Understanding such design principles is opening new possibilities in mesoscopic physics with potential applications.

  7. Marine biology

    Energy Technology Data Exchange (ETDEWEB)

    Thurman, H.V.; Webber, H.H.

    1984-01-01

    This book discusses both taxonomic and ecological topics on marine biology. Full coverage of marine organisms of all five kingdoms is provided, along with interesting and thorough discussion of all major marine habitats. Organization into six major parts allows flexibility. It also provides insight into important topics such as disposal of nuclear waste at sea, the idea that life began on the ocean floor, and how whales, krill, and people interact. A full-color photo chapter reviews questions, and exercises. The contents are: an overview marine biology: fundamental concepts/investigating life in the ocean; the physical ocean, the ocean floor, the nature of water, the nature and motion of ocean water; general ecology, conditions for life in the sea, biological productivity and energy transfer; marine organisms; monera, protista, mycota and metaphyta; the smaller marine animals, the large animals marine habitats, the intertidal zone/benthos of the continental shelf, the photic zone, the deep ocean, the ocean under stress, marine pollution, appendix a: the metric system and conversion factors/ appendix b: prefixes and suffixes/ appendix c: taxonomic classification of common marine organisms, and glossary, and index.

  8. Synthetic Biological Engineering of Photosynthesis

    Science.gov (United States)

    2015-11-16

    photosynthesis into artificial metabolic pathways. During the course of the granting period, we also made significant progress on understanding the...compartmentalization of carbon fixation and flux in relationship to photosynthesis and obtained 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND SUBTITLE...2014 Approved for Public Release; Distribution Unlimited Final Report: Synthetic Biological Engineering of Photosynthesis The views, opinions and/or

  9. Toxicity of spirotetramat to Bemisia tabaci biotype B and the impact on the biological parameters%螺虫乙酯对B型烟粉虱毒力及部分生物学参数的影响

    Institute of Scientific and Technical Information of China (English)

    戈大庆; 姜兴印; 王燕; 李俊虎; 段强

    2011-01-01

    In order to value the bioactivity and impact on the biology of spirotetramat against Bemisia tabaci biotype B, the toxicity of spirotetramat and imidacloprid (control agent) to different instar nymphs of B. tabaci biotype B and the effects of the longevity, fecundity and eggs hatchability were measured in the laboratory by using egg-dipping and leaf-dipping. The toxicity of the 2nd instar nymph is high after treatment by spirotetramat, the LCso was 4.07 mg/L, it was 2.73 times to the toxicity of imidacloprid, toxicity was low to the eggs and adults, and lower than that of imidacloprid. Longevity of the B. tabaci biotype B was 17.3 days after treatment with 12.5 mg/L spirotetramat, it was significantly shorted compared with the contrast experiment (treatment without pesticides), while imidacloprid was insignificant. The fecundity was 5 and the eggs hatching rate was 3.23% after treatment with 12.5 mg/L spirotetramat, which has significantly inhibition to the fecundity and the eggs hatching, and it was significantly lower than those treated with imidacloprid and the contrast experiment. It was no significant differences between imidacloprid and the contrast experiment. The repellent action was 52% to the adults of spirotetramat after 24 h treated with 100 mg/L spirotetramat, and the repellent action was not very good.%为系统评价新药剂螺虫乙酯(spirotetramat)对B型烟粉虱(Bem isia tabacibiotype B)的生物活性及生物学参数的影响,采用浸渍法测定了螺虫乙酯及对照药剂吡虫啉对B型烟粉虱各个虫态的室内毒力、成虫寿命、产卵量及所产卵孵化率的影响。结果表明,螺虫乙酯对2龄若虫毒力最高,LC50为4.07mg/L,为吡虫啉的2.73倍,对卵及成虫毒力较低,且显著低于吡虫啉;12.5 mg/L螺虫乙酯处理后,成虫寿命为17.3天,较空白对照显著缩短,吡虫啉与空白对照无显著差异;12.5mg/L螺虫乙酯处理后平均产卵量为5.0粒,所

  10. Biologic: Gene circuits and feedback in an introductory physics sequence for biology and premedical students

    CERN Document Server

    Cahn, S B

    2013-01-01

    Two synthetic gene circuits -- the genetic toggle switch and the repressilator -- are analyzed quantitatively and discussed in the context of an educational module on gene circuits and feedback that constitutes the final topic of a year-long introductory physics sequence, aimed at biology and premedical undergraduate students. The genetic toggle switch consists of two genes, each of whose protein product represses the other's expression, while the repressilator consists of three genes, each of whose protein product represses the next gene's expression. Analytic, numerical, and electronic treatments of the genetic toggle switch shows that this gene circuit realizes bistability. A simplified treatment of the repressilator reveals that this circuit can realize sustained oscillations. In both cases, a "phase diagram" is obtained, that specifies the region of parameter space in which bistability or oscillatory behavior, respectively, occurs.

  11. Systems biology characterization of engineered tissues.

    Science.gov (United States)

    Rajagopalan, Padmavathy; Kasif, Simon; Murali, T M

    2013-01-01

    Tissue engineering and molecular systems biology are inherently interdisciplinary fields that have been developed independently so far. In this review, we first provide a brief introduction to tissue engineering and to molecular systems biology. Next, we highlight some prominent applications of systems biology techniques in tissue engineering. Finally, we outline research directions that can successfully blend these two fields. Through these examples, we propose that experimental and computational advances in molecular systems biology can lead to predictive models of bioengineered tissues that enhance our understanding of bioengineered systems. In turn, the unique challenges posed by tissue engineering will usher in new experimental techniques and computational advances in systems biology.

  12. Biological trade and markets.

    Science.gov (United States)

    Hammerstein, Peter; Noë, Ronald

    2016-02-01

    Cooperation between organisms can often be understood, like trade between merchants, as a mutually beneficial exchange of services, resources or other 'commodities'. Mutual benefits alone, however, are not sufficient to explain the evolution of trade-based cooperation. First, organisms may reject a particular trade if another partner offers a better deal. Second, while human trade often entails binding contracts, non-human trade requires unwritten 'terms of contract' that 'self-stabilize' trade and prevent cheating even if all traders strive to maximize fitness. Whenever trading partners can be chosen, market-like situations arise in nature that biologists studying cooperation need to account for. The mere possibility of exerting partner choice stabilizes many forms of otherwise cheatable trade, induces competition, facilitates the evolution of specialization and often leads to intricate forms of cooperation. We discuss selected examples to illustrate these general points and review basic conceptual approaches that are important in the theory of biological trade and markets. Comparing these approaches with theory in economics, it turns out that conventional models-often called 'Walrasian' markets-are of limited relevance to biology. In contrast, early approaches to trade and markets, as found in the works of Ricardo and Cournot, contain elements of thought that have inspired useful models in biology. For example, the concept of comparative advantage has biological applications in trade, signalling and ecological competition. We also see convergence between post-Walrasian economics and biological markets. For example, both economists and biologists are studying 'principal-agent' problems with principals offering jobs to agents without being sure that the agents will do a proper job. Finally, we show that mating markets have many peculiarities not shared with conventional economic markets. Ideas from economics are useful for biologists studying cooperation but need

  13. Parameters estimation in quantum optics

    CERN Document Server

    D'Ariano, G M; Sacchi, M F; Paris, Matteo G. A.; Sacchi, Massimiliano F.

    2000-01-01

    We address several estimation problems in quantum optics by means of the maximum-likelihood principle. We consider Gaussian state estimation and the determination of the coupling parameters of quadratic Hamiltonians. Moreover, we analyze different schemes of phase-shift estimation. Finally, the absolute estimation of the quantum efficiency of both linear and avalanche photodetectors is studied. In all the considered applications, the Gaussian bound on statistical errors is attained with a few thousand data.

  14. Systems biology: experimental design.

    Science.gov (United States)

    Kreutz, Clemens; Timmer, Jens

    2009-02-01

    Experimental design has a long tradition in statistics, engineering and life sciences, dating back to the beginning of the last century when optimal designs for industrial and agricultural trials were considered. In cell biology, the use of mathematical modeling approaches raises new demands on experimental planning. A maximum informative investigation of the dynamic behavior of cellular systems is achieved by an optimal combination of stimulations and observations over time. In this minireview, the existing approaches concerning this optimization for parameter estimation and model discrimination are summarized. Furthermore, the relevant classical aspects of experimental design, such as randomization, replication and confounding, are reviewed.

  15. Biological Databases

    Directory of Open Access Journals (Sweden)

    Kaviena Baskaran

    2013-12-01

    Full Text Available Biology has entered a new era in distributing information based on database and this collection of database become primary in publishing information. This data publishing is done through Internet Gopher where information resources easy and affordable offered by powerful research tools. The more important thing now is the development of high quality and professionally operated electronic data publishing sites. To enhance the service and appropriate editorial and policies for electronic data publishing has been established and editors of article shoulder the responsibility.

  16. Variação dos parâmetros físicos, químicos e biológicos da água em um sistema de irrigação localizada Variation of physical, chemical and biological parameters of water in a trickle irrigation system

    Directory of Open Access Journals (Sweden)

    Túlio A. P. Ribeiro

    2005-09-01

    Full Text Available O presente trabalho teve como objetivo pesquisar, uma fonte hídrica superficial utilizada em um sistema de irrigação por gotejamento, com o fim de se analisar a variação temporal, durante um ano, dos principais parâmetros físicos, químicos e biológicos da sua água e que causam problemas de entupimento nos emissores: sólidos suspensos, turbidez, pH, ferro, sulfetos, condutividade elétrica, sólidos dissolvidos, dureza, índice de Langelier, algas e bactérias Os critérios para avaliação das impurezas presentes na água de irrigação se basearam em estudos realizados por Bucks & Nakayama (1986, no sentido de dar uma orientação de caracter quantitativo que propuseram uma classificação da água, indicando critérios para avaliação do risco de entupimento dos emissores nos sistemas de irrigação localizada. Os resultados mostraram que os parâmetros químicos apresentaram médio risco de obstrução aos emissores, foram pH, ferro e sulfetos, enquanto os parâmetros físicos e biológicos analisados indicaram baixo risco de entupimento dos emissores. Constatou-se correlação dos resultados entre os parâmetros físicos, turbidez e sólidos suspensos totais e o parâmetro biológico algas, com sólidos suspensos totais.This work had the objective to study a superficial water source utilized in a trickle irrigation system. The principal physical, chemical and biological parameters of the irrigation water that caused problems of obstrution in emitters: pH, turbidity, suspensded solids, dissolved solids, EC, hardness, Langelier index, algae and bacterium were analysed during the year. The evaluation criterion of the impurities present in the irrigation water were based on the studies conducted by Bucks & Nakayama (1986, in order to give quantitative orientation of risk of obstruction of drippers in trickle irrigation systems. The chemical factors which showed moderate clogging risk to the emitters were: pH, total iron and sulphite

  17. Nonlinear functional response parameter estimation in a stochastic predator-prey model.

    Science.gov (United States)

    Gilioli, Gianni; Pasquali, Sara; Ruggeri, Fabrizio

    2012-01-01

    Parameter estimation for the functional response of predator-prey systems is a critical methodological problem in population ecology. In this paper we consider a stochastic predator-prey system with non-linear Ivlev functional response and propose a method for model parameter estimation based on time series of field data. We tackle the problem of parameter estimation using a Bayesian approach relying on a Markov Chain Monte Carlo algorithm. The efficiency of the method is tested on a set of simulated data. Then, the method is applied to a predator-prey system of importance for Integrated Pest Management and biological control, the pest mite Tetranychus urticae and the predatory mite Phytoseiulus persimilis. The model is estimated on a dataset obtained from a field survey. Finally, the estimated model is used to forecast predator-prey dynamics in similar fields, with slightly different initial conditions.

  18. PARAMETER ESTIMATION IN BREAD BAKING MODEL

    OpenAIRE

    Hadiyanto Hadiyanto; AJB van Boxtel

    2012-01-01

    Bread product quality is highly dependent to the baking process. A model for the development of product quality, which was obtained by using quantitative and qualitative relationships, was calibrated by experiments at a fixed baking temperature of 200°C alone and in combination with 100 W microwave powers. The model parameters were estimated in a stepwise procedure i.e. first, heat and mass transfer related parameters, then the parameters related to product transformations and finally pro...

  19. Evaluation of Physicochemical and Microbiological Parameters of Smoked Sausages

    Directory of Open Access Journals (Sweden)

    Melinda Nagy

    2015-11-01

    Full Text Available Meat and meat products continue to supply nutrients and play a vital role in human life because of their high biological value protein, iron, zinc, selenium and vitamin B12 contents, being a crucial component of a well balanced diet. The objective of this paper was to analyse the microbiological and physicochemical characteristics of smoked sausage obtain by a modern recipe. The meat  material was obtained from local butchery (Cluj-Napoca, Romania. The physicochemical analyses highlighted the moisture (Drying-oven at 105 ºC, protein (Kjeldahl method and fat (Soxhlet method content, as well as nitrite (Griess method and sodium chloride concentrations (Mohr method of the final products. Microbiological and physicochemical analysis of the examined samples found no deviations from legal norms imposed for smoked sausage.  All of the quality parameters comply with the limits stipulated by STAS. 

  20. Biological biomaterials

    Energy Technology Data Exchange (ETDEWEB)

    Jorge-Herrero, E. [Servicio de Cirugia Experimental. Clinica Puerta de Hierro, Madrid (Spain)

    1997-05-01

    There are a number of situations in which substances of biological origin are employed as biomaterials. Most of them are macromolecules derived from isolated connective tissue or the connective tissue itself in membrane form, in both cases, the tissue can be used in its natural form or be chemically treated. In other cases, certain blood vessels can be chemically pretreated and used as vascular prostheses. Proteins such as albumin, collagen and fibrinogen are employed to coat vascular prostheses. Certain polysaccharides have also been tested for use in controlled drug release systems. Likewise, a number of tissues, such as dura mater, bovine pericardium, procine valves and human valves, are used in the preparation of cardiac prostheses. We also use veins from animals or humans in arterial replacement. In none of these cases are the tissues employed dissimilar to the native tissues as they have been chemically modified, becoming a new bio material with different physical and biochemical properties. In short, we find that natural products are being utilized as biomaterials and must be considered as such; thus, it is necessary to study both their chemicobiological and physicomechanical properties. In the present report, we review the current applications, problems and future prospects of some of these biological biomaterials. (Author) 84 refs.

  1. Synthetic Biology for Specialty Chemicals.

    Science.gov (United States)

    Markham, Kelly A; Alper, Hal S

    2015-01-01

    In this review, we address recent advances in the field of synthetic biology and describe how those tools have been applied to produce a wide variety of chemicals in microorganisms. Here we classify the expansion of the synthetic biology toolbox into three different categories based on their primary function in strain engineering-for design, for construction, and for optimization. Next, focusing on recent years, we look at how chemicals have been produced using these new synthetic biology tools. Advances in producing fuels are briefly described, followed by a more thorough treatment of commodity chemicals, specialty chemicals, pharmaceuticals, and nutraceuticals. Throughout this review, an emphasis is placed on how synthetic biology tools are applied to strain engineering. Finally, we discuss organism and host strain diversity and provide a future outlook in the field.

  2. varying elastic parameters distributions

    KAUST Repository

    Moussawi, Ali

    2014-12-01

    The experimental identication of mechanical properties is crucial in mechanics for understanding material behavior and for the development of numerical models. Classical identi cation procedures employ standard shaped specimens, assume that the mechanical elds in the object are homogeneous, and recover global properties. Thus, multiple tests are required for full characterization of a heterogeneous object, leading to a time consuming and costly process. The development of non-contact, full- eld measurement techniques from which complex kinematic elds can be recorded has opened the door to a new way of thinking. From the identi cation point of view, suitable methods can be used to process these complex kinematic elds in order to recover multiple spatially varying parameters through one test or a few tests. The requirement is the development of identi cation techniques that can process these complex experimental data. This thesis introduces a novel identi cation technique called the constitutive compatibility method. The key idea is to de ne stresses as compatible with the observed kinematic eld through the chosen class of constitutive equation, making possible the uncoupling of the identi cation of stress from the identi cation of the material parameters. This uncoupling leads to parametrized solutions in cases where 5 the solution is non-unique (due to unknown traction boundary conditions) as demonstrated on 2D numerical examples. First the theory is outlined and the method is demonstrated in 2D applications. Second, the method is implemented within a domain decomposition framework in order to reduce the cost for processing very large problems. Finally, it is extended to 3D numerical examples. Promising results are shown for 2D and 3D problems.

  3. When cell biology meets theory

    Science.gov (United States)

    Gonzalez-Gaitan, Marcos

    2015-01-01

    Cell biologists now have tools and knowledge to generate useful quantitative data. But how can we make sense of these data, and are we measuring the correct parameters? Moreover, how can we test hypotheses quantitatively? To answer these questions, the theory of physics is required and is essential to the future of quantitative cell biology. PMID:26416957

  4. When cell biology meets theory.

    Science.gov (United States)

    Gonzalez-Gaitan, Marcos; Roux, Aurélien

    2015-09-28

    Cell biologists now have tools and knowledge to generate useful quantitative data. But how can we make sense of these data, and are we measuring the correct parameters? Moreover, how can we test hypotheses quantitatively? To answer these questions, the theory of physics is required and is essential to the future of quantitative cell biology.

  5. Absolute biological needs.

    Science.gov (United States)

    McLeod, Stephen

    2014-07-01

    Absolute needs (as against instrumental needs) are independent of the ends, goals and purposes of personal agents. Against the view that the only needs are instrumental needs, David Wiggins and Garrett Thomson have defended absolute needs on the grounds that the verb 'need' has instrumental and absolute senses. While remaining neutral about it, this article does not adopt that approach. Instead, it suggests that there are absolute biological needs. The absolute nature of these needs is defended by appeal to: their objectivity (as against mind-dependence); the universality of the phenomenon of needing across the plant and animal kingdoms; the impossibility that biological needs depend wholly upon the exercise of the abilities characteristic of personal agency; the contention that the possession of biological needs is prior to the possession of the abilities characteristic of personal agency. Finally, three philosophical usages of 'normative' are distinguished. On two of these, to describe a phenomenon or claim as 'normative' is to describe it as value-dependent. A description of a phenomenon or claim as 'normative' in the third sense does not entail such value-dependency, though it leaves open the possibility that value depends upon the phenomenon or upon the truth of the claim. It is argued that while survival needs (or claims about them) may well be normative in this third sense, they are normative in neither of the first two. Thus, the idea of absolute need is not inherently normative in either of the first two senses.

  6. Photovoltaic module parameters acquisition model

    Science.gov (United States)

    Cibira, Gabriel; Koščová, Marcela

    2014-09-01

    This paper presents basic procedures for photovoltaic (PV) module parameters acquisition using MATLAB and Simulink modelling. In first step, MATLAB and Simulink theoretical model are set to calculate I-V and P-V characteristics for PV module based on equivalent electrical circuit. Then, limited I-V data string is obtained from examined PV module using standard measurement equipment at standard irradiation and temperature conditions and stated into MATLAB data matrix as a reference model. Next, the theoretical model is optimized to keep-up with the reference model and to learn its basic parameters relations, over sparse data matrix. Finally, PV module parameters are deliverable for acquisition at different realistic irradiation, temperature conditions as well as series resistance. Besides of output power characteristics and efficiency calculation for PV module or system, proposed model validates computing statistical deviation compared to reference model.

  7. Digital 'faces' of synthetic biology.

    Science.gov (United States)

    Friedrich, Kathrin

    2013-06-01

    In silicio design plays a fundamental role in the endeavour to synthesise biological systems. In particular, computer-aided design software enables users to manage the complexity of biological entities that is connected to their construction and reconfiguration. The software's graphical user interface bridges the gap between the machine-readable data on the algorithmic subface of the computer and its human-amenable surface represented by standardised diagrammatic elements. Notations like the Systems Biology Graphical Notation (SBGN), together with interactive operations such as drag & drop, allow the user to visually design and simulate synthetic systems as 'bio-algorithmic signs'. Finally, the digital programming process should be extended to the wet lab to manufacture the designed synthetic biological systems. By exploring the different 'faces' of synthetic biology, I argue that in particular computer-aided design (CAD) is pushing the idea to automatically produce de novo objects. Multifaceted software processes serve mutually aesthetic, epistemic and performative purposes by simultaneously black-boxing and bridging different data sources, experimental operations and community-wide standards. So far, synthetic biology is mainly a product of digital media technologies that structurally mimic the epistemological challenge to take both qualitative as well as quantitative aspects of biological systems into account in order to understand and produce new and functional entities.

  8. Synthetic biology as red herring.

    Science.gov (United States)

    Preston, Beth

    2013-12-01

    It has become commonplace to say that with the advent of technologies like synthetic biology the line between artifacts and living organisms, policed by metaphysicians since antiquity, is beginning to blur. But that line began to blur 10,000 years ago when plants and animals were first domesticated; and has been thoroughly blurred at least since agriculture became the dominant human subsistence pattern many millennia ago. Synthetic biology is ultimately only a late and unexceptional offshoot of this prehistoric development. From this perspective, then, synthetic biology is a red herring, distracting us from more thorough philosophical consideration of the most truly revolutionary human practice-agriculture. In the first section of this paper I will make this case with regard to ontology, arguing that synthetic biology crosses no ontological lines that were not crossed already in the Neolithic. In the second section I will construct a parallel case with regard to cognition, arguing that synthetic biology as biological engineering represents no cognitive advance over what was required for domestication and the new agricultural subsistence pattern it grounds. In the final section I will make the case with regard to human existence, arguing that synthetic biology, even if wildly successful, is not in a position to cause significant existential change in what it is to be human over and above the massive existential change caused by the transition to agriculture. I conclude that a longer historical perspective casts new light on some important issues in philosophy of technology and environmental philosophy.

  9. Dosimetry using environmental and biological materials. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Haskell, E.; Kenner, G.; Hayes, R.

    1998-02-01

    This report summarizes a five year effort to improve the sensitivity and reliability of retrospective dosimetry methods, to collaborate with laboratories engaged in related research and to share the technology with startup laboratories seeking similar capabilities. This research program has focused on validation of electron paramagnetic resonance (EPR) as a dosimetry tool and on optimization of the technique by reducing the lower limits of detection, simplifying the process of sample preparation and analysis and speeding analysis to allow greater throughput in routine measurement situations. The authors have investigated the dosimetric signal of hard tissues in enamel, deorganified dentin, synthetic carbonated apatites and synthetic hydroxyapatite. This research has resulted in a total of 27 manuscripts which have been published, are in press, or have been submitted for publication. Of these manuscripts, 14 are included in this report and were indexed separately for inclusion in the data base.

  10. Genetics and molecular biology of methanogen genes. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Konisky, J.

    1997-10-07

    Adenylate kinase has been isolated from four related methanogenic members of the Archaea. For each the optimum temperature for enzyme activity was similar to the temperature for optimal microbial growth and was approximately 30 C for Methanococcus voltage, 70 C for Methanococcus thermolithotrophicus, 80 C for Methanococcus igneus and 80--90 C for Methanococcus jannaschii. The enzymes were sensitive to the adenylate kinase inhibitor, Ap{sub 5}A [P{sup 1}, P{sup 5}-di(adenosine-5{prime}) pentaphosphate], a property that was exploited to purify the enzymes by CIBACRON Blue affinity chromatography. The enzymes had an estimated molecular weight (approximately 23--25 kDa) in the range common for adenylate kinases. Each of the enzymes had a region of amino acid sequence close to its N-terminus that was similar to the canonical P-loop sequence reported for all adenylate kinases. However, the methanogen sequences lacked a lysine residue that has previously been found to be invariant in adenylate kinases including an enzyme isolated from the Archeon, Sulfolobus acidocaldarius. If verified as a nucleotide binding domain, the methanogen sequence would represent a novel nucleotide binding motif. There was no correlation between amino acid abundance and the optimal temperature for enzyme activity.

  11. Molecular biological enhancement of coal desulfurization. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Krawiec, S.

    1995-01-01

    Fresh isolates of bacteria presumptively identified as R. erythropolis unequivocally have a DbtS{sup +} phenotype. The production of OH-BP from either DBT or DBTO{sub 2} was confirmed by difference spectroscopy, HPLC, and mass spectrometry. The temperature, pH, and means of supplying the thiophenic or sulfonic sole source of sulfur were optimized. The maximal rate of growth of the organism, its affinity for sulfone, and the extent to which substrate was converted to product were determined by using batch, fed batch, and continuous cultures. For strain N1-36, the maximum specific growth rate was 0.235 hr{sup -1} which corresponds to a minimal generation time of 2.95 hr. The K{sub s} was estimated to be 0.39 {mu}M. With 100 {mu}M DBT as the sole sulfur source, approximately 40 {mu}M OH-BP are produced (after 40 hr of growth); with 100 {mu}M DBTO{sub 2} as the sole sulfur source, approximately 70 {mu}M OH-BP are produced (after 40 hr of growth). The desulfurization activity is repressed by SO{sub 4}{sup =} OH-BP does not serve as a carbon source. The DbtS{sup +} phenotype of the R. erythropolis isolates is stable and discrete. The isolates selectively remove sulfur from DBT, a compound which models a refractory form of organic sulfur in compounds characteristic of fossil fuels. The desulfurization occurs with no oxidation of carbon-carbon bonds. The stability and specificity (along with genetic regulation) indicate that microbial desulfurization in a real phenomenon in which a noxious element is removed without significantly affecting the calorific value of the substrate. Additional characterization (and optimization) would provide the basis of a very important form of fossil fuel beneficiation.

  12. Biological control of Aleutian Island arctic fox: Final report

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Empirical and literature data on the resource utilization patterns of arctic fox (Alopex lagopus) and red fox (Vulpes vulpes) are evaluated to assess the potential...

  13. Molecular biological enhancement of coal desulfurization. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Krawiec, S.

    1994-12-31

    During the period from 1986 through 1993 the prospect of bacterial desulfurization of fossil fuel was transformed from a theoretically appealing concept to a demonstrable laboratory phenomenon. Results from several laboratories confirmed that there was not one but, rather, several metabolic bases of selectively removing sulfur from the carbon frame of sulfur-containing organic compounds characteristic of fossil fuels. Results in this report relate solely to the so-called ``4S`` pathway (named for the four sulfur-containing compounds in the sequence: (l) dibenzothiophene [DBT] {yields} (2) dibenzothiophene sulfoxide [DBTO] {yields} (3) dibenzosulfone [DBTO{sup 2}] {yields} (4) dibenzosulfonate {yields} monohydroxybiphenyl [OH-BP] + SO{sub 4}{sup =}. [An additional desulfurized product, biphenyl, has been hypothesized and another, o,o{prime}-biphenyl, observed.]) The following subjects are discussed: isolating bacteria with a DbtS{sup +} phenotype; confirming the production of a desulfurized product; determining the identity of the isolates; determining the growth characteristics of the isolates in batch and continuous cultures; determining the kinetics and yields of product in batch and continuous cultures.

  14. Dosimetry using environmental and biological materials. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Haskell, E.; Kenner, G.; Hayes, R.

    1996-09-01

    Although theoretical models have been the traditional tool for assessment of doses delivered by nuclear accidents, their use is now accompanied by increasing political and scientific demand for physical measurements which provide site specific dose information related directly to the original events, can be used to verify and augment the theoretical models, and can be performed and reflicated by independent laboratories. This report details a four year effort to improve the sensitivity and reliability of retrospective methods, to collaborate with laboratories engaged in related research, and to share the technology with startup laboratories seeking similar capabilities.

  15. Decommissioning of the ASTRA research reactor: Dismantling of the biological shield

    Directory of Open Access Journals (Sweden)

    Meyer Franz

    2006-01-01

    Full Text Available The paper describes the dismantling of the inactive and activated areas of the biological shield of the ASTRA research reactor at the Austrian Research Center in Seibersdorf. The calculation of the parameters determining the activated areas at the shield (reference nuclide, nuclide vector in the barite concrete and horizontal and vertical reduction behaviors of activity concentration and the activation profiles within the biological shield for unrestricted release, release restricted to permanent deposit and radioactive waste are presented. Considerations of located activation anomalies in the shield, e.g. in the vicinities of the beam-tubes, were made according to the reactor's operational history. Finally, an overview of the materials removed from the biological shield is given.

  16. Structural Biology Fact Sheet

    Science.gov (United States)

    ... Home > Science Education > Structural Biology Fact Sheet Structural Biology Fact Sheet Tagline (Optional) Middle/Main Content Area What is structural biology? Structural biology is a field of science focused ...

  17. Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Schuur, Edward [Northern Arizona Univ., Flagstaff, AZ (United States); Luo, Yiqi [Univ. of Oklahoma, Norman, OK (United States)

    2016-12-01

    This final grant report is a continuation of the final grant report submitted for DE-SC0006982 as the Principle Investigator (Schuur) relocated from the University of Florida to Northern Arizona University. This report summarizes the original project goals, as well as includes new project activities that were completed in the final period of the project.

  18. Identification of Critical Biological Parameters Affecting Gastrointestinal Absorption

    Science.gov (United States)

    1990-01-01

    segregation of the outer longitudinal layer of smooth muscle into three discrete bands called the teniae coli (see figure A-7); sacculations of the...intestinal wall called haustra that are caused by the fact that the teniae are shorter than the gut; and small fat-filled sacs of peritoneum attached along...the teniae (appendices epiploicae). Internally, the luminal surface possesses folds of mucosa that occur between adjacent haustra (plicae semilunares

  19. Soil Biological Parameters Influenced By Cocoa Management Systems

    Science.gov (United States)

    Cropping systems have a profound influence on the soil micro-fauna and they are responsible for nutrient cycling, and add stability to the soil. At Tarapoto, Peru, two field experiments were established on acidic medium fertility Alfisol to assess the influence of management systems on cacao rhizosp...

  20. Systems biology approach to bioremediation

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Romy; Wu, Cindy H.; Hazen, Terry C.

    2012-06-01

    Bioremediation has historically been approached as a ‘black box’ in terms of our fundamental understanding. Thus it succeeds and fails, seldom without a complete understanding of why. Systems biology is an integrated research approach to study complex biological systems, by investigating interactions and networks at the molecular, cellular, community, and ecosystem level. The knowledge of these interactions within individual components is fundamental to understanding the dynamics of the ecosystem under investigation. Finally, understanding and modeling functional microbial community structure and stress responses in environments at all levels have tremendous implications for our fundamental understanding of hydrobiogeochemical processes and the potential for making bioremediation breakthroughs and illuminating the ‘black box’.

  1. Synthetic biology - the state of play.

    Science.gov (United States)

    Kitney, Richard; Freemont, Paul

    2012-07-16

    Just over two years ago there was an article in Nature entitled "Five Hard Truths for Synthetic Biology". Since then, the field has moved on considerably. A number of economic commentators have shown that synthetic biology very significant industrial potential. This paper addresses key issues in relation to the state of play regarding synthetic biology. It first considers the current background to synthetic biology, whether it is a legitimate field and how it relates to foundational biological sciences. The fact that synthetic biology is a translational field is discussed and placed in the context of the industrial translation process. An important aspect of synthetic biology is platform technology, this topic is also discussed in some detail. Finally, examples of application areas are described.

  2. Simulating Biological and Non-Biological Motion

    Science.gov (United States)

    Bruzzo, Angela; Gesierich, Benno; Wohlschlager, Andreas

    2008-01-01

    It is widely accepted that the brain processes biological and non-biological movements in distinct neural circuits. Biological motion, in contrast to non-biological motion, refers to active movements of living beings. Aim of our experiment was to investigate the mechanisms underlying mental simulation of these two movement types. Subjects had to…

  3. A Brief Introduction to Chinese Biological Biological

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Chinese Biological Abstracts sponsored by the Library, the Shanghai Institutes for Biological Sciences, the Biological Documentation and Information Network, all of the Chinese Academy of Sciences, commenced publication in 1987 and was initiated to provide access to the Chinese information in the field of biology.

  4. Lumped-parameter models

    Energy Technology Data Exchange (ETDEWEB)

    Ibsen, Lars Bo; Liingaard, M.

    2006-12-15

    A lumped-parameter model represents the frequency dependent soil-structure interaction of a massless foundation placed on or embedded into an unbounded soil domain. In this technical report the steps of establishing a lumped-parameter model are presented. Following sections are included in this report: Static and dynamic formulation, Simple lumped-parameter models and Advanced lumped-parameter models. (au)

  5. Biological Correlates of Empathy

    Directory of Open Access Journals (Sweden)

    E. Timucin Oral

    2010-04-01

    Full Text Available Empathy can be defined as the capacity to know emotionally what another is experiencing from within the frame of reference of that other person and the capacity to sample the feelings of another or it can be metaphorized as to put oneself in another’s shoes. Although the concept of empathy was firstly described in psychological theories, researches studying the biological correlates of psychological theories have been increasing recently. Not suprisingly, dinamically oriented psychotherapists Freud, Kohut, Basch and Fenichel had suggested theories about the biological correlates of empathy concept and established the basis of this modality decades ago. Some other theorists emphasized the importance of empathy in the early years of lifetime regarding mother-child attachment in terms of developmental psychology and investigated its role in explanation of psychopathology. The data coming from some of the recent brain imaging and animal model studies also seem to support these theories. Although increased activity in different brain regions was shown in many of the brain imaging studies, the role of cingulate cortex for understanding mother-child relationship was constantly emphasized in nearly all of the studies. In addition to these studies, a group of Italian scientists has defined a group of neurons as “mirror neurons” in their studies observing rhesus macaque monkeys. Later, they also defined mirror neurons in human studies, and suggested them as “empathy neurons”. After the discovery of mirror neurons, the hopes of finding the missing part of the puzzle for understanding the biological correlates of empathy raised again. Although the roles of different biological parameters such as skin conductance and pupil diameter for defining empathy have not been certain yet, they are going to give us the opportunity to revise the inconsistent basis of structural validity in psychiatry and to stabilize descriptive validity. In this review, the

  6. Final Focus Test Stand final report

    CERN Document Server

    Jeremie, A; Burrows, P

    2013-01-01

    Future Linear colliders will need particle beam sizes in the nanometre range. The beam also needs to be stable all along the beam line and especially at the Final Focus section. A dedicated Final Focus test stand has been used for this study and is comprised of several sub-parts. First there is the Stabilisation/Isolation system with sensors and actuators stabilizing down to sub-nanometre level. Then the Magnet itself needs to comply with very specific design constraints. In addition to the mechanical items, the beam can be stabilized acting on the trajectory directly and Beam-based controls have been developed and tested on different accelerator facilities.

  7. Parameter Estimation in Continuous Time Domain

    Directory of Open Access Journals (Sweden)

    Gabriela M. ATANASIU

    2016-12-01

    Full Text Available This paper will aim to presents the applications of a continuous-time parameter estimation method for estimating structural parameters of a real bridge structure. For the purpose of illustrating this method two case studies of a bridge pile located in a highly seismic risk area are considered, for which the structural parameters for the mass, damping and stiffness are estimated. The estimation process is followed by the validation of the analytical results and comparison with them to the measurement data. Further benefits and applications for the continuous-time parameter estimation method in civil engineering are presented in the final part of this paper.

  8. Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Aristos Aristidou Natureworks); Robert Kean (NatureWorks); Tom Schechinger (IronHorse Farms, Mat); Stuart Birrell (Iowa State); Jill Euken (Wallace Foundation & Iowa State)

    2007-10-01

    /storage/transportation equipment and the processor would build and operate the plant. Pilot fermentation studies demonstrated dramatic improvements in yields and rates with optimization of batch fermentor parameters. Demonstrated yields and rates are approaching those necessary for profitable commercial operation for production of ethanol or lactic acid. The ability of the biocatalyst to adapt to biomass hydrolysate (both biomass sugars and toxins in the hydrolysate) was demonstrated and points towards ultimate successful commercialization of the technology. However, some of this work will need to be repeated and possibly extended to adapt the final selected biocatalyst for the specific commercial hydrolysate composition. The path from corn stover in the farm field to final products, involves a number of steps. Each of these steps has options, problems, and uncertainties; thus creating a very complex multidimensional obstacle to successful commercial development. Through the tasks of this project, the technical and commercial uncertainties of many of these steps have been addressed; thus providing for a clearer understanding of paths forward and commercial viability of a corn stover-based biorefinery.

  9. Principais parâmetros biológicos avaliados em erros na fase pré-analítica de laboratórios clínicos: revisão sistemática Main biological parameters evaluated in pre-analytical phase errors at clinical laboratories: a systematic review

    Directory of Open Access Journals (Sweden)

    Vivaldo Gomes da Costa

    2012-06-01

    comprises three phases: pre-analytical, analytical and post-analytical. Most errors occur in the pre-analytical phase. Thus, their determination and corresponding assessment maximize QAP efficiency. In this study, by means of a systematic review, which comprised 14 articles, we describe the main biological variations found in the pre-analytical phase at clinical laboratories. The biological parameters described in the review included glucose, cholesterol, triglycerides, enzymes and hormones. As far as venipuncture is concerned, a common error was the prolonged use of tourniquet. The main error causes were the following: storage time, tourniquet time, phlebotomy techniques, insufficient information to patients, incorrect blood/anticoagulant ratio, inadequate tubes, contaminated samples, medication and interlaboratory alterations. Our results corroborated other studies, although we did not find other investigations that specifically evaluated changes in the pre-analytical phase due to the use of medication. The most assessed biological parameters coincided with clinical tests. Accordingly, both the implementation of an efficient QAP and the development of professional awareness may prevent laboratory inaccuracies.

  10. Redefining solubility parameters: the partial solvation parameters.

    Science.gov (United States)

    Panayiotou, Costas

    2012-03-21

    The present work reconsiders a classical and universally accepted concept of physical chemistry, the solubility parameter. Based on the insight derived from modern quantum chemical calculations, a new definition of solubility parameter is proposed, which overcomes some of the inherent restrictions of the original definition and expands its range of applications. The original single solubility parameter is replaced by four partial solvation parameters reflecting the dispersion, the polar, the acidic and the basic character of the chemical compounds as expressed either in their pure state or in mixtures. Simple rules are adopted for the definition and calculation of these four parameters and their values are tabulated for a variety of common substances. In contrast, however, to the well known Hansen solubility parameters, their design and evaluation does not rely exclusively on the basic rule of "similarity matching" for solubility but it makes also use of the other basic rule of compatibility, namely, the rule of "complementarity matching". This complementarity matching becomes particularly operational with the sound definition of the acidic and basic components of the solvation parameter based on the third σ-moments of the screening charge distributions of the quantum mechanics-based COSMO-RS theory. The new definitions are made in a simple and straightforward manner, thus, preserving the strength and appeal of solubility parameter stemming from its simplicity. The new predictive method has been applied to a variety of solubility data for systems of pharmaceuticals and polymers. The results from quantum mechanics calculations are critically compared with the results from Abraham's acid/base descriptors.

  11. Cassini's Grand Finale: The Final Orbits

    Science.gov (United States)

    Spilker, Linda; Edgington, Scott

    2016-04-01

    The Cassini-Huygens mission, a joint collaboration between NASA, ESA and the Italian Space Agency, is approaching its last year of operations after nearly 12 years in orbit around Saturn. Cassini will send back its final bits of unique data on September 15th, 2017 as it plunges into Saturn's atmosphere, vaporizing and satisfying planetary protection requirements. Before that time Cassini will continue its legacy of exploration and discovery with 12 close flybys of Titan in 2016 and 2017 that will return new science data as well as sculpt the inclinations and periods of the final orbits. Even though all of our close icy satellite flybys, including those of Enceladus, are now completed, numerous Voyager-class flybys (summer solstice approaches. In November 2016 Cassini will transition to a series of orbits with peripases just outside Saturn's F ring. These 20 orbits will include close flybys of some tiny ring moons and excellent views of the F ring and outer A ring. The 126th and final close flyby of Titan will propel Cassini across Saturn's main rings and into its final orbits. Cassini's Grand Finale, starting in April 2017, is comprised of 22 orbits at an inclination of 63 degrees. Cassini will repeatedly dive between the innermost rings and the upper atmosphere of the planet providing insights into fundamental questions unattainable during the rest of the mission. Cassini will be the first spacecraft to explore this region. These close orbits provide the highest resolution observations of both the rings and Saturn, and direct in situ sampling of the ring particles, composition, plasma, Saturn's exosphere and the innermost radiation belts. Saturn's gravitational field will be measured to unprecedented accuracy, providing information on the interior structure of the planet, winds in the outer layers of Saturn's atmosphere, and the mass distribution in the rings. Probing the magnetic field will give insight into the nature of the magnetic dynamo, telling us: why the

  12. Parâmetros biológicos de fêmeas adultas Amblyomma cajennense alimentadas em coelhos tratados com bioterápico ultradiluído Biological parameters of Amblyomma cajennense adult females fed on rabbits treated with ultradiluted biotherapic

    Directory of Open Access Journals (Sweden)

    Luciana Rodrigues de Almeida

    2008-08-01

    Full Text Available Os bioterápicos são considerados medicamentos homeopáticos por serem preparados de acordo com a farmacotécnica homeopática, submetidos à diluição e dinamização. Com o objetivo de avaliar os efeitos da administração de bioterápico ultradiluído sobre parâmetros biológicos de carrapatos Amblyomma cajennense, oito coelhos de três meses de idade, separados em dois grupos de quatro animais, constituindo os grupos tratado e controle, receberam o bioterápico na potência 30 DH (Decimal Hering e soro fisiológico 30DH, respectivamente. Em seguida, os animais foram infestados experimentalmente com 10 casais de carrapatos A. cajennense e submetidos novamente aos referidos tratamentos. O bioterápico ultradiluído foi preparado a partir de carrapatos adultos machos e fêmeas de A. cajennense. Foram avaliados parâmetros biológicos relativos à postura e à eclosão larval de A. cajennense. De acordo com os resultados obtidos, não foram detectados efeitos significativos sobre os parâmetros biológicos de fêmeas A. cajennense alimentadas em coelhos tratados com o bioterápico, quando comparados ao grupo controle. Novos testes, envolvendo outras espécies hospedeiras e o acompanhamento de infestações subseqüentes, devem ser dedicados à avaliação do potencial terapêutico profilático dos bioterápicos ultradiluídos nas ectoparasitoses dos animais domésticos.The biotherapics are considered homeopathic medicine because are produced in agreement to the homeopathic pharmacotechnic being diluted and dinamizated. To evaluate the effects of ultradiluted biotherapic on biologic parameters of Amblyomma cajennense ticks, 8 rabbits, about 3 months old, were divided into 2 groups of 4 animals each: treated and control groups which received biotherapic 30 DH potency (Hering’s decimal and 30DH physiologic serum, respectively. Following, the animals were infested with 10 couples A. cajennense and treated again. The ultradiluted biotherapic was

  13. Nonlinear analysis of biological sequences

    Energy Technology Data Exchange (ETDEWEB)

    Torney, D.C.; Bruno, W.; Detours, V. [and others

    1998-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The main objectives of this project involved deriving new capabilities for analyzing biological sequences. The authors focused on tabulating the statistical properties exhibited by Human coding DNA sequences and on techniques of inferring the phylogenetic relationships among protein sequences related by descent.

  14. Cell biology perspectives in phage biology.

    Science.gov (United States)

    Ansaldi, Mireille

    2012-01-01

    Cellular biology has long been restricted to large cellular organisms. However, as the resolution of microscopic methods increased, it became possible to study smaller cells, in particular bacterial cells. Bacteriophage biology is one aspect of bacterial cell biology that has recently gained insight from cell biology. Despite their small size, bacteriophages could be successfully labeled and their cycle studied in the host cells. This review aims to put together, although non-extensively, several cell biology studies that recently pushed the elucidation of key mechanisms in phage biology, such as the lysis-lysogeny decision in temperate phages or genome replication and transcription, one step further.

  15. Biology Reflective Assessment Curriculum

    Science.gov (United States)

    Bayley, Cheryl Ann

    Often students and educators view assessments as an obligation and finality for a unit. In the current climate of high-stakes testing and accountability, the balance of time, resources and emphasis on students' scores related to assessment have been slanted considerably toward the summative side. This tension between assessment for accountability and assessment to inform teaching strains instruction and educators' ability to use that information to design learning opportunities that help students develop deeper conceptual understanding. A substantive body of research indicates that formative and reflective assessment can significantly improve student learning. Biology Reflective Assessment Curriculum (BRAC) examines support provided for high school science students through assessment practices. This investigation incorporates the usage of reflective assessments as a guiding practice for differentiated instruction and student choice. Reflective assessment is a metacognitive strategy that promotes self-monitoring and evaluation. The goals of the curriculum are to promote self-efficacy and conceptual understanding in students learning biology through developing their metacognitive awareness. BRAC was implemented in a high school biology classroom. Data from assessments, metacognitive surveys, self-efficacy surveys, reflective journals, student work, a culminating task and field notes were used to evaluate the effectiveness of the curriculum. The results suggest that students who develop their metacognitive skills developed a deeper conceptual understanding and improved feelings of self-efficacy when they were engaged in a reflective assessment unit embedded with student choice. BRAC is a tool for teachers to use assessments to assist students in becoming metacognitive and to guide student choice in learning opportunities.

  16. US Competitiveness in Synthetic Biology.

    Science.gov (United States)

    Gronvall, Gigi Kwik

    2015-01-01

    Synthetic biology is an emerging technical field that aims to make biology easier to engineer; the field has applications in strategically important sectors for the US economy. While the United States currently leads in synthetic biology R&D, other nations are heavily investing in order to boost their economies, which will inevitably diminish the US leadership position. This outcome is not entirely negative--additional investments will expand markets--but it is critical that the US government take steps to remain competitive: There are applications from which the US population and economy may benefit; there are specific applications with importance for national defense; and US technical leadership will ensure that US experts have a leading role in synthetic biology governance, regulation, and oversight. Measures to increase competitiveness in S&T generally are broadly applicable for synthetic biology and should be pursued. However, the US government will also need to take action on fundamental issues that will affect the field's development, such as countering anti-GMO (genetically modified organism) sentiments and anti-GMO legislation. The United States should maintain its regulatory approach so that it is the product that is regulated, not the method used to create a product. At the same time, the United States needs to ensure that the regulatory framework is updated so that synthetic biology products do not fall into regulatory gaps. Finally, the United States needs to pay close attention to how synthetic biology applications may be governed internationally, such as through the Nagoya Protocol of the Convention on Biological Diversity, so that beneficial applications may be realized.

  17. US Competitiveness in Synthetic Biology

    Science.gov (United States)

    2015-01-01

    Synthetic biology is an emerging technical field that aims to make biology easier to engineer; the field has applications in strategically important sectors for the US economy. While the United States currently leads in synthetic biology R&D, other nations are heavily investing in order to boost their economies, which will inevitably diminish the US leadership position. This outcome is not entirely negative—additional investments will expand markets—but it is critical that the US government take steps to remain competitive: There are applications from which the US population and economy may benefit; there are specific applications with importance for national defense; and US technical leadership will ensure that US experts have a leading role in synthetic biology governance, regulation, and oversight. Measures to increase competitiveness in S&T generally are broadly applicable for synthetic biology and should be pursued. However, the US government will also need to take action on fundamental issues that will affect the field's development, such as countering anti-GMO (genetically modified organism) sentiments and anti-GMO legislation. The United States should maintain its regulatory approach so that it is the product that is regulated, not the method used to create a product. At the same time, the United States needs to ensure that the regulatory framework is updated so that synthetic biology products do not fall into regulatory gaps. Finally, the United States needs to pay close attention to how synthetic biology applications may be governed internationally, such as through the Nagoya Protocol of the Convention on Biological Diversity, so that beneficial applications may be realized. PMID:26690379

  18. Functional quantum biology in photosynthesis and magnetoreception

    CERN Document Server

    Lambert, Neill; Cheng, Yuan-Chung; Li, Che-Ming; Chen, Guang-Yin; Nori, Franco

    2012-01-01

    Is there a functional role for quantum mechanics or coherent quantum effects in biological processes? While this question is as old as quantum theory, only recently have measurements on biological systems on ultra-fast time-scales shed light on a possible answer. In this review we give an overview of the two main candidates for biological systems which may harness such functional quantum effects: photosynthesis and magnetoreception. We discuss some of the latest evidence both for and against room temperature quantum coherence, and consider whether there is truly a functional role for coherence in these biological mechanisms. Finally, we give a brief overview of some more speculative examples of functional quantum biology including the sense of smell, long-range quantum tunneling in proteins, biological photoreceptors, and the flow of ions across a cell membrane.

  19. Correlation Effects in Biological Networks

    Directory of Open Access Journals (Sweden)

    A.A. Bagdasaryan

    2012-06-01

    Full Text Available Review of the complex network theory is presented and classification of such networks in accordance with the main statistical characteristics is considered. For the adjacency matrix of a real neural network the shortest distances for each pair of nodes as well as the node degree distribution and cluster coefficients are calculated. Comparison of the main statistical parameters with the random network is performed, and based on this, the conclusions about the correlation phenomena in biological system are made.

  20. Biological pest control in Mexico.

    Science.gov (United States)

    Williams, Trevor; Arredondo-Bernal, Hugo C; Rodríguez-del-Bosque, Luis A

    2013-01-01

    Mexico is a megadiverse country that forms part of the Mesoamerican biological corridor that connects North and South America. Mexico's biogeographical situation places it at risk from invasive exotic insect pests that enter from the United States, Central America, or the Caribbean. In this review we analyze the factors that contributed to some highly successful past programs involving classical biological control and/or the sterile insect technique (SIT). The present situation is then examined with reference to biological control, including SIT programs, targeted at seven major pests, with varying degrees of success. Finally, we analyze the current threats facing Mexico's agriculture industry from invasive pests that have recently entered the country or are about to do so. We conclude that despite a number of shortcomings, Mexico is better set to develop biological control-based pest control programs, particularly on an area-wide basis, than many other Latin American countries are. Classical and augmentative biological control and SIT-based programs are likely to provide effective and sustainable options for control of native and exotic pests, particularly when integrated into technology packages that meet farmers' needs across the great diversity of production systems in Mexico.

  1. Enhanced Nutrient Removal with Upflow Biological Aerated Filter for Reclaimed Water

    Institute of Scientific and Technical Information of China (English)

    WANG Hai-dong; PENG Yong-zhen; WANG Shu-ying; ZHANG Yan-ping

    2007-01-01

    A two-stage upflow biological aerated filter was designed as an advanced treatment process to optimize the operating parameters and study the correlative factors influencing the efficiency of nitrification, denitrification and phosphorus removal. The experimental results showed that the final effluent of the two-stage upflow biofilter process operated in series could meet the stringent limits of the reclaimed water for the total nitrogen of 2mg/L, and total phosphorus of 0.3mg/L. The high treatment efficiency allowed the reactor operating at very high hydraulic loadings and reaching nearly complete nitrification and denitrification.

  2. Biological warfare agents.

    Science.gov (United States)

    Pohanka, Miroslav; Kuca, Kamil

    2010-01-01

    Biological warfare agents are a group of pathogens and toxins of biological origin that can be potentially misused for military or criminal purposes. The present review attempts to summarize necessary knowledge about biological warfare agents. The historical aspects, examples of applications of these agents such as anthrax letters, biological weapons impact, a summary of biological warfare agents and epidemiology of infections are described. The last section tries to estimate future trends in research on biological warfare agents.

  3. Engineering parameters for expansion of MPT berths, Goa

    Digital Repository Service at National Institute of Oceanography (India)

    Jayakumar, S.; Chandramohan, P.; Jena, B.K.; Pednekar, P.S.

    Comprehensive program for a harbour development and management requires general and detailed information on the coastal environment including engineering characteristics in addition to physical, chemical and biological parameters. Mormugao Port...

  4. DCE Bio Detection System Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Lind, Michael A.; Batishko, Charles R.; Morgen, Gerald P.; Owsley, Stanley L.; Dunham, Glen C.; Warner, Marvin G.; Willett, Jesse A.

    2007-12-01

    The DCE (DNA Capture Element) Bio-Detection System (Biohound) was conceived, designed, built and tested by PNNL under a MIPR for the US Air Force under the technical direction of Dr. Johnathan Kiel and his team at Brooks City Base in San Antonio Texas. The project was directed toward building a measurement device to take advantage of a unique aptamer based assay developed by the Air Force for detecting biological agents. The assay uses narrow band quantum dots fluorophores, high efficiency fluorescence quenchers, magnetic micro-beads beads and selected aptamers to perform high specificity, high sensitivity detection of targeted biological materials in minutes. This final report summarizes and documents the final configuration of the system delivered to the Air Force in December 2008

  5. Estimating Cosmological Parameter Covariance

    CERN Document Server

    Taylor, Andy

    2014-01-01

    We investigate the bias and error in estimates of the cosmological parameter covariance matrix, due to sampling or modelling the data covariance matrix, for likelihood width and peak scatter estimators. We show that these estimators do not coincide unless the data covariance is exactly known. For sampled data covariances, with Gaussian distributed data and parameters, the parameter covariance matrix estimated from the width of the likelihood has a Wishart distribution, from which we derive the mean and covariance. This mean is biased and we propose an unbiased estimator of the parameter covariance matrix. Comparing our analytic results to a numerical Wishart sampler of the data covariance matrix we find excellent agreement. An accurate ansatz for the mean parameter covariance for the peak scatter estimator is found, and we fit its covariance to our numerical analysis. The mean is again biased and we propose an unbiased estimator for the peak parameter covariance. For sampled data covariances the width estimat...

  6. Aurora final report

    Energy Technology Data Exchange (ETDEWEB)

    Robert, Dross; Amedeo, Conti

    2013-12-06

    Final Technical report detailing the work done by Nuvera and its partners to fulfill the goals of the program "Transport Studies Enabling Efficiency Optimization of Cost-Competitive Fuel Cell Stacks" (a.k.a. AURORA)

  7. Final focus test beam

    Energy Technology Data Exchange (ETDEWEB)

    1991-03-01

    This report discusses the following: the Final Focus Test Beam Project; optical design; magnets; instrumentation; magnetic measurement and BPM calibration; mechanical alignment and stabilization; vacuum system; power supplies; control system; radiation shielding and personnel protection; infrastructure; and administration.

  8. Final focus nomenclature

    Energy Technology Data Exchange (ETDEWEB)

    Erickson, R.

    1986-08-08

    The formal names and common names for all devices in the final focus system of the SLC are listed. The formal names consist of a device type designator, microprocessor designator, and a four-digit unit number. (LEW)

  9. Transacsys PLC - Final Results

    CERN Multimedia

    2002-01-01

    Final results from Transacsys PLC. A subsidary of this company was set up to develop the CERN EDH system into a commercial product but incurred too much financial loss so the project was cancelled (1/2 page).

  10. WMO Marine Final Reports

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Final reports of the World Meteorological Organization (WMO) Commission for Marine Meteorology, Commission for Synoptic Meteorology, and Commission for Basic...

  11. Data breaches. Final rule.

    Science.gov (United States)

    2008-04-11

    This document adopts, without change, the interim final rule that was published in the Federal Register on June 22, 2007, addressing data breaches of sensitive personal information that is processed or maintained by the Department of Veterans Affairs (VA). This final rule implements certain provisions of the Veterans Benefits, Health Care, and Information Technology Act of 2006. The regulations prescribe the mechanisms for taking action in response to a data breach of sensitive personal information.

  12. CLIC Final Focus Studies

    CERN Document Server

    Tomás, R; Schulte, Daniel; Zimmermann, Frank

    2006-01-01

    The CLIC final focus system has been designed based on the local compensation scheme proposed by P. Raimondi and A. Seryi. However, there exist important chromatic aberrations that deteriorate the performance of the system. This paper studies the optimization of the final focus based on the computation of the higher orders of the map using MAD-X and PTC. The use of octupole tail folding to reduce the size of the halo in the locations with aperture limitations is also discussed.

  13. EFFECT OF MIXING CONDITIONS ON FLOCCULATION KINETICS OF WASTEWATERS CONTAINING PROTEINS AND OTHER BIOLOGICAL COMPOUNDS USING FIBROUS MATERIALS AND POLYELECTROLYTES

    Directory of Open Access Journals (Sweden)

    L.A. CHEN

    1998-12-01

    Full Text Available The application of a combined system of a polyelectrolyte, carboxymethyl cellulose (CMC, and highly fibrillated fibrous materials, cellulose triacetate fibrets (CTF, for the recovery of proteins and other biological compounds from model and actual biological systems has been demonstrated . In the present work, reaction batches were scaled-up to a one-liter agitated vessel, with a standard configuration. The effect of mixing conditions on the adsorption and flocculation process was studied. It was observed that flocculation time was very fast, occurring within the period of polymer addition. Long term shearing did not result in floc breakage and the values of percentage light transmission and protein concentration of the final filtrate remained the same during the incubation period. Increasing the shear rate resulted in improved process efficiency, up to an optimum value, above which performance was poorer. Perikinetic and orthokinetic rate parameters were calculated and results analyzed in view of these parameters.

  14. Determination of the dose of gamma radiation sterilization for assessment of biological parameters of male Ceratitis capitada (Diptera: Tephritidae), tsl - Vienna 8 strain; Determinacao da dose de radiacao gama esterilizante pela avaliacao dos parametros biologicos de machos de Ceratitis capitata (Diptera: Tephritidae), linhagem tsl - Vienna 8

    Energy Technology Data Exchange (ETDEWEB)

    Rocha, Aline Cristina Pereira da

    2011-07-01

    The Vienna-8, tsl (temperature sensitive lethal) strain of Ceratitis capitata, by presenting mutations that facilitate the mass rearing and release only of sterile males in the field, has been used in (Sterile Insect Technique) programmes. The objective of this study was to determine the radiation dose that provides the highest level of sterility for Vienna-8, tsl males assessing their biological parameters that indicate the quality of sterile males to be released. Brown pupae (males) of the tsl strain were obtained from the mass rearing of the Food Irradiation and Radio entomology laboratory of CENA/USP, and they were irradiated (with gamma radiation - {sup 60}Co) 24 hours before the emergence at rates of 0, 30, 60, 90 and 120 Gy. The determination of the sterilizing dose was based on fertility of sexually mature females of the bisexual strain and not irradiated, mated with males of different treatments. Eggs were collected daily during 6 days, were counted and it was possible to estimate fecundity, and assess the hatching rate. The emergence and flight ability were determined by following the protocol of quality control manual for FAO/IAEA/USDA (2003). To assess the longevity under nutritional stress, the insects were kept a period of 48 h after emergence in the absence of water and food, and after this period, mortality was recorded. The size of the testes (left and right) was obtained by dissecting irradiated and non-irradiated males at the eighth day of life, and measure the testes in an ocular micrometer, considering the maximum length and width of each sample. To determine the sperm number was necessary to dissect the males and break their testicles. No difference was observed in emergence rate, flight ability and longevity of irradiated and non-irradiated males, nor in the fecundity of females mated with males of different treatments. The sterilizing dose that resulted in lower fertility of females was 120 Gy, with 1.5% hatching. Considering the parameters

  15. EUD-based biological optimization for carbon ion therapy

    Energy Technology Data Exchange (ETDEWEB)

    Brüningk, Sarah C., E-mail: sarah.brueningk@icr.ac.uk; Kamp, Florian; Wilkens, Jan J. [Department of Radiation Oncology, Technische Universität München, Klinikum rechts der Isar, Ismaninger Str. 22, München 81675, Germany and Physik-Department, Technische Universität München, James-Franck-Str. 1, Garching 85748 (Germany)

    2015-11-15

    therapy, the optimization by biological objective functions resulted in slightly superior treatment plans in terms of final EUD for the organs at risk (OARs) compared to voxel-based optimization approaches. This observation was made independent of the underlying objective function metric. An absolute gain in OAR sparing was observed for quadratic objective functions, whereas intersecting DVHs were found for logistic approaches. Even for considerable under- or overestimations of the used effect- or dose–volume parameters during the optimization, treatment plans were obtained that were of similar quality as the results of a voxel-based optimization. Conclusions: EUD-based optimization with either of the presented concepts can successfully be applied to treatment plan optimization. This makes EUE-based optimization for carbon ion therapy a useful tool to optimize more specifically in the sense of biological outcome while voxel-to-voxel variations of the biological effectiveness are still properly accounted for. This may be advantageous in terms of computational cost during treatment plan optimization but also enables a straight forward comparison of different fractionation schemes or treatment modalities.

  16. Metales pesados en el riñón del delfín franciscana, Pontoporia blainvillei (Cetácea: Pontoporiidae y su relación con parámetros biológicos Heavy metals in kidney tissues of Franciscana dolphin, Pontoporia blainvillei (Cetacea: Pontoporiidae, and their relationship with biological parameters

    Directory of Open Access Journals (Sweden)

    María V Panebianco

    2011-11-01

    Full Text Available En este estudio se determinó los niveles de metales pesados (Cd, Pb, Zn, Cu, Cr y Ni en el tejido renal del delfín franciscana, Pontoporia blainvillei, y se estableció la influencia de los parámetros ecológicos y biológicos sobre la bioacumulación de estos elementos. Se analizaron muestras de 38 ejemplares colectados entre 2004 y 2010 en el sur de Buenos Aires, Argentina. La edad de los animales y el estado de madurez sexual se determinaron por métodos histológicos, y los niveles de metales pesados por Espectrofotometría de Absorción Atómica. No se determinaron diferencias significativas para las concentraciones de Zn, Cu y Cd entre ambos sexos. Los niveles de Cd presentaron diferencias según el estado de madurez sexual y se relacionaron positivamente con la longitud, peso corporal y edad. Los niveles de Cd, Cu y Zn resultaron menores a los informados en estudios previos realizados en el norte de Buenos Aires y Uruguay.Heavy metal (Cd, Pb, Zn, Cu, Cr,Ni concentrations were determined in the kidney tissue of the Franciscana dolphin, Pontoporia blainvillei, and the influence of ecological and biological parameters on the bioaccumulation of these elements was established. Samples from 38 specimens, collected between 2004 and 2010 off southern Buenos Aires, Argentina, were analyzed. Histological methods were used to determine both the age and sexual maturity of the animals. Heavy metal concentrations were measured by atomic absorption spectrophotometry. No significant differences were found by sex for Zn, Cu, and Cd. However, Cd levels differed between maturity stages and were positively related to length, body weight, and age. The Cd, Cu, and Zn levels reported here in were lower than those included in previous studies done off northern Buenos Aires and Uruguay.

  17. Influencia de Especies Arbóreas Implantadas sobre Parámetros Biológicos y Bioquímicos en un Suelo Forestal de Chubut, Argentina Influence of Implanted tree Species on Biological and Biochemical Parameters in a Forest soil of Chubut, Argentina

    Directory of Open Access Journals (Sweden)

    Diana N Effron

    2012-01-01

    Full Text Available Se estudió la influencia de algunas especies forestales sobre propiedades biológicas y bioquímicas de un suelo, con el propósito de contribuir a establecer criterios que logren un desarrollo sustentable para un sistema forestal. El sitio de estudio es un suelo forestal de Chubut, en la Patagonia Argentina. Se tomaron muestras superficiales de suelo de tres parcelas con una especie dominante cada una: Roble (Quercus robur, Fresno (Fraxinus excelsior L. y Pino radiata (Pinus radiata D. Don.. En ellas se determinaron carbono de respiración, actividad deshidrogenasa, actividad fosfatasa ácida, número de bacterias totales y amilolíticas, actinomicetes y hongos totales, mientras que en las hojas se determinó fósforo. Los resultados mostraron diferencias importantes de estos parámetros para las diferentes especies estudiadas, diferencias que son explicadas por la composición química de las diferentes especies vegetales.The influence of some tree species on biological and biochemical properties of a forest soil was studied with the purpose of establishing criteria to achieve a sustainable development of a forest system. The study site is a forest soil of Chubut, in the Argentinean Patagonia. Surface soil samples were taken of three plots with a dominant species each one: Oak (Quercus robur, Ash (Fraxinus excelsior L. and Radiata Pine (Pinus radiata D. Don.. Microbial respiration, dehydrogenase and acid phosphatase activities, counts of aerobic and amylolytic bacteria, actinomyces and fungi were determined in soil samples, while phosphorous was determines in leaves. The results showed important differences of these parameters for the different species considered in the study, differences that are explained by the different chemical composition of the vegetal species.

  18. Biological conversion system

    Science.gov (United States)

    Scott, C.D.

    A system for bioconversion of organic material comprises a primary bioreactor column wherein a biological active agent (zymomonas mobilis) converts the organic material (sugar) to a product (alcohol), a rejuvenator column wherein the biological activity of said biological active agent is enhanced, and means for circulating said biological active agent between said primary bioreactor column and said rejuvenator column.

  19. Sustainable operation of a biological wastewater treatment plant

    Science.gov (United States)

    Trikoilidou, E.; Samiotis, G.; Bellos, D.; Amanatidou, E.

    2016-11-01

    The sustainable operation of a biological wastewater treatment plant is significantly linked to its removal efficiency, cost of sludge management, energy consumption and monitoring cost. The biological treatment offers high organic removal efficiency, it also entails significant sludge production, which contains active (live) and inactive (dead) microorganisms and must be treated prior to final disposal, in order to prevent adverse impact on public health and environment. The efficiency of the activated sludge treatment process is correlated to an efficient solid-liquid separation, which is strongly depended on the biomass settling properties. The most commonly encountered settling problems in a wastewater treatment plant, which are usually associated with operating conditions and specific microorganisms growth, are sludge bulking, floating sludge, pin point flocs and straggler flocs. Sustainable management of sludge and less energy consumption are the two principal aspects that determine the operational cost of wastewater treatment plants. Sludge treatment and management accumulate more than 50% of the operating cost. Aerobic wastewater treatment plants have high energy requirements for covering the needs of aeration and recirculations. In order to ensure wastewater treatment plants’ effective operation, a large number of physicochemical parameters have to be monitored, thus further increasing the operational cost. As the operational parameters are linked to microbial population, a practical way of wastewater treatment plants’ controlling is the microscopic examination of sludge, which is proved to be an important tool for evaluating plants’ performance and assessing possible problems and symptoms. This study presents a biological wastewater treatment plant with almost zero biomass production, less energy consumption and a practical way for operation control through microbial manipulation and microscopic examination.

  20. An overview of biological processes and their potential for CO2 capture.

    Science.gov (United States)

    Goli, Amin; Shamiri, Ahmad; Talaiekhozani, Amirreza; Eshtiaghi, Nicky; Aghamohammadi, Nasrin; Aroua, Mohamed Kheireddine

    2016-12-01

    The extensive amount of available information on global warming suggests that this issue has become prevalent worldwide. Majority of countries have issued laws and policies in response to this concern by requiring their industrial sectors to reduce greenhouse gas emissions, such as CO2. Thus, introducing new and more effective treatment methods, such as biological techniques, is crucial to control the emission of greenhouse gases. Many studies have demonstrated CO2 fixation using photo-bioreactors and raceway ponds, but a comprehensive review is yet to be published on biological CO2 fixation. A comprehensive review of CO2 fixation through biological process is presented in this paper as biological processes are ideal to control both organic and inorganic pollutants. This process can also cover the classification of methods, functional mechanisms, designs, and their operational parameters, which are crucial for efficient CO2 fixation. This review also suggests the bio-trickling filter process as an appropriate approach in CO2 fixation to assist in creating a pollution-free environment. Finally, this paper introduces optimum designs, growth rate models, and CO2 fixation of microalgae, functions, and operations in biological CO2 fixation.

  1. Classification of hydrological parameter sensitivity and evaluation of parameter transferability across 431 US MOPEX basins

    Science.gov (United States)

    Ren, Huiying; Hou, Zhangshuan; Huang, Maoyi; Bao, Jie; Sun, Yu; Tesfa, Teklu; Ruby Leung, L.

    2016-05-01

    The Community Land Model (CLM) represents physical, chemical, and biological processes of the terrestrial ecosystems that interact with climate across a range of spatial and temporal scales. As CLM includes numerous sub-models and associated parameters, the high-dimensional parameter space presents a formidable challenge for quantifying uncertainty and improving Earth system predictions needed to assess environmental changes and risks. This study aims to evaluate the potential of transferring hydrologic model parameters in CLM through sensitivity analyses and classification across watersheds from the Model Parameter Estimation Experiment (MOPEX) in the United States. The sensitivity of CLM-simulated water and energy fluxes to hydrological parameters across 431 MOPEX basins are first examined using an efficient stochastic sampling-based sensitivity analysis approach. Linear, interaction, and high-order nonlinear impacts are all identified via statistical tests and stepwise backward removal parameter screening. The basins are then classified according to their parameter sensitivity patterns (internal attributes), as well as their hydrologic indices/attributes (external hydrologic factors) separately, using Principal component analysis (PCA) and expectation-maximization (EM) - based clustering approach. Similarities and differences among the parameter sensitivity-based classification system (S-Class), the hydrologic indices-based classification (H-Class), and the Koppen climate classification systems (K-Class) are discussed. Within each parameter sensitivity-based classification system (S-Class) with similar parameter sensitivity characteristics, similar inversion modeling setups can be used for parameter calibration, and the parameters and their contribution or significance to water and energy cycling may also be more transferrable. This classification study provides guidance on identifiable parameters, and on parameterization and inverse model design for CLM but the

  2. Lumped-parameter models

    DEFF Research Database (Denmark)

    Ibsen, Lars Bo; Liingaard, Morten

    A lumped-parameter model represents the frequency dependent soil-structure interaction of a massless foundation placed on or embedded into an unbounded soil domain. The lumped-parameter model development have been reported by (Wolf 1991b; Wolf 1991a; Wolf and Paronesso 1991; Wolf and Paronesso 19...

  3. Label-Free Biosensors for Cell Biology

    Directory of Open Access Journals (Sweden)

    Ye Fang

    2011-01-01

    Full Text Available Label-free biosensors for studying cell biology have finally come of age. Recent developments have advanced the biosensors from low throughput and high maintenance research tools to high throughput and low maintenance screening platforms. In parallel, the biosensors have evolved from an analytical tool solely for molecular interaction analysis to powerful platforms for studying cell biology at the whole cell level. This paper presents historical development, detection principles, and applications in cell biology of label-free biosensors. Future perspectives are also discussed.

  4. Synthetic biology: insights into biological computation.

    Science.gov (United States)

    Manzoni, Romilde; Urrios, Arturo; Velazquez-Garcia, Silvia; de Nadal, Eulàlia; Posas, Francesc

    2016-04-18

    Organisms have evolved a broad array of complex signaling mechanisms that allow them to survive in a wide range of environmental conditions. They are able to sense external inputs and produce an output response by computing the information. Synthetic biology attempts to rationally engineer biological systems in order to perform desired functions. Our increasing understanding of biological systems guides this rational design, while the huge background in electronics for building circuits defines the methodology. In this context, biocomputation is the branch of synthetic biology aimed at implementing artificial computational devices using engineered biological motifs as building blocks. Biocomputational devices are defined as biological systems that are able to integrate inputs and return outputs following pre-determined rules. Over the last decade the number of available synthetic engineered devices has increased exponentially; simple and complex circuits have been built in bacteria, yeast and mammalian cells. These devices can manage and store information, take decisions based on past and present inputs, and even convert a transient signal into a sustained response. The field is experiencing a fast growth and every day it is easier to implement more complex biological functions. This is mainly due to advances in in vitro DNA synthesis, new genome editing tools, novel molecular cloning techniques, continuously growing part libraries as well as other technological advances. This allows that digital computation can now be engineered and implemented in biological systems. Simple logic gates can be implemented and connected to perform novel desired functions or to better understand and redesign biological processes. Synthetic biological digital circuits could lead to new therapeutic approaches, as well as new and efficient ways to produce complex molecules such as antibiotics, bioplastics or biofuels. Biological computation not only provides possible biomedical and

  5. Translational environmental biology: cell biology informing conservation.

    Science.gov (United States)

    Traylor-Knowles, Nikki; Palumbi, Stephen R

    2014-05-01

    Typically, findings from cell biology have been beneficial for preventing human disease. However, translational applications from cell biology can also be applied to conservation efforts, such as protecting coral reefs. Recent efforts to understand the cell biological mechanisms maintaining coral health such as innate immunity and acclimatization have prompted new developments in conservation. Similar to biomedicine, we urge that future efforts should focus on better frameworks for biomarker development to protect coral reefs.

  6. Distributed Parameter Modelling Applications

    DEFF Research Database (Denmark)

    2011-01-01

    sands processing. The fertilizer granulation model considers the dynamics of MAP-DAP (mono and diammonium phosphates) production within an industrial granulator, that involves complex crystallisation, chemical reaction and particle growth, captured through population balances. A final example considers...

  7. Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Bult Carol J.

    2003-11-24

    The results of the DOE-funded Mouse Genome Sequence (MGS) project include a significant enhancement in the capacity of the community to connect biological knowledge with the mouse genome sequence in a comparative context. The resources developed as the result of the activities of the MGS project staff are used extensively by both individual researchers and other informatics groups.

  8. Nanoplasmonic and Microfluidic Devices for Biological Sensing

    KAUST Repository

    Perozziello, G.

    2017-02-16

    In this chapter we report about recent advances on the development and application of 2D and 3D plasmonic nanostructures used for sensing of biological samples by Raman spectroscopy at unprecedented resolution of analysis. Besides, we explain how the integration of these nanodevices in a microfluidic apparatus can simplify the analysis of biological samples. In the first part we introduce and motivate the convenience of using nanoplasmonic enhancers and Raman spectroscopy for biological sensing, describing the phenomena and the current approaches to fabricate nanoplasmonic structures. In the second part, we explain how specific multi-element devices produce the optimal enhancement of the Raman scattering. We report cases where biological sensing of DNA was performed at few molecules level with nanometer spatial resolutions. Finally, we show an example of microfluidic device integrating plasmonic nanodevices to sort and drive biological samples, like living cells, towards the optical probe in order to obtain optimal conditions of analysis.

  9. Computational Systems Chemical Biology

    OpenAIRE

    Oprea, Tudor I.; Elebeoba E. May; Leitão, Andrei; Tropsha, Alexander

    2011-01-01

    There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007).

  10. Monitoring of Biological Nitrogen Removal in Tannery Wastewater Using a Sequencing Batch Reactor

    Directory of Open Access Journals (Sweden)

    Carrasquero-Ferrer Sedolfo José

    2014-04-01

    Full Text Available The objective of this research was to relate the biological nitrogen removal in tannery wastewater with profiles of pH, alkalinity and redox potential (ORP using a sequencing batch reactor (SBR with a working volume of 2 L. The reactor worked under two operational sequences: anoxic-aerobic-anoxic (Ax/Ae/Ax and aerobic-anoxic (Ae/Ax, which were combined with two cell retention times (CRT (15 and 25 days, with an operation cycle time (OCT of 11 hours. The profiles were performed by measuring each 15 minutes the following parameters: pH, dissolved oxygen (DO, ORP, and each hour the parameters: total alkalinity, total chemical oxygen demand (DQOT, soluble chemical oxygen demand (DQOS, total Kjeldahl nitrogen (TKN, nitrite (NO2-, nitrate (NO3- and ammonia nitrogen (N-NH4+. Alkalinity and ORP profile were excellent indicators of the processes of biological nitrogen removal. However, pH could not be used as a control parameter, due to the buffering capacity of tannery wastewater. Finally, this research work showed that alkalinity and ORP values can be used as on-line control parameters to monitor the evolution of the nitrogen removal in tannery wastewater (nitrification and denitrification processes.

  11. Education science and biological anthropology.

    Science.gov (United States)

    Krebs, Uwe

    2014-01-01

    This contribution states deficits and makes proposals in order to overcome them. First there is the question as to why the Biological Anthropology--despite all its diversifications--hardly ever deals with educational aspects of its subject. Second it is the question as to why Educational Science neglects or even ignores data of Biological Anthropology which are recognizably important for its subject. It is postulated that the stated deficits are caused by several adverse influences such as, the individual identity of each of the involved single sciences; aspects of the recent history of the German Anthropology; a lack of conceptual understanding of each other; methodological differences and, last but not least, the structure of the universities. The necessity to remedy this situation was deduced from two groups of facts. First, more recent data of the Biological Anthropology (e.g. brain functions and learning, sex specificity and education) are of substantial relevance for the Educational Science. Second, the epistemological requirements of complex subjects like education need interdisciplinary approaches. Finally, a few suggestions of concrete topics are given which are related to both, Educational Science and Biological Anthropology.

  12. Biological signals classification and analysis

    CERN Document Server

    Kiasaleh, Kamran

    2015-01-01

    This authored monograph presents key aspects of signal processing analysis in the biomedical arena. Unlike wireless communication systems, biological entities produce signals with underlying nonlinear, chaotic nature that elude classification using the standard signal processing techniques, which have been developed over the past several decades for dealing primarily with standard communication systems. This book separates what is random from that which appears to be random, and yet is truly deterministic with random appearance. At its core, this work gives the reader a perspective on biomedical signals and the means to classify and process such signals. In particular, a review of random processes along with means to assess the behavior of random signals is also provided. The book also includes a general discussion of biological signals in order to demonstrate the inefficacy of the well-known techniques to correctly extract meaningful information from such signals. Finally, a thorough discussion of recently ...

  13. Supersymmetry Parameter Analysis

    CERN Document Server

    Kalinowski, Jan

    2002-01-01

    Supersymmetric particles can be produced copiously at future colliders. From the high-precision data taken at e+e- linear colliders, TESLA in particular, and combined with results from LHC, and CLIC later, the low-energy parameters of the supersymmetric model can be determined. Evolving the parameters from the low-energy scale to the high-scale by means of renormalization group techniques the fundamental supersymmetry parameters at the high scale, GUT or Planck, can be reconstructed to reveal the origin of supersymmetry breaking.

  14. Magnetic S-parameter

    DEFF Research Database (Denmark)

    Sannino, Francesco

    2010-01-01

    We propose a direct test of the existence of gauge duals for nonsupersymmetric asymptotically free gauge theories developing an infrared fixed point by computing the S-parameter in the electric and dual magnetic description. In particular we show that at the lower bound of the conformal window...... the magnetic S-parameter, i.e. the one determined via the dual magnetic gauge theory, assumes a simple expression in terms of the elementary magnetic degrees of freedom. The results further support our recent conjecture of the existence of a universal lower bound on the S parameter and indicates...

  15. [Biology molecular of glioblastomas].

    Science.gov (United States)

    Franco-Hernández, C; Martínez-Glez, V; Rey, J A

    2007-10-01

    Glioblastomas, the most frequent and malignant human brain tumors, may develop de novo (primary glioblastoma) or by progression from low-grade or anapalsic astrocytoma (secondary glioblastoma). The molecular alteration most frequent in these tumor-like types is the loss of heterozygosity on chromosome 10, in which several genes have been identified as tumors suppressor. The TP53/MDM2/P14arf and CDK4/RB1/ P16ink4 genetic pathways involved in cycle control are deregulated in the majority of gliomas as well as genes that promote the cellular division, EGFR. Finally the increase of growth and angiogenics factors is also involved in the development of glioblastomas. One of the objectives of molecular biology in tumors of glial ancestry is to try to find the genetic alterations that allow to approach better the classification of glioblastomas, its evolution prediction and treatment. The new pathmolecular classification of gliomas should improve the old one, especially being concerned about the oncogenesis and heterogeneity of these tumors. It is desirable that this classification had clinical applicability and integrates new molecular findings with some known histological features with pronostic value. In this paper we review the most frequent molecular mechanisms involved in the patogenesis of glioblastomas.

  16. The dawn of mathematical biology

    CERN Document Server

    Hoffmann, Daniel Sander

    2015-01-01

    In this paper I describe the early development of the so-called mathematical biophysics, as conceived by Nicolas Rashevsky back in the 1920's, as well as his latter idealization of a "relational biology". I also underline that the creation of the journal "The Bulletin of Mathematical Biophysics" was instrumental in legitimating the efforts of Rashevsky and his students, and I finally argue that his pioneering efforts, while still largely unacknowledged, were vital for the development of important scientific contributions, most notably the McCulloch-Pitts model of neural networks.

  17. Bioinspiration: applying mechanical design to experimental biology.

    Science.gov (United States)

    Flammang, Brooke E; Porter, Marianne E

    2011-07-01

    The production of bioinspired and biomimetic constructs has fostered much collaboration between biologists and engineers, although the extent of biological accuracy employed in the designs produced has not always been a priority. Even the exact definitions of "bioinspired" and "biomimetic" differ among biologists, engineers, and industrial designers, leading to confusion regarding the level of integration and replication of biological principles and physiology. By any name, biologically-inspired mechanical constructs have become an increasingly important research tool in experimental biology, offering the opportunity to focus research by creating model organisms that can be easily manipulated to fill a desired parameter space of structural and functional repertoires. Innovative researchers with both biological and engineering backgrounds have found ways to use bioinspired models to explore the biomechanics of organisms from all kingdoms to answer a variety of different questions. Bringing together these biologists and engineers will hopefully result in an open discourse of techniques and fruitful collaborations for experimental and industrial endeavors.

  18. Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, Chris [Altamont Environmental, Inc.

    2014-11-13

    The project, Capital Investment to Fund Equipment Purchases and Facility Modifications to Create a Sustainable Future for EnergyXchange served to replace landfill gas energy with alternative energy resources, primarily solar and wood waste. This is the final project closeout report.

  19. CAFE Project : final report

    NARCIS (Netherlands)

    Weber, A.; Carter, R.; Stanford, C.J.; Weber, A.

    2003-01-01

    [MAS E-0302] This is the final public report of the CAFE project (ESPRIT 7023). CAFE developed a secure conditional access architecture and implemented a multi-currency electronic purse system based on smart cards and infrared wallets. The electronic purse was tested in user trials at the European C

  20. MAGGIE Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Siuzdak, Gary

    2012-11-05

    The mass spectrometry component of the MAGGIE effort included the generation of novel GTL technologies and comprehensive characterization to elucidate functional relationships and pathways. Toward this goal Component 4 has generated unique surface-based mass spectrometry and bioinformatic technologies as well as helped identified new biological interactions. The informatics and analytical technology platforms that we developed as well as the biochemistry that it has been developed for, are presented in detail in the attached document.

  1. DHS Internship Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Tew, Karen [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2014-09-01

    I spent the last ten weeks working in the Systems Biology department at Sandia National Laboratories in Livermore, CA. Under the direction of Zachary Bent, I helped do preliminary testing/optimization of a vacuum-driven, capture-based system for pathogen RNA transcript enrichment. I also worked on a project to create mutant Yersinia enterocolitica strains in order to test which genes are involved in intracellular pathogen virulence, as well as sequencing several Klebsiella pneumoniae samples for use by a bioinformaticist.

  2. Structural Biology for A-Level Students

    Science.gov (United States)

    Philip, Judith

    2013-01-01

    The relationship between the structure and function of proteins is an important area in biochemistry. Pupils studying A-level Biology are introduced to the four levels of protein structure (primary, secondary, tertiary and quaternary) and how these can be used to describe the progressive folding of a chain of amino acid residues to a final,…

  3. NUMERICALLY SOLVING PERIODICALLY PERTURBED CONSERVATIVE SYSTEMS BY PARAMETER EMBEDDING METHODS

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The parameter embedding method is applied for numerically solving the perturbed conservative systems. By means of Newtonian iteration, a simple algorithm has been constructed. Finally, the convergence of the iteration is proved.

  4. System biology of gene regulation.

    Science.gov (United States)

    Baitaluk, Michael

    2009-01-01

    A famous joke story that exhibits the traditionally awkward alliance between theory and experiment and showing the differences between experimental biologists and theoretical modelers is when a University sends a biologist, a mathematician, a physicist, and a computer scientist to a walking trip in an attempt to stimulate interdisciplinary research. During a break, they watch a cow in a field nearby and the leader of the group asks, "I wonder how one could decide on the size of a cow?" Since a cow is a biological object, the biologist responded first: "I have seen many cows in this area and know it is a big cow." The mathematician argued, "The true volume is determined by integrating the mathematical function that describes the outer surface of the cow's body." The physicist suggested: "Let's assume the cow is a sphere...." Finally the computer scientist became nervous and said that he didn't bring his computer because there is no Internet connection up there on the hill. In this humorous but explanatory story suggestions proposed by theorists can be taken to reflect the view of many experimental biologists that computer scientists and theorists are too far removed from biological reality and therefore their theories and approaches are not of much immediate usefulness. Conversely, the statement of the biologist mirrors the view of many traditional theoretical and computational scientists that biological experiments are for the most part simply descriptive, lack rigor, and that much of the resulting biological data are of questionable functional relevance. One of the goals of current biology as a multidisciplinary science is to bring people from different scientific areas together on the same "hill" and teach them to speak the same "language." In fact, of course, when presenting their data, most experimentalist biologists do provide an interpretation and explanation for the results, and many theorists/computer scientists aim to answer (or at least to fully describe

  5. Tsonis final project report

    Energy Technology Data Exchange (ETDEWEB)

    Duane, Greg [University of Wisconsin-Milwaukee, WI (United States); Tsonis, Anastasios [University of Wisconsin-Milwaukee, WI (United States); Kocarev, Ljupco [University of Wisconsin-Milwaukee, WI (United States); Tribbia, Joseph [University of Wisconsin-Milwaukee, WI (United States)

    2014-11-20

    This collaborative reserach has several components but the main idea is that when imperfect copies of a given nonlinear dynamical system are coupled, they may synchronize for some set of coupling parameters. This idea is to be tested for several IPCC-like models each one with its own formulation and representing an “imperfect” copy of the true climate system. By computing the coupling parameters, which will lead the models to a synchronized state, a consensus on climate change simulations may be achieved.

  6. Inference for ordered parameters in multinomial distributions

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    This paper discusses inference for ordered parameters of multinomial distributions. We first show that the asymptotic distributions of their maximum likelihood estimators (MLEs) are not always normal and the bootstrap distribution estimators of the MLEs can be inconsistent. Then a class of weighted sum estimators (WSEs) of the ordered parameters is proposed. Properties of the WSEs are studied, including their asymptotic normality. Based on those results, large sample inferences for smooth functions of the ordered parameters can be made. Especially, the confidence intervals of the maximum cell probabilities are constructed. Simulation results indicate that this interval estimation performs much better than the bootstrap approaches in the literature. Finally, the above results for ordered parameters of multinomial distributions are extended to more general distribution models.

  7. [Hemodialysis with biological object].

    Science.gov (United States)

    Eventov, V L; Maksimenko, V A; Zhidkov, I L; Andrianova, M Iu

    2005-01-01

    The essence of the method of biodialysis (hemodialysis with biological object) developed and suggested by the authors for clinical use consists in that the healthy organism exerts, through a system of mass transfer, a therapeutic action on the sick organism. Blood from the affected and healthy organisms is perfused through individual mass exchangers (dialyzers, hemodiafilters and hemofilters), which are hydraulically connected by a circulating transport medium. Metabolites that accumulate in blood of the affected organism diffuse into the transport medium and, from there, into blood of the healthy organism, which metabolizes them. The reverse process occurs simultaneously: substances, whose concentration in blood of the sick organism is less versus the healthy organism, diffuse from blood of the healthy organism to blood of patient. The method suggested by us can be used in clinical practice for normalizing a variety of parameters in patients with hepatic and renal insufficiency. Besides, a number of substances can be transferred from the healthy donor to patient in the process of biodialysis, which opens promising potentialities for the treatment of many diseases.

  8. Stable States of Biological Organisms

    CERN Document Server

    Yukalov, V I; Yukalova, E P; Henry, J -Y; Cobb, J P

    2009-01-01

    A novel model of biological organisms is advanced, treating an organism as a self-consistent system subject to a pathogen flux. The principal novelty of the model is that it describes not some parts, but a biological organism as a whole. The organism is modeled by a five-dimensional dynamical system. The organism homeostasis is described by the evolution equations for five interacting components: healthy cells, ill cells, innate immune cells, specific immune cells, and pathogens. The stability analysis demonstrates that, in a wide domain of the parameter space, the system exhibits robust structural stability. There always exist four stable stationary solutions characterizing four qualitatively differing states of the organism: alive state, boundary state, critical state, and dead state.

  9. Synthetic biology, inspired by synthetic chemistry.

    Science.gov (United States)

    Malinova, V; Nallani, M; Meier, W P; Sinner, E K

    2012-07-16

    The topic synthetic biology appears still as an 'empty basket to be filled'. However, there is already plenty of claims and visions, as well as convincing research strategies about the theme of synthetic biology. First of all, synthetic biology seems to be about the engineering of biology - about bottom-up and top-down approaches, compromising complexity versus stability of artificial architectures, relevant in biology. Synthetic biology accounts for heterogeneous approaches towards minimal and even artificial life, the engineering of biochemical pathways on the organismic level, the modelling of molecular processes and finally, the combination of synthetic with nature-derived materials and architectural concepts, such as a cellular membrane. Still, synthetic biology is a discipline, which embraces interdisciplinary attempts in order to have a profound, scientific base to enable the re-design of nature and to compose architectures and processes with man-made matter. We like to give an overview about the developments in the field of synthetic biology, regarding polymer-based analogs of cellular membranes and what questions can be answered by applying synthetic polymer science towards the smallest unit in life, namely a cell.

  10. Resetting Biological Clocks

    Science.gov (United States)

    Winfree, Arthur T.

    1975-01-01

    Reports on experiments conducted on two biological clocks, in organisms in the plant and animal kingdoms, which indicate that biological oscillation can be arrested by a single stimulus of a definite strength delivered at the proper time. (GS)

  11. Biology is simple.

    Science.gov (United States)

    Newman, Tim

    2015-12-30

    This paper explores the potential for simplicity to reveal new biological understanding. Borrowing selectively from physics thinking, and contrasting with Crick's reductionist philosophy, the author argues that greater emphasis on simplicity is necessary to advance biology and its applications.

  12. Biology of Blood

    Science.gov (United States)

    ... here for the Professional Version Home Blood Disorders Biology of Blood Overview of Blood Resources In This ... Version. DOCTORS: Click here for the Professional Version Biology of Blood Overview of Blood Components of Blood ...

  13. Accurate kinetic parameter estimation during progress curve analysis of systems with endogenous substrate production.

    Science.gov (United States)

    Goudar, Chetan T

    2011-10-01

    We have identified an error in the published integral form of the modified Michaelis-Menten equation that accounts for endogenous substrate production. The correct solution is presented and the error in both the substrate concentration, S, and the kinetic parameters Vm , Km , and R resulting from the incorrect solution was characterized. The incorrect integral form resulted in substrate concentration errors as high as 50% resulting in 7-50% error in kinetic parameter estimates. To better reflect experimental scenarios, noise containing substrate depletion data were analyzed by both the incorrect and correct integral equations. While both equations resulted in identical fits to substrate depletion data, the final estimates of Vm , Km , and R were different and Km and R estimates from the incorrect integral equation deviated substantially from the actual values. Another observation was that at R = 0, the incorrect integral equation reduced to the correct form of the Michaelis-Menten equation. We believe this combination of excellent fits to experimental data, albeit with incorrect kinetic parameter estimates, and the reduction to the Michaelis-Menten equation at R = 0 is primarily responsible for the incorrectness to go unnoticed. However, the resulting error in kinetic parameter estimates will lead to incorrect biological interpretation and we urge the use of the correct integral form presented in this study.

  14. Estimation of optical parameters of highly scattering materials by time-of-flight spectroscopy

    Science.gov (United States)

    Plucinski, Jerzy

    2004-07-01

    Optical measurement methods are indispensable tool in biomedical research, providing invaluable information on optical properties of biological tissues. However, the application of these techniques is a big challenge, as most tissues are highly scattering materials whose optical properties cannot be measured in a straightforward way, due to multiple scattering of photons. Therefore, new optical measurement techniques and methods for highly scattering media are being developed to address this problem. One of the very promising techniques is time-of-flight spectroscopy. The paper presents problems encountered in reconstruction of basic optical parameters of tissues or other highly scattering materials from optical time-of-flight spectroscopy measurement data. To estimate the reconstruction accuracy of optical parameters (i.e. absorption coefficient, scattering coefficient, anisotropy factor and refractive index) the test data were generated by a computer program simulating light propagation in highly scattering material by Monte Carlo method. Following, a set of computer programs based on diffusion equation and optimization algorithms such as simplex method and genetic method were used to reconstruct optical parameters from the test data. Finally, by comparing reconstructed optical parameters with those used for generation of the test data, the accuracy of reconstructing algorithms it was estimated.

  15. Efeito de beauveria bassiana (bals. Vuillemin e Metarhizium anisopliae (metsch. sorokin nos parâmetros biológicos de trichogramma atopovirilia oatman & platner, 1983 (hymenoptera: trichogrammatidae Effect of Beauveria bassiana (Bals. Vuillemin and Metarhizium anisopliae (Metsch. Sorokin on the biological parameters of Trichogramma atopovirilia Oatman & Platner (Hymenoptera: Trichogrammatidae

    Directory of Open Access Journals (Sweden)

    Ricardo Antonio Polanczyk

    2010-12-01

    Full Text Available Dois experimentos foram realizados para avaliar o efeito de duas formulações comerciais à base de Beauveria bassiana (Bals. Vuillemin e Metarhizium anisopliae (Metsch., Sorokin sobre os parâmetros biológicos de Trichogramma atopovirilia Oatman & Platner, 1983. No primeiro experimento, cartelas com ovos de Spodoptera frugiperda, 1797 foram mergulhadas em suspensões preparadas com os produtos e, em seguida, colocadas à disposição dos parasitóides para oviposição, durante um período de 24 horas. No segundo, fêmeas do parasitóide foram alimentadas com uma solução mel e suspensão de conídios. Em ambos os experimentos as fêmeas mortas foram colocadas em uma câmara úmida para observar a esporulação dos fungos. Os tratamentos foram mantidos em câmara climatizada com temperatura de 25±1º C, umidade relativa de 70±10% e fotofase de 14 horas. Avaliou-se a longevidade e mortalidade dos adultos, índice de parasitismo, emergência do parasitóide, número de indivíduos por ovo e razão sexual dos descendentes. As formulações não interferiram nos parâmetros avaliados e não foi observada a esporulação do fungo no cadáver do parasitóide adulto. É possível inferir que T. atopovirilia e os fungos entomopatogênicos B. bassiana e M. anisopliae são compatíveis e podem ser empregados simultaneamente em programas de manejo integrado de S. frugiperda.Two bioassays were performed to evaluate the effect of two biopesticides based on Beauveria bassiana (Bals. Vuillemin and Metarhizium anisopliae (Metsch. Sorokin on the biological parameters of Trichogramma atopovirilia Oatman & Platner, 1983. In the first one, displays with S. frugiperda, 1797 eggs were dropped into the biopesticide suspension and offered to the parasitoid females for 24 hours. In the second one, parasitoid females were fed with a suspension containing honey and biopesticide suspension. In both cases, after the parasitoid death they were mantained into a humid

  16. Revisiting Cosmological parameter estimation

    CERN Document Server

    Prasad, Jayanti

    2014-01-01

    Constraining theoretical models with measuring the parameters of those from cosmic microwave background (CMB) anisotropy data is one of the most active areas in cosmology. WMAP, Planck and other recent experiments have shown that the six parameters standard $\\Lambda$CDM cosmological model still best fits the data. Bayesian methods based on Markov-Chain Monte Carlo (MCMC) sampling have been playing leading role in parameter estimation from CMB data. In one of the recent studies \\cite{2012PhRvD..85l3008P} we have shown that particle swarm optimization (PSO) which is a population based search procedure can also be effectively used to find the cosmological parameters which are best fit to the WMAP seven year data. In the present work we show that PSO not only can find the best-fit point, it can also sample the parameter space quite effectively, to the extent that we can use the same analysis pipeline to process PSO sampled points which is used to process the points sampled by Markov Chains, and get consistent res...

  17. Parameter Estimation Through Ignorance

    CERN Document Server

    Du, Hailiang

    2015-01-01

    Dynamical modelling lies at the heart of our understanding of physical systems. Its role in science is deeper than mere operational forecasting, in that it allows us to evaluate the adequacy of the mathematical structure of our models. Despite the importance of model parameters, there is no general method of parameter estimation outside linear systems. A new relatively simple method of parameter estimation for nonlinear systems is presented, based on variations in the accuracy of probability forecasts. It is illustrated on the Logistic Map, the Henon Map and the 12-D Lorenz96 flow, and its ability to outperform linear least squares in these systems is explored at various noise levels and sampling rates. As expected, it is more effective when the forecast error distributions are non-Gaussian. The new method selects parameter values by minimizing a proper, local skill score for continuous probability forecasts as a function of the parameter values. This new approach is easier to implement in practice than alter...

  18. MSSM without free parameters

    Science.gov (United States)

    Kitano, Ryuichiro; Motono, Ryuji; Nagai, Minoru

    2016-12-01

    It is often argued that the minimal supersymmetric standard model has O (100 ) free parameters, and the generic parameter region is already excluded by the null observation of the flavor and C P -violating processes as well as the constraints from the LHC experiments. This situation naturally leads us to consider the case where all the dangerous soft supersymmetry breaking terms, such as the scalar masses and scalar couplings, are absent, while only the unified gaugino mass term and the μ term are nonvanishing at the grand unification scale. We revisit this simple situation taking into account the observed Higgs boson mass, 125 GeV. Since the gaugino mass and the μ term are fixed in order to explain the Higgs boson and the Z boson masses, there is no free parameter left in this scenario. We find that there are three independent parameter sets that exist including ones which have not been discussed in the literature. We also find that the abundance of the dark matter can be explained by relic gravitinos which are nonthermally produced as decay products of the supersymmetry particles while satisfying constraints from big bang nucleosynthesis. We discuss the effects of the gravity mediation which generically gives a contribution to the soft terms of the order of the gravitino mass. It turns out that a newly found parameter set is preferable to explain the Higgs boson mass as well as the gravitino dark matter while satisfying the constraints from the electric dipole moments of the electron and the nucleon.

  19. Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Maxwell, Mike, J., P.E.

    2012-08-30

    The STI product is the Final Technical Report from ReliOn, Inc. for contract award DE-EE0000487: Recovery Act PEM Fuel Cell Systems Providing Emergency Reserve and Backup Power. The program covered the turnkey deployment of 431 ReliOn fuel cell systems at 189 individual sites for AT&T and PG&E with ReliOn functioning as the primary equipment supplier and the project manager. The Final Technical Report provides an executive level summary, a comparison of the actual accomplishments vs. the goals and objectives of the project, as well as a summary of the project activity from the contract award date of August 1, 2009 through the contract expiration date of December 31, 2011. Two photos are included in the body of the report which show hydrogen storage and bulk hydrogen refueling technologies developed as a result of this program.

  20. CMS Is Finally Completed

    CERN Multimedia

    2008-01-01

    Yet another step in the completion of the Large Hadron Collider was taken yesterday morning, as the final element of the Compact Muon Solenoid was lowered nearly 100 meters bellow ground. After more than eight years of work at the world's most powerful particle accelerator, scientists hope that they will be able to start initial experiments with the LHC until the end of this year.

  1. Designing synthetic biology.

    Science.gov (United States)

    Agapakis, Christina M

    2014-03-21

    Synthetic biology is frequently defined as the application of engineering design principles to biology. Such principles are intended to streamline the practice of biological engineering, to shorten the time required to design, build, and test synthetic gene networks. This streamlining of iterative design cycles can facilitate the future construction of biological systems for a range of applications in the production of fuels, foods, materials, and medicines. The promise of these potential applications as well as the emphasis on design has prompted critical reflection on synthetic biology from design theorists and practicing designers from many fields, who can bring valuable perspectives to the discipline. While interdisciplinary connections between biologists and engineers have built synthetic biology via the science and the technology of biology, interdisciplinary collaboration with artists, designers, and social theorists can provide insight on the connections between technology and society. Such collaborations can open up new avenues and new principles for research and design, as well as shed new light on the challenging context-dependence-both biological and social-that face living technologies at many scales. This review is inspired by the session titled "Design and Synthetic Biology: Connecting People and Technology" at Synthetic Biology 6.0 and covers a range of literature on design practice in synthetic biology and beyond. Critical engagement with how design is used to shape the discipline opens up new possibilities for how we might design the future of synthetic biology.

  2. BIOLOGICAL FOUNDATIONS OF LANGUAGE.

    Science.gov (United States)

    LENNEBERG, ERIC H.

    THE RELATIONSHIP BETWEEN BIOLOGY AND LANGUAGE IS EXPLORED IN THIS VOLUME. THE AUTHOR BELIEVES THAT "LANGUAGE IS THE MANIFESTATION OF SPECIES-SPECIFIC COGNITIVE PROPENSITIES. IT IS THE CONSEQUENCE OF THE BIOLOGICAL PECULIARITIES THAT MAKE A HUMAN TYPE OF COGNITION POSSIBLE." IN ATTEMPTING TO "REINSTATE THE CONCEPT OF THE BIOLOGICAL BASIS OF…

  3. Biology Myth-Killers

    Science.gov (United States)

    Lampert, Evan

    2014-01-01

    "Biology Myth-Killers" is an activity designed to identify and correct common misconceptions for high school and college introductory biology courses. Students identify common myths, which double as biology misconceptions, and use appropriate sources to share the "truth" about the myths. This learner-centered activity is a fun…

  4. Catarse e Final Feliz

    Directory of Open Access Journals (Sweden)

    Myriam Ávila

    2001-12-01

    Full Text Available Resumo: É a certeza de que nada mais – ou nada importante – pode acontecer após o final de um conto que permite o acontecimento da catarse. Se na maioria das narrativas existe algum tipo de dénouement, em algumas delas isso acontece de maneira especialmente satisfatória e afirmativa. O conto de fadas é uma dessas formas narrativas onde o efeito catártico é extremo e preenche objetivos específicos, de acordo com Bruno Bettelheim. Hollywood mimetizou essa forma como estratégia de sedução, iniciando a tradição do final feliz no cinema. A partir do conto de fadas Cinderela, em diferentes versões, juntamente com a animação homônima da Disney e ainda duas versões do filme Sabrina, será traçada aqui uma relação entre a catarse e o final feliz nos contos de fada, bem como seu uso pela indústria cultural. Palavras-chave: catarse, contos de fada, Hollywood

  5. Fundamental stellar parameters

    CERN Document Server

    Wittkowski, M

    2004-01-01

    I present a discussion of fundamental stellar parameters and their observational determination in the context of interferometric measurements with current and future optical/infrared interferometric facilities. Stellar parameters and the importance of their determination for stellar physics are discussed. One of the primary uses of interferometry in the field of stellar physics is the measurement of the intensity profile across the stellar disk, both as a function of position angle and of wavelength. High-precision fundamental stellar parameters are also derived by characterizations of binary and multiple system using interferometric observations. This topic is discussed in detail elsewhere in these proceedings. Comparison of observed spectrally dispersed center-to-limb intensity variations with models of stellar atmospheres and stellar evolution may result in an improved understanding of key phenomena in stellar astrophysics such as the precise evolutionary effects on the main sequence, the evolution of meta...

  6. Variations on tremor parameters

    Science.gov (United States)

    Boose, A.; Jentgens, Ch.; Spieker, S.; Dichgans, J.

    1995-03-01

    This paper describes our analysis procedure for long-term tremor EMG recordings, as well as three examples of applications. The description of the method focuses on how characteristics of the tremor (e.g. frequency, intensity, agonist-antagonist interaction) can be defined and calculated based on surface EMG data. The resulting quantitative characteristics are called ``tremor parameters.'' We discuss sinusoidally modulated, band-limited white noise as a model for pathological tremor-EMG, and show how the basic parameters can be extracted from this class of signals. The method is then applied to (1) estimate tremor severity in clinical studies, (2) quantify agonist-antagonist interaction, and (3) investigate the variations of the tremor parameters using simple methods from time-series analysis.

  7. Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    W. C. Griffith

    2007-01-01

    In this project we provide an example of how to develop multi-tiered models to go across levels of biological organization to provide a framework for relating results of studies of low doses of ionizing radiation. This framework allows us to better understand how to extrapolate laboratory results to policy decisions, and to identify future studies that will increase confidence in policy decisions. In our application of the conceptual Model we were able to move across multiple levels of biological assessment for rodents going from molecular to organism level for in vitro and in vivo endpoints and to relate these to human in vivo organism level effects. We used the rich literature on the effects of ionizing radiation on the developing brain in our models. The focus of this report is on disrupted neuronal migration due to radiation exposure and the structural and functional implications of these early biological effects. The cellular mechanisms resulting in pathogenesis are most likely due to a combination of the three mechanisms mentioned. For the purposes of a computational model, quantitative studies of low dose radiation effects on migration of neuronal progenitor cells in the cerebral mantle of experimental animals were used. In this project we were able to show now results from studies of low doses of radiation can be used in a multidimensional framework to construct linked models of neurodevelopment using molecular, cellular, tissue, and organ level studies conducted both in vitro and in vivo in rodents. These models could also be linked to behavioral endpoints in rodents which can be compared to available results in humans. The available data supported modeling to 10 cGy with limited data available at 5 cGy. We observed gradual but non-linear changes as the doses decreased. For neurodevelopment it appears that the slope of the dose response decreases from 25 cGy to 10 cGy. Future studies of neurodevelopment should be able to better define the dose response in

  8. Final Progress Report

    Energy Technology Data Exchange (ETDEWEB)

    Bernstein, Herbert J

    2012-02-06

    The BIOMOL grant was for 'Local System Support for PDB Biological Unit Search and Display' to augment Rasmol's [Bernstein 2000] [Sayle, Milner-White 1995] existing macromolecular display functions with new capabilities by taking advantage of recent increases in local computing power in order to move functionality that is now scattered among various local and remote systems into one local package. Work included new algorithms for molecular surface display, an extended format for Protein Data Bank Entries, work on issues relating to the integration of multiple diffraction images formats.

  9. Optomechanical parameter estimation

    CERN Document Server

    Ang, Shan Zheng; Bowen, Warwick P; Tsang, Mankei

    2013-01-01

    We propose a statistical framework for the problem of parameter estimation from a noisy optomechanical system. The Cram\\'er-Rao lower bound on the estimation errors in the long-time limit is derived and compared with the errors of radiometer and expectation-maximization (EM) algorithms in the estimation of the force noise power. When applied to experimental data, the EM estimator is found to have the lowest error and follow the Cram\\'er-Rao bound most closely. With its ability to estimate most of the system parameters, the EM algorithm is envisioned to be useful for optomechanical sensing, atomic magnetometry, and classical or quantum system identification applications in general.

  10. Schedulability Analysis for Java Finalizers

    DEFF Research Database (Denmark)

    Bøgholm, Thomas; Hansen, Rene Rydhof; Ravn, Anders P.;

    2010-01-01

    Java finalizers perform clean-up and finalisation of objects at garbage collection time. In real-time Java profiles the use of finalizers is either discouraged (RTSJ, Ravenscar Java) or even disallowed (JSR-302), mainly because of the unpredictability of finalizers and in particular their impact ...... programs. Finally, we extend the SARTS tool for automated schedulability analysis of Java bytecode programs to handle finalizers in a fully automated way.......Java finalizers perform clean-up and finalisation of objects at garbage collection time. In real-time Java profiles the use of finalizers is either discouraged (RTSJ, Ravenscar Java) or even disallowed (JSR-302), mainly because of the unpredictability of finalizers and in particular their impact...... on the schedulability analysis. In this paper we show that a controlled scoped memory model results in a structured and predictable execution of finalizers, more reminiscent of C++ destructors than Java finalizers. Furthermore, we incorporate finalizers into a (conservative) schedulability analysis for Predictable Java...

  11. Selection of Parameters in Ball-Spinning

    Institute of Scientific and Technical Information of China (English)

    Maosheng LI; Yongnian YAN; Shihong ZHANG; Dachang KANG

    2004-01-01

    Nowadays, with the development of spinning processes, more and more systematic research about spinning parameters has been published. Based on these results, a routing about how to select spinning parameters has been gradually formed. However, ball spinning, due to its own features plus research lack, is still unclear about its parameter selections. In addition, some manufacture-enterprises only notice the use of this technique whereas ignore the theory creation. The optimal parameters about the ball spinning although have been released from these enterprises but in fact not a helpful theory for other researchers and producers. Focus on selecting the parameters based on the trial-and-error, this article has carried a series of experiments to study the influence on the spinning working course from those parameters, especially the peeling phenomena, and the tube diameter bulging. An optimal graph of the working angle, the axial feeding rate, and the acceptable working course is put forward. Additionally, based on the theory of the minimal reduction rate, the selection of the ball diameter is finally described. Thus, it has given the rules to get the proper parameters in ball spinning.

  12. Final project report

    Energy Technology Data Exchange (ETDEWEB)

    Nitin S. Baliga and Leroy Hood

    2008-11-12

    The proposed overarching goal for this project was the following: Data integration, simulation and visualization will facilitate metabolic and regulatory network prediction, exploration, and formulation of hypotheses. We stated three specific aims to achieve the overarching goal of this project: (1) Integration of multiple levels of information such as mRNA and protein levels, predicted protein-protein interactions/associations and gene function will enable construction of models describing environmental response and dynamic behavior. (2) Flexible tools for network inference will accelerate our understanding of biological systems. (3) Flexible exploration and queries of model hypotheses will provide focus and reveal novel dependencies. The underlying philosophy of these proposed aims is that an iterative cycle of experiments, experimental design, and verification will lead to a comprehensive and predictive model that will shed light on systems level mechanisms involved in responses elicited by living systems upon sensing a change in their environment. In the previous years report we demonstrated considerable progress in development of data standards, regulatory network inference and data visualization and exploration. We are pleased to report that several manuscripts describing these procedures have been published in top international peer reviewed journals including Genome Biology, PNAS, and Cell. The abstracts of these manuscripts are given and they summarize our accomplishments in this project.

  13. Parameter Estimation of Partial Differential Equation Models

    KAUST Repository

    Xun, Xiaolei

    2013-09-01

    Partial differential equation (PDE) models are commonly used to model complex dynamic systems in applied sciences such as biology and finance. The forms of these PDE models are usually proposed by experts based on their prior knowledge and understanding of the dynamic system. Parameters in PDE models often have interesting scientific interpretations, but their values are often unknown and need to be estimated from the measurements of the dynamic system in the presence of measurement errors. Most PDEs used in practice have no analytic solutions, and can only be solved with numerical methods. Currently, methods for estimating PDE parameters require repeatedly solving PDEs numerically under thousands of candidate parameter values, and thus the computational load is high. In this article, we propose two methods to estimate parameters in PDE models: a parameter cascading method and a Bayesian approach. In both methods, the underlying dynamic process modeled with the PDE model is represented via basis function expansion. For the parameter cascading method, we develop two nested levels of optimization to estimate the PDE parameters. For the Bayesian method, we develop a joint model for data and the PDE and develop a novel hierarchical model allowing us to employ Markov chain Monte Carlo (MCMC) techniques to make posterior inference. Simulation studies show that the Bayesian method and parameter cascading method are comparable, and both outperform other available methods in terms of estimation accuracy. The two methods are demonstrated by estimating parameters in a PDE model from long-range infrared light detection and ranging data. Supplementary materials for this article are available online. © 2013 American Statistical Association.

  14. Band parameters of phosphorene

    DEFF Research Database (Denmark)

    Lew Yan Voon, L. C.; Wang, J.; Zhang, Y.;

    2015-01-01

    Phosphorene is a two-dimensional nanomaterial with a direct band-gap at the Brillouin zone center. In this paper, we present a recently derived effective-mass theory of the band structure in the presence of strain and electric field, based upon group theory. Band parameters for this theory...

  15. Response model parameter linking

    NARCIS (Netherlands)

    Barrett, Michelle Derbenwick

    2015-01-01

    With a few exceptions, the problem of linking item response model parameters from different item calibrations has been conceptualized as an instance of the problem of equating observed scores on different test forms. This thesis argues, however, that the use of item response models does not require

  16. Ovarian reserve parameters

    DEFF Research Database (Denmark)

    Bentzen, J G; Forman, Julie Lyng; Pinborg, Anja;

    2012-01-01

    was observed between duration of hormonal-contraception use and ovarian reserve parameters. No dose-response relation was found between the dose of ethinyloestradiol and AMH or AFC. This study indicates that ovarian reserve markers are lower in women using sex steroids for contraception. Thus, AMH...

  17. Computational systems chemical biology.

    Science.gov (United States)

    Oprea, Tudor I; May, Elebeoba E; Leitão, Andrei; Tropsha, Alexander

    2011-01-01

    There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology (SCB) (Nat Chem Biol 3: 447-450, 2007).The overarching goal of computational SCB is to develop tools for integrated chemical-biological data acquisition, filtering and processing, by taking into account relevant information related to interactions between proteins and small molecules, possible metabolic transformations of small molecules, as well as associated information related to genes, networks, small molecules, and, where applicable, mutants and variants of those proteins. There is yet an unmet need to develop an integrated in silico pharmacology/systems biology continuum that embeds drug-target-clinical outcome (DTCO) triplets, a capability that is vital to the future of chemical biology, pharmacology, and systems biology. Through the development of the SCB approach, scientists will be able to start addressing, in an integrated simulation environment, questions that make the best use of our ever-growing chemical and biological data repositories at the system-wide level. This chapter reviews some of the major research concepts and describes key components that constitute the emerging area of computational systems chemical biology.

  18. Quantum biological information theory

    CERN Document Server

    Djordjevic, Ivan B

    2016-01-01

    This book is a self-contained, tutorial-based introduction to quantum information theory and quantum biology. It serves as a single-source reference to the topic for researchers in bioengineering, communications engineering, electrical engineering, applied mathematics, biology, computer science, and physics. The book provides all the essential principles of the quantum biological information theory required to describe the quantum information transfer from DNA to proteins, the sources of genetic noise and genetic errors as well as their effects. Integrates quantum information and quantum biology concepts; Assumes only knowledge of basic concepts of vector algebra at undergraduate level; Provides a thorough introduction to basic concepts of quantum information processing, quantum information theory, and quantum biology; Includes in-depth discussion of the quantum biological channel modelling, quantum biological channel capacity calculation, quantum models of aging, quantum models of evolution, quantum models o...

  19. Parameter Estimation for a Computable General Equilibrium Model

    DEFF Research Database (Denmark)

    Arndt, Channing; Robinson, Sherman; Tarp, Finn

    . Second, it permits incorporation of prior information on parameter values. Third, it can be applied in the absence of copious data. Finally, it supplies measures of the capacity of the model to reproduce the historical record and the statistical significance of parameter estimates. The method is applied...

  20. Methodical errors of measurement of the human body tissues electrical parameters

    OpenAIRE

    Antoniuk, O.; Pokhodylo, Y.

    2015-01-01

    Sources of methodical measurement errors of immitance parameters of biological tissues are described. Modeling measurement errors of RC-parameters of biological tissues equivalent circuits into the frequency range is analyzed. Recommendations on the choice of test signal frequency for measurement of these elements is provided.

  1. Prometheus Project final report

    Science.gov (United States)

    Taylor, Randall

    2005-01-01

    This Final Report serves as an executive summary of the Prometheus Project's activities and deliverables from November 2002 through September 2005. It focuses on the challenges from a technical and management perspective, what was different and innovative about this project, and identifies the major options, decisions, and accomplishments of the Project team as a whole. However, the details of the activities performed by DOE NR and its contractors will be documented separately in accordance with closeout requirements of the DOE NR and consistent with agreements between NASA and NR.

  2. Service dogs. Final rule.

    Science.gov (United States)

    2012-09-05

    The Department of Veterans Affairs (VA) amends its regulations concerning veterans in need of service dogs. Under this final rule, VA will provide to veterans with visual, hearing, or mobility impairments benefits to support the use of a service dog as part of the management of such impairments. The benefits include assistance with veterinary care, travel benefits associated with obtaining and training a dog, and the provision, maintenance, and replacement of hardware required for the dog to perform the tasks necessary to assist such veterans.

  3. Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Sobecky, Patricia A; Taillefert, Martial

    2013-03-29

    This final technical report describes results and findings from a research project to examine the role of microbial phosphohydrolase enzymes in naturally occurring subsurface microorganisms for the purpose of promoting the immobilization of the radionuclide uranium through the production of insoluble uranium phosphate minerals. The research project investigated the microbial mechanisms and the physical and chemical processes promoting uranium biomineralization and sequestration in oxygenated subsurface soils. Uranium biomineralization under aerobic conditions can provide a secondary biobarrier strategy to immobilize radionuclides should the metal precipitates formed by microbial dissimilatory mechanisms remobilize due to a change in redox state.

  4. Assessment of Biological Kinetics in a Conventional Municipal WWTP by Means of the Oxygen Uptake Rate Method

    Directory of Open Access Journals (Sweden)

    Vincenzo Torretta

    2014-04-01

    Full Text Available Pollution control of surface water bodies requires stringent checks on wastewater treatment plants performances. The satisfactory operation of biological treatment, commonly performed by means of activated sludge processes, requires a number of controlling and monitoring procedures. Suitable respirometric techniques for the determination of the kinetic parameters that regulate biological processes have been implemented in order to achieve this aim. This paper describes the results of an experimental research carried out in a conventional Italian municipal wastewater treatment plant. Particularly, the research has been finalized to both evaluate the biological process for the removal of biodegradable pollutants, such as carbonaceous substrates and ammonia nitrogen, and to collect data in order to evaluate a possible plant upgrade. Heterotrophic and autotrophic biomass kinetic parameters have been examined using respirometric techniques based on oxygen uptake measurements. The research performed makes a valuable contribution toward verifying the reliability of the values proposed in the literature for some kinetic parameters, which have been commonly used for a long time.

  5. PARAMETER COORDINATION AND ROBUST OPTIMIZATION FOR MULTIDISCIPLINARY DESIGN

    Institute of Scientific and Technical Information of China (English)

    HU Jie; PENG Yinghong; XIONG Guangleng

    2006-01-01

    A new parameter coordination and robust optimization approach for multidisciplinary design is presented. Firstly, the constraints network model is established to support engineering change, coordination and optimization. In this model, interval boxes are adopted to describe the uncertainty of design parameters quantitatively to enhance the design robustness. Secondly, the parameter coordination method is presented to solve the constraints network model, monitor the potential conflicts due to engineering changes, and obtain the consistency solution space corresponding to the given product specifications. Finally, the robust parameter optimization model is established, and genetic arithmetic is used to obtain the robust optimization parameter. An example of bogie design is analyzed to show the scheme to be effective.

  6. Passive bloodstains: from an impact energy to a final dried pattern

    Science.gov (United States)

    Smith, Fiona; Brutin, David

    2016-11-01

    Tracking down the origin of a blood droplet present on a crime scene has become of major importance in bloodstain pattern analysis. Passive bloodstains are not yet well understood. Accordingly the purpose of this research is to provide new tools to forensic investigators in the analysis of bloodstains arising from blood droplets dripping naturally. The study aims to understand the link between the final dried pattern of a passive bloodstain and its impact energy. Currently no such tool exists, and no correlation has yet been proven. This research was therefore focusing on a new parameter, the thicker outer rim observed on the dried final pattern. To do so, we created several passive bloodstains with different impact energies. A correlation was highlighted between the inner diameter, the maximum spreading diameter, the initial diameter of a blood droplet and its impact energy. This correlation shows how the drying mechanism of a blood droplet is influenced by its impact energy as it alters the red blood cells dispersion inside the droplet. The biological deposit and the final dried pattern are subsequently modified. ANR funded project: D-Blood Project.

  7. Pathomics: Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Turteltaub, K W; Ascher, M; Langlois, R; Fodor, I; Kercher, J; Laughlin, K M; Nelson, D; Colston, W; Milanovich, F P

    2006-12-08

    Pathomics is a research project to explore the feasibility for developing biosignatures for early infectious disease detection in humans, particularly those that represent a threat from bioterrorism. Our goal is to use a science-based approach to better understand the underlying molecular basis of disease and to find sensitive, robust, and specific combinations of biological molecules (biosignatures) in the host that will indicate the presence of developing infection prior to overt symptoms (pre-syndromic). The ultimate goal is develop a national surveillance system for monitoring for the release and managing the consequences of a biothreat agent or an emerging disease. Developing the science for a more comprehensive understanding of the molecular basis of infectious disease and the development of biosignature-based diagnostics could help detect both emerging and engineered treats to humans.

  8. Lessons learned from quantitative dynamical modeling in systems biology.

    Directory of Open Access Journals (Sweden)

    Andreas Raue

    Full Text Available Due to the high complexity of biological data it is difficult to disentangle cellular processes relying only on intuitive interpretation of measurements. A Systems Biology approach that combines quantitative experimental data with dynamic mathematical modeling promises to yield deeper insights into these processes. Nevertheless, with growing complexity and increasing amount of quantitative experimental data, building realistic and reliable mathematical models can become a challenging task: the quality of experimental data has to be assessed objectively, unknown model parameters need to be estimated from the experimental data, and numerical calculations need to be precise and efficient. Here, we discuss, compare and characterize the performance of computational methods throughout the process of quantitative dynamic modeling using two previously established examples, for which quantitative, dose- and time-resolved experimental data are available. In particular, we present an approach that allows to determine the quality of experimental data in an efficient, objective and automated manner. Using this approach data generated by different measurement techniques and even in single replicates can be reliably used for mathematical modeling. For the estimation of unknown model parameters, the performance of different optimization algorithms was compared systematically. Our results show that deterministic derivative-based optimization employing the sensitivity equations in combination with a multi-start strategy based on latin hypercube sampling outperforms the other methods by orders of magnitude in accuracy and speed. Finally, we investigated transformations that yield a more efficient parameterization of the model and therefore lead to a further enhancement in optimization performance. We provide a freely available open source software package that implements the algorithms and examples compared here.

  9. Physical Parameter Eclipse Mapping

    CERN Document Server

    Vrielmann, S

    2000-01-01

    The tomographic method "Physical Parameter Eclipse Mapping" is a tool to reconstruct spatial distributions of physical parameters (like temperatures and surface densities) in accretion discs of cataclysmic variables. After summarizing the method, we apply it to multi-colour eclipse light curves of various dwarf novae and nova-likes like VZ Scl, IP Peg in outburst, UU Aqr, V2051 Oph and HT Cas in order to derive the temperatures (and surface densities) in the disc, the white dwarf temperature, the disc size, the effective temperatures and the viscosities. The results allows us to establish or refine a physical model for the accretion disc. Our maps of HT Cas and V2051 Oph, for example, indicate that the (quiescent) disc must be structured into a cool, optically thick inner disc sandwiched by hot, optically thin chromospheres. In addition, the disc of HT Cas must be patchy with a covering factor of about 40% caused by magnetic activity in the disc.

  10. Military display performance parameters

    Science.gov (United States)

    Desjardins, Daniel D.; Meyer, Frederick

    2012-06-01

    The military display market is analyzed in terms of four of its segments: avionics, vetronics, dismounted soldier, and command and control. Requirements are summarized for a number of technology-driving parameters, to include luminance, night vision imaging system compatibility, gray levels, resolution, dimming range, viewing angle, video capability, altitude, temperature, shock and vibration, etc., for direct-view and virtual-view displays in cockpits and crew stations. Technical specifications are discussed for selected programs.

  11. Setting Parameters by Example

    OpenAIRE

    1999-01-01

    We introduce a class of "inverse parametric optimization" problems, in which one is given both a parametric optimization problem and a desired optimal solution; the task is to determine parameter values that lead to the given solution. We describe algorithms for solving such problems for minimum spanning trees, shortest paths, and other "optimal subgraph" problems, and discuss applications in multicast routing, vehicle path planning, resource allocation, and board game programming.

  12. Imidazole: Having Versatile Biological Activities

    Directory of Open Access Journals (Sweden)

    Amita Verma

    2013-01-01

    Full Text Available Imidazoles have occupied a unique position in heterocyclic chemistry, and its derivatives have attracted considerable interests in recent years for their versatile properties in chemistry and pharmacology. Imidazole is nitrogen-containing heterocyclic ring which possesses biological and pharmaceutical importance. Thus, imidazole compounds have been an interesting source for researchers for more than a century. The imidazole ring is a constituent of several important natural products, including purine, histamine, histidine, and nucleic acid. Being a polar and ionisable aromatic compound, it improves pharmacokinetic characteristics of lead molecules and thus is used as a remedy to optimize solubility and bioavailability parameters of proposed poorly soluble lead molecules. There are several methods used for the synthesis of imidazole-containing compounds, and also their various structure reactions offer enormous scope in the field of medicinal chemistry. The imidazole derivatives possess extensive spectrum of biological activities such as antibacterial, anticancer, antitubercular, antifungal, analgesic, and anti-HIV activities. This paper aims to review the biological activities of imidazole during the past years.

  13. Classical osteoblastoma, atypical osteoblastoma, and osteosarcoma: a comparative study based on clinical, histological, and biological parameters Osteoblastoma clássico, osteoblastoma atípico e osteossarcoma: um estudo comparativo baseado em parâmetros clínicos, histológicos e biológicos

    Directory of Open Access Journals (Sweden)

    Cláudia Regina Gomes Cardim Mendes de Oliveira

    2007-01-01

    Full Text Available OBJECTIVE: To investigate the biological behavior of classical and atypical osteoblastomas in comparison to osteosarcomas. METHODS: Based on histological parameters, 30 osteoblastomas were subclassified as classical osteoblastomas (23/30 or atypical osteoblastoma (high cellularity, prominent blue osteoid, and epithelioid osteoblasts-7/30. Comparative immunohistochemical and clinical analysis was performed in 17 cases of patients with high-grade osteosarcoma. Formalin-fixed, paraffin-embedded archival tissue was immunostained for p53 and proliferation cell nuclear antigen. Tumors with positive p53 stain underwent molecular analyses for fragments of exon 10. RESULTS: The mean proliferating cell nuclear antigen indexes for classical osteoblastoma, atypical osteoblastoma, and osteosarcoma were 33%, 61%, and 79%, respectively. The atypical subgroup showed similar results to those of the osteosarcoma group (P 40 (P = 0.015. CONCLUSION: These results validate atypical osteoblastoma as an entity, with p53 and proliferation cell nuclear antigen immunoexpression closer to that of osteosarcoma than of classical osteoblastoma. Proliferating cell nuclear antigen labeling index and p53 may be useful predictors of recurrence.OBJETIVOS: Investigar o comportamento biológico de osteoblastomas clássicos e atípicos comparados com osteossarcomas. MÉTODOS: Com base em parâmetros histológicos classificamos um grupo de 30 osteoblastomas nos subgrupos de osteoblastomas clássicos (23/30 e de osteoblastomas atípicos (que apresentam como característica grande celularidade, osteóide azul proeminente e osteoblastos epitelióide-7/30. Como efeito de comparação dos resultados imunohistoquímicos e análise clínica, avaliamos 17 pacientes com osteosarcoma de grau avançado. Os cortes histológicos com bloco de parafina fixado em formalina foram imunocorados para p53 e antígeno nuclear de célula em proliferação. Tumores com coloração positiva para p53 tiveram

  14. Tav4SB: integrating tools for analysis of kinetic models of biological systems

    Directory of Open Access Journals (Sweden)

    Rybiński Mikołaj

    2012-04-01

    Full Text Available Abstract Background Progress in the modeling of biological systems strongly relies on the availability of specialized computer-aided tools. To that end, the Taverna Workbench eases integration of software tools for life science research and provides a common workflow-based framework for computational experiments in Biology. Results The Taverna services for Systems Biology (Tav4SB project provides a set of new Web service operations, which extend the functionality of the Taverna Workbench in a domain of systems biology. Tav4SB operations allow you to perform numerical simulations or model checking of, respectively, deterministic or stochastic semantics of biological models. On top of this functionality, Tav4SB enables the construction of high-level experiments. As an illustration of possibilities offered by our project we apply the multi-parameter sensitivity analysis. To visualize the results of model analysis a flexible plotting operation is provided as well. Tav4SB operations are executed in a simple grid environment, integrating heterogeneous software such as Mathematica, PRISM and SBML ODE Solver. The user guide, contact information, full documentation of available Web service operations, workflows and other additional resources can be found at the Tav4SB project’s Web page: http://bioputer.mimuw.edu.pl/tav4sb/. Conclusions The Tav4SB Web service provides a set of integrated tools in the domain for which Web-based applications are still not as widely available as for other areas of computational biology. Moreover, we extend the dedicated hardware base for computationally expensive task of simulating cellular models. Finally, we promote the standardization of models and experiments as well as accessibility and usability of remote services.

  15. The biologically effective dose in inhalation nanotoxicology.

    Science.gov (United States)

    Donaldson, Ken; Schinwald, Anja; Murphy, Fiona; Cho, Wan-Seob; Duffin, Rodger; Tran, Lang; Poland, Craig

    2013-03-19

    interactions with the lysosomal membrane can compromise the integrity of the NPs. Researchers have explored oxidative potential of NPs most extensively as an indicator of the BED: the ability of an NP to cause oxidative stress in cells is a key factor in determining cell toxicity, inflammogenicity, and oxidative DNA adduct formation. Finally we discuss BEDs for high aspect ratio nanoparticles because long fibers or nanoplatelets can cause inflammation and further effects. These consequences arise from the paradoxically small aerodynamic diameter of fibers or thin platelets. As a result, these NPs can deposit beyond the ciliated airways where their extended dimensions prevent them from being fully phagocytosed by macrophages, leading to frustrated phagocytosis. Although knowledge is accumulating on the BED for NPs, many questions and challenges remain in understanding and utilizing this important nanotoxicological parameter.

  16. Neural network parameters affecting image classification

    Directory of Open Access Journals (Sweden)

    K.C. Tiwari

    2001-07-01

    Full Text Available The study is to assess the behaviour and impact of various neural network parameters and their effects on the classification accuracy of remotely sensed images which resulted in successful classification of an IRS-1B LISS II image of Roorkee and its surrounding areas using neural network classification techniques. The method can be applied for various defence applications, such as for the identification of enemy troop concentrations and in logistical planning in deserts by identification of suitable areas for vehicular movement. Five parameters, namely training sample size, number of hidden layers, number of hidden nodes, learning rate and momentum factor were selected. In each case, sets of values were decided based on earlier works reported. Neural network-based classifications were carried out for as many as 450 combinations of these parameters. Finally, a graphical analysis of the results obtained was carried out to understand the relationship among these parameters. A table of recommended values for these parameters for achieving 90 per cent and higher classification accuracy was generated and used in classification of an IRS-1B LISS II image. The analysis suggests the existence of an intricate relationship among these parameters and calls for a wider series of classification experiments as also a more intricate analysis of the relationships.

  17. ILC Extraction Line Simulations with TDR Parameters

    CERN Document Server

    Marin, Eduardo

    2014-01-01

    The goal of this study is to evaluate the impact of the latest ILC beam parameters at the Interaction Point (IP), as specified in the 2013 ILC Technical Design Report (TDR), on beam losses in the extraction line. The previous beam loss evaluation was based on the parameters specified in the 2007 ILC Reference Design Report (RDR). The results of this study are compared to the results obtained in the past for the ``nominal'' and the ``low power'' (low-P) parameter options of the RDR. The initial disrupted beam distribution at IP was generated using Guinea-Pig code, and the beam losses were obtained in tracking simulations using DIMAD. The study is performed for 500 GeV center-of-mass beam energy and the extraction line optics corresponding to the latest final focus optics with L* = 4.5 m, with and without detector solenoid.

  18. Parameter likelihood of intrinsic ellipticity correlations

    CERN Document Server

    Capranico, Federica; Schaefer, Bjoern Malte

    2012-01-01

    Subject of this paper are the statistical properties of ellipticity alignments between galaxies evoked by their coupled angular momenta. Starting from physical angular momentum models, we bridge the gap towards ellipticity correlations, ellipticity spectra and derived quantities such as aperture moments, comparing the intrinsic signals with those generated by gravitational lensing, with the projected galaxy sample of EUCLID in mind. We investigate the dependence of intrinsic ellipticity correlations on cosmological parameters and show that intrinsic ellipticity correlations give rise to non-Gaussian likelihoods as a result of nonlinear functional dependencies. Comparing intrinsic ellipticity spectra to weak lensing spectra we quantify the magnitude of their contaminating effect on the estimation of cosmological parameters and find that biases on dark energy parameters are very small in an angular-momentum based model in contrast to the linear alignment model commonly used. Finally, we quantify whether intrins...

  19. Plant synthetic biology.

    Science.gov (United States)

    Liu, Wusheng; Stewart, C Neal

    2015-05-01

    Plant synthetic biology is an emerging field that combines engineering principles with plant biology toward the design and production of new devices. This emerging field should play an important role in future agriculture for traditional crop improvement, but also in enabling novel bioproduction in plants. In this review we discuss the design cycles of synthetic biology as well as key engineering principles, genetic parts, and computational tools that can be utilized in plant synthetic biology. Some pioneering examples are offered as a demonstration of how synthetic biology can be used to modify plants for specific purposes. These include synthetic sensors, synthetic metabolic pathways, and synthetic genomes. We also speculate about the future of synthetic biology of plants.

  20. Branching processes in biology

    CERN Document Server

    Kimmel, Marek

    2015-01-01

    This book provides a theoretical background of branching processes and discusses their biological applications. Branching processes are a well-developed and powerful set of tools in the field of applied probability. The range of applications considered includes molecular biology, cellular biology, human evolution and medicine. The branching processes discussed include Galton-Watson, Markov, Bellman-Harris, Multitype, and General Processes. As an aid to understanding specific examples, two introductory chapters, and two glossaries are included that provide background material in mathematics and in biology. The book will be of interest to scientists who work in quantitative modeling of biological systems, particularly probabilists, mathematical biologists, biostatisticians, cell biologists, molecular biologists, and bioinformaticians. The authors are a mathematician and cell biologist who have collaborated for more than a decade in the field of branching processes in biology for this new edition. This second ex...

  1. Final technical report

    Energy Technology Data Exchange (ETDEWEB)

    J.A. Rial; J. Lees

    2009-03-31

    As proposed, the main effort in this project is the development of software capable of performing real-time monitoring of micro-seismic activity recorded by an array of sensors deployed around an EGS. The main milestones are defined by the development of software to perform the following tasks: • Real-time micro-earthquake detection and location • Real-time detection of shear-wave splitting • Delayed-time inversion of shear-wave splitting These algorithms, which are discussed in detail in this report, make possible the automatic and real-time monitoring of subsurface fracture systems in geothermal fields from data collected by an array of seismic sensors. Shear wave splitting (SWS) is parameterized in terms of the polarization of the fast shear wave and the time delay between the fast and slow shear waves, which are automatically measured and stored. The measured parameters are then combined with previously measured SWS parameters at the same station and used to invert for the orientation (strike and dip) and intensity of cracks under that station. In addition, this grant allowed the collection of seismic data from several geothermal regions in the US (Coso) and Iceland (Hengill) to use in the development and testing of the software.

  2. Chemical Biology is.....

    OpenAIRE

    2007-01-01

    Chemical Biology is a relatively new field, and as such is not yet simply or succinctly defined. It includes such a wide range of fundamental problems that this commentary could only include just a few snapshots of potential areas of interest. Overarching themes and selected recent successes and ideas in chemical biology are described to illustrate broadly the scope of the field, but should not be taken as exhaustive. The Chemical Biology Section of Chemistry Central Journal is pleased to rec...

  3. Biological detector and method

    Energy Technology Data Exchange (ETDEWEB)

    Sillerud, Laurel; Alam, Todd M.; McDowell, Andrew F.

    2015-11-24

    A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

  4. Biological detector and method

    Science.gov (United States)

    Sillerud, Laurel; Alam, Todd M; McDowell, Andrew F

    2014-04-15

    A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

  5. Biological Individuality of Man

    Science.gov (United States)

    1974-12-01

    RECIPIENT’S CAT * LOO NUMBER Biological Individuality of Man 5 TlrPE OF REPORT a PERIOD COVERED Technical « PERFORMING ORO REPORT...Variability 13 A. Background , 13 B. Slatistictl Approaches to Biological Variability 13 C. Genetic Aspects of Biological Variability . 14 III...ioiological determinants of individuality. Only recently, have genetic infaienccs been investigated and the potentialities for future control of bio

  6. Biological detector and method

    Science.gov (United States)

    Sillerud, Laurel; Alam, Todd M; McDowell, Andrew F

    2013-02-26

    A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

  7. The PHENIX final texts

    Energy Technology Data Exchange (ETDEWEB)

    Vasile, A.; Fontaine, B.; Vanier, M.; Gauthe, P.; Pascal, V.; Prulhiere, G.; Jaecki, P.; Martin, L. [CEA Cadarache, 13 - Saint Paul lez Durance (France); Tenchine, D. [CEA Grenoble, 38 (France); Sauvage, J.F. [Electricite de France (EDF/SEPTEN), 69 - Villeurbanne (France); Dupraz, R.; Woaye Hune, A. [AREVA NP, 75 - Paris (France)

    2010-11-15

    The 250 MWe (140 MWe since 1993) PHENIX sodium cooled fast reactor was shut down on March 6, 2009. Before decommissioning, a final set of tests was performed during May 2009 - January 2010. These tests covered core physics, fuel behaviour and thermal-hydraulics areas. Detailed analysis of the tests results is ongoing. It will be used for the extension of the validation of ERANOS and DARWIN codes for core physics, TRIO{sub U} and CATHARE for thermal-hydraulics and GERMINAL for fuel behaviour. In addition, the program included 2 tests related to the comprehension of the four negative reactivity transients (AURN) experienced during the reactor operation in 1989 and 1990 and not yet fully explained. This was also a great opportunity to involve young engineers in the different processes like the design of the tests, their carrying out and the analysis of the results. The standard instrumentation of the reactor was completed by specifically designed devices. (authors)

  8. Final Progress Report

    Energy Technology Data Exchange (ETDEWEB)

    Josef Michl

    2011-10-31

    In this project we have established guidelines for the design on organic chromophores suitable for producing high triplet yields via singlet fission. We have proven their utility by identifying a chromophore of a structural class that had never been examined for singlet fission before, 1,3-diphenylisobenzofuran, and demonstrating in two independent ways that a thin layer of this material produces a triplet yield of 200% within experimental error. We have also designed a second chromophore of a very different type, again of a structural class that had not been examined for singlet fission before, and found that in a thin layer it produces a 70% triplet yield. Finally, we have enhanced the theoretical understanding of the quantum mechanical nature of the singlet fission process.

  9. DEWPOINT. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Riddle, R.A.

    1994-09-01

    The DEWPOINT (Directed Energy POwer INTegration) program was aimed at providing the large amounts of electric power required for a laser or accelerator based in space, or on an aircraft or satellite platform. This is our final report on our efforts as a part of this program which was cancelled before completion. This report summarizes the entire scope of effort funded by this program. It also includes some related information on cryogenically cooled microchannel heatsinks which was funded internally by LLNL. Specifically, the DEWPOINT program was to provide the electrical power for the proposed Neutral Particle Beam weapon system of the Strategic Defense Initiative. The Neutral Particle Beam called for a space-based accelerator driven by radio frequency power sources. The radio frequency solid-state power amplifiers generate waste heat which must be dissipated.

  10. AIPM Final Report

    Energy Technology Data Exchange (ETDEWEB)

    John Mookken

    2006-06-30

    The final AIPM project report consists of six sections. Each section includes information on the original AIPM project and extension work on the high temperature design. The first section (1) provides an overview of the program and highlights the significant targets to meet at the end of the program. The next section (2) summarizes the significant technical accomplishments by the SEMIKRON AIPM team during the course of the project. Greater technical details are provided in a collection of all the quarterly reports which can be found in the appendix. Section three (3) presents some the more significant technical data collected from technology demonstrators. Section four (4) analyzes the manufacturing cost or economic aspects of producing 100,000 units/yr. Section five (5) describes the commercialization efforts of the AIPM technology into the automotive market. The last section (6) recommends follow on work that will build on the efforts and achievements of the AIPM program.

  11. FINAL/ SCIENTIFIC TECHNICAL REPORT

    Energy Technology Data Exchange (ETDEWEB)

    McDonald, Henry; Singh, Suminderpal

    2006-08-28

    The overall objective of the Chattanooga fuel cell demonstrations project was to develop and demonstrate a prototype 5-kW grid-parallel, solid oxide fuel cell (SOFC) system that co-produces hydrogen, based on Ion America’s technology. The commercial viability of the 5kW SOFC system was tested by transporting, installing and commissioning the SOFC system at the Alternative Energy Laboratory at the University of Tennessee – Chattanooga. The system also demonstrated the efficiency and the reliability of the system running on natural gas. This project successfully contributed to the achievement of DOE technology validation milestones from the Technology Validation section of the Hydrogen, Fuel Cells and Infrastructure Technologies Program Multi-Year Research, Development and Demonstration Plan. Results of the project can be found in the final technical report.

  12. Final technical report

    DEFF Research Database (Denmark)

    Juhl, Thomas Winther; Nielsen, Jakob Skov

    This project entails research with the goal to extend laser cutting of steel based metals to thickness above 20 mm and laser powers in the 10 kW range, with adequate accuracy and economically viable cutting speeds. The technical approach is to develop mirror based cutting heads with truly coaxial....... Phase 2: Development of mirror based test cutting heads. Phase 3: Test and evaluation of the cutting heads on high power CO2 laser sources in the 6-12 kW power range. The test phase concentrates on cutting steels, applied in the heavy industry. In the first part of the project fundamental studies have...... gas jet chamber and laser beam path from the final focusing mirror. The project consists of three phases: Phase 1: Fundamental studies of cutting front mechanisms, beam propagation, nozzle design and chemical reactions in the cut kerf with special emphasize on high laser powers and thick sections...

  13. Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    John Tanis

    2005-11-25

    This document comprises the final technical report for atomic collisions research supported by DOE grant No. DE-FG02-87ER13778 from September 1, 2001 through August 31, 2004. The research involved the experimental investigation of excitation and charge-changing processes occurring in ion-atom and ion-molecule collisions. Major emphases of the study were: (1) interference effects resulting from coherent electron emission in H2, (2) production of doubly vacant K-shell (hollow ion) states due to electron correlation, and (3) formation of long-lived metastable states in electron transfer processes. During the period of the grant, this research resulted in 23 publications, 12 invited presentations, and 39 contributed presentations at national and international meetings and other institutions. Brief summaries of the completed research are presented below.

  14. Global sensitivity and identifiability implications in systems biology

    OpenAIRE

    Dobre, Simona; Bastogne, Thierry; Richard, Alain

    2010-01-01

    International audience; In systems biology, a common approach to model biological processes is to use large systems of differential equations.The associated parameter estimation problem requires to prior handle identifiability and sensitivity issues in a practical biological framework. The lack of method to assess global practical identifiability has leaded us to analyze and establish bridges between global sensitivity and identifiability measures. Specifically, we are interested in deriving ...

  15. A Personal Journey of Discovery: Developing Technology and Changing Biology

    Science.gov (United States)

    Hood, Lee

    2008-07-01

    This autobiographical article describes my experiences in developing chemically based, biological technologies for deciphering biological information: DNA, RNA, proteins, interactions, and networks. The instruments developed include protein and DNA sequencers and synthesizers, as well as ink-jet technology for synthesizing DNA chips. Diverse new strategies for doing biology also arose from novel applications of these instruments. The functioning of these instruments can be integrated to generate powerful new approaches to cloning and characterizing genes from a small amount of protein sequence or to using gene sequences to synthesize peptide fragments so as to characterize various properties of the proteins. I also discuss the five paradigm changes in which I have participated: the development and integration of biological instrumentation; the human genome project; cross-disciplinary biology; systems biology; and predictive, personalized, preventive, and participatory (P4) medicine. Finally, I discuss the origins, the philosophy, some accomplishments, and the future trajectories of the Institute for Systems Biology.

  16. Chemical space and biology.

    Science.gov (United States)

    Dobson, Christopher M

    2004-12-16

    Chemical space--which encompasses all possible small organic molecules, including those present in biological systems--is vast. So vast, in fact, that so far only a tiny fraction of it has been explored. Nevertheless, these explorations have greatly enhanced our understanding of biology, and have led to the development of many of today's drugs. The discovery of new bioactive molecules, facilitated by a deeper understanding of the nature of the regions of chemical space that are relevant to biology, will advance our knowledge of biological processes and lead to new strategies to treat disease.

  17. Polythiophenes in biological applications.

    Science.gov (United States)

    Sista, Prakash; Ghosh, Koushik; Martinez, Jennifer S; Rocha, Reginaldo C

    2014-01-01

    Polythiophene and its derivatives have shown tremendous potential for interfacing electrically conducting polymers with biological applications. These semiconducting organic polymers are relatively soft, conduct electrons and ions, have low cytotoxicity, and can undergo facile chemical modifications. In addition, the reduction in electrical impedance of electrodes coated with polythiophenes may prove to be invaluable for a stable and permanent connection between devices and biological tissues. This review article focuses on the synthesis and some key applications of polythiophenes in multidisciplinary areas at the interface with biology. These polymers have shown tremendous potential in biological applications such as diagnostics, therapy, drug delivery, imaging, implant devices and artificial organs.

  18. Biological wastewater treatment in brewhouses

    Directory of Open Access Journals (Sweden)

    Voronov Yuriy Viktorovich

    2014-03-01

    Full Text Available In the article the working principles of wastewater biological treatment for food companies is reviewed, including dairies and breweries, the waters of which are highly concentrated with dissolved organic contaminants and suspended solids. An example of successful implementation is anaerobic-aerobic treatment plants. Implementation of these treatment plants can achieve the required wastewater treatment at the lowest operational expenses and low volumes of secondary waste generated. Waste water from the food companies have high concentration of various organic contaminants (fats, proteins, starch, sugar, etc.. For such wastewater, high rates of suspended solids, grease and other contaminants are characteristic. Wastewater food industry requires effective purification flowsheets using biological treatment facilities. At the moment methods for the anaerobic-aerobic purification are applied. One of such methods is the treatment of wastewater at ASB-reactor (methane reactor and the further tertiary treatment on the OSB-reactor (aeration. Anaerobic process means water treatment processes in anoxic conditions. The anaerobic treatment of organic contamination is based on the process of methane fermentation - the process of converting substances to biogas. The role of biological effluent treatment is discussed with special attention given to combined anaerobic/aerobic treatment. Combining anaerobic pre-treatment with aerobic post-treatment integrates the advantages of both processes, amongst which there are reduced energy consumption (net energy production, reduced biological sludge production and limited space requirements. This combination allows for significant savings for operational costs as compared to complete aerobic treatment without compromising the required discharge standards. Anaerobic treatment is a proven and energy efficient method to treat industrial wastewater effluents. These days, more and more emphasis is laid on low energy use, a

  19. 21 CFR 640.103 - The final product.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 7 2010-04-01 2010-04-01 false The final product. 640.103 Section 640.103 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS....3 molar glycine and a preservative. (b) Protein composition. At least 96 percent of the...

  20. Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Church, Bruce W

    2008-10-15

    Most prokaryotes of interest to DOE are poorly understood. Even when full genomic sequences are available, the function of only a small number of gene products are clear. The critical question is how to best infer the most probable network architectures in cells that are poorly characterized. The project goal is to create a computational hypothesis testing (CHT) framework that combines large-scale dynamical simulation, a database of bioinformatics-derived probable interactions, and numerical parallel architecture data-fitting routines to explore many “what if ?” hypotheses about the functions of genes and proteins within pathways and their downstream effects on molecular concentration profiles and corresponding phenotypes. From this framework we expect to infer signal transduction pathways and gene expression networks in prokaryotes. Detailed mechanistic models of E. Coli have been developed that directly incorporate DNA sequence information. The CHT framework is implemented in the NIEngine network inference software. NIEngine has been applied to recover gene regulatory networks in E. coli to assess performance. Application to Shewanel la oneidensi and other organism of interest DOE will be conducted in partnership with Jim Collin's Lab at Boston University and other academic partners. The CHT framework has also found broad application in the automated learning of biology for purposes of improving human health.

  1. Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Michael Laub

    2008-12-29

    Our team of investigators from MIT (Michael Laub) and Stanford (Harley McAdams and Lucy Shapiro) conducted a multi-faceted, systematic experimental analysis of the 106 Caulobacter two-component signal transduction system proteins (62 histidine kinases and 44 response regulators) to understand how they coordinate cell cycle progression, metabolism, and response to environmental changes. These two-component signaling proteins were characterized at the genetic, biochemical, and genomic levels. The results generated by our laboratories have provided numerous insights into how Caulobacter cells sense and respond to a myriad of signals. As nearly all bacteria use two-component signaling for cell regulation, the results from this project help to deepen our general understanding of bacterial signal transduction. The tools and approaches developed can be applied to other bacteria. In particular, work from the Laub laboratory now enables the systematic, rational rewiring of two-component signaling proteins, a major advance that stands to impact synthetic biology and the development of biosensors and other designer molecular circuits. Results are summarized from our work. Each section lists publications and publicly-available resources which result from the work described.

  2. Timetable Attractiveness Parameters

    DEFF Research Database (Denmark)

    Schittenhelm, Bernd

    2008-01-01

    these timetables attractive. The travel time in the timetable depends on the characteristics of the infrastructure and rolling stock, the heterogeneity of the planned train traffic and the necessary number of transfers on the passenger’s journey. Planned interdependencies between trains, such as transfers......Timetable attractiveness is influenced by a set of key parameters that are described in this article. Regarding the superior structure of the timetable, the trend in Europe goes towards periodic regular interval timetables. Regular departures and focus on optimal transfer possibilities make...

  3. Measuring the chargino parameters

    Indian Academy of Sciences (India)

    J Kalinowski

    2000-07-01

    After the supersymmetric particles have been discovered, the priority will be to determine independently the fundamental parameters to reveal the structure of the underlying supersymmetric theory. In my talk I discuss how the chargino sector can be reconstructed completely by measuring the cross-sections with polarized beams at e+e- collider experiments: $\\tilde{X}^{+}_{i}\\tilde{X}^{-}_{j}[i,j=1,2]$. The closure of the two-chargino system can be investigated by analysing sum rules for the production cross-sections.

  4. Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models

    Directory of Open Access Journals (Sweden)

    Baker Syed

    2011-01-01

    Full Text Available Abstract In systems biology, experimentally measured parameters are not always available, necessitating the use of computationally based parameter estimation. In order to rely on estimated parameters, it is critical to first determine which parameters can be estimated for a given model and measurement set. This is done with parameter identifiability analysis. A kinetic model of the sucrose accumulation in the sugar cane culm tissue developed by Rohwer et al. was taken as a test case model. What differentiates this approach is the integration of an orthogonal-based local identifiability method into the unscented Kalman filter (UKF, rather than using the more common observability-based method which has inherent limitations. It also introduces a variable step size based on the system uncertainty of the UKF during the sensitivity calculation. This method identified 10 out of 12 parameters as identifiable. These ten parameters were estimated using the UKF, which was run 97 times. Throughout the repetitions the UKF proved to be more consistent than the estimation algorithms used for comparison.

  5. Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models.

    Science.gov (United States)

    Baker, Syed Murtuza; Poskar, C Hart; Junker, Björn H

    2011-10-11

    In systems biology, experimentally measured parameters are not always available, necessitating the use of computationally based parameter estimation. In order to rely on estimated parameters, it is critical to first determine which parameters can be estimated for a given model and measurement set. This is done with parameter identifiability analysis. A kinetic model of the sucrose accumulation in the sugar cane culm tissue developed by Rohwer et al. was taken as a test case model. What differentiates this approach is the integration of an orthogonal-based local identifiability method into the unscented Kalman filter (UKF), rather than using the more common observability-based method which has inherent limitations. It also introduces a variable step size based on the system uncertainty of the UKF during the sensitivity calculation. This method identified 10 out of 12 parameters as identifiable. These ten parameters were estimated using the UKF, which was run 97 times. Throughout the repetitions the UKF proved to be more consistent than the estimation algorithms used for comparison.

  6. Schedulability Analysis for Java Finalizers

    DEFF Research Database (Denmark)

    Bøgholm, Thomas; Hansen, Rene Rydhof; Søndergaard, Hans

    2010-01-01

    Java finalizers perform clean-up and finalisation of objects at garbage collection time. In real-time Java profiles the use of finalizers is either discouraged (RTSJ, Ravenscar Java) or even disallowed (JSR-302), mainly because of the unpredictability of finalizers and in particular their impact...... on the schedulability analysis. In this paper we show that a controlled scoped memory model results in a structured and predictable execution of finalizers, more reminiscent of C++ destructors than Java finalizers. Furthermore, we incorporate finalizers into a (conservative) schedulability analysis for Predictable Java...... programs. Finally, we extend the SARTS tool for automated schedulability analysis of Java bytecode programs to handle finalizers in a fully automated way....

  7. Parameter optimization in S-system models

    Directory of Open Access Journals (Sweden)

    Vasconcelos Ana

    2008-04-01

    Full Text Available Abstract Background The inverse problem of identifying the topology of biological networks from their time series responses is a cornerstone challenge in systems biology. We tackle this challenge here through the parameterization of S-system models. It was previously shown that parameter identification can be performed as an optimization based on the decoupling of the differential S-system equations, which results in a set of algebraic equations. Results A novel parameterization solution is proposed for the identification of S-system models from time series when no information about the network topology is known. The method is based on eigenvector optimization of a matrix formed from multiple regression equations of the linearized decoupled S-system. Furthermore, the algorithm is extended to the optimization of network topologies with constraints on metabolites and fluxes. These constraints rejoin the system in cases where it had been fragmented by decoupling. We demonstrate with synthetic time series why the algorithm can be expected to converge in most cases. Conclusion A procedure was developed that facilitates automated reverse engineering tasks for biological networks using S-systems. The proposed method of eigenvector optimization constitutes an advancement over S-system parameter identification from time series using a recent method called Alternating Regression. The proposed method overcomes convergence issues encountered in alternate regression by identifying nonlinear constraints that restrict the search space to computationally feasible solutions. Because the parameter identification is still performed for each metabolite separately, the modularity and linear time characteristics of the alternating regression method are preserved. Simulation studies illustrate how the proposed algorithm identifies the correct network topology out of a collection of models which all fit the dynamical time series essentially equally well.

  8. Final Project Report

    Energy Technology Data Exchange (ETDEWEB)

    Hood, Elizabeth E

    2017-03-27

    The purpose of this project was to develop technology that would facilitate production of sugars from agricultural residues to enable biofuels and biobased product manufacturing. Our primary technology is to use genetic engineering to put bacterial and fungal cellulase genes into corn kernels, using the grain as the production system for the enzymes. At the beginning of this DoE funded program, we were producing two cellulases—E1 endocellulase from a bacterium found in a hot spring at Yellowstone National Park, and CBH I exocellulase from a wood rot fungus. Our team developed several new regulatory sequences (promoters) that increased enzyme protein accumulation in two kernel compartments (embryo and endosperm). We were also able to capitalize on the diverse genetics of corn to increase protein accumulation. High oil germplasm in particular was instrumental in this increase. A second task in the program was to produce enzymes and proteins that enhanced the activity of the E1 and CBH I enzymes. Our team produced CBH II, from the same wood rot fungus at a level that enabled highly enhanced deconstruction activity of E1 and CBH I in a synergistic manner. We analyzed an additional protein, expansin from cucumber that was expressed in the maize grain expression system. This protein had been previously shown to enhance cellulase activity (D. Cosgrove, Penn State University), and required a large-scale production platform. Our team showed that the corn production system allows industrial amounts of active expansin to be harvested from the grain. One of the challenges of any new production system is to maximize recovery of active ingredient from the raw materials at a cost compatible with its final use. Our team showed that low pH extraction of grain solubilized the enzymes without contamination of native corn protein and active product could be concentrated through ultrafiltration. The final outcomes of this project were the following: 3 cellulase enzymes and the

  9. Biology Library Workbook.

    Science.gov (United States)

    Miller, Constance; And Others

    A library skills workbook provides college biology students with an introduction to biological library resources. Divided into two sections, the first contains explanations of the various steps in the library research process. The second consists of exercises keyed to the explanatory chapters of the first section. (RAA)

  10. Psoriasis : implications of biologics

    NARCIS (Netherlands)

    Lecluse, L.L.A.

    2010-01-01

    Since the end of 2004 several specific immunomodulating therapies: ‘biologic response modifiers’ or ‘biologics’ have been registered for moderate to severe psoriasis in Europe. This thesis is considering the implications of the introduction of the biologics for psoriasis patients, focusing on safety

  11. Biological Macromolecule Crystallization Database

    Science.gov (United States)

    SRD 21 Biological Macromolecule Crystallization Database (Web, free access)   The Biological Macromolecule Crystallization Database and NASA Archive for Protein Crystal Growth Data (BMCD) contains the conditions reported for the crystallization of proteins and nucleic acids used in X-ray structure determinations and archives the results of microgravity macromolecule crystallization studies.

  12. Experimenting with Mathematical Biology

    Science.gov (United States)

    Sanft, Rebecca; Walter, Anne

    2016-01-01

    St. Olaf College recently added a Mathematical Biology concentration to its curriculum. The core course, Mathematics of Biology, was redesigned to include a wet laboratory. The lab classes required students to collect data and implement the essential modeling techniques of formulation, implementation, validation, and analysis. The four labs…

  13. Introduction to systems biology

    NARCIS (Netherlands)

    Bruggeman, F.J.; Hornberg, J.J.; Boogerd, F.C.; Westerhoff, H.V.; Boogerd, F.C.; Bruggeman, F.J.; Hofmeyr, J.H.S.; Westerhoff, H.V.

    2007-01-01

    The developments in the molecular biosciences have made possible a shift to combined molecular and system-level approaches to biological research under the name of Systems Biology. It integrates many types of molecular knowledge, which can best be achieved by the synergistic use of models and experi

  14. The Phenix final tests

    Energy Technology Data Exchange (ETDEWEB)

    Vasile, A.; Fontaine, B.; Vanier, M.; Gauthe, P.; Pascal, V.; Prulhiere, G.; Jaecki, P. [CEA Cadarache, BP 1, 13108 St Paul Lez Durance (France); Tenchine, D. [CEA Grenoble (France); Martin, L. [Centrale Phenix - CEA Marcoule (France); Sauvage, J.F. [EDF / SEPTEN - 12 av. Dutrievoz 69628 Villeurbanne (France); Dupraz, R.; Woaye-Hune, A. [AREVA NP - 10 rue Juliette Recamier 69456 LYON Cedex (France)

    2010-07-01

    The 250 MWe (140 MWe since 1993) Phenix sodium cooled fast reactor was shut down on March 6, 2009. Before decommissioning, a final set of tests were performed during the May 2009 - January 2010 period covering core physics, fuel behaviour and thermal-hydraulics areas. Detailed analysis of the tests results is ongoing. It will be used for the extension of the validation of ERANOS and DARWIN codes for core physics, TRIO-U and CATHARE for Thermal-hydraulics and GERMINAL for fuel behaviour. In addition, the program included two tests related to the comprehension of the four negative reactivity transients (AURN in French acronym) experienced during the reactor operation in '89 and '90 and not yet fully explained. This was also a great opportunity to involve young engineers in the different processes like the design of the tests, their carrying out, and the analysis of the results. The standard instrumentation of the reactor was completed by specifically designed devises. (authors)

  15. Omega, the final multiplier

    Science.gov (United States)

    Buckley, T. N.

    2008-12-01

    The application of optimisation theory to vegetation processes has rarely extended beyond the context of diurnal to intra-annual gas exchange of individual leaves and crowns. One reason is that the Lagrange multipliers in the leaf-scale solutions, which are marginal products for allocatable photosynthetic resource inputs (water and nitrogen), are mysterious in origin, and their numerical values are difficult to measure -- let alone to predict or interpret in concrete physiological or ecological terms. These difficulties disappear, however, when the optimisation paradigm itself is extended to encompass carbon allocation and growth at the lifespan scale. The trajectories of leaf (and canopy) level marginal products are then implicit in the trajectory of plant and stand structure predicted by optimal carbon allocation. Furthermore, because the input and product are the same resource -- carbon -- in the whole plant optimisation, the product in one time step defines the input constraint, and hence implicitly the marginal product for carbon, in the next time step. This effectively converts the problem from a constrained optimisation of a definite integral, in which the multipliers are undetermined, to an unconstrained maximisation of a state, in which the multipliers are all implicit. This talk will explore how the marginal products for photosynthetic inputs as well as the marginal product for carbon -- i.e., the 'final multiplier,' omega -- are predicted to vary over time and in relation to environmental change during tree growth.

  16. Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Velasco, Mayda [Northwestern University

    2013-11-01

    This work is focused on the design and construction of novel beam diagnostic and instrumentation for charged particle accelerators required for the next generation of linear colliders. Our main interest is in non-invasive techniques. The Northwestern group of Velasco has been a member of the CLIC Test Facility 3 (CTF3) collaboration since 2003, and the beam instrumentation work is developed mostly at this facility1. This 4 kW electron beam facility has a 25-170 MeV electron LINAC. CTF3 performed a set of dedicated measurements to finalize the development of our RF-Pickup bunch length detectors. The RF-pickup based on mixers was fully commissioned in 2009 and the RF-pickup based on diodes was finished in time for the 2010-11 data taking. The analysis of all the data taken in by the summer of 2010 was finish in time and presented at the main conference of the year, LINAC 2010 in Japan.

  17. Tiger LDRD final report

    Energy Technology Data Exchange (ETDEWEB)

    Steich, D J; Brugger, S T; Kallman, J S; White, D A

    2000-02-01

    This final report describes our efforts on the Three-Dimensional Massively Parallel CEM Technologies LDRD project (97-ERD-009). Significant need exists for more advanced time domain computational electromagnetics modeling. Bookkeeping details and modifying inflexible software constitute a vast majority of the effort required to address such needs. The required effort escalates rapidly as problem complexity increases. For example, hybrid meshes requiring hybrid numerics on massively parallel platforms (MPPs). This project attempts to alleviate the above limitations by investigating flexible abstractions for these numerical algorithms on MPPs using object-oriented methods, providing a programming environment insulating physics from bookkeeping. The three major design iterations during the project, known as TIGER-I to TIGER-III, are discussed. Each version of TIGER is briefly discussed along with lessons learned during the development and implementation. An Application Programming Interface (API) of the object-oriented interface for Tiger-III is included in three appendices. The three appendices contain the Utilities, Entity-Attribute, and Mesh libraries developed during the project. The API libraries represent a snapshot of our latest attempt at insulated the physics from the bookkeeping.

  18. AIMES Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Katz, Daniel S [Univ. of Illinois, Urbana-Champaign, IL (United States). National Center for Supercomputing Applications (NCSA); Jha, Shantenu [Rutgers Univ., New Brunswick, NJ (United States); Weissman, Jon [Univ. of Minnesota, Minneapolis, MN (United States); Turilli, Matteo [Rutgers Univ., New Brunswick, NJ (United States)

    2017-01-31

    This is the final technical report for the AIMES project. Many important advances in science and engineering are due to large-scale distributed computing. Notwithstanding this reliance, we are still learning how to design and deploy large-scale production Distributed Computing Infrastructures (DCI). This is evidenced by missing design principles for DCI, and an absence of generally acceptable and usable distributed computing abstractions. The AIMES project was conceived against this backdrop, following on the heels of a comprehensive survey of scientific distributed applications. AIMES laid the foundations to address the tripartite challenge of dynamic resource management, integrating information, and portable and interoperable distributed applications. Four abstractions were defined and implemented: skeleton, resource bundle, pilot, and execution strategy. The four abstractions were implemented into software modules and then aggregated into the AIMES middleware. This middleware successfully integrates information across the application layer (skeletons) and resource layer (Bundles), derives a suitable execution strategy for the given skeleton and enacts its execution by means of pilots on one or more resources, depending on the application requirements, and resource availabilities and capabilities.

  19. Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Alexander Fridman

    2005-06-01

    This DOE project DE-FC36-04GO14052 ''Plasma Pilot Plant Test for Treating VOC Emissions from Wood Products Plants'' was conducted by Drexel University in cooperation with Georgia-Pacific (G-P) and Kurchatov Institute (KI). The objective of this project was to test the Plasma Pilot Plant capabilities in wood industry. The final goal of the project was to replace the current state-of-the-art, regenerative thermal oxidation (RTO) technology by Low-Temperature Plasma Technology (LTPT) in paper and wood industry for Volatile Organic Components (VOC) destruction in High Volume Low Concentration (HVLC) vent emissions. MetPro Corporation joined the team as an industrial partner from the environmental control business and a potential leader for commercialization. Concurrent Technology Corporation (CTC) has a separate contract with DOE for this technology evaluation. They prepared questionnaires for comparison of this technology and RTO, and made this comparison. These data are presented in this report along with the description of the technology itself. Experiments with the pilot plant were performed with average plasma power up to 3.6 kW. Different design of the laboratory and pilot plant pulsed coronas, as well as different analytical methods revealed many new peculiarities of the VOC abatement process. The work reported herein describes the experimental results for the VOCs removal efficiency with respect to energy consumption, residence time, water effect and initial concentration.

  20. Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Held, Isaac [Princeton Univ., NJ (United States); Balaji, V. [Princeton Univ., NJ (United States); Fueglistaler, Stephan [Princeton Univ., NJ (United States)

    2016-09-19

    We have constructed and analyzed a series of idealized models of tropical convection interacting with large-scale circulations, with 25-50km resolution and with 1-2km cloud resolving resolution to set the stage for rigorous tests of convection closure schemes in high resolution global climate models. Much of the focus has been on the climatology of tropical cyclogenesis in rotating systems and the related problem of the spontaneous aggregation of convection in non-rotating systems. The PI (Held) will be delivering the honorary Bjerknes lecture at the Fall 2016 AGU meeting in December on this work. We have also provided new analyses of long-standing issues related to the interaction between convection and the large-scale circulation: Kelvin waves in the upper troposphere and lower stratosphere, water vapor transport into the stratosphere, and upper tropospheric temperature trends. The results of these analyses help to improve our understanding of processes, and provide tests for future high resolution global modeling. Our final goal of testing new convections schemes in next-generation global atmospheric models at GFDL has been left for future work due to the complexity of the idealized model results meant as tests for these models uncovered in this work and to computational resource limitations. 11 papers have been published with support from this grant, 2 are in review, and another major summary paper is in preparation.

  1. Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Dmitriy Y. Anistratov; Marvin L. Adams; Todd S. Palmer; Kord S. Smith; Kevin Clarno; Hikaru Hiruta; Razvan Nes

    2003-08-04

    OAK B202 Final Technical Report. The present generation of reactor analysis methods uses few-group nodal diffusion approximations to calculate full-core eigenvalues and power distributions. The cross sections, diffusion coefficients, and discontinuity factors (collectively called ''group constants'') in the nodal diffusion equations are parameterized as functions of many variables, ranging from the obvious (temperature, boron concentration, etc.) to the more obscure (spectral index, moderator temperature history, etc.). These group constants, and their variations as functions of the many variables, are calculated by assembly-level transport codes. The current methodology has two main weaknesses that this project addressed. The first weakness is the diffusion approximation in the full-core calculation; this can be significantly inaccurate at interfaces between different assemblies. This project used the nodal diffusion framework to implement nodal quasidiffusion equations, which can capture transport effects to an arbitrary degree of accuracy. The second weakness is in the parameterization of the group constants; current models do not always perform well, especially at interfaces between unlike assemblies. The project developed a theoretical foundation for parameterization and homogenization models and used that theory to devise improved models. The new models were extended to tabulate information that the nodal quasidiffusion equations can use to capture transport effects in full-core calculations.

  2. Estimation of motility parameters from trajectory data

    DEFF Research Database (Denmark)

    Vestergaard, Christian L.; Pedersen, Jonas Nyvold; Mortensen, Kim I.;

    2015-01-01

    Given a theoretical model for a self-propelled particle or micro-organism, how does one optimally determine the parameters of the model from experimental data in the form of a time-lapse recorded trajectory? For very long trajectories, one has very good statistics, and optimality may matter little....... However, for biological micro-organisms, one may not control the duration of recordings, and then optimality can matter. This is especially the case if one is interested in individuality and hence cannot improve statistics by taking population averages over many trajectories. One can learn much about...

  3. Space biology research development

    Science.gov (United States)

    Bonting, Sjoerd L.

    1993-01-01

    The purpose of the Search for Extraterrestrial Intelligence (SETI) Institute is to conduct and promote research related activities regarding the search for extraterrestrial life, particularly intelligent life. Such research encompasses the broad discipline of 'Life in the Universe', including all scientific and technological aspects of astronomy and the planetary sciences, chemical evolution, the origin of life, biological evolution, and cultural evolution. The primary purpose was to provide funding for the Principal Investigator to collaborate with the personnel of the SETI Institute and the NASA-Ames Research center in order to plan and develop space biology research on and in connection with Space Station Freedom; to promote cooperation with the international partners in the space station; to conduct a study on the use of biosensors in space biology research and life support system operation; and to promote space biology research through the initiation of an annual publication 'Advances in Space Biology and Medicine'.

  4. Biological sample collector

    Science.gov (United States)

    Murphy, Gloria A.

    2010-09-07

    A biological sample collector is adapted to a collect several biological samples in a plurality of filter wells. A biological sample collector may comprise a manifold plate for mounting a filter plate thereon, the filter plate having a plurality of filter wells therein; a hollow slider for engaging and positioning a tube that slides therethrough; and a slide case within which the hollow slider travels to allow the tube to be aligned with a selected filter well of the plurality of filter wells, wherein when the tube is aligned with the selected filter well, the tube is pushed through the hollow slider and into the selected filter well to sealingly engage the selected filter well and to allow the tube to deposit a biological sample onto a filter in the bottom of the selected filter well. The biological sample collector may be portable.

  5. Perspective: Reaches of chemical physics in biology.

    Science.gov (United States)

    Gruebele, Martin; Thirumalai, D

    2013-09-28

    Chemical physics as a discipline contributes many experimental tools, algorithms, and fundamental theoretical models that can be applied to biological problems. This is especially true now as the molecular level and the systems level descriptions begin to connect, and multi-scale approaches are being developed to solve cutting edge problems in biology. In some cases, the concepts and tools got their start in non-biological fields, and migrated over, such as the idea of glassy landscapes, fluorescence spectroscopy, or master equation approaches. In other cases, the tools were specifically developed with biological physics applications in mind, such as modeling of single molecule trajectories or super-resolution laser techniques. In this introduction to the special topic section on chemical physics of biological systems, we consider a wide range of contributions, all the way from the molecular level, to molecular assemblies, chemical physics of the cell, and finally systems-level approaches, based on the contributions to this special issue. Chemical physicists can look forward to an exciting future where computational tools, analytical models, and new instrumentation will push the boundaries of biological inquiry.

  6. Biological transportation networks: Modeling and simulation

    KAUST Repository

    Albi, Giacomo

    2015-09-15

    We present a model for biological network formation originally introduced by Cai and Hu [Adaptation and optimization of biological transport networks, Phys. Rev. Lett. 111 (2013) 138701]. The modeling of fluid transportation (e.g., leaf venation and angiogenesis) and ion transportation networks (e.g., neural networks) is explained in detail and basic analytical features like the gradient flow structure of the fluid transportation network model and the impact of the model parameters on the geometry and topology of network formation are analyzed. We also present a numerical finite-element based discretization scheme and discuss sample cases of network formation simulations.

  7. Boolean networks with multiexpressions and parameters.

    Science.gov (United States)

    Zou, Yi Ming

    2013-01-01

    To model biological systems using networks, it is desirable to allow more than two levels of expression for the nodes and to allow the introduction of parameters. Various modeling and simulation methods addressing these needs using Boolean models, both synchronous and asynchronous, have been proposed in the literature. However, analytical study of these more general Boolean networks models is lagging. This paper aims to develop a concise theory for these different Boolean logic-based modeling methods. Boolean models for networks where each node can have more than two levels of expression and Boolean models with parameters are defined algebraically with examples provided. Certain classes of random asynchronous Boolean networks and deterministic moduli asynchronous Boolean networks are investigated in detail using the setting introduced in this paper. The derived theorems provide a clear picture for the attractor structures of these asynchronous Boolean networks.

  8. FINAL TECHNICAL REPORT

    Energy Technology Data Exchange (ETDEWEB)

    Loren F. Goodrich

    2011-05-31

    NIST has played a key role in many of the one-on-one, domestic, and international interlaboratory comparisons of measurements on superconductors. The history of interlaboratory comparisons of measurements on superconductors tells us that careful measurement methods are needed to obtain consistent results. Inconsistent results can lead to many problems including: a mistrust of the results of others, unfair advantages in commerce, and erroneous feedback in the optimization of conductor performance. NIST has experience in many interlaboratory comparisons; a long-term commitment to measurement accuracy; and independent, third-party laboratory status. The principal investigator's direct involvement in the measurements and daily supervision of sample mounting is the unique situation that has allowed important discoveries and evolution of our capabilities over the last 30 years. The principal investigator's research and metrology has helped to improve the accuracy of critical-current (I{sub c}) measurements in laboratories throughout the world. As conductors continue to improve and design limits are tested, the continuation of the long-term commitment to measurement accuracy could be vitally important to the success of new conductor development programs. It is extremely important to the U.S. wire manufacturers to get accurate (high certainty) I{sub c} measurements in order to optimize conductor performance. The optimization requires the adjustment of several fabrication parameters (such as reaction time, reaction temperature, conductor design, doping, diffusion barrier, Cu to non-Cu ratio, and twist pitch) based on the I{sub c} measurement of the conductor. If the I{sub c} measurements are made with high variability, it may be unclear whether or not the parameters are being adjusted in the optimal direction or whether or not the conductor meets the target specification. Our metrology is vital to the U.S. wire manufacturers in the highly competitive international

  9. FINAL TECHNICAL REPORT

    Energy Technology Data Exchange (ETDEWEB)

    Loren F. Goodrich

    2011-05-31

    NIST has played a key role in many of the one-on-one, domestic, and international interlaboratory comparisons of measurements on superconductors. The history of interlaboratory comparisons of measurements on superconductors tells us that careful measurement methods are needed to obtain consistent results. Inconsistent results can lead to many problems including: a mistrust of the results of others, unfair advantages in commerce, and erroneous feedback in the optimization of conductor performance. NIST has experience in many interlaboratory comparisons; a long-term commitment to measurement accuracy; and independent, third-party laboratory status. The principal investigator's direct involvement in the measurements and daily supervision of sample mounting is the unique situation that has allowed important discoveries and evolution of our capabilities over the last 30 years. The principal investigator's research and metrology has helped to improve the accuracy of critical-current (I{sub c}) measurements in laboratories throughout the world. As conductors continue to improve and design limits are tested, the continuation of the long-term commitment to measurement accuracy could be vitally important to the success of new conductor development programs. It is extremely important to the U.S. wire manufacturers to get accurate (high certainty) I{sub c} measurements in order to optimize conductor performance. The optimization requires the adjustment of several fabrication parameters (such as reaction time, reaction temperature, conductor design, doping, diffusion barrier, Cu to non-Cu ratio, and twist pitch) based on the I{sub c} measurement of the conductor. If the I{sub c} measurements are made with high variability, it may be unclear whether or not the parameters are being adjusted in the optimal direction or whether or not the conductor meets the target specification. Our metrology is vital to the U.S. wire manufacturers in the highly competitive international

  10. Estimation of kinetic parameters related to biochemical interactions between hydrogen peroxide and signal transduction proteins

    Science.gov (United States)

    Brito, Paula; Antunes, Fernando

    2014-10-01

    The lack of kinetic data concerning the biological effects of reactive oxygen species is slowing down the development of the field of redox signaling. Herein, we deduced and applied equations to estimate kinetic parameters from typical redox signaling experiments. H2O2-sensing mediated by the oxidation of a protein target and the switch-off of this sensor, by being converted back to its reduced form, are the two processes for which kinetic parameters are determined. The experimental data required to apply the equations deduced is the fraction of the H2O2 sensor protein in the reduced or in the oxidized state measured in intact cells or living tissues after exposure to either endogenous or added H2O2. Either non-linear fittings that do not need transformation of the experimental data or linearized plots in which deviations from the equations are easily observed can be used. The equations were shown to be valid by fitting to them virtual time courses simulated with a kinetic model. The good agreement between the kinetic parameters estimated in these fittings and those used to simulate the virtual time courses supported the accuracy of the kinetic equations deduced. Finally, equations were successfully tested with real data taken from published experiments that describe redox signaling mediated by the oxidation of two protein tyrosine phosphatases, PTP1B and SHP-2, which are two of the few H2O2-sensing proteins with known kinetic parameters. Whereas for PTP1B estimated kinetic parameters fitted in general the present knowledge, for SHP-2 results obtained suggest that reactivity towards H2O2 as well as the rate of SHP-2 regeneration back to its reduced form are higher than previously thought. In conclusion, valuable quantitative kinetic data can be estimated from typical redox signaling experiments, thus improving our understanding about the complex processes that underline the interplay between oxidative stress and redox signaling responses.

  11. Estimation of kinetic parameters related to biochemical interactions between hydrogen peroxide and signal transduction proteins

    Directory of Open Access Journals (Sweden)

    Paula Matos de Brito

    2014-10-01

    Full Text Available The lack of kinetic data concerning the biological effects of reactive oxygen species is slowing down the development of the field of redox signaling. Herein, we deduced and applied equations to estimate kinetic parameters from typical redox signaling experiments. H2O2-sensing mediated by the oxidation of a protein target and the switch-off of this sensor, by being converted back to its reduced form, are the two processes for which kinetic parameters are determined. The experimental data required to apply the equations deduced is the fraction of the H2O2 sensor protein in the reduced or in the oxidized state measured in intact cells or living tissues after exposure to either endogenous or added H2O2. Either non-linear fittings that do not need transformation of the experimental data or linearized plots in which deviations from the equations are easily observed can be used. The equations were shown to be valid by fitting to them virtual time courses simulated with a kinetic model. The good agreement between the kinetic parameters estimated in these fittings and those used to simulate the virtual time courses supported the accuracy of the kinetic equations deduced. Finally, equations were successfully tested with real data taken from published experiments that describe redox signaling mediated by the oxidation of two protein tyrosine phosphatases, PTP1B and SHP-2, which are two of the few H2O2-sensing proteins with known kinetic parameters. Whereas for PTP1B estimated kinetic parameters fitted in general the present knowledge, for SHP-2 results obtained suggest that reactivity towards H2O2 as well as the rate of SHP-2 regeneration back to its reduced form are higher than previously thought. In conclusion, valuable quantitative kinetic data can be estimated from typical redox signaling experiments, thus improving our understanding about the complex processes that underline the interplay between oxidative stress and redox signaling responses.

  12. Lake and lake-related drainage area parameters for site investigation program

    Energy Technology Data Exchange (ETDEWEB)

    Blomqvist, P.; Brunberg, A.K. [Uppsala Univ. (Sweden). Dept. of Limnology; Brydsten, L [Umeaa Univ. (Sweden). Dept. of Ecology and Environmental Science

    2000-09-01

    In this paper, a number of parameters of importance to a preliminary determination of the ecological function of lakes are presented. The choice of parameters have been made with respect to a model for the determination of the nature conservation values of lakes which is currently being developed by the authors of this report, but is also well suited for a general description of the lake type and the functioning of the inherent ecosystem. The parameters have been divided into five groups: (1) The location of the object relative important gradients in the surrounding nature; (2) The lake catchment area and its major constituents; (3) The lake morphometry; (4) The lake ecosystem; (5) Human-induced damages to the lake ecosystem. The first two groups, principally based on the climate, hydrology, geology and vegetation of the catchment area represent parameters that can be used to establish the rarity and representativity of the lake, and will in the context of site investigation program be used as a basis for generalisation of the results. The third group, the lake morphometry parameters, are standard parameters for the outline of sampling programmes and for calculations of the physical extension of different key habitats in the system. The fourth group, the ecosystem of the lake, includes physical, chemical and biological parameters required for determination of the stratification pattern, light climate, influence from the terrestrial ecosystem of the catchment area, trophic status, distribution of key habitats, and presence of fish and rare fauna and flora in the lake. In the context of site investigation program, the parameters in these two groups will be used for budget calculations of the flow of energy and material in the system. The fifth group, finally, describes the degree on anthropogenic influence on the ecosystem and will in the context of site investigation programmes be used to judge eventual malfunctioning within the entire, or parts of, the lake

  13. River and river-related drainage area parameters for site investigation program

    Energy Technology Data Exchange (ETDEWEB)

    Blomqvist, P.; Brunberg, A.K. [Uppsala Univ. (Sweden). Dept. of Limnology; Brydsten, L. [Umeaa Univ. (Sweden). Dept. of Ecology and Environmental Science

    2001-05-01

    In this paper, a number of parameters of importance to a determination of the function of running waters as transport channels for material from the continents to the sea are presented. We have assumed that retention mechanisms of material in the river and in the riparian zone will be covered by special investigations but tried to create a platform for such investigations by quantification of the extension of different main habitats. The choice of parameters has been made so that also the nature conservation value of the river can be preliminary established, and includes a general description of the river type and the inherent ecosystem. The material links directly to that presented in a previous report concerning site investigation programmes for lakes. The parameters have been divided into five groups: 1) The location of the object relative important gradients in the surrounding nature; 2) The river catchment area and its major constituents; 3) The river morphometry; 4) The river ecosystem; 5) Human-induced damages to the river ecosystem. The first two groups, principally based on the climate, hydrology, geology and vegetation of the catchment area, represent parameters that can be used to establish the rarity and representativity of the system, and will in the context of site investigation program be used as a basis for generalisation of the results. The third group, the river morphometry parameters, are standard parameters for the outline of sampling programmes and for calculations of the physical extension of key habitats in the system. The fourth group, the ecosystem of the river, includes physical, chemical and biological parameters required for determination of the influence from the terrestrial ecosystem of the catchment area, nutrient status, distribution of different habitats, and presence of fish in the system. In the context of site investigation program, the parameters in these two groups will be used for budget calculations of the flow of energy and

  14. MTX final report

    Energy Technology Data Exchange (ETDEWEB)

    Hooper, E.B. [ed.; Allen, S.L.; Brown, M.D.; Byers, J.A.; Casper, T.A.; Cohen, B.I.; Cohen, R.H.; Fenstermacher, M.E.; Foote, J.H.; Hoshino, K. [and others

    1994-01-01

    The MTX experiment was proposed in 1986 to apply high frequency microwaves generated by a free-electron laser (FEL) to electron cyclotron resonance heating (ECRH) in a high field, high density tokamak. As the absorption of microwaves at the electron cyclotron resonance requires high frequencies, the opportunity of applying a free-electron laser has appeal as the device is not limited to frequencies in the microwave or long millimeter wavelength regions, in contrast to many other sources. In addition, the FEL is inherently a high power source of microwaves, which would permit single units of 10 MW or more, optimum for reactors. Finally, it was recognized early in the study of the application of the FEL based on the induction linear accelerator, that the nonlinear effects associated with the intense pulses of microwaves naturally generated would offer several unique opportunities to apply ECRH to current drive, MHD control, and other plasma effects. It was consequently decided to adapt the induction accelerator based FEL to heating and controlling the tokamak, and to conduct experiments on the associated physics. To this end, the Alcator C tokamak was moved from the Massachusetts Institute of Technology (MIT) to the Lawrence Livermore National Laboratory where it was installed in Building 431 and operated from March, 1989, until the conclusion of the experiment in October, 1992. The FEL, based on the ETA-11 accelerator and IMP wiggler was brought into operation by the LLNL Electron Beam Group and power injected into the tokamak during an experimental run in the Fall, 1989. Following an upgrade by the MTX group, a second experimental run was made lasting from the Winter, 1992 through the end of the experiment. Significant contributions to the ECRH experiments were made by the Japan Atomic Energy Research Institute (JAERI).

  15. PARAMETER ESTIMATION IN BREAD BAKING MODEL

    Directory of Open Access Journals (Sweden)

    Hadiyanto Hadiyanto

    2012-05-01

    Full Text Available Bread product quality is highly dependent to the baking process. A model for the development of product quality, which was obtained by using quantitative and qualitative relationships, was calibrated by experiments at a fixed baking temperature of 200°C alone and in combination with 100 W microwave powers. The model parameters were estimated in a stepwise procedure i.e. first, heat and mass transfer related parameters, then the parameters related to product transformations and finally product quality parameters. There was a fair agreement between the calibrated model results and the experimental data. The results showed that the applied simple qualitative relationships for quality performed above expectation. Furthermore, it was confirmed that the microwave input is most meaningful for the internal product properties and not for the surface properties as crispness and color. The model with adjusted parameters was applied in a quality driven food process design procedure to derive a dynamic operation pattern, which was subsequently tested experimentally to calibrate the model. Despite the limited calibration with fixed operation settings, the model predicted well on the behavior under dynamic convective operation and on combined convective and microwave operation. It was expected that the suitability between model and baking system could be improved further by performing calibration experiments at higher temperature and various microwave power levels.  Abstrak  PERKIRAAN PARAMETER DALAM MODEL UNTUK PROSES BAKING ROTI. Kualitas produk roti sangat tergantung pada proses baking yang digunakan. Suatu model yang telah dikembangkan dengan metode kualitatif dan kuantitaif telah dikalibrasi dengan percobaan pada temperatur 200oC dan dengan kombinasi dengan mikrowave pada 100 Watt. Parameter-parameter model diestimasi dengan prosedur bertahap yaitu pertama, parameter pada model perpindahan masa dan panas, parameter pada model transformasi, dan

  16. Parameter and State Estimator for State Space Models

    Directory of Open Access Journals (Sweden)

    Ruifeng Ding

    2014-01-01

    Full Text Available This paper proposes a parameter and state estimator for canonical state space systems from measured input-output data. The key is to solve the system state from the state equation and to substitute it into the output equation, eliminating the state variables, and the resulting equation contains only the system inputs and outputs, and to derive a least squares parameter identification algorithm. Furthermore, the system states are computed from the estimated parameters and the input-output data. Convergence analysis using the martingale convergence theorem indicates that the parameter estimates converge to their true values. Finally, an illustrative example is provided to show that the proposed algorithm is effective.

  17. Modelling biological and chemically induced precipitation of calcium phosphate in enhanced biological phosphorus removal systems.

    Science.gov (United States)

    Barat, R; Montoya, T; Seco, A; Ferrer, J

    2011-06-01

    The biologically induced precipitation processes can be important in wastewater treatment, in particular treating raw wastewater with high calcium concentration combined with Enhanced Biological Phosphorus Removal. Currently, there is little information and experience in modelling jointly biological and chemical processes. This paper presents a calcium phosphate precipitation model and its inclusion in the Activated Sludge Model No 2d (ASM2d). The proposed precipitation model considers that aqueous phase reactions quickly achieve the chemical equilibrium and that aqueous-solid change is kinetically governed. The model was calibrated using data from four experiments in a Sequencing Batch Reactor (SBR) operated for EBPR and finally validated with two experiments. The precipitation model proposed was able to reproduce the dynamics of amorphous calcium phosphate (ACP) formation and later crystallization to hydroxyapatite (HAP) under different scenarios. The model successfully characterised the EBPR performance of the SBR, including the biological, physical and chemical processes.

  18. Computational systems biology in cancer brain metastasis.

    Science.gov (United States)

    Peng, Huiming; Tan, Hua; Zhao, Weiling; Jin, Guangxu; Sharma, Sambad; Xing, Fei; Watabe, Kounosuke; Zhou, Xiaobo

    2016-01-01

    Brain metastases occur in 20-40% of patients with advanced malignancies. A better understanding of the mechanism of this disease will help us to identify novel therapeutic strategies. In this review, we will discuss the systems biology approaches used in this area, including bioinformatics and mathematical modeling. Bioinformatics has been used for identifying the molecular mechanisms driving brain metastasis and mathematical modeling methods for analyzing dynamics of a system and predicting optimal therapeutic strategies. We will illustrate the strategies, procedures, and computational techniques used for studying systems biology in cancer brain metastases. We will give examples on how to use a systems biology approach to analyze a complex disease. Some of the approaches used to identify relevant networks, pathways, and possibly biomarkers in metastasis will be reviewed into details. Finally, certain challenges and possible future directions in this area will also be discussed.

  19. Biologics in the management of psoriasis.

    Science.gov (United States)

    Bahner, Jennifer D; Cao, Lauren Y; Korman, Neil J

    2009-07-23

    Psoriasis is a chronic inflammatory systemic disease for which there exist topical, ultraviolet, systemic, and biologic treatments. Biologic agents selectively interfere with the immune mechanisms responsible for psoriasis. Etanercept, infliximab, and adalimumab target tumor necrosis factor-alpha and have demonstrated efficacy in the treatment of psoriasis and psoriatic arthritis. Alefacept and efalizumab target T lymphocytes, are effective in the treatment of psoriasis, but are not approved for psoriatic arthritis. Finally, ustekinumab and ABT-874 target interleukin-12 and interleukin-23, and they have demonstrated efficacy in the treatment of psoriasis. The objective of this review is to present efficacy and safety data from randomized controlled trials of the biologic agents in the treatment of psoriasis.

  20. Insects as vectors: systematics and biology.

    Science.gov (United States)

    Rodhain, F

    2015-04-01

    Among the many complex relationships between insects and microorganisms such as viruses, bacteria and parasites, some have resulted in the establishment of biological systems within which the insects act as a biological vector for infectious agents. It is therefore advisable to understand the identity and biology of these vectors in depth, in order to define procedures for epidemiological surveillance and anti-vector control. The following are successively reviewed in this article: Anoplura (lice), Siphonaptera (fleas), Heteroptera (bugs: Cimicidae, Triatoma, Belostomatidae), Psychodidae (sandflies), Simuliidae (black flies), Ceratopogonidae (biting midges), Culicidae (mosquitoes), Tabanidae (horseflies) and Muscidae (tsetse flies, stable flies and pupipara). The authors provide a rapid overview of the morphology, systematics, development cycle and bio-ecology of each of these groups of vectors. Finally, their medical and veterinary importance is briefly reviewed.