WorldWideScience

Sample records for site response functions

  1. Designing a responsive web site

    OpenAIRE

    Fejzić , Diana

    2016-01-01

    Due to the increasing prevalence of smartphones and tablet computers design became a crucial part of web design. For a user, responsive web design enables the best user experience, regardless of whether a user is visiting the site via a mobile phone, a tablet or a computer. This thesis covers the process of planning, designing and responsive web site development, for a fictitious company named “Creative Design d.o.o.”, with the help of web technologies. In the initial part of the thesis, w...

  2. SITE COMPREHENSIVE LISTING (CERCLIS) (Superfund) - Responsible Parties at CERCLIS Sites

    Data.gov (United States)

    U.S. Environmental Protection Agency — Responsible Parties at CERCLIS Sites - The Comprehensive Environmental Response, Compensation and Liability Information System (CERCLIS) (Superfund) Public Access...

  3. Sacrifical sites, types and function

    Directory of Open Access Journals (Sweden)

    Örnulv Vorren

    1987-01-01

    Full Text Available Much has been written and said about Saami mythology and pre-Christian religion. There is, however, considerably less documentation of concrete cultural elements in scholarly descriptions. These investigations are considered important not only because they aim to provide documentation that can be used for studies of Saami mythology and pre-Christian religion. They also provide material that can throw light on the function of the holy places in a social context through analysis of their origin, their connections with certain families and persons, their associations with the siidas, their location within the areas where the Saamis from these siidas gained their livelihood, etc. The materials collected about the sacrificial sites also play an important role in studying the course of events leading up to the differentiation of Saami hunting and gathering culture. A question that has frequently arisen in the course of this work is with what powers or deities the different sacrificial sites were associated. This is naturally connected with their origin and their form. This, in turn, is reflected in the traditions and legends recounted concerning them. It is also reflected in their location in the physical environment and in the kinds of offerings that have been found. In the materials so far collected it is possible to distinguish between about eight different types of sacrificial site and holy mountain or fell according to their form and location: holy fells, rock formations, stone boulders, holes, cracks in fells, springs, lakes, ring-shaped sacrificial sites. Missionaries were urged to destroy the offering sites.

  4. Off-site response for radiological emergencies

    International Nuclear Information System (INIS)

    Eldridge, J.S.; Oakes, T.W.; Hubbard, H.M.; Hibbitts, H.W.

    1982-01-01

    Environmental radiological surveillance under emergency conditions at off-site locations is one of the advisory functions provided by DOE within the ORO jurisdiction. The Department of Environmental Management of ORNL has been requested to provide sampling and analytical assistance at such emergency response activities. We have assembled and identified specific individuals and equipment to provide a rapid response force to perform field measurements for environmental radioactivity releases as a consequence of nuclear accidents. Survey teams for sample collection and field measurements are provided along with analytical assistance to operate the radioactivity measuring equipment in the DOE emergency van

  5. GOES-R Advanced Baseline Imager: spectral response functions and radiometric biases with the NPP Visible Infrared Imaging Radiometer Suite evaluated for desert calibration sites.

    Science.gov (United States)

    Pearlman, Aaron; Pogorzala, David; Cao, Changyong

    2013-11-01

    The Advanced Baseline Imager (ABI), which will be launched in late 2015 on the National Oceanic and Atmospheric Administration's Geostationary Operational Environmental Satellite R-series satellite, will be evaluated in terms of its data quality postlaunch through comparisons with other satellite sensors such as the recently launched Visible Infrared Imaging Radiometer Suite (VIIRS) aboard the Suomi National Polar-orbiting Partnership satellite. The ABI has completed much of its prelaunch characterization and its developers have generated and released its channel spectral response functions (response versus wavelength). Using these responses and constraining a radiative transfer model with ground reflectance, aerosol, and water vapor measurements, we simulate observed top of atmosphere (TOA) reflectances for analogous visible and near infrared channels of the VIIRS and ABI sensors at the Sonoran Desert and White Sands National Monument sites and calculate the radiometric biases and their uncertainties. We also calculate sensor TOA reflectances using aircraft hyperspectral data from the Airborne Visible/Infrared Imaging Spectrometer to validate the uncertainties in several of the ABI and VIIRS channels and discuss the potential for validating the others. Once on-orbit, calibration scientists can use these biases to ensure ABI data quality and consistency to support the numerical weather prediction community and other data users. They can also use the results for ABI or VIIRS anomaly detection and resolution.

  6. SitesIdentify: a protein functional site prediction tool

    Directory of Open Access Journals (Sweden)

    Doig Andrew J

    2009-11-01

    Full Text Available Abstract Background The rate of protein structures being deposited in the Protein Data Bank surpasses the capacity to experimentally characterise them and therefore computational methods to analyse these structures have become increasingly important. Identifying the region of the protein most likely to be involved in function is useful in order to gain information about its potential role. There are many available approaches to predict functional site, but many are not made available via a publicly-accessible application. Results Here we present a functional site prediction tool (SitesIdentify, based on combining sequence conservation information with geometry-based cleft identification, that is freely available via a web-server. We have shown that SitesIdentify compares favourably to other functional site prediction tools in a comparison of seven methods on a non-redundant set of 237 enzymes with annotated active sites. Conclusion SitesIdentify is able to produce comparable accuracy in predicting functional sites to its closest available counterpart, but in addition achieves improved accuracy for proteins with few characterised homologues. SitesIdentify is available via a webserver at http://www.manchester.ac.uk/bioinformatics/sitesidentify/

  7. Site response calculations for nuclear power plants

    International Nuclear Information System (INIS)

    Wight, L.H.

    1975-01-01

    Six typical sites consisting of three soil profiles with average shear wave velocities of 800, 1800, and 5000 ft/sec as well as two soil depths of 200 and 400 ft were considered. Seismic input to these sites was a synthetic accelerogram applied at the surface and corresponding to a statistically representative response spectrum. The response of each of these six sites to this input was calculated with the SHAKE program. The results of these calculations are presented

  8. Function of site. Chapter 2

    International Nuclear Information System (INIS)

    1999-01-01

    In Semipalatinsk test site's history there are two stages for nuclear tests. In first stage (1949-1962) when the nuclear tests have being conducted in atmosphere, and second one (1963-1989) when underground nuclear explosions have being carried out. There were 456 nuclear tests, from which 117 were both the surface and the atmospheric explosions and other underground ones. In the chapter general characteristics of atmospheric nuclear tests, conducted on Semipalatinsk test site in 1949-1962 (chronology of conducting, release energy and kinds of nuclear explosions) are presented in tabular form. Most powerful of explosion was test of hydro- nuclear (hydrogen) bomb - prototype of thermonuclear charge in 1955 with capacity 1.6 Mt. In 1990-1992 the target-oriented radioecological investigation of territory around Semipalatinsk test site was carried out. Specialists dividing all atmospheric explosions by rate local traces, forming out of test site into 4 groups: with very strong contamination, with strong contamination, with weak contamination, and with very weak contamination. To nuclear explosions with very strong contamination were attributed the four explosions carrying out in 29.08.1949, 24.09.1951, 12.08.1953, 24.08.1956. Estimations of radiological situation including external doses of radiation and environment contamination and content of radioactive substances in human body was given by 10 European experts in collaboration with Kazakstan scientists. Results of investigation show that during past period surface contamination, called by nuclear weapons' fissile products was subjected to considerable decay. External doses completely coincidence with natural background. Remains of long living radionuclides are insignificant as well, and in 1995 its approximately were equal to annual exposition doses. One of most damaged settlements is Chagan. On it territory 530 radioactive sources with doses capacity from 100 up to 400 μR/h. Scientists of Semipalatinsk defined

  9. Recognition of functional sites in protein structures.

    Science.gov (United States)

    Shulman-Peleg, Alexandra; Nussinov, Ruth; Wolfson, Haim J

    2004-06-04

    Recognition of regions on the surface of one protein, that are similar to a binding site of another is crucial for the prediction of molecular interactions and for functional classifications. We first describe a novel method, SiteEngine, that assumes no sequence or fold similarities and is able to recognize proteins that have similar binding sites and may perform similar functions. We achieve high efficiency and speed by introducing a low-resolution surface representation via chemically important surface points, by hashing triangles of physico-chemical properties and by application of hierarchical scoring schemes for a thorough exploration of global and local similarities. We proceed to rigorously apply this method to functional site recognition in three possible ways: first, we search a given functional site on a large set of complete protein structures. Second, a potential functional site on a protein of interest is compared with known binding sites, to recognize similar features. Third, a complete protein structure is searched for the presence of an a priori unknown functional site, similar to known sites. Our method is robust and efficient enough to allow computationally demanding applications such as the first and the third. From the biological standpoint, the first application may identify secondary binding sites of drugs that may lead to side-effects. The third application finds new potential sites on the protein that may provide targets for drug design. Each of the three applications may aid in assigning a function and in classification of binding patterns. We highlight the advantages and disadvantages of each type of search, provide examples of large-scale searches of the entire Protein Data Base and make functional predictions.

  10. The nuclear response function

    International Nuclear Information System (INIS)

    Bertsch, G.F.

    1983-01-01

    These lectures present the theory of the nuclear response in the Random Phase Approximation (RPA). In the first lecture, various relations are derived between densities and currents which give rise to the well-known sum rules. Then RPA is derived via the time-dependent Hartree theory. The various formulations of RPA are shown: the configuration space representation, the coordinate space representation, the Landau theory of infinite systems and the RPA for separable interactions constrained by consistency. The remarkable success of RPA in describing the collective density oscillations of closed shell nuclei is illustrated with a few examples. In the final lecture, the σtau response is discussed with the application of simple theoretical considerations to the empirical data. Finally, we point out several problems which remain in the response theory. (author)

  11. Theory for site-site pair distribution functions of molecular fluids. II. Approximations for the Percus--Yevick site-site direct correlation functions

    International Nuclear Information System (INIS)

    Johnson, E.

    1977-01-01

    A theory for site-site pair distribution functions of molecular fluids is derived from the Ornstein-Zernike equation. Atom-atom pair distribution functions of this theory which were obtained by using different approximations for the Percus-Yevick site-site direct correlation functions are compared

  12. Kernel regression with functional response

    OpenAIRE

    Ferraty, Frédéric; Laksaci, Ali; Tadj, Amel; Vieu, Philippe

    2011-01-01

    We consider kernel regression estimate when both the response variable and the explanatory one are functional. The rates of uniform almost complete convergence are stated as function of the small ball probability of the predictor and as function of the entropy of the set on which uniformity is obtained.

  13. Site-Specific Seismic Site Response Model for the Waste Treatment Plant, Hanford, Washington

    Energy Technology Data Exchange (ETDEWEB)

    Rohay, Alan C.; Reidel, Steve P.

    2005-02-24

    This interim report documents the collection of site-specific geologic and geophysical data characterizing the Waste Treatment Plant site and the modeling of the site-specific structure response to earthquake ground motions.

  14. Hanford Site Welding Program Successfully Providing A Single Site Function For Use By Multiple Contractors

    International Nuclear Information System (INIS)

    Cannell, G.R.

    2009-01-01

    The Department of Energy, Richland Operations (DOE-RL) recently restructured its Hanford work scope, awarding two new contracts over the past several months for a total of three contracts to manage the sites cleanup efforts. DOE-RL met with key contractor personnel prior to and during contract transition to ensure site welding activities had appropriate oversight and maintained code compliance. The transition also provided an opportunity to establish a single site-wide function that would provide welding and materials engineering services to the Hanford site contractors: CH2M HILL Plateau Remediation Company (CHPRC); Mission Support Alliance (MSA); Washington River Protection Solutions (WRPS); and Washington Closure Hanford (WCH). Over the years, multiple and separate welding programs (amongst the several contractors) existed at the Hanford site leading to inefficiencies resulting from duplication of administrative efforts, maintenance of welding procedures, welder performance certifications, etc. The new, single program eliminates these inefficiencies. The new program, co-managed by two of the sites' new contractors, the CHPRC ('owner' of the program and responsible for construction welding services) and the MSA (provides maintenance welding services), provides more than just the traditional construction and maintenance welding services. Also provided, are welding engineering, specialty welding development/qualification for the closure of radioactive materials containers and materials evaluation/failure analysis. The following describes the new Hanford site welding program.

  15. Combining specificity determining and conserved residues improves functional site prediction

    Directory of Open Access Journals (Sweden)

    Gelfand Mikhail S

    2009-06-01

    Full Text Available Abstract Background Predicting the location of functionally important sites from protein sequence and/or structure is a long-standing problem in computational biology. Most current approaches make use of sequence conservation, assuming that amino acid residues conserved within a protein family are most likely to be functionally important. Most often these approaches do not consider many residues that act to define specific sub-functions within a family, or they make no distinction between residues important for function and those more relevant for maintaining structure (e.g. in the hydrophobic core. Many protein families bind and/or act on a variety of ligands, meaning that conserved residues often only bind a common ligand sub-structure or perform general catalytic activities. Results Here we present a novel method for functional site prediction based on identification of conserved positions, as well as those responsible for determining ligand specificity. We define Specificity-Determining Positions (SDPs, as those occupied by conserved residues within sub-groups of proteins in a family having a common specificity, but differ between groups, and are thus likely to account for specific recognition events. We benchmark the approach on enzyme families of known 3D structure with bound substrates, and find that in nearly all families residues predicted by SDPsite are in contact with the bound substrate, and that the addition of SDPs significantly improves functional site prediction accuracy. We apply SDPsite to various families of proteins containing known three-dimensional structures, but lacking clear functional annotations, and discusse several illustrative examples. Conclusion The results suggest a better means to predict functional details for the thousands of protein structures determined prior to a clear understanding of molecular function.

  16. Site response assessment using borehole seismic records

    Energy Technology Data Exchange (ETDEWEB)

    Park, Donghee; Chang, Chunjoong; Choi, Weonhack [KHNP Central Research Institute, Daejeon (Korea, Republic of)

    2014-05-15

    In regions with high seismic activity, such as Japan, the Western United States and Taiwan, borehole seismometers installed deep underground are used to monitor seismic activity during the course of seismic wave propagation at various depths and to study the stress changes due to earthquakes and analyze the connection to fault movements. The Korea Meteorological Administration (KMA) and the Korea Institute of Geology and Mining (KIGAM) have installed and are operating borehole seismometers at a depth of 70∼100 meters for the precise determination of epicenters. Also, Korea Hydro and Nuclear Power Co., Ltd. (KHNP) has installed and is operating 2 borehole seismic stations near Weolseong area to observe at a depth of 140 meters seismic activities connected to fault activity. KHNP plans to operate in the second half of 2014 a borehole seismic station for depths less than 300 and 600 meters in order to study the seismic response characteristics in deep strata. As a basic study for analyzing ground motion response characteristics at depths of about 300 to 600 meters in connection with the deep geological disposal of spent nuclear fuel, the present study examined the background noise response characteristics of the borehole seismic station operated by KHNP. In order to analyze the depth-dependent impact of seismic waves at deeper depths than in Korea, seismic data collected by Japan's KIK-net seismic stations were used and the seismic wave characteristics analyzed by size and depth. In order to analyze the borehole seismic observation data from the seismic station operated by KHNP, this study analyzed the background noise characteristics by using a probability density function.

  17. Site response assessment using borehole seismic records

    International Nuclear Information System (INIS)

    Park, Donghee; Chang, Chunjoong; Choi, Weonhack

    2014-01-01

    In regions with high seismic activity, such as Japan, the Western United States and Taiwan, borehole seismometers installed deep underground are used to monitor seismic activity during the course of seismic wave propagation at various depths and to study the stress changes due to earthquakes and analyze the connection to fault movements. The Korea Meteorological Administration (KMA) and the Korea Institute of Geology and Mining (KIGAM) have installed and are operating borehole seismometers at a depth of 70∼100 meters for the precise determination of epicenters. Also, Korea Hydro and Nuclear Power Co., Ltd. (KHNP) has installed and is operating 2 borehole seismic stations near Weolseong area to observe at a depth of 140 meters seismic activities connected to fault activity. KHNP plans to operate in the second half of 2014 a borehole seismic station for depths less than 300 and 600 meters in order to study the seismic response characteristics in deep strata. As a basic study for analyzing ground motion response characteristics at depths of about 300 to 600 meters in connection with the deep geological disposal of spent nuclear fuel, the present study examined the background noise response characteristics of the borehole seismic station operated by KHNP. In order to analyze the depth-dependent impact of seismic waves at deeper depths than in Korea, seismic data collected by Japan's KIK-net seismic stations were used and the seismic wave characteristics analyzed by size and depth. In order to analyze the borehole seismic observation data from the seismic station operated by KHNP, this study analyzed the background noise characteristics by using a probability density function

  18. Site Specific Ground Response Analysis for Quantifying Site Amplification at A Regolith Site

    Directory of Open Access Journals (Sweden)

    Bambang Setiawan

    2017-08-01

    Full Text Available DOI: 10.17014/ijog.4.3.159-167A numerical model has demonstrated that it can simulate reasonably well earthquake motions at the ground level during a seismic event. The most widely used model is an equivalent linear approach. The equivalent linear model was used to compute the free-field response of Adelaide regolith during the 1997 Burra earthquake. The aim of this study is to quantify the amplification at the investigated site. The model computed the ground response of horizontally layered soil deposits subjected to transient and vertically propagating shear waves through a one-dimensional-soil column. Each soil layer was assumed to be homogeneous, visco-elastic, and infinite in the horizontal extent. The results of this study were compared to other studies and forward computation of the geotechnical dynamic parameters of the investigated site. The amplification triggered by the 1997 Burra seismic event was deduced. This study reveals the amplification factor up to 3.6 at the studied site.

  19. Text mining improves prediction of protein functional sites.

    Directory of Open Access Journals (Sweden)

    Karin M Verspoor

    Full Text Available We present an approach that integrates protein structure analysis and text mining for protein functional site prediction, called LEAP-FS (Literature Enhanced Automated Prediction of Functional Sites. The structure analysis was carried out using Dynamics Perturbation Analysis (DPA, which predicts functional sites at control points where interactions greatly perturb protein vibrations. The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important. We assessed the significance of each of these methods by analyzing their performance in finding known functional sites (specifically, small-molecule binding sites and catalytic sites in about 100,000 publicly available protein structures. The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in a functional site. The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. Our analysis also yielded new high-quality predictions of many functional site residues that were not catalogued in the curated data sources we inspected. We conclude that both DPA and text mining independently provide valuable high-throughput protein functional site predictions, and that integrating the two methods using LEAP-FS further improves the quality of these predictions.

  20. Text Mining Improves Prediction of Protein Functional Sites

    Science.gov (United States)

    Cohn, Judith D.; Ravikumar, Komandur E.

    2012-01-01

    We present an approach that integrates protein structure analysis and text mining for protein functional site prediction, called LEAP-FS (Literature Enhanced Automated Prediction of Functional Sites). The structure analysis was carried out using Dynamics Perturbation Analysis (DPA), which predicts functional sites at control points where interactions greatly perturb protein vibrations. The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important. We assessed the significance of each of these methods by analyzing their performance in finding known functional sites (specifically, small-molecule binding sites and catalytic sites) in about 100,000 publicly available protein structures. The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in a functional site. The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. Our analysis also yielded new high-quality predictions of many functional site residues that were not catalogued in the curated data sources we inspected. We conclude that both DPA and text mining independently provide valuable high-throughput protein functional site predictions, and that integrating the two methods using LEAP-FS further improves the quality of these predictions. PMID:22393388

  1. Development of site specific response spectra

    International Nuclear Information System (INIS)

    Bernreuter, D.L.; Chen, J.C.; Savy, J.B.

    1987-03-01

    For a number of years the US Nuclear Regulatory Commission (NRC) has employed site specific spectra (SSSP) in their evaluation of the adequacy of the Safe Shutdown Earthquake (SSE). These spectra were developed only from the spectra of the horizontal components of the ground motion and from a very limited data set. As the data set has considerably increased for Eastern North America (ENA) and as more relevant data has become available from earthquakes occurring in other parts of the world (e.g., Italy), together with the fact that recent data indicated the importance of the vertical component, it became clear that an update of the SSSP's for ENA was desirable. The methodology used in this study is similar to the previous ones in that it used actual earthquake ground motion data with magnitudes within a certain range and recorded at distances and at sites similar to those that would be chosen for the definition of an SSE. An extensive analysis of the origin and size of the uncertainty is an important part of this study. The results of this analysis of the uncertainties is used to develop criteria for selecting the earthquake records to be used in the derivation of the SSSP's. We concluded that the SSSPs were not very sensitive to the distribution of the source to site distance of the earthquake records used in the analysis. That is, the variability (uncertainty) introduced by the range of distances was relatively small compared to the variability introduced by other factors. We also concluded that the SSSP are somewhat sensitive to the distribution of the magnitudes of these earthquakes, particularly at rock sites and, by inference, at shallow soil sites. We found that one important criterion in selecting records to generate SSSP is the depth of soil at the site

  2. Estimation of the pseudoacceleration response spectra in sites of Mexico

    International Nuclear Information System (INIS)

    Jara-Guerrero, J. M.; Jara-Diaz, M.; Hernandez, H.

    2007-01-01

    A methodology for the pseudoacceleration response spectra assessment using utility functions is presented. This methodology was applied to the seismic hazard analysis of several cities in Mexico. After the identification of the main seismic sources that could affect the site, attenuation laws are proposed using empirical models and the instrumental information collected. Historical seismicity data and recent seismic data obtained form the strong-motion networks installed on several sites of the country are used for evaluating the characteristics of the coastal earthquakes. Due to the lack of instrumental information, empirical data are employed in other seismic faults. Source parameters, characterized by the maximum magnitudes expected, are chosen according to the physical parameters of the faults and a Bayesian analysis approach. The subduction earthquake occurrences are established with a relation between the time since the last major event and the expected magnitude of the next one. Bayes theorem was applied twice to determine the probability distribution of the parameters in the lognormal distribution of the interoccurrence times for each of the Mexican subduction segments. Annual exceedence rates of the ground acceleration and pseudoacceleration response spectra parameters based on a utility function are obtained. (authors)

  3. THE KEPLER PIXEL RESPONSE FUNCTION

    International Nuclear Information System (INIS)

    Bryson, Stephen T.; Haas, Michael R.; Dotson, Jessie L.; Koch, David G.; Borucki, William J.; Tenenbaum, Peter; Jenkins, Jon M.; Chandrasekaran, Hema; Caldwell, Douglas A.; Klaus, Todd; Gilliland, Ronald L.

    2010-01-01

    Kepler seeks to detect sequences of transits of Earth-size exoplanets orbiting solar-like stars. Such transit signals are on the order of 100 ppm. The high photometric precision demanded by Kepler requires detailed knowledge of how the Kepler pixels respond to starlight during a nominal observation. This information is provided by the Kepler pixel response function (PRF), defined as the composite of Kepler's optical point-spread function, integrated spacecraft pointing jitter during a nominal cadence and other systematic effects. To provide sub-pixel resolution, the PRF is represented as a piecewise-continuous polynomial on a sub-pixel mesh. This continuous representation allows the prediction of a star's flux value on any pixel given the star's pixel position. The advantages and difficulties of this polynomial representation are discussed, including characterization of spatial variation in the PRF and the smoothing of discontinuities between sub-pixel polynomial patches. On-orbit super-resolution measurements of the PRF across the Kepler field of view are described. Two uses of the PRF are presented: the selection of pixels for each star that maximizes the photometric signal-to-noise ratio for that star, and PRF-fitted centroids which provide robust and accurate stellar positions on the CCD, primarily used for attitude and plate scale tracking. Good knowledge of the PRF has been a critical component for the successful collection of high-precision photometry by Kepler.

  4. Hanford Site emergency response needs, Volumes 1 and 2

    International Nuclear Information System (INIS)

    Good, D.E.

    1996-01-01

    This report presents the results of a comprehensive third party needs assessment of the Hanford Fire Department (HFD), conducted by Hughes Associates Inc. The assessment was commissioned with the intent of obtaining an unbiased report which could be used as a basis for identifying needed changes/modifications to the fire department and its services. This report serves several functions: (1) it documents current and future site operations and associated hazards and risks identified as a result of document review, site and facility surveys, and interviews with knowledgeable personnel; (2) describes the HFD in terms of organization, existing resources and response capabilities; (3) identifies regulatory and other requirements that are applicable to the HFD and includes a discussion of associated legal liabilities; and (4) provides recommendations based on applicable requirements and existing conditions. Each recommendation is followed by a supporting statement to clarify the intent or justification of the recommendation. This report will be followed by a Master Plan document which will present an implementation method for the recommendations (with associated costs) considered to be essential to maintaining adequate, cost effective emergency services at the Hanford site in the next five to seven years

  5. Hanford Site emergency response needs, Volumes 1 and 2

    Energy Technology Data Exchange (ETDEWEB)

    Good, D.E.

    1996-04-16

    This report presents the results of a comprehensive third party needs assessment of the Hanford Fire Department (HFD), conducted by Hughes Associates Inc. The assessment was commissioned with the intent of obtaining an unbiased report which could be used as a basis for identifying needed changes/modifications to the fire department and its services. This report serves several functions: (1) it documents current and future site operations and associated hazards and risks identified as a result of document review, site and facility surveys, and interviews with knowledgeable personnel; (2) describes the HFD in terms of organization, existing resources and response capabilities; (3) identifies regulatory and other requirements that are applicable to the HFD and includes a discussion of associated legal liabilities; and (4) provides recommendations based on applicable requirements and existing conditions. Each recommendation is followed by a supporting statement to clarify the intent or justification of the recommendation. This report will be followed by a Master Plan document which will present an implementation method for the recommendations (with associated costs) considered to be essential to maintaining adequate, cost effective emergency services at the Hanford site in the next five to seven years.

  6. Functional Complexity and Web Site Design : Evaluating the Online Presence of UNESCO World Heritage Sites

    NARCIS (Netherlands)

    De Jong, Menno D.T.; Wu, Yuguang

    2018-01-01

    Functional complexity is a widespread and underresearched phenomenon in Web sites. This article explores a specific case of functional complexity by analyzing the content of UNESCO World Heritage Web sites, which have to meet demands from both World Heritage and tourism perspectives. Based on a

  7. Seismic Hazard Assessment in Site Evaluation for Nuclear Installations: Ground Motion Prediction Equations and Site Response

    International Nuclear Information System (INIS)

    2016-07-01

    The objective of this publication is to provide the state-of-the-art practice and detailed technical elements related to ground motion evaluation by ground motion prediction equations (GMPEs) and site response in the context of seismic hazard assessments as recommended in IAEA Safety Standards Series No. SSG-9, Seismic Hazards in Site Evaluation for Nuclear Installations. The publication includes the basics of GMPEs, ground motion simulation, selection and adjustment of GMPEs, site characterization, and modelling of site response in order to improve seismic hazard assessment. The text aims at delineating the most important aspects of these topics (including current practices, criticalities and open problems) within a coherent framework. In particular, attention has been devoted to filling conceptual gaps. It is written as a reference text for trained users who are responsible for planning preparatory seismic hazard analyses for siting of all nuclear installations and/or providing constraints for anti-seismic design and retrofitting of existing structures

  8. Autoimmune Response Confers Decreased Cardiac Function in ...

    African Journals Online (AJOL)

    inflammatory response; rather, autoimmune response would keep affecting decreased heart function in. RHD patients who ... untreated children. Nearly 30 - 45 % of the affected children could ..... Technology Department of Anhui Province (PR.

  9. Semipalatinsk nuclear test site: History of building and function

    International Nuclear Information System (INIS)

    Sergazina, G.M.; Balmukhanov, S.B.

    1999-01-01

    A vast materials on history of Semipalatinsk nuclear test site creation and it building and function are presented. Authors with big reliability report one page of Kazakhstan's history. In steppe on naked place thousands of soldiers and officers, construct and military specialists have built the nuclear site on which during 40 years were conducting nuclear tests . Prolonged chronic radiation on population living near by site results to tragedy which is confessed by General Assembly of United Nations. In the book aspects of test site conversion and rehabilitation of injured population are considered. The book consists of introduction, three chapters and conclusion. The book is intended to wide circle of readers. (author)

  10. Active chemisorption sites in functionalized ionic liquids for carbon capture.

    Science.gov (United States)

    Cui, Guokai; Wang, Jianji; Zhang, Suojiang

    2016-07-25

    Development of novel technologies for the efficient and reversible capture of CO2 is highly desired. In the last decade, CO2 capture using ionic liquids has attracted intensive attention from both academia and industry, and has been recognized as a very promising technology. Recently, a new approach has been developed for highly efficient capture of CO2 by site-containing ionic liquids through chemical interaction. This perspective review focuses on the recent advances in the chemical absorption of CO2 using site-containing ionic liquids, such as amino-based ionic liquids, azolate ionic liquids, phenolate ionic liquids, dual-functionalized ionic liquids, pyridine-containing ionic liquids and so on. Other site-containing liquid absorbents such as amine-based solutions, switchable solvents, and functionalized ionic liquid-amine blends are also investigated. Strategies have been discussed for how to activate the existent reactive sites and develop novel reactive sites by physical and chemical methods to enhance CO2 absorption capacity and reduce absorption enthalpy. The carbon capture mechanisms of these site-containing liquid absorbents are also presented. Particular attention has been paid to the latest progress in CO2 capture in multiple-site interactions by amino-free anion-functionalized ionic liquids. In the last section, future directions and prospects for carbon capture by site-containing ionic liquids are outlined.

  11. Corporate Social Responsibility In Turkey: An Analysis Through Web Sites

    Directory of Open Access Journals (Sweden)

    Burcu EKER AKGÖZ

    2016-06-01

    Full Text Available In today’s business environment, there is no chance for a corporation to be succeeded simply by doing profit oriented business. Corporations are the living entities along with their stakeholders therefore corporations are expected to be responsive on the cultural, environmental and economic issues of society. Socially responsible programs that corporations execute would contribute the corporate image and reputation. Furthermore, these programs benefit both corporations and society. The aim of this study is to examine the presence and organization of information on corporate responsibility present on the corporate web sites of companies which are in the Capital top 500 list. We will choose the top 100 companies on the top 500 list. By using content analysis, identified corporate responsibility issues will be analyzed. In this study, the information given in the web sites of these top 100 companies will be analyzed. We will be examining how the information is organized, presented, and related to the corporate responsibilities.

  12. ARES: automated response function code. Users manual

    International Nuclear Information System (INIS)

    Maung, T.; Reynolds, G.M.

    1981-06-01

    This ARES user's manual provides detailed instructions for a general understanding of the Automated Response Function Code and gives step by step instructions for using the complete code package on a HP-1000 system. This code is designed to calculate response functions of NaI gamma-ray detectors, with cylindrical or rectangular geometries

  13. Sum rules in the response function method

    International Nuclear Information System (INIS)

    Takayanagi, Kazuo

    1990-01-01

    Sum rules in the response function method are studied in detail. A sum rule can be obtained theoretically by integrating the imaginary part of the response function over the excitation energy with a corresponding energy weight. Generally, the response function is calculated perturbatively in terms of the residual interaction, and the expansion can be described by diagrammatic methods. In this paper, we present a classification of the diagrams so as to clarify which diagram has what contribution to which sum rule. This will allow us to get insight into the contributions to the sum rules of all the processes expressed by Goldstone diagrams. (orig.)

  14. Cottonwood Response to Nitrogen Related To Plantation Age and Site

    Science.gov (United States)

    B.G. Blackmon

    1977-01-01

    When applied at plantation age 4,336 kg N/ha increased diameter growth of cottonwood on Sharkey clay by 33 percent over unfertilized controls. Fertilizing at ages 2 and 3 resulted in no response, nor was there any benefit from applying nitrogen fertilizer to cottonwood on Commerce silt loam. On both sites, foliar N levels were increased by fertilization regardless of...

  15. Site Response Analysis Using DeepSoil: Case Study of Bangka Site, Indonesia

    Energy Technology Data Exchange (ETDEWEB)

    Iswanto, Eko Rudi; Yee, Eric [KEPCO International Nuclear Graduate School, Ulsan (Korea, Republic of)

    2015-10-15

    Indonesia government declared through Act No. 17 year 2007 on the National Long-Term Development Plant Year 2005-2025 and Presidential Decree No. 5 year 2006 on the National Energy Policy (Indonesia 2007; Indonesia 2006), that nuclear energy is stated as a part of the national energy system. In order to undertake the above national policy, National Nuclear Energy Agency of Indonesia, as the promotor for the utilization of nuclear energy will conduct site study, which is a part of infrastructure preparation for NPP construction. Thorough preparation and steps are needed to operate an NPP and it takes between 10 to 15 years from the preliminary study (site selection, financial study, etc.) up to project implementation (manufacturing, construction, commissioning). During project implementation, it is necessary to prepare various documents relevant for permit application such as Safety Evaluation Report for site permit, Preliminary Safety Analysis Report and Environment Impact Assessment Report for construction permit. Considering the continuously increasing electricity energy demand, it is necessary to prepare for alternative NPP sites. The safety requirements of NPP's are stringent; amongst the various requirements is the ability to safely shut down in the wake of a possible earthquake. Ground response analysis of a potential site therefore needs to be carried out, parameter that affect the resistance of an NPP to earthquakes such as peak strain profiles is analysed. The objective of this paper is to analyse the ground response of the selected site for a NPP, using The Mw 7.9 in Sikuai Island, West Sumatra on September 12, 2007 as present input motion. This analysis will be carried out using a ground response analysis program, DeepSoil. In addition to this, an attempt was made to define the site specific input motion characteristics of the selected site for use in DeepSoil (DeepSoil 5.0). A site investigation at the WB site was performed primarily on the PS

  16. Coping responses as predictors of psychosocial functioning ...

    African Journals Online (AJOL)

    ... West Haven-Yale Multidimensional Pain Inventory and the Coping Responses Inventory – Adult Form. The prevalence of the use of Avoidance and Approach Coping, and the relationship between these responses and psychosocial functioning (Pain Severity, Interference, Support, Life Control, and Affective Distress) were ...

  17. Number of on-site personnel and their functions

    International Nuclear Information System (INIS)

    Recker, M.

    1986-01-01

    After the definition of the general tasks, the development of an organization chart for on-site personnel is shown, the number and qualifications are indicated relating to the specific jobs. The functions of the different people are explained in detail. (orig.)

  18. AGE STRUCTURE OR FUNCTIONAL RESPONSE? RECONCILING ...

    African Journals Online (AJOL)

    ... surplus production that differ from traditional single-species management models. ... Specifically, while the ECOSIM “Arena” functional response and the von ... as a proxy for age structure rather than as a function of predator/prey behaviour, ...

  19. Chief Business Officers' Functions: Responsibilities and Importance.

    Science.gov (United States)

    Calver, Richard A.; Vogler, Daniel E.

    1985-01-01

    Reports on a survey of 177 chief business officers of public community colleges regarding their responsibilities and the importance they assigned to various role functions. Highlights findings concerning the perceived importance of fiscal/financial duties; endowments as a job function; role in shared planning; and personal attention given to…

  20. Semiclassical theory for the nuclear response function

    International Nuclear Information System (INIS)

    Stroth, U.

    1986-01-01

    In the first part of this thesis it was demonstrated how on a semiclassical base a RPA theory is developed and applied to electron scattering. It was shown in which fields of nuclear physics this semiclassical theory can be applied and how it is to be understood. In this connection we dedicated an extensive discussion to the Fermi gas model. From the free response function we calculated the RPA response with a finite-range residual interaction which we completely antisymmetrize. In the second part of this thesis we studied with our theory (e,e') data for the separated response functions. (orig./HSI) [de

  1. Radiological emergency response - a functional approach

    International Nuclear Information System (INIS)

    Chowdhury, P.

    1998-01-01

    The state of Louisiana's radiological emergency response programme is based on the federal guidance 'Criteria for Preparation and Evaluation of Radiological Emergency Response Plans and Preparedness in Support of Nuclear Power Plants' (NUREG-0654, FEMA-REP-1 Rev. 1). Over the past 14 years, the planning and implementation of response capabilities became more organized and efficient; the training programme has strengthened considerably; co-ordination with all participating agencies has assumed a more co-operative role, and as a result, a fairly well integrated response planning has evolved. Recently, a more 'functional' approach is being adopted to maximize the programme's efficiency not only for nuclear power plant emergency response, but radiological emergency response as a whole. First, several broad-based 'components' are identified; clusters of 'nodes' are generated for each component; these 'nodes' may be divided into 'sub-nodes' which will contain some 'attributes'; 'relational bonds' among the 'attributes' will exist. When executed, the process begins and continues with the 'nodes' assuming a functional and dynamic role based on the nature and characteristics of the 'attributes'. The typical response based on stand-alone elements is thus eliminated, the overlapping of functions is avoided, and a well structured and efficient organization is produced, that is essential for today's complex nature of emergency response. (author)

  2. Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes.

    Directory of Open Access Journals (Sweden)

    Benjamin R Jack

    2016-05-01

    Full Text Available Functional residues in proteins tend to be highly conserved over evolutionary time. However, to what extent functional sites impose evolutionary constraints on nearby or even more distant residues is not known. Here, we report pervasive conservation gradients toward catalytic residues in a dataset of 524 distinct enzymes: evolutionary conservation decreases approximately linearly with increasing distance to the nearest catalytic residue in the protein structure. This trend encompasses, on average, 80% of the residues in any enzyme, and it is independent of known structural constraints on protein evolution such as residue packing or solvent accessibility. Further, the trend exists in both monomeric and multimeric enzymes and irrespective of enzyme size and/or location of the active site in the enzyme structure. By contrast, sites in protein-protein interfaces, unlike catalytic residues, are only weakly conserved and induce only minor rate gradients. In aggregate, these observations show that functional sites, and in particular catalytic residues, induce long-range evolutionary constraints in enzymes.

  3. Fast dynamics perturbation analysis for prediction of protein functional sites

    Directory of Open Access Journals (Sweden)

    Cohn Judith D

    2008-01-01

    Full Text Available Abstract Background We present a fast version of the dynamics perturbation analysis (DPA algorithm to predict functional sites in protein structures. The original DPA algorithm finds regions in proteins where interactions cause a large change in the protein conformational distribution, as measured using the relative entropy Dx. Such regions are associated with functional sites. Results The Fast DPA algorithm, which accelerates DPA calculations, is motivated by an empirical observation that Dx in a normal-modes model is highly correlated with an entropic term that only depends on the eigenvalues of the normal modes. The eigenvalues are accurately estimated using first-order perturbation theory, resulting in a N-fold reduction in the overall computational requirements of the algorithm, where N is the number of residues in the protein. The performance of the original and Fast DPA algorithms was compared using protein structures from a standard small-molecule docking test set. For nominal implementations of each algorithm, top-ranked Fast DPA predictions overlapped the true binding site 94% of the time, compared to 87% of the time for original DPA. In addition, per-protein recall statistics (fraction of binding-site residues that are among predicted residues were slightly better for Fast DPA. On the other hand, per-protein precision statistics (fraction of predicted residues that are among binding-site residues were slightly better using original DPA. Overall, the performance of Fast DPA in predicting ligand-binding-site residues was comparable to that of the original DPA algorithm. Conclusion Compared to the original DPA algorithm, the decreased run time with comparable performance makes Fast DPA well-suited for implementation on a web server and for high-throughput analysis.

  4. Site-Specific Antibody Functionalization Using Tetrazine-Styrene Cycloaddition.

    Science.gov (United States)

    Umlauf, Benjamin J; Mix, Kalie A; Grosskopf, Vanessa A; Raines, Ronald T; Shusta, Eric V

    2018-05-03

    Biologics, such as antibody-drug conjugates, are becoming mainstream therapeutics. Consequently, methods to functionalize biologics without disrupting their native properties are essential for identifying, characterizing, and translating candidate biologics from the bench to clinical practice. Here, we present a method for site-specific, carboxy-terminal modification of single-chain antibody fragments (scFvs). ScFvs displayed on the surface of yeast were isolated and functionalized by combining intein-mediated expressed protein ligation (EPL) with inverse electron-demand Diels-Alder (IEDDA) cycloaddition using a styrene-tetrazine pair. The high thiol concentration required to trigger EPL can hinder the subsequent chemoselective ligation reactions; therefore, the EPL reaction was used to append styrene to the scFv, limiting tetrazine exposure to damaging thiols. Subsequently, the styrene-functionalized scFv was reacted with tetrazine-conjugated compounds in an IEDDA cycloaddition to generate functionalized scFvs that retain their native binding activity. Rapid functionalization of yeast surface-derived scFv in a site-directed manner could find utility in many downstream laboratory and preclinical applications.

  5. Diagnostics for Linear Models With Functional Responses

    OpenAIRE

    Xu, Hongquan; Shen, Qing

    2005-01-01

    Linear models where the response is a function and the predictors are vectors are useful in analyzing data from designed experiments and other situations with functional observations. Residual analysis and diagnostics are considered for such models. Studentized residuals are defined and their properties are studied. Chi-square quantile-quantile plots are proposed to check the assumption of Gaussian error process and outliers. Jackknife residuals and an associated test are proposed to det...

  6. Frequency response functions for nonlinear convergent systems

    NARCIS (Netherlands)

    Pavlov, A.V.; Wouw, van de N.; Nijmeijer, H.

    2007-01-01

    Convergent systems constitute a practically important class of nonlinear systems that extends the class of asymptotically stable linear time-invariant systems. In this note, we extend frequency response functions defined for linear systems to nonlinear convergent systems. Such nonlinear frequency

  7. NaI(Tl) response functions

    International Nuclear Information System (INIS)

    Vega C, H. R.; Ortiz R, J. M.; Benites R, J. L.; De Leon M, H. A.

    2015-09-01

    The response functions of a NaI(Tl) detector have been estimated using Monte Carlo methods. Response functions were calculated for monoenergetic photon sources (0.05 to 3 MeV). Responses were calculated for point-like sources and for sources distributed in Portland cement cylinders. The responses were used to calculate the efficiency functions in term of photon energy. Commonly, sources used for calibration are point-like, and eventually sources to be measured have different features. In order to use the calibrated sources corrections due to solid angle, self-absorption and scattering, must be carried out. However, some of these corrections are not easy to perform. In this work, the calculated responses were used to estimate the detector efficiency of point-like sources, and sources distributed in Portland type cement. Samples of Portland paste were prepared and were exposed to photoneutrons produced by a 15 MV linac. Some of the elements in the cement were activated producing γ-emitting radionuclides that were measured with a NaI(Tl) gamma-ray spectrometer, that was calibrated with point-like sources. In order to determine the specific activity in the induced radioisotopes calculated efficiencies were used to make corrections due to the differences between the solid angle, photon absorption and photon scattering in the point-like calibration sources and the sources distributed in cement. During the interaction between photoneutrons and the cement samples three radioisotopes were induced: 56 Mn, 24 Na, and 28 Al. (Author)

  8. Development of Biomimetic and Functionally Responsive Surfaces

    Science.gov (United States)

    Anastasiadis, Spiros H.

    2010-03-01

    Controlling the surface morphology of solids and manufacturing of functional surfaces with special responsive properties has been the subject of intense research. We report a methodology for creating multifunctionally responsive surfaces by irradiating silicon wafers with femtosecond laser pulses and subsequently coating them with different types of functional conformal coatings. Such surfaces exhibit controlled dual-scale roughness at the micro- and the nano-scale, which mimics the hierarchical morphology of water repellent natural surfaces. When a simple alkylsilane coating is utilized, highly water repellent surfaces are produced that quantitatively compare to those of the Lotus leaf. When a polymer brush is ``grafted from" these surfaces based on a pH-sensitive polymer, the surfaces can alter their behavior from super-hydrophilic (after immersion in a low pH buffer) to super-hydrophobic and water-repellent (following immersion to a high pH buffer). We quantify the water repellency of such responsive systems by drop elasticity measurements whereas we demonstrate that the water repellent state of such surface requires appropriate hydrophobicity of the functionalizing polymer. When a photo-responsive azobenzene-type polymer is deposited, a dynamic optical control of the wetting properties is obtained and the surface can be switched from super-hydrophilic (following UV irradiation) to hydrophobic (following green irradiation). In all the above cases we show that the principal effect of roughness is to cause amplification of the response to the different external stimuli.

  9. Radiological emergency response - a functional approach

    Energy Technology Data Exchange (ETDEWEB)

    Chowdhury, Prosanta [Louisiana Radiation Protection Div., Baton Rouge, LA (United States)

    1997-12-31

    The radiological emergency response program in the State of Louisiana is discussed. The improved approach intends to maximize the efficiency for both nuclear power plant and radiological emergency response as a whole. Several broad-based components are identified: cluster of `nodes` are generated for each component; these `nodes` may be divided into `sub-nodes` which will contain some `attributes`; `relational bonds` among the `attributes` will exist. When executed, the process begins and continues with the `nodes` assuming a functional and dynamic role based on the nature and characteristics of the `attributes`. The typical response based on stand-alone elements is eliminated; overlapping of functions is avoided, and is produced a well-structure and efficient organization 1 ref., 6 figs.; e-mail: prosanta at deq.state.la.us

  10. Radiological emergency response - a functional approach

    International Nuclear Information System (INIS)

    Chowdhury, Prosanta

    1997-01-01

    The radiological emergency response program in the State of Louisiana is discussed. The improved approach intends to maximize the efficiency for both nuclear power plant and radiological emergency response as a whole. Several broad-based components are identified: cluster of 'nodes' are generated for each component; these 'nodes' may be divided into 'sub-nodes' which will contain some 'attributes'; 'relational bonds' among the 'attributes' will exist. When executed, the process begins and continues with the 'nodes' assuming a functional and dynamic role based on the nature and characteristics of the 'attributes'. The typical response based on stand-alone elements is eliminated; overlapping of functions is avoided, and is produced a well-structure and efficient organization

  11. Modeling Nonlinear Site Response Uncertainty in Broadband Ground Motion Simulations for the Los Angeles Basin

    Science.gov (United States)

    Assimaki, D.; Li, W.; Steidl, J. M.; Schmedes, J.

    2007-12-01

    source parameters for the ensemble of site conditions. Elastic, equivalent linear and nonlinear simulations are implemented for the deterministic description of the base-model velocity and attenuation structures and nonlinear soil properties, to examine the variability in ground motion predictions as a function of ground motion amplitude and frequency content, and nonlinear site response methodology. The modeling site response uncertainty introduced in the broadband ground motion predictions is reported by means of the COV of site amplification, defined as the ratio of the predicted peak ground acceleration (PGA) and spectral acceleration (SA) at short and long periods to the corresponding intensity measure on the ground surface of a typical NEHRP BC boundary profile (Vs30=760m/s), for the ensemble of approximate and incremental nonlinear models implemented. A frequency index is developed to describe the frequency content of incident ground motion. In conjunction with the rock-outcrop acceleration level, this index is used to identify the site and ground motion conditions where incremental nonlinear analyses should be employed in lieu of approximate methodologies. Finally, the effects of modeling uncertainty in ground response analysis is evaluated in the estimation of site amplification factors, which are successively compared to recently published factors of the New Generation Attenuation Relations (NGA) and the currently employed Seismic Code Provisions (NEHRP).

  12. Response of Korean pine's functional traits to geography and climate.

    Directory of Open Access Journals (Sweden)

    Yichen Dong

    Full Text Available This study analyzed the characteristics of Korean pine (Pinus koraiensis functional trait responses to geographic and climatic factors in the eastern region of Northeast China (41°-48°N and the linear relationships among Korean pine functional traits, to explore this species' adaptability and ecological regulation strategies under different environmental conditions. Korean pine samples were collected from eight sites located at different latitudes, and the following factors were determined for each site: geographic factors-latitude, longitude, and altitude; temperature factors-mean annual temperature (MAT, growth season mean temperature (GST, and mean temperature of the coldest month (MTCM; and moisture factors-annual precipitation (AP, growth season precipitation (GSP, and potential evapotranspiration (PET. The Korean pine functional traits examined were specific leaf area (SLA, leaf thickness (LT, leaf dry matter content (LDMC, specific root length (SRL, leaf nitrogen content (LNC, leaf phosphorus content (LPC, root nitrogen content (RNC, and root phosphorus content (RPC. The results showed that Korean pine functional traits were significantly correlated to latitude, altitude, GST, MTCM, AP, GSP, and PET. Among the Korean pine functional traits, SLA showed significant linear relationships with LT, LDMC, LNC, LPC, and RPC, and LT showed significant linear relationships with LDMC, SRL, LNC, LPC, RNC, and RPC; the linear relationships between LNC, LPC, RNC, and RPC were also significant. In conclusion, Korean pine functional trait responses to latitude resulted in its adaptation to geographic and climatic factors. The main limiting factors were precipitation and evapotranspiration, followed by altitude, latitude, GST, and MTCM. The impacts of longitude and MAT were not obvious. Changes in precipitation and temperature were most responsible for the close correlation among Korean pine functional traits, reflecting its adaption to habitat

  13. The knowledge-based off-site emergency response system for a nuclear power plant

    International Nuclear Information System (INIS)

    Ho, L.W.; Loa, W.W.; Wang, C.L.

    1987-01-01

    A knowledge-based expert system for a nuclear power plant off-site emergency response system is described. The system incorporates the knowledge about the nuclear power plant behaviours, site environment and site geographic factors, etc. The system is developed using Chinshan nuclear power station of Taipower Company, Taiwan, ROC as a representative model. The objectives of developing this system are to provide an automated intelligent system with functions of accident simulation, prediction and with learning capabilities to supplement the actions of the emergency planners and accident managers in order to protect the plant personnel and the surrounding population, and prevent or mitigate property damages resulting from the plant accident. The system is capable of providing local and national authorities with rapid retrieval data from the site characteristics and accident progression. The system can also provide the framework for allocation of available resources and can handle the uncertainties in data and models

  14. Response functions of superfluid neutron matter

    Energy Technology Data Exchange (ETDEWEB)

    Keller, Jochen; Sedrakian, Armen [Institut fuer Theoretische Physik, Goethe Universitaet, 60438 Frankfurt/Main (Germany)

    2011-07-01

    We investigate the response of pair-correlated neutron matter under conditions relevant to neutron stars to external weak probes and compute its neutrino emissivity in vector and axialvector channels. To derive the response functions we sum up an infinite chain of particle-hole ladder diagrams within finite-temperature Green's function theory. The polarization tensor of matter is evaluated in the limit of small momentum transfers. The calculated neutrino emission via the weak neutral current processes of pair-breaking and recombination of Cooper-pairs in neutron stars causes a cooling of their baryonic interior, and represents an important mechanism for the thermal evolution of the star within a certain time domain.

  15. Optical response from functionalized atomically thin nanomaterials

    Energy Technology Data Exchange (ETDEWEB)

    Malic, Ermin; Berghaeuser, Gunnar; Feierabend, Maja [Department of Physics, Chalmers University of Technology, Gothenburg (Sweden); Knorr, Andreas [Institut fuer Theoretische Physik, Technische Universitaet Berlin (Germany)

    2017-10-15

    Chemical functionalization of atomically thin nanostructures presents a promising strategy to create new hybrid nanomaterials with remarkable and externally controllable properties. Here, we review our research in the field of theoretical modeling of carbon nanotubes, graphene, and transition metal dichalcogenides located in molecular dipole fields. In particular, we provide a microscopic view on the change of the optical response of these technologically promising nanomaterials due to the presence of photo-active spiropyran molecules. The feature article presents a review of recent theoretical work providing microscopic view on the optical response of chemically functionalized carbon nanotubes, graphene, and monolayered transition metal dichalcogenides. In particular, we propose a novel sensor mechanism based on the molecule-induced activation of dark excitons. This results in a pronounced additional peak presenting an unambiguous optical fingerprint for the attached molecules. (copyright 2017 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  16. Site Response and Basin Waves in the Sacramento–San Joaquin Delta, California

    Science.gov (United States)

    Fletcher, Jon Peter B.; Boatwright, John

    2013-01-01

    The Sacramento–San Joaquin Delta is an inland delta at the western extent of the Central Valley. Levees were built around swampy islands starting after the Civil War to reclaim these lands for farming. Various studies show that these levees could fail in concert from shaking from a major local or regional earthquake resulting in salty water from the San Francisco Bay contaminating the water in the Delta. We installed seismographs around the Delta and on levees to assess the contribution of site response to the seismic hazard of the levees. Cone penetrometer testing shows that the upper 10 s of meters of soil in the Delta have shear‐wave velocities of about 200  m/s, which would give a strong site response. Seismographs were sited following two strategies: pairs of stations to compare the response of the levees to nearby sites, and a more regional deployment in the Delta. Site response was determined in two different ways: a traditional spectral ratio (TSR) approach of S waves using station BDM of the Berkeley Digital Seismic Net as a reference site, and using SH/SV ratios of noise (or Nakamura’s method). Both estimates usually agree in spectral character for stations whose response is dominated by a resonant peak, but the most obvious peaks in the SH/SV ratios usually are about two‐thirds as large as the main peaks in the TSRs. Levee sites typically have large narrow resonances in the site response function compared to sites in the farmland of the Delta. These resonances, at a frequency of about 1–3 Hz, have amplitudes of about 15 with TSR and 10–12 with Nakamura’s method. Sites on farmland in the Delta also have amplifications, but these are typically broader and not as resonant in appearance. Late (slow) Rayleigh waves were recorded at stations in the Delta, have a dominant period of about one second, and are highly monochromatic. Results from a three‐station array at the Holland Marina suggest that they have a phase velocity of about

  17. NaI(Tl) response functions

    Energy Technology Data Exchange (ETDEWEB)

    Vega C, H. R.; Ortiz R, J. M. [Universidad Autonoma de Zacatecas, Unidad Academica de Estudios Nucleares, Cipres No. 10, Fracc. La Penuela, 98068 Zacatecas, Zac. (Mexico); Benites R, J. L. [Centro Estatal de Cancerologia de Nayarit, Calz. de la Cruz 118 Sur, Tepic, Nayarit (Mexico); De Leon M, H. A., E-mail: fermineutron@yahoo.com.mx [Instituto Tecnologico de Aguascalientes, Av. Adolfo Lopez Mateos 1801 Ote., 20155 Aguascalientes, Ags. (Mexico)

    2015-09-15

    The response functions of a NaI(Tl) detector have been estimated using Monte Carlo methods. Response functions were calculated for monoenergetic photon sources (0.05 to 3 MeV). Responses were calculated for point-like sources and for sources distributed in Portland cement cylinders. The responses were used to calculate the efficiency functions in term of photon energy. Commonly, sources used for calibration are point-like, and eventually sources to be measured have different features. In order to use the calibrated sources corrections due to solid angle, self-absorption and scattering, must be carried out. However, some of these corrections are not easy to perform. In this work, the calculated responses were used to estimate the detector efficiency of point-like sources, and sources distributed in Portland type cement. Samples of Portland paste were prepared and were exposed to photoneutrons produced by a 15 MV linac. Some of the elements in the cement were activated producing γ-emitting radionuclides that were measured with a NaI(Tl) gamma-ray spectrometer, that was calibrated with point-like sources. In order to determine the specific activity in the induced radioisotopes calculated efficiencies were used to make corrections due to the differences between the solid angle, photon absorption and photon scattering in the point-like calibration sources and the sources distributed in cement. During the interaction between photoneutrons and the cement samples three radioisotopes were induced: {sup 56}Mn, {sup 24}Na, and {sup 28}Al. (Author)

  18. The functional response of a generalist predator.

    Directory of Open Access Journals (Sweden)

    Sophie Smout

    Full Text Available BACKGROUND: Predators can have profound impacts on the dynamics of their prey that depend on how predator consumption is affected by prey density (the predator's functional response. Consumption by a generalist predator is expected to depend on the densities of all its major prey species (its multispecies functional response, or MSFR, but most studies of generalists have focussed on their functional response to only one prey species. METHODOLOGY AND PRINCIPAL FINDINGS: Using Bayesian methods, we fit an MSFR to field data from an avian predator (the hen harrier Circus cyaneus feeding on three different prey species. We use a simple graphical approach to show that ignoring the effects of alternative prey can give a misleading impression of the predator's effect on the prey of interest. For example, in our system, a "predator pit" for one prey species only occurs when the availability of other prey species is low. CONCLUSIONS AND SIGNIFICANCE: The Bayesian approach is effective in fitting the MSFR model to field data. It allows flexibility in modelling over-dispersion, incorporates additional biological information into the parameter priors, and generates estimates of uncertainty in the model's predictions. These features of robustness and data efficiency make our approach ideal for the study of long-lived predators, for which data may be sparse and management/conservation priorities pressing.

  19. Nuclear event time histories and computed site transfer functions for locations in the Los Angeles region

    Science.gov (United States)

    Rogers, A.M.; Covington, P.A.; Park, R.B.; Borcherdt, R.D.; Perkins, D.M.

    1980-01-01

    This report presents a collection of Nevada Test Site (NTS) nuclear explosion recordings obtained at sites in the greater Los Angeles, Calif., region. The report includes ground velocity time histories, as well as, derived site transfer functions. These data have been collected as part of a study to evaluate the validity of using low-level ground motions to predict the frequency-dependent response of a site during an earthquake. For this study 19 nuclear events were recorded at 98 separate locations. Some of these sites have recorded more than one of the nuclear explosions, and, consequently, there are a total of 159, three-component station records. The location of all the recording sites are shown in figures 1–5, the station coordinates and abbreviations are given in table 1. The station addresses are listed in table 2, and the nuclear explosions that were recorded are listed in table 3. The recording sites were chosen on the basis of three criteria: (1) that the underlying geological conditions were representative of conditions over significant areas of the region, (2) that the site was the location of a strong-motion recording of the 1971 San Fernando earthquake, or (3) that more complete geographical coverage was required in that location.

  20. System transient response to loss of off-site power

    International Nuclear Information System (INIS)

    Sozer, A.

    1990-01-01

    A simultaneous trip of the reactor, main circulation pumps, secondary coolant pumps, and pressurizer pump due to loss of off-site power at the High Flux Isotope Reactor (HFIR) located at the Oak Ridge National Laboratory (ORNL) has been analyzed to estimate available safety margin. A computer model based on the Modular Modeling System code has been used to calculate the transient response of the system. The reactor depressurizes from 482.7 psia down to about 23 psia in about 50 seconds and remains stable thereafter. Available safety margin has been estimated in terms of the incipient boiling heat flux ratio. It is a conservative estimate due to assumed less than available primary and secondary flows and higher than normal depressurization rate. The ratio indicates no incipient boiling conditions at the hot spot. No potential damage to the fuel is likely to occur during this transient. 2 refs., 6 figs

  1. Prediction of functional sites in proteins using conserved functional group analysis.

    Science.gov (United States)

    Innis, C Axel; Anand, A Prem; Sowdhamini, R

    2004-04-02

    A detailed knowledge of a protein's functional site is an absolute prerequisite for understanding its mode of action at the molecular level. However, the rapid pace at which sequence and structural information is being accumulated for proteins greatly exceeds our ability to determine their biochemical roles experimentally. As a result, computational methods are required which allow for the efficient processing of the evolutionary information contained in this wealth of data, in particular that related to the nature and location of functionally important sites and residues. The method presented here, referred to as conserved functional group (CFG) analysis, relies on a simplified representation of the chemical groups found in amino acid side-chains to identify functional sites from a single protein structure and a number of its sequence homologues. We show that CFG analysis can fully or partially predict the location of functional sites in approximately 96% of the 470 cases tested and that, unlike other methods available, it is able to tolerate wide variations in sequence identity. In addition, we discuss its potential in a structural genomics context, where automation, scalability and efficiency are critical, and an increasing number of protein structures are determined with no prior knowledge of function. This is exemplified by our analysis of the hypothetical protein Ydde_Ecoli, whose structure was recently solved by members of the North East Structural Genomics consortium. Although the proposed active site for this protein needs to be validated experimentally, this example illustrates the scope of CFG analysis as a general tool for the identification of residues likely to play an important role in a protein's biochemical function. Thus, our method offers a convenient solution to rapidly and automatically process the vast amounts of data that are beginning to emerge from structural genomics projects.

  2. Functional and structural responses to marine urbanisation

    Science.gov (United States)

    Mayer-Pinto, M.; Cole, V. J.; Johnston, E. L.; Bugnot, A.; Hurst, H.; Airoldi, L.; Glasby, T. M.; Dafforn, K. A.

    2018-01-01

    Urban areas have broad ecological footprints with complex impacts on natural systems. In coastal areas, growing populations are advancing their urban footprint into the ocean through the construction of seawalls and other built infrastructure. While we have some understanding of how urbanisation might drive functional change in terrestrial ecosystems, coastal systems have been largely overlooked. This study is one of the first to directly assess how changes in diversity relate to changes in ecosystem properties and functions (e.g. productivity, filtration rates) of artificial and natural habitats in one of the largest urbanised estuaries in the world, Sydney Harbour. We complemented our surveys with an extensive literature search. We found large and important differences in the community structure and function between artificial and natural coastal habitats. However, differences in diversity and abundance of organisms do not necessarily match observed functional changes. The abundance and composition of important functional groups differed among habitats with rocky shores having 40% and 70% more grazers than seawalls or pilings, respectively. In contrast, scavengers were approximately 8 times more abundant on seawalls than on pilings or rocky shores and algae were more diverse on natural rocky shores and seawalls than on pilings. Our results confirm previous findings in the literature. Oysters were more abundant on pilings than on rocky shores, but were also smaller. Interestingly, these differences in oyster populations did not affect in situ filtration rates between habitats. Seawalls were the most invaded habitats while pilings supported greater secondary productivity than other habitats. This study highlights the complexity of the diversity-function relationship and responses to ocean sprawl in coastal systems. Importantly, we showed that functional properties should be considered independently from structural change if we are to design and manage artificial

  3. Response function of a moving contact line

    Science.gov (United States)

    Perrin, H.; Belardinelli, D.; Sbragaglia, M.; Andreotti, B.

    2018-04-01

    The hydrodynamics of a liquid-vapor interface in contact with a heterogeneous surface is largely impacted by the presence of defects at the smaller scales. Such defects introduce morphological disturbances on the contact line and ultimately determine the force exerted on the wedge of liquid in contact with the surface. From the mathematical point of view, defects introduce perturbation modes, whose space-time evolution is governed by the interfacial hydrodynamic equations of the contact line. In this paper we derive the response function of the contact line to such generic perturbations. The contact line response may be used to design simplified one-dimensional time-dependent models accounting for the complexity of interfacial flows coupled to nanoscale defects, yet offering a more tractable mathematical framework to explore contact line motion through a disordered energy landscape.

  4. Differential regulation of the human progesterone receptor gene through an estrogen response element half site and Sp1 sites.

    Science.gov (United States)

    Petz, Larry N; Ziegler, Yvonne S; Schultz, Jennifer R; Kim, Hwajin; Kemper, J Kim; Nardulli, Ann M

    2004-02-01

    The progesterone receptor (PR) gene is regulated by estrogen in normal reproductive tissues and in MCF-7 human breast cancer cells. Although it is generally thought that estrogen responsiveness is mediated by interaction of the ligand-occupied estrogen receptor (ER) with estrogen response elements (EREs) in target genes, the human progesterone receptor (PR) gene lacks a palindromic ERE. Promoter A of the PR gene does, however, contain an ERE half site upstream of two adjacent Sp1 sites from +571 to +595, the +571 ERE/Sp1 site. We have examined the individual contributions of the ERE half site and the two Sp1 sites in regulating estrogen responsiveness. Transient transfection assays demonstrated that both Sp1 sites were critical for estrogen-mediated activation of the PR gene. Interestingly, rather than decreasing transcription, mutations in the ERE half site increased transcription substantially suggesting that this site plays a role in limiting transcription. Chromatin immunoprecipitation assays demonstrated that Sp1 was associated with the +571 ERE/Sp1 site in the endogenous PR gene in the absence and in the presence of estrogen, but that ERalpha was only associated with this region of the PR gene after MCF-7 cells had been treated with estrogen. Our studies provide evidence that effective regulation of transcription through the +571 ERE/Sp1 site requires the binding of ERalpha and Sp1 to their respective cis elements and the appropriate interaction of ERalpha and Sp1 with other coregulatory proteins and transcription factors.

  5. Spontaneous symmetry breaking and response functions

    International Nuclear Information System (INIS)

    Beraudo, A.; De Pace, A.; Martini, M.; Molinari, A.

    2005-01-01

    We study the quantum phase transition occurring in an infinite homogeneous system of spin 1/2 fermions in a non-relativistic context. As an example we consider neutrons interacting through a simple spin-spin Heisenberg force. The two critical values of the coupling strength-signaling the onset into the system of a finite magnetization and of the total magnetization, respectively-are found and their dependence upon the range of the interaction is explored. The spin response function of the system in the region where the spin-rotational symmetry is spontaneously broken is also studied. For a ferromagnetic interaction the spin response along the direction of the spontaneous magnetization occurs in the particle-hole continuum and displays, for not too large momentum transfers, two distinct peaks. The response along the direction orthogonal to the spontaneous magnetization displays instead, beyond a softened and depleted particle-hole continuum, a collective mode to be identified with a Goldstone boson of type II. Notably, the random phase approximation on a Hartree-Fock basis accounts for it, in particular for its quadratic-close to the origin-dispersion relation. It is shown that the Goldstone boson contributes to the saturation of the energy-weighted sum rule for ∼25% when the system becomes fully magnetized (that is in correspondence of the upper critical value of the interaction strength) and continues to grow as the interaction strength increases

  6. Conserved Functional Motifs and Homology Modeling to Predict Hidden Moonlighting Functional Sites

    KAUST Repository

    Wong, Aloysius Tze; Gehring, Christoph A; Irving, Helen R.

    2015-01-01

    Moonlighting functional centers within proteins can provide them with hitherto unrecognized functions. Here, we review how hidden moonlighting functional centers, which we define as binding sites that have catalytic activity or regulate protein function in a novel manner, can be identified using targeted bioinformatic searches. Functional motifs used in such searches include amino acid residues that are conserved across species and many of which have been assigned functional roles based on experimental evidence. Molecules that were identified in this manner seeking cyclic mononucleotide cyclases in plants are used as examples. The strength of this computational approach is enhanced when good homology models can be developed to test the functionality of the predicted centers in silico, which, in turn, increases confidence in the ability of the identified candidates to perform the predicted functions. Computational characterization of moonlighting functional centers is not diagnostic for catalysis but serves as a rapid screening method, and highlights testable targets from a potentially large pool of candidates for subsequent in vitro and in vivo experiments required to confirm the functionality of the predicted moonlighting centers.

  7. Conserved Functional Motifs and Homology Modeling to Predict Hidden Moonlighting Functional Sites

    KAUST Repository

    Wong, Aloysius Tze

    2015-06-09

    Moonlighting functional centers within proteins can provide them with hitherto unrecognized functions. Here, we review how hidden moonlighting functional centers, which we define as binding sites that have catalytic activity or regulate protein function in a novel manner, can be identified using targeted bioinformatic searches. Functional motifs used in such searches include amino acid residues that are conserved across species and many of which have been assigned functional roles based on experimental evidence. Molecules that were identified in this manner seeking cyclic mononucleotide cyclases in plants are used as examples. The strength of this computational approach is enhanced when good homology models can be developed to test the functionality of the predicted centers in silico, which, in turn, increases confidence in the ability of the identified candidates to perform the predicted functions. Computational characterization of moonlighting functional centers is not diagnostic for catalysis but serves as a rapid screening method, and highlights testable targets from a potentially large pool of candidates for subsequent in vitro and in vivo experiments required to confirm the functionality of the predicted moonlighting centers.

  8. Functional, Responsive Materials Assembled from Recombinant Oleosin

    Science.gov (United States)

    Hammer, Daniel

    Biological cells are surrounded by a plasma membrane made primarily of phospholipids that form a bilayer. This membrane is permselective and compartmentalizes the cell. A simple form of artificial cell is the vesicle, in which a phospholipid bilayer membrane surrounds an aqueous solution. However, there is no a priori reason why a membrane needs to be made of phospholipids. It could be made of any surfactant that forms a bilayer. We have assembled membranes and other structures from the recombinant plant protein oleosin. The ability to assemble from a recombinant protein means that every molecule is identical, we have complete control over the sequence, and hence can build in designer functionality with high fidelity, including adhesion and enzymatic activity. Such incorporation is trivial using the tools of molecular biology. We find that while many variants of oleosin make membranes, others make micelles and sheets. We show how the type of supramolecular structure can be altered by the conditions of solvent, such as ionic strength, and the architecture of the surfactant itself. We show that protease cleavable domains can be incorporated within oleosin, and be engineered to protect other functional domains such as adhesive motifs, to make responsive materials whose activity and shape depend on the action of proteases. We will also present the idea of making ``Franken''-oleosins, where large domains of native oleosin are replaced with domains from other functional proteins, to make hybrids conferred by the donor protein. Thus, we can view oleosin as a template upon which a vast array of designer functionalities can be imparted..

  9. Response predictions using the observed autocorrelation function

    DEFF Research Database (Denmark)

    Nielsen, Ulrik Dam; H. Brodtkorb, Astrid; Jensen, Jørgen Juncher

    2018-01-01

    This article studies a procedure that facilitates short-time, deterministic predictions of the wave-induced motion of a marine vessel, where it is understood that the future motion of the vessel is calculated ahead of time. Such predictions are valuable to assist in the execution of many marine......-induced response in study. Thus, predicted (future) values ahead of time for a given time history recording are computed through a mathematical combination of the sample autocorrelation function and previous measurements recorded just prior to the moment of action. Importantly, the procedure does not need input...... show that predictions can be successfully made in a time horizon corresponding to about 8-9 wave periods ahead of current time (the moment of action)....

  10. Resting state functional connectivity predicts neurofeedback response

    Directory of Open Access Journals (Sweden)

    Dustin eScheinost

    2014-09-01

    Full Text Available Tailoring treatments to the specific needs and biology of individual patients – personalized medicine – requires delineation of reliable predictors of response. Unfortunately, these have been slow to emerge, especially in neuropsychiatric disorders. We have recently described a real-time functional magnetic resonance imaging (rt-fMRI neurofeedback protocol that can reduce contamination-related anxiety, a prominent symptom of many cases of obsessive-compulsive disorder (OCD. Individual response to this intervention is variable. Here we used patterns of brain functional connectivity, as measured by baseline resting-state fMRI (rs-fMRI, to predict improvements in contamination anxiety after neurofeedback training. Activity of a region of the orbitofrontal cortex (OFC and anterior prefrontal cortex, Brodmann area (BA 10, associated with contamination anxiety in each subject was measured in real time and presented as a neurofeedback signal, permitting subjects to learn to modulate this target brain region. We have previously reported both enhanced OFC/BA 10 control and improved anxiety in a group of subclinically anxious subjects after neurofeedback. Five individuals with contamination-related OCD who underwent the same protocol also showed improved clinical symptomatology. In both groups, these behavioral improvements were strongly correlated with baseline whole-brain connectivity in the OFC/BA 10, computed from rs-fMRI collected several days prior to neurofeedback training. These pilot data suggest that rs-fMRI can be used to identify individuals likely to benefit from rt-fMRI neurofeedback training to control contamination anxiety.

  11. Wetland survey of selected areas in the K-24 Site Area of responsibility

    Energy Technology Data Exchange (ETDEWEB)

    Rosensteel, B.A.; Awl, D.J. [JAYCOR, Environmental Division, Oak Ridge, TN (United States)

    1995-07-01

    In accordance with DOE Regulations for Compliance with Floodplain/Wetlands Environmental Review Requirements, wetland surveys were conducted in selected areas within the K-25 Area of Responsibility during the summer of 1994. These areas are Mitchell Branch, Poplar Creek, the K-770 OU, Duct Island Peninsula, the Powerhouse area, and the K-25 South Corner. Previously surveyed areas included in this report are the main plant area of the K-25 Site, the K-901 OU, the AVLIS site, and the K-25 South Site. Wetland determinations were based on the USACE methodology. Forty-four separate wetland areas, ranging in size from 0.13 to 4.23 ha, were identified. Wetlands were identified in all of the areas surveyed with the exception of the interior of the Duct Island Peninsula and the main plant area of the K-25 Site. Wetlands perform functions such as floodflow alteration, sediment stabilization, sediment and toxicant retention, nutrient transformation, production export, and support of aquatic species and wildlife diversity and abundance. The forested, scrub-shrub, and emergent wetlands identified in the K-25 area perform some or all of these functions to varying degrees.

  12. Wetland survey of selected areas in the K-24 Site Area of responsibility

    International Nuclear Information System (INIS)

    Rosensteel, B.A.; Awl, D.J.

    1995-07-01

    In accordance with DOE Regulations for Compliance with Floodplain/Wetlands Environmental Review Requirements, wetland surveys were conducted in selected areas within the K-25 Area of Responsibility during the summer of 1994. These areas are Mitchell Branch, Poplar Creek, the K-770 OU, Duct Island Peninsula, the Powerhouse area, and the K-25 South Corner. Previously surveyed areas included in this report are the main plant area of the K-25 Site, the K-901 OU, the AVLIS site, and the K-25 South Site. Wetland determinations were based on the USACE methodology. Forty-four separate wetland areas, ranging in size from 0.13 to 4.23 ha, were identified. Wetlands were identified in all of the areas surveyed with the exception of the interior of the Duct Island Peninsula and the main plant area of the K-25 Site. Wetlands perform functions such as floodflow alteration, sediment stabilization, sediment and toxicant retention, nutrient transformation, production export, and support of aquatic species and wildlife diversity and abundance. The forested, scrub-shrub, and emergent wetlands identified in the K-25 area perform some or all of these functions to varying degrees

  13. Parallel sites implicate functional convergence of the hearing gene prestin among echolocating mammals.

    Science.gov (United States)

    Liu, Zhen; Qi, Fei-Yan; Zhou, Xin; Ren, Hai-Qing; Shi, Peng

    2014-09-01

    Echolocation is a sensory system whereby certain mammals navigate and forage using sound waves, usually in environments where visibility is limited. Curiously, echolocation has evolved independently in bats and whales, which occupy entirely different environments. Based on this phenotypic convergence, recent studies identified several echolocation-related genes with parallel sites at the protein sequence level among different echolocating mammals, and among these, prestin seems the most promising. Although previous studies analyzed the evolutionary mechanism of prestin, the functional roles of the parallel sites in the evolution of mammalian echolocation are not clear. By functional assays, we show that a key parameter of prestin function, 1/α, is increased in all echolocating mammals and that the N7T parallel substitution accounted for this functional convergence. Moreover, another parameter, V1/2, was shifted toward the depolarization direction in a toothed whale, the bottlenose dolphin (Tursiops truncatus) and a constant-frequency (CF) bat, the Stoliczka's trident bat (Aselliscus stoliczkanus). The parallel site of I384T between toothed whales and CF bats was responsible for this functional convergence. Furthermore, the two parameters (1/α and V1/2) were correlated with mammalian high-frequency hearing, suggesting that the convergent changes of the prestin function in echolocating mammals may play important roles in mammalian echolocation. To our knowledge, these findings present the functional patterns of echolocation-related genes in echolocating mammals for the first time and rigorously demonstrate adaptive parallel evolution at the protein sequence level, paving the way to insights into the molecular mechanism underlying mammalian echolocation. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Estimating Derived Response Levels at the Savannah River Site for Use with Emergency Response Models

    International Nuclear Information System (INIS)

    Simpkins, A.A.

    2002-01-01

    Emergency response computer models at the Savannah River Site (SRS) are coupled with real-time meteorological data to estimate dose to individuals downwind of accidental radioactive releases. Currently, these models estimate doses for inhalation and shine pathways, but do not consider dose due to ingestion of contaminated food products. The Food and Drug Administration (FDA) has developed derived intervention levels (DIL) which refer to the radionuclide-specific concentration in food present throughout the relevant period of time, with no intervention, that could lead to an individual receiving a radiation dose equal to the protective action guide. In the event of an emergency, concentrations in various food types are compared with these levels to make interdictions decisions. Prior to monitoring results being available, concentrations in the environmental media (i.e. soil), called derived response levels (DRLs), can be estimated from the DILs and directly compared with computer output to provide preliminary guidance as to whether intervention is necessary. Site-specific derived response levels (DRLs) are developed for ingestion pathways pertinent to SRS: milk, meat, fish, grain, produce, and beverage. This provides decision-makers with an additional tool for use immediately following an accident prior to the acquisition of food monitoring data

  15. Stimuli-Responsive Nanodiamond-Based Biosensor for Enhanced Metastatic Tumor Site Detection.

    Science.gov (United States)

    Wang, Xin; Gu, Mengjie; Toh, Tan Boon; Abdullah, Nurrul Lissa Binti; Chow, Edward Kai-Hua

    2018-02-01

    Metastasis is often critical to cancer progression and linked to poor survival and drug resistance. Early detection of metastasis, as well as identification of metastatic tumor sites, can improve cancer patient survival. Thus, developing technology to improve the detection of cancer metastasis biomarkers can improve both diagnosis and treatment. In this study, we investigated the use of nanodiamonds to develop a stimuli-responsive metastasis detection complex that utilizes matrix metalloproteinase 9 (MMP9) as a metastasis biomarker, as MMP9 increased expression has been shown to be indicative of metastasis. The nanodiamond-MMP9 biosensor complex consists of nanodiamonds functionalized with MMP9-specific fluorescent-labeled substrate peptides. Using this design, protease activity of MMP9 can be accurately measured and correlated to MMP9 expression. The nanodiamond-MMP9 biosensor also demonstrated an enhanced ability to protect the base sensor peptide from nonspecific serum protease cleavage. This enhanced peptide stability, combined with a quantitative stimuli-responsive output function, provides strong evidence for the further development of a nanodiamond-MMP9 biosensor for metastasis site detection. More importantly, this work provides the foundation for use of nanodiamonds as a platform for stimuli-responsive biosensors and theranostic complexes that can be implemented across a wide range of biomedical applications.

  16. Interactivity in brand web sites: cognitive, affective, and behavioral responses explained by consumers’ online flow experience

    NARCIS (Netherlands)

    van Noort, G.; Voorveld, H.A.M.; van Reijmersdal, E.A.

    2012-01-01

    Web site interactivity creates numerous opportunities for marketers to persuade online consumers and receives extensive attention in the marketing literature. However, research on cognitive and behavioral responses to web site interactivity is scarce, and more importantly, it does not provide

  17. Site quality in Appalachian hardwoods: the biological and economic response under selection silviculture

    Science.gov (United States)

    Orris D. McCauley; George R., Jr. Trimble

    1975-01-01

    The relative or percentage value response after 12 years of selective cutting practices on low- and high-quality sites in Appalachian hardwoods amounted to a 119-percent increase on the low-quality site and 145 percent on the high-quality site. The absolute value or actual dollar response, on the other hand, showed that the low-quality site increased in value only $76/...

  18. RISM theory distribution functions for Lennard--Jones interaction site fluids

    International Nuclear Information System (INIS)

    Johnson, E.; Hazoume, R.P.

    1978-01-01

    Reference interaction site model (RISM) theory distribution functions for Lennard-Jones interaction site fluids are discussed. The comparison with computer simulation results suggests that these distribution functions are as accurate as RISM distribution functions for fused hard sphere molecular fluids

  19. A three-dimensional model of mammalian tyrosinase active site accounting for loss of function mutations.

    Science.gov (United States)

    Schweikardt, Thorsten; Olivares, Concepción; Solano, Francisco; Jaenicke, Elmar; García-Borrón, José Carlos; Decker, Heinz

    2007-10-01

    Tyrosinases are the first and rate-limiting enzymes in the synthesis of melanin pigments responsible for colouring hair, skin and eyes. Mutation of tyrosinases often decreases melanin production resulting in albinism, but the effects are not always understood at the molecular level. Homology modelling of mouse tyrosinase based on recently published crystal structures of non-mammalian tyrosinases provides an active site model accounting for loss-of-function mutations. According to the model, the copper-binding histidines are located in a helix bundle comprising four densely packed helices. A loop containing residues M374, S375 and V377 connects the CuA and CuB centres, with the peptide oxygens of M374 and V377 serving as hydrogen acceptors for the NH-groups of the imidazole rings of the copper-binding His367 and His180. Therefore, this loop is essential for the stability of the active site architecture. A double substitution (374)MS(375) --> (374)GG(375) or a single M374G mutation lead to a local perturbation of the protein matrix at the active site affecting the orientation of the H367 side chain, that may be unable to bind CuB reliably, resulting in loss of activity. The model also accounts for loss of function in two naturally occurring albino mutations, S380P and V393F. The hydroxyl group in S380 contributes to the correct orientation of M374, and the substitution of V393 for a bulkier phenylalanine sterically impedes correct side chain packing at the active site. Therefore, our model explains the mechanistic necessity for conservation of not only active site histidines but also adjacent amino acids in tyrosinase.

  20. How do probiotics and prebiotics function at distant sites?

    Science.gov (United States)

    Reid, G; Abrahamsson, T; Bailey, M; Bindels, L B; Bubnov, R; Ganguli, K; Martoni, C; O'Neill, C; Savignac, H M; Stanton, C; Ship, N; Surette, M; Tuohy, K; van Hemert, S

    2017-08-24

    The realisation that microbes regarded as beneficial to the host can impart effects at sites distant from their habitat, has raised many possibilities for treatment of diseases. The objective of a workshop hosted in Turku, Finland, by the International Scientific Association for Probiotics and Prebiotics, was to assess the evidence for these effects and the extent to which early life microbiome programming influences how the gut microbiota communicates with distant sites. In addition, we examined how probiotics and prebiotics might affect the skin, airways, heart, brain and metabolism. The growing levels of scientific and clinical evidence showing how microbes influence the physiology of many body sites, leads us to call for more funding to advance a potentially exciting avenue for novel therapies for many chronic diseases.

  1. Seismic site-response characterization of high-velocity sites using advanced geophysical techniques: application to the NAGRA-Net

    Science.gov (United States)

    Poggi, V.; Burjanek, J.; Michel, C.; Fäh, D.

    2017-08-01

    The Swiss Seismological Service (SED) has recently finalised the installation of ten new seismological broadband stations in northern Switzerland. The project was led in cooperation with the National Cooperative for the Disposal of Radioactive Waste (Nagra) and Swissnuclear to monitor micro seismicity at potential locations of nuclear-waste repositories. To further improve the quality and usability of the seismic recordings, an extensive characterization of the sites surrounding the installation area was performed following a standardised investigation protocol. State-of-the-art geophysical techniques have been used, including advanced active and passive seismic methods. The results of all analyses converged to the definition of a set of best-representative 1-D velocity profiles for each site, which are the input for the computation of engineering soil proxies (traveltime averaged velocity and quarter-wavelength parameters) and numerical amplification models. Computed site response is then validated through comparison with empirical site amplification, which is currently available for any station connected to the Swiss seismic networks. With the goal of a high-sensitivity network, most of the NAGRA stations have been installed on stiff-soil sites of rather high seismic velocity. Seismic characterization of such sites has always been considered challenging, due to lack of relevant velocity contrast and the large wavelengths required to investigate the frequency range of engineering interest. We describe how ambient vibration techniques can successfully be applied in these particular conditions, providing practical recommendations for best practice in seismic site characterization of high-velocity sites.

  2. Proposed Site-Specific Response Spectra for Surabaya-Madura Bridge

    Directory of Open Access Journals (Sweden)

    Dyah Kusumastuti

    2008-01-01

    Full Text Available This paper presents a site-specific seismic hazard study to determine the recommended seismic design criteria for Suramadu Bridge. The study is performed using probabilistic seismic hazard approach to determine maximum acceleration and response spectra at bedrock and followed by local site effect analysis to determine maximum acceleration and response spectra at ground surface. The probabilistic seismic hazard analysis (PSHA is carried out using 3-dimension (3-D seismic source models (fault source model. Two hazard levels are analysed to represent 150 and 3,300 years return period of ground motion around site location. The local site effect analysis is performed using 1-dimension (1-D shear wave propagation theory to obtain peak ground acceleration and response spectra at ground surface. Finally, the site-specific surface response spectra with 5 percent damping are developed based on the mean plus one standard deviation concept from the result of local site effect analysis.

  3. Computer analysis of protein functional sites projection on exon structure of genes in Metazoa.

    Science.gov (United States)

    Medvedeva, Irina V; Demenkov, Pavel S; Ivanisenko, Vladimir A

    2015-01-01

    Study of the relationship between the structural and functional organization of proteins and their coding genes is necessary for an understanding of the evolution of molecular systems and can provide new knowledge for many applications for designing proteins with improved medical and biological properties. It is well known that the functional properties of proteins are determined by their functional sites. Functional sites are usually represented by a small number of amino acid residues that are distantly located from each other in the amino acid sequence. They are highly conserved within their functional group and vary significantly in structure between such groups. According to this facts analysis of the general properties of the structural organization of the functional sites at the protein level and, at the level of exon-intron structure of the coding gene is still an actual problem. One approach to this analysis is the projection of amino acid residue positions of the functional sites along with the exon boundaries to the gene structure. In this paper, we examined the discontinuity of the functional sites in the exon-intron structure of genes and the distribution of lengths and phases of the functional site encoding exons in vertebrate genes. We have shown that the DNA fragments coding the functional sites were in the same exons, or in close exons. The observed tendency to cluster the exons that code functional sites which could be considered as the unit of protein evolution. We studied the characteristics of the structure of the exon boundaries that code, and do not code, functional sites in 11 Metazoa species. This is accompanied by a reduced frequency of intercodon gaps (phase 0) in exons encoding the amino acid residue functional site, which may be evidence of the existence of evolutionary limitations to the exon shuffling. These results characterize the features of the coding exon-intron structure that affect the functionality of the encoded protein and

  4. Multi-Functional Stimuli-Responsive Materials

    Data.gov (United States)

    National Aeronautics and Space Administration — Supramolecular polymers based on non-covalent interactions can display a wide array of stimuli-responsive attributes. They can be tailored to change shape, actuate...

  5. Site characterization and site response in Port-au-Prince, Haiti

    Science.gov (United States)

    Hough, Susan E.; Yong, Alan K.; Altidor, Jean Robert; Anglade, Dieuseul; Given, Douglas D.; Mildor, Saint-Louis

    2011-01-01

    Waveform analysis of aftershocks of the Mw7.0 Haiti earthquake of 12 January 2010 reveals amplification of ground motions at sites within the Cul de Sac valley in which Port-au-Prince is situated. Relative to ground motions recorded at a hard-rock reference site, peak acceleration values are amplified by a factor of approximately 1.8 at sites on low-lying Mio-Pliocene deposits in central Port-au-Prince and by a factor of approximately 2.5–3 on a steep foothill ridge in the southern Port-au-Prince metropolitan region. The observed amplitude, predominant periods, variability, and polarization of amplification are consistent with predicted topographic amplification by a steep, narrow ridge. A swath of unusually high damage in this region corresponds with the extent of the ridge where high weak-motion amplifications are observed. We use ASTER (Advanced Spaceborne Thermal Emission and Reflection Radiometer) imagery to map local geomorphology, including characterization of both near-surface and of small-scale topographic structures that correspond to zones of inferred amplification.

  6. Functional mimicry of a discontinuous antigenic site by a designed synthetic peptide

    NARCIS (Netherlands)

    Villen, J.; Borras, E.; Schaaper, W.M.M.; Meloen, R.H.; Davila, M.; Domingo, E.; Giralt, E.; Andreu, D.

    2002-01-01

    Functional reproduction of the discontinuous antigenic site D of foot-and-mouth disease virus (FMDV) has been achieved by means of synthetic peptide constructions that integrate each of the three protein loops that define the antigenic site into a single molecule. The site D mimics were designed on

  7. Cerebral blood flow response to functional activation

    DEFF Research Database (Denmark)

    Paulson, Olaf B; Hasselbalch, Steen G; Rostrup, Egill

    2010-01-01

    Cerebral blood flow (CBF) and cerebral metabolic rate are normally coupled, that is an increase in metabolic demand will lead to an increase in flow. However, during functional activation, CBF and glucose metabolism remain coupled as they increase in proportion, whereas oxygen metabolism only inc...... the cerebral tissue's increased demand for glucose supply during neural activation with recent evidence supporting a key function for astrocytes in rCBF regulation....

  8. Sites Requiring Facility Response Plans, Geographic NAD83, EPA (2006) [facility_response_plan_sites_la_EPA_2007

    Data.gov (United States)

    Louisiana Geographic Information Center — Locations of facilities in Louisiana requiring Oil Pollution Act (OPA) Facility Response Plans (FRP). The dataset was provided by the Region 6 OSCARS program....

  9. Site Response in Las Vegas Valley, Nevada from NTS Explosions and Earthquake Data

    Science.gov (United States)

    Rodgers, Arthur; Tkalcic, Hrvoje; McCallen, David; Larsen, Shawn; Snelson, Catherine

    2006-01-01

    We report site response in Las Vegas Valley (LVV) from historical recordings of Nevada Test Site (NTS) nuclear explosions and earthquake recordings from permanent and temporary seismic stations. Our data set significantly improves the spatial coverage of LVV over previous studies, especially in the northern, deeper parts of the basin. Site response at stations in LVV was measured for frequencies in the range 0.2 5.0 Hz using Standard Spectral Ratios (SSR) and Horizontal-Vertical Spectral Ratios (HVR). For the SSR measurements we used a reference site (approximately NEHRP B ``rock'' classification) located on Frenchman Mountain outside the basin. Site response at sedimentary sites is variable in LVV with average amplifications approaching a factor of 10 at some frequencies. We observed peaks in the site response curves at frequencies clustered near 0.6, 1.2 and 2.0 Hz, with some sites showing additional lower amplitude peaks at higher frequencies. The spatial pattern of site response is strongly correlated with the reported depth to basement for frequencies between 0.2 and 3.0 Hz, although the frequency of peak amplification does not show a similar correlation. For a few sites where we have geotechnical shear velocities, the amplification shows a correlation with the average upper 30-meter shear velocities, V 30. We performed two-dimensional finite difference simulations and reproduced the observed peak site amplifications at 0.6 and 1.2 Hz with a low velocity near-surface layer with shear velocities 600 750 m/s and a thickness of 100 200 m. These modeling results indicate that the amplitude and frequencies of site response peaks in LVV are strongly controlled by shallow velocity structure.

  10. Mercury Binding Sites in Thiol-Functionalized Mesostructured Silica

    International Nuclear Information System (INIS)

    Billinge, Simon J.L.; McKimmey, Emily J.; Shatnawi, Mouath; Kim, HyunJeong; Petkov, Valeri; Wermeille, Didier; Pinnavaia, Thomas J.

    2005-01-01

    Thiol-functionalized mesostructured silica with anhydrous compositions of (SiO 2 ) 1-x (LSiO 1.5 ) x , where L is a mercaptopropyl group and x is the fraction of functionalized framework silicon centers, are effective trapping agents for the removal of mercuric(II) ions from water. In the present work, we investigate the mercury-binding mechanism for representative thiol-functionalized mesostructures by atomic pair distribution function (PDF) analysis of synchrotron X-ray powder diffraction data and by Raman spectroscopy. The mesostructures with wormhole framework structures and compositions corresponding to x = 0.30 and 0.50 were prepared by direct assembly methods in the presence of a structure-directing amine porogen. PDF analyses of five mercury-loaded compositions with Hg/S ratios of 0.50-1.30 provided evidence for the bridging of thiolate sulfur atoms to two metal ion centers and the formation of chain structures on the pore surfaces. We find no evidence for Hg-O bonds and can rule out oxygen coordination of the mercury at greater than the 10% level. The relative intensities of the PDF peaks corresponding to Hg-S and Hg-Hg atomic pairs indicate that the mercury centers cluster on the functionalized surfaces by virtue of thiolate bridging, regardless of the overall mercury loading. However, the Raman results indicate that the complexation of mercury centers by thiolate depends on the mercury loading. At low mercury loadings (Hg/S (le) 0.5), the dominant species is an electrically neutral complex in which mercury most likely is tetrahedrally coordinated to bridging thiolate ligands, as in Hg(SBu t ) 2 . At higher loadings (Hg/S 1.0-1.3), mercury complex cations predominate, as evidenced by the presence of charge-balancing anions (nitrate) on the surface. This cationic form of bound mercury is assigned a linear coordination to two bridging thiolate ligands.

  11. ARES: automated response function code. Users manual. [HPGAM and LSQVM

    Energy Technology Data Exchange (ETDEWEB)

    Maung, T.; Reynolds, G.M.

    1981-06-01

    This ARES user's manual provides detailed instructions for a general understanding of the Automated Response Function Code and gives step by step instructions for using the complete code package on a HP-1000 system. This code is designed to calculate response functions of NaI gamma-ray detectors, with cylindrical or rectangular geometries.

  12. Anismus: a marker of multi-site functional disorders?

    Science.gov (United States)

    Bouchoucha, Michel; Devroede, Ghislain; Arsac, Michel

    2004-07-01

    This study was undertaken to assess the clinical significance of anismus in patients who complain of constipation. Thirty control subjects and 93 consecutive patients complaining of functional constipation took part in the study. Colonic transit time study and anorectal manometry were performed. Questions about depression and urinary and sexual diseases were added to a questionnaire based on the Rome II criteria, and visual analog scales about four items (constipation, diarrhoea, abdominal bloating and abdominal pain). Constipated patients have lower threshold sensation volume, lower constant sensation volume, and lower maximum tolerable volume than controls. Thirty-seven patients (40%) were found to have anismus, based on anorectal manometry. No significant difference was found between constipated patients with anismus and constipated patients without anismus, using anorectal manometry. Constipated patients had longer colorectal transit time than controls, but neither total nor segmental colonic transit time was correlated with the presence or absence of anismus. In patients with anismus, a higher frequency of oesophageal symptoms, dysmotility-like dyspepsia, aerophagia, functional bowel disorders, functional abdominal pain, soiling, and dyschezia was found. In addition, a higher frequency of urinary complaints, sexual complaints, and depression was found. Anismus was associated with increased awareness of constipation, abdominal bloating, and abdominal pain, but not with diarrhoea.

  13. Longitudinal and transverse quasielastic response functions of light nuclei

    International Nuclear Information System (INIS)

    Carlson, J.; Jourdan, J.; Sick, I.; Schiavilla, R.

    2002-01-01

    The 3 He and 4 He longitudinal and transverse response functions are determined from an analysis of the world data on quasielastic inclusive electron scattering. The corresponding Euclidean response functions are derived and compared to those calculated with Green's function Monte Carlo methods, using realistic interactions and currents. Large contributions associated with two-body currents are found, particularly in the 4 He transverse response, in agreement with data. The contributions of the two-body charge and current operators in the 3 He, 4 He, and 6 Li response functions are also studied via sum-rule techniques. A semiquantitative explanation for the observed systematics in the excess of transverse quasielastic strength, as function of mass number and momentum transfer, is provided. Finally, a number of model studies with simplified interactions, currents, and wave functions are carried out to elucidate the role played, in the full calculation, by tensor interactions and correlations

  14. Adaptive Feeding behavior and functional responses in pelagic copepods

    DEFF Research Database (Denmark)

    Kiørboe, Thomas; Saiz, Enrico; Tiselius, Peter

    2018-01-01

    Zooplankton may modify their feeding behavior in response to prey availability and presence of predators with implications to populations of both predators and prey. Optimal foraging theory predicts that such responses result in a type II functional response for passive foragers and a type III re...

  15. SITEX 2.0: Projections of protein functional sites on eukaryotic genes. Extension with orthologous genes.

    Science.gov (United States)

    Medvedeva, Irina V; Demenkov, Pavel S; Ivanisenko, Vladimir A

    2017-04-01

    Functional sites define the diversity of protein functions and are the central object of research of the structural and functional organization of proteins. The mechanisms underlying protein functional sites emergence and their variability during evolution are distinguished by duplication, shuffling, insertion and deletion of the exons in genes. The study of the correlation between a site structure and exon structure serves as the basis for the in-depth understanding of sites organization. In this regard, the development of programming resources that allow the realization of the mutual projection of exon structure of genes and primary and tertiary structures of encoded proteins is still the actual problem. Previously, we developed the SitEx system that provides information about protein and gene sequences with mapped exon borders and protein functional sites amino acid positions. The database included information on proteins with known 3D structure. However, data with respect to orthologs was not available. Therefore, we added the projection of sites positions to the exon structures of orthologs in SitEx 2.0. We implemented a search through database using site conservation variability and site discontinuity through exon structure. Inclusion of the information on orthologs allowed to expand the possibilities of SitEx usage for solving problems regarding the analysis of the structural and functional organization of proteins. Database URL: http://www-bionet.sscc.ru/sitex/ .

  16. Hot Spots in a Network of Functional Sites

    Science.gov (United States)

    Ozbek, Pemra; Soner, Seren; Haliloglu, Turkan

    2013-01-01

    It is of significant interest to understand how proteins interact, which holds the key phenomenon in biological functions. Using dynamic fluctuations in high frequency modes, we show that the Gaussian Network Model (GNM) predicts hot spot residues with success rates ranging between S 8–58%, C 84–95%, P 5–19% and A 81–92% on unbound structures and S 8–51%, C 97–99%, P 14–50%, A 94–97% on complex structures for sensitivity, specificity, precision and accuracy, respectively. High specificity and accuracy rates with a single property on unbound protein structures suggest that hot spots are predefined in the dynamics of unbound structures and forming the binding core of interfaces, whereas the prediction of other functional residues with similar dynamic behavior explains the lower precision values. The latter is demonstrated with the case studies; ubiquitin, hen egg-white lysozyme and M2 proton channel. The dynamic fluctuations suggest a pseudo network of residues with high frequency fluctuations, which could be plausible for the mechanism of biological interactions and allosteric regulation. PMID:24023934

  17. Functional impact of HIV coreceptor-binding site mutations

    International Nuclear Information System (INIS)

    Biscone, Mark J.; Miamidian, John L.; Muchiri, John M.; Baik, Sarah S.W.; Lee, Fang-Hua; Doms, Robert W.; Reeves, Jacqueline D.

    2006-01-01

    The bridging sheet region of the gp120 subunit of the HIV-1 Env protein interacts with the major virus coreceptors, CCR5 and CXCR4. We examined the impact of mutations in and adjacent to the bridging sheet region of an X4 tropic HIV-1 on membrane fusion and entry inhibitor susceptibility. When the V3-loop of this Env was changed so that CCR5 was used, the effects of these same mutations on CCR5 use were assayed as well. We found that coreceptor-binding site mutations had greater effects on CXCR4-mediated fusion and infection than when CCR5 was used as a coreceptor, perhaps related to differences in coreceptor affinity. The mutations also reduced use of the alternative coreceptors CCR3 and CCR8 to varying degrees, indicating that the bridging sheet region is important for the efficient utilization of both major and minor HIV coreceptors. As seen before with a primary R5 virus strain, bridging sheet mutations increased susceptibility to the CCR5 inhibitor TAK-779, which correlated with CCR5 binding efficiency. Bridging sheet mutations also conferred increased susceptibility to the CXCR4 ligand AMD-3100 in the context of the X4 tropic Env. However, these mutations had little effect on the rate of membrane fusion and little effect on susceptibility to enfuvirtide, a membrane fusion inhibitor whose activity is dependent in part on the rate of Env-mediated membrane fusion. Thus, mutations that reduce coreceptor binding and enhance susceptibility to coreceptor inhibitors can affect fusion and enfuvirtide susceptibility in an Env context-dependent manner

  18. Responses to Deficiencies and Suggestions, AIHA Site Assessment July 12-14, 2016

    Energy Technology Data Exchange (ETDEWEB)

    Bennett, Jack T. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Harding, Ruth N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-08-11

    These are the responses to the deficiencies and suggestions found during the American Industrial Hygiene Association external site assessment carried out July 12-14, 2016 in the Analytical Services and Instrumentation Division Analytical Laboratory.

  19. Buckling Response of Thick Functionally Graded Plates

    Directory of Open Access Journals (Sweden)

    BOUAZZA MOKHTAR

    2014-11-01

    Full Text Available In this paper, the buckling of a functionally graded plate is studied by using first order shear deformation theory (FSDT. The material properties of the plate are assumed to be graded continuously in the direction of thickness. The variation of the material properties follows a simple power-law distribution in terms of the volume fractions of constituents. The von Karman strains are used to construct the equilibrium equations of the plates subjected to two types of thermal loading, linear temperature rise and gradient through the thickness are considered. The governing equations are reduced to linear differential equation with boundary conditions yielding a simple solution procedure. In addition, the effects of temperature field, volume fraction distributions, and system geometric parameters are investigated. The results are compared with the results of the no shear deformation theory (classic plate theory, CPT.

  20. Explanation of procedure on site medical emergency response for nuclear accident

    International Nuclear Information System (INIS)

    Liu Yulong; Jiang Zhong

    2012-01-01

    National occupational health standard-Procedure on Site Medical Emergency Response for Nuclear Accident has been approved and issued by the Ministry of Health. This standard is formulated according to the Emergency Response Law of the People's Republic of China, Law of the People 's Republic of China on Prevention and Control of Occupational Diseases, Regulations on Emergency Measures for Nuclear Accidents at Nuclear Power Plants, and Health Emergency Plans for Nuclear and Radiological Accidents of Ministry of Health, supporting the use of On-site Medical Emergency Planning and Preparedness for Nuclear Accidents and Off-site Medical Emergency Planning and Preparedness for Nuclear Accidents. Nuclear accident on-site medical response procedure is a part of the on-site emergency plan. The standard specifies the basic content and requirements of the nuclear accident on-site medical emergency response procedures of nuclear facilities operating units to guide and regulate the work of nuclear accident on-site medical emergency response of nuclear facilities operating units. The criteria-related contents were interpreted in this article. (authors)

  1. Comments and responses on the Remedial Action Plan and site design for stabilization of the Inactive Uranium Mill Tailings Site, Grand Junction, Colorado. Revision 1

    International Nuclear Information System (INIS)

    1994-01-01

    This report contains information concerning public comments and responses on the remedial action plan and site design for stabilization of the inactive uranium mill tailings site in Grand Junction, Colorado

  2. Taxonomic and functional responses to fire and post-fire management of a Mediterranean hymenoptera community.

    Science.gov (United States)

    Mateos, Eduardo; Santos, Xavier; Pujade-Villar, Juli

    2011-11-01

    Fire is one of the commonest disturbances worldwide, transforming habitat structure and affecting ecosystem functioning. Understanding how species respond to such environmental disturbances is a major conservation goal that should be monitored using functionally and taxonomically diverse groups such as Hymenoptera. In this respect, we have analyzed the taxonomic and functional response to fire and post-fire management of a Hymenoptera community from a Mediterranean protected area. Thus, Hymenoptera were sampled at fifteen sites located in three burnt areas submitted to different post-fire practices, as well as at five sites located in peripheral unburnt pine forest. A total of 4882 specimens belonging to 33 families, which were classified into six feeding groups according to their dietary preferences, were collected. ANOVA and Redundancy Analyses showed a taxonomic and functional response to fire as all burnt areas had more Hymenoptera families, different community composition and higher numbers of parasitoids than the unburnt area. Taxonomic differences were also found between burnt areas in terms of the response of Hymenoptera to post-fire management. In general the number of parasitoids was positively correlated to the number of potential host arthropods. Parasitoids are recognized to be sensitive to habitat changes, thus highlighting their value for monitoring the functional responses of organisms to habitat disturbance. The taxonomic and functional responses of Hymenoptera suggest that some pine-forest fires can enhance habitat heterogeneity and arthropod diversity, hence increasing interspecific interactions such as those established by parasitoids and their hosts.

  3. Taxonomic and Functional Responses to Fire and Post-Fire Management of a Mediterranean Hymenoptera Community

    Science.gov (United States)

    Mateos, Eduardo; Santos, Xavier; Pujade-Villar, Juli

    2011-11-01

    Fire is one of the commonest disturbances worldwide, transforming habitat structure and affecting ecosystem functioning. Understanding how species respond to such environmental disturbances is a major conservation goal that should be monitored using functionally and taxonomically diverse groups such as Hymenoptera. In this respect, we have analyzed the taxonomic and functional response to fire and post-fire management of a Hymenoptera community from a Mediterranean protected area. Thus, Hymenoptera were sampled at fifteen sites located in three burnt areas submitted to different post-fire practices, as well as at five sites located in peripheral unburnt pine forest. A total of 4882 specimens belonging to 33 families, which were classified into six feeding groups according to their dietary preferences, were collected. ANOVA and Redundancy Analyses showed a taxonomic and functional response to fire as all burnt areas had more Hymenoptera families, different community composition and higher numbers of parasitoids than the unburnt area. Taxonomic differences were also found between burnt areas in terms of the response of Hymenoptera to post-fire management. In general the number of parasitoids was positively correlated to the number of potential host arthropods. Parasitoids are recognized to be sensitive to habitat changes, thus highlighting their value for monitoring the functional responses of organisms to habitat disturbance. The taxonomic and functional responses of Hymenoptera suggest that some pine-forest fires can enhance habitat heterogeneity and arthropod diversity, hence increasing interspecific interactions such as those established by parasitoids and their hosts.

  4. Y-12 site-specific earthquake response analysis and soil liquefaction assessment

    International Nuclear Information System (INIS)

    Ahmed, S.B.; Hunt, R.J.; Manrod, W.E. III.

    1995-01-01

    A site-specific earthquake response analysis and soil liquefaction assessment were performed for the Oak Ridge Y-12 Plant. The main purpose of these studies was to use the results of the analyses for evaluating the safety of the performance category -1, -2, and -3 facilities against the natural phenomena seismic hazards. Earthquake response was determined for seven (7), one dimensional soil columns (Fig. 12) using two horizontal components of the PC-3 design basis 2000-year seismic event. The computer program SHAKE 91 (Ref. 7) was used to calculate the absolute response accelerations on top of ground (soil/weathered shale) and rock outcrop. The SHAKE program has been validated for horizontal response calculations at periods less than 2.0 second at several sites and consequently is widely accepted in the geotechnical earthquake engineering area for site response analysis

  5. ANL site response for the DOE FY1994 information resources management long-range plan

    Energy Technology Data Exchange (ETDEWEB)

    Boxberger, L.M.

    1992-03-01

    Argonne National Laboratory's ANL Site Response for the DOE FY1994 Information Resources Management (IRM) Long-Range Plan (ANL/TM 500) is one of many contributions to the DOE information resources management long-range planning process and, as such, is an integral part of the DOE policy and program planning system. The Laboratory has constructed this response according to instructions in a Call issued in September 1991 by the DOE Office of IRM Policy, Plans and Oversight. As one of a continuing series, this Site Response is an update and extension of the Laboratory's previous submissions. The response contains both narrative and tabular material. It covers an eight-year period consisting of the base year (FY1991), the current year (FY1992), the budget year (FY1993), the plan year (FY1994), and the out years (FY1995-FY1998). This Site Response was compiled by Argonne National Laboratory's Computing and Telecommunications Division (CTD), which has the responsibility to provide leadership in optimizing computing and information services and disseminating computer-related technologies throughout the Laboratory. The Site Response consists of 5 parts: (1) a site overview, describes the ANL mission, overall organization structure, the strategic approach to meet information resource needs, the planning process, major issues and points of contact. (2) a software plan for DOE contractors, Part 2B, Software Plan FMS plan for DOE organizations, (3) computing resources telecommunications, (4) telecommunications, (5) printing and publishing.

  6. ANL site response for the DOE FY1994 information resources management long-range plan

    Energy Technology Data Exchange (ETDEWEB)

    Boxberger, L.M.

    1992-03-01

    Argonne National Laboratory`s ANL Site Response for the DOE FY1994 Information Resources Management (IRM) Long-Range Plan (ANL/TM 500) is one of many contributions to the DOE information resources management long-range planning process and, as such, is an integral part of the DOE policy and program planning system. The Laboratory has constructed this response according to instructions in a Call issued in September 1991 by the DOE Office of IRM Policy, Plans and Oversight. As one of a continuing series, this Site Response is an update and extension of the Laboratory`s previous submissions. The response contains both narrative and tabular material. It covers an eight-year period consisting of the base year (FY1991), the current year (FY1992), the budget year (FY1993), the plan year (FY1994), and the out years (FY1995-FY1998). This Site Response was compiled by Argonne National Laboratory`s Computing and Telecommunications Division (CTD), which has the responsibility to provide leadership in optimizing computing and information services and disseminating computer-related technologies throughout the Laboratory. The Site Response consists of 5 parts: (1) a site overview, describes the ANL mission, overall organization structure, the strategic approach to meet information resource needs, the planning process, major issues and points of contact. (2) a software plan for DOE contractors, Part 2B, ``Software Plan FMS plan for DOE organizations, (3) computing resources telecommunications, (4) telecommunications, (5) printing and publishing.

  7. Functional Roles of Syk in Macrophage-Mediated Inflammatory Responses

    Science.gov (United States)

    Yi, Young-Su; Son, Young-Jin; Ryou, Chongsuk; Sung, Gi-Ho; Kim, Jong-Hoon; Cho, Jae Youl

    2014-01-01

    Inflammation is a series of complex biological responses to protect the host from pathogen invasion. Chronic inflammation is considered a major cause of diseases, such as various types of inflammatory/autoimmune diseases and cancers. Spleen tyrosine kinase (Syk) was initially found to be highly expressed in hematopoietic cells and has been known to play crucial roles in adaptive immune responses. However, recent studies have reported that Syk is also involved in other biological functions, especially in innate immune responses. Although Syk has been extensively studied in adaptive immune responses, numerous studies have recently presented evidence that Syk has critical functions in macrophage-mediated inflammatory responses and is closely related to innate immune response. This review describes the characteristics of Syk-mediated signaling pathways, summarizes the recent findings supporting the crucial roles of Syk in macrophage-mediated inflammatory responses and diseases, and discusses Syk-targeted drug development for the therapy of inflammatory diseases. PMID:25045209

  8. Functional Roles of Syk in Macrophage-Mediated Inflammatory Responses

    Directory of Open Access Journals (Sweden)

    Young-Su Yi

    2014-01-01

    Full Text Available Inflammation is a series of complex biological responses to protect the host from pathogen invasion. Chronic inflammation is considered a major cause of diseases, such as various types of inflammatory/autoimmune diseases and cancers. Spleen tyrosine kinase (Syk was initially found to be highly expressed in hematopoietic cells and has been known to play crucial roles in adaptive immune responses. However, recent studies have reported that Syk is also involved in other biological functions, especially in innate immune responses. Although Syk has been extensively studied in adaptive immune responses, numerous studies have recently presented evidence that Syk has critical functions in macrophage-mediated inflammatory responses and is closely related to innate immune response. This review describes the characteristics of Syk-mediated signaling pathways, summarizes the recent findings supporting the crucial roles of Syk in macrophage-mediated inflammatory responses and diseases, and discusses Syk-targeted drug development for the therapy of inflammatory diseases.

  9. Linear density response function in the projector augmented wave method

    DEFF Research Database (Denmark)

    Yan, Jun; Mortensen, Jens Jørgen; Jacobsen, Karsten Wedel

    2011-01-01

    We present an implementation of the linear density response function within the projector-augmented wave method with applications to the linear optical and dielectric properties of both solids, surfaces, and interfaces. The response function is represented in plane waves while the single...... functions of Si, C, SiC, AlP, and GaAs compare well with previous calculations. While optical properties of semiconductors, in particular excitonic effects, are generally not well described by ALDA, we obtain excellent agreement with experiments for the surface loss function of graphene and the Mg(0001...

  10. A discrimlnant function approach to ecological site classification in northern New England

    Science.gov (United States)

    James M. Fincher; Marie-Louise Smith

    1994-01-01

    Describes one approach to ecologically based classification of upland forest community types of the White and Green Mountain physiographic regions. The classification approach is based on an intensive statistical analysis of the relationship between the communities and soil-site factors. Discriminant functions useful in distinguishing between types based on soil-site...

  11. Both ATPase sites of Escherichia coli UvrA have functional roles in nucleotide excision repair

    International Nuclear Information System (INIS)

    Thiagalingam, S.; Grossman, L.

    1991-01-01

    The roles of the two tandemly arranged putative ATP binding sites of Escherichia coli UvrA in UvrABC endonuclease-mediated excision repair were analyzed by site-directed mutagenesis and biochemical characterization of the representative mutant proteins. Evidence is presented that UvrA has two functional ATPase sites which coincide with the putative ATP binding motifs predicted from its amino acid sequence. The individual ATPase sites can independently hydrolyze ATP. The C-terminal ATPase site has a higher affinity for ATP than the N-terminal site. The invariable lysine residues at the ends of the glycine-rich loops of the consensus Walker type A motifs are indispensable for ATP hydrolysis. However, the mutations at these lysine residues do not significantly affect ATP binding. UvrA, with bound ATP, forms the most favored conformation for DNA binding. The initial binding of UvrA to DNA is chiefly at the undamaged sites. In contrast to the wild type UvrA, the ATPase site mutants bind equally to damaged and undamaged sites. Dissociation of tightly bound nucleoprotein complexes from the undamaged sites requires hydrolysis of ATP by the C-terminal ATPase site of UvrA. Thus, both ATP binding and hydrolysis are required for the damage recognition step enabling UvrA to discriminate between damaged and undamaged sites on DNA

  12. Sweetgum Response to Nitrogen Fertilization on Sites of Different Quality and Land Use History

    Science.gov (United States)

    D. Andrew Scott; Donald J. Kaczmarek; James A. Burger; Michael B. Kane

    2002-01-01

    Nitrogen (N) fertilizer management in young hardwood plantations is difficult due to our lack of understanding of the site-specific mechanisms that control tree response. Differences in landuse history and soil characteristics can alter the plant response to added N considerably. Foliage biomass, N content, N concentration, resorption, and soil N supply characteristics...

  13. Estimating and coping with public response to radioactive waste repository siting

    International Nuclear Information System (INIS)

    Payne, B.A.

    1984-01-01

    The siting, construction, and operation of a radioactive waste repository is likely to be controversial in the communities being considered and at the state and national levels as well. Public response can be conceptualized at two levels: individual and group or organizational. At the individual level, public response is the behavior of people motivated by their attitudes, knowledge, and perceptions of radioactive waste and its hazards and risks. Groups or organizations provide a structure to public response through which to pool resources and talents, set up a division of labor, hire experts, develop a skilled leadership, take legal action, and so on. A broad range of organizations is possible: ad hoc, existing community groups with an added purpose, nationally-recognized organizations, or government offices and agencies. Two cases of response to radioactive waste disposal sites illustrate these sources and kinds of response and suggest indicators to estimate the nature and level of response. Specific coping strategies take different forms, depending on the nature and level of response (either supporting or opposing) to the proposed siting, the past experience of community members with similar projects, with federal agencies, and with citizens' action groups, and sources and accuracy of information individuals and groups have. All strategies are based on a policy of honesty and straight-forwardness, with a sincere effort on the part of site evaluators and decision-makers to be attentive and responsive to the public's concerns

  14. Using a Full Complex Site Transfer Function to Estimate Strong Ground Motion in Port-au-Prince (Haiti).

    Science.gov (United States)

    ST Fleur, S.; Courboulex, F.; Bertrand, E.; Mercier De Lepinay, B. F.; Hough, S. E.; Boisson, D.; Momplaisir, R.

    2017-12-01

    To assess the possible impact of a future earthquake in the urban area of Port-au-Prince (Haiti), we have implemented a simulation approach for complex ground motions produced by an earthquake. To this end, we have integrated local site effect in the prediction of strong ground motions in Port-au-Prince using the complex transfer functions method, which takes into account amplitude changes as well as phase changes. This technique is particularly suitable for basins where a conventional 1D digital approach proves inadequate, as is the case in Port-au-Prince. To do this, we use the results of the Standard Spectral Ratio (SSR) approach of St Fleur et al. (2016) to estimate the amplitude of the response of the site to a nearby rock site. Then, we determine the phase difference between sites, interpreted as changes in the phase of the signal related to local site conditions, using the signals of the 2010 earthquake aftershocks records. Finally, the accelerogram of the simulated earthquake is obtain using the technique of the inverse Fourier transform. The results of this study showed that the strongest soil motions are expected in neighborhoods of downtown Port-au-Prince and adjacent hills. In addition, this simulation method by complex transfer functions was validated by comparison with recorded actual data. Our simulated response spectra reproduce very well both the amplitude and the shape of the response spectra of recorded earthquakes. This new approach allowed to reproduce the lengthening of the signal that could be generated by surface waves at certain stations in the city of Port-au-Prince. However, two points of vigilance must be considered: (1) a good signal-to-noise ratio is necessary to obtain a robust estimate of the site-reference phase shift (ratio at least equal to 10); (2) unless the amplitude and phase changes are measured on strong motion records, this technique does not take non-linear effects into account.

  15. Response functions of free mass gravitational wave antennas

    Science.gov (United States)

    Estabrook, F. B.

    1985-01-01

    The work of Gursel, Linsay, Spero, Saulson, Whitcomb and Weiss (1984) on the response of a free-mass interferometric antenna is extended. Starting from first principles, the earlier work derived the response of a 2-arm gravitational wave antenna to plane polarized gravitational waves. Equivalent formulas (generalized slightly to allow for arbitrary elliptical polarization) are obtained by a simple differencing of the '3-pulse' Doppler response functions of two 1-arm antennas. A '4-pulse' response function is found, with quite complicated angular dependences for arbitrary incident polarization. The differencing method can as readily be used to write exact response functions ('3n+1 pulse') for antennas having multiple passes or more arms.

  16. Evaluation of the detector response function digital conventional radiology

    International Nuclear Information System (INIS)

    Arino Gil, A.; Hernandez Rodriguez, J.; Mateos Salvador, P.; Rodriguez Lopez, B.; Font Gelabert, J. C.

    2013-01-01

    The objective of this work is to obtain the response function that relates the air kerma at the entrance of the detector and pixel value, for a series of digital detectors of conventional Radiology model Optimus DigitalDiagnost Philips () and 6000 Definium General Electric. From the set of measurements is obtained a response function for each reference type of detector, and compared with those published in the literature for these teams. (Author)

  17. Tumor Suppressor Genes within Common Fragile Sites Are Active Players in the DNA Damage Response.

    Directory of Open Access Journals (Sweden)

    Idit Hazan

    2016-12-01

    Full Text Available The role of common fragile sites (CFSs in cancer remains controversial. Two main views dominate the discussion: one suggests that CFS loci are hotspots of genomic instability leading to inactivation of genes encoded within them, while the other view proposes that CFSs are functional units and that loss of the encoded genes confers selective pressure, leading to cancer development. The latter view is supported by emerging evidence showing that expression of a given CFS is associated with genome integrity and that inactivation of CFS-resident tumor suppressor genes leads to dysregulation of the DNA damage response (DDR and increased genomic instability. These two viewpoints of CFS function are not mutually exclusive but rather coexist; when breaks at CFSs are not repaired accurately, this can lead to deletions by which cells acquire growth advantage because of loss of tumor suppressor activities. Here, we review recent advances linking some CFS gene products with the DDR, genomic instability, and carcinogenesis and discuss how their inactivation might represent a selective advantage for cancer cells.

  18. The response of electrostatic probes via the λ-function

    DEFF Research Database (Denmark)

    Rerup, T.O.; Crichton, George C; McAllister, Iain Wilson

    1994-01-01

    The response of an electrostatic probe is examined with reference to a planar spacer. The study involves the numerical calculation of the probe λ-function, from which response-related characteristic parameters can be derived. These parameters enable the probe detection sensitivity and spatial...

  19. Improving ATLAS grid site reliability with functional tests using HammerCloud

    CERN Document Server

    Legger, F; The ATLAS collaboration

    2012-01-01

    With the exponential growth of LHC (Large Hadron Collider) data in 2011, and more coming in 2012, distributed computing has become the established way to analyse collider data. The ATLAS grid infrastructure includes almost 100 sites worldwide, ranging from large national computing centers to smaller university clusters. These facilities are used for data reconstruction and simulation, which are centrally managed by the ATLAS production system, and for distributed user analysis. To ensure the smooth operation of such a complex system, regular tests of all sites are necessary to validate the site capability of successfully executing user and production jobs. We report on the development, optimization and results of an automated functional testing suite using the HammerCloud framework. Functional tests are short light-weight applications covering typical user analysis and production schemes, which are periodically submitted to all ATLAS grid sites. Results from those tests are collected and used to evaluate site...

  20. 32 CFR 352a.4 - Responsibilities and functions.

    Science.gov (United States)

    2010-07-01

    ...) ORGANIZATIONAL CHARTERS DEFENSE FINANCE AND ACCOUNTING SERVICE (DFAS) § 352a.4 Responsibilities and functions. (a) The Director, Defense Finance and Accounting Service (DFAS), is the principal DoD executive for finance and accounting requirements, systems, and functions identified in DoD Directive 5118.3, 1 and...

  1. Site classification of Indian strong motion network using response spectra ratios

    Science.gov (United States)

    Chopra, Sumer; Kumar, Vikas; Choudhury, Pallabee; Yadav, R. B. S.

    2018-03-01

    In the present study, we tried to classify the Indian strong motion sites spread all over Himalaya and adjoining region, located on varied geological formations, based on response spectral ratio. A total of 90 sites were classified based on 395 strong motion records from 94 earthquakes recorded at these sites. The magnitude of these earthquakes are between 2.3 and 7.7 and the hypocentral distance for most of the cases is less than 50 km. The predominant period obtained from response spectral ratios is used to classify these sites. It was found that the shape and predominant peaks of the spectra at these sites match with those in Japan, Italy, Iran, and at some of the sites in Europe and the same classification scheme can be applied to Indian strong motion network. We found that the earlier schemes based on description of near-surface geology, geomorphology, and topography were not able to capture the effect of sediment thickness. The sites are classified into seven classes (CL-I to CL-VII) with varying predominant periods and ranges as proposed by Alessandro et al. (Bull Seismol Soc Am 102:680-695 2012). The effect of magnitudes and hypocentral distances on the shape and predominant peaks were also studied and found to be very small. The classification scheme is robust and cost-effective and can be used in region-specific attenuation relationships for accounting local site effect.

  2. Functional analysis of a potential regulatory K+-binding site in the Na+, K+-ATPase

    DEFF Research Database (Denmark)

    Schack, Vivien Rodacker; Vilsen, Bente

    The Na+, K+-ATPase functions by actively transporting 3 Na+ ions out of and 2 K+ ions into the cell, thereby creating ion gradients crucial for many physiological processes. Recently, a combined structural and functional study of the closely related Ca2+-ATPase indicated the presence...... of a regulatory K+-binding site in the P-domain of the enzyme, identifying E732 as being of particular importance (Sorensen, Clausen et al. 2004). In addition, P709 is thought to play a significant role in the structural organization of this site. Both E732 and P709 are highly conserved among P-type ATPases (E732...... is present as either glutamic acid or aspartic acid), which supports their importance and additionally raises the question whether this site may play a general role among P-type ATPases. In Na+, K+-ATPase, K+ functions directly as a substrate for membrane binding sites, however, an additional regulatory...

  3. Multi-Site Diagnostic Classification of Schizophrenia Using Discriminant Deep Learning with Functional Connectivity MRI

    Directory of Open Access Journals (Sweden)

    Ling-Li Zeng

    2018-04-01

    Full Text Available Background: A lack of a sufficiently large sample at single sites causes poor generalizability in automatic diagnosis classification of heterogeneous psychiatric disorders such as schizophrenia based on brain imaging scans. Advanced deep learning methods may be capable of learning subtle hidden patterns from high dimensional imaging data, overcome potential site-related variation, and achieve reproducible cross-site classification. However, deep learning-based cross-site transfer classification, despite less imaging site-specificity and more generalizability of diagnostic models, has not been investigated in schizophrenia. Methods: A large multi-site functional MRI sample (n = 734, including 357 schizophrenic patients from seven imaging resources was collected, and a deep discriminant autoencoder network, aimed at learning imaging site-shared functional connectivity features, was developed to discriminate schizophrenic individuals from healthy controls. Findings: Accuracies of approximately 85·0% and 81·0% were obtained in multi-site pooling classification and leave-site-out transfer classification, respectively. The learned functional connectivity features revealed dysregulation of the cortical-striatal-cerebellar circuit in schizophrenia, and the most discriminating functional connections were primarily located within and across the default, salience, and control networks. Interpretation: The findings imply that dysfunctional integration of the cortical-striatal-cerebellar circuit across the default, salience, and control networks may play an important role in the “disconnectivity” model underlying the pathophysiology of schizophrenia. The proposed discriminant deep learning method may be capable of learning reliable connectome patterns and help in understanding the pathophysiology and achieving accurate prediction of schizophrenia across multiple independent imaging sites. Keywords: Schizophrenia, Deep learning, Connectome, f

  4. Multi-Site Diagnostic Classification of Schizophrenia Using Discriminant Deep Learning with Functional Connectivity MRI.

    Science.gov (United States)

    Zeng, Ling-Li; Wang, Huaning; Hu, Panpan; Yang, Bo; Pu, Weidan; Shen, Hui; Chen, Xingui; Liu, Zhening; Yin, Hong; Tan, Qingrong; Wang, Kai; Hu, Dewen

    2018-04-01

    A lack of a sufficiently large sample at single sites causes poor generalizability in automatic diagnosis classification of heterogeneous psychiatric disorders such as schizophrenia based on brain imaging scans. Advanced deep learning methods may be capable of learning subtle hidden patterns from high dimensional imaging data, overcome potential site-related variation, and achieve reproducible cross-site classification. However, deep learning-based cross-site transfer classification, despite less imaging site-specificity and more generalizability of diagnostic models, has not been investigated in schizophrenia. A large multi-site functional MRI sample (n = 734, including 357 schizophrenic patients from seven imaging resources) was collected, and a deep discriminant autoencoder network, aimed at learning imaging site-shared functional connectivity features, was developed to discriminate schizophrenic individuals from healthy controls. Accuracies of approximately 85·0% and 81·0% were obtained in multi-site pooling classification and leave-site-out transfer classification, respectively. The learned functional connectivity features revealed dysregulation of the cortical-striatal-cerebellar circuit in schizophrenia, and the most discriminating functional connections were primarily located within and across the default, salience, and control networks. The findings imply that dysfunctional integration of the cortical-striatal-cerebellar circuit across the default, salience, and control networks may play an important role in the "disconnectivity" model underlying the pathophysiology of schizophrenia. The proposed discriminant deep learning method may be capable of learning reliable connectome patterns and help in understanding the pathophysiology and achieving accurate prediction of schizophrenia across multiple independent imaging sites. Copyright © 2018 German Center for Neurodegenerative Diseases (DZNE). Published by Elsevier B.V. All rights reserved.

  5. Assigning Quantitative Function to Post-Translational Modifications Reveals Multiple Sites of Phosphorylation That Tune Yeast Pheromone Signaling Output

    Energy Technology Data Exchange (ETDEWEB)

    Pincus, David; Ryan, Christopher J.; Smith, Richard D.; Brent, Roger; Resnekov, Orna; Hakimi, Mohamed Ali

    2013-03-12

    Cell signaling systems transmit information by post-­translationally modifying signaling proteins, often via phosphorylation. While thousands of sites of phosphorylation have been identified in proteomic studies, the vast majority of sites have no known function. Assigning functional roles to the catalog of uncharacterized phosphorylation sites is a key research challenge. Here we present a general approach to address this challenge and apply it to a prototypical signaling pathway, the pheromone response pathway in Saccharomyces cerevisiae. The pheromone pathway includes a mitogen activated protein kinase (MAPK) cascade activated by a G-­protein coupled receptor (GPCR). We used mass spectrometry-based proteomics to identify sites whose phosphorylation changed when the system was active, and evolutionary conservation to assign priority to a list of candidate MAPK regulatory sites. We made targeted alterations in those sites, and measured the effects of the mutations on pheromone pathway output in single cells. Our work identified six new sites that quantitatively tuned system output. We developed simple computational models to find system architectures that recapitulated the quantitative phenotypes of the mutants. Our results identify a number of regulated phosphorylation events that contribute to adjust the input-­output relationship of this model eukaryotic signaling system. We believe this combined approach constitutes a general means not only to reveal modification sites required to turn a pathway on and off, but also those required for more subtle quantitative effects that tune pathway output. Our results further suggest that relatively small quantitative influences from individual regulatory phosphorylation events endow signaling systems with plasticity that evolution may exploit to quantitatively tailor signaling outcomes.

  6. Comment and response document for the final remedial action plan and site design for stabilization of the inactive uranium mill tailings sites at Slick Rock, Colorado. Revision 2

    International Nuclear Information System (INIS)

    1996-05-01

    This document for the final remedial action plan and site design has been prepared for US Department of Energy Environmental Restoration Division as part of the Uranium Mill Tailings Remedial Action plan. Comments and responses are included for the site design for stabilization of the inactive uranium mill tailings sites at Slick Rock, Colorado

  7. Dynamic response function and large-amplitude dissipative collective motion

    International Nuclear Information System (INIS)

    Wu Xizhen; Zhuo Yizhong; Li Zhuxia; Sakata, Fumihiko.

    1993-05-01

    Aiming at exploring microscopic dynamics responsible for the dissipative large-amplitude collective motion, the dynamic response and correlation functions are introduced within the general theory of nuclear coupled-master equations. The theory is based on the microscopic theory of nuclear collective dynamics which has been developed within the time-dependent Hartree-Fock (TDHF) theory for disclosing complex structure of the TDHF-manifold. A systematic numerical method for calculating the dynamic response and correlation functions is proposed. By performing numerical calculation for a simple model Hamiltonian, it is pointed out that the dynamic response function gives an important information in understanding the large-amplitude dissipative collective motion which is described by an ensemble of trajectories within the TDHF-manifold. (author)

  8. Development of emergency response training program for on-site commanders (1)

    International Nuclear Information System (INIS)

    Hikono, Masaru; Matsui, Yuko; Kanayama, Masaki

    2017-01-01

    Since the Great East Japan Earthquake of 2011, there have been increasing calls for developing the leadership capabilities of managers who are in charge of command and control of the on-site emergency response center at nuclear power plants. Training programs to improve non-technical skills are being developed and introduced. The authors developed an active learning exercise that can be repeatedly performed on-site, targeting on-site commander teams in charge of the initial response in an emergency situation. The exercise forms the core element of a non-technical skills training curriculum. This paper outlines the developed exercise, evaluates the stress on the participants caused by the exercise, and identifies any issues before actually introducing it to a site. (author)

  9. Spiral ganglion cell site of excitation I: comparison of scala tympani and intrameatal electrode responses.

    Science.gov (United States)

    Cartee, Lianne A; Miller, Charles A; van den Honert, Chris

    2006-05-01

    To determine the site of excitation on the spiral ganglion cell in response to electrical stimulation similar to that from a cochlear implant, single-fiber responses to electrical stimuli delivered by an electrode positioned in the scala tympani were compared to responses from stimuli delivered by an electrode placed in the internal auditory meatus. The response to intrameatal stimulation provided a control set of data with a known excitation site, the central axon of the spiral ganglion cell. For both intrameatal and scala tympani stimuli, the responses to single-pulse, summation, and refractory stimulus protocols were recorded. The data demonstrated that summation pulses, as opposed to single pulses, are likely to give the most insightful measures for determination of the site of excitation. Single-fiber summation data for both scala tympani and intrameatally stimulated fibers were analyzed with a clustering algorithm. Combining cluster analysis and additional numerical modeling data, it was hypothesized that the scala tympani responses corresponded to central excitation, peripheral excitation adjacent to the cell body, and peripheral excitation at a site distant from the cell body. Fibers stimulated by an intrameatal electrode demonstrated the greatest range of jitter measurements indicating that greater fiber independence may be achieved with intrameatal stimulation.

  10. Silicon Drift Detector response function for PIXE spectra fitting

    Science.gov (United States)

    Calzolai, G.; Tapinassi, S.; Chiari, M.; Giannoni, M.; Nava, S.; Pazzi, G.; Lucarelli, F.

    2018-02-01

    The correct determination of the X-ray peak areas in PIXE spectra by fitting with a computer program depends crucially on accurate parameterization of the detector peak response function. In the Guelph PIXE software package, GUPIXWin, one of the most used PIXE spectra analysis code, the response of a semiconductor detector to monochromatic X-ray radiation is described by a linear combination of several analytical functions: a Gaussian profile for the X-ray line itself, and additional tail contributions (exponential tails and step functions) on the low-energy side of the X-ray line to describe incomplete charge collection effects. The literature on the spectral response of silicon X-ray detectors for PIXE applications is rather scarce, in particular data for Silicon Drift Detectors (SDD) and for a large range of X-ray energies are missing. Using a set of analytical functions, the SDD response functions were satisfactorily reproduced for the X-ray energy range 1-15 keV. The behaviour of the parameters involved in the SDD tailing functions with X-ray energy is described by simple polynomial functions, which permit an easy implementation in PIXE spectra fitting codes.

  11. Methodological substantiation of the professional functions of Responsible persons of pharmaceutical and hospital institutions

    Directory of Open Access Journals (Sweden)

    N. O. Vetiutneva

    2018-03-01

    Full Text Available The aim of the work is the content analysis and methodological justification of the professional functions of the Responsible persons for quality assurance of medicines in pharmaceutical and hospital institutions. Materials and methods. The following research methods were used: system and comparative analysis, generalization, systematization, graphic modeling, observation. Research materials: normative legal acts, normative documents, recommendations of international organizations, information of wholesale and retail pharmaceutical companies, pharmaceutical and hospital institutions, professional non-governmental organizations, placed on official web-sites and collected in the process of direct observation. Results. The personnel and qualification aspects of professional activity of Responsible persons of pharmaceutical and hospital institutions were discussed. On the basis of analysis of the modern legal and regulatory framework, a general list of professional functions of the Responsible persons of health care institutions had been formed. The content analysis and comparison of the number of the functions of Responsible persons performed in health care institutions of different types is carried out. The new functions of the Responsible persons of health care institutions are considered. The managerial nature of the professional functions of the Responsible persons and the expediency of their complementing with the leadership functions are substantiated. On the basis of international management standards, requirements of GPP and GPEP, systematization of the functions of the Responsible persons of health care institutions in the groups and subgroups was performed. Conclusions. The generalization and systematization of the professional functions of the Responsible persons of health care institutions had been carried out for five classification groups of functions, namely: leadership, planning, organizational, control and information, of which the

  12. In silico determination of intracellular glycosylation and phosphorylation sites in human selectins: Implications for biological function

    DEFF Research Database (Denmark)

    Ahmad, I.; Hoessli, D.C.; Gupta, Ramneek

    2007-01-01

    Post-translational modifications provide the proteins with the possibility to perform functions in addition to those determined by their primary sequence. However, analysis of multifunctional protein structures in the environment of cells and body fluids is made especially difficult by the presence...... both modifications are likely to occur can also be predicted (YinYang sites), to suggest further functional versatility. Structural modifications of hydroxyl groups of P-, E-, and L-selectins have been predicted and possible functions resulting from such modifications are proposed. Functional changes...... of the three selectins are based on the assumption that transitory and reversible protein modifications by phosphate and O-GlcNAc cause specific conformational changes and generate binding sites for other proteins. The computer-assisted prediction of glycosylation and phosphorylation sites in selectins should...

  13. Science in Emergency Response at CDC: Structure and Functions.

    Science.gov (United States)

    Iskander, John; Rose, Dale A; Ghiya, Neelam D

    2017-09-01

    Recent high-profile activations of the US Centers for Disease Control and Prevention (CDC) Emergency Operations Center (EOC) include responses to the West African Ebola and Zika virus epidemics. Within the EOC, emergency responses are organized according to the Incident Management System, which provides a standardized structure and chain of command, regardless of whether the EOC activation occurs in response to an outbreak, natural disaster, or other type of public health emergency. By embedding key scientific roles, such as the associate director for science, and functions within a Scientific Response Section, the current CDC emergency response structure ensures that both urgent and important science issues receive needed attention. Key functions during emergency responses include internal coordination of scientific work, data management, information dissemination, and scientific publication. We describe a case example involving the ongoing Zika virus response that demonstrates how the scientific response structure can be used to rapidly produce high-quality science needed to answer urgent public health questions and guide policy. Within the context of emergency response, longer-term priorities at CDC include both streamlining administrative requirements and funding mechanisms for scientific research.

  14. Development of uniform hazard response spectra for Tarapur, Trombay and Kakrapar sites

    International Nuclear Information System (INIS)

    Ghosh, A.K.; Rao, K.S.; Kushwaha, H.S.

    2003-08-01

    Traditionally, the seismic design basis ground motion has been specified by normalised response spectral shapes and peak ground acceleration (PGA). The mean recurrence interval (MRI) used to be computed for PGA only. The present work develops uniform hazard response spectra i.e. spectra having the same MRI at all frequencies for Tarapur, Trombay and Kakrapar sites. These results determine the seismic hazard at the given site and the associated uncertainties. Typical examples are given to show the sensitivity of the results to changes in various parameters. (author)

  15. Density functional study the interaction of oxygen molecule with defect sites of graphene

    Energy Technology Data Exchange (ETDEWEB)

    Qi Xuejun [State Key Laboratory of Coal Combustion, Wuhan 430074 (China); Guo Xin, E-mail: guoxin@mail.hust.edu.cn [State Key Laboratory of Coal Combustion, Wuhan 430074 (China); Zheng Chuguang [State Key Laboratory of Coal Combustion, Wuhan 430074 (China)

    2012-10-15

    Highlights: Black-Right-Pointing-Pointer The defect sites existed on the graphite surface create active sites and enhance the reactivity of carbonaceous material. Black-Right-Pointing-Pointer Oxygen molecule more favor chemisorbed on the graphene surface contains defect sites than the perfect surface. Black-Right-Pointing-Pointer The single active oxygen atom adsorbed on the defect surfaces, it completely insert into the surface. - Abstract: The present article reports a theoretical study of oxygen interacted with graphene surface containing defect sites on the atomic level by employing the density functional theory combined with the graphene cluster model. It was founded that oxygen molecule prefers to be chemisorbed on the graphene surface containing defect sites compared to the perfect surface. The adsorption energy of O{sub 2} on the double defect site is about 2.5 times as large as that on the perfect graphene surface. Moreover, the oxygen molecule interacts with S-W defect site gives rise to stable epoxy structure, which pulling the carbon atom outward from the original site in the direction perpendicular to the surface. If the oxygen molecule is adsorbed on the single vacancy site, two C-O bonds are formed on the graphene surface. However, when the oxygen molecule is chemisorbed on the double vacancy site, the oxygen atoms substitute the missing carbon atom's position in the carbon plane and form a hexagonal structure on the graphene network. The results indicate that single active oxygen atom approaches the defect site, it's completely adsorbed in the plane and high energy is released. In all cases, the interaction of an oxygen atom with defect surface involves an exothermic process. The defect site creates active sites on the surface of graphene and produces catalytic effects during the process of oxidation of carbonaceous materials.

  16. Estimating and coping with public response to radioactive waste repository siting

    International Nuclear Information System (INIS)

    Payne, B.A.

    1984-01-01

    The siting and construction of a radioactive waste disposal operation is likely to be controversial in the communities being considered, and at the state and national levels as well. Public response can be conceptualized at two levels: individual, and group or organizational. At the individual level, public response is the behavior of people motivated by their attitudes, knowledge, and perceptions of radioactive waste and its hazards and risks. On the group or organizational level, public response is the organized activity of individuals. Organizations provide the ability to pool resources and talents, set up a division of labor, hire experts, develop a skilled leadership, take legal action, and so on. A broad range of organizations is possible: ad hoc, existing community groups with an added purpose, nationally-recognized organizations, or government offices and agencies. Two cases of response to radioactive waste disposal sites illustrate these sources and kinds of response and lead to indicators to estimate the nature and level of response. Finally, drawing from the theoretical discussion of the sources and levels of public response, on the estimation techniques, and on the examples, specific coping strategies are developed. These strategies take different forms, based on the nature and level of response (either supporting or opposing) to the proposed siting, and the past experience of the community members with similar projects, with other federal requirements, and with citizens' action groups, as well as sources and accuracy of information individuals and groups have. However, all strategies are based on a policy of honesty and straight-forwardness, with a sincere effort on the part of site evaluators and decision-makers to be attentive and responsive to the public's concerns. 10 references

  17. Mitochondrial respiration controls lysosomal function during inflammatory T cell responses

    Science.gov (United States)

    Baixauli, Francesc; Acín-Pérez, Rebeca; Villarroya-Beltrí, Carolina; Mazzeo, Carla; Nuñez-Andrade, Norman; Gabandé-Rodriguez, Enrique; Dolores Ledesma, Maria; Blázquez, Alberto; Martin, Miguel Angel; Falcón-Pérez, Juan Manuel; Redondo, Juan Miguel; Enríquez, Jose Antonio; Mittelbrunn, Maria

    2016-01-01

    Summary The endolysosomal system is critical for the maintenance of cellular homeostasis. However, how endolysosomal compartment is regulated by mitochondrial function is largely unknown. We have generated a mouse model with defective mitochondrial function in CD4+ T lymphocytes by genetic deletion of the mitochondrial transcription factor A (Tfam). Mitochondrial respiration-deficiency impairs lysosome function, promotes p62 and sphingomyelin accumulation and disrupts endolysosomal trafficking pathways and autophagy, thus linking a primary mitochondrial dysfunction to a lysosomal storage disorder. The impaired lysosome function in Tfam-deficient cells subverts T cell differentiation toward pro-inflammatory subsets and exacerbates the in vivo inflammatory response. Restoration of NAD+ levels improves lysosome function and corrects the inflammatory defects in Tfam-deficient T cells. Our results uncover a mechanism by which mitochondria regulate lysosome function to preserve T cell differentiation and effector functions, and identify novel strategies for intervention in mitochondrial-related diseases. PMID:26299452

  18. Source Spectra and Site Response for Two Indonesian Earthquakes: the Tasikmalaya and Kerinci Events of 2009

    Science.gov (United States)

    Gunawan, I.; Cummins, P. R.; Ghasemi, H.; Suhardjono, S.

    2012-12-01

    Indonesia is very prone to natural disasters, especially earthquakes, due to its location in a tectonically active region. In September-October 2009 alone, intraslab and crustal earthquakes caused the deaths of thousands of people, severe infrastructure destruction and considerable economic loss. Thus, both intraslab and crustal earthquakes are important sources of earthquake hazard in Indonesia. Analysis of response spectra for these intraslab and crustal earthquakes are needed to yield more detail about earthquake properties. For both types of earthquakes, we have analysed available Indonesian seismic waveform data to constrain source and path parameters - i.e., low frequency spectral level, Q, and corner frequency - at reference stations that appear to be little influenced by site response.. We have considered these analyses for the main shocks as well as several aftershocks. We obtain corner frequencies that are reasonably consistent with the constant stress drop hypothesis. Using these results, we consider using them to extract information about site response form other stations form the Indonesian strong motion network that appear to be strongly affected by site response. Such site response data, as well as earthquake source parameters, are important for assessing earthquake hazard in Indonesia.

  19. Local and linear chemical reactivity response functions at finite temperature in density functional theory

    International Nuclear Information System (INIS)

    Franco-Pérez, Marco; Ayers, Paul W.; Gázquez, José L.; Vela, Alberto

    2015-01-01

    We explore the local and nonlocal response functions of the grand canonical potential density functional at nonzero temperature. In analogy to the zero-temperature treatment, local (e.g., the average electron density and the local softness) and nonlocal (e.g., the softness kernel) intrinsic response functions are defined as partial derivatives of the grand canonical potential with respect to its thermodynamic variables (i.e., the chemical potential of the electron reservoir and the external potential generated by the atomic nuclei). To define the local and nonlocal response functions of the electron density (e.g., the Fukui function, the linear density response function, and the dual descriptor), we differentiate with respect to the average electron number and the external potential. The well-known mathematical relationships between the intrinsic response functions and the electron-density responses are generalized to nonzero temperature, and we prove that in the zero-temperature limit, our results recover well-known identities from the density functional theory of chemical reactivity. Specific working equations and numerical results are provided for the 3-state ensemble model

  20. Improving ATLAS grid site reliability with functional tests using HammerCloud

    CERN Document Server

    Legger, F; The ATLAS collaboration; Medrano Llamas, R; Sciacca, G; Van der Ster, D C

    2012-01-01

    With the exponential growth of LHC (Large Hadron Collider) data in 2011, and more coming in 2012, distributed computing has become the established way to analyse collider data. The ATLAS grid infrastructure includes more than 80 sites worldwide, ranging from large national computing centers to smaller university clusters. These facilities are used for data reconstruction and simulation, which are centrally managed by the ATLAS production system, and for distributed user analysis. To ensure the smooth operation of such a complex system, regular tests of all sites are necessary to validate the site capability of successfully executing user and production jobs. We report on the development, optimization and results of an automated functional testing suite using the HammerCloud framework. Functional tests are short light-weight applications covering typical user analysis and production schemes, which are periodically submitted to all ATLAS grid sites. Results from those tests are collected and used to evaluate si...

  1. Functional neural networks underlying response inhibition in adolescents and adults.

    Science.gov (United States)

    Stevens, Michael C; Kiehl, Kent A; Pearlson, Godfrey D; Calhoun, Vince D

    2007-07-19

    This study provides the first description of neural network dynamics associated with response inhibition in healthy adolescents and adults. Functional and effective connectivity analyses of whole brain hemodynamic activity elicited during performance of a Go/No-Go task were used to identify functionally integrated neural networks and characterize their causal interactions. Three response inhibition circuits formed a hierarchical, inter-dependent system wherein thalamic modulation of input to premotor cortex by fronto-striatal regions led to response suppression. Adolescents differed from adults in the degree of network engagement, regional fronto-striatal-thalamic connectivity, and network dynamics. We identify and characterize several age-related differences in the function of neural circuits that are associated with behavioral performance changes across adolescent development.

  2. Response variance in functional maps: neural darwinism revisited.

    Directory of Open Access Journals (Sweden)

    Hirokazu Takahashi

    Full Text Available The mechanisms by which functional maps and map plasticity contribute to cortical computation remain controversial. Recent studies have revisited the theory of neural Darwinism to interpret the learning-induced map plasticity and neuronal heterogeneity observed in the cortex. Here, we hypothesize that the Darwinian principle provides a substrate to explain the relationship between neuron heterogeneity and cortical functional maps. We demonstrate in the rat auditory cortex that the degree of response variance is closely correlated with the size of its representational area. Further, we show that the response variance within a given population is altered through training. These results suggest that larger representational areas may help to accommodate heterogeneous populations of neurons. Thus, functional maps and map plasticity are likely to play essential roles in Darwinian computation, serving as effective, but not absolutely necessary, structures to generate diverse response properties within a neural population.

  3. Response variance in functional maps: neural darwinism revisited.

    Science.gov (United States)

    Takahashi, Hirokazu; Yokota, Ryo; Kanzaki, Ryohei

    2013-01-01

    The mechanisms by which functional maps and map plasticity contribute to cortical computation remain controversial. Recent studies have revisited the theory of neural Darwinism to interpret the learning-induced map plasticity and neuronal heterogeneity observed in the cortex. Here, we hypothesize that the Darwinian principle provides a substrate to explain the relationship between neuron heterogeneity and cortical functional maps. We demonstrate in the rat auditory cortex that the degree of response variance is closely correlated with the size of its representational area. Further, we show that the response variance within a given population is altered through training. These results suggest that larger representational areas may help to accommodate heterogeneous populations of neurons. Thus, functional maps and map plasticity are likely to play essential roles in Darwinian computation, serving as effective, but not absolutely necessary, structures to generate diverse response properties within a neural population.

  4. Functionally unidimensional item response models for multivariate binary data

    DEFF Research Database (Denmark)

    Ip, Edward; Molenberghs, Geert; Chen, Shyh-Huei

    2013-01-01

    The problem of fitting unidimensional item response models to potentially multidimensional data has been extensively studied. The focus of this article is on response data that have a strong dimension but also contain minor nuisance dimensions. Fitting a unidimensional model to such multidimensio......The problem of fitting unidimensional item response models to potentially multidimensional data has been extensively studied. The focus of this article is on response data that have a strong dimension but also contain minor nuisance dimensions. Fitting a unidimensional model...... to such multidimensional data is believed to result in ability estimates that represent a combination of the major and minor dimensions. We conjecture that the underlying dimension for the fitted unidimensional model, which we call the functional dimension, represents a nonlinear projection. In this article we investigate...... tool. An example regarding a construct of desire for physical competency is used to illustrate the functional unidimensional approach....

  5. Effective summary evaluators for deep nuclear waste repositories: geohydrologic response function

    International Nuclear Information System (INIS)

    Nelson, R.W.; Dove, F.H.

    1981-03-01

    Useful insight has been gained over the past four years as hydrologic system modeling has been applied to evaluate hypothetical, waste-repository sites in various geologic media. The Geohydrologic Response Functions, described in this paper, are shown to: blend extensive results of technical analysis into simple summary relationships, and to potentially help the public and decision makers to evaluate the magnitude of any loss in repository integrity

  6. Investigation of the metal binding site in methionine aminopeptidase by density functional theory

    DEFF Research Database (Denmark)

    Jørgensen, Anne Techau; Norrby, Per-Ola; Liljefors, Tommy

    2002-01-01

    All methionine aminopeptidases exhibit the same conserved metal binding site. The structure of this site with either Co2+ ions or Zn2+ ions was investigated using density functional theory. The calculations showed that the structure of the site was not influenced by the identity of the metal ions....... This was the case for both of the systems studied; one based on the X-ray structure of the human methionine aminopeptidase type 2 (hMetAP-2) and the other based on the X-ray structure of the E. coli methionine aminopeptidase type 1 (eMetAP-1). Another important structural issue is the identity of the bridging...

  7. Improving ATLAS grid site reliability with functional tests using HammerCloud

    Science.gov (United States)

    Elmsheuser, Johannes; Legger, Federica; Medrano Llamas, Ramon; Sciacca, Gianfranco; van der Ster, Dan

    2012-12-01

    With the exponential growth of LHC (Large Hadron Collider) data in 2011, and more coming in 2012, distributed computing has become the established way to analyse collider data. The ATLAS grid infrastructure includes almost 100 sites worldwide, ranging from large national computing centers to smaller university clusters. These facilities are used for data reconstruction and simulation, which are centrally managed by the ATLAS production system, and for distributed user analysis. To ensure the smooth operation of such a complex system, regular tests of all sites are necessary to validate the site capability of successfully executing user and production jobs. We report on the development, optimization and results of an automated functional testing suite using the HammerCloud framework. Functional tests are short lightweight applications covering typical user analysis and production schemes, which are periodically submitted to all ATLAS grid sites. Results from those tests are collected and used to evaluate site performances. Sites that fail or are unable to run the tests are automatically excluded from the PanDA brokerage system, therefore avoiding user or production jobs to be sent to problematic sites.

  8. MACK/MACKLIB system for nuclear response functions

    International Nuclear Information System (INIS)

    Abdou, M.A.; Gohar, Y.

    1978-01-01

    The MACK computer program calculates energy pointwise and multigroup nuclear response functions from basic nuclear data in ENDF/B format. The new version of the program, MACK-IV, incorporates major developments and improvements aimed at maximizing the utilization of available nuclear data and ensuring energy conservation in nuclear heating calculations. A new library, MACKLIB-IV, of nuclear response functions was generated in the CTR energy group structure of 171 neutron groups and 36 gamma groups. The library was prepared using MACK-IV, and ENDF/B-IV, and is suitable for fusion, fusion--fission hybrids, and fission applications. 3 figures, 4 tables

  9. MACK/MACKLIB system for nuclear response functions

    International Nuclear Information System (INIS)

    Abdou, M.A.; Gohar, Y.M.

    1978-01-01

    The MACK computer program calculates energy pointwise and multigroup nuclear response functions from basic nuclear data in ENDF/B format. The new version of the program MACK-IV, incorporates major developments and improvements aimed at maximizing the utilization of available nuclear data and ensuring energy conservation in nuclear heating calculations. A new library, MACKLIB-IV, of nuclear response functions was generated in the CTR energy group structure of 171 neutron groups and 36 gamma groups. The library was prepared using MACK-IV and ENDF/B-IV and is suitable for fusion, fusion-fission hydrids, and fission applications

  10. Computations of nuclear response functions with MACK-IV

    International Nuclear Information System (INIS)

    Abdou, M.A.; Gohar, Y.

    1978-01-01

    The MACK computer program calculates energy pointwise and multigroup nuclear response functions from basic nuclear data in ENDF/B format. The new version of the program, MACK-IV, incorporates major developments and improvements aimed at maximizing the utilization of available nuclear data and ensuring energy conservation in nuclear heating calculations. A new library, MACKLIB-IV, of nuclear response functions was generated in the CTR energy group structure of 171 neutron groups and 36 gamma groups. The library was prepared using MACK-IV and ENDF/B-IV and is suitable for fusion, fusion-fission hybrids, and fission applications

  11. Computations of nuclear response functions with MACK-IV

    Energy Technology Data Exchange (ETDEWEB)

    Abdou, M A; Gohar, Y

    1978-01-01

    The MACK computer program calculates energy pointwise and multigroup nuclear response functions from basic nuclear data in ENDF/B format. The new version of the program, MACK-IV, incorporates major developments and improvements aimed at maximizing the utilization of available nuclear data and ensuring energy conservation in nuclear heating calculations. A new library, MACKLIB-IV, of nuclear response functions was generated in the CTR energy group structure of 171 neutron groups and 36 gamma groups. The library was prepared using MACK-IV and ENDF/B-IV and is suitable for fusion, fusion-fission hybrids, and fission applications.

  12. MACK/MACKLIB system for nuclear response functions

    Energy Technology Data Exchange (ETDEWEB)

    Abdou, M.A.; Gohar, Y.M.

    1978-03-15

    The MACK computer program calculates energy pointwise and multigroup nuclear response functions from basic nuclear data in ENDF/B format. The new version of the program MACK-IV, incorporates major developments and improvements aimed at maximizing the utilization of available nuclear data and ensuring energy conservation in nuclear heating calculations. A new library, MACKLIB-IV, of nuclear response functions was generated in the CTR energy group structure of 171 neutron groups and 36 gamma groups. The library was prepared using MACK-IV and ENDF/B-IV and is suitable for fusion, fusion-fission hydrids, and fission applications.

  13. Community functional responses to soil and climate at multiple spatial scales: when does intraspecific variation matter?

    Directory of Open Access Journals (Sweden)

    Andrew Siefert

    Full Text Available Despite increasing evidence of the importance of intraspecific trait variation in plant communities, its role in community trait responses to environmental variation, particularly along broad-scale climatic gradients, is poorly understood. We analyzed functional trait variation among early-successional herbaceous plant communities (old fields across a 1200-km latitudinal extent in eastern North America, focusing on four traits: vegetative height, leaf area, specific leaf area (SLA, and leaf dry matter content (LDMC. We determined the contributions of species turnover and intraspecific variation to between-site functional dissimilarity at multiple spatial scales and community trait responses to edaphic and climatic factors. Among-site variation in community mean trait values and community trait responses to the environment were generated by a combination of species turnover and intraspecific variation, with species turnover making a greater contribution for all traits. The relative importance of intraspecific variation decreased with increasing geographic and environmental distance between sites for SLA and leaf area. Intraspecific variation was most important for responses of vegetative height and responses to edaphic compared to climatic factors. Individual species displayed strong trait responses to environmental factors in many cases, but these responses were highly variable among species and did not usually scale up to the community level. These findings provide new insights into the role of intraspecific trait variation in plant communities and the factors controlling its relative importance. The contribution of intraspecific variation to community trait responses was greatest at fine spatial scales and along edaphic gradients, while species turnover dominated at broad spatial scales and along climatic gradients.

  14. Preliminary evaluation of the Accident Response Mobile Manipulation System for accident site salvage operations

    International Nuclear Information System (INIS)

    Trujillo, J.M.; Morse, W.D.; Jones, D.P.

    1994-01-01

    This paper describes and evaluates operational experiences with the Accident Response Mobile Manipulation System (ARMMS) during simulated accident site salvage operations which might involve nuclear weapons. The ARMMS is based upon a teleoperated mobility platform with two Schilling Titan 7F Manipulators

  15. Response of Competing Vegetation to Site Preparation on West Gulf Coastal Plain Commercial Forest Land

    Science.gov (United States)

    Gale L. Wolters; Henry A. Pearson; Ronald E. Thill; V. Clark Baldwin; Alton Martin

    1995-01-01

    The response of woody and herbaceous vegetation to site preparation, subsoil texture, and fertilization was measured on the West Gulf Coastal Plain. The influences of these treatments on competing vegetation were short-term. Drastic soil disturbance and fertilization briefly increased herbage production. Shear-windrow and shear-disk were generally the most effective...

  16. Rebuilding trust in online shops on consumer review sites : sellers’ responses to user-generated complaints

    NARCIS (Netherlands)

    Matzat, U.; Snijders, C.C.P.

    2012-01-01

    How do online shops re-build trust on consumer-generated review sites after customers accuse them of misbehaving? Theories suggest that the effectiveness of responses depends on the type of accusation, yet online research indicates that apologies are superior to denials regardless of the type of

  17. 40 CFR 300.440 - Procedures for planning and implementing off-site response actions.

    Science.gov (United States)

    2010-07-01

    ... unless the Remedial Project Manager or OSC assures the proper management of the CERCLA waste samples or... OIL AND HAZARDOUS SUBSTANCES POLLUTION CONTINGENCY PLAN Hazardous Substance Response § 300.440... § 300.440(d). (5) Off-site transfers of those laboratory samples and treatability study CERCLA wastes...

  18. Growth and nutrition response of young sweetgum plantations to repeated nitrogen fertilization on two site types

    Science.gov (United States)

    D. Andrew Scott; James A. Burger; Donald J. Kaczmarek; Michael B. Kane

    2004-01-01

    Short-rotation intensive tree culture is being investigated in the southern United States as a method of producing hardwood fiber, but little is known about the early productivity and nutritional needs of these systems, especially on different site types. We studied the growth and foliar nutrition response of two sweetgum (Liquidambar styraciflua L...

  19. Functional criteria for emergency response facilities. Technical report (final)

    International Nuclear Information System (INIS)

    1981-02-01

    This report describes the facilities and systems to be used by nuclear power plant licensees to improve responses to emergency situations. The facilities include the Technical Support Center (TSC), Onsite Operational Support Center (OSC), and Nearsite Emergency Operations Facility (EOF), as well as a brief discussion of the emergency response function of the control room. The data systems described are the Safety Parameter Display System (SPDS) and Nuclear Data Link (NDL). Together, these facilities and systems make up the total Emergency Response Facilities (ERFs). Licensees should follow the guidance provided both in this report and in NUREG-0654 (FEMA-REP-1), Revision 1, for design and implementation of the ERFs

  20. Analysis of functional importance of binding sites in the Drosophila gap gene network model.

    Science.gov (United States)

    Kozlov, Konstantin; Gursky, Vitaly V; Kulakovskiy, Ivan V; Dymova, Arina; Samsonova, Maria

    2015-01-01

    The statistical thermodynamics based approach provides a promising framework for construction of the genotype-phenotype map in many biological systems. Among important aspects of a good model connecting the DNA sequence information with that of a molecular phenotype (gene expression) is the selection of regulatory interactions and relevant transcription factor bindings sites. As the model may predict different levels of the functional importance of specific binding sites in different genomic and regulatory contexts, it is essential to formulate and study such models under different modeling assumptions. We elaborate a two-layer model for the Drosophila gap gene network and include in the model a combined set of transcription factor binding sites and concentration dependent regulatory interaction between gap genes hunchback and Kruppel. We show that the new variants of the model are more consistent in terms of gene expression predictions for various genetic constructs in comparison to previous work. We quantify the functional importance of binding sites by calculating their impact on gene expression in the model and calculate how these impacts correlate across all sites under different modeling assumptions. The assumption about the dual interaction between hb and Kr leads to the most consistent modeling results, but, on the other hand, may obscure existence of indirect interactions between binding sites in regulatory regions of distinct genes. The analysis confirms the previously formulated regulation concept of many weak binding sites working in concert. The model predicts a more or less uniform distribution of functionally important binding sites over the sets of experimentally characterized regulatory modules and other open chromatin domains.

  1. Orthogonal use of a human tRNA synthetase active site to achieve multi-functionality

    Science.gov (United States)

    Zhou, Quansheng; Kapoor, Mili; Guo, Min; Belani, Rajesh; Xu, Xiaoling; Kiosses, William B.; Hanan, Melanie; Park, Chulho; Armour, Eva; Do, Minh-Ha; Nangle, Leslie A.; Schimmel, Paul; Yang, Xiang-Lei

    2011-01-01

    Protein multi-functionality is an emerging explanation for the complexity of higher organisms. In this regard, while aminoacyl tRNA synthetases catalyze amino acid activation for protein synthesis, some also act in pathways for inflammation, angiogenesis, and apoptosis. How multiple functions evolved and their relationship to the active site is not clear. Here structural modeling analysis, mutagenesis, and cell-based functional studies show that the potent angiostatic, natural fragment of human TrpRS associates via Trp side chains that protrude from the cognate cellular receptor VE-cadherin. Modeling indicates that (I prefer the way it was because the conclusion was reached not only by modeling, but more so by experimental studies.)VE-cadherin Trp side chains fit into the Trp-specific active site of the synthetase. Thus, specific side chains of the receptor mimic (?) amino acid substrates and expand the functionality of the active site of the synthetase. We propose that orthogonal use of the same active site may be a general way to develop multi-functionality of human tRNA synthetases and other proteins. PMID:20010843

  2. Response report from US Department of Energy Hearings on proposed salt site nominations

    International Nuclear Information System (INIS)

    1983-11-01

    As required by the Nuclear Waste Policy Act (US Congress, 1983, Pub. L. 97-425, Section 112(b) (2)), the US Department of Energy (DOE) conducted a series of nine formal public hearings during April and May 1983, in Louisiana, Mississippi, Texas, and Utah and in the state capitals of Mississippi, Texas, and Utah. The hearings were held in local communities in the vicinity of sites identified as potentially suitable for further study in the program to select a site for the nation's first repository for high-level nuclear waste. The public hearings for potential sites in salt focused on the proposed nomination of the Vacherie salt dome site in Louisiana; the Richton and Cypress Creek salt dome sites in Mississippi; the Deaf Smith County and Swisher County bedded salt sites in Texas; and the Davis and Lavender Canyon bedded salt sites in Utah. The oral and written comments made during the course of the nine formal public hearings were analyzed, paraphrased into almost 1100 comments, and grouped into 62 issues or subjects within the following nine major topical areas: National Waste Terminal Storage Program Planning Process, Consultation and Cooperation, Engineering/Repository Design, Geology, Hydrology, Transportation, Public Health and Safety, Environmental Quality, and Socioeconomics. This document provides general responses to each of the 62 major issues raised during the hearings. 137 references, 7 figures, 12 tables

  3. Response report from US Department of Energy hearings on proposed salt site nominations

    International Nuclear Information System (INIS)

    1983-11-01

    As required by the Nuclear Waste Policy Act (US Congress, 1983, Pub. L. 97-425, Section 112(b)(2)), the US Department of Energy (DOE) conducted a series of nine formal public hearings during April and May 1983, in Louisiana, Mississippi, Texas, and Utah and in the state capitals of Mississippi, Texas, and Utah. The hearings were held in local communities in the vicinity of sites identified as potentially suitable for further study in the program to select a site for the nation's first repository for high-level nuclear waste. The public hearings for potential sites in salt focused on the proposed nomination of the Vacherie salt dome site in Louisiana; the Richton and Cypress Creek salt dome sites in Mississippi; the Deaf Smith County and Swisher County bedded salt sites in Texas; and the Davis and Lavender Canyon bedded salt sites in Utah. The oral and written comments made during the course of the nine formal public hearings were analyzed, paraphrased into almost 1100 comments, and grouped into 62 issues or subjects within the following nine major topical areas: National Waste Terminal Storage program Planning Process, Consultation and Cooperation, Engineering/Repository Design, Geology, Hydrology, Transportation, Public Health and Safety, Environmental Quality, and Socioeconomics. This document provides general responses to each of the 62 major issues raised during the hearings

  4. Using a site-specific technical error to establish training responsiveness: a preliminary explorative study.

    Science.gov (United States)

    Weatherwax, Ryan M; Harris, Nigel K; Kilding, Andrew E; Dalleck, Lance C

    2018-01-01

    Even though cardiorespiratory fitness (CRF) training elicits numerous health benefits, not all individuals have positive training responses following a structured CRF intervention. It has been suggested that the technical error (TE), a combination of biological variability and measurement error, should be used to establish specific training responsiveness criteria to gain further insight on the effectiveness of the training program. To date, most training interventions use an absolute change or a TE from previous findings, which do not take into consideration the training site and equipment used to establish training outcomes or the specific cohort being evaluated. The purpose of this investigation was to retrospectively analyze training responsiveness of two CRF training interventions using two common criteria and a site-specific TE. Sixteen men and women completed two maximal graded exercise tests and verification bouts to identify maximal oxygen consumption (VO 2 max) and establish a site-specific TE. The TE was then used to retrospectively analyze training responsiveness in comparison to commonly used criteria: percent change of >0% and >+5.6% in VO 2 max. The TE was found to be 7.7% for relative VO 2 max. χ 2 testing showed significant differences in all training criteria for each intervention and pooled data from both interventions, except between %Δ >0 and %Δ >+7.7% in one of the investigations. Training nonresponsiveness ranged from 11.5% to 34.6%. Findings from the present study support the utility of site-specific TE criterion to quantify training responsiveness. A similar methodology of establishing a site-specific and even cohort specific TE should be considered to establish when true cardiorespiratory training adaptations occur.

  5. Characterisation of the zebrafish serotonin transporter functionally links TM10 to the ligand binding site

    DEFF Research Database (Denmark)

    Severinsen, Kasper; Müller, Heidi Kaastrup; Wiborg, Ove

    2008-01-01

    and [(3)H]-escitalopram binding in transiently transfected human embryonic kidney cells; HEK-293-MSR. Residues responsible for altered affinities inhibitors were pinpointed by generating cross-species chimeras and subsequent point mutations by site directed mutagenesis. drSERT has a higher affinity...

  6. Response spectra by blind faults for design purpose of stiff structures on rock site

    International Nuclear Information System (INIS)

    Hiroyuki Mizutani; Kenichi Kato; Masayuki Takemura; Kazuhiko Yashiro; Kazuo Dan

    2005-01-01

    The goal of this paper is to propose the response spectra by blind faults for seismic design of nuclear power facilities. It is impossible to evaluate earthquake ground motions from blind faults, because the size and the location of blind fault cannot be identified even if the detailed geological surveys are conducted. From the viewpoint of seismic design, it is crucial to investigate the upper level of earthquake ground motions due to blind faults. In this paper, 41 earthquakes that occurred in the upper crust in Japan and California are selected and classified into the active and the blind fault types. On the basis of near-source strong motion records observed on rock sites, upper level of response spectra by blind faults is examined. The estimated upper level is as follows: the peak ground acceleration is 450 cm/s 2 , the flat level of the acceleration response spectra is 1200 cm/s 2 , and the flat level of the velocity response spectra is 100 cm/s on rock sites with shear wave velocity Vs of about 700 m/s. The upper level can envelop the observed response spectra in near-source region on rock sites. (authors)

  7. Development of uniform hazard response spectra for rock sites considering line and point sources of earthquakes

    International Nuclear Information System (INIS)

    Ghosh, A.K.; Kushwaha, H.S.

    2001-12-01

    Traditionally, the seismic design basis ground motion has been specified by normalised response spectral shapes and peak ground acceleration (PGA). The mean recurrence interval (MRI) used to computed for PGA only. It is shown that the MRI associated with such response spectra are not the same at all frequencies. The present work develops uniform hazard response spectra i.e. spectra having the same MRI at all frequencies for line and point sources of earthquakes by using a large number of strong motion accelerograms recorded on rock sites. Sensitivity of the number of the results to the changes in various parameters has also been presented. This work is an extension of an earlier work for aerial sources of earthquakes. These results will help to determine the seismic hazard at a given site and the associated uncertainities. (author)

  8. Functional MRI of food-induced brain responses

    NARCIS (Netherlands)

    Smeets, P.A.M.

    2006-01-01

    The ultimate goal of this research was to find central biomarkers of satiety, i.e., physiological measures in the brain that relate to subjectively rated appetite, actual food intake, or both. This thesis describes the changes in brain activity in response to food stimuli as measured by functional

  9. Semiparametric Item Response Functions in the Context of Guessing

    Science.gov (United States)

    Falk, Carl F.; Cai, Li

    2016-01-01

    We present a logistic function of a monotonic polynomial with a lower asymptote, allowing additional flexibility beyond the three-parameter logistic model. We develop a maximum marginal likelihood-based approach to estimate the item parameters. The new item response model is demonstrated on math assessment data from a state, and a computationally…

  10. Fitting of transfer functions to frequency response measurements

    International Nuclear Information System (INIS)

    Moret, J.M.

    1994-12-01

    An algorithm for approximating a given complex frequency response with a rational function of two polynomials with real coefficients is presented, together with its extension to distributed parameter systems, the corresponding error analysis and its application to a real case. (author) 5 figs., 4 refs

  11. Functionalized mesoporous silica nanoparticles for stimuli-responsive and targeted

    Energy Technology Data Exchange (ETDEWEB)

    Knezevic, Nikola [Iowa State Univ., Ames, IA (United States)

    2009-12-15

    Construction of functional supramolecular nanoassemblies has attracted great deal of attention in recent years for their wide spectrum of practical applications. Mesoporous silica nanoparticles (MSN) in particular were shown to be effective scaffolds for the construction of drug carriers, sensors and catalysts. Herein, we describe the synthesis and characterization of stimuli-responsive, controlled release MSN-based assemblies for drug delivery.

  12. Response efficiency during functional communication training: effects of effort on response allocation.

    OpenAIRE

    Richman, D M; Wacker, D P; Winborn, L

    2001-01-01

    An analogue functional analysis revealed that the problem behavior of a young child with developmental delays was maintained by positive reinforcement. A concurrent-schedule procedure was then used to vary the amount of effort required to emit mands. Results suggested that response effort can be an important variable when developing effective functional communication training programs.

  13. Superfund tio videos: Set A. Overview of superfund, response activities and responsibilities, site discovery, notification, and evaluation. Part 1. Audio-Visual

    International Nuclear Information System (INIS)

    1990-01-01

    The videotape is divided into three sections. Section 1 discusses the development and framework of CERCLA and the Superfund Program and outlines the implementing rules that guide Superfund site cleanups. The Superfund response actions - remedial, removal, and enforcement - are reviewed. Section 2 outlines On-Scene Coordinator's (OSC) and Remedial Project Manager's (RPM) roles and responsibilities in Superfund removal, remedial, and enforcement activities. The other players involved in Superfund response activities also are identified. Section 3 describes how EPA learns of potential Superfund sites and lists the authorities that determine the requirements for site discovery. The procedures used to prioritize the sites and to identify and select sites for remediation are discussed

  14. Effect of uncertainty in VS-N correlations on seismic site response ...

    Indian Academy of Sciences (India)

    57

    2005-08-16

    Aug 16, 2005 ... Strong to weak ground. 34 ... VS and N values are related through a power law relationship: VS = 71 ... analysis. Some studies on the uncertainty of VS and nonlinear soil ... Variability in the input ground motions may sometimes affect the site ..... of amplification spectra which is basically the transfer function ...

  15. Analysis of ground response data at Lotung large-scale soil- structure interaction experiment site

    International Nuclear Information System (INIS)

    Chang, C.Y.; Mok, C.M.; Power, M.S.

    1991-12-01

    The Electric Power Research Institute (EPRI), in cooperation with the Taiwan Power Company (TPC), constructed two models (1/4-scale and 1/2-scale) of a nuclear plant containment structure at a site in Lotung (Tang, 1987), a seismically active region in northeast Taiwan. The models were constructed to gather data for the evaluation and validation of soil-structure interaction (SSI) analysis methodologies. Extensive instrumentation was deployed to record both structural and ground responses at the site during earthquakes. The experiment is generally referred to as the Lotung Large-Scale Seismic Test (LSST). As part of the LSST, two downhole arrays were installed at the site to record ground motions at depths as well as at the ground surface. Structural response and ground response have been recorded for a number of earthquakes (i.e. a total of 18 earthquakes in the period of October 1985 through November 1986) at the LSST site since the completion of the installation of the downhole instruments in October 1985. These data include those from earthquakes having magnitudes ranging from M L 4.5 to M L 7.0 and epicentral distances range from 4.7 km to 77.7 km. Peak ground surface accelerations range from 0.03 g to 0.21 g for the horizontal component and from 0.01 g to 0.20 g for the vertical component. The objectives of the study were: (1) to obtain empirical data on variations of earthquake ground motion with depth; (2) to examine field evidence of nonlinear soil response due to earthquake shaking and to determine the degree of soil nonlinearity; (3) to assess the ability of ground response analysis techniques including techniques to approximate nonlinear soil response to estimate ground motions due to earthquake shaking; and (4) to analyze earth pressures recorded beneath the basemat and on the side wall of the 1/4 scale model structure during selected earthquakes

  16. Stone tool function at the paleolithic sites of Starosele and Buran Kaya III, Crimea: behavioral implications.

    Science.gov (United States)

    Hardy, B L; Kay, M; Marks, A E; Monigal, K

    2001-09-11

    Stone tools are often the most abundant type of cultural remains at Paleolithic sites, yet their function is often poorly understood. Investigations of stone tool function, including microscopic use-wear and residue analyses, were performed on a sample of artifacts from the Paleolithic sites of Starosele (40,000-80,000 years BP) and Buran Kaya III (32,000-37,000 years BP). The Middle Paleolithic levels at Starosele exhibit a typical variant of the local Micoquian Industry. The artifacts from Buran Kaya III most closely resemble an Early Streletskayan Industry associated with the early Upper Paleolithic. The results of the functional analyses suggest that hominids at both sites were exploiting woody and starchy plant material as well as birds and mammals. Both sites show evidence of hafting of a wide variety of tools and the possible use of projectile or thrusting spears. These analyses were performed by using two different techniques conducted by independent researchers. Combined residue and use-wear analyses suggest that both the Upper Paleolithic and Middle Paleolithic hominids at these sites were broad-based foragers capable of exploiting a wide range of resources.

  17. Functional characterization of autophosphorylation sites of the activated insulin receptor-tyrosine kinase

    International Nuclear Information System (INIS)

    Flores-Riveros, J.R.; Lane, M.D.

    1987-01-01

    Insulin receptor, solubilized from 3T3-L1 cellular membranes and then purified, was autophosphorylated with [γ- 32 P]ATP in the absence or presence of insulin. Specific phosphopeptides generated by trypsin digestion of the 32 P-labeled β-subunit were identified and separated by reverse phase HPLC. In the absence of insulin, radioactivity of the phosphopeptides is evenly distributed among four major peaks designated as sites I, II, III and IV, according to their order of elution. This pattern is maintained for at least the first 30 min of autophosphorylation. When the reaction is carried out in the presence of insulin, > 50% of the total 32 P radioactivity is found in site I and the rate of 32 P incorporation into this site is markedly higher than into sites II, III and IV. Maximal activation of tyrosine kinase activity, as estimated by substrate phosphorylation, is coincident with the nearly complete phosphorylation of site I. Delayed activation of previously autophosphorylated receptor by insulin, but not by EGF or IGF-I, produced a similar pattern where phosphorylated site I predominates. These observations indicate that one major insulin-regulated autophosphorylation site in the β-subunit is responsible for activation of the insulin receptor tyrosine kinase. The isolation of this phosphopeptide on a preparative scale and its characterization are now in progress

  18. Conceptual DFT: the chemical relevance of higher response functions.

    Science.gov (United States)

    Geerlings, P; De Proft, F

    2008-06-07

    In recent years conceptual density functional theory offered a perspective for the interpretation/prediction of experimental/theoretical reactivity data on the basis of a series of response functions to perturbations in the number of electrons and/or external potential. This approach has enabled the sharp definition and computation, from first principles, of a series of well-known but sometimes vaguely defined chemical concepts such as electronegativity and hardness. In this contribution, a short overview of the shortcomings of the simplest, first order response functions is illustrated leading to a description of chemical bonding in a covalent interaction in terms of interacting atoms or groups, governed by electrostatics with the tendency to polarize bonds on the basis of electronegativity differences. The second order approach, well known until now, introduces the hardness/softness and Fukui function concepts related to polarizability and frontier MO theory, respectively. The introduction of polarizability/softness is also considered in a historical perspective in which polarizability was, with some exceptions, mainly put forward in non covalent interactions. A particular series of response functions, arising when the changes in the external potential are solely provoked by changes in nuclear configurations (the "R-analogues") are also systematically considered. The main part of the contribution is devoted to third order response functions which, at first sight, may be expected not to yield chemically significant information, as turns out to be for the hyperhardness. A counterexample is the dual descriptor and its R analogue, the initial hardness response, which turns out to yield a firm basis to regain the Woodward-Hoffmann rules for pericyclic reactions based on a density-only basis, i.e. without involving the phase, sign, symmetry of the wavefunction. Even the second order nonlinear response functions are shown possibly to bear interesting information, e

  19. Response functions for infinite fermion systems with velocity dependent interactions

    International Nuclear Information System (INIS)

    Garcia-Recio, C.; Salcedo, L.L.; Navarro, J.; Nguyen Van Giai

    1991-01-01

    Response functions of infinite Fermi systems are studied in the framework of the self-consistent Random Phase Approximation. Starting from an effective interaction with velocity and density dependence, or equivalently from a local energy density functional, algebraic expressions for the RPA response function are derived. Simple formulae for the energy-weighted and polarizability sum rules are obtained. The method is illustrated by applications to nuclear matter and liquid 3 He. In nuclear matter, it is shown that existing Skyrme interactions give spin-isospin response functions close to those calculated with finite range interactions. The different renormalization of longitudinal and transverse Coulomb sum rules in nuclear matter is discussed. In 3 He, the low-lying collective spin oscillation can be well described in a wide range of momenta with a Skyrme-type interaction if the relevant Landau parameters are fitted. For the high-lying density oscillation, the introduction of a finite range term in the energy functional improves considerably the agreement with the data. (author) 54 refs., 19 figs., 4 tabs

  20. Optimal hemodynamic response model for functional near-infrared spectroscopy

    Directory of Open Access Journals (Sweden)

    Muhammad Ahmad Kamran

    2015-06-01

    Full Text Available Functional near-infrared spectroscopy (fNIRS is an emerging non-invasive brain imaging technique and measures brain activities by means of near-infrared light of 650-950 nm wavelengths. The cortical hemodynamic response (HR differs in attributes at different brain regions and on repetition of trials, even if the experimental paradigm is kept exactly the same. Therefore, an HR model that can estimate such variations in the response is the objective of this research. The canonical hemodynamic response function (cHRF is modeled by using two Gamma functions with six unknown parameters. The HRF model is supposed to be linear combination of HRF, baseline and physiological noises (amplitudes and frequencies of physiological noises are supposed to be unknown. An objective function is developed as a square of the residuals with constraints on twelve free parameters. The formulated problem is solved by using an iterative optimization algorithm to estimate the unknown parameters in the model. Inter-subject variations in HRF and physiological noises have been estimated for better cortical functional maps. The accuracy of the algorithm has been verified using ten real and fifteen simulated data sets. Ten healthy subjects participated in the experiment and their HRF for finger-tapping tasks have been estimated and analyzed. The statistical significance of the estimated activity strength parameters has been verified by employing statistical analysis, i.e., (t-value >tcritical and p-value < 0.05.

  1. Low nucleosome occupancy is encoded around functional human transcription factor binding sites

    Directory of Open Access Journals (Sweden)

    Daenen Floris

    2008-07-01

    Full Text Available Abstract Background Transcriptional regulation of genes in eukaryotes is achieved by the interactions of multiple transcription factors with arrays of transcription factor binding sites (TFBSs on DNA and with each other. Identification of these TFBSs is an essential step in our understanding of gene regulatory networks, but computational prediction of TFBSs with either consensus or commonly used stochastic models such as Position-Specific Scoring Matrices (PSSMs results in an unacceptably high number of hits consisting of a few true functional binding sites and numerous false non-functional binding sites. This is due to the inability of the models to incorporate higher order properties of sequences including sequences surrounding TFBSs and influencing the positioning of nucleosomes and/or the interactions that might occur between transcription factors. Results Significant improvement can be expected through the development of a new framework for the modeling and prediction of TFBSs that considers explicitly these higher order sequence properties. It would be particularly interesting to include in the new modeling framework the information present in the nucleosome positioning sequences (NPSs surrounding TFBSs, as it can be hypothesized that genomes use this information to encode the formation of stable nucleosomes over non-functional sites, while functional sites have a more open chromatin configuration. In this report we evaluate the usefulness of the latter feature by comparing the nucleosome occupancy probabilities around experimentally verified human TFBSs with the nucleosome occupancy probabilities around false positive TFBSs and in random sequences. Conclusion We present evidence that nucleosome occupancy is remarkably lower around true functional human TFBSs as compared to non-functional human TFBSs, which supports the use of this feature to improve current TFBS prediction approaches in higher eukaryotes.

  2. UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures.

    Science.gov (United States)

    Lua, Rhonald C; Wilson, Stephen J; Konecki, Daniel M; Wilkins, Angela D; Venner, Eric; Morgan, Daniel H; Lichtarge, Olivier

    2016-01-04

    The structure and function of proteins underlie most aspects of biology and their mutational perturbations often cause disease. To identify the molecular determinants of function as well as targets for drugs, it is central to characterize the important residues and how they cluster to form functional sites. The Evolutionary Trace (ET) achieves this by ranking the functional and structural importance of the protein sequence positions. ET uses evolutionary distances to estimate functional distances and correlates genotype variations with those in the fitness phenotype. Thus, ET ranks are worse for sequence positions that vary among evolutionarily closer homologs but better for positions that vary mostly among distant homologs. This approach identifies functional determinants, predicts function, guides the mutational redesign of functional and allosteric specificity, and interprets the action of coding sequence variations in proteins, people and populations. Now, the UET database offers pre-computed ET analyses for the protein structure databank, and on-the-fly analysis of any protein sequence. A web interface retrieves ET rankings of sequence positions and maps results to a structure to identify functionally important regions. This UET database integrates several ways of viewing the results on the protein sequence or structure and can be found at http://mammoth.bcm.tmc.edu/uet/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. Do On-Site Mental Health Professionals Change Pediatricians' Responses to Children's Mental Health Problems?

    Science.gov (United States)

    McCue Horwitz, Sarah; Storfer-Isser, Amy; Kerker, Bonnie D; Szilagyi, Moira; Garner, Andrew S; O'Connor, Karen G; Hoagwood, Kimberly E; Green, Cori M; Foy, Jane M; Stein, Ruth E K

    2016-01-01

    To assess the availability of on-site mental health professionals (MHPs) in primary care; to examine practice/pediatrician characteristics associated with on-site MHPs; and to determine whether the presence of on-site MHPs is related to pediatricians' comanaging or more frequently identifying, treating/managing, or referring mental health (MH) problems. Analyses included American Academy of Pediatrics (AAP) members who participated in an AAP Periodic Survey in 2013 and who practiced general pediatrics (n = 321). Measures included sociodemographics, practice characteristics, questions about on-site MHPs, comanagement of MH problems, and pediatricians' behaviors in response to 5 prevalent MH problems. Weighted univariate, bivariate, and multivariable analyses were performed. Thirty-five percent reported on-site MHPs. Practice characteristics (medical schools, universities, health maintenance organizations, managed, or referred 5 common child MH problems. Among the subset of pediatricians who reported comanaging, there was an association with comanagement when the on-site MHP was a child psychiatrist, substance abuse counselor, or social worker. On-site MHPs are more frequent in settings where low-income children are served and where pediatricians train. Pediatricians who comanage MH problems are more likely to do so when the on-site MHP is a child psychiatrist, substance abuse counselor, or social worker. Overall, on-site MHPs were not associated with comanagement or increased likelihood of pediatricians identifying, treating/managing, or referring children with 5 common child MH problems. Copyright © 2016 Academic Pediatric Association. Published by Elsevier Inc. All rights reserved.

  4. Limitation and applicability of microtremor records for site-response estimation

    Science.gov (United States)

    Song, G.; Kang, T.; Park, S.

    2010-12-01

    Site effects are the modifications of seismic motions which are traveling through near-surface materials. The impedance contrast between the topmost layer and bedrock may significantly amplify ground motions and augment their durations. Inelastic behavior of the geological media such as highly fractured/weathered rocks and unconsolidated sediments may absorb seismic energy, and thus damp the resulting ground motions. It is inherently most desirable to evaluate the site effects using seismic records from large earthquakes. If there are only small events that will be recorded by several seismograph stations, it becomes difficult to evaluate site effects using earthquake data. Recently a number of studies pay attention to microtremor records to assess site effects. The main reason of such efforts is that measurements are relatively easy regardless of site condition and cost-effective without necessity of waiting for earthquakes or of using active sources. Especially microtremor measurements are exclusively a useful option to assess site effects, and thus seismic microzonation, in the urban area and/or region of low to moderate seismicity. Spectral ratios of horizontal components to vertical component (HVSR) of microtremor records have been popular for estimation of site resonant frequency. Although some studies have shown that the amplitude of spectral ratios is an indicator of site amplification relative to bedrock motion, there are still debates on it. This discrepancy may originate from the deficiency of our understanding on the nature of microtremor. Therefore, it is important to understand the limitation and applicability of microtremor records for site-effect assessments. The focus on this problem is how microtremor responses on the subsurface structures and their physical properties, and how parameters deduced from microtremor analyses are related to site responses during earthquake ground motions. In order to investigate how these issues have a practical

  5. Site-selective three-component reaction for dual-functionalization of peptides

    DEFF Research Database (Denmark)

    Munch, Henrik Kofoed; Rasmussen, Jakob Ewald; Popa, Gina

    2013-01-01

    A site-selective dual-functionalization of peptides is presented, involving readily available maleimides as well as N-hydroxylamines. The modification proceeds through a three component 1,3-dipolar cycloaddition, forming a stable product. This was exemplified by the one-pot attachment of two...

  6. Probing dopamine transporter structure and function by Zn2+-site engineering

    DEFF Research Database (Denmark)

    Loland, Claus Juul; Norgaard-Nielsen, Kristine; Gether, Ulrik

    2003-01-01

    , it will be described how we have used Zn2+-binding sites as a tool to probe the structure and function of Na+/Cl--coupled biogenic amine transporters with specific focus on the human DAT (hDAT). The work has not only led to the definition of the first structural constrains in the tertiary structure of this class...

  7. Stimulus-response functions of single avian olfactory bulb neurones.

    Science.gov (United States)

    McKeegan, Dorothy E F; Demmers, Theodorus G M; Wathes, Christopher M; Jones, R Bryan; Gentle, Michael J

    2002-10-25

    This study investigated olfactory processing in a functional context by examining the responses of single avian olfactory bulb neurones to two biologically important gases over relevant concentration ranges. Recordings of extracellular spike activity were made from 80 single units in the left olfactory bulb of 11 anaesthetised, freely breathing adult hens (Gallus domesticus). The units were spontaneously active, exhibiting widely variable firing rates (0.07-47.28 spikes/s) and variable temporal firing patterns. Single units were tested for their response to an ascending concentration series of either ammonia (2.5-100 ppm) or hydrogen sulphide (1-50 ppm), delivered directly to the olfactory epithelium. Stimulation with a calibrated gas delivery system resulted in modification of spontaneous activity causing either inhibition (47% of units) or excitation (53%) of firing. For ammonia, 20 of the 35 units tested exhibited a response, while for hydrogen sulphide, 25 of the 45 units tested were responsive. Approximate response thresholds for ammonia (median threshold 3.75 ppm (range 2.5-60 ppm, n=20)) and hydrogen sulphide (median threshold 1 ppm (range 1-10 ppm, n=25)) were determined with most units exhibiting thresholds near the lower end of these ranges. Stimulus response curves were constructed for 23 units; 16 (the most complete) were subjected to a linear regression analysis to determine whether they were best fitted by a linear, log or power function. No single function provided the best fit for all the curves (seven were linear, eight were log, one was power). These findings show that avian units respond to changes in stimulus concentration in a manner generally consistent with reported responses in mammalian olfactory bulb neurones. However, this study illustrates a level of fine-tuning to small step changes in concentration (<5 ppm) not previously demonstrated in vertebrate single olfactory bulb neurones.

  8. Design basis of off-site emergency response plans for fuel cycle installations

    International Nuclear Information System (INIS)

    Rzepka, J.P.; Dubiau, Ph.; Jouve, A.C.; Charles, T.; Mercier, J.P.

    1995-01-01

    In France, the term 'off-site emergency response plan' refers to all the arrangements which should be made by the government authorities to protect the population in the event of an accident affecting the installations of the site considered. The outline of the method of defining typical accidents, evaluation of 'source-terms' and health consequences is presented. Two applications to installations from the front-end and from the back-end of the fuel cycle are discussed. (K.A.). 1 tab

  9. Taxonomic and functional diversity provides insight into microbial pathways and stress responses in the saline Qinghai Lake, China.

    Directory of Open Access Journals (Sweden)

    Qiuyuan Huang

    Full Text Available Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m saline (1.4% lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E. Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change.

  10. Ambient Vibrations Measurements and 1D Site Response Modelling as a Tool for Soil and Building Properties Investigation

    Directory of Open Access Journals (Sweden)

    Sebastiano Imposa

    2018-03-01

    Full Text Available The safety of historic buildings heritage is an important task that becomes more substantial when the buildings are directed to educational purposes. The present study aims at evaluating the dynamic features of the Benedettini complex, an historic monastery located in downtown Catania, which is at present the headquarters of the humanistic studies department of the University of Catania. Both the building’s complex response to a seismic input and the soil-to-structure interaction were investigated using ambient noise recordings. The results point out a multiple dynamic behaviour of the monastery structure that shows several oscillation modes, whereas the identification of a single natural frequency can be observed in some sites where the structure can more freely oscillate. This observation is also confirmed by the variability of computed damping values that appear linked to the different rigidity of the structure, as a function of the either the longitudinal or transversal orientation of the investigated structural elements. Moreover, the comparison between the building’s fundamental period and spectral ratios frequencies, which were obtained from free field ambient noise measurements located outside the monastery, outline the presence of potential resonance effects between the site and structure during a seismic event. Numerical modelling of the local seismic response confirms the obtained experimental site frequencies, setting into evidence that higher amplification factors are reached in the same frequency range characterizing the building.

  11. Aging and response conflict solution: behavioural and functional connectivity changes.

    Science.gov (United States)

    Langner, Robert; Cieslik, Edna C; Behrwind, Simone D; Roski, Christian; Caspers, Svenja; Amunts, Katrin; Eickhoff, Simon B

    2015-01-01

    Healthy aging has been found associated with less efficient response conflict solution, but the cognitive and neural mechanisms have remained elusive. In a two-experiment study, we first examined the behavioural consequences of this putative age-related decline for conflicts induced by spatial stimulus-response incompatibility. We then used resting-state functional magnetic resonance imaging data from a large, independent sample of adults (n = 399; 18-85 years) to investigate age differences in functional connectivity between the nodes of a network previously found associated with incompatibility-induced response conflicts in the very same paradigm. As expected, overcoming interference from conflicting response tendencies took longer in older adults, even after accounting for potential mediator variables (general response speed and accuracy, motor speed, visuomotor coordination ability, and cognitive flexibility). Experiment 2 revealed selective age-related decreases in functional connectivity between bilateral anterior insula, pre-supplementary motor area, and right dorsolateral prefrontal cortex. Importantly, these age effects persisted after controlling for regional grey-matter atrophy assessed by voxel-based morphometry. Meta-analytic functional profiling using the BrainMap database showed these age-sensitive nodes to be more strongly linked to highly abstract cognition, as compared with the remaining network nodes, which were more strongly linked to action-related processing. These findings indicate changes in interregional coupling with age among task-relevant network nodes that are not specifically associated with conflict resolution per se. Rather, our behavioural and neural data jointly suggest that healthy aging is associated with difficulties in properly activating non-dominant but relevant task schemata necessary to exert efficient cognitive control over action.

  12. Development of the Parent Responses to School Functioning Questionnaire.

    Science.gov (United States)

    Barber Garcia, Brittany N; Gray, Laura S; Simons, Laura E; Logan, Deirdre E

    2017-10-01

    Parents play an important role in supporting school functioning in youth with chronic pain, but no validated tools exists to assess parental responses to child and adolescent pain behaviors in the school context. Such a tool would be useful in identifying targets of change to reduce pain-related school impairment. The goal of this study was to develop and preliminarily validate the Parent Responses to School Functioning Questionnaire (PRSF), a parent self-report measure of this construct. After initial expert review and pilot testing, the measure was administered to 418 parents of children (ages 6-17 years) seen for initial multidisciplinary chronic pain clinic evaluation. The final 16-item PRSF showed evidence of good internal consistency (α = .82) and 2-week test-retest reliability (intraclass correlation coefficient = .87). Criterion validity was demonstrated by significant correlations with school absence rates and overall school functioning, and construct validity was demonstrated by correlations with general parental responses to pain. Three subscales emerged capturing parents' personal distress, parents' level of distrust of the school, and parents' expectations and behaviors related to their child's management of challenging school situations. These results provide preliminary support for the PRSF as a psychometrically sound tool to assess parents' responses to child pain in the school setting. The 16-item PRSF measures parental responses to their child's chronic pain in the school context. The clinically useful measure can inform interventions aimed reducing functional disability in children with chronic pain by enhancing parents' ability to respond adaptively to child pain behaviors. Copyright © 2017 American Pain Society. Published by Elsevier Inc. All rights reserved.

  13. Better estimation of protein-DNA interaction parameters improve prediction of functional sites

    Directory of Open Access Journals (Sweden)

    O'Flanagan Ruadhan A

    2008-12-01

    Full Text Available Abstract Background Characterizing transcription factor binding motifs is a common bioinformatics task. For transcription factors with variable binding sites, we need to get many suboptimal binding sites in our training dataset to get accurate estimates of free energy penalties for deviating from the consensus DNA sequence. One procedure to do that involves a modified SELEX (Systematic Evolution of Ligands by Exponential Enrichment method designed to produce many such sequences. Results We analyzed low stringency SELEX data for E. coli Catabolic Activator Protein (CAP, and we show here that appropriate quantitative analysis improves our ability to predict in vitro affinity. To obtain large number of sequences required for this analysis we used a SELEX SAGE protocol developed by Roulet et al. The sequences obtained from here were subjected to bioinformatic analysis. The resulting bioinformatic model characterizes the sequence specificity of the protein more accurately than those sequence specificities predicted from previous analysis just by using a few known binding sites available in the literature. The consequences of this increase in accuracy for prediction of in vivo binding sites (and especially functional ones in the E. coli genome are also discussed. We measured the dissociation constants of several putative CAP binding sites by EMSA (Electrophoretic Mobility Shift Assay and compared the affinities to the bioinformatics scores provided by methods like the weight matrix method and QPMEME (Quadratic Programming Method of Energy Matrix Estimation trained on known binding sites as well as on the new sites from SELEX SAGE data. We also checked predicted genome sites for conservation in the related species S. typhimurium. We found that bioinformatics scores based on SELEX SAGE data does better in terms of prediction of physical binding energies as well as in detecting functional sites. Conclusion We think that training binding site detection

  14. Ecosystem functional response across precipitation extremes in a sagebrush steppe.

    Science.gov (United States)

    Tredennick, Andrew T; Kleinhesselink, Andrew R; Taylor, J Bret; Adler, Peter B

    2018-01-01

    Precipitation is predicted to become more variable in the western United States, meaning years of above and below average precipitation will become more common. Periods of extreme precipitation are major drivers of interannual variability in ecosystem functioning in water limited communities, but how ecosystems respond to these extremes over the long-term may shift with precipitation means and variances. Long-term changes in ecosystem functional response could reflect compensatory changes in species composition or species reaching physiological thresholds at extreme precipitation levels. We conducted a five year precipitation manipulation experiment in a sagebrush steppe ecosystem in Idaho, United States. We used drought and irrigation treatments (approximately 50% decrease/increase) to investigate whether ecosystem functional response remains consistent under sustained high or low precipitation. We recorded data on aboveground net primary productivity (ANPP), species abundance, and soil moisture. We fit a generalized linear mixed effects model to determine if the relationship between ANPP and soil moisture differed among treatments. We used nonmetric multidimensional scaling to quantify community composition over the five years. Ecosystem functional response, defined as the relationship between soil moisture and ANPP, was similar among irrigation and control treatments, but the drought treatment had a greater slope than the control treatment. However, all estimates for the effect of soil moisture on ANPP overlapped zero, indicating the relationship is weak and uncertain regardless of treatment. There was also large spatial variation in ANPP within-years, which contributes to the uncertainty of the soil moisture effect. Plant community composition was remarkably stable over the course of the experiment and did not differ among treatments. Despite some evidence that ecosystem functional response became more sensitive under sustained drought conditions, the response

  15. Development of a Online Nuclear Emergency Response System (ONERS) for Kalpakkam site - the design aspects

    Energy Technology Data Exchange (ETDEWEB)

    Raja Shekhar, S. S.; Bhatawadekar, Shantanu; Krishna Murthy, Y. V.N., [Regional Remote Sensing Service Centre, Department of Space, Nagpur (India); Srinivas, C. V.; Venkatesan, [Radiological Safety Division, Radiological Safety and Environmental Group, Indira Gandhi Centre for Atomic Research, Kalapakkam (India)

    2012-07-01

    An Online Nuclear Emergency Response System (ONERS) is developed for the nuclear power plant site at Kalpakkam as part of the Department of Atomic Energy (DAE) initiative. ONERS is a GIS based spatial analysis system designed indigenously to provide decision support in the event of a radioactive leak or accident from any of the nuclear facilities by assessing the dispersion and deposition patterns of the atmospheric releases, integrate with spatial geographical database for impact assessment and guidance for mitigation. The system is designed with open software tools (UMN Map server, MYSQL, PHP, Java scripts) and its main features include assessment of dose, short and long term forecast, counter measure support, impact assessment to minimize potential threat to man and environment during radiological emergencies. The system is implemented in live mode with integration of numerical models and spatial data base for the site region and is presently operational for the Kalpakkam site. (author)

  16. Development of a Online Nuclear Emergency Response System (ONERS) for Kalpakkam site - the design aspects

    International Nuclear Information System (INIS)

    Raja Shekhar, S.S.; Bhatawadekar, Shantanu; Krishna Murthy, Y.V.N.; Srinivas, C.V.; Venkatesan

    2012-01-01

    An Online Nuclear Emergency Response System (ONERS) is developed for the nuclear power plant site at Kalpakkam as part of the Department of Atomic Energy (DAE) initiative. ONERS is a GIS based spatial analysis system designed indigenously to provide decision support in the event of a radioactive leak or accident from any of the nuclear facilities by assessing the dispersion and deposition patterns of the atmospheric releases, integrate with spatial geographical database for impact assessment and guidance for mitigation. The system is designed with open software tools (UMN Map server, MYSQL, PHP, Java scripts) and its main features include assessment of dose, short and long term forecast, counter measure support, impact assessment to minimize potential threat to man and environment during radiological emergencies. The system is implemented in live mode with integration of numerical models and spatial data base for the site region and is presently operational for the Kalpakkam site. (author)

  17. The Ironbridge Gorge Heritage Site and its local and regional functions

    Directory of Open Access Journals (Sweden)

    Cudny Waldemar

    2017-06-01

    Full Text Available The article is devoted to the issue of heritage and its functions. Based on the existing literature, the author presents the definition of heritage, the classification of heritage resources, and its most important impacts. The aim of the article was to show the functions that may be performed by a heritage site, locally and regionally. The example used by the author is the Ironbridge Gorge Heritage Site in the United Kingdom. Most heritage functions described by other authors are confirmed in this case study. The cultural heritage of the Ironbridge Gorge creates an opportunity to undertake various local and regional activities, having first of all an educational influence on the inhabitants, school youth and tourists. We must not ignore the economicinfluences, such as financing the activity of the Ironbridge Trust (the institution administering the site, generating income for local firms providing service to tourists, or for construction companies. This income helps to preserve and conserve the tangible heritage of the Ironbridge Gorge, as well as to generate jobs in heritage management, conservation and heritage tourism. Other effects of the Ironbridge Gorge Site include a socio-cultural impact or that related to sustainable development.

  18. Development of uniform hazard response spectra from accelerograms recorded on rock sites

    International Nuclear Information System (INIS)

    Ghosh, A.K.; Kushwaha, H.S.

    2000-05-01

    Traditionally, the seismic design basis ground motion has been specified by response spectral shapes and the peak ground acceleration (PGA). The mean recurrence interval (MRI) is evaluated for PGA only. The present work has developed response spectra having the same MRI at all frequencies. This report extends the work of Cornell (on PGA) to consider an aerial source model and a general form of the spectral acceleration at various frequencies. The latter has been derived from a number of strong motion earthquake recorded on rock sites. Sensitivity of the results to the changes in various parameters has also been presented. These results will help to determine the seismic hazard at a given site and the associated uncertainties. (author)

  19. Executing application function calls in response to an interrupt

    Science.gov (United States)

    Almasi, Gheorghe; Archer, Charles J.; Giampapa, Mark E.; Gooding, Thomas M.; Heidelberger, Philip; Parker, Jeffrey J.

    2010-05-11

    Executing application function calls in response to an interrupt including creating a thread; receiving an interrupt having an interrupt type; determining whether a value of a semaphore represents that interrupts are disabled; if the value of the semaphore represents that interrupts are not disabled: calling, by the thread, one or more preconfigured functions in dependence upon the interrupt type of the interrupt; yielding the thread; and if the value of the semaphore represents that interrupts are disabled: setting the value of the semaphore to represent to a kernel that interrupts are hard-disabled; and hard-disabling interrupts at the kernel.

  20. Three-dimensional site response at KiK-net downhole arrays

    Science.gov (United States)

    Thompson, Eric M.; Tanaka, Yasuo; Baise, Laurie G.; Kayen, Robert E.

    2010-01-01

    Ground motions at two Kiban-Kyoshin Network (KiK-net) strong motion downhole array sites in Hokkaido, Japan (TKCH08 in Taiki and TKCH05 in Honbetsu) illustrate the importance of three-dimensional (3D) site effects. These sites recorded the M8.0 2003 Tokachi-Oki earthquake, with recorded accelerations above 0.4 g at both sites as well as numerous ground motions from smaller events. Weak ground motions indicate that site TKCH08 is well modeled with the assumption of plane SH waves traveling through a 1D medium (SH1D), while TKCH05 is characteristic of a poor fit to the SH1D theoretical response. We hypothesized that the misfit at TKCH05results from the heterogeneity of the subsurface. To test this hypothesis, we measured four S-wave velocity profiles in the vicinity (KiK-net site pair is ideal for assessing the relative importance of 3D site effects and nonlinear site effects. The linear ground motions at TKCH05 isolate the 3D site effects, as we hypothesized from the linear ground motions and confirmed with our subsequent SASW surveys. The Tokachi-Oki time history at TKCH08 isolates the effects of nonlinearity from spatial heterogeneity because the 3D effects are negligible. The Tokachi-Oki time history at TKCH05 includes both nonlinear and 3D site effects. Comparisons of the accuracy of the SH1D model predictions of these surface time histories from the downhole time histories indicates that the 3D site effects are at least as important as nonlinear effects in this case. The errors associated with the assumption of a 1D medium and 1D wave propagation will be carried into a nonlinear analysis that relies on these same assumptions. Thus, the presence of 3D effects should be ruled out prior to a 1D nonlinear analysis. The SH1D residuals show that 3D effects can be mistaken for nonlinear effects.

  1. SAVANNAH RIVER SITE CAPABILITIES FOR CONDUCTING INGESTION PATHWAY CONSEQUENCE ASSESSMENTS FOR EMERGENCY RESPONSE

    Energy Technology Data Exchange (ETDEWEB)

    Hunter, C

    2007-12-11

    Potential airborne releases of radioactivity from facilities operated for the U. S. Department of Energy at the Savannah River Site could pose significant consequences to the public through the ingestion pathway. The Savannah River National Laboratory has developed a suite of technologies needed to conduct assessments of ingestion dose during emergency response, enabling emergency manager at SRS to develop initial protective action recommendation for state agencies early in the response and to make informed decisions on activation of additional Federal assets that would be needed to support long-term monitoring and assessment activities.

  2. Estimations of On-site Directional Wave Spectra from Measured Ship Responses

    DEFF Research Database (Denmark)

    Nielsen, Ulrik Dam

    2006-01-01

    include an quivalence of energy in the governing equations and, as regards the parametric concept, a frequency dependent spreading of the waves is introduced. The paper includes an extensive analysis of full-scale measurements for which the directional wave spectra are estimated by the two ship response......In general, two main concepts can be applied to estimate the on-site directional wave spectrum on the basis of ship response measurements: 1) a parametric method which assumes the wave spectrum to be composed by parameterised wave spectra, or 2) a non-parametric method where the directional wave...

  3. BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server

    Directory of Open Access Journals (Sweden)

    Jiang Hualiang

    2010-01-01

    Full Text Available Abstract Background Genome sequencing and post-genomics projects such as structural genomics are extending the frontier of the study of sequence-structure-function relationship of genes and their products. Although many sequence/structure-based methods have been devised with the aim of deciphering this delicate relationship, there still remain large gaps in this fundamental problem, which continuously drives researchers to develop novel methods to extract relevant information from sequences and structures and to infer the functions of newly identified genes by genomics technology. Results Here we present an ultrafast method, named BSSF(Binding Site Similarity & Function, which enables researchers to conduct similarity searches in a comprehensive three-dimensional binding site database extracted from PDB structures. This method utilizes a fingerprint representation of the binding site and a validated statistical Z-score function scheme to judge the similarity between the query and database items, even if their similarities are only constrained in a sub-pocket. This fingerprint based similarity measurement was also validated on a known binding site dataset by comparing with geometric hashing, which is a standard 3D similarity method. The comparison clearly demonstrated the utility of this ultrafast method. After conducting the database searching, the hit list is further analyzed to provide basic statistical information about the occurrences of Gene Ontology terms and Enzyme Commission numbers, which may benefit researchers by helping them to design further experiments to study the query proteins. Conclusions This ultrafast web-based system will not only help researchers interested in drug design and structural genomics to identify similar binding sites, but also assist them by providing further analysis of hit list from database searching.

  4. Invertebrate succession on open coast coal post mining sites in response to the type of restoration

    OpenAIRE

    Hromádková, Šárka

    2014-01-01

    This review deals with development of invertebrates on sites after brown coal mining in response to the type of restoration. When the soil properties are improved, it is then necessary to mitigate negative threats such as landslides and erosion or low pH. The following is an overlap of fertile soil. Soil characteristics can be locally modified by diversifying of plantations of fast and slow growing wood species. After a succession of plants and the subsequent increase in litter layer, the dev...

  5. Biological response to purification and acid functionalization of carbon nanotubes

    Science.gov (United States)

    Figarol, Agathe; Pourchez, Jérémie; Boudard, Delphine; Forest, Valérie; Tulliani, Jean-Marc; Lecompte, Jean-Pierre; Cottier, Michèle; Bernache-Assollant, Didier; Grosseau, Philippe

    2014-07-01

    Acid functionalization has been considered as an easy way to enhance the dispersion and biodegradation of carbon nanotubes (CNT). However, inconsistencies between toxicity studies of acid functionalized CNT remain unexplained. This could be due to a joint effect of the main physicochemical modifications resulting from an acid functionalization: addition of surface acid groups and purification from catalytic metallic impurities. In this study, the impact on CNT biotoxicity of these two physiochemical features was assessed separately. The in vitro biological response of RAW 264.7 macrophages was evaluated after exposure to 15-240 µg mL-1 of two types of multi-walled CNT. For each type of CNT (small: 20 nm diameter, and big: 90 nm diameter), three different surface chemical properties were studied (total of six CNT samples): pristine, acid functionalized and desorbed. Desorbed CNT were purified by the acid functionalization but presented a very low amount of surface acid groups due to a thermal treatment under vacuum. A Janus effect of acid functionalization with two opposite impacts is highlighted. The CNT purification decreased the overall toxicity, while the surface acid groups intensified it when present at a specific threshold. These acid groups especially amplified the pro-inflammatory response. The threshold mechanism which seemed to regulate the impact of acid groups should be further studied to determine its value and potential link to the other physicochemical state of the CNT. The results suggest that, for a safer-design approach, the benefit-risk balance of an acid functionalization has to be considered, depending on the CNT primary state of purification. Further research should be conducted in this direction.

  6. Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins

    Science.gov (United States)

    Kinjo, Akira R.; Nakamura, Haruki

    2012-01-01

    Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures. PMID:22347478

  7. Structure-based Markov random field model for representing evolutionary constraints on functional sites.

    Science.gov (United States)

    Jeong, Chan-Seok; Kim, Dongsup

    2016-02-24

    Elucidating the cooperative mechanism of interconnected residues is an important component toward understanding the biological function of a protein. Coevolution analysis has been developed to model the coevolutionary information reflecting structural and functional constraints. Recently, several methods have been developed based on a probabilistic graphical model called the Markov random field (MRF), which have led to significant improvements for coevolution analysis; however, thus far, the performance of these models has mainly been assessed by focusing on the aspect of protein structure. In this study, we built an MRF model whose graphical topology is determined by the residue proximity in the protein structure, and derived a novel positional coevolution estimate utilizing the node weight of the MRF model. This structure-based MRF method was evaluated for three data sets, each of which annotates catalytic site, allosteric site, and comprehensively determined functional site information. We demonstrate that the structure-based MRF architecture can encode the evolutionary information associated with biological function. Furthermore, we show that the node weight can more accurately represent positional coevolution information compared to the edge weight. Lastly, we demonstrate that the structure-based MRF model can be reliably built with only a few aligned sequences in linear time. The results show that adoption of a structure-based architecture could be an acceptable approximation for coevolution modeling with efficient computation complexity.

  8. Response function of spin-isospin nuclear excitations

    International Nuclear Information System (INIS)

    Salvetti, A.R.

    1986-01-01

    The selected aspects of spin-isospir nuclear excitations are studied. The spreading width of M/ states in even Ca isotopes for the purpose of trying to understand the missing strenght specially in 44 Ca, was estimated. The doorway calculation, was used, considering the level of complexity next to the independent particle M/ state. Using a nuclear matter context, the system response function to a spin-isospin probe and verify how the response function behaves for free fermions and in the ring approximation was studied. Higher correlations to polarization propagation such as the induced interaction and self-energy corrections was introduced. The dopping of colletive effects by such collisions terms was verified. It was investigate how to estimate the short range term of the effective interaction in the spin-isospin channel and the possibility of detecting a difference between these short range terms in the longitudinal and the transverse channel, for understanding the absence of pior condensation precursor states and negative results in a recent attempt to detect differences between longitudinal and transverse response functions one naively expects theoretically. (author) [pt

  9. Optimal hemodynamic response model for functional near-infrared spectroscopy.

    Science.gov (United States)

    Kamran, Muhammad A; Jeong, Myung Yung; Mannan, Malik M N

    2015-01-01

    Functional near-infrared spectroscopy (fNIRS) is an emerging non-invasive brain imaging technique and measures brain activities by means of near-infrared light of 650-950 nm wavelengths. The cortical hemodynamic response (HR) differs in attributes at different brain regions and on repetition of trials, even if the experimental paradigm is kept exactly the same. Therefore, an HR model that can estimate such variations in the response is the objective of this research. The canonical hemodynamic response function (cHRF) is modeled by two Gamma functions with six unknown parameters (four of them to model the shape and other two to scale and baseline respectively). The HRF model is supposed to be a linear combination of HRF, baseline, and physiological noises (amplitudes and frequencies of physiological noises are supposed to be unknown). An objective function is developed as a square of the residuals with constraints on 12 free parameters. The formulated problem is solved by using an iterative optimization algorithm to estimate the unknown parameters in the model. Inter-subject variations in HRF and physiological noises have been estimated for better cortical functional maps. The accuracy of the algorithm has been verified using 10 real and 15 simulated data sets. Ten healthy subjects participated in the experiment and their HRF for finger-tapping tasks have been estimated and analyzed. The statistical significance of the estimated activity strength parameters has been verified by employing statistical analysis (i.e., t-value > t critical and p-value < 0.05).

  10. Dual and multi-stimuli responsive polymeric nanoparticles for programmed site-specific drug delivery.

    Science.gov (United States)

    Cheng, Ru; Meng, Fenghua; Deng, Chao; Klok, Harm-Anton; Zhong, Zhiyuan

    2013-05-01

    In the past decades, polymeric nanoparticles have emerged as a most promising and viable technology platform for targeted and controlled drug delivery. As vehicles, ideal nanoparticles are obliged to possess high drug loading levels, deliver drug to the specific pathological site and/or target cells without drug leakage on the way, while rapidly unload drug at the site of action. To this end, various "intelligent" polymeric nanoparticles that release drugs in response to an internal or external stimulus such as pH, redox, temperature, magnetic and light have been actively pursued. These stimuli-responsive nanoparticles have demonstrated, though to varying degrees, improved in vitro and/or in vivo drug release profiles. In an effort to further improve drug release performances, novel dual and multi-stimuli responsive polymeric nanoparticles that respond to a combination of two or more signals such as pH/temperature, pH/redox, pH/magnetic field, temperature/reduction, double pH, pH and diols, temperature/magnetic field, temperature/enzyme, temperature/pH/redox, temperature/pH/magnetic, pH/redox/magnetic, temperature/redox/guest molecules, and temperature/pH/guest molecules have recently been developed. Notably, these combined responses take place either simultaneously at the pathological site or in a sequential manner from nanoparticle preparation, nanoparticle transporting pathways, to cellular compartments. These dual and multi-stimuli responsive polymeric nanoparticles have shown unprecedented control over drug delivery and release leading to superior in vitro and/or in vivo anti-cancer efficacy. With programmed site-specific drug delivery feature, dual and multi-stimuli responsive nanoparticulate drug formulations have tremendous potential for targeted cancer therapy. In this review paper, we highlight the recent exciting developments in dual and multi-stimuli responsive polymeric nanoparticles for precision drug delivery applications, with a particular focus

  11. Functional diversity of benthic ciliate communities in response to environmental gradients in a wetland of Yangtze Estuary, China.

    Science.gov (United States)

    Xu, Yuan; Fan, Xinpeng; Warren, Alan; Zhang, Liquan; Xu, Henglong

    2018-02-01

    Researches on the functional diversity of benthic ecosystems have mainly focused on macrofauna, and studies on functional structure of ciliate communities have been based only on trophic- or size-groups. Current research was carried out on the changing patterns of classical and functional diversity of benthic ciliates in response to environmental gradients at three sites in a wetland in Yangtze Estuary. The results showed that changes of environmental factors (e.g. salinity, sediment grain size and hydrodynamic conditions) in the Yangtze Estuary induce variability in species composition and functional trait distribution. Furthermore, increased species richness and diversity did not lead to significant changes in functional diversity due to functional redundancy. However, salt water intrusion of Yangtze Estuary during the dry season could cause reduced functional diversity of ciliate communities. Current study provides the first insight into the functional diversity of ciliate communities in response to environmental gradients. Copyright © 2018 Elsevier Ltd. All rights reserved.

  12. Identification of Key Functional Residues in the Active Site of Human β1,4-Galactosyltransferase 7

    Science.gov (United States)

    Talhaoui, Ibtissam; Bui, Catherine; Oriol, Rafael; Mulliert, Guillermo; Gulberti, Sandrine; Netter, Patrick; Coughtrie, Michael W. H.; Ouzzine, Mohamed; Fournel-Gigleux, Sylvie

    2010-01-01

    Glycosaminoglycans (GAGs) play a central role in many pathophysiological events, and exogenous xyloside substrates of β1,4-galactosyltransferase 7 (β4GalT7), a major enzyme of GAG biosynthesis, have interesting biomedical applications. To predict functional peptide regions important for substrate binding and activity of human β4GalT7, we conducted a phylogenetic analysis of the β1,4-galactosyltransferase family and generated a molecular model using the x-ray structure of Drosophila β4GalT7-UDP as template. Two evolutionary conserved motifs, 163DVD165 and 221FWGWGREDDE230, are central in the organization of the enzyme active site. This model was challenged by systematic engineering of point mutations, combined with in vitro and ex vivo functional assays. Investigation of the kinetic properties of purified recombinant wild-type β4GalT7 and selected mutants identified Trp224 as a key residue governing both donor and acceptor substrate binding. Our results also suggested the involvement of the canonical carboxylate residue Asp228 acting as general base in the reaction catalyzed by human β4GalT7. Importantly, ex vivo functional tests demonstrated that regulation of GAG synthesis is highly responsive to modification of these key active site amino acids. Interestingly, engineering mutants at position 224 allowed us to modify the affinity and to modulate the specificity of human β4GalT7 toward UDP-sugars and xyloside acceptors. Furthermore, the W224H mutant was able to sustain decorin GAG chain substitution but not GAG synthesis from exogenously added xyloside. Altogether, this study provides novel insight into human β4GalT7 active site functional domains, allowing manipulation of this enzyme critical for the regulation of GAG synthesis. A better understanding of the mechanism underlying GAG assembly paves the way toward GAG-based therapeutics. PMID:20843813

  13. A note on monotonicity of item response functions for ordered polytomous item response theory models.

    Science.gov (United States)

    Kang, Hyeon-Ah; Su, Ya-Hui; Chang, Hua-Hua

    2018-03-08

    A monotone relationship between a true score (τ) and a latent trait level (θ) has been a key assumption for many psychometric applications. The monotonicity property in dichotomous response models is evident as a result of a transformation via a test characteristic curve. Monotonicity in polytomous models, in contrast, is not immediately obvious because item response functions are determined by a set of response category curves, which are conceivably non-monotonic in θ. The purpose of the present note is to demonstrate strict monotonicity in ordered polytomous item response models. Five models that are widely used in operational assessments are considered for proof: the generalized partial credit model (Muraki, 1992, Applied Psychological Measurement, 16, 159), the nominal model (Bock, 1972, Psychometrika, 37, 29), the partial credit model (Masters, 1982, Psychometrika, 47, 147), the rating scale model (Andrich, 1978, Psychometrika, 43, 561), and the graded response model (Samejima, 1972, A general model for free-response data (Psychometric Monograph no. 18). Psychometric Society, Richmond). The study asserts that the item response functions in these models strictly increase in θ and thus there exists strict monotonicity between τ and θ under certain specified conditions. This conclusion validates the practice of customarily using τ in place of θ in applied settings and provides theoretical grounds for one-to-one transformations between the two scales. © 2018 The British Psychological Society.

  14. Nonlinear Site Response Validation Studies Using KIK-net Strong Motion Data

    Science.gov (United States)

    Asimaki, D.; Shi, J.

    2014-12-01

    Earthquake simulations are nowadays producing realistic ground motion time-series in the range of engineering design applications. Of particular significance to engineers are simulations of near-field motions and large magnitude events, for which observations are scarce. With the engineering community slowly adopting the use of simulated ground motions, site response models need to be re-evaluated in terms of their capabilities and limitations to 'translate' the simulated time-series from rock surface output to structural analyses input. In this talk, we evaluate three one-dimensional site response models: linear viscoelastic, equivalent linear and nonlinear. We evaluate the performance of the models by comparing predictions to observations at 30 downhole stations of the Japanese network KIK-Net that have recorded several strong events, including the 2011 Tohoku earthquake. Velocity profiles are used as the only input to all models, while additional parameters such as quality factor, density and nonlinear dynamic soil properties are estimated from empirical correlations. We quantify the differences of ground surface predictions and observations in terms of both seismological and engineering intensity measures, including bias ratios of peak ground response and visual comparisons of elastic spectra, and inelastic to elastic deformation ratio for multiple ductility ratios. We observe that PGV/Vs,30 — as measure of strain— is a better predictor of site nonlinearity than PGA, and that incremental nonlinear analyses are necessary to produce reliable estimates of high-frequency ground motion components at soft sites. We finally discuss the implications of our findings on the parameterization of nonlinear amplification factors in GMPEs, and on the extensive use of equivalent linear analyses in probabilistic seismic hazard procedures.

  15. Temperature response functions (G-functions) for single pile heat exchangers

    International Nuclear Information System (INIS)

    Loveridge, Fleur; Powrie, William

    2013-01-01

    Foundation piles used as heat exchangers as part of a ground energy system have the potential to reduce energy use and carbon dioxide emissions from new buildings. However, current design approaches for pile heat exchangers are based on methods developed for boreholes which have a different geometry, with a much larger aspect (length to diameter) ratio. Current methods also neglect the transient behaviour of the pile concrete, instead assuming a steady state resistance for design purposes. As piles have a much larger volume of concrete than boreholes, this neglects the significant potential for heat storage within the pile. To overcome these shortcomings this paper presents new pile temperature response functions (G-functions) which are designed to reflect typical geometries of pile heat exchangers and include the transient response of the pile concrete. Owing to the larger number of pile sizes and pipe configurations which are possible with pile heat exchangers it is not feasible to developed a single unified G-function and instead upper and lower bound solutions are provided for different aspects ratios. - Highlights: • We present new temperature response functions for pile heat exchangers. • The functions include transient heat transfer within the pile concrete. • Application of the functions reduces the resulting calculated temperature ranges. • Greater energy efficiency is possible by accounting for heat storage in the pile

  16. Two site spin correlation function in Bethe-Peierls approximation for Ising model

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, D [Roorkee Univ. (India). Dept. of Physics

    1976-07-01

    Two site spin correlation function for an Ising model above Curie temperature has been calculated by generalising Bethe-Peierls approximation. The results derived by a graphical method due to Englert are essentially the same as those obtained earlier by Elliott and Marshall, and Oguchi and Ono. The earlier results were obtained by a direct generalisation of the cluster method of Bethe, while these results are derived by retaining that class of diagrams , which is exact on Bethe lattice.

  17. An error-related negativity potential investigation of response monitoring function in individuals with Internet addiction disorder

    Directory of Open Access Journals (Sweden)

    Zhenhe eZhou

    2013-09-01

    Full Text Available Internet addiction disorder (IAD is an impulse disorder or at least related to impulse control disorder. Deficits in executive functioning, including response monitoring, have been proposed as a hallmark feature of impulse control disorders. The error-related negativity (ERN reflects individual’s ability to monitor behavior. Since IAD belongs to a compulsive-impulsive spectrum disorder, theoretically, it should present response monitoring functional deficit characteristics of some disorders, such as substance dependence, ADHD or alcohol abuse, testing with an Erikson flanker task. Up to now, no studies on response monitoring functional deficit in IAD were reported. The purpose of the present study was to examine whether IAD displays response monitoring functional deficit characteristics in a modified Erikson flanker task.23 subjects were recruited as IAD group. 23 matched age, gender and education healthy persons were recruited as control group. All participants completed the modified Erikson flanker task while measured with event-related potentials (ERPs. IAD group made more total error rates than did controls (P < 0.01; Reactive times for total error responses in IAD group were shorter than did controls (P < 0.01. The mean ERN amplitudes of total error response conditions at frontal electrode sites and at central electrode sites of IAD group were reduced compared with control group (all P < 0.01. These results revealed that IAD displays response monitoring functional deficit characteristics and shares ERN characteristics of compulsive-impulsive spectrum disorder.

  18. Defining a similarity threshold for a functional proteinsequence pattern: The signal peptide cleavage site

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Engelbrecht, Jacob; von Heijne, Gunnar

    1996-01-01

    When preparing data sets of amino acid or nucleotide sequences it is necessary to exclude redundant or homologous sequences in order to avoid overestimating the predictive performance of an algorithm. For some time methods for doing this have been available in the area of protein structure...... prediction. We have developed a similar procedure based on pair-wise alignments for sequences with functional sites. We show how a correlation coefficient between sequence similarity and functional homology can be used to compare the efficiency of different similarity measures and choose a nonarbitrary...

  19. Leaders as Corporate Responsibility Spokesperson: How Leaders Explain Liabilites Via Corporate Web Sites?

    Directory of Open Access Journals (Sweden)

    Burcu Öksüz

    2014-12-01

    Full Text Available The aim of this paper is to reveal the corporate social responsibility (CSR understandings of corporations from the leaders’ perspective and discuss how leaders define and explain CSR practices their organizations executed as spokesperson via social media channels of their organizations.  In this context, a content analysis aiming to display the ideas of Turkey’s top 250 corporations’ leaders (CEO, chairman of the board, general manager designated by Istanbul Chamber of Industry in 2013. The leader messages about different dimensions of CSR and CSR practices that are partaking in corporate web sites were examined. According to the results of the analysis, it is found that the leaders act as responsible leaders, and also the spokesperson of their corporations. In addition it is found out that responsible leaders included multiplexed information on different dimensions and various practices of CSR in their social media messages.

  20. Response function of a p type - HPGe detector

    International Nuclear Information System (INIS)

    Lopez-Pino, Neivy; Cabral, Fatima Padilla; D'Alessandro, Katia; Maidana, Nora Lia; Vanin, Vito Roberto

    2011-01-01

    The response function of a HPGe detector depends on Ge crystal dimensions and dead layers thicknesses; most of them are not given by the manufacturers or change with detector damage from neutrons or contact with the atmosphere and therefore must be experimentally determined. The response function is obtained by a Monte-Carlo simulation procedure based on the Ge crystal characteristics. In this work, a p-type coaxial HPGe detector with 30% efficiency, manufactured in 1989, was investigated. The crystal radius and length and the inner hole dimensions were obtained scanning the capsule both in the radial and axial directions using 4 mm collimated beams from 137 Cs, 207 Bi point sources placed on a x-y table in steps of 2,00 mm. These dimensions were estimated comparing the experimental peak areas with those obtained by simulation using several hole configurations. In a similar procedure, the frontal dead layer thickness was determined using 2 mm collimated beams of the 59 keV gamma-rays from 241 Am and 81 keV from 133 Ba sources hitting the detector at 90 deg and 45 deg with respect to the capsule surface. The Monte Carlo detector model included, besides the crystal, hole and capsules sizes, the Ge dead-layers. The obtained spectra were folded with a gaussian resolution function to account for electronic noise. The comparison of simulated and experimental response functions for 4 mm collimated beams of 60 Co, 137 Cs, and 207 Bi points sources placed at distances of 7, 11 and 17 cm from the detector end cap showed relative deviations of about 10% in general and below 10% in the peak. The frontal dead layer thickness determined by our procedure was different from that specified by the detector manufacturer. (author)

  1. Are Microbial Nanowires Responsible for Geoelectrical Changes at Hydrocarbon Contaminated Sites?

    Science.gov (United States)

    Hager, C.; Atekwana, E. A.; Gorby, Y. A.; Duris, J. W.; Allen, J. P.; Atekwana, E. A.; Ownby, C.; Rossbach, S.

    2007-05-01

    Significant advances in near-surface geophysics and biogeophysics in particular, have clearly established a link between geoelectrical response and the growth and enzymatic activities of microbes in geologic media. Recent studies from hydrocarbon contaminated sites suggest that the activities of distinct microbial populations, specifically syntrophic, sulfate reducing, and dissimilatory iron reducing microbial populations are a contributing factor to elevated sediment conductivity. However, a fundamental mechanistic understanding of the processes and sources resulting in the measured electrical response remains uncertain. The recent discovery of bacterial nanowires and their electron transport capabilities suggest that if bacterial nanowires permeate the subsurface, they may in part be responsible for the anomalous conductivity response. In this study we investigated the microbial population structure, the presence of nanowires, and microbial-induced alterations of a hydrocarbon contaminated environment and relate them to the sediments' geoelectrical response. Our results show that microbial communities varied substantially along the vertical gradient and at depths where hydrocarbons saturated the sediments, ribosomal intergenic spacer analysis (RISA) revealed signatures of microbial communities adapted to hydrocarbon impact. In contrast, RISA profiles from a background location showed little community variations with depth. While all sites showed evidence of microbial activity, a scanning electron microscope (SEM) study of sediment from the contaminated location showed pervasive development of "nanowire-like structures" with morphologies consistent with nanowires from laboratory experiments. SEM analysis suggests extensive alteration of the sediments by microbial Activity. We conclude that, excess organic carbon (electron donor) but limited electron acceptors in these environments cause microorganisms to produce nanowires to shuttle the electrons as they seek for

  2. Identifying functional transcription factor binding sites in yeast by considering their positional preference in the promoters.

    Directory of Open Access Journals (Sweden)

    Fu-Jou Lai

    Full Text Available Transcription factor binding site (TFBS identification plays an important role in deciphering gene regulatory codes. With comprehensive knowledge of TFBSs, one can understand molecular mechanisms of gene regulation. In the recent decades, various computational approaches have been proposed to predict TFBSs in the genome. The TFBS dataset of a TF generated by each algorithm is a ranked list of predicted TFBSs of that TF, where top ranked TFBSs are statistically significant ones. However, whether these statistically significant TFBSs are functional (i.e. biologically relevant is still unknown. Here we develop a post-processor, called the functional propensity calculator (FPC, to assign a functional propensity to each TFBS in the existing computationally predicted TFBS datasets. It is known that functional TFBSs reveal strong positional preference towards the transcriptional start site (TSS. This motivates us to take TFBS position relative to the TSS as the key idea in building our FPC. Based on our calculated functional propensities, the TFBSs of a TF in the original TFBS dataset could be reordered, where top ranked TFBSs are now the ones with high functional propensities. To validate the biological significance of our results, we perform three published statistical tests to assess the enrichment of Gene Ontology (GO terms, the enrichment of physical protein-protein interactions, and the tendency of being co-expressed. The top ranked TFBSs in our reordered TFBS dataset outperform the top ranked TFBSs in the original TFBS dataset, justifying the effectiveness of our post-processor in extracting functional TFBSs from the original TFBS dataset. More importantly, assigning functional propensities to putative TFBSs enables biologists to easily identify which TFBSs in the promoter of interest are likely to be biologically relevant and are good candidates to do further detailed experimental investigation. The FPC is implemented as a web tool at http://santiago.ee.ncku.edu.tw/FPC/.

  3. Fatal attraction: vegetation responses to nutrient inputs attract herbivores to infectious anthrax carcass sites.

    Science.gov (United States)

    Turner, Wendy C; Kausrud, Kyrre L; Krishnappa, Yathin S; Cromsigt, Joris P G M; Ganz, Holly H; Mapaure, Isaac; Cloete, Claudine C; Havarua, Zepee; Küsters, Martina; Getz, Wayne M; Stenseth, Nils Chr

    2014-11-22

    Parasites can shape the foraging behaviour of their hosts through cues indicating risk of infection. When cues for risk co-occur with desired traits such as forage quality, individuals face a trade-off between nutrient acquisition and parasite exposure. We evaluated how this trade-off may influence disease transmission in a 3-year experimental study of anthrax in a guild of mammalian herbivores in Etosha National Park, Namibia. At plains zebra (Equus quagga) carcass sites we assessed (i) carcass nutrient effects on soils and grasses, (ii) concentrations of Bacillus anthracis (BA) on grasses and in soils, and (iii) herbivore grazing behaviour, compared with control sites, using motion-sensing camera traps. We found that carcass-mediated nutrient pulses improved soil and vegetation, and that BA is found on grasses up to 2 years after death. Host foraging responses to carcass sites shifted from avoidance to attraction, and ultimately to no preference, with the strength and duration of these behavioural responses varying among herbivore species. Our results demonstrate that animal carcasses alter the environment and attract grazing hosts to parasite aggregations. This attraction may enhance transmission rates, suggesting that hosts are limited in their ability to trade off nutrient intake with parasite avoidance when relying on indirect cues. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  4. Site-Specific Multilevel Modeling of Potato Response to Nitrogen Fertilization

    Directory of Open Access Journals (Sweden)

    Serge-Étienne Parent

    2017-12-01

    Full Text Available Technologies of precision agriculture, digital soil maps, and meteorological stations provide a minimum data set to guide precision farming operations. However, determining optimal nutrient requirements for potato (Solanum tuberosum L. crops at subfield scale remains a challenge given specific climatic, edaphic, and managerial conditions. Multilevel modeling can generalize yield response to fertilizer additions using data easily accessible to growers. Our objective was to elaborate a multilevel N fertilizer response model for potato crops using the Mitscherlich equation and a core data set of 93 N fertilizer trials conducted in Québec, Canada. Daily climatic data were collected at 10 × 10 km resolution. Soils were characterized by organic matter content, pH, and texture in the arable layer, and by texture and tools of pedometrics across a gleization-podzolization continuum in subsoil layers. There were five categories of preceding crops and five cultivar maturity orders. The three Mitscherlich parameters (Asymptote, Rate, and Environment were most often site-specific. Sensitivity analysis showed that optimum N dosage increased with non-leguminous high-residue preceding crops, coarser soils, podzolization, drier climatic condition, and late cultivar maturity. The inferential model could guide site-specific N fertilization using an accessible minimum data set to support fertilization decisions. As decision-support system, the model could also provide a range of optimum N doses across a large spectrum of site-specific conditions including climate change.

  5. How linear features alter predator movement and the functional response.

    KAUST Repository

    McKenzie, Hannah W

    2012-01-18

    In areas of oil and gas exploration, seismic lines have been reported to alter the movement patterns of wolves (Canis lupus). We developed a mechanistic first passage time model, based on an anisotropic elliptic partial differential equation, and used this to explore how wolf movement responses to seismic lines influence the encounter rate of the wolves with their prey. The model was parametrized using 5 min GPS location data. These data showed that wolves travelled faster on seismic lines and had a higher probability of staying on a seismic line once they were on it. We simulated wolf movement on a range of seismic line densities and drew implications for the rate of predator-prey interactions as described by the functional response. The functional response exhibited a more than linear increase with respect to prey density (type III) as well as interactions with seismic line density. Encounter rates were significantly higher in landscapes with high seismic line density and were most pronounced at low prey densities. This suggests that prey at low population densities are at higher risk in environments with a high seismic line density unless they learn to avoid them.

  6. How linear features alter predator movement and the functional response.

    KAUST Repository

    McKenzie, Hannah W; Merrill, Evelyn H; Spiteri, Raymond J; Lewis, Mark A

    2012-01-01

    In areas of oil and gas exploration, seismic lines have been reported to alter the movement patterns of wolves (Canis lupus). We developed a mechanistic first passage time model, based on an anisotropic elliptic partial differential equation, and used this to explore how wolf movement responses to seismic lines influence the encounter rate of the wolves with their prey. The model was parametrized using 5 min GPS location data. These data showed that wolves travelled faster on seismic lines and had a higher probability of staying on a seismic line once they were on it. We simulated wolf movement on a range of seismic line densities and drew implications for the rate of predator-prey interactions as described by the functional response. The functional response exhibited a more than linear increase with respect to prey density (type III) as well as interactions with seismic line density. Encounter rates were significantly higher in landscapes with high seismic line density and were most pronounced at low prey densities. This suggests that prey at low population densities are at higher risk in environments with a high seismic line density unless they learn to avoid them.

  7. 3D Information System of Historical Site – Proposal and Realisation of a Functional Prototype

    Directory of Open Access Journals (Sweden)

    J. Hodač

    2005-01-01

    Full Text Available The development of methods for 3D data acquisition, together with progress in information technologies raises the question of creating and using 3D models and 3D information systems (IS of historical sites and buildings. This paper presents the current state of the “Live Theatre” project. The theme of the project is the proposal and realisation of a 3D IS of the baroque theatre at Eeský Krumlov castle (UNESCO site.The project is divided into three main stages – creation of a 3D model, proposal of a conception for a 3D IS, and realisation of a functional prototype. 3D data was acquired by means of photogrammetric and surveying methods. An accurate 3D model (photo-realistic, textured was built up with MicroStation CAD system. The proposal of a conception of a 3D IS was the main outcome of the author’s dissertation. The essential feature of the proposed conception is the creation of subsystems targeted on three spheres – management, research and presentation of the site. The functionality of each subsystem is connected with its related sphere; however, each subsystem uses the same database. The present stage of the project involves making a functional prototype (with sample data. During this stage we are working on several basic technological topics. At present we are concerned with 3D data, its formats, format conversions (e.g. DGN _ VRML and its connection to other types of data. After that, we will be seeking a convenient technical solution based on network technologies (Internet and an appropriate layout for the data (database. The project is being carried out in close co-operation with the administration of the castle and some other partners. This stage of the project will be completed in December 2005.A functional prototype and the information acquired by testing it will form the basis for the final proposal of a complex IS of a historical site. The final proposal and appropriate technology will be the outcome of the project. The

  8. Functional Associations by Response Overlap (FARO), a functional genomics approach matching gene expression phenotypes

    DEFF Research Database (Denmark)

    Nielsen, Henrik Bjørn; Mundy, J.; Willenbrock, Hanni

    2007-01-01

    The systematic comparison of transcriptional responses of organisms is a powerful tool in functional genomics. For example, mutants may be characterized by comparing their transcript profiles to those obtained in other experiments querying the effects on gene expression of many experimental facto...

  9. Identification and Validation of Novel Hedgehog-Responsive Enhancers Predicted by Computational Analysis of Ci/Gli Binding Site Density

    Science.gov (United States)

    Richards, Neil; Parker, David S.; Johnson, Lisa A.; Allen, Benjamin L.; Barolo, Scott; Gumucio, Deborah L.

    2015-01-01

    The Hedgehog (Hh) signaling pathway directs a multitude of cellular responses during embryogenesis and adult tissue homeostasis. Stimulation of the pathway results in activation of Hh target genes by the transcription factor Ci/Gli, which binds to specific motifs in genomic enhancers. In Drosophila, only a few enhancers (patched, decapentaplegic, wingless, stripe, knot, hairy, orthodenticle) have been shown by in vivo functional assays to depend on direct Ci/Gli regulation. All but one (orthodenticle) contain more than one Ci/Gli site, prompting us to directly test whether homotypic clustering of Ci/Gli binding sites is sufficient to define a Hh-regulated enhancer. We therefore developed a computational algorithm to identify Ci/Gli clusters that are enriched over random expectation, within a given region of the genome. Candidate genomic regions containing Ci/Gli clusters were functionally tested in chicken neural tube electroporation assays and in transgenic flies. Of the 22 Ci/Gli clusters tested, seven novel enhancers (and the previously known patched enhancer) were identified as Hh-responsive and Ci/Gli-dependent in one or both of these assays, including: Cuticular protein 100A (Cpr100A); invected (inv), which encodes an engrailed-related transcription factor expressed at the anterior/posterior wing disc boundary; roadkill (rdx), the fly homolog of vertebrate Spop; the segment polarity gene gooseberry (gsb); and two previously untested regions of the Hh receptor-encoding patched (ptc) gene. We conclude that homotypic Ci/Gli clustering is not sufficient information to ensure Hh-responsiveness; however, it can provide a clue for enhancer recognition within putative Hedgehog target gene loci. PMID:26710299

  10. Investigation of Nonlinear Site Response and Seismic Compression from Case History Analysis and Laboratory Testing

    Science.gov (United States)

    Yee, Eric

    In this thesis I address a series of issues related to ground failure and ground motions during earthquakes. A major component is the evaluation of cyclic volumetric strain behavior of unsaturated soils, more commonly known as seismic compression, from advanced laboratory testing. Another major component is the application of nonlinear and equivalent linear ground response analyses to large-strain problems involving highly nonlinear dynamic soil behavior. These two components are merged in the analysis of a truly unique and crucial field case history of nonlinear site response and seismic compression. My first topic concerns dynamic soil testing for relatively small strain dynamic soil properties such as threshold strains, gammatv. Such testing is often conducted using specialized devices such as dual-specimen simple-shear, as devices configured for large strain testing produce noisy signals in the small strain range. Working with a simple shear device originally developed for large-strain testing, I extend its low-strain capabilities by characterizing noisy signals and utilizing several statistical methods to extract meaningful responses in the small strain range. I utilize linear regression of a transformed variable to estimate the cyclic shear strain from a noisy signal and the confidence interval on its amplitude. I utilize Kernel regression with the Nadaraya-Watson estimator and a Gaussian kernel to evaluate vertical strain response. A practical utilization of these techniques is illustrated by evaluating threshold shear strains for volume change with a procedure that takes into account uncertainties in the measured shear and vertical strains. My second topic concerns the seismic compression characteristics of non-plastic and low-plasticity silty sands with varying fines content (10 ≤ FC ≤ 60%). Simple shear testing was performed on various sand-fines mixtures at a range of modified Proctor relative compaction levels ( RC) and degrees-of-saturation (S

  11. Polychaete response to fresh food supply at organically enriched coastal sites: Repercussion on bioturbation potential and trophic structure

    Science.gov (United States)

    Venturini, N.; Pires-Vanin, A. M. S.; Salhi, M.; Bessonart, M.; Muniz, P.

    2011-12-01

    We investigated the vertical distribution, abundance, specific and functional structure of polychaete assemblages at four organically enriched sites. The effects of fresh organic matter input from the water column driving by upwelling were evaluated. Temperature and salinity values indicate the intrusion of South Atlantic Central Water (SACW) in spring, a nutrient-rich water mass. The dominance of the conveyor belt transport (CONV) in the station influenced by SACW, in the spring survey, is associated with fresh organic matter input as indicated by higher amounts of polyunsaturated fatty acids. Conversely, the predominance of the diffusive mixing (DIFF) bioturbation category, in the sites without SACW influence is related to the preferential accumulation of more refractive food resources as indicated by higher concentrations of short chain saturated fatty acids. At the site influenced by SACW, the changes in polychaete assemblages were not all evident during proceeding upwelling conditions, but may persist at the end of the upwelling. Polychaetes in the study area seemed to be limited by the quality but not the quantity of food. The delay in polychaete response to fresh food supply may be related to the organic enrichment and the prevalence of refractory material in the sediments.

  12. That Was Then, This Is Now: Replacing the Mobile-Optimized Site with Responsive Design

    Directory of Open Access Journals (Sweden)

    Laurie M. Bridges

    2013-12-01

    Full Text Available As mobile technologies continue to evolve, libraries seek sustainable ways to keep up with these changes and to best serve our users.  Previous library mobile usability research has examined tasks users predict they might be likely to perform, but little is known about what users actually do on a mobile-optimized library site.  This research used a combination of survey methodology and web analytics to examine what tasks users actually carry out on a library mobile site.  The results indicate that users perform an array of passive and active tasks and do not want content choices to be limited on mobile devices.  Responsive design is described as a long-term solution for addressing both designers and users’ needs.

  13. Nuclear response functions at large energy and momentum transfer

    International Nuclear Information System (INIS)

    Bertozzi, W.; Moniz, E.J.; Lourie, R.W.

    1991-01-01

    Quasifree nucleon processes are expected to dominate the nuclear electromagnetic response function for large energy and momentum transfers, i.e., for energy transfers large compared with nuclear single particle energies and momentum transfers large compared with typical nuclear momenta. Despite the evident success of the quasifree picture in providing the basic frame work for discussing and understanding the large energy, large momentum nuclear response, the limits of this picture have also become quite clear. In this article a selected set of inclusive and coincidence data are presented in order to define the limits of the quasifree picture more quantitatively. Specific dynamical mechanisms thought to be important in going beyond the quasifree picture are discussed as well. 75 refs, 37 figs

  14. Shear wave profiles from surface wave inversion: the impact of uncertainty on seismic site response analysis

    International Nuclear Information System (INIS)

    Boaga, J; Vignoli, G; Cassiani, G

    2011-01-01

    Inversion is a critical step in all geophysical techniques, and is generally fraught with ill-posedness. In the case of seismic surface wave studies, the inverse problem can lead to different equivalent subsoil models and consequently to different local seismic response analyses. This can have a large impact on an earthquake engineering design. In this paper, we discuss the consequences of non-uniqueness of surface wave inversion on seismic responses, with both numerical and experimental data. Our goal is to evaluate the consequences on common seismic response analysis in the case of different impedance contrast conditions. We verify the implications of inversion uncertainty, and consequently of data information content, on realistic local site responses. A stochastic process is used to generate a set of 1D shear wave velocity profiles from several specific subsurface models. All these profiles are characterized as being equivalent, i.e. their responses, in terms of a dispersion curve, are compatible with the uncertainty in the same surface wave data. The generated 1D shear velocity models are then subjected to a conventional one-dimensional seismic ground response analysis using a realistic input motion. While recent analyses claim that the consequences of surface wave inversion uncertainties are very limited, our test points out that a relationship exists between inversion confidence and seismic responses in different subsoils. In the case of regular and relatively smooth increase of shear wave velocities with depth, as is usual in sedimentary plains, our results show that the choice of a specific model among equivalent solutions strongly influences the seismic response. On the other hand, when the shallow subsoil is characterized by a strong impedance contrast (thus revealing a characteristic soil resonance period), as is common in the presence of a shallow bedrock, equivalent solutions provide practically the same seismic amplification, especially in the

  15. The polyproline site in hinge 2 influences the functional capacity of truncated dystrophins.

    Directory of Open Access Journals (Sweden)

    Glen B Banks

    2010-05-01

    Full Text Available Mutations in dystrophin can lead to Duchenne muscular dystrophy or the more mild form of the disease, Becker muscular dystrophy. The hinge 3 region in the rod domain of dystrophin is particularly prone to deletion mutations. In-frame deletions of hinge 3 are predicted to lead to BMD, however the severity of disease can vary considerably. Here we performed extensive structure-function analyses of truncated dystrophins with modified hinges and spectrin-like repeats in mdx mice. We found that the polyproline site in hinge 2 profoundly influences the functional capacity of a microdystrophin(DeltaR4-R23/DeltaCT with a large deletion in the hinge 3 region. Inclusion of polyproline in microdystrophin(DeltaR4-R23/DeltaCT led to small myofibers (12% smaller than wild-type, Achilles myotendinous disruption, ringed fibers, and aberrant neuromuscular junctions in the mdx gastrocnemius muscles. Replacing hinge 2 of microdystrophin(DeltaR4-R23/DeltaCT with hinge 3 significantly improved the functional capacity to prevent muscle degeneration, increase muscle fiber area, and maintain the junctions. We conclude that the rigid alpha-helical structure of the polyproline site significantly impairs the functional capacity of truncated dystrophins to maintain appropriate connections between the cytoskeleton and extracellular matrix.

  16. Site-Specific Incorporation of Functional Components into RNA by an Unnatural Base Pair Transcription System

    Directory of Open Access Journals (Sweden)

    Rie Kawai

    2012-03-01

    Full Text Available Toward the expansion of the genetic alphabet, an unnatural base pair between 7-(2-thienylimidazo[4,5-b]pyridine (Ds and pyrrole-2-carbaldehyde (Pa functions as a third base pair in replication and transcription, and provides a useful tool for the site-specific, enzymatic incorporation of functional components into nucleic acids. We have synthesized several modified-Pa substrates, such as alkylamino-, biotin-, TAMRA-, FAM-, and digoxigenin-linked PaTPs, and examined their transcription by T7 RNA polymerase using Ds-containing DNA templates with various sequences. The Pa substrates modified with relatively small functional groups, such as alkylamino and biotin, were efficiently incorporated into RNA transcripts at the internal positions, except for those less than 10 bases from the 3′-terminus. We found that the efficient incorporation into a position close to the 3′-terminus of a transcript depended on the natural base contexts neighboring the unnatural base, and that pyrimidine-Ds-pyrimidine sequences in templates were generally favorable, relative to purine-Ds-purine sequences. The unnatural base pair transcription system provides a method for the site-specific functionalization of large RNA molecules.

  17. Intra-operative multi-site stimulation: Expanding methodology for cortical brain mapping of language functions.

    Science.gov (United States)

    Gonen, Tal; Gazit, Tomer; Korn, Akiva; Kirschner, Adi; Perry, Daniella; Hendler, Talma; Ram, Zvi

    2017-01-01

    Direct cortical stimulation (DCS) is considered the gold-standard for functional cortical mapping during awake surgery for brain tumor resection. DCS is performed by stimulating one local cortical area at a time. We present a feasibility study using an intra-operative technique aimed at improving our ability to map brain functions which rely on activity in distributed cortical regions. Following standard DCS, Multi-Site Stimulation (MSS) was performed in 15 patients by applying simultaneous cortical stimulations at multiple locations. Language functioning was chosen as a case-cognitive domain due to its relatively well-known cortical organization. MSS, performed at sites that did not produce disruption when applied in a single stimulation point, revealed additional language dysfunction in 73% of the patients. Functional regions identified by this technique were presumed to be significant to language circuitry and were spared during surgery. No new neurological deficits were observed in any of the patients following surgery. Though the neuro-electrical effects of MSS need further investigation, this feasibility study may provide a first step towards sophistication of intra-operative cortical mapping.

  18. Exactly solvable model for the time response function of RPCs

    International Nuclear Information System (INIS)

    Mangiarotti, A.; Fonte, P.; Gobbi, A.

    2004-01-01

    The fluctuation theory for the growth of several avalanches is briefly summarized and extended to include the case of electronegative gas mixtures. Based on such physical picture, the intrinsic time response function of an RPC can be calculated in a closed form and its average and rms extracted from series representations. The corresponding timing resolution, expressed in units of 1/((α-η)vd), is a universal function of the mean number of 'effective' clusters n0 reduced by electron attachment: n0(1-η/α). A comparison to a few selected good-quality experimental data is attempted for the timing resolution of both 1-gap and 4-gaps RPCs, finding a reasonable agreement

  19. Plant responses to environmental stress: regulation and functions of the Arabidopsis TCH genes

    Science.gov (United States)

    Braam, J.; Sistrunk, M. L.; Polisensky, D. H.; Xu, W.; Purugganan, M. M.; Antosiewicz, D. M.; Campbell, P.; Johnson, K. A.; McIntire, L. V. (Principal Investigator)

    1997-01-01

    Expression of the Arabidopsis TCH genes is markedly upregulated in response to a variety of environmental stimuli including the seemingly innocuous stimulus of touch. Understanding the mechanism(s) and factors that control TCH gene regulation will shed light on the signaling pathways that enable plants to respond to environmental conditions. The TCH proteins include calmodulin, calmodulin-related proteins and a xyloglucan endotransglycosylase. Expression analyses and localization of protein accumulation indicates that the potential sites of TCH protein function include expanding cells and tissues under mechanical strain. We hypothesize that at least a subset of the TCH proteins may collaborate in cell wall biogenesis.

  20. Efficient multi-site two-photon functional imaging of neuronal circuits.

    Science.gov (United States)

    Castanares, Michael Lawrence; Gautam, Vini; Drury, Jack; Bachor, Hans; Daria, Vincent R

    2016-12-01

    Two-photon imaging using high-speed multi-channel detectors is a promising approach for optical recording of cellular membrane dynamics at multiple sites. A main bottleneck of this technique is the limited number of photons captured within a short exposure time (~1ms). Here, we implement temporal gating to improve the two-photon fluorescence yield from holographically projected multiple foci whilst maintaining a biologically safe incident average power. We observed up to 6x improvement in the signal-to-noise ratio (SNR) in Fluorescein and cultured hippocampal neurons showing evoked calcium transients. With improved SNR, we could pave the way to achieving multi-site optical recording of fluorogenic probes with response times in the order of ~1ms.

  1. Improvement of worker safety through the investigation of the site response to rockbursts.

    CSIR Research Space (South Africa)

    Durrheim, RJ

    1997-12-01

    Full Text Available Committee DRAFT FINAL REPORT Improvement of worker safety through the investigation of the site response to rockbursts R J Durrheim, A M Milev, S M Spottiswoode, and B Vakalisa Research agency CSIR: Division of Mining Technology Project number GAP2OI... in the application of current technology, such as numerical modelling for mine design, were also identified. It was also found that published guidelines, e.g. for pillar design, have limitations which are not explicitly stated. The performance of new technologies...

  2. Assessing Riparian Vegetation Condition and Function in Disturbed Sites of the Arid Northwestern Mexico

    Directory of Open Access Journals (Sweden)

    Lara Cornejo-Denman

    2018-01-01

    Full Text Available Transformation or modification of vegetation distribution and structure in arid riparian ecosystems can lead to the loss of ecological function. Mexico has 101,500,000 ha of arid lands, however there is a general lack of information regarding how arid riparian ecosystems are being modified. To assess these modifications, we use eight sites in the San Miguel River (central Sonora to analyze (1 riparian vegetation composition, structure and distribution using field sampling and remote sensing data from Unmanned Aerial Vehicles (UAV; (2 productivity (proxies, using vegetation indices derived from satellite data; and (3 variability posed by riparian vegetation and vegetation adjacent to riparian habitats. The development of a simple yet informative Anthropogenic-disturbance Index (ADI allowed us to classify and describe each study site. We found sharp differences in vegetation composition and structure between sites due to the absence/presence of obligate-riparian species. We also report significant difference between EVI (Enhanced Vegetation Index values for the dry season among vegetation types that develop near the edges of the river but differ in composition, suggesting that land cover changes form obligate-riparian to facultative-riparian species can lead to a loss in potential productivity. Finally, our tests suggest that sites with higher disturbance present lower photosynthetic activity.

  3. Savannah River Site management response plan for chemical safety vulnerability field assessment. Revision 1

    International Nuclear Information System (INIS)

    Kahal, E.J.; Murphy, S.L.; Salaymeh, S.R.

    1994-09-01

    As part of the U.S. Department of Energy's (DOE) initiative to identify potential chemical safety vulnerabilities in the DOE complex, the Chemical Safety Vulnerability Core Working Group issued a field verification assessment report. While the report concluded that Savannah River Site (SRS) is moving in a positive direction, the report also identified five chemical safety vulnerabilities with broad programmatic impact that are not easily nor quickly remedied. The May 1994 SRS Management Response Plan addressed the five SRS vulnerabilities identified in the field assessment report. The SRS response plan listed observations supporting the vulnerabilities and any actions taken or planned toward resolution. Many of the observations were resolved by simple explanations, such as the existence of implementation plans for Safety Analysis Report updates. Recognizing that correcting individual observations does not suffice in remedying the vulnerabilities, a task team was assembled to address the broader programmatic issues and to recommend corrective actions

  4. Functions of microRNA in response to cocaine stimulation.

    Science.gov (United States)

    Xu, L-F; Wang, J; Lv, F B; Song, Q

    2013-12-04

    MicroRNAs (miRNAs) are a type of non-protein-coding single-stranded RNA, which are typically 20-25 nt in length. miRNAs play important roles in various biological processes, including development, cell proliferation, differentiation, and apoptosis. We aimed to detect the miRNA response to cocaine stimulations and their target genes. Using the miRNA expression data GSE21901 downloaded from the Gene Expression Omnibus database, we screened out the differentially expressed miRNA after short-term (1 h) and longer-term (6 h) cocaine stimulations based on the fold change >1.2. Target genes of differentially expressed miRNAs were retrieved from TargetScan database with the context score -0.3. Functional annotation enrichment analysis was performed for all the target genes with DAVID. A total of 121 differentially expressed miRNAs between the 1-h treatment and the control samples, 58 between the 6-h treatment and the control samples, and 69 between the 1-h and the 6-h treatment samples. Among them, miR-212 results of particular interest, since its expression level was constantly elevated responding to cocaine treatment. After functional and pathway annotations of target genes, we proved that miR-212 was a critical element in cocaine-addiction, because of its involvement in regulating several important cell cycle events. The results may pave the way for further understanding the regulatory mechanisms of cocaine-response in human bodies.

  5. Study on response function of CdTe detector

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hyunduk; Cho, Gyuseong [Department of Nuclear and Quantum Engineering, Korea Advanced Institute of Science and Technology, Daejeon 305-701 (Korea, Republic of); Kang, Bo-Sun [Department of Radiological Science, Catholic University of Daegu, Kyoungsan, Kyoungbuk 712-702 (Korea, Republic of)], E-mail: bskang@cu.ac.kr

    2009-10-21

    So far the origin of the mechanism of light emission in the sonoluminescence has not elucidated whether it is due to blackbody radiation or bremsstrahlung. The final goal of our study is measuring X-ray energy spectrum using high-sensitivity cadmium telluride (CdTe) detector in order to obtain information for understanding sonoluminescence phenomena. However, the scope of this report is the measurement of X-ray spectrum using a high-resolution CdTe detector and determination of CdTe detector response function to obtain the corrected spectrum from measured soft X-ray source spectrum. In general, the measured spectrum was distorted by the characteristics of CdTe detector. Monte Carlo simulation code, MCNP, was used to obtain the reference response function of the CdTe detector. The X-ray spectra of {sup 57}Co, {sup 133}Ba, and {sup 241}Am were obtained by a 4x4x1.0(t) mm{sup 3} CdTe detector at room temperature.

  6. Visual functions in amblyopia as determinants of response to treatment.

    Science.gov (United States)

    Singh, Vinita; Agrawal, Siddharth

    2013-01-01

    To describe the visual functions in amblyopia as determinants of response to treatment. Sixty-nine patients with unilateral and bilateral amblyopia (114 amblyopic eyes) 3 to 15 years old (mean age: 8.80 ± 2.9 years), 40 males (58%) and 29 females (42%), were included in this study. All patients were treated by conventional occlusion 6 hours per day for mild to moderate amblyopia (visual acuity 0.70 or better) and full-time for 4 weeks followed by 6 hours per day for severe amblyopia (visual acuity 0.8 or worse). During occlusion, near activities requiring hand-eye coordination were advised. The follow-up examination was done at 3 and 6 months. Improvement in visual acuity was evaluated on the logMAR chart and correlated with the visual functions. Statistical analysis was done using Wilcoxon rank sum test (Mann-Whitney U test) and Kruskal-Wallis analysis. There was a statistically significant association of poor contrast sensitivity with the grade of amblyopia (P amblyopia (P amblyopia therapy. The grade of amblyopia (initial visual acuity) and accommodation are strong determinants of response to amblyopia therapy, whereas stereopsis and mesopic visual acuity have some value as determinants. Copyright 2013, SLACK Incorporated.

  7. Status of environmental response efforts at radioactively contaminated sites in the united states air force installation restoration program

    International Nuclear Information System (INIS)

    Rowe, W.D. Jr.; McEntee, T.E. Jr.; Johnson, B.; Manning, L.

    1995-01-01

    The United States Air Force has identified approximately 170 radioactively contaminated sites at its domestic installations. These sites contain a variety of low level radioactive and mixed wastes and are classified as burial sites, landfills, buildings, and other disposal sites. Of these 170, approximately 70 are presently being evaluated under the Air Force Installation Restoration Program (IRP) in accordance with applicable laws and regulations. Removal and/or remedial actions have been taken at specific sites using site-specific residual radioactivity criteria. The remaining sites are either under investigation to determine the need for possible action or have been classified as response complete based on restricted or unrestricted future use. This paper describes past Air Force operations that generated radioactive waste materials; examines the current inventory of resulting radioactively contaminated sites in the Air Force IRP; reviews criteria used to evaluate sites for removal and/or remedial actions; provides summary information on actions taken at sites; and focuses on response actions and cleanup levels at two completed sites. The paper concludes with an assessment of outstanding issues relevant to the remediation of radioactively contaminated sites. (author)

  8. Insect community structure and function in Upper Three Runs, Savannah River Site, South Carolina

    Energy Technology Data Exchange (ETDEWEB)

    Morse, J.C.; English, W.R. [Clemson Univ., SC (United States). Dept. of Entomology; Looney, B.B. [Westinghouse Savannah River Co., Aiken, SC (United States)

    1993-07-08

    A project to document the insect species in the upper reaches of Upper Three Runs at the Savannah River site was recently completed. This research was supported by the US Department of Energy under the National Environmental Research Park Program. The work was performed by the Department of Entomology at Clemson University in clemson, SC, by John C. Morse (principal investigator), William R. English and their colleagues. The major output from this study was the dissertation of Dr. William R. English entitled ``Ecosystem Dynamics of a South Carolina Sandhills Stream.`` He investigated selected environmental resources and determined their dynamics and the dynamics of the aquatic invertebrate community structure in response to them.

  9. Equivalent linear and nonlinear site response analysis for design and risk assessment of safety-related nuclear structures

    International Nuclear Information System (INIS)

    Bolisetti, Chandrakanth; Whittaker, Andrew S.; Mason, H. Benjamin; Almufti, Ibrahim; Willford, Michael

    2014-01-01

    Highlights: • Performed equivalent linear and nonlinear site response analyses using industry-standard numerical programs. • Considered a wide range of sites and input ground motions. • Noted the practical issues encountered while using these programs. • Examined differences between the responses calculated from different programs. • Results of biaxial and uniaxial analyses are compared. - Abstract: Site response analysis is a precursor to soil-structure interaction analysis, which is an essential component in the seismic analysis of safety-related nuclear structures. Output from site response analysis provides input to soil-structure interaction analysis. Current practice in calculating site response for safety-related nuclear applications mainly involves the equivalent linear method in the frequency-domain. Nonlinear time-domain methods are used by some for the assessment of buildings, bridges and petrochemical facilities. Several commercial programs have been developed for site response analysis but none of them have been formally validated for large strains and high frequencies, which are crucial for the performance assessment of safety-related nuclear structures. This study sheds light on the applicability of some industry-standard equivalent linear (SHAKE) and nonlinear (DEEPSOIL and LS-DYNA) programs across a broad range of frequencies, earthquake shaking intensities, and sites ranging from stiff sand to hard rock, all with a focus on application to safety-related nuclear structures. Results show that the equivalent linear method is unable to reproduce the high frequency acceleration response, resulting in almost constant spectral accelerations in the short period range. Analysis using LS-DYNA occasionally results in some unrealistic high frequency acceleration ‘noise’, which can be removed by smoothing the piece-wise linear backbone curve. Analysis using DEEPSOIL results in abrupt variations in the peak strains of consecutive soil layers

  10. Positive selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins.

    LENUS (Irish Health Repository)

    Morgan, Claire C

    2010-01-01

    ABSTRACT: BACKGROUND: Reproductive proteins are central to the continuation of all mammalian species. The evolution of these proteins has been greatly influenced by environmental pressures induced by pathogens, rival sperm, sexual selection and sexual conflict. Positive selection has been demonstrated in many of these proteins with particular focus on primate lineages. However, the mammalia are a diverse group in terms of mating habits, population sizes and germ line generation times. We have examined the selective pressures at work on a number of novel reproductive proteins across a wide variety of mammalia. RESULTS: We show that selective pressures on reproductive proteins are highly varied. Of the 10 genes analyzed in detail, all contain signatures of positive selection either across specific sites or in specific lineages or a combination of both. Our analysis of SP56 and Col1a1 are entirely novel and the results show positively selected sites present in each gene. Our findings for the Col1a1 gene are suggestive of a link between positive selection and severe disease type. We find evidence in our dataset to suggest that interacting proteins are evolving in symphony: most likely to maintain interacting functionality. CONCLUSION: Our in silico analyses show positively selected sites are occurring near catalytically important regions suggesting selective pressure to maximize efficient fertilization. In those cases where a mechanism of protein function is not fully understood, the sites presented here represent ideal candidates for mutational study. This work has highlighted the widespread rate heterogeneity in mutational rates across the mammalia and specifically has shown that the evolution of reproductive proteins is highly varied depending on the species and interacting partners. We have shown that positive selection and disease are closely linked in the Col1a1 gene.

  11. Response Function of the Crayfish Caudal Photoreceptor to Hydrodynamic Stimuli

    Science.gov (United States)

    Breite, Sally; Bahar, Sonya; Neiman, Alexander; Moss, Frank

    2002-03-01

    In its abdominal 6th ganglion the crayfish houses 2 light-sensitive neurons (caudal photoreceptors, or CPRs). It is known that these neurons work in tandem with a mechanosensory system of tiny hairs spread across the tailfan, which make synaptic contact with the photoreceptors. A stochastic resonance effect has been shown in this system in which light enhances the transduction of a weak, periodic mechanosensory (hydrodynamic) stimulus. It is not known, however, whether an optimal response from the CPR is induced by a single sine wave cycle or some other waveform. We have experimentally investigated this favorable waveform by driving a tailfan preparation with mechanical 10 Hz correlated Ornstein-Uhlenbeck noise and calculating the response function from the spike-triggered average of the applied noise waveform. We will discuss differences in the shape of the optimal waveform under dark and light conditions, as well as what seems to be a noticeable difference in the magnitude of the animals' response to a noisy stimulus in comparison with a periodic stimulus.

  12. Dynamic Response of Functionally Graded Carbon Nanotube Reinforced Sandwich Plate

    Science.gov (United States)

    Mehar, Kulmani; Panda, Subrata Kumar

    2018-03-01

    In this article, the dynamic response of the carbon nanotube-reinforced functionally graded sandwich composite plate has been studied numerically with the help of finite element method. The face sheets of the sandwich composite plate are made of carbon nanotube- reinforced composite for two different grading patterns whereas the core phase is taken as isotropic material. The final properties of the structure are calculated using the rule of mixture. The geometrical model of the sandwich plate is developed and discretized suitably with the help of available shell element in ANSYS library. Subsequently, the corresponding numerical dynamic responses computed via batch input technique (parametric design language code in ANSYS) of ANSYS including Newmark’s integration scheme. The stability of the sandwich structural numerical model is established through the proper convergence study. Further, the reliability of the sandwich model is checked by comparison study between present and available results from references. As a final point, some numerical problems have been solved to examine the effect of different design constraints (carbon nanotube distribution pattern, core to face thickness ratio, volume fractions of the nanotube, length to thickness ratio, aspect ratio and constraints at edges) on the time-responses of sandwich plate.

  13. Identification and functional analysis of novel phosphorylation sites in the RNA surveillance protein Upf1.

    Science.gov (United States)

    Lasalde, Clarivel; Rivera, Andrea V; León, Alfredo J; González-Feliciano, José A; Estrella, Luis A; Rodríguez-Cruz, Eva N; Correa, María E; Cajigas, Iván J; Bracho, Dina P; Vega, Irving E; Wilkinson, Miles F; González, Carlos I

    2014-02-01

    One third of inherited genetic diseases are caused by mRNAs harboring premature termination codons as a result of nonsense mutations. These aberrant mRNAs are degraded by the Nonsense-Mediated mRNA Decay (NMD) pathway. A central component of the NMD pathway is Upf1, an RNA-dependent ATPase and helicase. Upf1 is a known phosphorylated protein, but only portions of this large protein have been examined for phosphorylation sites and the functional relevance of its phosphorylation has not been elucidated in Saccharomyces cerevisiae. Using tandem mass spectrometry analyses, we report the identification of 11 putative phosphorylated sites in S. cerevisiae Upf1. Five of these phosphorylated residues are located within the ATPase and helicase domains and are conserved in higher eukaryotes, suggesting a biological significance for their phosphorylation. Indeed, functional analysis demonstrated that a small carboxy-terminal motif harboring at least three phosphorylated amino acids is important for three Upf1 functions: ATPase activity, NMD activity and the ability to promote translation termination efficiency. We provide evidence that two tyrosines within this phospho-motif (Y-738 and Y-742) act redundantly to promote ATP hydrolysis, NMD efficiency and translation termination fidelity.

  14. Natural responses to Quaternary climatic change in the Nevada Test Site region

    International Nuclear Information System (INIS)

    Gibson, J.D.

    1993-01-01

    Migration of hazardous contaminants within geologic settings depends on natural processes. Climatic fluctuations can affect the magnitudes and rates of many of these processes. In any long-term environmental evaluation of natural processes, responses to climatic change must be considered. Four generalized categories of natural responses to Quaternary climatic change are recognized for the Nevada Test Site (NTS) region of southwestern Nevada and adjacent California: (1) biologic, (2) geomorphic, (3) hydrologic (including surface and subsurface) and (4) pedologic/diagenetic. Specific examples that correspond to the four categories illustrate the broad range of complex natural processes the are affected by climatic change. These responses dictate the potential effects of climatic change on contaminant transport, effects that are being examined by existing and planned environmental-restoration and waste-management programs within the region. Regulatory requirements for many of these programs include long-term (>10,000-year) waste isolation because of radiologic components. The purpose here is not to be exhaustive in documenting all known natural responses to climatic change in the NTS region, but rather to give a flavor of the scope of interdisciplinary and interrelated fields of Quaternary science that must be considered in evaluating the possible effects of climatic change on long-term environmental programs

  15. HECTR [Hydrogen Event: Containment Transient Response] analyses of the Nevada Test Site (NTS) premixed combustion experiments

    International Nuclear Information System (INIS)

    Wong, C.C.

    1988-11-01

    The HECTR (Hydrogen Event: Containment Transient Response) computer code has been developed at Sandia National Laboratories to predict the transient pressure and temperature responses within reactor containments for hypothetical accidents involving the transport and combustion of hydrogen. Although HECTR was designed primarily to investigate these phenomena in LWRs, it may also be used to analyze hydrogen transport and combustion experiments as well. It is in this manner that HECTR is assessed and empirical correlations, such as the combustion completeness and flame speed correlations for the hydrogen combustion model, if necessary, are upgraded. In this report, we present HECTR analyses of the large-scale premixed hydrogen combustion experiments at the Nevada Test Site (NTS) and comparison with the test results. The existing correlations in HECTR version 1.0, under certain conditions, have difficulty in predicting accurately the combustion completeness and burn time for the NTS experiments. By combining the combustion data obtained from the NTS experiments with other experimental data (FITS, VGES, ACUREX, and Whiteshell), a set of new and better combustion correlations was generated. HECTR prediction of the containment responses, using a single-compartment model and EPRI-provided combustion completeness and burn time, compares reasonably well against the test results. However, HECTR prediction of the containment responses using a multicompartment model does not compare well with the test results. This discrepancy shows the deficiency of the homogeneous burning model used in HECTR. To overcome this deficiency, a flame propagation model is highly recommended. 16 refs., 84 figs., 5 tabs

  16. Guide to ground water remediation at CERCLA response action and RCRA corrective action sites

    International Nuclear Information System (INIS)

    1995-10-01

    This Guide contains the regulatory and policy requirements governing remediation of ground water contaminated with hazardous waste [including radioactive mixed waste (RMW)], hazardous substances, or pollutants/contaminants that present (or may present) an imminent and substantial danger. It was prepared by the Office of Environmental Policy and Assistance, RCRA/CERCLA Division (EH-413), to assist Environmental Program Managers (ERPMs) who often encounter contaminated ground water during the performance of either response actions under CERCLA or corrective actions under Subtitle C of RCRA. The Guide begins with coverage of the regulatory and technical issues that are encountered by ERPM's after a CERCLA Preliminary Assessment/Site Investigation (PA/SI) or the RCRA Facility Assessment (RFA) have been completed and releases into the environment have been confirmed. It is based on the assumption that ground water contamination is present at the site, operable unit, solid waste management unit, or facility. The Guide's scope concludes with completion of the final RAs/corrective measures and a determination by the appropriate regulatory agencies that no further response action is necessary

  17. Response spectra for nuclear structures on rock sites considering the near-fault directivity effect

    Institute of Scientific and Technical Information of China (English)

    Xu Longiun; Yang Shengchao; Xie Lili

    2010-01-01

    Near-fault ground motions, potentially with large amplitude and typical velocity pulses, may significantly impact the performance of a wide range of structures. The current study is aimed at evaluating the safety implications of the near-fault effect on nuclear power plant facilities designed according to the Chinese code. To this end, a set of near-fault ground motions at rock sites with typical forward-directivity effect is examined with special emphasis on several key parameters and response spectra. Spectral comparison of the selected records with the Chinese and other code design spectra was conducted. The bi-normalized response spectra in terms of different comer periods are utilized to derive nuclear design spectra. It is concluded that nuclear design spectra on rock sites derived from typical rupture directivity records are significantly influenced both by the earthquake magnitude and the rupture distance. The nuclear design spectra specified in the code needs to be adjusted to reflect the near-fault directivity effect of large earthquakes.

  18. A report on upgraded seismic monitoring stations in Myanmar: Station performance and site response

    Science.gov (United States)

    Thiam, Hrin Nei; Min Htwe, Yin Myo; Kyaw, Tun Lin; Tun, Pa Pa; Min, Zaw; Htwe, Sun Hninn; Aung, Tin Myo; Lin, Kyaw Kyaw; Aung, Myat Min; De Cristofaro, Jason; Franke, Mathias; Radman, Stefan; Lepiten, Elouie; Wolin, Emily; Hough, Susan E.

    2017-01-01

    Myanmar is in a tectonically complex region between the eastern edge of the Himalayan collision zone and the northern end of the Sunda megathrust. Until recently, earthquake monitoring and research efforts have been hampered by a lack of modern instrumentation and communication infrastructure. In January 2016, a major upgrade of the Myanmar National Seismic Network (MNSN; network code MM) was undertaken to improve earthquake monitoring capability. We installed five permanent broadband and strong‐motion seismic stations and real‐time data telemetry using newly improved cellular networks. Data are telemetered to the MNSN hub in Nay Pyi Taw and archived at the Incorporated Research Institutions for Seismology Data Management Center. We analyzed station noise characteristics and site response using noise and events recorded over the first six months of station operation. Background noise characteristics vary across the array, but indicate that the new stations are performing well. MM stations recorded more than 20 earthquakes of M≥4.5 within Myanmar and its immediate surroundings, including an M 6.8 earthquake located northwest of Mandalay on 13 April 2016 and the Mw 6.8 Chauk event on 24 August 2016. We use this new dataset to calculate horizontal‐to‐vertical spectral ratios, which provide a preliminary characterization of site response of the upgraded MM stations.

  19. Dynamic selection of ship responses for estimation of on-site directional wave spectra

    DEFF Research Database (Denmark)

    Andersen, Ingrid Marie Vincent; Storhaug, Gaute

    2012-01-01

    -estimate of the wave spectrum is suggested. The selection method needs to be robust for what reason a parameterised uni-directional, two-parameter wave spectrum is treated. The parameters included are the zero up-crossing period, the significant wave height and the main wave direction relative to the ship’s heading...... with the best overall agreement are selected for the actual estimation of the directional wave spectrum. The transfer functions for the ship responses can be determined using different computational methods such as striptheory, 3D panel codes, closed form expressions or model tests. The uncertainty associated......Knowledge of the wave environment in which a ship is operating is crucial for most on-board decision support systems. Previous research has shown that the directional wave spectrum can be estimated by the use of measured global ship responses and a set of transfer functions determined...

  20. Directional topographic site response at Tarzana observed in aftershocks of the 1994 Northridge, California, earthquake: Implications for mainshock motions

    Science.gov (United States)

    Spudich, P.; Hellweg, M.; Lee, W.H.K.

    1996-01-01

    The Northridge earthquake caused 1.78 g acceleration in the east-west direction at a site in Tarzana, California, located about 6 km south of the mainshock epicenter. The accelerograph was located atop a hill about 15-m high, 500-m long, and 130-m wide, striking about N78??E. During the aftershock sequence, a temporary array of 21 three-component geophones was deployed in six radial lines centered on the accelerograph, with an average sensor spacing of 35 m. Station COO was located about 2 m from the accelerograph. We inverted aftershock spectra to obtain average relative site response at each station as a function of direction of ground motion. We identified a 3.2-Hz resonance that is a transverse oscillation of the hill (a directional topographic effect). The top/base amplification ratio at 3.2 Hz is about 4.5 for horizontal ground motions oriented approximately perpendicular to the long axis of the hill and about 2 for motions parallel to the hill. This resonance is seen most strongly within 50 m of COO. Other resonant frequencies were also observed. A strong lateral variation in attenuation, probably associated with a fault, caused substantially lower motion at frequencies above 6 Hz at the east end of the hill. There may be some additional scattered waves associated with the fault zone and seen at both the base and top of the hill, causing particle motions (not spectral ratios) at the top of the hill to be rotated about 20?? away from the direction transverse to the hill. The resonant frequency, but not the amplitude, of our observed topographic resonance agrees well with theory, even for such a low hill. Comparisons of our observations with theoretical results indicate that the 3D shape of the hill and its internal structure are important factors affecting its response. The strong transverse resonance of the hill does not account for the large east-west mainshock motions. Assuming linear soil response, mainshock east-west motions at the Tarzana accelerograph

  1. Site specific interaction between ZnO nanoparticles and tyrosine: A density functional theory study

    Science.gov (United States)

    Singh, Satvinder; Singh, Janpreet; Singh, Baljinder; Singh, Gurinder; Kaura, Aman; Tripathi, S. K.

    2018-05-01

    First Principles Calculations have been performed on ZnO/Tyrosine atomic complex to study site specific interaction of Tyrosine and ZnO nanoparticles. Calculated results shows that -COOH group present in Tyrosine is energetically more favorable than -NH2 group. Interactions show ionic bonding between ZnO and Tyrosine. All the calculations have been performed under the Density Functional Theory (DFT) framework. Structural and electronic properties of (ZnO)3/Tyrosine complex have been studied. Gaussian basis set approach has been adopted for the calculations. A ring type most stable (ZnO)3 atomic cluster has been modeled, analyzed and used for the calculations.

  2. Structural and Functional Consequences of Chaperone Site Deletion in αA-Crystallin

    Science.gov (United States)

    Santhoshkumar, Puttur; Karmakar, Srabani; Sharma, Krishna K.

    2016-01-01

    The chaperone-like activity of αA-crystallin has an important role in maintaining lens transparency. Previously we identified residues 70–88 as a chaperone site in αA-crystallin. In this study, we deleted the chaperone site residues to generate αAΔ70–76 and αAΔ70–88 mutants and investigated if there are additional substrate-binding sites in αA-crystallin. Both mutant proteins when expressed in E. coli formed inclusion bodies, and on solubilizing and refolding, they exhibited similar structural properties, with a 2- to 3-fold increase in molar mass compared to the molar mass of wild-type protein. The deletion mutants were less stable than the wild-type αA-crystallin. Functionally αAΔ70–88 was completely inactive as a chaperone, while αAΔ70–76 demonstrated a 40–50% reduction in anti-aggregation activity against alcohol dehydrogenase (ADH). Deletion of residues 70–88 abolished the ADH binding sites in αA-crystallin at physiological temperature. At 45 °C, cryptic ADH binding site(s) became exposed, which contributed subtly to the chaperone-like activity of αAΔ70–88. Both of the deletion mutants were completely inactive in suppressing aggregation of βL-crystallin at 53 °C. The mutants completely lost the anti-apoptotic property that αA-crystallin exhibits while they protected ARPE-19 (a human retinal pigment epithelial cell line) and primary human lens epithelial (HLE) cells from oxidative stress. Our studies demonstrate that residues 70–88 in αA-crystallin act as a primary substrate binding site and account for the bulk of the total chaperone activity. The β3 and β4 strands in αA-crystallin comprising 70–88 residues play an important role in maintenance of the structure and in preventing aggregation of denaturing proteins. PMID:27524665

  3. Site response assessment at the city of Alkhobar, Eastern Saudi Arabia from microtremor and boring data

    Science.gov (United States)

    Fnais, M. S.

    2014-12-01

    The AlKhobar City affected by distant earthquakes from Zagros fold-fault belt of subduction zone. These earthquakes produced great site effects on the sedimentary layers that in turn significantly influenced earthquake ground motions in the area. Mapping of site response using microtremor measurements compared with geological and borehole data of Alkhobar city is the main target of this work. The resonance frequency and their H/V values have been calculated using Nakamura technique through deployed of seismograph instruments at 113 sites in AlKhobar city for different time periods. The recording length was about one hour with sampling frequency of 100 Hz. Most of the measured sites present three peaks for the resonance frequency; the first peak ranges from 0.33 to 1.03 Hz, the second peak ranges from 1.03 to 1.23 Hz, while the third peak ranges from 1.23-1.73. Tests have been conducted to ensure that these peaks are natural in origin. The northern zones of AlKhobar City have lower values of resonance frequency indicating great thickness of sediments. In contrast, the southern parts of the city have higher values of resonance frequency illustrating shallow depths of the bedrock. Furthermore, twenty of boreholes have been conducted through AlKhobar City to different depth. Standard penetration test (SPT) data has been corrected and used to calculate the resonance frequency at their locations. Borehole results clarified that the resonance frequency values range from 0.27 to 1.95 Hz. These results are correlated well with that of the microtremor measurements. Accordingly, the first peak have been interpreted due to the impedance contrast between the limestone and the overlying sediments, while the third peak is originated from a boundary between the upper most surface layer and the underlying sediments. These results must be applied for earthquake risk mitigation in AlKhobar City.

  4. Presence of a predator image in potential breeding sites and oviposition responses of a dengue vector.

    Science.gov (United States)

    Dieng, Hamady; Satho, Tomomitsu; Suradi, Nur Farrahana Binti; Hakim, Hafijah; Abang, Fatimah; Aliasan, Nur Ezzati; Miake, Fumio; Zuharah, Wan Fatma; Kassim, Nur Faeza A; Majid, Abdul Hafiz A; Fadzly, Nik; Vargas, Ronald E Morales; Morales, Noppawan P; Noweg, Gabriel Tonga

    2017-12-01

    In dengue vector control, attempts to minimize or replace the use of pesticides have mostly involved use of predators, but success has been severely impeded by difficulties associated with financial and environmental costs, predator mass production, and persistence in target habitats. Visual deterrents have been used successfully to control animal pests, in some cases in an effort to replace pesticide use. Despite evidence that visual signals are crucial in site choice for egg deposition by dengue vectors, and that female mosquitoes respond to artificial predation, the role of predator intimidation as it affects the oviposition behavior of dengue vectors remains largely unexplored. Here, we examined the oviposition responses of Aedes aegypti exposed to various mosquito predator pictures. Gravid females were presented with equal opportunities to oviposit in two cups with predator images [Toxorhynchites splendens-TXI, Goldfish (Carassius auratus)-small (SFI) and large (LFI) and Tx. splendens+Goldfish-TXFI] and two others without pictures. Differences in egg deposition were examined between sites with and without these images. When given a chance to oviposit in cups with and without TXI, Ae. aegypti females were similarly attracted to both sites. When provided an opportunity to oviposit in cups displaying pictures of fish (SFI or LFI) and blank cups, egg deposition rates were much lower in the fish picture sites. Females showed a preference for blank cups over TXFI for egg deposition. They also equally avoided cups with pictures of fish, regardless of the size of the picture. Our results indicate that the presence of images of goldfish and their association with Tx. larvae significantly reduced egg deposition by Ae. aegypti, and this was not the case with the predatory larvae alone. The observations that the images of natural predators can repel gravid females of a dengue vector provide novel possibilities to develop effective and inexpensive alternative tools to

  5. Seismic site-response characterization of high-velocity sites using advanced geophysical techniques: application to the NAGRA-Net

    Czech Academy of Sciences Publication Activity Database

    Poggi, V.; Burjánek, Jan; Michel, C.; Fäh, D.

    2017-01-01

    Roč. 210, č. 2 (2017), s. 645-659 ISSN 0956-540X Institutional support: RVO:67985530 Keywords : joint inversion * earthquake ground motions * seismic noise * site effects Subject RIV: DC - Siesmology, Volcanology, Earth Structure OBOR OECD: Volcanology Impact factor: 2.414, year: 2016

  6. Lithic technological responses to Late Pleistocene glacial cycling at Pinnacle Point Site 5-6, South Africa

    Science.gov (United States)

    Brown, Kyle S.; Oestmo, Simen; Pereira, Telmo; Ranhorn, Kathryn L.; Schoville, Benjamin J.; Marean, Curtis W.

    2017-01-01

    There are multiple hypotheses for human responses to glacial cycling in the Late Pleistocene, including changes in population size, interconnectedness, and mobility. Lithic technological analysis informs us of human responses to environmental change because lithic assemblage characteristics are a reflection of raw material transport, reduction, and discard behaviors that depend on hunter-gatherer social and economic decisions. Pinnacle Point Site 5–6 (PP5-6), Western Cape, South Africa is an ideal locality for examining the influence of glacial cycling on early modern human behaviors because it preserves a long sequence spanning marine isotope stages (MIS) 5, 4, and 3 and is associated with robust records of paleoenvironmental change. The analysis presented here addresses the question, what, if any, lithic assemblage traits at PP5-6 represent changing behavioral responses to the MIS 5-4-3 interglacial-glacial cycle? It statistically evaluates changes in 93 traits with no a priori assumptions about which traits may significantly associate with MIS. In contrast to other studies that claim that there is little relationship between broad-scale patterns of climate change and lithic technology, we identified the following characteristics that are associated with MIS 4: increased use of quartz, increased evidence for outcrop sources of quartzite and silcrete, increased evidence for earlier stages of reduction in silcrete, evidence for increased flaking efficiency in all raw material types, and changes in tool types and function for silcrete. Based on these results, we suggest that foragers responded to MIS 4 glacial environmental conditions at PP5-6 with increased population or group sizes, ‘place provisioning’, longer and/or more intense site occupations, and decreased residential mobility. Several other traits, including silcrete frequency, do not exhibit an association with MIS. Backed pieces, once they appear in the PP5-6 record during MIS 4, persist through MIS

  7. FDG PET/CT for therapeutic response monitoring in multi-site non-respiratory tuberculosis

    International Nuclear Information System (INIS)

    Geng Tian; Yong Xiao; Bin Chen; Jun Xia; Hong Guan; Qunyi Deng

    2010-01-01

    Background: Tuberculosis (TB) can produce positive signals during 18 F-fluorodeoxyglucose positron emission/computed tomography (FDG PET/CT) scanning. Until now, there has been no better method than clinical assessment to evaluate the therapeutic response of non-respiratory TB (NRTB). Purpose: To retrospectively assess the ability of FDG PET/CT to evaluate the response to anti-TB treatment in patients with NRTB. Material and Methods: Three patients with multi-site NRTB underwent repeat PET/CT scans during anti-TB treatment. Changes in maximal standard uptake value (SUVmax) of the TB lesions on PET/CT images were analyzed between two scans. Initial PET/CT scans were performed before the start of anti-TB treatment, and later scans were performed after completion of the treatment. Results: Patient 1, a 63-year-old female, and patient 2, a 50-year-old male, were diagnosed as multi-site NRTB by biopsy. Patient 3, a 37-year-old male was diagnosed clinically. These patients demonstrated multiple FDG-avid lesions in whole body on initial PET/CT images. The highest SUVmax of patient 1, 2, and 3 were 13.6, 17.7, and 13.9 separately. After completion of the treatment, all positive signals of patient 1, 2, and 3 decreased to undetectable value on repeated PET/CT scans with intervals of 318 days, 258 days, and 182 days separately. Conclusion: FDG PET/CT scan may be useful for monitoring responses to anti-TB treatment in patients with NRTB

  8. Effects of functionalization on the targeting site of carbon nanotubes inside cells

    International Nuclear Information System (INIS)

    Porter, A E; Bendall, J S; Welland, M; Gass, M; Muller, K; Skepper, J; Midgley, P

    2010-01-01

    Functionalized single-walled carbon nanotubes (SWNTs) are currently being investigated for a variety of applications, including contrast agents for medical imaging 1 . However before they can be used commercially it is necessary to assess whether they enter cells, the site they target within the cell and whether they cause any cytotoxicity. Here we characterize uptake of unlabelled, acid-treated, COO - functionalized SWNTs by human monocyte derived macrophage cells using both low-loss and energy loss spectroscopy and compare our findings to previous work on unpurified SWNTs. The acid-treated SWNTs were less aggregated within cells than unpurified SWNTs. Acid treatment was found to affect the distribution of intracellular SWNTs. Bundles, and also individual acid treated SWNTs, were found frequently inside lysosomes, cytoplasm and also inserting into the plasma membrane whereas unpurified non-functionalised SWNTs entered lysosomes and occasionally the nucleus.

  9. Effects of functionalization on the targeting site of carbon nanotubes inside cells

    Energy Technology Data Exchange (ETDEWEB)

    Porter, A E; Bendall, J S; Welland, M [UK SuperSTEM, Daresbury Laboratory, Daresbury, Cheshire WA4 4AD (United Kingdom); Gass, M [The Nanoscience Centre, University of Cambridge, 11 J. J. Thompson Avenue, Cambridge CB3 OFF (United Kingdom); Muller, K; Skepper, J [Multiimaging Centre, Department of PDN, Physiology, Development and Neuroscience, Anatomy Building, University of Cambridge, Downing Street, Cambridge CB2 3DY (United Kingdom); Midgley, P, E-mail: a.porter@imperial.ac.u [Department of Materials Science and Metallurgy, University of Cambridge, Pembroke Street, Cambridge CB2 3QZ (United Kingdom)

    2010-07-01

    Functionalized single-walled carbon nanotubes (SWNTs) are currently being investigated for a variety of applications, including contrast agents for medical imaging{sup 1}. However before they can be used commercially it is necessary to assess whether they enter cells, the site they target within the cell and whether they cause any cytotoxicity. Here we characterize uptake of unlabelled, acid-treated, COO{sup -} functionalized SWNTs by human monocyte derived macrophage cells using both low-loss and energy loss spectroscopy and compare our findings to previous work on unpurified SWNTs. The acid-treated SWNTs were less aggregated within cells than unpurified SWNTs. Acid treatment was found to affect the distribution of intracellular SWNTs. Bundles, and also individual acid treated SWNTs, were found frequently inside lysosomes, cytoplasm and also inserting into the plasma membrane whereas unpurified non-functionalised SWNTs entered lysosomes and occasionally the nucleus.

  10. PKA regulates calcineurin function through the phosphorylation of RCAN1: Identification of a novel phosphorylation site

    International Nuclear Information System (INIS)

    Kim, Seon Sook; Lee, Eun Hye; Lee, Kooyeon; Jo, Su-Hyun; Seo, Su Ryeon

    2015-01-01

    Calcineurin is a calcium/calmodulin-dependent phosphatase that has been implicated in T cell activation through the induction of nuclear factors of activated T cells (NFAT). We have previously suggested that endogenous regulator of calcineurin (RCAN1, also known as DSCR1) is targeted by protein kinase A (PKA) for the control of calcineurin activity. In the present study, we characterized the PKA-mediated phosphorylation site in RCAN1 by mass spectrometric analysis and revealed that PKA directly phosphorylated RCAN1 at the Ser 93. PKA-induced phosphorylation and the increase in the half-life of the RCAN1 protein were prevented by the substitution of Ser 93 with Ala (S93A). Furthermore, the PKA-mediated phosphorylation of RCAN1 at Ser 93 potentiated the inhibition of calcineurin-dependent pro-inflammatory cytokine gene expression by RCAN1. Our results suggest the presence of a novel phosphorylation site in RCAN1 and that its phosphorylation influences calcineurin-dependent inflammatory target gene expression. - Highlights: • We identify novel phosphorylation sites in RCAN1 by LC-MS/MS analysis. • PKA-dependent phosphorylation of RCAN1 at Ser 93 inhibits calcineurin-mediated intracellular signaling. • We show the immunosuppressive function of RCAN1 phosphorylation at Ser 93 in suppressing cytokine expression

  11. Effect of self-deflection on a totally asymmetric simple exclusion process with functions of site assignments

    Science.gov (United States)

    Tsuzuki, Satori; Yanagisawa, Daichi; Nishinari, Katsuhiro

    2018-04-01

    This study proposes a model of a totally asymmetric simple exclusion process on a single-channel lane with functions of site assignments along the pit lane. The system model attempts to insert a new particle to the leftmost site at a certain probability by randomly selecting one of the empty sites in the pit lane, and reserving it for the particle. Thereafter, the particle is directed to stop at the site only once during its travel. Recently, the system was determined to show a self-deflection effect, in which the site usage distribution biases spontaneously toward the leftmost site, and the throughput becomes maximum when the site usage distribution is slightly biased to the rightmost site. Our exact analysis describes this deflection effect and show a good agreement with simulations.

  12. Simulation of ecological processes using response functions method

    International Nuclear Information System (INIS)

    Malkina-Pykh, I.G.; Pykh, Yu. A.

    1998-01-01

    The article describes further development and applications of the already well-known response functions method (MRF). The method is used as a basis for the development of mathematical models of a wide set of ecological processes. The model of radioactive contamination of the ecosystems is chosen as an example. The mathematical model was elaborated for the description of 90 Sr dynamics in the elementary ecosystems of various geographical zones. The model includes the blocks corresponding with the main units of any elementary ecosystem: lower atmosphere, soil, vegetation, surface water. Parameters' evaluation was provided on a wide set of experimental data. A set of computer simulations was done on the model to prove the possibility of the model's use for ecological forecasting

  13. Forest ecotone response to climate change: sensitivity to temperature response functional forms

    Energy Technology Data Exchange (ETDEWEB)

    Loehle, C. [National Council for Air and Stream Improvement, Naperville, IL (United States)

    2000-10-01

    Past simulation studies have been in general agreement that climatic change could have adverse effects on forests, including geographic range shrinkages, conversion to grassland, and catastrophic forest decline or dieback. Some other recent studies, however, concluded that this agreement is generally based on parabolic temperature response rather than functional responses or data, and may therefore exaggerate dieback effects. This paper proposes a new model of temperature response that is based on a trade-off between cold tolerance and growth rate. In this model, the growth rate increases at first, and then levels off with increasing growing degree-days. Species from more southern regions have a higher minimum temperature and a faster maximum height growth rate. It is argued that faster growth rates of southern types lead to their competitive superiority in warmer environments and that such temperature response should produce less dieback and slower rates of change than the more common parabolic response model. Theoretical justification of this model is provided, followed by application of the model to a simulated ecotone under a warming scenario. Results of the study based on the proposed asymptotic model showed no dieback and only a gradual ecotone movement north, suggesting that ecotone shifts will, in fact, take many hundreds to thousands of years, with the result that species will not face the risk of extinction. 56 refs., 1 tab., 8 figs.

  14. Immune responses at brain barriers and implications for brain development and neurological function in later life

    Directory of Open Access Journals (Sweden)

    Helen B. Stolp

    2013-08-01

    Full Text Available For a long time the brain has been considered an immune-privileged site due to a muted inflammatory response and the presence of protective brain barriers. It is now recognised that neuroinflammation may play an important role in almost all neurological disorders and that the brain barriers may be contributing through either normal immune signalling, or disruption of their basic physiological mechanisms. The distinction between normal function and dysfunction at the barriers is difficult to dissect, partly due to a lack of understanding of normal barrier function and partly because of physiological changes that occur as part of normal development and ageing. Brain barriers consist of a number of interacting structural and physiological elements including tight junctions between adjacent barrier cells and an array of influx and efflux transporters. Despite these protective mechanisms, the capacity for immune-surveillance of the brain is maintained, and there is evidence of inflammatory signalling at the brain barriers that may be an important part of the body’s response to damage or infection. This signalling system appears to change both with normal ageing, and during disease. Changes may affect diapedesis of immune cells and active molecular transfer, or cause rearrangement of the tight junctions and an increase in passive permeability across barrier interfaces. Here we review the many elements that contribute to brain barrier functions and how they respond to inflammation, particularly during development and aging. The implications of inflammation–induced barrier dysfunction for brain development and subsequent neurological function are also discussed.

  15. Site response, shallow shear-wave velocity, and damage in Los Gatos, California, from the 1989 Loma Prieta earthquake

    Science.gov (United States)

    Hartzell, S.; Carver, D.; Williams, R.A.

    2001-01-01

    Aftershock records of the 1989 Loma Prieta earthquake are used to calculate site response in the frequency band of 0.5-10 Hz at 24 locations in Los Gatos, California, on the edge of the Santa Clara Valley. Two different methods are used: spectral ratios relative to a reference site on rock and a source/site spectral inversion method. These two methods complement each other and give consistent results. Site amplification factors are compared with surficial geology, thickness of alluvium, shallow shear-wave velocity measurements, and ground deformation and structural damage resulting from the Loma Prieta earthquake. Higher values of site amplification are seen on Quaternary alluvium compared with older Miocene and Cretaceous units of Monterey and Franciscan Formation. However, other more detailed correlations with surficial geology are not evident. A complex pattern of alluvial sediment thickness, caused by crosscutting thrust faults, is interpreted as contributing to the variability in site response and the presence of spectral resonance peaks between 2 and 7 Hz at some sites. Within the range of our field measurements, there is a correlation between lower average shear-wave velocity of the top 30 m and 50% higher values of site amplification. An area of residential homes thrown from their foundations correlates with high site response. This damage may also have been aggravated by local ground deformation. Severe damage to commercial buildings in the business district, however, is attributed to poor masonry construction.

  16. Evolutionarily conserved sites in yeast tropomyosin function in cell polarity, transport and contractile ring formation

    Directory of Open Access Journals (Sweden)

    Susanne Cranz-Mileva

    2015-08-01

    Full Text Available Tropomyosin is a coiled-coil protein that binds and regulates actin filaments. The tropomyosin gene in Schizosaccharomyces pombe, cdc8, is required for formation of actin cables, contractile rings, and polar localization of actin patches. The roles of conserved residues were investigated in gene replacement mutants. The work validates an evolution-based approach to identify tropomyosin functions in living cells and sites of potential interactions with other proteins. A cdc8 mutant with near-normal actin affinity affects patch polarization and vacuole fusion, possibly by affecting Myo52p, a class V myosin, function. The presence of labile residual cell attachments suggests a delay in completion of cell division and redistribution of cell patches following cytokinesis. Another mutant with a mild phenotype is synthetic negative with GFP-fimbrin, inferring involvement of the mutated tropomyosin sites in interaction between the two proteins. Proteins that assemble in the contractile ring region before actin do so in a mutant cdc8 strain that cannot assemble condensed actin rings, yet some cells can divide. Of general significance, LifeAct-GFP negatively affects the actin cytoskeleton, indicating caution in its use as a biomarker for actin filaments.

  17. Exploring functionally related enzymes using radially distributed properties of active sites around the reacting points of bound ligands

    Directory of Open Access Journals (Sweden)

    Ueno Keisuke

    2012-04-01

    Full Text Available Abstract Background Structural genomics approaches, particularly those solving the 3D structures of many proteins with unknown functions, have increased the desire for structure-based function predictions. However, prediction of enzyme function is difficult because one member of a superfamily may catalyze a different reaction than other members, whereas members of different superfamilies can catalyze the same reaction. In addition, conformational changes, mutations or the absence of a particular catalytic residue can prevent inference of the mechanism by which catalytic residues stabilize and promote the elementary reaction. A major hurdle for alignment-based methods for prediction of function is the absence (despite its importance of a measure of similarity of the physicochemical properties of catalytic sites. To solve this problem, the physicochemical features radially distributed around catalytic sites should be considered in addition to structural and sequence similarities. Results We showed that radial distribution functions (RDFs, which are associated with the local structural and physicochemical properties of catalytic active sites, are capable of clustering oxidoreductases and transferases by function. The catalytic sites of these enzymes were also characterized using the RDFs. The RDFs provided a measure of the similarity among the catalytic sites, detecting conformational changes caused by mutation of catalytic residues. Furthermore, the RDFs reinforced the classification of enzyme functions based on conventional sequence and structural alignments. Conclusions Our results demonstrate that the application of RDFs provides advantages in the functional classification of enzymes by providing information about catalytic sites.

  18. Functional Associations by Response Overlap (FARO, a functional genomics approach matching gene expression phenotypes.

    Directory of Open Access Journals (Sweden)

    Henrik Bjørn Nielsen

    2007-08-01

    Full Text Available The systematic comparison of transcriptional responses of organisms is a powerful tool in functional genomics. For example, mutants may be characterized by comparing their transcript profiles to those obtained in other experiments querying the effects on gene expression of many experimental factors including treatments, mutations and pathogen infections. Similarly, drugs may be discovered by the relationship between the transcript profiles effectuated or impacted by a candidate drug and by the target disease. The integration of such data enables systems biology to predict the interplay between experimental factors affecting a biological system. Unfortunately, direct comparisons of gene expression profiles obtained in independent, publicly available microarray experiments are typically compromised by substantial, experiment-specific biases. Here we suggest a novel yet conceptually simple approach for deriving 'Functional Association(s by Response Overlap' (FARO between microarray gene expression studies. The transcriptional response is defined by the set of differentially expressed genes independent from the magnitude or direction of the change. This approach overcomes the limited comparability between studies that is typical for methods that rely on correlation in gene expression. We apply FARO to a compendium of 242 diverse Arabidopsis microarray experimental factors, including phyto-hormones, stresses and pathogens, growth conditions/stages, tissue types and mutants. We also use FARO to confirm and further delineate the functions of Arabidopsis MAP kinase 4 in disease and stress responses. Furthermore, we find that a large, well-defined set of genes responds in opposing directions to different stress conditions and predict the effects of different stress combinations. This demonstrates the usefulness of our approach for exploiting public microarray data to derive biologically meaningful associations between experimental factors. Finally, our

  19. Single-site Green function of the Dirac equation for full-potential electron scattering

    Energy Technology Data Exchange (ETDEWEB)

    Kordt, Pascal

    2012-05-30

    I present an elaborated analytical examination of the Green function of an electron scattered at a single-site potential, for both the Schroedinger and the Dirac equation, followed by an efficient numerical solution, in both cases for potentials of arbitrary shape without an atomic sphere approximation. A numerically stable way to calculate the corresponding regular and irregular wave functions and the Green function is via the angular Lippmann-Schwinger integral equations. These are solved based on an expansion in Chebyshev polynomials and their recursion relations, allowing to rewrite the Lippmann-Schwinger equations into a system of algebraic linear equations. Gonzales et al. developed this method for the Schroedinger equation, where it gives a much higher accuracy compared to previous perturbation methods, with only modest increase in computational effort. In order to apply it to the Dirac equation, I developed relativistic Lippmann-Schwinger equations, based on a decomposition of the potential matrix into spin spherical harmonics, exploiting certain properties of this matrix. The resulting method was embedded into a Korringa-Kohn-Rostoker code for density functional calculations. As an example, the method is applied by calculating phase shifts and the Mott scattering of a tungsten impurity. (orig.)

  20. Single-site Green function of the Dirac equation for full-potential electron scattering

    International Nuclear Information System (INIS)

    Kordt, Pascal

    2012-01-01

    I present an elaborated analytical examination of the Green function of an electron scattered at a single-site potential, for both the Schroedinger and the Dirac equation, followed by an efficient numerical solution, in both cases for potentials of arbitrary shape without an atomic sphere approximation. A numerically stable way to calculate the corresponding regular and irregular wave functions and the Green function is via the angular Lippmann-Schwinger integral equations. These are solved based on an expansion in Chebyshev polynomials and their recursion relations, allowing to rewrite the Lippmann-Schwinger equations into a system of algebraic linear equations. Gonzales et al. developed this method for the Schroedinger equation, where it gives a much higher accuracy compared to previous perturbation methods, with only modest increase in computational effort. In order to apply it to the Dirac equation, I developed relativistic Lippmann-Schwinger equations, based on a decomposition of the potential matrix into spin spherical harmonics, exploiting certain properties of this matrix. The resulting method was embedded into a Korringa-Kohn-Rostoker code for density functional calculations. As an example, the method is applied by calculating phase shifts and the Mott scattering of a tungsten impurity. (orig.)

  1. Functional outcomes following surgical-site infections after operative fixation of closed ankle fractures.

    Science.gov (United States)

    Naumann, Markus G; Sigurdsen, Ulf; Utvåg, Stein Erik; Stavem, Knut

    2017-12-01

    To compare the functional outcomes between patients with and without postoperative surgical-site infection (SSI) after surgical treatment in closed ankle fractures. Retrospective cohort study with prospective follow-up. Of 1011 treated patients, 959 were eligible for inclusion in a postal survey. Functional outcomes were assessed using three self-reported questionnaires. In total 567 patients responded a median of 4.3 years (range 3.1-6.2 years) after surgery. In total 29/567 had an SSI. The mean Olerud and Molander Ankle Score was 19.8 points lower for patients with a deep SSI (p=0.02), the Lower Extremity Functional Scale score was 10.2 points lower (p<0.01) and the Self-Reported Foot & Ankle Questionnaire score was 5.0 points higher (p=0.10) than for those without an SSI, after adjusting for age, sex, smoking status, diabetes, physical status, fracture classification and duration of surgery. Patients with a deep SSI had worse long-term functional outcomes than those without an SSI. Copyright © 2016 European Foot and Ankle Society. Published by Elsevier Ltd. All rights reserved.

  2. Electromagnetic and neutral-weak response functions of light nuclei

    Science.gov (United States)

    Lovato, Alessandro

    2015-10-01

    A major goal of nuclear theory is to understand the strong interaction in nuclei as it manifests itself in terms of two- and many-body forces among the nuclear constituents, the protons and neutrons, and the interactions of these constituents with external electroweak probes via one- and many-body currents. Using imaginary-time projection technique, quantum Monte Carlo allows for solving the time-independent Schrödinger equation even for Hamiltonians including highly spin-isospin dependent two- and three- body forces. I will present a recent Green's function Monte Carlo calculation of the quasi-elastic electroweak response functions in light nuclei, needed to describe electron and neutrino scattering. We found that meson-exchange two-body currents generate excess transverse strength from threshold to the quasielastic to the dip region and beyond. These results challenge the conventional picture of quasi elastic inclusive scattering as being largely dominated by single-nucleon knockout processes. These findings are of particular interest for the interpretation of neutrino oscillation signals.

  3. A comprehensive software suite for protein family construction and functional site prediction.

    Directory of Open Access Journals (Sweden)

    David Renfrew Haft

    Full Text Available In functionally diverse protein families, conservation in short signature regions may outperform full-length sequence comparisons for identifying proteins that belong to a subgroup within which one specific aspect of their function is conserved. The SIMBAL workflow (Sites Inferred by Metabolic Background Assertion Labeling is a data-mining procedure for finding such signature regions. It begins by using clues from genomic context, such as co-occurrence or conserved gene neighborhoods, to build a useful training set from a large number of uncharacterized but mutually homologous proteins. When training set construction is successful, the YES partition is enriched in proteins that share function with the user's query sequence, while the NO partition is depleted. A selected query sequence is then mined for short signature regions whose closest matches overwhelmingly favor proteins from the YES partition. High-scoring signature regions typically contain key residues critical to functional specificity, so proteins with the highest sequence similarity across these regions tend to share the same function. The SIMBAL algorithm was described previously, but significant manual effort, expertise, and a supporting software infrastructure were required to prepare the requisite training sets. Here, we describe a new, distributable software suite that speeds up and simplifies the process for using SIMBAL, most notably by providing tools that automate training set construction. These tools have broad utility for comparative genomics, allowing for flexible collection of proteins or protein domains based on genomic context as well as homology, a capability that can greatly assist in protein family construction. Armed with this new software suite, SIMBAL can serve as a fast and powerful in silico alternative to direct experimentation for characterizing proteins and their functional interactions.

  4. SOFTWARE QUALITY ASSURANCE FOR EMERGENCY RESPONSE CONSEQUENCE ASSESSMENT MODELS AT DOE'S SAVANNAH RIVER SITE

    International Nuclear Information System (INIS)

    Hunter, C

    2007-01-01

    The Savannah River National Laboratory's (SRNL) Atmospheric Technologies Group develops, maintains, and operates computer-based software applications for use in emergency response consequence assessment at DOE's Savannah River Site. These applications range from straightforward, stand-alone Gaussian dispersion models run with simple meteorological input to complex computational software systems with supporting scripts that simulate highly dynamic atmospheric processes. A software quality assurance program has been developed to ensure appropriate lifecycle management of these software applications. This program was designed to meet fully the overall structure and intent of SRNL's institutional software QA programs, yet remain sufficiently practical to achieve the necessary level of control in a cost-effective manner. A general overview of this program is described

  5. Call for information on coastal energy facility siting: an analysis of responses

    International Nuclear Information System (INIS)

    Anon.

    1977-01-01

    The Call for Information issued by the New Jersey Department of Environmental Protection in December 1975 consisted of an eight page questionnaire which was sent to industries, government agencies, and private organizations. Its objective was to seek the help of these groups in plans for the siting of energy facilities in the coastal zone. Potential development of oil and gas from the Baltimore Canyon region adjacent to New Jersey has made planning for energy facilities a priority issue both at the state and federal level. The Call for Information invited government and the energy industry to submit (a) suggested criteria for locating energy and energy-related facilities within the New Jersey coastal zone, (b) analyses by governmental and private agencies or groups of the need to locate energy facilities in specific sites within New Jersey's coastal zone, or in generalized portions thereof, and (c) identification of the land-use parameters, appropriate to the various types of facilities which may be proposed, now or later, for coastal siting. The findings obtained from the draft call and the final call issued seven months later are presented. The results of the industries' responses show that the electric and gas utilities gave some useful information while this was true of only a few of the oil companies. The reluctance to give informatign was perhaps aggravated by lack of clear state and federal policies. The appendices illustrate specific information on manpower, cost and facility requirements to develop oil refineries, establish a gas processing plant as well as information from the US Coast Guard and the Environmental Protection Agency. There is also a listing of the companies that bid in the August 1976 lease sale indicating which bids were accepted, a map of the offshore tracts, and a list of which companies responded to the Call for Information

  6. Cascadia Onshore-Offshore Site Response, Submarine Sediment Mobilization, and Earthquake Recurrence

    Science.gov (United States)

    Gomberg, J.

    2018-02-01

    Local geologic structure and topography may modify arriving seismic waves. This inherent variation in shaking, or "site response," may affect the distribution of slope failures and redistribution of submarine sediments. I used seafloor seismic data from the 2011 to 2015 Cascadia Initiative and permanent onshore seismic networks to derive estimates of site response, denoted Sn, in low- and high-frequency (0.02-1 and 1-10 Hz) passbands. For three shaking metrics (peak velocity and acceleration and energy density) Sn varies similarly throughout Cascadia and changes primarily in the direction of convergence, roughly east-west. In the two passbands, Sn patterns offshore are nearly opposite and range over an order of magnitude or more across Cascadia. Sn patterns broadly may be attributed to sediment resonance and attenuation. This and an abrupt step in the east-west trend of Sn suggest that changes in topography and structure at the edge of the continental margin significantly impact shaking. These patterns also correlate with gravity lows diagnostic of marginal basins and methane plumes channeled within shelf-bounding faults. Offshore Sn exceeds that onshore in both passbands, and the steepest slopes and shelf coincide with the relatively greatest and smallest Sn estimates at low and high frequencies, respectively; these results should be considered in submarine shaking-triggered slope stability failure studies. Significant north-south Sn variations are not apparent, but sparse sampling does not permit rejection of the hypothesis that the southerly decrease in intervals between shaking-triggered turbidites and great earthquakes inferred by Goldfinger et al. (2012, 2013, 2016) and Priest et al. (2017) is due to inherently stronger shaking southward.

  7. Comparison of blood volume pulse and skin conductance responses to mental and affective stimuli at different anatomical sites

    International Nuclear Information System (INIS)

    Kushki, Azadeh; Fairley, Jillian; Merja, Satyam; King, Gillian; Chau, Tom

    2011-01-01

    Measurements of blood volume pulse (BVP) and skin conductance are commonly used as indications of psychological arousal in affective computing and human–machine interfaces. To date, palmar surfaces remain the primary site for these measurements. Placement of sensors on palmar surfaces, however, is undesirable when recordings are fraught with motion and pressure artifacts. These artifacts are frequent when the human participant has involuntary movements as in hyperkinetic cerebral palsy. This motivates the use of alternative measurement sites. The present study examined the correlation between measurements of blood volume pulse and skin conductance obtained from three different sites on the body (fingers, toes and ear for BVP; fingers, toes and arch of the foot for skin conductance) in response to cognitive and affective stimuli. The results of this pilot study indicated significant inter-site correlation among signal features derived from different sites, with the exception of BVP amplitude, the number of electrodermal reactions and the slope of the electrodermal activity response. We attribute these differences in part to inter-site discrepancies in local skin conditions, such as skin temperature. Despite these differences, significant changes from baseline were present in the responses to the cognitive and affective stimuli at non-palmar sites, suggesting that these sites may provide viable signal measurements for use in affective computing and human–machine interface applications

  8. Temperature response functions introduce high uncertainty in modelled carbon stocks in cold temperature regimes

    Science.gov (United States)

    Portner, H.; Wolf, A.; Bugmann, H.

    2009-04-01

    Many biogeochemical models have been applied to study the response of the carbon cycle to changes in climate, whereby the process of carbon uptake (photosynthesis) has usually gained more attention than the equally important process of carbon release by respiration. The decomposition of soil organic matter is driven by a combination of factors with a prominent one being soil temperature [Berg and Laskowski(2005)]. One uncertainty concerns the response function used to describe the sensitivity of soil organic matter decomposition to temperature. This relationship is often described by one out of a set of similar exponential functions, but it has not been investigated how uncertainties in the choice of the response function influence the long term predictions of biogeochemical models. We built upon the well-established LPJ-GUESS model [Smith et al.(2001)]. We tested five candidate functions and calibrated them against eight datasets from different Ameriflux and CarboEuropeIP sites [Hibbard et al.(2006)]. We used a simple Exponential function with a constant Q10, the Arrhenius function, the Gaussian function [Tuomi et al.(2008), O'Connell(1990)], the Van't Hoff function [Van't Hoff(1901)] and the Lloyd&Taylor function [Lloyd and Taylor(1994)]. We assessed the impact of uncertainty in model formulation of temperature response on estimates of present and future long-term carbon storage in ecosystems and hence on the CO2 feedback potential to the atmosphere. We specifically investigated the relative importance of model formulation and the error introduced by using different data sets for the parameterization. Our results suggested that the Exponential and Arrhenius functions are inappropriate, as they overestimated the respiration rates at lower temperatures. The Gaussian, Van't Hoff and Lloyd&Taylor functions all fit the observed data better, whereby the functions of Gaussian and Van't Hoff underestimated the response at higher temperatures. We suggest, that the

  9. Transcriptional activation of transforming growth factor alpha by estradiol: requirement for both a GC-rich site and an estrogen response element half-site.

    Science.gov (United States)

    Vyhlidal, C; Samudio, I; Kladde, M P; Safe, S

    2000-06-01

    17beta-Estradiol (E2) induces transforming growth factor alpha (TGFalpha) gene expression in MCF-7 cells and previous studies have identified a 53 bp (-252 to -200) sequence containing two imperfect estrogen responsive elements (EREs) that contribute to E2 responsiveness. Deletion analysis of the TGFalpha gene promoter in this study identified a second upstream region of the promoter (-623 to -549) that is also E2 responsive. This sequence contains three GC-rich sites and an imperfect ERE half-site, and the specific cis-elements and trans-acting factors were determined by promoter analysis in transient transfection experiments, gel mobility shift assays and in vitro DNA footprinting. The results are consistent with an estrogen receptor alpha (ERalpha)/Sp1 complex interacting with an Sp1(N)(30) ERE half-site ((1/2)) motif in which both ERalpha and Sp1 bind promoter DNA. The ER/Sp1-DNA complex is formed using nuclear extracts from MCF-7 cells but not with recombinant human ERalpha or Sp1 proteins, suggesting that other nuclear factor(s) are required for complex stabilization. The E2-responsive Sp1(N)(x)ERE(1/2) motif identified in the TGFalpha gene promoter has also been characterized in the cathepsin D and heat shock protein 27 gene promoters; however, in the latter two promoters the numbers of intervening nucleotides are 23 and 10 respectively.

  10. Site-response Estimation by 1D Heterogeneous Velocity Model using Borehole Log and its Relationship to Damping Factor

    International Nuclear Information System (INIS)

    Sato, Hiroaki

    2014-01-01

    In the Niigata area, which suffered from several large earthquakes such as the 2007 Chuetsu-oki earthquake, geographical observation that elucidates the S-wave structure of the underground is advancing. Modeling of S-wave velocity structure in the subsurface is underway to enable simulation of long-period ground motion. The one-dimensional velocity model by inverse analysis of micro-tremors is sufficiently appropriate for long-period site response but not for short-period, which is important for ground motion evaluation at NPP sites. The high-frequency site responses may be controlled by the strength of heterogeneity of underground structure because the heterogeneity of the 1D model plays an important role in estimating high-frequency site responses and is strongly related to the damping factor of the 1D layered velocity model. (author)

  11. Finite element analysis of functionally graded bone plate at femur bone fracture site

    Science.gov (United States)

    Satapathy, Pravat Kumar; Sahoo, Bamadev; Panda, L. N.; Das, S.

    2018-03-01

    This paper focuses on the analysis of fractured Femur bone with functionally graded bone plate. The Femur bone is modeled by using the data from the CT (Computerized Tomography) scan and the material properties are assigned using Mimics software. The fracture fixation plate used here is composed of Functionally Graded Material (FGM). The functionally graded bone plate is considered to be composed of different layers of homogeneous materials. Finite element method approach is adopted for analysis. The volume fraction of the material is calculated by considering its variation along the thickness direction (z) according to a power law and the effective properties of the homogeneous layers are estimated. The model developed is validated by comparing numerical results available in the literature. Static analysis has been performed for the bone plate system by considering both axial compressive load and torsional load. The investigation shows that by introducing FG bone plate instead of titanium, the stress at the fracture site increases by 63 percentage and the deformation decreases by 15 percentage, especially when torsional load is taken into consideration. The present model yields better results in comparison with the commercially available bone plates.

  12. Analysis of recorded earthquake response data at the Hualien large-scale seismic test site

    International Nuclear Information System (INIS)

    Hyun, C.H.; Tang, H.T.; Dermitzakis, S.; Esfandiari, S.

    1997-01-01

    A soil-structure interaction (SSI) experiment is being conducted in a seismically active region in Hualien, Taiwan. To obtain earthquake data for quantifying SSI effects and providing a basis to benchmark analysis methods, a 1/4-th scale cylindrical concrete containment model similar in shape to that of a nuclear power plant containment was constructed in the field where both the containment model and its surrounding soil, surface and sub-surface, are extensively instrumented to record earthquake data. In between September 1993 and May 1995, eight earthquakes with Richter magnitudes ranging from 4.2 to 6.2 were recorded. The author focuses on studying and analyzing the recorded data to provide information on the response characteristics of the Hualien soil-structure system, the SSI effects and the ground motion characteristics. An effort was also made to directly determine the site soil physical properties based on correlation analysis of the recorded data. No modeling simulations were attempted to try to analytically predict the SSI response of the soil and the structure. These will be the scope of a subsequent study

  13. Comprehensive proteome analysis of lysosomes reveals the diverse function of macrophages in immune responses.

    Science.gov (United States)

    Gao, Yanpan; Chen, Yanyu; Zhan, Shaohua; Zhang, Wenhao; Xiong, Feng; Ge, Wei

    2017-01-31

    Phagocytosis and autophagy in macrophages have been shown to be essential to both innate and adaptive immunity. Lysosomes are the main catabolic subcellular organelles responsible for degradation and recycling of both extracellular and intracellular material, which are the final steps in phagocytosis and autophagy. However, the molecular mechanisms underlying lysosomal functions after infection remain obscure. In this study, we conducted a quantitative proteomics analysis of the changes in constitution and glycosylation of proteins in lysosomes derived from murine RAW 264.7 macrophage cells treated with different types of pathogens comprising examples of bacteria (Listeria monocytogenes, L. m), DNA viruses (herpes simplex virus type-1, HSV-1) and RNA viruses (vesicular stomatitis virus, VSV). In total, 3,704 lysosome-related proteins and 300 potential glycosylation sites on 193 proteins were identified. Comparative analysis showed that the aforementioned pathogens induced distinct alterations in the proteome of the lysosome, which is closely associated with the immune functions of macrophages, such as toll-like receptor activation, inflammation and antigen-presentation. The most significant changes in proteins and fluctuations in glycosylation were also determined. Furthermore, Western blot analysis showed that the changes in expression of these proteins were undetectable at the whole cell level. Thus, our study provides unique insights into the function of lysosomes in macrophage activation and immune responses.

  14. Response function of semiconductor detectors, Ge and Si(Li)

    International Nuclear Information System (INIS)

    Zevallos Chavez, Juan Yury

    2003-01-01

    The Response Function (RF) for Ge and Si(Li) semiconductor detectors was obtained. The RF was calculated for five detectors, four Hp Ge with active volumes of 89 cm 3 , 50 cm 3 , 8 cm 3 and 5 cm 3 , and one Si(Li) with 0.143 cm 3 of active volume. The interval of energy studied ranged from 6 keV up to 1.5 MeV. Two kinds of studies were done in this work. The first one was the RF dependence with the detection geometry. Here the calculation of the RF for a geometry named as simple and an extrapolation of that RF, were both done. The extrapolation process analyzed both, spectra obtained with a shielding geometry and spectra where the source-detector distance was modified. The second one was the RF dependence with the detection electronics. This study was done varying the shaping time of the pulse in the detection electronics. The purpose was to verify the effect of the ballistic deficit in the resolution of the detector. This effect was not observed. The RF components that describe the region of the total absorption of the energy of the incident photons, and the partial absorption of this energy, were both treated. In particular, empirical functions were proposed for the treatment of both, the multiple scattering originated in the detector (crystal), and the photon scattering originated in materials of the neighborhood of the crystal. Another study involving Monte Carlo simulations was also done in order to comprehend the photon scattering structures produced in an iron shield. A deconvolution method is suggested, for spectra related to scattered radiation in order to assess the dose delivered to the scatterer. (author)

  15. Dual function of CD70 in viral infection: modulator of early cytokine responses and activator of adaptive responses1

    OpenAIRE

    Allam, Atef; Swiecki, Melissa; Vermi, William; Ashwell, Jonathan D.; Colonna, Marco

    2014-01-01

    The role of the tumor necrosis factor family member CD70 in adaptive T cell responses has been intensively studied but its function in innate responses is still under investigation. Here we show that CD70 inhibits the early innate response to murine cytomegalovirus (MCMV) but is essential for the optimal generation of virus-specific CD8 T cells. CD70-/- mice reacted to MCMV infection with a robust type I interferon and proinflammatory cytokine response. This response was sufficient for initia...

  16. Historical precipitation predictably alters the shape and magnitude of microbial functional response to soil moisture.

    Science.gov (United States)

    Averill, Colin; Waring, Bonnie G; Hawkes, Christine V

    2016-05-01

    Soil moisture constrains the activity of decomposer soil microorganisms, and in turn the rate at which soil carbon returns to the atmosphere. While increases in soil moisture are generally associated with increased microbial activity, historical climate may constrain current microbial responses to moisture. However, it is not known if variation in the shape and magnitude of microbial functional responses to soil moisture can be predicted from historical climate at regional scales. To address this problem, we measured soil enzyme activity at 12 sites across a broad climate gradient spanning 442-887 mm mean annual precipitation. Measurements were made eight times over 21 months to maximize sampling during different moisture conditions. We then fit saturating functions of enzyme activity to soil moisture and extracted half saturation and maximum activity parameter values from model fits. We found that 50% of the variation in maximum activity parameters across sites could be predicted by 30-year mean annual precipitation, an indicator of historical climate, and that the effect is independent of variation in temperature, soil texture, or soil carbon concentration. Based on this finding, we suggest that variation in the shape and magnitude of soil microbial response to soil moisture due to historical climate may be remarkably predictable at regional scales, and this approach may extend to other systems. If historical contingencies on microbial activities prove to be persistent in the face of environmental change, this approach also provides a framework for incorporating historical climate effects into biogeochemical models simulating future global change scenarios. © 2016 John Wiley & Sons Ltd.

  17. Controlled, Site-Specific Functionalization of Carbon Nanotubes with Diazonium Salts

    Science.gov (United States)

    Tour, James M.

    2013-01-01

    capacities and uses. Site-specific functionalization may enable the use of nanotubes in molecular electronic applications because device functionality is critical at the cross points.

  18. Evaluation of functionality and biological response of the multilayer flow modulator in porcine animal models.

    Science.gov (United States)

    Sultan, Sherif; Kavanagh, Edel P; Hynes, Niamh; Diethrich, Edward B

    2016-02-01

    This study outlines the use of non-aneurysmal porcine animal models to study device functionality and biological response of the Multilayer Flow Modulator (MFM) (Cardiatis, Isnes, Belgium), with an emphasis on preclinical device functionality and biological response characteristics in an otherwise healthy aorta. Twelve animals were implanted with the study device in the abdominal aorta, in 6 animals for 1 month and 6 animals for 6 months. Upon completion of the study period, each animal underwent a necropsy to examine how the implanted device had affected the artery and surrounding tissue. Neointima and stenosis formation were recorded via morphometry, and endothelialization via histopathological analysis. The MFM devices were delivered to their respective implantation sites without difficulty. Six of the implanted stents were oversized with percentages ranging from 2.6% to 18.8%. Statistical analysis was carried out and showed no significance between the regular sized stent group and oversized stent group for neointimal area (P=0.17), neointimal thickness (P=0.17), and percentage area stenosis (P=0.65). Histopathological findings showed in most areas flattened endothelium like cells lined the luminal surface of the neointima. Scanning electron microscopy also showed the devices were well tolerated, inciting only a minimal neointimal covering and little fibrin or platelet deposition. Neointimal thickness of 239.7±55.6 μm and 318.3±130.4 μm, and percentage area stenosis of 9.6±2.6% and 12.6±5% were recorded at 1 and 6 months respectively. No statistical differences were found between these results. The MFM devices were delivered to their respective implantation sites without difficulty and incited little neointimal and stenosis formation in the aorta, affirming its functionality and biocompatibility.

  19. A functional genetic variant in fragile-site gene FATS modulates the risk of breast cancer in triparous women

    International Nuclear Information System (INIS)

    Song, Fangfang; Zhang, Jun; Qiu, Li; Zhao, Yawen; Xing, Pan; Lu, Jiachun; Chen, Kexin; Li, Zheng

    2015-01-01

    The fragile-site associated tumor suppressor (FATS, formerly known as C10orf90), a regulator of p53-p21 pathway has been involved in the onset of breast cancer. Recent data support the idea that the crosstalk between FATS and p53 may be of physiological importance for reproduction during evolution. The aim of the current study was to test the hypothesis that FATS genetic polymorphism can influence the risk of breast cancer. We conducted population-based studies in two independent cohorts comprising 1 532 cases and 1 573 controls in Tianjin of North China, and 804 cases and 835 controls in Guangzhou of South China, coupled with functional validation methods, to investigate the role of FATS genetic variant in breast cancer risk. We identified a functional variant rs11245007 (905C > T, 262D/N) in fragile-site gene FATS that modulates p53 activation. FATS-262 N exhibited stronger E3 activity to polyubiquitinate p53 than did FATS-262D, leading to the stronger transcriptional activity of p53 and more pronounced stabilization of p53 protein and its activation in response to DNA damage. Case–control studies found that CT or TT genotype was significantly associated with a protective effect on breast cancer risk in women with parity ≥ 3, which was not affected by family history. Our findings suggest the role of FATS-p53 signaling cascade in suppressing pregnancy-related carcinogenesis and potential application of FATS genotyping in breast cancer prevention. The online version of this article (doi:10.1186/s12885-015-1570-9) contains supplementary material, which is available to authorized users

  20. Response function measurement of plastic scintillator for high energy neutrons

    International Nuclear Information System (INIS)

    Sanami, Toshiya; Ban, Syuichi; Takahashi, Kazutoshi; Takada, Masashi

    2003-01-01

    The response function and detection efficiency of 2''φ x 2''L plastic (PilotU) and NE213 liquid (2''NE213) scintillators, which were used for the measurement of secondary neutrons from high energy electron induced reactions, were measured at Heavy Ion Medical Accelerator in Chiba (HIMAC). High energy neutrons were produced via 400 MeV/n C beam bombardment on a thick graphite target. The detectors were placed at 15 deg with respect to C beam axis, 5 m away from the target. As standard, a 5''φ x 5''L NE213 liquid scintillator (5''NE213) was also placed at same position. Neutron energy was determined by the time-of-flight method with the beam pickup scintillator in front of the target. In front of the detectors, veto scintillators were placed to remove charged particle events. All detector signals were corrected with list mode event by event. We deduce neutron spectrum for each detectors. The efficiency curves for pilotU and 2''NE213 were determined on the bases of 5 N E213 neutron spectrum and its efficiency calculated by CECIL code. (author)

  1. Zero-field magnetic response functions in Landau levels

    Science.gov (United States)

    Gao, Yang; Niu, Qian

    2017-07-01

    We present a fresh perspective on the Landau level quantization rule; that is, by successively including zero-field magnetic response functions at zero temperature, such as zero-field magnetization and susceptibility, the Onsager’s rule can be corrected order by order. Such a perspective is further reinterpreted as a quantization of the semiclassical electron density in solids. Our theory not only reproduces Onsager’s rule at zeroth order and the Berry phase and magnetic moment correction at first order but also explains the nature of higher-order corrections in a universal way. In applications, those higher-order corrections are expected to curve the linear relation between the level index and the inverse of the magnetic field, as already observed in experiments. Our theory then provides a way to extract the correct value of Berry phase as well as the magnetic susceptibility at zero temperature from Landau level fan diagrams in experiments. Moreover, it can be used theoretically to calculate Landau levels up to second-order accuracy for realistic models.

  2. Evaluation of site effects on ground motions based on equivalent linear site response analysis and liquefaction potential in Chennai, south India

    Science.gov (United States)

    Nampally, Subhadra; Padhy, Simanchal; Trupti, S.; Prabhakar Prasad, P.; Seshunarayana, T.

    2018-05-01

    We study local site effects with detailed geotechnical and geophysical site characterization to evaluate the site-specific seismic hazard for the seismic microzonation of the Chennai city in South India. A Maximum Credible Earthquake (MCE) of magnitude 6.0 is considered based on the available seismotectonic and geological information of the study area. We synthesized strong ground motion records for this target event using stochastic finite-fault technique, based on a dynamic corner frequency approach, at different sites in the city, with the model parameters for the source, site, and path (attenuation) most appropriately selected for this region. We tested the influence of several model parameters on the characteristics of ground motion through simulations and found that stress drop largely influences both the amplitude and frequency of ground motion. To minimize its influence, we estimated stress drop after finite bandwidth correction, as expected from an M6 earthquake in Indian peninsula shield for accurately predicting the level of ground motion. Estimates of shear wave velocity averaged over the top 30 m of soil (V S30) are obtained from multichannel analysis of surface wave (MASW) at 210 sites at depths of 30 to 60 m below the ground surface. Using these V S30 values, along with the available geotechnical information and synthetic ground motion database obtained, equivalent linear one-dimensional site response analysis that approximates the nonlinear soil behavior within the linear analysis framework was performed using the computer program SHAKE2000. Fundamental natural frequency, Peak Ground Acceleration (PGA) at surface and rock levels, response spectrum at surface level for different damping coefficients, and amplification factors are presented at different sites of the city. Liquefaction study was done based on the V S30 and PGA values obtained. The major findings suggest show that the northeast part of the city is characterized by (i) low V S30 values

  3. Surface binding sites in carbohydrate active enzymes: An emerging picture of structural and functional diversity

    DEFF Research Database (Denmark)

    Svensson, Birte; Cockburn, Darrell

    2013-01-01

    is not universal and is in fact rare among some families of enzymes. In some cases an alternative to possessing a CBM is for the enzyme to bind to the substrate at a site on the catalytic domain, but away from the active site. Such a site is termed a surface (or secondary) binding site (SBS). SBSs have been...

  4. The conserved WW-domain binding sites in Dystroglycan C-terminus are essential but partially redundant for Dystroglycan function

    Directory of Open Access Journals (Sweden)

    Deng W-M

    2009-02-01

    Full Text Available Abstract Background Dystroglycan (Dg is a transmembrane protein that is a part of the Dystrophin Glycoprotein Complex (DGC which connects the extracellular matrix to the actin cytoskeleton. The C-terminal end of Dg contains a number of putative SH3, SH2 and WW domain binding sites. The most C-terminal PPXY motif has been established as a binding site for Dystrophin (Dys WW-domain. However, our previous studies indicate that both Dystroglycan PPXY motives, WWbsI and WWbsII can bind Dystrophin protein in vitro. Results We now find that both WW binding sites are important for maintaining full Dg function in the establishment of oocyte polarity in Drosophila. If either WW binding site is mutated, the Dg protein can still be active. However, simultaneous mutations in both WW binding sites abolish the Dg activities in both overexpression and loss-of-function oocyte polarity assays in vivo. Additionally, sequence comparisons of WW binding sites in 12 species of Drosophila, as well as in humans, reveal a high level of conservation. This preservation throughout evolution supports the idea that both WW binding sites are functionally required. Conclusion Based on the obtained results we propose that the presence of the two WW binding sites in Dystroglycan secures the essential interaction between Dg and Dys and might further provide additional regulation for the cytoskeletal interactions of this complex.

  5. A new functional site W115 in CdtA is critical for Aggregatibacter actinomycetemcomitans cytolethal distending toxin.

    Directory of Open Access Journals (Sweden)

    Lu Li

    Full Text Available Aggregatibacter actinomycetemcomitans, a specific pathogen of localized aggressive periodontitis, produces a cytolethal distending toxin (CDT that arrests eukaryotic cells irreversibly in G0/G1 or G2/M phase of the cell cycle. Although structural studies show that the aromatic patch region of CdtA plays an important role in its biological activity, the functional sites of CdtA have not been firmly established. In this study, site-specific mutagenesis strategy was employed for cdtA point mutations construction so as to examine the contributions of individual amino acids to receptor binding and the biological activity of holotoxin. The binding ability was reduced in CdtA(Y181ABC holotoxin and the biological function of CDT was not weaken in CdtA(Y105ABC, CdtA(Y125ABC, CdtA(F109ABC and CdtA(S106NBC holotoxin suggesting that these sites were not critical to CDT. But the binding activity and cell cycle arrest ability of holotoxin complexes were inhibited in CdtA(W115GBC. And this site did not affect the holotoxin assembly by size exclusion chromatography. Therefore, W115 might be a critical site of CdtA binding ability. These findings suggest that the functional sites of CdtA are not only in the aromatic patch region. W115, the new functional site is critical for receptor binding and cell cycle arrest, which provides potential targets for pharmacological disruption of CDT activity.

  6. Structure-based stabilization of HIV-1 gp120 enhances humoral immune responses to the induced co-receptor binding site.

    Directory of Open Access Journals (Sweden)

    Barna Dey

    2009-05-01

    Full Text Available The human immunodeficiency virus type 1 (HIV-1 exterior envelope glycoprotein, gp120, possesses conserved binding sites for interaction with the primary virus receptor, CD4, and also for the co-receptor, generally CCR5. Although gp120 is a major target for virus-specific neutralizing antibodies, the gp120 variable elements and its malleable nature contribute to evasion of effective host-neutralizing antibodies. To understand the conformational character and immunogenicity of the gp120 receptor binding sites as potential vaccine targets, we introduced structure-based modifications to stabilize gp120 core proteins (deleted of the gp120 major variable regions into the conformation recognized by both receptors. Thermodynamic analysis of the re-engineered core with selected ligands revealed significant stabilization of the receptor-binding regions. Stabilization of the co-receptor-binding region was associated with a marked increase in on-rate of ligand binding to this site as determined by surface plasmon resonance. Rabbit immunization studies showed that the conformational stabilization of core proteins, along with increased ligand affinity, was associated with strikingly enhanced humoral immune responses against the co-receptor-binding site. These results demonstrate that structure-based approaches can be exploited to stabilize a conformational site in a large functional protein to enhance immunogenic responses specific for that region.

  7. Role of a database-driven web site in the immediate disaster response and recovery of Academic Health Center: the Katrina experience.

    Science.gov (United States)

    Fordis, Michael; Alexander, J Douglas; McKellar, Julie

    2007-08-01

    In the wake of Hurricane Katrina's landfall on August 29, 2005, and the subsequent levee failures, operations of Tulane University School of Medicine became unsustainable. As New Orleans collapsed, faculty, students, residents, and staff were scattered nationwide. In response, four Texas medical schools created an alliance to assist Tulane in temporarily relocating operations to south Texas. Resuming operations in a three- to four-week time span required developing and implementing a coordinated communication plan in the face of widespread communication infrastructure disruptions. A keystone of the strategy involved rapidly creating a "recovery Web site" to provide essential information on immediate recovery plans, mechanisms for reestablishing communications with displaced persons, housing relocation options (over 200 students, faculty, and staff were relocated using Web site resources), classes and residency training, and other issues (e.g., financial services, counseling support) vitally important to affected individuals. The database-driven Web site was launched in four days on September 11, 2005, by modifying an existing system and completing new programming. Additional functions were added during the next week, and the site operated continuously until March 2006, providing about 890,000 pages of information in over 100,000 visitor sessions. The site proved essential in disseminating announcements, reestablishing communications among the Tulane family, and supporting relocation and recovery. This experience shows the importance of information technology in collaborative efforts of academic health centers in early disaster response and recovery, reinforcing recommendations published recently by the Association of Academic Health Centers and the National Academy of Sciences.

  8. Convergent phylogenetic and functional responses to altered fire regimes in mesic savanna grasslands of North America and South Africa.

    Science.gov (United States)

    Forrestel, Elisabeth J; Donoghue, Michael J; Smith, Melinda D

    2014-08-01

    The importance of fire in the creation and maintenance of mesic grassland communities is well recognized. Improved understanding of how grasses--the dominant clade in these important ecosystems--will respond to alterations in fire regimes is needed in the face of anthropogenically driven climate and land-use change. Here, we examined how grass communities shift in response to experimentally manipulated fire regimes at multiple levels of community diversity--taxonomic, phylogenetic and functional--in C4-dominanted mesic savanna grassland sites with similar structure and physiognomy, yet disparate biogeographic histories. We found that the grass communities were similar in their phylogenetic response and aspects of their functional response to high fire frequency. Both sites exhibited phylogenetic clustering of highly abundant species in annually burned plots, driven by species of the Andropogoneae, and a narrow range of functional strategies associated with rapid post-fire regeneration in a high-light, nitrogen-limited environment. By examining multiple facets of diversity in a comparative context, we identified convergent phylogenetic and functional responses to altered fire regimes in two mesic savanna grasslands. Our results highlight the importance of a common filtering process associated with fire that is consistent across grasslands of disparate biogeographic histories and taxonomic representation. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  9. Evolutionary rates at codon sites may be used to align sequences and infer protein domain function

    Directory of Open Access Journals (Sweden)

    Hazelhurst Scott

    2010-03-01

    Full Text Available Abstract Background Sequence alignments form part of many investigations in molecular biology, including the determination of phylogenetic relationships, the prediction of protein structure and function, and the measurement of evolutionary rates. However, to obtain meaningful results, a significant degree of sequence similarity is required to ensure that the alignments are accurate and the inferences correct. Limitations arise when sequence similarity is low, which is particularly problematic when working with fast-evolving genes, evolutionary distant taxa, genomes with nucleotide biases, and cases of convergent evolution. Results A novel approach was conceptualized to address the "low sequence similarity" alignment problem. We developed an alignment algorithm termed FIRE (Functional Inference using the Rates of Evolution, which aligns sequences using the evolutionary rate at codon sites, as measured by the dN/dS ratio, rather than nucleotide or amino acid residues. FIRE was used to test the hypotheses that evolutionary rates can be used to align sequences and that the alignments may be used to infer protein domain function. Using a range of test data, we found that aligning domains based on evolutionary rates was possible even when sequence similarity was very low (for example, antibody variable regions. Furthermore, the alignment has the potential to infer protein domain function, indicating that domains with similar functions are subject to similar evolutionary constraints. These data suggest that an evolutionary rate-based approach to sequence analysis (particularly when combined with structural data may be used to study cases of convergent evolution or when sequences have very low similarity. However, when aligning homologous gene sets with sequence similarity, FIRE did not perform as well as the best traditional alignment algorithms indicating that the conventional approach of aligning residues as opposed to evolutionary rates remains the

  10. Ser298 of MITF, a mutation site in Waardenburg syndrome type 2, is a phosphorylation site with functional significance.

    Science.gov (United States)

    Takeda, K; Takemoto, C; Kobayashi, I; Watanabe, A; Nobukuni, Y; Fisher, D E; Tachibana, M

    2000-01-01

    MITF (microphthalmia-associated transcription factor) is a basic-helix-loop-helix-leucine zipper (bHLHZip) factor which regulates expression of tyrosinase and other melanocytic genes via a CATGTG promoter sequence, and is involved in melanocyte differentiation. Mutations of MITF in mice or humans with Waardenburg syndrome type 2 (WS2) often severely disrupt the bHLHZip domain, suggesting the importance of this structure. Here, we show that Ser298, which locates downstream of the bHLHZip and was previously found to be mutated in individuals with WS2, plays an important role in MITF function. Glycogen synthase kinase 3 (GSK3) was found to phosphorylate Ser298 in vitro, thereby enhancing the binding of MITF to the tyrosinase promoter. The same serine was found to be phosphorylated in vivo, and expression of dominant-negative GSK3beta selectively suppressed the ability of MITF to transactivate the tyrosinase promoter. Moreover, mutation of Ser298, as found in a WS2 family, disabled phos-phorylation of MITF by GSK3beta and impaired MITF function. These findings suggest that the Ser298 is important for MITF function and is phosphorylated probably by GSK3beta.

  11. Inconsistent Growth Response to Fertilization and Thinning of Lodgepole Pine in the Rocky Mountain Foothills Is Linked to Site Index

    Directory of Open Access Journals (Sweden)

    Bradley D. Pinno

    2012-01-01

    Full Text Available Fertilization of conifers often results in highly variable growth responses across sites which are difficult to predict. The goal of this study was to predict the growth response of lodgepole pine (Pinus contorta var. latifolia crop trees to thinning and fertilization using basic site and foliar characteristics. Fifteen harvest-origin stands along the foothills of the Rocky Mountains of Alberta were subjected to six treatments including two levels of thinning (thinning to 2500 stems per hectare and a control and three types of fertilization (nitrogen-only fertilization, complete fertilization including nitrogen with added P, K, S, Mg, and B, and no fertilization. After three growing seasons, the growth response and foliar status of the crop trees were examined and this response was related to site and foliar characteristics. There was a small and highly variable additive response to fertilization and thinning; diameter growth of crop trees increased relative to the controls an average of 0.3 cm with thinning, 0.3 cm with either N-only or complete fertilization and 0.6 cm when thinned and fertilized. The increase in diameter growth with thinning and nitrogen-only fertilization was positively related to site index but not to any other site factors or pretreatment foliar variables such as nutrient concentrations, ratios, or thresholds.

  12. IgG-Fc-mediated effector functions: molecular definition of interaction sites for effector ligands and the role of glycosylation.

    Science.gov (United States)

    Jefferis, R; Lund, J; Pound, J D

    1998-06-01

    The Fc region of human IgG expresses interaction sites for many effector ligands. In this review the topographical distributions of ten of these sites are discussed in relation to functional requirement. It is apparent that interaction sites localised to the inter-CH2-CH3 domain region of the Fc allow for functional divalency, whereas sites localised to the hinge proximal region of the CH2 domain are functionally monovalent, with expression of the latter sites being particularly dependent on glycosylation. All x-ray crystal structures for Fc and Fc-ligand complexes report that the protein structure of the hinge proximal region of the CH2 domain is "disordered", suggesting "internal mobility". We propose a model in which such "internal mobility" results in the generation of a dynamic equilibrium between multiple conformers, certain of which express interaction sites specific to individual ligands. The emerging understanding of the influence of oligosaccharide/protein interactions on protein conformation and biological function of IgG antibodies suggests a potential to generate novel glycoforms of antibody molecules having unique profiles of effector functions.

  13. Multi-method Near-surface Geophysical Surveys for Site Response and Earthquake Damage Assessments at School Sites in Washington, USA

    Science.gov (United States)

    Cakir, R.; Walsh, T. J.; Norman, D. K.

    2017-12-01

    We, Washington Geological Survey (WGS), have been performing multi-method near surface geophysical surveys to help assess potential earthquake damage at public schools in Washington. We have been conducting active and passive seismic surveys, and estimating Shear-wave velocity (Vs) profiles, then determining the NEHRP soil classifications based on Vs30m values at school sites in Washington. The survey methods we have used: 1D and 2D MASW and MAM, P- and S-wave refraction, horizontal-to-vertical spectral ratio (H/V), and 2ST-SPAC to measure Vs and Vp at shallow (0-70m) and greater depths at the sites. We have also run Ground Penetrating Radar (GPR) surveys at the sites to check possible horizontal subsurface variations along and between the seismic survey lines and the actual locations of the school buildings. The seismic survey results were then used to calculate Vs30m for determining the NEHRP soil classifications at school sites, thus soil amplification effects on the ground motions. Resulting shear-wave velocity profiles generated from these studies can also be used for site response and liquefaction potential studies, as well as for improvement efforts of the national Vs30m database, essential information for ShakeMap and ground motion modeling efforts in Washington and Pacific Northwest. To estimate casualties, nonstructural, and structural losses caused by the potential earthquakes in the region, we used these seismic site characterization results associated with structural engineering evaluations based on ASCE41 or FEMA 154 (Rapid Visual Screening) as inputs in FEMA Hazus-Advanced Engineering Building Module (AEBM) analysis. Compelling example surveys will be presented for the school sites in western and eastern Washington.

  14. The Effectors and Sensory Sites of Formaldehyde-responsive Regulator FrmR and Metal-sensing Variant *

    Science.gov (United States)

    Osman, Deenah; Piergentili, Cecilia; Chen, Junjun; Sayer, Lucy N.; Usón, Isabel; Huggins, Thomas G.; Robinson, Nigel J.; Pohl, Ehmke

    2016-01-01

    The DUF156 family of DNA-binding transcriptional regulators includes metal sensors that respond to cobalt and/or nickel (RcnR, InrS) or copper (CsoR) plus CstR, which responds to persulfide, and formaldehyde-responsive FrmR. Unexpectedly, the allosteric mechanism of FrmR from Salmonella enterica serovar Typhimurium is triggered by metals in vitro, and variant FrmRE64H gains responsiveness to Zn(II) and cobalt in vivo. Here we establish that the allosteric mechanism of FrmR is triggered directly by formaldehyde in vitro. Sensitivity to formaldehyde requires a cysteine (Cys35 in FrmR) conserved in all DUF156 proteins. A crystal structure of metal- and formaldehyde-sensing FrmRE64H reveals that an FrmR-specific amino-terminal Pro2 is proximal to Cys35, and these residues form the deduced formaldehyde-sensing site. Evidence is presented that implies that residues spatially close to the conserved cysteine tune the sensitivities of DUF156 proteins above or below critical thresholds for different effectors, generating the semblance of specificity within cells. Relative to FrmR, RcnR is less responsive to formaldehyde in vitro, and RcnR does not sense formaldehyde in vivo, but reciprocal mutations FrmRP2S and RcnRS2P, respectively, impair and enhance formaldehyde reactivity in vitro. Formaldehyde detoxification by FrmA requires S-(hydroxymethyl)glutathione, yet glutathione inhibits formaldehyde detection by FrmR in vivo and in vitro. Quantifying the number of FrmR molecules per cell and modeling formaldehyde modification as a function of [formaldehyde] demonstrates that FrmR reactivity is optimized such that FrmR is modified and frmRA is derepressed at lower [formaldehyde] than required to generate S-(hydroxymethyl)glutathione. Expression of FrmA is thereby coordinated with the accumulation of its substrate. PMID:27474740

  15. Response functions for computing absorbed dose to skeletal tissues from photon irradiation-an update

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Perry B; Bahadori, Amir A [Nuclear and Radiological Engineering, University of Florida, Gainesville, FL 32611 (United States); Eckerman, Keith F [Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 (United States); Lee, Choonsik [Radiation Epidemiology Branch, National Cancer Institute, Bethesda, MD 20892 (United States); Bolch, Wesley E, E-mail: wbolch@ufl.edu [Nuclear and Radiological/Biomedical Engineering, University of Florida, Gainesville, FL 32611 (United States)

    2011-04-21

    A comprehensive set of photon fluence-to-dose response functions (DRFs) is presented for two radiosensitive skeletal tissues-active and total shallow marrow-within 15 and 32 bone sites, respectively, of the ICRP reference adult male. The functions were developed using fractional skeletal masses and associated electron-absorbed fractions as reported for the UF hybrid adult male phantom, which in turn is based upon micro-CT images of trabecular spongiosa taken from a 40 year male cadaver. The new DRFs expand upon both the original set of seven functions produced in 1985, and a 2007 update calculated under the assumption of secondary electron escape from spongiosa. In this study, it is assumed that photon irradiation of the skeleton will yield charged particle equilibrium across all spongiosa regions at energies exceeding 200 keV. Kerma coefficients for active marrow, inactive marrow, trabecular bone and spongiosa at higher energies are calculated using the DRF algorithm setting the electron-absorbed fraction for self-irradiation to unity. By comparing kerma coefficients and DRF functions, dose enhancement factors and mass energy-absorption coefficient (MEAC) ratios for active marrow to spongiosa were derived. These MEAC ratios compared well with those provided by the NIST Physical Reference Data Library (mean difference of 0.8%), and the dose enhancement factors for active marrow compared favorably with values calculated in the well-known study published by King and Spiers (1985 Br. J. Radiol. 58 345-56) (mean absolute difference of 1.9 percentage points). Additionally, dose enhancement factors for active marrow were shown to correlate well with the shallow marrow volume fraction (R{sup 2} = 0.91). Dose enhancement factors for the total shallow marrow were also calculated for 32 bone sites representing the first such derivation for this target tissue.

  16. Priority and construction sites of water storage in a watershed in response to climate change

    Science.gov (United States)

    Lin, Cheng-Yu; Zhang, Wen-Yan; Lin, Chao-Yuan

    2014-05-01

    Taiwan is located at the Eastern Asia Monsoon climate zone. Typhoons and/or convectional rains occur frequently and result in high intensity storms in the summer season. Once the detention facilities are shortage or soil infiltration rate become worse in a watershed due to land use, surface runoff is easily to concentrate and threaten the protected areas. Therefore, it is very important to examine the functionality of water storage for a watershed. The purpose of this study is to solve the issue of flooding in the Puzi Creek. A case study of Yizen Bridge Watershed, in which the SCS curve number was used as an index to extract the spatial distribution of the strength of water storage, and the value of watershed mean CN along the main channel was calculated using area-weighting method. Therefore, the hotspot management sites were then derived and the priority method was applied to screen the depression sites for the reference of management authorities in detention ponds placement. The results show that the areas of subzone A with the characteristics of bad condition in topography and soil, which results in poor infiltration. However, the areas are mostly covered with forest and are difficult to create the artificial water storage facilities. Detention dams are strongly recommended at the site of depression in the river channel to decrease discharge velocity and reduce impact from flood disaster. The areas of subzone B are mainly located at the agriculture slope land. The topographic depressions in the farmland are the suitable places to construct the farm ponds for the use of flood detention and sediment deposition in the rainy seasons and irrigation in the dry seasons. Areas of subzone C are mainly occupied the gentle slope land with a better ability in water storage due to low CN value. Farm ponds constructed in the riparian to bypass the nearby river channel can create multifunctional wetland to effectively decrease the peak discharge in the downstream during

  17. Comparison of equivalent linear and non linear methods on ground response analysis: case study at West Bangka site

    International Nuclear Information System (INIS)

    Eko Rudi Iswanto; Eric Yee

    2016-01-01

    Within the framework of identifying NPP sites, site surveys are performed in West Bangka (WB), Bangka-Belitung Island Province. Ground response analysis of a potential site has been carried out using peak strain profiles and peak ground acceleration. The objective of this research is to compare Equivalent Linear (EQL) and Non Linear (NL) methods of ground response analysis on the selected NPP site (West Bangka) using Deep Soil software. Equivalent linear method is widely used because requires soil data in simple way and short time of computational process. On the other hand, non linear method is capable of representing the actual soil behaviour by considering non linear soil parameter. The results showed that EQL method has similar trends to NL method. At surface layer, the acceleration values for EQL and NL methods are resulted as 0.425 g and 0.375 g respectively. NL method is more reliable in capturing higher frequencies of spectral acceleration compared to EQL method. (author)

  18. Physiological responses to taste signals of functional food components.

    Science.gov (United States)

    Narukawa, Masataka

    2018-02-01

    The functions of food have three categories: nutrition, palatability, and bioregulation. As the onset of lifestyle-related diseases has increased, many people have shown interest in functional foods that are beneficial to bioregulation. We believe that functional foods should be highly palatable for increased acceptance from consumers. In order to design functional foods with a high palatability, we have investigated about the palatability, especially in relation to the taste of food. In this review, we discuss (1) the identification of taste receptors that respond to functional food components; (2) an analysis of the peripheral taste transduction system; and (3) the investigation of the relationship between physiological functions and taste signals.

  19. Effects of Permafrost and Seasonally Frozen Ground on the Seismic Response of Transportation Infrastructure Sites

    Science.gov (United States)

    2010-02-01

    This interdisciplinary project combined seismic data recorded at bridge sites with computer models to identify how highway bridges built on permanently and seasonally frozen ground behave during an earthquake. Two sites one in Anchorage and one in...

  20. The responsibility of business enterprises to restore access to essential public service at resettlement sites

    NARCIS (Netherlands)

    van der Ploeg, Lidewij; Vanclay, Francis; Lourenço, Ivo; Hesselman, Marlies; Hallo de Wolf, Antenor; Toebes, Brigit

    2017-01-01

    This chapter examines the provision of essential public services in resettlement sites associated with project induced displacement. Restoring and improving access to essential public services in resettlement sites is an important aspect of livelihood restoration of affected peoples. Project

  1. Comment and response document for the long-term surveillance plan for the Falls City disposal site, Falls City, Texas

    International Nuclear Information System (INIS)

    1996-11-01

    This is the Comment and Response Document dated November 1996 for the Long-Term Surveillance Plan for the Falls City Disposal Site in Falls City, Texas. The site is part of the U.S. DOE's Uranium Mill Tailings Remedial Action Project (UMTRA). Several comments regarding the hydrology and surface erosion described in the Long-Term Surveillance Plan are addressed in this document

  2. Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions.

    Science.gov (United States)

    Su, Min-Gang; Weng, Julia Tzu-Ya; Hsu, Justin Bo-Kai; Huang, Kai-Yao; Chi, Yu-Hsiang; Lee, Tzong-Yi

    2017-12-21

    Protein post-translational modification (PTM) plays an essential role in various cellular processes that modulates the physical and chemical properties, folding, conformation, stability and activity of proteins, thereby modifying the functions of proteins. The improved throughput of mass spectrometry (MS) or MS/MS technology has not only brought about a surge in proteome-scale studies, but also contributed to a fruitful list of identified PTMs. However, with the increase in the number of identified PTMs, perhaps the more crucial question is what kind of biological mechanisms these PTMs are involved in. This is particularly important in light of the fact that most protein-based pharmaceuticals deliver their therapeutic effects through some form of PTM. Yet, our understanding is still limited with respect to the local effects and frequency of PTM sites near pharmaceutical binding sites and the interfaces of protein-protein interaction (PPI). Understanding PTM's function is critical to our ability to manipulate the biological mechanisms of protein. In this study, to understand the regulation of protein functions by PTMs, we mapped 25,835 PTM sites to proteins with available three-dimensional (3D) structural information in the Protein Data Bank (PDB), including 1785 modified PTM sites on the 3D structure. Based on the acquired structural PTM sites, we proposed to use five properties for the structural characterization of PTM substrate sites: the spatial composition of amino acids, residues and side-chain orientations surrounding the PTM substrate sites, as well as the secondary structure, division of acidity and alkaline residues, and solvent-accessible surface area. We further mapped the structural PTM sites to the structures of drug binding and PPI sites, identifying a total of 1917 PTM sites that may affect PPI and 3951 PTM sites associated with drug-target binding. An integrated analytical platform (CruxPTM), with a variety of methods and online molecular docking

  3. Site geological and geotechnical studies, determination of soil characteristics and soil response studies

    International Nuclear Information System (INIS)

    1985-08-01

    RFS or Regles Fondamentales de Surete (Basic Safety Rules) applicable to certain types of nuclear facilities lay down requirements with which compliance, for the type of facilities and within the scope of application covered by the RFS, is considered to be equivalent to compliance with technical French regulatory practice. The object of the RFS is to take advantage of standardization in the field of safety, while allowing for technical progress in that field. They are designed to enable the operating utility and contractors to know the rules pertaining to various subjects which are considered to be acceptable by the Service Central de Surete des Installations Nucleaires, or the SCSIN (Central Department for the Safety of Nuclear Facilities). These RFS should make safety analysis easier and lead to better understanding between experts and individuals concerned with the problems of nuclear safety. The SCSIN reserves the right to modify, when considered necessary, any RFS and specify, if need be, the terms under which a modification is deemed retroactive. The purpose of this RFS is to specify the soil characteristics to be determined and the soil response studies to be performed as part of site geological and geotechnical studies

  4. Polyester textile functionalization through incorporation of pH/thermo-responsive microgels. Part II: polyester functionalization and characterization

    NARCIS (Netherlands)

    Glampedaki, P.; Calvimontes, A.; Dutschk, Victoria; Warmoeskerken, Marinus

    2012-01-01

    A new approach to functionalize the surface of polyester textiles is described in this study. Functionalization was achieved by incorporating pH/temperature-responsive polyelectrolyte microgels into the textile surface layer using UV irradiation. The aim of functionalization was to regulate

  5. Asthma, respiratory symptoms and lung function in children living near a petrochemical site.

    NARCIS (Netherlands)

    Rovira, E.; Cuadras, A.; Aguilar, X.; Esteban, L.; Borràs-Santos, A.; Zock, J.P.; Sunyer, J.

    2014-01-01

    Residential proximity to environmental hazards has been related to adverse health outcomes. Respiratory health and allergies in children living near petrochemical sites have not been extensively studied. We evaluated the association between residential proximity to the petrochemical site of

  6. Quantifying Fast and Slow Responses of Terrestrial Carbon Exchange across a Water Availability Gradient in North American Flux Sites

    Science.gov (United States)

    Biederman, J. A.; Scott, R. L.; Goulden, M.

    2014-12-01

    Climate change is predicted to increase the frequency and severity of water limitation, altering terrestrial ecosystems and their carbon exchange with the atmosphere. Here we compare site-level temporal sensitivity of annual carbon fluxes to interannual variations in water availability against cross-site spatial patterns over a network of 19 eddy covariance flux sites. This network represents one order of magnitude in mean annual productivity and includes western North American desert shrublands and grasslands, savannahs, woodlands, and forests with continuous records of 4 to 12 years. Our analysis reveals site-specific patterns not identifiable in prior syntheses that pooled sites. We interpret temporal variability as an indicator of ecosystem response to annual water availability due to fast-changing factors such as leaf stomatal response and microbial activity, while cross-site spatial patterns are used to infer ecosystem adjustment to climatic water availability through slow-changing factors such as plant community and organic carbon pools. Using variance decomposition, we directly quantify how terrestrial carbon balance depends on slow- and fast-changing components of gross ecosystem production (GEP) and total ecosystem respiration (TER). Slow factors explain the majority of variance in annual net ecosystem production (NEP) across the dataset, and their relative importance is greater at wetter, forest sites than desert ecosystems. Site-specific offsets from spatial patterns of GEP and TER explain one third of NEP variance, likely due to slow-changing factors not directly linked to water, such as disturbance. TER and GEP are correlated across sites as previously shown, but our site-level analysis reveals surprisingly consistent linear relationships between these fluxes in deserts and savannahs, indicating fast coupling of TER and GEP in more arid ecosystems. Based on the uncertainty associated with slow and fast factors, we suggest a framework for improved

  7. Contributions of individual domains to function of the HIV-1 Rev response element.

    Science.gov (United States)

    O'Carroll, Ina P; Thappeta, Yashna; Fan, Lixin; Ramirez-Valdez, Edric A; Smith, Sean; Wang, Yun-Xing; Rein, Alan

    2017-08-16

    The HIV-1 Rev response element (RRE) is a 351-base element in unspliced and partially spliced viral RNA; binding of the RRE by the viral Rev protein induces nuclear export of RRE-containing RNAs, as required for virus replication. It contains one long, imperfect double helix (domain I), one branched domain (domain II) containing a high-affinity Rev-binding site, and two or three additional domains. We previously reported that the RRE assumes an "A" shape in solution and suggested that the location of the Rev binding sites in domains I and II, opposite each other on the two legs of the A, is optimal for Rev binding and explains Rev's specificity for RRE-containing RNAs. Using SAXS and a quantitative functional assay, we have now analyzed a panel of RRE mutants. All the results support the essential role of the A shape for RRE function. Moreover, they suggest that the distal portion of domain I and the three crowning domains all contribute to the maintenance of the A shape. Domains I and II are necessary and sufficient for substantial RRE function, provided they are joined by a flexible linker that allows the two domains to face each other. IMPORTANCE Retroviral replication requires that some of the viral RNAs transcribed in the cell nucleus be exported to the cytoplasm without being spliced. To achieve this, HIV-1 encodes a protein, Rev, which binds to a complex, highly structured element within viral RNA, the Rev Response Element (RRE), and escorts RRE-containing RNAs from the nucleus. We previously reported that the RRE is "A"-shaped and suggested that this architecture, with the 2 legs opposite one another, can explain the specificity of Rev for the RRE. We have analyzed the functional contributions of individual RRE domains, and now report that several domains contribute, with some redundancy, to maintenance of the overall RRE shape. The data strongly support the hypothesis that the opposed placement of the 2 legs is essential for RRE function. Copyright © 2017

  8. Functional characterization of Foxp3-specific spontaneous immune responses

    DEFF Research Database (Denmark)

    Larsen, Susanne Købke; Munir, S; Andersen, Anders Woetmann

    2013-01-01

    Tumor-infiltrating CD4+CD25+ regulatory T cells (Tregs) are associated with an impaired prognosis in several cancers. The transcription factor forkhead box P3 (Foxp3) is generally expressed in Tregs. Here, we identify and characterize spontaneous cytotoxic immune responses to Foxp3-expressing cel....... Consequently, induction of Foxp3-specific cytotoxic T-cell responses appears as an attractive tool to boost spontaneous or therapeutically provoked immune responses, for example, for the therapy of cancer....

  9. Do Quercus ilex woodlands undergo abrupt non-linear functional changes in response to human disturbance along a climatic gradient?

    Science.gov (United States)

    Bochet, Esther; García-Fayos, Patricio; José Molina, Maria; Moreno de las Heras, Mariano; Espigares, Tíscar; Nicolau, Jose Manuel; Monleon, Vicente

    2017-04-01

    Theoretical models predict that drylands are particularly prone to suffer critical transitions with abrupt non-linear changes in their structure and functions as a result of the existing complex interactions between climatic fluctuations and human disturbances. However, so far, few studies provide empirical data to validate these models. We aim at determining how holm oak (Quercus ilex) woodlands undergo changes in their functions in response to human disturbance along an aridity gradient (from semi-arid to sub-humid conditions), in eastern Spain. For that purpose, we used (a) remote-sensing estimations of precipitation-use-efficiency (PUE) from enhanced vegetation index (EVI) observations performed in 231x231 m plots of the Moderate Resolution Imaging Spectroradiometer (MODIS); (b) biological and chemical soil parameter determinations (extracellular soil enzyme activity, soil respiration, nutrient cycling processes) from soil sampled in the same plots; (c) vegetation parameter determinations (ratio of functional groups) from vegetation surveys performed in the same plots. We analyzed and compared the shape of the functional change (in terms of PUE and soil and vegetation parameters) in response to human disturbance intensity for our holm oak sites along the aridity gradient. Overall, our results evidenced important differences in the shape of the functional change in response to human disturbance between climatic conditions. Semi-arid areas experienced a more accelerated non-linear decrease with an increasing disturbance intensity than sub-humid ones. The proportion of functional groups (herbaceous vs. woody cover) played a relevant role in the shape of the functional response of the holm oak sites to human disturbance.

  10. Distinct phosphorylation sites on the ghrelin receptor, GHSR1a, establish a code that determines the functions of ß-arrestins

    Science.gov (United States)

    Bouzo-Lorenzo, Monica; Santo-Zas, Icía; Lodeiro, Maria; Nogueiras, Rubén; Casanueva, Felipe F.; Castro, Marian; Pazos, Yolanda; Tobin, Andrew B; Butcher, Adrian J.; Camiña, Jesús P.

    2016-01-01

    The growth hormone secretagogue receptor, GHSR1a, mediates the biological activities of ghrelin, which includes the secretion of growth hormone, as well as the stimulation of appetite, food intake and maintenance of energy homeostasis. Mapping phosphorylation sites on GHSR1a and knowledge of how these sites control specific functional consequences unlocks new strategies for the development of therapeutic agents targeting individual functions. Herein, we have identified the phosphorylation of different sets of sites within GHSR1a which engender distinct functionality of ß-arrestins. More specifically, the Ser362, Ser363 and Thr366 residues at the carboxyl-terminal tail were primarily responsible for ß-arrestin 1 and 2 binding, internalization and ß-arrestin-mediated proliferation and adipogenesis. The Thr350 and Ser349 are not necessary for ß-arrestin recruitment, but are involved in the stabilization of the GHSR1a-ß-arrestin complex in a manner that determines the ultimate cellular consequences of ß-arrestin signaling. We further demonstrated that the mitogenic and adipogenic effect of ghrelin were mainly dependent on the ß-arrestin bound to the phosphorylated GHSR1a. In contrast, the ghrelin function on GH secretion was entirely mediated by G protein signaling. Our data is consistent with the hypothesis that the phosphorylation pattern on the C terminus of GHSR1a determines the signaling and physiological output. PMID:26935831

  11. Frequency Response Function Based Damage Identification for Aerospace Structures

    Science.gov (United States)

    Oliver, Joseph Acton

    Structural health monitoring technologies continue to be pursued for aerospace structures in the interests of increased safety and, when combined with health prognosis, efficiency in life-cycle management. The current dissertation develops and validates damage identification technology as a critical component for structural health monitoring of aerospace structures and, in particular, composite unmanned aerial vehicles. The primary innovation is a statistical least-squares damage identification algorithm based in concepts of parameter estimation and model update. The algorithm uses frequency response function based residual force vectors derived from distributed vibration measurements to update a structural finite element model through statistically weighted least-squares minimization producing location and quantification of the damage, estimation uncertainty, and an updated model. Advantages compared to other approaches include robust applicability to systems which are heavily damped, large, and noisy, with a relatively low number of distributed measurement points compared to the number of analytical degrees-of-freedom of an associated analytical structural model (e.g., modal finite element model). Motivation, research objectives, and a dissertation summary are discussed in Chapter 1 followed by a literature review in Chapter 2. Chapter 3 gives background theory and the damage identification algorithm derivation followed by a study of fundamental algorithm behavior on a two degree-of-freedom mass-spring system with generalized damping. Chapter 4 investigates the impact of noise then successfully proves the algorithm against competing methods using an analytical eight degree-of-freedom mass-spring system with non-proportional structural damping. Chapter 5 extends use of the algorithm to finite element models, including solutions for numerical issues, approaches for modeling damping approximately in reduced coordinates, and analytical validation using a composite

  12. NON-FORMAL EDUCATION WITHIN THE FUNCTION OF RESPONSIBLE PARENTING

    Directory of Open Access Journals (Sweden)

    Dragana Bogavac

    2017-06-01

    Full Text Available The aim of this survey was to discover to what degree parental non-formal education is present within the function of responsible parenting. The questionnaire research method was used in the survey. For the purpose of this research a questionnaire of 13 questions was constructed relating to the forms of non-formal education, and another questionnaire of 10 questions relating to the parents’ expectations of non-formal education. The sample included 198 parents. Examination of the scores concerning the presence of certain forms of parental non-formal education realized in cooperation with the school leads to the conclusion that the parents possess a positive attitude towards non-formal education. The analysis showed that the parents’ expectations were not on a satisfactory level. According to the results, the fathers displayed a greater interest towards non-formal education (7.72±1.35 than the mothers (6.93±1.85, (p<0.05. Unemployed parents had a greater score (7.85±1.30 than the employed parents (7.22±1.71, (p<0.05. A difference in the acceptance of non-formal education in accordance with the level of formal education was also noticeable (p<0.001. Respondents with a high school degree displayed the highest level of acceptance (7.97±0.78, while the lowest interest was seen in respondents with an associate degree (6.41±2.29. Univariate linear regression analysis showed that statistically important predictors were: gender (OR: -0.23 (-1.24 – -0.33, p< 0.001, work status (OR: -0.14 (-1.24 – -0.01, < 0.05 and the level of formal education (OR: -0.33 (-0.81 – -0.34, p< 0.001. The final results lead to the conclusion that parental non-formal education supports the concept of lifelong education.

  13. When the shifting agriculture is gone: functionality of Atlantic Coastal Forest in abandoned farming sites

    Directory of Open Access Journals (Sweden)

    Rogério Ribeiro de Oliveira

    Full Text Available Slash-and-burn agriculture has been practiced for a very long time by the traditional populations (caiçaras on Ilha Grande, Rio de Janeiro State, Brazil. After a few years of use the plots are abandoned to fallow. We examined the processes of litter production and decomposition and the relationships between forest lands used by caiçara populations and landscape functionality. Five and 25-year-old forests growing on areas once used for subsistence agriculture were compared to a near-climax forest site. No significant differences between the three areas were noted in terms of litter production over a 2-yr period; the average litter productions were 9,927, 8,707 and 10,031 kg/ha/yr for the 5-year, 25-year and climax forests respectively. N and K nutrient input through litter was greatest in the climax forest; P and Mg input was greatest in the 5-yr forest; and Na greatest in the 25-yr forest. Ground litter accumulation (3,040-3,730 kg/ha/yr was not significantly different in the three areas. Litter turnover times (1/K were 0.33, 0.42 and 0.38 for the 5-yr, 25-yr and climax forests respectively. These secondary forests cover almost all of Ilha Grande and demonstrate low species diversity, but they have production and decomposition systems similar to those of mature forests.

  14. Asymmetric Responses of Primary Productivity to Altered Precipitation Simulated by Land Surface Models across Three Long-term Grassland Sites

    Science.gov (United States)

    Wu, D.; Ciais, P.; Viovy, N.; Knapp, A.; Wilcox, K.; Bahn, M.; Smith, M. D.; Ito, A.; Arneth, A.; Harper, A. B.; Ukkola, A.; Paschalis, A.; Poulter, B.; Peng, C.; Reick, C. H.; Hayes, D. J.; Ricciuto, D. M.; Reinthaler, D.; Chen, G.; Tian, H.; Helene, G.; Zscheischler, J.; Mao, J.; Ingrisch, J.; Nabel, J.; Pongratz, J.; Boysen, L.; Kautz, M.; Schmitt, M.; Krohn, M.; Zeng, N.; Meir, P.; Zhang, Q.; Zhu, Q.; Hasibeder, R.; Vicca, S.; Sippel, S.; Dangal, S. R. S.; Fatichi, S.; Sitch, S.; Shi, X.; Wang, Y.; Luo, Y.; Liu, Y.; Piao, S.

    2017-12-01

    Changes in precipitation variability including the occurrence of extreme events strongly influence plant growth in grasslands. Field measurements of aboveground net primary production (ANPP) in temperate grasslands suggest a positive asymmetric response with wet years resulting in ANPP gains larger than ANPP declines in dry years. Whether land surface models used for historical simulations and future projections of the coupled carbon-water system in grasslands are capable to simulate such non-symmetrical ANPP responses remains an important open research question. In this study, we evaluate the simulated responses of grassland primary productivity to altered precipitation with fourteen land surface models at the three sites of Colorado Shortgrass Steppe (SGS), Konza prairie (KNZ) and Stubai Valley meadow (STU) along a rainfall gradient from dry to wet. Our results suggest that: (i) Gross primary production (GPP), NPP, ANPP and belowground NPP (BNPP) show nonlinear response curves (concave-down) in all the models, but with different curvatures and mean values. In contrast across the sites, primary production increases and then saturates along increasing precipitation with a flattening at the wetter site. (ii) Slopes of spatial relationships between modeled primary production and precipitation are steeper than the temporal slopes (obtained from inter-annual variations). (iii) Asymmetric responses under nominal precipitation range with modeled inter-annual primary production show large uncertainties, and model-ensemble median generally suggests negative asymmetry (greater declines in dry years than increases in wet years) across the three sites. (iv) Primary production at the drier site is predicted to more sensitive to precipitation compared to wetter site, and median sensitivity consistently indicates greater negative impacts of reduced precipitation than positive effects of increased precipitation under extreme conditions. This study implies that most models

  15. Transmembrane helix M6 in sarco(endo)plasmic reticulum Ca(2+)-ATPase forms a functional interaction site with phospholamban. Evidence for physical interactions at other sites.

    Science.gov (United States)

    Asahi, M; Kimura, Y; Kurzydlowski, K; Tada, M; MacLennan, D H

    1999-11-12

    In an earlier study (Kimura, Y., Kurzydlowski, K., Tada, M., and MacLennan, D. H. (1997) J. Biol. Chem. 272, 15061-15064), mutation of amino acids on one face of the phospholamban (PLN) transmembrane helix led to loss of PLN inhibition of sarco(endo)plasmic reticulum Ca(2+)-ATPase (SERCA) molecules. This helical face was proposed to form a site of PLN interaction with a transmembrane helix in SERCA molecules. To determine whether predicted transmembrane helices M4, M5, M6, or M8 in SERCA1a interact with PLN, SERCA1a mutants were co-expressed with wild-type PLN and effects on Ca(2+) dependence of Ca(2+) transport were measured. Wild-type inhibitory interactions shifted apparent Ca(2+) affinity of SERCA1a by an average of -0.34 pCa units, but four of the seven mutations in M4 led to a more inhibitory shift in apparent Ca(2+) affinity, averaging -0.53 pCa units. Seven mutations in M5 led to an average shift of -0.32 pCa units and seven mutations in M8 led to an average shift of -0.30 pCa units. Among 11 mutations in M6, 1, Q791A, increased the inhibitory shift (-0.59 pCa units) and 5, V795A (-0.11), L802A (-0.07), L802V (-0.04), T805A (-0.11), and F809A (-0.12), reduced the inhibitory shift, consistent with the view that Val(795), Leu(802), Thr(805), and Phe(809), located on one face of a predicted M6 helix, form a site in SERCA1a for interaction with PLN. Those mutations in M4, M6, or M8 of SERCA1a that enhanced PLN inhibitory function did not enhance PLN physical association with SERCA1a, but mutants V795A and L802A in M6, which decreased PLN inhibitory function, decreased physical association, as measured by co-immunoprecipitation. In related studies, those PLN mutants that gained inhibitory function also increased levels of co-immunoprecipitation of wild-type SERCA1a and those that lost inhibitory function also reduced association, correlating functional interaction sites with physical interaction sites. Thus, both functional and physical data confirm that PLN

  16. Effects of B site doping on electronic structures of InNbO4 based on hybrid density functional calculations

    Science.gov (United States)

    Lu, M. F.; Zhou, C. P.; Li, Q. Q.; Zhang, C. L.; Shi, H. F.

    2018-01-01

    In order to improve the photocatalytic activity under visible-light irradiation, we adopted first principle calculations based on density functional theory (DFT) to calculate the electronic structures of B site transition metal element doped InNbO4. The results indicated that the complete hybridization of Nb 4d states and some Ti 3d states contributed to the new conduction band of Ti doped InNbO4, barely changing the position of band edge. For Cr doping, some localized Cr 3d states were introduced into the band gap. Nonetheless, the potential of localized levels was too positive to cause visible-light reaction. When it came to Cu doping, the band gap was almost same with that of InNbO4 as well as some localized Cu 3d states appeared above the top of VB. The introduction of localized energy levels benefited electrons to migrate from valence band (VB) to conduction band (CB) by absorbing lower energy photons, realizing visible-light response.

  17. Reorganization of a dense granular assembly: The unjamming response function

    Science.gov (United States)

    Kolb, Évelyne; Cviklinski, Jean; Lanuza, José; Claudin, Philippe; Clément, Éric

    2004-03-01

    We investigate the mechanical properties of a static dense granular assembly in response to a local forcing. To this end, a small cyclic displacement is applied on a grain in the bulk of a two-dimensional disordered packing under gravity and the displacement fields are monitored. We evidence a dominant long range radial response in the upper half part above the solicitation and after a large number of cycles the response is “quasireversible” with a remanent dissipation field exhibiting long range streams and vortexlike symmetry.

  18. V S30, slope, H 800 and f 0: performance of various site-condition proxies in reducing ground-motion aleatory variability and predicting nonlinear site response

    Science.gov (United States)

    Derras, Boumédiène; Bard, Pierre-Yves; Cotton, Fabrice

    2017-09-01

    The aim of this paper is to investigate the ability of various site-condition proxies (SCPs) to reduce ground-motion aleatory variability and evaluate how SCPs capture nonlinearity site effects. The SCPs used here are time-averaged shear-wave velocity in the top 30 m ( V S30), the topographical slope (slope), the fundamental resonance frequency ( f 0) and the depth beyond which V s exceeds 800 m/s ( H 800). We considered first the performance of each SCP taken alone and then the combined performance of the 6 SCP pairs [ V S30- f 0], [ V S30- H 800], [ f 0-slope], [ H 800-slope], [ V S30-slope] and [ f 0- H 800]. This analysis is performed using a neural network approach including a random effect applied on a KiK-net subset for derivation of ground-motion prediction equations setting the relationship between various ground-motion parameters such as peak ground acceleration, peak ground velocity and pseudo-spectral acceleration PSA ( T), and M w, R JB, focal depth and SCPs. While the choice of SCP is found to have almost no impact on the median ground-motion prediction, it does impact the level of aleatory uncertainty. V S30 is found to perform the best of single proxies at short periods ( T < 0.6 s), while f 0 and H 800 perform better at longer periods; considering SCP pairs leads to significant improvements, with particular emphasis on [ V S30- H 800] and [ f 0-slope] pairs. The results also indicate significant nonlinearity on the site terms for soft sites and that the most relevant loading parameter for characterising nonlinear site response is the "stiff" spectral ordinate at the considered period.[Figure not available: see fulltext.

  19. Matrix of response functions for xenon gamma-ray detector

    International Nuclear Information System (INIS)

    Shustov, A.E.; Vlasik, K.F.; Grachev, V.M.; Dmitrenko, V.V.; Novikov, A.S.; P'ya, S.N.; Ulin, S.E.; Uteshev, Z.M.; Chernysheva, I.V.

    2014-01-01

    An approach of creation of response matrix using simulation GEANT4 gamma-ray Monte-Carlo method has been described for gamma-ray spectrometer based on high pressure xenon impulse ionization chamber with a shielding grid [ru

  20. A method for improving global pyranometer measurements by modeling responsivity functions

    Energy Technology Data Exchange (ETDEWEB)

    Lester, A. [Smith College, Northampton, MA 01063 (United States); Myers, D.R. [National Renewable Energy Laboratory, 1617 Cole Blvd., Golden, CO 80401 (United States)

    2006-03-15

    Accurate global solar radiation measurements are crucial to climate change research and the development of solar energy technologies. Pyranometers produce an electrical signal proportional to global irradiance. The signal-to-irradiance ratio is the responsivity (RS) of the instrument (RS=signal/irradiance=microvolts/(W/m{sup 2})). Most engineering measurements are made using a constant RS. It is known that RS varies with day of year, zenith angle, and net infrared radiation. This study proposes a method to find an RS function to model a pyranometer's changing RS. Using a reference irradiance calculated from direct and diffuse instruments, we found instantaneous RS for two global pyranometers over 31 sunny days in a two-year period. We performed successive independent regressions of the error between the constant and instantaneous RS with respect to zenith angle, day of year, and net infrared to obtain an RS function. An alternative method replaced the infrared regression with an independently developed technique to account for thermal offset. Results show improved uncertainties with the function method than with the single-calibration value. Lower uncertainties also occur using a black-and-white (8-48), rather than all-black (PSP), shaded pyranometer as the diffuse reference instrument. We conclude that the function method is extremely effective in reducing uncertainty in the irradiance measurements for global PSP pyranometers if they are calibrated at the deployment site. Furthermore, it was found that the function method accounts for the pyranometer's thermal offset, rendering further corrections unnecessary. The improvements in irradiance data achieved in this study will serve to increase the accuracy of solar energy assessments and atmospheric research. (author)

  1. Blogging within a Social Networking Site as a Form of Literature Response in a Teacher Education Course

    Science.gov (United States)

    Hutchison, Amy; Wang, Wei

    2012-01-01

    The purpose of this qualitative study was to document how pre-service teachers in a children's literature course experienced blogging on a social networking site as a form of literature response. Understanding how pre-service teachers experience these tools can inform the ways we instruct them to integrate Web 2.0 tools into their teaching.…

  2. 76 FR 10028 - Settlement Agreement for Recovery of Past Response Costs 10,000 Havana Street Site, Commerce City...

    Science.gov (United States)

    2011-02-23

    ... ENVIRONMENTAL PROTECTION AGENCY [FRL-9269-7] Settlement Agreement for Recovery of Past Response Costs 10,000 Havana Street Site, Commerce City, Adams County, CO AGENCY: Environmental Protection Agency. ACTION: Notice and request for public comment. SUMMARY: In accordance with the requirements of Section...

  3. International Benchmark on Numerical Simulations for 1D, Nonlinear Site Response (PRENOLIN) : Verification Phase Based on Canonical Cases

    NARCIS (Netherlands)

    Régnier, Julie; Bonilla, Luis-Fabian; Bard, Pierre-Yves; Bertrand, Etienne; Hollender, Fabrice; Kawase, Hiroshi; Sicilia, Deborah; Arduino, Pedro; Amorosi, Angelo; Asimaki, Dominiki; Pisano, F.

    2016-01-01

    PREdiction of NOn‐LINear soil behavior (PRENOLIN) is an international benchmark aiming to test multiple numerical simulation codes that are capable of predicting nonlinear seismic site response with various constitutive models. One of the objectives of this project is the assessment of the

  4. Do On-site Mental Health Professionals Change Pediatricians’ Responses to Children’s Mental Health Problems?

    Science.gov (United States)

    Horwitz, Sarah McCue; Storfer-Isser, Amy; Kerker, Bonnie D.; Szilagyi, Moira; Garner, Andrew S.; O’Connor, Karen G.; Hoagwood, Kimberly E.; Green, Cori M.; Foy, Jane M.; Stein, Ruth E.K.

    2016-01-01

    Objective The objectives were to: assess the availability of on-site mental health professionals (MHP) in primary care; examine practice/pediatrician characteristics associated with on-site MHPs; and determine whether presence of on-site MHPs is related to pediatricians’ co-managing or more frequently identifying, treat/managing or referring MH problems. Methods Analyses included AAP members who participated in an AAP Periodic Survey in 2013 and who practiced general pediatrics (N=321). Measures included socio-demographics, practice characteristics, questions on about on-site MHPs, co-management of MH problems and pediatricians’ behaviors in response to 5 prevalent MH problems. Weighted univariate, bivariate and multivariable analyses were performed. Results Thirty-five percent reported on-site MHPs. Practice characteristics (medical schools/universities/HMOs, <100 visits/week, <80% of patients privately insured), and interactions of practice location (urban) with visits and patient insurance, were associated with on-site MHPs. There was no overall association between co-location and co-management or whether pediatricians usually identified, treat/managed or referred 5 common child MH problems. Among the subset of pediatricians who reported co-managing there was an association with co-management when the on-site MHP was a child psychiatrist, SA counselor, or social worker. Conclusions On-site MHPs are more frequent in settings where low-income children are served and where pediatricians train. Pediatricians who co-manage MH problems are more likely to do so when the on-site MHP is a child psychiatrist, SA counselor, or social worker. Overall, on-site MHPs were not associated with co-management or increased likelihood of pediatricians identifying, treating/managing, or referring children with 5 common child MH problems. PMID:27064141

  5. Polarization response functions and the (/rvec e/,e'/rvec p/) reaction

    International Nuclear Information System (INIS)

    Picklesimer, A.; Van Orden, J.W.

    1988-01-01

    The first comprehensive study of the full set of eighteen response functions relevant to the (/rvec e/,e'/rvec p/) reaction is presented. Benchmark analytical features and limiting cases of the response functions are described. Numerical predictions contrasting nonrelativistic and relativistic (Dirac) dynamics and on- and off- shell final state interaction effects are presented. Basic physical characteristics and dependences of the response functions are identified. The outlook for future experimental studies of the (/rvec e/,e'/rvec p/) polarization response functions is discussed. 56 refs., 5 figs., 1 tab

  6. The ArcSDE GIS Dynamic Population Model Tool for Savannah River Site Emergency Response

    International Nuclear Information System (INIS)

    MCLANE, TRACY; JONES, DWIGHT

    2005-01-01

    The Savannah River Site (SRS) is a 310-square-mile Department of Energy site located near Aiken, South Carolina. With a workforce of over 10,000 employees and subcontractors, SRS emergency personnel must be able to respond to an emergency event in a timely and effective manner, in order to ensure the safety and security of the Site. Geographic Information Systems (GIS) provides the technology needed to give managers and emergency personnel the information they need to make quick and effective decisions. In the event of a site evacuation, knowing the number of on-site personnel to evacuate from a given area is an essential piece of information for emergency staff. SRS has developed a GIS Dynamic Population Model Tool to quickly communicate real-time information that summarizes employee populations by facility area and building and then generates dynamic maps that illustrate output statistics

  7. Long latency postural responses are functionally modified by cognitive set.

    Science.gov (United States)

    Beckley, D J; Bloem, B R; Remler, M P; Roos, R A; Van Dijk, J G

    1991-10-01

    We examined how cognitive set influences the long latency components of normal postural responses in the legs. We disturbed the postural stability of standing human subjects with sudden toe-up ankle rotations. To influence the subjects' cognitive set, we varied the rotation amplitude either predictably (serial 4 degrees versus serial 10 degrees) or unpredictably (random mixture of 4 degrees and 10 degrees). The subjects' responses to these ankle rotations were assessed from the EMG activity of the tibialis anterior, the medial gastrocnemius, and the vastus lateralis muscles of the left leg. The results indicate that, when the rotation amplitude is predictable, only the amplitude of the long latency (LL) response in tibialis anterior and vastus lateralis varied directly with perturbation size. Furthermore, when the rotation amplitude is unpredictable, the central nervous system selects a default amplitude for the LL response in the tibialis anterior. When normal subjects are exposed to 2 perturbation amplitudes which include the potential risk of falling, the default LL response in tibialis anterior appropriately anticipates the larger amplitude perturbation rather than the smaller or an intermediate one.

  8. Functional analysis of rice HOMEOBOX4 (Oshox4) gene reveals a negative function in gibberellin responses.

    Science.gov (United States)

    Dai, Mingqiu; Hu, Yongfeng; Ma, Qian; Zhao, Yu; Zhou, Dao-Xiu

    2008-02-01

    The homeodomain-leucine zipper (HD-Zip) putative transcription factor genes are divided into 4 families. In this work, we studied the function of a rice HD-Zip I gene, H OME O BO X4 (Oshox4). Oshox4 transcripts were detected in leaf and floral organ primordia but excluded from the shoot apical meristem and the protein was nuclear localized. Over-expression of Oshox4 in rice induced a semi-dwarf phenotype that could not be complemented by applied GA3. The over-expression plants accumulated elevated levels of bioactive GA, while the GA catabolic gene GA2ox3 was upregulated in the transgenic plants. In addition, over-expression of Oshox4 blocked GA-dependent alpha-amylase production. However, down-regulation of Oshox4 in RNAi transgenic plants induced no phenotypic alteration. Interestingly, the expression of YAB1 that is involved in the negative feedback regulation of the GA biosynthesis was upregulated in the Oshox4 over-expressing plants. One-hybrid assays showed that Oshox4 could interact with YAB1 promoter in yeast. In addition, Oshox4 expression was upregulated by GA. These data together suggest that Oshox4 may be involved in the negative regulation of GA signalling and may play a role to fine tune GA responses in rice.

  9. Can ammonia tolerance amongst lichen functional groups be explained by physiological responses?

    International Nuclear Information System (INIS)

    Munzi, S.; Cruz, C.; Branquinho, C.; Pinho, P.; Leith, I.D.; Sheppard, L.J.

    2014-01-01

    Ammonia (NH 3 ) empirical critical levels for Europe were re-evaluated in 2009, based mainly on the ecological responses of lichen communities without acknowledging the physiological differences between oligotrophic and nitrophytic species. Here, we compare a nitrogen sensitive lichen (Evernia prunastri) with a nitrogen tolerant one (Xanthoria parietina), focussing on their physiological response (Fv/Fm) to short-term NH 3 exposure and their frequency of occurrence along an NH 3 field gradient. Both frequency and Fv/Fm of E. prunastri decreased abruptly above 3 μg m −3 NH 3 suggesting direct adverse effects of NH 3 on its photosynthetic performance. By contrast, X. parietina increased its frequency with NH 3 , despite showing decreased capacity of photosystem II above 50 μg m −3 NH 3 , suggesting that the ecological success of X. parietina at ammonia-rich sites might be related to indirect effects of increased nitrogen (NH 3 ) availability. These results highlight the need to establish NH 3 critical levels based on oligotrophic lichen species. - Highlights: • Physiological response and ecological behavior were compared in two contrasting lichens. • NH 3 reduces Fv/Fm in both the N sensitive E. prunastri and the N tolerant X. parietina. • In the field frequency of occurrence correlated with NH 3 concentration. • NH 3 indirectly provides the nitrophytic X. parietina with ecological advantages. • Oligotrophs more accurately indicate increasing NH 3 concentrations than nitrophytes. - Physiological response to ammonia helps to explain lichen functional groups

  10. Systematic mapping of contact sites reveals tethers and a function for the peroxisome-mitochondria contact

    NARCIS (Netherlands)

    Shai, Nadav; Yifrach, Eden; van Roermund, Carlo W T; Cohen, Nir; Bibi, Chen; IJlst, Lodewijk; Cavellini, Laetitia; Meurisse, Julie; Schuster, Ramona; Zada, Lior; Mari, Muriel C; Reggiori, Fulvio M; Hughes, Adam L; Escobar-Henriques, Mafalda; Cohen, Mickael M; Waterham, Hans R; Wanders, Ronald J A; Schuldiner, Maya; Zalckvar, Einat

    2018-01-01

    The understanding that organelles are not floating in the cytosol, but rather held in an organized yet dynamic interplay through membrane contact sites, is altering the way we grasp cell biological phenomena. However, we still have not identified the entire repertoire of contact sites, their

  11. Features generated for computational splice-site prediction correspond to functional elements

    Directory of Open Access Journals (Sweden)

    Wilbur W John

    2007-10-01

    Full Text Available Abstract Background Accurate selection of splice sites during the splicing of precursors to messenger RNA requires both relatively well-characterized signals at the splice sites and auxiliary signals in the adjacent exons and introns. We previously described a feature generation algorithm (FGA that is capable of achieving high classification accuracy on human 3' splice sites. In this paper, we extend the splice-site prediction to 5' splice sites and explore the generated features for biologically meaningful splicing signals. Results We present examples from the observed features that correspond to known signals, both core signals (including the branch site and pyrimidine tract and auxiliary signals (including GGG triplets and exon splicing enhancers. We present evidence that features identified by FGA include splicing signals not found by other methods. Conclusion Our generated features capture known biological signals in the expected sequence interval flanking splice sites. The method can be easily applied to other species and to similar classification problems, such as tissue-specific regulatory elements, polyadenylation sites, promoters, etc.

  12. Function of ZFAND3 in the DNA Damage Response

    Science.gov (United States)

    2013-06-01

    Cantor SB, Naka- tani Y, Livingston DM. 2006. Multifactorial contribu- tions to an acute DNA damage response by BRCA1/ BARD1-containing complexes. Genes...Cutaneous T Cell Lymphoma. PLoS ONE 8(7): e68915. doi:10.1371/journal.pone.0068915 Editor: Sue Cotterill, St. Georges University of London, United

  13. Comment and response document for the UMTRA Project vitro processing site completion report Salt Lake City, Utah. Revision 1

    International Nuclear Information System (INIS)

    1995-03-01

    This Comment and Response Document is a series of UMTRA document review forms regarding the UMTRA Project Vitro Processing Site Completion Report for Salt Lake City, Utah in March, 1995. The completion report provides evidence that the final Salt Lake City, Utah, processing site property conditions are in accordance with the approved design and that all U.S. Environmental Protection Agency (EPA) standards have been satisfied. Included as appendices to support the stated conclusions are the record drawings; a summary of grid test results; contract specifications and construction drawings, the EPA standards (40 CFR Part 192); the audit, inspection, and surveillance summary; the permit information; and project photographs. The principal objective of the remedial action at Salt Lake City is to remove the tailings from the processing site, render the site free of contamination to EPA standards, and restore the site to the final design grade elevations. Each section is evaluated in detail to check all aspects of above report, especially the inclusion of adequate verification data. Each review form contains a section entitled State of Utah Response and Action, which is an explanation or correction of DOE criticisms of the report

  14. Processing of response functions obtained by radiotracer measurements. XIII

    International Nuclear Information System (INIS)

    Thyn, J.; Havlicek, A.

    1982-01-01

    The segregation of fodder mixtures during filling and emptying of storage tanks was evaluated statistically using significance tests and by the frequency characteristics method evaluating system by the gain coefficient. The gain coefficient is determined from the self-correlation function of tracer concentration variations during filling and from the self-correlation function of tracer concentration variations during emptying. The described methods of experimental data processing were used for the evaluation of industrial cylindrical storage tanks with differently shaped hoppers (rectangular or circular central hole). 24 Na in the form of ground sodium carb--onate was used as a tracer. (author)

  15. A Quantitative Assessment of the Structure and Functions of a Mature Bottomland Hardwood Community: The Iatt Creek Ecosystem Site

    Science.gov (United States)

    Calvin E. Meier; John A. Stanturf; Emile S. Gardiner; Paul B. Hamel; Melvin L. Warren

    1999-01-01

    We report our efforts, initiated in 1995, to quantify ecological processes and functions in a relatively undisturbed, mature hardwood forest. The 320-ha site is located in central Louisiana on the upper reaches of Iatt Creek, an anastomosing minor stream bottom. The forest is a mature sweetgum (Liquidambar styraciflua L.)-cherrybark oak (

  16. Geographic Response Plan (GRP) Sensitive Site Points (Editable), Guam, 2016, US EPA Region 9

    Data.gov (United States)

    U.S. Environmental Protection Agency — This is an editable point feature data set with points over Apra Harbor in Guam. These points represent sensitive sites such as access points for public use and...

  17. Identification of sites within the Palo Duro Basin. Volume 3. Responses to comments

    International Nuclear Information System (INIS)

    1984-11-01

    This document responds to comments received by the US Department of Energy (DOE) on the draft report entitled Identification of Sites Within the Palo Duro Basin: Volume I - Palo Duro Location A (in Deaf Smith County) and Volume II - Palo Duro Location B (in Swisher County), BMI/ONWI-531, February 1984. The purpose of the report was to review existing geologic, environmental, and socioeconomic data for previously identified potentially acceptable sites consisting of approximately 200 square miles in Swisher County and 400 square miles in Deaf Smith County in the Texas Panhandle and to narrow them to preferred smaller sites for possible further study for a nuclear waste repository. The smaller sites thus identified within the two counties would then be more comparable in size to those in salt deposits in Louisiana, Mississippi, and Utah

  18. Diuretic response and renal function in heart failure

    NARCIS (Netherlands)

    ter Maaten, Jozine Magdalena

    2016-01-01

    In patients with heart failure fluid overload is a frequently occurring problem, which is among others caused by an impaired function of the heart. This fluid overload may lead to severe dyspnea warranting an acute hospitalization. The first choice treatment of this fluid overload is administration

  19. Functional MRI of human hypothalamic responses following glucose ingestion

    NARCIS (Netherlands)

    Smeets, P.A.M.; Graaf, C. de; Stafleu, A.; Osch, M.J.P. van; Grond, J. van der

    2005-01-01

    The hypothalamus is intimately involved in the regulation of food intake, integrating multiple neural and hormonal signals. Several hypothalamic nuclei contain glucose-sensitive neurons, which play a crucial role in energy homeostasis. Although a few functional magnetic resonance imaging (fMRI)

  20. Insight the C-site pocket conformational changes responsible for sirtuin 2 activity using molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Sugunadevi Sakkiah

    Full Text Available Sirtuin belongs to a family of typical histone deacetylase which regulates the fundamental cellular biological processes including gene expression, genome stability, mitosis, nutrient metabolism, aging, mitochondrial function, and cell motility. Michael et. al. reported that B-site mutation (Q167A and H187A decreased the SIRT2 activity but still the structural changes were not reported. Hence, we performed 5 ns molecular dynamics (MD simulation on SIRT2 Apo-form and complexes with substrate/NAD(+ and inhibitor of wild type (WT, Q167A, and H187A. The results revealed that the assembly and disassembly of C-site induced by presence of substrate/NAD(+ and inhibitor, respectively. This assembly and disassembly was mainly due to the interaction between the substrate/NAD(+ and inhibitor and F96 and the distance between F96 and H187 which are present at the neck of the C-site. MD simulations suggest that the conformational change of L3 plays a major role in assembly and disassembly of C-site. Our current results strongly suggest that the distinct conformational change of L3 as well as the assembly and disassembly of C-site plays an important role in SIRT2 deacetylation function. Our study unveiled the structural changes of SIRT2 in presence of NAD(+ and inhibitor which should be helpful to improve the inhibitory potency of SIRT2.

  1. Assessing the structural conservation of protein pockets to study functional and allosteric sites: implications for drug discovery

    Directory of Open Access Journals (Sweden)

    Daura Xavier

    2010-03-01

    Full Text Available Abstract Background With the classical, active-site oriented drug-development approach reaching its limits, protein ligand-binding sites in general and allosteric sites in particular are increasingly attracting the interest of medicinal chemists in the search for new types of targets and strategies to drug development. Given that allostery represents one of the most common and powerful means to regulate protein function, the traditional drug discovery approach of targeting active sites can be extended by targeting allosteric or regulatory protein pockets that may allow the discovery of not only novel drug-like inhibitors, but activators as well. The wealth of available protein structural data can be exploited to further increase our understanding of allosterism, which in turn may have therapeutic applications. A first step in this direction is to identify and characterize putative effector sites that may be present in already available structural data. Results We performed a large-scale study of protein cavities as potential allosteric and functional sites, by integrating publicly available information on protein sequences, structures and active sites for more than a thousand protein families. By identifying common pockets across different structures of the same protein family we developed a method to measure the pocket's structural conservation. The method was first parameterized using known active sites. We characterized the predicted pockets in terms of sequence and structural conservation, backbone flexibility and electrostatic potential. Although these different measures do not tend to correlate, their combination is useful in selecting functional and regulatory sites, as a detailed analysis of a handful of protein families shows. We finally estimated the numbers of potential allosteric or regulatory pockets that may be present in the data set, finding that pockets with putative functional and effector characteristics are widespread across

  2. Food supply and demand, a simulation model of the functional response of grazing ruminants

    NARCIS (Netherlands)

    Smallegange, I.M.; Brunsting, A.M.H.

    2002-01-01

    A dynamic model of the functional response is a first prerequisite to be able to bridge the gap between local feeding ecology and grazing rules that pertain to larger scales. A mechanistic model is presented that simulates the functional response, growth and grazing time of ruminants. It is based on

  3. Use of Geohydrologic Response Functions in the assessment of deep nuclear waste repositories: assessment of effectiveness of geologic isolation systems

    International Nuclear Information System (INIS)

    Nelson, R.W.

    1981-05-01

    Geohydrologic Response Functions (GRFs) interrelate the three vital factors needed in the repository decision-making process: the quantity, arrival time, and location of contamination reaching the biosphere. GRFs further focus attention upon two related and additive parameters: the initial delay time and delay spread time. After the principal site selection, the GRFs may be applied to obtain more detailed performance evaluations concerning specific nuclides or waste components, specific results for various types of accidental release, and effects of a variety of contaminant source terms or leach models. The response functions may be applied to consider contaminant reductions and delays through material sorption as well as through a variety of other interactions and effects

  4. Functionalization of silicon-doped single walled carbon nanotubes at the doping site: An ab initio study

    International Nuclear Information System (INIS)

    Song Chen; Xia Yueyuan; Zhao Mingwen; Liu Xiangdong; Li Feng; Huang Boda; Zhang Hongyu; Zhang Bingyun

    2006-01-01

    We performed ab initio calculations on the cytosine-functionalized silicon-doped single walled carbon nanotubes (SWNT). The results show that silicon substitutional doping to SWNT can dramatically change the atomic and electronic structures of the SWNT. And more importantly, it may provide an efficient pathway for further sidewall functionalization to synthesize more complicated SWNT based complex materials, for example, our previously proposed base-functionalized SWNTs, because the doping silicon atom can improve the reaction activity of the tube at the doping site due to its preference to form sp3 hybridization bonding

  5. Evaluation and Monte Carlo modelling of the response function of the Leake neutron area survey instrument

    International Nuclear Information System (INIS)

    Tagziria, H.; Tanner, R.J.; Bartlett, D.T.; Thomas, D.J.

    2004-01-01

    All available measured data for the response characteristics of the Leake counter have been gathered together. These data, augmented by previously unpublished work, have been compared to Monte Carlo simulations of the instrument's response characteristics in the energy range from thermal to 20 MeV. A response function has been derived, which is recommended as the best currently available for the instrument. Folding this function with workplace energy distributions has enabled an assessment of the impact of this new response function to be made. Similar work, which will be published separately, has been carried out for the NM2 and the Studsvik 2202D neutron area survey instruments

  6. Compositional differences in simulated root exudates elicit a limited functional and compositional response in soil microbial communities.

    Science.gov (United States)

    Strickland, Michael S; McCulley, Rebecca L; Nelson, Jim A; Bradford, Mark A

    2015-01-01

    Inputs of low molecular weight carbon (LMW-C) to soil - primarily via root exudates- are expected to be a major driver of microbial activity and source of stable soil organic carbon. It is expected that variation in the type and composition of LMW-C entering soil will influence microbial community composition and function. If this is the case then short-term changes in LMW-C inputs may alter processes regulated by these communities. To determine if change in the composition of LMW-C inputs influences microbial community function and composition, we conducted a 90 day microcosm experiment whereby soils sourced from three different land covers (meadows, deciduous forests, and white pine stands) were amended, at low concentrations, with one of eight simulated root exudate treatments. Treatments included no addition of LMW-C, and the full factorial combination of glucose, glycine, and oxalic acid. After 90 days, we conducted a functional response assay and determined microbial composition via phospholipid fatty acid analysis. Whereas we noted a statistically significant effect of exudate treatments, this only accounted for ∼3% of the variation observed in function. In comparison, land cover and site explained ∼46 and ∼41% of the variation, respectively. This suggests that exudate composition has little influence on function compared to site/land cover specific factors. Supporting the finding that exudate effects were minor, we found that an absence of LMW-C elicited the greatest difference in function compared to those treatments receiving any LMW-C. Additionally, exudate treatments did not alter microbial community composition and observable differences were instead due to land cover. These results confirm the strong effects of land cover/site legacies on soil microbial communities. In contrast, short-term changes in exudate composition, at meaningful concentrations, may have little impact on microbial function and composition.

  7. Response functions for computing absorbed dose to skeletal tissues from neutron irradiation

    Science.gov (United States)

    Bahadori, Amir A.; Johnson, Perry; Jokisch, Derek W.; Eckerman, Keith F.; Bolch, Wesley E.

    2011-11-01

    Spongiosa in the adult human skeleton consists of three tissues—active marrow (AM), inactive marrow (IM) and trabecularized mineral bone (TB). AM is considered to be the target tissue for assessment of both long-term leukemia risk and acute marrow toxicity following radiation exposure. The total shallow marrow (TM50), defined as all tissues lying within the first 50 µm of the bone surfaces, is considered to be the radiation target tissue of relevance for radiogenic bone cancer induction. For irradiation by sources external to the body, kerma to homogeneous spongiosa has been used as a surrogate for absorbed dose to both of these tissues, as direct dose calculations are not possible using computational phantoms with homogenized spongiosa. Recent micro-CT imaging of a 40 year old male cadaver has allowed for the accurate modeling of the fine microscopic structure of spongiosa in many regions of the adult skeleton (Hough et al 2011 Phys. Med. Biol. 56 2309-46). This microstructure, along with associated masses and tissue compositions, was used to compute specific absorbed fraction (SAF) values for protons originating in axial and appendicular bone sites (Jokisch et al 2011 Phys. Med. Biol. 56 6857-72). These proton SAFs, bone masses, tissue compositions and proton production cross sections, were subsequently used to construct neutron dose-response functions (DRFs) for both AM and TM50 targets in each bone of the reference adult male. Kerma conditions were assumed for other resultant charged particles. For comparison, AM, TM50 and spongiosa kerma coefficients were also calculated. At low incident neutron energies, AM kerma coefficients for neutrons correlate well with values of the AM DRF, while total marrow (TM) kerma coefficients correlate well with values of the TM50 DRF. At high incident neutron energies, all kerma coefficients and DRFs tend to converge as charged-particle equilibrium is established across the bone site. In the range of 10 eV to 100 Me

  8. Tonal response on the stairway of the main pyramid at La Ciudadela, Teotihuacan archaeological site

    Science.gov (United States)

    Beristain, Sergio; Coss, Cecilia; Aquino, Gabriela; Negrete, Jose; Lizana, Pablo

    2002-11-01

    This paper presents new research on the very interesting audible effects produced by the stairways of many archaeological sites in Mexico. This investigation was made at the main stairway of the pyramid at La Ciudadela, Teotihuacan archaeological site. The effect previously studied was a chirped echo reflected from the stairway at normal incidence, which resembles the singing of the Quetzal. Now it is presented with the impulsive sound source and the listeners located at different angles, where apart from the characteristic chirped sound, several musical notes could be obtained and identified, covering a range of at least one half an octave. This evaluation was made at the site, where the effect is clearly audible, and it is supported with simple mathematics.

  9. Identification of E-cadherin signature motifs functioning as cleavage sites for Helicobacter pylori HtrA

    Science.gov (United States)

    Schmidt, Thomas P.; Perna, Anna M.; Fugmann, Tim; Böhm, Manja; Jan Hiss; Haller, Sarah; Götz, Camilla; Tegtmeyer, Nicole; Hoy, Benjamin; Rau, Tilman T.; Neri, Dario; Backert, Steffen; Schneider, Gisbert; Wessler, Silja

    2016-03-01

    The cell adhesion protein and tumour suppressor E-cadherin exhibits important functions in the prevention of gastric cancer. As a class-I carcinogen, Helicobacter pylori (H. pylori) has developed a unique strategy to interfere with E-cadherin functions. In previous studies, we have demonstrated that H. pylori secretes the protease high temperature requirement A (HtrA) which cleaves off the E-cadherin ectodomain (NTF) on epithelial cells. This opens cell-to-cell junctions, allowing bacterial transmigration across the polarised epithelium. Here, we investigated the molecular mechanism of the HtrA-E-cadherin interaction and identified E-cadherin cleavage sites for HtrA. Mass-spectrometry-based proteomics and Edman degradation revealed three signature motifs containing the [VITA]-[VITA]-x-x-D-[DN] sequence pattern, which were preferentially cleaved by HtrA. Based on these sites, we developed a substrate-derived peptide inhibitor that selectively bound and inhibited HtrA, thereby blocking transmigration of H. pylori. The discovery of HtrA-targeted signature sites might further explain why we detected a stable 90 kDa NTF fragment during H. pylori infection, but also additional E-cadherin fragments ranging from 105 kDa to 48 kDa in in vitro cleavage experiments. In conclusion, HtrA targets E-cadherin signature sites that are accessible in in vitro reactions, but might be partially masked on epithelial cells through functional homophilic E-cadherin interactions.

  10. Perceived risk, trust in government, and response to repository siting in the United States

    International Nuclear Information System (INIS)

    Kraft, M.E.

    1991-01-01

    Conflicts over the siting of high-level radioactive waste repositories have been intense and unrelenting. Public and state opposition to implementation of the US Nuclear Waste Policy Act is tied closely to the perception of unacceptably high repository risks and to lack of trust and confidence in governmental agencies, particularly the DOE. This paper explores the relationship of perceived risk, trust in government, and opposition to repository siting in the US in an attempt to clarify the conditions of successful implementation of nuclear waste policy in the decades ahead

  11. US Department of Energy response to standards for remedial actions at inactive uranium processing sites: Proposed rule

    International Nuclear Information System (INIS)

    1988-01-01

    The Title I groundwater standards for inactive uranium mill tailings sites, which were promulgated on January 5, 1983, by the US Environmental Protection Agency (EPA) for the Uranium Mill Tailings Remedial Action (UMTRA) Project, were remanded to the EPA on September 3, 1985, by the US Tenth Circuit Court of Appeals. The Court instructed the EPA to compile general groundwater standards for all Title I sites. On September 24, 1987, the EPA published proposed standards (52FR36000-36008) in response to the remand. This report includes an evaluation of the potential effects of the proposed EPA groundwater standards on the UMTRA Project, as well as a discussion of the DOE's position on the proposed standards. The report also contains and appendix which provides supporting information and cost analyses. In order to assess the impacts of the proposed EPA standards, this report summarizes the proposed EPA standards in Section 2.0. The next three sections assess the impacts of the three parts of the EPA standards: Subpart A considers disposal sites; Subpart B is concerned with restoration at processing sites; and Subpart C addresses supplemental standards. Section 6.0 integrates previous sections into a recommendations section. Section 7.0 contains the DOE response to questions posed by the EPA in the preamble to the proposed standards. 6 refs., 5 figs., 3 tabs

  12. Responsiveness summary for the engineering evaluation/cost analysis for decontamination at the St. Louis Downtown Site, St. Louis, Missouri

    International Nuclear Information System (INIS)

    Picel, M.H.; Peterson, J.M.; Williams, M.J.

    1991-12-01

    The US Department of Energy (DOE) is responsible for conducting remedial actions at the Mallinckrodt Chemical Plant, also referred to as the St. Louis Downtown Site (SLDS), located in the city of St. Louis, Missouri. Remedial activities at the SLDS are being carried out under DOE's Formerly Utilized Sites Remedial Action Program (FUSRAP) as part of the overall cleanup planned for three noncontiguous areas in St. Louis, which are collectively referred to as the St. Louis Site. Potential response action alternatives for managing the contaminated material generated at the SLDS have been evaluated in accordance with US Environmental Protection Agency (EPA) guidance for conducting interim actions under the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA), as amended. An engineering evaluation/cost analysis (EE/CA) report was prepared to document this process. On the basis of the analysis presented in the EE/CA, the preferred alternative for the management of contaminated wastes generated by DOE-supported plant activities is the provision of temporary storage capacity, which can be made available by modifying an existing building (i.e., Building 116) at SLDS. This alternative would enable DOE and Mallinckrodt to coordinate efforts to prevent the uncontrolled relocation of contamination and ensure that ultimate site cleanup objectives are not complicated by plant activities implemented by Mallinckrodt. The EE/CA, dated May 1991, was issued to the general public on June 7, 1991, and a public comment period was held from June 7 through July 10, 1991, in accordance with the public participation process identified in CERCLA. Comments on the proposed action were received in writing from the Missouri Department of Health, private citizen Kay Drey, and the EPA Region 7. This responsiveness summary has been prepared to respond to issues identified in these comment letters on the proposed action

  13. Functional responses of North Atlantic fish eggs to increasing temperature

    DEFF Research Database (Denmark)

    Tsoukali, Stavroula; Visser, Andre; MacKenzie, Brian

    2016-01-01

    -days and survival of fish eggs from 32 populations of 17 species in the North Atlantic to different temperatures in order to determine potential consequences of global warming for these species. The response of development time exhibited a similar decreasing trend with respect to temperature across species....... There was an overall decrease, across species, in an index of thermal requirement (cumulative degree-days) for egg development with increasing temperature. Within an empirically derived optimal thermal range for egg survival, the thermal requirement was more variable in species adapted to cold waters compared...... to species adapted to warmer waters. Moreover, the sensitivity of survival of eggs from different species to increases in temperature differed, reflecting a pattern of sensitivity along a stenotherm-eurytherm gradient of vulnerability to temperature among species. The results quantify physiological effects...

  14. Method of detecting system function by measuring frequency response

    Science.gov (United States)

    Morrison, John L [Butte, MT; Morrison, William H [Manchester, CT; Christophersen, Jon P [Idaho Falls, ID

    2012-04-03

    Real-time battery impedance spectrum is acquired using a one-time record. Fast Summation Transformation (FST) is a parallel method of acquiring a real-time battery impedance spectrum using a one-time record that enables battery diagnostics. An excitation current to a battery is a sum of equal amplitude sine waves of frequencies that are octave harmonics spread over a range of interest. A sample frequency is also octave and harmonically related to all frequencies in the sum. The time profile of this signal has a duration that is a few periods of the lowest frequency. The voltage response of the battery, average deleted, is the impedance of the battery in the time domain. Since the excitation frequencies are known and octave and harmonically related, a simple algorithm, FST, processes the time record by rectifying relative to the sine and cosine of each frequency. Another algorithm yields real and imaginary components for each frequency.

  15. Method of detecting system function by measuring frequency response

    Science.gov (United States)

    Morrison, John L.; Morrison, William H.; Christophersen, Jon P.; Motloch, Chester G.

    2013-01-08

    Methods of rapidly measuring an impedance spectrum of an energy storage device in-situ over a limited number of logarithmically distributed frequencies are described. An energy storage device is excited with a known input signal, and a response is measured to ascertain the impedance spectrum. An excitation signal is a limited time duration sum-of-sines consisting of a select number of frequencies. In one embodiment, magnitude and phase of each frequency of interest within the sum-of-sines is identified when the selected frequencies and sample rate are logarithmic integer steps greater than two. This technique requires a measurement with a duration of one period of the lowest frequency. In another embodiment, where selected frequencies are distributed in octave steps, the impedance spectrum can be determined using a captured time record that is reduced to a half-period of the lowest frequency.

  16. Functional changes in littoral macroinvertebrate communities in response to watershed-level anthropogenic stress.

    Directory of Open Access Journals (Sweden)

    Katya E Kovalenko

    Full Text Available Watershed-scale anthropogenic stressors have profound effects on aquatic communities. Although several functional traits of stream macroinvertebrates change predictably in response to land development and urbanization, little is known about macroinvertebrate functional responses in lakes. We assessed functional community structure, functional diversity (Rao's quadratic entropy and voltinism in macroinvertebrate communities sampled across the full gradient of anthropogenic stress in Laurentian Great Lakes coastal wetlands. Functional diversity and voltinism significantly decreased with increasing development, whereas agriculture had smaller or non-significant effects. Functional community structure was affected by watershed-scale development, as demonstrated by an ordination analysis followed by regression. Because functional community structure affects energy flow and ecosystem function, and functional diversity is known to have important implications for ecosystem resilience to further environmental change, these results highlight the necessity of finding ways to remediate or at least ameliorate these effects.

  17. Consumer Response to Web Sites and Their Influence on Advertising Effectiveness.

    Science.gov (United States)

    Goldsmith, Ronald E.; Lafferty, Barbara A.

    2002-01-01

    Describes a study of undergraduates that tested four hypotheses regarding the effects of viewing Web sites on Internet advertising. Highlights include attitudes toward ads in marketing communications and advertising research; recalling brand names seen on the Internet; perceived advantages and disadvantages of online advertising; and recalling ads…

  18. Black walnut response to subsoiling, irrigation, and vegetation management on a site with a shallow fragipan

    Science.gov (United States)

    F. D. McBride; J. W. Van Sambeek

    1995-01-01

    Vegetation management with glyphosate and simazine proved to be more effective than preplant subsoiling or irrigation for achieving acceptable walnut biomass growth on an upland old field site (SI = 70 for white oak). In 1980, we direct seeded germinating black walnut seed on an upland, slightly eroded, old field ridge with a 45 to 60 cm deep fragipan. We tested all...

  19. Biomass of Speckled Alder on an Air-Polluted Mountain Site and its Response to Fertilization

    Czech Academy of Sciences Publication Activity Database

    Kuneš, I.; Baláš, M.; Koňasová, T.; Špulák, O.; Balcar, V.; Bednářová Millerová, K.; Kacálek, D.; Jakl, M.; Zahradník, D.; Vítámvás, J.; Šťastná, J.; Jaklová Dytrtová, Jana

    2014-01-01

    Roč. 54, č. 6 (2014), s. 1421-1433 ISSN 0364-152X Grant - others:GA MZe(CZ) QH92087 Institutional support: RVO:61388963 Keywords : Alnus incana * site amelioration * biological amelioration * slow-acting amendments * ecosystem restoration Subject RIV: GK - Forestry Impact factor: 1.724, year: 2014

  20. Longleaf pine site response to repeated fertilization and forest floor removal by raking and prescribed burning

    Science.gov (United States)

    Kim Ludovici; Robert Eaton; Stanley Zarnoch

    2018-01-01

    Removal of forest floor litter by pine needle raking and prescribed burning is a common practice in longleaf pine (Pinus palustris Mill.) stands on Coastal Plain sites in the Southeastern United States. Repeated removal of litter by raking and the loss of surface organic matter from controlled burns can affect the...

  1. Dual function of CD70 in viral infection: modulator of early cytokine responses and activator of adaptive responses1

    Science.gov (United States)

    Allam, Atef; Swiecki, Melissa; Vermi, William; Ashwell, Jonathan D.; Colonna, Marco

    2014-01-01

    The role of the tumor necrosis factor family member CD70 in adaptive T cell responses has been intensively studied but its function in innate responses is still under investigation. Here we show that CD70 inhibits the early innate response to murine cytomegalovirus (MCMV) but is essential for the optimal generation of virus-specific CD8 T cells. CD70-/- mice reacted to MCMV infection with a robust type I interferon and proinflammatory cytokine response. This response was sufficient for initial control of MCMV, although at later time points, CD70-/- mice became more susceptible to MCMV infection. The heightened cytokine response during the early phase of MCMV infection in CD70-/- mice was paralleled by a reduction in regulatory T cells (Treg). Treg from naïve CD70-/- mice were not as efficient at suppressing T cell proliferation compared to Treg from naïve WT mice and depletion of Treg during MCMV infection in Foxp3-DTR mice or in WT mice recapitulated the phenotype observed in CD70-/- mice. Our study demonstrates that while CD70 is required for the activation of the antiviral adaptive response, it has a regulatory role in early cytokine responses to viruses such as MCMV, possibly through maintenance of Treg survival and function. PMID:24913981

  2. Site-specific differences in the association between plantar tactile perception and mobility function in older adults

    Directory of Open Access Journals (Sweden)

    Yenisel eCruz-Almeida

    2014-04-01

    Full Text Available Introduction Impaired somatosensation is common in older adults and contributes to age-related loss of mobility function. However, little is known about whether somatosensation at different sites on the plantar surface of the foot are differentially related to mobility function. Such a finding may have important implications for clinical care of older adults and other at-risk populations, such as for optimizing interventions (e.g., footwear for augmenting somatosensory feedback and for improving the efficiency of clinical assessment. Materials and Methods Tactile perception was evaluated with a 10g monofilament at four sites on the plantar surface of each foot: great toe (GT, first metatarsal head (MT1, heel (H and fifth metatarsal head (MT5. Mobility function was assessed with the Berg Balance Scale and walking speed. Results Sixty-one older adults participated. Tactile perception was significantly positively associated with Berg Balance Score (adjusted R2 = 0.30 - 0.75; p = 0.03 - Discussion The present findings indicate that tactile perception at MT1 is more closely linked to mobility function than is tactile perception at GT, MT5 or H. These findings warrant further research to examine whether interventions (e.g., textured insoles and assessments that preferentially or exclusively focus on the site of MT1 may be more effective for optimizing clinical care.

  3. Versatile and Efficient Site-Specific Protein Functionalization by Tubulin Tyrosine Ligase.

    Science.gov (United States)

    Schumacher, Dominik; Helma, Jonas; Mann, Florian A; Pichler, Garwin; Natale, Francesco; Krause, Eberhard; Cardoso, M Cristina; Hackenberger, Christian P R; Leonhardt, Heinrich

    2015-11-09

    A novel chemoenzymatic approach for simple and fast site-specific protein labeling is reported. Recombinant tubulin tyrosine ligase (TTL) was repurposed to attach various unnatural tyrosine derivatives as small bioorthogonal handles to proteins containing a short tubulin-derived recognition sequence (Tub-tag). This novel strategy enables a broad range of high-yielding and fast chemoselective C-terminal protein modifications on isolated proteins or in cell lysates for applications in biochemistry, cell biology, and beyond, as demonstrated by the site-specific labeling of nanobodies, GFP, and ubiquitin. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Planning for off-site response to radiation accidents in nuclear facilities

    International Nuclear Information System (INIS)

    1981-01-01

    The purpose of this publication is to give guidance to those who are responsible for the protection of the public in the event of an accident occurring at a land-based nuclear facility. This guidance should assist in the advance preparation of emergency response plans and implementing procedures. Basic principles of protective measures along with their advantages and disadvantages are discussed. Other principles related to emergency planning and the operational response to an emergency are outlined. Although the guidance is primarily oriented towards land-based nuclear power facilities, the guidance does have general application to other types of nuclear facility

  5. Planning for off-site response to radiation accidents in nuclear facilities

    International Nuclear Information System (INIS)

    1979-01-01

    The purpose of this manual is to give guidance to those who are responsible for the protection of the public in the event of an accident occurring at a land-based nuclear facility. This guidance should assist in the advance preparation of emergency response plans and implementing procedures. Basic principles of protective measures along with their advantages and disadvantages are discussed. Other principles related to emergency planning and the operational response to an emergency are outlined. Although the guidance is primarily oriented toward land-based nuclear power facilities, the guidance does have general application to other types of nuclear facilities

  6. Final environmental impact statement for the Nevada test site and off-site locations in the State of Nevada. Public comment and response document, Volume 3, Part B responses

    International Nuclear Information System (INIS)

    1996-08-01

    This sitewide EIS evaluates the potential environmental impacts of four possible land-use alternatives being considered for the Nevada Test Site (NTS), the Tonopah Test Range, and the formerly operated DOE sites in the state of Nevada: the Project Shoal Area, the Central Nevada Test Area, and portions of the Nellis Air Force Range Complex. Three additional sites in Nevada-Eldorado Valley, Dry Lake Valley, and Coyote Spring Valley-are evaluated for collocation of solar energy production facilities. The four alternatives include Continue Current Operations (No Action, continue to operate at the level maintained for the past 3 to 5 years); Discontinue Operations 1 (discontinue operations and interagency programs); Expanded Use (increased use of NTS and its resources to support defense and nondefense programs); and Alternate Use of Withdrawn Lands (discontinue all defense-related activities at NTS; continue waste management operations in support of NTS environmental restoration efforts; expand nondefense research). Environmental impacts were assessed for each alternative by analyzing, to the extent possible, the discrete and cumulative environmental impacts associated with Defense Waste Management, Environmental Restoration, Nondefense Research and Development, and Work for Others Programs. A framework for a Resource Management Plan is included as Volume 2 of this EIS and represents the development of an ecosystem based planning process closely integrated with the National Environmental Policy Act process. This EIS, among other things, analyzed the impacts of transportation of low level waste, and site characterization activities related to the Yucca Mountain Project but did not analyze the suitability of the site as a repository. This EIS does not analyze the suitability of the Yucca Mountain site as a repository as this is an action beyond the scope of the EIS. Volume 3 of this EIS contains the public comments and the responses to the comments

  7. Decreased prefrontal functional brain response during memory testing in women with Cushing's syndrome in remission.

    Science.gov (United States)

    Ragnarsson, Oskar; Stomby, Andreas; Dahlqvist, Per; Evang, Johan A; Ryberg, Mats; Olsson, Tommy; Bollerslev, Jens; Nyberg, Lars; Johannsson, Gudmundur

    2017-08-01

    Neurocognitive dysfunction is an important feature of Cushing's syndrome (CS). Our hypothesis was that patients with CS in remission have decreased functional brain responses in the prefrontal cortex and hippocampus during memory testing. In this cross-sectional study we included 19 women previously treated for CS and 19 controls matched for age, gender, and education. The median remission time was 7 (IQR 6-10) years. Brain activity was studied with functional magnetic resonance imaging during episodic- and working-memory tasks. The primary regions of interest were the prefrontal cortex and the hippocampus. A voxel-wise comparison of functional brain responses in patients and controls was performed. During episodic-memory encoding, patients displayed lower functional brain responses in the left and right prefrontal gyrus (pright inferior occipital gyrus (pbrain responses in the left posterior hippocampus in patients (p=0.05). During episodic-memory retrieval, the patients displayed lower functional brain responses in several brain areas with the most predominant difference in the right prefrontal cortex (pbrain response during a more complex working memory task compared with a simpler one. In conclusion, women with CS in long-term remission have reduced functional brain responses during episodic and working memory testing. This observation extends previous findings showing long-term adverse effects of severe hypercortisolaemia on brain function. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Measuring bovine gamma delta T cell function at the site of Mycobacterium bovis infection

    Science.gov (United States)

    Bovine gamma delta T cells are amongst the first cells to accumulate at the site of Mycobacterium bovis infection; however, their role in the developing lesion remains unclear. We utilized transcriptomics analysis, in situ hybridization, and a macrophage/gamma delta T cell co-culture system to eluc...

  9. DPP6 domains responsible for its localization and function.

    Science.gov (United States)

    Lin, Lin; Long, Laura K; Hatch, Michael M; Hoffman, Dax A

    2014-11-14

    Dipeptidyl peptidase-like protein 6 (DPP6) is an auxiliary subunit of the Kv4 family of voltage-gated K(+) channels known to enhance channel surface expression and potently accelerate their kinetics. DPP6 is a single transmembrane protein, which is structurally remarkable for its large extracellular domain. Included in this domain is a cysteine-rich motif, the function of which is unknown. Here we show that this cysteine-rich domain of DPP6 is required for its export from the ER and expression on the cell surface. Disulfide bridges formed at C349/C356 and C465/C468 of the cysteine-rich domain are necessary for the enhancement of Kv4.2 channel surface expression but not its interaction with Kv4.2 subunits. The short intracellular N-terminal and transmembrane domains of DPP6 associates with and accelerates the recovery from inactivation of Kv4.2, but the entire extracellular domain is necessary to enhance Kv4.2 surface expression and stabilization. Our findings show that the cysteine-rich domain of DPP6 plays an important role in protein folding of DPP6 that is required for transport of DPP6/Kv4.2 complexes out of the ER. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. Modification of response functions of cat visual cortical cells by spatially congruent perturbing stimuli.

    Science.gov (United States)

    Kabara, J F; Bonds, A B

    2001-12-01

    Responses of cat striate cortical cells to a drifting sinusoidal grating were modified by the superimposition of a second, perturbing grating (PG) that did not excite the cell when presented alone. One consequence of the presence of a PG was a shift in the tuning curves. The orientation tuning of all 41 cells exposed to a PG and the spatial frequency tuning of 83% of the 23 cells exposed to a PG showed statistically significant dislocations of both the response function peak and center of mass from their single grating values. As found in earlier reports, the presence of PGs suppressed responsiveness. However, reductions measured at the single grating optimum orientation or spatial frequency were on average 1.3 times greater than the suppression found at the peak of the response function modified by the presence of the PG. Much of the loss in response seen at the single grating optimum is thus a result of a shift in the tuning function rather than outright suppression. On average orientation shifts were repulsive and proportional (approximately 0.10 deg/deg) to the angle between the perturbing stimulus and the optimum single grating orientation. Shifts in the spatial frequency response function were both attractive and repulsive, resulting in an overall average of zero. For both simple and complex cells, PGs generally broadened orientation response function bandwidths. Similarly, complex cell spatial frequency response function bandwidths broadened. Simple cell spatial frequency response functions usually did not change, and those that did broadened only 4% on average. These data support the hypothesis that additional sinusoidal components in compound stimuli retune cells' response functions for orientation and spatial frequency.

  11. IN SITU COMPARISON OF TREE-RING RESPONSES TO CLIMATE AND POPULATION GENETICS: THE NEED TO CONTROL FOR LOCAL CLIMATE AND SITE VARIABLES

    Directory of Open Access Journals (Sweden)

    Johann Mathias Housset

    2016-10-01

    Full Text Available Tree species responses to climate change will be greatly influenced by their evolutionary potential and their phenotypic plasticity. Investigating tree-rings responses to climate and population genetics at the regional scale is therefore crucial in assessing the tree behaviour to climate change. This study combined in situ dendroclimatology and population genetics over a latitudinal gradient and compared the variations between the two at the intra- and inter-population levels. This approach was applied on the northern marginal populations of Thuja occidentalis (eastern white-cedar in the Canadian boreal forest. We aimed first to assess the radial growth variability (response functional trait within populations across the gradient and to compare it with the genetic diversity (microsatellites. Second, we investigated the variability in the growth response to climate at the regional scale through the radial growth-climate relationships, and tested its correlation with environmental variables and population genetic structure. Model selection based on the Akaike Information Criteria revealed that the growth synchronicity between pairs of trees of a population covariates with both the genetic diversity of this population and the amount of precipitation (inverse correlation, although these variables only explained a small fraction of the observed variance. At the regional scale, variance partitioning and partial redundancy analysis indicate that the growth response to climate was greatly modulated by stand environmental variables, suggesting predominant plastic variations in growth-response to climate. Combining in situ dendroclimatology and population genetics is a promising way to investigate species’ response capacity to climate change in natural stands. We stress the need to control for local climate and site conditions effects on dendroclimatic response to climate to avoid misleading conclusions regarding the associations with genetic variables.

  12. Productivity, mortality, and response to disturbance of nesting Swainson's hawks on the Hanford Site

    Energy Technology Data Exchange (ETDEWEB)

    Poole, L.D.; Marr, N.V.; McCorquodale, S.M.

    1988-03-01

    The objectives of this study were to characterize Swainson's hawk (Buteo swainson) use of the US Department of Energy (DOE) Hanford Site and to evaluate the potential for engineering and other human activities on the Hanford Site to negatively affect the nesting Swainson's hawk population. Activities associated with the Basalt Waste Isolation Project (BWIP) were used as the primary external stimuli in studying hawk responses to potential human disturbance. Parked and moving vehicles were the most common disturbance sources observed in Swainson's hawk territories. Hawks appeared to be sensitive to disturbance from pedestrians and slow-moving vehicles near nests. Novel stimuli were much more likely to evoke strong responses than were recurring events. Adult hawks reacted more frequently and vigorously than did juveniles. When disturbed, adult hawks usually flew toward the location of the disturbance; juvenile hawks usually flew away from disturbances. Human activity associated with BWIP may have had negative on one pair of nesting Swainson's hawks and may have precluded the use of an additional traditional nesting territory. Negative impacts to nesting Swainson's hawks from human activity could be minimized by confining activities to the non-nesting period or to distances greater than 2.2 km from nest sites. Tree groves and elevated perches, including utility poles, across the Hanford Site are probably critical to the success of nesting Swainson's hawks. Potential mitigation strategies associated with energy research and development activities on the Hanford Site could include provisions for maintenance and establishment of drought-tolerant trees and native vegetation. 22 refs., 5 figs., 3 tabs.

  13. Calibration of the time response functions of a quenched plastic scintillator for neutron time of flight

    CERN Document Server

    Chen, J B; Peng, H S; Tang, C H; Zhang, B H; Ding, Y K; Chen, M; Chen, H S; Li, C G; Wen, T S; Yu, R Z

    2002-01-01

    The time response functions of an ultrafast quenched plastic scintillation detector used to measure neutron time of flight spectra were calibrated by utilizing cosmic rays and implosion neutrons from DT-filled capsules at the Shenguang II laser facility. These sources could be regarded as delta function pulses due to their much narrower time widths than those of the time response functions of the detection system. The results showed that the detector responses to DT neutrons and to cosmic rays were 1.18 and 0.96 ns FWHM, respectively.

  14. Identification of two novel functional p53 responsive elements in the herpes simplex virus-1 genome.

    Science.gov (United States)

    Hsieh, Jui-Cheng; Kuta, Ryan; Armour, Courtney R; Boehmer, Paul E

    2014-07-01

    Analysis of the herpes simplex virus-1 (HSV-1) genome reveals two candidate p53 responsive elements (p53RE), located in proximity to the replication origins oriL and oriS, referred to as p53RE-L and p53RE-S, respectively. The sequences of p53RE-L and p53RE-S conform to the p53 consensus site and are present in HSV-1 strains KOS, 17, and F. p53 binds to both elements in vitro and in virus-infected cells. Both p53RE-L and p53RE-S are capable of conferring p53-dependent transcriptional activation onto a heterologous reporter gene. Importantly, expression of the essential immediate early viral transactivator ICP4 and the essential DNA replication protein ICP8, that are adjacent to p53RE-S and p53RE-L, are repressed in a p53-dependent manner. Taken together, this study identifies two novel functional p53RE in the HSV-1 genome and suggests a complex mechanism of viral gene regulation by p53 which may determine progression of the lytic viral replication cycle or the establishment of latency. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. Structural and functional implications in the eubacterial ribosome as revealed by protein-rRNA and antibiotic contact sites.

    Science.gov (United States)

    Wittmann-Liebold, B; Uhlein, M; Urlaub, H; Müller, E C; Otto, A; Bischof, O

    1995-01-01

    Contact sites between protein and rRNA in 30S and 50S ribosomal subunits of Escherichia coli and Bacillus stearothermophilus were investigated at the molecular level using UV and 2-iminothiolane as cross-linkers. Thirteen ribosomal proteins (S3, S4, S7, S14, S17, L2, L4, L6, L14, L27, L28, L29, and L36) from these organisms were cross-linked in direct contact with the RNAs, and the peptide stretches as well as amino acids involved were identified. Further, the binding sites of puromycin and spiramycin were established at the peptide level in several proteins that were found to constitute the antibiotic-binding sites. Peptide stretches of puromycin binding were identified from proteins S7, S14, S18, L18, AND L29; those of spiramycin attachment were derived from proteins S12, S14, L17, L18, L27, and L35. Comparison of the RNA-peptide contact sites with the peptides identified for antibiotic binding and with those altered in antibiotic-resistant mutants clearly showed identical peptide areas to be involved and, hence, demonstrated the functional importance of these peptides. Further evidence for a functional implication of ribosomal proteins in the translational process came from complementation experiments in which protein L2 from Halobacterium marismortui was incorporated into the E. coli ribosomes that were active. The incorporated protein was present in 50S subunits and 70S particles, in disomes, and in higher polysomes. These results clearly demonstrate the functional implication of protein L2 in protein biosynthesis. Incorporation studies with a mutant of HmaL2 with a replacement of histidine-229 by glycine completely abolished the functional activity of the ribosome. Accordingly, protein L2 with histidine-229 is a crucial element of the translational machinery.

  16. Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures.

    Directory of Open Access Journals (Sweden)

    Hong Jin

    Full Text Available The NK homeodomain factor Tinman is a crucial regulator of early mesoderm patterning and, together with the GATA factor Pannier and the Dorsocross T-box factors, serves as one of the key cardiogenic factors during specification and differentiation of heart cells. Although the basic framework of regulatory interactions driving heart development has been worked out, only about a dozen genes involved in heart development have been designated as direct Tinman target genes to date, and detailed information about the functional architectures of their cardiac enhancers is lacking. We have used immunoprecipitation of chromatin (ChIP from embryos at two different stages of early cardiogenesis to obtain a global overview of the sequences bound by Tinman in vivo and their linked genes. Our data from the analysis of ~50 sequences with high Tinman occupancy show that the majority of such sequences act as enhancers in various mesodermal tissues in which Tinman is active. All of the dorsal mesodermal and cardiac enhancers, but not some of the others, require tinman function. The cardiac enhancers feature diverse arrangements of binding motifs for Tinman, Pannier, and Dorsocross. By employing these cardiac and non-cardiac enhancers in machine learning approaches, we identify a novel motif, termed CEE, as a classifier for cardiac enhancers. In vivo assays for the requirement of the binding motifs of Tinman, Pannier, and Dorsocross, as well as the CEE motifs in a set of cardiac enhancers, show that the Tinman sites are essential in all but one of the tested enhancers; although on occasion they can be functionally redundant with Dorsocross sites. The enhancers differ widely with respect to their requirement for Pannier, Dorsocross, and CEE sites, which we ascribe to their different position in the regulatory circuitry, their distinct temporal and spatial activities during cardiogenesis, and functional redundancies among different factor binding sites.

  17. A new approach to evaluate the response functions for conical and cylindrical collimators

    International Nuclear Information System (INIS)

    Gigante, G.E.

    1989-01-01

    A new approach to the evaluation of the conical collimator response function is shown. The basic collimator formulae are reviewed. The collimator response function has been found in a very easy way. An approximate solution has been introduced. Studying the response of a measuring system, the use of this approximation strongly reduces the complexity of the relations to be used; therefore it would provide a useful starting point for a Monte Carlo calculation. The errors introduced are less than 10%. Approximate relations that allow the evaluation of the response of conical and cylindrical collimators to plane and line sources are also given. (orig.)

  18. Clinical, pathological and functional characterization of riboflavin-responsive neuropathy.

    Science.gov (United States)

    Manole, Andreea; Jaunmuktane, Zane; Hargreaves, Iain; Ludtmann, Marthe H R; Salpietro, Vincenzo; Bello, Oscar D; Pope, Simon; Pandraud, Amelie; Horga, Alejandro; Scalco, Renata S; Li, Abi; Ashokkumar, Balasubramaniem; Lourenço, Charles M; Heales, Simon; Horvath, Rita; Chinnery, Patrick F; Toro, Camilo; Singleton, Andrew B; Jacques, Thomas S; Abramov, Andrey Y; Muntoni, Francesco; Hanna, Michael G; Reilly, Mary M; Revesz, Tamas; Kullmann, Dimitri M; Jepson, James E C; Houlden, Henry

    2017-11-01

    Brown-Vialetto-Van Laere syndrome represents a phenotypic spectrum of motor, sensory, and cranial nerve neuropathy, often with ataxia, optic atrophy and respiratory problems leading to ventilator-dependence. Loss-of-function mutations in two riboflavin transporter genes, SLC52A2 and SLC52A3, have recently been linked to Brown-Vialetto-Van Laere syndrome. However, the genetic frequency, neuropathology and downstream consequences of riboflavin transporter mutations are unclear. By screening a large cohort of 132 patients with early-onset severe sensory, motor and cranial nerve neuropathy we confirmed the strong genetic link between riboflavin transporter mutations and Brown-Vialetto-Van Laere syndrome, identifying 22 pathogenic mutations in SLC52A2 and SLC52A3, 14 of which were novel. Brain and spinal cord neuropathological examination of two cases with SLC52A3 mutations showed classical symmetrical brainstem lesions resembling pathology seen in mitochondrial disease, including severe neuronal loss in the lower cranial nerve nuclei, anterior horns and corresponding nerves, atrophy of the spinothalamic and spinocerebellar tracts and posterior column-medial lemniscus pathways. Mitochondrial dysfunction has previously been implicated in an array of neurodegenerative disorders. Since riboflavin metabolites are critical components of the mitochondrial electron transport chain, we hypothesized that reduced riboflavin transport would result in impaired mitochondrial activity, and confirmed this using in vitro and in vivo models. Electron transport chain complex I and complex II activity were decreased in SLC52A2 patient fibroblasts, while global knockdown of the single Drosophila melanogaster riboflavin transporter homologue revealed reduced levels of riboflavin, downstream metabolites, and electron transport chain complex I activity. This in turn led to abnormal mitochondrial membrane potential, respiratory chain activity and morphology. Riboflavin transporter knockdown in

  19. An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins.

    Directory of Open Access Journals (Sweden)

    Angela F Harper

    2017-02-01

    Full Text Available Peroxiredoxins (Prxs or Prdxs are a large protein superfamily of antioxidant enzymes that rapidly detoxify damaging peroxides and/or affect signal transduction and, thus, have roles in proliferation, differentiation, and apoptosis. Prx superfamily members are widespread across phylogeny and multiple methods have been developed to classify them. Here we present an updated atlas of the Prx superfamily identified using a novel method called MISST (Multi-level Iterative Sequence Searching Technique. MISST is an iterative search process developed to be both agglomerative, to add sequences containing similar functional site features, and divisive, to split groups when functional site features suggest distinct functionally-relevant clusters. Superfamily members need not be identified initially-MISST begins with a minimal representative set of known structures and searches GenBank iteratively. Further, the method's novelty lies in the manner in which isofunctional groups are selected; rather than use a single or shifting threshold to identify clusters, the groups are deemed isofunctional when they pass a self-identification criterion, such that the group identifies itself and nothing else in a search of GenBank. The method was preliminarily validated on the Prxs, as the Prxs presented challenges of both agglomeration and division. For example, previous sequence analysis clustered the Prx functional families Prx1 and Prx6 into one group. Subsequent expert analysis clearly identified Prx6 as a distinct functionally relevant group. The MISST process distinguishes these two closely related, though functionally distinct, families. Through MISST search iterations, over 38,000 Prx sequences were identified, which the method divided into six isofunctional clusters, consistent with previous expert analysis. The results represent the most complete computational functional analysis of proteins comprising the Prx superfamily. The feasibility of this novel method is

  20. Mechanical Control of ATP Synthase Function: Activation Energy Difference between Tight and Loose Binding Sites

    KAUST Repository

    Beke-Somfai, Tamás

    2010-01-26

    Despite exhaustive chemical and crystal structure studies, the mechanistic details of how FoF1-ATP synthase can convert mechanical energy to chemical, producing ATP, are still not fully understood. On the basis of quantum mechanical calculations using a recent highresolution X-ray structure, we conclude that formation of the P-O bond may be achieved through a transition state (TS) with a planar PO3 - ion. Surprisingly, there is a more than 40 kJ/mol difference between barrier heights of the loose and tight binding sites of the enzyme. This indicates that even a relatively small change in active site conformation, induced by the γ-subunit rotation, may effectively block the back reaction in βTP and, thus, promote ATP. © 2009 American Chemical Society.

  1. Modeling injury rates as a function of industrialized versus on-site construction techniques.

    Science.gov (United States)

    Rubio-Romero, J C; Suárez-Cebador, M; Abad, Jesús

    2014-05-01

    It is often predicted that the industrialization of building activities will lead to a reduction of accident rates in the construction sector, particularly as a result of switching activities from building sites to factories. However, to date no scientific research has provided objective quantitative results to back up this claim. The aim of this paper is to evaluate how industrialization affects the accident rate in different industrialized building systems in Spain. Our results revealed that the industrialized steel modular system presents the lowest accident rate, while the highest accident rate was recorded in the construction method with cast-in-place concrete. The lightweight construction system also presents a high accident rate. Accordingly, industrialized building systems cannot claim to be safer than traditional ones. The different types of "on-site work" seem to be the main variable which would explain the accident rates recorded in industrialized construction systems. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Modeling injury rates as a function of industrialized versus on-site construction techniques

    OpenAIRE

    Rubio Romero, Juan Carlos; Suárez Cebador, Manuel; Abad Puente, Jesús

    2014-01-01

    It is often predicted that the industrialization of building activities will lead to a reduction of accident rates in the construction sector, particularly as a result of switching activities from building sites to factories. However, to date no scientific research has provided objective quantitative results to back up this claim. The aim of this paper is to evaluate how industrialization affects the accident rate in different industrialized building systems in Spain. Our results revealed tha...

  3. Decreases in soil microbial function and functional diversity in response to depleted uranium

    International Nuclear Information System (INIS)

    Meyer, M.C.; Paschke, M.W.; McLendon, T.

    1998-01-01

    A soil microcosm experiment was used to analyze effects of depleted uranium (DU) on soil function, and the concomitant changes in bacterial functional diversity. Uranium treatment levels were 0, 50, 500, 5000, 10,000 and 25,000 mg DU kg -1 soil. Three measures of soil function were made. Overall soil biological activity was assessed via measurement of soil respiration. Decomposition was assessed by measurement of mass loss of four different plant litter types: wood sticks, cellulose paper, high-N grass, and low-N grass. Mineral N availability in the microcosms was estimated using ion-exchange resin bags. Functional diversity of the microcosms was analyzed through the use of the Biolog-system of sole-C-utilization patterns. Soil respiration was the most sensitive measure of functional changes, with significant decreases observed starting at the 500 mg kg -1 treatment. No differences in N availability were observed across the U treatments. Litter decomposition was significantly decreased at the 25,000 mg kg -1 level relative to the control for all litter types except the high-N grass. Wood decomposition was reduced by 84% at the 25,000 mg kg - treatment, cellulose paper by 68%, and low-N grass by 15%. Decreases in the functional diversity of the bacterial community were related to the observed decrease in soil respiration, and to the greater effect on decomposition of the lower-quality litter types

  4. Does the site of platelet sequestration predict the response to splenectomy in adult patients with immune thrombocytopenic purpura?

    Science.gov (United States)

    Navez, Julie; Hubert, Catherine; Gigot, Jean-François; Navez, Benoit; Lambert, Catherine; Jamar, François; Danse, Etienne; Lannoy, Valérie; Jabbour, Nicolas

    2015-01-01

    Splenectomy is the only potentially curative treatment for chronic immune thrombocytopenic purpura (ITP) in adults. However, one-third of the patients relapse without predictive factors identified. We evaluate the predictive value of the site of platelet sequestration on the response to splenectomy in patients with ITP. Eighty-two consecutive patients with ITP treated by splenectomy between 1992 and 2013 were retrospectively reviewed. Platelet sequestration site was studied by (111)Indium-oxinate-labeled platelets in 93% of patients. Response to splenectomy was defined at last follow-up as: complete response (CR) for platelet count (PC) ≥100 × 10(9)/L, response (R) for PC≥30 × 10(9)/L and splenectomy was performed in 81 patients (conversion rate of 16%), and open approach in one patient. Median follow-up was 57 months (range, 1-235). Platelet sequestration study was performed in 93% of patients: 50 patients (61%) exhibited splenic sequestration, 9 (11%) hepatic sequestration and 14 patients (17%) mixed sequestration. CR was obtained in 72% of patients, R in 25% and NR in 4% (two with splenic sequestration, one with hepatic sequestration). Preoperative PC, age at diagnosis, hepatic sequestration and male gender were significant for predicting CR in univariate analysis, but only age (HR = 1.025 by one-year increase, 95% CI [1.004-1.047], p = 0.020) and pre-operative PC (HR = 0.112 for > 100 versus splenectomy was independent of the site of platelet sequestration in patients with ITP. Pre-operative platelet sequestration study in these patients cannot be recommended.

  5. Nuclear power plants in Germany. Recent developments in off-site nuclear emergency preparedness and response; Kernkraftwerke in Deutschland. Neue Entwicklungen im anlagenexternen Notfallschutz

    Energy Technology Data Exchange (ETDEWEB)

    Gering, Florian [Bundesamt fuer Strahlenschutz, Oberschleissheim/Neuherberg (Germany). Abt. SW 2.2 Entscheidungshilfesysteme, Lageermittlung und Kommunikation

    2014-10-15

    The reactor accident in Fukushima, Japan, in 2011 triggered a thorough review of the off-site emergency preparedness and response for nuclear power plants in Germany. ''Off-site emergency preparedness and response'' includes all actions to protect the public outside the fence of a nuclear power plant. This review resulted in several changes in off-site emergency preparedness and response, which are briefly described in this article. Additionally, several recent activities are described which may influence emergency preparedness and response in the future.

  6. Ceruloplasmin revisited: structural and functional roles of various metal cation-binding sites

    International Nuclear Information System (INIS)

    Bento, Isabel; Peixoto, Cristina; Zaitsev, Vjacheslav N.; Lindley, Peter F.

    2007-01-01

    The three-dimensional molecular structure of human serum ceruloplasmin has been reinvestigated using X-ray synchrotron data collected at 100 K from a crystal frozen to liquid-nitrogen temperature. The three-dimensional molecular structure of human serum ceruloplasmin has been reinvestigated using X-ray synchrotron data collected at 100 K from a crystal frozen to liquid-nitrogen temperature. The resulting model, with an increase in resolution from 3.1 to 2.8 Å, gives an overall improvement of the molecular structure, in particular the side chains. In addition, it enables the clear definition of previously unidentified Ca 2+ -binding and Na + -binding sites. The Ca 2+ cation is located in domain 1 in a configuration very similar to that found in the activated bovine factor Va. The Na + sites appear to play a structural role in providing rigidity to the three protuberances on the top surface of the molecule. These features probably help to steer substrates towards the mononuclear copper sites prior to their oxidation and to restrict the size of the approaching substrate. The trinuclear copper centre appears to differ from the room-temperature structure in that a dioxygen moiety is bound in a similar way to that found in the endospore coat protein CotA from Bacillus subtilis

  7. The determination of frequency response function of the RSG Gas by laplace transform analysis

    International Nuclear Information System (INIS)

    Tukiran, S.; Surian, P.; Jujuratisbela, U.

    1997-01-01

    The response function of the RSG-GAS reactor system to the reactivity perturbations is necessary to be analyzed due to the interrelation with reliability and safety of reactor operation. the response depends on the power frequency response function H(s), while H(s) depends on the zero power frequency response function Z(s) and dynamic power coefficient of reactivity Kp(s) determination of the frequency response function of the RSG-GAS reactor was done by Fourier transform analysis method. Z(s) was obtained by fourier transform of P(t) and Cj(t) became P(S) and Cj(s) in point kinetic equations. Second order of simpson rule was used for completion of its numerical integration. then. LYMPR (Laplace transform for multipurpose reactor) code was made with fortran 77 computer language in vax 8550 system. the LTMPR code is able to determine the frequency response function and period-reactivity relation of RSG-GAS reactor by rod drop method. Profile of power as rod drop, zero power (without reactivity feedback) was used for determination frequency response of RSG-GAS reactor. The results of calculations are in a good agreement with experiment result, so the LTMPR code can be used for analysis response frequency of the RSG-GAS reactor

  8. Cyclic and dynamic response of a bridge pier model located at the Volvi European test site in Greece

    International Nuclear Information System (INIS)

    Manos, G.C.; Kourtides, V.; Soulis, V.J.

    2005-01-01

    This paper presents results of the measured and predicted response of a bridge pier model-structures which has been erected at the Volvi-Greece European Test Site for Earthquake Engineering. The disadvantage at the Test Site is that one is unable to produce significant in-situ levels of ground motion, when desired, as can be generated by an earthquake simulator. However, one is having the advantage at the Test Site of realistic foundations conditions, which are present for model structures that are built there and are supported on the soft soil deposits in-situ. The current extension of the in-situ facility includes the possibility of subjecting large-scale model structures to low to medium intensity man-made dynamic excitations. At this point in time the model structures that are built at the test site include: a) A 6-story Reinforced Concrete building model with masonry in fills; b) A single bridge pier model, built for the purposes of the currently running Euro-Risk program, which is supported by the European Union. The variation of the dynamic characteristics of the 6-story 1/3 3-D frame model structure was measured over a period of ten years. So far, only one earthquake of moderate intensity has subjected the 6-story model structure to seismic loads and excited the permanent instrumentation system. The main objective of the recent tests, which are partially presented in this paper and involve the bridge pier model, is to include influences on the dynamic structural response arising from the flexible foundation support conditions. The bridge pier model was initially studied at the laboratory under cyclic horizontal loads that were applied simultaneously with vertical forces. Thus, the cyclic post-elastic behavior of this bridge pier model was recorded at the laboratory. Next, a series of low intensity excitations were performed at the test site over a period of two years. During this period, the pier model structure was in various configurations that included

  9. Planning, Coordinating, and Managing Off-Site Storage is an Area of Increasing, Professional Responsibility for Special Collections Departments

    Directory of Open Access Journals (Sweden)

    Melissa Goertzen

    2016-03-01

    Full Text Available Objective – To measure the use of off-site storage for special collections materials and to examine how this use impacts core special collections activities. Design – Survey questionnaire containing both structured and open ended questions. Follow-up interviews were also conducted. Setting – Association of Research Libraries (ARL member institutions in the United States of America. Subjects – 108 directors of special collections. Methods – Participants were recruited via email; contact information was compiled through professional directories, web searches, and referrals from professionals at ARL member libraries. The survey was sent out on October 31, 2013, and two reminder emails were distributed before it closed three weeks later. The survey was created and distributed using Qualtrics, a research software that supports online data collection and analysis. All results were analyzed using Microsoft Excel and Qualtrics. Main Results – The final response rate was 58% (63 out of 108. The majority (51 participants, or 81% reported use of off-site storage for library collections. Of this group, 91% (47 out of 51 house a variety of special collections in off-site storage. The criteria most frequently utilized to designate these materials to off-site storage are use (87%, size (66%, format (60%, and value (57%. The authors found that special collections directors are most likely to send materials to off-site storage facilities that are established and in use by other departments at their home institution; access to established workflows, especially those linked to transit and delivery, and space for expanding collections are benefits. In regard to core special collections activities, results indicated that public service was most impacted by off-site storage. The authors discussed challenges related to patron use and satisfaction. In regard to management and processing, directors faced challenges using the same level of staff to maintain

  10. Redox Modulation Matters: Emerging Functions for Glutaredoxins in Plant Development and Stress Responses

    Directory of Open Access Journals (Sweden)

    Shutian Li

    2014-11-01

    Full Text Available Glutaredoxins (GRXs are small ubiquitous glutathione (GSH-dependent oxidoreductases that catalyze the reversible reduction of protein disulfide bridges or protein-GSH mixed disulfide bonds via a dithiol or monothiol mechanism, respectively. Three major classes of GRXs, with the CPYC-type, the CGFS-type or the CC-type active site, have been identified in many plant species. In spite of the well-characterized roles for GRXs in Escherichia coli, yeast and humans, the biological functions of plant GRXs have been largely enigmatic. The CPYC-type and CGFS-type GRXs exist in all organisms, from prokaryotes to eukaryotes, whereas the CC-type class has thus far been solely identified in land plants. Only the number of the CC-type GRXs has enlarged dramatically during the evolution of land plants, suggesting their participation in the formation of more complex plants adapted to life on land. A growing body of evidence indicates that plant GRXs are involved in numerous cellular pathways. In this review, emphasis is placed on the recently emerging functions for GRXs in floral organ development and disease resistance. Notably, CC-type GRXs have been recruited to participate in these two seemingly unrelated processes. Besides, the current knowledge of plant GRXs in the assembly and delivery of iron-sulfur clusters, oxidative stress responses and arsenic resistance is also presented. As GRXs require GSH as an electron donor to reduce their target proteins, GSH-related developmental processes, including the control of flowering time and the development of postembryonic roots and shoots, are further discussed. Profiling the thiol redox proteome using high-throughput proteomic approaches and measuring cellular redox changes with fluorescent redox biosensors will help to further unravel the redox-regulated physiological processes in plants.

  11. Assessing item fit for unidimensional item response theory models using residuals from estimated item response functions.

    Science.gov (United States)

    Haberman, Shelby J; Sinharay, Sandip; Chon, Kyong Hee

    2013-07-01

    Residual analysis (e.g. Hambleton & Swaminathan, Item response theory: principles and applications, Kluwer Academic, Boston, 1985; Hambleton, Swaminathan, & Rogers, Fundamentals of item response theory, Sage, Newbury Park, 1991) is a popular method to assess fit of item response theory (IRT) models. We suggest a form of residual analysis that may be applied to assess item fit for unidimensional IRT models. The residual analysis consists of a comparison of the maximum-likelihood estimate of the item characteristic curve with an alternative ratio estimate of the item characteristic curve. The large sample distribution of the residual is proved to be standardized normal when the IRT model fits the data. We compare the performance of our suggested residual to the standardized residual of Hambleton et al. (Fundamentals of item response theory, Sage, Newbury Park, 1991) in a detailed simulation study. We then calculate our suggested residuals using data from an operational test. The residuals appear to be useful in assessing the item fit for unidimensional IRT models.

  12. The bacterial response regulator ArcA uses a diverse binding site architecture to regulate carbon oxidation globally.

    Directory of Open Access Journals (Sweden)

    Dan M Park

    Full Text Available Despite the importance of maintaining redox homeostasis for cellular viability, how cells control redox balance globally is poorly understood. Here we provide new mechanistic insight into how the balance between reduced and oxidized electron carriers is regulated at the level of gene expression by mapping the regulon of the response regulator ArcA from Escherichia coli, which responds to the quinone/quinol redox couple via its membrane-bound sensor kinase, ArcB. Our genome-wide analysis reveals that ArcA reprograms metabolism under anaerobic conditions such that carbon oxidation pathways that recycle redox carriers via respiration are transcriptionally repressed by ArcA. We propose that this strategy favors use of catabolic pathways that recycle redox carriers via fermentation akin to lactate production in mammalian cells. Unexpectedly, bioinformatic analysis of the sequences bound by ArcA in ChIP-seq revealed that most ArcA binding sites contain additional direct repeat elements beyond the two required for binding an ArcA dimer. DNase I footprinting assays suggest that non-canonical arrangements of cis-regulatory modules dictate both the length and concentration-sensitive occupancy of DNA sites. We propose that this plasticity in ArcA binding site architecture provides both an efficient means of encoding binding sites for ArcA, σ(70-RNAP and perhaps other transcription factors within the same narrow sequence space and an effective mechanism for global control of carbon metabolism to maintain redox homeostasis.

  13. A review of fire effects on vegetation and soils in the Great Basin region: response and ecological site characteristics

    Science.gov (United States)

    Miller, Richard F.; Chambers, Jeanne C.; Pyke, David A.; Pierson, Fred B.; Williams, C. Jason

    2013-01-01

    This review synthesizes the state of knowledge on fire effects on vegetation and soils in semi-arid ecosystems in the Great Basin Region, including the central and northern Great Basin and Range, Columbia River Basin, and the Snake River Plain. We summarize available literature related to: (1) the effects of environmental gradients, ecological site, and vegetation characteristics on resilience to disturbance and resistance to invasive species; (2) the effects of fire on individual plant species and communities, biological soil crusts, seed banks, soil nutrients, and hydrology; and (3) the role of fire severity, fire versus fire surrogate treatments, and post-fire grazing in determining ecosystem response. From this, we identify knowledge gaps and present a framework for predicting plant successional trajectories following wild and prescribed fires and fire surrogate treatments. Possibly the three most important ecological site characteristics that influence a site’s resilience (ability of the ecological site to recover from disturbance) and resistance to invasive species are soil temperature/moisture regimes and the composition and structure of vegetation on the ecological site just prior to the disturbance event.

  14. Herbicide and fertilizers promote analogous phylogenetic responses but opposite functional responses in plant communities

    DEFF Research Database (Denmark)

    Pellissier, Loïc; Wisz, Mary S.; Strandberg, Beate

    2014-01-01

    on long-term experiment we show that fertilizer and herbicides (glyphosate) have contrasting effects on functional structure, but can increase phylogenetic diversity in semi-natural plant communities. We found that an increase in nitrogen promoted an increase in the average specific leaf area and canopy...... height at the community level, but an increase in glyphosate promoted a decrease in those traits. Phylogenetic diversity of plant communities increased when herbicide and fertilizer were applied together, likely because functional traits facilitating plant success in those conditions were......Throughout the world, herbicides and fertilizers change species composition in agricultural communities, but how do the cumulative effects of these chemicals impact the functional and phylogenetic structure of non-targeted communities when they drift into adjacent semi-natural habitats? Based...

  15. Phenological responses of juvenile pecan and white oak on an upland site

    Science.gov (United States)

    Pecan (Carya illinoiensis) and white oak (Quercus alba) produce multiple products and wildlife values, but their phenological responses to N fertilization have not been well characterized in an mixed species agroforestry practice. We compared tree height at planting and for six consecutive growing ...

  16. Improvement of worker safety through the investigation of the site response to rockbursts

    CSIR Research Space (South Africa)

    Hagan, TO

    1998-12-01

    Full Text Available of GAP 201 and consists of two main enabling areas namely: a comprehensive investigation of rockbursts that have caused damage and posed a hazard to workers; measurement and analysis of the dynamic response of the rock surrounding excavations following...

  17. Phenological responses of juvenile pecan and white oak on an upland site

    Science.gov (United States)

    D. M. Burner; D. K. Brauer; J. L. Snider; C. A. Harrington; P. A. Moore

    2014-01-01

    Pecan (Carya illinoiensis) and white oak (Quercus alba) produce multiple products and wildlife values, but their phenological responses to N fertilization have not been well characterized. We compared tree growth at planting and for six consecutive growing seasons during establishment (2003–2008, Test 1), and determined if...

  18. Assessment of exposure-response functions for rocket-emission toxicants

    National Research Council Canada - National Science Library

    Subcommittee on Rocket-Emission Toxicants, National Research Council

    ... aborted launch that results in a rocket being destroyed near the ground. Assessment of Exposure-Response Functions for Rocket-Emmission Toxicants evaluates the model and the data used for three rocket emission toxicants...

  19. Measurement and simulation of neutron response function of organic liquid scintillator detector

    International Nuclear Information System (INIS)

    Gohil, M.; Banerjee, K.; Bhattacharya, S.; Bhattacharya, C.; Kundu, S.; Rana, T.K.; Mukherjee, G.; Meena, J.K.; Pandey, R.; Pai, H.; Ghosh, T.K.; Dey, A.; Mukhopadhyay, S.; Pandit, D.; Pal, S.; Banerjee, S.R.; Bandhopadhyay, T.

    2012-01-01

    Response functions of monoenergetic neutrons at various energies, corresponding to a measured neutron energy spectrum have been extracted. The experimental response functions for neutron energies in the range of ∼2-20 MeV have been compared with the respective GEANT4 predictions. It has been found that, there is some discrepancy between the experimental and the GEANT4 simulated neutron response functions at lower pulse height regions, which increases with the increase of neutron energy. This might be due to the incompleteness of the physics processes used in the present GEANT4 simulations. In particular, higher order reaction processes which become more significant at higher energies should be properly taken into account in the calculation of response function.

  20. Estimated Quality of Multistage Process on the Basis of Probabilistic Approach with Continuous Response Functions

    Directory of Open Access Journals (Sweden)

    Yuri B. Tebekin

    2011-11-01

    Full Text Available The article is devoted to the problem of the quality management for multiphase processes on the basis of the probabilistic approach. Method with continuous response functions is offered from the application of the method of Lagrange multipliers.

  1. Summary of canister overheating incident at the Carbon Tetrachloride Expedited Response Action site

    Energy Technology Data Exchange (ETDEWEB)

    Driggers, S.A.

    1994-03-10

    The granular activated carbon (GAC)-filled canister that overheated was being used to adsorb carbon tetrachloride vapors drawn from a well near the 216-Z-9 Trench, a subsurface disposal site in the 200 West Area of the Hanford Site. The overheating incident resulted in a band of discolored paint on the exterior surface of the canister. Although there was no other known damage to equipment, no injuries to operating personnel, and no releases of hazardous materials, the incident is of concern because it was not anticipated. It also poses the possibility of release of carbon tetrachloride and other hazardous vapors if the incident were to recur. All soil vapor extraction system (VES) operations were halted until a better understanding of the cause of the incident could be determined and controls implemented to reduce the possibility of a recurrence. The focus of this report and the intent of all the activities associated with understanding the overheating incident has been to provide information that will allow safe restart of the VES operations, develop operational limits and controls to prevent recurrence of an overheating incident, and safely optimize recovery of carbon tetrachloride from the ground.

  2. Response of deep-sea benthic foraminifera to Miocene paleoclimatic events, DSDP site 289

    International Nuclear Information System (INIS)

    Woodruff, F.; Douglas, R.G.

    1981-01-01

    Changes in the Miocene deep-sea benthic foraminifera at DSDP Site 289 closely correlate to the climatically induced variations in deep and bottom waters in the Pacific Ocean. In early Miocene time, oxygen and carbon isotopes indicate that bottom waters were relatively warm and poorly oxygenated. Benthic foraminiferal assemblages are characterized by various species inherited from the Oligocene. Expansion of the Antarctic icecap in the early middle Miocene, 14-16 m.y. ago, increased oxygen isotope values, produced cold, more oxygenated bottom waters and lead to a turnover in the benthic foraminifera. An Oligocene-early Miocene assemblage was replaced by a cibicidoid-dominated assemblage. Some species became extinct and benthic faunas became more bathymetrically restricted with the increased stratification of deep waters in the ocean. In mid-Miocene time, Epistominella exigua and E. umbonifera, indicative of young, oxygenated bottom waters, are relatively common at DSDP Site 289. Further glacial expansion 5-9 m.y. ago lowered sealevel, increased oceanic upwelling and associated biological productivity and intensified the oxygen minima. Abundant hispid and costate uvigerines become a dominant faunal element at shallow depths above 2500 m as E. umbonifera becomes common to abundant below 2500 m. By late Miocene time, benthic faunas similar in species composition and proportion to modern faunas on the Ontong-Java plateau, had become established. (Auth.)

  3. Non-host disease resistance response in pea (Pisum sativum) pods: Biochemical function of DRR206 and phytoalexin pathway localization.

    Science.gov (United States)

    Seneviratne, Herana Kamal; Dalisay, Doralyn S; Kim, Kye-Won; Moinuddin, Syed G A; Yang, Hong; Hartshorn, Christopher M; Davin, Laurence B; Lewis, Norman G

    2015-05-01

    Continually exposed to potential pathogens, vascular plants have evolved intricate defense mechanisms to recognize encroaching threats and defend themselves. They do so by inducing a set of defense responses that can help defeat and/or limit effects of invading pathogens, of which the non-host disease resistance response is the most common. In this regard, pea (Pisum sativum) pod tissue, when exposed to Fusarium solani f. sp. phaseoli spores, undergoes an inducible transcriptional activation of pathogenesis-related genes, and also produces (+)-pisatin, its major phytoalexin. One of the inducible pathogenesis-related genes is Disease Resistance Response-206 (DRR206), whose role in vivo was unknown. DRR206 is, however, related to the dirigent protein (DP) family. In this study, its biochemical function was investigated in planta, with the metabolite associated with its gene induction being pinoresinol monoglucoside. Interestingly, both pinoresinol monoglucoside and (+)-pisatin were co-localized in pea pod endocarp epidermal cells, as demonstrated using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging. In addition, endocarp epidermal cells are also the site for both chalcone synthase and DRR206 gene expression. Taken together, these data indicate that both (+)-pisatin and pinoresinol monoglucoside function in the overall phytoalexin responses. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. A paradox of transcriptional and functional innate interferon responses of human intestinal enteroids to enteric virus infection

    Science.gov (United States)

    Saxena, Kapil; Simon, Lukas M.; Zeng, Xi-Lei; Blutt, Sarah E.; Crawford, Sue E.; Sastri, Narayan P.; Karandikar, Umesh C.; Ajami, Nadim J.; Zachos, Nicholas C.; Kovbasnjuk, Olga; Donowitz, Mark; Conner, Margaret E.; Shaw, Chad A.; Estes, Mary K.

    2017-01-01

    The intestinal epithelium can limit enteric pathogens by producing antiviral cytokines, such as IFNs. Type I IFN (IFN-α/β) and type III IFN (IFN-λ) function at the epithelial level, and their respective efficacies depend on the specific pathogen and site of infection. However, the roles of type I and type III IFN in restricting human enteric viruses are poorly characterized as a result of the difficulties in cultivating these viruses in vitro and directly obtaining control and infected small intestinal human tissue. We infected nontransformed human intestinal enteroid cultures from multiple individuals with human rotavirus (HRV) and assessed the host epithelial response by using RNA-sequencing and functional assays. The dominant transcriptional pathway induced by HRV infection is a type III IFN-regulated response. Early after HRV infection, low levels of type III IFN protein activate IFN-stimulated genes. However, this endogenous response does not restrict HRV replication because replication-competent HRV antagonizes the type III IFN response at pre- and posttranscriptional levels. In contrast, exogenous IFN treatment restricts HRV replication, with type I IFN being more potent than type III IFN, suggesting that extraepithelial sources of type I IFN may be the critical IFN for limiting enteric virus replication in the human intestine. PMID:28069942

  5. Functional response of a near-surface soil microbial community to a simulated underground CO2 storage leak.

    Science.gov (United States)

    Morales, Sergio E; Holben, William E

    2013-01-01

    Understanding the impacts of leaks from geologic carbon sequestration, also known as carbon capture and storage, is key to developing effective strategies for carbon dioxide (CO2) emissions management and mitigation of potential negative effects. Here, we provide the first report on the potential effects of leaks from carbon capture and storage sites on microbial functional groups in surface and near-surface soils. Using a simulated subsurface CO2 storage leak scenario, we demonstrate how CO2 flow upward through the soil column altered both the abundance (DNA) and activity (mRNA) of microbial functional groups mediating carbon and nitrogen transformations. These microbial responses were found to be seasonally dependent and correlated to shifts in atmospheric conditions. While both DNA and mRNA levels were affected by elevated CO2, they did not react equally, suggesting two separate mechanisms for soil microbial community response to high CO2 levels. The results did not always agree with previous studies on elevated atmospheric (rather than subsurface) CO2 using FACE (Free-Air CO2 Enrichment) systems, suggesting that microbial community response to CO2 seepage from the subsurface might differ from its response to atmospheric CO2 increases.

  6. Summary Report of the Consultants' Meeting on EXFOR Data in Resonance Region and Spectrometer Response Function

    International Nuclear Information System (INIS)

    Gunsing, F.; Schillebeeckx, P.; Semkova, V.

    2013-12-01

    The Consultants' Meeting 'EXFOR Data in Resonance Region and Spectrometer Response Function' was held at the IAEA Headquarters in Vienna from 8 to 10 October 2013. A summary of the presentations and discussions that took place during the meeting is reported here. The participants have agreed on recommendations on data reporting for EXFOR and on the need of documenting spectrometer response functions. Recommendations are given for experimentalists, for compilers, and for evaluators. (author)

  7. Development and evaluation of fixed phrase registration function for disaster response management system

    International Nuclear Information System (INIS)

    Suzuki, Takeyasu; Tsuda, Teppei

    2012-01-01

    It is important that three elements such as what happened, how it will advance, and how people should act are intelligibly transferred in disaster information from administrative organs to local residents. In this paper, authors developed the fixed phrase registration function and it was implemented in disaster response management system authors have previously developed. The system was applied to disaster response exercise in Mitsuke City, Niigata prefecture and the function was highly evaluated by employees of Mitsuke City. (author)

  8. Corn stover fractions as a function of hybrid, maturity, site and year

    Energy Technology Data Exchange (ETDEWEB)

    Lizotte, P.L. [Laval Univ., Quebec City, PQ (Canada). Dept. des sols et de genie agroalimentaire; Savoie, P. [Agriculture and Agri-Food Canada, Quebec City, PQ (Canada); Lefsrud, M. [McGill Univ., Macdonald College, Ste-Anne-de-Bellevue, PQ (Canada). Dept. of Biosystems Engineering

    2010-07-01

    Corn stover is usually left on the ground following corn harvest so that it can be incorporated into the soil as organic matter and to protect against erosion. Part of the corn stover is oxidized in the atmosphere. Corn stover represents between 40 and 50 per cent of the dry matter (DM) contained in the aerial biomass of corn plants. Recent studies have shown that half of the corn stover could be harvested sustainably on low-sloping land under no-till practice. In Quebec, where 400,000 ha of corn are planted each year, corn stover could provide one million t DM of currently neglected biomass. Various hybrids of corn were monitored from early September to late November at 4 different sites during 2007, 2008 and 2009. Whole plants cut at 100 mm above the ground were collected weekly and separated into 7 fractions, notably the grain, the cob, the husk, the stalk below the ear, the stalk above the ear, the leaves below the ear and the leaves above the ear. In 2007, corn ears on average, were at 0.96 m above the ground at a site with low crop heat units (CHU). Hybrids grown in a warmer site were taller and their ears were 1.21 m above the ground. The DM partitioned in 7 components was 54 per cent grain, 14 per cent bottom stalk, 6 per cent top stalk, 5 per cent bottom leaves, 7 per cent top leaves, 5 per cent husk and 9 per cent cob. The total mass of fibre during harvest decreased from 8.9 to 6.6 t DM/ha for a low CHU hybrid and from 9.3 to 8.3 t DM/ha for a high CHU hybrid. Grain yield increased in 2008 from 3.8 to 7.6 t DM/ha over a 12-week period.

  9. Thunder Bay Terminals Ltd. Site selection to operation: the management function

    Energy Technology Data Exchange (ETDEWEB)

    Cook, P.R.

    1979-08-01

    Thunder Bay Terminals Ltd. is a link in a new transportation system for Canada's natural resources stretching over 3000 miles from British Columbia's mountains to Ontario's lower Great Lakes. Thunder Bay Terminals' plant, now in operation, cost about $70 million and was completed on time and under budget. The paper is the project manager's account of this accomplishment. From site selection through feasibility, engineering and construction to realization, he emphasizes the necessary philosophies for the control of time and money. The computer as a tool is discussed, as well as techniques for procurement.

  10. Contrasting physiological responses of two co-occurring eucalypts to seasonal drought at restored bauxite mine sites.

    Science.gov (United States)

    Szota, Christopher; Farrell, Claire; Koch, John M; Lambers, Hans; Veneklaas, Erik J

    2011-10-01

    This study describes the physiological response of two co-occurring tree species (Eucalyptus marginata and Corymbia calophylla) to seasonal drought at low- and high-quality restored bauxite mine sites in south-western Australia. Seasonal changes in photosynthesis (A), stomatal conductance (g(s)), leaf water potential (ψ), leaf osmotic potential (ψ), leaf relative water content (RWC) and pressure-volume analysis were captured over an 18-month field study to (i) determine the nature and severity of physiological stress in relation to site quality and (ii) identify any physiological differences between the two species. Root system restriction at the low-quality site reduced maximum rates of gas exchange (g(s) and A) and increased water stress (midday ψ and daily RWC) in both species during drought. Both species showed high stomatal sensitivity during drought; however, E. marginata demonstrated a higher dehydration tolerance where ψ and RWC fell to -3.2 MPa and 73% compared with -2.4 MPa and 80% for C. calophylla. Corymbia calophylla showed lower g(s) and higher ψ and RWC during drought, indicating higher drought tolerance. Pressure-volume curves showed that cell-wall elasticity of E. marginata leaves increased in response to drought, while C. calophylla leaves showed lower osmotic potential at zero turgor in summer than in winter, indicating osmotic adjustment. Both species are clearly able to tolerate seasonal drought at hostile sites; however, by C. calophylla closing stomata earlier in the drought cycle, maintaining a higher water status during drought and having the additional mechanism of osmotic adjustment, it may have a greater capacity to survive extended periods of drought.

  11. Geomagnetic-cutoff distribution functions for use in estimating detector response to neutrinos of atmospheric origin

    International Nuclear Information System (INIS)

    Cooke, D.J.

    1983-01-01

    A procedure has been developed for deriving functions which characterize the effect of geomagnetic cutoffs on the charged primary cosmic rays that give rise to neutrinos arriving in any given direction at specified points on or in the earth. These cutoff distribution functions, for use in atmospheric-neutrino flux calculations, have been determined for eight nucleon-decay--experiment sites, by use of a technique which employs the Stormer cutoff expression, and which assumes collinear motion of neutrino and parent primary

  12. Dose-response relationship between cigarette smoking and site-specific cancer risk: protocol for a systematic review with an original design combining umbrella and traditional reviews.

    Science.gov (United States)

    Lugo, Alessandra; Bosetti, Cristina; Peveri, Giulia; Rota, Matteo; Bagnardi, Vincenzo; Gallus, Silvano

    2017-11-01

    Only a limited number of meta-analyses providing risk curve functions of dose-response relationships between various smoking-related variables and cancer-specific risk are available. To identify all relevant original publications on the issue, we will conduct a series of comprehensive systematic reviews based on three subsequent literature searches: (1) an umbrella review, to identify meta-analyses, pooled analyses and systematic reviews published before 28 April 2017 on the association between cigarette smoking and the risk of 28 (namely all) malignant neoplasms; (2) for each cancer site, an updated review of original publications on the association between cigarette smoking and cancer risk, starting from the last available comprehensive review identified through the umbrella review; and (3) a review of all original articles on the association between cigarette smoking and site-specific cancer risk included in the publications identified through the umbrella review and the updated reviews. The primary outcomes of interest will be (1) the excess incidence/mortality of various cancers for smokers compared with never smokers; and (2) the dose-response curves describing the association between smoking intensity, duration and time since stopping and incidence/mortality for various cancers. For each cancer site, we will perform a meta-analysis by pooling study-specific estimates for smoking status. We will also estimate the dose-response curves for other smoking-related variables through random-effects meta-regression models based on a non-linear dose-response relationship framework. Ethics approval is not required for this study. Main results will be published in peer-reviewed journals and will also be included in a publicly available website. We will provide therefore the most complete and updated estimates on the association between various measures of cigarette smoking and site-specific cancer risk. This will allow us to obtain precise estimates on the cancer burden

  13. Review of off-site emergency preparedness and response plan of Indian NPPs based on experience of Fukushima nuclear accident

    International Nuclear Information System (INIS)

    Singh, Hukum; Dash, M.; Shukla, Vikas; Vijayan, P.; Krishnamurthy, P.R.

    2012-01-01

    Nuclear power plants in India are designed, constructed and operated based on the principle of the highest priority to nuclear safety. To deal with any unlikely situation of radiological emergency, the emergency preparedness and response plans are ensured to be in place at all NPPs prior to their commissioning. These plans are periodically reviewed and tested by conducting emergency exercise with the participation of various agencies such as Nuclear Power Corporation of India Limited, NDMA, district authorities, regulatory body and general public. On March 11, 2011 an earthquake of magnitude 9.0 hit the Fukushima Dai-ichi and Dai-ni followed by tsunami waves of height 15 meters above reference sea level. This resulted in large scale release of radioactive material from Fukushima Dai-ichi NPS. This led to the evacuation of a large number of people from the areas surrounding the affected nuclear power plants. The event was rated as level 7 event in International Nuclear Event Scale (INES). The event also revealed the challenges in handling radiological emergency situation in adverse environmental conditions, The experience of managing radiological emergency situation during Fukushima nuclear accident provides opportunities to review and improve emergency preparedness and response programme. The present paper presents the chronology of the emergency situation, challenges faced and handled in Fukushima. Even though the possibility of a Fukushima type nuclear accident in India is very remote due to the low probability of a high intensity earthquake followed by tsunami at NPP sites, the efforts needs to be initiated from the regulatory point of view for an effective Nuclear and Radiological Emergency Preparedness and Response Plans. The Emergency Preparedness and Response Plans of NPP sites were reviewed in the light of unique challenges of accident at Fukushima. It is realized that multi unit events are the realities that must be addressed as part of Emergency

  14. Review of off-site emergency preparedness and response plan of Indian NPPs based on experience of Fukushima nuclear accident

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Hukum; Dash, M.; Shukla, Vikas; Vijayan, P.; Krishnamurthy, P.R., E-mail: vshukla@aerb.gov.in [Operating Plants Safety Division, Atomic Energy Regulatory Board, Mumbai (India)

    2012-07-01

    Nuclear power plants in India are designed, constructed and operated based on the principle of the highest priority to nuclear safety. To deal with any unlikely situation of radiological emergency, the emergency preparedness and response plans are ensured to be in place at all NPPs prior to their commissioning. These plans are periodically reviewed and tested by conducting emergency exercise with the participation of various agencies such as Nuclear Power Corporation of India Limited, NDMA, district authorities, regulatory body and general public. On March 11, 2011 an earthquake of magnitude 9.0 hit the Fukushima Dai-ichi and Dai-ni followed by tsunami waves of height 15 meters above reference sea level. This resulted in large scale release of radioactive material from Fukushima Dai-ichi NPS. This led to the evacuation of a large number of people from the areas surrounding the affected nuclear power plants. The event was rated as level 7 event in International Nuclear Event Scale (INES). The event also revealed the challenges in handling radiological emergency situation in adverse environmental conditions, The experience of managing radiological emergency situation during Fukushima nuclear accident provides opportunities to review and improve emergency preparedness and response programme. The present paper presents the chronology of the emergency situation, challenges faced and handled in Fukushima. Even though the possibility of a Fukushima type nuclear accident in India is very remote due to the low probability of a high intensity earthquake followed by tsunami at NPP sites, the efforts needs to be initiated from the regulatory point of view for an effective Nuclear and Radiological Emergency Preparedness and Response Plans. The Emergency Preparedness and Response Plans of NPP sites were reviewed in the light of unique challenges of accident at Fukushima. It is realized that multi unit events are the realities that must be addressed as part of Emergency

  15. Functional trait responses to sediment deposition reduce macrofauna-mediated ecosystem functioning in an estuarine mudflat

    Science.gov (United States)

    Mestdagh, Sebastiaan; Bagaço, Leila; Braeckman, Ulrike; Ysebaert, Tom; De Smet, Bart; Moens, Tom; Van Colen, Carl

    2018-05-01

    Human activities, among which dredging and land use change in river basins, are altering estuarine ecosystems. These activities may result in changes in sedimentary processes, affecting biodiversity of sediment macrofauna. As macrofauna controls sediment chemistry and fluxes of energy and matter between water column and sediment, changes in the structure of macrobenthic communities could affect the functioning of an entire ecosystem. We assessed the impact of sediment deposition on intertidal macrobenthic communities and on rates of an important ecosystem function, i.e. sediment community oxygen consumption (SCOC). An experiment was performed with undisturbed sediment samples from the Scheldt river estuary (SW Netherlands). The samples were subjected to four sedimentation regimes: one control and three with a deposited sediment layer of 1, 2 or 5 cm. Oxygen consumption was measured during incubation at ambient temperature. Luminophores applied at the surface, and a seawater-bromide mixture, served as tracers for bioturbation and bio-irrigation, respectively. After incubation, the macrofauna was extracted, identified, and counted and then classified into functional groups based on motility and sediment reworking capacity. Total macrofaunal densities dropped already under the thinnest deposits. The most affected fauna were surficial and low-motility animals, occurring at high densities in the control. Their mortality resulted in a drop in SCOC, which decreased steadily with increasing deposit thickness, while bio-irrigation and bioturbation activity showed increases in the lower sediment deposition regimes but decreases in the more extreme treatments. The initial increased activity likely counteracted the effects of the drop in low-motility, surficial fauna densities, resulting in a steady rather than sudden fall in oxygen consumption. We conclude that the functional identity in terms of motility and sediment reworking can be crucial in our understanding of the

  16. Functional trait responses to sediment deposition reduce macrofauna-mediated ecosystem functioning in an estuarine mudflat

    Directory of Open Access Journals (Sweden)

    S. Mestdagh

    2018-05-01

    Full Text Available Human activities, among which dredging and land use change in river basins, are altering estuarine ecosystems. These activities may result in changes in sedimentary processes, affecting biodiversity of sediment macrofauna. As macrofauna controls sediment chemistry and fluxes of energy and matter between water column and sediment, changes in the structure of macrobenthic communities could affect the functioning of an entire ecosystem. We assessed the impact of sediment deposition on intertidal macrobenthic communities and on rates of an important ecosystem function, i.e. sediment community oxygen consumption (SCOC. An experiment was performed with undisturbed sediment samples from the Scheldt river estuary (SW Netherlands. The samples were subjected to four sedimentation regimes: one control and three with a deposited sediment layer of 1, 2 or 5 cm. Oxygen consumption was measured during incubation at ambient temperature. Luminophores applied at the surface, and a seawater–bromide mixture, served as tracers for bioturbation and bio-irrigation, respectively. After incubation, the macrofauna was extracted, identified, and counted and then classified into functional groups based on motility and sediment reworking capacity. Total macrofaunal densities dropped already under the thinnest deposits. The most affected fauna were surficial and low-motility animals, occurring at high densities in the control. Their mortality resulted in a drop in SCOC, which decreased steadily with increasing deposit thickness, while bio-irrigation and bioturbation activity showed increases in the lower sediment deposition regimes but decreases in the more extreme treatments. The initial increased activity likely counteracted the effects of the drop in low-motility, surficial fauna densities, resulting in a steady rather than sudden fall in oxygen consumption. We conclude that the functional identity in terms of motility and sediment reworking can be crucial in our

  17. Site-Specific Multilevel Modeling of Potato Response to Nitrogen Fertilization

    OpenAIRE

    Serge-Étienne Parent; Michaël A. Leblanc; Annie-Claude Parent; Zonlehoua Coulibali; Léon E. Parent

    2017-01-01

    Technologies of precision agriculture, digital soil maps, and meteorological stations provide a minimum data set to guide precision farming operations. However, determining optimal nutrient requirements for potato (Solanum tuberosum L.) crops at subfield scale remains a challenge given specific climatic, edaphic, and managerial conditions. Multilevel modeling can generalize yield response to fertilizer additions using data easily accessible to growers. Our objective was to elaborate a multile...

  18. Data Equivalency of an Interactive Voice Response System for Home Assessment of Back Pain and Function

    Directory of Open Access Journals (Sweden)

    William S Shaw

    2007-01-01

    Full Text Available BACKGROUND: Interactive voice response (IVR systems that collect survey data using automated, push-button telephone responses may be useful to monitor patients’ pain and function at home; however, its equivalency to other data collection methods has not been studied.

  19. Semi-classical calculation of the spin-isospin response functions

    International Nuclear Information System (INIS)

    Chanfray, G.

    1987-03-01

    We present a semi-classical calculation of the nuclear response functions beyond the Thomas-Fermi approximation. We apply our formalism to the spin-isospin responses and show that the surface peaked h/2π corrections considerably decrease the ratio longitudinal/transverse as obtained through hadronic probes

  20. Off-site emergency response plans in case of technological catastrophes: the case Angra dos Reis

    International Nuclear Information System (INIS)

    Souza Junior, M.D. de.

    1990-04-01

    In the first part of the thesis a discussion of the technical, operational and methodological features of the current practices for emergency planning in case of a nuclear fallout. Based on this general reference is possible to evaluate the features in the natural and social environment of Angra dos Reis that probably will obstruct the application of the protective countermeasures to the public. These critical points are enhanced to permit the discussion of a methodological approach that is supposed to be suitable to the reality of Angra dos Reis. The approach was developed specifically to this region and was introduced as a part of the general emergency off-site plan to the Central Nuclear Almirante Alvaro Alberto (CNAAA). Starting from this experience will be possible to enlarge this approach in a further research, in order to study this potential hazards of other industrial plants. (author)

  1. Identification and functional analysis of a second RBF-2 binding site within the HIV-1 promoter

    International Nuclear Information System (INIS)

    Dahabieh, Matthew S.; Ooms, Marcel; Malcolm, Tom; Simon, Viviana; Sadowski, Ivan

    2011-01-01

    Transcription from the HIV-1 long terminal repeat (LTR) is mediated by numerous host transcription factors. In this study we characterized an E-box motif (RBE1) within the core promoter that was previously implicated in both transcriptional activation and repression. We show that RBE1 is a binding site for the RBF-2 transcription factor complex (USF1, USF2, and TFII-I), previously shown to bind an upstream viral element, RBE3. The RBE1 and RBE3 elements formed complexes of identical mobility and protein constituents in gel shift assays, both with Jurkat T-cell nuclear extracts and recombinant USF/TFII-I. Furthermore, both elements are regulators of HIV-1 expression; mutations in LTR-luciferase reporters and in HIV-1 molecular clones resulted in decreased transcription, virion production, and proviral expression in infected cells. Collectively, our data indicate that RBE1 is a bona fide RBF-2 binding site and that the RBE1 and RBE3 elements are necessary for mediating proper transcription from the HIV-1 LTR.

  2. Calculation of the spin-isospin response functions in an extended semi-classical theory

    International Nuclear Information System (INIS)

    Chanfray, G.

    1987-01-01

    We present a semi-classical calculation of the spin isospin response-functions beyond Thomas-Fermi theory. We show that surface-peaked ℎ 2 corrections reduce the collective effects predicted by Thomas-Fermi calculations. These effects, small for a volume response, become important for surface responses probed by hadrons. This yields a considerable improvement of the agreement with the (p, p') Los Alamos data

  3. Anaesthetic induction with alfaxalone in the ball python (Python regius): dose response and effect of injection site.

    Science.gov (United States)

    James, Lauren E; Williams, Catherine Ja; Bertelsen, Mads F; Wang, Tobias

    2018-05-01

    To characterise the minimum dose of intramuscular alfaxalone required to facilitate intubation for mechanical ventilation, and to investigate the impact of cranial versus caudal injection on anaesthetic depth. Randomised crossover study. Six healthy juvenile ball pythons (Python regius). Three dosages (10, 20 and 30 mg kg -1 ) of alfaxalone were administered to each python in a caudal location with a minimum 2 weeks washout. Induction and recovery were monitored by assessing muscle tone, righting reflex, response to a noxious stimulus and the ability to intubate. A subsequent experiment assessed the influence of injection site by comparing administration of 20 mg kg -1 alfaxalone in a cranial location (1 cm cranial to the heart) with the caudal site. Respiration rate was monitored throughout, and when intubation was possible, snakes were mechanically ventilated. Regardless of dose and injection site, maximum effect was reached within 10.0 ± 2.7 minutes. When administered at the caudal injection site, intubation was only successful after a dosage of 30 mg kg- 1 , which is higher than in previous reports for other reptiles. However, intubation was possible in all cases after 7.2 ± 1.6 minutes upon cranial administration of 20 mg kg -1 , and anaesthetic duration was significantly lengthened (p pythons, and may serve as a useful induction agent prior to provision of volatile anaesthetics. The same dosage injected in the cranial site led to deeper anaesthesia than when injected caudally, suggesting that shunting to the liver and first-pass metabolism of alfaxalone occur when injected caudally, via the renal portal system. Copyright © 2018 Association of Veterinary Anaesthetists and American College of Veterinary Anesthesia and Analgesia. Published by Elsevier Ltd. All rights reserved.

  4. Activity-Based Probes for Isoenzyme- and Site-Specific Functional Characterization of Glutathione S -Transferases

    Energy Technology Data Exchange (ETDEWEB)

    Stoddard, Ethan G. [Chemical Biology and Exposure; Killinger, Bryan J. [Chemical Biology and Exposure; Nair, Reji N. [Chemical Biology and Exposure; Sadler, Natalie C. [Chemical Biology and Exposure; Volk, Regan F. [Chemical Biology and Exposure; Purvine, Samuel O. [Chemical Biology and Exposure; Shukla, Anil K. [Chemical Biology and Exposure; Smith, Jordan N. [Chemical Biology and Exposure; Wright, Aaron T. [Chemical Biology and Exposure

    2017-11-01

    Glutathione S-transferases (GSTs) comprise a highly diverse family of phase II drug metabolizing enzymes whose shared function is the conjugation of reduced glutathione to various endo- and xenobiotics. Although the conglomerate activity of these enzymes can be measured by colorimetric assays, measurement of the individual contribution from specific isoforms and their contribution to the detoxification of xenobiotics in complex biological samples has not been possible. For this reason, we have developed two activity-based probes that characterize active glutathione transferases in mammalian tissues. The GST active site is comprised of a glutathione binding “G site” and a distinct substrate binding “H site”. Therefore, we developed (1) a glutathione-based photoaffinity probe (GSH-ABP) to target the “G site”, and (2) a probe designed to mimic a substrate molecule and show “H site” activity (GST-ABP). The GSH-ABP features a photoreactive moiety for UV-induced covalent binding to GSTs and glutathione-binding enzymes. The GST-ABP is a derivative of a known mechanism-based GST inhibitor that binds within the active site and inhibits GST activity. Validation of probe targets and “G” and “H” site specificity was carried out using a series of competitors in liver homogenates. Herein, we present robust tools for the novel characterization of enzyme- and active site-specific GST activity in mammalian model systems.

  5. CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome.

    Science.gov (United States)

    Zhang, Zijun; Xing, Yi

    2017-09-19

    Crosslinking or RNA immunoprecipitation followed by sequencing (CLIP-seq or RIP-seq) allows transcriptome-wide discovery of RNA regulatory sites. As CLIP-seq/RIP-seq reads are short, existing computational tools focus on uniquely mapped reads, while reads mapped to multiple loci are discarded. We present CLAM (CLIP-seq Analysis of Multi-mapped reads). CLAM uses an expectation-maximization algorithm to assign multi-mapped reads and calls peaks combining uniquely and multi-mapped reads. To demonstrate the utility of CLAM, we applied it to a wide range of public CLIP-seq/RIP-seq datasets involving numerous splicing factors, microRNAs and m6A RNA methylation. CLAM recovered a large number of novel RNA regulatory sites inaccessible by uniquely mapped reads. The functional significance of these sites was demonstrated by consensus motif patterns and association with alternative splicing (splicing factors), transcript abundance (AGO2) and mRNA half-life (m6A). CLAM provides a useful tool to discover novel protein-RNA interactions and RNA modification sites from CLIP-seq and RIP-seq data, and reveals the significant contribution of repetitive elements to the RNA regulatory landscape of the human transcriptome. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Real-time and on-site γ-ray radiation response testing system for semiconductor devices and its applications

    Energy Technology Data Exchange (ETDEWEB)

    Mu, Yifei, E-mail: Y.Mu@student.liverpool.ac.uk [Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool L69 3GJ (United Kingdom); Zhao, Ce Zhou, E-mail: cezhou.zhao@xjtlu.edu.cn [Department of Electrical and Electronic Engineering, Xi’an Jiaotong-Liverpool University, Suzhou 215123 (China); Qi, Yanfei, E-mail: yanfei.qi01@xjtlu.edu.cn [Department of Electrical and Electronic Engineering, Xi’an Jiaotong-Liverpool University, Suzhou 215123 (China); Lam, Sang, E-mail: s.lam@xjtlu.edu.cn [Department of Electrical and Electronic Engineering, Xi’an Jiaotong-Liverpool University, Suzhou 215123 (China); Zhao, Chun, E-mail: garyzhao@ust.hk [Nano and Advanced Materials Institute, Hong Kong University of Science and Technology, Kowloon (Hong Kong); Lu, Qifeng, E-mail: qifeng@liverpool.ac.uk [Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool L69 3GJ (United Kingdom); Cai, Yutao, E-mail: yutao.cai@xjtlu.edu.cn [Department of Electrical and Electronic Engineering, Xi’an Jiaotong-Liverpool University, Suzhou 215123 (China); Mitrovic, Ivona Z., E-mail: ivona@liverpool.ac.uk [Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool L69 3GJ (United Kingdom); Taylor, Stephen, E-mail: s.taylor@liverpool.ac.uk [Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool L69 3GJ (United Kingdom); Chalker, Paul R., E-mail: pchalker@liverpool.ac.uk [Center for Materials and Structures, School of Engineering, University of Liverpool, Liverpool L69 3GH (United Kingdom)

    2016-04-01

    The construction of a turnkey real-time and on-site radiation response testing system for semiconductor devices is reported. Components of an on-site radiation response probe station, which contains a 1.11 GBq Cs{sup 137} gamma (γ)-ray source, and equipment of a real-time measurement system are described in detail for the construction of the whole system. The real-time measurement system includes a conventional capacitance–voltage (C–V) and stress module, a pulse C–V and stress module, a conventional current–voltage (I–V) and stress module, a pulse I–V and stress module, a DC on-the-fly (OTF) module and a pulse OTF module. Electrical characteristics of MOS capacitors or MOSFET devices are measured by each module integrated in the probe station under continuous γ-ray exposure and the measurement results are presented. The dose rates of different gate dielectrics are calculated by a novel calculation model based on the Cs{sup 137} γ-ray source placed in the probe station. For the sake of operators’ safety, an equivalent dose rate of 70 nSv/h at a given operation distance is indicated by a dose attenuation model in the experimental environment. HfO{sub 2} thin films formed by atomic layer deposition are employed to investigate the radiation response of the high-κ material by using the conventional C–V and pulse C–V modules. The irradiation exposure of the sample is carried out with a dose rate of 0.175 rad/s and ±1 V bias in the radiation response testing system. Analysis of flat-band voltage shifts (ΔV{sub FB}) of the MOS capacitors suggests that the on-site and real-time/pulse measurements detect more serious degradation of the HfO{sub 2} thin films compared with the off-site irradiation and conventional measurement techniques.

  7. Herbicide and fertilizers promote analogous phylogenetic responses but opposite functional responses in plant communities

    International Nuclear Information System (INIS)

    Pellissier, Loïc; Wisz, Mary S; Strandberg, Beate; Damgaard, Christian

    2014-01-01

    Throughout the world, herbicides and fertilizers change species composition in agricultural communities, but how do the cumulative effects of these chemicals impact the functional and phylogenetic structure of non-targeted communities when they drift into adjacent semi-natural habitats? Based on long-term experiment we show that fertilizer and herbicides (glyphosate) have contrasting effects on functional structure, but can increase phylogenetic diversity in semi-natural plant communities. We found that an increase in nitrogen promoted an increase in the average specific leaf area and canopy height at the community level, but an increase in glyphosate promoted a decrease in those traits. Phylogenetic diversity of plant communities increased when herbicide and fertilizer were applied together, likely because functional traits facilitating plant success in those conditions were not phylogenetically conserved. Species richness also decreased with increasing levels of nitrogen and glyphosate. Our results suggest that predicting the cumulative effects of agrochemicals is more complex than anticipated due to their distinct selection of traits that may or may not be conserved phylogenetically. Precautionary efforts to mitigate drift of agricultural chemicals into semi-natural habitats are warranted to prevent unforeseeable biodiversity shifts. (paper)

  8. The alkylation response protein AidB is localized at the new poles and constriction sites in Brucella abortus

    Directory of Open Access Journals (Sweden)

    Dotreppe Delphine

    2011-11-01

    Full Text Available Abstract Background Brucella abortus is the etiological agent of a worldwide zoonosis called brucellosis. This alpha-proteobacterium is dividing asymmetrically, and PdhS, an essential histidine kinase, was reported to be an old pole marker. Results We were interested to identify functions that could be recruited to bacterial poles. The Brucella ORFeome, a collection of cloned predicted coding sequences, was placed in fusion with yellow fluorescent protein (YFP coding sequence and screened for polar localizations in B. abortus. We report that AidB-YFP was systematically localized to the new poles and at constrictions sites in B. abortus, either in culture or inside infected HeLa cells or RAW264.7 macrophages. AidB is an acyl-CoA dehydrogenase (ACAD homolog, similar to E. coli AidB, an enzyme putatively involved in destroying alkylating agents. Accordingly, a B. abortus aidB mutant is more sensitive than the wild-type strain to the lethality induced by methanesulphonic acid ethyl ester (EMS. The exposure to EMS led to a very low frequency of constriction events, suggesting that cell cycle is blocked during alkylation damage. The localization of AidB-YFP at the new poles and at constriction sites seems to be specific for this ACAD homolog since two other ACAD homologs fused to YFP did not show specific localization. The overexpression of aidB, but not the two other ACAD coding sequences, leads to multiple morphological defects. Conclusions Data reported here suggest that AidB is a marker of new poles and constriction sites, that could be considered as sites of preparation of new poles in the sibling cells originating from cell division. The possible role of AidB in the generation or the function of new poles needs further investigation.

  9. Functional response to cholinesterase inhibitor therapy in a naturalistic Alzheimer’s disease cohort

    Directory of Open Access Journals (Sweden)

    Wattmo Carina

    2012-11-01

    Full Text Available Abstract Background Activities of daily living (ADL are an essential part of the diagnostic criteria for Alzheimer’s disease (AD. A decline in ADL affects independent living and has a strong negative impact on caregiver burden. Functional response to cholinesterase inhibitor (ChEI treatment and factors that might influence this response in naturalistic AD patients need investigating. The aim of this study was to identify the socio-demographic and clinical factors that affect the functional response after 6 months of ChEI therapy. Methods This prospective, non-randomised, multicentre study in a routine clinical setting included 784 AD patients treated with donepezil, rivastigmine or galantamine. At baseline and after 6 months of treatment, patients were assessed using several rating scales, including the Instrumental Activities of Daily Living (IADL scale, Physical Self-Maintenance Scale (PSMS and Mini-Mental State Examination (MMSE. Demographic and clinical characteristics were investigated at baseline. The functional response and the relationships of potential predictors were analysed using general linear models. Results After 6 months of ChEI treatment, 49% and 74% of patients showed improvement/no change in IADL and in PSMS score, respectively. The improved/unchanged patients exhibited better cognitive status at baseline; regarding improved/unchanged PSMS, patients were younger and used fewer anti-depressants. A more positive functional response to ChEI was observed in younger individuals or among those having the interaction effect of better preserved cognition and lower ADL ability. Patients with fewer concomitant medications or those using NSAIDs/acetylsalicylic acid showed a better PSMS response. Conclusions Critical characteristics that may influence the functional response to ChEI in AD were identified. Some predictors differed from those previously shown to affect cognitive response, e.g., lower cognitive ability and older age

  10. Data-driven haemodynamic response function extraction using Fourier-wavelet regularised deconvolution

    NARCIS (Netherlands)

    Wink, Alle Meije; Hoogduin, Hans; Roerdink, Jos B.T.M.

    2008-01-01

    Background: We present a simple, data-driven method to extract haemodynamic response functions (HRF) from functional magnetic resonance imaging (fMRI) time series, based on the Fourier-wavelet regularised deconvolution (ForWaRD) technique. HRF data are required for many fMRI applications, such as

  11. Data-driven haemodynamic response function extraction using Fourier-wavelet regularised deconvolution

    NARCIS (Netherlands)

    Wink, Alle Meije; Hoogduin, Hans; Roerdink, Jos B.T.M.

    2010-01-01

    Background: We present a simple, data-driven method to extract haemodynamic response functions (HRF) from functional magnetic resonance imaging (fMRI) time series, based on the Fourier-wavelet regularised deconvolution (ForWaRD) technique. HRF data are required for many fMRI applications, such as

  12. Lung function and bronchial responsiveness after Mycoplasma pneumoniae infection in early childhood

    DEFF Research Database (Denmark)

    Boysen, Birgitte Kjær; Jensen, Jørgen S; Nielsen, Kim G

    2008-01-01

    by whole-body plethysmography and bronchial hyperresponsiveness was assessed by cold, dry air hyperventilation. Neither baseline lung function nor bronchial response to cold dry air hyperventilation differed between M. pneumoniae-positive and -negative children: mean baseline lung function were 1.17 versus...

  13. Linking and Psychological Functioning in a Chinese Sample: The Multiple Mediation of Response to Positive Affect

    Science.gov (United States)

    Yang, Hongfei; Li, Juan

    2016-01-01

    The present study examined the associations between linking, response to positive affect, and psychological functioning in Chinese college students. The results of conducting multiple mediation analyses indicated that emotion- and self-focused positive rumination mediated the relationship between linking and psychological functioning, whereas…

  14. ERP Responses to Violations in the Hierarchical Structure of Functional Categories in Japanese Verb Conjugation

    Science.gov (United States)

    Kobayashi, Yuki; Sugioka, Yoko; Ito, Takane

    2018-01-01

    An event-related potential experiment was conducted in order to investigate readers' response to violations in the hierarchical structure of functional categories in Japanese, an agglutinative language where functional heads like Negation (Neg) as well as Tense (Tns) are realized as suffixes. A left-lateralized negativity followed by a P600 was…

  15. Responsiveness of the OARSI-OMERACT osteoarthritis pain and function measures

    DEFF Research Database (Denmark)

    Bond, M; Davis, A; Lohmander, Stefan

    2012-01-01

    To assess the responsiveness of the Intermittent and Constant Osteoarthritis Pain (ICOAP) measure, Hip Disability and Osteoarthritis Outcome Score Physical Function Short Form (HOOS-PS), and the Knee Disability and Osteoarthritis Outcome Score Physical Function Short Form (KOOS-PS) in a pharmacol...

  16. Maturation of Sensori-Motor Functional Responses in the Preterm Brain.

    Science.gov (United States)

    Allievi, Alessandro G; Arichi, Tomoki; Tusor, Nora; Kimpton, Jessica; Arulkumaran, Sophie; Counsell, Serena J; Edwards, A David; Burdet, Etienne

    2016-01-01

    Preterm birth engenders an increased risk of conditions like cerebral palsy and therefore this time may be crucial for the brain's developing sensori-motor system. However, little is known about how cortical sensori-motor function matures at this time, whether development is influenced by experience, and about its role in spontaneous motor behavior. We aimed to systematically characterize spatial and temporal maturation of sensori-motor functional brain activity across this period using functional MRI and a custom-made robotic stimulation device. We studied 57 infants aged from 30 + 2 to 43 + 2 weeks postmenstrual age. Following both induced and spontaneous right wrist movements, we saw consistent positive blood oxygen level-dependent functional responses in the contralateral (left) primary somatosensory and motor cortices. In addition, we saw a maturational trend toward faster, higher amplitude, and more spatially dispersed functional responses; and increasing integration of the ipsilateral hemisphere and sensori-motor associative areas. We also found that interhemispheric functional connectivity was significantly related to ex-utero exposure, suggesting the influence of experience-dependent mechanisms. At term equivalent age, we saw a decrease in both response amplitude and interhemispheric functional connectivity, and an increase in spatial specificity, culminating in the establishment of a sensori-motor functional response similar to that seen in adults. © The Author 2015. Published by Oxford University Press.

  17. Intake rates and the functional response in shorebirds (Charadriiformes) eating macro-invertebrates

    NARCIS (Netherlands)

    Goss-Custard, John D.; West, Andrew D.; Yates, Michael G.; Caldow, Richard W. G.; Stillman, Richard A.; Bardsley, Louise; Castilla, Juan; Castro, Macarena; Dierschke, Volker; Durell, Sarah E. A. Le V. Dit; Eichhorn, Goetz; Ens, Bruno J.; Exo, Klaus-Michael; Udayangani-Fernando, P. U.; Ferns, Peter N.; Hockey, Philip A. R.; Gill, Jennifer A.; Johnstone, Ian; Kalejta-Summers, Bozena; Masero, Jose A.; Moreira, Francisco; Nagarajan, Rajarathina Velu; Owens, Ian P. F.; Pacheco, Cristian; Perez-Hurtado, Alejandro; Rogers, Danny; Scheiffarth, Gregor; Sitters, Humphrey; Sutherland, William J.; Triplet, Patrick; Worrall, Dave H.; Zharikov, Yuri; Zwarts, Leo; Pettifor, Richard A.

    2006-01-01

    As field determinations take much effort, it would be useful to be able to predict easily the coefficients describing the functional response of free-living predators, the function relating food intake rate to the abundance of food organisms in the environment. As a means easily to parameterise an

  18. Functional studies of elongation factor Tu from Escherichia coli : Site-directed mutagenesis and antibiotic action

    NARCIS (Netherlands)

    Krab, Ivo Maarten

    2001-01-01

    This PhD thesis describes several studies into the structure and function of Escherichia coli Elongation Factor Tu (EF-Tu). EF-Tu plays a central role in the bacterial protein synthesis machinery as the carrier of "coded building blocks" for protein synthesis, aminoacylated tRNA (aa-tRNA). Without

  19. Conductance of Sidewall-Functionalized Carbon Nanotubes: Universal Dependence on Adsorption Sites

    DEFF Research Database (Denmark)

    García-Lastra, J.M.; Thygesen, Kristian Sommer; Strange, Mikkel

    2008-01-01

    We use density functional theory to study the effect of molecular adsorbates on the conductance of metallic carbon nanotubes (CNT). The five molecules considered (NO2, NH2, H, COOH, OH) lead to very similar scattering of the electrons. The adsorption of a single molecule suppresses one of the two...

  20. Pigment binding sites occupancy and functional architecture of the Photosystem II antenna complex Lhcb5

    NARCIS (Netherlands)

    Ballottari, M.; Mozzo, M.; Croce, R.; Morosinotto, T.; Bassi, R.

    2009-01-01

    Lhcb5 is an antenna protein that is highly conserved in plants and green algae. It is part of the inner layer of photosystem II antenna system retained in high light acclimated plants. To study the structure-function relation and the role of individual pigments in this complex, we (i) "knocked out"

  1. Comparison of dose response functions for EBT3 model GafChromic™ film dosimetry system.

    Science.gov (United States)

    Aldelaijan, Saad; Devic, Slobodan

    2018-05-01

    Different dose response functions of EBT3 model GafChromic™ film dosimetry system have been compared in terms of sensitivity as well as uncertainty vs. error analysis. We also made an assessment of the necessity of scanning film pieces before and after irradiation. Pieces of EBT3 film model were irradiated to different dose values in Solid Water (SW) phantom. Based on images scanned in both reflection and transmission mode before and after irradiation, twelve different response functions were calculated. For every response function, a reference radiochromic film dosimetry system was established by generating calibration curve and by performing the error vs. uncertainty analysis. Response functions using pixel values from the green channel demonstrated the highest sensitivity in both transmission and reflection mode. All functions were successfully fitted with rational functional form, and provided an overall one-sigma uncertainty of better than 2% for doses above 2 Gy. Use of pre-scanned images to calculate response functions resulted in negligible improvement in dose measurement accuracy. Although reflection scanning mode provides higher sensitivity and could lead to a more widespread use of radiochromic film dosimetry, it has fairly limited dose range and slightly increased uncertainty when compared to transmission scan based response functions. Double-scanning technique, either in transmission or reflection mode, shows negligible improvement in dose accuracy as well as a negligible increase in dose uncertainty. Normalized pixel value of the images scanned in transmission mode shows linear response in a dose range of up to 11 Gy. Copyright © 2018 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  2. PASSPORT-seq: A Novel High-Throughput Bioassay to Functionally Test Polymorphisms in Micro-RNA Target Sites

    Directory of Open Access Journals (Sweden)

    Joseph Ipe

    2018-06-01

    Full Text Available Next-generation sequencing (NGS studies have identified large numbers of genetic variants that are predicted to alter miRNA–mRNA interactions. We developed a novel high-throughput bioassay, PASSPORT-seq, that can functionally test in parallel 100s of these variants in miRNA binding sites (mirSNPs. The results are highly reproducible across both technical and biological replicates. The utility of the bioassay was demonstrated by testing 100 mirSNPs in HEK293, HepG2, and HeLa cells. The results of several of the variants were validated in all three cell lines using traditional individual luciferase assays. Fifty-five mirSNPs were functional in at least one of three cell lines (FDR ≤ 0.05; 11, 36, and 27 of them were functional in HEK293, HepG2, and HeLa cells, respectively. Only four of the variants were functional in all three cell lines, which demonstrates the cell-type specific effects of mirSNPs and the importance of testing the mirSNPs in multiple cell lines. Using PASSPORT-seq, we functionally tested 111 variants in the 3′ UTR of 17 pharmacogenes that are predicted to alter miRNA regulation. Thirty-three of the variants tested were functional in at least one cell line.

  3. [Responses of functional diversity of aquatic insect community to land use change in middle reach of Qiantang River, East China].

    Science.gov (United States)

    Zhang, Lian-Bo; Liu, Dong-Xiao; Liu, Shuo-Ru; Zhang, Yong; Tong, Xiao-Li; Wang, Bei-Xin

    2013-10-01

    Based on the biological traits such as life history, resistance ability against environmental disturbance, and physiological characteristics of aquatic insects, and by using the fourth-corner statistical method, this paper studied the responses of the functional diversity of aquatic insect community to land use change in the middle reach of Qiantang River, Zhejiang Province of East China. For the test aquatic insect community, some of its biological traits were sensitive to land use change, and altered along human disturbance gradients as expected. With the increasing intensity of human disturbance, the maximal insect body length decreased gradually, the dominant respiration pattern evolved from gill respiration to tegument respiration, and the abundance of burrowers increased significantly. At the same time, the functional diversity measured as Rao's quadratic entropy was significantly higher in reference sites than in disturbed sites (P aquatic community were mainly induced by the land use change caused by human activities, which resulted in the decline of stream water quality and habitat quality and the variations of aquatic insect community composition and biological traits. The aquatic insect biological traits and functional diversity could be the potentially effective indicators in the stream health assessment in the future.

  4. Development of emergency response training program for on-site commanders (2). Extraction of non-technical skills

    International Nuclear Information System (INIS)

    Matsui, Yuko; Hikono, Masaru; Iwasaki, Mari; Morita, Miduho

    2017-01-01

    This study aimed at characterizing a non-technical skill exercise for on-site managers in charge of initial response at an emergency response center by extracting and clarifying the behavior examples of non-technical skills shown in the exercise scenario. From video observations, the non-technical skill examples were identified from seven of the eight non-technical skill categories which had been defined when the training program was developed. At the same time, the limitation when extracting the cases by observations was identified. The extracted non-technical skill cases are expected to be used for characterizing exercise scenarios, as well as provide knowledge to raise the awareness of exercise participants. (author)

  5. Influence of turbulence, orientation, and site configuration on the response of buildings to extreme wind.

    Science.gov (United States)

    Aly, Aly Mousaad

    2014-01-01

    Atmospheric turbulence results from the vertical movement of air, together with flow disturbances around surface obstacles which make low- and moderate-level winds extremely irregular. Recent advancements in wind engineering have led to the construction of new facilities for testing residential homes at relatively high Reynolds numbers. However, the generation of a fully developed turbulence in these facilities is challenging. The author proposed techniques for the testing of residential buildings and architectural features in flows that lack fully developed turbulence. While these methods are effective for small structures, the extension of the approach for large and flexible structures is not possible yet. The purpose of this study is to investigate the role of turbulence in the response of tall buildings to extreme winds. In addition, the paper presents a detailed analysis to investigate the influence of upstream terrain conditions, wind direction angle (orientation), and the interference effect from the surrounding on the response of high-rise buildings. The methodology presented can be followed to help decision makers to choose among innovative solutions like aerodynamic mitigation, structural member size adjustment, and/or damping enhancement, with an objective to improve the resiliency and the serviceability of buildings.

  6. Influence of Turbulence, Orientation, and Site Configuration on the Response of Buildings to Extreme Wind

    Science.gov (United States)

    2014-01-01

    Atmospheric turbulence results from the vertical movement of air, together with flow disturbances around surface obstacles which make low- and moderate-level winds extremely irregular. Recent advancements in wind engineering have led to the construction of new facilities for testing residential homes at relatively high Reynolds numbers. However, the generation of a fully developed turbulence in these facilities is challenging. The author proposed techniques for the testing of residential buildings and architectural features in flows that lack fully developed turbulence. While these methods are effective for small structures, the extension of the approach for large and flexible structures is not possible yet. The purpose of this study is to investigate the role of turbulence in the response of tall buildings to extreme winds. In addition, the paper presents a detailed analysis to investigate the influence of upstream terrain conditions, wind direction angle (orientation), and the interference effect from the surrounding on the response of high-rise buildings. The methodology presented can be followed to help decision makers to choose among innovative solutions like aerodynamic mitigation, structural member size adjustment, and/or damping enhancement, with an objective to improve the resiliency and the serviceability of buildings. PMID:24701140

  7. Assessment of stability of the response versus scan angle for the S-NPP VIIRS reflective solar bands using pseudo-invariant desert and Dome C sites

    Science.gov (United States)

    Wu, Aisheng; Xiong, Xiaoxiong J.; Cao, Changyong

    2017-09-01

    The Visible Infrared Imaging Radiometer Suite (VIIRS) on the Suomi NPP (National Polar-orbiting Partnership) satellite has been in operation for over five years. VIIRS has 22 bands with a spectral range from 0.4 μm to 2.2 μm for the reflective solar bands (RSB). The Earth view swath covers a distance of 3000 km over scan angles of +/- 56.0° off nadir. The on-board calibration of the RSB relies on a solar diffuser (SD) located at a fixed scan angle and a solar diffuser stability monitor (SDSM). The response versus scan angle (RVS) was characterized prelaunch in ambient conditions and is currently used to determine the on-orbit response for all scan angles relative to the SD scan angle. Since the RVS is vitally important to the quality of calibrated level 1B products, it is important to monitor its on-orbit stability, particularly at the short wavelengths (blue) where the most degradation occurs. In this study, the RVS stability is examined based on reflectance trends collected at various scan angles over the selected pseudo-invariant desert sites in Northern Africa and the Dome C snow site in Antarctica. These trends are corrected by the site dependent BRDF (bi-directional reflectance function) model to reduce seasonally related fluctuations. The BRDF corrected trends are examined so any systematic drifts in the scan angle direction would indicate a potential change in RVS. The results of this study provide useful information on VIIRS RVS on-orbit stability performance.

  8. Response of PCB contamination in stream fish to abatement actions at an industrial site

    International Nuclear Information System (INIS)

    Southworth, G.R.; Peterson, M.J.; McCarthy, J.F.; Milne, G.

    1995-01-01

    The Paducah Gaseous Diffusion Plant (PGDP) in Paducah, Kentucky, used large quantities of PCBs in equipment associated with the great electric power requirements of isotopic enrichment of uranium. Historic losses of PCBs in the 1950s and 1960s have left a legacy of contamination at the site. A biological monitoring program implemented in 1987 found PCBs in PGDP effluents and in fish downstream from facility discharges. As a consequence, a fish consumption advisory was posted on Little Bayou Creek by the Commonwealth of Kentucky in 1987, and regulatory discharge limits for PCBs at PGDP were reduced. Monitoring at multiple locations in receiving streams indicated that PGDP discharges were more important than in stream sediment contamination as sources of PCBs to fish. Environmental management and compliance staff at PGDP led an effort to reduce PCB discharges and monitor the effects of those actions. The active discharge of uncontaminated process water to historically PCB-contaminated drainage systems was found to mobilize PCBs into KPDES (Clean Water Act) regulated effluents. Efforts to locate PCB sources within the plant, coupled with improvements in management practices and remedial actions, appear to have been successful in reducing PCB discharges from these sources. Actions included emplacing passive monitors in the plant drainage system to identify this as a chronic source, and consolidating and re-routing effluents to minimize flow through PCB-contaminated channels. As a consequence, PCB contamination in fish in small streams receiving plant discharges decreased 75% over from 1992--1995

  9. Model-experiment synthesis at two FACE sites in the southeastern US. Forest ecosystem responses to elevated CO[2]. (Invited)

    Science.gov (United States)

    Walker, A. P.; Zaehle, S.; De Kauwe, M. G.; Medlyn, B. E.; Dietze, M.; Hickler, T.; Iversen, C. M.; Jain, A. K.; Luo, Y.; McCarthy, H. R.; Parton, W. J.; Prentice, C.; Thornton, P. E.; Wang, S.; Wang, Y.; Warlind, D.; Warren, J.; Weng, E.; Hanson, P. J.; Oren, R.; Norby, R. J.

    2013-12-01

    Ecosystem observations from two long-term Free-Air CO[2] Enrichment (FACE) experiments (Duke forest and Oak Ridge forest) were used to evaluate the assumptions of 11 terrestrial ecosystem models and the consequences of those assumptions for the responses of ecosystem water, carbon (C) and nitrogen (N) fluxes to elevated CO[2] (eCO[2]). Nitrogen dynamics were the main constraint on simulated productivity responses to eCO[2]. At Oak Ridge some models reproduced the declining response of C and N fluxes, while at Duke none of the models were able to maintain the observed sustained responses. C and N cycles are coupled through a number of complex interactions, which causes uncertainty in model simulations in multiple ways. Nonetheless, the major difference between models and experiments was a larger than observed increase in N-use efficiency and lower than observed response of N uptake. The results indicate that at Duke there were mechanisms by which trees accessed additional N in response to eCO[2] that were not represented in the ecosystem models, and which did not operate with the same efficiency at Oak Ridge. Sequestration of the additional productivity under eCO[2] into forest biomass depended largely on C allocation. Allocation assumptions were classified into three main categories--fixed partitioning coefficients, functional relationships and a partial (leaf allocation only) optimisation. The assumption which best constrained model results was a functional relationship between leaf area and sapwood area (pipe-model) and increased root allocation when nitrogen or water were limiting. Both, productivity and allocation responses to eCO[2] determined the ecosystem-level response of LAI, which together with the response of stomatal conductance (and hence water-use efficiency; WUE) determined the ecosystem response of transpiration. Differences in the WUE response across models were related to the representation of the relationship of stomatal conductance to CO[2] and

  10. The spin polarized linear response from density functional theory: Theory and application to atoms

    Energy Technology Data Exchange (ETDEWEB)

    Fias, Stijn, E-mail: sfias@vub.ac.be; Boisdenghien, Zino; De Proft, Frank; Geerlings, Paul [General Chemistry (ALGC), Vrije Universiteit Brussel (Free University Brussels – VUB), Pleinlaan 2, 1050 Brussels (Belgium)

    2014-11-14

    Within the context of spin polarized conceptual density functional theory, the spin polarized linear response functions are introduced both in the [N, N{sub s}] and [N{sub α}, N{sub β}] representations. The mathematical relations between the spin polarized linear response functions in both representations are examined and an analytical expression for the spin polarized linear response functions in the [N{sub α}, N{sub β}] representation is derived. The spin polarized linear response functions were calculated for all atoms up to and including argon. To simplify the plotting of our results, we integrated χ(r, r′) to a quantity χ(r, r{sup ′}), circumventing the θ and ϕ dependence. This allows us to plot and to investigate the periodicity throughout the first three rows in the periodic table within the two different representations. For the first time, χ{sub αβ}(r, r{sup ′}), χ{sub βα}(r, r{sup ′}), and χ{sub SS}(r, r{sup ′}) plots have been calculated and discussed. By integration of the spin polarized linear response functions, different components to the polarisability, α{sub αα}, α{sub αβ}, α{sub βα}, and α{sub ββ} have been calculated.

  11. Association of ideomotor apraxia with lesion site, etiology, neglect, and functional independence in patients with first ever stroke.

    Science.gov (United States)

    Civelek, Gul Mete; Atalay, Ayce; Turhan, Nur

    2015-04-01

    Ideomotor apraxia (IMA) is characterized by the inability to correctly imitate hand gestures and voluntarily pantomime tool use. The relationship between IMA and characteristics of stroke has not been totally elucidated. This study aimed to find out associations between presence of IMA and stroke etiology, site of the lesions, neglect, and temporal and functional parameters of stroke in patients with first ever stroke. Thirty-nine patients with first ever stroke were included. Patients with severe cognitive deficits were excluded. Assessment tools included Ideomotor Apraxia Test, Functional Independence Measure (FIM), Brunnstrom recovery stages, Mini Mental Test (MMT), and star cancellation test. Etiology (hemorrhagic or ischemic) and site of stroke was assessed through brain imaging methods. Location and size of ischemic lesion was determined by using the Oxfordshire Community Stroke Project system. IMA was identified in 35.9% of the patients. Patients with IMA had significantly lower FIM scores both on admission and discharge (P = 0.001, P = 0.001). Presence of IMA was significantly associated with the presence of neglect (P = 0.004), total anterior circulation ischemia (TACI) (P stroke etiology had no impact on the presence of IMA. IMA was in concordance with poor cognitive and functional state and was not limited to left hemisphere lesions. The study revealed strong associations between IMA, neglect, and TACI. Every patient with stroke should be evaluated for the presence of IMA on admission to rehabilitation unit.

  12. Response functions for crystals and surfaces, with applications to surface scattering

    International Nuclear Information System (INIS)

    Barker, J.A.; Steele, W.A.

    1978-01-01

    A general solution of the equations of forced motion of a harmonic crystal or other vibrating system with arbitrary time-dependent forces acting on the atoms is given. The solution is given in terms of dynamical 'response functions', for which expressions in terms of the normal mode frequencies and eigenvectors (polarization vectors) are given. Numerical calculations of the response functions are described for (111) and (100) surfaces of face-centered cubic crystals interacting with Lennard-Jones 6-12 potentials, and the qualitative features of the surface and bulk response functions are discussed. The use of these functions in problems of atomic scattering from surface is outlined, and convenient parametrized forms for this application are given. (Auth.)

  13. Long-term change of site response after the M W 9.0 Tohoku earthquake in Japan

    Science.gov (United States)

    Wu, Chunquan; Peng, Zhigang

    2012-12-01

    The recent M W 9.0 off the Pacific coast of Tohoku earthquake is the largest recorded earthquake in Japan's history. The Tohoku main shock and its aftershocks generated widespread strong shakings as large as ~3000 Gal along the east coast of Japan. Wu and Peng (2011) found clear drop of resonant frequency of up to 70% during the Tohoku main shock at 6 sites and correlation of resonance (peak) frequency and peak ground acceleration (PGA) during the main shock. Here we follow that study and systematically analyze long-term changes of material properties in the shallow crust from one year before to 5 months after the Tohoku main shock, using seismic data recorded by the Japanese Strong Motion Network KiK-Net. We use sliding window spectral ratios computed from a pair of surface and borehole stations to track the temporal changes in the site response of 6 sites. Our results show two stages of logarithmic recovery after a sharp drop of resonance frequency during the Tohoku main shock. The first stage is a rapid recovery within several hundred seconds to several hours, and the second stage is a slow recovery of more than five months. We also investigate whether the damage caused by the Tohoku main shock could make the near surface layers more susceptible to further damages, but we do not observe clear changes in susceptibility to further damage before and after the Tohoku main shock.

  14. Public Responses to CO2 Storage Sites. Lessons from Five European Cases

    Energy Technology Data Exchange (ETDEWEB)

    Oltra, C.; Boso, A. [Centro de Investigaciones Energeticas, Medioambientales y Tecnologicas CIEMAT, Madrid (Spain); Upham, P. [Finnish Environment Institute, Helsinki and Centre for Integrated Energy Research, University of Leeds, Leeds (United Kingdom); Riesch, H. [Centre for Environmental Policy, Imperial College London, London (United Kingdom); Brunsting, S. [ECN Policy Studies, Energy Research Centre of the Netherlands ECN, Amsterdam (Netherlands); Duetschke, E. [Fraunhofer-Institut fuer System- und Innovationsforschung ISI, Karlsruhe (Germany); Lis, A. [Department of Sociology and Social Anthropology, Central European University, Budapest (Hungary)

    2012-05-24

    Studies of the factors involved in public perceptions of CO2 storage projects reveal a level of complexity and diversity that arguably confounds a comprehensive theoretical account. To some extent, a conceptual approach that simply organises the relevant social scientific knowledge thematically, rather than seeking an integrated explanation, is as useful as any single account that fails to do justice to the contingencies involved. This paper reviews and assembles such knowledge in terms of six themes and applies these themes to five European cases of carbon capture and storage (CCS) implementation. We identify the main factors involved in community responses to CCS as relating to: the characteristics of the project; the engagement process; risk perceptions; the actions of the stakeholders; the characteristics of the community, and the socio-political context.

  15. Site response - a critical problem in soil-structure interaction analyses for embedded structures

    International Nuclear Information System (INIS)

    Seed, H.B.; Lysmer, J.

    1986-01-01

    Soil-structure interaction analyses for embedded structures must necessarily be based on a knowledge of the manner in which the soil would behave in the absence of any structure - that is on a knowledge and understanding of the spatial distribution of motions in the ground within the depth of embedment of the structure. The nature of these spatial variations is discussed and illustrated by examples of recorded motions. It is shown that both the amplitude of peak acceleration and the form of the acceleration response spectrum for earthquake motions will necessarily vary with depth and failure to take these variations into account may introduce an unwarranted degree of conservatism into the soil-structure interaction analysis procedure

  16. Thyroid nodules in the population living around semipalatinsk nuclear test site. Possible implications for dose-response relationships study

    International Nuclear Information System (INIS)

    Zhumadilov, Z.

    2006-01-01

    The risk of radiation-induced nodules is higher than the risk for radiation-induced cancer. Risk factors and specific modifiers of the dose-response relationship may vary among different populations and not be well recognized. Many thyroid studies have considered thyroid nodularity itself, but not specific morphological types of thyroid nodules. There are many specific types of thyroid nodules which follow a morphological classification of thyroid lesions, including some congenital and tumor-like conditions. Modern equipment and technique can help us to identify particular specific types of thyroid nodules. In this study we report some results of a clinically applicable approach to materials derived from three studies. From 1999 through 2002, we have screened 571 current residents from 4 exposed and 1 control village near the Semipalatinsk Nuclear Test Site area, who were of similar ages (<20) at the time of major radiation fallout events at the Semipalatinsk Nuclear Test Site (SNTS). Prevalent nodules were identified by ultrasound and fine-needle aspiration biopsy, cytopathology results. Analysis of ultrasound images and cytopathology of thyroid lesions among exposed and non-exposed population allowed us to distinguish some interesting ultrasound features for specific types of thyroid nodules. We believe that it would be interesting and possibly more informative for thyroid dosimetry studies to consider specific morphological types of thyroid nodules. We need more detailed research to clarify the feasibility of applying these findings for study of the dose-response relationship. (author)

  17. Preliminary results from EMERSITO, a rapid response network for site-effect studies

    Directory of Open Access Journals (Sweden)

    Paola Bordoni

    2012-10-01

    Full Text Available On May 20, 2012, at 02:03 UTC, a Ml 5.9 reverse-fault earthquake occurred in the Emilia-Romagna region, northern Italy, at a hypocentral depth of 6.3 km (http://iside.rm.ingv.it/, close to the cities of Modena and Ferrara in the plain of the Po River. The epicenter was near the village of Finale Emilia where macroseismic intensity was assessed at 7 EMS98 [Tertulliani et al. 2012, this issue], while the closest accelerometric station, MRN, located less than 20 km west-ward at Mirandola (Figure 1 recorded peaks of ground accelerations of about 300 cm/s2 (www.protezionecivile.gov.it/resources/cms/documents/Report_DPC_1_Emilia_EQSd.pdf. The mainshock triggered liquefaction phenomena a few kilometers eastwards of the epicenter, around the village of San Carlo. On the same day, two other shocks of Ml 5.1 followed (02:07, 13:18 GMT; http://iside.rm.ingv.it/. On May 29, 2012, at 07:00 UTC another Ml 5.8 earthquake hit the region (http://iside.rm.ingv.it/, with the epicenter close to the village of Mirandola (Figure 1. Three other strong aftershocks occurred afterwards, of Ml 5.3 (May 29, at 10:55, Ml 5.2 (May 29, at 11:00 and Ml 5.1 (June 3, at 19:20. For a detailed description of the seismic sequence, see Moretti et al. [2012], Scognamiglio et al. [2012], and Massa et al. [2012], in this issue. The Emilia seismic sequence resulted in 25 casualties, several of whom were among the workers in the many factories that collapsed during working hours, and there was extensive damage to monuments, public buildings, industrial sites, and private homes. […

  18. Functional groups of macro-benthos of selected sites of upstream of Hron River and Hnilec River

    International Nuclear Information System (INIS)

    Rufusova, A.

    2011-01-01

    The author used six functional groups of macro-benthos based on 'species traits', which are indicated with the Greek letters α to ζ. In the work authors applied this method to the macroinvertebrate communities of selected sites of upstream of the Hron River and the Hnilec River. The method appropriately captured increasing gradient of anthropogenic changes in the direction of the river continuum. Although the method was used for Slovak rivers for the first time, it seems to be promising for use in the future. (author)

  19. Manipulation of the membrane binding site of vitamin K-dependent proteins: Enhanced biological function of human factor VII

    OpenAIRE

    Shah, Amit M.; Kisiel, Walter; Foster, Donald C.; Nelsestuen, Gary L.

    1998-01-01

    Recent studies suggested that modification of the membrane contact site of vitamin K-dependent proteins may enhance the membrane affinity and function of members of this protein family. The properties of a factor VII mutant, factor VII-Q10E32, relative to wild-type factor VII (VII, containing P10K32), have been compared. Membrane affinity of VII-Q10E32 was about 20-fold higher than that of wild-type factor VII. The rate of autoactivation VII-Q10E32 with soluble tissue factor was 100-fold fast...

  20. Vegetation response to invasive Tamarix control in southwestern U.S. rivers: a collaborative study including 416 sites.

    Science.gov (United States)

    González, Eduardo; Sher, Anna A; Anderson, Robert M; Bay, Robin F; Bean, Daniel W; Bissonnete, Gabriel J; Bourgeois, Bérenger; Cooper, David J; Dohrenwend, Kara; Eichhorst, Kim D; El Waer, Hisham; Kennard, Deborah K; Harms-Weissinger, Rebecca; Henry, Annie L; Makarick, Lori J; Ostoja, Steven M; Reynolds, Lindsay V; Robinson, W Wright; Shafroth, Patrick B

    2017-09-01

    Most studies assessing vegetation response following control of invasive Tamarix trees along southwestern U.S. rivers have been small in scale (e.g., river reach), or at a regional scale but with poor spatial-temporal replication, and most have not included testing the effects of a now widely used biological control. We monitored plant composition following Tamarix control along hydrologic, soil, and climatic gradients in 244 treated and 172 reference sites across six U.S. states. This represents the largest comprehensive assessment to date on the vegetation response to the four most common Tamarix control treatments. Biocontrol by a defoliating beetle (treatment 1) reduced the abundance of Tamarix less than active removal by mechanically using hand and chain-saws (2), heavy machinery (3) or burning (4). Tamarix abundance also decreased with lower temperatures, higher precipitation, and follow-up treatments for Tamarix resprouting. Native cover generally increased over time in active Tamarix removal sites, however, the increases observed were small and was not consistently increased by active revegetation. Overall, native cover was correlated to permanent stream flow, lower grazing pressure, lower soil salinity and temperatures, and higher precipitation. Species diversity also increased where Tamarix was removed. However, Tamarix treatments, especially those generating the highest disturbance (burning and heavy machinery), also often promoted secondary invasions of exotic forbs. The abundance of hydrophytic species was much lower in treated than in reference sites, suggesting that management of southwestern U.S. rivers has focused too much on weed control, overlooking restoration of fluvial processes that provide habitat for hydrophytic and floodplain vegetation. These results can help inform future management of Tamarix-infested rivers to restore hydrogeomorphic processes, increase native biodiversity and reduce abundance of noxious species. © 2017 by the

  1. Secretagogue stimulation of neurosecretory cells elicits filopodial extensions uncovering new functional release sites.

    Science.gov (United States)

    Papadopulos, Andreas; Martin, Sally; Tomatis, Vanesa M; Gormal, Rachel S; Meunier, Frederic A

    2013-12-04

    Regulated exocytosis in neurosecretory cells relies on the timely fusion of secretory granules (SGs) with the plasma membrane. Secretagogue stimulation leads to an enlargement of the cell footprint (surface area in contact with the coverslip), an effect previously attributed to exocytic fusion of SGs with the plasma membrane. Using total internal reflection fluorescence microscopy, we reveal the formation of filopodia-like structures in bovine chromaffin and PC12 cells driving the footprint expansion, suggesting the involvement of cortical actin network remodeling in this process. Using exocytosis-incompetent PC12 cells, we demonstrate that footprint enlargement is largely independent of SG fusion, suggesting that vesicular exocytic fusion plays a relatively minor role in filopodial expansion. The footprint periphery, including filopodia, undergoes extensive F-actin remodeling, an effect abolished by the actomyosin inhibitors cytochalasin D and blebbistatin. Imaging of both Lifeact-GFP and the SG marker protein neuropeptide Y-mCherry reveals that SGs actively translocate along newly forming actin tracks before undergoing fusion. Together, these data demonstrate that neurosecretory cells regulate the number of SGs undergoing exocytosis during sustained stimulation by controlling vesicular mobilization and translocation to the plasma membrane through actin remodeling. Such remodeling facilitates the de novo formation of fusion sites.

  2. Compositional differences in simulated root exudates elicit a limited functional and compositional response in soil microbial communities

    Directory of Open Access Journals (Sweden)

    Michael S Strickland

    2015-08-01

    Full Text Available Inputs of low molecular weight carbon (LMW-C to soil −primarily via root exudates− are expected to be a major driver of microbial activity and source of stable soil organic carbon. It is expected that variation in the type and composition of LMW-C entering soil will influence microbial community composition and function. If this is the case then short-term changes in LMW-C inputs may alter processes regulated by these communities. To determine if change in the composition of LMW-C inputs influences microbial community function and composition, we conducted a 90 day microcosm experiment whereby soils sourced from three different land covers (meadows, deciduous forests, and white pine stands were amended, at low concentrations, with one of eight simulated root exudate treatments. Treatments included no addition of LMW-C, and the full factorial combination of glucose, glycine, and oxalic acid. After 90 days, we conducted a functional response assay and determined microbial composition via phospholipid fatty acid analysis. Whereas we noted a statistically significant effect of exudate treatments, this only accounted for ~3% of the variation observed in function. In comparison, land cover and site explained ~46 and ~41% of the variation, respectively. This suggests that exudate composition has little influence on function

  3. SIZE AND FIELD OF ACTIVITY INFLUENCE ON WEB SITES FUNCTIONALITY FOR ROMANIAN COMPANIES

    Directory of Open Access Journals (Sweden)

    Tarca Ioan

    2008-05-01

    Full Text Available The internet became an important part of the company’s informational system. In order to take advantage on the Internet’s interactive nature, a lot of companies have created their own websites. Companies use the website for numerous applications: to promote themselves, online shopping, and communication with targeted clients. This study reveals the fact that the company’s size and field of activity have influence on website’s functionality and interactivity. Small companies use the website to successfully compete corporations which do not have yet necessary stimulants to fully exploit the internet capacities.

  4. Concordance and discordance between taxonomic and functional homogenization: responses of soil mite assemblages to forest conversion.

    Science.gov (United States)

    Mori, Akira S; Ota, Aino T; Fujii, Saori; Seino, Tatsuyuki; Kabeya, Daisuke; Okamoto, Toru; Ito, Masamichi T; Kaneko, Nobuhiro; Hasegawa, Motohiro

    2015-10-01

    The compositional characteristics of ecological assemblages are often simplified; this process is termed "biotic homogenization." This process of biological reorganization occurs not only taxonomically but also functionally. Testing both aspects of homogenization is essential if ecosystem functioning supported by a diverse mosaic of functional traits in the landscape is concerned. Here, we aimed to infer the underlying processes of taxonomic/functional homogenization at the local scale, which is a scale that is meaningful for this research question. We recorded species of litter-dwelling oribatid mites along a gradient of forest conversion from a natural forest to a monoculture larch plantation in Japan (in total 11 stands), and collected data on the functional traits of the recorded species to quantify functional diversity. We calculated the taxonomic and functional β-diversity, an index of biotic homogenization. We found that both the taxonomic and functional β-diversity decreased with larch dominance (stand homogenization). After further deconstructing β-diversity into the components of turnover and nestedness, which reflect different processes of community organization, a significant decrease in the response to larch dominance was observed only for the functional turnover. As a result, there was a steeper decline in the functional β-diversity than the taxonomic β-diversity. This discordance between the taxonomic and functional response suggests that species replacement occurs between species that are functionally redundant under environmental homogenization, ultimately leading to the stronger homogenization of functional diversity. The insights gained from community organization of oribatid mites suggest that the functional characteristics of local assemblages, which support the functionality of ecosystems, are of more concern in human-dominated forest landscapes.

  5. Transcriptional activation of rat creatine kinase B by 17beta-estradiol in MCF-7 cells involves an estrogen responsive element and GC-rich sites.

    Science.gov (United States)

    Wang, F; Samudio, I; Safe, S

    2001-01-01

    The rat creatine kinase B (CKB) gene is induced by estrogen in the uterus, and constructs containing rat CKB gene promoter inserts are highly estrogen-responsive in cell culture. Analysis of the upstream -568 to -523 region of the promoter in HeLa cells has identified an imperfect palindromic estrogen response element (ERE) that is required for hormone inducibility. Analysis of the CKB gene promoter in MCF-7 breast cancer cells confirmed that pCKB7 (containing the -568 to -523 promoter insert) was estrogen-responsive in transient transfection studies. However, mutation and deletion analysis of this region of the promoter showed that two GC-rich sites and the concensus ERE were functional cis-elements that bound estrogen receptor alpha (ERalpha)/Sp1 and ERalpha proteins, respectively. The role of these elements was confirmed in gel mobility shift and chromatin immunoprecipitation assays and transfection studies in MDA-MB-231 and Schneider Drosophila SL-2 cells. These results show that transcriptional activation of CKB by estrogen is dependent, in part, on ERalpha/Sp1 action which is cell context-dependent. Copyright 2001 Wiley-Liss, Inc.

  6. A mathematical function for the description of nutrient-response curve.

    Directory of Open Access Journals (Sweden)

    Hamed Ahmadi

    Full Text Available Several mathematical equations have been proposed to modeling nutrient-response curve for animal and human justified on the goodness of fit and/or on the biological mechanism. In this paper, a functional form of a generalized quantitative model based on Rayleigh distribution principle for description of nutrient-response phenomena is derived. The three parameters governing the curve a has biological interpretation, b may be used to calculate reliable estimates of nutrient response relationships, and c provide the basis for deriving relationships between nutrient and physiological responses. The new function was successfully applied to fit the nutritional data obtained from 6 experiments including a wide range of nutrients and responses. An evaluation and comparison were also done based simulated data sets to check the suitability of new model and four-parameter logistic model for describing nutrient responses. This study indicates the usefulness and wide applicability of the new introduced, simple and flexible model when applied as a quantitative approach to characterizing nutrient-response curve. This new mathematical way to describe nutritional-response data, with some useful biological interpretations, has potential to be used as an alternative approach in modeling nutritional responses curve to estimate nutrient efficiency and requirements.

  7. Thermo-responsive cell culture carrier: Effects on macrophage functionality and detachment efficiency.

    Science.gov (United States)

    Rennert, Knut; Nitschke, Mirko; Wallert, Maria; Keune, Natalie; Raasch, Martin; Lorkowski, Stefan; Mosig, Alexander S

    2017-01-01

    Harvesting cultivated macrophages for tissue engineering purposes by enzymatic digestion of cell adhesion molecules can potentially result in unintended activation, altered function, or behavior of these cells. Thermo-responsive polymer is a promising tool that allows for gentle macrophage detachment without artificial activation prior to subculture within engineered tissue constructs. We therefore characterized different species of thermo-responsive polymers for their suitability as cell substrate and to mediate gentle macrophage detachment by temperature shift. Primary human monocyte- and THP-1-derived macrophages were cultured on thermo-responsive polymers and characterized for phagocytosis and cytokine secretion in response to lipopolysaccharide stimulation. We found that both cell types differentially respond in dependence of culture and stimulation on thermo-responsive polymers. In contrast to THP-1 macrophages, primary monocyte-derived macrophages showed no signs of impaired viability, artificial activation, or altered functionality due to culture on thermo-responsive polymers compared to conventional cell culture. Our study demonstrates that along with commercially available UpCell carriers, two other thermo-responsive polymers based on poly(vinyl methyl ether) blends are attractive candidates for differentiation and gentle detachment of primary monocyte-derived macrophages. In summary, we observed similar functionality and viability of primary monocyte-derived macrophages cultured on thermo-responsive polymers compared to standard cell culture surfaces. While this first generation of custom-made thermo-responsive polymers does not yet outperform standard culture approaches, our results are very promising and provide the basis for exploiting the unique advantages offered by custom-made thermo-responsive polymers to further improve macrophage culture and recovery in the future, including the covalent binding of signaling molecules and the reduction of

  8. Numerical and functional responses of intestinal helminths in three rajid skates: evidence for competition between parasites?

    Science.gov (United States)

    Randhawa, Haseeb S

    2012-11-01

    Host-parasite interactions generally involve communities of parasites. Within these communities, species will co-exist and/or interact with one another in a manner either benefiting the species involved or to the detriment of one or more of the species. At the level of helminth infracommunities, evidence for intra- and inter-specific competition includes numerical responses, i.e. those regulating helminth intensity of infection, and functional responses, i.e. where the presence of competitors modifies the realised niche of infrapopulations. The objectives of this study are to assess the numerical and functional responses of helminths in infracommunities from 3 rajid skates using general linear models. Despite a lack of numerical responses, functional responses to intra- and inter-specific interactions were observed. A positive correlation between the number of individuals in an infrapopulation and its niche breadth (functional response) was observed for the tapeworms Pseudanthobothrium spp. and Echeneibothrium spp., in all their respective hosts, and for the nematode Pseudanisakis sp. in the little skate. Evidence for inter-specific competition includes niche shifts in Pseudanthobothrium purtoni (ex little skate) and Pseudanisakis sp. (ex thorny skate) in the presence of Pseudanisakis sp. and the tapeworm Grillotia sp., respectively. These results are consistent with other studies in providing evidence for competition between helminths of skates.

  9. Frequent Use of Social Networking Sites Is Associated with Poor Psychological Functioning Among Children and Adolescents.

    Science.gov (United States)

    Sampasa-Kanyinga, Hugues; Lewis, Rosamund F

    2015-07-01

    Social networking sites (SNSs) have gained substantial popularity among youth in recent years. However, the relationship between the use of these Web-based platforms and mental health problems in children and adolescents is unclear. This study investigated the association between time spent on SNSs and unmet need for mental health support, poor self-rated mental health, and reports of psychological distress and suicidal ideation in a representative sample of middle and high school children in Ottawa, Canada. Data for this study were based on 753 students (55% female; Mage=14.1 years) in grades 7-12 derived from the 2013 Ontario Student Drug Use and Health Survey. Multinomial logistic regression was used to examine the associations between mental health variables and time spent using SNSs. Overall, 25.2% of students reported using SNSs for more than 2 hours every day, 54.3% reported using SNSs for 2 hours or less every day, and 20.5% reported infrequent or no use of SNSs. Students who reported unmet need for mental health support were more likely to report using SNSs for more than 2 hours every day than those with no identified unmet need for mental health support. Daily SNS use of more than 2 hours was also independently associated with poor self-rating of mental health and experiences of high levels of psychological distress and suicidal ideation. The findings suggest that students with poor mental health may be greater users of SNSs. These results indicate an opportunity to enhance the presence of health service providers on SNSs in order to provide support to youth.

  10. Functional analysis of truncated and site-directed mutagenesis dextransucrases to produce different type dextrans.

    Science.gov (United States)

    Wang, Chao; Zhang, Hong-Bin; Li, Meng-Qi; Hu, Xue-Qin; Li, Yao

    2017-07-01

    Dextrans with distinct molecular size and structure are increasingly being used in the food and pharmaceutical industries. Dextran is produced by d