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Sample records for allocation model sam

  1. SAM Photovoltaic Model Technical Reference

    SciTech Connect

    Gilman, P.

    2015-05-27

    This manual describes the photovoltaic performance model in the System Advisor Model (SAM). The U.S. Department of Energy’s National Renewable Energy Laboratory maintains and distributes SAM, which is available as a free download from https://sam.nrel.gov. These descriptions are based on SAM 2015.1.30 (SSC 41).

  2. Spatial Analysis and Modeling Systems (SAMS)

    NASA Technical Reports Server (NTRS)

    Vermillion, Charles; Chan, Paul; Hill, John; Jaske, Robert; Rochon, Gilbert; Stetina, Fran

    1991-01-01

    The objective is to develop a uniform environmental data gathering and distribution system to support (1) emergency management for environmental disasters, and (2) the calibration and validation of remotely sensed data. Initial activities will be to select a data test site and to demonstrate multi-discipline applications using simulated or satellite data in a non real-time mode. Rainfall and flooding are chosen as the testbeds for the SAMS concept because of the abundance of data and the availability of models. The capability to display and process GOES data and analyze GOES generated rain-rate maps will be integrated into SAMS.

  3. System Advisor Model, SAM 2014.1.14: General Description

    SciTech Connect

    Blair, N.; Dobos, A. P.; Freeman, J.; Neises, T.; Wagner, M.; Ferguson, T.; Gilman, P.; Janzou, S.

    2014-02-01

    This document describes the capabilities of the U.S. Department of Energy and National Renewable Energy Laboratory's System Advisor Model (SAM), Version 2013.9.20, released on September 9, 2013. SAM is a computer model that calculates performance and financial metrics of renewable energy systems. Project developers, policy makers, equipment manufacturers, and researchers use graphs and tables of SAM results in the process of evaluating financial, technology, and incentive options for renewable energy projects. SAM simulates the performance of photovoltaic, concentrating solar power, solar water heating, wind, geothermal, biomass, and conventional power systems. The financial model can represent financial structures for projects that either buy and sell electricity at retail rates (residential and commercial) or sell electricity at a price determined in a power purchase agreement (utility). SAM's advanced simulation options facilitate parametric and sensitivity analyses, and statistical analysis capabilities are available for Monte Carlo simulation and weather variability (P50/P90) studies. SAM can also read input variables from Microsoft Excel worksheets. For software developers, the SAM software development kit (SDK) makes it possible to use SAM simulation modules in their applications written in C/C++, C#, Java, Python, and MATLAB. NREL provides both SAM and the SDK as free downloads at http://sam.nrel.gov. Technical support and more information about the software are available on the website.

  4. Technical Manual for the SAM Physical Trough Model

    SciTech Connect

    Wagner, M. J.; Gilman, P.

    2011-06-01

    NREL, in conjunction with Sandia National Lab and the U.S Department of Energy, developed the System Advisor Model (SAM) analysis tool for renewable energy system performance and economic analysis. This paper documents the technical background and engineering formulation for one of SAM's two parabolic trough system models in SAM. The Physical Trough model calculates performance relationships based on physical first principles where possible, allowing the modeler to predict electricity production for a wider range of component geometries than is possible in the Empirical Trough model. This document describes the major parabolic trough plant subsystems in detail including the solar field, power block, thermal storage, piping, auxiliary heating, and control systems. This model makes use of both existing subsystem performance modeling approaches, and new approaches developed specifically for SAM.

  5. Wind Technology Modeling Within the System Advisor Model (SAM) (Poster)

    SciTech Connect

    Blair, N.; Dobos, A.; Ferguson, T.; Freeman, J.; Gilman, P.; Whitmore, J.

    2014-05-01

    This poster provides detail for implementation and the underlying methodology for modeling wind power generation performance in the National Renewable Energy Laboratory's (NREL's) System Advisor Model (SAM). SAM's wind power model allows users to assess projects involving one or more large or small wind turbines with any of the detailed options for residential, commercial, or utility financing. The model requires information about the wind resource, wind turbine specifications, wind farm layout (if applicable), and costs, and provides analysis to compare the absolute or relative impact of these inputs. SAM is a system performance and economic model designed to facilitate analysis and decision-making for project developers, financers, policymakers, and energy researchers. The user pairs a generation technology with a financing option (residential, commercial, or utility) to calculate the cost of energy over the multi-year project period. Specifically, SAM calculates the value of projects which buy and sell power at retail rates for residential and commercial systems, and also for larger-scale projects which operate through a power purchase agreement (PPA) with a utility. The financial model captures complex financing and rate structures, taxes, and incentives.

  6. System Advisor Model, SAM 2011.12.2: General Description

    SciTech Connect

    Gilman, P.; Dobos, A.

    2012-02-01

    This document describes the capabilities of the U.S. Department of Energy and National Renewable Energy Laboratory's System Advisor Model (SAM), Version 2011.12.2, released on December 2, 2011. SAM is software that models the cost and performance of renewable energy systems. Project developers, policy makers, equipment manufacturers, and researchers use graphs and tables of SAM results in the process of evaluating financial, technology, and incentive options for renewable energy projects. SAM simulates the performance of solar, wind, geothermal, biomass, and conventional power systems. The financial model can represent financing structures for projects that either buy and sell electricity at retail rates (residential and commercial) or sell electricity at a price determined in a power purchase agreement (utility). Advanced analysis options facilitate parametric, sensitivity, and statistical analyses, and allow for interfacing SAM with Microsoft Excel or with other computer programs. SAM is available as a free download at http://sam.nrel.gov. Technical support and more information about the software are available on the website.

  7. Technoeconomic Modeling of Battery Energy Storage in SAM

    SciTech Connect

    DiOrio, Nicholas; Dobos, Aron; Janzou, Steven; Nelson, Austin; Lundstrom, Blake

    2015-09-01

    Detailed comprehensive lead-acid and lithium-ion battery models have been integrated with photovoltaic models in an effort to allow System Advisor Model (SAM) to offer the ability to predict the performance and economic benefit of behind the meter storage. In a system with storage, excess PV energy can be saved until later in the day when PV production has fallen, or until times of peak demand when it is more valuable. Complex dispatch strategies can be developed to leverage storage to reduce energy consumption or power demand based on the utility rate structure. This document describes the details of the battery performance and economic models in SAM.

  8. The fSAM Model of False Recall

    ERIC Educational Resources Information Center

    Kimball, Daniel R.; Smith, Troy A.; Kahana, Michael J.

    2007-01-01

    The authors report a new theory of false memory building upon existing associative memory models and implemented in fSAM, the first fully specified quantitative model of false recall. Participants frequently intrude unstudied critical words while recalling lists comprising their strongest semantic associates but infrequently produce other…

  9. Technical Manual for the SAM Biomass Power Generation Model

    SciTech Connect

    Jorgenson, J.; Gilman, P.; Dobos, A.

    2011-09-01

    This technical manual provides context for the implementation of the biomass electric power generation performance model in the National Renewable Energy Laboratory's (NREL's) System Advisor Model (SAM). Additionally, the report details the engineering and scientific principles behind the underlying calculations in the model. The framework established in this manual is designed to give users a complete understanding of behind-the-scenes calculations and the results generated.

  10. Introducing the aerosol-climate model MAECHAM5-SAM2

    NASA Astrophysics Data System (ADS)

    Hommel, R.; Timmreck, C.; Graf, H. F.

    2009-04-01

    We are presenting a new global aerosol model MAECHAM5-SAM2 to study the aerosol dynamics in the UTLS under background and volcanic conditions. The microphysical core modul SAM2 treats the formation, the evolution and the transport of stratospheric sulphuric acid aerosol. The aerosol size distribution and the weight percentage of the sulphuric acid solution is calculated dependent on the concentrations of H2SO4 and H2O, their vapor pressures, the atmospheric temperature and pressure. The fixed sectional method is used to resolve an aerosol distribution between 1 nm and 2.6 micron in particle radius. Homogeneous nucleation, condensation and evaporation, coagulation, water-vapor growth, sedimentation and sulphur chemistry are included. The module is applied in the middle-atmosphere MAECHAM5 model, resolving the atmosphere up to 0.01 hPa (~80 km) in 39 layers. It is shown here that MAECHAM5-SAM2 well represents in-situ measured size distributions of stratospheric background aerosol in the northern hemisphere mid-latitudes. Distinct differences can be seen when derived integrated aerosol parameters (surface area, effective radius) are compared with aerosol climatologies based on the SAGE II satellite instrument (derived by the University of Oxford and the NASA AMES laboratory). The bias between the model and the SAGE II data increases as the moment of the aerosol size distribution decreases. Thus the modeled effective radius show the strongest bias, followed by the aerosol surface area density. Correspondingly less biased are the higher moments volume area density and the mass density of the global stratospheric aerosol coverage. This finding supports the key finding No. 2 of the SPARC Assessment of Stratospheric Aerosol Properties (2006), where it was shown that during periods of very low aerosol load in the stratosphere, the consistency between in-situ and satellite measurements, which exist in a volcanically perturbed stratosphere, breaks down and significant

  11. A Spatial Analysis and Modeling System (SAMS) for environment management

    NASA Technical Reports Server (NTRS)

    Stetina, Fran; Hill, John; Chan, Paul; Jaske, Robert; Rochon, Gilbert

    1993-01-01

    This is a proposal to develop a uniform global environmental data gathering and distribution system to support the calibration and validation of remotely sensed data. SAMS is based on an enhanced version of FEMA's Integrated Emergency Management Information Systems and the Department of Defense's Air land Battlefield Environment Software Systems. This system consists of state-of-the-art graphics and visualization techniques, simulation models, database management and expert systems for conducting environmental and disaster preparedness studies. This software package will be integrated into various Landsat and UNEP-GRID stations which are planned to become direct readout stations during the EOS (Earth Observing System) timeframe. This system would be implemented as a pilot program to support the Tropical Rainfall Measuring Mission (TRMM). This will be a joint NASA-FEMA-University-Industry project.

  12. A Spatial Analysis and Modeling System (SAMS) for environment management

    NASA Technical Reports Server (NTRS)

    Vermillion, Charles H.; Stetina, Fran; Hill, John; Chan, Paul; Jaske, Robert; Rochon, Gilbert

    1992-01-01

    This is a proposal to develop a uniform global environmental data gathering and distribution system to support the calibration and validation of remotely sensed data. SAMS is based on an enhanced version of FE MA's Integrated Emergency Management Information Systems and the Department of Defense's Air Land Battlefield Environment Software Systems. This system consists of state-of-the-art graphics and visualization techniques, simulation models, database management and expert systems for conducting environmental and disaster preparedness studies. This software package will be integrated into various Landsat and UNEP-GRID stations which are planned to become direct readout stations during the EOS timeframe. This system would be implemented as a pilot program to support the Tropical Rainfall Measuring Mission (TRMM). This will be a joint NASA-FEMA-University-Industry project.

  13. Minority Transportation Expenditure Allocation Model

    SciTech Connect

    Vyas, Anant D.; Santini, Danilo J.; Marik, Sheri K.

    1993-04-12

    MITRAM (Minority TRansportation expenditure Allocation Model) can project various transportation related attributes of minority (Black and Hispanic) and majority (white) populations. The model projects vehicle ownership, vehicle miles of travel, workers, new car and on-road fleet fuel economy, amount and share of household income spent on gasoline, and household expenditures on public transportation and taxis. MITRAM predicts reactions to sustained fuel price changes for up to 10 years after the change.

  14. Molten Salt Power Tower Cost Model for the System Advisor Model (SAM)

    SciTech Connect

    Turchi, C. S.; Heath, G. A.

    2013-02-01

    This report describes a component-based cost model developed for molten-salt power tower solar power plants. The cost model was developed by the National Renewable Energy Laboratory (NREL), using data from several prior studies, including a contracted analysis from WorleyParsons Group, which is included herein as an Appendix. The WorleyParsons' analysis also estimated material composition and mass for the plant to facilitate a life cycle analysis of the molten salt power tower technology. Details of the life cycle assessment have been published elsewhere. The cost model provides a reference plant that interfaces with NREL's System Advisor Model or SAM. The reference plant assumes a nominal 100-MWe (net) power tower running with a nitrate salt heat transfer fluid (HTF). Thermal energy storage is provided by direct storage of the HTF in a two-tank system. The design assumes dry-cooling. The model includes a spreadsheet that interfaces with SAM via the Excel Exchange option in SAM. The spreadsheet allows users to estimate the costs of different-size plants and to take into account changes in commodity prices. This report and the accompanying Excel spreadsheet can be downloaded at https://sam.nrel.gov/cost.

  15. Accept/decline decision module for the liver simulated allocation model.

    PubMed

    Kim, Sang-Phil; Gupta, Diwakar; Israni, Ajay K; Kasiske, Bertram L

    2015-03-01

    Simulated allocation models (SAMs) are used to evaluate organ allocation policies. An important component of SAMs is a module that decides whether each potential recipient will accept an offered organ. The objective of this study was to develop and test accept-or-decline classifiers based on several machine-learning methods in an effort to improve the SAM for liver allocation. Feature selection and imbalance correction methods were tested and best approaches identified for application to organ transplant data. Then, we used 2011 liver match-run data to compare classifiers based on logistic regression, support vector machines, boosting, classification and regression trees, and Random Forests. Finally, because the accept-or-decline module will be embedded in a simulation model, we also developed an evaluation tool for comparing performance of predictors, which we call sample-path accuracy. The Random Forest method resulted in the smallest overall error rate, and boosting techniques had greater accuracy when both sensitivity and specificity were simultaneously considered important. Our comparisons show that no method dominates all others on all performance measures of interest. A logistic regression-based classifier is easy to implement and allows for pinpointing the contribution of each feature toward the probability of acceptance. Other methods we tested did not have a similar interpretation. The Scientific Registry of Transplant Recipients decided to use the logistic regression-based accept-decline decision module in the next generation of liver SAM.

  16. Computational models and resource allocation for supercomputers

    NASA Technical Reports Server (NTRS)

    Mauney, Jon; Agrawal, Dharma P.; Harcourt, Edwin A.; Choe, Young K.; Kim, Sukil

    1989-01-01

    There are several different architectures used in supercomputers, with differing computational models. These different models present a variety of resource allocation problems that must be solved. The computational needs of a program must be cast in terms of the computational model supported by the supercomputer, and this must be done in a way that makes effective use of the machine's resources. This is the resource allocation problem. The computational models of available supercomputers and the associated resource allocation techniques are surveyed. It is shown that many problems and solutions appear repeatedly in very different computing environments. Some case studies are presented, showing concrete computational models and the allocation strategies used.

  17. Parabolic Trough Reference Plant for Cost Modeling with the Solar Advisor Model (SAM)

    SciTech Connect

    Turchi, C.

    2010-07-01

    This report describes a component-based cost model developed for parabolic trough solar power plants. The cost model was developed by the National Renewable Energy Laboratory (NREL), assisted by WorleyParsons Group Inc., for use with NREL's Solar Advisor Model (SAM). This report includes an overview and explanation of the model, two summary contract reports from WorleyParsons, and an Excel spreadsheet for use with SAM. The cost study uses a reference plant with a 100-MWe capacity and six hours of thermal energy storage. Wet-cooling and dry-cooling configurations are considered. The spreadsheet includes capital and operating cost by component to allow users to estimate the impact of changes in component costs.

  18. Construct Validation of the Louisiana School Analysis Model (SAM) Instructional Staff Questionnaire

    ERIC Educational Resources Information Center

    Bray-Clark, Nikki; Bates, Reid

    2005-01-01

    The purpose of this study was to validate the Louisiana SAM Instructional Staff Questionnaire, a key component of the Louisiana School Analysis Model. The model was designed as a comprehensive evaluation tool for schools. Principle axis factoring with oblique rotation was used to uncover the underlying structure of the SISQ. (Contains 1 table.)

  19. Case Studies Comparing System Advisor Model (SAM) Results to Real Performance Data: Preprint

    SciTech Connect

    Blair, N.; Dobos, A.; Sather, N.

    2012-06-01

    NREL has completed a series of detailed case studies comparing the simulations of the System Advisor Model (SAM) and measured performance data or published performance expectations. These case studies compare PV measured performance data with simulated performance data using appropriate weather data. The measured data sets were primarily taken from NREL onsite PV systems and weather monitoring stations.

  20. Integration, Validation, and Application of a PV Snow Coverage Model in SAM

    SciTech Connect

    Ryberg, David; Freeman, Janine

    2015-09-01

    Due to the increasing deployment of PV systems in snowy climates, there is significant interest in a method capable of estimating PV losses resulting from snow coverage that has been verified for a wide variety of system designs and locations. A scattering of independent snow coverage models have been developed over the last 15 years; however, there has been very little effort spent on verifying these models beyond the system design and location on which they were based. Moreover, none of the major PV modeling software products have incorporated any of these models into their workflow. In response to this deficiency, we have integrated the methodology of the snow model developed in the paper by Marion et al. [1] into the National Renewable Energy Laboratory's (NREL) System Advisor Model (SAM). In this work we describe how the snow model is implemented in SAM and discuss our demonstration of the model's effectiveness at reducing error in annual estimations for two PV arrays. Following this, we use this new functionality in conjunction with a long term historical dataset to estimate average snow losses across the United States for a typical PV system design. The open availability of the snow loss estimation capability in SAM to the PV modeling community, coupled with our results of the nation-wide study, will better equip the industry to accurately estimate PV energy production in areas affected by snowfall.

  1. Linear modelling of attentional resource allocation

    NASA Technical Reports Server (NTRS)

    Pierce, B.

    1978-01-01

    Eight subjects time-shared performance of two compensatory tracking tasks under conditions when both were of constant difficulty, and when the control order of one task (designated primary) was varied over time within a trial. On line performance feedback was presented on half of the trials. The data are interpreted in terms of a linear model of the operator's attention allocation system, and suggest that this allocation is strongly suboptimal. Furthermore, the limitations in reallocating attentional resources between tasks, in response to difficulty fluctuations were not reduced by augmented performance feedback. Some characteristics of the allocation system are described, and reasons for its limitations suggested.

  2. The SAM framework: modeling the effects of management factors on human behavior in risk analysis.

    PubMed

    Murphy, D M; Paté-Cornell, M E

    1996-08-01

    Complex engineered systems, such as nuclear reactors and chemical plants, have the potential for catastrophic failure with disastrous consequences. In recent years, human and management factors have been recognized as frequent root causes of major failures in such systems. However, classical probabilistic risk analysis (PRA) techniques do not account for the underlying causes of these errors because they focus on the physical system and do not explicitly address the link between components' performance and organizational factors. This paper describes a general approach for addressing the human and management causes of system failure, called the SAM (System-Action-Management) framework. Beginning with a quantitative risk model of the physical system, SAM expands the scope of analysis to incorporate first the decisions and actions of individuals that affect the physical system. SAM then links management factors (incentives, training, policies and procedures, selection criteria, etc.) to those decisions and actions. The focus of this paper is on four quantitative models of action that describe this last relationship. These models address the formation of intentions for action and their execution as a function of the organizational environment. Intention formation is described by three alternative models: a rational model, a bounded rationality model, and a rule-based model. The execution of intentions is then modeled separately. These four models are designed to assess the probabilities of individual actions from the perspective of management, thus reflecting the uncertainties inherent to human behavior. The SAM framework is illustrated for a hypothetical case of hazardous materials transportation. This framework can be used as a tool to increase the safety and reliability of complex technical systems by modifying the organization, rather than, or in addition to, re-designing the physical system.

  3. Evolution of SAM in an enhanced model for Monitoring WLCG services

    NASA Astrophysics Data System (ADS)

    Collados, David; Shade, John; Traylen (Cern, Steve; Imamagic (Srce, Emir

    2010-04-01

    It is four years now since the first prototypes of tools and tests started to monitor the Worldwide LHC Computing Grid (WLCG) services. One of these tools is the Service Availability Monitoring (SAM) framework, which superseded the SFT tool, and has become a keystone for the monthly WLCG availability and reliability computations. During this time, the grid has evolved into a robust, production-level infrastructure, in no small part thanks to the extensive monitoring infrastructure which includes testing, visualization and reporting. Experience gained with monitoring has led to emerging grid monitoring standards, and provided valuable input for the Operations Automation Strategy aimed at the regionalization of monitoring services. This change in scope, together with an ever-increasing number of services and infrastructures, make enhancements in the architecture of existing monitoring tools a necessity. This paper describes the present architecture of SAM, an enhanced and distributed model for monitoring WLCG services, and the required changes in SAM to adopt this new model inside the EGEE-III project.

  4. Parabolic Trough Collector Cost Update for the System Advisor Model (SAM)

    SciTech Connect

    Kurup, Parthiv; Turchi, Craig S.

    2015-11-01

    This report updates the baseline cost for parabolic trough solar fields in the United States within NREL's System Advisor Model (SAM). SAM, available at no cost at https://sam.nrel.gov/, is a performance and financial model designed to facilitate decision making for people involved in the renewable energy industry. SAM is the primary tool used by NREL and the U.S. Department of Energy (DOE) for estimating the performance and cost of concentrating solar power (CSP) technologies and projects. The study performed a bottom-up build and cost estimate for two state-of-the-art parabolic trough designs -- the SkyTrough and the Ultimate Trough. The SkyTrough analysis estimated the potential installed cost for a solar field of 1500 SCAs as $170/m2 +/- $6/m2. The investigation found that SkyTrough installed costs were sensitive to factors such as raw aluminum alloy cost and production volume. For example, in the case of the SkyTrough, the installed cost would rise to nearly $210/m2 if the aluminum alloy cost was $1.70/lb instead of $1.03/lb. Accordingly, one must be aware of fluctuations in the relevant commodities markets to track system cost over time. The estimated installed cost for the Ultimate Trough was only slightly higher at $178/m2, which includes an assembly facility of $11.6 million amortized over the required production volume. Considering the size and overall cost of a 700 SCA Ultimate Trough solar field, two parallel production lines in a fully covered assembly facility, each with the specific torque box, module and mirror jigs, would be justified for a full CSP plant.

  5. Senescence-accelerated mouse (SAM): a novel murine model of senescence.

    PubMed

    Takeda, T; Hosokawa, M; Higuchi, K

    1997-01-01

    The Senescence-Accelerated Mouse (SAM) has been under development by our research team at Kyoto University since 1970 through the selective inbreeding of the AKR/J strain of mice donated by the Jackson Laboratory in 1968, based on a graded score for senescence, life span, and pathologic phenotype. At present, there are 12 lines of SAM: nine senescence-prone inbred strains (SAMP) including SAMP1, SAMP2, SAMP3, SAMP6, SAMP7, SAMP8, SAMP9, SAMP10, and SAMP11; and three senescence-resistant inbred strains (SAMR) including SAMR1, SAMR4, and SAMR5. Data from survival curves, Gompertzian function, and grading score of senescence, together with growth patterns of body weight of these SAMP and SAMR, revealed that the characteristic feature of aging common to all SAMP mice is "accelerated senescence;" early onset and irreversible advance of senescence manifested by several signs and gross lesions such as the loss of normal behavior, various skin lesions, increased lordokyphosis, etc., after a period of normal development. In the course of SAM development, it became evident that SAMP strains manifest various pathologic phenotypes that are characteristic enough to differentiate the SAM strains. The genetic background and significance of SAM development are discussed. PMID:9088907

  6. Resource Allocation Models and Accountability: A Jamaican Case Study

    ERIC Educational Resources Information Center

    Nkrumah-Young, Kofi K.; Powell, Philip

    2008-01-01

    Higher education institutions (HEIs) may be funded privately, by the state or by a mixture of the two. Nevertheless, any state financing of HE necessitates a mechanism to determine the level of support and the channels through which it is to be directed; that is, a resource allocation model. Public funding, through resource allocation models,…

  7. Senescence-accelerated mouse (SAM) with special references to neurodegeneration models, SAMP8 and SAMP10 mice.

    PubMed

    Takeda, Toshio

    2009-04-01

    The SAM strains, a group of related inbred strains consisting of senescence-prone inbred strains (SAMP) and senescence-resistant inbred strains (SAMR), have been successfully developed by selective inbreeding of the AKR/J strain of mice donated by the Jackson laboratory in 1968. The characteristic feature of aging common to the SAMP and SAMR is accelerated senescence and normal aging, respectively. Furthermore, SAMP and SAMR strains of mice manifest various pathobiological phenotypes spontaneously. Among SAMP strains, SAMP8 and SAMP10 mice show age-related behavioral deterioration such as deficits in learning and memory, emotional disorders (reduced anxiety-like behavior and depressive behavior) and altered circadian rhythm associated with certain pathological, biochemical and pharmacological changes. Here, the previous and recent literature on SAM mice are reviewed with an emphasis on SAMP8 and SAMP10 mice. A spontaneous model like SAM with distinct advantages over the gene-modified model is hoped by investigators to be used more widely as a biogerontological resource to explore the etiopathogenesis of accelerated senescence and neurodegenerative disorders. PMID:19199030

  8. Senescence-accelerated mouse (SAM) as an animal model of senile dementia: pharmacological, neurochemical and molecular biological approach.

    PubMed

    Okuma, Y; Nomura, Y

    1998-12-01

    To elucidate the fundamental mechanism of age-related deficiencies of learning and to develop effective drugs for intervention in age-related diseases such as learning dysfunctions, pertinent animal models that have characteristics closely similar to human dysfunctions should be established. SAM (senescence-accelerated mouse) has been established as a murine model of the SAM strains, groups of related inbred strains including nine strains of accelerated senescence-prone, short-lived mice (SAMP) and three strains of accelerated senescence-resistant, long-lived mice (SAMR). SAMP-strain mice show relatively strain-specific age-associated phenotypic pathologies such as shortened life span and early manifestation of senescence. Among the SAMP-strain mice, SAMP8 mice show an age-related deterioration in learning ability. Here, the neuropathological, neurochemical and pharmacological features of SAM are reported, especially for SAMP8. Moreover, the effects of several drugs on the biochemical and behavioral alterations in SAMP8 and the etiologic manifestation of accelerated senescence are also discussed. PMID:9920195

  9. Tracking the MSL-SAM methane detection source location Through Mars Regional Atmospheric Modeling System (MRAMS)

    NASA Astrophysics Data System (ADS)

    Pla-García, Jorge

    2016-04-01

    1. Introduction: The putative in situ detection of methane by Sample Analysis at Mars (SAM) instrument suite on Curiosi-ty at Gale crater has garnered significant attention because of the potential implications for the presence of geological methane sources or indigenous Martian organisms [1, 2]. SAM reported detection of back-ground levels of atmospheric methane of mean value 0.69±0.25 parts per billion by volume (ppbv) at the 95% confidence interval (CI). Additionally, in four sequential measurements spanning a 60-sol period, SAM observed elevated levels of methane of 7.2±2.1 ppbv (95% CI), implying that Mars is episodically producing methane from an additional unknown source. There are many major unresolved questions regard-ing this detection: 1) What are the potential sources of the methane release? 2) What causes the rapid decrease in concentration? and 3) Where is the re-lease location? 4) How spatially extensive is the re-lease? 5) For how long is CH4 released? Regarding the first question, the source of methane, is so far not identified. It could be related with geo-logical process like methane release from clathrates [3], serpentinisation [4] and volcanism [5]; or due to biological activity from methanogenesis [6]. To answer the second question, the rapid decrease in concentration, it is important to note that the photo-chemical lifetime of methane is of order 100 years, much longer than the atmospheric mixing time scale, and thus the gas should tend to be well mixed except near a source or shortly after an episodic release. The observed spike of 7 ppb from the background of <1 ppb, and then the rapid return to the background lev-el could be due to a sink (destruction) or due to at-mospheric mixing. A wind mediated erosion process of ordinary quartz crystals was proposed to produce activated quartz grains, which sequester methane by forming covalent Si-C bonds. If this process is op-erational on Mars today, which some recent prelimi-nary studies on

  10. Linear programming model for optimum resource allocation in rural systems

    SciTech Connect

    Devadas, V.

    1997-07-01

    The article presents a model for optimum resource allocation in a rural system. Making use of linear programming, the objective function of the linear programming model is to maximize the revenue of the rural system, and optimum resource allocation is made subject to a number of energy- and nonenergy-related constraints relevant to the rural system. The model also quantifies the major yields as well as the by-products of different sectors of the rural economic system.

  11. Dosimetric comparison of the specific anthropomorphic mannequin (SAM) to 14 anatomical head models using a novel definition for the mobile phone positioning

    NASA Astrophysics Data System (ADS)

    Kainz, Wolfgang; Christ, Andreas; Kellom, Tocher; Seidman, Seth; Nikoloski, Neviana; Beard, Brian; Kuster, Niels

    2005-07-01

    This paper presents new definitions for obtaining reproducible results in numerical phone dosimetry. Numerous numerical dosimetric studies have been published about the exposure of mobile phone users which concluded with conflicting results. However, many of these studies lack reproducibility due to shortcomings in the description of the phone positioning. The new approach was tested by two groups applying two different numerical program packages to compare the specific anthropomorphic mannequin (SAM) to 14 anatomically correct head models. A novel definition for the positioning of mobile phones next to anatomically correct head models is given along with other essential parameters to be reported. The definition is solely based on anatomical characteristics of the head. A simple up-to-date phone model was used to determine the peak spatial specific absorption rate (SAR) of mobile phones in SAM and in the anatomically correct head models. The results were validated by measurements. The study clearly shows that SAM gives a conservative estimate of the exposure in anatomically correct head models for head only tissue. Depending on frequency, phone position and head size the numerically calculated 10 g averaged SAR in the pinna can be up to 2.1 times greater than the peak spatial SAR in SAM. Measurements in small structures, such as the pinna, will significantly increase the uncertainty; therefore SAM was designed for SAR assessment in the head only. Whether SAM will provide a conservative value for the pinna depends on the pinna SAR limit of the safety standard considered.

  12. Tracking the MSL-SAM methane detection source location Through Mars Regional Atmospheric Modeling System (MRAMS)

    NASA Astrophysics Data System (ADS)

    Pla-García, Jorge

    2016-04-01

    1. Introduction: The putative in situ detection of methane by Sample Analysis at Mars (SAM) instrument suite on Curiosi-ty at Gale crater has garnered significant attention because of the potential implications for the presence of geological methane sources or indigenous Martian organisms [1, 2]. SAM reported detection of back-ground levels of atmospheric methane of mean value 0.69±0.25 parts per billion by volume (ppbv) at the 95% confidence interval (CI). Additionally, in four sequential measurements spanning a 60-sol period, SAM observed elevated levels of methane of 7.2±2.1 ppbv (95% CI), implying that Mars is episodically producing methane from an additional unknown source. There are many major unresolved questions regard-ing this detection: 1) What are the potential sources of the methane release? 2) What causes the rapid decrease in concentration? and 3) Where is the re-lease location? 4) How spatially extensive is the re-lease? 5) For how long is CH4 released? Regarding the first question, the source of methane, is so far not identified. It could be related with geo-logical process like methane release from clathrates [3], serpentinisation [4] and volcanism [5]; or due to biological activity from methanogenesis [6]. To answer the second question, the rapid decrease in concentration, it is important to note that the photo-chemical lifetime of methane is of order 100 years, much longer than the atmospheric mixing time scale, and thus the gas should tend to be well mixed except near a source or shortly after an episodic release. The observed spike of 7 ppb from the background of <1 ppb, and then the rapid return to the background lev-el could be due to a sink (destruction) or due to at-mospheric mixing. A wind mediated erosion process of ordinary quartz crystals was proposed to produce activated quartz grains, which sequester methane by forming covalent Si-C bonds. If this process is op-erational on Mars today, which some recent prelimi-nary studies on

  13. A model for analysis of TDA budget allocation

    NASA Technical Reports Server (NTRS)

    Remer, D. S.; Buchanan, H. R.

    1994-01-01

    There is an ever-increasing need to achieve greater efficiency in the operation of the Deep Space Network (DSN), i.e., increased productivity at reduced cost. One of the tools used in the course of a planning workshop on this subject was a methodology for budget allocation applicable to long-range planning. This article presents a model for analysis of the TDA budget allocation. For the 1994 through 1999 period, the percentage of the total TDA budget allocated to capacity and capability is being cut in half, whereas the percentage spent on efficiency of delivery will be increasing.

  14. A Model for Resource Allocation Using Operational Knowledge Assets

    ERIC Educational Resources Information Center

    Andreou, Andreas N.; Bontis, Nick

    2007-01-01

    Purpose: The paper seeks to develop a business model that shows the impact of operational knowledge assets on intellectual capital (IC) components and business performance and use the model to show how knowledge assets can be prioritized in driving resource allocation decisions. Design/methodology/approach: Quantitative data were collected from 84…

  15. Modelling C allocation in response to nutrient availability

    NASA Astrophysics Data System (ADS)

    Stocker, Benjamin; Prentice, Colin

    2015-04-01

    Carbon (C) allocation in ecosystems is a key variable of the global terrestrial C cycle. While photosynthesis governs the amount of C that enters ecosystems, its subsequent allocation to compartments with different life times determines its over-all residence time and variations in allocation patterns drive changes in ecosystem C balance and its response to environmental change. A better understanding of the controls on allocation is thus key to improving global vegetation models that commonly rely on using fixed partitioning factors. Observational data suggests variations of ecosystem structure and functioning along large-scale gradients of resource availability. Below-ground C allocation, inferred as gross primary production minus above-ground biomass production increases along gradients of decreasing nutrient availability. This is not only due to more root growth, but also due to enhanced production of exudates and stimulation of root symbionts and has been interpreted to reflect optimal plant allocation decisions under a varying soil fertility status. Here, we propose a model that accounts for trade-offs between (i) growth in above-ground and (ii) below-ground plant compartments, (iii) exudation to the rhizosphere and root symbionts and (iv) temporary storage in non-structural pools. By postulating the maximization of long-term growth under a given (seasonal regime) of soil nitrogen (N) availability, we attempt to reproduce observed large-scale gradients. The model is formulated based on a C cost for different N uptake decisions, where the cost is a function of N availability, root mass, and soil temperature (for biological N fixation). On a daily time scale, ecosystem N uptake may be realized by C exudation to the rhizosphere and/or symbiotic fixation of atmospheric N2. On an annual time scale, allocation to roots versus leaves is adjusted to soil inorganic N availability and modeled to yield maximum total growth. Exudation versus temporary storage of C is

  16. ReefSAM - Reef Sedimentary Accretion Model: A new 3D coral reef evolution model/simulator

    NASA Astrophysics Data System (ADS)

    Barrett, Samuel; Webster, Jody

    2013-04-01

    Coral reefs show characteristic morphological patterns (e.g. coral dominated margins with detrital carbonate dominated lagoons/back-reef) and temporal development (e.g. Hopley et al. 2007). While the processes which lead to predictable patterns on a range of scales have been discussed qualitatively, a full quantitative understanding of the range of processes and parameters involved requires modelling. Previous attempts to model complex Holocene reef systems (i.e. One Tree Reef, GBR - Barrett and Webster 2012) using a carbonate stratigraphic forward model (Carbonate3D - Warrlich et al. 2002) identified a number of important but unsimulated processes and potential model improvements. ReefSAM has been written from scratch in Matlab using these findings and experiences from using Carbonate3D. It simulates coralgal accretion and carbonate sand production and transport. Specific improvements include: 1. a more complex hydrodynamic model based on wave refraction and incorporating vertical (depth) and lateral (substrate dependent) variations in transport energy and erosion. 2. a complex reef growth model incorporating depth, wave energy/turbidity and substrate composition. 3. Paleo-water depth, paleo-wave energy and bio-zone (combination of paleo-water depth and wave energy) model outputs allowing coralgal habitat changes through time and space to be simulated and compared to observational data. The model is compared to the well studied One Tree Reef - tests similar to those undertaken in Barrett and Webster 2012 with Carbonate3D are presented. Model development coincides with plans for further intensive drilling at One Tree Reef (mid 2013) providing an opportunity to test the model predictively. The model is still in active development. References: Barrett, S.J., Webster, J.M.,2012. Holocene evolution of the Great Barrier Reef: Insights from 3D numerical modelling. Sedimentary Geology 265-266, 56-71. Warrlich, G.M.D., Waltham, D.A., Bosence D.W.J., 2002. Quantifying the

  17. The SAM software system for modeling severe accidents at nuclear power plants equipped with VVER reactors on full-scale and analytic training simulators

    NASA Astrophysics Data System (ADS)

    Osadchaya, D. Yu.; Fuks, R. L.

    2014-04-01

    The architecture of the SAM software package intended for modeling beyond-design-basis accidents at nuclear power plants equipped with VVER reactors evolving into a severe stage with core melting and failure of the reactor pressure vessel is presented. By using the SAM software package it is possible to perform comprehensive modeling of the entire emergency process from the failure initiating event to the stage of severe accident involving meltdown of nuclear fuel, failure of the reactor pressure vessel, and escape of corium onto the concrete basement or into the corium catcher with retention of molten products in it.

  18. In the interests of time: improving HIV allocative efficiency modelling via optimal time-varying allocations

    PubMed Central

    Shattock, Andrew J; Kerr, Cliff C; Stuart, Robyn M; Masaki, Emiko; Fraser, Nicole; Benedikt, Clemens; Gorgens, Marelize; Wilson, David P; Gray, Richard T

    2016-01-01

    Introduction International investment in the response to HIV and AIDS has plateaued and its future level is uncertain. With many countries committed to ending the epidemic, it is essential to allocate available resources efficiently over different response periods to maximize impact. The objective of this study is to propose a technique to determine the optimal allocation of funds over time across a set of HIV programmes to achieve desirable health outcomes. Methods We developed a technique to determine the optimal time-varying allocation of funds (1) when the future annual HIV budget is pre-defined and (2) when the total budget over a period is pre-defined, but the year-on-year budget is to be optimally determined. We use this methodology with Optima, an HIV transmission model that uses non-linear relationships between programme spending and associated programmatic outcomes to quantify the expected epidemiological impact of spending. We apply these methods to data collected from Zambia to determine the optimal distribution of resources to fund the right programmes, for the right people, at the right time. Results and discussion Considering realistic implementation and ethical constraints, we estimate that the optimal time-varying redistribution of the 2014 Zambian HIV budget between 2015 and 2025 will lead to a 7.6% (7.3% to 7.8%) decrease in cumulative new HIV infections compared with a baseline scenario where programme allocations remain at 2014 levels. This compares to a 5.1% (4.6% to 5.6%) reduction in new infections using an optimal allocation with constant programme spending that recommends unrealistic programmatic changes. Contrasting priorities for programme funding arise when assessing outcomes for a five-year funding period over 5-, 10- and 20-year time horizons. Conclusions Countries increasingly face the need to do more with the resources available. The methodology presented here can aid decision-makers in planning as to when to expand or contract

  19. Allocating the Book Budget: A Model

    ERIC Educational Resources Information Center

    Kohut, Joseph D.

    1974-01-01

    Inflation is currently affecting library book budgets, particularly the acquisition of serials. This model would balance the purchase of serials against the purchase of monographs by individual funding units within the academic library. Consideration is given to inflation as a cost factor. The model is applied to a specific example. (Author/LS)

  20. Resource Allocation Procedure at Queensland University: A Dynamic Modelling Project.

    ERIC Educational Resources Information Center

    Galbraith, Peter L.; Carss, Brian W.

    A structural reorganization of the University of Queensland, Australia, was undertaken to promote efficient resource management, and a resource allocation model was developed to aid in policy evaluation and planning. The operation of the restructured system was based on creating five resource groups to manage the distribution of academic resources…

  1. Error rate information in attention allocation pilot models

    NASA Technical Reports Server (NTRS)

    Faulkner, W. H.; Onstott, E. D.

    1977-01-01

    The Northrop urgency decision pilot model was used in a command tracking task to compare the optimized performance of multiaxis attention allocation pilot models whose urgency functions were (1) based on tracking error alone, and (2) based on both tracking error and error rate. A matrix of system dynamics and command inputs was employed, to create both symmetric and asymmetric two axis compensatory tracking tasks. All tasks were single loop on each axis. Analysis showed that a model that allocates control attention through nonlinear urgency functions using only error information could not achieve performance of the full model whose attention shifting algorithm included both error and error rate terms. Subsequent to this analysis, tracking performance predictions for the full model were verified by piloted flight simulation. Complete model and simulation data are presented.

  2. SECURITY MODELING FOR MARITIME PORT DEFENSE RESOURCE ALLOCATION

    SciTech Connect

    Harris, S.; Dunn, D.

    2010-09-07

    Redeployment of existing law enforcement resources and optimal use of geographic terrain are examined for countering the threat of a maritime based small-vessel radiological or nuclear attack. The evaluation was based on modeling conducted by the Savannah River National Laboratory that involved the development of options for defensive resource allocation that can reduce the risk of a maritime based radiological or nuclear threat. A diverse range of potential attack scenarios has been assessed. As a result of identifying vulnerable pathways, effective countermeasures can be deployed using current resources. The modeling involved the use of the Automated Vulnerability Evaluation for Risks of Terrorism (AVERT{reg_sign}) software to conduct computer based simulation modeling. The models provided estimates for the probability of encountering an adversary based on allocated resources including response boats, patrol boats and helicopters over various environmental conditions including day, night, rough seas and various traffic flow rates.

  3. Age and equity in liver transplantation: An organ allocation model.

    PubMed

    Cucchetti, Alessandro; Ross, Lainie Friedman; Thistlethwaite, J Richard; Vitale, Alessandro; Ravaioli, Matteo; Cescon, Matteo; Ercolani, Giorgio; Burra, Patrizia; Cillo, Umberto; Pinna, Antonio Daniele

    2015-10-01

    A moral liver allocation policy must be fair. We considered a 2-step, 2-principle allocation system called "age mapping." Its first principle, equal opportunity, ensures that candidates of all ages have an equal chance of getting an organ. Its second principle, prudential lifespan equity, allocates younger donor grafts to younger candidates and older donors to older candidates in order to increase the likelihood that all recipients achieve a "full lifespan." Data from 2476 candidates and 1371 consecutive adult liver transplantations (from 1999 to 2012) were used to determine whether age mapping can reduce the gap in years of life lost (YLL) between younger and older recipients. A parametric Weibull prognostic model was developed to estimate total life expectancy after transplantation using survival of the general population matched by sex and age as a reference. Life expectancy from birth was calculated by adding age at transplant and total life expectancy after transplantation. In multivariate analysis, recipient age, hepatitis C virus status, Model for End-Stage Liver Disease score at transplant of >30, and donor age were significantly related to prognosis after surgery (P < 0.05). The mean (and standard deviation) number of years of life from birth, calculated from the current allocation model, for various age groups were: recipients 18-47 years (n = 340) = 65.2 (3.3); 48-55 years (n = 387) = 72.7 (2.1); 56-61 years (n = 372) = 74.7 (1.7) and for recipients >61 years (n = 272) = 77.4 (1.4). The total number of YLL equaled 523 years. Redistributing liver grafts, using an age mapping algorithm, reduces the lifespan gap between younger and older candidates by 33% (from 12.3% to 8.3%) and achieves a 14% overall reduction of YLL (73 years) compared to baseline liver distribution. In conclusion, deliberately incorporating age into an allocation algorithm promotes fairness and increases efficiency.

  4. Comparing Different Model Structures for Carbon Allocation in the Community Land Model (CLM)

    NASA Astrophysics Data System (ADS)

    Montane, F.; Fox, A. M.; Arellano, A. F.; Scaven, V. L.; Alexander, M. R.; Moore, D. J.

    2015-12-01

    Quantifying the intensity of feedback mechanisms between terrestrial ecosystems and climate is a central challenge for understanding the global carbon cycle. Part of this challenge includes understanding how climate affects not only NPP, but also C allocation in different plant tissues (leaves, stem and roots) which determines the C residence time. For instance, C could be sequestered over longer time periods if changes in climate increase allocation to long-lived plant tissue (e.g. woody components) with respect to short-lived tissues (e.g. leaves). Networks of eddy covariance towers like AmeriFlux provide the infrastructure necessary to study relationships between ecosystem processes and climate forcing. We ran the Community Land Model (CLM) for six temperate forests in North America (AmeriFlux sites) using different model structures for the C allocation module: i) standard carbon allocation module in CLM, which allocates C to the stem and leaves as a dynamic function of NPP and with fixed coefficients for the rest of parameters; ii) alternative C allocation module, which allocates C to the root and stem as a dynamic function of NPP and with fixed coefficients for the rest of parameters; and iii) alternative C allocation module with fixed coefficients for all the parameters. We compare C allocation patterns and climate sensitivities betwen the different model structures and available observations for the sites. We suggest some future approaches to reduce model uncertainty in the current scheme for C allocation in CLM and its climate sensitivity.

  5. Modeling the allocation system: principles for robust design before restructuring.

    PubMed

    Mehrotra, Sanjay; Kilambi, Vikram; Gilroy, Richard; Ladner, Daniela P; Klintmalm, Goran B; Kaplan, Bruce

    2015-02-01

    The United Network for Organ Sharing is poised to resolve geographic disparity in liver transplantation and promote allocation based on medical urgency. At the time of writing, United Network for Organ Sharing is considering redistricting the organ procurement and transplantation network so that patient model for end-stage liver disease scores at transplant is more uniform across regions.We review the proposal with a systems-engineering focus and find that although the proposal is promising, it currently lacks evidence that it would perform effectively under realistic departures from its underlying data and assumptions. Moreover, we caution against prematurely focusing on redistricting as the only method to mitigate disparity. We describe system modeling principles which, if followed, will ensure that the redesigned allocation system is effective and efficient in achieving the intended goals.

  6. SAP Minutes No.2015-03 for FIFRA meeting held 9/15-17/2015. A set of scientific issues being considered by the Environmental Protection Agency regarding development of a spatial aquatic model(SAM)for pesticide risk assessment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    On September 15-17th, 2014, the US Environmental Protection Agency convened a public meeting of the FIFRA Scientific Advisory Panel (SAP) to address scientific issues associated with the agency’s “Development of a Spatial Aquatic Model (SAM) for Pesticide Risk Assessment”. The goal of SAM is to impr...

  7. Heterotypic Sam-Sam association between Odin-Sam1 and Arap3-Sam: binding affinity and structural insights.

    PubMed

    Mercurio, Flavia A; Marasco, Daniela; Pirone, Luciano; Scognamiglio, Pasqualina L; Pedone, Emilia M; Pellecchia, Maurizio; Leone, Marilisa

    2013-01-01

    Arap3 is a phosphatidylinositol 3 kinase effector protein that plays a role as GTPase activator (GAP) for Arf6 and RhoA. Arap3 contains a sterile alpha motif (Sam) domain that has high sequence homology with the Sam domain of the EphA2-receptor (EphA2-Sam). Both Arap3-Sam and EphA2-Sam are able to associate with the Sam domain of the lipid phosphatase Ship2 (Ship2-Sam). Recently, we reported a novel interaction between the first Sam domain of Odin (Odin-Sam1), a protein belonging to the ANKS (ANKyrin repeat and Sam domain containing) family, and EphA2-Sam. In our latest work, we applied NMR spectroscopy, surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) to characterize the association between Arap3-Sam and Odin-Sam1. We show that these two Sam domains interact with low micromolar affinity. Moreover, by means of molecular docking techniques, supported by NMR data, we demonstrate that Odin-Sam1 and Arap3-Sam might bind with a topology that is common to several Sam-Sam complexes. The revealed structural details form the basis for the design of potential peptide antagonists that could be used as chemical tools to investigate functional aspects related to heterotypic Arap3-Sam associations.

  8. On species sampling sequences induced by residual allocation models

    PubMed Central

    Rodríguez, Abel; Quintana, Fernando A.

    2014-01-01

    We discuss fully Bayesian inference in a class of species sampling models that are induced by residual allocation (sometimes called stick-breaking) priors on almost surely discrete random measures. This class provides a generalization of the well-known Ewens sampling formula that allows for additional flexibility while retaining computational tractability. In particular, the procedure is used to derive the exchangeable predictive probability functions associated with the generalized Dirichlet process of Hjort (2000) and the probit stick-breaking prior of Chung and Dunson (2009) and Rodriguez and Dunson (2011). The procedure is illustrated with applications to genetics and nonparametric mixture modeling. PMID:25477705

  9. On species sampling sequences induced by residual allocation models.

    PubMed

    Rodríguez, Abel; Quintana, Fernando A

    2015-02-01

    We discuss fully Bayesian inference in a class of species sampling models that are induced by residual allocation (sometimes called stick-breaking) priors on almost surely discrete random measures. This class provides a generalization of the well-known Ewens sampling formula that allows for additional flexibility while retaining computational tractability. In particular, the procedure is used to derive the exchangeable predictive probability functions associated with the generalized Dirichlet process of Hjort (2000) and the probit stick-breaking prior of Chung and Dunson (2009) and Rodriguez and Dunson (2011). The procedure is illustrated with applications to genetics and nonparametric mixture modeling. PMID:25477705

  10. Traffic Behavior Recognition Using the Pachinko Allocation Model

    PubMed Central

    Huynh-The, Thien; Banos, Oresti; Le, Ba-Vui; Bui, Dinh-Mao; Yoon, Yongik; Lee, Sungyoung

    2015-01-01

    CCTV-based behavior recognition systems have gained considerable attention in recent years in the transportation surveillance domain for identifying unusual patterns, such as traffic jams, accidents, dangerous driving and other abnormal behaviors. In this paper, a novel approach for traffic behavior modeling is presented for video-based road surveillance. The proposed system combines the pachinko allocation model (PAM) and support vector machine (SVM) for a hierarchical representation and identification of traffic behavior. A background subtraction technique using Gaussian mixture models (GMMs) and an object tracking mechanism based on Kalman filters are utilized to firstly construct the object trajectories. Then, the sparse features comprising the locations and directions of the moving objects are modeled by PAM into traffic topics, namely activities and behaviors. As a key innovation, PAM captures not only the correlation among the activities, but also among the behaviors based on the arbitrary directed acyclic graph (DAG). The SVM classifier is then utilized on top to train and recognize the traffic activity and behavior. The proposed model shows more flexibility and greater expressive power than the commonly-used latent Dirichlet allocation (LDA) approach, leading to a higher recognition accuracy in the behavior classification. PMID:26151213

  11. Traffic Behavior Recognition Using the Pachinko Allocation Model.

    PubMed

    Huynh-The, Thien; Banos, Oresti; Le, Ba-Vui; Bui, Dinh-Mao; Yoon, Yongik; Lee, Sungyoung

    2015-01-01

    CCTV-based behavior recognition systems have gained considerable attention in recent years in the transportation surveillance domain for identifying unusual patterns, such as traffic jams, accidents, dangerous driving and other abnormal behaviors. In this paper, a novel approach for traffic behavior modeling is presented for video-based road surveillance. The proposed system combines the pachinko allocation model (PAM) and support vector machine (SVM) for a hierarchical representation and identification of traffic behavior. A background subtraction technique using Gaussian mixture models (GMMs) and an object tracking mechanism based on Kalman filters are utilized to firstly construct the object trajectories. Then, the sparse features comprising the locations and directions of the moving objects are modeled by PAMinto traffic topics, namely activities and behaviors. As a key innovation, PAM captures not only the correlation among the activities, but also among the behaviors based on the arbitrary directed acyclic graph (DAG). The SVM classifier is then utilized on top to train and recognize the traffic activity and behavior. The proposed model shows more flexibility and greater expressive power than the commonly-used latent Dirichlet allocation (LDA) approach, leading to a higher recognition accuracy in the behavior classification. PMID:26151213

  12. Results and Comparison from the SAM Linear Fresnel Technology Performance Model: Preprint

    SciTech Connect

    Wagner, M. J.

    2012-04-01

    This paper presents the new Linear Fresnel technology performance model in NREL's System Advisor Model. The model predicts the financial and technical performance of direct-steam-generation Linear Fresnel power plants, and can be used to analyze a range of system configurations. This paper presents a brief discussion of the model formulation and motivation, and provides extensive discussion of the model performance and financial results. The Linear Fresnel technology is also compared to other concentrating solar power technologies in both qualitative and quantitative measures. The Linear Fresnel model - developed in conjunction with the Electric Power Research Institute - provides users with the ability to model a variety of solar field layouts, fossil backup configurations, thermal receiver designs, and steam generation conditions. This flexibility aims to encompass current market solutions for the DSG Linear Fresnel technology, which is seeing increasing exposure in fossil plant augmentation and stand-alone power generation applications.

  13. Synthia Tonn, SAM Engineer

    NASA Video Gallery

    The Sample Analysis at Mars (SAM) is a suite of instruments developed for use on the Mars Science Laboratory, designed to help find out whether or not Mars ever supported life. This video profiles ...

  14. Cache Allocation in CDN: An Evolutionary Game Generalized Particle Model

    NASA Astrophysics Data System (ADS)

    Feng, Xiang; Lau, Francis C. M.; Gao, Daqi

    Content distribution networks (CDNs) increasingly have been used to reduce the response times experienced by Internet users through placing surrogates close to the clients. This paper presents an object replacement approach based on an evolutionary game generalized particle model (G-GPM). We first propose a problem model for CDNs. The CDN model is then fit into a gravitational field. The origin servers and surrogates are regarded as two kinds of particles which are located in two force-fields. The cache allocation problem is thus transformed into the kinematics and dynamics of the particles in the annular and the round force-fields. The G-GPM approach is unique in four aspects: 1) direct viewing of individual and overall optimization; 2) parallel computing (lower time complexity); 3) multi-objective solution; and 4) being able to deal with some social interactions behaviors.

  15. Fast and slow responses of Southern Ocean sea surface temperature to SAM in coupled climate models

    NASA Astrophysics Data System (ADS)

    Krishnamurti, T. N.; Kumar, Vinay; Simon, Anu; Thomas, Aype; Bhardwaj, Amit; Das, Sweta; Senroy, Soma; Roy Bhowmik, S. K.

    2016-06-01

    A major rain storm in Uttarakhand (India) caused heavy rains and major loss of life from floods and land slide during 16-18 June, 2013. The observed daily maximum rainfall rates (3-hourly) during the 16th and 17th June were 220 and 340 mm respectively. This event is addressed via sensitivity studies using a cloud resolving non-hydrostatic model with detailed microphysics. The streaming of moist air from the east-south-east and warmer air from the south-west contributed to the sustained large population and amplitude of buoyancy and the associated CAPE contributed to the longer period of heavy rains. This study addresses the concept of Buoyancy as a means for large vertical accelerations, stronger vertical motions, extreme rain rates and the mechanisms that relate to the time rates of change. A post-processing algorithm provides an analysis of time rate of change for the buoyancy. Moist air streams and warm/moist air intrusions into heavily raining clouds are part of this buoyancy enhancement framework. Improvements in modeling of the extreme rain event came from adaptive observational strategy that showed lack of moisture data sets in these vital regions. We show that a moist boundary layer near the Bay of Bengal leads to moist rivers of moisture where the horizontal convergence confines a large population of buoyancy elements with large magnitudes of buoyancy that streams towards the region of extreme orographic rains. The areas covered in this study include: (i) Use of high resolution cloud modeling (1-km), (ii) Now casting of rains using physical initialization with a Newtonian relaxation, (iii) Use of an adaptive observational strategy, (iii) Sensitivity of the evolution of fields and population of buoyancy elements to boundary layer moisture, (iv) Role of orography and details of buoyancy budget.

  16. A Thermodynamics Model for the Emergence of a Stripe-like Binary SAM on a Nanoparticle Surface.

    PubMed

    Ge, Xinwei; Ke, Pu Chun; Davis, Thomas P; Ding, Feng

    2015-10-01

    It has been under debate if a self-assembled monolayer (SAM) with two immiscible ligands of different chain lengths and/or bulkiness can form a stripe-like pattern on a nanoparticle (NP) surface. The entropic gain upon such pattern formation due to difference in chain lengths and/or bulkiness has been proposed as the driving force in literature. Using atomistic discrete molecular dynamics simulations it is shown that stripe-like pattern could indeed emerge, but only for a subset of binary SAM systems. In addition to entropic contributions, the formation of a striped pattern also strongly depends upon interligand interactions governed by the physicochemical properties of the ligand constituents. Due to the interplay between entropy and enthalpy, a binary SAM system can be categorized into three different types depending on whether and under what condition a striped pattern can emerge. The results help clarify the ongoing debate and our proposed principle can aid in the engineering of novel binary SAMs on a NP surface.

  17. The senescence-accelerated mouse (SAM): a higher oxidative stress and age-dependent degenerative diseases model.

    PubMed

    Chiba, Yoichi; Shimada, Atsuyoshi; Kumagai, Naoko; Yoshikawa, Keisuke; Ishii, Sanae; Furukawa, Ayako; Takei, Shiro; Sakura, Masaaki; Kawamura, Noriko; Hosokawa, Masanori

    2009-04-01

    The SAM strain of mice is actually a group of related inbred strains consisting of a series of SAMP (accelerated senescence-prone) and SAMR (accelerated senescence-resistant) strains. Compared with the SAMR strains, the SAMP strains show a more accelerated senescence process, a shorter lifespan, and an earlier onset and more rapid progress of age-associated pathological phenotypes similar to human geriatric disorders. The higher oxidative stress status observed in SAMP mice is partly caused by mitochondrial dysfunction, and may be a cause of this senescence acceleration and age-dependent alterations in cell structure and function. Based on our recent observations, we discuss a possible mechanism for mitochondrial dysfunction resulting in the excessive production of reactive oxygen species, and a role for the hyperoxidative stress status in neurodegeneration in SAMP mice. These SAM strains can serve as a useful tool to understand the cellular mechanisms of age-dependent degeneration, and to develop clinical interventions. PMID:18688709

  18. Adapting SAM for CDF

    SciTech Connect

    D. Bonham et al.

    2003-10-13

    The CDF and D0 experiments probe the high-energy frontier and as they do so have accumulated hundreds of Terabytes of data on the way to petabytes of data over the next two years. The experiments have made a commitment to use the developing Grid based on the SAM system to handle these data. The D0 SAM has been extended for use in CDF as common patterns of design emerged to meet the similar requirements of these experiments. The process by which the merger was achieved is explained with particular emphasis on lessons learned concerning the database design patterns plus realization of the use cases.

  19. Modeling healthcare data using multiple-channel latent Dirichlet allocation.

    PubMed

    Lu, Hsin-Min; Wei, Chih-Ping; Hsiao, Fei-Yuan

    2016-04-01

    Information and communications technologies have enabled healthcare institutions to accumulate large amounts of healthcare data that include diagnoses, medications, and additional contextual information such as patient demographics. To gain a better understanding of big healthcare data and to develop better data-driven clinical decision support systems, we propose a novel multiple-channel latent Dirichlet allocation (MCLDA) approach for modeling diagnoses, medications, and contextual information in healthcare data. The proposed MCLDA model assumes that a latent health status group structure is responsible for the observed co-occurrences among diagnoses, medications, and contextual information. Using a real-world research testbed that includes one million healthcare insurance claim records, we investigate the utility of MCLDA. Our empirical evaluation results suggest that MCLDA is capable of capturing the comorbidity structures and linking them with the distribution of medications. Moreover, MCLDA is able to identify the pairing between diagnoses and medications in a record based on the assigned latent groups. MCLDA can also be employed to predict missing medications or diagnoses given partial records. Our evaluation results also show that, in most cases, MCLDA outperforms alternative methods such as logistic regressions and the k-nearest-neighbor (KNN) model for two prediction tasks, i.e., medication and diagnosis prediction. Thus, MCLDA represents a promising approach to modeling healthcare data for clinical decision support.

  20. Modeling healthcare data using multiple-channel latent Dirichlet allocation.

    PubMed

    Lu, Hsin-Min; Wei, Chih-Ping; Hsiao, Fei-Yuan

    2016-04-01

    Information and communications technologies have enabled healthcare institutions to accumulate large amounts of healthcare data that include diagnoses, medications, and additional contextual information such as patient demographics. To gain a better understanding of big healthcare data and to develop better data-driven clinical decision support systems, we propose a novel multiple-channel latent Dirichlet allocation (MCLDA) approach for modeling diagnoses, medications, and contextual information in healthcare data. The proposed MCLDA model assumes that a latent health status group structure is responsible for the observed co-occurrences among diagnoses, medications, and contextual information. Using a real-world research testbed that includes one million healthcare insurance claim records, we investigate the utility of MCLDA. Our empirical evaluation results suggest that MCLDA is capable of capturing the comorbidity structures and linking them with the distribution of medications. Moreover, MCLDA is able to identify the pairing between diagnoses and medications in a record based on the assigned latent groups. MCLDA can also be employed to predict missing medications or diagnoses given partial records. Our evaluation results also show that, in most cases, MCLDA outperforms alternative methods such as logistic regressions and the k-nearest-neighbor (KNN) model for two prediction tasks, i.e., medication and diagnosis prediction. Thus, MCLDA represents a promising approach to modeling healthcare data for clinical decision support. PMID:26898516

  1. Communication Interface for SAMS

    NASA Technical Reports Server (NTRS)

    Koffman, M.; Hartley, F.

    1995-01-01

    An interface is described that supplies communications between the flight instruments and the analog input of an existing conventional recording unit for the Shuttle Space Acceleration Measurement System (SAMS), a data acquisition unit. The architecture and current implementation of an STD bus/LonTalk communication interface are described.

  2. A Model of Resource Allocation in Public School Districts: A Theoretical and Empirical Analysis.

    ERIC Educational Resources Information Center

    Chambers, Jay G.

    This paper formulates a comprehensive model of resource allocation in a local public school district. The theoretical framework specified could be applied equally well to any number of local public social service agencies. Section 1 develops the theoretical model describing the process of resource allocation. This involves the determination of the…

  3. Bringing the Budget Back into Academic Work Allocation Models: A Management Perspective

    ERIC Educational Resources Information Center

    Robertson, Michael; Germov, John

    2015-01-01

    Issues surrounding increasingly constrained resources and reducing levels of sector-based funding require consideration of a different Academic Work Allocation Model (AWAM) approach. Evidence from the literature indicates that an effective work allocation model is founded on the principles of equity and transparency in the distribution and…

  4. Peptide Fragments of Odin-Sam1: Conformational Analysis and Interaction Studies with EphA2-Sam.

    PubMed

    Mercurio, Flavia A; Di Natale, Concetta; Pirone, Luciano; Scognamiglio, Pasqualina L; Marasco, Daniela; Pedone, Emilia M; Saviano, Michele; Leone, Marilisa

    2015-07-27

    Odin is a protein belonging to the ANKS family, and has two tandem Sam domains. The first, Odin-Sam1, binds to the Sam domain of the EphA2 receptor (EphA2-Sam); this interaction could be crucial for the regulation of receptor endocytosis and might have an impact on cancer. Odin-Sam1 associates with EphA2-Sam by adopting a "mid-loop/end-helix" model. In this study three peptide sequences, encompassing the mid-loop interacting portion of Odin-Sam1 and its C-terminal α5 helix, were designed. Their conformational properties were analyzed by CD and NMR. In addition, their abilities to interact with EphA2-Sam were investigated by SPR studies. The peptides adopt a predominantly disordered state in aqueous buffer, but a higher helical content is evident in the presence of the cosolvent trifluoroethanol. Dissociation constants towards EphA2-Sam were in the high micromolar range. The structural findings suggest further routes for the design of potential anti-cancer therapeutics as inhibitors of EphA2-Sam heterotypic interactions.

  5. Peptide Fragments of Odin-Sam1: Conformational Analysis and Interaction Studies with EphA2-Sam.

    PubMed

    Mercurio, Flavia A; Di Natale, Concetta; Pirone, Luciano; Scognamiglio, Pasqualina L; Marasco, Daniela; Pedone, Emilia M; Saviano, Michele; Leone, Marilisa

    2015-07-27

    Odin is a protein belonging to the ANKS family, and has two tandem Sam domains. The first, Odin-Sam1, binds to the Sam domain of the EphA2 receptor (EphA2-Sam); this interaction could be crucial for the regulation of receptor endocytosis and might have an impact on cancer. Odin-Sam1 associates with EphA2-Sam by adopting a "mid-loop/end-helix" model. In this study three peptide sequences, encompassing the mid-loop interacting portion of Odin-Sam1 and its C-terminal α5 helix, were designed. Their conformational properties were analyzed by CD and NMR. In addition, their abilities to interact with EphA2-Sam were investigated by SPR studies. The peptides adopt a predominantly disordered state in aqueous buffer, but a higher helical content is evident in the presence of the cosolvent trifluoroethanol. Dissociation constants towards EphA2-Sam were in the high micromolar range. The structural findings suggest further routes for the design of potential anti-cancer therapeutics as inhibitors of EphA2-Sam heterotypic interactions. PMID:26120079

  6. From Theory to Practice: Implementation of a Resource Allocation Model in Health Departments

    PubMed Central

    Yaylali, Emine; Farnham, Paul G.; Schneider, Karen L.; Landers, Stewart J.; Kouzouian, Oskian; Lasry, Arielle; Purcell, David W.; Green, Timothy A.; Sansom, Stephanie L.

    2016-01-01

    Objective To develop a resource allocation model to optimize health departments’ Centers for Disease Control and Prevention (CDC)–funded HIV prevention budgets to prevent the most new cases of HIV infection and to evaluate the model’s implementation in 4 health departments. Design, Settings, and Participants We developed a linear programming model combined with a Bernoulli process model that allocated a fixed budget among HIV prevention interventions and risk subpopulations to maximize the number of new infections prevented. The model, which required epidemiologic, behavioral, budgetary, and programmatic data, was implemented in health departments in Philadelphia, Chicago, Alabama, and Nebraska. Main Outcome Measures The optimal allocation of funds, the site-specific cost per case of HIV infection prevented rankings by intervention, and the expected number of HIV cases prevented. Results The model suggested allocating funds to HIV testing and continuum-of-care interventions in all 4 health departments. The most cost-effective intervention for all sites was HIV testing in nonclinical settings for men who have sex with men, and the least cost-effective interventions were behavioral interventions for HIV-negative persons. The pilot sites required 3 to 4 months of technical assistance to develop data inputs and generate and interpret the results. Although the sites found the model easy to use in providing quantitative evidence for allocating HIV prevention resources, they criticized the exclusion of structural interventions and the use of the model to allocate only CDC funds. Conclusions Resource allocation models have the potential to improve the allocation of limited HIV prevention resources and can be used as a decision-making guide for state and local health departments. Using such models may require substantial staff time and technical assistance. These model results emphasize the allocation of CDC funds toward testing and continuum-of-care interventions and

  7. Integrated optimal allocation model for complex adaptive system of water resources management (I): Methodologies

    NASA Astrophysics Data System (ADS)

    Zhou, Yanlai; Guo, Shenglian; Xu, Chong-Yu; Liu, Dedi; Chen, Lu; Ye, Yushi

    2015-12-01

    Due to the adaption, dynamic and multi-objective characteristics of complex water resources system, it is a considerable challenge to manage water resources in an efficient, equitable and sustainable way. An integrated optimal allocation model is proposed for complex adaptive system of water resources management. The model consists of three modules: (1) an agent-based module for revealing evolution mechanism of complex adaptive system using agent-based, system dynamic and non-dominated sorting genetic algorithm II methods, (2) an optimal module for deriving decision set of water resources allocation using multi-objective genetic algorithm, and (3) a multi-objective evaluation module for evaluating the efficiency of the optimal module and selecting the optimal water resources allocation scheme using project pursuit method. This study has provided a theoretical framework for adaptive allocation, dynamic allocation and multi-objective optimization for a complex adaptive system of water resources management.

  8. Optimization Model for cooperative water allocation and valuation in large river basins regarding environmental constraints

    NASA Astrophysics Data System (ADS)

    Pournazeri, S.

    2011-12-01

    A comprehensive optimization model named Cooperative Water Allocation Model (CWAM) is developed for equitable and efficient water allocation and valuation of Zab river basin in order to solve the draught problems of Orumieh Lake in North West of Iran. The model's methodology consists of three phases. The first represents an initial water rights allocation among competing users. The second comprises the water reallocation process for complete usage by consumers. The third phase performs an allocation of the net benefit of the stakeholders participating in a coalition by applying cooperative game theory. The environmental constraints are accounted for in the water allocation model by entering probable environmental damage in a target function, and inputting the minimum water requirement of users. The potential of underground water usage is evaluated in order to compensate for the variation in the amount of surface water. This is conducted by applying an integrated economic- hydrologic river basin model. A node-link river basin network is utilized in CWAM which consists of two major blocks. The first indicates the internal water rights allocation and the second is associated to water and net benefit reallocation. System control, loss in links by evaporation or seepage, modification of inflow into the node, loss in nodes and loss in outflow are considered in this model. Water valuation is calculated for environmental, industrial, municipal and agricultural usage by net benefit function. It can be seen that the water rights are allocated efficiently and incomes are distributed appropriately based on quality and quantity limitations.

  9. Model-based metrics of human-automation function allocation in complex work environments

    NASA Astrophysics Data System (ADS)

    Kim, So Young

    Function allocation is the design decision which assigns work functions to all agents in a team, both human and automated. Efforts to guide function allocation systematically has been studied in many fields such as engineering, human factors, team and organization design, management science, and cognitive systems engineering. Each field focuses on certain aspects of function allocation, but not all; thus, an independent discussion of each does not address all necessary issues with function allocation. Four distinctive perspectives emerged from a review of these fields: technology-centered, human-centered, team-oriented, and work-oriented. Each perspective focuses on different aspects of function allocation: capabilities and characteristics of agents (automation or human), team structure and processes, and work structure and the work environment. Together, these perspectives identify the following eight issues with function allocation: 1) Workload, 2) Incoherency in function allocations, 3) Mismatches between responsibility and authority, 4) Interruptive automation, 5) Automation boundary conditions, 6) Function allocation preventing human adaptation to context, 7) Function allocation destabilizing the humans' work environment, and 8) Mission Performance. Addressing these issues systematically requires formal models and simulations that include all necessary aspects of human-automation function allocation: the work environment, the dynamics inherent to the work, agents, and relationships among them. Also, addressing these issues requires not only a (static) model, but also a (dynamic) simulation that captures temporal aspects of work such as the timing of actions and their impact on the agent's work. Therefore, with properly modeled work as described by the work environment, the dynamics inherent to the work, agents, and relationships among them, a modeling framework developed by this thesis, which includes static work models and dynamic simulation, can capture the

  10. A methodological note on location-allocation models.

    PubMed Central

    Scarpaci, J L

    1984-01-01

    Three conditions render the use of standard methodologies inappropriate in solving location-allocation problems. This paper presents one alternative method for assigning an emergency aircraft to one of three hospitals in northern Chile when standard approaches are not suitable. Graph analyses and the demographic potential measures are used in the case presented. The main advantages of this alternative approach are its computational ease and the use of more than one method. PMID:6476173

  11. Neural Network Based Modeling and Analysis of LP Control Surface Allocation

    NASA Technical Reports Server (NTRS)

    Langari, Reza; Krishnakumar, Kalmanje; Gundy-Burlet, Karen

    2003-01-01

    This paper presents an approach to interpretive modeling of LP based control allocation in intelligent flight control. The emphasis is placed on a nonlinear interpretation of the LP allocation process as a static map to support analytical study of the resulting closed loop system, albeit in approximate form. The approach makes use of a bi-layer neural network to capture the essential functioning of the LP allocation process. It is further shown via Lyapunov based analysis that under certain relatively mild conditions the resulting closed loop system is stable. Some preliminary conclusions from a study at Ames are stated and directions for further research are given at the conclusion of the paper.

  12. A mathematical modeling approach to resource allocation for railroad-highway crossing safety upgrades.

    PubMed

    Konur, Dinçer; Golias, Mihalis M; Darks, Brandon

    2013-03-01

    State Departments of Transportation (S-DOT's) periodically allocate budget for safety upgrades at railroad-highway crossings. Efficient resource allocation is crucial for reducing accidents at railroad-highway crossings and increasing railroad as well as highway transportation safety. While a specific method is not restricted to S-DOT's, sorting type of procedures are recommended by the Federal Railroad Administration (FRA), United States Department of Transportation for the resource allocation problem. In this study, a generic mathematical model is proposed for the resource allocation problem for railroad-highway crossing safety upgrades. The proposed approach is compared to sorting based methods for safety upgrades of public at-grade railroad-highway crossings in Tennessee. The comparison shows that the proposed mathematical modeling approach is more efficient than sorting methods in reducing accidents and severity.

  13. SAM II Data and Information

    Atmospheric Science Data Center

    2016-07-06

    ... Data obtained from the Stratospheric Aerosol Measurement (SAM) II instrument, which flew on board the Nimbus-7 ... Spatial Resolution:  The altitude profiles of aerosol extinction have a 1 km vertical resolution. Temporal ...

  14. Faces of Marshall: Sam Ortega

    NASA Video Gallery

    Several Marshall employees were interviewed as part of Marshall's 50th Anniversary activities. Engineer Sam Ortega tells his story of how he came to work as an engineer at Marshall and how sewing a...

  15. A Mathematical Programming Model for the Efficient Allocation of Vocational Technical Education Funds.

    ERIC Educational Resources Information Center

    McNamara, James F.

    This mathematical programing model was developed to provide the State Board of Education with complete information for evaluating decisions about the efficient allocation of vocational education funds to local school districts. The model, based on a supply-demand criterion, was tested on a set of occupational training programs within a given Labor…

  16. The Health Resources Allocation Model (HRAM) for the 21st century.

    PubMed

    Maire, Nicolas; Hegnauer, Michael; Nguyen, Dana; Godelmann, Lucas; Hoffmann, Axel; de Savigny, Don; Tanner, Marcel

    2012-05-01

    The Health Resources Allocation Model (HRAM) is an eLearning tool for health cadres and scientists introducing basic concepts of sub-national, rational district-based health planning and systems thinking under resources constraint. HRAM allows the evaluation of resource allocation strategies in relation to key outcome measures such as coverage, equity of services achieved and number of deaths and disability-adjusted life years (DALYs) prevented. In addition, the model takes into account geographical and demographic characteristics and populations' health seeking behaviour. It can be adapted to different socio-ecological and health system settings. PMID:22639131

  17. The Health Resources Allocation Model (HRAM) for the 21st century.

    PubMed

    Maire, Nicolas; Hegnauer, Michael; Nguyen, Dana; Godelmann, Lucas; Hoffmann, Axel; de Savigny, Don; Tanner, Marcel

    2012-05-01

    The Health Resources Allocation Model (HRAM) is an eLearning tool for health cadres and scientists introducing basic concepts of sub-national, rational district-based health planning and systems thinking under resources constraint. HRAM allows the evaluation of resource allocation strategies in relation to key outcome measures such as coverage, equity of services achieved and number of deaths and disability-adjusted life years (DALYs) prevented. In addition, the model takes into account geographical and demographic characteristics and populations' health seeking behaviour. It can be adapted to different socio-ecological and health system settings.

  18. Modelling information exchange in worker–queen conflict over sex allocation

    PubMed Central

    Pen, Ido; Taylor, Peter D

    2005-01-01

    We investigate the conflict between queen and worker over sex allocation, specifically the allocation of the queen's eggs between workers and reproductives and the allocation of the reproductive eggs between male and female. In contrast to previous models, we allow workers to observe and use information about the strategy of the queen. We consider three conflict models: simultaneous (no information exchange), sequential (a one-way information exchange) and negotiated (an iterated two-way information exchange). We find that the first model produces sex ratios intermediate between the classic queen (1 : 1) and worker (1 : 3) optima. The second model, in which the worker has information about the queen's decisions, produces a different result and one that is somewhat counter-intuitive in that the sex ratios are less female-biased than for the other two models, and in fact are often male-biased. The third model predicts sex ratios intermediate between the first two models. We discuss how these findings may shed new light on observed sex allocation patterns in social insects and we suggest some experimental tests. PMID:16243692

  19. Testing new approaches to carbonate system simulation at the reef scale: the ReefSam model first results, application to a question in reef morphology and future challenges.

    NASA Astrophysics Data System (ADS)

    Barrett, Samuel; Webster, Jody

    2016-04-01

    Numerical simulation of the stratigraphy and sedimentology of carbonate systems (carbonate forward stratigraphic modelling - CFSM) provides significant insight into the understanding of both the physical nature of these systems and the processes which control their development. It also provides the opportunity to quantitatively test conceptual models concerning stratigraphy, sedimentology or geomorphology, and allows us to extend our knowledge either spatially (e.g. between bore holes) or temporally (forwards or backwards in time). The later is especially important in determining the likely future development of carbonate systems, particularly regarding the effects of climate change. This application, by its nature, requires successful simulation of carbonate systems on short time scales and at high spatial resolutions. Previous modelling attempts have typically focused on the scales of kilometers and kilo-years or greater (the scale of entire carbonate platforms), rather than at the scale of centuries or decades, and tens to hundreds of meters (the scale of individual reefs). Previous work has identified limitations in common approaches to simulating important reef processes. We present a new CFSM, Reef Sedimentary Accretion Model (ReefSAM), which is designed to test new approaches to simulating reef-scale processes, with the aim of being able to better simulate the past and future development of coral reefs. Four major features have been tested: 1. A simulation of wave based hydrodynamic energy with multiple simultaneous directions and intensities including wave refraction, interaction, and lateral sheltering. 2. Sediment transport simulated as sediment being moved from cell to cell in an iterative fashion until complete deposition. 3. A coral growth model including consideration of local wave energy and composition of the basement substrate (as well as depth). 4. A highly quantitative model testing approach where dozens of output parameters describing the reef

  20. Visual Attention Allocation Between Robotic Arm and Environmental Process Control: Validating the STOM Task Switching Model

    NASA Technical Reports Server (NTRS)

    Wickens, Christopher; Vieanne, Alex; Clegg, Benjamin; Sebok, Angelia; Janes, Jessica

    2015-01-01

    Fifty six participants time shared a spacecraft environmental control system task with a realistic space robotic arm control task in either a manual or highly automated version. The former could suffer minor failures, whose diagnosis and repair were supported by a decision aid. At the end of the experiment this decision aid unexpectedly failed. We measured visual attention allocation and switching between the two tasks, in each of the eight conditions formed by manual-automated arm X expected-unexpected failure X monitoring- failure management. We also used our multi-attribute task switching model, based on task attributes of priority interest, difficulty and salience that were self-rated by participants, to predict allocation. An un-weighted model based on attributes of difficulty, interest and salience accounted for 96 percent of the task allocation variance across the 8 different conditions. Task difficulty served as an attractor, with more difficult tasks increasing the tendency to stay on task.

  1. Ethical models in bioethics: theory and application in organ allocation policies.

    PubMed

    Petrini, C

    2010-12-01

    Policies for allocating organs to people awaiting a transplant constitute a major ethical challenge. First and foremost, they demand balance between the principles of beneficence and justice, but many other ethically relevant principles are also involved: autonomy, responsibility, equity, efficiency, utility, therapeutic outcome, medical urgency, and so forth. Various organ allocation models can be developed based on the hierarchical importance assigned to a given principle over the others, but none of the principles should be completely disregarded. An ethically acceptable organ allocation policy must therefore be in conformity, to a certain extent, with the requirements of all the principles. Many models for organ allocation can be derived. The utilitarian model aims to maximize benefits, which can be of various types on a social or individual level, such as the number of lives saved, prognosis, and so forth. The prioritarian model favours the neediest or those who suffer most. The egalitarian model privileges equity and justice, suggesting that all people should have an equal opportunity (casual allocation) or priority should be given to those who have been waiting longer. The personalist model focuses on each individual patient, attempting to mesh together all the various aspects affecting the person: therapeutic needs (urgency), fairness, clinical outcomes, respect for persons. In the individualistic model the main element is free choice and the system of opting-in is privileged. Contrary to the individualistic model, the communitarian model identities in the community the fundamental elements for the legitimacy of choices: therefore, the system of opting-out is privileged. This article does not aim at suggesting practical solutions. Rather, it furnishes to decision makers an overview on the possible ethical approach to this matter.

  2. Ethical models in bioethics: theory and application in organ allocation policies.

    PubMed

    Petrini, C

    2010-12-01

    Policies for allocating organs to people awaiting a transplant constitute a major ethical challenge. First and foremost, they demand balance between the principles of beneficence and justice, but many other ethically relevant principles are also involved: autonomy, responsibility, equity, efficiency, utility, therapeutic outcome, medical urgency, and so forth. Various organ allocation models can be developed based on the hierarchical importance assigned to a given principle over the others, but none of the principles should be completely disregarded. An ethically acceptable organ allocation policy must therefore be in conformity, to a certain extent, with the requirements of all the principles. Many models for organ allocation can be derived. The utilitarian model aims to maximize benefits, which can be of various types on a social or individual level, such as the number of lives saved, prognosis, and so forth. The prioritarian model favours the neediest or those who suffer most. The egalitarian model privileges equity and justice, suggesting that all people should have an equal opportunity (casual allocation) or priority should be given to those who have been waiting longer. The personalist model focuses on each individual patient, attempting to mesh together all the various aspects affecting the person: therapeutic needs (urgency), fairness, clinical outcomes, respect for persons. In the individualistic model the main element is free choice and the system of opting-in is privileged. Contrary to the individualistic model, the communitarian model identities in the community the fundamental elements for the legitimacy of choices: therefore, the system of opting-out is privileged. This article does not aim at suggesting practical solutions. Rather, it furnishes to decision makers an overview on the possible ethical approach to this matter. PMID:21196904

  3. Location-allocation models and new solution methodologies in telecommunication networks

    NASA Astrophysics Data System (ADS)

    Dinu, S.; Ciucur, V.

    2016-08-01

    When designing a telecommunications network topology, three types of interdependent decisions are combined: location, allocation and routing, which are expressed by the following design considerations: how many interconnection devices - consolidation points/concentrators should be used and where should they be located; how to allocate terminal nodes to concentrators; how should the voice, video or data traffic be routed and what transmission links (capacitated or not) should be built into the network. Including these three components of the decision into a single model generates a problem whose complexity makes it difficult to solve. A first method to address the overall problem is the sequential one, whereby the first step deals with the location-allocation problem and based on this solution the subsequent sub-problem (routing the network traffic) shall be solved. The issue of location and allocation in a telecommunications network, called "The capacitated concentrator location- allocation - CCLA problem" is based on one of the general location models on a network in which clients/demand nodes are the terminals and facilities are the concentrators. Like in a location model, each client node has a demand traffic, which must be served, and the facilities can serve these demands within their capacity limit. In this study, the CCLA problem is modeled as a single-source capacitated location-allocation model whose optimization objective is to determine the minimum network cost consisting of fixed costs for establishing the locations of concentrators, costs for operating concentrators and costs for allocating terminals to concentrators. The problem is known as a difficult combinatorial optimization problem for which powerful algorithms are required. Our approach proposes a Fuzzy Genetic Algorithm combined with a local search procedure to calculate the optimal values of the location and allocation variables. To confirm the efficiency of the proposed algorithm with respect

  4. Language Preference and Time Allocation in the Joint Languages Diversification Model.

    ERIC Educational Resources Information Center

    Kenning, Marie-Madeleine

    1994-01-01

    Presents a follow-up study of a joint languages diversification model. The research focuses on the evolution of the relative popularity of the three languages involved in the scheme (French, German, and Italian) and the impact of a timetable that allocates different amounts of time to two languages with a switch halfway through the year. (five…

  5. Omega-3 polyunsaturated fatty acids ameliorate the severity of ileitis in the senescence accelerated mice (SAM)P1/Yit mice model

    PubMed Central

    Matsunaga, H; Hokari, R; Kurihara, C; Okada, Y; Takebayashi, K; Okudaira, K; Watanabe, C; Komoto, S; Nakamura, M; Tsuzuki, Y; Kawaguchi, A; Nagao, S; Miura, S

    2009-01-01

    Clinical studies using omega-3 polyunsaturated fatty acids (ω3-PUFA) to Crohn's disease (CD) are conflicting. Beneficial effects of dietary ω3-PUFA intake in various experimental inflammatory bowel disease (IBD) models have been reported. However, animal models of large intestinal inflammation have been used in all previous studies, and the effect of ω3 fat in an animal model of small intestinal inflammation has not been reported. We hypothesized that the effects of ω3 fat are different between large and small intestine. The aim of this study was to determine whether the direct effect of ω3 fat is beneficial for small intestinal inflammation. Senescence accelerated mice (SAM)P1/Yit mice showed remarkable inflammation of the terminal ileum spontaneously. The numbers of F4/80-positive monocyte–macrophage cells as well as β7-integrin-positive lymphocytes in the intestinal mucosa were increased significantly compared with those in the control mice (AKR-J mice). The area of mucosal addressin cell adhesion molecule-1 (MAdCAM-1)-positive vessels was also increased. The degree of expression levels of monocyte chemoattractant protein-1 (MCP-1), interleukin (IL)-6 and interferon (IFN)-γ mRNA were increased significantly compared with those in the control mice. The feeding of two different kinds of ω3 fat (fish-oil-rich and perilla-oil-rich diets) for 16 weeks to SAMP1/Yit mice ameliorated inflammation of the terminal ileum significantly. In both the ω3-fat-rich diet groups, enhanced infiltration of F4/80-positive monocytes/macrophages in intestinal mucosa of SAMP1/Yit mice cells and the increased levels of MCP-1, IL-6 and IFN-γ mRNA expression were ameliorated significantly compared with those in the control diet group. The results suggest that ω3 fat is beneficial for small intestinal inflammation by inhibition of monocyte recruitment to inflamed intestinal mucosa. PMID:19793338

  6. A modeling framework for inferring tree growth and allocation from physiological, morphological and allometric traits.

    PubMed

    Ogle, Kiona; Pacala, Stephen W

    2009-04-01

    Predictions of forest succession, diversity and function require an understanding of how species differ in their growth, allocation patterns and susceptibility to mortality. These processes in turn are affected by allometric constraints and the physiological state of the tree, both of which are coupled to the tree's labile carbon status. Ultimately, insight into the hidden labile pools and the processes affecting the allocation of labile carbon to storage, maintenance and growth will improve our ability to predict tree growth, mortality and forest dynamics. We developed the 'Allometrically Constrained Growth and Carbon Allocation' (ACGCA) model that explicitly couples tree growth, mortality, allometries and labile carbon. This coupling results in (1) a semi-mechanistic basis for predicting tree death, (2) an allocation scheme that simultaneously satisfies allometric relationships and physiology-based carbon dynamics and (3) a range of physiological states that are consistent with tree behavior (e.g., healthy, static, shrinking, recovering, recovered and dead). We present the ACGCA model and illustrate aspects of its behavior by conducting simulations under different forest gap dynamics scenarios and with parameter values obtained for two ecologically dissimilar species: loblolly pine (Pinus taeda L.) and red maple (Acer rubrum L.). The model reproduces growth and mortality patterns of these species that are consistent with their shade-tolerance and succession status. The ACGCA framework provides an alternative, and potentially improved, approach for predicting tree growth, mortality and forest dynamics. PMID:19203984

  7. On LAM's and SAM's for Halley's rotation

    NASA Technical Reports Server (NTRS)

    Peale, Stanton J.

    1992-01-01

    Non principal axis rotation for comet Halley is inferred from dual periodicities evident in the observations. The modes where the spin axis precesses around the axis of minimum moment of inertia (long axis mode or LAM) and where it precesses around the axis of maximum moment of inertia (short axis mode or SAM) are described from an inertial point of view. The currently favored LAM model for Halley's rotation state satisfies observational and dynamical constraints that apparently no SAM can satisfy. But it cannot reproduce the observed post perihelion brightening through seasonal illumination of localized sources on the nucleus, whereas a SAM can easily produce post or pre perihelion brightening by this mechanism. However, the likelihood of a LAM rotation for elongated nuclei of periodic comets such as Halley together with Halley's extreme post perihelion behavior far from the Sun suggest that Halley's post perihelion brightening may be due to effects other than seasonal illumination of localized sources, and therefore such brightening may not constrain its rotation state.

  8. Modeling forest C and N allocation responses to free-air CO2 enrichment

    NASA Astrophysics Data System (ADS)

    Luus, Kristina; De Kauwe, Martin; Walker, Anthony; Werner, Christian; Iversen, Colleen; McCarthy, Heather; Medlyn, Belinda; Norby, Richard; Oren, Ram; Zak, Donald; Zaehle, Sönke

    2015-04-01

    Vegetation allocation patterns and soil-vegetation partitioning of C and N are predicted to change in response to rising atmospheric concentrations of CO2. These allocation responses to rising CO2 have been examined at the ecosystem level through through free-air CO2 enrichment (FACE) experiments, and their global implications for the timing of progressive N limitation (PNL) and C sequestration have been predicted for ~100 years using a variety of ecosystem models. However, recent FACE model-data syntheses studies [1,2,3] have indicated that ecosystem models do not capture the 5-10 year site-level ecosystem allocation responses to elevated CO2. This may be due in part to the missing representation of the rhizosphere interactions between plants and soil biota in models. Ecosystem allocation of C and N is altered by interactions between soil and vegetation through the priming effect: as plant N availability diminishes, plants respond physiologically by altering their tissue allocation strategies so as to increase rates of root growth and rhizodeposition. In response, either soil organic material begins to accumulate, which hastens the onset of PNL, or soil microbes start to decompose C more rapidly, resulting in increased N availability for plant uptake, which delays PNL. In this study, a straightforward approach for representing rhizosphere interactions in ecosystem models was developed through which C and N allocation to roots and rhizodeposition responds dynamically to elevated CO2 conditions, modifying soil decomposition rates without pre-specification of the direction in which soil C and N accumulation should shift in response to elevated CO2. This approach was implemented in a variety of ecosystem models ranging from stand (G'DAY), to land surface (CLM 4.5, O-CN), to dynamic global vegetation (LPJ-GUESS) models. Comparisons against data from three forest FACE sites (Duke, Oak Ridge & Rhinelander) indicated that representing rhizosphere interactions allowed

  9. Technical documentation and user's guide for City-County Allocation Model (CCAM). Version 1. 0

    SciTech Connect

    Clark, L.T. Jr.; Scott, M.J.; Hammer, P.

    1986-05-01

    The City-County Allocation Model (CCAM) was developed as part of the Monitored Retrievable Storage (MRS) Program. The CCAM model was designed to allocate population changes forecasted by the MASTER model to specific local communities within commuting distance of the MRS facility. The CCAM model was designed to then forecast the potential changes in demand for key community services such as housing, police protection, and utilities for these communities. The CCAM model uses a flexible on-line data base on demand for community services that is based on a combination of local service levels and state and national service standards. The CCAM model can be used to quickly forecast the potential community service consequence of economic development for local communities anywhere in the country. The remainder of this document is organized as follows. The purpose of this manual is to assist the user in understanding and operating the City-County Allocation Model (CCAM). The annual explains the data sources for the model and code modifications as well as the operational procedures.

  10. Sperm competition games: the risk model can generate higher sperm allocation to virgin females.

    PubMed

    Ball, M A; Parker, G A

    2007-03-01

    We examine the risk model in sperm competition games for cases where female fertility increases significantly with sperm numbers (sperm limitation). Without sperm competition, sperm allocation increases with sperm limitation. We define 'average risk' as the probability q that females in the population mate twice, and 'perceived risk' as the information males gain about the sperm competition probability with individual females. If males obtain no information from individual females, sperm numbers increase with q unless sperm limitation is high and one of the two competing ejaculates is strongly disfavoured. If males can distinguish between virgin and mated females, greater sperm allocation to virgins is favoured by high sperm limitation, high q, and by the second male's ejaculate being disfavoured. With high sperm limitation, sperm allocation to virgins increases and to mated females decreases with q at high q levels. With perfect information about female mating pattern, sperm allocation (i) to virgins that will mate again exceeds that to mated females and to virgins that will mate only once, (ii) to virgins that mate only once exceeds that for mated females if q is high and there is high second male disadvantage and (iii) to each type of female can decrease with q if sperm limitation is high, although the average allocation increases at least across low q levels. In general, higher sperm allocation to virgins is favoured by: strong disadvantage to the second ejaculate, high sperm limitation, high average risk and increased information (perceived risk). These conditions may apply in a few species, especially spiders. PMID:17305842

  11. How a new funding model will shift allocations from the Global Fund to Fight AIDS, tuberculosis, and malaria.

    PubMed

    Fan, Victoria Y; Glassman, Amanda; Silverman, Rachel L

    2014-12-01

    Policy makers deciding how to fund global health programs in low- and middle-income countries face important but difficult questions about how to allocate resources across countries. In this article we present a typology of three allocation methodologies to align allocations with priorities. We then apply our typology to the Global Fund to Fight AIDS, Tuberculosis, and Malaria. We examined the Global Fund's historical HIV allocations and its predicted allocations under a new funding model that creates an explicit allocation methodology. We found that under the new funding model, substantial shifts in the Global Fund's portfolio are likely to result from concentrating resources in countries with more HIV cases and lower per capita incomes. For example, South Africa, which had 15.8 percent of global HIV cases in 2009, could see its Global Fund HIV funding more than triple, from historic levels that averaged 3.0 percent to 9.7 percent of total Global Fund allocations. The new funding model methodology is expected, but not guaranteed, to improve the efficiency of Global Fund allocations in comparison to historical practice. We conclude with recommendations for the Global Fund and other global health donors to further develop their allocation methodologies and processes to improve efficiency and transparency.

  12. Solution structure of the first Sam domain of Odin and binding studies with the EphA2 receptor.

    PubMed

    Mercurio, Flavia Anna; Marasco, Daniela; Pirone, Luciano; Pedone, Emilia Maria; Pellecchia, Maurizio; Leone, Marilisa

    2012-03-13

    The EphA2 receptor plays key roles in many physiological and pathological events, including cancer. The process of receptor endocytosis and the consequent degradation have attracted attention as possible means of overcoming the negative outcomes of EphA2 in cancer cells and decreasing tumor malignancy. A recent study indicates that Sam (sterile alpha motif) domains of Odin, a member of the ANKS (ankyrin repeat and sterile alpha motif domain-containing) family of proteins, are important for the regulation of EphA2 endocytosis. Odin contains two tandem Sam domains (Odin-Sam1 and -Sam2). Herein, we report on the nuclear magnetic resonance (NMR) solution structure of Odin-Sam1; through a variety of assays (employing NMR, surface plasmon resonance, and isothermal titration calorimetry techniques), we clearly demonstrate that Odin-Sam1 binds to the Sam domain of EphA2 in the low micromolar range. NMR chemical shift perturbation experiments and molecular modeling studies point out that the two Sam domains interact with a head-to-tail topology characteristic of several Sam-Sam complexes. This binding mode is similar to that we have previously proposed for the association between the Sam domains of the lipid phosphatase Ship2 and EphA2. This work further validates structural elements relevant for the heterotypic Sam-Sam interactions of EphA2 and provides novel insights for the design of potential therapeutic compounds that can modulate receptor endocytosis.

  13. Allocation Variable-Based Probabilistic Algorithm to Deal with Label Switching Problem in Bayesian Mixture Models

    PubMed Central

    Pan, Jia-Chiun; Liu, Chih-Min; Hwu, Hai-Gwo; Huang, Guan-Hua

    2015-01-01

    The label switching problem occurs as a result of the nonidentifiability of posterior distribution over various permutations of component labels when using Bayesian approach to estimate parameters in mixture models. In the cases where the number of components is fixed and known, we propose a relabelling algorithm, an allocation variable-based (denoted by AVP) probabilistic relabelling approach, to deal with label switching problem. We establish a model for the posterior distribution of allocation variables with label switching phenomenon. The AVP algorithm stochastically relabel the posterior samples according to the posterior probabilities of the established model. Some existing deterministic and other probabilistic algorithms are compared with AVP algorithm in simulation studies, and the success of the proposed approach is demonstrated in simulation studies and a real dataset. PMID:26458185

  14. Employing resource allocation modeling to inform HIV prevention planning for the state of Iowa.

    PubMed

    Holtgrave, David R; Young, Patricia A; Mayer, Randall R; Maulsby, Cathy; Kim, J Janet

    2013-10-01

    In fiscal year (FY) 2012, the Centers for Disease Control and Prevention (CDC) reallocated their HIV prevention funding to U.S. states, territories, and some cities so as to be more highly correlated with 2008 HIV prevalence. A jurisdiction's HIV prevention funding could drop as low as $750,000 for FY 2016. Iowa was one state that experienced a substantial funding drop, and it chose to undertake a mathematical modeling exercise to inform the following questions: (a) Given current HIV prevention funding for the state, what is the optimal allocation of resources to maximize infections averted? (b) With this "optimal" resource allocation, how many (and what percentage of) HIV infections in the state can be averted? (c) Is the optimal resource allocation sufficient to achieve the National HIV/AIDS Strategy goal of 25% reduction in HIV incidence? and (d) With the "optimal" resource allocation, is the return on the investment such that it might be considered cost-effective? Here, we describe the results of the policy analysis, and the uses of the results. PMID:24059879

  15. SAM Overview: The Habitability of Mars

    NASA Video Gallery

    Featuring an interview with Paul Mahaffy, SAM's Principal Investigator, this video gives a general overview of SAM's mission aboard the Mars Science Laboratory, otherwise known as the Curiosity rover.

  16. SAM II Data and Information (ASCII)

    Atmospheric Science Data Center

    2016-09-01

    SAM II (ASCII) Data and Information Data obtained from the Stratospheric Aerosol Measurement (SAM) II instrument, ... Guide Documents:  Project Guide Data Set Guide Readme Files:  Data Set (Text file) ...

  17. The Vesicle Protein SAM-4 Regulates the Processivity of Synaptic Vesicle Transport

    PubMed Central

    Zheng, Qun; Ahlawat, Shikha; Schaefer, Anneliese; Mahoney, Tim; Koushika, Sandhya P.; Nonet, Michael L.

    2014-01-01

    Axonal transport of synaptic vesicles (SVs) is a KIF1A/UNC-104 mediated process critical for synapse development and maintenance yet little is known of how SV transport is regulated. Using C. elegans as an in vivo model, we identified SAM-4 as a novel conserved vesicular component regulating SV transport. Processivity, but not velocity, of SV transport was reduced in sam-4 mutants. sam-4 displayed strong genetic interactions with mutations in the cargo binding but not the motor domain of unc-104. Gain-of-function mutations in the unc-104 motor domain, identified in this study, suppress the sam-4 defects by increasing processivity of the SV transport. Genetic analyses suggest that SAM-4, SYD-2/liprin-α and the KIF1A/UNC-104 motor function in the same pathway to regulate SV transport. Our data support a model in which the SV protein SAM-4 regulates the processivity of SV transport. PMID:25329901

  18. Resources allocation in healthcare for cancer: a case study using generalised additive mixed models.

    PubMed

    Musio, Monica; Sauleau, Erik A; Augustin, Nicole H

    2012-11-01

    Our aim is to develop a method for helping resources re-allocation in healthcare linked to cancer, in order to replan the allocation of providers. Ageing of the population has a considerable impact on the use of health resources because aged people require more specialised medical care due notably to cancer. We propose a method useful to monitor changes of cancer incidence in space and time taking into account two age categories, according to healthcar general organisation. We use generalised additive mixed models with a Poisson response, according to the methodology presented in Wood, Generalised additive models: an introduction with R. Chapman and Hall/CRC, 2006. Besides one-dimensional smooth functions accounting for non-linear effects of covariates, the space-time interaction can be modelled using scale invariant smoothers. Incidence data collected by a general cancer registry between 1992 and 2007 in a specific area of France is studied. Our best model exhibits a strong increase of the incidence of cancer along time and an obvious spatial pattern for people more than 70 years with a higher incidence in the central band of the region. This is a strong argument for re-allocating resources for old people cancer care in this sub-region. PMID:23242683

  19. Resources allocation in healthcare for cancer: a case study using generalised additive mixed models.

    PubMed

    Musio, Monica; Sauleau, Erik A; Augustin, Nicole H

    2012-11-01

    Our aim is to develop a method for helping resources re-allocation in healthcare linked to cancer, in order to replan the allocation of providers. Ageing of the population has a considerable impact on the use of health resources because aged people require more specialised medical care due notably to cancer. We propose a method useful to monitor changes of cancer incidence in space and time taking into account two age categories, according to healthcar general organisation. We use generalised additive mixed models with a Poisson response, according to the methodology presented in Wood, Generalised additive models: an introduction with R. Chapman and Hall/CRC, 2006. Besides one-dimensional smooth functions accounting for non-linear effects of covariates, the space-time interaction can be modelled using scale invariant smoothers. Incidence data collected by a general cancer registry between 1992 and 2007 in a specific area of France is studied. Our best model exhibits a strong increase of the incidence of cancer along time and an obvious spatial pattern for people more than 70 years with a higher incidence in the central band of the region. This is a strong argument for re-allocating resources for old people cancer care in this sub-region.

  20. Integrated optimal allocation model for complex adaptive system of water resources management (II): Case study

    NASA Astrophysics Data System (ADS)

    Zhou, Yanlai; Guo, Shenglian; Xu, Chong-Yu; Liu, Dedi; Chen, Lu; Wang, Dong

    2015-12-01

    Climate change, rapid economic development and increase of the human population are considered as the major triggers of increasing challenges for water resources management. This proposed integrated optimal allocation model (IOAM) for complex adaptive system of water resources management is applied in Dongjiang River basin located in the Guangdong Province of China. The IOAM is calibrated and validated under baseline period 2010 year and future period 2011-2030 year, respectively. The simulation results indicate that the proposed model can make a trade-off between demand and supply for sustainable development of society, economy, ecology and environment and achieve adaptive management of water resources allocation. The optimal scheme derived by multi-objective evaluation is recommended for decision-makers in order to maximize the comprehensive benefits of water resources management.

  1. Equity weights in the allocation of health care: the rank-dependent QALY model.

    PubMed

    Bleichrodt, Han; Diecidue, Enrico; Quiggin, John

    2004-01-01

    This paper introduces the rank-dependent quality-adjusted life-years (QALY) model, a new method to aggregate QALYs in economic evaluations of health care. The rank-dependent QALY model permits the formalization of influential concepts of equity in the allocation of health care, such as the fair innings approach, and it includes as special cases many of the social welfare functions that have been proposed in the literature. An important advantage of the rank-dependent QALY model is that it offers a straightforward procedure to estimate equity weights for QALYs. We characterize the rank-dependent QALY model and argue that its central condition has normative appeal.

  2. A model for dynamic allocation of human attention among multiple tasks

    NASA Technical Reports Server (NTRS)

    Sheridan, T. B.; Tulga, M. K.

    1978-01-01

    The problem of multi-task attention allocation with special reference to aircraft piloting is discussed with the experimental paradigm used to characterize this situation and the experimental results obtained in the first phase of the research. A qualitative description of an approach to mathematical modeling, and some results obtained with it are also presented to indicate what aspects of the model are most promising. Two appendices are given which (1) discuss the model in relation to graph theory and optimization and (2) specify the optimization algorithm of the model.

  3. PID feedback controller used as a tactical asset allocation technique: The G.A.M. model

    NASA Astrophysics Data System (ADS)

    Gandolfi, G.; Sabatini, A.; Rossolini, M.

    2007-09-01

    The objective of this paper is to illustrate a tactical asset allocation technique utilizing the PID controller. The proportional-integral-derivative (PID) controller is widely applied in most industrial processes; it has been successfully used for over 50 years and it is used by more than 95% of the plants processes. It is a robust and easily understood algorithm that can provide excellent control performance in spite of the diverse dynamic characteristics of the process plant. In finance, the process plant, controlled by the PID controller, can be represented by financial market assets forming a portfolio. More specifically, in the present work, the plant is represented by a risk-adjusted return variable. Money and portfolio managers’ main target is to achieve a relevant risk-adjusted return in their managing activities. In literature and in the financial industry business, numerous kinds of return/risk ratios are commonly studied and used. The aim of this work is to perform a tactical asset allocation technique consisting in the optimization of risk adjusted return by means of asset allocation methodologies based on the PID model-free feedback control modeling procedure. The process plant does not need to be mathematically modeled: the PID control action lies in altering the portfolio asset weights, according to the PID algorithm and its parameters, Ziegler-and-Nichols-tuned, in order to approach the desired portfolio risk-adjusted return efficiently.

  4. Game Theoretic Modeling of Water Resources Allocation Under Hydro-Climatic Uncertainty

    NASA Astrophysics Data System (ADS)

    Brown, C.; Lall, U.; Siegfried, T.

    2005-12-01

    Typical hydrologic and economic modeling approaches rely on assumptions of climate stationarity and economic conditions of ideal markets and rational decision-makers. In this study, we incorporate hydroclimatic variability with a game theoretic approach to simulate and evaluate common water allocation paradigms. Game Theory may be particularly appropriate for modeling water allocation decisions. First, a game theoretic approach allows economic analysis in situations where price theory doesn't apply, which is typically the case in water resources where markets are thin, players are few, and rules of exchange are highly constrained by legal or cultural traditions. Previous studies confirm that game theory is applicable to water resources decision problems, yet applications and modeling based on these principles is only rarely observed in the literature. Second, there are numerous existing theoretical and empirical studies of specific games and human behavior that may be applied in the development of predictive water allocation models. With this framework, one can evaluate alternative orderings and rules regarding the fraction of available water that one is allowed to appropriate. Specific attributes of the players involved in water resources management complicate the determination of solutions to game theory models. While an analytical approach will be useful for providing general insights, the variety of preference structures of individual players in a realistic water scenario will likely require a simulation approach. We propose a simulation approach incorporating the rationality, self-interest and equilibrium concepts of game theory with an agent-based modeling framework that allows the distinct properties of each player to be expressed and allows the performance of the system to manifest the integrative effect of these factors. Underlying this framework, we apply a realistic representation of spatio-temporal hydrologic variability and incorporate the impact of

  5. SAMS Acceleration Measurements on MIR

    NASA Technical Reports Server (NTRS)

    Moskowitz, Milton E.; Hrovat, Kenneth; Finkelstein, Robert; Reckart, Timothy

    1997-01-01

    During NASA Increment 3 (September 1996 to January 1997), about 5 gigabytes of acceleration data were collected by the Space Acceleration Measurement System (SAMS) onboard the Russian Space Station, Mir. The data were recorded on 11 optical disks and were returned to Earth on STS-81. During this time, SAMS data were collected in the Priroda module to support the following experiments: the Mir Structural Dynamics Experiment (MiSDE) and Binary Colloidal Alloy Tests (BCAT). This report points out some of the salient features of the microgravity environment to which these experiments were exposed. Also documented are mission events of interest such as the docked phase of STS-81 operations, a Progress engine burn, attitude control thruster operation, and crew exercise. Also included are a description of the Mir module orientations, and the panel notations within the modules. This report presents an overview of the SAMS acceleration measurements recorded by 10 Hz and 100 Hz sensor heads. Variations in the acceleration environment caused by unique activities such as crew exercise and life-support fans are presented. The analyses included herein complement those presented in previous mission summary reports published by the Principal Investigator Microgravity Services (PIMS) group.

  6. Basin Economic Allocation Model (BEAM): An economic model of water use developed for the Aral Sea Basin

    NASA Astrophysics Data System (ADS)

    Riegels, Niels; Kromann, Mikkel; Karup Pedersen, Jesper; Lindgaard-Jørgensen, Palle; Sokolov, Vadim; Sorokin, Anatoly

    2013-04-01

    The water resources of the Aral Sea basin are under increasing pressure, particularly from the conflict over whether hydropower or irrigation water use should take priority. The purpose of the BEAM model is to explore the impact of changes to water allocation and investments in water management infrastructure on the overall welfare of the Aral Sea basin. The BEAM model estimates welfare changes associated with changes to how water is allocated between the five countries in the basin (Kazakhstan, Kyrgyz Republic, Tajikistan, Turkmenistan and Uzbekistan; water use in Afghanistan is assumed to be fixed). Water is allocated according to economic optimization criteria; in other words, the BEAM model allocates water across time and space so that the economic welfare associated with water use is maximized. The model is programmed in GAMS. The model addresses the Aral Sea Basin as a whole - that is, the rivers Syr Darya, Amu Darya, Kashkadarya, and Zarafshan, as well as the Aral Sea. The model representation includes water resources, including 14 river sections, 6 terminal lakes, 28 reservoirs and 19 catchment runoff nodes, as well as land resources (i.e., irrigated croplands). The model covers 5 sectors: agriculture (crops: wheat, cotton, alfalfa, rice, fruit, vegetables and others), hydropower, nature, households and industry. The focus of the model is on welfare impacts associated with changes to water use in the agriculture and hydropower sectors. The model aims at addressing the following issues of relevance for economic management of water resources: • Physical efficiency (estimating how investments in irrigation efficiency affect economic welfare). • Economic efficiency (estimating how changes in how water is allocated affect welfare). • Equity (who will gain from changes in allocation of water from one sector to another and who will lose?). Stakeholders in the region have been involved in the development of the model, and about 10 national experts, including

  7. Co-allocation model for complex equipment project risk based on gray information

    NASA Astrophysics Data System (ADS)

    Zhi-geng, Fang; Jin-yu, Sun

    2013-10-01

    As the fact that complex equipment project is a multi-level co-development network system and milestones connect with each other in accordance with the logical relationship between different levels, we can decompose the complex equipment project into several multi-level milestones. This paper has designed several connecting nodes of collaborative milestone and established a new co-allocation model for complex equipment project risk based on gray information. Take comprehensive trial phase of a large aircraft developed project as an example to prove the effectiveness and feasibility of the above models and algorithms, which provides a new analysis methods and research ideas.

  8. Carbon allocation under light and nitrogen resource gradients in two model marine phytoplankton(1).

    PubMed

    Bittar, Thais B; Lin, Yajuan; Sassano, Lara R; Wheeler, Benjamin J; Brown, Susan L; Cochlan, William P; Johnson, Zackary I

    2013-06-01

    Marine phytoplankton have conserved elemental stoichiometry, but there can be significant deviations from this Redfield ratio. Moreover, phytoplankton allocate reduced carbon (C) to different biochemical pools based on nutritional status and light availability, adding complexity to this relationship. This allocation influences physiology, ecology, and biogeochemistry. Here, we present results on the physiological and biochemical properties of two evolutionarily distinct model marine phytoplankton, a diatom (cf. Staurosira sp. Ehrenberg) and a chlorophyte (Chlorella sp. M. Beijerinck) grown under light and nitrogen resource gradients to characterize how carbon is allocated under different energy and substrate conditions. We found that nitrogen (N)-replete growth rate increased monotonically with light until it reached a threshold intensity (~200 μmol photons · m(-2)  · s(-1) ). For Chlorella sp., the nitrogen quota (pg · μm(-3) ) was greatest below this threshold, beyond which it was reduced by the effect of N-stress, while for Staurosira sp. there was no trend. Both species maintained constant maximum quantum yield of photosynthesis (mol C · mol photons(-1) ) over the range of light and N-gradients studied (although each species used different photophysiological strategies). In both species, C:chl a (g · g(-1) ) increased as a function of light and N-stress, while C:N (mol · mol(-1) ) and relative neutral lipid:C (rel. lipid · g(-1) ) were most strongly influenced by N-stress above the threshold light intensity. These results demonstrated that the interaction of substrate (N-availability) and energy gradients influenced C-allocation, and that general patterns of biochemical responses may be conserved among phytoplankton; they provided a framework for predicting phytoplankton biochemical composition in ecological, biogeochemical, or biotechnological applications.

  9. Towards optimal allocation of computer resources: trade-offs between uncertainty, discretization and model reduction

    NASA Astrophysics Data System (ADS)

    Zinkhahn, M.; Leube, P.; Nowak, W.; de Barros, F. P. J.

    2012-04-01

    In recent years, there has been an increase in the computational complexity of hydro(geo)logical models. This has been driven by new problems addressing large-scale relationships like global warming, reactive transport on the catchment scale or CO2 sequestration. Computational model complexity becomes even more drastic, when facing the ubiquitous need for uncertainty quantification and risk assessment in the environmental sciences. Complexity can be broken down into contributions ranging from spatial, temporal and stochastic resolution, e.g., spatial grid resolution, time step size and number of repeated simulations dedicated to quantify uncertainty. Controlling these resolutions allows keeping the computational cost at a tractable level whilst guaranteeing accurate and robust predictions. Having this possibility at hand triggers our overall driving question: What is the optimal resolution for independent variables (i.e. time and space) to achieve reliable prediction in the presence of uncertainty? Can we determine an overall optimum combination of the number of realizations, spatial and temporal resolutions, needed for overall statistical/physical convergence of model predictions? If so, how can we find it? In other words, how can we optimally allocate available computational resources in order to achieve highest accuracy associated with a given prediction goal? In this work, we present an approach that allows to determine the compromise among different model dimensions (space, time, probability) when allocating computational resources. The overall goal is to maximize the prediction accuracy given limited computational resources. Our analysis is based on the idea to jointly consider the discretization errors and computational costs of all individual model dimensions. This yields a cost-to-error surface which serves to aid modelers in finding an optimal allocation of the computational resources. As a pragmatic way to proceed, we propose running small cost

  10. Towards Optimal Allocation of Computer Resources: Trade-offs between Uncertainty, Discretization and Model Reduction

    NASA Astrophysics Data System (ADS)

    Nowak, W.; Leube, P.; Zinkhahn, M.; de Barros, F.; Rajagopal, R.

    2012-12-01

    In recent years, there has been an increase in the computational complexity of hydro(geo)logical models. This has been driven by new problems addressing large-scale relationships like global warming, reactive transport on the catchment scale or CO2 sequestration. Computational model complexity becomes even more drastic, when facing the ubiquitous need for uncertainty quantification and risk assessment in the environmental sciences. Computational complexity can be broken down into contributions ranging from spatial, temporal and stochastic resolution, e.g., spatial grid resolution, time step size and number of repeated simulations dedicated to quantify uncertainty. Controlling these resolutions allows keeping the computational cost at a tractable level whilst guaranteeing accurate and robust predictions. Having this possibility at hand triggers our overall driving question: What is the optimal resolution for independent variables (i.e. time and space) to achieve reliable prediction in the presence of uncertainty? Can we determine an overall optimum combination of the number of realizations, spatial and temporal resolutions, needed for overall statistical/physical convergence of model predictions? If so, how can we find it? In other words, how can we optimally allocate available computational resources in order to achieve highest accuracy associated with a given prediction goal? In this work, we present an approach that allows to determine the compromise among different model dimensions (space, time, probability) when allocating computational resources. The overall goal is to maximize the prediction accuracy given limited computational resources. Our analysis is based on the idea to jointly consider the discretization errors and computational costs of all individual model dimensions. This yields a cost-to-error surface which serves to aid modelers in finding an optimal allocation of the computational resources. As a pragmatic way to proceed, we propose running small

  11. Primary health-care network monitoring: a hierarchical resource allocation modeling approach.

    PubMed

    Pur, Aleksander; Bohanec, Marko; Lavrac, Nada; Cestnik, Bojan

    2010-01-01

    Management of a primary health-care network (PHCN) is a difficult task in every country. A suitable monitoring system can provide useful information for PHCN management, especially given a large quantity of health-care data that is produced daily in the network. This paper proposes a methodology for structured development of monitoring systems and a PHCN resource allocation monitoring model based on this methodology. The purpose of the monitoring model is to improve the allocation of health-care resources. The proposed methodology is based on modules that are organized into a hierarchy, where each module monitors a particular aspect of the system. This methodology was used to design a PHCN monitoring model for Slovenia. Specific aspects of the Slovenian PHCN were taken into account such as varying needs of patients from different municipalities, existence of small municipalities having less than 1000 residents, the fact that many patients visit physicians in other municipalities, and that physicians may work at more than one location or organization. The main modules in the model are focused on the overall assessment of the PHCN, monitoring of patients visits to health-care providers (HCPs), physical accessibility of health services, segment of patients in municipalities who have not selected a personal physician, assessment of the availability of HCPs for patients, physicians working on more than one location, and available human resources in the PHCN. Most of the model's components are general and can be adapted for other national health-care systems.

  12. Sam.

    ERIC Educational Resources Information Center

    Wilson, James C.

    1988-01-01

    A father writes about his six-year-old son born with hydrocephalus. He describes such day-to-day experiences as going to a baseball game and the grocery store, reactions of friends and strangers to his son's social interactions, and a special day at preschool. The boy's medical treatment, including surgeries, are also described. (VW)

  13. Comparing administered and market-based water allocation systems using an agent-based modeling approach

    NASA Astrophysics Data System (ADS)

    Zhao, J.; Cai, X.; Wang, Z.

    2009-12-01

    It also has been well recognized that market-based systems can have significant advantages over administered systems for water allocation. However there are not many successful water markets around the world yet and administered systems exist commonly in water allocation management practice. This paradox has been under discussion for decades and still calls for attention for both research and practice. This paper explores some insights for the paradox and tries to address why market systems have not been widely implemented for water allocation. Adopting the theory of agent-based system we develop a consistent analytical model to interpret both systems. First we derive some theorems based on the analytical model, with respect to the necessary conditions for economic efficiency of water allocation. Following that the agent-based model is used to illustrate the coherence and difference between administered and market-based systems. The two systems are compared from three aspects: 1) the driving forces acting on the system state, 2) system efficiency, and 3) equity. Regarding economic efficiency, penalty on the violation of water use permits (or rights) under an administered system can lead to system-wide economic efficiency, as well as being acceptable by some agents, which follows the theory of the so-call rational violation. Ideal equity will be realized if penalty equals incentive with an administered system and if transaction costs are zero with a market system. The performances of both agents and the over system are explained with an administered system and market system, respectively. The performances of agents are subject to different mechanisms of interactions between agents under the two systems. The system emergency (i.e., system benefit, equilibrium market price, etc), resulting from the performance at the agent level, reflects the different mechanism of the two systems, the “invisible hand” with the market system and administrative measures (penalty

  14. Modelling the effect of environmental factors on resource allocation in mixed plants systems

    NASA Astrophysics Data System (ADS)

    Gayler, Sebastian; Priesack, Eckart

    2010-05-01

    In most cases, growth of plants is determined by competition against neighbours for the local resources light, water and nutrients and by defending against herbivores and pathogens. Consequently, it is important for a plant to grow fast without neglecting defence. However, plant internal substrates and energy required to support maintenance, growth and defence are limited and the total demand for these processes cannot be met in most cases. Therefore, allocation of carbohydrates to growth related primary metabolism or to defence related secondary metabolism can be seen as a trade-off between the demand of plants for being competitive against neighbours and for being more resistant against pathogens. A modelling approach is presented which can be used to simulate competition for light, water and nutrients between plant individuals in mixed canopies. The balance of resource allocation between growth processes and synthesis of secondary compounds is modelled by a concept originating from different plant defence hypothesis. The model is used to analyse the impact of environmental factors such as soil water and nitrogen availability, planting density and atmospheric concentration of CO2 on growth of plant individuals within mixed canopies and variations in concentration of carbon-based secondary metabolites in plant tissues.

  15. Bit allocation algorithm with novel view synthesis distortion model for multiview video plus depth coding.

    PubMed

    Chung, Tae-Young; Sim, Jae-Young; Kim, Chang-Su

    2014-08-01

    An efficient bit allocation algorithm based on a novel view synthesis distortion model is proposed for the rate-distortion optimized coding of multiview video plus depth sequences in this paper. We decompose an input frame into nonedge blocks and edge blocks. For each nonedge block, we linearly approximate its texture and disparity values, and derive a view synthesis distortion model, which quantifies the impacts of the texture and depth distortions on the qualities of synthesized virtual views. On the other hand, for each edge block, we use its texture and disparity gradients for the distortion model. In addition, we formulate a bit-rate allocation problem in terms of the quantization parameters for texture and depth data. By solving the problem, we can optimally divide a limited bit budget between the texture and depth data, in order to maximize the qualities of synthesized virtual views, as well as those of encoded real views. Experimental results demonstrate that the proposed algorithm yields the average PSNR gains of 1.98 and 2.04 dB in two-view and three-view scenarios, respectively, as compared with a benchmark conventional algorithm.

  16. Variability in Parameter Estimates and Model Fit across Repeated Allocations of Items to Parcels

    ERIC Educational Resources Information Center

    Sterba, Sonya K.; MacCallum, Robert C.

    2010-01-01

    Different random or purposive allocations of items to parcels within a single sample are thought not to alter structural parameter estimates as long as items are unidimensional and congeneric. If, additionally, numbers of items per parcel and parcels per factor are held fixed across allocations, different allocations of items to parcels within a…

  17. A New Model for Equitable and Efficient Resource Allocation to Schools: The Israeli Case

    ERIC Educational Resources Information Center

    BenDavid-Hadar, Iris; Ziderman, Adrian

    2011-01-01

    This paper sets out a new budget allocation formula for schools, designed to achieve a more equitable distribution of educational achievement. In addition to needs-based elements, the suggested composite allocation formula includes an improvement component, whereby schools receive budgetary allocations based on a new incentive measure developed in…

  18. Decomposing biodiversity data using the Latent Dirichlet Allocation model, a probabilistic multivariate statistical method.

    PubMed

    Valle, Denis; Baiser, Benjamin; Woodall, Christopher W; Chazdon, Robin

    2014-12-01

    We propose a novel multivariate method to analyse biodiversity data based on the Latent Dirichlet Allocation (LDA) model. LDA, a probabilistic model, reduces assemblages to sets of distinct component communities. It produces easily interpretable results, can represent abrupt and gradual changes in composition, accommodates missing data and allows for coherent estimates of uncertainty. We illustrate our method using tree data for the eastern United States and from a tropical successional chronosequence. The model is able to detect pervasive declines in the oak community in Minnesota and Indiana, potentially due to fire suppression, increased growing season precipitation and herbivory. The chronosequence analysis is able to delineate clear successional trends in species composition, while also revealing that site-specific factors significantly impact these successional trajectories. The proposed method provides a means to decompose and track the dynamics of species assemblages along temporal and spatial gradients, including effects of global change and forest disturbances.

  19. Concurrent airline fleet allocation and aircraft design with profit modeling for multiple airlines

    NASA Astrophysics Data System (ADS)

    Govindaraju, Parithi

    A "System of Systems" (SoS) approach is particularly beneficial in analyzing complex large scale systems comprised of numerous independent systems -- each capable of independent operations in their own right -- that when brought in conjunction offer capabilities and performance beyond the constituents of the individual systems. The variable resource allocation problem is a type of SoS problem, which includes the allocation of "yet-to-be-designed" systems in addition to existing resources and systems. The methodology presented here expands upon earlier work that demonstrated a decomposition approach that sought to simultaneously design a new aircraft and allocate this new aircraft along with existing aircraft in an effort to meet passenger demand at minimum fleet level operating cost for a single airline. The result of this describes important characteristics of the new aircraft. The ticket price model developed and implemented here enables analysis of the system using profit maximization studies instead of cost minimization. A multiobjective problem formulation has been implemented to determine characteristics of a new aircraft that maximizes the profit of multiple airlines to recognize the fact that aircraft manufacturers sell their aircraft to multiple customers and seldom design aircraft customized to a single airline's operations. The route network characteristics of two simple airlines serve as the example problem for the initial studies. The resulting problem formulation is a mixed-integer nonlinear programming problem, which is typically difficult to solve. A sequential decomposition strategy is applied as a solution methodology by segregating the allocation (integer programming) and aircraft design (non-linear programming) subspaces. After solving a simple problem considering two airlines, the decomposition approach is then applied to two larger airline route networks representing actual airline operations in the year 2005. The decomposition strategy serves

  20. Perceptions and Attitudes of Health Professionals in Kenya on National Health Care Resource Allocation Mechanisms: A Structural Equation Modeling

    PubMed Central

    Owili, Patrick Opiyo; Hsu, Yi-Hsin Elsa; Chern, Jin-Yuan; Chiu, Chiung-Hsuan Megan; Wang, Bill; Huang, Kuo-Cherh; Muga, Miriam Adoyo

    2015-01-01

    Background Health care resource allocation is key towards attaining equity in the health system. However, health professionals’ perceived impact and attitude towards health care resource allocation in Sub-Saharan Africa is unknown; furthermore, they occupy a position which makes them notice the impact of different policies in their health system. This study explored perceptions and attitudes of health professionals in Kenya on health care resource allocation mechanism. Method We conducted a survey of a representative sample of 341 health professionals in Moi Teaching and Referral Hospital from February to April 2012, consisting of over 3000 employees. We assessed health professionals’ perceived impact and attitudes on health care resource allocation mechanism in Kenya. We used structural equation modeling and applied a Confirmatory Factor Analysis using Robust Maximum Likelihood estimation procedure to test the hypothesized model. Results We found that the allocation mechanism was negatively associated with their perceived positive impact (-1.04, p < .001), health professionals’ satisfaction (-0.24, p < .01), and professionals’ attitudes (-1.55, p < .001) while it was positively associated with perceived negative impact (1.14, p < .001). Perceived positive impact of the allocation mechanism was negatively associated with their overall satisfaction (-0.08) and attitude (-0.98) at p < .001, respectively. Furthermore, overall satisfaction was negatively associated with attitude (-1.10, p <.001). On the other hand, perceived negative impact of the allocation was positively associated with overall satisfaction (0.29, p <.001) but was not associated with attitude. Conclusion The result suggests that health care resource allocation mechanism has a negative effect towards perceptions, attitudes and overall satisfaction of health professionals who are at the frontline in health care. These findings can serve as a crucial reference for policymakers as the Kenyan

  1. Resource Allocation Modelling in Vocational Rehabilitation: A Prototype Developed with the Michigan and Rhode Island VR Agencies.

    ERIC Educational Resources Information Center

    Leff, H. Stephen; Turner, Ralph R.

    This report focuses on the use of linear programming models to address the issues of how vocational rehabilitation (VR) resources should be allocated in order to maximize program efficiency within given resource constraints. A general introduction to linear programming models is first presented that describes the major types of models available,…

  2. SAM-2 ground-truth plan: Correlative measurements for the Stratospheric Aerosol Measurement-2 (SAM 2) sensor on the Nimbus G satellite

    NASA Technical Reports Server (NTRS)

    Russell, P. B.; Mccormick, M. P.; Mcmaster, L. R.; Pepin, T. J.; Chu, W. P.; Swissler, T. J.

    1978-01-01

    The SAM-2 will fly aboard the Nimbus-G satellite for launch in the fall of 1978 and measure stratospheric vertical profiles of aerosol extinction in high latitude bands. The plan gives details of the location and times for the simultaneous satellite/correlative measurements for the nominal launch time, the rationale and choice of the correlative sensors, their characteristics and expected accuracies, and the conversion of their data to extinction profiles. The SAM-2 expected instrument performance and data inversion results are presented. Various atmospheric models representative of polar stratospheric aerosols are used in the SAM-2 and correlative sensor analyses.

  3. Model Predictive Obstacle Avoidance and Wheel Allocation Control of Mobile Robots Using Embedded CPU

    NASA Astrophysics Data System (ADS)

    Takahashi, Naoki; Nonaka, Kenichiro

    In this study, we propose a real-time model predictive control method for leg/wheel mobile robots which simultaneously achieves both obstacle avoidance and wheel allocation at a flexible position. The proposed method generates both obstacle avoidance path and dynamical wheel positions, and controls the heading angle depending on the slope of the predicted path so that the robot can keep a good balance between stability and mobility in narrow and complex spaces like indoor environments. Moreover, we reduce the computational effort of the algorithm by deleting usage of mathematical function in the repetitive numerical computation. Thus the proposed real-time optimization method can be applied to low speed on-board CPUs used in commercially-produced vehicles. We conducted experiments to verify efficacy and feasibility of the real-time implementation of the proposed method. We used a leg/wheel mobile robot which is equipped with two laser range finders to detect obstacles and an embedded CPU whose clock speed is only 80MHz. Experiments indicate that the proposed method achieves improved obstacle avoidance comparing with the previous method in the sense that it generates an avoidance path with balanced allocation of right and left side wheels.

  4. Statistical mechanics of competitive resource allocation using agent-based models

    NASA Astrophysics Data System (ADS)

    Chakraborti, Anirban; Challet, Damien; Chatterjee, Arnab; Marsili, Matteo; Zhang, Yi-Cheng; Chakrabarti, Bikas K.

    2015-01-01

    Demand outstrips available resources in most situations, which gives rise to competition, interaction and learning. In this article, we review a broad spectrum of multi-agent models of competition (El Farol Bar problem, Minority Game, Kolkata Paise Restaurant problem, Stable marriage problem, Parking space problem and others) and the methods used to understand them analytically. We emphasize the power of concepts and tools from statistical mechanics to understand and explain fully collective phenomena such as phase transitions and long memory, and the mapping between agent heterogeneity and physical disorder. As these methods can be applied to any large-scale model of competitive resource allocation made up of heterogeneous adaptive agent with non-linear interaction, they provide a prospective unifying paradigm for many scientific disciplines.

  5. Interim report on revising the resource allocation and mine costing model. [By states for 8 sulfur content ranges

    SciTech Connect

    Not Available

    1980-03-07

    The purpose of this contract is to provide the Coal and Electric Power Analysis Division, EIA, with a revised and fully documented Resource Allocation and Mine Costing (RAMC) model to be used in developing coal supply curves for use in the Mid-range Energy Forecasting System and the National Coal Model. The project is structured in three phases, as follows: establish conceptual underpinnings of revised supply curve methodology; revise mine costing methodology; and revise resource allocation methodology. The first three tasks in Phase I were to review and critique the current RAMC approach, review and critique the NUS deep mine and the Fluor Utah surface mine costing methodologies, and to propose revisions to the current approach. This Interim Report documents our findings under these three tasks. Our review of the current RAMC concludes that the resource allocation methodology is reasonable; however, the mine costing methodology has a number of deficiencies. Hence, Section 5 presents a number of alternative approaches for implementing an improved costing methodology in the RAMC model. Although the resource allocation approach is reasonable, the data used to drive the model need to be improved. The Appendices discuss a number of these data issues, affecting both mine costing and resource allocation.

  6. Context dependence of maternal effects: testing assumptions of optimal egg size, differential, and sex allocation models.

    PubMed

    Krist, Miloš; Munclinger, Pavel

    2015-10-01

    If offspring develop in adverse conditions, the maternal component of their phenotypic variation might increase due to the stronger dependence of offspring traits on parental investment. This should result in increased parental investment to individual offspring, as assumed by the model of optimal egg size. The opposite pattern, i.e., stronger dependence of offspring fitness on parental investment and consequently larger parental investment under good conditions is assumed by both the theory of differential allocation if attractive males provide material benefits, and reproductive compensation if they invest less into paternal care. Another influential idea is the Trivers-Willard model, which assumes sex-specific dependence of offspring fitness on parental investment. Here we tested these ideas by examining the effects of egg size on offspring fitness across many postnatal contexts in the Collared Flycatcher Ficedula albicollis. We employed a cross-fostering design that generated variation in egg size within nests and used brood means of fledgling mass as a functional measure of the quality of rearing conditions. Effects of egg size on three offspring traits, including lifetime reproductive success of recruits, were more pronounced in low-quality broods. These results support the assumption of the model of optimal egg size. Based on female preference for males providing material benefits, this pattern could support differential allocation, if attractive males invest less in paternal care, or reproductive compensation, if they invest more. By comparison, we did not find any evidence for sex specificity of fitness returns that might explain sex monomorphism of egg size in this species. The challenge for future studies will be the integration of components of parental investment and offspring fitness into their global measures and testing how the former affects the latter across gradients of postnatal conditions.

  7. Belowground carbon allocation patterns in a dry Mediterranean ecosystem: a comparison of two models.

    NASA Astrophysics Data System (ADS)

    María, Almagro; Jorge, López; Carolina, Boix-Fayos; Juan, Albadalejo; María, Martínez-Mena

    2010-05-01

    Total belowground C allocation (TBCA) represents a large fraction of gross primary production; it can exceed aboveground net primary production, and provides the primary source of detrital C to mineral soil. Here, we measure soil respiration, water erosion, litterfall and estimated annual changes in C stored in mineral soil, litter and roots, in three representative land uses in a Mediterranean ecosystem (late-successional forest, abandoned agricultural field, rain-fed olive grove), and use two C balance approaches (steady-state and non-steady-state) to estimate TBCA. Both TBCA approaches are compared to assess how different C fluxes (outputs and inputs) affect our estimates of TBCA within each land use. In addition, annual net ecosystem productivity is determined and C allocation patterns are examined for each land use. We hypothesized that changes in C stored in mineral soil, litter and roots will be minor compared to soil respiration, but will still have a significant effect on the estimates of TBCA. Annual net ecosystem productivity was 648, 541 and 324 g C m-2 yr-1 for forest, abandoned field and olive grove, respectively. Across land uses, more than 60 % of the C was allocated belowground. Soil respiration (FS) was the largest component in the TBCA approaches across all land uses. Annual C losses through water erosion were negligible compared to FS (less than 1%) and had little effect on the estimates of TBCA. Annual changes in C stored in the soil, litter layer and roots were low compared to FS (16, 24 and 10 % for forest, abandoned field and olive grove, respectively), but had a significant effect on the estimates of TBCA. In our sites, an assumption that ?[CS + CR + CL]/?t= 0 will give biased estimates of TBCA, particularly in the abandoned agricultural field, where soil C storage may be increasing more rapidly. Therefore, the steady-state model is unsuited to these Mediterranean ecosystems and the full model is recommended. The results from this study

  8. Does Distraction Reduce the Alcohol-Aggression Relation? A Cognitive and Behavioral Test of the Attention-Allocation Model

    ERIC Educational Resources Information Center

    Gallagher, Kathryn E.; Parrott, Dominic J.

    2011-01-01

    Objective: This study provided the first direct test of the cognitive underpinnings of the attention-allocation model and attempted to replicate and extend past behavioral findings for this model as an explanation for alcohol-related aggression. Method: A diverse community sample (55% African American) of men (N = 159) between 21 and 35 years of…

  9. Optimizing Real-Time Vaccine Allocation in a Stochastic SIR Model

    PubMed Central

    Nguyen, Chantal; Carlson, Jean M.

    2016-01-01

    Real-time vaccination following an outbreak can effectively mitigate the damage caused by an infectious disease. However, in many cases, available resources are insufficient to vaccinate the entire at-risk population, logistics result in delayed vaccine deployment, and the interaction between members of different cities facilitates a wide spatial spread of infection. Limited vaccine, time delays, and interaction (or coupling) of cities lead to tradeoffs that impact the overall magnitude of the epidemic. These tradeoffs mandate investigation of optimal strategies that minimize the severity of the epidemic by prioritizing allocation of vaccine to specific subpopulations. We use an SIR model to describe the disease dynamics of an epidemic which breaks out in one city and spreads to another. We solve a master equation to determine the resulting probability distribution of the final epidemic size. We then identify tradeoffs between vaccine, time delay, and coupling, and we determine the optimal vaccination protocols resulting from these tradeoffs. PMID:27043931

  10. South San Francisco bay water quality modeling and waste load allocation study

    SciTech Connect

    Wang, P.F.; Ambrose, R.B.; Novo-Gradac, K.K.

    1993-03-01

    A waste load allocation modeling study was conducted in South San Francisco Bay, California. Relatively numerous reports on hydrodynamics and less complete data for water quality, especially sediment levels, in the Bay were reviewed for use in the study. Simulations were based on the premise that sediments maintain equilibrium over long periods of time. Copper concentrations were simulated using different loading conditions describing different scenarios. Nontidal transport results were obtained for suspended solids, copper, nickel, and lead. The wide ranges of historical water quality data were addressed through sensitivity analysis of unsteady nonpoint source loads. For demonstration purposes, the domain for tidal simulations covered only the regions south of Dumbarton Bridge. The effects of the reduction of point-source loads over the past few years and of the droughts that began in 1987 were simulated using appropriate loading conditions.

  11. A modelization of the task allocation problem for prescribing activity in an ICU.

    PubMed Central

    Renard, J. M.; Bricon-Souf, N.; Guigue, L.; Beuscart, R.

    2000-01-01

    The improvement of coordination between Health Care Professionals belonging different specialities and who are extremely mobile, is a crucial problem in Medicine. A workflow System is one example of the new informatics tools which facilitate the transfer of information and responsibility between health care providers. Medical informatics systems in particular should be reactive enough to cope with the flexibility of real work situations: in this paper, we present the task allocation problem. We distinguish between the workflow control process and the notifying process, which concerns the sharing out of the tasks between the actors concerned. We focus on the impact of strategies of notification on the progress of coordinated work. We propose a simulator to model and study the different ways of sharing tasks between actors in an Intensive Care Unit's activity of prescription. PMID:11079971

  12. A Schelling model with switching agents: decreasing segregation via random allocation and social mobility

    NASA Astrophysics Data System (ADS)

    Hazan, Aurélien; Randon-Furling, Julien

    2013-10-01

    We study the behaviour of a Schelling-class system in which a fraction f of spatially-fixed switching agents is introduced. This new model allows for multiple interpretations, including: (i) random, non-preferential allocation (e.g. by housing associations) of given, fixed sites in an open residential system, and (ii) superimposition of social and spatial mobility in a closed residential system. We find that the presence of switching agents in a segregative Schelling-type dynamics can lead to the emergence of intermediate patterns (e.g. mixture of patches, fuzzy interfaces) as the ones described in [E. Hatna, I. Benenson, J. Artif. Soc. Social. Simul. 15, 6 (2012)]. We also investigate different transitions between segregated and mixed phases both at f = 0 and along lines of increasing f, where the nature of the transition changes.

  13. Competitive allocation of resources on a network: an agent-based model of air companies competing for the best routes

    NASA Astrophysics Data System (ADS)

    Gurtner, Gérald; Valori, Luca; Lillo, Fabrizio

    2015-05-01

    We present a stylized model of the allocation of resources on a network. By considering as a concrete example the network of sectors of the airspace, where each node is a sector characterized by a maximal number of simultaneously present aircraft, we consider the problem of air companies competing for the allocation of the airspace. Each company is characterized by a cost function, weighting differently punctuality and length of the flight. We consider the model in the presence of pure and mixed populations of types of airline companies and we study how the equilibria depends on the characteristics of the network.

  14. Characterization of the SAM domain of the PKD-related protein ANKS6 and its interaction with ANKS3

    PubMed Central

    2014-01-01

    Background Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic disorder leading to end-stage renal failure in humans. In the PKD/Mhm(cy/+) rat model of ADPKD, the point mutation R823W in the sterile alpha motif (SAM) domain of the protein ANKS6 is responsible for disease. SAM domains are known protein-protein interaction domains, capable of binding each other to form polymers and heterodimers. Despite its physiological importance, little is known about the function of ANKS6 and how the R823W point mutation leads to PKD. Recent work has revealed that ANKS6 interacts with a related protein called ANKS3. Both ANKS6 and ANKS3 have a similar domain structure, with ankyrin repeats at the N-terminus and a SAM domain at the C-terminus. Results The SAM domain of ANKS3 is identified as a direct binding partner of the ANKS6 SAM domain. We find that ANKS3-SAM polymerizes and ANKS6-SAM can bind to one end of the polymer. We present crystal structures of both the ANKS3-SAM polymer and the ANKS3-SAM/ANKS6-SAM complex, revealing the molecular details of their association. We also learn how the R823W mutation disrupts ANKS6 function by dramatically destabilizing the SAM domain such that the interaction with ANKS3-SAM is lost. Conclusions ANKS3 is a direct interacting partner of ANKS6. By structurally and biochemically characterizing the interaction between the ANKS3 and ANKS6 SAM domains, our work provides a basis for future investigation of how the interaction between these proteins mediates kidney function. PMID:24998259

  15. Location-Allocation and Accessibility Models for Improving the Spatial Planning of Public Health Services

    PubMed Central

    Polo, Gina; Acosta, C. Mera; Ferreira, Fernando; Dias, Ricardo Augusto

    2015-01-01

    This study integrated accessibility and location-allocation models in geographic information systems as a proposed strategy to improve the spatial planning of public health services. To estimate the spatial accessibility, we modified the two-step floating catchment area (2SFCA) model with a different impedance function, a Gaussian weight for competition among service sites, a friction coefficient, distances along a street network based on the Dijkstra’s algorithm and by performing a vectorial analysis. To check the accuracy of the strategy, we used the data from the public sterilization program for the dogs and cats of Bogot´a, Colombia. Since the proposed strategy is independent of the service, it could also be applied to any other public intervention when the capacity of the service is known. The results of the accessibility model were consistent with the sterilization program data, revealing that the western, central and northern zones are the most isolated areas under the sterilization program. Spatial accessibility improvement was sought by relocating the sterilization sites using the maximum coverage with finite demand and the p-median models. The relocation proposed by the maximum coverage model more effectively maximized the spatial accessibility to the sterilization service given the non-uniform distribution of the populations of dogs and cats throughout the city. The implementation of the proposed strategy would provide direct benefits by improving the effectiveness of different public health interventions and the use of financial and human resources. PMID:25775411

  16. Simulation of tree-ring widths with a model for primary production, carbon allocation, and growth

    NASA Astrophysics Data System (ADS)

    Li, G.; Harrison, S. P.; Prentice, I. C.; Falster, D.

    2014-12-01

    We present a simple, generic model of annual tree growth, called "T". This model accepts input from a first-principles light-use efficiency model (the "P" model). The P model provides values for gross primary production (GPP) per unit of absorbed photosynthetically active radiation (PAR). Absorbed PAR is estimated from the current leaf area. GPP is allocated to foliage, transport tissue, and fine-root production and respiration in such a way as to satisfy well-understood dimensional and functional relationships. Our approach thereby integrates two modelling approaches separately developed in the global carbon-cycle and forest-science literature. The T model can represent both ontogenetic effects (the impact of ageing) and the effects of environmental variations and trends (climate and CO2) on growth. Driven by local climate records, the model was applied to simulate ring widths during the period 1958-2006 for multiple trees of Pinus koraiensis from the Changbai Mountains in northeastern China. Each tree was initialised at its actual diameter at the time when local climate records started. The model produces realistic simulations of the interannual variability in ring width for different age cohorts (young, mature, and old). Both the simulations and observations show a significant positive response of tree-ring width to growing-season total photosynthetically active radiation (PAR0) and the ratio of actual to potential evapotranspiration (α), and a significant negative response to mean annual temperature (MAT). The slopes of the simulated and observed relationships with PAR0 and α are similar; the negative response to MAT is underestimated by the model. Comparison of simulations with fixed and changing atmospheric CO2 concentration shows that CO2 fertilisation over the past 50 years is too small to be distinguished in the ring-width data, given ontogenetic trends and interannual variability in climate.

  17. Modeling Resources Allocation in Attacker-Defender Games with "Warm Up" CSF.

    PubMed

    Guan, Peiqiu; Zhuang, Jun

    2016-04-01

    Like many other engineering investments, the attacker's and defender's investments may have limited impact without initial capital to "warm up" the systems. This article studies such "warm up" effects on both the attack and defense equilibrium strategies in a sequential-move game model by developing a class of novel and more realistic contest success functions. We first solve a single-target attacker-defender game analytically and provide numerical solutions to a multiple-target case. We compare the results of the models with and without consideration of the investment "warm up" effects, and find that the defender would suffer higher expected damage, and either underestimate the attacker effort or waste defense investment if the defender falsely believes that no investment "warm up" effects exist. We illustrate the model results with real data, and compare the results of the models with and without consideration of the correlation between the "warm up" threshold and the investment effectiveness. Interestingly, we find that the defender is suggested to give up defending all the targets when the attack or the defense "warm up" thresholds are sufficiently high. This article provides new insights and suggestions on policy implications for homeland security resource allocation. PMID:26713543

  18. Modeling Resources Allocation in Attacker-Defender Games with "Warm Up" CSF.

    PubMed

    Guan, Peiqiu; Zhuang, Jun

    2016-04-01

    Like many other engineering investments, the attacker's and defender's investments may have limited impact without initial capital to "warm up" the systems. This article studies such "warm up" effects on both the attack and defense equilibrium strategies in a sequential-move game model by developing a class of novel and more realistic contest success functions. We first solve a single-target attacker-defender game analytically and provide numerical solutions to a multiple-target case. We compare the results of the models with and without consideration of the investment "warm up" effects, and find that the defender would suffer higher expected damage, and either underestimate the attacker effort or waste defense investment if the defender falsely believes that no investment "warm up" effects exist. We illustrate the model results with real data, and compare the results of the models with and without consideration of the correlation between the "warm up" threshold and the investment effectiveness. Interestingly, we find that the defender is suggested to give up defending all the targets when the attack or the defense "warm up" thresholds are sufficiently high. This article provides new insights and suggestions on policy implications for homeland security resource allocation.

  19. Patterning NHS-terminated SAMs on germanium.

    PubMed

    Morris, Carleen J; Shestopalov, Alexander A; Gold, Brian H; Clark, Robert L; Toone, Eric J

    2011-05-17

    Here we report a simple, robust approach to patterning functional SAMs on germanium. The protocol relies on catalytic soft-lithographic pattern transfer from an elastomeric stamp bearing pendant immobilized sulfonic acid moieties to an NHS-functionalized bilayer molecular system comprising a primary ordered alkyl monolayer and a reactive ester secondary overlayer. The catalytic polyurethane-acrylate stamp was used to form micrometer-scale features of chemically distinct SAMs on germanium. The methodology represents the first example of patterned SAMs on germanium, a semiconductor material.

  20. SAM-FS: LSC's New Solaris-Based Storage Management Product

    NASA Technical Reports Server (NTRS)

    Angell, Kent

    1996-01-01

    SAM-FS is a full featured hierarchical storage management (HSM) device that operates as a file system on Solaris-based machines. The SAM-FS file system provides the user with all of the standard UNIX system utilities and calls, and adds some new commands, i.e. archive, release, stage, sls, sfind, and a family of maintenance commands. The system also offers enhancements such as high performance virtual disk read and write, control of the disk through an extent array, and the ability to dynamically allocate block size. SAM-FS provides 'archive sets' which are groupings of data to be copied to secondary storage. In practice, as soon as a file is written to disk, SAM-FS will make copies onto secondary media. SAM-FS is a scalable storage management system. The system can manage millions of files per system, though this is limited today by the speed of UNIX and its utilities. In the future, a new search algorithm will be implemented that will remove logical and performance restrictions on the number of files managed.

  1. Modeling virtual organizations with Latent Dirichlet Allocation: a case for natural language processing.

    PubMed

    Gross, Alexander; Murthy, Dhiraj

    2014-10-01

    This paper explores a variety of methods for applying the Latent Dirichlet Allocation (LDA) automated topic modeling algorithm to the modeling of the structure and behavior of virtual organizations found within modern social media and social networking environments. As the field of Big Data reveals, an increase in the scale of social data available presents new challenges which are not tackled by merely scaling up hardware and software. Rather, they necessitate new methods and, indeed, new areas of expertise. Natural language processing provides one such method. This paper applies LDA to the study of scientific virtual organizations whose members employ social technologies. Because of the vast data footprint in these virtual platforms, we found that natural language processing was needed to 'unlock' and render visible latent, previously unseen conversational connections across large textual corpora (spanning profiles, discussion threads, forums, and other social media incarnations). We introduce variants of LDA and ultimately make the argument that natural language processing is a critical interdisciplinary methodology to make better sense of social 'Big Data' and we were able to successfully model nested discussion topics from forums and blog posts using LDA. Importantly, we found that LDA can move us beyond the state-of-the-art in conventional Social Network Analysis techniques. PMID:24930023

  2. Modeling virtual organizations with Latent Dirichlet Allocation: a case for natural language processing.

    PubMed

    Gross, Alexander; Murthy, Dhiraj

    2014-10-01

    This paper explores a variety of methods for applying the Latent Dirichlet Allocation (LDA) automated topic modeling algorithm to the modeling of the structure and behavior of virtual organizations found within modern social media and social networking environments. As the field of Big Data reveals, an increase in the scale of social data available presents new challenges which are not tackled by merely scaling up hardware and software. Rather, they necessitate new methods and, indeed, new areas of expertise. Natural language processing provides one such method. This paper applies LDA to the study of scientific virtual organizations whose members employ social technologies. Because of the vast data footprint in these virtual platforms, we found that natural language processing was needed to 'unlock' and render visible latent, previously unseen conversational connections across large textual corpora (spanning profiles, discussion threads, forums, and other social media incarnations). We introduce variants of LDA and ultimately make the argument that natural language processing is a critical interdisciplinary methodology to make better sense of social 'Big Data' and we were able to successfully model nested discussion topics from forums and blog posts using LDA. Importantly, we found that LDA can move us beyond the state-of-the-art in conventional Social Network Analysis techniques.

  3. CARBON AND NITROGEN ALLOCATION MODEL FOR THE SUB-TROPICAL SEAGRASS THALASSIA TESTUDINUM AND THE TEMPERATE SEAGRASS ZOSTER MARINA

    EPA Science Inventory

    Our understanding of seagrass physiology is based on crude estimates of production and biomass. To better understand the complex physiological relationships between the plants and the environment we developed a model of carbon and nitrogen allocation in the sub-tropical seagrass ...

  4. NES Live Video Chat: Engineer Sam Ortega

    NASA Video Gallery

    The NES project invited all K-12 students to participate in a one-hour-long NASA video webchat on April 19, 2011 with NASA engineer Sam Ortega. Ortega answered questions about building and testing ...

  5. Stay lean without dieting: Lose Sam68.

    PubMed

    Huot, Marc-Étienne; Richard, Stéphane

    2012-10-01

    Alternative splicing is well known to be tissue-specific. Although several genes have been shown to undergo alternative splicing in adipocytes, little is known about the mechanism that regulates alternative splicing during adipogenesis. We recently reported that Sam68(-/-) mice exhibit a lean phenotype and are protected against diet-induced obesity. Our genome-wide exon array analysis in white adipose tissue (WAT) from wild-type and Sam68(-/-) mice revealed that Sam68 deficiency leads to an abnormal splicing of the mTOR gene. This has been shown to reduce the overall mTOR protein content and activity during in vitro adipose differentiation. In Sam68(-/-) mice, this situation leads to an increased energy expenditure, decreased adipogenesis and WAT formation. PMID:23700540

  6. STS-134 Crew Talks With Sam Ting

    NASA Video Gallery

    The STS-134 crew talks with Sam Ting, principal investigator for the Alpha Magnetic Spectrometer, following the installation of the particle physics detector on the International Space Station duri...

  7. Global Modeling of Withdrawal, Allocation and Consumptive Use of Surface Water and Groundwater Resources

    NASA Astrophysics Data System (ADS)

    Wada, Y.; Wisser, D.; Bierkens, M. F.

    2014-12-01

    To sustain growing food demand and increasing standard of living, global water withdrawal and consumptive water use have been increasing rapidly. To analyze the human perturbation on water resources consistently over large scales, a number of macro-scale hydrological models (MHMs) have been developed in recent decades. However, few models consider the interaction between terrestrial water fluxes, and human activities and associated water use, and even fewer models distinguish water use from surface water and groundwater resources. Here, we couple a global water demand model with a global hydrological model and dynamically simulate daily water withdrawal and consumptive water use over the period 1979-2010, using two re-analysis products: ERA-Interim and MERRA. We explicitly take into account the mutual feedback between supply and demand, and implement a newly developed water allocation scheme to distinguish surface water and groundwater use. Moreover, we include a new irrigation scheme, which works dynamically with a daily surface and soil water balance, and incorporate the newly available extensive global reservoir data set (GRanD). Simulated surface water and groundwater withdrawals generally show good agreement with reported national and sub-national statistics. The results show a consistent increase in both surface water and groundwater use worldwide, with a more rapid increase in groundwater use since the 1990s. Human impacts on terrestrial water storage (TWS) signals are evident, altering the seasonal and inter-annual variability. This alteration is particularly large over heavily regulated basins such as the Colorado and the Columbia, and over the major irrigated basins such as the Mississippi, the Indus, and the Ganges. Including human water use and associated reservoir operations generally improves the correlation of simulated TWS anomalies with those of the GRACE observations.

  8. A System Dynamics Model to Improve Water Resources Allocation in the Conchos River

    NASA Astrophysics Data System (ADS)

    Gastelum, J. R.; Valdes, J. B.; Stewart, S.

    2005-12-01

    The Conchos river located in Chihuahua state on a semiarid region is the most important Mexican river contributing water deliveries to USA as established by the Water treaty of 1944 signed between Mexico and USA. Historically, Mexico has delivered to UNITED STATES 550 Hm3 (445,549.5 ACF) per year of water since the treaty was established, which is 25% above the yearly water volume Mexico is required to deliver. The Conchos river has contributed with 54% of the historic Mexican water treaty deliveries to the UNITED STATES, which represents the highest percentage of the 6 Mexican rivers considered on the water treaty. However, during drought situations the basin has proven to be vulnerable, for instance, because of the severe drought of the 90's, several cities in 1992 on Chihuahua state where declared disaster areas, and from 1992 to 2001 Mexico had accumulated a water treaty deficit of 2111.6 Hm3 (1,710,586 ACF). This has conduced to economic, social, and political difficulties in both countries. Because of the cited problematic and considering the poor understanding of the relationship between water supply and demand factors on the basin, a decision support system (DSS) has been developed aimed to improve the decision making process related with the water resources allocation process. This DSS has been created using System Dynamics (SD). It is a semi-distributed model and is running on monthly time step basis. For both the short and long term, three important water resources management strategies have been evaluated: several water allocation policies from reservoirs to water users; bulk water rights transfers inside and outside Irrigation Districts; and improvement of water distribution efficiencies. The model results have provided very useful regard to gain more quantitative understanding of the different strategies being implemented. They have also indicated that the different water resources alternatives change its degree of importance according to the

  9. Resource Allocation.

    ERIC Educational Resources Information Center

    Stennett, R. G.

    A research allocation formula employed in London, Ontario elementary schools, as well as supporting data on the method, are provided in this report. Attempts to improve on the traditional methods of resource allocation in London's schools were based on two principles: (1) that need for a particular service could and should be determined…

  10. Polycystic kidney disease in Han:SPRD Cy rats is associated with elevated expression and mislocalization of SamCystin

    PubMed Central

    Nagao, Shizuko; Morita, Miwa; Kugita, Masanori; Yoshihara, Daisuke; Yamaguchi, Tamio; Kurahashi, Hiroki; Calvet, James P.

    2010-01-01

    Polycystic kidney disease (PKD) in Han:SPRD Cy rats is caused by a missense mutation in Anks6 (also called Pkdr1), leading to an R823W substitution in SamCystin, a protein that contains ankyrin repeats and a sterile alpha motif (SAM). The cellular function of SamCystin and the role of the Cy (R823W) mutation in cyst formation are unknown. In normal SPRD rats, SamCystin was found to be expressed in proximal tubules and glomeruli; protein expression was highest at 7 days of age and declined by ∼50–60% at 45–84 days of age. In Cy/+ and Cy/Cy kidneys, expression of SamCystin was lower than in +/+ kidneys at 3 and 7 days but became elevated at 21 days. Immunohistochemical analysis revealed that SamCystin was distributed on the brush border of proximal tubules in normal rat kidneys. In Cy/+ kidneys, there were robust SamCystin staining in cyst-lining epithelial cells and loss of apical localization, and increased number of PCNA-positive cells in cyst-lining epithelia. Verapamil, an L-type Ca2+ channel blocker, accelerated PKD progression in this model and caused a further increase in the expression and abnormal distribution of SamCystin. We conclude that aberrant expression and mislocalization of R823W SamCystin lead to increased cell proliferation and renal cyst formation. PMID:20719982

  11. Where does the carbon go? A model-data intercomparison of vegetation carbon allocation and turnover processes at two temperate forest free-air CO2 enrichment sites.

    PubMed

    De Kauwe, Martin G; Medlyn, Belinda E; Zaehle, Sönke; Walker, Anthony P; Dietze, Michael C; Wang, Ying-Ping; Luo, Yiqi; Jain, Atul K; El-Masri, Bassil; Hickler, Thomas; Wårlind, David; Weng, Ensheng; Parton, William J; Thornton, Peter E; Wang, Shusen; Prentice, I Colin; Asao, Shinichi; Smith, Benjamin; McCarthy, Heather R; Iversen, Colleen M; Hanson, Paul J; Warren, Jeffrey M; Oren, Ram; Norby, Richard J

    2014-08-01

    Elevated atmospheric CO2 concentration (eCO2) has the potential to increase vegetation carbon storage if increased net primary production causes increased long-lived biomass. Model predictions of eCO2 effects on vegetation carbon storage depend on how allocation and turnover processes are represented. We used data from two temperate forest free-air CO2 enrichment (FACE) experiments to evaluate representations of allocation and turnover in 11 ecosystem models. Observed eCO2 effects on allocation were dynamic. Allocation schemes based on functional relationships among biomass fractions that vary with resource availability were best able to capture the general features of the observations. Allocation schemes based on constant fractions or resource limitations performed less well, with some models having unintended outcomes. Few models represent turnover processes mechanistically and there was wide variation in predictions of tissue lifespan. Consequently, models did not perform well at predicting eCO2 effects on vegetation carbon storage. Our recommendations to reduce uncertainty include: use of allocation schemes constrained by biomass fractions; careful testing of allocation schemes; and synthesis of allocation and turnover data in terms of model parameters. Data from intensively studied ecosystem manipulation experiments are invaluable for constraining models and we recommend that such experiments should attempt to fully quantify carbon, water and nutrient budgets.

  12. Comparing administered and market-based water allocation systems through a consistent agent-based modeling framework.

    PubMed

    Zhao, Jianshi; Cai, Ximing; Wang, Zhongjing

    2013-07-15

    Water allocation can be undertaken through administered systems (AS), market-based systems (MS), or a combination of the two. The debate on the performance of the two systems has lasted for decades but still calls for attention in both research and practice. This paper compares water users' behavior under AS and MS through a consistent agent-based modeling framework for water allocation analysis that incorporates variables particular to both MS (e.g., water trade and trading prices) and AS (water use violations and penalties/subsidies). Analogous to the economic theory of water markets under MS, the theory of rational violation justifies the exchange of entitled water under AS through the use of cross-subsidies. Under water stress conditions, a unique water allocation equilibrium can be achieved by following a simple bargaining rule that does not depend upon initial market prices under MS, or initial economic incentives under AS. The modeling analysis shows that the behavior of water users (agents) depends on transaction, or administrative, costs, as well as their autonomy. Reducing transaction costs under MS or administrative costs under AS will mitigate the effect that equity constraints (originating with primary water allocation) have on the system's total net economic benefits. Moreover, hydrologic uncertainty is shown to increase market prices under MS and penalties/subsidies under AS and, in most cases, also increases transaction, or administrative, costs. PMID:23597927

  13. [A simulation model for predicting the dry matter allocation in cut lily plants under effects of substrate water potential].

    PubMed

    Dong, Yong-Yi; Li, Gang; An, Dong-Sheng; Luo, Wei-Hong

    2012-04-01

    Dry matter allocation and translocation is the base of the formation of appearance quality of ornamental plants, and strongly affected by water supply. Taking cut lily cultivar 'Sorbonne' as test material, a culture experiment of different planting dates and water supply levels was conducted in a multi-span greenhouse in Nanjing from March 2009 to January 2010 to quantitatively analyze the seasonal changes of the dry matter allocation and translocation in 'Sorbonne' plants and the effects of substrate water potential on the dry matter allocation indices for different organs (flower, stem, leaf, bulb, and root), aimed to define the critical substrate water potential for the normal growth of the cultivar, and establish a simulation model for predicting the dry matter allocation in cut lily plants under effects of substrate water potential. The model established in this study gave a good prediction on the dry mass of plant organs, with the coefficient of determination and the relative root mean square error between the simulated and measured values of the cultivar' s flower dry mass, stem dry mass, leaf dry mass, bulb dry mass, and root dry mass being 0.96 and 19.2%, 0.95 and 12.4%, 0.86 and 19.4%, 0.95 and 12.2%, and 0.85 and 31.7%, respectively. The critical water potential for the water management of cut lily could be -15 kPa.

  14. Comparing administered and market-based water allocation systems through a consistent agent-based modeling framework.

    PubMed

    Zhao, Jianshi; Cai, Ximing; Wang, Zhongjing

    2013-07-15

    Water allocation can be undertaken through administered systems (AS), market-based systems (MS), or a combination of the two. The debate on the performance of the two systems has lasted for decades but still calls for attention in both research and practice. This paper compares water users' behavior under AS and MS through a consistent agent-based modeling framework for water allocation analysis that incorporates variables particular to both MS (e.g., water trade and trading prices) and AS (water use violations and penalties/subsidies). Analogous to the economic theory of water markets under MS, the theory of rational violation justifies the exchange of entitled water under AS through the use of cross-subsidies. Under water stress conditions, a unique water allocation equilibrium can be achieved by following a simple bargaining rule that does not depend upon initial market prices under MS, or initial economic incentives under AS. The modeling analysis shows that the behavior of water users (agents) depends on transaction, or administrative, costs, as well as their autonomy. Reducing transaction costs under MS or administrative costs under AS will mitigate the effect that equity constraints (originating with primary water allocation) have on the system's total net economic benefits. Moreover, hydrologic uncertainty is shown to increase market prices under MS and penalties/subsidies under AS and, in most cases, also increases transaction, or administrative, costs.

  15. A multiprocessor computer simulation model employing a feedback scheduler/allocator for memory space and bandwidth matching and TMR processing

    NASA Technical Reports Server (NTRS)

    Bradley, D. B.; Irwin, J. D.

    1974-01-01

    A computer simulation model for a multiprocessor computer is developed that is useful for studying the problem of matching multiprocessor's memory space, memory bandwidth and numbers and speeds of processors with aggregate job set characteristics. The model assumes an input work load of a set of recurrent jobs. The model includes a feedback scheduler/allocator which attempts to improve system performance through higher memory bandwidth utilization by matching individual job requirements for space and bandwidth with space availability and estimates of bandwidth availability at the times of memory allocation. The simulation model includes provisions for specifying precedence relations among the jobs in a job set, and provisions for specifying precedence execution of TMR (Triple Modular Redundant and SIMPLEX (non redundant) jobs.

  16. PSOLA: A Heuristic Land-Use Allocation Model Using Patch-Level Operations and Knowledge-Informed Rules.

    PubMed

    Liu, Yaolin; Peng, Jinjin; Jiao, Limin; Liu, Yanfang

    2016-01-01

    Optimizing land-use allocation is important to regional sustainable development, as it promotes the social equality of public services, increases the economic benefits of land-use activities, and reduces the ecological risk of land-use planning. Most land-use optimization models allocate land-use using cell-level operations that fragment land-use patches. These models do not cooperate well with land-use planning knowledge, leading to irrational land-use patterns. This study focuses on building a heuristic land-use allocation model (PSOLA) using particle swarm optimization. The model allocates land-use with patch-level operations to avoid fragmentation. The patch-level operations include a patch-edge operator, a patch-size operator, and a patch-compactness operator that constrain the size and shape of land-use patches. The model is also integrated with knowledge-informed rules to provide auxiliary knowledge of land-use planning during optimization. The knowledge-informed rules consist of suitability, accessibility, land use policy, and stakeholders' preference. To validate the PSOLA model, a case study was performed in Gaoqiao Town in Zhejiang Province, China. The results demonstrate that the PSOLA model outperforms a basic PSO (Particle Swarm Optimization) in the terms of the social, economic, ecological, and overall benefits by 3.60%, 7.10%, 1.53% and 4.06%, respectively, which confirms the effectiveness of our improvements. Furthermore, the model has an open architecture, enabling its extension as a generic tool to support decision making in land-use planning.

  17. PSOLA: A Heuristic Land-Use Allocation Model Using Patch-Level Operations and Knowledge-Informed Rules.

    PubMed

    Liu, Yaolin; Peng, Jinjin; Jiao, Limin; Liu, Yanfang

    2016-01-01

    Optimizing land-use allocation is important to regional sustainable development, as it promotes the social equality of public services, increases the economic benefits of land-use activities, and reduces the ecological risk of land-use planning. Most land-use optimization models allocate land-use using cell-level operations that fragment land-use patches. These models do not cooperate well with land-use planning knowledge, leading to irrational land-use patterns. This study focuses on building a heuristic land-use allocation model (PSOLA) using particle swarm optimization. The model allocates land-use with patch-level operations to avoid fragmentation. The patch-level operations include a patch-edge operator, a patch-size operator, and a patch-compactness operator that constrain the size and shape of land-use patches. The model is also integrated with knowledge-informed rules to provide auxiliary knowledge of land-use planning during optimization. The knowledge-informed rules consist of suitability, accessibility, land use policy, and stakeholders' preference. To validate the PSOLA model, a case study was performed in Gaoqiao Town in Zhejiang Province, China. The results demonstrate that the PSOLA model outperforms a basic PSO (Particle Swarm Optimization) in the terms of the social, economic, ecological, and overall benefits by 3.60%, 7.10%, 1.53% and 4.06%, respectively, which confirms the effectiveness of our improvements. Furthermore, the model has an open architecture, enabling its extension as a generic tool to support decision making in land-use planning. PMID:27322619

  18. PSOLA: A Heuristic Land-Use Allocation Model Using Patch-Level Operations and Knowledge-Informed Rules

    PubMed Central

    Liu, Yaolin; Peng, Jinjin; Jiao, Limin; Liu, Yanfang

    2016-01-01

    Optimizing land-use allocation is important to regional sustainable development, as it promotes the social equality of public services, increases the economic benefits of land-use activities, and reduces the ecological risk of land-use planning. Most land-use optimization models allocate land-use using cell-level operations that fragment land-use patches. These models do not cooperate well with land-use planning knowledge, leading to irrational land-use patterns. This study focuses on building a heuristic land-use allocation model (PSOLA) using particle swarm optimization. The model allocates land-use with patch-level operations to avoid fragmentation. The patch-level operations include a patch-edge operator, a patch-size operator, and a patch-compactness operator that constrain the size and shape of land-use patches. The model is also integrated with knowledge-informed rules to provide auxiliary knowledge of land-use planning during optimization. The knowledge-informed rules consist of suitability, accessibility, land use policy, and stakeholders’ preference. To validate the PSOLA model, a case study was performed in Gaoqiao Town in Zhejiang Province, China. The results demonstrate that the PSOLA model outperforms a basic PSO (Particle Swarm Optimization) in the terms of the social, economic, ecological, and overall benefits by 3.60%, 7.10%, 1.53% and 4.06%, respectively, which confirms the effectiveness of our improvements. Furthermore, the model has an open architecture, enabling its extension as a generic tool to support decision making in land-use planning. PMID:27322619

  19. Allocation of environmental loads in recycling: a model based in the qualitative value of recycled material

    NASA Astrophysics Data System (ADS)

    Ferreira, Jose V. R.; Domingos, Idalina; Antunes, Paula

    2001-02-01

    When the life cycle of a product, material or service, studied in a Life Cycle Assessment (LCA) affect other life cycles not included in the system in analysis, it is necessary to apply allocation rules. Allocation can be defined, in LCA context, as the act of assigning the environmental loads of a system to the functions of that system in proportionate shares. Most of the available allocation methods are of generic application, they do not take into account the quality of the materials to be recycled and the few that do take it into account attribute to it a quantitative value. Methods that are both generic and scientifically correct are generally difficult to apply. Rules that are too simple for a case by case application could lead to studies of life cycle assessment that cannot be compared. This way, the best will be to dispose of simple methods but just and mathematically correct with a fundamentally driven application to a sector of economic activity. In this study a method of allocation is proposed which takes into account primarily the "qualitative" value of the material to be recycled, irrespective of being a pos-consumption product/material or a secondary material of a production process. Through a case study, the potential of application of the proposed method is demonstrated, in the recycling of products coming from wood industries and its derivatives, when compared with other allocation methods.

  20. Surface adhesion and confinement variation of Staphylococcus aurius on SAM surfaces

    NASA Astrophysics Data System (ADS)

    Amroski, Alicia; Olsen, Morgan; Calabrese, Joseph; Senevirathne, Reshani; Senevirathne, Indrajith

    2012-02-01

    Controlled surface adhesion of non - pathogenic gram positive strain, Staphylococcus aureus is interesting as a model system due to possible development of respective biosensors for prevention and detection of the pathogenic strain methicillin resistant Staphylococcus aureus (MRSA) and further as a study for bio-machine interfacing. Self Assembled Monolayers (SAM) with engineered surfaces of linear thiols on Au(111) were used as the substrate. Sub cultured S. aureus were used for the analysis. The SAM layered surfaces were dipped in 2 -- 4 Log/ml S. aureus solution. Subsequent surface adhesion at different bacterial dilutions on surfaces will be discussed, and correlated with quantitative and qualitative adhesion properties of bacteria on the engineered SAM surfaces. The bacteria adhered SAM surfaces were investigated using intermittent contact, noncontact, lateral force and contact modes of Atomic Force Microscopy (AFM).

  1. Modelling the climatic drivers determining photosynthesis and carbon allocation in evergreen Mediterranean forests using multiproxy long time series

    NASA Astrophysics Data System (ADS)

    Gea-Izquierdo, G.; Guibal, F.; Joffre, R.; Ourcival, J. M.; Simioni, G.; Guiot, J.

    2015-02-01

    Climatic drivers limit several important physiological processes involved in ecosystem carbon dynamics including gross primary productivity (GPP) and carbon allocation in vegetation. Climatic variability limits these two processes differently. We developed an existing mechanistic model to analyse photosynthesis and variability in carbon allocation in two evergreen species at two Mediterranean forests. The model was calibrated using a combination of eddy covariance CO2 flux data, dendrochronological time series of secondary growth and forest inventory data. The model was modified to be climate explicit in the key processes addressing acclimation of photosynthesis and allocation. It succeeded to fit both the high- and the low-frequency response of stand GPP and carbon allocation to the stem. This would support its capability to address both carbon source and sink limitations. Simulations suggest a decrease in mean stomatal conductance in response to environmental changes and an increase in mean annual intrinsic water use efficiency (iWUE) in both species during the last 50 years. However, this was not translated on a parallel increase in ecosystem water use efficiency (WUE). A long-term decrease in annual GPP matched the local trend in precipitation since the 1970s observed in one site. In contrast, GPP did not show a negative trend and the trees buffered the climatic variability observed at the site where long-term precipitation remained stable. In our simulations these temporal changes would be partly related to increasing [CO2] because the model includes biochemical equations where photosynthesis is directly linked to [CO2]. Long-term trends in GPP did not match those in growth, in agreement with the C-sink hypothesis. There is a great potential to use the model with abundant dendrochronological data and analyse forest performance under climate change. This would help to understand how different interfering environmental factors produce instability in the climatic

  2. Time Utility Functions for Modeling and Evaluating Resource Allocations in a Heterogeneous Computing System

    SciTech Connect

    Briceno, Luis Diego; Khemka, Bhavesh; Siegel, Howard Jay; Maciejewski, Anthony A; Groer, Christopher S; Koenig, Gregory A; Okonski, Gene D; Poole, Stephen W

    2011-01-01

    This study considers a heterogeneous computing system and corresponding workload being investigated by the Extreme Scale Systems Center (ESSC) at Oak Ridge National Laboratory (ORNL). The ESSC is part of a collaborative effort between the Department of Energy (DOE) and the Department of Defense (DoD) to deliver research, tools, software, and technologies that can be integrated, deployed, and used in both DOE and DoD environments. The heterogeneous system and workload described here are representative of a prototypical computing environment being studied as part of this collaboration. Each task can exhibit a time-varying importance or utility to the overall enterprise. In this system, an arriving task has an associated priority and precedence. The priority is used to describe the importance of a task, and precedence is used to describe how soon the task must be executed. These two metrics are combined to create a utility function curve that indicates how valuable it is for the system to complete a task at any given moment. This research focuses on using time-utility functions to generate a metric that can be used to compare the performance of different resource schedulers in a heterogeneous computing system. The contributions of this paper are: (a) a mathematical model of a heterogeneous computing system where tasks arrive dynamically and need to be assigned based on their priority, precedence, utility characteristic class, and task execution type, (b) the use of priority and precedence to generate time-utility functions that describe the value a task has at any given time, (c) the derivation of a metric based on the total utility gained from completing tasks to measure the performance of the computing environment, and (d) a comparison of the performance of resource allocation heuristics in this environment.

  3. The ALICE Glance Shift Accounting Management System (SAMS)

    NASA Astrophysics Data System (ADS)

    Martins Silva, H.; Abreu Da Silva, I.; Ronchetti, F.; Telesca, A.; Maidantchik, C.

    2015-12-01

    ALICE (A Large Ion Collider Experiment) is an experiment at the CERN LHC (Large Hadron Collider) studying the physics of strongly interacting matter and the quark-gluon plasma. The experiment operation requires a 24 hours a day and 7 days a week shift crew at the experimental site, composed by the ALICE collaboration members. Shift duties are calculated for each institute according to their correlated members. In order to ensure the full coverage of the experiment operation as well as its good quality, the ALICE Shift Accounting Management System (SAMS) is used to manage the shift bookings as well as the needed training. ALICE SAMS is the result of a joint effort between the Federal University of Rio de Janeiro (UFRJ) and the ALICE Collaboration. The Glance technology, developed by the UFRJ and the ATLAS experiment, sits at the basis of the system as an intermediate layer isolating the particularities of the databases. In this paper, we describe the ALICE SAMS development process and functionalities. The database has been modelled according to the collaboration needs and is fully integrated with the ALICE Collaboration repository to access members information and respectively roles and activities. Run, period and training coordinators can manage their subsystem operation and ensure an efficient personnel management. Members of the ALICE collaboration can book shifts and on-call according to pre-defined rights. ALICE SAMS features a user profile containing all the statistics and user contact information as well as the Institutes profile. Both the user and institute profiles are public (within the scope of the collaboration) and show the credit balance in real time. A shift calendar allows the Run Coordinator to plan data taking periods in terms of which subsystems shifts are enabled or disabled and on-call responsible people and slots. An overview display presents the shift crew present in the control room and allows the Run Coordination team to confirm the presence

  4. Genetic characterization of senescence-accelerated mouse (SAM).

    PubMed

    Higuchi, K

    1997-01-01

    The Senescence-Accelerated Mouse (SAM) strains are unique and appropriate models for genetic studies on aging because the SAMP strains have an "accelerated senescence" phenotype for which the SAMR strains are controls, and each SAMP strain has a strain-specific age-associated disorder. Furthermore, because they have gone through sufficient generations of sister-brother mating, they can be considered inbred strains, which can be analyzed genetically. There are now 11 SAMP strains and 3 SAMR strains descended from the progenitor litters. Analysis with the Gompertz function shows that the SAMP strains have the same initial mortality rate (IMR) as the SAMR strains but a shorter mortality rate doubling time (MRDT), presumably due to genes that accelerated the rate of senescence in the SAMP strains. This accelerated senescence may also occur in cultured fibroblast-like cells. We performed molecular genetic characterization of all the SAM strains to acquire a base of genetic information from which we could develop hypotheses on the mechanism of development of SAM strains and genetic factors that contribute to accelerated senescence. PMID:9088910

  5. Basis for ligand discrimination between ON and OFF state riboswitch conformations: the case of the SAM-I riboswitch.

    PubMed

    Boyapati, Vamsi Krishna; Huang, Wei; Spedale, Jessica; Aboul-Ela, Fareed

    2012-06-01

    Riboswitches are RNA elements that bind to effector ligands and control gene expression. Most consist of two domains. S-Adenosyl Methionine (SAM) binds the aptamer domain of the SAM-I riboswitch and induces conformational changes in the expression domain to form an intrinsic terminator (transcription OFF state). Without SAM the riboswitch forms the transcription ON state, allowing read-through transcription. The mechanistic link between the SAM/aptamer recognition event and subsequent secondary structure rearrangement by the riboswitch is unclear. We probed for those structural features of the Bacillus subtilis yitJ SAM-I riboswitch responsible for discrimination between the ON and OFF states by SAM. We designed SAM-I riboswitch RNA segments forming "hybrid" structures of the ON and OFF states. The choice of segment constrains the formation of a partial P1 helix, characteristic of the OFF state, together with a partial antiterminator (AT) helix, characteristic of the ON state. For most choices of P1 vs. AT helix lengths, SAM binds with micromolar affinity according to equilibrium dialysis. Mutational analysis and in-line probing confirm that the mode of SAM binding by hybrid structures is similar to that of the aptamer. Altogether, binding measurements and in-line probing are consistent with the hypothesis that when SAM is present, stacking interactions with the AT helix stabilize a partially formed P1 helix in the hybrids. Molecular modeling indicates that continuous stacking between the P1 and the AT helices is plausible with SAM bound. Our findings raise the possibility that conformational intermediates may play a role in ligand-induced aptamer folding.

  6. The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch

    PubMed Central

    Huang, Wei; Kim, Joohyun; Jha, Shantenu; Aboul-ela, Fareed

    2013-01-01

    Riboswitches sense cellular concentrations of small molecules and use this information to adjust synthesis rates of related metabolites. Riboswitches include an aptamer domain to detect the ligand and an expression platform to control gene expression. Previous structural studies of riboswitches largely focused on aptamers, truncating the expression domain to suppress conformational switching. To link ligand/aptamer binding to conformational switching, we constructed models of an S-adenosyl methionine (SAM)-I riboswitch RNA segment incorporating elements of the expression platform, allowing formation of an antiterminator (AT) helix. Using Anton, a computer specially developed for long timescale Molecular Dynamics (MD), we simulated an extended (three microseconds) MD trajectory with SAM bound to a modeled riboswitch RNA segment. Remarkably, we observed a strand migration, converting three base pairs from an antiterminator (AT) helix, characteristic of the transcription ON state, to a P1 helix, characteristic of the OFF state. This conformational switching towards the OFF state is observed only in the presence of SAM. Among seven extended trajectories with three starting structures, the presence of SAM enhances the trend towards the OFF state for two out of three starting structures tested. Our simulation provides a visual demonstration of how a small molecule (<500 MW) binding to a limited surface can trigger a large scale conformational rearrangement in a 40 kDa RNA by perturbing the Free Energy Landscape. Such a mechanism can explain minimal requirements for SAM binding and transcription termination for SAM-I riboswitches previously reported experimentally. PMID:23704854

  7. Validation of SAM 2 and SAGE satellite

    NASA Technical Reports Server (NTRS)

    Kent, G. S.; Wang, P.-H.; Farrukh, U. O.; Yue, G. K.

    1987-01-01

    Presented are the results of a validation study of data obtained by the Stratospheric Aerosol and Gas Experiment I (SAGE I) and Stratospheric Aerosol Measurement II (SAM II) satellite experiments. The study includes the entire SAGE I data set (February 1979 - November 1981) and the first four and one-half years of SAM II data (October 1978 - February 1983). These data sets have been validated by their use in the analysis of dynamical, physical and chemical processes in the stratosphere. They have been compared with other existing data sets and the SAGE I and SAM II data sets intercompared where possible. The study has shown the data to be of great value in the study of the climatological behavior of stratospheric aerosols and ozone. Several scientific publications and user-oriented data summaries have appeared as a result of the work carried out under this contract.

  8. Sam, Brookhaven, and the Physical Review

    NASA Astrophysics Data System (ADS)

    Blume, Martin

    2010-03-01

    Sam Goudsmit came to Brookhaven National Laboratory in 1948, just after the first year of operation of the new institution, and after a year of his postwar appointment as Professor of Physics at Northwestern University. He was named an associate editor of the Physical Review at that time, under the then Managing Editor John T. Tate of the University of Minnesota. Tate had been Editor since 1926, and had presided over the growth of Physical Review to leadership of publication in the world of physics. Tate died in 1950, and after a search under an interim Editor Sam was, in 1951, named Managing Editor. In 1952 he became Chair of the Brookhaven Physics Department, founded Physical Review Letters, and served as department chair until 1960, when he stepped down but remained an Associate Chair. I will discuss my own interactions with Sam during this later period, when I learned of his many faceted talents and accomplishments.

  9. Modulation of Conformational Equilibria in the S-Adenosylmethionine (SAM) II Riboswitch by SAM, Mg(2+), and Trimethylamine N-Oxide.

    PubMed

    McPhie, Peter; Brown, Patrick; Chen, Bin; Dayie, Theodore K; Minton, Allen P

    2016-09-13

    The dependence of the conformation of the S-adenosylmethionine (SAM) II riboswitch on the concentration of added Mg(2+) ions and SAM, individually and in mixtures, was monitored by circular dichroism (CD) spectroscopy and by measurement of the diffusion coefficient. The results are analyzed in the context of two complementary quantitative models, both of which are consistent with a single underlying physical model. Magnesium binding sites in the open state have an affinity on average higher than the affinity of those in the compact state, but formation of the compact state is accompanied by an increase in the number of binding sites. Consequently, at low Mg(2+) concentrations, Mg(2+) binds preferentially to the open state, favoring its formation, but at high concentrations, Mg(2+) binds preferentially to the compact state. The affinity of the riboswitch for SAM increases drastically with an increased level of binding of Mg(2+) to the compact pseudoknot conformation. The effect of increasing concentrations of trimethylamine N-oxide (TMAO), a well-studied molecular crowding agent, on the conformation of the riboswitch and its affinity for SAM were also monitored by CD spectroscopy and measurement of diffusion. In the absence of added Mg(2+), high concentrations of TMAO were found to induce a conformational change compatible with the formation of the pseudoknot form but have only a small effect on the affinity of the RNA for SAM. PMID:27552169

  10. An Optimization Model for the Allocation of University Based Merit Aid

    ERIC Educational Resources Information Center

    Sugrue, Paul K.

    2010-01-01

    The allocation of merit-based financial aid during the college admissions process presents postsecondary institutions with complex and financially expensive decisions. This article describes the application of linear programming as a decision tool in merit based financial aid decisions at a medium size private university. The objective defined for…

  11. Light Competition and Carbon Partitioning-Allocation in an improved Forest Ecosystem Model

    NASA Astrophysics Data System (ADS)

    Collalti, Alessio; Santini, Monia; Valentini Valentini, Riccardo

    2010-05-01

    . Hence, the presence of a cohort in a storey determines the amount of light received for the photosynthetic processes. The population density (numbers of trees per cell) represents a good competition index for determining the tree crown structure and tree crown dimension within a forest population. The tree crown tend to branch out horizontally to intercept as much light as possible. The model assess the structure of the tree crown both vertically and horizontally on the base of the population density and it up-scales the result to the whole stand. The canopy depth and the percentage of horizontal coverage determines moreover a crowding competition index that lead to a specific biomass partitioning-allocation ratio among the different tree components (foliage, roots and stem) and especially for the stem affecting Height-Diameter (at breast height) ratio. In this model, Height-Diameter ratio is used as an alternative competition index in determining the vigour and the strength of competition on free growth status of trees. The forest dominant vegetative cover affects moreover the presence of a dominated layer, it influences its yield and its Carbon stocking capacity and hence it influences the forest ecosystem CO2 carbon balance. From this model it is possible to simulate the impact of Climate Change on forests, the feedback of one or more dominated layers in terms of CO2 uptake in a forest stand and the effects of forest management activities for the next years.

  12. The value of models in informing resource allocation in colorectal cancer screening – 1 the case of the Netherlands

    PubMed Central

    van Hees, Frank; Zauber, Ann G.; van Veldhuizen, Harriët; Heijnen, Marie-Louise A.; Penning, Corine; de Koning, Harry J.; van Ballegooijen, Marjolein; Lansdorp-Vogelaar, Iris

    2015-01-01

    In May 2011, the Dutch government decided to implement a national programme for colorectal cancer (CRC) screening using biennial faecal immunochemical test (FIT) screening between ages 55 and 75.[1] Decision modelling played an important role in informing this decision, as well as in the planning and implementation of the programme afterwards. In this overview, we illustrate the value of models in informing resource allocation in CRC screening, using the role that decision modelling has played in the Dutch CRC screening programme as an example. PMID:26063755

  13. Genetic typing of the senescence-accelerated mouse (SAM) strains with microsatellite markers.

    PubMed

    Xia, C; Higuchi, K; Shimizu, M; Matsushita, T; Kogishi, K; Wang, J; Chiba, T; Festing, M F; Hosokawa, M

    1999-03-01

    The Senescence-Accelerated Mouse (SAM) strains constitute a murine model of accelerated senescence originating from the ancestral AKR/J strains and consist of nine senescence-prone (SAMP) strains and four senescence-resistant (SAMR) strains. The chromosomes (Chrs) of the SAM strains were typed with 581 microsatellite markers amplified by PCR, and the fundamental genetic information of the SAM strains was obtained. One-third of the examined markers displayed polymorphism among the strains, and only two alleles were detected in almost all loci among the SAM and AKR/J strains. However, in 12 loci (5.6% of total 215 polymorphic markers), the third allele was detected among the SAM strains. The genetic typing and developmental history suggested that the SAM strains were related inbred strains developed by the accidental crossing between the AKR/J strain and other unknown strain(s). Comparison of the distribution of the loci in the SAMP and the SAMR series revealed notable differences in the four regions on Chrs 4, 14, 16, and 17. This indicated that some of these chromosomal sites might contain the genes responsible for accelerated senescence in the SAMP series. PMID:10051317

  14. Discrimination between closely related cellular metabolites by the SAM-I riboswitch.

    PubMed

    Montange, Rebecca K; Mondragón, Estefanía; van Tyne, Daria; Garst, Andrew D; Ceres, Pablo; Batey, Robert T

    2010-02-26

    The SAM-I riboswitch is a cis-acting element of genetic control found in bacterial mRNAs that specifically binds S-adenosylmethionine (SAM). We previously determined the 2.9-A X-ray crystal structure of the effector-binding domain of this RNA element, revealing details of RNA-ligand recognition. To improve this structure, variations were made to the RNA sequence to alter lattice contacts, resulting in a 0.5-A improvement in crystallographic resolution and allowing for a more accurate refinement of the crystallographic model. The basis for SAM specificity was addressed by a structural analysis of the RNA complexed to S-adenosylhomocysteine (SAH) and sinefungin and by measuring the affinity of SAM and SAH for a series of mutants using isothermal titration calorimetry. These data illustrate the importance of two universally conserved base pairs in the RNA that form electrostatic interactions with the positively charged sulfonium group of SAM, thereby providing a basis for discrimination between SAM and SAH. PMID:20006621

  15. Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch

    PubMed Central

    Montange, Rebecca K.; Mondragón, Estefanía; van Tyne, Daria; Garst, Andrew D.; Ceres, Pablo; Batey, Robert T.

    2009-01-01

    The SAM-I riboswitch is a cis-acting element of genetic control found in bacterial mRNAs that specifically binds S-adenosylmethionine (SAM). We previously determined the 2.9-Å X-ray crystal structure of the effector-binding domain of this RNA element, revealing details of RNA–ligand recognition. To improve this structure, variations were made to the RNA sequence to alter lattice contacts, resulting in a 0.5-Å improvement in crystallographic resolution and allowing for a more accurate refinement of the crystallographic model. The basis for SAM specificity was addressed by a structural analysis of the RNA complexed to S-adenosylhomocysteine (SAH) and sinefungin and by measuring the affinity of SAM and SAH for a series of mutants using isothermal titration calorimetry. These data illustrate the importance of two universally conserved base pairs in the RNA that form electrostatic interactions with the positively charged sulfonium group of SAM, thereby providing a basis for discrimination between SAM and SAH. PMID:20006621

  16. Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch

    SciTech Connect

    Montange, R.; Mondragon, E; van Tyne, D; Garst, A; Ceres, P; Batey, R

    2010-01-01

    The SAM-I riboswitch is a cis-acting element of genetic control found in bacterial mRNAs that specifically binds S-adenosylmethionine (SAM). We previously determined the 2.9-{angstrom} X-ray crystal structure of the effector-binding domain of this RNA element, revealing details of RNA-ligand recognition. To improve this structure, variations were made to the RNA sequence to alter lattice contacts, resulting in a 0.5-{angstrom} improvement in crystallographic resolution and allowing for a more accurate refinement of the crystallographic model. The basis for SAM specificity was addressed by a structural analysis of the RNA complexed to S-adenosylhomocysteine (SAH) and sinefungin and by measuring the affinity of SAM and SAH for a series of mutants using isothermal titration calorimetry. These data illustrate the importance of two universally conserved base pairs in the RNA that form electrostatic interactions with the positively charged sulfonium group of SAM, thereby providing a basis for discrimination between SAM and SAH.

  17. Modelling the climatic drivers determining photosynthesis and carbon allocation in evergreen Mediterranean forests using multiproxy long time series

    NASA Astrophysics Data System (ADS)

    Gea-Izquierdo, G.; Guibal, F.; Joffre, R.; Ourcival, J. M.; Simioni, G.; Guiot, J.

    2015-06-01

    Climatic drivers limit several important physiological processes involved in ecosystem carbon dynamics including gross primary productivity (GPP) and carbon allocation in vegetation. Climatic variability limits these two processes differently. We developed an existing mechanistic model to analyse photosynthesis and variability in carbon allocation in two evergreen species at two Mediterranean forests. The model was calibrated using a combination of eddy covariance CO2 flux data, dendrochronological time series of secondary growth and forest inventory data. The model was modified to be climate explicit in the key processes addressing the acclimation of photosynthesis and the pattern of C allocation, particularly to water stress. It succeeded in fitting both the high- and the low-frequency response of stand GPP and carbon allocation to stem growth. This would support its capability to address both C-source and C-sink limitations. Simulations suggest a decrease in mean stomatal conductance in response to a recent enhancement in water stress and an increase in mean annual intrinsic water use efficiency (iWUE) in both species during the last 50 years. However, this was not translated into a parallel increase in ecosystem water use efficiency (WUE). The interannual variability in WUE closely followed that in iWUE at both sites. Nevertheless, long-term decadal variability in WUE followed the long-term decrease in annual GPP matching the local trend in annual precipitation observed since the late 1970s at one site. In contrast, at the site where long-term precipitation remained stable, GPP and WUE did not show a negative trend and the trees buffered the climatic variability. In our simulations these temporal changes were related to acclimation processes at the canopy level, including modifications in LAI and stomatal conductance, but also partly related to increasing [CO2] because the model includes biochemical equations where photosynthesis is directly linked to [CO2

  18. Optimization model for the allocation of water resources based on the maximization of employment in the agriculture and industry sectors

    NASA Astrophysics Data System (ADS)

    Habibi Davijani, M.; Banihabib, M. E.; Nadjafzadeh Anvar, A.; Hashemi, S. R.

    2016-02-01

    In many discussions, work force is mentioned as the most important factor of production. Principally, work force is a factor which can compensate for the physical and material limitations and shortcomings of other factors to a large extent which can help increase the production level. On the other hand, employment is considered as an effective factor in social issues. The goal of the present research is the allocation of water resources so as to maximize the number of jobs created in the industry and agriculture sectors. An objective that has attracted the attention of policy makers involved in water supply and distribution is the maximization of the interests of beneficiaries and consumers in case of certain policies adopted. The present model applies the particle swarm optimization (PSO) algorithm in order to determine the optimum amount of water allocated to each water-demanding sector, area under cultivation, agricultural production, employment in the agriculture sector, industrial production and employment in the industry sector. Based on the results obtained from this research, by optimally allocating water resources in the central desert region of Iran, 1096 jobs can be created in the industry and agriculture sectors, which constitutes an improvement of about 13% relative to the previous situation (non-optimal water utilization). It is also worth mentioning that by optimizing the employment factor as a social parameter, the other areas such as the economic sector are influenced as well. For example, in this investigation, the resulting economic benefits (incomes) have improved from 73 billion Rials at baseline employment figures to 112 billion Rials in the case of optimized employment condition. Therefore, it is necessary to change the inter-sector and intra-sector water allocation models in this region, because this change not only leads to more jobs in this area, but also causes an improvement in the region's economic conditions.

  19. Budgeting based on need: a model to determine sub-national allocation of resources for health services in Indonesia

    PubMed Central

    2012-01-01

    Background Allocating national resources to regions based on need is a key policy issue in most health systems. Many systems utilise proxy measures of need as the basis for allocation formulae. Increasingly these are underpinned by complex statistical methods to separate need from supplier induced utilisation. Assessment of need is then used to allocate existing global budgets to geographic areas. Many low and middle income countries are beginning to use formula methods for funding however these attempts are often hampered by a lack of information on utilisation, relative needs and whether the budgets allocated bear any relationship to cost. An alternative is to develop bottom-up estimates of the cost of providing for local need. This method is viable where public funding is focused on a relatively small number of targeted services. We describe a bottom-up approach to developing a formula for the allocation of resources. The method is illustrated in the context of the state minimum service package mandated to be provided by the Indonesian public health system. Methods A standardised costing methodology was developed that is sensitive to the main expected drivers of local cost variation including demographic structure, epidemiology and location. Essential package costing is often undertaken at a country level. It is less usual to utilise the methods across different parts of a country in a way that takes account of variation in population needs and location. Costing was based on best clinical practice in Indonesia and province specific data on distribution and costs of facilities. The resulting model was used to estimate essential package costs in a representative district in each province of the country. Findings Substantial differences in the costs of providing basic services ranging from USD 15 in urban Yogyakarta to USD 48 in sparsely populated North Maluku. These costs are driven largely by the structure of the population, particularly numbers of births

  20. Emerging themes in radical SAM chemistry

    PubMed Central

    Shisler, Krista A; Broderick, Joan B

    2014-01-01

    Enzymes in the radical SAM (RS) superfamily catalyze a wide variety of reactions through unique radical chemistry. The characteristic markers of the superfamily include a [4Fe–4S] cluster coordinated to the protein via a cysteine triad motif, typically CX3CX2C, with the fourth iron coordinated by S-adenosylmethionine (SAM). The SAM serves as a precursor for a 5′-deoxyadenosyl radical, the central intermediate in nearly all RS enzymes studied to date. The SAM-bound [4Fe–4S] cluster is located within a partial or full triosephosphate isomerase (TIM) barrel where the radical chemistry occurs protected from the surroundings. In addition to the TIM barrel and a RS [4Fe–4S] cluster, many members of the superfamily contain additional domains and/or additional Fe–S clusters. Recently characterized superfamily members are providing new examples of the remarkable range of reactions that can be catalyzed, as well as new structural and mechanistic insights into these fascinating reactions. PMID:23141873

  1. Sam's Journey to "Reach for the Stars"

    ERIC Educational Resources Information Center

    Mayer, Sue

    2007-01-01

    In this article, the author shares her experiences as a parent of a child with Down syndrome. Although her son Sam's first years were filled with numerous hospitalizations and visits to pediatricians, which she feared would further delay his development, she soon discovered an organization known as the National Association of Child Development…

  2. Structural Basis for Methyl Transfer by a Radical SAM Enzyme

    SciTech Connect

    Boal, Amie K.; Grove, Tyler L.; McLaughlin, Monica I.; Yennawar, Neela H.; Booker, Squire J.; Rosenzweig, Amy C.

    2014-10-02

    The radical S-adenosyl-l-methionine (SAM) enzymes RlmN and Cfr methylate 23S ribosomal RNA, modifying the C2 or C8 position of adenosine 2503. The methyl groups are installed by a two-step sequence involving initial methylation of a conserved Cys residue (RlmN Cys{sup 355}) by SAM. Methyl transfer to the substrate requires reductive cleavage of a second equivalent of SAM. Crystal structures of RlmN and RlmN with SAM show that a single molecule of SAM coordinates the [4Fe-4S] cluster. Residue Cys{sup 355} is S-methylated and located proximal to the SAM methyl group, suggesting the SAM that is involved in the initial methyl transfer binds at the same site. Thus, RlmN accomplishes its complex reaction with structural economy, harnessing the two most important reactivities of SAM within a single site.

  3. SAM II Data and Information (HDF-EOS)

    Atmospheric Science Data Center

    2016-09-01

    SAM II Data and Information (HDF-EOS) Data obtained from the Stratospheric Aerosol Measurement (SAM) II instrument, ... Guide Documents:  Project Guide Data Set Guide Readme Files:  Data Set (Text file) ...

  4. Introducing health gains in location-allocation models: A stochastic model for planning the delivery of long-term care

    NASA Astrophysics Data System (ADS)

    Cardoso, T.; Oliveira, M. D.; Barbosa-Póvoa, A.; Nickel, S.

    2015-05-01

    Although the maximization of health is a key objective in health care systems, location-allocation literature has not yet considered this dimension. This study proposes a multi-objective stochastic mathematical programming approach to support the planning of a multi-service network of long-term care (LTC), both in terms of services location and capacity planning. This approach is based on a mixed integer linear programming model with two objectives - the maximization of expected health gains and the minimization of expected costs - with satisficing levels in several dimensions of equity - namely, equity of access, equity of utilization, socioeconomic equity and geographical equity - being imposed as constraints. The augmented ε-constraint method is used to explore the trade-off between these conflicting objectives, with uncertainty in the demand and delivery of care being accounted for. The model is applied to analyze the (re)organization of the LTC network currently operating in the Great Lisbon region in Portugal for the 2014-2016 period. Results show that extending the network of LTC is a cost-effective investment.

  5. Characterization of flourocarbon SAM coated MEMS tribogauge

    NASA Astrophysics Data System (ADS)

    Vijayasai, Ashwin; Ramachandran, Gautham; Sivakumar, Ganapathy; Anderson, Charlie; Gale, Richard; Dallas, Tim

    2012-03-01

    A MEMS tribogauge was used for on-chip and in-situ characterization of nano-tribological phenomena (stiction, friction, and wear of coated polysilicon surfaces). The device was fabricated using the SUMMiT-V process. Measurements were made on sidewall surfaces on the polysilicon-3 layer. The device consists of two orthogonally positioned comb-drive assemblies that are used for both actuation and sensing. One assembly is used to apply a normal load (Fn) to contacting surface, while the other induces a tangential load (FT). Precise position control is tracked by employing a LabVIEW controlled AD7747 capacitance sense mechanism. The resolution of the characterization apparatus is +/-10nm. Three MEMS tribogauge devices are tested; two of them have a chemisorbed layer of self-assembled monolayer (SAM) coatings and one with no SAM coating. The two types of SAM coatings are FOTS and 'Sandia vapor-SAM' (SVSAM). The tribogauge with no FSAM coating is either UV-Ozone or 'air plasma' treated to remove organic contaminants leaving behind -OH bonds on top of the MEMS surface (native oxide, SiO2). Characterization using the tribogauge for each coating type includes: measurement of baseline stiction force [see manuscript], static and dynamic coefficient of friction [see manuscript], induced stiction force calculated after specific load cycles [see manuscript]. Experiments showed that the induced stiction force increases in proportion to the increase in the number of load cycles, indicating degradation of the FSAM coating and topographical changes to the interacting surfaces. The UV-Ozone /air plasma treated pristine tribogauge was used to measure the stiction force of the device with no SAM coating [see manuscript].

  6. A negative binomial model for student allocation to higher education in Portugal during the pre-Bologna period

    NASA Astrophysics Data System (ADS)

    Oliveira, Raquel; Gonçalves, A. Manuela; Vasconcelos, Rosa M.

    2013-10-01

    This paper aims to describe and characterize student allocation in the Portuguese public higher education system, namely in academic engineering programs, during the so-called pre-Bologna period. With this study, we achieved a better understanding of some of the variables which could describe the access to higher education engineering programs after the implementation of the Bologna process. The data used in this paper covers the years from 1997 to 2005 and was provided by the Portuguese Ministry of Education. We use regression analysis applied to count data, by estimating negative binomial models, and we obtained a satisfactory performance of the model.

  7. Development of integrated model for continuous berth allocation problem and quay crane scheduling with non crossing constraint

    NASA Astrophysics Data System (ADS)

    Basri, Azyanzuhaila Hasan; Zainuddin, Zaitul Marlizawati

    2014-09-01

    High efficiency of port operation is required to succeed in the competition between port container terminals. Berth Allocation and Quay Crane Scheduling are the most important part in container terminal operations. The integrated model is formulated as a MIP problem with the objective to minimize the sum of the dwell times, where a vessel's dwell time is measured between arrival and departure including both times waiting to be berthed and servicing time while berthed. The construction of suitable mathematical model is formulated by considering various practical constraints.

  8. Changing model of nursing care from individual patient allocation to team nursing in the acute inpatient environment.

    PubMed

    Fairbrother, Greg; Jones, Aaron; Rivas, Ketty

    2010-06-01

    Agreement was reached with 12 acute medical and surgical wards/units at Sydney's Prince of Wales Hospital to participate in a trial of team nursing (TN). Six units employed action research principles to undertake a change to a team nursing model and six remained with the pre-existing individual patient allocation (IPA) model. Task-based teaming was widely discarded by the team nursing units in favour of allocating patients within the team and introducing more supportive and communicative processes aimed at fostering responsibility sharing. Localised team-based models of care arose in the change wards and were outlined, implemented and refined using social action research principles. A 12-month prospective experimental comparison of job satisfaction and staff retention between the TN and IPA groups indicated statistically significant job satisfaction benefits and practically important staff retention benefits associated with moving away from an IPA model of nursing care delivery towards a team-based model of care delivery. Perhaps not surprisingly, job satisfaction gains were most marked among new graduate nurses, who reported real benefits from a teaming inspired shift in model of care in the acute inpatient environment. PMID:20950201

  9. 77 FR 50493 - Sam Rayburn Dam Project Power Rate

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-21

    ... Southwestern Power Administration Sam Rayburn Dam Project Power Rate AGENCY: Southwestern Power Administration, DOE. ACTION: Notice of proposed extension. SUMMARY: The current Sam Rayburn Dam Project rate was... 46 microwave and VHF radio sites. Costs associated ] with the Sam Rayburn and Robert D. Willis...

  10. Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues.

    PubMed

    Ji, Xinjian; Li, Yongzhen; Xie, Liqi; Lu, Haojie; Ding, Wei; Zhang, Qi

    2016-09-19

    Radical S-adenosyl-l-methionine (SAM) enzymes utilize a [4Fe-4S] cluster to bind SAM and reductively cleave its carbon-sulfur bond to produce a highly reactive 5'-deoxyadenosyl (dAdo) radical. In almost all cases, the dAdo radical abstracts a hydrogen atom from the substrates or from enzymes, thereby initiating a highly diverse array of reactions. Herein, we report a change of the dAdo radical-based chemistry from hydrogen abstraction to radical addition in the reaction of the radical SAM enzyme NosL. This change was achieved by using a substrate analogue containing an olefin moiety. We also showed that two SAM analogues containing different nucleoside functionalities initiate the radical-based reactions with high efficiencies. The radical adduct with the olefin produced in the reaction was found to undergo two divergent reactions, and the mechanistic insights into this process were investigated in detail. Our study demonstrates a promising strategy in expanding radical SAM chemistry, providing an effective way to access nucleoside-containing compounds by using radical SAM-dependent reactions. PMID:27573794

  11. Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues.

    PubMed

    Ji, Xinjian; Li, Yongzhen; Xie, Liqi; Lu, Haojie; Ding, Wei; Zhang, Qi

    2016-09-19

    Radical S-adenosyl-l-methionine (SAM) enzymes utilize a [4Fe-4S] cluster to bind SAM and reductively cleave its carbon-sulfur bond to produce a highly reactive 5'-deoxyadenosyl (dAdo) radical. In almost all cases, the dAdo radical abstracts a hydrogen atom from the substrates or from enzymes, thereby initiating a highly diverse array of reactions. Herein, we report a change of the dAdo radical-based chemistry from hydrogen abstraction to radical addition in the reaction of the radical SAM enzyme NosL. This change was achieved by using a substrate analogue containing an olefin moiety. We also showed that two SAM analogues containing different nucleoside functionalities initiate the radical-based reactions with high efficiencies. The radical adduct with the olefin produced in the reaction was found to undergo two divergent reactions, and the mechanistic insights into this process were investigated in detail. Our study demonstrates a promising strategy in expanding radical SAM chemistry, providing an effective way to access nucleoside-containing compounds by using radical SAM-dependent reactions.

  12. Make or buy analysis model based on tolerance allocation to minimize manufacturing cost and fuzzy quality loss

    NASA Astrophysics Data System (ADS)

    Rosyidi, C. N.; Puspitoingrum, W.; Jauhari, W. A.; Suhardi, B.; Hamada, K.

    2016-02-01

    The specification of tolerances has a significant impact on the quality of product and final production cost. The company should carefully pay attention to the component or product tolerance so they can produce a good quality product at the lowest cost. Tolerance allocation has been widely used to solve problem in selecting particular process or supplier. But before merely getting into the selection process, the company must first make a plan to analyse whether the component must be made in house (make), to be purchased from a supplier (buy), or used the combination of both. This paper discusses an optimization model of process and supplier selection in order to minimize the manufacturing costs and the fuzzy quality loss. This model can also be used to determine the allocation of components to the selected processes or suppliers. Tolerance, process capability and production capacity are three important constraints that affect the decision. Fuzzy quality loss function is used in this paper to describe the semantic of the quality, in which the product quality level is divided into several grades. The implementation of the proposed model has been demonstrated by solving a numerical example problem that used a simple assembly product which consists of three components. The metaheuristic approach were implemented to OptQuest software from Oracle Crystal Ball in order to obtain the optimal solution of the numerical example.

  13. Regional bit allocation and rate distortion optimization for multiview depth video coding with view synthesis distortion model.

    PubMed

    Zhang, Yun; Kwong, Sam; Xu, Long; Hu, Sudeng; Jiang, Gangyi; Kuo, C-C Jay

    2013-09-01

    In this paper, we propose a view synthesis distortion model (VSDM) that establishes the relationship between depth distortion and view synthesis distortion for the regions with different characteristics: color texture area corresponding depth (CTAD) region and color smooth area corresponding depth (CSAD), respectively. With this VSDM, we propose regional bit allocation (RBA) and rate distortion optimization (RDO) algorithms for multiview depth video coding (MDVC) by allocating more bits on CTAD for rendering quality and fewer bits on CSAD for compression efficiency. Experimental results show that the proposed VSDM based RBA and RDO can improve the coding efficiency significantly for the test sequences. In addition, for the proposed overall MDVC algorithm that integrates VSDM based RBA and RDO, it achieves 9.99% and 14.51% bit rate reduction on average for the high and low bit rate, respectively. It can improve virtual view image quality 0.22 and 0.24 dB on average at the high and low bit rate, respectively, when compared with the original joint multiview video coding model. The RD performance comparisons using five different metrics also validate the effectiveness of the proposed overall algorithm. In addition, the proposed algorithms can be applied to both INTRA and INTER frames.

  14. Effects of nonlinear model response on allocation of streamflow depletion: exemplified by the case of Beaver Creek, USA

    NASA Astrophysics Data System (ADS)

    Ahlfeld, David P.; Schneider, James C.; Spalding, Charles P.

    2016-06-01

    Anomalies found when apportioning responsibility for streamflow depletion are examined. The anomalies arise when responsibility is assigned to the two states that contribute to depletion of Beaver Creek in the Republican River Basin in the United States. The apportioning procedure for this basin presumes that the sum of streamflow depletions, computed by comparing simulation model runs with and without groundwater pumping from individual states, approximates the streamflow depletion when both states are pumping. In the case study presented here, this presumed superposition fails dramatically. The stream drying and aquifer-storage depletion, as represented in the simulation model used for allocation, are examined in detail to understand the hydrologic and numerical basis for the severe nonlinear response. Users of apportioning procedures that rely on superposition should be aware of the presence and likely magnitude of nonlinear responses in modeling tools.

  15. Optimal control model predictions of system performance and attention allocation and their experimental validation in a display design study

    NASA Technical Reports Server (NTRS)

    Johannsen, G.; Govindaraj, T.

    1980-01-01

    The influence of different types of predictor displays in a longitudinal vertical takeoff and landing (VTOL) hover task is analyzed in a theoretical study. Several cases with differing amounts of predictive and rate information are compared. The optimal control model of the human operator is used to estimate human and system performance in terms of root-mean-square (rms) values and to compute optimized attention allocation. The only part of the model which is varied to predict these data is the observation matrix. Typical cases are selected for a subsequent experimental validation. The rms values as well as eye-movement data are recorded. The results agree favorably with those of the theoretical study in terms of relative differences. Better matching is achieved by revised model input data.

  16. Ambient STM Study of Long Chain Hydrophobic Thiol SAMs on HOPG and Au-capped HOPG

    NASA Astrophysics Data System (ADS)

    Maurer, Mackenzie; Bowers, Alexis; Senevirathne, Indrajith

    2015-03-01

    Thiol-based self-assembled monolayers (SAM) surfaces are ubiquitous in many device applications including sensor engineering. The conductivity characteristics and surface molecular structure and orientation of these SAMs are important as physiochemical properties are dependent on the surface arrangement. This study attempts to quantify and model long chain -R terminated (hydrophobic) 1-dodecanethiol on both Highly Oriented Pyrolytic Graphite (HOPG) and thermally annealed Au thin films capped on HOPG substrates. Study uses Scanning Tunneling Microscopy (STM), contact angle measurements and reflective spectroscopy to assess the SAM layered surface. 5mM concentrated solutions of 1-dodecanethiol dissolved in 200 proof ethanol were prepared for the self-assembly process. These solutions were used in developing SAMs on freshly cleaved HOPG. Au thin layers were sputter deposited on HOPG and subsequently annealed. Data indicated Au deposition changes the surface consistency. Uniqueness of this study is the ambient conditions under which data was obtained. Surface structure, consistency and possible thiol molecular arrangement of the SAM layer will be discussed.

  17. Approaches to Resource Allocation

    ERIC Educational Resources Information Center

    Dressel, Paul; Simon, Lou Anna Kimsey

    1976-01-01

    Various budgeting patterns and strategies are currently in use, each with its own particular strengths and weaknesses. Neither cost-benefit analysis nor cost-effectiveness analysis offers any better solution to the allocation problem than do the unsupported contentions of departments or the historical unit costs. An operable model that performs…

  18. Applying the Attention-Allocation Model to the Explanation of Alcohol-Related Aggression: Implications for Prevention

    PubMed Central

    Giancola, Peter R.; Josephs, Robert A.; DeWall, C. Nathan; Gunn, Rachel L.

    2009-01-01

    The primary purpose of this article is to apply the attention allocation model (AAM; Steele & Josephs, 1990) to the explanation, as well as the prevention, of alcohol-related violence. The AAM contends that alcohol has a “myopic” effect on attentional capacity that presumably facilitates aggression by narrowing attentional focus on the most salient provocative cues, that are naturally present in hostile situations, rather than less salient inhibitory cues. Data are presented to demonstrate support for the AAM with regard to alcohol-related aggression. The model has also been expanded to suggest some intermediary mechanisms that may account for how distracting attention away from provocative cues might be involved in the reduction of aggression. Finally, a number of practical suggestions are put forth regarding how the AAM can be applied to the prevention of intoxicated aggression. PMID:19938917

  19. A variation reduction allocation model for quality improvement to minimize investment and quality costs by considering suppliers’ learning curve

    NASA Astrophysics Data System (ADS)

    Rosyidi, C. N.; Jauhari, WA; Suhardi, B.; Hamada, K.

    2016-02-01

    Quality improvement must be performed in a company to maintain its product competitiveness in the market. The goal of such improvement is to increase the customer satisfaction and the profitability of the company. In current practice, a company needs several suppliers to provide the components in assembly process of a final product. Hence quality improvement of the final product must involve the suppliers. In this paper, an optimization model to allocate the variance reduction is developed. Variation reduction is an important term in quality improvement for both manufacturer and suppliers. To improve suppliers’ components quality, the manufacturer must invest an amount of their financial resources in learning process of the suppliers. The objective function of the model is to minimize the total cost consists of investment cost, and quality costs for both internal and external quality costs. The Learning curve will determine how the employee of the suppliers will respond to the learning processes in reducing the variance of the component.

  20. Obituary: Sam Roweis (1972-2010)

    NASA Astrophysics Data System (ADS)

    Hogg, David

    2011-12-01

    Computer scientist and statistical astronomer Sam Roweis took his own life in New York City on 2010 January 12. He was a brilliant and accomplished researcher in the field of machine learning, and a strong advocate for the use of computational statistics for automating discovery and scientific data analysis. He made several important contributions to astronomy and was working on adaptive astronomical data analysis at the time of his death. Roweis obtained his PhD in 1999 from the California Institute of Technology, where he worked on a remarkable range of subjects, including DNA computing, modeling of dynamical systems, signal processing, and speech recognition. During this time he unified and clarified some of the most important data analysis techniques, including Principal Component Analysis, Hidden Markov Models, and Expectation Maximization. His work was aimed at making data analysis and modeling faster, but also better justified scientifically. The last years of his PhD were spent in Princeton NJ, where he came in contact with a young generation of cosmologists thinking about microwave background and large-scale structure data. In a postdoc at University College London, Roweis co-created the Locally Linear Embedding (LLE) algorithm; a simple but flexible technique for mapping a large data set onto a low-dimensional manifold. The LLE paper obtained more than 2700 citations in 9 years, launched a new sub-field of machine learning known as "manifold learning," and inspired work in data visualization, search, and applied mathematics. In 2001, Roweis took a faculty job at the University of Toronto Computer Science Department. He continued working on data analysis methods that have probabilistic interpretation and therefore scientific applicability, but at the same time have good performance on large data sets. He was awarded a Sloan Fellowship, a Canada Research Chair, and a fellowship of the Canadian Institute for Advanced Research, among other honors and awards

  1. Senescence-accelerated mouse (SAM): a biogerontological resource in aging research.

    PubMed

    Takeda, T

    1999-01-01

    The senescence-accelerated mouse (SAM), consisting of 14 senescence-prone inbred strains (SAMP) and 4 senescence-resistant inbred strains (SAMR) has been under development since 1970 through the selective inbreeding of AKR/J strain mice donated by the Jackson laboratory in 1968, based on the data of the grading score of senescence, life span, and pathologic phenotypes. The characteristic feature of aging common to all SAMP and SAMR mice is accelerated senescence and normal aging, respectively. Furthermore, SAMP and SAMR strains manifest various pathobiological phenotypes which include such neurobiological phenotypes as deficits in learning and memory, emotional disorders, abnormal circadian rhythms, brain atrophy, hearing impairment, etc., and are often characteristic enough to differentiate the strains. Various efforts are currently being made using the SAM model to clarify the underlying mechanisms in accelerated senescence as well as the etiopathogenic mechanisms in age-associated pathobiologies. Genetic background and significance of SAM development are discussed. PMID:10537019

  2. AFM-assisted fabrication of thiol SAM pattern with alternating quantified surface potential

    PubMed Central

    2011-01-01

    Thiol self-assembled monolayers (SAMs) are widely used in many nano- and bio-technology applications. We report a new approach to create and characterize a thiol SAMs micropattern with alternating charges on a flat gold-coated substrate using atomic force microscopy (AFM) and Kelvin probe force microscopy (KPFM). We produced SAMs-patterns made of alternating positively charged, negatively charged, and hydrophobic-terminated thiols by an automated AFM-assisted manipulation, or nanografting. We show that these thiol patterns possess only small topographical differences as revealed by AFM, and distinguished differences in surface potential (20-50 mV), revealed by KPFM. The pattern can be helpful in the development of biosensor technologies, specifically for selective binding of biomolecules based on charge and hydrophobicity, and serve as a model for creating surfaces with quantified alternating surface potential distribution. PMID:21711703

  3. A Systems Approach for Allocating Educational Space.

    ERIC Educational Resources Information Center

    Florida Univ., Gainesville. Center for Community Needs Assessment.

    A computer simulation model for allocating facilities and physical space is presented as a means of optimally allocating available educational resources. The model allows the decisionmaker to change specific program allocations, system parameters, and other controllable variables in order to determine the effects, both cost and utility, of these…

  4. Water consumption and allocation strategies along the river oases of Tarim River based on large-scale hydrological modelling

    NASA Astrophysics Data System (ADS)

    Yu, Yang; Disse, Markus; Yu, Ruide

    2016-04-01

    With the mainstream of 1,321km and located in an arid area in northwest China, the Tarim River is China's longest inland river. The Tarim basin on the northern edge of the Taklamakan desert is an extremely arid region. In this region, agricultural water consumption and allocation management are crucial to address the conflicts among irrigation water users from upstream to downstream. Since 2011, the German Ministry of Science and Education BMBF established the Sino-German SuMaRiO project, for the sustainable management of river oases along the Tarim River. The project aims to contribute to a sustainable land management which explicitly takes into account ecosystem functions and ecosystem services. SuMaRiO will identify realizable management strategies, considering social, economic and ecological criteria. This will have positive effects for nearly 10 million inhabitants of different ethnic groups. The modelling of water consumption and allocation strategies is a core block in the SuMaRiO cluster. A large-scale hydrological model (MIKE HYDRO Basin) was established for the purpose of sustainable agricultural water management in the main stem Tarim River. MIKE HYDRO Basin is an integrated, multipurpose, map-based decision support tool for river basin analysis, planning and management. It provides detailed simulation results concerning water resources and land use in the catchment areas of the river. Calibration data and future predictions based on large amount of data was acquired. The results of model calibration indicated a close correlation between simulated and observed values. Scenarios with the change on irrigation strategies and land use distributions were investigated. Irrigation scenarios revealed that the available irrigation water has significant and varying effects on the yields of different crops. Irrigation water saving could reach up to 40% in the water-saving irrigation scenario. Land use scenarios illustrated that an increase of farmland area in the

  5. MMW, IR, and SAM signature collection

    NASA Astrophysics Data System (ADS)

    Reichstetter, Fred; Ward, Mary E.

    2002-08-01

    During the development of smart weapon's seeker/sensors, it is imperative to collect high quality signatures of the targets the system is intended to engage. These signatures are used to support algorithm development so the system can find and engage the targets of interest in the specific kill area on the target. Englin AFB FL is the AF development center for munitions; and in support of the development effort, the 46th Test Wing (46 TW) has initiated significant improvements in collection capabilities for signatures in the MMW, Infrared and Seismic, Acoustic and Magnetic (SAM) spectrum. Additionally, the Joint Munitions Test and Evaluation program office maintains a fleet of foreign ground vehicle targets used for such signature collection including items such as tanks, SCUD missile launchers, air defense units such as SA-06, SA-8, SA-13, and associated ground support trucks and general purpose vehicles. The major test facility includes a 300 ft tower used for mounting the instrumentation suite that currently includes, 10, 35 and 94 GHz MMW and 2-5(mu) and 8-12(mu) IR instrumentation systems. This facility has undergone major improvements in terms of background signature reduction, construction of a high bay building to house the turntable on which the targets are mounted, and an additional in- ground stationary turntable primarily for IR signature collection. Our experience using this facility to collect signatures for the smart weapons development community has confirmed a significant improvement in quality and efficiency. The need for the stationary turntable signature collection capability was driven by the requirements of the IR community who are interested in collecting signatures in clutter. This tends to be contrary to the MMW community that desires minimum background clutter. The resulting location, adjacent to the MMW tower, allows variations in the type and amount of clutter background that could be incorporated and also provides maximum utilization of

  6. On inclusion of water resource management in Earth system models - Part 2: Representation of water supply and allocation and opportunities for improved modeling

    NASA Astrophysics Data System (ADS)

    Nazemi, A.; Wheater, H. S.

    2015-01-01

    Human water use has significantly increased during the recent past. Water withdrawals from surface and groundwater sources have altered terrestrial discharge and storage, with large variability in time and space. These withdrawals are driven by sectoral demands for water, but are commonly subject to supply constraints, which determine water allocation. Water supply and allocation, therefore, should be considered together with water demand and appropriately included in Earth system models to address various large-scale effects with or without considering possible climate interactions. In a companion paper, we review the modeling of demand in large-scale models. Here, we review the algorithms developed to represent the elements of water supply and allocation in land surface and global hydrologic models. We note that some potentially important online implications, such as the effects of large reservoirs on land-atmospheric feedbacks, have not yet been fully investigated. Regarding offline implications, we find that there are important elements, such as groundwater availability and withdrawals, and the representation of large reservoirs, which should be improved. We identify major sources of uncertainty in current simulations due to limitations in data support, water allocation algorithms, host large-scale models as well as propagation of various biases across the integrated modeling system. Considering these findings with those highlighted in our companion paper, we note that advancements in computation and coupling techniques as well as improvements in natural and anthropogenic process representation and parameterization in host large-scale models, in conjunction with remote sensing and data assimilation can facilitate inclusion of water resource management at larger scales. Nonetheless, various modeling options should be carefully considered, diagnosed and intercompared. We propose a modular framework to develop integrated models based on multiple hypotheses for

  7. Multi-objective models of waste load allocation toward a sustainable reuse of drainage water in irrigation.

    PubMed

    Allam, Ayman; Tawfik, Ahmed; Yoshimura, Chihiro; Fleifle, Amr

    2016-06-01

    The present study proposes a waste load allocation (WLA) framework for a sustainable quality management of agricultural drainage water (ADW). Two multi-objective models, namely, abatement-performance and abatement-equity-performance, were developed through the integration of a water quality model (QAUL2Kw) and a genetic algorithm, by considering (1) the total waste load abatement, and (2) the inequity among waste dischargers. For successfully accomplishing modeling tasks, we developed a comprehensive overall performance measure (E wla ) reflecting possible violations of Egyptian standards for ADW reuse in irrigation. This methodology was applied to the Gharbia drain in the Nile Delta, Egypt, during both summer and winter seasons of 2012. Abatement-performance modeling results for a target of E wla = 100 % corresponded to the abatement ratio of the dischargers ranging from 20.7 to 75.6 % and 29.5 to 78.5 % in summer and in winter, respectively, alongside highly shifting inequity values. Abatement-equity-performance modeling results for a target of E wla = 90 % unraveled the necessity of increasing treatment efforts in three out of five dischargers during summer, and four out of five in winter. The trade-off curves obtained from WLA models proved their reliability in selecting appropriate WLA procedures as a function of budget constraints, principles of social equity, and desired overall performance level. Hence, the proposed framework of methodologies is of great importance to decision makers working toward a sustainable reuse of the ADW in irrigation. PMID:26951225

  8. Halomethane production in plants: Structure of the biosynthetic SAM-dependent halide methyltransferase from Arabidopsis thaliana**

    PubMed Central

    Schmidberger, Jason W.; James, Agata B.; Edwards, Robert; Naismith, James H.; O’Hagan, David

    2012-01-01

    A product structure of the halomethane producing enzyme in plants (Arabidopsis thaliana) is reported and a model for presentation of chloride/bromide ion to the methyl group of S-adenosyl-L-methionine (SAM) is presented to rationalise nucleophilic halide attack for halomethane production, gaseous natural products that are produced globally. PMID:20376845

  9. The Role of Integrated Modelling and Assessment for Decision-Making: Lessons from Water Allocation Issues in Australia

    NASA Astrophysics Data System (ADS)

    Jakeman, A. J.; Guillaume, J. H. A.; El Sawah, S.; Hamilton, S.

    2014-12-01

    Integrated modelling and assessment (IMA) is best regarded as a process that can support environmental decision-making when issues are strongly contested and uncertainties pervasive. To be most useful, the process must be multi-dimensional and phased. Principally, it must be tailored to the problem context to encompass diverse issues of concern, management settings and stakeholders. This in turn requires the integration of multiple processes and components of natural and human systems and their corresponding spatial and temporal scales. Modellers therefore need to be able to integrate multiple disciplines, methods, models, tools and data, and many sources and types of uncertainty. These dimensions are incorporated into iteration between the various phases of the IMA process, including scoping, problem framing and formulation, assessing options and communicating findings. Two case studies in Australia are employed to share the lessons of how integration can be achieved in these IMA phases using a mix of stakeholder participation processes and modelling tools. One case study aims to improve the relevance of modelling by incorporating stakeholder's views of irrigated viticulture and water management decision making. It used a novel methodology with the acronym ICTAM, consisting of Interviews to elicit mental models, Cognitive maps to represent and analyse individual and group mental models, Time-sequence diagrams to chronologically structure the decision making process, an All-encompassing conceptual model, and computational Models of stakeholder decision making. The second case uses a hydro-economic river network model to examine basin-wide impacts of water allocation cuts and adoption of farm innovations. The knowledge exchange approach used in each case was designed to integrate data and knowledge bearing in mind the contextual dimensions of the problem at hand, and the specific contributions that environmental modelling was thought to be able to make.

  10. The SAM domain of ANKS6 has different interacting partners and mutations can induce different cystic phenotypes.

    PubMed

    Bakey, Zeineb; Bihoreau, Marie-Thérèse; Piedagnel, Rémi; Delestré, Laure; Arnould, Catherine; de Villiers, Alexandre d'Hotman; Devuyst, Olivier; Hoffmann, Sigrid; Ronco, Pierre; Gauguier, Dominique; Lelongt, Brigitte

    2015-08-01

    The ankyrin repeat and sterile α motif (SAM) domain-containing six gene (Anks6) is a candidate for polycystic kidney disease (PKD). Originally identified in the PKD/Mhm(cy/+) rat model of PKD, the disease is caused by a mutation (R823W) in the SAM domain of the encoded protein. Recent studies support the etiological role of the ANKS6 SAM domain in human cystic diseases, but its function in kidney remains unknown. To investigate the role of ANKS6 in cyst formation, we screened an archive of N-ethyl-N-nitrosourea-treated mice and derived a strain carrying a missense mutation (I747N) within the SAM domain of ANKS6. This mutation is only six amino acids away from the PKD-causing mutation (R823W) in cy/+ rats. Evidence of renal cysts in these mice confirmed the crucial role of the SAM domain of ANKS6 in kidney function. Comparative phenotype analysis in cy/+ rats and our Anks6(I747N) mice further showed that the two models display noticeably different PKD phenotypes and that there is a defective interaction between ANKS6 with ANKS3 in the rat and between ANKS6 and BICC1 (bicaudal C homolog 1) in the mouse. Thus, our data demonstrate the importance of ANKS6 for kidney structure integrity and the essential mediating role of its SAM domain in the formation of protein complexes.

  11. Understanding the SAM influence on the South Pacific ENSO teleconnection

    NASA Astrophysics Data System (ADS)

    Fogt, Ryan L.; Bromwich, David H.; Hines, Keith M.

    2011-04-01

    The relationship between the El Niño Southern Oscillation (ENSO) and the Southern Hemisphere Annular Mode (SAM) is examined, with the goal of understanding how various strong SAM events modulate the ENSO teleconnection to the South Pacific (45°-70°S, 150°-70°W). The focus is on multi-month, multi-event variations during the last 50 years. A significant ( p < 0.10) relationship is observed, most marked during the austral summer and in the 1970s and 1990s. In most cases, the significant relationship is brought about by La Niña (El Niño) events occurring with positive (negative) phases of the SAM more often than expected by chance. The South Pacific teleconnection magnitude is found to be strongly dependent on the SAM phase. Only when ENSO events occur with a weak SAM or when a La Niña (El Niño) occurs with a positive (negative) SAM phase are significant South Pacific teleconnections found. This modulation in the South Pacific ENSO teleconnection is directly tied to the interaction of the anomalous ENSO and SAM transient eddy momentum fluxes. During La Niña/SAM+ and El Niño/SAM- combinations, the anomalous transient momentum fluxes in the Pacific act to reinforce the circulation anomalies in the midlatitudes, altering the circulation in such a way to maintain the ENSO teleconnections. In La Niña/SAM- and El Niño/SAM+ cases, the anomalous transient eddies oppose each other in the midlatitudes, overall acting to reduce the magnitude of the high latitude ENSO teleconnection.

  12. Inhibition of Sam68 triggers adipose tissue browning

    PubMed Central

    Zhou, Junlan; Cheng, Min; Boriboun, Chan; Ardehali, Mariam Mina; Jiang, Changfei; Liu, Qinghua; Han, Shuling; Goukassian, David A.; Tang, Yao-Liang; Zhao, Ting C.; Zhao, Ming; Cai, Lu; Richard, Stéphane; Kishore, Raj; Qin, Gangjian

    2015-01-01

    Obesity is associated with insulin resistance and type 2 diabetes; molecular mechanisms promoting energy expenditure may be utilized for effective therapy. Src-associated-in-mitosis-of-68kDa (Sam68) is potentially significant because knockout (KO) of Sam68 leads to markedly-reduced adiposity. Here we sought to determine the mechanism by which Sam68 regulates adiposity and energy homeostasis. We firstly found in Sam68-KO mice a significantly-reduced body weight with the difference explained entirely by decreased adiposity. Interestingly, these effects were not mediated by a difference in food intake, but rather associated with enhanced physical activity. When fed high-fat diet, Sam68-KO mice gained much lesser body weight and fat mass as compared to wild-type (WT) littermates and displayed an improved glucose and insulin tolerance. The brown adipose tissue (BAT), inguinal and epididymal depots are smaller and their adipocytes less hypertrophy in Sam68-KO mice than in WT littermates. The BAT of Sam68-KO mice exhibited reduced lipid stores and expressed higher levels of Ucp1 and key thermogenic and fatty-acid-oxidation genes. Similarly, depots of inguinal and epididymal white adipose tissue (WAT) in Sam68-KO mice appeared browner, their multilocular Ucp1-positive cells were much more abundant, and the expression of Ucp1, Cidea, Prdm16 and Ppargc1a genes was greater as compared to WT controls, suggesting that loss of Sam68 also promotes WAT browning. Furthermore, in all fat depots of Sam68-KO mice, the expression of M2 macrophage markers were upregulated and M1 markers downregulated. Thus Sam68 plays a crucial role in the control of thermogenesis and may be targeted to combat obesity and associated disorders. PMID:25934704

  13. Inhibition of Sam68 triggers adipose tissue browning.

    PubMed

    Zhou, Junlan; Cheng, Min; Boriboun, Chan; Ardehali, Mariam M; Jiang, Changfei; Liu, Qinghua; Han, Shuling; Goukassian, David A; Tang, Yao-Liang; Zhao, Ting C; Zhao, Ming; Cai, Lu; Richard, Stéphane; Kishore, Raj; Qin, Gangjian

    2015-06-01

    Obesity is associated with insulin resistance and type 2 diabetes; molecular mechanisms that promote energy expenditure can be utilized for effective therapy. Src-associated in mitosis of 68 kDa (Sam68) is potentially significant, because knockout (KO) of Sam68 leads to markedly reduced adiposity. In the present study, we sought to determine the mechanism by which Sam68 regulates adiposity and energy homeostasis. We first found that Sam68 KO mice have a significantly reduced body weight as compared to controls, and the difference is explained entirely by decreased adiposity. Interestingly, these effects were not mediated by a difference in food intake; rather, they were associated with enhanced physical activity. When they were fed a high-fat diet, Sam68 KO mice gained much less body weight and fat mass than their WT littermates did, and they displayed an improved glucose and insulin tolerance. In Sam68 KO mice, the brown adipose tissue (BAT), inguinal, and epididymal depots were smaller, and their adipocytes were less hypertrophied as compared to their WT littermates. The BAT of Sam68 KO mice exhibited reduced lipid stores and expressed higher levels of Ucp1 and key thermogenic and fatty acid oxidation genes. Similarly, depots of inguinal and epididymal white adipose tissue (WAT) in Sam68 KO mice appeared browner, their multilocular Ucp1-positive cells were much more abundant, and the expression of Ucp1, Cidea, Prdm16, and Ppargc1a genes was greater as compared to WT controls, which suggests that the loss of Sam68 also promotes WAT browning. Furthermore, in all of the fat depots of the Sam68 KO mice, the expression of M2 macrophage markers was up-regulated, and that of M1 markers was down-regulated. Thus, Sam68 plays a crucial role in controlling thermogenesis and may be targeted to combat obesity and associated disorders.

  14. Competition for light and water increases tree carbon allocation to fine roots and leaves in a next-generation dynamic vegetation model

    NASA Astrophysics Data System (ADS)

    Lichstein, J. W.; Zhang, T.; Weng, E.; Farrior, C.; Dybzinski, R.; Birdsey, R.; Pacala, S. W.

    2015-12-01

    The response of the terrestrial carbon (C) cycle to climate change is a key uncertainty in land models. An important component of this uncertainty concerns plant functional diversity, which is typically represented in land models by ~10 functional types (PFTs) with fixed traits. However, few land models include the individual-level competitive mechanisms that largely determine how plant functional traits are distributed in time and space in real ecosystems. We have developed a new land model that represents height-structured competition for light with a simple canopy space-filling algorithm, the perfect plasticity approximation (PPA). The new land model, LM3-PPA, allows for an arbitrary number of PFTs (or 'species') whose spatial-temporal distributions are determined by the outcome of competition for light and water. We performed experiments with a modified version of LM3-PPA in 10 eastern U.S. grid cells and across simulated precipitation gradients to determine how competition for light and water affects tree C allocation to leaves, fine roots, and wood across climate gradients and in response to episodic drought. We studied the performance of 16 allocational types ('species') in monoculture and in competition with each other to determine the competitively-optimal, NPP-maximizing, and biomass-maximizing C allocation strategy under different environmental conditions. Under chronically moist conditions, competitively-optimal, NPP-maximizing, and biomass-maximizing trees all had similar C allocation. However, under chronically dry conditions, competitively-optimal trees allocated more C to both fine roots and leaves, and less C to wood, compared to NPP- or biomass-maximizing strategies. When subject to episodic drought, the most drought-tolerant allocational strategies had relatively low allocation to leaves (and thus low leaf area and low water demand). Thus, the "over-investment" in leaves that results from resource competition increases the vulnerability of

  15. Using SAM Assessment and Training for Office 2003

    ERIC Educational Resources Information Center

    Whittle, Gary

    2005-01-01

    This presentation will demonstrate the uses of SAM 2003 from Course Technology as a skills assessment and training software that is used via the Internet. Historically, testing in computer education has taken the form of pencil and paper or standardized testing. The actual computer skills of the student have not been properly assessed. With SAM,…

  16. A sub-canopy structure for simulating oil palm in the Community Land Model: phenology, allocation and yield

    NASA Astrophysics Data System (ADS)

    Fan, Y.; Roupsard, O.; Bernoux, M.; Le Maire, G.; Panferov, O.; Kotowska, M. M.; Knohl, A.

    2015-06-01

    Land surface modelling has been widely used to characterize the two-way interactions between climate and human activities in terrestrial ecosystems such as deforestation, agricultural expansion, and urbanization. Towards an effort to quantify the effects of forests to oil palm conversion occurring in the tropics on land-atmosphere carbon, water and energy fluxes, we introduce a new perennial crop plant functional type (PFT) for oil palm. Due to the modular and sequential nature of oil palm growth (around 40 stacked phytomers) and yield (fruit bunches axillated on each phytomer), we developed a specific sub-canopy structure for simulating palm's growth and yield within the framework of the Community Land Model (CLM4.5). In this structure each phytomer has its own prognostic leaf growth and fruit yield capacity like a PFT but with shared stem and root components among all phytomers. Phenology and carbon and nitrogen allocation operate on the different phytomers in parallel but at unsynchronized steps, so that multiple fruit yields per annum are enabled in terms of carbon and nitrogen outputs. An important phenological phase is identified for the palm PFT - the storage growth period of bud and "spear" leaves which are photosynthetically inactive before expansion. Agricultural practices such as transplanting, fertilization, and leaf pruning are represented. Parameters introduced for the new PFT were calibrated and validated with field measurements of leaf area index (LAI) and yield from Sumatra, Indonesia. In calibration with a mature oil palm plantation, the cumulative yields from 2005 to 2014 matched perfectly between simulation and observation (mean percentage error = 4 %). Simulated inter-annual dynamics of PFT-level and phytomer-level LAI were both within the range of field measurements. Validation from eight independent oil palm sites shows the ability of the model to adequately predict the average leaf growth and fruit yield across sites but also indicates that

  17. [Anti-aging studies on the senescence accelerated mouse (SAM) strains].

    PubMed

    Takahashi, Ryoya

    2010-01-01

    Senescence accelerated mouse (SAM), a murine model of accelerated senescence, was established by Toshio Takeda and colleagues. SAM consists of series of SAMP (prone) and SAMR (resistant) lines. All SAMP lines (from SAMP1 to SAMP11) are characterized by accelerated accumulation of senile features, earlier onset and faster progress of age-associated pathological phenotypes, such as amyloidosis, impaired immune response, senile osteoporosis and deficits in learning and memory. These SAMP lines are useful for evaluation of putative anti-aging therapies. For example, SAMP1 line is used to study the anti-aging effect of the antioxidant containing foods and various anti-oxidants, such as coenzyme Q10, vitamin C, lycopene. SAMP8 line exhibiting an early onset of impaired learning and memory is often used for test strategies for therapeutic intervention of dementia of early onset. SAMP6 is used as an animal model for developing new strategies for the treatment of osteoporosis in humans. Various lines of SAM (P1, P6, P8, P10 and R1) are now commercially available for research. In this review, I will briefly introduce various usages of SAM in anti-aging research. PMID:20046059

  18. A Fuzzy Robust Optimization Model for Waste Allocation Planning Under Uncertainty.

    PubMed

    Xu, Ye; Huang, Guohe; Xu, Ling

    2014-10-01

    In this study, a fuzzy robust optimization (FRO) model was developed for supporting municipal solid waste management under uncertainty. The Development Zone of the City of Dalian, China, was used as a study case for demonstration. Comparing with traditional fuzzy models, the FRO model made improvement by considering the minimization of the weighted summation among the expected objective values, the differences between two extreme possible objective values, and the penalty of the constraints violation as the objective function, instead of relying purely on the minimization of expected value. Such an improvement leads to enhanced system reliability and the model becomes especially useful when multiple types of uncertainties and complexities are involved in the management system. Through a case study, the applicability of the FRO model was successfully demonstrated. Solutions under three future planning scenarios were provided by the FRO model, including (1) priority on economic development, (2) priority on environmental protection, and (3) balanced consideration for both. The balanced scenario solution was recommended for decision makers, since it respected both system economy and reliability. The model proved valuable in providing a comprehensive profile about the studied system and helping decision makers gain an in-depth insight into system complexity and select cost-effective management strategies. PMID:25317037

  19. A Fuzzy Robust Optimization Model for Waste Allocation Planning Under Uncertainty

    PubMed Central

    Xu, Ye; Huang, Guohe; Xu, Ling

    2014-01-01

    Abstract In this study, a fuzzy robust optimization (FRO) model was developed for supporting municipal solid waste management under uncertainty. The Development Zone of the City of Dalian, China, was used as a study case for demonstration. Comparing with traditional fuzzy models, the FRO model made improvement by considering the minimization of the weighted summation among the expected objective values, the differences between two extreme possible objective values, and the penalty of the constraints violation as the objective function, instead of relying purely on the minimization of expected value. Such an improvement leads to enhanced system reliability and the model becomes especially useful when multiple types of uncertainties and complexities are involved in the management system. Through a case study, the applicability of the FRO model was successfully demonstrated. Solutions under three future planning scenarios were provided by the FRO model, including (1) priority on economic development, (2) priority on environmental protection, and (3) balanced consideration for both. The balanced scenario solution was recommended for decision makers, since it respected both system economy and reliability. The model proved valuable in providing a comprehensive profile about the studied system and helping decision makers gain an in-depth insight into system complexity and select cost-effective management strategies. PMID:25317037

  20. The SAM domain of polyhomeotic forms a helical polymer.

    PubMed

    Kim, Chongwoo A; Gingery, Mari; Pilpa, Rosemarie M; Bowie, James U

    2002-06-01

    The polycomb group (PcG) proteins are important in the maintenance of stable repression patterns during development. Several PcG members contain a protein protein interaction module called a SAM domain (also known as SPM, PNT and HLH). Here we report the high-resolution structure of the SAM domain of polyhomeotic (Ph). Ph-SAM forms a helical polymer structure, providing a likely mechanism for the extension of PcG complexes. The structure of the polymer resembles that formed by the SAM domain of another transcriptional repressor, TEL. The formation of these polymer structures by SAM domains in two divergent repressors suggests a conserved mode of repression involving a higher order chromatin structure.

  1. Student Activities in Meteorology (SAM), June 1994

    SciTech Connect

    Meier, B.L.; Passarelli, E.

    1994-06-01

    In an effort to inspire student interest in science and technology, scientists from the Forecast Systems Laboratory, a laboratory within the National Oceanic and Atmospheric Administration's (NOAA) Environmental Research Laboratories, and classroom teachers from the Boulder Valley School District collaborated to produce a series of classroom science activities on meteorology and atmospheric science. We call this series 'Student Activities in Meteorology,' or SAM. The goal is to provide activities that are interesting to students, and at the same time convenient and easy to use for teachers. The activity topics chosen are to incorporate trend setting scientific research and cutting edge technology. Several of the activities focus on the meteorological concerns of the Denver metropolitan area because many of NOAA's research labs are located in Boulder, where much of the research and testing for the region is performed. We believe that these activities are versatile and can be easily integrated into current science, environmental studies, health, social studies, and math curricula.

  2. Obituary: Sam Roweis (1972-2010)

    NASA Astrophysics Data System (ADS)

    Hogg, David

    2011-12-01

    Computer scientist and statistical astronomer Sam Roweis took his own life in New York City on 2010 January 12. He was a brilliant and accomplished researcher in the field of machine learning, and a strong advocate for the use of computational statistics for automating discovery and scientific data analysis. He made several important contributions to astronomy and was working on adaptive astronomical data analysis at the time of his death. Roweis obtained his PhD in 1999 from the California Institute of Technology, where he worked on a remarkable range of subjects, including DNA computing, modeling of dynamical systems, signal processing, and speech recognition. During this time he unified and clarified some of the most important data analysis techniques, including Principal Component Analysis, Hidden Markov Models, and Expectation Maximization. His work was aimed at making data analysis and modeling faster, but also better justified scientifically. The last years of his PhD were spent in Princeton NJ, where he came in contact with a young generation of cosmologists thinking about microwave background and large-scale structure data. In a postdoc at University College London, Roweis co-created the Locally Linear Embedding (LLE) algorithm; a simple but flexible technique for mapping a large data set onto a low-dimensional manifold. The LLE paper obtained more than 2700 citations in 9 years, launched a new sub-field of machine learning known as "manifold learning," and inspired work in data visualization, search, and applied mathematics. In 2001, Roweis took a faculty job at the University of Toronto Computer Science Department. He continued working on data analysis methods that have probabilistic interpretation and therefore scientific applicability, but at the same time have good performance on large data sets. He was awarded a Sloan Fellowship, a Canada Research Chair, and a fellowship of the Canadian Institute for Advanced Research, among other honors and awards

  3. Optimality-based modeling of nitrogen allocation and photoacclimation in photosynthesis

    NASA Astrophysics Data System (ADS)

    Armstrong, Robert A.

    2006-03-01

    The ability to predict phytoplankton growth rates under light and nutrient limitation is fundamental to modeling the ocean carbon cycle. Equally fundamental is the ability to predict chlorophyll:carbon ratios, since satellite-based chlorophyll estimates are one of the few data sets to which model output can be compared globally. Because the Geider et al. [Geider, R.J., MacIntyre, H.L., Kana, T.M., 1998. A dynamic regulatory model of phytoplanktonic acclimation to light, nutrients, and temperature. Limnology and Oceanography 43, 679-694] model addresses both desiderata, it has become the model of choice for representing photosynthesis in a wide range of ecosystem models. The Geider et al. [Geider, R.J., MacIntyre, H.L., Kana, T.M., 1998. A dynamic regulatory model of phytoplanktonic acclimation to light, nutrients, and temperature. Limnology and Oceanography 43, 679-694] model follows previous models in positing that maximum photosynthetic rate can be reached only when nitrogen cell quota (nitrogen:carbon ratio) reaches a fixed maximum value qN,maxC. Empirically, this assumption is contradicted by the extremely thorough data set of Laws and Bannister [Laws, E.A., Bannister, T.T., 1980. Nutrient- and light-limited growth of Thalassiosira fluviatilis in continuous culture, with implications for phytoplankton growth in the ocean. Limnology and Oceanography 25, 457-473] and by other studies: maximum growth rate does not seem to require maximum nitrogen cell quota. To the extent that existing models do not reflect this key characteristic, they may fail to yield reliable predictions of chlorophyll:carbon ratios as functions of nitrogen:carbon ratios. They also may fail to reflect differences in growth rates of competing phytoplankton species, an essential feature of state-of-the-art ecosystem models used in biogeochemistry simulations. In the present paper I replace the nitrogen limitation function of previous models by one that does not require maximum nitrogen cell

  4. Economic Analysis Case Studies of Battery Energy Storage with SAM

    SciTech Connect

    DiOrio, Nicholas; Dobos, Aron; Janzou, Steven

    2015-11-01

    Interest in energy storage has continued to increase as states like California have introduced mandates and subsidies to spur adoption. This energy storage includes customer sited behind-the-meter storage coupled with photovoltaics (PV). This paper presents case study results from California and Tennessee, which were performed to assess the economic benefit of customer-installed systems. Different dispatch strategies, including manual scheduling and automated peak-shaving were explored to determine ideal ways to use the storage system to increase the system value and mitigate demand charges. Incentives, complex electric tariffs, and site specific load and PV data were used to perform detailed analysis. The analysis was performed using the free, publically available System Advisor Model (SAM) tool. We find that installation of photovoltaics with a lithium-ion battery system priced at $300/kWh in Los Angeles under a high demand charge utility rate structure and dispatched using perfect day-ahead forecasting yields a positive net-present value, while all other scenarios cost the customer more than the savings accrued. Different dispatch strategies, including manual scheduling and automated peak-shaving were explored to determine ideal ways to use the storage system to increase the system value and mitigate demand charges. Incentives, complex electric tariffs, and site specific load and PV data were used to perform detailed analysis. The analysis was performed using the free, publically available System Advisor Model (SAM) tool. We find that installation of photovoltaics with a lithium-ion battery system priced at $300/kWh in Los Angeles under a high demand charge utility rate structure and dispatched using perfect day-ahead forecasting yields a positive net-present value, while all other scenarios cost the customer more than the savings accrued.

  5. District Allocation of Human Resources Utilizing the Evidence Based Model: A Study of One High Achieving School District in Southern California

    ERIC Educational Resources Information Center

    Lane, Amber Marie

    2013-01-01

    This study applies the Gap Analysis Framework to understand the gaps that exist in human resource allocation of one Southern California school district. Once identified, gaps are closed with the reallocation of human resources, according to the Evidenced Based Model, requiring the re-purposing of core classroom teachers, specialists, special…

  6. A Minimalistic Resource Allocation Model to Explain Ubiquitous Increase in Protein Expression with Growth Rate

    PubMed Central

    Keren, Leeat; Segal, Eran; Milo, Ron

    2016-01-01

    Most proteins show changes in level across growth conditions. Many of these changes seem to be coordinated with the specific growth rate rather than the growth environment or the protein function. Although cellular growth rates, gene expression levels and gene regulation have been at the center of biological research for decades, there are only a few models giving a base line prediction of the dependence of the proteome fraction occupied by a gene with the specific growth rate. We present a simple model that predicts a widely coordinated increase in the fraction of many proteins out of the proteome, proportionally with the growth rate. The model reveals how passive redistribution of resources, due to active regulation of only a few proteins, can have proteome wide effects that are quantitatively predictable. Our model provides a potential explanation for why and how such a coordinated response of a large fraction of the proteome to the specific growth rate arises under different environmental conditions. The simplicity of our model can also be useful by serving as a baseline null hypothesis in the search for active regulation. We exemplify the usage of the model by analyzing the relationship between growth rate and proteome composition for the model microorganism E.coli as reflected in recent proteomics data sets spanning various growth conditions. We find that the fraction out of the proteome of a large number of proteins, and from different cellular processes, increases proportionally with the growth rate. Notably, ribosomal proteins, which have been previously reported to increase in fraction with growth rate, are only a small part of this group of proteins. We suggest that, although the fractions of many proteins change with the growth rate, such changes may be partially driven by a global effect, not necessarily requiring specific cellular control mechanisms. PMID:27073913

  7. Evaluation of a digital model for estuarine water quality simulation in waste allocation studies

    USGS Publications Warehouse

    Seaburn, G.E.; Jennings, Marshall E.; Merritt, Michael L.

    1979-01-01

    Hydrologic and water-quality data were collected on 4 estuaries in Pasco, Citrus, and Pinellas Counties, Florida, to evaluate modeling results. Current and predicted waste loading of the four estuaries was simulated by use of a two-dimensional steady-state, intertidal-condition model. Concentrations of DO, carbonaceous and nitrogenous BOD, and chloride were simulated as averages over a tidal cycle. General equations for the model are based on the law of conservation of mass. Assumption of steady-state required that water-quality data for calibration be averaged over an appropriate time cycle with respect to volume and cross-section. Diurnal DO fluctuation was determined in 2 estuaries for evaluating the influence of photosynthesis and respiration. The estuary model is best applied by calibrating it for a particular set of observed conditions, and then using this calibrated model for sensitivity analyses without attempting to verify the chosen parameter values against a second set of conditions. Sensitivity analyses included dispersion coefficient , decay rates, photosynthesis, and respiration. (Woodard-USGS)

  8. Comparing Surfaces and Engineered Interfaces using Self-Assembled Monolayers (SAMs) and Injected SAMs Silanes

    SciTech Connect

    Morris, Mark J.; Simmons, Kevin L.

    2003-11-01

    The objective of this study was to show a comparison between property changes by formation of a self-assembled monolayer on the surface of PPG synthetic precipitated silica, which is a technique developed at PNNL, and by adding the SAMs silane chemical directly into the mixing bowl. These coatings have the potential to greatly increase the bond strength and enhance other properties between the particle and the rubber matrix of a rubber compound. Tensile testing measured peak stress and elongation at break. The increase in tensile strength shows how well the polymer-filler interfacial adhesion is doing. The study used five different SAM systems with a sulfur cured styrene butadiene rubber (SBR) tire rubber formulation. The three propylsilanes were propyl triethoxysilane, allyl triethoxysilane and 3-mercaptopropyl triethoxysilane. Five combinations of silanes were used in this study. The application of the silanes were 100% propyl triethoxy silane (100% Alkyl); a 10/90 mixture of allyl and propyl triethoxy silanes (10% vinyl/90% alkyl); a 50/50 mixture of the allyl and propyl (50% vinyl/50% alkyl); a 10/90mixture of 3-mercaptopropyl trimethoxysilane and propyl trimethoxysilane (10% mercaptan/90% alkyl) and lastly a 50/50 3-mercaptopropyl and propylsilanes (50% mercaptan/alkyl). The data not only shows improvement with SAMs, the peak stress data (ultimate strength) shows that the by changing the amount of silane content can change the physical properties

  9. Influence of vegetation dynamic modeling on the allocation of green and blue waters

    NASA Astrophysics Data System (ADS)

    Ruiz-Pérez, Guiomar; Francés, Félix

    2015-04-01

    The long history of the Mediterranean region is dominated by the interactions and co-evolution between man and its natural environment. It is important to consider that the Mediterranean region is recurrently or permanently confronted with the scarcity of the water. The issue of climate change is (and will be) aggravating this situation. This raises the question of a loss of services that ecosystems provide to human and also the amount of available water to be used by vegetation. The question of the water cycle, therefore, should be considered in an integrated manner by taking into account both blue water (water in liquid form used for the human needs or which flows into the oceans) and green water (water having the vapor for resulting from evaporation and transpiration processes). In spite of this, traditionally, very few hydrological models have incorporated the vegetation dynamic as a state variable. In fact, most of them are able to represent fairly well the observed discharge, but usually including the vegetation as a static parameter. However, in the last decade, the number of hydrological models which explicitly take into account the vegetation development as a state variable has increased substantially. In this work, we want to analyze if it is really necessary to use a dynamic vegetation model to quantify adequately the distribution of water into blue and green water. The study site is located in the Public Forest Monte de la Hunde y Palomeras (Spain). The vegetation in the study area is dominated by Aleppo pine of high tree density with scant presence of other species. Two different daily models were applied (with static and dynamic vegetation representation respectively) in three different scenarios: dry year (2005), normal year (2008) and wet year (2010). The static vegetation model simulates the evapotranspiration considering the vegetation as a stationary parameter. Contrarily, the dynamic vegetation model connects the hydrological model with a

  10. CARBON AND NITROGEN ALLOCATION MODEL FOR THE SEAGRASS THALASSIA TESTUDUNUM IN LOWER LAGUNA MADRE

    EPA Science Inventory

    Inverse modeling methods are a powerful tool for understanding complex physiological relationships between seagrasses and their environment. The power of the method is a result of using ranges of data in a system of constraints to describe the biological system, in this case, t...

  11. Towards Decentralized and Goal-Oriented Models of Institutional Resource Allocation: The Spanish Case

    ERIC Educational Resources Information Center

    Lopez, Maria Jose Gonzalez

    2006-01-01

    The search for more flexibility in financial management of public universities demands adjustments in budgeting strategies. International studies on this topic recommend wider financial autonomy for management units, the use of budgeting models based on performance, the implementation of formula systems for the determination of financial needs of…

  12. Spectral mapping of morphological features on the moon with MGM and SAM

    NASA Astrophysics Data System (ADS)

    Kodikara, Gayantha R. L.; Champati ray, P. K.; Chauhan, Prakash; Chatterjee, R. S.

    2016-02-01

    Three types of morphological features observed in different lunar crustal terrains were studied and mapped using hyperspectral Moon mineralogy mapper (M3) data onboard Chandrayaan 1 mission in order to assess the utility of cascaded MGM-SAM spectral mixture modeling approach to characterize the surface materials, which may occur as mineral mixtures, at different topography of the lunar surface. Selected morphological features include: the impact melts in Orientale basin, sinuous rilles in Procellarum KREEP Terrane (PKT) and a rayed crater in Feldspathic Highland Terrane (FHT). Methodology involves extraction of spectrally pure pixels (endmembers) of the area using Pixel Purity Index (PPI), identification of mineralogy of the selected endmember spectrum using the Modified Gaussian Method (MGM) and mapping of mineralogically identified endmembers using the Spectral Angle Mapper (SAM) method. Mapping results demonstrate both the capabilities and the limitations of the MGM method of spectral deconvolution and the SAM method of spectral matching as effective tools for compositional characterizations of morphological features on the lunar surface. As a method of spectral deconvolution, MGM was able to identify and characterize both high- and low - Ca pyroxenes along with plagioclase feldspar. The Spectral Angle Mapper (SAM) was able to map identified mineral mixtures from MGM.

  13. SAM68 is a physiological regulator of SMN2 splicing in spinal muscular atrophy

    PubMed Central

    Pagliarini, Vittoria; Pelosi, Laura; Bustamante, Maria Blaire; Nobili, Annalisa; Berardinelli, Maria Grazia; D’Amelio, Marcello; Musarò, Antonio

    2015-01-01

    Spinal muscular atrophy (SMA) is a neurodegenerative disease caused by loss of motor neurons in patients with null mutations in the SMN1 gene. The almost identical SMN2 gene is unable to compensate for this deficiency because of the skipping of exon 7 during pre–messenger RNA (mRNA) processing. Although several splicing factors can modulate SMN2 splicing in vitro, the physiological regulators of this disease-causing event are unknown. We found that knockout of the splicing factor SAM68 partially rescued body weight and viability of SMAΔ7 mice. Ablation of SAM68 function promoted SMN2 splicing and expression in SMAΔ7 mice, correlating with amelioration of SMA-related defects in motor neurons and skeletal muscles. Mechanistically, SAM68 binds to SMN2 pre-mRNA, favoring recruitment of the splicing repressor hnRNP A1 and interfering with that of U2AF65 at the 3′ splice site of exon 7. These findings identify SAM68 as the first physiological regulator of SMN2 splicing in an SMA mouse model. PMID:26438828

  14. Agent based model of effects of task allocation strategies in flat organizations

    NASA Astrophysics Data System (ADS)

    Sobkowicz, Pawel

    2016-09-01

    A common practice in many organizations is to pile the work on the best performers. It is easy to implement by the management and, despite the apparent injustice, appears to be working in many situations. In our work we present a simple agent based model, constructed to simulate this practice and to analyze conditions under which the overall efficiency of the organization (for example measured by the backlog of unresolved issues) breaks down, due to the cumulative effect of the individual overloads. The model confirms that the strategy mentioned above is, indeed, rational: it leads to better global results than an alternative one, using equal workload distribution among all workers. The presented analyses focus on the behavior of the organizations close to the limit of the maximum total throughput and provide results for the growth of the unprocessed backlog in several situations, as well as suggestions related to avoiding such buildup.

  15. A Numerical model to evaluate proposed ground-water allocations in southwest Kansas

    USGS Publications Warehouse

    Jorgensen, D.G.; Grubb, H.F.; Baker, C.H.; Hilmes, G.E.; Jenkins, E.D.

    1982-01-01

    A computer model was developed to assist the Southwest Kansas Groundwater Management District No. 3 in the evaluation of applications to appropriate ground water. The model calculated the drawdown due from a proposed well at all existing wells in the section of the proposed well and at all wells in the adjacent eight sections. The depletion expected in the 9-square-mile area due to all existing wells and the proposed well is computed and compared with allowable limits defined by the management district. An optional program permits the evaluation of allowable depletion for one or more townships. All options are designed to run interactively, thus allowing for immediate evaluation of proposed ground-water withdrawals. (USGS)

  16. Microeconomics-based resource allocation in overlay networks by using non-strategic behavior modeling

    NASA Astrophysics Data System (ADS)

    Analoui, Morteza; Rezvani, Mohammad Hossein

    2011-01-01

    Behavior modeling has recently been investigated for designing self-organizing mechanisms in the context of communication networks in order to exploit the natural selfishness of the users with the goal of maximizing the overall utility. In strategic behavior modeling, the users of the network are assumed to be game players who seek to maximize their utility with taking into account the decisions that the other players might make. The essential difference between the aforementioned researches and this work is that it incorporates the non-strategic decisions in order to design the mechanism for the overlay network. In this solution concept, the decisions that a peer might make does not affect the actions of the other peers at all. The theory of consumer-firm developed in microeconomics is a model of the non-strategic behavior that we have adopted in our research. Based on it, we have presented distributed algorithms for peers' "joining" and "leaving" operations. We have modeled the overlay network as a competitive economy in which the content provided by an origin server can be viewed as commodity and the origin server and the peers who multicast the content to their downside are considered as the firms. On the other hand, due to the dual role of the peers in the overlay network, they can be considered as the consumers as well. On joining to the overlay economy, each peer is provided with an income and tries to get hold of the service regardless to the behavior of the other peers. We have designed the scalable algorithms in such a way that the existence of equilibrium price (known as Walrasian equilibrium price) is guaranteed.

  17. Mathematical modelling of diurnal regulation of carbohydrate allocation by osmo-related processes in plants.

    PubMed

    Pokhilko, Alexandra; Ebenhöh, Oliver

    2015-03-01

    Plants synthesize sucrose in source tissues (mainly mature leafs) and supply it for growth of sink tissues (young leafs). Sucrose is derived from photosynthesis during daytime and from starch at night. Because the diurnal regulation of sucrose fluxes is not completely understood, we built a mathematical model designed to reproduce all key experimental observations. For this, assumptions were made about the molecular mechanisms underlying the regulations, which are all motivated by experimental facts. The key regulators in our model are two kinases (SnRK1 and osmo-sensitive kinase OsmK) under the control of the circadian clock. SnRK1 is activated in the night to prepare for regularly occurring carbon-limiting conditions, whereas OsmK is activated during the day to prepare for water deficit, which often occurs in the afternoon. Decrease of SnRK1 and increase of OsmK result in partitioning of carbon towards sucrose to supply growing sink tissues. Concomitantly, increasing levels of the growth regulator trehalose-6-phosphate stimulates the development of new sink tissues and thus sink demand, which further activates sucrose supply in a positive feedback loop. We propose that OsmK acts as a timer to measure the length of the photoperiod and suggest experiments how this hypothesis can be validated. PMID:25631572

  18. SAM Gcms Chromatography Performed at Mars : Elements of Interpretation

    NASA Astrophysics Data System (ADS)

    Szopa, C.; Coll, P. J.; Buch, A.; François, P.; Cabane, M.; Coscia, D.; Teinturier, S.; Navarro-Gonzalez, R.; Glavin, D. P.; Freissinet, C.; Mahaffy, P. R.

    2013-12-01

    The characterisation of the chemical and mineralogical composition of regolith samples collected with the Curiosity rover is a primary objective of the SAM experiment. These data should provide essential clues on the past habitability of Gale crater. Interpretation of the data collected after SAM pyrolysis evolved gas analysis (EGA) and gas chromatography mass spectrometry (GC-MS) experiments on the first soil samples collected by MSL at the Rocknest Aeolian Deposit in Gale Crater has been challenging due to the concomitant presence in the ovens of an oxychlorine phase present in the samples, and a derivatization agent coming from the SAM wet chemistry experiment (Glavin et al., 2013). Moreover, accurate identification and quantification, in the SAM EGA mode, of volatiles released from the heated sample, or generated by reactions occurring in the SAM pyrolysis oven, is also difficult for a few compounds due to evolution over similar temperature ranges and overlap of their MS signatures. Hence, the GC analyses, coupled with MS, enabled the separation and identification and quantification of most of the volatile compounds detected. These results can have been obtained through tests and calibration done with GC individual spare components and with the SAM testbed. This paper will present a view of the interpretation of the chromatograms obtained when analyzing the Rocknest and John Klein solid samples delivered to SAM, on sols 96 and 199 respectively, supported by laboratory calibrations.

  19. Beta test results for the CAA mini-SAM system

    SciTech Connect

    Johnson, R.C.; Monagle, M.

    1997-04-01

    The mission of the Chemical Analysis Automation (CAA) Program is to automate methods for chemical analysis of environmental samples. To accomplish this mission, the CAA team has developed automated laboratory systems based on a plug-and-work strategy for integrating components. Realizing that standardization is the key to implementing this strategy, CAA has developed, demonstrated, and encouraged commercialization of standards for laboratory automation. While the CAA mission is driven by the analyses in support of the extensive remediation programs of the Departments of Energy and Defense, it also impacts any industry that depends upon high volumes of repetitive chemical analysis. A Standard Analysis Method (SAM) is any collection of hardware and software used to automate part or all of a method. The method automated for the Mini-SAM testing is EPA Method 3550, which outlines semivolatiles extraction by sonication. The list of semivolatiles includes the polychlorinated biphenyl (PCB) analytes of interest. The basic building block of a SAM is the Standard Laboratory Module (SLM). For the Mini-SAM test an automated sonication SLM and an automated concentration SLM were configured to perform the extraction and concentration processes. The Mini-SAM differs from the Full-SAM in that a fully automated delivery of materials, samples, and extracts is not required. The intent of the Beta Test of the Mini-SAM was threefold. Firstly, the Mini-SAM Beta Test met a milestone mandated by the Department of Energy in the course of the program effort. Secondly, the CAA Program secured an independent assessment of the equipment and its capabilities from Assagai Analytical Laboratory. Lastly, the Program captured real-world sample data. The independent assessment, coupled with CAA observation of equipment performance, was used to determine strengths and weaknesses of the Mini-SAM and to compile possible modifications for CAA engineers to address.

  20. Increased forest carbon storage with increased atmospheric CO2 despite nitrogen limitation: a game-theoretic allocation model for trees in competition for nitrogen and light.

    PubMed

    Dybzinski, Ray; Farrior, Caroline E; Pacala, Stephen W

    2015-03-01

    Changes in resource availability often cause competitively driven changes in tree allocation to foliage, wood, and fine roots, either via plastic changes within individuals or through turnover of individuals with differing strategies. Here, we investigate how optimally competitive tree allocation should change in response to elevated atmospheric CO2 along a gradient of nitrogen and light availability, together with how those changes should affect carbon storage in living biomass. We present a physiologically-based forest model that includes the primary functions of wood and nitrogen. From a tree's perspective, wood is an offensive and defensive weapon used against neighbors in competition for light. From a biogeochemical perspective, wood is the primary living reservoir of stored carbon. Nitrogen constitutes a tree's photosynthetic machinery and the support systems for that machinery, and its limited availability thus reduces a tree's ability to fix carbon. This model has been previously successful in predicting allocation to foliage, wood, and fine roots along natural productivity gradients. Using game theory, we solve the model for competitively optimal foliage, wood, and fine root allocation strategies for trees in competition for nitrogen and light as a function of CO2 and nitrogen mineralization rate. Instead of down-regulating under nitrogen limitation, carbon storage under elevated CO2 relative to carbon storage at ambient CO2 is approximately independent of the nitrogen mineralization rate. This surprising prediction is a consequence of both increased competition for nitrogen driving increased fine root biomass and increased competition for light driving increased allocation to wood under elevated CO2 .

  1. Increased forest carbon storage with increased atmospheric CO2 despite nitrogen limitation: a game-theoretic allocation model for trees in competition for nitrogen and light.

    PubMed

    Dybzinski, Ray; Farrior, Caroline E; Pacala, Stephen W

    2015-03-01

    Changes in resource availability often cause competitively driven changes in tree allocation to foliage, wood, and fine roots, either via plastic changes within individuals or through turnover of individuals with differing strategies. Here, we investigate how optimally competitive tree allocation should change in response to elevated atmospheric CO2 along a gradient of nitrogen and light availability, together with how those changes should affect carbon storage in living biomass. We present a physiologically-based forest model that includes the primary functions of wood and nitrogen. From a tree's perspective, wood is an offensive and defensive weapon used against neighbors in competition for light. From a biogeochemical perspective, wood is the primary living reservoir of stored carbon. Nitrogen constitutes a tree's photosynthetic machinery and the support systems for that machinery, and its limited availability thus reduces a tree's ability to fix carbon. This model has been previously successful in predicting allocation to foliage, wood, and fine roots along natural productivity gradients. Using game theory, we solve the model for competitively optimal foliage, wood, and fine root allocation strategies for trees in competition for nitrogen and light as a function of CO2 and nitrogen mineralization rate. Instead of down-regulating under nitrogen limitation, carbon storage under elevated CO2 relative to carbon storage at ambient CO2 is approximately independent of the nitrogen mineralization rate. This surprising prediction is a consequence of both increased competition for nitrogen driving increased fine root biomass and increased competition for light driving increased allocation to wood under elevated CO2 . PMID:25392967

  2. SAM 2 and SAGE data management and processing

    NASA Technical Reports Server (NTRS)

    Osborn, M. T.; Trepte, C. R.

    1987-01-01

    The data management and processing supplied by ST Systems Corporation (STX) for the Stratospheric Aerosol Measurement 2 (SAM 2) and Stratospheric Aerosol and Gas Experiment (SAGE) experiments for the years 1983 to 1986 are described. Included are discussions of data validation, documentation, and scientific analysis, as well as the archival schedule met by the operational reduction of SAM 2 and SAGE data. Work under this contract resulted in the archiving of the first seven years of SAM 2 data and all three years of SAGE data. A list of publications and presentations supported was also included.

  3. Recent Advances in Radical SAM Enzymology: New Structures and Mechanisms

    PubMed Central

    2015-01-01

    The radical S-adenosylmethionine (SAM) superfamily of enzymes catalyzes an amazingly diverse variety of reactions ranging from simple hydrogen abstraction to complicated multistep rearrangements and insertions. The reactions they catalyze are important for a broad range of biological functions, including cofactor and natural product biosynthesis, DNA repair, and tRNA modification. Generally conserved features of the radical SAM superfamily include a CX3CX2C motif that binds an [Fe4S4] cluster essential for the reductive cleavage of SAM. Here, we review recent advances in our understanding of the structure and mechanisms of these enzymes that, in some cases, have overturned widely accepted mechanisms. PMID:25009947

  4. SAM 2 and SAGE data management and processing

    NASA Astrophysics Data System (ADS)

    Osborn, M. T.; Trepte, C. R.

    1987-02-01

    The data management and processing supplied by ST Systems Corporation (STX) for the Stratospheric Aerosol Measurement 2 (SAM 2) and Stratospheric Aerosol and Gas Experiment (SAGE) experiments for the years 1983 to 1986 are described. Included are discussions of data validation, documentation, and scientific analysis, as well as the archival schedule met by the operational reduction of SAM 2 and SAGE data. Work under this contract resulted in the archiving of the first seven years of SAM 2 data and all three years of SAGE data. A list of publications and presentations supported was also included.

  5. Methodologies for optimal resource allocation to the national space program and new space utilizations. Volume 2: Resource allocation and smoothing model, programmer's manual

    NASA Technical Reports Server (NTRS)

    1971-01-01

    Appendixes are presented that provide model input requirements, a sample case, flow charts, and a program listing. At the beginning of each appendix, descriptive details and technical comments are provided to indicate any special instructions applicable to the use of that appendix. In addition, the program listing includes comment cards that state the purpose of each subroutine in the complete program and describe operations performed within that subroutine. The input requirements includes details on the many options that adapt the program to the specific needs of the analyst for a particular problem.

  6. Simulating smoke transport from wildland fires with a regional-scale air quality model: sensitivity to spatiotemporal allocation of fire emissions.

    PubMed

    Garcia-Menendez, Fernando; Hu, Yongtao; Odman, Mehmet T

    2014-09-15

    Air quality forecasts generated with chemical transport models can provide valuable information about the potential impacts of fires on pollutant levels. However, significant uncertainties are associated with fire-related emission estimates as well as their distribution on gridded modeling domains. In this study, we explore the sensitivity of fine particulate matter concentrations predicted by a regional-scale air quality model to the spatial and temporal allocation of fire emissions. The assessment was completed by simulating a fire-related smoke episode in which air quality throughout the Atlanta metropolitan area was affected on February 28, 2007. Sensitivity analyses were carried out to evaluate the significance of emission distribution among the model's vertical layers, along the horizontal plane, and into hourly inputs. Predicted PM2.5 concentrations were highly sensitive to emission injection altitude relative to planetary boundary layer height. Simulations were also responsive to the horizontal allocation of fire emissions and their distribution into single or multiple grid cells. Additionally, modeled concentrations were greatly sensitive to the temporal distribution of fire-related emissions. The analyses demonstrate that, in addition to adequate estimates of emitted mass, successfully modeling the impacts of fires on air quality depends on an accurate spatiotemporal allocation of emissions. PMID:24973934

  7. Simulating smoke transport from wildland fires with a regional-scale air quality model: sensitivity to spatiotemporal allocation of fire emissions.

    PubMed

    Garcia-Menendez, Fernando; Hu, Yongtao; Odman, Mehmet T

    2014-09-15

    Air quality forecasts generated with chemical transport models can provide valuable information about the potential impacts of fires on pollutant levels. However, significant uncertainties are associated with fire-related emission estimates as well as their distribution on gridded modeling domains. In this study, we explore the sensitivity of fine particulate matter concentrations predicted by a regional-scale air quality model to the spatial and temporal allocation of fire emissions. The assessment was completed by simulating a fire-related smoke episode in which air quality throughout the Atlanta metropolitan area was affected on February 28, 2007. Sensitivity analyses were carried out to evaluate the significance of emission distribution among the model's vertical layers, along the horizontal plane, and into hourly inputs. Predicted PM2.5 concentrations were highly sensitive to emission injection altitude relative to planetary boundary layer height. Simulations were also responsive to the horizontal allocation of fire emissions and their distribution into single or multiple grid cells. Additionally, modeled concentrations were greatly sensitive to the temporal distribution of fire-related emissions. The analyses demonstrate that, in addition to adequate estimates of emitted mass, successfully modeling the impacts of fires on air quality depends on an accurate spatiotemporal allocation of emissions.

  8. Crystal structures of the SAM-III/S[subscript MK] riboswitch reveal the SAM-dependent translation inhibition mechanism

    SciTech Connect

    Lu, C.; Smith, A.M.; Fuchs, R.T.; Ding, F.; Rajashankar, K.; Henkin, T.M.; Ke, A.

    2010-01-07

    Three distinct classes of S-adenosyl-L-methionine (SAM)-responsive riboswitches have been identified that regulate bacterial gene expression at the levels of transcription attenuation or translation inhibition. The SMK box (SAM-III) translational riboswitch has been identified in the SAM synthetase gene in members of the Lactobacillales. Here we report the 2.2-{angstrom} crystal structure of the Enterococcus faecalis SMK box riboswitch. The Y-shaped riboswitch organizes its conserved nucleotides around a three-way junction for SAM recognition. The Shine-Dalgarno sequence, which is sequestered by base-pairing with the anti-Shine-Dalgarno sequence in response to SAM binding, also directly participates in SAM recognition. The riboswitch makes extensive interactions with the adenosine and sulfonium moieties of SAM but does not appear to recognize the tail of the methionine moiety. We captured a structural snapshot of the SMK box riboswitch sampling the near-cognate ligand S-adenosyl-L-homocysteine (SAH) in which SAH was found to adopt an alternative conformation and fails to make several key interactions.

  9. Vibrational Stark Effect of the Electric-Field Reporter 4-Mercaptobenzonitrile as a Tool for Investigating Electrostatics at Electrode/SAM/Solution Interfaces

    PubMed Central

    Schkolnik, Gal; Salewski, Johannes; Millo, Diego; Zebger, Ingo; Franzen, Stefan; Hildebrandt, Peter

    2012-01-01

    4-mercaptobenzonitrile (MBN) in self-assembled monolayers (SAMs) on Au and Ag electrodes was studied by surface enhanced infrared absorption and Raman spectroscopy, to correlate the nitrile stretching frequency with the local electric field exploiting the vibrational Stark effect (VSE). Using MBN SAMs in different metal/SAM interfaces, we sorted out the main factors controlling the nitrile stretching frequency, which comprise, in addition to external electric fields, the metal-MBN bond, the surface potential, and hydrogen bond interactions. On the basis of the linear relationships between the nitrile stretching and the electrode potential, an electrostatic description of the interfacial potential distribution is presented that allows for determining the electric field strengths on the SAM surface, as well as the effective potential of zero-charge of the SAM-coated metal. Comparing this latter quantity with calculated values derived from literature data, we note a very good agreement for Au/MBN but distinct deviations for Ag/MBN which may reflect either the approximations and simplifications of the model or the uncertainty in reported structural parameters for Ag/MBN. The present electrostatic model consistently explains the electric field strengths for MBN SAMs on Ag and Au as well as for thiophenol and mercaptohexanoic acid SAMs with MBN incorporated as a VSE reporter. PMID:22837705

  10. Divergence in plant and microbial allocation strategies explains continental patterns in microbial allocation and biogeochemical fluxes.

    PubMed

    Averill, Colin

    2014-10-01

    Allocation trade-offs shape ecological and biogeochemical phenomena at local to global scale. Plant allocation strategies drive major changes in ecosystem carbon cycling. Microbial allocation to enzymes that decompose carbon vs. organic nutrients may similarly affect ecosystem carbon cycling. Current solutions to this allocation problem prioritise stoichiometric tradeoffs implemented in plant ecology. These solutions may not maximise microbial growth and fitness under all conditions, because organic nutrients are also a significant carbon resource for microbes. I created multiple allocation frameworks and simulated microbial growth using a microbial explicit biogeochemical model. I demonstrate that prioritising stoichiometric trade-offs does not optimise microbial allocation, while exploiting organic nutrients as carbon resources does. Analysis of continental-scale enzyme data supports the allocation patterns predicted by this framework, and modelling suggests large deviations in soil C loss based on which strategy is implemented. Therefore, understanding microbial allocation strategies will likely improve our understanding of carbon cycling and climate.

  11. The dynamic of annual carbon allocation to wood in European forests is consistent with a combined source-sink limitation of growth: implications for modelling

    NASA Astrophysics Data System (ADS)

    Guillemot, J.; Martin-StPaul, N. K.; Dufrêne, E.; François, C.; Soudani, K.; Ourcival, J. M.; Delpierre, N.

    2015-02-01

    The extent to which forest growth is limited by carbon (C) supply (source control) or by cambial activity (sink control) will condition the response of trees to global changes. However, the physiological processes responsible for the limitation of forest growth are still under debate. The aim of this study is to evaluate the key drivers of the annual carbon allocation to wood along large soil and climate regional gradients in five tree species representative of the main European forest biomes (Fagus sylvatica, Quercus petraea, Quercus ilex, Quercus robur and Picea abies). Combining field measurements and process-based simulations at 49 sites (931 site-years), we assessed the stand biomass growth dependences at both inter-site and inter-annual scales. Specifically, the relative influence of forest C balance (source control), direct environmental control (water and temperature controls of sink activity) and allocation adjustments related to age, past climate conditions, competition intensity and soil nutrient availability on growth were quantified. The inter-site variability in stand C allocation to wood was predominantly driven by an age-related decline. The direct control of temperature or water stress on sink activity (i.e. independently from their effects on C supply) exerted a strong influence on the annual stand woody growth in all the species considered, including deciduous temperate species. The lagged effect of the past environment conditions was a significant driver of the annual C allocation to wood. Carbon supply appeared to strongly limit growth only in deciduous temperate species. We provide an evaluation of the spatio-temporal dynamics of annual carbon allocation to wood in European forests. Our study supports the premise that European forest growth is under a complex control including both source and sink limitations. The relative influences of the different growth drivers strongly vary across years and spatial ecological gradients. We suggest a

  12. Scenario-Based Multi-Objective Optimum Allocation Model for Earthquake Emergency Shelters Using a Modified Particle Swarm Optimization Algorithm: A Case Study in Chaoyang District, Beijing, China

    PubMed Central

    Zhao, Xiujuan; Xu, Wei; Ma, Yunjia; Hu, Fuyu

    2015-01-01

    The correct location of earthquake emergency shelters and their allocation to residents can effectively reduce the number of casualties by providing safe havens and efficient evacuation routes during the chaotic period of the unfolding disaster. However, diverse and strict constraints and the discrete feasible domain of the required models make the problem of shelter location and allocation more difficult. A number of models have been developed to solve this problem, but there are still large differences between the models and the actual situation because the characteristics of the evacuees and the construction costs of the shelters have been excessively simplified. We report here the development of a multi-objective model for the allocation of residents to earthquake shelters by considering these factors using the Chaoyang district, Beijing, China as a case study. The two objectives of this model were to minimize the total weighted evacuation time from residential areas to a specified shelter and to minimize the total area of all the shelters. The two constraints were the shelter capacity and the service radius. Three scenarios were considered to estimate the number of people who would need to be evacuated. The particle swarm optimization algorithm was first modified by applying the von Neumann structure in former loops and global structure in later loops, and then used to solve this problem. The results show that increasing the shelter area can result in a large decrease in the total weighted evacuation time from scheme 1 to scheme 9 in scenario A, from scheme 1 to scheme 9 in scenario B, from scheme 1 to scheme 19 in scenario C. If the funding were not a limitation, then the final schemes of each scenario are the best solutions, otherwise the earlier schemes are more reasonable. The modified model proved to be useful for the optimization of shelter allocation, and the result can be used as a scientific reference for planning shelters in the Chaoyang district

  13. Curiosity Shakes, Bakes, and Tastes Mars with SAM

    NASA Video Gallery

    NASA's Curiosity rover analyzed its first solid sample of Mars with a variety of instruments, including the Sample Analysis at Mars (SAM) instrument suite. Developed at NASA's Goddard Space Flight ...

  14. In vivo CH3(CH2)11SAu SAM electrodes in the beating heart: in situ analytical studies relevant to pacemakers and interstitial biosensors.

    PubMed

    Chou, Howard A; Zavitz, Daniel H; Ovadia, Marc

    2003-01-01

    To study in vivo modification of the SAM equivalent circuit when a highly ordered SAM is used as a bioelectrode, dodecanethiolate SAM-Au intramuscular electrodes were studied in living rat heart in a challenging in situ perfused rat model by impedance spectroscopy, cyclic voltammetry, and neutron activation analysis (NAA). The SAM layer experienced disintegration in vivo biological system, as NAA detected the presence of Au atoms that had leached into the surrounding living tissue. Therefore, the underlying Au surface became exposed during biological implant. Study by impedance spectroscopy, however, revealed perfect capacitive behavior for the SAM, similar to in vitro behavior. Electrodes showed a pure capacitive Nyquist plot with 86.1-89.4 degrees near-vertical line segments as the equivalent circuit locus, as for a parallel plate capacitor. Impedance magnitude varied linearly with 1/omega excluding diffusionally limited ionic charge transport. There was no diffusional conductive element Z(W infinity ) or spatially confined Warburg impedance Z(D). The effect of in vivo exposure of a highly ordered SAM is a 'sealing over' effect of new defects by the binding of proteinaceous or lipid species in the biological milieu, a fact of significance for SAM electrodes used either as pacemaker electrodes or as a platform for in vivo biosensors.

  15. Auxiliary iron-sulfur cofactors in radical SAM enzymes.

    PubMed

    Lanz, Nicholas D; Booker, Squire J

    2015-06-01

    A vast number of enzymes are now known to belong to a superfamily known as radical SAM, which all contain a [4Fe-4S] cluster ligated by three cysteine residues. The remaining, unligated, iron ion of the cluster binds in contact with the α-amino and α-carboxylate groups of S-adenosyl-l-methionine (SAM). This binding mode facilitates inner-sphere electron transfer from the reduced form of the cluster into the sulfur atom of SAM, resulting in a reductive cleavage of SAM to methionine and a 5'-deoxyadenosyl radical. The 5'-deoxyadenosyl radical then abstracts a target substrate hydrogen atom, initiating a wide variety of radical-based transformations. A subset of radical SAM enzymes contains one or more additional iron-sulfur clusters that are required for the reactions they catalyze. However, outside of a subset of sulfur insertion reactions, very little is known about the roles of these additional clusters. This review will highlight the most recent advances in the identification and characterization of radical SAM enzymes that harbor auxiliary iron-sulfur clusters. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.

  16. HPA and SAM axis responses as correlates of self- vs parental ratings of anxiety in boys with an Autistic Disorder.

    PubMed

    Bitsika, Vicki; Sharpley, Christopher F; Sweeney, John A; McFarlane, James R

    2014-03-29

    Anxiety and Autistic Disorder (AD) are both neurological conditions and both disorders share some features that make it difficult to precisely allocate specific symptoms to each disorder. HPA and SAM axis activities have been conclusively associated with anxiety, and may provide a method of validating anxiety rating scale assessments given by parents and their children with AD about those children. Data from HPA axis (salivary cortisol) and SAM axis (salivary alpha amylase) responses were collected from a sample of 32 high-functioning boys (M age=11yr) with an Autistic Disorder (AD) and were compared with the boys' and their mothers' ratings of the boys' anxiety. There was a significant difference between the self-ratings given by the boys and ratings given about them by their mothers. Further, only the boys' self-ratings of their anxiety significantly predicted the HPA axis responses and neither were significantly related to SAM axis responses. Some boys showed cortisol responses which were similar to that previously reported in children who had suffered chronic and severe anxiety arising from stressful social interactions. As well as suggesting that some boys with an AD can provide valid self-assessments of their anxiety, these data also point to the presence of very high levels of chronic HPA-axis arousal and consequent chronic anxiety in these boys.

  17. Developing a bi-objective optimization model for solving the availability allocation problem in repairable series-parallel systems by NSGA II

    NASA Astrophysics Data System (ADS)

    Amiri, Maghsoud; Khajeh, Mostafa

    2016-11-01

    Bi-objective optimization of the availability allocation problem in a series-parallel system with repairable components is aimed in this paper. The two objectives of the problem are the availability of the system and the total cost of the system. Regarding the previous studies in series-parallel systems, the main contribution of this study is to expand the redundancy allocation problems to systems that have repairable components. Therefore, the considered systems in this paper are the systems that have repairable components in their configurations and subsystems. Due to the complexity of the model, a meta-heuristic method called as non-dominated sorting genetic algorithm is applied to find Pareto front. After finding the Pareto front, a procedure is used to select the best solution from the Pareto front.

  18. Computer Processor Allocator

    2004-03-01

    The Compute Processor Allocator (CPA) provides an efficient and reliable mechanism for managing and allotting processors in a massively parallel (MP) computer. It maintains information in a database on the health. configuration and allocation of each processor. This persistent information is factored in to each allocation decision. The CPA runs in a distributed fashion to avoid a single point of failure.

  19. SAMS Acceleration Measurements on Mir from June to November 1995

    NASA Technical Reports Server (NTRS)

    DeLombard, Richard; Hrovat, Ken; Moskowitz, Milton; McPherson, Kevin

    1996-01-01

    The NASA Microgravity Science and Applications Division (MSAD) sponsors science experiments on a variety of microgravity carriers, including sounding rockets, drop towers, parabolic aircraft, and Orbiter missions. The MSAD sponsors the Space Acceleration Measurement System (SAMS) to support microgravity science experiments with acceleration measurements to characterize the microgravity environment to which the experiments were exposed. The Principal Investigator Microgravity Services project at the NASA Lewis Research Center supports principal investigators of microgravity experiments as they evaluate the effects of varying acceleration levels on their experiments. In 1993, a cooperative effort was started between the United States and Russia involving science utilization of the Russian Mir space station by scientists from the United States and Russia. MSAD is currently sponsoring science experiments participating in the Shuttle-Mir Science Program in cooperation with the Russians on the Mir space station. Included in the complement of MSAD experiments and equipment is a SAMS unit In a manner similar to Orbiter mission support, the SAMS unit supports science experiments from the U.S. and Russia by measuring the microgravity environment during experiment operations. The initial SAMS supported experiment was a Protein Crystal Growth (PCG) experiment from June to November 1995. SAMS data were obtained during the PCG operations on Mir in accordance with the PCG Principal Investigator's requirements. This report presents an overview of the SAMS data recorded to support this PCG experiment. The report contains plots of the SAMS 100 Hz sensor head data as an overview of the microgravity environment, including the STS-74 Shuttle-Mir docking.

  20. Thematic Mapper data for forest resource allocation

    NASA Technical Reports Server (NTRS)

    Zeff, Ilene S.; Merry, Carolyn J.

    1993-01-01

    A technique for classifying a Landsat Thematic Mapper image was demonstrated on the Wayne National Forest of southeastern Ohio. The classified image was integrated into a geographic information system database, and prescriptive forest land use allocation models were developed using the techniques of cartographic modeling. Timber harvest sites and accompanying haul roads were allocated.

  1. Eco-hydrologic Modeling of Rangelands: Evaluating a New Carbon Allocation Approach and Simulating Ecosystem Response to Changing Climate and Management Conditions

    NASA Astrophysics Data System (ADS)

    Reyes, J. J.; Tague, C.; Choate, J. S.; Adam, J. C.

    2014-12-01

    More than one-third of the United States' land cover is comprised of rangelands, which support both forage production and livestock grazing. For grasses in both semi-arid and humid environments, small changes in precipitation and temperature, as well as grazing, can have disproportionately larger impacts on ecosystem processes. For example, these areas may experience large response pulses under highly variable precipitation and other potential future changes. The ultimate goal of this study is to provide information on the interactions between management activities, climate and ecosystem processes to inform sustainable rangeland management. The specific objectives of this paper are to (1) evaluate a new carbon allocation strategy for grasses and (2) test the sensitivity of this improved strategy to changes in climate and grazing strategies. The Regional Hydro-ecologic Simulation System (RHESSys) is a process-based, watershed-scale model that simulates hydrology and biogeochemical cycling with dynamic soil and vegetation modules. We developed a new carbon allocation algorithm for partitioning net primary productivity (NPP) between roots and leaves for grasses. The 'hybrid' approach represents a balance between preferential partitioning due to environmental conditions and age-related growth. We evaluated this new allocation scheme at the point-scale at a variety of rangeland sites in the U.S. using observed biomass measurements and against existing allocation schemes used in RHESSys. Additionally, changes in the magnitude, frequency, and intensity of precipitation and temperature were used to assess ecosystem responses using our new allocation scheme. We found that changes in biomass and NPP were generally more sensitive to changes in precipitation than changes in temperature. At more arid sites, larger percent reductions in historic baseline precipitation affected biomass and NPP more negatively. We incorporated grazing impacts through biomass removal. We found that

  2. CONSORT: Sam68 Is Directly Regulated by MiR-204 and Promotes the Self-Renewal Potential of Breast Cancer Cells by Activating the Wnt/Beta-Catenin Signaling Pathway

    PubMed Central

    Wang, Lan; Tian, Han; Yuan, Jie; Wu, Hongmei; Wu, Jueheng; Zhu, Xun

    2015-01-01

    Abstract Breast cancer stem cells (BCSCs) are considered to be responsible for recurrence in breast cancer. The 68 kDa Src-associated protein in mitosis (Sam68) has been linked to the development and progression of breast cancer; however, the posttranscriptional regulation and role of Sam68 in BCSC self-renewal remain unclear. Sam68 was ectopically overexpressed or knocked down using a siRNA; the self-renewal potential of breast cancer cell lines was assessed using flow cytometry, in vitro mammosphere culture and a xenograft model in NOD/SCID mice. Activation of beta-catenin was assessed by immunohistochemical staining, Western blotting, and luciferase reporter gene assays. The ArrayExpress dataset GSE45666 was used to identify conserved microRNAs downregulated in breast cancer; real-time PCR, Western blotting, luciferase reporter assay, and xenografted tumor model were used to confirm miR-204 regulated Sam68. We found that endogenous Sam68 expression correlated positively with the self-renewal potential of breast cancer cell lines. Overexpression of Sam68 promoted, whereas knockdown reduced, breast cancer cell self-renewal potential in vitro and tumorigenicity in vivo. The Wnt/beta-catenin pathway was identified as a functional mediator of Sam68-induced self-renewal in SKBR-3 and MCF-7 cells. Furthermore, miR-204 was found to be frequently downregulated in human breast cancer and confirmed to directly target Sam68; miR-204 inhibited the self-renewal of breast cancer cell lines by targeting and suppressing Sam68. Our study reveals that Sam68 is regulated by miR-204 and may play an important role in the self-renewal of BCSCs via activating the Wnt/beta-catenin pathway. Sam68 may represent a novel therapeutic target for breast cancer. PMID:26656364

  3. Validation of the Model of End-Stage Liver Disease for Liver Transplant Allocation in Alberta: Implications for Future Directions in Canada

    PubMed Central

    Burak, Kelly W.; Meeberg, Glenda A.; Myers, Robert P.; Fick, Gordon H.; Swain, Mark G.; Bain, Vincent G.; Kneteman, Norman M.; Hilsden, Robert J.

    2016-01-01

    Background. Since 2002, the Model of End-Stage Liver Disease (MELD) has been used for allocation of liver transplants (LT) in the USA. In Canada, livers were allocated by the CanWAIT algorithm. The aim of this study was to compare the abilities of MELD, Child-Pugh (CP), and CanWAIT status to predict 3-month and 1-year mortality before LT in Canadian patients and to describe the use of MELD in Canada. Methods. Validation of MELD was performed in 320 patients listed for LT in Alberta (1998–2002). In October 2014, a survey of MELD use by Canadian LT centers was conducted. Results. Within 1 year of listing, 47 patients were removed from the waiting list (29 deaths, 18 too ill for LT). Using logistic regression, the MELD and CP were better than the CanWAIT at predicting 3-month (AUROC: 0.79, 0.78, and 0.59; p = 0.0002) and 1-year waitlist mortality (AUROC: 0.70, 0.70, and 0.55; p = 0.0023). Beginning in 2004, MELD began to be adopted by Canadian LT programs but its use was not standardized. Conclusions. Compared with the CanWAIT system, the MELD score was significantly better at predicting LT waitlist mortality. MELD-sodium (MELD-Na) has now been adopted for LT allocation in Canada. PMID:27446823

  4. Optimizing reproductive phenology in a two-resource world: a dynamic allocation model of plant growth predicts later reproduction in phosphorus-limited plants

    PubMed Central

    Nord, Eric A.; Shea, Katriona; Lynch, Jonathan P.

    2011-01-01

    Background and Aims Timing of reproduction is a key life-history trait that is regulated by resource availability. Delayed reproduction in soils with low phosphorus availability is common among annuals, in contrast to the accelerated reproduction typical of other low-nutrient environments. It is hypothesized that this anomalous response arises from the high marginal value of additional allocation to root growth caused by the low mobility of phosphorus in soils. Methods To better understand the benefits and costs of such delayed reproduction, a two-resource dynamic allocation model of plant growth and reproduction is presented. The model incorporates growth, respiration, and carbon and phosphorus acquisition of both root and shoot tissue, and considers the reallocation of resources from senescent leaves. The model is parameterized with data from Arabidopsis and the optimal reproductive phenology is explored in a range of environments. Key Results The model predicts delayed reproduction in low-phosphorus environments. Reproductive timing in low-phosphorus environments is quite sensitive to phosphorus mobility, but is less sensitive to the temporal distribution of mortality risks. In low-phosphorus environments, the relative metabolic cost of roots was greater, and reproductive allocation reduced, compared with high-phosphorus conditions. The model suggests that delayed reproduction in response to low phosphorus availability may be reduced in plants adapted to environments where phosphorus mobility is greater. Conclusions Delayed reproduction in low-phosphorus soils can be a beneficial response allowing for increased acquisition and utilization of phosphorus. This finding has implications both for efforts to breed crops for low-phosphorus soils, and for efforts to understand how climate change may impact plant growth and productivity in low-phosphorus environments. PMID:21712299

  5. The dynamic of the annual carbon allocation to wood in European tree species is consistent with a combined source-sink limitation of growth: implications for modelling

    NASA Astrophysics Data System (ADS)

    Guillemot, J.; Martin-StPaul, N. K.; Dufrene, E.; Francois, C.; Soudani, K.; Ourcival, J. M.; Delpierre, N.

    2015-05-01

    appeared to strongly limit growth only in temperate deciduous species. We provide an evaluation of the spatio-temporal dynamics of the annual C allocation to wood in French forests. Our study supports the premise that the growth of European tree species is subject to complex control processes that include both source and sink limitations. The relative influences of the growth drivers strongly vary with time and across spatial ecological gradients. We suggest a straightforward modelling framework with which to implement these combined forest growth limitations into terrestrial biosphere models.

  6. SAM-T08, HMM-based protein structure prediction

    PubMed Central

    Karplus, Kevin

    2009-01-01

    The SAM-T08 web server is a protein structure prediction server that provides several useful intermediate results in addition to the final predicted 3D structure: three multiple sequence alignments of putative homologs using different iterated search procedures, prediction of local structure features including various backbone and burial properties, calibrated E-values for the significance of template searches of PDB and residue–residue contact predictions. The server has been validated as part of the CASP8 assessment of structure prediction as having good performance across all classes of predictions. The SAM-T08 server is available at http://compbio.soe.ucsc.edu/SAM_T08/T08-query.html PMID:19483096

  7. Total maximum allocated load calculation of nitrogen pollutants by linking a 3D biogeochemical-hydrodynamic model with a programming model in Bohai Sea

    NASA Astrophysics Data System (ADS)

    Dai, Aiquan; Li, Keqiang; Ding, Dongsheng; Li, Yan; Liang, Shengkang; Li, Yanbin; Su, Ying; Wang, Xiulin

    2015-12-01

    The equal percent removal (EPR) method, in which pollutant reduction ratio was set as the same in all administrative regions, failed to satisfy the requirement for water quality improvement in the Bohai Sea. Such requirement was imposed by the developed Coastal Pollution Total Load Control Management. The total maximum allocated load (TMAL) of nitrogen pollutants in the sea-sink source regions (SSRs) around the Bohai Rim, which is the maximum pollutant load of every outlet under the limitation of water quality criteria, was estimated by optimization-simulation method (OSM) combined with loop approximation calculation. In OSM, water quality is simulated using a water quality model and pollutant load is calculated with a programming model. The effect of changes in pollutant loads on TMAL was discussed. Results showed that the TMAL of nitrogen pollutants in 34 SSRs was 1.49×105 ton/year. The highest TMAL was observed in summer, whereas the lowest in winter. TMAL was also higher in the Bohai Strait and central Bohai Sea and lower in the inner area of the Liaodong Bay, Bohai Bay and Laizhou Bay. In loop approximation calculation, the TMAL obtained was considered satisfactory for water quality criteria as fluctuation of concentration response matrix with pollutant loads was eliminated. Results of numerical experiment further showed that water quality improved faster and were more evident under TMAL input than that when using the EPR method

  8. The methylthiolation reaction mediated by the Radical-SAM enzymes

    PubMed Central

    Atta, Mohamed; Arragain, Simon; Fontecave, Marc; Mulliez, Etienne; Hunt, John F.; Luff, Jon D.; Forouhar, Farhad

    2014-01-01

    Over the past ten years, considerable progress has been made in our understanding of the mechanistic enzymology of the Radical-SAM enzymes. It is now clear that these enzymes appear to be involved in a remarkably wide range of chemically challenging reactions. This review article highlights mechanistic and structural aspects of the methylthiotransferases (MTTases) sub-class of the Radical-SAM enzymes. The mechanism of methylthio insertion, now observed to be performed by three different enzymes is an exciting unsolved problem. PMID:22178611

  9. Developing an Agent-based Model for the Depot-based Water Allocation System in the Bakken Field in Western North Dakota

    NASA Astrophysics Data System (ADS)

    Lin, T.; Lin, Z.; Lim, S.; Borders, M.

    2015-12-01

    The oil production at the Bakken Shale increased more than ten times from 2008 to 2013 due to technological advancement in hydraulic fracturing and North Dakota has become the second largest oil producing state in the U.S. behind only Texas since 2012. On average it requires about 2-4 million gallons of freshwater to complete one oil well in the Bakken field and the number of oil well completions (i.e., hydraulic fracturing) in the Bakken field increased from 500 in 2008 to 2085 in 2013. A large quantity of freshwater used for hydraulic fracturing renders a significant impact on water resource management in the semi-arid region. A novel water allocation system - water depots - was spontaneously created to distribute surface and ground water for industrial uses. A GIS-based multi-agent model is developed to simulate the emergent patterns and dynamics of the water depot-based water allocation system and to explore its economic and environmental consequences. Four different types of water depot are defined as agents and water price, climate condition, water source, geology, and other physical and economic constraints are considered in the model. Decentralized optimization algorithm will be used to determine the agents' behaviors. The agent-based model for water depots will be coupled with hydrological models to improve the region's water resources management.

  10. THE 1985 NAPAP EMISSIONS INVENTORY: DEVELOPMENT OF SPECIES ALLOCATION FACTORS

    EPA Science Inventory

    The report describes the methodologies and data bases used to develop species allocation factors and data processing software used to develop the 1985 National Acid Precipitation Assessment Program (NAPAP) Modelers' Emissions Inventory (Version 2). Species allocation factors were...

  11. Atomic-level insights into metabolite recognition and specificity of the SAM-II riboswitch

    PubMed Central

    Doshi, Urmi; Kelley, Jennifer M.; Hamelberg, Donald

    2012-01-01

    Although S-adenosylhomocysteine (SAH), a metabolic by-product of S-adenosylmethionine (SAM), differs from SAM only by a single methyl group and an overall positive charge, SAH binds the SAM-II riboswitch with more than 1000-fold less affinity than SAM. Using atomistic molecular dynamics simulations, we investigated the molecular basis of such high selectivity in ligand recognition by SAM-II riboswitch. The biosynthesis of SAM exclusively generates the (S,S) stereoisomer, and (S,S)-SAM can spontaneously convert to the (R,S) form. We, therefore, also examined the effects of (R,S)-SAM binding to SAM-II and its potential biological function. We find that the unfavorable loss in entropy in SAM-II binding is greater for (S,S)- and (R,S)-SAM than SAH, which is compensated by stabilizing electrostatic interactions with the riboswitch. The positively charged sulfonium moiety on SAM acts as the crucial anchor point responsible for the formation of key ionic interactions as it fits favorably in the negatively charged binding pocket. In contrast, SAH, with its lone pair of electrons on the sulfur, experiences repulsion in the binding pocket of SAM-II and is enthalpically destabilized. In the presence of SAH, similar to the unbound riboswitch, the pseudoknot structure of SAM-II is not completely formed, thus exposing the Shine-Dalgarno sequence. Unlike SAM, this may further facilitate ribosomal assembly and translation initiation. Our analysis of the conformational ensemble sampled by SAM-II in the absence of ligands and when bound to SAM or SAH reveals that ligand binding follows a combination of conformational selection and induced-fit mechanisms. PMID:22194311

  12. Sam68 functions as a transcriptional coactivator of the p53 tumor suppressor

    PubMed Central

    Li, Naomi; Richard, Stéphane

    2016-01-01

    Sam68 is a known sequence-specific RNA binding protein that regulates alternative splicing events during the cell cycle and apoptosis. Sam68 has also been shown to influence transcription, but the molecular mechanism remains undefined. Herein we identify Sam68 as a transcriptional coactivator of the p53 tumor suppressor in response to DNA damage. Using CRISPR/Cas9 generated isogenic HCT116 Sam68−/− cell lines wild type or deficient for p53, we show that Sam68 is required for the efficient transactivation of p53 target genes. Consistently, Sam68 depletion caused defects in DNA damage-induced cell cycle arrest and apoptosis mediated by p53. Mechanistically, we demonstrate that Sam68 physically interacted with p53 in an RNA-dependent manner, and that this interaction was essential for the coactivator function of Sam68. Furthermore, we show that both Sam68 and p53 were recruited to promoters of p53-responsive genes, suggesting interdependence. Finally, Sam68 acted in concert with the p53 long noncoding RNA (lncRNA) target PR-lncRNA-1 for p53 recruitment, implicating a positive-feedback mechanism in which lncRNAs induced by the Sam68/p53 complex can enhance p53 transcriptional activity. These findings define a hitherto novel mechanism of action for Sam68 in governing p53 transcriptional activation, and represent the first report of Sam68 in the regulation of tumor suppressor activities. PMID:27365047

  13. Improved waiting-list outcomes in Argentina after the adoption of a model for end-stage liver disease-based liver allocation policy.

    PubMed

    Cejas, Nora Gabriela; Villamil, Federico G; Lendoire, Javier C; Tagliafichi, Viviana; Lopez, Arturo; Krogh, Daniela Hansen; Soratti, Carlos A; Bisigniano, Liliana

    2013-07-01

    In July 2005, Argentina became the first country after the United States to introduce the Model for End-Stage Liver Disease (MELD) for organ allocation. In this study, we investigated waiting-list (WL) outcomes (n = 3272) and post-liver transplantation (LT) survival in 2 consecutive periods of 5 years before and after the implementation of a MELD-based allocation policy. Data were obtained from the database of the national institute for organ allocation in Argentina. After the adoption of the MELD system, there were significant reductions in WL mortality [28.5% versus 21.9%, P < 0.001, hazard ratio (HR) = 1.57, 95% confidence interval (CI) = 1.37-1.81] and total dropout rates (38.6% versus 29.1%, P < 0.001, HR = 1.31, 95% CI = 1.16-1.48) despite significantly less LT accessibility (57.4% versus 50.7%, P < 0.001, HR = 1.53, 95% CI = 1.39-1.68). The annual number of deaths per 1000 patient-years at risk decreased from 273 in 2005 to 173 in 2010, and the number of LT procedures per 1000 patient-years at risk decreased from 564 to 422. MELD and Model for End-Stage Liver Disease-Sodium scores were excellent predictors of 3-month WL mortality with c statistics of 0.828 and 0.857, respectively (P < 0.001). No difference was observed in 1-year posttransplant survival between the 2 periods (81.1% versus 81.3%). Although patients with a MELD score > 30 had lower posttransplant survival, the global accuracy of the score for predicting outcomes was poor, as indicated by a c statistic of only 0.523. Patients with granted MELD exceptions (158 for hepatocellular carcinoma and 52 for other reasons) had significantly higher access to LT (80.4%) in comparison with nonexception patients with equivalent listing priority (MELD score = 18-25; 54.6%, P < 0.001, HR = 0.49, 95% CI = 0.40-0.61). In conclusion, the adoption of the MELD model in Argentina has resulted in improved liver organ allocation without compromising

  14. Global model estimates of carbon and nitrogen storage in litter and soil pools: response to changes in vegetation quality and biomass allocation

    NASA Astrophysics Data System (ADS)

    Potter, Christopher S.; Klooster, Steven A.

    1997-02-01

    Changes in plant production, structure, and tissue composition are primary drivers for terrestrial biogeochemistry under future environmental conditions. Consequently, there is a need for process-oriented assessment of the potential global importance of vegetation controls over extended periods of C and N sequestration in terrestrial ecosystems. In this study, plant litter quality (lignin content) and carbon allocation to woody tissues are used as surrogates for testing the hypothetical effects of vegetation change on C and N cycles. We tested the CASA (Carnegie-Ames-Stanford approach) biosphere model, which uses global gridded (1°) satellite imagery on a monthly time interval to simulate seasonal patterns in net ecosystem carbon balance and near steady-state C/N storage in detritus and soils. Under contemporary "reference" settings, combined organic matter storage (litter plus surface soil to c. 30cm depth) for C and N is estimated highest in tropical and boreal forest ecosystem zones, and in cultivated ecosystems. The worldwide C:N ratio (by weight) for standing litter plus surface soil organic matter (SOM) is estimated at 23. About 14% of the projected global pool of 1327Pg (1015 g) soil C resides in "modern" form, in the sense that this proportion is in near-steady state exchange with plant production and decomposition on time scales of several decades. Likewise, about 12% of the projected global pool of 104Pg soil N is in modern form. Sensitivity tests treated litter quality and allocation effects independently from other direct effects of changes in climate, atmospheric CO2 levels, and primary production. For forested ecosystems, the model predicts that a hypothetical 50% decrease in litter lignin concentration would result in a long-term net loss of about 10% C from surface litter and soil organic matter pools. A 50% decrease in C allocation to woody tissues would invoke approximately the same net loss of C as a 50% decrease in litter lignin. With respect

  15. Skill Acquisition Measures (SAM). Elementary Mathematics Level IV. Teacher's Manual.

    ERIC Educational Resources Information Center

    Lancaster City School District, PA.

    The Skill Acquisition Measures (SAM) were designed by the Lancaster (Pennsylvania) School District as criterion referenced tests for mathematics. This manual consists of copies of the student test forms for level 4, with additional information for the teacher's use. Each of the test items is presented with the correct answers and the criteria for…

  16. 78 FR 47695 - Sam Rayburn Dam Power Rate

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-06

    ... September 30, 2013 (77 FR 67813, November. 14, 2012). The Administrator, Southwestern Power Administration (Southwestern), has prepared Current and Revised 2013 Power Repayment Studies which show the need for an... Southwestern Power Administration Sam Rayburn Dam Power Rate AGENCY: Southwestern Power Administration,...

  17. 77 FR 67813 - Sam Rayburn Dam Project Power Rate

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-14

    ... Rayburn power rate extension were announced by a Federal Register (77 FR 50493) notice published on August... published notice in the Federal Register, (77 FR 50493), of the proposed rate extension for the Rayburn... Southwestern Power Administration Sam Rayburn Dam Project Power Rate AGENCY: Southwestern Power...

  18. Social Activity Method (SAM): A Fractal Language for Mathematics

    ERIC Educational Resources Information Center

    Dowling, Paul

    2013-01-01

    In this paper I shall present and develop my organisational language, "social activity method" (SAM), and illustrate some of its applications. I shall introduce a new scheme for "modes of recontextualisation" that enables the analysis of the ways in which one activity--which might be school mathematics or social research or any…

  19. SAMS Acceleration Measurement on Mir From March to September 1996

    NASA Technical Reports Server (NTRS)

    Moskowitz, Milton E.; Hrovat, Ken; Truong, Duc; Reckart, Timothy

    1997-01-01

    During NASA Increment 2 (March to September 1996), over 15 gigabytes of acceleration data were collected by the Space Acceleration Measurement System (SAMS) onboard the Russian Space Station, Mir. The data were recorded on 55 optical disks and were returned to Earth on STS-79. During this time, SAMS data were collected in the Kristall and Kvant modules, and in the Priroda module to support the following experiments: the Queen's University Experiments in Liquid Diffusion (QUELD), the Technological Evaluation of the MIM (TEM), the Forced Flow Flame Spreading Test (FFFT), and Candle Flames in Microgravity (CFM). This report points out some of the salient features of the microgravity environment to which these experiments were exposed. Also documented are mission events of interest such as the docked phase of STS-76 operations, an extravehicular activity (EVA) to install and deploy solar panels on the Kvant module, a Progress engine burn to raise Mir's altitude, and an on-orbit SAMS calibration procedure. Also included are a description of the Mir module orientations, and the panel notations within the modules. This report presents an overview of the SAMS acceleration measurements recorded by 10 Hz and 100 Hz sensor heads. Variations in the acceleration environment caused by unique activities such as crew exercise and life-support fans are presented. The analyses included herein complement those presented in previous mission summary reports published by the Principal Investigator Microgravity Services (PIMS) group.

  20. Role of Sam68 in post-transcriptional gene regulation.

    PubMed

    Sánchez-Jiménez, Flora; Sánchez-Margalet, Víctor

    2013-11-28

    The STAR family of proteins links signaling pathways to various aspects of post-transcriptional regulation and processing of RNAs. Sam68 belongs to this class of heteronuclear ribonucleoprotein particle K (hnRNP K) homology (KH) single domain-containing family of RNA-binding proteins that also contains some domains predicted to bind critical components in signal transduction pathways. In response to phosphorylation and other post-transcriptional modifications, Sam68 has been shown to have the ability to link signal transduction pathways to downstream effects regulating RNA metabolism, including transcription, alternative splicing or RNA transport. In addition to its function as a docking protein in some signaling pathways, this prototypic STAR protein has been identified to have a nuclear localization and to take part in the formation of both nuclear and cytosolic multi-molecular complexes such as Sam68 nuclear bodies and stress granules. Coupling with other proteins and RNA targets, Sam68 may play a role in the regulation of differential expression and mRNA processing and translation according to internal and external signals, thus mediating important physiological functions, such as cell death, proliferation or cell differentiation.

  1. Role of Sam68 in Post-Transcriptional Gene Regulation

    PubMed Central

    Sánchez-Jiménez, Flora; Sánchez-Margalet, Víctor

    2013-01-01

    The STAR family of proteins links signaling pathways to various aspects of post-transcriptional regulation and processing of RNAs. Sam68 belongs to this class of heteronuclear ribonucleoprotein particle K (hnRNP K) homology (KH) single domain-containing family of RNA-binding proteins that also contains some domains predicted to bind critical components in signal transduction pathways. In response to phosphorylation and other post-transcriptional modifications, Sam68 has been shown to have the ability to link signal transduction pathways to downstream effects regulating RNA metabolism, including transcription, alternative splicing or RNA transport. In addition to its function as a docking protein in some signaling pathways, this prototypic STAR protein has been identified to have a nuclear localization and to take part in the formation of both nuclear and cytosolic multi-molecular complexes such as Sam68 nuclear bodies and stress granules. Coupling with other proteins and RNA targets, Sam68 may play a role in the regulation of differential expression and mRNA processing and translation according to internal and external signals, thus mediating important physiological functions, such as cell death, proliferation or cell differentiation. PMID:24287914

  2. Information System through ANIS at CeSAM

    NASA Astrophysics Data System (ADS)

    Moreau, C.; Agneray, F.; Gimenez, S.

    2015-09-01

    ANIS (AstroNomical Information System) is a web generic tool developed at CeSAM to facilitate and standardize the implementation of astronomical data of various kinds through private and/or public dedicated Information Systems. The architecture of ANIS is composed of a database server which contains the project data, a web user interface template which provides high level services (search, extract and display imaging and spectroscopic data using a combination of criteria, an object list, a sql query module or a cone search interfaces), a framework composed of several packages, and a metadata database managed by a web administration entity. The process to implement a new ANIS instance at CeSAM is easy and fast : the scientific project has to submit data or a data secure access, the CeSAM team installs the new instance (web interface template and the metadata database), and the project administrator can configure the instance with the web ANIS-administration entity. Currently, the CeSAM offers through ANIS a web access to VO compliant Information Systems for different projects (HeDaM, HST-COSMOS, CFHTLS-ZPhots, ExoDAT,...).

  3. EFFECTS OF POLYCYCLIC AROMATIC HYDROCARBON OF SAM-COATED ELECTRODES USING FERRYICYANIDE AS THE REDOX INDICATOR

    EPA Science Inventory

    Electrochemical responses on self-assembled monolayer (SAM)-coated polycrystalline gold electrodes were investigated using cyclic voltammetry and square wave voltammetry with a three electrode system. Experimental results show potential in the application of pyrene-imprinted SAM...

  4. Improving methionine and ATP availability by MET6 and SAM2 co-expression combined with sodium citrate feeding enhanced SAM accumulation in Saccharomyces cerevisiae.

    PubMed

    Chen, Hailong; Wang, Zhou; Wang, Zhilai; Dou, Jie; Zhou, Changlin

    2016-04-01

    S-adenosyl-L-methionine (SAM), biosynthesized from methionine and ATP, exhibited diverse pharmaceutical applications. To enhance SAM accumulation in S. cerevisiae CGMCC 2842 (wild type), improvement of methionine and ATP availability through MET6 and SAM2 co-expression combined with sodium citrate feeding was investigated here. Feeding 6 g/L methionine at 12 h into medium was found to increase SAM accumulation by 38 % in wild type strain. Based on this result, MET6, encoding methionine synthase, was overexpressed, which caused a 59 % increase of SAM. To redirect intracellular methionine into SAM, MET6 and SAM2 (encoding methionine adenosyltransferase) were co-expressed to obtain the recombinant strain YGSPM in which the SAM accumulation was 2.34-fold of wild type strain. The data obtained showed that co-expression of MET6 and SAM2 improved intracellular methionine availability and redirected the methionine to SAM biosynthesis. To elevate intracellular ATP levels, 6 g/L sodium citrate, used as an auxiliary energy substrate, was fed into the batch fermentation medium, and an additional 19 % increase of SAM was observed after sodium citrate addition. Meanwhile, it was found that addition of sodium citrate improved the isocitrate dehydrogenase activity which was associated with the intracellular ATP levels. The results demonstrated that addition of sodium citrate improved intracellular ATP levels which promoted conversion of methionine into SAM. This study presented a feasible approach with considerable potential for developing highly SAM-productive strains based on improving methionine and ATP availability.

  5. Spatio-angularly multiplexed (SAM) holographic storage in photorefractive crystals

    NASA Astrophysics Data System (ADS)

    Tao, Shiquan

    In this thesis a novel multiplexing scheme for dense holographic storage in photorefractive crystals, Spatio-Angular Multiplexing (or SAM), is described in detail. In SAM Fourier transform holograms are formed in spatially overlapping regions of a crystal and are distinguished from one another by using variously angled reference beams. SAM takes advantage of both the high storage density possible using angularly multiplexed volume holograms and also the low crosstalk possible using spatially multiplexed Fourier transform holograms. Compared to pure spatial multiplexing, SAM increases the storage capacity by fully utilising the volume of the storage medium. On the other hand, SAM reduces the number of holograms overlapping any one hologram in a given volume, and so increases the diffraction efficiency achievable as compared to pure angular multiplexing. SAM offers the possibility of incorporating the recorded crystal into a content addressable memory (CAM) system for parallel access of all stored patterns. In order to obtain the maximum diffraction efficiency and signal to noise ratio, the hologram must be replayed by a readout beam incident at the correct angle of readout beam. The optimum angle may be shifted away from the angle used in recording by a ''Bragg-shift", caused (under certain conditions) by phase coupling between the two writing beams during recording. Although this Bragg shift is small, a large diffraction efficiency enhancement is obtained when the grating is read out at the optimum angle. We have calculated the Bragg shift, using a numerical calculation based on an earlier theory, and have obtained good agreement with experiment. Using the novel SAM scheme, we have succeeded in storing 756 high resolution binary patterns in an Fe:LiNbO3 crystal of volume 1cm3, with an average diffraction efficiency of 0.5%. This large database is designed for practical use in a novel associative memory system, called a high order feedback neural network (HOFNET

  6. SuMoToRI, an Ecophysiological Model to Predict Growth and Sulfur Allocation and Partitioning in Oilseed Rape (Brassica napus L.) Until the Onset of Pod Formation.

    PubMed

    Brunel-Muguet, Sophie; Mollier, Alain; Kauffmann, François; Avice, Jean-Christophe; Goudier, Damien; Sénécal, Emmanuelle; Etienne, Philippe

    2015-01-01

    Sulfur (S) nutrition in rapeseed (Brassica napus L.) is a major concern for this high S-demanding crop, especially in the context of soil S oligotrophy. Therefore, predicting plant growth, S plant allocation (between the plant's compartments) and S pool partitioning (repartition of the mobile-S vs. non-mobile-S fractions) until the onset of reproductive phase could help in the diagnosis of S deficiencies during the early stages. For this purpose, a process-based model, SuMoToRI (Sulfur Model Toward Rapeseed Improvement), was developed up to the onset of pod formation. The key features rely on (i) the determination of the S requirements used for growth (structural and metabolic functions) through critical S dilution curves and (ii) the estimation of a mobile pool of S that is regenerated by daily S uptake and remobilization from senescing leaves. This study describes the functioning of the model and presents the model's calibration and evaluation. SuMoToRI was calibrated and evaluated with independent datasets from greenhouse experiments under contrasting S supply conditions. It is run with a small number of parameters with generic values, except in the case of the radiation use efficiency, which was shown to be modulated by S supply. The model gave satisfying predictions of the dynamics of growth, S allocation between compartments and S partitioning, such as the mobile-S fraction in the leaves, which is an indicator of the remobilization potential toward growing sinks. The mechanistic features of SuMoToRI provide a process-based framework that has enabled the description of the S remobilizing process in a species characterized by senescence during the vegetative phase. We believe that this model structure could be useful for modeling S dynamics in other arable crops that have similar senescence-related characteristics. PMID:26635825

  7. Characterization of sams genes of Amoeba proteus and the endosymbiotic X-bacteria.

    PubMed

    Jeon, Taeck J; Jeon, Kwang W

    2003-01-01

    As a result of harboring obligatory bacterial endosymbionts, the xD strain of Amoeba proteus no longer produces its own S-adenosylmethionine synthetase (SAMS). When symbiont-free D amoebae are infected with symbionts (X-bacteria), the amount of amoeba SAMS decreases to a negligible level within four weeks, but about 47% of the SAMS activity, which apparently comes from another source, is still detected. Complete nucleotide sequences of sams genes of D and xD amoebae are presented and show that there are no differences between the two. Long-established xD amoebae contain an intact sams gene and thus the loss of xD amoeba's SAMS is not due to the loss of the gene itself. The open reading frame of the amoeba's sams gene has 1,281 nucleotides, encoding SAMS of 426 amino acids with a mass of 48 kDa and pI of 6.5. The amino acid sequence of amoeba SAMS is longer than the SAMS of other organisms by having an extra internal stretch of 28 amino acids. The 5'-flanking region of amoeba sams contains consensus-binding sites for several transcription factors that are related to the regulation of sams genes in E. coli and yeast. The complete nucleotide sequence of the symbiont's sams gene is also presented. The open reading frame of X-bacteria sams is 1,146 nucleotides long, encoding SAMS of 381 amino acids with a mass of 41 kDa and pI of 6.0. The X-bacteria SAMS has 45% sequence identity with that of A. proteus.

  8. Selective Plasma Deposition of Fluorocarbon Films on SAMs

    NASA Technical Reports Server (NTRS)

    Crain, Mark M., III; Walsh, Kevin M.; Cohn, Robert W.

    2006-01-01

    A dry plasma process has been demonstrated to be useful for the selective modification of self-assembled monolayers (SAMs) of alkanethiolates. These SAMs are used, during the fabrication of semiconductor electronic devices, as etch masks on gold layers that are destined to be patterned and incorporated into the devices. The selective modification involves the formation of fluorocarbon films that render the SAMs more effective in protecting the masked areas of the gold against etching by a potassium iodide (KI) solution. This modification can be utilized, not only in the fabrication of single electronic devices but also in the fabrication of integrated circuits, microelectromechanical systems, and circuit boards. In the steps that precede the dry plasma process, a silicon mold in the desired pattern is fabricated by standard photolithographic techniques. A stamp is then made by casting polydimethylsiloxane (commonly known as silicone rubber) in the mold. The stamp is coated with an alkanethiol solution, then the stamp is pressed on the gold layer of a device to be fabricated in order to deposit the alkanethiol to form an alkanethiolate SAM in the desired pattern (see figure). Next, the workpiece is exposed to a radio-frequency plasma generated from a mixture of CF4 and H2 gases. After this plasma treatment, the SAM is found to be modified, while the exposed areas of gold remain unchanged. This dry plasma process offers the potential for forming masks superior to those formed in a prior wet etching process. Among the advantages over the wet etching process are greater selectivity, fewer pin holes in the masks, and less nonuniformity of the masks. The fluorocarbon films formed in this way may also be useful as intermediate layers for subsequent fabrication steps and as dielectric layers to be incorporated into finished products.

  9. SuMoToRI, an Ecophysiological Model to Predict Growth and Sulfur Allocation and Partitioning in Oilseed Rape (Brassica napus L.) Until the Onset of Pod Formation

    PubMed Central

    Brunel-Muguet, Sophie; Mollier, Alain; Kauffmann, François; Avice, Jean-Christophe; Goudier, Damien; Sénécal, Emmanuelle; Etienne, Philippe

    2015-01-01

    Sulfur (S) nutrition in rapeseed (Brassica napus L.) is a major concern for this high S-demanding crop, especially in the context of soil S oligotrophy. Therefore, predicting plant growth, S plant allocation (between the plant’s compartments) and S pool partitioning (repartition of the mobile-S vs. non-mobile-S fractions) until the onset of reproductive phase could help in the diagnosis of S deficiencies during the early stages. For this purpose, a process-based model, SuMoToRI (Sulfur Model Toward Rapeseed Improvement), was developed up to the onset of pod formation. The key features rely on (i) the determination of the S requirements used for growth (structural and metabolic functions) through critical S dilution curves and (ii) the estimation of a mobile pool of S that is regenerated by daily S uptake and remobilization from senescing leaves. This study describes the functioning of the model and presents the model’s calibration and evaluation. SuMoToRI was calibrated and evaluated with independent datasets from greenhouse experiments under contrasting S supply conditions. It is run with a small number of parameters with generic values, except in the case of the radiation use efficiency, which was shown to be modulated by S supply. The model gave satisfying predictions of the dynamics of growth, S allocation between compartments and S partitioning, such as the mobile-S fraction in the leaves, which is an indicator of the remobilization potential toward growing sinks. The mechanistic features of SuMoToRI provide a process-based framework that has enabled the description of the S remobilizing process in a species characterized by senescence during the vegetative phase. We believe that this model structure could be useful for modeling S dynamics in other arable crops that have similar senescence-related characteristics. PMID:26635825

  10. Integrating a distributed hydrological model and SEEA-Water for improving water account and water allocation management under a climate change context.

    NASA Astrophysics Data System (ADS)

    Jauch, Eduardo; Almeida, Carina; Simionesei, Lucian; Ramos, Tiago; Neves, Ramiro

    2015-04-01

    The crescent demand and situations of water scarcity and droughts are a difficult problem to solve by water managers, with big repercussions in the entire society. The complexity of this question is increased by trans-boundary river issues and the environmental impacts of the usual adopted solutions to store water, like reservoirs. To be able to answer to the society requirements regarding water allocation in a sustainable way, the managers must have a complete and clear picture of the present situation, as well as being able to understand the changes in the water dynamics both in the short and long time period. One of the available tools for the managers is the System of Environmental-Economic Accounts for Water (SEEA-Water), a subsystem of SEEA with focus on water accounts, developed by the United Nations Statistical Division (UNSD) in collaboration with the London Group on Environmental Accounting, This system provides, between other things, with a set of tables and accounts for water and water related emissions, organizing statistical data making possible the derivation of indicators that can be used to assess the relations between economy and environment. One of the main issues with the SEEA-Water framework seems to be the requirement of large amounts of data, including field measurements of water availability in rivers/lakes/reservoirs, soil and groundwater, as also precipitation, irrigation and other water sources and uses. While this is an incentive to collecting and using data, it diminishes the usefulness of the system on countries where this data is not yet available or is incomplete, as it can lead to a poor understanding of the water availability and uses. Distributed hydrological models can be used to fill missing data required by the SEEA-Water framework. They also make it easier to assess different scenarios (usually soil use, water demand and climate changes) for a better planning of water allocation. In the context of the DURERO project (www

  11. Optimal Resource Allocation in Library Systems

    ERIC Educational Resources Information Center

    Rouse, William B.

    1975-01-01

    Queueing theory is used to model processes as either waiting or balking processes. The optimal allocation of resources to these processes is defined as that which maximizes the expected value of the decision-maker's utility function. (Author)

  12. The allocation of ecosystem net primary productivity in tropical forests

    PubMed Central

    Malhi, Yadvinder; Doughty, Christopher; Galbraith, David

    2011-01-01

    The allocation of the net primary productivity (NPP) of an ecosystem between canopy, woody tissue and fine roots is an important descriptor of the functioning of that ecosystem, and an important feature to correctly represent in terrestrial ecosystem models. Here, we collate and analyse a global dataset of NPP allocation in tropical forests, and compare this with the representation of NPP allocation in 13 terrestrial ecosystem models. On average, the data suggest an equal partitioning of allocation between all three main components (mean 34 ± 6% canopy, 39 ± 10% wood, 27 ± 11% fine roots), but there is substantial site-to-site variation in allocation to woody tissue versus allocation to fine roots. Allocation to canopy (leaves, flowers and fruit) shows much less variance. The mean allocation of the ecosystem models is close to the mean of the data, but the spread is much greater, with several models reporting allocation partitioning outside of the spread of the data. Where all main components of NPP cannot be measured, litterfall is a good predictor of overall NPP (r2 = 0.83 for linear fit forced through origin), stem growth is a moderate predictor and fine root production a poor predictor. Across sites the major component of variation of allocation is a shifting allocation between wood and fine roots, with allocation to the canopy being a relatively invariant component of total NPP. This suggests the dominant allocation trade-off is a ‘fine root versus wood’ trade-off, as opposed to the expected ‘root–shoot’ trade-off; such a trade-off has recently been posited on theoretical grounds for old-growth forest stands. We conclude by discussing the systematic biases in estimates of allocation introduced by missing NPP components, including herbivory, large leaf litter and root exudates production. These biases have a moderate effect on overall carbon allocation estimates, but are smaller than the observed range in allocation values across sites. PMID

  13. Spectral-spatial hyperspectral classification based on multi-center SAM and MRF

    NASA Astrophysics Data System (ADS)

    Tang, Bo; Liu, Zhi; Xiao, Xiaoyan; Nie, Mingyu; Chang, Jun; Jiang, Wei; Li, Xiaomei; Zheng, Chengyun

    2015-12-01

    In this paper, a novel framework for an accurate spectral-spatial classification of hyperspectral images is proposed to address nonlinear classification problems. The algorithm is based on the spectral angle mapper (SAM), which is achieved by introducing the multi-center model and Markov random fields (MRF) into a probabilistic decision framework to obtain an accurate classification. Experimental comparisons between several traditional classification methods and the proposed MSAM-MRF algorithm have demonstrated that the performance of the proposed MSAM-MRF algorithm outperforms the traditional classification algorithms.

  14. [Preliminary study on autoregulation of samR involved in development and differentiation of Streptomyces ansochromogenes].

    PubMed

    Yang, Yan-ling; Yang, Hai-hua; Tan, Hua-rong

    2005-02-01

    The previous result showed that samR plays an important role in the development progress of Streptomyces ansochromogenes. It was reported that the differentiation progress of S. ansochromogenes was accelerated by a recombinant plasmid containing an extra copy of samR gene. However, the differentiation progress of S. ansochromogenes was not further accelerated by a multicopy plasmid containing samR gene. Electrophoresis mobility shift assay (EMSA) demonstrated that SamR binds to its own promoter region specifically. All these results hint that samR is an autoregulatory gene in Streptomyces ansochromogenes. PMID:15847153

  15. SAM Technical Review Committee Final Report: Summary and Key Recommendations from the Onsite TRC Meeting Held April 22-23, 2013

    SciTech Connect

    Blair, N.; Dobos, S.; Janzou, S.; Gilman, P.; Freeman, J.; Kaffine, L.

    2013-08-01

    The System Advisor Model (SAM) is a broad and robust set of models and frameworks for analyzing both system performance and system financing. It does this across a range of technologies dominated by solar technologies including photovoltaics (PV) and concentrated solar power (CSP). The U.S. Department of Energy (DOE) Solar Energy Technology Program requested the SAM development team to review the photovoltaic performance modeling with the development community and specifically, with the independent engineering community. The report summarizes the major effort for this technical review committee (TRC).

  16. Leptin receptor activation increases Sam68 tyrosine phosphorylation and expression in human trophoblastic cells.

    PubMed

    Sánchez-Jiménez, Flora; Pérez-Pérez, Antonio; González-Yanes, Carmen; Najib, Souad; Varone, Cecilia L; Sánchez-Margalet, Víctor

    2011-01-30

    Leptin is produced in placenta where it has been found to be an important autocrine signal for trophoblastic growth during pregnancy, promoting antiapoptotic and trophic effects. Leptin receptor is present in trophoblastic cells and leptin may fully activate signaling. We have previously implicated the RNA-binding protein Sam68 in leptin signal transduction in immune cells. In the present work, we have studied the possible role of Sam68 in leptin receptor signaling in trophoblastic cells (JEG-3 cells). Leptin dose-dependently stimulated Sam68 phosphorylation in JEG-3 cells, as assessed by immunoprecipitation and immunoblot with anti-phosphotyrosine antibodies. As previously observed in other systems, tyrosine phosphorylation of Sam68 in response to leptin inhibits its RNA binding capacity. Besides, leptin stimulation dose-dependently increases Sam68 expression in JEG-3 cells, as assessed by quantitative PCR. Consistently, the amount of Sam68 protein is increased after 24h of leptin stimulation of trophoblastic cells. In order to study the possible role of Sam68 on leptin receptor synthesis, we employed antisense strategy to knockdown the expression of Sam68. We have found that a decrease in Sam68 expression leads to a decrease in leptin receptor amount in JEG-3 cells, as assessed both by quantitative PCR and immunoblot. These results strongly suggest the participation of Sam68 in leptin receptor signaling in human trophoblastic cells, and therefore, Sam68 may mediate some of the leptin effects in placenta. PMID:21035519

  17. First use of SAM onboard calibration gas cell

    NASA Astrophysics Data System (ADS)

    Malespin, C.; Trainer, M. G.; Manning, H. L.; Franz, H. B.; Conrad, P. G.; Raaen, E.; Webster, C. R.; Flesch, G.; Eigenbrode, J. L.; Wong, M. H.; Mahaffy, P. R.

    2015-12-01

    The Sample Analysis at Mars (SAM) instrument (Mahaffy et al 2012) suite on Curiosity completed its first measurement of the onboard calibration gas cell on MSL Mission Sol 1042. The cell consists of a gas mixture of four primary gases, along with trace fluorinated hydrocarbon high mass calibrants. The mix is comprised of approximately 25% CO2, N2, Xe and Ar, where the 129Xe has been given a three times enrichment relative to terrestrial xenon in order to distinguish it isotopically from Martian atmospheric Xe. Analysis of the calibration cell is intended to identify changes in instrument performance between pre-launch calibrations and operations on Mars, for any of the three main subsystems in SAM: the Quadrupole Mass Spectrometer (QMS), Tunable Laser Spectrometer (TLS), and Gas Chromatograph (GC). Here we present the experimental approach, results, and implications for instrument performance after almost three years of measurements on Mars.

  18. The water quality of Sam Rayburn Reservoir, eastern Texas

    USGS Publications Warehouse

    Rawson, Jack; Lansford, Myra W.

    1971-01-01

    Results of periodic surveys indicate that dissolved-oxygen concentrations at three sites in the 19-mile reach of the Angelina River downstream from Sam Rayburn Dam were low in late summer and early fall after periods of summer stagnation in the reservoir. Moreover, the amount of reaeration that occurred in the reach was insignificant. During periods when the dissolved-oxygen deficiency was large, the concentrations of iron and manganese at each of the three sites increased greatly.

  19. GLAO4ELT: trade study and SAM experience

    NASA Astrophysics Data System (ADS)

    Tokovinin, A.

    2011-09-01

    It is expected that a large fraction of wave-front distortions at ELTs will be anisoplanatic, being produced jointly by near-ground and dome turbulence, wind buffeting, flexures, and vibrations. We compare various strategies for sensing this "ground" component using (i) several sodium LGSs, (ii) one or several Rayleigh LGSs and (ii) NGSs in a wide field. The experience gained so far with the RLGS GLAO system SAM at 4-m telescope will be presented and discussed.

  20. SAMS Acceleration Measurements on Mir (NASA Increment 4)

    NASA Technical Reports Server (NTRS)

    DeLombard, Richard

    1998-01-01

    During NASA Increment 4 (January to May 1997), about 5 gigabytes of acceleration data were collected by the Space Acceleration Measurements System (SAMS) onboard the Russian Space Station, Mir. The data were recorded on 28 optical disks which were returned to Earth on STS-84. During this increment, SAMS data were collected in the Priroda module to support the Mir Structural Dynamics Experiment (MiSDE), the Binary Colloidal Alloy Tests (BCAT), Angular Liquid Bridge (ALB), Candle Flames in Microgravity (CFM), Diffusion Controlled Apparatus Module (DCAM), Enhanced Dynamic Load Sensors (EDLS), Forced Flow Flame Spreading Test (FFFr), Liquid Metal Diffusion (LMD), Protein Crystal Growth in Dewar (PCG/Dewar), Queen's University Experiments in Liquid Diffusion (QUELD), and Technical Evaluation of MIM (TEM). This report points out some of the salient features of the microgravity environment to which these experiments were exposed. Also documented are mission events of interest such as the docked phase of STS-84 operations, a Progress engine bum, Soyuz vehicle docking and undocking, and Progress vehicle docking. This report presents an overview of the SAMS acceleration measurements recorded by 10 Hz and 100 Hz sensor heads. The analyses included herein complement those presented in previous summary reports prepared by the Principal Investigator Microgravity Services (PIMS) group.

  1. Mechanistic Enzymology of the Radical SAM Enzyme DesII

    PubMed Central

    2016-01-01

    DesII is a member of the radical SAM family of enzymes that catalyzes radical-mediated transformations of TDP-4-amino-4,6-didexoy-D-glucose as well as other sugar nucleotide diphosphates. Like nearly all radical SAM enzymes, the reactions begin with the reductive homolysis of SAM to produce a 5′-deoxyadenosyl radical which is followed by regiospecific hydrogen atom abstraction from the substrate. What happens next, however, depends on the nature of the substrate radical so produced. In the case of the biosynthetically relevant substrate, a radical-mediated deamination ensues; however, when this amino group is replaced with a hydroxyl, one instead observes dehydrogenation. The factors that govern the fate of the initially generated substrate radical as well as the mechanistic details underlying these transformations have been a key focus of research into the chemistry of DesII. This review will discuss recent discoveries pertaining to the enzymology of DesII, how it may relate to understanding other radical-mediated lyases and dehydrogenases and the working hypotheses currently being investigated regarding the mechanism of DesII catalysis.

  2. Deposition of DNA rafts on cationic SAMs on silicon [100].

    PubMed

    Sarveswaran, Koshala; Hu, Wenchuang; Huber, Paul W; Bernstein, Gary H; Lieberman, Marya

    2006-12-19

    We demonstrate a guided self-assembly approach to the fabrication of DNA nanostructures on silicon substrates. DNA oligonucleotides self-assemble into "rafts" 8 x 37 x 2 nm in size. The rafts bind to cationic SAMs on silicon wafers. Electron-beam lithography of a thin poly(methyl methacrylate) (PMMA) resist layer was used to define trenches, and (3-aminopropyl)triethoxysilane (APTES), a cationic SAM precursor, was deposited from aqueous solution onto the exposed silicon dioxide at the trench bottoms. The remaining PMMA can be cleanly stripped off with dichloromethane, leaving APTES layers 0.7-1.2 nm in thickness and 110 nm in width. DNA rafts bind selectively to the resulting APTES stripes. The coverage of DNA rafts on adjacent areas of silicon dioxide is 20 times lower than on the APTES stripes. The topographic features of the rafts, measured by AFM, are identical to those of rafts deposited on wide-area SAMs. Binding to the APTES stripes appears to be very strong as indicated by "jamming" of the rafts at a saturation coverage of 42% and the stability to repeated AFM scanning in air.

  3. CE-SAM: a conversational interface for ISR mission support

    NASA Astrophysics Data System (ADS)

    Pizzocaro, Diego; Parizas, Christos; Preece, Alun; Braines, Dave; Mott, David; Bakdash, Jonathan Z.

    2013-05-01

    There is considerable interest in natural language conversational interfaces. These allow for complex user interactions with systems, such as fulfilling information requirements in dynamic environments, without requiring extensive training or a technical background (e.g. in formal query languages or schemas). To leverage the advantages of conversational interactions we propose CE-SAM (Controlled English Sensor Assignment to Missions), a system that guides users through refining and satisfying their information needs in the context of Intelligence, Surveillance, and Reconnaissance (ISR) operations. The rapidly-increasing availability of sensing assets and other information sources poses substantial challenges to effective ISR resource management. In a coalition context, the problem is even more complex, because assets may be "owned" by different partners. We show how CE-SAM allows a user to refine and relate their ISR information needs to pre-existing concepts in an ISR knowledge base, via conversational interaction implemented on a tablet device. The knowledge base is represented using Controlled English (CE) - a form of controlled natural language that is both human-readable and machine processable (i.e. can be used to implement automated reasoning). Users interact with the CE-SAM conversational interface using natural language, which the system converts to CE for feeding-back to the user for confirmation (e.g. to reduce misunderstanding). We show that this process not only allows users to access the assets that can support their mission needs, but also assists them in extending the CE knowledge base with new concepts.

  4. The Unobtrusive Memory Allocator

    2003-03-31

    This library implements a memory allocator/manager which ask its host program or library for memory refions to manage rather than requesting them from the operating system. This allocator supports multiple distinct heaps within a single executable, each of which may grow either upward or downward in memory. The GNU mmalloc library has been modified in such a way that its allocation algorithms have been preserved, but the manner in which it obtains regions to managemore » has been changed to request memory from the host program or library. Additional modifications allow the allocator to manage each heap as either upward or downward-growing. By allowing the hosting program or library to determine what memory is managed, this package allows a greater degree of control than other memory allocation/management libraries. Additional distinguishing features include the ability to manage multiple distinct heaps with in a single executable, each of which may grow either upward or downward in memory. The most common use of this library is in conjunction with the Berkeley Unified Parallel C (UPC) Runtime Library. This package is a modified version of the LGPL-licensed "mmalloc" allocator from release 5.2 of the "gdb" debugger's source code.« less

  5. In situ analysis of martian regolith with the SAM experiment during the first mars year of the MSL mission: Identification of organic molecules by gas chromatography from laboratory measurements

    NASA Astrophysics Data System (ADS)

    Millan, M.; Szopa, C.; Buch, A.; Coll, P.; Glavin, D. P.; Freissinet, C.; Navarro-Gonzalez, R.; François, P.; Coscia, D.; Bonnet, J. Y.; Teinturier, S.; Cabane, M.; Mahaffy, P. R.

    2016-09-01

    The Sample Analysis at Mars (SAM) instrument onboard the Curiosity rover, is specifically designed for in situ molecular and isotopic analyses of martian surface materials and atmosphere. It contributes to the Mars Science Laboratory (MSL) missions primary scientific goal to characterize the potential past, present or future habitability of Mars. In all of the analyses of solid samples delivered to SAM so far, chlorinated organic compounds have been detected above instrument background levels and identified by gas chromatography coupled to mass spectrometry (GC-MS) (Freissinet et al., 2015; Glavin et al., 2013). While some of these may originate from reactions between oxychlorines and terrestrial organic carbon present in the instrument background (Glavin et al., 2013), others have been demonstrated to originate from indigenous organic carbon present in samples (Freissinet et al., 2015). We present here laboratory calibrations that focused on the analyses performed with the MXT-CLP GC column (SAM GC-5 channel) used for nearly all of the GC-MS analyses of the martian soil samples carried out with SAM to date. Complementary to the mass spectrometric data, gas chromatography allows us to separate and identify the species analyzable in a nominal SAM-GC run time of about 21 min. To characterize the analytical capabilities of this channel within the SAM Flight Model (FM) operating conditions on Mars, and their implications on the detection of organic matter, it is required to perform laboratory experimental tests and calibrations on spare model components. This work assesses the SAM flight GC-5 column efficiency, confirms the identification of the molecules based on their retention time, and enables a better understanding of the behavior of the SAM injection trap (IT) and its release of organic molecules. This work will enable further optimization of the SAM-GC runs for additional samples to be analyzed during the MSL mission.

  6. The SAMS: Smartphone Addiction Management System and verification.

    PubMed

    Lee, Heyoung; Ahn, Heejune; Choi, Samwook; Choi, Wanbok

    2014-01-01

    While the popularity of smartphones has given enormous convenience to our lives, their pathological use has created a new mental health concern among the community. Hence, intensive research is being conducted on the etiology and treatment of the condition. However, the traditional clinical approach based surveys and interviews has serious limitations: health professionals cannot perform continual assessment and intervention for the affected group and the subjectivity of assessment is questionable. To cope with these limitations, a comprehensive ICT (Information and Communications Technology) system called SAMS (Smartphone Addiction Management System) is developed for objective assessment and intervention. The SAMS system consists of an Android smartphone application and a web application server. The SAMS client monitors the user's application usage together with GPS location and Internet access location, and transmits the data to the SAMS server. The SAMS server stores the usage data and performs key statistical data analysis and usage intervention according to the clinicians' decision. To verify the reliability and efficacy of the developed system, a comparison study with survey-based screening with the K-SAS (Korean Smartphone Addiction Scale) as well as self-field trials is performed. The comparison study is done using usage data from 14 users who are 19 to 50 year old adults that left at least 1 week usage logs and completed the survey questionnaires. The field trial fully verified the accuracy of the time, location, and Internet access information in the usage measurement and the reliability of the system operation over more than 2 weeks. The comparison study showed that daily use count has a strong correlation with K-SAS scores, whereas daily use times do not strongly correlate for potentially addicted users. The correlation coefficients of count and times with total K-SAS score are CC = 0.62 and CC =0.07, respectively, and the t-test analysis for the

  7. [Senescence-accelerated mouse (SAM): with special reference to age-associated pathologies and their modulation].

    PubMed

    Takeda, T

    1996-07-01

    The senescence-accelerated mouse (SAM) has been under development by our research team at Kyoto University since 1970 through selective inbreeding of the AKR/J strain of mice donated by the Jackson Laboratory in 1968, based on the data of the grading score of senescence, life span, and pathologic phenotypes. At present, there are 12 lines of SAM; the 9 senescence-prone inbred strains (SAMP) include SAMP1, SAMP2, SAMP3, SAMP6, SAMP7, SAMP8, SAMP9, SAMP10 and SAMP11, and the 3 senescence-resistant inbred strains (SAMR) SAMR1, SANR4 and SAMR5. Data from survival curves, the Gompertzian function and the grading score of senescence, together with growth patterns of body weight of these SAMP and SAMR mice revealed that the characteristic feature of aging common to all SAMP mice is "accelerated senescence": early onset and irreversible advance of senescence manifested by several signs and gross lesions such as the loss of normal behavior, various skin lesions, increased lordokyphosis, etc., after a period of normal development. Routine postmortem examinations and the pathobiological features revealed by systematically designed studies have shown several pathologic phenotypes, which are often characteristic enough to differentiate among the various SAM strains: senile amyloidosis in SAMP1, -P2, -P7, -P9, -P10 and -P11, secondary amyloidosis in SAMP2 and -P6, contracted kidney in SAMP1, -P2, -P10, -P11, immunoblastic lymphoma in SAMR1 and -R4, histiocytic sarcoma in SAMR1 and -R4, ovarian cysts in SAMR1, impaired immune response in SAMP1, -P2 and -P8, hyperinflation of the lungs in SAMP1, hearing impairment in SAMP1, degenerative temporomandibular joint disease in SAMP3, senile osteoporosis in SAMP6, deficits in learning and memory in SAMP8 and -P10, emotional disorders in SAMP8 and -P10, cataracts in SAMP9, and brain atrophy in SAMP10. These are all age-associated pathologies, the incidence and severity of which increase with advancing age. The SAM model in which these

  8. Unliganded EphA3 dimerization promoted by the SAM domain

    NASA Astrophysics Data System (ADS)

    Hristova, Kalina; Singh, Deo; King, Christopher; Ahmed, Fozia; Pasquale, Elena

    The EphA3 receptor tyrosine kinase regulates morphogenesis during development, and is overexpressed and mutated in a variety of cancers. EphA3 activation is believed to follow a ``seeding mechanism'' model, in which ligand binding to the monomeric receptor acts as a trigger for signal-productive receptor clustering. We use a novel approach to study EphA3 lateral interactions on the surface of live cells, and we demonstrate that EphA3 forms dimers in the absence of ligand binding. We further show that these dimers are stabilized by interactions involving the EphA3 SAM domain. The discovery of unliganded EphA3 dimers challenges the current understanding of the chain of EphA3 activation events, and suggests that EphA3 may follow the ``pre-formed dimer'' model of activation known to be relevant for other receptor tyrosine kinases. This work also establishes a new role for the SAM domain in promoting Eph receptor lateral interactions and signaling on the cell surface.

  9. Unliganded EphA3 dimerization promoted by the SAM domain

    PubMed Central

    Singh, Deo R.; Cao, QingQing; King, Christopher; Salotto, Matt; Ahmed, Fozia; Zhou, Xiang Yang; Pasquale, Elena B.; Hristova, Kalina

    2015-01-01

    The erythropoietin-producing hepatocellular carcinoma A3 (EphA3) receptor tyrosine kinase (RTK) regulates morphogenesis during development and is overexpressed and mutated in a variety of cancers. EphA3 activation is believed to follow a ‘seeding mechanism’ model, in which ligand binding to the monomeric receptor acts as a trigger for signal-productive receptor clustering. We study EphA3 lateral interactions on the surface of live cells and we demonstrate that EphA3 forms dimers in the absence of ligand binding. We further show that these dimers are stabilized by interactions involving the EphA3 sterile α-motif (SAM) domain. The discovery of unliganded EphA3 dimers challenges the current understanding of the chain of EphA3 activation events and suggests that EphA3 may follow the ‘pre-formed dimer’ model of activation known to be relevant for other receptor tyrosine kinases. The present work also establishes a new role for the SAM domain in promoting Eph receptor lateral interactions and signalling on the cell surface. PMID:26232493

  10. Carbon allocation to ectomycorrhizal fungi correlates with belowground allocation in culture studies.

    PubMed

    Hobbie, Erik A

    2006-03-01

    Ectomycorrhizal fungi form symbioses with most temperate and boreal tree species, but difficulties in measuring carbon allocation to these symbionts have prevented the assessment of their importance in forest ecosystems. Here, I surveyed allocation patterns in 14 culture studies and five field studies of ectomycorrhizal plants. In culture studies, allocation to ectomycorrhizal fungi (NPPf) was linearly related to total belowground net primary production (NPPb) by the equation NPPf = 41.5% x NPPb - 11.3% (r2 = 0.55, P < 0.001) and ranged from 1% to 21% of total net primary production. As a percentage of NPP, allocation to ectomycorrhizal fungi was highest at lowest plant growth rates and lowest nutrient availabilities. Because total belowground allocation can be estimated using carbon balance techniques, these relationships should allow ecologists to incorporate mycorrhizal fungi into existing ecosystem models. In field studies, allocation to ectomycorrhizal fungi ranged from 0% to 22% of total allocation, but wide differences in measurement techniques made intercomparisons difficult. Techniques such as fungal in-growth cores, root branching-order studies, and isotopic analyses could refine our estimates of turnover rates of fine roots, mycorrhizae, and extraradical hyphae. Together with ecosystem modeling, such techniques could soon provide good estimates of the relative importance of root vs. fungal allocation in belowground carbon budgets.

  11. Systematic biochemical characterization of the SAM domains in Eph receptor family from Mus Musculus.

    PubMed

    Wang, Yue; Li, Qingxia; Zheng, Yunhua; Li, Gang; Liu, Wei

    2016-05-13

    The Eph receptor family is the largest subfamily of receptor tyrosine kinases and well-known for their pivotal roles in axon guidance, synaptogenesis, artery/venous differentiation and tumorigenesis, etc. Activation of the Eph receptor needs multimerization of the receptors. The intracellular C-terminal SAM domain of Eph receptor was reported to mediate self-association of Eph receptors via the homo SAM-SAM interaction. In this study, we systematically expressed and purified the SAM domain proteins of all fourteen Eph receptors of Mus musculus in Escherichia coli. The FPLC (fast protein liquid chromatography) results showed the recombinant SAM domains were highly homogeneous. Using CD (circular dichroism) spectrometry, we found that the secondary structure of all the SAM domains was typically alpha helical folded and remarkably similar. The thermo-stability tests showed that they were quite stable in solution. SEC-MALS (size exclusion chromatography coupled with multiple angle light scattering) results illustrated 200 μM Eph SAM domains behaved as good monomers in the size-exclusion chromatography. More importantly, DLS (dynamic light scattering) results revealed the overwhelming majority of SAM domains was not multimerized in solution either at 200 μM or 2000 μM protein concentration, which indicating the SAM domain alone was not sufficient to mediate the polymerization of Eph receptor. In summary, our studies provided the systematic biochemical characterizations of the Eph receptor SAM domains and implied their roles in Eph receptor mediated signaling pathways. PMID:27086853

  12. A Model of the Regulation of Nitrogenase Electron Allocation in Legume Nodules (II. Comparison of Empirical and Theoretical Studies in Soybean).

    PubMed Central

    Moloney, A. H.; Guy, R. D.; Layzell, D. B.

    1994-01-01

    In N2-fixing legumes, the proportion of total electron flow through nitrogenase (total nitrogenase activity, TNA) that is used for N2 fixation is called the electron allocation coefficient (EAC). Previous studies have proposed that EAC is regulated by the competitive inhibition of H2 on N2 fixation and that the degree of H2 inhibition can be affected by a nodule's permeability to gas diffusion. To test this hypothesis, EAC was measured in soybean (Glycine max L. Merr.) nodules exposed to various partial pressures of H2 and N2, with or without changes in TNA or nodule permeability to gas diffusion, and the results were compared with the predictions of a mathematical model that combined equations for gas diffusion and competitive inhibition of N2 fixation (A. Moloney and D.B. Layzell [1993] Plant Physiol 103: 421-428). The empirical data clearly showed that decreases in EAC were associated with increases in external pH2, decreases in external pN2, and decreases in nodule permeability to O2 diffusion. The model predicted similar trends in EAC, and the small deviations that occurred between measured and predicted values could be readily accounted for by altering one or more of the following model assumptions: K1(H2) of nitrogenase (range from 2-4% H2), Km(N2) of nitrogenase (range from 4-5% N2), the allocation of less than 100% of whole-nodule respiration to tissues within the diffusion barrier, and the presence of a diffusion pathway that is open pore versus closed pore. The differences in the open-pore and closed-pore versions of the model suggest that it may be possible to use EAC measurements as a tool for the study of legume nodule diffusion barrier structure and function. The ability of the model to predict EAC provided strong support for the hypothesis that H2 inhibition of N2 fixation plays a major role in the in vivo control of EAC and that the presence of a variable barrier to gas diffusion affects the H2 and N2 concentration in the infected cell and

  13. A sub-canopy structure for simulating oil palm in the Community Land Model (CLM-Palm): phenology, allocation and yield

    NASA Astrophysics Data System (ADS)

    Fan, Y.; Roupsard, O.; Bernoux, M.; Le Maire, G.; Panferov, O.; Kotowska, M. M.; Knohl, A.

    2015-11-01

    In order to quantify the effects of forests to oil palm conversion occurring in the tropics on land-atmosphere carbon, water and energy fluxes, we develop a new perennial crop sub-model CLM-Palm for simulating a palm plant functional type (PFT) within the framework of the Community Land Model (CLM4.5). CLM-Palm is tested here on oil palm only but is meant of generic interest for other palm crops (e.g., coconut). The oil palm has monopodial morphology and sequential phenology of around 40 stacked phytomers, each carrying a large leaf and a fruit bunch, forming a multilayer canopy. A sub-canopy phenological and physiological parameterization is thus introduced so that each phytomer has its own prognostic leaf growth and fruit yield capacity but with shared stem and root components. Phenology and carbon and nitrogen allocation operate on the different phytomers in parallel but at unsynchronized steps, separated by a thermal period. An important phenological phase is identified for the oil palm - the storage growth period of bud and "spear" leaves which are photosynthetically inactive before expansion. Agricultural practices such as transplanting, fertilization and leaf pruning are represented. Parameters introduced for the oil palm were calibrated and validated with field measurements of leaf area index (LAI), yield and net primary production (NPP) from Sumatra, Indonesia. In calibration with a mature oil palm plantation, the cumulative yields from 2005 to 2014 matched notably well between simulation and observation (mean percentage error = 3 %). Simulated inter-annual dynamics of PFT-level and phytomer-level LAI were both within the range of field measurements. Validation from eight independent oil palm sites shows the ability of the model to adequately predict the average leaf growth and fruit yield across sites and sufficiently represent the significant nitrogen- and age-related site-to-site variability in NPP and yield. Results also indicate that seasonal dynamics

  14. Shear-Induced Detachment of Polystyrene Beads from SAM-Coated Surfaces.

    PubMed

    Cho, Kwun Lun; Rosenhahn, Axel; Thelen, Richard; Grunze, Michael; Lobban, Matthew; Karahka, Markus Leopold; Kreuzer, H Jürgen

    2015-10-13

    In this work we experimentally and theoretically analyze the detachment of microscopic polystyrene beads from different self-assembled monolayer (SAM) surfaces in a shear flow in order to develop a mechanistic model for the removal of cells from surfaces. The detachment of the beads from the surface is treated as a thermally activated process applying an Arrhenius Ansatz to determine the activation barrier and attempt frequency of the rate determing step in bead removal. The statistical analysis of the experimental shear detachment data obtained in phosphate-buffered saline buffer results in an activation energy around 20 kJ/mol, which is orders of magnitude lower than the adhesion energy measured by atomic force microscopy (AFM). The same order of magnitude for the adhesion energy measured by AFM is derived from ab initio calculations of the van der Waals interaction energy between the polystyrene beads and the SAM-covered gold surface. We conclude that the rate determing step for detachment of the beads is the initiation of rolling on the surface (overcoming static friction) and not physical detachment, i.e., lifting the particle off the surface. PMID:26401759

  15. Shear-Induced Detachment of Polystyrene Beads from SAM-Coated Surfaces.

    PubMed

    Cho, Kwun Lun; Rosenhahn, Axel; Thelen, Richard; Grunze, Michael; Lobban, Matthew; Karahka, Markus Leopold; Kreuzer, H Jürgen

    2015-10-13

    In this work we experimentally and theoretically analyze the detachment of microscopic polystyrene beads from different self-assembled monolayer (SAM) surfaces in a shear flow in order to develop a mechanistic model for the removal of cells from surfaces. The detachment of the beads from the surface is treated as a thermally activated process applying an Arrhenius Ansatz to determine the activation barrier and attempt frequency of the rate determing step in bead removal. The statistical analysis of the experimental shear detachment data obtained in phosphate-buffered saline buffer results in an activation energy around 20 kJ/mol, which is orders of magnitude lower than the adhesion energy measured by atomic force microscopy (AFM). The same order of magnitude for the adhesion energy measured by AFM is derived from ab initio calculations of the van der Waals interaction energy between the polystyrene beads and the SAM-covered gold surface. We conclude that the rate determing step for detachment of the beads is the initiation of rolling on the surface (overcoming static friction) and not physical detachment, i.e., lifting the particle off the surface.

  16. Measuring the conformational space of square four-helical bundles with the program samCC.

    PubMed

    Dunin-Horkawicz, Stanislaw; Lupas, Andrei N

    2010-05-01

    Four-helical bundles are the most abundant topological motif among helical folds. Their constituent helices show crossing angles that mainly cluster around +20 degrees (aligned) or -50 degrees (orthogonal). Bundles with all helices aligned are called 'square' and comprise four-helical coiled coils as their structurally most regular form. Since coiled coils can be described fully by parametric equations, they can serve as a reference point for quantifying the conformational space of all square bundles. To this end we have developed a program, samCC, which measures the deviation of a given bundle from an idealized coiled coil and decomposes this into axial rotation and axial, radial, and angular shifts. We present examples of analyses performed with the program and focus in particular on the axial rotation states of helices in coiled coils, in order to gain further insight into a proposed mechanism for transmembrane signal transduction, which involves a 26 degrees axial rotation of helices between a canonical coiled coil and a variant called the Alacoil. We find that, unlike expected from the mechanistic model, coiled coils show a continuum of axial rotation states, suggesting that the Alacoil does not represent a single, defined state. We also find that one of the originally proposed Alacoil proteins, Rop, in fact has canonical packing. SamCC is freely available as a web service athttp://toolkit.tuebingen.mpg.de/samcc.

  17. Benchmark Simulations of the Thermal-Hydraulic Responses during EBR-II Inherent Safety Tests using SAM

    SciTech Connect

    Hu, Rui; Sumner, Tyler S.

    2016-01-01

    An advanced system analysis tool SAM is being developed for fast-running, improved-fidelity, and wholeplant transient analyses at Argonne National Laboratory under DOE-NE’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. As an important part of code development, companion validation activities are being conducted to ensure the performance and validity of the SAM code. This paper presents the benchmark simulations of two EBR-II tests, SHRT-45R and BOP- 302R, whose data are available through the support of DOE-NE’s Advanced Reactor Technology (ART) program. The code predictions of major primary coolant system parameter are compared with the test results. Additionally, the SAS4A/SASSYS-1 code simulation results are also included for a code-to-code comparison.

  18. Detection of Nitric Oxide by the Sample Analysis at Mars (SAM) Instrument Implications for the Presence of Nitrates

    NASA Technical Reports Server (NTRS)

    Navarro-Gonzalez, R.; Stern, J.; Freissinet, C.; Franz, H. B.; Eigenbrode, J. L..; McKay, C. P.; Coll, P.; Sutter, B.; Archer, D.; McAdam, A.; Cabane, M.; Ming, D. W.; Glavin, D.; Leshin, L.; Wong, M.; Atreya, S.; Wray, J. J.; Steele, A.; Buch, A.; Prats, B. D.; Szopa, C.; Coscia, D.; Teinturier, S.; Conrad, P.; Owen, T. C.; Mahaffy, P.; Grotzinger, J. P.

    2014-01-01

    One of the main goals of the Mars Science Laboratory is to determine whether the planet ever had environmental conditions able to support microbial life. Nitrogen is a fundamental element for life, and is present in structural (e.g., proteins), catalytic (e.g., enzymes and ribozymes), energy transfer (e.g., ATP) and information storage (RNA and DNA) biomolecules. Planetary models suggest that molecular nitrogen was abundant in the early Martian atmosphere, but was rapidly lost to space by photochemistry, sputtering impact erosion, and oxidized and deposited to the surface as nitrate. Nitrates are a fundamental source for nitrogen to terrestrial microorganisms. Therefore, the detection of nitrates in soils and rocks is important to assess the habitability of a Martian environment. SAM is capable of detecting nitrates by their thermal decomposition into nitric oxide, NO. Here we analyze the release of NO from soils and rocks examined by the SAM instrument at Gale crater, and discuss its origin.

  19. Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.

    PubMed

    Fenwick, Michael K; Mehta, Angad P; Zhang, Yang; Abdelwahed, Sameh H; Begley, Tadhg P; Ealick, Steven E

    2015-03-27

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.

  20. Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase

    SciTech Connect

    Fenwick, Michael K.; Mehta, Angad P.; Zhang, Yang; Abdelwahed, Sameh H.; Begley, Tadhg P.; Ealick, Steven E.

    2015-03-27

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.

  1. Localization of event-related activity by SAM(erf).

    PubMed

    Robinson, S E

    2004-01-01

    Synthetic aperture magnetometry (SAM) has been used to image source power or source signal-to-noise ratio from MEG. However, the locations of maximal event-related oscillatory activity (or changes from resting state) do not necessarily coincide with those sites that are phase-locked to external events (i.e., localized by dipole fit to the averaged evoked response). Since an estimate of the source time-series may also be obtained by applying the beamformer coefficients to the MEG signal, one can image event-related activity by mapping some function reflecting the reliability of the averaged source waveform at each location. We have devised a new analysis method, SAM(erf), for obtaining a functional image of event-related brain activity and revealing the corresponding waveforms for activated sites. The mapping function used is the ratio of RMS amplitude of the averaged source waveform to that of the +/- average waveform, for a selected time window. This function is computed at each coordinate on a three-dimensional grid in the head. In addition to the SAM(erf) functional image, the averaged source waveforms for each local maximum in the image can be computed and displayed. This procedure can reveal multiple locations and waveforms at sites in the brain engaged in event-related activities. When this method is applied to evoked response studies, phase-locked activity can sometimes be found in areas distant from primary sensory cortex. Given the sensitivity of this functional imaging method to areas outside primary sensory cortex, it has the potential for detecting subtle changes in brain activity in health and disease. PMID:16012649

  2. Latent IBP Compound Dirichlet Allocation.

    PubMed

    Archambeau, Cedric; Lakshminarayanan, Balaji; Bouchard, Guillaume

    2015-02-01

    We introduce the four-parameter IBP compound Dirichlet process (ICDP), a stochastic process that generates sparse non-negative vectors with potentially an unbounded number of entries. If we repeatedly sample from the ICDP we can generate sparse matrices with an infinite number of columns and power-law characteristics. We apply the four-parameter ICDP to sparse nonparametric topic modelling to account for the very large number of topics present in large text corpora and the power-law distribution of the vocabulary of natural languages. The model, which we call latent IBP compound Dirichlet allocation (LIDA), allows for power-law distributions, both, in the number of topics summarising the documents and in the number of words defining each topic. It can be interpreted as a sparse variant of the hierarchical Pitman-Yor process when applied to topic modelling. We derive an efficient and simple collapsed Gibbs sampler closely related to the collapsed Gibbs sampler of latent Dirichlet allocation (LDA), making the model applicable in a wide range of domains. Our nonparametric Bayesian topic model compares favourably to the widely used hierarchical Dirichlet process and its heavy tailed version, the hierarchical Pitman-Yor process, on benchmark corpora. Experiments demonstrate that accounting for the power-distribution of real data is beneficial and that sparsity provides more interpretable results. PMID:26353244

  3. Paramagnetic Intermediates Generated by Radical S-Adenosylmethionine (SAM) Enzymes

    PubMed Central

    2015-01-01

    Conspectus A [4Fe–4S]+ cluster reduces a bound S-adenosylmethionine (SAM) molecule, cleaving it into methionine and a 5′-deoxyadenosyl radical (5′-dA•). This step initiates the varied chemistry catalyzed by each of the so-called radical SAM enzymes. The strongly oxidizing 5′-dA• is quenched by abstracting a H-atom from a target species. In some cases, this species is an exogenous molecule of substrate, for example, l-tyrosine in the [FeFe] hydrogenase maturase, HydG. In other cases, the target is a proteinaceous residue as in all the glycyl radical forming enzymes. The generation of this initial radical species and the subsequent chemistry involving downstream radical intermediates is meticulously controlled by the enzyme so as to prevent unwanted reactions. But the manner in which this control is exerted is unknown. Electron paramagnetic resonance (EPR) spectroscopy has proven to be a valuable tool used to gain insight into these mechanisms. In this Account, we summarize efforts to trap such radical intermediates in radical SAM enzymes and highlight four examples in which EPR spectroscopic results have shed significant light on the corresponding mechanism. For lysine 2,3-aminomutase, nearly each possible intermediate, from an analogue of the initial 5′-dA• to the product radical l-β-lysine, has been explored. A paramagnetic intermediate observed in biotin synthase is shown to involve an auxiliary [FeS] cluster whose bridging sulfide is a co-substrate for the final step in the biosynthesis of vitamin B7. In HydG, the l-tyrosine substrate is converted in unprecedented fashion to a 4-oxidobenzyl radical on the way to generating CO and CN– ligands for the [FeFe] cluster of hydrogenase. And finally, EPR has confirmed a mechanistic proposal for the antibiotic resistance protein Cfr, which methylates the unactivated sp2-hybridized C8-carbon of an adenosine base of 23S ribosomal RNA. These four systems provide just a brief survey of the ever-growing set

  4. Comparative studies of aerosol extinction measurements made by the SAM II and SAGE II satellite experiments

    NASA Technical Reports Server (NTRS)

    Yue, Glenn K.; Mccormick, M. P.; Chu, W. P.; Wang, P.; Osborn, M. T.

    1989-01-01

    Results from the Stratospheric Aerosol Measurement (SAM) II and Stratospheric Aerosol and Gas Experiment (SAGE) II are compared for measurement locations which are coincident in time and space. At 1.0 micron, the SAM II and SAGE II aerosol extinction profiles are similar within their measurement errors. In addition, sunrise and sunset aerosol extinction data at four different wavelengths are compared for occasions when the SAGE II and SAM II measurements are nearly coincident in space and about 12 hours apart.

  5. Regulation of gene expression by the RNA-binding protein Sam68 in cancer.

    PubMed

    Rajan, Prabhakar; Gaughan, Luke; Dalgliesh, Caroline; El-Sherif, Amira; Robson, Craig N; Leung, Hing Y; Elliott, David J

    2008-06-01

    Sam68 (Src-associated in mitosis 68 kDa) is the prototypical member of the STAR (signal transducer and activator of RNA) family of RNA-binding proteins. Sam68 is implicated in a number of cellular processes including signal transduction, transcription, RNA metabolism, cell cycle regulation and apoptosis. In the present review, we summarize the functions of Sam68 as a transcriptional and post-transcriptional regulator of gene expression, with particular relevance to cancer. PMID:18481990

  6. Tree Biomass Allocation and Its Model Additivity for Casuarina equisetifolia in a Tropical Forest of Hainan Island, China

    PubMed Central

    Xue, Yang; Yang, Zhongyang; Wang, Xiaoyan; Lin, Zhipan; Li, Dunxi; Su, Shaofeng

    2016-01-01

    Casuarina equisetifolia is commonly planted and used in the construction of coastal shelterbelt protection in Hainan Island. Thus, it is critical to accurately estimate the tree biomass of Casuarina equisetifolia L. for forest managers to evaluate the biomass stock in Hainan. The data for this work consisted of 72 trees, which were divided into three age groups: young forest, middle-aged forest, and mature forest. The proportion of biomass from the trunk significantly increased with age (P<0.05). However, the biomass of the branch and leaf decreased, and the biomass of the root did not change. To test whether the crown radius (CR) can improve biomass estimates of C. equisetifolia, we introduced CR into the biomass models. Here, six models were used to estimate the biomass of each component, including the trunk, the branch, the leaf, and the root. In each group, we selected one model among these six models for each component. The results showed that including the CR greatly improved the model performance and reduced the error, especially for the young and mature forests. In addition, to ensure biomass additivity, the selected equation for each component was fitted as a system of equations using seemingly unrelated regression (SUR). The SUR method not only gave efficient and accurate estimates but also achieved the logical additivity. The results in this study provide a robust estimation of tree biomass components and total biomass over three groups of C. equisetifolia. PMID:27002822

  7. Tree Biomass Allocation and Its Model Additivity for Casuarina equisetifolia in a Tropical Forest of Hainan Island, China.

    PubMed

    Xue, Yang; Yang, Zhongyang; Wang, Xiaoyan; Lin, Zhipan; Li, Dunxi; Su, Shaofeng

    2016-01-01

    Casuarina equisetifolia is commonly planted and used in the construction of coastal shelterbelt protection in Hainan Island. Thus, it is critical to accurately estimate the tree biomass of Casuarina equisetifolia L. for forest managers to evaluate the biomass stock in Hainan. The data for this work consisted of 72 trees, which were divided into three age groups: young forest, middle-aged forest, and mature forest. The proportion of biomass from the trunk significantly increased with age (P<0.05). However, the biomass of the branch and leaf decreased, and the biomass of the root did not change. To test whether the crown radius (CR) can improve biomass estimates of C. equisetifolia, we introduced CR into the biomass models. Here, six models were used to estimate the biomass of each component, including the trunk, the branch, the leaf, and the root. In each group, we selected one model among these six models for each component. The results showed that including the CR greatly improved the model performance and reduced the error, especially for the young and mature forests. In addition, to ensure biomass additivity, the selected equation for each component was fitted as a system of equations using seemingly unrelated regression (SUR). The SUR method not only gave efficient and accurate estimates but also achieved the logical additivity. The results in this study provide a robust estimation of tree biomass components and total biomass over three groups of C. equisetifolia.

  8. The nuclear protein Sam68 is cleaved by the FMDV 3C protease redistributing Sam68 to the cytoplasm during FMDV infection of host cells

    SciTech Connect

    Lawrence, Paul; Schafer, Elizabeth A.; Rieder, Elizabeth

    2012-03-30

    Picornavirus infection can lead to disruption of nuclear pore traffic, shut-off of cell translation machinery, and cleavage of proteins involved in cellular signal transduction and the innate response to infection. Here, we demonstrated that the FMDV 3C{sup pro} induced the cleavage of nuclear RNA-binding protein Sam68 C-terminus containing the nuclear localization sequence (NLS). Consequently, it stimulated the redistribution of Sam68 to the cytoplasm. The siRNA knockdown of Sam68 resulted in a 1000-fold reduction in viral titers, which prompted us to study the effect of Sam68 on FMDV post-entry events. Interestingly, Sam68 interacts with the internal ribosomal entry site within the 5 Prime non-translated region of the FMDV genome, and Sam68 knockdown decreased FMDV IRES-driven activity in vitro suggesting that it could modulate translation of the viral genome. The results uncover a novel role for Sam68 in the context of picornaviruses and the proteolysis of a new cellular target of the FMDV 3C{sup pro}.

  9. The first year: Development of a LANDSAT capability at Sam Houston State University

    NASA Technical Reports Server (NTRS)

    Bounds, J. H.

    1981-01-01

    Problems encountered in initiating a LANDSAT data processing capability at Sam Houston State University are discussed. Computer requirements, financing, and academic and administrative support are addressed.

  10. Biomass Resource Allocation among Competing End Uses

    SciTech Connect

    Newes, E.; Bush, B.; Inman, D.; Lin, Y.; Mai, T.; Martinez, A.; Mulcahy, D.; Short, W.; Simpkins, T.; Uriarte, C.; Peck, C.

    2012-05-01

    The Biomass Scenario Model (BSM) is a system dynamics model developed by the U.S. Department of Energy as a tool to better understand the interaction of complex policies and their potential effects on the biofuels industry in the United States. However, it does not currently have the capability to account for allocation of biomass resources among the various end uses, which limits its utilization in analysis of policies that target biomass uses outside the biofuels industry. This report provides a more holistic understanding of the dynamics surrounding the allocation of biomass among uses that include traditional use, wood pellet exports, bio-based products and bioproducts, biopower, and biofuels by (1) highlighting the methods used in existing models' treatments of competition for biomass resources; (2) identifying coverage and gaps in industry data regarding the competing end uses; and (3) exploring options for developing models of biomass allocation that could be integrated with the BSM to actively exchange and incorporate relevant information.

  11. Allocation of authority in European health policy.

    PubMed

    Adolph, Christopher; Greer, Scott L; Massard da Fonseca, Elize

    2012-11-01

    Although many study the effects of different allocations of health policy authority, few ask why countries assign responsibility over different policies as they do. We test two broad theories: fiscal federalism, which predicts rational governments will concentrate information-intensive operations at lower levels, and redistributive and regulatory functions at higher levels; and "politicized federalism", which suggests a combination of systematic and historically idiosyncratic political variables interfere with efficient allocation of authority. Drawing on the WHO Health in Transition country profiles, we present new data on the allocation of responsibility for key health care policy tasks (implementation, provision, finance, regulation, and framework legislation) and policy areas (primary, secondary and tertiary care, public health and pharmaceuticals) in the 27 EU member states and Switzerland. We use a Bayesian multinomial mixed logit model to analyze how different countries arrive at different allocations of authority over each task and area of health policy, and find the allocation of powers broadly follows fiscal federalism. Responsibility for pharmaceuticals, framework legislation, and most finance lodges at the highest levels of government, acute and primary care in the regions, and provision at the local and regional levels. Where allocation does not follow fiscal federalism, it appears to reflect ethnic divisions, the population of states and regions, the presence of mountainous terrain, and the timing of region creation. PMID:22858423

  12. Investigation and incorporation of water inflow uncertainties through stochastic modelling in a combined optimisation methodology for water allocation in Alfeios River (Greece)

    NASA Astrophysics Data System (ADS)

    Bekri, Eleni; Yannopoulos, Panayotis; Disse, Markus

    2014-05-01

    The Alfeios River plays a vital role for Western Peloponnisos in Greece from natural, ecological, social and economic aspect. The main river and its six tributaries, forming the longest watercourse and the highest streamflow rate of Peloponnisose, represent a significant source of water supply for the region, aiming at delivering and satisfying the expected demands from a variety of water users, including irrigation, drinking water supply, hydropower production and recreation. In the previous EGU General Assembly, a fuzzy-boundary-interval linear programming methodology, based on Li et al. (2010) and Bekri et al. (2012), has been presented for optimal water allocation under uncertain and vague system conditions in the Alfeios River Basin. Uncertainties associated with the benefit and cost coefficient in the objective function of the main water uses (hydropower production and irrigation) were expressed as probability distributions and fuzzy boundary intervals derived by associated α-cut levels. The uncertainty of the monthly water inflows was not incorporated in the previous initial application and the analysis of all other sources of uncertainty has been applied to two extreme hydrologic years represented by a selected wet and dry year. To manage and operate the river system, decision makers should be able to analyze and evaluate the impact of various hydrologic scenarios. In the present work, the critical uncertain parameter of water inflows is analyzed and its incorporation as an additional type of uncertainty in the suggested methodology is investigated, in order to enable the assessment of optimal water allocation for hydrologic and socio-economic scenarios based both on historical data and projected climate change conditions. For this purpose, stochastic simulation analysis for a part of the Alfeios river system is undertaken, testing various stochastic models from simple stationary ones (AR and ARMA), Thomas-Fiering, ARIMA as well as more sophisticated and

  13. A fuzzy multi-objective model for capacity allocation and pricing policy of provider in data communication service with different QoS levels

    NASA Astrophysics Data System (ADS)

    Pan, Wei; Wang, Xianjia; Zhong, Yong-guang; Yu, Lean; Jie, Cao; Ran, Lun; Qiao, Han; Wang, Shouyang; Xu, Xianhao

    2012-06-01

    Data communication service has an important influence on e-commerce. The key challenge for the users is, ultimately, to select a suitable provider. However, in this article, we do not focus on this aspect but the viewpoint and decision-making of providers for order allocation and pricing policy when orders exceed service capacity. It is a multiple criteria decision-making problem such as profit and cancellation ratio. Meanwhile, we know realistic situations in which much of the input information is uncertain. Thus, it becomes very complex in a real-life environment. In this situation, fuzzy sets theory is the best tool for solving this problem. Our fuzzy model is formulated in such a way as to simultaneously consider the imprecision of information, price sensitive demand, stochastic variables, cancellation fee and the general membership function. For solving the problem, a new fuzzy programming is developed. Finally, a numerical example is presented to illustrate the proposed method. The results show that it is effective for determining the suitable order set and pricing policy of provider in data communication service with different quality of service (QoS) levels.

  14. In situ analysis of Mars soil sample with the sam gcms instrumentation onboard Curiosity : interpretation and comparison of measurements done at Rocknest and Yelloknife bay sites

    NASA Astrophysics Data System (ADS)

    Szopa, Cyril; Coll, Patrice; Cabane, Michel; Coscia, David; Buch, Arnaud; Francois, Pascaline; Millan, Maeva; Teinturier, Sammy; Navarro-Gonzales, Rafael; Glavin, Daniel; Freissinet, Caro; Steele, Andrew; Eigenbrode, Jen; Mahaffy, Paul

    2014-05-01

    The characterisation of the chemical and mineralogical composition of regolith samples collected with the Curiosity rover is a primary objective of the SAM experiment. These data should provide essential clues on the past habitability of Gale crater. Amongst the SAM suite of instruments [1], SAM-GC (Gas Chromatograph) is devoted to identify and quantify volatiles evolved from the thermal (heating up to about 900°C)/chemical (derivatization procedure) treatment of any soil sample collected by the Curiosity rover. With the aim to search for potential organic molecules outgassed from the samples, a SAM-GC analytical channel composed of thermal-desorption injector and a MXT-CLP chromatographic column was chosen to achieve all the measurements done up today, as it was designed for the separation of a wide range of volatile organic molecules. Three solid samples have been analyzed with GCMS, one sand sample collected at the Rocknest site, and two rock samples (John Klein and Cumberland respectively) collected at the Yellowknife Bay site using the Curiosity driller. All the measurements were successful and they produced complex chromatograms with both detectors used for SAM GC, i.e. a thermal conductivity detector and the SAM quandrupole mass spectrometer. Their interpretation already revealed the presence of an oxychlorine phase present in the sample which is at the origin of chlorohydrocarbons clearly identified [2] but this represents only a fraction of the GCMS signal recorded [3,4]. This work presents a systematic comparison of the GCMS measurements done for the different samples collected, supported by reference data obtained in laboratory with different spare models of the gas chromatograph, with the aim to bring new elements of interpretation of the SAM measurements. References: [1] Mahaffy, P. et al. (2012) Space Sci Rev, 170, 401-478. [2] Glavin, D. et al. (2013), JGR. [3] Leshin L. et al. (2013), Science, [4] Ming D. et al. (2013), Science, 32, 64

  15. GENERATING SOPHISTICATED SPATIAL SURROGATES USING THE MIMS SPATIAL ALLOCATOR

    EPA Science Inventory

    The Multimedia Integrated Modeling System (MIMS) Spatial Allocator is open-source software for generating spatial surrogates for emissions modeling, changing the map projection of Shapefiles, and performing other types of spatial allocation that does not require the use of a comm...

  16. Myrmics Memory Allocator

    SciTech Connect

    Lymperis, S.

    2011-09-23

    MMA is a stand-alone memory management system for MPI clusters. It implements a shared Partitioned Global Address Space, where multiple MPI processes request objects from the allocator and the latter provides them with system-wide unique memory addresses for each object. It provides applications with an intuitive way of managing the memory system in a unified way, thus enabling easier writing of irregular application code.

  17. Chemical analyses of hydroxyapatite formation on SAM surfaces modified with COOH, NH(2), CH(3), and OH functions.

    PubMed

    Hirata, Isao; Akamatsu, Mai; Fujii, Eri; Poolthong, Suchit; Okazaki, Masayuki

    2010-08-01

    Hydroxyapatite formation was examined at the surface of self-assembled monolayers (SAMs) modified with four functional groups, -COOH, -NH(2), -CH(3), and -OH. For COOH-SAM and NH(2)-SAM, scanning electron spectroscopic observation showed that flake-like sheet crystals covered the whole wafer and small broccoli-like crystals were observed occasionally on the flake-like crystal base layer. For CH(3)-SAM and OH-SAM, no flake-like sheet crystals were observed; broccoli-like crystals were observed in a dispersed manner for CH(3)-SAM, but in localized spots for OH-SAM. X-ray diffraction patterns showed a strong apatite pattern oriented toward the c-axis direction for COOH-SAM. ESCA analysis revealed distinct Ca, P, O peaks for COOH-, NH(2)-, CH(3)-, and OH-SAM. Surface plasmon resonance (SPR) analysis indicated that during the supply of supersaturated calcium phosphate solution, the deposition of precipitates increased monotonically with time for COOH-SAM, increased slightly for NH(2)-SAM, but little increase in deposition was detected for CH(3)-SAM and OH-SAM.

  18. Unanticipated coordination of tris buffer to the Radical SAM cluster of the RimO methylthiotransferase.

    PubMed

    Molle, Thibaut; Clémancey, Martin; Latour, Jean-Marc; Kathirvelu, Velavan; Sicoli, Giuseppe; Forouhar, Farhad; Mulliez, Etienne; Gambarelli, Serge; Atta, Mohamed

    2016-07-01

    Radical SAM enzymes generally contain a [4Fe-4S](2+/1+) (RS cluster) cluster bound to the protein via the three cysteines of a canonical motif CxxxCxxC. The non-cysteinyl iron is used to coordinate SAM via its amino-carboxylate moiety. The coordination-induced proximity between the cluster acting as an electron donor and the adenosyl-sulfonium bond of SAM allows for the homolytic cleavage of the latter leading to the formation of the reactive 5'-deoxyadenosyl radical used for substrate activation. Most of the structures of Radical SAM enzymes have been obtained in the presence of SAM, and therefore, little is known about the situation when SAM is not present. In this report, we show that RimO, a methylthiotransferase belonging to the radical SAM superfamily, binds a Tris molecule in the absence of SAM leading to specific spectroscopic signatures both in Mössbauer and pulsed EPR spectroscopies. These data provide a cautionary note for researchers who work with coordinative unsaturated iron sulfur clusters. PMID:27259294

  19. Sam68 Regulates S6K1 Alternative Splicing during Adipogenesis

    PubMed Central

    Song, Jingwen

    2015-01-01

    The requirement for alternative splicing during adipogenesis is poorly understood. The Sam68 RNA binding protein is a known regulator of alternative splicing, and mice deficient for Sam68 exhibit adipogenesis defects due to defective mTOR signaling. Sam68 null preadipocytes were monitored for alternative splicing imbalances in components of the mTOR signaling pathway. Herein, we report that Sam68 regulates isoform expression of the ribosomal S6 kinase gene (Rps6kb1). Sam68-deficient adipocytes express Rps6kb1-002 and its encoded p31S6K1 protein, in contrast to wild-type adipocytes that do not express this isoform. Sam68 binds an RNA sequence encoded by Rps6kb1 intron 6 and prevents serine/arginine-rich splicing factor 1 (SRSF1)-mediated alternative splicing of Rps6kb1-002, as assessed by cross-linking and immunoprecipitation (CLIP) and minigene assays. Depletion of p31S6K1 with small interfering RNAs (siRNAs) partially restored adipogenesis of Sam68-deficient preadipocytes. The ectopic expression of p31S6K1 in wild-type 3T3-L1 cells resulted in adipogenesis differentiation defects, showing that p31S6K1 is an inhibitor of adipogenesis. Our findings indicate that Sam68 is required to prevent the expression of p31S6K1 in adipocytes for adipogenesis to occur. PMID:25776557

  20. Overview of SAM results obtained at Gale Crater during the 180 first sols

    NASA Astrophysics Data System (ADS)

    Coll, P.; Mahaffy, P. R.; Cabane, M.; Webster, C. R.; Archer, D.; Atreya, S. K.; Benna, M.; Brinckerhoff, W. B.; Brunner, A.; Buch, A.; Conrad, P.; Coscia, D.; Dobson, N.; Dworkin, J.; Eigenbrode, J.; Farley, K.; Flesch, G.; Franz, H.; Freissinet, C.; Galvin, D.; Gorevan, S.; Harpold, D.; Hengemihle, J.; Jaeger, F.; Johnson, C.; Johnson, M.; Jones, J.; Lefavor, M.; Leshin, L.; Lyness, E.; Malespin, C.; Manning, H.; Martin, D.; McAdam, A.; McKay, C.; Miller, K.; Ming, D. W.; Morris, R. V.; Navarro-González, R.; Niles, P.; Nolan, T.; Owen, T.; Pavolv, A.; Prats, B.; Pepin, R.; Raaen, E.; Raulin, F.; Steele, A.; Stern, J.; Squyres, S.; Sutter, B.; Summons, R. E.; Szopa, C.; Tan, F.; Teinturier, S.; Trainer, M.; Wong, M.; Wray, J.

    2013-09-01

    During the first 180 sols of Curiosity's landed mission on Mars (8/6/2012 to 2/7/2013) SAM sampled the atmosphere more than a dozen times, the dusty sandpile named Rocknest and a basin site named John Klein on the floor of Gale crater. The atmospheric experiments utilized SAM's quadrupole mass spectrometer (QMS) and its tunable laser spectrometer (TLS) while the solid sample experiments also utilized the gas chromatograph (GC). Although a number of core experiments were pre-programmed and stored in SAM EEProm, the high level SAM scripting language enabled the team to often optimize experiments based on prior runs. SAM and its Experiment Sequences exercised during the First 120 Sols: The SAM instruments, its gas processing system (GPS) and its sample manipulation system (SMS) have been already described [1]. During the first few weeks of the landed mission SAM carried out a variety of instrument health checks and then began a series of atmospheric experiments to measure atmospheric composition and isotope ratios. From sol 56 to 102 Curiosity lingered at Rocknest to clean out the surfaces of the sample processing system by scooping several times into this fine grained material, vibrating to abrade possible contamination from surfaces, and then discarding before delivery of sample to SAM from the 5th scoop.

  1. Winning Attitude & Dedication to Physical Therapy Keep Sam Schmidt on Track

    ERIC Educational Resources Information Center

    Bosley, Nikki Prevenslik

    2006-01-01

    This article relates how Sam Schmidt returned to living a productive life after an accident left him with spinal cord injury. Schmidt was a former Indy Racing League driver who founded Sam Schmidt Motorsports after his accident in 2000. Schmidt's car hit the wall as he exited turn two during a practice session at Walt Disney World Speedway in…

  2. Dielectric behavior of the frog lens in the 100 Hz to 500 MHz range. Simulation with an allocated ellipsoidal-shells model.

    PubMed Central

    Watanabe, M; Suzaki, T; Irimajiri, A

    1991-01-01

    In an attempt to correlate the passive electrical properties of the lens tissue with its structure, we measured ac admittances for isolated frog lenses, lens nuclei, and homogenate of cortical fiber cells, over the frequency range 10(2)-5.10(8) Hz. The whole lenses molded into discoid shape show a characteristic "two-step" dielectric dispersion with a huge permittivity increment of the order of 10(5) at 1 kHz. Of the two subdispersions disclosed, dispersion 1 has a permittivity increment (delta epsilon) of 2.10(5) with a characteristic frequency (fc) of 2 kHz, and dispersion 2 has a delta epsilon of 400 with an fc of 2 MHz. In terms of loss tangent, these dispersions are more clearly located as two separate peaks. Data are analyzed using an allocated ellipsoidal-shells model which has been developed by taking into account fiber orientation inside the lens tissue. Dispersion 1 is assigned to the equatorial cortex, where fiber cells run parallel to the applied electric field, and dispersion 2 to the nucleus with a complex fiber arrangement and also to the polar cortex, in which the fiber alignment is predominantly perpendicular. In addition, the model analysis reveals that, in the frog lens, the nucleus occupies approximately 30% in volume and that relative permittivity and conductivity for the cell interior are, respectively, 45 and 3 mS/cm for the cortical cells, and 28 and 0.3 mS/cm for the nuclear cells. Images FIGURE 5 PMID:2015379

  3. Synaptic Tagging During Memory Allocation

    PubMed Central

    Rogerson, Thomas; Cai, Denise; Frank, Adam; Sano, Yoshitake; Shobe, Justin; Aranda, Manuel L.; Silva, Alcino J.

    2014-01-01

    There is now compelling evidence that the allocation of memory to specific neurons (neuronal allocation) and synapses (synaptic allocation) in a neurocircuit is not random and that instead specific mechanisms, such as increases in neuronal excitability and synaptic tagging and capture, determine the exact sites where memories are stored. We propose an integrated view of these processes, such that neuronal allocation, synaptic tagging and capture, spine clustering and metaplasticity reflect related aspects of memory allocation mechanisms. Importantly, the properties of these mechanisms suggest a set of rules that profoundly affect how memories are stored and recalled. PMID:24496410

  4. NaCo/SAM observations of sources at the Galactic Center

    NASA Astrophysics Data System (ADS)

    Sanchez-Bermudez, J.; Schödel, R.; Alberdi, A.; Pott, J. U.

    2012-07-01

    Sparse aperture masking (SAM) interferometry combined with Adaptive Optics (AO) is a technique that is uniquely suited to investigate structures near the diffraction limit of large telescopes. The strengths of the technique are a robust calibration of the Point Spread Function (PSF) while maintaining a relatively high dynamic range. We used SAM+AO observations to investigate the circumstellar environment of several bright sources with infrared excess in the central parsec of the Galaxy. For our observations, unstable atmospheric conditions as well as significant residuals after the background subtraction presented serious problems for the standard approach of calibrating SAM data via interspersed observations of reference stars. We circumvented these difficulties by constructing a synthesized calibrator directly from sources within the field-of-view. When observing crowded fields, this novel method can boost the efficiency of SAM observations because it renders interspersed calibrator observations unnecessary. Here, we presented the first NaCo/SAM images reconstructed using this method.

  5. Radical SAM catalysis via an organometallic intermediate with an Fe-[5'-C]-deoxyadenosyl bond.

    PubMed

    Horitani, Masaki; Shisler, Krista; Broderick, William E; Hutcheson, Rachel U; Duschene, Kaitlin S; Marts, Amy R; Hoffman, Brian M; Broderick, Joan B

    2016-05-13

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to cleave SAM to initiate diverse radical reactions. These reactions are thought to involve the 5'-deoxyadenosyl radical intermediate, which has not yet been detected. We used rapid freeze-quenching to trap a catalytically competent intermediate in the reaction catalyzed by the radical SAM enzyme pyruvate formate-lyase activating enzyme. Characterization of the intermediate by electron paramagnetic resonance and (13)C, (57)Fe electron nuclear double-resonance spectroscopies reveals that it contains an organometallic center in which the 5' carbon of a SAM-derived deoxyadenosyl moiety forms a bond with the unique iron site of the [4Fe-4S] cluster. Discovery of this intermediate extends the list of enzymatic bioorganometallic centers to the radical SAM enzymes, the largest enzyme superfamily known, and reveals intriguing parallels to B12 radical enzymes.

  6. S.A.M., the Italian Martian simulation chamber.

    PubMed

    Galletta, G; Ferri, F; Fanti, G; D'Alessandro, M; Bertoloni, G; Pavarin, D; Bettanini, C; Cozza, P; Pretto, P; Bianchini, G; Debei, S

    2006-12-01

    The Martian Environment Simulator (SAM "Simulatore di Ambiente Marziano") is a interdisciplinary project of Astrobiology done at University of Padua. The research is aimed to the study of the survival of the microorganisms exposed to the "extreme" planetary environment. The facility has been designed in order to simulate Mars' environmental conditions in terms of atmospheric pressure, temperature cycles and UV radiation dose. The bacterial cells, contained into dedicated capsules, will be exposed to thermal cycles simulating diurnal and seasonal Martian cycles. The metabolism of the different biological samples will be analysed at different phases of the experiment, to study their survival and eventual activity of protein synthesis (mortality, mutations and capability of DNA repairing). We describe the experimental facility and provide the perspectives of the biological experiments we will perform in order to provide hints on the possibility of life on Mars either autochthonous or imported from Earth.

  7. Radical SAM-Mediated Methylation of Ribosomal RNA

    PubMed Central

    Stojkovic, Vanja; Fujimori, Danica Galonić

    2015-01-01

    Post-transcriptional modifications of RNA play an important role in a wide range of biological processes. In ribosomal RNA (rRNA), methylation of nucleotide bases is the predominant modification. In recent years, methylation of adenosine 2503 (A2503) in bacterial 23S rRNA has attracted significant attention due to both the unusual regioselectivity of the methyl group incorporation, as well as the pathophysiological roles of the resultant methylations. Specifically, A2503 is methylated at the C2 and C8 positions of the adenine ring, and the introduced modifications have a profound impact on translational fidelity and antibiotic resistance, respectively. These modifications are performed by RlmN and Cfr, two members, of the recently discovered class of radical S-adenosylmethionine (radical SAM) methylsynthases. Here, we present several methods that can be used to evaluate the activity of these enzymes, under both in vivo and in vitro conditions. PMID:26253978

  8. S.A.M., the Italian Martian Simulation Chamber

    NASA Astrophysics Data System (ADS)

    Galletta, G.; Ferri, F.; Fanti, G.; D'Alessandro, M.; Bertoloni, G.; Pavarin, D.; Bettanini, C.; Cozza, P.; Pretto, P.; Bianchini, G.; Debei, S.

    2006-12-01

    The Martian Environment Simulator (SAM “Simulatore di Ambiente Marziano”) is a interdisciplinary project of Astrobiology done at University of Padua. The research is aimed to the study of the survival of the microorganisms exposed to the “extreme” planetary environment. The facility has been designed in order to simulate Mars’ environmental conditions in terms of atmospheric pressure, temperature cycles and UV radiation dose. The bacterial cells, contained into dedicated capsules, will be exposed to thermal cycles simulating diurnal and seasonal Martian cycles. The metabolism of the different biological samples will be analysed at different phases of the experiment, to study their survival and eventual activity of protein synthesis (mortality, mutations and capability of DNA reparing). We describe the experimental facility and provide the perspectives of the biological experiments we will perform in order to provide hints on the possibility of life on Mars either autochthonous or imported from Earth.

  9. Presentation on a Space Acceleration Measurement System (SAMS)

    NASA Technical Reports Server (NTRS)

    Chase, Theodore L.

    1990-01-01

    The primary objective of the Space Acceleration Measurement Systems (SAMS) project is to provide an acceleration measurement system capable of serving a wide variety of space experiments. The design of the system being developed under this project takes into consideration requirements for experiments located in the middeck, in the orbiter bay, and in Spacelab. In addition to measuring, conditioning, and recording accelerations, the system will be capable of performing complex calculations and interactive control. The main components consist of a remote triaxial optical storage device. In operation, the triaxial sensor head produces output signals in response to acceleration inputs. These signals are preamplified, filtered and converted into digital data which is then transferred to optical memory. The system design is modular, facilitating both software and hardware upgrading as technology advances. Two complete acceleration measurement flight systems will be build and tested under this project.

  10. 50 CFR 660.323 - Pacific whiting allocations, allocation attainment, and inseason allocation reapportionment.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Pacific whiting allocations, allocation attainment, and inseason allocation reapportionment. 660.323 Section 660.323 Wildlife and Fisheries FISHERY...) FISHERIES OFF WEST COAST STATES West Coast Groundfish Fisheries § 660.323 Pacific whiting...

  11. Social activity method (SAM): A fractal language for mathematics

    NASA Astrophysics Data System (ADS)

    Dowling, Paul

    2013-09-01

    In this paper I shall present and develop my organisational language, social activity method (SAM), and illustrate some of its applications. I shall introduce a new scheme for modes of recontextualisation that enables the analysis of the ways in which one activity - which might be school mathematics or social research or any empirically observed regularity of practice - recontextualises the practice of another and I shall also present, deploy, and develop an existing scheme - domains of action - in an analysis of school mathematics examination papers and in the structuring of what I refer to as the esoteric domain. This domain is here conceived as a hybrid domain of, first, linguistic and extralinguistic resources that are unambiguously mathematical in terms of both expression and content and, second, pedagogic theory - often tacit - that enables the mathematical gaze onto other practices and so recontextualises them. A second and more general theme that runs through the paper is the claim that there is nothing that is beyond semiosis, that there is nothing to which we have direct access, unmediated by interpretation. This state of affairs has implications for mathematics education. Specifically, insofar as an individual's mathematical semiotic system is under continuous development - the curriculum never being graspable all at once - understanding - as a stable semiotic moment - of any aspect or object of mathematics is always localised to the individual and is at best transient, and the sequencing of such moments may well also be more individualised than consistent in some correspondence with the sequencing of the curriculum. This being the case, a concentration on understanding as a goal may well serve to inhibit the pragmatic acquisition and deployment of mathematical technologies, which should be the principal aim of mathematics teaching and learning. The paper is primarily concerned with mathematics education. SAM, however, is a language that is available for

  12. Sam68 is Overexpressed in Epithelial Ovarian Cancer and Promotes Tumor Cell Proliferation.

    PubMed

    Dong, Lijuan; Che, Hailuo; Li, Mingmei; Li, Xuepeng

    2016-01-01

    BACKGROUND Epithelial ovarian cancer (EOC) is the deadliest gynecological malignancy, and evidence is accumulating on how molecular markers may be associated with the origin and process of EOC. Sam68 (Src-associated in mitosis, of 68 kD), is a K homology domain RNA-binding protein that has been investigated as a risk factor in multiple types of tumors. The aim of the present study was to investigate the contribution of the Sam68 gene in the pathogenesis of EOC. MATERIAL AND METHODS Western blot assay and real-time quantitative PCR methods were performed to examine Sam68 expression in EOC tissue specimens. The association of Sam68 expression with clinic-pathologic variables of EOC was evaluated. Then gain-of-function and loss-of-function strategies were adopted to examine the regulation of Sam68 on the proliferation of EOC OVCAR-3 cells using CCK-8 and colony forming assays. RESULTS Sam68 was overexpressed in both mRNA and protein levels in EOC tumor tissue (n=152) in an association with malignant factors of EOC such as International Federation of Gynecology and Obstetrics (FIGO) stage, residual tumor size (cm), histological grade, and lymph node metastasis. In vitro results demonstrated that Sam68 overexpression was upregulated while Sam68 knockdown downregulated the proliferation of EOC OVCAR-3 cells via regulation of cell growth and colony formation. CONCLUSIONS Sam68 was overexpressed in EOC tissue in association with such cancer malignant factors of FIGO stage, histological grade, and lymph node metastasis, and also positively regulated the proliferation of EOC cells. Our research suggests that Sam68 might accelerate cell cycle progression, and present as a prognostic marker for EOC. PMID:27623016

  13. Sam68 is Overexpressed in Epithelial Ovarian Cancer and Promotes Tumor Cell Proliferation

    PubMed Central

    Dong, Lijuan; Che, Hailuo; Li, Mingmei; Li, Xuepeng

    2016-01-01

    Background Epithelial ovarian cancer (EOC) is the deadliest gynecological malignancy, and evidence is accumulating on how molecular markers may be associated with the origin and process of EOC. Sam68 (Src-associated in mitosis, of 68 kD), is a K homology domain RNA-binding protein that has been investigated as a risk factor in multiple types of tumors. The aim of the present study was to investigate the contribution of the Sam68 gene in the pathogenesis of EOC. Material/Methods Western blot assay and real-time quantitative PCR methods were performed to examine Sam68 expression in EOC tissue specimens. The association of Sam68 expression with clinic-pathologic variables of EOC was evaluated. Then gain-of-function and loss-of-function strategies were adopted to examine the regulation of Sam68 on the proliferation of EOC OVCAR-3 cells using CCK-8 and colony forming assays. Results Sam68 was overexpressed in both mRNA and protein levels in EOC tumor tissue (n=152) in an association with malignant factors of EOC such as International Federation of Gynecology and Obstetrics (FIGO) stage, residual tumor size (cm), histological grade, and lymph node metastasis. In vitro results demonstrated that Sam68 overexpression was upregulated while Sam68 knockdown downregulated the proliferation of EOC OVCAR-3 cells via regulation of cell growth and colony formation. Conclusions Sam68 was overexpressed in EOC tissue in association with such cancer malignant factors of FIGO stage, histological grade, and lymph node metastasis, and also positively regulated the proliferation of EOC cells. Our research suggests that Sam68 might accelerate cell cycle progression, and present as a prognostic marker for EOC. PMID:27623016

  14. Simplifying rules for optimal allocation of preventive care resources.

    PubMed

    Gandjour, Afschin

    2012-04-01

    Given the limited resources for preventive care, policy-makers need to consider the efficiency/cost-effectiveness of preventive measures, such as drugs and vaccines, when allocating preventive care resources. However, in many settings only limited information on lifetime costs and effects of preventive measures exists. Therefore, it seems useful to provide policy-makers with some simplifying rules when allocating preventive care resources. The purpose of this article is to investigate the relevance of risk and severity of the disease to be prevented for the optimal allocation of preventive care resources. The report shows - based on a constrained optimization model - that optimal allocation of preventive care resources does, in fact, depend on both factors. Resources should be allocated to the prevention of diseases with a higher probability of occurrence or larger severity. This article also identifies situations where preventive care resources should be allocated to the prevention of less severe disease.

  15. Constrained Allocation Flux Balance Analysis.

    PubMed

    Mori, Matteo; Hwa, Terence; Martin, Olivier C; De Martino, Andrea; Marinari, Enzo

    2016-06-01

    New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis. We introduce here Constrained Allocation Flux Balance Analysis, CAFBA, in which the biosynthetic costs associated to growth are accounted for in an effective way through a single additional genome-wide constraint. Its roots lie in the experimentally observed pattern of proteome allocation for metabolic functions, allowing to bridge regulation and metabolism in a transparent way under the principle of growth-rate maximization. We provide a simple method to solve CAFBA efficiently and propose an "ensemble averaging" procedure to account for unknown protein costs. Applying this approach to modeling E. coli metabolism, we find that, as the growth rate increases, CAFBA solutions cross over from respiratory, growth-yield maximizing states (preferred at slow growth) to fermentative states with carbon overflow (preferred at fast growth). In addition, CAFBA allows for quantitatively accurate predictions on the rate of acetate excretion and growth yield based on only 3 parameters determined by empirical growth laws.

  16. Constrained Allocation Flux Balance Analysis.

    PubMed

    Mori, Matteo; Hwa, Terence; Martin, Olivier C; De Martino, Andrea; Marinari, Enzo

    2016-06-01

    New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis. We introduce here Constrained Allocation Flux Balance Analysis, CAFBA, in which the biosynthetic costs associated to growth are accounted for in an effective way through a single additional genome-wide constraint. Its roots lie in the experimentally observed pattern of proteome allocation for metabolic functions, allowing to bridge regulation and metabolism in a transparent way under the principle of growth-rate maximization. We provide a simple method to solve CAFBA efficiently and propose an "ensemble averaging" procedure to account for unknown protein costs. Applying this approach to modeling E. coli metabolism, we find that, as the growth rate increases, CAFBA solutions cross over from respiratory, growth-yield maximizing states (preferred at slow growth) to fermentative states with carbon overflow (preferred at fast growth). In addition, CAFBA allows for quantitatively accurate predictions on the rate of acetate excretion and growth yield based on only 3 parameters determined by empirical growth laws. PMID:27355325

  17. Constrained Allocation Flux Balance Analysis

    PubMed Central

    Mori, Matteo; Hwa, Terence; Martin, Olivier C.

    2016-01-01

    New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis. We introduce here Constrained Allocation Flux Balance Analysis, CAFBA, in which the biosynthetic costs associated to growth are accounted for in an effective way through a single additional genome-wide constraint. Its roots lie in the experimentally observed pattern of proteome allocation for metabolic functions, allowing to bridge regulation and metabolism in a transparent way under the principle of growth-rate maximization. We provide a simple method to solve CAFBA efficiently and propose an “ensemble averaging” procedure to account for unknown protein costs. Applying this approach to modeling E. coli metabolism, we find that, as the growth rate increases, CAFBA solutions cross over from respiratory, growth-yield maximizing states (preferred at slow growth) to fermentative states with carbon overflow (preferred at fast growth). In addition, CAFBA allows for quantitatively accurate predictions on the rate of acetate excretion and growth yield based on only 3 parameters determined by empirical growth laws. PMID:27355325

  18. [Organ allocation. Ethical issues].

    PubMed

    Cattorini, P

    2010-01-01

    The criteria for allocating organs are one of the most debated ethical issue in the transplantation programs. The article examines some rules and principles followed by "Nord Italia Transplant program", summarized in its Principles' Charter and explained in a recent interdisciplinary book. General theories of justice and their application to individual clinical cases are commented and evaluated, in order to foster a public, democratic, transparent debate among professionals and citizens, scientific associations and customers' organizations. Some specific moral dilemmas are focused regarding the concepts of proportionate treatment, unselfish donation by living persons, promotion of local institutions efficiency. PMID:20677677

  19. Task mapping for non-contiguous allocations.

    SciTech Connect

    Leung, Vitus Joseph; Bunde, David P.; Ebbers, Johnathan; Price, Nicholas W.; Swank, Matthew.; Feer, Stefan P.; Rhodes, Zachary D.

    2013-02-01

    This paper examines task mapping algorithms for non-contiguously allocated parallel jobs. Several studies have shown that task placement affects job running time for both contiguously and non-contiguously allocated jobs. Traditionally, work on task mapping either uses a very general model where the job has an arbitrary communication pattern or assumes that jobs are allocated contiguously, making them completely isolated from each other. A middle ground between these two cases is the mapping problem for non-contiguous jobs having a specific communication pattern. We propose several task mapping algorithms for jobs with a stencil communication pattern and evaluate them using experiments and simulations. Our strategies improve the running time of a MiniApp by as much as 30% over a baseline strategy. Furthermore, this improvement increases markedly with the job size, demonstrating the importance of task mapping as systems grow toward exascale.

  20. Discrete Resource Allocation in Visual Working Memory

    ERIC Educational Resources Information Center

    Barton, Brian; Ester, Edward F.; Awh, Edward

    2009-01-01

    Are resources in visual working memory allocated in a continuous or a discrete fashion? On one hand, flexible resource models suggest that capacity is determined by a central resource pool that can be flexibly divided such that items of greater complexity receive a larger share of resources. On the other hand, if capacity in working memory is…

  1. MSL/SAM Measurements of Volatile Isotopes, and their Implications for Atmospheric Loss

    NASA Astrophysics Data System (ADS)

    Atreya, Sushil K.; Mahaffy, Paul; Webster, Christopher; Wong, Michael; Conrad, Pamela; Franz, Heather; Grotzinger, John; Jones, John; Leshin, Laurie; Malespin, Charles; Manning, Heidi; Navarro-Gonzalez, Raphael; Owen, Tobias; Pepin, Robert; Schwenzer, Susanne; Trainer, Melissa

    2014-05-01

    High precision measurements of the isotopes of carbon and oxygen in CO2, hydrogen in H2O, nitrogen in N2, and argon in the martian atmosphere have been made by the Sample Analysis at Mars (SAM) instrument on the Curiosity Rover [1,2,3,4]. The resulting values in per mil are 46 for δ13C (relative to VPDB reference standard), 48 for δ18O (VSMOW), 5880 for δD (VSMOW), 572 for δ15N (relative to earth atmosphere), and 4.2 for 36Ar/38Ar (or δ38Ar=310 relative to sun reference standard). The observed enrichment of the heavier isotope over the lighter isotope means that loss to space rather than loss to the surface dominates the isotopic composition in the martian atmosphere. Vertical mixing transports the volatiles from the surface up to the upper atmosphere. While eddy diffusion and molecular diffusion control the distribution of the noble gases, photochemistry also plays a significant role in the distribution of the other volatiles as they diffuse to the upper atmosphere. The above SAM data on the isotopic ratios of carbon, oxygen, hydrogen, nitrogen and argon implies a massive loss of the atmosphere from Mars in the past four billion years. Only hydrogen (hence water) is likely to escape thermally due to the low exospheric temperature of Mars. However, the lack of intrinsic magnetic field on Mars allows solar wind to interact directly with the atmosphere, thus opening up a myriad of possibilities for escape of volatiles from Mars. One such mechanism studied by the ion mass analyzer instrument on Mars Express finds that at current rate of erosion by solar wind, Mars may have lost between 0.2 and 4 millibar of the CO2 atmosphere in the past 3.5 billion years [5]. However, these authors [5] stress that other mechanisms including photochemical, sputtering and cold plasma escape may result in up to 1000 times greater rate of atmospheric loss based on models. Any fractionation in the isotopes of the heavy noble gas, xenon, would have occurred prior to approximately 4 Ga

  2. Computationally efficient control allocation

    NASA Technical Reports Server (NTRS)

    Durham, Wayne (Inventor)

    2001-01-01

    A computationally efficient method for calculating near-optimal solutions to the three-objective, linear control allocation problem is disclosed. The control allocation problem is that of distributing the effort of redundant control effectors to achieve some desired set of objectives. The problem is deemed linear if control effectiveness is affine with respect to the individual control effectors. The optimal solution is that which exploits the collective maximum capability of the effectors within their individual physical limits. Computational efficiency is measured by the number of floating-point operations required for solution. The method presented returned optimal solutions in more than 90% of the cases examined; non-optimal solutions returned by the method were typically much less than 1% different from optimal and the errors tended to become smaller than 0.01% as the number of controls was increased. The magnitude of the errors returned by the present method was much smaller than those that resulted from either pseudo inverse or cascaded generalized inverse solutions. The computational complexity of the method presented varied linearly with increasing numbers of controls; the number of required floating point operations increased from 5.5 i, to seven times faster than did the minimum-norm solution (the pseudoinverse), and at about the same rate as did the cascaded generalized inverse solution. The computational requirements of the method presented were much better than that of previously described facet-searching methods which increase in proportion to the square of the number of controls.

  3. The Use of Student Outcomes in Resource Allocation Decisions.

    ERIC Educational Resources Information Center

    Elfner, Eliot S.

    Resource allocation processes suitable for use in not-for-profit institutions are discussed and a conceptual model for resource allocation in institutions of higher education is presented. The objectives of higher education include the personal development and education of students, not merely the certification of students by conferring degrees.…

  4. On the Allocation of Resources for Secondary Schools

    ERIC Educational Resources Information Center

    Haelermans, Carla; De Witte, Kristof; Blank, Jos L. T.

    2012-01-01

    This paper studies the optimal allocation of resources--in terms of school management, teachers, supporting employees and materials--in secondary schools. We use a flexible budget constrained output distance function model to estimate both technical and allocative efficiency scores for 448 Dutch secondary schools between 2002 and 2007. The results…

  5. The nuclear protein Sam68 is recruited to the cytoplasmic stress granules during enterovirus 71 infection.

    PubMed

    Zhang, Hua; Chen, Ning; Li, Pengfei; Pan, Ziye; Ding, Yun; Zou, Dehua; Li, Liyang; Xiao, Lijie; Shen, Binglei; Liu, Shuxia; Cao, Hongwei; Cui, Yudong

    2016-07-01

    Our previous study found that the nuclear protein, 68-kDa Src-associated in mitosis protein (Sam68), is translocated to the cytoplasm and forms punctate pattern during enterovirus 71 (EV71) infection [Virus Research, 180 (2014), 1-11]. However, the exact function of this punctate pattern in cytoplasm during EV71 infection remains unknown. In this study, we firstly have examined this punctate pattern of Sam68 re-localization in the cytoplasm, and observed the obvious recruitments of Sam68 to the EV71-induced stress granules (SGs). Sam68, belongs to the KH domain family of RNA binding proteins (RBPs), was then confirmed that its KH domain was essential for this recruitment. Nevertheless, Knockdown of Sam68 expression using ShRNA had no effects on SGs assembly, indicating that Sam68 is not a constitutive component of the SGs during EV71 infection. Lastly, we investigated the importance of microtubulin transport to SGs aggregation, and revealed that microtubule depolymerization inhibited SGs formation, suggesting that EV71-induced SGs move throughout the cytoplasm in a microtubule-dependent manner. Taken together, these results illuminated that EV71 infections can induce SGs formation, and Sam68, as a SGs component, migrates alone with SGs dependent on intact microtubule upon the viral infections. These findings may provide novel underlying mechanism for delineating the role of SGs during EV71 infection. PMID:27057671

  6. The integrated conjugative plasmid pSAM2 of Streptomyces ambofaciens is related to temperate bacteriophages.

    PubMed

    Boccard, F; Smokvina, T; Pernodet, J L; Friedmann, A; Guérineau, M

    1989-03-01

    Streptomyces ambofaciens ATCC23877 and derivatives contain the 11-kb element pSAM2 present in an integrated state or as a free and integrated plasmid. This element, able to integrate site-specifically in the genome of different Streptomyces species, is conjugative and mobilizes chromosomal markers. Besides these plasmid functions, we have shown that the site-specific recombination system of pSAM2 presents strong similarities with that of several temperate phages. The integration event is promoted by a site-specific recombinase of the integrase family. The int gene encoding this integrase is closely linked to the plasmid attachment site (attP). A small open reading frame (ORF) overlaps the int gene and the predicted protein exhibits similarities with Xis proteins involved in phages excision. The integrated copy of pSAM2 in strain ATCC23877 is flanked by att sequences (attL and attR). Another att sequence (attX) is present in this strain and attX and attL are the boundaries of a 42-kb fragment (xSAM1) absent, as well as pSAM2, from S.ambofaciens DSM40697. Sequences partially similar to pSAM2 int gene are found near the chromosomal integration zone in both S.ambofaciens strains. The possible origin of pSAM2, an element carrying plasmid as well as phage features, is discussed.

  7. Generalized multidimensional dynamic allocation method.

    PubMed

    Lebowitsch, Jonathan; Ge, Yan; Young, Benjamin; Hu, Feifang

    2012-12-10

    Dynamic allocation has received considerable attention since it was first proposed in the 1970s as an alternative means of allocating treatments in clinical trials which helps to secure the balance of prognostic factors across treatment groups. The purpose of this paper is to present a generalized multidimensional dynamic allocation method that simultaneously balances treatment assignments at three key levels: within the overall study, within each level of each prognostic factor, and within each stratum, that is, combination of levels of different factors Further it offers capabilities for unbalanced and adaptive designs for trials. The treatment balancing performance of the proposed method is investigated through simulations which compare multidimensional dynamic allocation with traditional stratified block randomization and the Pocock-Simon method. On the basis of these results, we conclude that this generalized multidimensional dynamic allocation method is an improvement over conventional dynamic allocation methods and is flexible enough to be applied for most trial settings including Phases I, II and III trials.

  8. Sam68 Mediates the Activation of Insulin and Leptin Signalling in Breast Cancer Cells

    PubMed Central

    Pérez-Pérez, Antonio; Sánchez-Jiménez, Flora; Vilariño-García, Teresa; de la Cruz, Luis; Virizuela, Juan A.; Sánchez-Margalet, Víctor

    2016-01-01

    Obesity is a well-known risk factor for breast cancer development in postmenopausal women. High insulin and leptin levels seem to have a role modulating the growth of these tumours. Sam68 is an RNA-binding protein with signalling functions that has been found to be overexpressed in breast cancer. Moreover, Sam68 may be recruited to insulin and leptin signalling pathways, mediating its effects on survival, growth and proliferation in different cellular types. We aimed to study the expression of Sam68 and its phosphorylation level upon insulin and leptin stimulation, and the role of Sam68 in the proliferative effect and signalling pathways that are activated by insulin or leptin in human breast adenocarcinoma cells. In the human breast adenocarcinoma cell lines MCF7, MDA-MB-231 and BT-474, Sam68 protein quantity and gene expression were increased upon leptin or insulin stimulation, as it was checked by qPCR and immunoblot. Moreover, both insulin and leptin stimulation promoted an increase in Sam68 tyrosine phosphorylation and negatively regulated its RNA binding capacity. siRNA was used to downregulate Sam68 expression, which resulted in lower proliferative effects of both insulin and leptin, as well as a lower activation of MAPK and PI3K pathways promoted by both hormones. These effects may be partly explained by the decrease in IRS-1 expression by down-regulation of Sam68. These results suggest the participation of Sam68 in both leptin and insulin receptor signaling in human breast cancer cells, mediating the trophic effects of these hormones in proliferation and cellular growth. PMID:27415018

  9. Function Allocation in Complex Socio-Technical Systems: Procedure usage in nuclear power and the Context Analysis Method for Identifying Design Solutions (CAMIDS) Model

    NASA Astrophysics Data System (ADS)

    Schmitt, Kara Anne

    This research aims to prove that strict adherence to procedures and rigid compliance to process in the US Nuclear Industry may not prevent incidents or increase safety. According to the Institute of Nuclear Power Operations, the nuclear power industry has seen a recent rise in events, and this research claims that a contributing factor to this rise is organizational, cultural, and based on peoples overreliance on procedures and policy. Understanding the proper balance of function allocation, automation and human decision-making is imperative to creating a nuclear power plant that is safe, efficient, and reliable. This research claims that new generations of operators are less engaged and thinking because they have been instructed to follow procedures to a fault. According to operators, they were once to know the plant and its interrelations, but organizationally more importance is now put on following procedure and policy. Literature reviews were performed, experts were questioned, and a model for context analysis was developed. The Context Analysis Method for Identifying Design Solutions (CAMIDS) Model was created, verified and validated through both peer review and application in real world scenarios in active nuclear power plant simulators. These experiments supported the claim that strict adherence and rigid compliance to procedures may not increase safety by studying the industry's propensity for following incorrect procedures, and when it directly affects the outcome of safety or security of the plant. The findings of this research indicate that the younger generations of operators rely highly on procedures, and the organizational pressures of required compliance to procedures may lead to incidents within the plant because operators feel pressured into following the rules and policy above performing the correct actions in a timely manner. The findings support computer based procedures, efficient alarm systems, and skill of the craft matrices. The solution to

  10. Denitrification of the polar winter stratosphere - Implications of SAM II cloud formation temperatures

    NASA Technical Reports Server (NTRS)

    Hamill, Patrick; Toon, O. B.

    1990-01-01

    The SAM II extinction profiles and the associated temperature profiles are used to determine the amount of denitrification of the winter polar stratospheres. Clear evidence of the denitrification process in the Antarctic data is seen. There are indications in the Arctic data that denitrification mechanisms may be at work there also. At the latitudes observed by the SAM II satellite system, denitrification begins before the formation of extensive ice clouds and may be due to sedimentation of nitric acid particles. However, the possibility of dinitrification by type II PSCs at latitudes not observed by SAM II cannot be excluded.

  11. Mixed-SAM surfaces monitoring CTX-protein part I: Using atomic force microscope measurements.

    PubMed

    Chang, Joe-Ming; Tseng, Fan-Gang; Chieng, Ching-Chang

    2010-12-01

    Fast and efficient detection of Cobra cardiotoxin (CTX) protein molecules on biochip surfaces is an example of application in biotechnology. One potential application of mixed self assembled monolayers (SAMs) as chip surfaces yield different binding affinities of the CTX proteins, a series of studies on the interaction force between CTX proteins and the mixed SAMs surfaces formed from mixtures of two thiols with the same/different chain lengths and/or with the same/different terminal groups will be investigated. In these dual papers, the mixed SAMs of n-alkinethiol SAMs of different chain lengths are chosen as the first examples of this series due to the simple functions of the mixed SAMs surface structure. Thus, the adhesion force measurements of CTX protein molecules on mixed SAMs of n-alkinethiol SAMs of different chain lengths: 1-decanethiol (C9) and 1-hexanethiol (C5) with different mixing ratios are developed and conducted using atomic force microscope (AFM). There are two major tasks in Part I of the dual papers: the development of the AFM measurements providing reliable information, and selection of the surface with highest binding affinity among this mixed SAMs group. Results indicate that the adhesion forces for CTX protein molecules on mixed SAMs with mixing ratio (χ(C9)) of 0.25, 0.5, 0.75 and 1, are 1.26, 1.8, 1.38, and 1.25 folds respectively, compared with the adhesion force of CTX protein molecules on the C5 surface only. Therefore, the SAM surfaces of χ(C9) = 0.5 is the best choice as a biomaterial sensor of this group of mixed SAMs because the strongest binding force and highest efficiency. Effects of the loading force of the AFM operation, the radius of curvature of the AFM tip, and the AFM tip endurance as well as control experiments were examined to ensure the quantitative determination of adhesion force for AFM measurement. The physical mechanism of protein adsorption on SAM surfaces will be studied and analyzed by molecular dynamics (MD

  12. A comparative study of aerosol extinction measurements made by the SAM II and SAGE satellite experiments

    NASA Technical Reports Server (NTRS)

    Yue, G. K.; Mccormick, M. P.; Chu, W. P.

    1984-01-01

    SAM II and SAGE are two satellite experiments designed to measure stratospheric aerosol extinction using the technique of solar occultation or limb extinction. Although each sensor is mounted aboard a different satellite, there are occasions when their measurement locations are nearly coincident, thereby providing opportunities for a measurement comparison. In this paper, the aerosol extinction profiles and daily contour plots for some of these events in 1979 are reported. The comparisons shown in this paper demonstrate that SAM II and SAGE are producing similar aerosol extinction profiles within their measurement errors and that since SAM II has been previously validated, these results show the validity of the SAGE aerosol measurements.

  13. Large scale study on the variation of RF energy absorption in the head & brain regions of adults and children and evaluation of the SAM phantom conservativeness

    NASA Astrophysics Data System (ADS)

    Keshvari, J.; Kivento, M.; Christ, A.; Bit-Babik, G.

    2016-04-01

    This paper presents the results of two computational large scale studies using highly realistic exposure scenarios, MRI based human head and hand models, and two mobile phone models. The objectives are (i) to study the relevance of age when people are exposed to RF by comparing adult and child heads and (ii) to analyze and discuss the conservativeness of the SAM phantom for all age groups. Representative use conditions were simulated using detailed CAD models of two mobile phones operating between 900 MHz and 1950 MHz including configurations with the hand holding the phone, which were not considered in most previous studies. The peak spatial-average specific absorption rate (psSAR) in the head and the pinna tissues is assessed using anatomically accurate head and hand models. The first of the two mentioned studies involved nine head-, four hand- and two phone-models, the second study included six head-, four hand- and three simplified phone-models (over 400 configurations in total). In addition, both studies also evaluated the exposure using the SAM phantom. Results show no systematic differences between psSAR induced in the adult and child heads. The exposure level and its variation for different age groups may be different for particular phones, but no correlation between psSAR and model age was found. The psSAR from all exposure conditions was compared to the corresponding configurations using SAM, which was found to be conservative in the large majority of cases.

  14. Random Walk Model for the Growth of Monolayer in Dip Pen Nanolithography

    NASA Astrophysics Data System (ADS)

    Kim, H.; Ha, S.; Jang, J.

    2013-02-01

    By using a simple random-walk model, we simulate the growth of a self-assembled monolayer (SAM) pattern generated in dip pen nanolithography (DPN). In this model, the SAM pattern grows mainly via the serial pushing of molecules deposited from the tip. We examine various SAM patterns, such as lines, crosses, and letters by changing the tip scan speed.

  15. Research on allocation efficiency of the daisy chain allocation algorithm

    NASA Astrophysics Data System (ADS)

    Shi, Jingping; Zhang, Weiguo

    2013-03-01

    With the improvement of the aircraft performance in reliability, maneuverability and survivability, the number of the control effectors increases a lot. How to distribute the three-axis moments into the control surfaces reasonably becomes an important problem. Daisy chain method is simple and easy to be carried out in the design of the allocation system. But it can not solve the allocation problem for entire attainable moment subset. For the lateral-directional allocation problem, the allocation efficiency of the daisy chain can be directly measured by the area of its subset of attainable moments. Because of the non-linear allocation characteristic, the subset of attainable moments of daisy-chain method is a complex non-convex polygon, and it is difficult to solve directly. By analyzing the two-dimensional allocation problems with a "micro-element" idea, a numerical calculation algorithm is proposed to compute the area of the non-convex polygon. In order to improve the allocation efficiency of the algorithm, a genetic algorithm with the allocation efficiency chosen as the fitness function is proposed to find the best pseudo-inverse matrix.

  16. Sam Goudsmit--His Physics and His Statesmanship

    NASA Astrophysics Data System (ADS)

    Bederson, Benjamin

    2010-03-01

    Sam Goudsmit was already a famous theoretical physicist in his thirties, mainly because of his co-discovery of electron spin with George Uhlenbeck while both were students of Paul Ehrenfest in Holland in 1925. He and Uhlenbeck continued their thriving careers at the University of Michigan. Goudsmit's style as a physicist was always to make as close a connection between theory and experiment as possible. Thus, for example, his development with his student Robert Bacher of the technique called ``fractional parentage'' used fruitfully in both atomic and nuclear physics to compute energy levels of unknown states in terms of know ones. He also delved deeply into problems related to determinations of nuclear spins and moments. Partly because of his service as scientific leader of the Alsos project at the end of WWII he became a leading statesman of science. I will describe some of his achievements both as a physicist and as a statesman, prior to his becoming Editor in Chief of the American Physical Society.

  17. Sam Shepard and the dysfunctional American family: therapeutic perspectives.

    PubMed

    Sparr, L F; Erstling, S S; Boehnlein, J K

    1990-10-01

    In depicting dysfunctional families Sam Shepard brought a greater intensity level to family portrayals than had previously been seen in modern American theater. In part, his plays appear to reflect the tumultuous tone of the late 1960s and early 1970s when American society was in flux and when the national uncertainty reached down to the basic unit of society, the family. Yet, despite addressing recently emerging social issues, Shepard's plays also depict universal family conflicts. There have been and always will be compelling forces that threaten domestic cohesiveness. While Shepard's families reflect extremely high levels of disorganization, they also demonstrate scenarios recognizable to all family therapists. They reassert the family's power and its influence on individual development. They also indirectly ask us to reflect on our current clinical practice and research. Family therapists need to continue to pay attention the content issues of family organization as well as therapeutic techniques. Shepard's plays remind therapists to look beyond internal dynamics in order to consider connections and affiliations that integrate families with outside communities. He underscores the importance of knowing the meaning and context of traditional rites of passage within families. Family therapists or other care providers may unwittingly undermine the significance of these family rituals by prescription of "expert" advice.

  18. CD and NMR conformational studies of a peptide encompassing the Mid Loop interface of Ship2-Sam.

    PubMed

    Mercurio, Flavia A; Scognamiglio, Pasqualina L; Di Natale, Concetta; Marasco, Daniela; Pellecchia, Maurizio; Leone, Marilisa

    2014-11-01

    The lipid phosphatase Ship2 is a protein that intervenes in several diseases such as diabetes, cancer, neurodegeneration, and atherosclerosis. It is made up of a catalytic domain and several protein docking modules such as a C-terminal Sam (Sterile alpha motif) domain. The Sam domain of Ship2 (Ship2-Sam) binds to the Sam domains of the EphA2 receptor (EphA2-Sam) and the PI3K effector protein Arap3 (Arap3-Sam). These heterotypic Sam-Sam interactions occur through formation of dimers presenting the canonical "Mid Loop/End Helix" binding mode. The central region of Ship2-Sam, spanning the C-terminal end of α2, the α3 and α4 helices together with the α2α3 and α3α4 interhelical loops, forms the Mid Loop surface that is needed to bind partners Sam domains. A peptide encompassing most of the Ship2-Sam Mid Loop interface (Shiptide) capable of binding to both EphA2-Sam and Arap3-Sam, was previously identified. Here we investigated the conformational features of this peptide, through solution CD and NMR studies in different conditions. These studies reveal that the peptide is highly flexible in aqueous buffer, while it adopts a helical conformation in presence of 2,2,2-trifluoroethanol. The discovered structural insights and in particular the identification of a helical motif, may lead to the design of more constrained and possibly cell permeable Shiptide analogs that could work as efficient antagonists of Ship2-Sam heterotypic interactions and embrace therapeutic applications.

  19. Development of and flight results from the Space Acceleration Measurement System (SAMS)

    NASA Technical Reports Server (NTRS)

    Delombard, Richard; Finley, Brian D.; Baugher, Charles R.

    1992-01-01

    Described here is the development of and the flight results from the Space Acceleration Measurement System (SAMS) flight units used in the Orbiter middeck, Spacelab module, and the Orbitercargo bay. The SAMS units are general purpose microgravity accelerometers designed to support a variety of science experiments with microgravity acceleration measurements. A total of six flight units have been fabricated; four for use in the Orbiter middeck and Spacelab module, and two for use in the Orbiter cargo bay. The design of the units is briefly described. The initial two flights of SAMS units on STS-40 (June 1991) and STS-43 (August 1991) resulted in 371 megabytes and 2.6 gigabytes of data respectively. Analytical techniques developed to examine this quantity of acceleration data are described and sample plots of analyzed data are illustrated. Future missions for the SAMS units are listed.

  20. Introduction to the thematic minireview series on radical S-adenosylmethionine (SAM) enzymes.

    PubMed

    Banerjee, Ruma

    2015-02-13

    In the early days, radical enzyme reactions that use S-adenosylmethionine (SAM) coordinated to an Fe-S cluster, which Perry Frey described as a "poor man's coenzyme B12," were believed to be relatively rare chemical curiosities. Today, bioinformatics analyses have revealed the wide prevalence and sheer numbers of radical SAM enzymes, conferring superfamily status. In this thematic minireview series, the JBC presents six articles on radical SAM enzymes that accomplish wide-ranging chemical transformations. We learn that despite the diversity of the reactions catalyzed, family members share some common structural and mechanistic themes. Still in its infancy, continued explorations promise to be fertile grounds for discoveries that will undoubtedly further broaden our understanding of the catalytic repertoire and deepen our understanding of the chemical strategies used by radical SAM enzymes. PMID:25477525

  1. Radical SAM enzymes in the biosynthesis of sugar-containing natural products.

    PubMed

    Ruszczycky, Mark W; Ogasawara, Yasushi; Liu, Hung-Wen

    2012-11-01

    Carbohydrates play a key role in the biological activity of numerous natural products. In many instances their biosynthesis requires radical mediated rearrangements, some of which are catalyzed by radical SAM enzymes. BtrN is one such enzyme responsible for the dehydrogenation of a secondary alcohol in the biosynthesis of 2-deoxystreptamine. DesII is another example that catalyzes a deamination reaction necessary for the net C4 deoxygenation of a glucose derivative en route to desosamine formation. BtrN and DesII represent the two most extensively characterized radical SAM enzymes involved in carbohydrate biosynthesis. In this review, we summarize the biosynthetic roles of these two enzymes, their mechanisms of catalysis, the questions that have arisen during these investigations and the insight they can offer for furthering our understanding of radical SAM enzymology. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology. PMID:22172915

  2. Radical SAM enzymes in the biosynthesis of sugar-containing natural products☆

    PubMed Central

    Ruszczycky, Mark W.; Ogasawara, Yasushi; Liu, Hung-wen

    2012-01-01

    Carbohydrates play a key role in the biological activity of numerous natural products. In many instances their biosynthesis requires radical mediated rearrangements, some of which are catalyzed by radical SAM enzymes. BtrN is one such enzyme responsible for the dehydrogenation of a secondary alcohol in the biosynthesis of 2-deoxystreptamine. DesII is another example that catalyzes a deamination reaction necessary for the net C4 deoxygenation of a glucose derivative en route to desosamine formation. BtrN and DesII represent the two most extensively characterized radical SAM enzymes involved in carbohydrate biosynthesis. In this review, we summarize the biosynthetic roles of these two enzymes, their mechanisms of catalysis, the questions that have arisen during these investigations and the insight they can offer for furthering our understanding of radical SAM enzymology. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology. PMID:22172915

  3. SAmBA: an interactive software for optimizing the design of biological macromolecules crystallization experiments.

    PubMed

    Audic, S; Lopez, F; Claverie, J M; Poirot, O; Abergel, C

    1997-10-01

    SAmBA is a new software for the design of minimal experimental protocols using the notion of orthogonal arrays of strength 2. The main application of SAmBA is the search of protein crystallization conditions. Given a user input defining the relevant effectors/variables (e.g., pH, temperature, salts) and states (e.g., pH: 5, 6, 7 and 8), this software proposes an optimal set of experiments in which all tested variables and the pairwise interactions between them are symmetrically sampled. No a priori restrictions on the number and range of experimental variables is imposed. SAmBA consists of two complementary programs, SAm and BA, using a simulated annealing approach and a backtracking algorithm, respectively. The software is freely available as C code or as an interactive JAVA applet at http:/(/)igs-server.cnrs-mrs.fr. PMID:9329089

  4. Radical SAM enzymes involved in the biosynthesis of purine-based natural products

    PubMed Central

    Bandarian, Vahe

    2013-01-01

    The radical S-adenosyl-L-methionine (SAM) superfamily is a widely distributed group of iron-sulfur containing proteins that exploit the reactivity of the high energy intermediate, 5’-deoxyadenosyl radical, which is produced by reductive cleavage of SAM, to carry-out complex radical-mediated transformations. The reactions catalyzed by radical SAM enzymes range from simple group migrations to complex reactions in protein and RNA modification. This review will highlight three radical SAM enzymes that catalyze reactions involving modified guanosines in the biosynthesis pathways of the hypermodified tRNA base wybutosine; secondary metabolites of 7-deazapurine structure, including the hypermodified tRNA base queuosine; and the redox cofactor F420. PMID:22902275

  5. Tandem SAM Domain Structure of Human Caskin1: A Presynaptic, Self-Assembling Scaffold for CASK

    SciTech Connect

    Stafford, Ryan L.; Hinde, Elizabeth; Knight, Mary Jane; Pennella, Mario A.; Ear, Jason; Digman, Michelle A.; Gratton, Enrico; Bowie, James U.

    2012-02-07

    The synaptic scaffolding proteins CASK and Caskin1 are part of the fibrous mesh of proteins that organize the active zones of neural synapses. CASK binds to a region of Caskin1 called the CASK interaction domain (CID). Adjacent to the CID, Caskin1 contains two tandem sterile a motif (SAM) domains. Many SAM domains form polymers so they are good candidates for forming the fibrous structures seen in the active zone. We show here that the SAM domains of Caskin1 form a new type of SAM helical polymer. The Caskin1 polymer interface exhibits a remarkable segregation of charged residues, resulting in a high sensitivity to ionic strength in vitro. The Caskin1 polymers can be decorated with CASK proteins, illustrating how these proteins may work together to organize the cytomatrix in active zones.

  6. The Principal as Resource Allocator.

    ERIC Educational Resources Information Center

    Peterson, Kent D.

    The effect of political influences on the allocation of personnel, money, facilities, and equipment by elementary school principals is discussed in this paper. The use of Zald's political economy framework as a tool for understanding the principal's role in allocating resources is described by the author. He suggests that the principal occupies a…

  7. Bringing a Chemical Laboratory Named Sam to Mars on the 2011 Curiosity Rover

    NASA Astrophysics Data System (ADS)

    Mahaffy, P. R.; Bleacher, L.; Jones, A.; Atreya, S. K.; Manning, H. L.; Cabane, M.; Webster, C. R.; Sam Team

    2010-12-01

    Introduction: An important goal of upcoming missions to Mars is to understand if life could have developed there. The task of the Sample Analysis at Mars (SAM) suite of instruments [1] and the other Curiosity investigations [2] is to move us steadily toward that goal with an assessment of the habitability of our neighboring planet through a series of chemical and geological measurements. SAM is designed to search for organic compounds and inorganic volatiles and measure isotope ratios. Other instruments on Curiosity will provide elemental analysis and identify minerals. SAM will analyze both atmospheric samples and gases evolved from powdered rocks that may have formed billions of years ago with Curiosity providing access to interesting sites scouted by orbiting cameras and spectrometers. SAM Instrument Suite: SAM’s instruments are a Quadrupole Mass Spectrometer (QMS), a 6-column Gas Chromatograph (GC), and a 2-channel Tunable Laser Spectrometer (TLS). SAM can identify organic compounds in Mars rocks to sub-ppb sensitivity and secure precise isotope ratios for C, H, and O in carbon dioxide and water and measure trace levels of methane and its carbon 13 isotope. The SAM gas processing system consists of valves, heaters, pressure sensors, gas scrubbers and getters, traps, and gas tanks used for calibration or combustion experiments [2]. A variety of calibrant compounds interior and exterior to SAM will allow the science and engineering teams to assess SAM’s performance. SAM has been calibrated and tested in a Mars-like environment. Keeping Educators and the Public Informed: The Education and Public Outreach (EPO) goals of the SAM team are to make this complex chemical laboratory and its data widely available to educators, students, and the public. Formal education activities include developing templates for professional development workshops for educators to teach them about SAM and Curiosity, incorporating data into Mars Student Data Teams, and writing articles

  8. Inkless microcontact printing on SAMs of Boc- and TBS-protected thiols.

    PubMed

    Shestopalov, Alexander A; Clark, Robert L; Toone, Eric J

    2010-01-01

    We report a new inkless catalytic muCP technique that achieves accurate, fast, and complete pattern reproduction on SAMs of Boc- and TBS-protected thiols immobilized on gold using a polyurethane-acrylate stamp functionalized with covalently bound sulfonic acids. Pattern transfer is complete at room temperature just after one minute of contact and renders sub-200 nm size structures of chemically differentiated SAMs.

  9. The Combustion Experiment on the Sample Analysis at Mars (SAM) Instrument Suite on the Curiosity Rover

    NASA Technical Reports Server (NTRS)

    Stern, J. C.; Malespin, C. A.; Eigenbrode, J. L.; Graham, H. V.; Archer, P. D., Jr.; Brunner, A. E.; Freissinet, C.; Franz, H. B.; Fuentes, J.; Glavin, D. P.; Leshin, L. A.; Mahaffy, P. R.; McAdam, A. C.; Ming, D. W.; Navvaro-Gonzales, R.; Niles, P. B.; Steele, A.

    2014-01-01

    The combustion experiment on the Sample Analysis at Mars (SAM) suite on Curiosity will heat a sample of Mars regolith in the presence of oxygen and measure composition of the evolved gases using quadrupole mass spectrometry (QMS) and tunable laser spectrometry (TLS). QMS will enable detection of combustion products such as CO, CO2, NO, and other oxidized species, while TLS will enable precise measurements of the abundance and carbon isotopic composition (delta(sup 13)C) of the evolved CO2 and hydrogen isotopic composition (deltaD) of H2O. SAM will perform a two-step combustion to isolate combustible materials below approx.550 C and above approx.550 C. The combustion experiment on SAM, if properly designed and executed, has the potential to answer multiple questions regarding the origins of volatiles seen thus far in SAM evolved gas analysis (EGA) on Mars. Constraints imposed by SAM and MSL time and power resources, as well as SAM consumables (oxygen gas), will limit the number of SAM combustion experiments, so it is imperative to design an experiment targeting the most pressing science questions. Low temperature combustion experiments will primarily target the quantification of carbon (and nitrogen) contributed by SAM wet chemistry reagants MTBSTFA (N-Methyl-N-tert-butyldimethylsilyltrifluoroacetamide) and DMF (Dimethylformamide), which have been identified in the background of blank and sample runs and may adsorb to the sample while the cup is in the Sample Manipulation System (SMS). In addition, differences between the sample and "blank" may yield information regarding abundance and delta(sup 13)C of bulk (both organic and inorganic) martian carbon. High temperature combustion experiments primarily aim to detect refractory organic matter, if present in Cumberland fines, as well as address the question of quantification and deltaD value of water evolution associated with hydroxyl hydrogen in clay minerals.

  10. Identification of trans-acting factors regulating SamDC expression in Oryza sativa

    SciTech Connect

    Basu, Supratim; Roychoudhury, Aryadeep; Sengupta, Dibyendu N.

    2014-03-07

    Highlights: • Identification of cis elements responsible for SamDC expression by in silico analysis. • qPCR analysis of SamDC expression to abiotic and biotic stress treatments. • Detection of SamDC regulators using identified cis-elements as probe by EMSA. • Southwestern Blot analysis to predict the size of the trans-acting factors. - Abstract: Abiotic stress affects the growth and productivity of crop plants; to cope with the adverse environmental conditions, plants have developed efficient defense machinery comprising of antioxidants like phenolics and flavonoids, and osmolytes like polyamines. SamDC is a key enzyme in the polyamine biosynthesis pathway in plants. In our present communication we have done in silico analysis of the promoter region of SamDC to look for the presence of different cis-regulatory elements contributing to its expression. Based on the presence of different cis-regulatory elements we completed comparative analysis of SamDC gene expression in rice lamina of IR-29 and Nonabokra by qPCR in response to the abiotic stress treatments of salinity, drought, cold and the biotic stress treatments of ABA and light. Additionally, to explore the role of the cis-regulatory elements in regulating the expression of SamDC gene in plants we comparatively analyzed the binding of rice nuclear proteins prepared from IR-29 and Nonabokra undergoing various stress treatments. The intensity of the complex formed was low and inducible in IR-29 in contrast to Nonabokra. Southwestern blot analysis helped in predicting the size of the trans-acting factors binding to these cis-elements. To our knowledge this is the first report on the comprehensive analysis of SamDC gene expression in rice and identification of the trans-acting factors regulating its expression.

  11. 24 CFR 92.50 - Formula allocation.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false Formula allocation. 92.50 Section... Development HOME INVESTMENT PARTNERSHIPS PROGRAM Allocation Formula § 92.50 Formula allocation. (a) Jurisdictions eligible for a formula allocation. HUD will provide allocations of funds in amounts determined...

  12. 23 CFR 1240.15 - Allocations.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 23 Highways 1 2010-04-01 2010-04-01 false Allocations. 1240.15 Section 1240.15 Highways NATIONAL... GUIDELINES SAFETY INCENTIVE GRANTS FOR USE OF SEAT BELTS-ALLOCATIONS BASED ON SEAT BELT USE RATES Determination of Allocations § 1240.15 Allocations. (a) Funds allocated under this part shall be available...

  13. Contribution of sams-1 and pmt-1 to lipid homoeostasis in adult Caenorhabditis elegans.

    PubMed

    Li, Yingxiu; Na, Keun; Lee, Hyoung-Joo; Lee, Eun-Young; Paik, Young-Ki

    2011-05-01

    Accumulation of lipids inside the cell is primarily caused by disorders of lipid metabolism. S-adenosylmethionine synthetase (SAMS) produces SAM, an important methyl donor in various phospholipid methyltransferase reactions catalysed by phosphoethanolamine N-methyltransferase (PMT-1). A gel-based, quantitative proteomic analysis of the RNA interference (RNAi)-mediated inactivation of the pod-2 gene, which encodes acetyl-CoA carboxylase, showed a substantial down-regulation of SAMS-1. Consequently, RNAi of either sams-1 or pmt-1 caused a significant increase in lipid droplet size in the intestine of Caenorhabditis elegans. Lipid droplets exhibited increased triacylglycerol (TG) and decreased phosphatidylcholine (PC) levels, suggesting a reciprocal relationship between TG and PC regulation. These lipid-associated phenotypes were rescued by choline feeding. Among the five fat metabolism-related genes examined, two genes were highly induced by inactivation of sams-1 or pmt-1: pod-2 and stearoyl-CoA desaturase (fat-7). Thus, both SAMS-1 and PMT-1 were shown to contribute to the homoeostasis of TG and PC levels in C. elegans, which would provide an important survival strategy under harsh environmental conditions.

  14. Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase

    DOE PAGES

    Fenwick, Michael K.; Mehta, Angad P.; Zhang, Yang; Abdelwahed, Sameh H.; Begley, Tadhg P.; Ealick, Steven E.

    2015-03-27

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active sitemore » metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.« less

  15. Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase

    NASA Astrophysics Data System (ADS)

    Fenwick, Michael K.; Mehta, Angad P.; Zhang, Yang; Abdelwahed, Sameh H.; Begley, Tadhg P.; Ealick, Steven E.

    2015-03-01

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5‧-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.

  16. Sam68 Is Required for DNA Damage Responses via Regulating Poly(ADP-ribosyl)ation

    PubMed Central

    Hodgson, Andrea; Wier, Eric M.; Wen, Matthew G.; Kamenyeva, Olena; Xia, Xue; Koo, Lily Y.

    2016-01-01

    The rapid and robust synthesis of polymers of adenosine diphosphate (ADP)-ribose (PAR) chains, primarily catalyzed by poly(ADP-ribose) polymerase 1 (PARP1), is crucial for cellular responses to DNA damage. However, the precise mechanisms through which PARP1 is activated and PAR is robustly synthesized are not fully understood. Here, we identified Src-associated substrate during mitosis of 68 kDa (Sam68) as a novel signaling molecule in DNA damage responses (DDRs). In the absence of Sam68, DNA damage-triggered PAR production and PAR-dependent DNA repair signaling were dramatically diminished. With serial cellular and biochemical assays, we demonstrated that Sam68 is recruited to and significantly overlaps with PARP1 at DNA lesions and that the interaction between Sam68 and PARP1 is crucial for DNA damage-initiated and PARP1-conferred PAR production. Utilizing cell lines and knockout mice, we illustrated that Sam68-deleted cells and animals are hypersensitive to genotoxicity caused by DNA-damaging agents. Together, our findings suggest that Sam68 plays a crucial role in DDR via regulating DNA damage-initiated PAR production. PMID:27635653

  17. Sam68 Is Required for DNA Damage Responses via Regulating Poly(ADP-ribosyl)ation.

    PubMed

    Sun, Xin; Fu, Kai; Hodgson, Andrea; Wier, Eric M; Wen, Matthew G; Kamenyeva, Olena; Xia, Xue; Koo, Lily Y; Wan, Fengyi

    2016-09-01

    The rapid and robust synthesis of polymers of adenosine diphosphate (ADP)-ribose (PAR) chains, primarily catalyzed by poly(ADP-ribose) polymerase 1 (PARP1), is crucial for cellular responses to DNA damage. However, the precise mechanisms through which PARP1 is activated and PAR is robustly synthesized are not fully understood. Here, we identified Src-associated substrate during mitosis of 68 kDa (Sam68) as a novel signaling molecule in DNA damage responses (DDRs). In the absence of Sam68, DNA damage-triggered PAR production and PAR-dependent DNA repair signaling were dramatically diminished. With serial cellular and biochemical assays, we demonstrated that Sam68 is recruited to and significantly overlaps with PARP1 at DNA lesions and that the interaction between Sam68 and PARP1 is crucial for DNA damage-initiated and PARP1-conferred PAR production. Utilizing cell lines and knockout mice, we illustrated that Sam68-deleted cells and animals are hypersensitive to genotoxicity caused by DNA-damaging agents. Together, our findings suggest that Sam68 plays a crucial role in DDR via regulating DNA damage-initiated PAR production. PMID:27635653

  18. The Dynamic of Annual Carbon Allocation to Wood in European Forests Is Consistent with a Combined Source-Sink Limitation of Growth: Implications on Growth Simulations in a Terrestrial Biosphere Model

    NASA Astrophysics Data System (ADS)

    Guillemot, J.; Martin-StPaul, N. K.; Dufrêne, E.; François, C.; Soudani, K.; Ourcival, J. M.; Leadley, P.; Delpierre, N.

    2014-12-01

    The extent to which forest growth is limited by carbon (C) supply (source control) or by cambial activity (sink control) will strongly determines the responses of trees to global changes. However, the physiological processes responsible for the limitation of forest growth are still under debate. The aim of this study was i) to evaluate the key drivers of the annual carbon allocation to wood along large soil and climate regional gradients in four tree species representative of the main European forest biomes (Fagus sylvatica, Quercus petraea, Quercus ilex and Picea abies) ii) to implement the identified key drivers in a new C allocation scheme within the CASTANEA terrestrial biosphere model (TBM). Combining field measurements and process-based simulations at 49 sites (931 site-years), our analyses revealed that the inter-site variability in C allocation to wood was predominantly driven by an age-related decline. The direct control of temperature or water stress on sink activity (i.e. independently from their effects on C supply) exerted a strong influence on the annual woody growth in all the species considered, including deciduous temperate species. The lagged effect of the past environment conditions was a significant driver of the annual C allocation to wood. Carbon supply appeared to strongly limit growth only in deciduous temperate species. Our study supports the premise that European forest growth is under a complex panel of source- and sink- limitations, contradicting the simple source control implemented in most TBMs. The implementation of these combined forest growth limitations in the CASTANEA model significantly improved its performance when evaluated against independent stand growth data at the regional scale (mainland France, >103 plots). We finally discuss how the sink imitation affects the CASTANEA simulated projections of forest productivity along the 21th century, especially with respect to the expected fertilizing effect of increasing atmospheric

  19. Active Region Soft X-Ray Spectra and Temperature Analyses based on Sounding Rocket Measurements from the Solar Aspect Monitor (SAM), - a Modified SDO/EVE Instrument

    NASA Astrophysics Data System (ADS)

    Didkovsky, Leonid V.; Wieman, Seth; Woods, Thomas N.; Jones, Andrew; Moore, Christopher

    2016-05-01

    Some initial results of soft x-ray spectral (0.5 to 3.0 nm) observations of active regions (AR11877 and AR11875) from a sounding rocket flight NASA 36.290 on 21 October 2013 at about 18:30 UT are reported. These observations were made by a Solar Aspect Monitor (SAM), a rocket version of the EUV Variability Experiment’s (EVE) channel, a pinhole camera modified for EVE rocket suite of instruments to include a free-standing transmission grating (200 nm period), which provided spectrally-resolved images of the solar disk. Intensity ratios for strong emission lines extracted from temporally averaged SAM spectral profiles of the ARs were compared to appropriately convolved modeled CHIANTI spectra. These ratios represent the AR’s temperature structures, which are compared to the structures derived from some other observations and temperature models.

  20. Adaptive Control Allocation in the Presence of Actuator Failures

    NASA Technical Reports Server (NTRS)

    Liu, Yu; Crespo, Luis G.

    2010-01-01

    In this paper, a novel adaptive control allocation framework is proposed. In the adaptive control allocation structure, cooperative actuators are grouped and treated as an equivalent control effector. A state feedback adaptive control signal is designed for the equivalent effector and allocated to the member actuators adaptively. Two adaptive control allocation algorithms are proposed, which guarantee closed-loop stability and asymptotic state tracking in the presence of uncertain loss of effectiveness and constant-magnitude actuator failures. The proposed algorithms can be shown to reduce the controller complexity with proper grouping of the actuators. The proposed adaptive control allocation schemes are applied to two linearized aircraft models, and the simulation results demonstrate the performance of the proposed algorithms.

  1. Resource Balancing Control Allocation

    NASA Technical Reports Server (NTRS)

    Frost, Susan A.; Bodson, Marc

    2010-01-01

    Next generation aircraft with a large number of actuators will require advanced control allocation methods to compute the actuator commands needed to follow desired trajectories while respecting system constraints. Previously, algorithms were proposed to minimize the l1 or l2 norms of the tracking error and of the control effort. The paper discusses the alternative choice of using the l1 norm for minimization of the tracking error and a normalized l(infinity) norm, or sup norm, for minimization of the control effort. The algorithm computes the norm of the actuator deflections scaled by the actuator limits. Minimization of the control effort then translates into the minimization of the maximum actuator deflection as a percentage of its range of motion. The paper shows how the problem can be solved effectively by converting it into a linear program and solving it using a simplex algorithm. Properties of the algorithm are investigated through examples. In particular, the min-max criterion results in a type of resource balancing, where the resources are the control surfaces and the algorithm balances these resources to achieve the desired command. A study of the sensitivity of the algorithms to the data is presented, which shows that the normalized l(infinity) algorithm has the lowest sensitivity, although high sensitivities are observed whenever the limits of performance are reached.

  2. Detecting non-binomial sex allocation when developmental mortality operates.

    PubMed

    Wilkinson, Richard D; Kapranas, Apostolos; Hardy, Ian C W

    2016-11-01

    Optimal sex allocation theory is one of the most intricately developed areas of evolutionary ecology. Under a range of conditions, particularly under population sub-division, selection favours sex being allocated to offspring non-randomly, generating non-binomial variances of offspring group sex ratios. Detecting non-binomial sex allocation is complicated by stochastic developmental mortality, as offspring sex can often only be identified on maturity with the sex of non-maturing offspring remaining unknown. We show that current approaches for detecting non-binomiality have limited ability to detect non-binomial sex allocation when developmental mortality has occurred. We present a new procedure using an explicit model of sex allocation and mortality and develop a Bayesian model selection approach (available as an R package). We use the double and multiplicative binomial distributions to model over- and under-dispersed sex allocation and show how to calculate Bayes factors for comparing these alternative models to the null hypothesis of binomial sex allocation. The ability to detect non-binomial sex allocation is greatly increased, particularly in cases where mortality is common. The use of Bayesian methods allows for the quantification of the evidence in favour of each hypothesis, and our modelling approach provides an improved descriptive capability over existing approaches. We use a simulation study to demonstrate substantial improvements in power for detecting non-binomial sex allocation in situations where current methods fail, and we illustrate the approach in real scenarios using empirically obtained datasets on the sexual composition of groups of gregarious parasitoid wasps.

  3. Accounting for Parcel-Allocation Variability in Practice: Combining Sources of Uncertainty and Choosing the Number of Allocations.

    PubMed

    Sterba, Sonya K; Rights, Jason D

    2016-01-01

    Item parceling remains widely used under conditions that can lead to parcel-allocation variability in results. Hence, researchers may be interested in quantifying and accounting for parcel-allocation variability within sample. To do so in practice, three key issues need to be addressed. First, how can we combine sources of uncertainty arising from sampling variability and parcel-allocation variability when drawing inferences about parameters in structural equation models? Second, on what basis can we choose the number of repeated item-to-parcel allocations within sample? Third, how can we diagnose and report proportions of total variability per estimate arising due to parcel-allocation variability versus sampling variability? This article addresses these three methodological issues. Developments are illustrated using simulated and empirical examples, and software for implementing them is provided.

  4. SAM-Like Evolved Gas Analyses of Phyllosilicate Minerals and Applications to SAM Analyses of the Sheepbed Mudstone, Gale Crater, Mars

    NASA Technical Reports Server (NTRS)

    McAdam, A. C.; Franz, H. B.; Mahaffy, P. R.; Eigenbrode, J. L.; Stern, J. C.; Brunner, B.; Sutter, B.; Archer, P. D.; Ming , D. W.; Morris, R. V.; Bish, D. L.; Atreya, S. K.

    2014-01-01

    While in Yellowknife Bay, the Mars Science Laboratory Curiosity rover collected two drilled samples, John Klein (hereafter "JK") and Cumberland ("CB"), from the Sheepbed mudstone, as well as a scooped sample from the Rocknest aeolian bedform ("RN"). These samples were sieved by Curiosity's sample processing system and then several subsamples of these materials were delivered to the Sample Analysis at Mars (SAM) instrument suite and the CheMin X-ray diffraction/X-ray fluorescence instrument. CheMin provided the first in situ X-ray diffraction-based evidence of clay minerals on Mars, which are likely trioctahedral smectites (e.g., Fe-saponite) and comprise 20 wt% of the mudstone samples [1]. SAM's evolved gas analysis (EGA) mass spectrometry analyses of JK and CB subsamples, as well as RN subsamples, detected H2O, CO2, O2, H2, SO2, H2S, HCl, NO, OCS, CS2 and other trace gases evolved during pyrolysis. The identity of evolved gases and temperature( s) of evolution can augment mineral detection by CheMin and place constraints on trace volatile-bearing phases present below the CheMin detection limit or those phases difficult to characterize with XRD (e.g., X-ray amorphous phases). Here we will focus on the SAM H2O data, in the context of CheMin analyses, and comparisons to laboratory SAM-like analyses of several phyllosilicate minerals including smectites.

  5. Probing the nature and resistance of the molecule-electrode contact in SAM-based junctions

    NASA Astrophysics Data System (ADS)

    Suchand Sangeeth, C. S.; Wan, Albert; Nijhuis, Christian A.

    2015-07-01

    It is challenging to quantify the contact resistance and to determine the nature of the molecule-electrode contacts in molecular two-terminal junctions. Here we show that potentiodynamic and temperature dependent impedance measurements give insights into the nature of the SAM-electrode interface and other bottlenecks of charge transport (the capacitance of the SAM (CSAM) and the resistance of the SAM (RSAM)), unlike DC methods, independently of each other. We found that the resistance of the top-electrode-SAM contact for junctions with the form of AgTS-SCn//GaOx/EGaIn with n = 10, 12, 14, 16 or 18 is bias and temperature independent and hence Ohmic (non-rectifying) in nature, and is orders of magnitude smaller than RSAM. The CSAM and RSAM are independent of the temperature, indicating that the mechanism of charge transport in these SAM-based junctions is coherent tunneling and the charge carrier trapping at the interfaces is negligible.It is challenging to quantify the contact resistance and to determine the nature of the molecule-electrode contacts in molecular two-terminal junctions. Here we show that potentiodynamic and temperature dependent impedance measurements give insights into the nature of the SAM-electrode interface and other bottlenecks of charge transport (the capacitance of the SAM (CSAM) and the resistance of the SAM (RSAM)), unlike DC methods, independently of each other. We found that the resistance of the top-electrode-SAM contact for junctions with the form of AgTS-SCn//GaOx/EGaIn with n = 10, 12, 14, 16 or 18 is bias and temperature independent and hence Ohmic (non-rectifying) in nature, and is orders of magnitude smaller than RSAM. The CSAM and RSAM are independent of the temperature, indicating that the mechanism of charge transport in these SAM-based junctions is coherent tunneling and the charge carrier trapping at the interfaces is negligible. Electronic supplementary information (ESI) available: Detailed experimental procedure, Nyquist

  6. Ethical considerations surrounding survival benefit-based liver allocation.

    PubMed

    Keller, Eric J; Kwo, Paul Y; Helft, Paul R

    2014-02-01

    The disparity between the demand for and supply of donor livers has continued to grow over the last 2 decades, and this has placed greater weight on the need for efficient and effective liver allocation. Although the use of extended criteria donors has shown great potential, it remains unregulated. A survival benefit-based model was recently proposed to answer calls to increase efficiency and reduce futile transplants. However, it was previously determined that the current allocation system was not in need of modification and that instead geographic disparities should be addressed. In contrast, we believe that there is a significant need to replace the current allocation system and complement efforts to improve donor liver distribution. We illustrate this need first by identifying major ethical concerns shaping liver allocation and then by using these concerns to identify strengths and shortcomings of the Model for End-Stage Liver Disease/Pediatric End-Stage Liver Disease system and a survival benefit-based model. The latter model is a promising means of improving liver allocation: it incorporates a greater number of ethical principles, uses a sophisticated statistical model to increase efficiency and reduce waste, minimizes bias, and parallels developments in the allocation of other organs. However, it remains limited in its posttransplant predictive accuracy and may raise potential issues regarding informed consent. In addition, the proposed model fails to include quality-of-life concerns and prioritize younger patients. We feel that it is time to take the next steps toward better liver allocation not only through reductions in geographic disparities but also through the adoption of a model better equipped to balance the many ethical concerns shaping organ allocation. Thus, we support the development of a similar model with suggested amendments. PMID:24166860

  7. Collaborative Resource Allocation

    NASA Technical Reports Server (NTRS)

    Wang, Yeou-Fang; Wax, Allan; Lam, Raymond; Baldwin, John; Borden, Chester

    2007-01-01

    Collaborative Resource Allocation Networking Environment (CRANE) Version 0.5 is a prototype created to prove the newest concept of using a distributed environment to schedule Deep Space Network (DSN) antenna times in a collaborative fashion. This program is for all space-flight and terrestrial science project users and DSN schedulers to perform scheduling activities and conflict resolution, both synchronously and asynchronously. Project schedulers can, for the first time, participate directly in scheduling their tracking times into the official DSN schedule, and negotiate directly with other projects in an integrated scheduling system. A master schedule covers long-range, mid-range, near-real-time, and real-time scheduling time frames all in one, rather than the current method of separate functions that are supported by different processes and tools. CRANE also provides private workspaces (both dynamic and static), data sharing, scenario management, user control, rapid messaging (based on Java Message Service), data/time synchronization, workflow management, notification (including emails), conflict checking, and a linkage to a schedule generation engine. The data structure with corresponding database design combines object trees with multiple associated mortal instances and relational database to provide unprecedented traceability and simplify the existing DSN XML schedule representation. These technologies are used to provide traceability, schedule negotiation, conflict resolution, and load forecasting from real-time operations to long-range loading analysis up to 20 years in the future. CRANE includes a database, a stored procedure layer, an agent-based middle tier, a Web service wrapper, a Windows Integrated Analysis Environment (IAE), a Java application, and a Web page interface.

  8. The Search for Nitrates on Mars by the Sample Analysis at Mars (SAM) Instrument

    NASA Technical Reports Server (NTRS)

    Navarro-Gonzalez, Rafael; Stern, Jennifer C.; Freissinet, Caroline; McKay, Chirstopher P.; Sutter, Brad; Archer, P. Douglas, Jr.; McAdam, Amy; Franz, Heather; Coll, Partice J.; Glavin, Daniel Patrick; Eigenbrode, Jennifer L.; Wong, Mike; Atreya, Sushiil K.; Wray, James J.; Steele, Andrew; Prats, Benito D.; Szopa, Cyril; Coscia, David; Teinturier, Samuel; Buch, Arnaud; Leshin, Laurie A.; Ming, Douglas W.; Conrad, Pamela Gales; Cabane, Michel; Mahaffy, Paul R.; Grotzinger, John P.

    2013-01-01

    Planetary models suggest that nitrogen was abundant in the early Martian atmosphere as N2 but it was lost by sputtering and photochemical loss to space, impact erosion, and chemical oxidation to nitrates. A nitrogen cycle may exist on Mars where nitrates, produced early in Mars' history, may have been later decomposed back into N2 by the current impact flux. Nitrates are a fundamental source of nitrogen for terrestrial microorganisms, and they have evolved metabolic pathways to perform both oxidation and reduction to drive a complete biological nitrogen cycle. Therefore, the characterization of nitrogen in Martian soils is important to assess habitability of the Martian environment, particularly with respect to the presence of nitrates. The only previous mission that was designed to search for soil nitrates was the Phoenix mission but N-containing species were not detected by TEGA or the MECA WCL. Nitrates have been tentatively identified in Nakhla meteorites, and if nitrogen was oxidized on Mars, this has important implications for the habitability potential of Mars. Here we report the results from the Sample Analysis at Mars (SAM) instrument suite aboard the Curiosity rover during the first year of surface operations in Gale Crater. Samples from the Rocknest aeolian deposit and sedimentary rocks (John Klein) were heated to approx 835degC under helium flow and the evolved gases were analyzed by MS and GC-MS. Two and possibly three peaks may be associated with the release of m/z 30 at temperatures ranging from 180degC to 500degC. M/z 30 has been tentatively identified as NO; other plausible contributions include CH2O and an isotopologue of CO, 12C18O. NO, CH2O, and CO may be reaction products of reagents (MTBSTFA/DMF) carried from Earth for the wet chemical derivatization experiments with SAM and/or derived from indigenous soil nitrogenated organics. Laboratory analyses indicate that it is also possible that <550degC evolved NO is produced via reaction of HCl with

  9. Fluorocarbon Contamination from the Drill on the Mars Science Laboratory: Potential Science Impact on Detecting Martian Organics by Sample Analysis at Mars (SAM)

    NASA Technical Reports Server (NTRS)

    Eigenbrode, J. L.; McAdam, A.; Franz, H.; Freissinet, C.; Bower, H.; Floyd, M.; Conrad, P.; Mahaffy, P.; Feldman, J.; Hurowitz, J.; Evans, J.; Anderson, M.; Jandura, L.; Brown, K.; Logan, C.; Kuhn, S.; Anderson, R.; Beegle, L.; Limonadi, D.; Rainen, R.; Umland, J.

    2013-01-01

    Polytetrafluoroethylene (PTFE or trade name: Teflon by Dupont Co.) has been detected in rocks drilled during terrestrial testing of the Mars Science Laboratory (MSL) drilling hardware. The PTFE in sediments is a wear product of the seals used in the Drill Bit Assemblies (DBAs). It is expected that the drill assembly on the MSL flight model will also shed Teflon particles into drilled samples. One of the primary goals of the Sample Analysis at Mars (SAM) instrument suite on MSL is to test for the presence of martian organics in samples. Complications introduced by the potential presence of PTFE in drilled samples to the SAM evolved gas analysis (EGA or pyrolysisquadrupole mass spectrometry, pyr-QMS) and pyrolysis- gas chromatography mass spectrometry (Pyr- GCMS) experiments was investigated.

  10. Adaptive allocation for binary outcomes using decreasingly informative priors.

    PubMed

    Sabo, Roy T

    2014-01-01

    A method of outcome-adaptive allocation is presented using Bayes methods, where a natural lead-in is incorporated through the use of informative yet skeptical prior distributions for each treatment group. These prior distributions are modeled on unobserved data in such a way that their influence on the allocation scheme decreases as the trial progresses. Simulation studies show this method to behave comparably to the Bayesian adaptive allocation method described by Thall and Wathen (2007), who incorporate a natural lead-in through sample-size-based exponents.

  11. New insight into the electrochemical desorption of alkanethiol SAMs on gold.

    PubMed

    Pensa, Evangelina; Vericat, Carolina; Grumelli, Doris; Salvarezza, Roberto C; Park, Sung Hyun; Longo, Gabriel S; Szleifer, Igal; Méndez De Leo, Lucila P

    2012-09-21

    A combination of Polarization Modulation Infrared Reflection Absorption Spectroscopy (PMIRRAS) under electrochemical control, Electrochemical Scanning Tunneling Microscopy (ECSTM) and Molecular Dynamics (MD) simulations has been used to shed light on the reductive desorption process of dodecanethiol (C12) and octadecanethiol (C18) SAMs on gold in aqueous electrolytes. Experimental PMIRRAS, ECSTM and MD simulations data for C12 desorption are consistent with formation of randomly distributed micellar aggregates stabilized by Na(+) ions, coexisting with a lying-down phase of molecules. The analysis of pit and Au island coverage before and after desorption is consistent with the thiolate-Au adatoms models. On the other hand, PMIRRAS and MD data for C18 indicate that the desorbed alkanethiolates adopt a Na(+) ion-stabilized bilayer of interdigitated alkanethiolates, with no evidence of lying down molecules. MD simulations also show that both the degree of order and tilt angle of the desorbed alkanethiolates change with the surface charge on the metal, going from bilayers to micelles. These results demonstrate the complexity of the alkanethiol desorption in the presence of water and the fact that chain length and counterions play a key role in a complex structure.

  12. Possible Detection of Nitrates on Mars by the Sample Analysis at Mars (SAM) Instrument

    NASA Technical Reports Server (NTRS)

    Navarro-Gonzalez, R.; Stern, J.; Sutter, B.; Archer, D.; McAdam, A.; Franz, H. B.; McKay, C. P.; Coll, P.; Cabane, M.; Ming, D. W.; Brunner, A. E.; Glavin, D.; Eigenbrode, J. L.; Jones, J. H.; Freissinet, C.; Leshin, L.; Wong, M.; Atreya, S.; Wray, J. J.; Steele, A.; Buch, A.; Prats, B. D.; Szopa, C.; Conrad, P.; Mahaffy, P.

    2013-01-01

    Planetary models suggest that nitrogen was abundant in the early Martian atmosphere as dinitrogen (N2). However, it has been lost by sputtering and photochemical loss to space [1, 2], impact erosion [3], and chemical oxidation to nitrates [4]. Nitrates, produced early in Mars history, are later decomposed back into N2 by the current impact flux [5], making possible a nitrogen cycle on Mars. It is estimated that a layer of about 3 m of pure NaNO3 should be distributed globally on Mars [5]. Nitrates are a fundamental source for nitrogen to terrestrial microorganisms. Therefore, the detection of soil nitrates is important to assess habitability in the Martian environment. The only previous mission that was designed to search for soil nitrates was the Phoenix mission but was unable to detect evolved N-containing species by TEGA and the MECA WCL [6]. Nitrates have been tentatively identified in the Nakhla meteorite [7]. The purpose of this work is to determine if nitrates were detected in first solid sample (Rocknest) in Gale Crater examined by the SAM instrument.

  13. Carbon-sulfur bond-forming reaction catalysed by the radical SAM enzyme HydE

    NASA Astrophysics Data System (ADS)

    Rohac, Roman; Amara, Patricia; Benjdia, Alhosna; Martin, Lydie; Ruffié, Pauline; Favier, Adrien; Berteau, Olivier; Mouesca, Jean-Marie; Fontecilla-Camps, Juan C.; Nicolet, Yvain

    2016-05-01

    Carbon-sulfur bond formation at aliphatic positions is a challenging reaction that is performed efficiently by radical S-adenosyl-L-methionine (SAM) enzymes. Here we report that 1,3-thiazolidines can act as ligands and substrates for the radical SAM enzyme HydE, which is involved in the assembly of the active site of [FeFe]-hydrogenase. Using X-ray crystallography, in vitro assays and NMR spectroscopy we identified a radical-based reaction mechanism that is best described as the formation of a C-centred radical that concomitantly attacks the sulfur atom of a thioether. To the best of our knowledge, this is the first example of a radical SAM enzyme that reacts directly on a sulfur atom instead of abstracting a hydrogen atom. Using theoretical calculations based on our high-resolution structures we followed the evolution of the electronic structure from SAM through to the formation of S-adenosyl-L-cysteine. Our results suggest that, at least in this case, the widely proposed and highly reactive 5‧-deoxyadenosyl radical species that triggers the reaction in radical SAM enzymes is not an isolable intermediate.

  14. Expression and functions of the star proteins Sam68 and T-STAR in mammalian spermatogenesis.

    PubMed

    Ehrmann, Ingrid; Elliott, David J

    2010-01-01

    Spermatogenesis is one of the few major developmental pathways which are still ongoing in the adult. In this chapter we review the properties of Sam68 and T-STAR, which are the STAR proteins functionally implicated in mammalian spermatogenesis. Sam68 is a ubiquitously expressed member of the STAR family, but has an essential role in spermatogenesis. Sam68 null mice are male infertile and at least in part this is due to a failure in important translational controls that operate during and after meiosis. The homologous T-STAR protein has a much more restricted anatomic expression pattern than Sam68, with highest levels seen in the testis and the developing brain. The focus of this chapter is the functional role of Sam68 and T-STAR proteins in male germ cell development. Since these proteins are known to have many cellular functions we extrapolate from other cell types and tissues to speculate on each of their likely functions within male germ cells, including control of alternative pre-mRNA splicing patterns in male germ cells.

  15. Study of SAM surface morphology, integrity and film quality on various Au surfaces

    NASA Astrophysics Data System (ADS)

    Murphy, John; Senevirathne, Indrajith

    2013-03-01

    SAM (Self Assembled Monolayer) surfaces have many possible applications from polymer based electronics to sensor engineering. Common substrate architecture for such systems happens to be Au(111) on mica. Au on layered mica lacks mechanical resilience towards engineering applications. Solutions of 1-dodecanethiol (hydrophobic -R), dissolved in 200 proof Ethanol with 5mM concentration were prepared. These solutions were used in developing SAMs on purchased, clean flat Au(111) on mica (standard), Au sputter deposited on mica, Hydrogen flame annealed Au layers on glass, and Hydrogen flame annealed Au layers on mica. Resulting SAM surfaces were investigated with regular and custom built hydrophilic and hydrophobic AFM (Atomic Force Microcopy) probes via contact, and non contact AFM with topography and phase imaging. Surface integrity, roughness, corrugation and morphology on SAM surfaces were estimated. Preliminary data indicated total RMS surface roughness at ~ 2.8nm for SAMs on typical gold surfaces on mica purchased (standard) while varying RMS surface roughness estimates on subsequent surfaces with flame annealed samples showing similar RMS surface roughness. LHU Nanotechnology Program, PASSHE FPDC (LOU # 2010-LHU-03).

  16. Characterization of a S-adenosyl-l-methionine (SAM)-accumulating strain of Scheffersomyces stipitis.

    PubMed

    Križanović, Stela; Butorac, Ana; Mrvčić, Jasna; Krpan, Maja; Cindrić, Mario; Bačun-Družina, Višnja; Stanzer, Damir

    2015-06-01

    S-adenosyl-l-methionine (SAM) is an important molecule in the cellular metabolism of mammals. In this study, we examined several of the physiological characteristics of a SAM-accumulating strain of the yeast Scheffersomyces stipitis (M12), including SAM production, ergosterol content, and ethanol tolerance. S. stipitis M12 accumulated up to 52.48 mg SAM/g dry cell weight. Proteome analyses showed that the disruption of C-24 methylation in ergosterol biosynthesis, a step mediated by C-24 sterol methyltransferase (Erg6p), results in greater SAM accumulation by S. stipitis M12 compared to the wild-type strain. A comparative proteome-wide analysis identified 25 proteins that were differentially expressed by S. stipitis M12. These proteins are involved in ribosome biogenesis, translation, the stress response, ubiquitin-dependent catabolic processes, the cell cycle, ethanol tolerance, posttranslational modification, peroxisomal membrane stability, epigenetic regulation, the actin cytoskeleton and cell morphology, iron and copper homeostasis, cell signaling, and energy metabolism.

  17. The relative influence of ENSO and SAM on Antarctic Peninsula climate

    NASA Astrophysics Data System (ADS)

    Clem, Kyle R.; Renwick, James A.; McGregor, James; Fogt, Ryan L.

    2016-08-01

    Recent warming of the Antarctic Peninsula during austral autumn, winter, and spring has been linked to sea surface temperature (SST) trends in the tropical Pacific and tropical Atlantic, while warming of the northeast Peninsula during summer has been linked to a strengthening of westerly winds traversing the Peninsula associated with a positive trend in the Southern Annular Mode (SAM). Here we demonstrate that circulation changes associated with the SAM dominate interannual temperature variability across the entire Antarctic Peninsula during both summer and autumn, while relationships with tropical Pacific SST variability associated with the El Niño-Southern Oscillation (ENSO) are strongest and statistically significant primarily during winter and spring only. We find the ENSO-Peninsula temperature relationship during autumn to be weak on interannual time scales and regional circulation anomalies associated with the SAM more important for interannual temperature variability across the Peninsula during autumn. Consistent with previous studies, western Peninsula temperatures during autumn, winter, and spring are closely tied to changes in the Amundsen Sea Low (ASL) and associated meridional wind anomalies. The interannual variability of ASL depth is most strongly correlated with the SAM index during autumn, while the ENSO relationship is strongest during winter and spring. Investigation of western and northeast Peninsula temperatures separately reveals that interannual variability of northeast Peninsula temperatures is primarily sensitive to zonal wind anomalies crossing the Peninsula and resultant leeside adiabatic warming rather than to meridional wind anomalies, which is closely tied to variability in the zonal portion of the SAM pattern.

  18. Structural and functional comparison of HemN to other radical SAM enzymes.

    PubMed

    Layer, Gunhild; Kervio, Eric; Morlock, Gaby; Heinz, Dirk W; Jahn, Dieter; Retey, Janos; Schubert, Wolf-Dieter

    2005-10-01

    Radical SAM enzymes have only recently been recognized as an ancient family sharing an unusual radical-based reaction mechanism. This late appreciation is due to the extreme oxygen sensitivity of most radical SAM enzymes, making their characterization particularly arduous. Nevertheless, realization that the novel apposition of the established cofactors S-adenosylmethionine and [4Fe-4S] cluster creates an explosive source of catalytic radicals, the appreciation of the sheer size of this previously neglected family, and the rapid succession of three successfully solved crystal structures within a year have ensured that this family has belatedly been noted. In this review, we report the characterization of two enzymes: the established radical SAM enzyme, HemN or oxygen-independent coproporphyrinogen III oxidase from Escherichia coli, and littorine mutase, a presumed radical SAM enzyme, responsible for the conversion of littorine to hyoscyamine in plants. The enzymes are compared to other radical SAM enzymes and in particular the three reported crystal structures from this family, HemN, biotin synthase and MoaA, are discussed.

  19. A Distributed Cooperative Power Allocation Method for Campus Buildings

    SciTech Connect

    Hao, He; Sun, Yannan; Carroll, Thomas E.; Somani, Abhishek

    2015-09-01

    We propose a coordination algorithm for cooperative power allocation among a collection of commercial buildings within a campus. We introduced thermal and power models of a typical commercial building Heating, Ventilation, and Air Conditioning (HVAC) system, and utilize model predictive control to characterize their power flexibility. The power allocation problem is formulated as a cooperative game using the Nash Bargaining Solution (NBS) concept, in which buildings collectively maximize the product of their utilities subject to their local flexibility constraints and a total power limit set by the campus coordinator. To solve the optimal allocation problem, a distributed protocol is designed using dual decomposition of the Nash bargaining problem. Numerical simulations are performed to demonstrate the efficacy of our proposed allocation method

  20. Sex allocation pattern of the diatom Cyclotella meneghiniana.

    PubMed

    Shirokawa, Y; Shimada, M

    2013-06-22

    Sex allocation is one of the most successful applications of evolutionary game theory. This theory has usually been applied to multicellular organisms; however, conditional sex allocation in unicellular organisms remains an unexplored field of research. Observations at the cellular level are indispensable for an understanding of the phenotypic sex allocation strategy among individuals within clonal unicellular organisms. The diatom Cyclotella meneghiniana, in which the sexes are generated from vegetative cells, is suitable for investigating effects of phenotypic plasticity factors on sex allocation while excluding genetic differences. We designed a microfluidic system that allowed us to trace the fate of individual cells. Sex allocation by individual mother cells was affected by cell lineage, cell size and cell density. Sibling cell pairs tended to differentiate into the same fates (split sex ratio). We found a significant negative correlation between the cell area of the mother cell and sex ratio of the two sibling cells. The male-biased sex ratio declined with higher local cell population density, supporting the fertility insurance hypothesis. Our results characterize multiple non-genetic factors that affect the phenotypic single cell-level sex allocation. Sex allocation in diatoms may provide a model system for testing evolutionary game theory in unicellular organisms. PMID:23760641

  1. Sex allocation pattern of the diatom Cyclotella meneghiniana

    PubMed Central

    Shirokawa, Y.; Shimada, M.

    2013-01-01

    Sex allocation is one of the most successful applications of evolutionary game theory. This theory has usually been applied to multicellular organisms; however, conditional sex allocation in unicellular organisms remains an unexplored field of research. Observations at the cellular level are indispensable for an understanding of the phenotypic sex allocation strategy among individuals within clonal unicellular organisms. The diatom Cyclotella meneghiniana, in which the sexes are generated from vegetative cells, is suitable for investigating effects of phenotypic plasticity factors on sex allocation while excluding genetic differences. We designed a microfluidic system that allowed us to trace the fate of individual cells. Sex allocation by individual mother cells was affected by cell lineage, cell size and cell density. Sibling cell pairs tended to differentiate into the same fates (split sex ratio). We found a significant negative correlation between the cell area of the mother cell and sex ratio of the two sibling cells. The male-biased sex ratio declined with higher local cell population density, supporting the fertility insurance hypothesis. Our results characterize multiple non-genetic factors that affect the phenotypic single cell-level sex allocation. Sex allocation in diatoms may provide a model system for testing evolutionary game theory in unicellular organisms. PMID:23760641

  2. 15 CFR 335.4 - Allocation.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 15 Commerce and Foreign Trade 2 2010-01-01 2010-01-01 false Allocation. 335.4 Section 335.4... § 335.4 Allocation. (a) For HTS 9902.51.11 and HTS 9902.51.15 each Tariff Rate Quota will be allocated separately. Allocation will be based on an applicant's Worsted Wool Suit production, on a weighted...

  3. Preserving the allocation ratio at every allocation with biased coin randomization and minimization in studies with unequal allocation.

    PubMed

    Kuznetsova, Olga M; Tymofyeyev, Yevgen

    2012-04-13

    The demand for unequal allocation in clinical trials is growing. Most commonly, the unequal allocation is achieved through permuted block randomization. However, other allocation procedures might be required to better approximate the allocation ratio in small samples, reduce the selection bias in open-label studies, or balance on baseline covariates. When these allocation procedures are generalized to unequal allocation, special care is to be taken to preserve the allocation ratio at every allocation step. This paper offers a way to expand the biased coin randomization to unequal allocation that preserves the allocation ratio at every allocation. The suggested expansion works with biased coin randomization that balances only on treatment group totals and with covariate-adaptive procedures that use a random biased coin element at every allocation. Balancing properties of the allocation ratio preserving biased coin randomization and minimization are described through simulations. It is demonstrated that these procedures are asymptotically protected against the shift in the rerandomization distribution identified for some examples of minimization with 1:2 allocation. The asymptotic shift in the rerandomization distribution of the difference in treatment means for an arbitrary unequal allocation procedure is explicitly derived in the paper.

  4. Detection of Organics at Mars: How Wet Chemistry Onboard SAM Helps

    NASA Technical Reports Server (NTRS)

    Buch, A.; Freissinet, Caroline; Szopa, C.; Glavin, D.; Coll, P.; Cabane, M.; Eigenbrode, J.; Navarro-Gonzalez, R.; Coscia, D.; Teinturier, S.; Mahaffy, P.

    2013-01-01

    For the first time in the history of space exploration, a mission of interest to astrobiology could be able to analyze refractory organic compounds in the soil of Mars. Wet chemistry experiment allow organic components to be altered in such a way that improves there detection either by releasing the compounds from sample matricies or by changing the chemical structure to be amenable to analytical conditions. The latter is particular important when polar compounds are present. Sample Analysis at Mars (SAM), on the Curiosity rover of the Mars Science Laboratory mission, has onboard two wet chemistry experiments: derivatization and thermochemolysis. Here we report on the nature of the MTBSTFA derivatization experiment on SAM, the detection of MTBSTFA in initial SAM results, and the implications of this detection.

  5. Distributed processing and analysis of physics data in the D0 SAM system at Fermilab

    SciTech Connect

    Igor V. Terekhov

    2001-08-30

    SAM (Sequential Access through Meta-data) is the data access system for the D0 high energy physics (HEP) experiment at Fermilab. The system is being developed and used to handle the Petabyte-scale experiment data. The D0 applications, like virtually all HEP applications, are data-intensive, which poses special problems for the data management and job control facilities in the distributed environment. The fundamental problem is to bring the user applications and the data together, and SAM attacks the problems from both sides. First, we describe how the system moves the data through the distributed disk cache. Second, we describe how SAM interacts with the batch system to synchronize parallel user jobs with the data availability. All the design solutions herein have been implemented in a real system that handles the mission-critical data of the D0 experiment; thus, we present our work from the standpoint of real experience.

  6. SPASM and Twitch Domains in S-Adenosylmethionine (SAM) Radical Enzymes*

    PubMed Central

    Grell, Tsehai A. J.; Goldman, Peter J.; Drennan, Catherine L.

    2015-01-01

    S-Adenosylmethionine (SAM, also known as AdoMet) radical enzymes use SAM and a [4Fe-4S] cluster to catalyze a diverse array of reactions. They adopt a partial triose-phosphate isomerase (TIM) barrel fold with N- and C-terminal extensions that tailor the structure of the enzyme to its specific function. One extension, termed a SPASM domain, binds two auxiliary [4Fe-4S] clusters and is present within peptide-modifying enzymes. The first structure of a SPASM-containing enzyme, anaerobic sulfatase-maturating enzyme (anSME), revealed unexpected similarities to two non-SPASM proteins, butirosin biosynthetic enzyme 2-deoxy-scyllo-inosamine dehydrogenase (BtrN) and molybdenum cofactor biosynthetic enzyme (MoaA). The latter two enzymes bind one auxiliary cluster and exhibit a partial SPASM motif, coined a Twitch domain. Here we review the structure and function of auxiliary cluster domains within the SAM radical enzyme superfamily. PMID:25477505

  7. The crystal structure of a novel SAM-dependent methyltransferase PH1915 from Pyrococcus horikoshii.

    SciTech Connect

    Sun, W.; Xu, X.; Pavlova, M.; Edwards, A.; Joachimiak, A.; Savchenko, A.; Christendat, D.; Biosciences Division; Univ. of Toronto; Univ. Health Network

    2005-01-01

    The S-adenosyl-L-methionine (SAM)-dependent methyltransferases represent a diverse and biologically important class of enzymes. These enzymes utilize the ubiquitous methyl donor SAM as a cofactor to methylate proteins, small molecules, lipids, and nucleic acids. Here we present the crystal structure of PH1915 from Pyrococcus horikoshii OT3, a predicted SAM-dependent methyltransferase. This protein belongs to the Cluster of Orthologous Group 1092, and the presented crystal structure is the first representative structure of this protein family. Based on sequence and 3D structure analysis, we have made valuable functional insights that will facilitate further studies for characterizing this group of proteins. Specifically, we propose that PH1915 and its orthologs are rRNA- or tRNA-specific methyltransferases.

  8. Bringing a Chemical Laboratory Named Sam to Mars on the 2011 Curiosity Rover

    NASA Technical Reports Server (NTRS)

    Mahaffy, P. R.; Bleacher, L.; Jones, A.; Conrad, P. G.; Cabane, M.; Webster, C. R.; Atreya, S. A.; Manning, H.

    2010-01-01

    An important goal of upcoming missions to Mars is to understand if life could have developed there. The task of the Sample Analysis at Mars (SAM) suite of instruments [1] and the other Curiosity investigations [2] is to move us steadily toward that goal with an assessment of the habitability of our neighboring planet through a series of chemical and geological measurements. SAM is designed to search for organic compounds and inorganic volatiles and measure isotope ratios. Other instruments on Curiosity will provide elemental analysis and identify minerals. SAM will analyze both atmospheric samples and gases evolved from powdered rocks that may have formed billions of years ago with Curiosity providing access to interesting sites scouted by orbiting cameras and spectrometers.

  9. Data handling with SAM and art at the NOνA experiment

    NASA Astrophysics Data System (ADS)

    Aurisano, A.; Backhouse, C.; Davies, G. S.; Illingworth, R.; Mayer, N.; Mengel, M.; Norman, A.; Rocco, D.; Zirnstein, J.

    2015-12-01

    During operations, NOvA produces between 5,000 and 7,000 raw files per day with peaks in excess of 12,000. These files must be processed in several stages to produce fully calibrated and reconstructed analysis files. In addition, many simulated neutrino interactions must be produced and processed through the same stages as data. To accommodate the large volume of data and Monte Carlo, production must be possible both on the Fermilab grid and on off-site farms, such as the ones accessible through the Open Science Grid. To handle the challenge of cataloging these files and to facilitate their off-line processing, we have adopted the SAM system developed at Fermilab. SAM indexes files according to metadata, keeps track of each file's physical locations, provides dataset management facilities, and facilitates data transfer to off-site grids. To integrate SAM with Fermilab's art software framework and the NOvA production workflow, we have developed methods to embed metadata into our configuration files, art files, and standalone ROOT files. A module in the art framework propagates the embedded information from configuration files into art files, and from input art files to output art files, allowing us to maintain a complete processing history within our files. Embedding metadata in configuration files also allows configuration files indexed in SAM to be used as inputs to Monte Carlo production jobs. Further, SAM keeps track of the input files used to create each output file. Parentage information enables the construction of self-draining datasets which have become the primary production paradigm used at NOvA. In this paper we will present an overview of SAM at NOvA and how it has transformed the file production framework used by the experiment.

  10. Data handling with SAM and art at the NOvA experiment

    DOE PAGES

    Aurisano, A.; Backhouse, C.; Davies, G. S.; Illingworth, R.; Mayer, N.; Mengel, M.; Norman, A.; Rocco, D.; Zirnstein, J.

    2015-12-23

    During operations, NOvA produces between 5,000 and 7,000 raw files per day with peaks in excess of 12,000. These files must be processed in several stages to produce fully calibrated and reconstructed analysis files. In addition, many simulated neutrino interactions must be produced and processed through the same stages as data. To accommodate the large volume of data and Monte Carlo, production must be possible both on the Fermilab grid and on off-site farms, such as the ones accessible through the Open Science Grid. To handle the challenge of cataloging these files and to facilitate their off-line processing, we havemore » adopted the SAM system developed at Fermilab. SAM indexes files according to metadata, keeps track of each file's physical locations, provides dataset management facilities, and facilitates data transfer to off-site grids. To integrate SAM with Fermilab's art software framework and the NOvA production workflow, we have developed methods to embed metadata into our configuration files, art files, and standalone ROOT files. A module in the art framework propagates the embedded information from configuration files into art files, and from input art files to output art files, allowing us to maintain a complete processing history within our files. Embedding metadata in configuration files also allows configuration files indexed in SAM to be used as inputs to Monte Carlo production jobs. Further, SAM keeps track of the input files used to create each output file. Parentage information enables the construction of self-draining datasets which have become the primary production paradigm used at NOvA. In this study we will present an overview of SAM at NOvA and how it has transformed the file production framework used by the experiment.« less

  11. Results from the Curiosity Rover's SAM Investigation at Gale Crater and links to Habitability of Mars

    NASA Astrophysics Data System (ADS)

    Coll, P. J.; Mahaffy, P. R.; Webster, C. R.; Cabane, M.; Atreya, S. K.; Conrad, P. G.; Navarro-gonzalez, R.; SAM; MSL Science Teams

    2013-05-01

    The Mars Science Laboratory Mission (MSL) has as its goal an exploration of the potential of the ancient Gale Crater to support life. The Sample Analysis at Mars (SAM) instrument suite (3) contributes to this exploration of habitability with (1) a search for organic compounds in rocks and soils, (2) a determination of the composition of inorganic volatiles compounds in the atmosphere or extracted from solid materials, and (3) measurements of the isotopic composition of several of these volatiles. The initial exploration of the region near the landing point has revealed a diverse geology and SAM has made measurements of both atmospheric and solid samples. Additional prime exploration targets are the clay and sulfate layers in the central mound (Mt. Sharp) of Gale crater. SAM is located in the interior of the Curiosity rover. Nine other instruments complete the payload including an XRD/XRF instrument and a variety of imaging, laser induced breakdown spectroscopy, and elemental analysis instrumentation. Several of these instruments serve to locate sampling sites and interrogate candidate materials before solid sample is collected either with a drill or a scoop for delivery to SAM and the XRD/XRF instruments. SAM's instruments are a quadrupole mass spectrometer (QMS), a tunable laser spectrometer (TLS), and a 6-column gas chromatograph (GC) coupled through a solid sample transport system and a gas processing and enrichment system. SAM atmospheric runs include a determination of: new volume mixing ratios for the 5 major isotopic constituents; an upper limit for the volume mixing ratio of methane; C and O isotope ratios in CO2; D/H in water; and the 40Ar/36Ar ratio. Major evolved gases from fines scooped from an eolian drift were H2O, CO2, O2, SO2, and a number of minor species. Chlorine containing compounds in this material were tentatively identified as perchlorates.

  12. Searching for Reduced Carbon on the Surface of Mars: The SAM Combustion Experiment

    NASA Technical Reports Server (NTRS)

    Stern, J. C.; Malespin, C. A.; Mahaffy, P. R.; Webster, C. R.; Eigenbrode, J. L.; Archer, P. D., Jr.; Brunner, A. E.; Freissinet, C.; Franz, H. B.; Glavin, D. P.; Graham, H. V.; McAdam, A. C.; Ming, D. W.; Navarro-Gonzalez, R.; Niles, P. B.; Steele, A.; Sutter, B.; Trainer, M. G.

    2014-01-01

    The search for reduced carbon has been a major focus of past and present missions to Mars. Thermal evolved gas analysis was used by the Viking and Phoenix landers and is currently in use by the Sample Analysis at Mars (SAM) instrument suite on the Mars Science Laboratory (MSL) to characterize volatiles evolved from solid samples, including those associated with reduced organic species. SAM has the additional capability to perform a combustion experiment, in which a sample of Mars regolith is heated in the presence of oxygen and the composition of the evolved gases is measured using quadrupole mass spectrometry (QMS) and tunable laser spectrometry (TLS) [1]. Organics detection on the Martian surface has been complicated by oxidation and destruction during heating by soil oxidants [2], including oxychlorine compounds, and terrestrial organics in the SAM background contributed by one of the SAM wet chemistry reagents MTBSTFA (N-Methyl-N-tertbutyldimethylsilyl- trifluoroacetamide) [3,4]. Thermal Evolved Gas Analysis (TEGA) results from Phoenix show a mid temperature CO2 release between 400 C - 680 C speculated to be carbonate, CO2 adsorbed to grains, or combustion of organics by soil oxidants [5]. Low temperature CO2 evolutions (approx. 200 C - 400 C) were also present at all three sites in Gale Crater where SAM Evolved Gas Analysis (EGA) was performed, and potential sources include combustion of terrestrial organics from SAM, as well as combustion and/or decarboxylation either indigenous martian or exogenous organic carbon [4,6]. By performing an experiment to intentionally combust all reduced materials in the sample, we hope to compare the bulk abundance of CO2 and other oxidized species evolved by combustion to that evolved during an EGA experiment to estimate how much CO2 could be contributed by reduced carbon sources. In addition, C, O, and H isotopic compositions of CO2 and H2O measured by TLS can contribute information regarding the potential sources of these

  13. The survey of autobiographical memory (SAM): a novel measure of trait mnemonics in everyday life.

    PubMed

    Palombo, Daniela J; Williams, Lynne J; Abdi, Hervé; Levine, Brian

    2013-06-01

    Compared to the abundance of laboratory-based memory tasks, few measures exist to assess self-reported memory function. This need is particularly important for naturalistic mnemonic capacities, such as autobiographical memory (recall of events and facts from one's past), because it is difficult to reliably assess in the laboratory. Furthermore, naturalistic mnemonic capacities may show stable individual differences that evade the constraints of laboratory testing. The Survey of Autobiographical Memory (SAM) was designed to assess such trait mnemonics, or the dimensional characterization of self-reported mnemonic characteristics. The SAM comprises items assessing self-reported episodic autobiographical, semantic, and spatial memory, as well as future prospection. In a large sample of healthy young adults, the latent dimensional structure of the SAM was characterized with multiple correspondence analysis (MCA). This analysis revealed dimensions corresponding to general mnemonic abilities (i.e., good vs poor memory across subtypes), spatial memory, and future prospection. While episodic and semantic items did not separate in this data-driven analysis, these categories did show expected dissociations in relation to depression history and to laboratory-based measures of recollection. Remote spatial memory as assessed by the SAM showed the expected advantage for males over females. Spatial memory was also related to autobiographical memory performance. Brief versions of the SAM are provided for efficient research applications. Individual differences in memory function are likely related to other health-related factors, including personality, psychopathology, dementia risk, brain structure and function, and genotype. In conjunction with laboratory or performance based assessments, the SAM can provide a useful measure of naturalistic self-report trait mnemonics for probing these relationships. PMID:23063319

  14. Collective credit allocation in science

    PubMed Central

    Shen, Hua-Wei; Barabási, Albert-László

    2014-01-01

    Collaboration among researchers is an essential component of the modern scientific enterprise, playing a particularly important role in multidisciplinary research. However, we continue to wrestle with allocating credit to the coauthors of publications with multiple authors, because the relative contribution of each author is difficult to determine. At the same time, the scientific community runs an informal field-dependent credit allocation process that assigns credit in a collective fashion to each work. Here we develop a credit allocation algorithm that captures the coauthors’ contribution to a publication as perceived by the scientific community, reproducing the informal collective credit allocation of science. We validate the method by identifying the authors of Nobel-winning papers that are credited for the discovery, independent of their positions in the author list. The method can also compare the relative impact of researchers working in the same field, even if they did not publish together. The ability to accurately measure the relative credit of researchers could affect many aspects of credit allocation in science, potentially impacting hiring, funding, and promotion decisions. PMID:25114238

  15. Collective credit allocation in science.

    PubMed

    Shen, Hua-Wei; Barabási, Albert-László

    2014-08-26

    Collaboration among researchers is an essential component of the modern scientific enterprise, playing a particularly important role in multidisciplinary research. However, we continue to wrestle with allocating credit to the coauthors of publications with multiple authors, because the relative contribution of each author is difficult to determine. At the same time, the scientific community runs an informal field-dependent credit allocation process that assigns credit in a collective fashion to each work. Here we develop a credit allocation algorithm that captures the coauthors' contribution to a publication as perceived by the scientific community, reproducing the informal collective credit allocation of science. We validate the method by identifying the authors of Nobel-winning papers that are credited for the discovery, independent of their positions in the author list. The method can also compare the relative impact of researchers working in the same field, even if they did not publish together. The ability to accurately measure the relative credit of researchers could affect many aspects of credit allocation in science, potentially impacting hiring, funding, and promotion decisions. PMID:25114238

  16. The nucleation and growth of calcium oxalate monohydrate on self- assembled monolayers (SAMs)

    SciTech Connect

    Campbell, A.A.; Tarasevich, B.J.; Graff, G.L.; Fryxell, G.E.; Rieke, P.C.

    1992-05-01

    A physical chemical approach was used to study calcium oxalate monohydrate (COM) nucleation and growth on various organic interfaces. Self-assembling monolayers (SAMs), containing derivatized organic functional groups, were designed to mimic various amino acid residues present in both urine and stone matrix macromolecules. Derivatized surfaces include SAMs with terminal methyl, bromo, imidazole, and thiazolidine-carboxylic acid functional groups. Pronounced differences in COM deposition were observed for the various interfaces with the imidazole and thiazolidine surfaces having the greatest effect and the methyl and bromo groups having little or no nucleating potential.

  17. Mineral classification map using MF and SAM techniques: A case study in the Nohwa Island, Korea

    SciTech Connect

    Son, Young-Sun; Yoon, Wang-Jung

    2015-03-10

    The purpose of this study is to map pyprophyllite distribution at surface of the Nohwa deposit, Korea by using Advanced Spaceborne Thermal Emission and Reflectance Radiometer (ASTER) data. For this, combined Spectral Angle Mapper (SAM), and Matched Filtering (MF) technique based on mathematical algorithm was applied. The regional distribution of high-grade and low-grade pyrophyllite in the Nohwa deposit area could be differentiated by this method. The results of this study show that ASTER data analysis using combination of SAM and MF techniques will assist in exploration of pyrophyllite at the exposed surface.

  18. The Combustion Experiment on the Sample Analysis at Mars (SAM) Instrument Suite on the Curiosity Rover

    NASA Technical Reports Server (NTRS)

    Stern, J. C.; Malespin, C. A.; Eigenbrode, J.; Graham, H. V.; Archer, P. D.; Brunner, A.; Freissinet, C.; Franz, H. B.; Fuentes, J.; Glavin, D. P.; Mahaffy, P. R.; McAdam, A. C.; Ming, D. W.; Niles, P. B.; Steele, A.

    2014-01-01

    The combustion experiment on the Sample Analysis at Mars (SAM) suite on Curiosity will heat a sample of Mars regolith in the presence of oxygen and measure composition of the evolved gases using quadrupole mass spectrometry (QMS) and tunable laser spectrometry (TLS). QMS will enable detection of combustion products such as CO, CO2, NO, and other oxidized species, while TLS will enable precision measurements of the abundance and carbon isotopic composition (delta C-13) of the evolved CO2 and hydrogen isotopic composition (delta D) of H2O. SAM will perform a two-step combustion to isolate combustible materials below approx. 550 C and above approx. 550 C.

  19. In Situ Analysis of Mars Soil and Rocks Sample with the Sam Gcms Instrumentation Onboard Curiosity : Interpretation and Comparison of Measurements Done during the First Martian Year of Curiosity on Mars

    NASA Astrophysics Data System (ADS)

    Szopa, C.; Coll, P. J.; Cabane, M.; Buch, A.; Coscia, D.; Millan, M.; Francois, P.; Belmahadi, I.; Teinturier, S.; Navarro-Gonzalez, R.; Glavin, D. P.; Freissinet, C.; Steele, A.; Eigenbrode, J. L.; Mahaffy, P. R.

    2014-12-01

    The characterisation of the chemical and mineralogical composition of solid surface samples collected with the Curiosity rover is a primary objective of the SAM experiment. These data should provide essential clues on the past habitability of Gale crater. Amongst the SAM suite of instruments [1], SAM-GC (Gas Chromatograph) is devoted to identify and quantify volatiles evolved from the thermal (heating up to about 900°C)/chemical (derivatization procedure) treatment of any soil sample collected by the Curiosity rover. With the aim to search for potential organic molecules outgassed from the samples, SAM-GC analytical channels composed of thermal-desorption injector, and a MXT-CLP or a MXT-Q chromatographic column was chosen to achieve all the measurements done up today, with the aim to separate of a wide range of volatile inorganic and organic molecules. Four solid samples have been analyzed with GCMS, one sand sample collected at the Rocknest site, two rock samples (John Klein and Cumberland respectively) collected at the Yellowknife Bay site using the Curiosity driller, and one rock sample collected at the Kimberly site. All the measurements were successful and they produced complex chromatograms with both detectors used for SAM GC, i.e. a thermal conductivity detector and the SAM quandrupole mass spectrometer. Their interpretation already revealed the presence of an oxychlorine phase present in the sample which is at the origin of chlorohydrocarbons clearly identified [2] but this represents only a fraction of the GCMS signal recorded [3,4]. This work presents a systematic comparison of the GCMS measurements done for the different samples collected, supported by reference data obtained in laboratory with different spare models of the gas chromatograph, with the aim to bring new elements of interpretation of the SAM measurements. References: [1] Mahaffy, P. et al. (2012) Space Sci Rev, 170, 401-478. [2] Glavin, D. et al. (2013), JGR. [3] Leshin L. et al. (2013

  20. Optimal allocation of trend following strategies

    NASA Astrophysics Data System (ADS)

    Grebenkov, Denis S.; Serror, Jeremy

    2015-09-01

    We consider a portfolio allocation problem for trend following (TF) strategies on multiple correlated assets. Under simplifying assumptions of a Gaussian market and linear TF strategies, we derive analytical formulas for the mean and variance of the portfolio return. We construct then the optimal portfolio that maximizes risk-adjusted return by accounting for inter-asset correlations. The dynamic allocation problem for n assets is shown to be equivalent to the classical static allocation problem for n2 virtual assets that include lead-lag corrections in positions of TF strategies. The respective roles of asset auto-correlations and inter-asset correlations are investigated in depth for the two-asset case and a sector model. In contrast to the principle of diversification suggesting to treat uncorrelated assets, we show that inter-asset correlations allow one to estimate apparent trends more reliably and to adjust the TF positions more efficiently. If properly accounted for, inter-asset correlations are not deteriorative but beneficial for portfolio management that can open new profit opportunities for trend followers. These concepts are illustrated using daily returns of three highly correlated futures markets: the E-mini S&P 500, Euro Stoxx 50 index, and the US 10-year T-note futures.

  1. Software For Allocation Of Tolerances

    NASA Technical Reports Server (NTRS)

    Fernandez, Ken; Raman, Shivakumar; Pulat, Simin

    1992-01-01

    Collection of computer programs being developed to assist engineers in allocating tolerances to dimensions of components and assemblies. System reflects tolerancing expertise of design and manufacturing engineers; helps engineers maintain comprehensive tolerancing policy and overview that might otherwise get lost when attending to details of design and manufacturing processes. Necessary to allocate tolerances for three main reasons: tolerances allow for variations in dimensions of components as manufactured; assembly of two or more components, dimensions lie between specified limits; and part replaced must fit in place.

  2. Analysis of the interactions between host factor Sam68 and viral elements during foot-and-mouth disease virus infection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The nuclear protein Src-associated protein of 68 kDa in mitosis (Sam68) is known to bind RNA and be involved in cellular processes triggered in response to environmental stresses, including virus infection. Interestingly, Sam68, is a multi-functional protein implicated in the life cycle of retroviru...

  3. Organic chemistry on surfaces: Direct cyclopropanation by dihalocarbene addition to vinyl terminated self-assembled monolayers (SAMs)

    PubMed Central

    Adamkiewicz, Malgorzata

    2014-01-01

    Summary C11-Vinyl-terminated self-assembled monolayers (SAMs) on silica surfaces are successfully modified in C–C bond forming reactions with dihalocarbenes to generate SAMs, terminated with dihalo- (fluoro, chloro, bromo) cyclopropane motifs with about 30% surface coverage. PMID:25550756

  4. Sam68 is tyrosine phosphorylated and recruited to signalling in peripheral blood mononuclear cells from HIV infected patients

    PubMed Central

    Najib, S; Rodríguez-Baño, J; Ríos, M J; Muniain, M A; Goberna, R; Sánchez-Margalet, V

    2005-01-01

    Human immunodeficiency virus (HIV) codes for a protein, Rev, that mediates the viral RNA export from the nucleus to the cytoplasm. Recently, it has been found that Sam68, the substrate of Src associated in mitosis, is a functional homologue of Rev, and a synergistic activator of Rev activity. Thus, it has been suggested that Sam68 may play an important role in the post-transcriptional regulation of HIV. Sam68 contains an RNA binding motif named KH [homology to the nuclear ribonucleoprotein (hnRNP) K]. Tyrosine phosphorylation of Sam68 and binding to SH3 domains have been found to negatively regulate its RNA binding capacity. Besides, tyrosine phosphorylation of Sam68 allows the formation of signalling complexes with other proteins containing SH2 and SH3 domains, suggesting a role in signal transduction of different systems in human lymphocytes, such as the T cell receptor, and leptin receptor, or the insulin receptor in other cell types. In the present work, we have found that Sam68 is tyrosine phosphorylated in peripheral blood mononuclear cells (PBMC) from HIV infected subjects, leading to the formation of signalling complexes with p85 the regulatory subunit of PI3K, GAP and STAT-3, and decreasing its RNA binding capacity. In contrast, PBMC from HIV infected subjects have lower expression levels of Sam68 compared with controls. These results suggest that Sam68 may play some role in the immune function of lymphocytes in HIV infection. PMID:16045742

  5. Task allocation among multiple intelligent robots

    NASA Technical Reports Server (NTRS)

    Gasser, L.; Bekey, G.

    1987-01-01

    Researchers describe the design of a decentralized mechanism for allocating assembly tasks in a multiple robot assembly workstation. Currently, the approach focuses on distributed allocation to explore its feasibility and its potential for adaptability to changing circumstances, rather than for optimizing throughput. Individual greedy robots make their own local allocation decisions using both dynamic allocation policies which propagate through a network of allocation goals, and local static and dynamic constraints describing which robots are elibible for which assembly tasks. Global coherence is achieved by proper weighting of allocation pressures propagating through the assembly plan. Deadlock avoidance and synchronization is achieved using periodic reassessments of local allocation decisions, ageing of allocation goals, and short-term allocation locks on goals.

  6. Estimation of head tissue-specific exposure from mobile phones based on measurements in the homogeneous SAM head.

    PubMed

    Gosselin, Marie-Christine; Kühn, Sven; Crespo-Valero, Pedro; Cherubini, Emilio; Zefferer, Marcel; Christ, Andreas; Kuster, Niels

    2011-09-01

    The maximum spatial peak exposure of each commercial mobile phone determined in compliance with the relevant safety and product standards is publicly available. However, this information is not sufficient for epidemiological studies aiming to correlate the use of mobile phones with specific cancers or to behavioral alterations, as the dominant location of the exposure may be anywhere in the head between the chin to above the ear, depending on the phone design. The objective of this study was to develop a methodology to determine tissue-specific exposure by expanding the post-processing of the measured surface or volume scans using standardized compliance testing equipment, that is, specific absorption rate (SAR) scanners. The transformation matrix was developed using the results from generic dipoles to evaluate the relation between the SAR in many brain regions of the Virtual Family anatomical phantoms and in virtual brain regions mapped onto the homogeneous SAM head. A set of transformation factors was derived to correlate the SAR induced in the SAM head to the SAR in the anatomical heads. The evaluation included the uncertainty associated with each factor, arising from the anatomical differences between the phantoms (typically less than 6 dB (4×)). The applicability of these factors was validated by performing simulations of four head models exposed to four realistic mobile phone models. The new methodology enables the reliable determination of the maximum and averaged exposure of specific tissues and functional brain regions to mobile phones when combined with mobile phone power control data, and therefore greatly strengthens epidemiological evaluations and improves information for the consumer.

  7. Estimation of head tissue-specific exposure from mobile phones based on measurements in the homogeneous SAM head.

    PubMed

    Gosselin, Marie-Christine; Kühn, Sven; Crespo-Valero, Pedro; Cherubini, Emilio; Zefferer, Marcel; Christ, Andreas; Kuster, Niels

    2011-09-01

    The maximum spatial peak exposure of each commercial mobile phone determined in compliance with the relevant safety and product standards is publicly available. However, this information is not sufficient for epidemiological studies aiming to correlate the use of mobile phones with specific cancers or to behavioral alterations, as the dominant location of the exposure may be anywhere in the head between the chin to above the ear, depending on the phone design. The objective of this study was to develop a methodology to determine tissue-specific exposure by expanding the post-processing of the measured surface or volume scans using standardized compliance testing equipment, that is, specific absorption rate (SAR) scanners. The transformation matrix was developed using the results from generic dipoles to evaluate the relation between the SAR in many brain regions of the Virtual Family anatomical phantoms and in virtual brain regions mapped onto the homogeneous SAM head. A set of transformation factors was derived to correlate the SAR induced in the SAM head to the SAR in the anatomical heads. The evaluation included the uncertainty associated with each factor, arising from the anatomical differences between the phantoms (typically less than 6 dB (4×)). The applicability of these factors was validated by performing simulations of four head models exposed to four realistic mobile phone models. The new methodology enables the reliable determination of the maximum and averaged exposure of specific tissues and functional brain regions to mobile phones when combined with mobile phone power control data, and therefore greatly strengthens epidemiological evaluations and improves information for the consumer. PMID:21416476

  8. 78 FR 3024 - Sam D. Hamilton Noxubee National Wildlife Refuge, MS; Intent To Prepare a Comprehensive...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-15

    ... of issues to consider in the planning process. DATES: To ensure consideration, we must receive your... determine how the public can use each refuge. The planning process is a way for us and the public to... our process for developing a CCP for Sam D. Hamilton Noxubee NWR in Mississippi. This notice...

  9. The transcription factor FBI-1 inhibits SAM68-mediated BCL-X alternative splicing and apoptosis

    PubMed Central

    Bielli, Pamela; Busà, Roberta; Di Stasi, Savino M; Munoz, Manuel J; Botti, Flavia; Kornblihtt, Alberto R; Sette, Claudio

    2014-01-01

    Alternative splicing (AS) is tightly coupled to transcription for the majority of human genes. However, how these two processes are linked is not well understood. Here, we unveil a direct role for the transcription factor FBI-1 in the regulation of AS. FBI-1 interacts with the splicing factor SAM68 and reduces its binding to BCL-X mRNA. This, in turn, results in the selection of the proximal 5′ splice site in BCL-X exon 2, thereby favoring the anti-apoptotic BCL-XL variant and counteracting SAM68-mediated apoptosis. Conversely, depletion of FBI-1, or expression of a SAM68 mutant lacking the FBI-1 binding region, restores the ability of SAM68 to induce BCL-XS splicing and apoptosis. FBI-1's role in splicing requires the activity of histone deacetylases, whose pharmacological inhibition recapitulates the effects of FBI-1 knockdown. Our study reveals an unexpected function for FBI-1 in splicing modulation with a direct impact on cell survival. PMID:24514149

  10. The transcription factor FBI-1 inhibits SAM68-mediated BCL-X alternative splicing and apoptosis.

    PubMed

    Bielli, Pamela; Busà, Roberta; Di Stasi, Savino M; Munoz, Manuel J; Botti, Flavia; Kornblihtt, Alberto R; Sette, Claudio

    2014-04-01

    Alternative splicing (AS) is tightly coupled to transcription for the majority of human genes. However, how these two processes are linked is not well understood. Here, we unveil a direct role for the transcription factor FBI-1 in the regulation of AS. FBI-1 interacts with the splicing factor SAM68 and reduces its binding to BCL-X mRNA. This, in turn, results in the selection of the proximal 5' splice site in BCL-X exon 2, thereby favoring the anti-apoptotic BCL-XL variant and counteracting SAM68-mediated apoptosis. Conversely, depletion of FBI-1, or expression of a SAM68 mutant lacking the FBI-1 binding region, restores the ability of SAM68 to induce BCL-XS splicing and apoptosis. FBI-1's role in splicing requires the activity of histone deacetylases, whose pharmacological inhibition recapitulates the effects of FBI-1 knockdown. Our study reveals an unexpected function for FBI-1 in splicing modulation with a direct impact on cell survival.

  11. Cross-Reactive Sensor Array for Metal Ion Sensing Based on Fluorescent SAMs

    PubMed Central

    Basabe-Desmonts, Lourdes; van der Baan, Frederieke; Zimmerman, Rebecca S.; Reinhoudt, David N.; Crego-Calama, Mercedes

    2007-01-01

    Fluorescent self assembled monolayers (SAMs) on glass were previously developed in our group as new sensing materials for metal ions. These fluorescent SAMs are comprised by fluorophores and small molecules sequentially deposited on a monolayer on glass. The preorganization provided by the surface avoids the need for complex receptor design, allowing for a combinatorial approach to sensing systems based on small molecules. Now we show the fabrication of an effective microarray for the screening of metal ions and the properties of the sensing SAMs. A collection of fluorescent sensing SAMs was generated by combinatorial methods and immobilized on the glass surfaces of a custom-made 140 well microtiter-plate. The resulting libraries are easily measured and show varied responses to a series cations such as Cu2+, Co2+, Pb2+, Ca2+ and Zn2+. These surfaces are not designed to complex selectively a unique analyte but rather they are intended to produce fingerprint type responses to a range of analytes by less specific interactions. The unselective responses of the library to the presence of different cations generate a characteristic pattern for each analyte, a “finger print” response.

  12. Skills Assessment Module (S.A.M.): A Unique & Practical Approach to the Assessment Process.

    ERIC Educational Resources Information Center

    Rosinek, Michele

    The Skills Assessment Module (SAM) is designed to assess special needs students' affective, cognitive, and manipulative strengths and weaknesses in relation to vocational skills required in various training programs within a school system. Initial sections outline procedures and techniques (including paper-pencil tests, hands-on skill modules and…

  13. Treating Obsessive-Compulsive Disorder and Schizophrenia: The Case of Sam

    ERIC Educational Resources Information Center

    Peasley-Miklus, Catherine; Massie, Elise; Baslett, Gaston; Carmin, Cheryl

    2005-01-01

    This article describes the case of Sam, a 22-year-old male with obsessive-compulsive disorder (OCD) and schizophrenia. The patient's background, the development and characteristics of his OCD and schizophrenia, and the history of what became a rather complicated treatment are described. In addition, four problem areas of therapy are identified.

  14. The formation of ACC and competition between polyamines and ethylene for SAM

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ethylene biosynthesis involves the conversion of S-adenosylmethionine (SAM) to 1-aminocyclopropane-1-carboxylic acid (ACC) by ACC synthase (ACS). ACC is then converted to ethylene. The genes that encode enzymes in this pathway all belong to a family of genes. Differential transcriptional regulation ...

  15. 19. (4"X5" image enlarged from 2 1/4" negative) Sam Fowler, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    19. (4"X5" image enlarged from 2 1/4" negative) Sam Fowler, Photographer, February 1998 VIEW OF GEORGIA DOT BRIDGE NO. 051-00025D-01986N (JAMES P. HOULIHAN BRIDGE). NAVIGATIONAL LIGHT LOCATED ON TOP OF FENDER - Georgia DOT Bridge No. 051-00025D-01986N, US 17 & State Route 25 Spanning Savannah River, Port Wentworth, Chatham County, GA

  16. The Methodist Recruiting Officer Myth: Sir Sam Hughes and World War I Recruitment in French Canada.

    ERIC Educational Resources Information Center

    Morton, Desmond

    1986-01-01

    During World War I, so the story goes, recruiting in French Canada went slowly because the Minister of Militia, Sir Sam Hughes, was a bigoted Ontario Orangeman with the gall to appoint a Methodist minister as recruiting officer for Quebec. Secondary students analyze primary source materials regarding this matter. (RM)

  17. SamACO: variable sampling ant colony optimization algorithm for continuous optimization.

    PubMed

    Hu, Xiao-Min; Zhang, Jun; Chung, Henry Shu-Hung; Li, Yun; Liu, Ou

    2010-12-01

    An ant colony optimization (ACO) algorithm offers algorithmic techniques for optimization by simulating the foraging behavior of a group of ants to perform incremental solution constructions and to realize a pheromone laying-and-following mechanism. Although ACO is first designed for solving discrete (combinatorial) optimization problems, the ACO procedure is also applicable to continuous optimization. This paper presents a new way of extending ACO to solving continuous optimization problems by focusing on continuous variable sampling as a key to transforming ACO from discrete optimization to continuous optimization. The proposed SamACO algorithm consists of three major steps, i.e., the generation of candidate variable values for selection, the ants' solution construction, and the pheromone update process. The distinct characteristics of SamACO are the cooperation of a novel sampling method for discretizing the continuous search space and an efficient incremental solution construction method based on the sampled values. The performance of SamACO is tested using continuous numerical functions with unimodal and multimodal features. Compared with some state-of-the-art algorithms, including traditional ant-based algorithms and representative computational intelligence algorithms for continuous optimization, the performance of SamACO is seen competitive and promising.

  18. Arrays of high quality SAM-based junctions and their application in molecular diode based logic.

    PubMed

    Wan, Albert; Suchand Sangeeth, C S; Wang, Lejia; Yuan, Li; Jiang, Li; Nijhuis, Christian A

    2015-12-14

    This paper describes a method to fabricate a microfluidic top-electrode that can be utilized to generate arrays of self-assembled monolayer (SAM)-based junctions. The top-electrodes consist of a liquid-metal of GaOx/EGaIn mechanically stabilized in microchannels and through-holes in polydimethylsiloxane (PDMS); these top-electrodes form molecular junctions by directly placing them onto the SAM supported by template-stripped (TS) Ag or Au bottom-electrodes. Unlike conventional techniques to form multiple junctions, our method does not require lithography to pattern the bottom-electrode and is compatible with TS bottom-electrodes, which are ultra-flat with large grains, free from potential contamination of photoresist residues, and do not have electrode-edges where the molecules are unable to pack well. We formed tunneling junctions with n-alkanethiolate SAMs in yields of ∼80%, with good reproducibility and electrical stability. Temperature dependent J(V) measurements indicated that the mechanism of charge transport across the junction is coherent tunneling. To demonstrate the usefulness of these junctions, we formed molecular diodes based on SAMs with Fc head groups. These junctions rectify currents with a rectification ratio R of 45. These molecular diodes were incorporated in simple electronic circuitry to demonstrate molecular diode-based Boolean logic.

  19. Statement of Facts for 1977 City-Wide Mock Trial Competitions. Walker Thomas v. Sam Nomad.

    ERIC Educational Resources Information Center

    National Inst. for Citizen Education in the Law, Washington, DC.

    Prepared by the District of Columbia Street Law Project for its annual city-wide mock trial competition, this instructional handout provides material for a civil case over an automobile accident. Walker Thomas is suing Sam Nomad for damages that resulted from a collision, for which both parties blame the other. The handout clarifies the laws and…

  20. SAM-based Cell Transfer to Photopatterned Hydrogels for Microengineering Vascular-Like Structures

    PubMed Central

    Sadr, Nasser; Zhu, Mojun; Osaki, Tatsuya; Kakegawa, Takahiro; Yang, Yunzhi; Moretti, Matteo; Fukuda, Junji; Khademhosseini, Ali

    2011-01-01

    A major challenge in tissue engineering is to reproduce the native 3D microvascular architecture fundamental for in vivo functions. Current approaches still lack a network of perfusable vessels with native 3D structural organization. Here we present a new method combining self-assembled monolayer (SAM)-based cell transfer and gelatin methacrylate hydrogel photopatterning techniques for microengineering vascular structures. Human umbilical vein cell (HUVEC) transfer from oligopeptide SAM-coated surfaces to the hydrogel revealed two SAM desorption mechanisms: photoinduced and electrochemically triggered. The former, occurs concomitantly to hydrogel photocrosslinking, and resulted in efficient (>97%) monolayer transfer. The latter, prompted by additional potential application, preserved cell morphology and maintained high transfer efficiency of VE-cadherin positive monolayers over longer culture periods. This approach was also applied to transfer HUVECs to 3D geometrically defined vascular-like structures in hydrogels, which were then maintained in perfusion culture for 15 days. As a step toward more complex constructs, a cell-laden hydrogel layer was photopatterned around the endothelialized channel to mimic the vascular smooth muscle structure of distal arterioles. This study shows that the coupling of the SAM-based cell transfer and hydrogel photocrosslinking could potentially open up new avenues in engineering more complex, vascularized tissue constructs for regenerative medicine and tissue engineering applications. PMID:21802723

  1. North Slope, Alaska: A case study of Sedimentary AeroMagnetics (SAM)

    SciTech Connect

    McConnell, T.J.

    1995-12-31

    Sedimentary AeroMagnetics (SAM) is the application of very high resolution aeromagnetic data to the exploration for hydrocarbons in the sedimentary section of a basin. Basically SAM provides very high spatial resolution of very low amplitude (<1 nT) anomalies originating from structures within the weakly magnetic sedimentary column. These sedimentary anomalies are superimposed upon the conventional high amplitude magnetic anomalies created by the crystalline basement. These low intensity anomalies generated from within the sediments are related to changes in the magnetic composition of the rocks. This can occur when rocks of differing magnetic susceptibilities are juxtaposed across a fault, or at a stratigraphic truncation. Fluid flow along faults, or at a stratigraphic truncation. Fluid flow along faults and fracture zones can also produce magnetization effects which can allow direct delineament of the fault or fracture zone. Stratigraphic units of weakly magnetic shale and sandstone also create subtle plateau effects in the magnetic amplitude maps. SAM data is a result of combining improvements in aeromagnetic data acquisition technology with new ideas on the design of the survey parameters. SAM surveys are generally flown at 200 - 800 meter line spacing with a terrain clearance of 60 - 150 meters. Data processing techniques are used which preserve the broad band frequency spectrum of the acquired data thereby allowing interpretation of the separate and distinct anomaly sources of the sedimentary column and of the crystalline basement.

  2. Making Time for Instructional Leadership. Volume 1: The Evolution of the SAM Process

    ERIC Educational Resources Information Center

    Goldring, Ellen; Grissom, Jason A.; Neumerski, Christine M.; Murphy, Joseph; Blissett, Richard; Porter, Andy

    2015-01-01

    This three-volume report describes the "SAM (School Administration Manager) process," an approach that about 700 schools around the nation are using to direct more of principals' time and effort to improve teaching and learning in classrooms. Research has shown that a principal's instructional leadership is second only to teaching among…

  3. Regulating nutrient allocation in plants

    SciTech Connect

    Udvardi, Michael; Yang, Jiading; Worley, Eric

    2014-12-09

    The invention provides coding and promoter sequences for a VS-1 and AP-2 gene, which affects the developmental process of senescence in plants. Vectors, transgenic plants, seeds, and host cells comprising heterologous VS-1 and AP-2 genes are also provided. Additionally provided are methods of altering nutrient allocation and composition in a plant using the VS-1 and AP-2 genes.

  4. Administrators' Decisions about Resource Allocation

    ERIC Educational Resources Information Center

    Knight, William E.; Folkins, John W.; Hakel, Milton D.; Kennell, Richard P.

    2011-01-01

    Do academic administrators make decisions about resource allocation differently depending on the discipline receiving the funding? Does an administrator's academic identity influence these decisions? This study explored those questions with a sample of 1,690 academic administrators at doctoral-research universities. Participants used fictional…

  5. Report on Tribal Priority Allocations.

    ERIC Educational Resources Information Center

    Bureau of Indian Affairs (Dept. of Interior), Washington, DC.

    As part of Bureau of Indian Affairs (BIA) funding, Tribal Priority Allocations (TPA) are the principal source of funds for tribal governments and agency offices at the reservation level. According to their unique needs and circumstances, tribes may prioritize funding among eight general categories: government, human services, education, public…

  6. The Discipline of Asset Allocation.

    ERIC Educational Resources Information Center

    Petzel, Todd E.

    2000-01-01

    Discussion of asset allocation for college/university endowment funds focuses on three levels of risk: (1) the absolute risk of the portfolio (usually leading to asset diversification); (2) the benchmark risk (usually comparison with peer institutions; and (3) personal career risk (which may incline managers toward maximizing short-term returns,…

  7. Structure-guided discovery of carboxy-SAM as a novel metabolite modulating tRNA function

    PubMed Central

    Kim, Jungwook; Xiao, Hui; Bonanno, Jeffrey B.; Kalyanaraman, Chakrapani; Brown, Shoshana; Tang, Xiangying; Al-Obaidi, Nawar F.; Patskovsky, Yury; Babbitt, Patricia C.; Jacobson, Matthew P.; Lee, Young-Sam; Almo, Steven C.

    2014-01-01

    Identifying novel metabolites and characterizing their biological functions are major challenges of the post-genomic era. X-ray crystallography can reveal unanticipated ligands which persist through purification and crystallization. These adventitious protein:ligand complexes provide insights into new activities, pathways and regulatory mechanisms. We describe a new metabolite, carboxy-S-adenosylmethionine (Cx-SAM), its biosynthetic pathway and its role in tRNA modification. The structure of CmoA, a member of the SAM-dependent methyltransferase superfamily, revealed a ligand in the catalytic site consistent with Cx-SAM. Mechanistic analyses demonstrated an unprecedented role for prephenate as the carboxyl donor and the involvement of a unique ylide intermediate as the carboxyl acceptor in the CmoA-mediated conversion of SAM to Cx-SAM. A second member of the SAM-dependent methyltransferase superfamily, CmoB, recognizes Cx-SAM and acts as a carboxymethyltransferase to convert 5-hydroxyuridine (ho5U) into 5-oxyacetyl uridine (cmo5U) at the wobble position of multiple tRNAs in Gram negative bacteria1, resulting in expanded codon-recognition properties2,3. CmoA and CmoB represent the first documented synthase and transferase for Cx-SAM. These findings reveal new functional diversity in the SAM-dependent methyltransferase superfamily and expand the metabolic and biological contributions of SAM-based biochemistry. These discoveries highlight the value of structural genomics approaches for identifying ligands in the context of their physiologically relevant macromolecular binding partners and for aiding in functional assignment. PMID:23676670

  8. Mechanism elucidation of the radical SAM enzyme spore photoproduct lyase (SPL)

    PubMed Central

    Li, Lei

    2011-01-01

    Spore photoproduct lyase (SPL) repairs a special thymine dimer 5-thyminyl-5,6-dihydrothymine, which is commonly called spore photoproduct or SP at the bacterial early germination phase. SP is the exclusive DNA photo-damage product in bacterial endospores; its generation and swift repair by SPL are responsible for the spores’ extremely high UV resistance. The early in vivo studies suggested that SPL utilizes a direct reversal strategy to repair the SP in the absence of light. The research in the past decade further established SPL as a radical SAM enzyme, which utilizes a tri-cysteine CXXXCXXC motif to harbor a [4Fe-4S] cluster. At the 1+ oxidation state, the cluster provides an electron to the S-adenosylmethionine (SAM), which binds to the cluster in a bidentate manner as the fourth and fifth ligands, to reductively cleave the C-S bond associated with the sulfonium ion in SAM, generating a reactive 5′-deoxyadenosyl (5′-dA) radical. This 5′-dA radical abstracts the proR hydrogen atom from the C6 carbon of SP to initiate the repair process; the resulting SP radical subsequently fragments to generate a putative thymine methyl radical, which accepts a back-donated H atom to yield the repaired TpT. SAM is suggested to be regenerated at the end of each catalytic cycle; and only a catalytic amount of SAM is needed in the SPL reaction. The H atom source for the back donation step is suggested to be a cysteine residue (C141 in B. subtilis SPL), and the H-atom transfer reaction leaves a thiyl radical behind on the protein. This thiyl radical thus must participate in the SAM regeneration process; however how the thiyl radical abstracts an H atom from the 5′-dA to regenerate SAM is unknown. This paper reviews and discusses the history and the latest progress in the mechanistic elucidation of SPL. Despite some recent breakthroughs, more questions are raised in the mechanistic understanding of this intriguing DNA repair enzyme. PMID:22197590

  9. Analysis of chlorocarbon compounds identified in the SAM Investigation of the Mars Science Laboratory mission

    NASA Astrophysics Data System (ADS)

    Freissinet, Caroline; Mahaffy, P.; Glavin, D.; Buch, A.; Brunner, A.; Eigenbrode, J.; Martin, M.; Miller, K.; Steele, A.; Szopa, C.; SAM; MSL science Team

    2013-10-01

    The gas chromatograph mass spectrometer (GCMS) mode of the Sample Analysis at Mars (SAM) experiment was designed for the separation and identification of the chemical components of the gases released from a solid sample or trapped from the atmosphere. Gases from solid samples are either produced by heating a cell from ambient to >800-1100oC (EGA mode) or by wet chemistry extraction and reactions (not yet employed on Mars). Prior to EGA analysis of portions of the first 3 solid samples (Rocknest, John Klein and Cumberland) collected by MSL and delivered to SAM, an internal SAM blank run was carried out with an empty quartz cup. These blank analyses are required to understand the background signal intrinsic to the GCMS and its gas manifolds and traps. Several peaks have been identified as part of SAM background, some of them below the nmol level, which attests of the sensitivity of the instrument and as-designed performance of the GCMS. The origin of each peak has been investigated, and two major contributors are revealed; residual vapor from one of the chemicals used for SAM wet chemistry experiment: N-methyl-N-tert-butyldimethylsilyl-trifluoroacetamide (MTBSTFA), and the Tenax from the hydrocarbon trap. Supporting lab experiments are in progress to understand the reaction pathways of the molecules identified in the SAM background. These experiments help elucidate which molecules may be interpreted as indigenous to Mars. Of the three solid samples analyzed on 11 runs, it was possible to detect and identify several chlorinated compounds including several chlorohydrocarbons. The chlorine is likely derived from the decomposition of martian perchlorates or other indigenous Cl-containing species while the origin of the carbon is presently under investigation for each detected molecule. To date, a subset these molecules have been identified in lab studies and a terrestrial contribution to the observed products are more easily explained. The combined results from SAM and

  10. A Response to Sam McKegney's "Strategies for Ethical Engagement: An Open Letter Concerning Non-Native Scholars of Native Literatures"

    ERIC Educational Resources Information Center

    Appleford, Rob

    2009-01-01

    This article presents the author's response to Sam McKegney's "Strategies for Ethical Engagement: An Open Letter Concerning Non-Native Scholars of Native Literatures." In his response to Sam's diagnosis of the malaise currently afflicting non-Aboriginal critics of this literature, the author attempts to consider the "cure" Sam offers (albeit…

  11. Molecular cloning, characterization and expression analysis of the SAMS gene during adventitious root development in IBA-induced tetraploid black locust.

    PubMed

    Quan, Jine; Zhang, Sheng; Zhang, Chunxia; Meng, Sen; Zhao, Zhong; Xu, Xuexuan

    2014-01-01

    S-Adenosylmethionine synthetase (SAMS) catalyzes the synthesis of S-adenosylmethionine (SAM), a precursor for ethylene and polyamine biosynthesis. Here, we report the isolation of the 1498 bp full-length cDNA sequence encoding tetraploid black locust (Robinia pseudoacacia L.) SAMS (TrbSAMS), which contains an open reading frame of 1179 bp encoding 392 amino acids. The amino acid sequence of TrbSAMS has more than 94% sequence identity to SAMSs from other plants, with a closer phylogenetic relationship to SAMSs from legumes than to SAMS from other plants. The TrbSAMS monomer consists of N-terminal, central, and C-terminal domains. Subcellular localization analysis revealed that the TrbSAMS protein localizes mainly to in the cell membrane and cytoplasm of onion epidermal cells and Arabidopsis mesophyll cell protoplasts. Indole-3-butyric acid (IBA)-treated cuttings showed higher levels of TrbSAMS transcript than untreated control cuttings during root primordium and adventitious root formation. TrbSAMS and its downstream genes showed differential expression in shoots, leaves, bark, and roots, with the highest expression observed in bark. IBA-treated cuttings also showed higher SAMS activity than control cuttings during root primordium and adventitious root formation. These results indicate that TrbSAMS might play an important role in the regulation of IBA-induced adventitious root development in tetraploid black locust cuttings. PMID:25285660

  12. Molecular Cloning, Characterization and Expression Analysis of the SAMS Gene during Adventitious Root Development in IBA-Induced Tetraploid Black Locust

    PubMed Central

    Quan, Jine; Zhang, Sheng; Zhang, Chunxia; Meng, Sen; Zhao, Zhong; Xu, Xuexuan

    2014-01-01

    S-Adenosylmethionine synthetase (SAMS) catalyzes the synthesis of S-adenosylmethionine (SAM), a precursor for ethylene and polyamine biosynthesis. Here, we report the isolation of the 1498 bp full-length cDNA sequence encoding tetraploid black locust (Robinia pseudoacacia L.) SAMS (TrbSAMS), which contains an open reading frame of 1179 bp encoding 392 amino acids. The amino acid sequence of TrbSAMS has more than 94% sequence identity to SAMSs from other plants, with a closer phylogenetic relationship to SAMSs from legumes than to SAMS from other plants. The TrbSAMS monomer consists of N-terminal, central, and C-terminal domains. Subcellular localization analysis revealed that the TrbSAMS protein localizes mainly to in the cell membrane and cytoplasm of onion epidermal cells and Arabidopsis mesophyll cell protoplasts. Indole-3-butyric acid (IBA)-treated cuttings showed higher levels of TrbSAMS transcript than untreated control cuttings during root primordium and adventitious root formation. TrbSAMS and its downstream genes showed differential expression in shoots, leaves, bark, and roots, with the highest expression observed in bark. IBA-treated cuttings also showed higher SAMS activity than control cuttings during root primordium and adventitious root formation. These results indicate that TrbSAMS might play an important role in the regulation of IBA-induced adventitious root development in tetraploid black locust cuttings. PMID:25285660

  13. The egg-sharing model for human therapeutic cloning research: managing donor selection criteria, the proportion of shared oocytes allocated to research, and amount of financial subsidy given to the donor.

    PubMed

    Heng, Boon Chin; Tong, Guo Qing; Stojkovic, Miodrag

    2006-01-01

    Recent advances in human therapeutic cloning made by Hwang and colleagues have opened up new avenues of therapy for various human diseases. However, the major bottleneck of this new technology is the severe shortage of human donor oocytes. Egg-sharing in return for subsidized fertility treatment has been suggested as an ethically justifiable and practical solution to overcome the shortage of donor oocytes for therapeutic cloning. Because the utilization of shared oocytes in therapeutic cloning research does not result in any therapeutic benefit to a second party, this would necessitate a different management strategy compared to their use for the assisted conception of infertile women who are unable to produce any oocytes of their own. It is proposed that the pool of prospective egg-sharers in therapeutic cloning research be limited only to younger women (below 30 years of age) with indications for either male partner sub-fertility or tubal blockage. With regards to the proportion of the shared gametes being allocated to research, a threshold number of retrieved oocytes should be set that if not exceeded, would result in the patient being automatically removed from the egg-sharing scheme. Any excess supernumerary oocyte above this threshold number can be contributed to science, and allocation should be done in a randomized manner. Perhaps, a total of 10 retrieved oocytes from the patient may be considered a suitable threshold, since the chances of conception are unlikely to be impaired. With regards to the amount of subsidy being given to the patient, it is suggested that the proportion of financial subsidy should be equal to the proportion of the patient's oocytes being allocated to research. No doubt, the promise of future therapeutic benefit may be offered to the patient instead of financial subsidy. However, this is ethically controversial because therapeutic cloning has not yet been demonstrated to be a viable model of clinical therapy and any promises made to

  14. Monetizing Benefits Under Alternative River Recreation Use Allocation Systems

    NASA Astrophysics Data System (ADS)

    Loomis, John B.

    1980-02-01

    An optimal capacity, when the binding use constraint is ecological damage, and monetization of recreational benefits, under alternative means of rationing that capacity, were conceptually and empirically developed. The model was developed by first estimating the demand to float Westwater Canyon, derived from a modified travel cost model. Recreational benefits of 6,500 under a hypothetical capacity of 50 trips, when pricing was used to allocate the permits, and a range of benefits from as low as 880 to an expected value of $3,690, if a lottery system is used, were estimated using this model. The monetization of the efficiency losses associated with more equitable allocation systems allows managers to be more objective in making the equity-efficiency trade-offs involved in picking a recreation use allocation system.

  15. System Advisor Model

    2010-03-01

    The System Advisor Model (SAM) is a performance and economic model designed to facilitate decision making for people involved in the renewable energy industry, ranging from project managers and engineers to incentive program designers, technology developers, and researchers.

  16. Sam68/KHDRBS1 is critical for colon tumorigenesis by regulating genotoxic stress-induced NF-κB activation

    PubMed Central

    Fu, Kai; Sun, Xin; Wier, Eric M; Hodgson, Andrea; Liu, Yue; Sears, Cynthia L; Wan, Fengyi

    2016-01-01

    Nuclear factor kappa B (NF-κB)-mediated transcription is an important mediator for cellular responses to DNA damage. Genotoxic agents trigger a 'nuclear-to-cytoplasmic' NF-κB activation signaling pathway; however, the early nuclear signaling cascade linking DNA damage and NF-κB activation is poorly understood. Here we report that Src-associated-substrate-during-mitosis-of-68kDa/KH domain containing, RNA binding, signal transduction associated 1 (Sam68/KHDRBS1) is a key NF-κB regulator in genotoxic stress-initiated signaling pathway. Sam68 deficiency abolishes DNA damage-stimulated polymers of ADP-ribose (PAR) production and the PAR-dependent NF-κB transactivation of anti-apoptotic genes. Sam68 deleted cells are hypersensitive to genotoxicity caused by DNA damaging agents. Upregulated Sam68 coincides with elevated PAR production and NF-κB-mediated anti-apoptotic transcription in human and mouse colon cancer. Knockdown of Sam68 sensitizes human colon cancer cells to genotoxic stress-induced apoptosis and genetic deletion of Sam68 dampens colon tumor burden in mice. Together our data reveal a novel function of Sam68 in the genotoxic stress-initiated nuclear signaling, which is crucial for colon tumorigenesis. DOI: http://dx.doi.org/10.7554/eLife.15018.001 PMID:27458801

  17. Direct Patterning of Organic Self-Assembled Monolayer (SAM) on GaAs Surfaces via Dip-Pen Nanolithography (DPN)

    NASA Astrophysics Data System (ADS)

    Xiong, Peng; Keiper, Timothy; Wang, Xiaolei; Zhao, Jianhua

    2015-03-01

    Hybrid structures of functional molecules and solid-state (SS) materials have attracted extensive interest in surface nanoscience and molecular electronics. The formation and micro/nano patterning of organic SAMs on SS surfaces are a key step in fabricating such devices. Here we report realization of high quality MHA SAMs on GaAs and direct formation of micro/nanoscale patterns of MHA SAM on the surface by micro-contact printing (μ CP) and DPN. The process begins with the preparation of an oxide-free surface of GaAs, for which we employed treatment by an ammonium polysulfide ((NH4)2 Sx) solution. The treatment strips native oxides from GaAs creating an atomic layer of sulfur covalently bonded to the fresh surface. Formation of high-quality SAMs of thiol molecules on GaAs then proceeds through exchange of the sulfur and the thiol terminal of the molecules. The effects of the sulfur-passivation and formation of MHA SAM on the treated surface were confirmed by XPS, HRTEM, and DPN. To the best of our knowledge, this is a first realization of direct DPN of nanoscale organic SAM on a semiconductor free of surface oxide. We further evidence the utility of the hybrid platform by demonstrating directed self-assembly of Au nanoparticles onto MHA/ODT SAM templates on GaAs.

  18. Stability of phosphonic self assembled monolayers (SAMs) on cobalt chromium (Co-Cr) alloy under oxidative conditions

    NASA Astrophysics Data System (ADS)

    Bhure, Rahul; Abdel-Fattah, Tarek M.; Bonner, Carl; Hall, Felicia; Mahapatro, Anil

    2011-04-01

    Cobalt chromium (Co-Cr) alloys have been widely used in the biomedical arena for cardiovascular, orthopedic and dental applications. Surface modification of the alloy allows us to tailor the interfacial properties to address critical challenges of Co-Cr alloy in medical applications. Self assembled monolayers (SAMs) of Octadecylphosphonic acid (ODPA) have been used to form thin films on the oxide layer of the Co-Cr alloy surface by solution deposition technique. The SAMs formed were investigated for their stability to oxidative conditions of ambient laboratory environment over periods of 1, 3, 7 and 14 days. The samples were then characterized for their stability using X-ray Photoelectron Spectroscopy (XPS), Atomic Force Microscopy (AFM) and contact angle measurements. Detailed high energy XPS elemental scans confirmed the presence of the phosphonic monolayer after oxidative exposure which suggested that the SAMs were firmly attached to the oxide layer of Co-Cr alloy. AFM images gave topographical data of the surface and showed islands of SAMs on Co-Cr alloy surface, before and after SAM formation and also over the duration of the oxidative exposure. Contact angle measurements confirmed the hydrophobicity of the surface over 14 days. Thus the SAMs were found to be stable for the duration of the study. These SAMs could be subsequently tailored by modifying the terminal functional groups and could be used for various potential biomedical applications such as drug delivery, biocompatibility and tissue integration.

  19. 40 CFR 74.26 - Allocation formula.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...) SULFUR DIOXIDE OPT-INS Allowance Calculations for Combustion Sources § 74.26 Allocation formula. (a) The Administrator will calculate the annual allowance allocation for a combustion source based on the data... 40 Protection of Environment 16 2010-07-01 2010-07-01 false Allocation formula. 74.26 Section...

  20. 49 CFR 262.5 - Allocation requirements.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 4 2010-10-01 2010-10-01 false Allocation requirements. 262.5 Section 262.5... IMPROVEMENT PROJECTS § 262.5 Allocation requirements. At least fifty percent of all grant funds awarded under... than $20,000,000 each. Designated, high-priority projects will be excluded from this allocation...

  1. 39 CFR 3060.12 - Asset allocation.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 39 Postal Service 1 2010-07-01 2010-07-01 false Asset allocation. 3060.12 Section 3060.12 Postal... COMPETITIVE PRODUCTS ENTERPRISE § 3060.12 Asset allocation. Within 6 months of January 23, 2009, and for each... competitive products enterprise using a method of allocation based on appropriate revenue or cost...

  2. 15 CFR 923.110 - Allocation formula.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 15 Commerce and Foreign Trade 3 2010-01-01 2010-01-01 false Allocation formula. 923.110 Section... MANAGEMENT COASTAL ZONE MANAGEMENT PROGRAM REGULATIONS Allocation of Section 306 Program Administration Grants § 923.110 Allocation formula. (a) As required by subsection 306(a), the Secretary may make...

  3. 25 CFR 39.902 - Allocation.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Allocation. 39.902 Section 39.902 Indians BUREAU OF... Maintenance and Minor Repair Fund § 39.902 Allocation. (a) Interim Maintenance and Minor Repair funds shall be... determining school allocations shall be taken from the facilities inventory maintained by the Division...

  4. 24 CFR 945.203 - Allocation plan.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 4 2010-04-01 2010-04-01 false Allocation plan. 945.203 Section... FAMILIES Application and Approval Procedures § 945.203 Allocation plan. (a) Applicable terminology. (1) As used in this section, the terms “initial allocation plan” refers to the PHA's first submission of...

  5. 24 CFR 594.15 - Allocation amounts.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 3 2010-04-01 2010-04-01 false Allocation amounts. 594.15 Section... DEVELOPMENT COMMUNITY FACILITIES JOHN HEINZ NEIGHBORHOOD DEVELOPMENT PROGRAM Funding Allocation and Criteria § 594.15 Allocation amounts. (a) Amounts and match requirement. HUD will make grants, in the form...

  6. Using Regression Analysis in Departmental Budget Allocations. IR Applications, Volume 24, November 1, 2009

    ERIC Educational Resources Information Center

    Luna, Andrew L.; Brennan, Kelly A.

    2009-01-01

    This study uses a regression model to determine if a significant difference exists between the actual budget allocation that an academic department received and the model's predicted budget allocation for that same department. Budget data from a Southeastern Master's/Comprehensive state university were used as the dependent variable, and the…

  7. Sub-Optimal Allocation of Time in Sequential Movements

    PubMed Central

    Wu, Shih-Wei; Dal Martello, Maria F.; Maloney, Laurence T.

    2009-01-01

    The allocation of limited resources such as time or energy is a core problem that organisms face when planning complex actions. Most previous research concerning planning of movement has focused on the planning of single, isolated movements. Here we investigated the allocation of time in a pointing task where human subjects attempted to touch two targets in a specified order to earn monetary rewards. Subjects were required to complete both movements within a limited time but could freely allocate the available time between the movements. The time constraint presents an allocation problem to the subjects: the more time spent on one movement, the less time is available for the other. In different conditions we assigned different rewards to the two tokens. How the subject allocated time between movements affected their expected gain on each trial. We also varied the angle between the first and second movements and the length of the second movement. Based on our results, we developed and tested a model of speed-accuracy tradeoff for sequential movements. Using this model we could predict the time allocation that would maximize the expected gain of each subject in each experimental condition. We compared human performance with predicted optimal performance. We found that all subjects allocated time sub-optimally, spending more time than they should on the first movement even when the reward of the second target was five times larger than the first. We conclude that the movement planning system fails to maximize expected reward in planning sequences of as few as two movements and discuss possible interpretations drawn from economic theory. PMID:20011047

  8. Communication patterns and allocation strategies.

    SciTech Connect

    Leung, Vitus Joseph; Mache, Jens Wolfgang; Bunde, David P.

    2004-01-01

    Motivated by observations about job runtimes on the CPlant system, we use a trace-driven microsimulator to begin characterizing the performance of different classes of allocation algorithms on jobs with different communication patterns in space-shared parallel systems with mesh topology. We show that relative performance varies considerably with communication pattern. The Paging strategy using the Hilbert space-filling curve and the Best Fit heuristic performed best across several communication patterns.

  9. Solving the optimal attention allocation problem in manual control

    NASA Technical Reports Server (NTRS)

    Kleinman, D. L.

    1976-01-01

    Within the context of the optimal control model of human response, analytic expressions for the gradients of closed-loop performance metrics with respect to human operator attention allocation are derived. These derivatives serve as the basis for a gradient algorithm that determines the optimal attention that a human should allocate among several display indicators in a steady-state manual control task. Application of the human modeling techniques are made to study the hover control task for a CH-46 VTOL flight tested by NASA.

  10. Early Evolved Gas Results from the Curiosity Rover’s SAM Investigation at Gale Crater

    NASA Astrophysics Data System (ADS)

    Mahaffy, Paul R.; Franz, H.; McAdam, A.; Brunner, A.; Eigenbrode, J.; Stern, J.; SAM Science Team; MSL Science Team

    2013-10-01

    The Mars Science Laboratory Mission is designed to explore the habitability of the selected landing site at Gale crater. The Sample Analysis at Mars (SAM) instrument suite contributes to this study with a search for organic compounds, an analysis of the composition of inorganic volatiles, and measurements of the isotopic composition light elements. Both atmospheric and solid samples are analyzed. The layers in the central mound (Mt. Sharp) of Gale crater are important targets for the MSL mission. However, in situ measurements made during the past year of interesting regions close to the Bradbury landing site have revealed a diverse geology and several primary mission objectives have already been realized. SAM is located in the interior of the Curiosity rover. The MSL cameras, a laser induced breakdown spectrometer, and elemental analysis instrumentation serves to locate sampling sites and interogate candidate materials before solid sample is collected either with a drill or a scoop for delivery to SAM and the XRD instrument CheMin. SAM integrates a quadrupole mass spectrometer (QMS), a tunable laser spectrometer (TLS), and a 6-column gas chromatograph (GC) with a solid sample transport system and a gas processing and enrichment system. Results of SAM atmospheric composition analyses have already been reported (1,2). To date, multiple SAM evolved gas experiments have examined samples from fines scooped from an aeolian drift and from two drilled samples of a mudstone. Major evolved gases are H2O, CO2, O2, SO2, H2S, H2, and a number of minor species. These data help confirm the likely presence of perchlorates, the presence of phylosillicates, and both reduced and oxidized compounds evolved from the same sample. 1) P.R. Mahaffy et al., Abundance and Isotopic Composition of Gases in the Martian Atmosphere from the Curiosity Rover, Science 343, (2013). 2) C.R. Webster et al., Isotope Ratios of H, C and O in Martian Atmospheric Carbon Dioxide and Water Measured by the

  11. Early Results from the Curiosity Rover's SAM Investigation at Gale Crater

    NASA Astrophysics Data System (ADS)

    Mahaffy, Paul; Webster, Chris; Cabane, Michael; Coll, Patrice

    2013-04-01

    The goals of the Mars Science Laboratory Mission (1, 2) are to explore the potential of the Gale Crater landing site to support life either in the distant past or the present. The contribution of the Sample Analysis at Mars (SAM) instrument suite (3) in this exploration of habitability is (A) to search for organic compounds in rocks and soils, (B) to determine the composition of inorganic volatiles compounds in the atmosphere or extracted from solid materials, and (C) to measure the isotopic composition of several of these volatiles. While prime exploration targets of MSL's Curiosity Rover are the layers in the central mound (Mt. Sharp) of Gale crater the initial exploration of region near the landing point has revealed a diverse geology and the early part of the mission has been spent both commissioning the 10 Curiosity instruments and the Rover subsystems and making first time measurements of both atmospheric and solid samples. SAM is located in the interior of MSL's Curiosity rover next to the XRD/XRF CheMin instrument. A variety of imaging, laser induced breakdown spectroscopy, and elemental analysis instrumentation serves to locate sampling sites and interogate candidate materials before solid sample is collected either with a drill or a scoop for delivery to SAM and CheMin. SAM's instruments are a quadrupole mass spectrometer (QMS), a tunable laser spectrometer (TLS), and a 6-column gas chromatograph (GC). These are coupled through a solid sample transport system and a gas processing and enrichment system. The SAM suite is able to measure a suite of light isotopes and to analyze volatiles directly from the atmosphere or thermally released from solid samples. Early results from SAM atmospheric runs include a determination of: new volume mixing ratios for the 5 major isotopic constituents showing Ar approximately equal to N2; an upper limit of 3.5 ppb for the volume mixing ratio of methane; C and O isotope ratios showing both heavier than terrestrial averages

  12. Application of Neutron-Absorbing Structural-Amorphous Metal (SAM) Coatings for Spent Nuclear Fuel (SNF) Container to Enhance Criticality Safety Control

    SciTech Connect

    Choi, J

    2007-01-12

    This report describes the analysis and modeling approaches used in the evaluation for criticality-control applications of the neutron-absorbing structural-amorphous metal (SAM) coatings. The applications of boron-containing high-performance corrosion-resistant material (HPCRM)--amorphous metal as the neutron-absorbing coatings to the metallic support structure can enhance criticality safety controls for spent nuclear fuel in baskets inside storage containers, transportation casks, and disposal containers. The use of these advanced iron-based, corrosion-resistant materials to prevent nuclear criticality in transportation, aging, and disposal containers would be extremely beneficial to the nuclear waste management programs.

  13. Curiosity's Sample Analysis at Mars (SAM) Investigation: Overview of Results from the First 120 Sols on Mars

    NASA Technical Reports Server (NTRS)

    Mahaffy, P. R.; Cabane, M.; Webster, C. R.; Archer, P. D.; Atreya, S. K.; Benna, M.; Brinckerhoff, W. B.; Brunner, A. E.; Buch, A.; Coll, P.; Conrad, P. G.; Coscia, D.; Dobson, N.; Dworkin, J. P.; Eigenbrode, J. L.; Farley, K. A.; Flesch, G.; Franz, H. B.; Freissinet, C.; Gorevan, S.; Glavin, D. P.; Grotzinger, J. P.; Harpold, D. N.; Hengemihle, J.; Jaeger, F.

    2013-01-01

    During the first 120 sols of Curiosity s landed mission on Mars (8/6/2012 to 12/7/2012) SAM sampled the atmosphere 9 times and an eolian bedform named Rocknest 4 times. The atmospheric experiments utilized SAM s quadrupole mass spectrometer (QMS) and tunable laser spectrometer (TLS) while the solid sample experiments also utilized the gas chromatograph (GC). Although a number of core experiments were pre-programmed and stored in EEProm, a high level SAM scripting language enabled the team to optimize experiments based on prior runs.

  14. Denitrification of the polar winter stratosphere: Implications of SAM II (Stratospheric Aerosol Measurement II) cloud formation temperatures

    SciTech Connect

    Hamill, P. ); Toon, O.B. )

    1990-03-01

    The authors use the Stratospheric Aerosol Measurement II (SAM II) extinction profiles and the associated temperature profiles to determine the amount of denitrification of the winter polar stratospheres. The authors see clear evidence of the denitrification process in the Antarctic data. There are indications in the Arctic data that denitrification mechanisms may be at work there also. At the latitudes observed by the SAM II satellite system, denitrification begins before the formation of extensive ice clouds and may be due to sedimentation of nitric acid particles. However, they cannot exclude the possibility of denitrification by type II PSC's at latitudes not observed by SAM II.

  15. Prey risk allocation in a grazing ecosystem.

    PubMed

    Gude, Justin A; Garrott, Robert A; Borkowski, John J; King, Fred

    2006-02-01

    Understanding the behaviorally mediated indirect effects of predators in ecosystems requires knowledge of predator-prey behavioral interactions. In predator-ungulate-plant systems, empirical research quantifying how predators affect ungulate group sizes and distribution, in the context of other influential variables, is particularly needed. The risk allocation hypothesis proposes that prey behavioral responses to predation risk depend on background frequencies of exposure to risk, and it can be used to make predictions about predator-ungulate-plant interactions. We determined non-predation variables that affect elk (Cervus elaphus) group sizes and distribution on a winter range in the Greater Yellowstone Ecosystem (GYE) using logistic and log-linear regression on surveys of 513 1-km2 areas conducted over two years. Employing model selection techniques, we evaluated risk allocation and other a priori hypotheses of elk group size and distributional responses to wolf (Canis lupus) predation risk while accounting for influential non-wolf-predation variables. We found little evidence that wolves affect elk group sizes, which were strongly influenced by habitat type and hunting by humans. Following predictions from the risk allocation hypothesis, wolves likely created a more dynamic elk distribution in areas that they frequently hunted, as elk tended to move following wolf encounters in those areas. This response should dilute elk foraging pressure on plant communities in areas where they are frequently hunted by wolves. We predict that this should decrease the spatial heterogeneity of elk impacts on grasslands in areas that wolves frequently hunt. We also predict that this should decrease browsing pressure on heavily browsed woody plant stands in certain areas, which is supported by recent research in the GYE. PMID:16705980

  16. Updates to the Demographic and Spatial Allocation Models to Produce Integrated Climate and Land Use Scenarios (Iclus) (Version 2) (External Review Draft)

    EPA Science Inventory

    The U.S. EPA's Integrated Climate and Land Use Scenarios (ICLUS) version 2 (v2) modeling tool furthered land change modeling by providing nationwide housing development scenarios up to 2100. ICLUS V2 includes updated population and land use data sets and addressing limitations i...

  17. Optimal Allocation of Node Capacity in Cascade-Robustness Networks.

    PubMed

    Chen, Zhen; Zhang, Jun; Du, Wen-Bo; Lordan, Oriol; Tang, Jiangjun

    2015-01-01

    The robustness of large scale critical infrastructures, which can be modeled as complex networks, is of great significance. One of the most important means to enhance robustness is to optimize the allocation of resources. Traditional allocation of resources is mainly based on the topology information, which is neither realistic nor systematic. In this paper, we try to build a framework for searching for the most favorable pattern of node capacity allocation to reduce the vulnerability to cascading failures at a low cost. A nonlinear and multi-objective optimization model is proposed and tackled using a particle swarm optimization algorithm (PSO). It is found that the network becomes more robust and economical when less capacity is left on the heavily loaded nodes and the optimized network performs better resisting noise. Our work is helpful in designing a robust economical network. PMID:26496705

  18. Using hierarchical P-median problem for public school allocation

    NASA Astrophysics Data System (ADS)

    Nasir, Noryanti; Shariff, S. Sarifah Radiah

    2014-09-01

    Student's orientation from primary to the secondary schools is a vital process and need to be considered as yearly problem by The District Education Office of Ministry of Education Malaysia. The allocation of students to the right schools becomes complicated due to several constraints like capacity of seats in secondary schools, widespread demand areas as well as preferences by the parents. Considering all the constraints, this study proposes the application of location model to allocate students the right school. The allocation of student from primary to secondary school is based on total number of students, the availability of seats from primary and at the secondary schools, and distance from student's home to the nearest schools, both primary and secondary schools. The problem is modelled as hierarchical P-median problem as there are two hierarchical levels in this orientation. An alternative Genetic Algorithm (GA) based heuristic is applied to solve the problem and results are compared with Excel Solver.

  19. Optimal Allocation of Node Capacity in Cascade-Robustness Networks

    PubMed Central

    Chen, Zhen; Zhang, Jun; Du, Wen-Bo; Lordan, Oriol; Tang, Jiangjun

    2015-01-01

    The robustness of large scale critical infrastructures, which can be modeled as complex networks, is of great significance. One of the most important means to enhance robustness is to optimize the allocation of resources. Traditional allocation of resources is mainly based on the topology information, which is neither realistic nor systematic. In this paper, we try to build a framework for searching for the most favorable pattern of node capacity allocation to reduce the vulnerability to cascading failures at a low cost. A nonlinear and multi-objective optimization model is proposed and tackled using a particle swarm optimization algorithm (PSO). It is found that the network becomes more robust and economical when less capacity is left on the heavily loaded nodes and the optimized network performs better resisting noise. Our work is helpful in designing a robust economical network. PMID:26496705

  20. Evolved Gas Analyses of Sedimentary Materials in Gale Crater, Mars: Results of the Curiosity Rover's Sample Analysis at Mars (SAM) Instrument from Yellowknife Bay to the Stimson Formation

    NASA Technical Reports Server (NTRS)

    Sutter, B.; McAdam, A. C.; Rampe, E. B.; Ming, D. W.; Mahaffy, P. R.; Navarro-Gonzalez, R.; Stern, J. C.; Eigenbrode, J. L.; Archer, P. D.

    2016-01-01

    The Sample Analysis at Mars (SAM) instrument aboard the Mars Science Laboratory rover has analyzed 10 samples from Gale Crater. All SAM evolved gas analyses have yielded a multitude of volatiles (e.g, H2O, SO2, H2S, CO2, CO, NO, O2, HC1). The objectives of this work are to 1) Characterize the evolved H2O, SO2, CO2, and O2 gas traces of sediments analyzed by SAM through sol 1178, 2) Constrain sediment mineralogy/composition based on SAM evolved gas analysis (SAM-EGA), and 3) Discuss the implications of these results releative to understanding the geochemical history of Gale Crater.