Identification of suitable sites for mountain ginseng cultivation using GIS and geo-temperature.

PubMed

Kang, Hag Mo; Choi, Soo Im; Kim, Hyun

2016-01-01

This study was conducted to explore an accurate site identification technique using a geographic information system (GIS) and geo-temperature (gT) for locating suitable sites for growing cultivated mountain ginseng (CMG; Panax ginseng), which is highly sensitive to the environmental conditions in which it grows. The study site was Jinan-gun, South Korea. The spatial resolution for geographic data was set at 10 m × 10 m, and the temperatures for various climatic factors influencing CMG growth were calculated by averaging the 3-year temperatures obtained from the automatic weather stations of the Korea Meteorological Administration. Identification of suitable sites for CMG cultivation was undertaken using both a conventional method and a new method, in which the gT was added as one of the most important factors for crop cultivation. The results yielded by the 2 methods were then compared. When the gT was added as an additional factor (new method), the proportion of suitable sites identified decreased by 0.4 % compared with the conventional method. However, the proportion matching real CMG cultivation sites increased by 3.5 %. Moreover, only 68.2 % corresponded with suitable sites identified using the conventional factors; i.e., 31.8 % were newly detected suitable sites. The accuracy of GIS-based identification of suitable CMG cultivation sites improved by applying the temperature factor (i.e., gT) in addition to the conventionally used factors.

Methods of linking mothers and infants using health plan data for studies of pregnancy outcomes.

PubMed

Johnson, Karin E; Beaton, Sarah J; Andrade, Susan E; Cheetham, T Craig; Scott, Pamela E; Hammad, Tarek A; Dashevsky, Inna; Cooper, William O; Davis, Robert L; Pawloski, Pamala A; Raebel, Marsha A; Smith, David H; Toh, Sengwee; Li, De-Kun; Haffenreffer, Katherine; Dublin, Sascha

2013-07-01

Research on medication safety in pregnancy often utilizes health plan and birth certificate records. This study discusses methods used to link mothers with infants, a crucial step in such research. We describe how eight sites participating in the Medication Exposure in Pregnancy Risk Evaluation Program created linkages between deliveries, infants and birth certificates for the 2001-2007 birth cohorts. We describe linkage rates across sites, and for two sites, we compare the characteristics of populations linked using different methods. Of 299,260 deliveries, 256,563 (86%; range by site, 74-99%) could be linked to infants using a deterministic algorithm. At two sites, using birth certificate data to augment mother-infant linkage increased the representation of mothers who were Hispanic or non-White, younger, Medicaid recipients, or had low educational level. A total of 236,460 (92%; range by site, 82-100%) deliveries could be linked to a birth certificate. Tailored approaches enabled linking most deliveries to infants and to birth certificates, even when data systems differed. The methods used may affect the composition of the population identified. Linkages established with such methods can support sound pharmacoepidemiology studies of maternal drug exposure outside the context of a formal registry. Copyright © 2013 John Wiley & Sons, Ltd.

Comparison of on-site field measured inorganic arsenic in rice with laboratory measurements using a field deployable method: Method validation.

PubMed

Mlangeni, Angstone Thembachako; Vecchi, Valeria; Norton, Gareth J; Raab, Andrea; Krupp, Eva M; Feldmann, Joerg

2018-10-15

A commercial arsenic field kit designed to measure inorganic arsenic (iAs) in water was modified into a field deployable method (FDM) to measure iAs in rice. While the method has been validated to give precise and accurate results in the laboratory, its on-site field performance has not been evaluated. This study was designed to test the method on-site in Malawi in order to evaluate its accuracy and precision in determination of iAs on-site by comparing with a validated reference method and giving original data on inorganic arsenic in Malawian rice and rice-based products. The method was validated by using the established laboratory-based HPLC-ICPMS. Statistical tests indicated there were no significant differences between on-site and laboratory iAs measurements determined using the FDM (p = 0.263, ά = 0.05) and between on-site measurements and measurements determined using HPLC-ICP-MS (p = 0.299, ά = 0.05). This method allows quick (within 1 h) and efficient screening of rice containing iAs concentrations on-site. Copyright © 2018 Elsevier Ltd. All rights reserved.

Computer Program for Point Location And Calculation of ERror (PLACER)

USGS Publications Warehouse

Granato, Gregory E.

1999-01-01

A program designed for point location and calculation of error (PLACER) was developed as part of the Quality Assurance Program of the Federal Highway Administration/U.S. Geological Survey (USGS) National Data and Methodology Synthesis (NDAMS) review process. The program provides a standard method to derive study-site locations from site maps in highwayrunoff, urban-runoff, and other research reports. This report provides a guide for using PLACER, documents methods used to estimate study-site locations, documents the NDAMS Study-Site Locator Form, and documents the FORTRAN code used to implement the method. PLACER is a simple program that calculates the latitude and longitude coordinates of one or more study sites plotted on a published map and estimates the uncertainty of these calculated coordinates. PLACER calculates the latitude and longitude of each study site by interpolating between the coordinates of known features and the locations of study sites using any consistent, linear, user-defined coordinate system. This program will read data entered from the computer keyboard and(or) from a formatted text file, and will write the results to the computer screen and to a text file. PLACER is readily transferable to different computers and operating systems with few (if any) modifications because it is written in standard FORTRAN. PLACER can be used to calculate study site locations in latitude and longitude, using known map coordinates or features that are identifiable in geographic information data bases such as USGS Geographic Names Information System, which is available on the World Wide Web.

Selection of Atmospheric Environmental Monitoring Sites based on Geographic Parameters Extraction of GIS and Fuzzy Matter-Element Analysis.

PubMed

Wu, Jianfa; Peng, Dahao; Ma, Jianhao; Zhao, Li; Sun, Ce; Ling, Huanzhang

2015-01-01

To effectively monitor the atmospheric quality of small-scale areas, it is necessary to optimize the locations of the monitoring sites. This study combined geographic parameters extraction by GIS with fuzzy matter-element analysis. Geographic coordinates were extracted by GIS and transformed into rectangular coordinates. These coordinates were input into the Gaussian plume model to calculate the pollutant concentration at each site. Fuzzy matter-element analysis, which is used to solve incompatible problems, was used to select the locations of sites. The matter element matrices were established according to the concentration parameters. The comprehensive correlation functions KA (xj) and KB (xj), which reflect the degree of correlation among monitoring indices, were solved for each site, and a scatter diagram of the sites was drawn to determine the final positions of the sites based on the functions. The sites could be classified and ultimately selected by the scatter diagram. An actual case was tested, and the results showed that 5 positions can be used for monitoring, and the locations conformed to the technical standard. In the results of this paper, the hierarchical clustering method was used to improve the methods. The sites were classified into 5 types, and 7 locations were selected. Five of the 7 locations were completely identical to the sites determined by fuzzy matter-element analysis. The selections according to these two methods are similar, and these methods can be used in combination. In contrast to traditional methods, this study monitors the isolated point pollutant source within a small range, which can reduce the cost of monitoring.

The Path to Graduation: A Model Interactive Web Site Design Supporting Doctoral Students

ERIC Educational Resources Information Center

Simmons-Johnson, Nicole

2012-01-01

Objective. This 2-phase mixed method study assessed 2nd-year doctoral students' and dissertation students' perceptions of the current Graduate School of Education dissertation support Web site, with implications for designing a model dissertation support Web site. Methods. Phase 1 collected quantitative and qualitative data through an…

Evaluation of pier-scour measurement methods and pier-scour predictions with observed scour measurements at selected bridge sites in New Hampshire, 1995-98

DOT National Transportation Integrated Search

2000-11-01

In a previous study, 44 of 48 bridge sites examined in New Hampshire were categorized as scour critical. This report summarizes research conducted to evaluate pier-scour measurement methods and predictions at many of these sites. This evaluation incl...

Site Selection in Experiments: An Assessment of Site Recruitment and Generalizability in Two Scale-Up Studies

ERIC Educational Resources Information Center

Tipton, Elizabeth; Fellers, Lauren; Caverly, Sarah; Vaden-Kiernan, Michael; Borman, Geoffrey; Sullivan, Kate; Ruiz de Castilla, Veronica

2016-01-01

Recently, statisticians have begun developing methods to improve the generalizability of results from large-scale experiments in education. This work has included the development of methods for improved site selection when random sampling is infeasible, including the use of stratification and targeted recruitment strategies. This article provides…

Evaluation of local site effect from microtremor measurements in Babol City, Iran

NASA Astrophysics Data System (ADS)

Rezaei, Sadegh; Choobbasti, Asskar Janalizadeh

2018-03-01

Every year, numerous casualties and a large deal of financial losses are incurred due to earthquake events. The losses incurred by an earthquake vary depending on local site effect. Therefore, in order to conquer drastic effects of an earthquake, one should evaluate urban districts in terms of the local site effect. One of the methods for evaluating the local site effect is microtremor measurement and analysis. Aiming at evaluation of local site effect across the city of Babol, the study area was gridded and microtremor measurements were performed with an appropriate distribution. The acquired data was analyzed through the horizontal-to-vertical noise ratio (HVNR) method, and fundamental frequency and associated amplitude of the H/V peak were obtained. The results indicate that fundamental frequency of the study area is generally lower than 1.25 Hz, which is acceptably in agreement with the findings of previous studies. Also, in order to constrain and validate the seismostratigraphic model obtained with this method, the results were compared with geotechnical, geological, and seismic data. Comparing the results of different methods, it was observed that the presented geophysical method can successfully determine the values of fundamental frequency across the study area as well as local site effect. Using the data obtained from the analysis of microtremor, a microzonation map of fundamental frequency across the city of Babol was prepared. This map has numerous applications in designing high-rise building and urban development plans.

Simulation of electron-proton coupling with a Monte Carlo method: application to cytochrome c3 using continuum electrostatics.

PubMed Central

Baptista, A M; Martel, P J; Soares, C M

1999-01-01

A new method is presented for simulating the simultaneous binding equilibrium of electrons and protons on protein molecules, which makes it possible to study the full equilibrium thermodynamics of redox and protonation processes, including electron-proton coupling. The simulations using this method reflect directly the pH and electrostatic potential of the environment, thus providing a much closer and realistic connection with experimental parameters than do usual methods. By ignoring the full binding equilibrium, calculations usually overlook the twofold effect that binding fluctuations have on the behavior of redox proteins: first, they affect the energy of the system by creating partially occupied sites; second, they affect its entropy by introducing an additional empty/occupied site disorder (here named occupational entropy). The proposed method is applied to cytochrome c3 of Desulfovibrio vulgaris Hildenborough to study its redox properties and electron-proton coupling (redox-Bohr effect), using a continuum electrostatic method based on the linear Poisson-Boltzmann equation. Unlike previous studies using other methods, the full reduction order of the four hemes at physiological pH is successfully predicted. The sites more strongly involved in the redox-Bohr effect are identified by analysis of their titration curves/surfaces and the shifts of their midpoint redox potentials and pKa values. Site-site couplings are analyzed using statistical correlations, a method much more realistic than the usual analysis based on direct interactions. The site found to be more strongly involved in the redox-Bohr effect is propionate D of heme I, in agreement with previous studies; other likely candidates are His67, the N-terminus, and propionate D of heme IV. Even though the present study is limited to equilibrium conditions, the possible role of binding fluctuations in the concerted transfer of protons and electrons under nonequilibrium conditions is also discussed. The occupational entropy contributions to midpoint redox potentials and pKa values are computed and shown to be significant. PMID:10354425

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

Rowe, M.D.; Pierce, B.L.

This report presents results of tests of different final site selection methods used for siting large-scale facilities such as nuclear power plants. Test data are adapted from a nuclear power plant siting study conducted on Long Island, New York. The purpose of the tests is to determine whether or not different final site selection methods produce different results, and to obtain some understanding of the nature of any differences found. Decision rules and weighting methods are included. Decision rules tested are Weighting Summation, Power Law, Decision Analysis, Goal Programming, and Goal Attainment; weighting methods tested are Categorization, Ranking, Rating Ratiomore » Estimation, Metfessel Allocation, Indifferent Tradeoff, Decision Analysis lottery, and Global Evaluation. Results show that different methods can, indeed, produce different results, but that the probability that they will do so is controlled by the structure of differences among the sites being evaluated. Differences in weights and suitability scores attributable to methods have reduced significance if the alternatives include one or two sites that are superior to all others in many attributes. The more tradeoffs there are among good and bad levels of different attributes at different sites, the more important are the specifics of methods to the final decision. 5 refs., 14 figs., 19 tabs.« less

X-ray and synchrotron methods in studies of cultural heritage sites

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

Koval’chuk, M. V.; Yatsishina, E. B.; Blagov, A. E.

2016-09-15

X-ray and synchrotron methods that are most widely used in studies of cultural heritage objects (including archaeological sites)—X-ray diffraction analysis, X-ray spectroscopy, and visualization techniques— have been considered. The reported examples show high efficiency and informativeness of natural science studies when solving most diverse problems of archaeology, history, the study of art, museology, etc.

A Hierarchical Modeling Approach to Data Analysis and Study Design in a Multi-Site Experimental fMRI Study

ERIC Educational Resources Information Center

Zhou, Bo; Konstorum, Anna; Duong, Thao; Tieu, Kinh H.; Wells, William M.; Brown, Gregory G.; Stern, Hal S.; Shahbaba, Babak

2013-01-01

We propose a hierarchical Bayesian model for analyzing multi-site experimental fMRI studies. Our method takes the hierarchical structure of the data (subjects are nested within sites, and there are multiple observations per subject) into account and allows for modeling between-site variation. Using posterior predictive model checking and model…

mHealth Series: mHealth project in Zhao County, rural China – Description of objectives, field site and methods

PubMed Central

van Velthoven, Michelle Helena; Li, Ye; Wang, Wei; Du, Xiaozhen; Wu, Qiong; Chen, Li; Majeed, Azeem; Rudan, Igor; Zhang, Yanfeng; Car, Josip

2013-01-01

Background We set up a collaboration between researchers in China and the UK that aimed to explore the use of mHealth in China. This is the first paper in a series of papers on a large mHealth project part of this collaboration. This paper included the aims and objectives of the mHealth project, our field site, and the detailed methods of two studies. Field site The field site for this mHealth project was Zhao County, which lies 280 km south of Beijing in Hebei Province, China. Methods We described the methodology of two studies: (i) a mixed methods study exploring factors influencing sample size calculations for mHealth–based health surveys and (ii) a cross–over study determining validity of an mHealth text messaging data collection tool. The first study used mixed methods, both quantitative and qualitative, including: (i) two surveys with caregivers of young children, (ii) interviews with caregivers, village doctors and participants of the cross–over study, and (iii) researchers’ views. We combined data from caregivers, village doctors and researchers to provide an in–depth understanding of factors influencing sample size calculations for mHealth–based health surveys. The second study, a cross–over study, used a randomised cross–over study design to compare the traditional face–to–face survey method to the new text messaging survey method. We assessed data equivalence (intrarater agreement), the amount of information in responses, reasons for giving different responses, the response rate, characteristics of non–responders, and the error rate. Conclusions This paper described the objectives, field site and methods of a large mHealth project part of a collaboration between researchers in China and the UK. The mixed methods study evaluating factors that influence sample size calculations could help future studies with estimating reliable sample sizes. The cross–over study comparing face–to–face and text message survey data collection could help future studies with developing their mHealth tools. PMID:24363919

Standardization of Laboratory Methods for the PERCH Study

PubMed Central

Karron, Ruth A.; Morpeth, Susan C.; Bhat, Niranjan; Levine, Orin S.; Baggett, Henry C.; Brooks, W. Abdullah; Feikin, Daniel R.; Hammitt, Laura L.; Howie, Stephen R. C.; Knoll, Maria Deloria; Kotloff, Karen L.; Madhi, Shabir A.; Scott, J. Anthony G.; Thea, Donald M.; Adrian, Peter V.; Ahmed, Dilruba; Alam, Muntasir; Anderson, Trevor P.; Antonio, Martin; Baillie, Vicky L.; Dione, Michel; Endtz, Hubert P.; Gitahi, Caroline; Karani, Angela; Kwenda, Geoffrey; Maiga, Abdoul Aziz; McClellan, Jessica; Mitchell, Joanne L.; Morailane, Palesa; Mugo, Daisy; Mwaba, John; Mwansa, James; Mwarumba, Salim; Nyongesa, Sammy; Panchalingam, Sandra; Rahman, Mustafizur; Sawatwong, Pongpun; Tamboura, Boubou; Toure, Aliou; Whistler, Toni; O’Brien, Katherine L.; Murdoch, David R.

2017-01-01

Abstract The Pneumonia Etiology Research for Child Health study was conducted across 7 diverse research sites and relied on standardized clinical and laboratory methods for the accurate and meaningful interpretation of pneumonia etiology data. Blood, respiratory specimens, and urine were collected from children aged 1–59 months hospitalized with severe or very severe pneumonia and community controls of the same age without severe pneumonia and were tested with an extensive array of laboratory diagnostic tests. A standardized testing algorithm and standard operating procedures were applied across all study sites. Site laboratories received uniform training, equipment, and reagents for core testing methods. Standardization was further assured by routine teleconferences, in-person meetings, site monitoring visits, and internal and external quality assurance testing. Targeted confirmatory testing and testing by specialized assays were done at a central reference laboratory. PMID:28575358

Evaluation of Restoration Methods to Minimize Canada Thistle (Cirsium arvense) Infestation

USGS Publications Warehouse

Larson, Diane L.

2009-01-01

The National Wildlife Refuge System has an active habitat restoration program and annually seeds thousands of hectares with native plant species. The noxious weed, Canada thistle (Cirsium arvense), plagues these restorations. This study evaluates planting methodology and seed mixes with the goal of recommending optimal methods to reduce infestation of noxious weeds, especially Canada thistle, in new restorations. Three planting methods (dormant season broadcast, growing season [summer] broadcast, and growing season [summer] drill) were fully crossed with three levels of seed diversity (10, 20, and 34 species [plus a fourth level, 58 species, on the three sites in Iowa]) in a completely randomized design replicated on nine sites in Minnesota and Iowa. The propagule bank of Canada thistle was evaluated at each site. Planting occurred in winter 2004 and spring-summer 2005. Here I report on results through summer 2007. None of the planting methods or seed mix diversities consistently resulted in reduced abundance of Canada thistle. Soil texture had the strongest influence; sites with greater proportions of clay had greater frequency and cover of Canada thistle than did sandy sites. At the Minnesota study sites, the dormant broadcast planting method combined with the highest seed diversity resulted in both the greatest cover of planted species as well as the greatest richness of planted species. At the Iowa sites, planted species richness was slightly greater in the summer drill plots, but cover of planted species was greatest in the dormant broadcast plots. Richness of planted species at the Iowa sites was maximized in the high diversity plots, with the extra-high diversity seed mix resulting in significantly lower species richness. Individual species responded to planting methods idiosyncratically, which suggests that particular species could be favored by tailoring planting methods to that species.

Application of the BMWP-Costa Rica biotic index in aquatic biomonitoring: sensitivity to collection method and sampling intensity.

PubMed

Gutiérrez-Fonseca, Pablo E; Lorion, Christopher M

2014-04-01

The use of aquatic macroinvertebrates as bio-indicators in water quality studies has increased considerably over the last decade in Costa Rica, and standard biomonitoring methods have now been formulated at the national level. Nevertheless, questions remain about the effectiveness of different methods of sampling freshwater benthic assemblages, and how sampling intensity may influence biomonitoring results. In this study, we compared the results of qualitative sampling using commonly applied methods with a more intensive quantitative approach at 12 sites in small, lowland streams on the southern Caribbean slope of Costa Rica. Qualitative samples were collected following the official protocol using a strainer during a set time period and macroinvertebrates were field-picked. Quantitative sampling involved collecting ten replicate Surber samples and picking out macroinvertebrates in the laboratory with a stereomicroscope. The strainer sampling method consistently yielded fewer individuals and families than quantitative samples. As a result, site scores calculated using the Biological Monitoring Working Party-Costa Rica (BMWP-CR) biotic index often differed greatly depending on the sampling method. Site water quality classifications using the BMWP-CR index differed between the two sampling methods for 11 of the 12 sites in 2005, and for 9 of the 12 sites in 2006. Sampling intensity clearly had a strong influence on BMWP-CR index scores, as well as perceived differences between reference and impacted sites. Achieving reliable and consistent biomonitoring results for lowland Costa Rican streams may demand intensive sampling and requires careful consideration of sampling methods.

Characterization studies and indicated remediation methods for plutonium contaminated soils at the Nevada Test Site

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

Murarik, T.M.; Wenstrand, T.K.; Rogers, L.A.

An initial soil characterization study was conducted to help identify possible remediation methods to remove plutonium from the Nevada Test Site and Tonapah Test Range surface soils. Results from soil samples collected across various isopleths at five sites indicate that the size-fraction distribution patterns of plutonium remain similar to findings from the Nevada Applied Ecology Group (NAEG) (1970's). The plutonium remains in the upper 10--15 cm of soils, as indicated in previous studies. Distribution of fine particles downwind'' of ground zero at each site is suggested. Whether this pattern was established immediately after each explosion or this resulted from post-shotmore » wind movement of deposited material is unclear. Several possible soil treatment scenarios are presented. Removal of plutonium from certain size fractions of the soils would alleviate the sites of much of the plutonium burden. However, the nature of association of plutonium with soil components will determine which remediation methods will most likely succeed.« less

Characterization studies and indicated remediation methods for plutonium contaminated soils at the Nevada Test Site

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

Murarik, T.M.; Wenstrand, T.K.; Rogers, L.A.

An initial soil characterization study was conducted to help identify possible remediation methods to remove plutonium from the Nevada Test Site and Tonapah Test Range surface soils. Results from soil samples collected across various isopleths at five sites indicate that the size-fraction distribution patterns of plutonium remain similar to findings from the Nevada Applied Ecology Group (NAEG) (1970`s). The plutonium remains in the upper 10--15 cm of soils, as indicated in previous studies. Distribution of fine particles ``downwind`` of ground zero at each site is suggested. Whether this pattern was established immediately after each explosion or this resulted from post-shotmore » wind movement of deposited material is unclear. Several possible soil treatment scenarios are presented. Removal of plutonium from certain size fractions of the soils would alleviate the sites of much of the plutonium burden. However, the nature of association of plutonium with soil components will determine which remediation methods will most likely succeed.« less

Site preference of alloying elements in DO22-Ni3V phase: Phase-field and first-principles study

NASA Astrophysics Data System (ADS)

Zhang, Ding-Ni; Shangguan, Qian-Qian; Liu, Fu; Zhang, Ming-Yi

2015-07-01

Site preference of alloying elements in DO22-Ni3V phase was investigated using phase-field and first-principles method. The concentrations of alloying elements on sublattices of DO22-Ni3V phase were quantitatively studied using phase-field model based on microscopic diffusion equations. The phase-field computation results demonstrate that the concentration differences of alloying elements on the NiI and NiII site are attributed to the coordination environment difference. Host atoms Ni and substitutional ternary additions Al prefer to occupy NiI site. Antisite atoms V show site preference on the NiII site. Further reason of site preference of alloying elements on the two different Ni sites were studied using first-principles method to calculate the electronic structure of DO22-Ni3V phase. Calculation of density of states, orbitals population and charge population of the optimized Ni3V structure found that the electronic structures of NiI and NiII sites are different. Electronic structure difference, which is caused by coordination environment difference, is the essential reason for site selectivity behaviors of alloying elements on NiI and NiII sites.

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

McLaughlin, E.; Gupta, S.

This project mainly involves a molecular dynamics and Monte Carlo study of the effect of molecular shape on thermophysical properties of bulk fluids with an emphasis on the aromatic hydrocarbon liquids. In this regard we have studied the modeling, simulation methodologies, and predictive and correlating methods for thermodynamic properties of fluids of nonspherical molecules. In connection with modeling we have studied the use of anisotropic site-site potentials, through a modification of the Gay-Berne Gaussian overlap potential, to successfully model the aromatic rings after adding the necessary electrostatic moments. We have also shown these interaction sites should be located at themore » geometric centers of the chemical groups. In connection with predictive methods, we have shown two perturbation type theories to work well for fluids modeled using one-center anisotropic potentials and the possibility exists for extending these to anisotropic site-site models. In connection with correlation methods, we have studied, through simulations, the effect of molecular shape on the attraction term in the generalized van der Waals equation of state for fluids of nonspherical molecules and proposed a possible form which is to be studied further. We have successfully studied the vector and parallel processing aspects of molecular simulations for fluids of nonspherical molecules.« less

The holy grail of soil metal contamination site assessment: reducing risk and increasing confidence of decision making using infield portable X-ray Fluorescence (pXRF) technology

NASA Astrophysics Data System (ADS)

Rouillon, M.; Taylor, M. P.; Dong, C.

2016-12-01

This research assesses the advantages of integrating field portable X-ray Fluorescence (pXRF) technology for reducing the risk and increase confidence of decision making for metal-contaminated site assessments. Metal-contaminated sites are often highly heterogeneous and require a high sampling density to accurately characterize the distribution and concentration of contaminants. The current regulatory assessment approaches rely on a small number of samples processed using standard wet-chemistry methods. In New South Wales (NSW), Australia, the current notification trigger for characterizing metal-contaminated sites require the upper 95% confidence interval of the site mean to equal or exceed the relevant guidelines. The method's low `minimum' sampling requirements can misclassify sites due to the heterogeneous nature of soil contamination, leading to inaccurate decision making. To address this issue, we propose integrating infield pXRF analysis with the established sampling method to overcome sampling limitations. This approach increases the minimum sampling resolution and reduces the 95% CI of the site mean. Infield pXRF analysis at contamination hotspots enhances sample resolution efficiently and without the need to return to the site. In this study, the current and proposed pXRF site assessment methods are compared at five heterogeneous metal-contaminated sites by analysing the spatial distribution of contaminants, 95% confidence intervals of site means, and the sampling and analysis uncertainty associated with each method. Finally, an analysis of costs associated with both the current and proposed methods is presented to demonstrate the advantages of incorporating pXRF into metal-contaminated site assessments. The data shows that pXRF integrated site assessments allows for faster, cost-efficient, characterisation of metal-contaminated sites with greater confidence for decision making.

Site Classification using Multichannel Channel Analysis of Surface Wave (MASW) method on Soft and Hard Ground

NASA Astrophysics Data System (ADS)

Ashraf, M. A. M.; Kumar, N. S.; Yusoh, R.; Hazreek, Z. A. M.; Aziman, M.

2018-04-01

Site classification utilizing average shear wave velocity (Vs(30) up to 30 meters depth is a typical parameter. Numerous geophysical methods have been proposed for estimation of shear wave velocity by utilizing assortment of testing configuration, processing method, and inversion algorithm. Multichannel Analysis of Surface Wave (MASW) method is been rehearsed by numerous specialist and professional to geotechnical engineering for local site characterization and classification. This study aims to determine the site classification on soft and hard ground using MASW method. The subsurface classification was made utilizing National Earthquake Hazards Reduction Program (NERHP) and international Building Code (IBC) classification. Two sites are chosen to acquire the shear wave velocity which is in the state of Pulau Pinang for soft soil and Perlis for hard rock. Results recommend that MASW technique can be utilized to spatially calculate the distribution of shear wave velocity (Vs(30)) in soil and rock to characterize areas.

Multiscale site-response mapping: A case study of Parkfield, California

USGS Publications Warehouse

Thompson, E.M.; Baise, L.G.; Kayen, R.E.; Morgan, E.C.; Kaklamanos, J.

2011-01-01

The scale of previously proposed methods for mapping site-response ranges from global coverage down to individual urban regions. Typically, spatial coverage and accuracy are inversely related.We use the densely spaced strong-motion stations in Parkfield, California, to estimate the accuracy of different site-response mapping methods and demonstrate a method for integrating multiple site-response estimates from the site to the global scale. This method is simply a weighted mean of a suite of different estimates, where the weights are the inverse of the variance of the individual estimates. Thus, the dominant site-response model varies in space as a function of the accuracy of the different models. For mapping applications, site-response models should be judged in terms of both spatial coverage and the degree of correlation with observed amplifications. Performance varies with period, but in general the Parkfield data show that: (1) where a velocity profile is available, the square-rootof- impedance (SRI) method outperforms the measured VS30 (30 m divided by the S-wave travel time to 30 m depth) and (2) where velocity profiles are unavailable, the topographic slope method outperforms surficial geology for short periods, but geology outperforms slope at longer periods. We develop new equations to estimate site response from topographic slope, derived from the Next Generation Attenuation (NGA) database.

Updated techniques for estimating monthly streamflow-duration characteristics at ungaged and partial-record sites in central Nevada

USGS Publications Warehouse

Hess, Glen W.

2002-01-01

Techniques for estimating monthly streamflow-duration characteristics at ungaged and partial-record sites in central Nevada have been updated. These techniques were developed using streamflow records at six continuous-record sites, basin physical and climatic characteristics, and concurrent streamflow measurements at four partial-record sites. Two methods, the basin-characteristic method and the concurrent-measurement method, were developed to provide estimating techniques for selected streamflow characteristics at ungaged and partial-record sites in central Nevada. In the first method, logarithmic-regression analyses were used to relate monthly mean streamflows (from all months and by month) from continuous-record gaging sites of various percent exceedence levels or monthly mean streamflows (by month) to selected basin physical and climatic variables at ungaged sites. Analyses indicate that the total drainage area and percent of drainage area at altitudes greater than 10,000 feet are the most significant variables. For the equations developed from all months of monthly mean streamflow, the coefficient of determination averaged 0.84 and the standard error of estimate of the relations for the ungaged sites averaged 72 percent. For the equations derived from monthly means by month, the coefficient of determination averaged 0.72 and the standard error of estimate of the relations averaged 78 percent. If standard errors are compared, the relations developed in this study appear generally to be less accurate than those developed in a previous study. However, the new relations are based on additional data and the slight increase in error may be due to the wider range of streamflow for a longer period of record, 1995-2000. In the second method, streamflow measurements at partial-record sites were correlated with concurrent streamflows at nearby gaged sites by the use of linear-regression techniques. Statistical measures of results using the second method typically indicated greater accuracy than for the first method. However, to make estimates for individual months, the concurrent-measurement method requires several years additional streamflow data at more partial-record sites. Thus, exceedence values for individual months are not yet available due to the low number of concurrent-streamflow-measurement data available. Reliability, limitations, and applications of both estimating methods are described herein.

Using network screening methods to determine locations with specific safety issues: A design consistency case study.

PubMed

Butsick, Andrew J; Wood, Jonathan S; Jovanis, Paul P

2017-09-01

The Highway Safety Manual provides multiple methods that can be used to identify sites with promise (SWiPs) for safety improvement. However, most of these methods cannot be used to identify sites with specific problems. Furthermore, given that infrastructure funding is often specified for use related to specific problems/programs, a method for identifying SWiPs related to those programs would be very useful. This research establishes a method for Identifying SWiPs with specific issues. This is accomplished using two safety performance functions (SPFs). This method is applied to identifying SWiPs with geometric design consistency issues. Mixed effects negative binomial regression was used to develop two SPFs using 5 years of crash data and over 8754km of two-lane rural roadway. The first SPF contained typical roadway elements while the second contained additional geometric design consistency parameters. After empirical Bayes adjustments, sites with promise (SWiPs) were identified. The disparity between SWiPs identified by the two SPFs was evident; 40 unique sites were identified by each model out of the top 220 segments. By comparing sites across the two models, candidate road segments can be identified where a lack design consistency may be contributing to an increase in expected crashes. Practitioners can use this method to more effectively identify roadway segments suffering from reduced safety performance due to geometric design inconsistency, with detailed engineering studies of identified sites required to confirm the initial assessment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Prediction of allosteric sites on protein surfaces with an elastic-network-model-based thermodynamic method.

PubMed

Su, Ji Guo; Qi, Li Sheng; Li, Chun Hua; Zhu, Yan Ying; Du, Hui Jing; Hou, Yan Xue; Hao, Rui; Wang, Ji Hua

2014-08-01

Allostery is a rapid and efficient way in many biological processes to regulate protein functions, where binding of an effector at the allosteric site alters the activity and function at a distant active site. Allosteric regulation of protein biological functions provides a promising strategy for novel drug design. However, how to effectively identify the allosteric sites remains one of the major challenges for allosteric drug design. In the present work, a thermodynamic method based on the elastic network model was proposed to predict the allosteric sites on the protein surface. In our method, the thermodynamic coupling between the allosteric and active sites was considered, and then the allosteric sites were identified as those where the binding of an effector molecule induces a large change in the binding free energy of the protein with its ligand. Using the proposed method, two proteins, i.e., the 70 kD heat shock protein (Hsp70) and GluA2 alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptor, were studied and the allosteric sites on the protein surface were successfully identified. The predicted results are consistent with the available experimental data, which indicates that our method is a simple yet effective approach for the identification of allosteric sites on proteins.

Prediction of allosteric sites on protein surfaces with an elastic-network-model-based thermodynamic method

NASA Astrophysics Data System (ADS)

Su, Ji Guo; Qi, Li Sheng; Li, Chun Hua; Zhu, Yan Ying; Du, Hui Jing; Hou, Yan Xue; Hao, Rui; Wang, Ji Hua

2014-08-01

Allostery is a rapid and efficient way in many biological processes to regulate protein functions, where binding of an effector at the allosteric site alters the activity and function at a distant active site. Allosteric regulation of protein biological functions provides a promising strategy for novel drug design. However, how to effectively identify the allosteric sites remains one of the major challenges for allosteric drug design. In the present work, a thermodynamic method based on the elastic network model was proposed to predict the allosteric sites on the protein surface. In our method, the thermodynamic coupling between the allosteric and active sites was considered, and then the allosteric sites were identified as those where the binding of an effector molecule induces a large change in the binding free energy of the protein with its ligand. Using the proposed method, two proteins, i.e., the 70 kD heat shock protein (Hsp70) and GluA2 alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptor, were studied and the allosteric sites on the protein surface were successfully identified. The predicted results are consistent with the available experimental data, which indicates that our method is a simple yet effective approach for the identification of allosteric sites on proteins.

Empirical estimation of school siting parameter towards improving children's safety

NASA Astrophysics Data System (ADS)

Aziz, I. S.; Yusoff, Z. M.; Rasam, A. R. A.; Rahman, A. N. N. A.; Omar, D.

2014-02-01

Distance from school to home is a key determination in ensuring the safety of hildren. School siting parameters are made to make sure that a particular school is located in a safe environment. School siting parameters are made by Department of Town and Country Planning Malaysia (DTCP) and latest review was on June 2012. These school siting parameters are crucially important as they can affect the safety, school reputation, and not to mention the perception of the pupil and parents of the school. There have been many studies to review school siting parameters since these change in conjunction with this ever-changing world. In this study, the focus is the impact of school siting parameter on people with low income that live in the urban area, specifically in Johor Bahru, Malaysia. In achieving that, this study will use two methods which are on site and off site. The on site method is to give questionnaires to people and off site is to use Geographic Information System (GIS) and Statistical Product and Service Solutions (SPSS), to analyse the results obtained from the questionnaire. The output is a maps of suitable safe distance from school to house. The results of this study will be useful to people with low income as their children tend to walk to school rather than use transportation.

Pan-Canadian assessment of pandemic immunization data collection: study methodology

PubMed Central

2010-01-01

Background The collection of individual-level pandemic (H1N1) 2009 influenza immunization data was considered important to facilitate optimal vaccine delivery and accurate assessment of vaccine coverage. These data are also critical for research aimed at evaluating the new vaccine's safety and effectiveness. Systems used to collect immunization data include manual approaches in which data are collected and retained on paper, electronic systems in which data are captured on computer at the point of vaccination and hybrid systems which are comprised of both computerized and manual data collection components. This study's objective was to compare the efficiencies and perceptions of data collection methods employed during Canada's pandemic (H1N1) 2009 influenza vaccination campaign. Methods/Design A pan-Canadian observational study was conducted in a convenience sample of public health clinics and healthcare institutions during the H1N1 vaccination campaign in the fall of 2009. The study design consisted of three stages: Stage 1 involved passive observation of the site's layout, processes and client flow; Stage 2 entailed timing site staff on 20 clients through five core immunization tasks: i) client registration, ii) medical history collection, iii) medical history review, iv) vaccine administration record keeping and v) preparation of proof of vaccine administration for the client; in Stage 3, site staff completed a questionnaire regarding perceived usability of the site's data collection approach. Before the national study began, a pilot study was conducted in three seasonal influenza vaccination sites in Ontario, to both test that the proposed methodology was logistically feasible and to determine inter-rater reliability in the measurements of the research staff. Comparative analyses will be conducted across the range of data collection methods with respect to time required to collect immunization data, number and type of individual-level data elements collected, and clinic staff perceptions of the usability of the method employed at their site, using analysis of variance (ANOVA). Discussion Various data collection methods were employed at immunization sites across Canada during the pandemic (H1N1) 2009 influenza vaccination campaign. Our comparison of methods can facilitate planning an efficient, coordinated approach for collecting immunization data in future influenza seasons. PMID:20624270

Preliminary Evaluation of Method to Monitor Landfills Resilience against Methane Emission

NASA Astrophysics Data System (ADS)

Chusna, Noor Amalia; Maryono, Maryono

2018-02-01

Methane emission from landfill sites contribute to global warming and un-proper methane treatment can pose an explosion hazard. Stakeholder and government in the cities in Indonesia been found significant difficulties to monitor the resilience of landfill from methane emission. Moreover, the management of methane gas has always been a challenging issue for long waste management service and operations. Landfills are a significant contributor to anthropogenic methane emissions. This study conducted preliminary evaluation of method to manage methane gas emission by assessing LandGem and IPCC method. From the preliminary evaluation, this study found that the IPCC method is based on the availability of current and historical country specific data regarding the waste disposed of in landfills while from the LandGEM method is an automated tool for estimating emission rates for total landfill gas this method account total gas of methane, carbon dioxide and other. The method can be used either with specific data to estimate emissions in the site or default parameters if no site-specific data are available. Both of method could be utilize to monitor the methane emission from landfill site in cities of Central Java.

Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome

PubMed Central

Alquezar-Planas, David E.; Ishida, Yasuko; Courtiol, Alexandre; Timms, Peter; Johnson, Rebecca N.; Lenz, Dorina; Helgen, Kristofer M.; Roca, Alfred L.; Hartman, Stefanie

2016-01-01

Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small. PMID:27069793

Independent mapping methods reveal rotational activation near pulmonary veins where atrial fibrillation terminates before pulmonary vein isolation.

PubMed

Navara, Rachita; Leef, George; Shenasa, Fatemah; Kowalewski, Christopher; Rogers, Albert J; Meckler, Gabriela; Zaman, Junaid A B; Baykaner, Tina; Park, Shirley; Turakhia, Mintu P; Zei, Paul; Viswanathan, Mohan; Wang, Paul J; Narayan, Sanjiv M

2018-01-29

To investigate mechanisms by which atrial fibrillation (AF) may terminate during ablation near the pulmonary veins before the veins are isolated (PVI). It remains unstudied how AF may terminate during ablation before PVs are isolated, or how patients with PV reconnection can be arrhythmia-free. We studied patients in whom PV antral ablation terminated AF before PVI, using two independent mapping methods. We studied patients with AF referred for ablation, in whom biatrial contact basket electrograms were studied by both an activation/phase mapping method and by a second validated mapping method reported not to create false rotational activity. In 22 patients (age 60.1 ± 10.4, 36% persistent AF), ablation at sites near the PVs terminated AF (77% to sinus rhythm) prior to PVI. AF propagation revealed rotational (n  =  20) and focal (n  =  2) patterns at sites of termination by mapping method 1 and method 2. Both methods showed organized sites that were spatially concordant (P < 0.001) with similar stability (P < 0.001). Vagal slowing was not observed at sites of AF termination. PV antral regions where ablation terminated AF before PVI exhibited rotational and focal activation by two independent mapping methods. These data provide an alternative mechanism for the success of PVI, and may explain AF termination before PVI or lack of arrhythmias despite PV reconnection. Mapping such sites may enable targeted PV lesion sets and improved freedom from AF. © 2018 Wiley Periodicals, Inc.

Study on detecting leachate leakage of municipal solid waste landfill site.

PubMed

Liu, Jiangang; Cao, Xianxian; Ai, Yingbo; Zhou, Dongdong; Han, Qiting

2015-06-01

The article studies the detection of the leakage passage of leachate in a waste landfill dam. The leachate of waste landfill has its own features, like high conductivity, high chroma and an increasing temperature, also, the horizontal flow velocity of groundwater on the leakage site increases. This article proposes a comprehensive tracing method to identify the leakage site of an impermeable membrane by using these features. This method has been applied to determine two leakage sites of the Yahu municipal solid waste landfill site in Pingshan District, Shenzhen, China, which shows that there are two leachate leakage passages in the waste landfill dam A between NZK-2 and NZK-3, and between NZK-6 and NZK-7. © The Author(s) 2015.

Brief and precarious lives: infant mortality in contrasting sites from medieval and post-medieval England (AD 850-1859).

PubMed

Lewis, Mary E; Gowland, Rebecca

2007-09-01

This study compares the infant mortality profiles of 128 infants from two urban and two rural cemetery sites in medieval England. The aim of this paper is to assess the impact of urbanization and industrialization in terms of endogenous or exogenous causes of death. In order to undertake this analysis, two different methods of estimating gestational age from long bone lengths were used: a traditional regression method and a Bayesian method. The regression method tended to produce more marked peaks at 38 weeks, while the Bayesian method produced a broader range of ages and were more comparable with the expected "natural" mortality profiles.At all the sites, neonatal mortality (28-40 weeks) outweighed post-neonatal mortality (41-48 weeks) with rural Raunds Furnells in Northamptonshire, showing the highest number of neonatal deaths and post-medieval Spitalfields, London, showing a greater proportion of deaths due to exogenous or environmental factors. Of the four sites under study, Wharram Percy in Yorkshire showed the most convincing "natural" infant mortality profile, suggesting the inclusion of all births at the site (i.e., stillbirths and unbaptised infants). (c) 2007 Wiley-Liss, Inc.

Systematic data ingratiation of clinical trial recruitment locations for geographic-based query and visualization

PubMed Central

Luo, Jake; Chen, Weiheng; Wu, Min; Weng, Chunhua

2018-01-01

Background Prior studies of clinical trial planning indicate that it is crucial to search and screen recruitment sites before starting to enroll participants. However, currently there is no systematic method developed to support clinical investigators to search candidate recruitment sites according to their interested clinical trial factors. Objective In this study, we aim at developing a new approach to integrating the location data of over one million heterogeneous recruitment sites that are stored in clinical trial documents. The integrated recruitment location data can be searched and visualized using a map-based information retrieval method. The method enables systematic search and analysis of recruitment sites across a large amount of clinical trials. Methods The location data of more than 1.4 million recruitment sites of over 183,000 clinical trials was normalized and integrated using a geocoding method. The integrated data can be used to support geographic information retrieval of recruitment sites. Additionally, the information of over 6000 clinical trial target disease conditions and close to 4000 interventions was also integrated into the system and linked to the recruitment locations. Such data integration enabled the construction of a novel map-based query system. The system will allow clinical investigators to search and visualize candidate recruitment sites for clinical trials based on target conditions and interventions. Results The evaluation results showed that the coverage of the geographic location mapping for the 1.4 million recruitment sites was 99.8%. The evaluation of 200 randomly retrieved recruitment sites showed that the correctness of geographic information mapping was 96.5%. The recruitment intensities of the top 30 countries were also retrieved and analyzed. The data analysis results indicated that the recruitment intensity varied significantly across different countries and geographic areas. Conclusion This study contributed a new data processing framework to extract and integrate the location data of heterogeneous recruitment sites from clinical trial documents. The developed system can support effective retrieval and analysis of potential recruitment sites using target clinical trial factors. PMID:29132636

Application of nonparametric regression methods to study the relationship between NO2 concentrations and local wind direction and speed at background sites.

PubMed

Donnelly, Aoife; Misstear, Bruce; Broderick, Brian

2011-02-15

Background concentrations of nitrogen dioxide (NO(2)) are not constant but vary temporally and spatially. The current paper presents a powerful tool for the quantification of the effects of wind direction and wind speed on background NO(2) concentrations, particularly in cases where monitoring data are limited. In contrast to previous studies which applied similar methods to sites directly affected by local pollution sources, the current study focuses on background sites with the aim of improving methods for predicting background concentrations adopted in air quality modelling studies. The relationship between measured NO(2) concentration in air at three such sites in Ireland and locally measured wind direction has been quantified using nonparametric regression methods. The major aim was to analyse a method for quantifying the effects of local wind direction on background levels of NO(2) in Ireland. The method was expanded to include wind speed as an added predictor variable. A Gaussian kernel function is used in the analysis and circular statistics employed for the wind direction variable. Wind direction and wind speed were both found to have a statistically significant effect on background levels of NO(2) at all three sites. Frequently environmental impact assessments are based on short term baseline monitoring producing a limited dataset. The presented non-parametric regression methods, in contrast to the frequently used methods such as binning of the data, allow concentrations for missing data pairs to be estimated and distinction between spurious and true peaks in concentrations to be made. The methods were found to provide a realistic estimation of long term concentration variation with wind direction and speed, even for cases where the data set is limited. Accurate identification of the actual variation at each location and causative factors could be made, thus supporting the improved definition of background concentrations for use in air quality modelling studies. Copyright © 2010 Elsevier B.V. All rights reserved.

TENORM Resources

EPA Pesticide Factsheets

Studies of existing TENORM sites provide information needed to select appropriate methods for estimating risks from these sites, the best ways to clean up the sites, and the most economical and environmentally friendly ways to dispose of the TENORM.

Quantum coupled mutation finder: predicting functionally or structurally important sites in proteins using quantum Jensen-Shannon divergence and CUDA programming.

PubMed

Gültas, Mehmet; Düzgün, Güncel; Herzog, Sebastian; Jäger, Sven Joachim; Meckbach, Cornelia; Wingender, Edgar; Waack, Stephan

2014-04-03

The identification of functionally or structurally important non-conserved residue sites in protein MSAs is an important challenge for understanding the structural basis and molecular mechanism of protein functions. Despite the rich literature on compensatory mutations as well as sequence conservation analysis for the detection of those important residues, previous methods often rely on classical information-theoretic measures. However, these measures usually do not take into account dis/similarities of amino acids which are likely to be crucial for those residues. In this study, we present a new method, the Quantum Coupled Mutation Finder (QCMF) that incorporates significant dis/similar amino acid pair signals in the prediction of functionally or structurally important sites. The result of this study is twofold. First, using the essential sites of two human proteins, namely epidermal growth factor receptor (EGFR) and glucokinase (GCK), we tested the QCMF-method. The QCMF includes two metrics based on quantum Jensen-Shannon divergence to measure both sequence conservation and compensatory mutations. We found that the QCMF reaches an improved performance in identifying essential sites from MSAs of both proteins with a significantly higher Matthews correlation coefficient (MCC) value in comparison to previous methods. Second, using a data set of 153 proteins, we made a pairwise comparison between QCMF and three conventional methods. This comparison study strongly suggests that QCMF complements the conventional methods for the identification of correlated mutations in MSAs. QCMF utilizes the notion of entanglement, which is a major resource of quantum information, to model significant dissimilar and similar amino acid pair signals in the detection of functionally or structurally important sites. Our results suggest that on the one hand QCMF significantly outperforms the previous method, which mainly focuses on dissimilar amino acid signals, to detect essential sites in proteins. On the other hand, it is complementary to the existing methods for the identification of correlated mutations. The method of QCMF is computationally intensive. To ensure a feasible computation time of the QCMF's algorithm, we leveraged Compute Unified Device Architecture (CUDA).The QCMF server is freely accessible at http://qcmf.informatik.uni-goettingen.de/.

Validation of a radiosonde-based cloud layer detection method against a ground-based remote sensing method at multiple ARM sites

NASA Astrophysics Data System (ADS)

Zhang, Jinqiang; Li, Zhanqing; Chen, Hongbin; Cribb, Maureen

2013-01-01

Cloud vertical structure is a key quantity in meteorological and climate studies, but it is also among the most difficult quantities to observe. In this study, we develop a long-term (10 years) radiosonde-based cloud profile product for the U.S. Department of Energy's Atmospheric Radiation Measurement (ARM) program Southern Great Plains (SGP), Tropical Western Pacific (TWP), and North Slope of Alaska (NSA) sites and a shorter-term product for the ARM Mobile Facility (AMF) deployed in Shouxian, Anhui Province, China (AMF-China). The AMF-China site was in operation from 14 May to 28 December 2008; the ARM sites have been collecting data for over 15 years. The Active Remote Sensing of Cloud (ARSCL) value-added product (VAP), which combines data from the 95-GHz W-band ARM Cloud Radar (WACR) and/or the 35-GHz Millimeter Microwave Cloud Radar (MMCR), is used in this study to validate the radiosonde-based cloud layer retrieval method. The performance of the radiosonde-based cloud layer retrieval method applied to data from different climate regimes is evaluated. Overall, cloud layers derived from the ARSCL VAP and radiosonde data agree very well at the SGP and AMF-China sites. At the TWP and NSA sites, the radiosonde tends to detect more cloud layers in the upper troposphere.

Evaluation of Terrestrial LIDAR for Monitoring Geomorphic Change at Archeological Sites in Grand Canyon National Park, Arizona

USGS Publications Warehouse

Collins, Brian D.; Brown, Kristin M.; Fairley, Helen C.

2008-01-01

This report presents the results of an evaluation of terrestrial light detection and ranging (LIDAR) for monitoring geomorphic change at archeological sites located within Grand Canyon National Park, Ariz. Traditionally, topographic change-detection studies have used total station methods for the collection of data related to key measurable features of site erosion such as the location of thalwegs and knickpoints of gullies that traverse archeological sites (for example, Pederson and others, 2003). Total station methods require survey teams to walk within and on the features of interest within the archeological sites to take accurate measurements. As a result, site impacts may develop such as trailing, damage to cryptogamic crusts, and surface compaction that can exacerbate future erosion of the sites. National Park Service (NPS) resource managers have become increasingly concerned that repeated surveys for research and monitoring purposes may have a detrimental impact on the resources that researchers are trying to study and protect. Beginning in 2006, the Sociocultural Program of the U.S. Geological Survey's (USGS) Grand Canyon Monitoring and Research Center (GCMRC) initiated an evaluation of terrestrial LIDAR as a new monitoring tool that might enhance data quality and reduce site impacts. This evaluation was conducted as one part of an ongoing study to develop objective, replicable, quantifiable monitoring protocols for tracking the status and trend of variables affecting archeological site condition along the Colorado River corridor. The overall study consists of two elements: (1) an evaluation of the methodology through direct comparison to geomorphologic metrics already being collected by total station methods (this report) and (2) an evaluation of terrestrial LIDAR's ability to detect topographic change through the collection of temporally different datasets (a report on this portion of the study is anticipated early in 2009). The main goals of the first element of study were to 1. test the methodology and survey protocols of terrestrial LIDAR surveying under actual archeological site field conditions, 2. examine the ability to collect topographic data of entire archeological sites given such constraints as vegetation and rough topography, and 3. evaluate the ability of terrestrial LIDAR to accurately map the locations of key geomorphic features already being collected by total station methods such as gully thalweg and knickpoint locations. This report focuses on the ability of terrestrial LIDAR to duplicate total station methods, including typical erosion-related change features such as the plan view gully thalweg location and the gully thalweg long profile. The report also presents information concerning the use of terrestrial LIDAR for archeological site monitoring in a general sense. In addition, a detailed comparison of the site impacts caused by both total station and terrestrial LIDAR survey methods is presented using a suite of indicators, including total field survey time, field footstep count, and data-processing time. A thorough discussion of the relative benefits and limitations of using terrestrial LIDAR for monitoring erosion-induced changes at archeological sites in Grand Canyon National Park concludes this report.

Molecular detection of airborne Coccidioides in Tucson, Arizona

USGS Publications Warehouse

Chow, Nancy A.; Griffin, Dale W.; Barker, Bridget M.; Loparev, Vladimir N.; Litvintseva, Anastasia P.

2016-01-01

Environmental surveillance of the soil-dwelling fungus Coccidioides is essential for the prevention of Valley fever, a disease primarily caused by inhalation of the arthroconidia. Methods for collecting and detectingCoccidioides in soil samples are currently in use by several laboratories; however, a method utilizing current air sampling technologies has not been formally demonstrated for the capture of airborne arthroconidia. In this study, we collected air/dust samples at two sites (Site A and Site B) in the endemic region of Tucson, Arizona, and tested a variety of air samplers and membrane matrices. We then employed a single-tube nested qPCR assay for molecular detection. At both sites, numerous soil samples (n = 10 at Site A and n = 24 at Site B) were collected and Coccidioides was detected in two samples (20%) at Site A and in eight samples (33%) at Site B. Of the 25 air/dust samples collected at both sites using five different air sampling methods, we detected Coccidioides in three samples from site B. All three samples were collected using a high-volume sampler with glass-fiber filters. In this report, we describe these methods and propose the use of these air sampling and molecular detection strategies for environmental surveillance of Coccidioides.

VS30, site amplifications and some comparisons: The Adapazari (Turkey) case

NASA Astrophysics Data System (ADS)

Ozcep, Tazegul; Ozcep, Ferhat; Ozel, Oguz

The aim of this study was to investigate the role of VS30 in site amplifications in the Adapazari region, Turkey. To fulfil this aim, amplifications from VS30 measurements were compared with earthquake data for different soil types in the seismic design codes. The Adapazari area was selected as the study area, and shear-wave velocity distribution was obtained by the multichannel analysis of surface waves (MASWs) method at 100 sites for the top 50 m of soil. Aftershock data following the Mw 7.4 Izmit earthquake of 17 August 1999 gave magnitudes between 4.0 and 5.6 at six stations installed in and around the Adapazari Basin, at Babalı, Şeker, Genç, Hastane, Toyota and Imar. This data was used to estimate site amplifications by the reference-station method. In addition, the fundamental periods of the station sites were estimated by the single station method. Site classifications based on VS30 in the seismic design codes were compared with the fundamental periods and amplification values. It was found that site amplifications (from earthquake data) and relevant spectra (from VS30) are not in good agreement for soils in Adapazari (Turkey).

Contribution of the 40Ar/39Ar method to improve Middle-Pleistocene archaeological/palaeontological sites from the Italian Peninsula

NASA Astrophysics Data System (ADS)

Nomade, Sebastien, ,, Dr.; Pereira, MSc. Alison; voinchet, Pierre, ,, Dr.; Bahain, Jean-Jacques, ,, Dr.; Aureli, Daniele, ,, Dr.; Arzarello, Marta, ,, Dr.; Anzidei, Anna-Paola, ,, Dr.; Biddittu, Italo, ,, Dr.; Bulgarelli, Maria-Grazia, ,, Dr.; Falguères, Christophe, ,, Dr.; Giaccio, Biagio, ,, Dr.; Guillou, Hervé, ,, Dr.; Manzi, Gorgio, ,, Dr.; Moncel, Marie-Hélène, ,, Dr.; Nicoud, Elisa, ,, Dr.; Pagli, Maria, ,, Dr.; Parenti, Fabio, ,, Dr.; Peretto, Carlo, ,, Dr.; Piperno, Marcello, ,, Dr.; Rocca, Roxane, ,, Dr.

2017-04-01

European Middle-Pleistocene archaeological and/or paleontological sites lack a unified and precise chronological framework. Despite recent efforts mostly focused on methods such as OSL, ESR/U-series or cosmogenic nuclides, the age of numerous sites from this period fundamentally still relies on qualitative and speculative palaeoenvironmental and/or palaeontological/palaeoanthropological considerations. The lack of robust chronologies, along with the scarcity of human fossils, prevent coherent correlations between European sites which in turn limits our understanding of human diffusion dynamics, understand techno-cultural evolution or correlate archaeological sites with palaeoclimatic and environmental records. With the goal of providing an accurate and precise chronological framework based on a multi-method approach, a research network including geochronologists, archaeologist and paleoanthropologists from various French and Italian institutions launched in 2010 a wide study of Middle-Pleistocene archaeological sites of central and southern Italy. This study combining the 39Ar/40Ar method with palaeo-dosimetric methods applied to European sites in the age range of 700 ka to 300 ka is unprecedented. In parallel, a large effort has been done to improve the regional Middle-Pleistocene tephrostratigraphic database through a massive application of both high-precision 40Ar/39Ar geochronological and geochemical investigations. We illustrate our approach and results in addressing several key-sites such as Notarchirico, Valle Giumentina; Ceprano-Campogrande and La Polledrara di Cecanibbio. The accurate and precise chronological framework we built permits us to replace all the investigated archaeological and palaeontological records into a coherent climatic and environmental context. Furthermore, our work provides the opportunity to compare lithic industries from a technical and evolutionary point of view within a homogeneous temporal frame. These preliminary results border the current limitations of the 40Ar/39Ar method and will guide expected advances to apply our approach to other European sites.

Evapotranspiration from areas of native vegetation in west-central Florida

USGS Publications Warehouse

Bidlake, W.R.; Woodham, W.M.; Lopez, M.A.

1993-01-01

A study was made to examine the suitability of three different micrometeorological methods for estimating evapotranspiration from selected areas of native vegetation in west-central Florida and to estimate annual evapotranspiration from those areas. Evapotranspiration was estimated using the energy- balance Bowen ratio and eddy correlation methods. Potential evapotranspiration was computed using the Penman equation. The energy-balance Bowen ratio method was used to estimate diurnal evapotrans- piration at unforested sites and yielded reasonable results; however, measurements indicated that the magnitudes of air temperature and vapor-pressure gradients above the forested sites were too small to obtain reliable evapotranspiration measurements with the energy balance Bowen ratio system. Analysis of the surface energy-balance indicated that sensible and latent heat fluxes computed using standard eddy correlation computation methods did not adequately account for available energy. Eddy correlation data were combined with the equation for the surface energy balance to yield two additional estimates of evapotranspiration. Daily potential evapotranspiration and evapotranspira- tion estimated using the energy-balance Bowen ratio method were not correlated at a unforested, dry prairie site, but they were correlated at a marsh site. Estimates of annual evapotranspiration for sites within the four vegetation types, which were based on energy-balance Bowen ratio and eddy correlation measurements, were 1,010 millimeters for dry prairie sites, 990 millimeters for marsh sites, 1,060 millimeters for pine flatwood sites, and 970 millimeters for a cypress swamp site.

An alternative approach to characterize nonlinear site effects

USGS Publications Warehouse

Zhang, R.R.; Hartzell, S.; Liang, J.; Hu, Y.

2005-01-01

This paper examines the rationale of a method of nonstationary processing and analysis, referred to as the Hilbert-Huang transform (HHT), for its application to a recording-based approach in quantifying influences of soil nonlinearity in site response. In particular, this paper first summarizes symptoms of soil nonlinearity shown in earthquake recordings, reviews the Fourier-based approach to characterizing nonlinearity, and offers justifications for the HHT in addressing nonlinearity issues. This study then uses the HHT method to analyze synthetic data and recordings from the 1964 Niigata and 2001 Nisqually earthquakes. In doing so, the HHT-based site response is defined as the ratio of marginal Hilbert amplitude spectra, alternative to the Fourier-based response that is the ratio of Fourier amplitude spectra. With the Fourier-based approach in studies of site response as a reference, this study shows that the alternative HHT-based approach is effective in characterizing soil nonlinearity and nonlinear site response.

Alternative methods of salt disposal at the seven salt sites for a nuclear waste repository

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

Not Available

1987-02-01

This study discusses the various alternative salt management techniques for the disposal of excess mined salt at seven potentially acceptable nuclear waste repository sites: Deaf Smith and Swisher Counties, Texas; Richton and Cypress Creek Domes, Mississippi; Vacherie Dome, Louisiana; and Davis and Lavender Canyons, Utah. Because the repository development involves the underground excavation of corridors and waste emplacement rooms, in either bedded or domed salt formations, excess salt will be mined and must be disposed of offsite. The salt disposal alternatives examined for all the sites include commercial use, ocean disposal, deep well injection, landfill disposal, and underground mine disposal.more » These alternatives (and other site-specific disposal methods) are reviewed, using estimated amounts of excavated, backfilled, and excess salt. Methods of transporting the excess salt are discussed, along with possible impacts of each disposal method and potential regulatory requirements. A preferred method of disposal is recommended for each potentially acceptable repository site. 14 refs., 5 tabs.« less

Laboratory Study of Polychlorinated Biphenyl Contamination and Mitigation in Buildings -- Part 4. Evaluation of the Activated Metal Treatment System (AMTS) for On-site Destruction of PCBs

EPA Science Inventory

This is the fourth, also the last, report of the report series entitled “Laboratory Study of Polychlorinated Biphenyl (PCB) Contamination and Mitigation in Buildings.” This report evaluates the performance of an on-site PCB destruction method, known as the AMTS method...

Laboratory Study of Polychlorinated Biphenyl (PCB) Contamination and Mitigation in Buildings -- Part 4. Evaluation of the Activated Metal Treatment System (AMTS) for On-site Destruction of PCBs

EPA Science Inventory

This is the fourth, also the last, report of the report series entitled “Laboratory Study of Polychlorinated Biphenyl (PCB) Contamination and Mitigation in Buildings.” This report evaluates the performance of an on-site PCB destruction method, known as the AMTS method, developed ...

Verification of chemistry reference ranges using a simple method in sub-Saharan Africa

PubMed Central

Taylor, Douglas; Mandala, Justin; Nanda, Kavita; Van Campenhout, Christel; Agingu, Walter; Madurai, Lorna; Barsch, Eva-Maria; Deese, Jennifer; Van Damme, Lut; Crucitti, Tania

2016-01-01

Background Chemistry safety assessments are interpreted by using chemistry reference ranges (CRRs). Verification of CRRs is time consuming and often requires a statistical background. Objectives We report on an easy and cost-saving method to verify CRRs. Methods Using a former method introduced by Sigma Diagnostics, three study sites in sub-Saharan Africa, Bondo, Kenya, and Pretoria and Bloemfontein, South Africa, verified the CRRs for hepatic and renal biochemistry assays performed during a clinical trial of HIV antiretroviral pre-exposure prophylaxis. The aspartate aminotransferase/alanine aminotransferase, creatinine and phosphorus results from 10 clinically-healthy participants at the screening visit were used. In the event the CRRs did not pass the verification, new CRRs had to be calculated based on 40 clinically-healthy participants. Results Within a few weeks, the study sites accomplished verification of the CRRs without additional costs. The aspartate aminotransferase reference ranges for the Bondo, Kenya site and the alanine aminotransferase reference ranges for the Pretoria, South Africa site required adjustment. The phosphorus CRR passed verification and the creatinine CRR required adjustment at every site. The newly-established CRR intervals were narrower than the CRRs used previously at these study sites due to decreases in the upper limits of the reference ranges. As a result, more toxicities were detected. Conclusion To ensure the safety of clinical trial participants, verification of CRRs should be standard practice in clinical trials conducted in settings where the CRR has not been validated for the local population. This verification method is simple, inexpensive, and can be performed by any medical laboratory. PMID:28879112

Site classification for National Strong Motion Observation Network System (NSMONS) stations in China using an empirical H/V spectral ratio method

NASA Astrophysics Data System (ADS)

Ji, Kun; Ren, Yefei; Wen, Ruizhi

2017-10-01

Reliable site classification of the stations of the China National Strong Motion Observation Network System (NSMONS) has not yet been assigned because of lacking borehole data. This study used an empirical horizontal-to-vertical (H/V) spectral ratio (hereafter, HVSR) site classification method to overcome this problem. First, according to their borehole data, stations selected from KiK-net in Japan were individually assigned a site class (CL-I, CL-II, or CL-III), which is defined in the Chinese seismic code. Then, the mean HVSR curve for each site class was computed using strong motion recordings captured during the period 1996-2012. These curves were compared with those proposed by Zhao et al. (2006a) for four types of site classes (SC-I, SC-II, SC-III, and SC-IV) defined in the Japanese seismic code (JRA, 1980). It was found that an approximate range of the predominant period Tg could be identified by the predominant peak of the HVSR curve for the CL-I and SC-I sites, CL-II and SC-II sites, and CL-III and SC-III + SC-IV sites. Second, an empirical site classification method was proposed based on comprehensive consideration of peak period, amplitude, and shape of the HVSR curve. The selected stations from KiK-net were classified using the proposed method. The results showed that the success rates of the proposed method in identifying CL-I, CL-II, and CL-III sites were 63%, 64%, and 58% respectively. Finally, the HVSRs of 178 NSMONS stations were computed based on recordings from 2007 to 2015 and the sites classified using the proposed method. The mean HVSR curves were re-calculated for three site classes and compared with those from KiK-net data. It was found that both the peak period and the amplitude were similar for the mean HVSR curves derived from NSMONS classification results and KiK-net borehole data, implying the effectiveness of the proposed method in identifying different site classes. The classification results have good agreement with site classes based on borehole data of 81 stations in China, which indicates that our site classification results are acceptable and that the proposed method is practicable.

Delineation of contaminant plume for an inorganic contaminated site using electrical resistivity tomography: comparison with direct-push technique.

PubMed

Liao, Qing; Deng, Yaping; Shi, Xiaoqing; Sun, Yuanyuan; Duan, Weidong; Wu, Jichun

2018-03-03

Precise delineation of contaminant plume distribution is essential for effective remediation of contaminated sites. Traditional in situ investigation methods like direct-push (DP) sampling are accurate, but are usually intrusive and costly. Electrical resistivity tomography (ERT) method, as a non-invasive geophysical technique to map spatiotemporal changes in resistivity of the subsurface, is becoming increasingly popular in environmental science. However, the resolution of ERT for delineation of contaminant plumes still remains controversial. In this study, ERT and DP technique were both conducted at a real inorganic contaminated site. The reliability of the ERT method was validated by the direct comparisons of their investigation results that the resistivity acquired by ERT method is in accordance with the total dissolved solid concentration in groundwater and the overall variation of the total iron content in soil obtained by DP technique. After testifying the applicability of ERT method for contaminant identification, the extension of contaminant plume at the study site was revealed by supplementary ERT surveys conducted subsequently in the surrounding area of the contaminant source zone.

Full-vector geomagnetic field records from the East Eifel, Germany

NASA Astrophysics Data System (ADS)

Monster, Marilyn W. L.; Langemeijer, Jaap; Wiarda, Laura R.; Dekkers, Mark J.; Biggin, Andy J.; Hurst, Elliot A.; Groot, Lennart V. de

2018-01-01

To create meaningful models of the geomagnetic field, high-quality directional and intensity input data are needed. However, while it is fairly straightforward to obtain directional data, intensity data are much scarcer, especially for periods before the Holocene. Here, we present data from twelve flows (age range ∼ 200 to ∼ 470 ka) in the East Eifel volcanic field (Germany). These sites had been previously studied and are resampled to further test the recently proposed multi-method palaeointensity approach. Samples are first subjected to classic palaeomagnetic and rock magnetic analyses to optimise the subsequent palaeointensity experiments. Four different palaeointensity methods - IZZI-Thellier, the multispecimen method, calibrated pseudo-Thellier, and microwave-Thellier - are being used in the present study. The latter should be considered as supportive because only one or two specimens per site could be processed. Palaeointensities obtained for ten sites pass our selection criteria: two sites are successful with a single approach, four sites with two approaches, three more sites work with three approaches, and one site with all four approaches. Site-averaged intensity values typically range between 30 and 35 μT. No typically low palaeointensity values are found, in line with paleodirectional results which are compatible with regular palaeosecular variation of the Earth's magnetic field. Results from different methods are remarkably consistent and generally agree well with the values previously reported. They appear to be below the average for the Brunhes chron; there are no indications for relatively higher palaeointensities for units younger than 300 ka. However, our young sites could be close in age, and therefore may not represent the average intensity of the paleofield. Three of our sites are even considered coeval; encouragingly, these do yield the same palaeointensity within uncertainty bounds.

Does Categorization Method Matter in Exploring Volume-Outcome Relation? A Multiple Categorization Methods Comparison in Coronary Artery Bypass Graft Surgery Surgical Site Infection.

PubMed

Yu, Tsung-Hsien; Tung, Yu-Chi; Chung, Kuo-Piao

2015-08-01

Volume-infection relation studies have been published for high-risk surgical procedures, although the conclusions remain controversial. Inconsistent results may be caused by inconsistent categorization methods, the definitions of service volume, and different statistical approaches. The purpose of this study was to examine whether a relation exists between provider volume and coronary artery bypass graft (CABG) surgical site infection (SSI) using different categorization methods. A population-based cross-sectional multi-level study was conducted. A total of 10,405 patients who received CABG surgery between 2006 and 2008 in Taiwan were recruited. The outcome of interest was surgical site infection for CABG surgery. The associations among several patient, surgeon, and hospital characteristics was examined. The definition of surgeons' and hospitals' service volume was the cumulative CABG service volumes in the previous year for each CABG operation and categorized by three types of approaches: Continuous, quartile, and k-means clustering. The results of multi-level mixed effects modeling showed that hospital volume had no association with SSI. Although the relation between surgeon volume and surgical site infection was negative, it was inconsistent among the different categorization methods. Categorization of service volume is an important issue in volume-infection study. The findings of the current study suggest that different categorization methods might influence the relation between volume and SSI. The selection of an optimal cutoff point should be taken into account for future research.

Non-Invasive Seismic Methods for Earthquake Site Classification Applied to Ontario Bridge Sites

NASA Astrophysics Data System (ADS)

Bilson Darko, A.; Molnar, S.; Sadrekarimi, A.

2017-12-01

How a site responds to earthquake shaking and its corresponding damage is largely influenced by the underlying ground conditions through which it propagates. The effects of site conditions on propagating seismic waves can be predicted from measurements of the shear wave velocity (Vs) of the soil layer(s) and the impedance ratio between bedrock and soil. Currently the seismic design of new buildings and bridges (2015 Canadian building and bridge codes) requires determination of the time-averaged shear-wave velocity of the upper 30 metres (Vs30) of a given site. In this study, two in situ Vs profiling methods; Multichannel Analysis of Surface Waves (MASW) and Ambient Vibration Array (AVA) methods are used to determine Vs30 at chosen bridge sites in Ontario, Canada. Both active-source (MASW) and passive-source (AVA) surface wave methods are used at each bridge site to obtain Rayleigh-wave phase velocities over a wide frequency bandwidth. The dispersion curve is jointly inverted with each site's amplification function (microtremor horizontal-to-vertical spectral ratio) to obtain shear-wave velocity profile(s). We apply our non-invasive testing at three major infrastructure projects, e.g., five bridge sites along the Rt. Hon. Herb Gray Parkway in Windsor, Ontario. Our non-invasive testing is co-located with previous invasive testing, including Standard Penetration Test (SPT), Cone Penetration Test and downhole Vs data. Correlations between SPT blowcount and Vs are developed for the different soil types sampled at our Ontario bridge sites. A robust earthquake site classification procedure (reliable Vs30 estimates) for bridge sites across Ontario is evaluated from available combinations of invasive and non-invasive site characterization methods.

Social Networking Sites as Virtual Communities of Practice: A Mixed Method Study

ERIC Educational Resources Information Center

Davis, Lorretta J.

2010-01-01

Membership in social networking sites is increasing rapidly. Social networking sites serve many purposes including networking, communication, recruitment, and sharing knowledge. Social networking sites, public or private, may be hosted on applications such as Facebook and LinkedIn. As individuals begin to follow and participate in social…

SUMMARY OF TECHNIQUES AND UNIQUE USES FOR DIRECT PUSH METHODS IN SITE CHARACTERIZATION ON CONTAMINATED FIELD SITES

EPA Science Inventory

Site characterization of subsurface contaminant transport is often hampered by a lack of knowledge of site heterogeneity and temporal variations in hydrogeochemistry. Two case studies are reviewed to illustrate the utility of macro-scale mapping information along with spatially-...

Study of Site Response in the Seattle and Tacoma Basins, Washington, Using Spectral Ratio Methods

NASA Astrophysics Data System (ADS)

Keshvardoost, R.; Wolf, L. W.

2014-12-01

Sedimentary basins are known to have a pronounced influence on earthquake-generated ground motions, affecting both predominant frequencies and wave amplification. These site characteristics are important elements in estimating ground shaking and seismic hazard. In this study, we use three-component broadband and strong motion seismic data from three recent earthquakes to determine site response characteristics in the Seattle and Tacoma basins, Washington. Resonant frequencies and relative amplification of ground motions were determined using Fourier spectral ratios of velocity and acceleration records from the 2012 Mw 6.1 Vancouver Island earthquake, the 2012 Mw 7.8 Queen Charlotte Island earthquake, and the 2014 Mw 6.6 Vancouver Island earthquake. Recordings from sites within and adjacent to the Seattle and Tacoma basins were selected for the study based on their signal to noise ratios. Both the Standard Spectral Ratio (SSR) and the Horizontal-to-Vertical Spectral Ratio (HVSR) methods were used in the analysis, and results from each were compared to examine their agreement and their relation to local geology. Although 57% of the sites (27 out of 48) exhibited consistent results between the two methods, other sites varied considerably. In addition, we use data from the Seattle Liquefaction Array (SLA) to evaluate the site response at 4 different depths. Results indicate that resonant frequencies remain the same at different depths but amplification decreases significantly over the top 50 m.

Analysis and Prediction of Myristoylation Sites Using the mRMR Method, the IFS Method and an Extreme Learning Machine Algorithm.

PubMed

Wang, ShaoPeng; Zhang, Yu-Hang; Huang, GuoHua; Chen, Lei; Cai, Yu-Dong

2017-01-01

Myristoylation is an important hydrophobic post-translational modification that is covalently bound to the amino group of Gly residues on the N-terminus of proteins. The many diverse functions of myristoylation on proteins, such as membrane targeting, signal pathway regulation and apoptosis, are largely due to the lipid modification, whereas abnormal or irregular myristoylation on proteins can lead to several pathological changes in the cell. To better understand the function of myristoylated sites and to correctly identify them in protein sequences, this study conducted a novel computational investigation on identifying myristoylation sites in protein sequences. A training dataset with 196 positive and 84 negative peptide segments were obtained. Four types of features derived from the peptide segments following the myristoylation sites were used to specify myristoylatedand non-myristoylated sites. Then, feature selection methods including maximum relevance and minimum redundancy (mRMR), incremental feature selection (IFS), and a machine learning algorithm (extreme learning machine method) were adopted to extract optimal features for the algorithm to identify myristoylation sites in protein sequences, thereby building an optimal prediction model. As a result, 41 key features were extracted and used to build an optimal prediction model. The effectiveness of the optimal prediction model was further validated by its performance on a test dataset. Furthermore, detailed analyses were also performed on the extracted 41 features to gain insight into the mechanism of myristoylation modification. This study provided a new computational method for identifying myristoylation sites in protein sequences. We believe that it can be a useful tool to predict myristoylation sites from protein sequences. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Pan-Canadian assessment of pandemic immunization data collection: study methodology.

PubMed

Pereira, Jennifer A; Quach, Susan; Heidebrecht, Christine; Foisy, Julie; Quan, Sherman; Finkelstein, Michael; Sikora, Christopher A; Bettinger, Julie A; Buckeridge, David L; McCarthy, Anne; Deeks, Shelley; Kwong, Jeffrey C

2010-06-08

The collection of individual-level pandemic (H1N1) 2009 influenza immunization data was considered important to facilitate optimal vaccine delivery and accurate assessment of vaccine coverage. These data are also critical for research aimed at evaluating the new vaccine's safety and effectiveness. Systems used to collect immunization data include manual approaches in which data are collected and retained on paper, electronic systems in which data are captured on computer at the point of vaccination and hybrid systems which are comprised of both computerized and manual data collection components. This study's objective was to compare the efficiencies and perceptions of data collection methods employed during Canada's pandemic (H1N1) 2009 influenza vaccination campaign. A pan-Canadian observational study was conducted in a convenience sample of public health clinics and healthcare institutions during the H1N1 vaccination campaign in the fall of 2009. The study design consisted of three stages: Stage 1 involved passive observation of the site's layout, processes and client flow; Stage 2 entailed timing site staff on 20 clients through five core immunization tasks: i) client registration, ii) medical history collection, iii) medical history review, iv) vaccine administration record keeping and v) preparation of proof of vaccine administration for the client; in Stage 3, site staff completed a questionnaire regarding perceived usability of the site's data collection approach. Before the national study began, a pilot study was conducted in three seasonal influenza vaccination sites in Ontario, to both test that the proposed methodology was logistically feasible and to determine inter-rater reliability in the measurements of the research staff. Comparative analyses will be conducted across the range of data collection methods with respect to time required to collect immunization data, number and type of individual-level data elements collected, and clinic staff perceptions of the usability of the method employed at their site, using analysis of variance (ANOVA). Various data collection methods were employed at immunization sites across Canada during the pandemic (H1N1) 2009 influenza vaccination campaign. Our comparison of methods can facilitate planning an efficient, coordinated approach for collecting immunization data in future influenza seasons.

Implementation of Evidence-Based Employment Services in Specialty Mental Health

PubMed Central

Hamilton, Alison B; Cohen, Amy N; Glover, Dawn L; Whelan, Fiona; Chemerinski, Eran; McNagny, Kirk P; Mullins, Deborah; Reist, Christopher; Schubert, Max; Young, Alexander S

2013-01-01

Objective. Study a quality improvement approach for implementing evidence-based employment services at specialty mental health clinics. Data Sources/Study Setting. Semistructured interviews with clinicians and administrators before, during, and after implementation. Qualitative field notes, structured baseline and follow-up interviews with patients, semistructured interviews with patients after implementation, and administrative data. Study Design. Site-level controlled trial at four implementation and four control sites. Hybrid implementation–effectiveness study with mixed methods intervention evaluation design. Data Collection/Extraction Methods. Site visits, in-person and telephone interviews, patient surveys, patient self-assessment. A total of 801 patients completed baseline surveys and 53 clinicians and other clinical key stakeholders completed longitudinal qualitative interviews. Principal Findings. At baseline, sites varied in the availability, utilization, and quality of supported employment. Each site needed quality improvement for this service, though for differing reasons, with some needing development of the service itself and others needing increased service capacity. Improvements in knowledge, attitudes, beliefs, and referral behaviors were evident in mid- and postimplementation interviews, though some barriers persisted. Half of patients expressed an interest in working at baseline. Patients at implementation sites were 2.3 times more likely to receive employment services during the study year. Those who had a service visit were more likely to be employed at follow-up than those who did not. Conclusions. Studies of implementation and effectiveness require mixed methods to both enhance implementation in real time and provide context for interpretation of complex results. In this study, a quality improvement approach resulted in superior patient-level outcomes and improved clinician knowledge, attitudes, and behaviors, in the context of substantial variation among sites. PMID:24138608

Suicide and the Internet: Changes in the accessibility of suicide-related information between 2007 and 2014.

PubMed

Biddle, Lucy; Derges, Jane; Mars, Becky; Heron, Jon; Donovan, Jenny L; Potokar, John; Piper, Martyn; Wyllie, Clare; Gunnell, David

2016-01-15

Following the ongoing concerns about cyber-suicide, we investigate changes between 2007 and 2014 in material likely to be accessed by suicidal individuals searching for methods of suicide. 12 search terms relating to suicide methods were applied to four search engines and the top ten hits from each were categorised and analysed for content. The frequency of each category of site across all searches, using particular search terms and engines, was counted. Key changes: growth of blogs and discussion forums (from 3% of hits, 2007 to 18.5% of hits, 2014); increase in hits linking to general information sites - especially factual sites that detail and evaluate suicide methods (from 9%, 2007 to 21.7%, 2014). Hits for dedicated suicide sites increased (from 19% to 23%), while formal help sites were less visible (from 13% to 6.5%). Overall, 54% of hits contained information about new high-lethality methods. We did not search for help sites so cannot assess the balance of suicide promoting versus preventing sites available online. Social media was beyond the scope of this study. Working with ISPs and search engines would help optimise support sites. Better site moderation and implementation of suicide reporting guidelines should be encouraged. Copyright © 2015 Elsevier B.V. All rights reserved.

System-wide identification of wild-type SUMO-2 conjugation sites

PubMed Central

Hendriks, Ivo A.; D'Souza, Rochelle C.; Chang, Jer-Gung; Mann, Matthias; Vertegaal, Alfred C. O.

2015-01-01

SUMOylation is a reversible post-translational modification (PTM) regulating all nuclear processes. Identification of SUMOylation sites by mass spectrometry (MS) has been hampered by bulky tryptic fragments, which thus far necessitated the use of mutated SUMO. Here we present a SUMO-specific protease-based methodology which circumvents this problem, dubbed Protease-Reliant Identification of SUMO Modification (PRISM). PRISM allows for detection of SUMOylated proteins as well as identification of specific sites of SUMOylation while using wild-type SUMO. The method is generic and could be widely applied to study lysine PTMs. We employ PRISM in combination with high-resolution MS to identify SUMOylation sites from HeLa cells under standard growth conditions and in response to heat shock. We identified 751 wild-type SUMOylation sites on endogenous proteins, including 200 dynamic SUMO sites in response to heat shock. Thus, we have developed a method capable of quantitatively studying wild-type mammalian SUMO at the site-specific and system-wide level. PMID:26073453

Site-specific fab fragment biotinylation at the conserved nucleotide binding site for enhanced Ebola detection.

PubMed

Mustafaoglu, Nur; Alves, Nathan J; Bilgicer, Basar

2015-07-01

The nucleotide binding site (NBS) is a highly conserved region between the variable light and heavy chains at the Fab domains of all antibodies, and a small molecule that we identified, indole-3-butyric acid (IBA), binds specifically to this site. Fab fragment, with its small size and simple production methods compared to intact antibody, is good candidate for use in miniaturized diagnostic devices and targeted therapeutic applications. However, commonly used modification techniques are not well suited for Fab fragments as they are often more delicate than intact antibodies. Fab fragments are of particular interest for sensor surface functionalization but immobilization results in damage to the antigen binding site and greatly reduced activity due to their truncated size that allows only a small area that can bind to surfaces without impeding antigen binding. In this study, we describe an NBS-UV photocrosslinking functionalization method (UV-NBS(Biotin) in which a Fab fragment is site-specifically biotinylated with an IBA-EG11-Biotin linker via UV energy exposure (1 J/cm(2)) without affecting its antigen binding activity. This study demonstrates successful immobilization of biotinylated Ebola detecting Fab fragment (KZ52 Fab fragment) via the UV-NBS(Biotin) method yielding 1031-fold and 2-fold better antigen detection sensitivity compared to commonly used immobilization methods: direct physical adsorption and NHS-Biotin functionalization, respectively. Utilization of the UV-NBS(Biotin) method for site-specific conjugation to Fab fragment represents a proof of concept use of Fab fragment for various diagnostic and therapeutic applications with numerous fluorescent probes, affinity molecules and peptides. © 2015 Wiley Periodicals, Inc.

Traffic operational evaluation of traffic impact analysis (TIA) case sites.

DOT National Transportation Integrated Search

2010-09-22

This report summarizes traffic operational evaluation of six select traffic impact analysis (TIA) case sites and the effectiveness of forecasting methods used in TIA studies. Six TIA case sites comprising 15 signalized intersections and 2 unsignalize...

Representativeness of the ground observational sites and up-scaling of the point soil moisture measurements

NASA Astrophysics Data System (ADS)

Chen, Jinlei; Wen, Jun; Tian, Hui

2016-02-01

Soil moisture plays an increasingly important role in the cycle of energy-water exchange, climate change, and hydrologic processes. It is usually measured at a point site, but regional soil moisture is essential for validating remote sensing products and numerical modeling results. In the study reported in this paper, the minimal number of required sites (NRS) for establishing a research observational network and the representative single sites for regional soil moisture estimation are discussed using the soil moisture data derived from the ;Maqu soil moisture observational network; (101°40‧-102°40‧E, 33°30‧-35°45‧N), which is supported by Chinese Academy of Science. Furthermore, the best up-scaling method suitable for this network has been studied by evaluating four commonly used up-scaling methods. The results showed that (1) Under a given accuracy requirement R ⩾ 0.99, RMSD ⩽ 0.02 m3/m3, NRS at both 5 and 10 cm depth is 10. (2) Representativeness of the sites has been validated by time stability analysis (TSA), time sliding correlation analysis (TSCA) and optimal combination of sites (OCS). NST01 is the most representative site at 5 cm depth for the first two methods; NST07 and NST02 are the most representative sites at 10 cm depth. The optimum combination sites at 5 cm depth are NST01, NST02, and NST07. NST05, NST08, and NST13 are the best group at 10 cm depth. (3) Linear fitting, compared with other three methods, is the best up-scaling method for all types of representative sites obtained above, and linear regression equations between a single site and regional soil moisture are established hereafter. ;Single site; obtained by OCS has the greatest up-scaling effect, and TSCA takes the second place. (4) Linear fitting equations show good practicability in estimating the variation of regional soil moisture from July 3, 2013 to July 3, 2014, when a large number of observed soil moisture data are lost.

Study on evaluation methods for Rayleigh wave dispersion characteristic

USGS Publications Warehouse

Shi, L.; Tao, X.; Kayen, R.; Shi, H.; Yan, S.

2005-01-01

The evaluation of Rayleigh wave dispersion characteristic is the key step for detecting S-wave velocity structure. By comparing the dispersion curves directly with the spectra analysis of surface waves (SASW) method, rather than comparing the S-wave velocity structure, the validity and precision of microtremor-array method (MAM) can be evaluated more objectively. The results from the China - US joint surface wave investigation in 26 sites in Tangshan, China, show that the MAM has the same precision with SASW method in 83% of the 26 sites. The MAM is valid for Rayleigh wave dispersion characteristic testing and has great application potentiality for site S-wave velocity structure detection.

Analysis of Multi-Criteria Evaluation Method of Landfill Site Selection for Municipal Solid Waste Management

NASA Astrophysics Data System (ADS)

Mohammed, Habiba Ibrahim; Majid, Zulkepli; Yusof, Norhakim Bin; Bello Yamusa, Yamusa

2018-03-01

Landfilling remains the most common systematic technique of solid waste disposal in most of the developed and developing countries. Finding a suitable site for landfill is a very challenging task. Landfill site selection process aims to provide suitable areas that will protect the environment and public health from pollution and hazards. Therefore, various factors such as environmental, physical, socio-economic, and geological criteria must be considered before siting any landfill. This makes the site selection process vigorous and tedious because it involves the processing of large amount of spatial data, rules and regulations from different agencies and also policy from decision makers. This allows the incorporation of conflicting objectives and decision maker preferences into spatial decision models. This paper particularly analyzes the multi-criteria evaluation (MCE) method of landfill site selection for solid waste management by means of literature reviews and surveys. The study will help the decision makers and waste management authorities to choose the most effective method when considering landfill site selection.

XenoSite: accurately predicting CYP-mediated sites of metabolism with neural networks.

PubMed

Zaretzki, Jed; Matlock, Matthew; Swamidass, S Joshua

2013-12-23

Understanding how xenobiotic molecules are metabolized is important because it influences the safety, efficacy, and dose of medicines and how they can be modified to improve these properties. The cytochrome P450s (CYPs) are proteins responsible for metabolizing 90% of drugs on the market, and many computational methods can predict which atomic sites of a molecule--sites of metabolism (SOMs)--are modified during CYP-mediated metabolism. This study improves on prior methods of predicting CYP-mediated SOMs by using new descriptors and machine learning based on neural networks. The new method, XenoSite, is faster to train and more accurate by as much as 4% or 5% for some isozymes. Furthermore, some "incorrect" predictions made by XenoSite were subsequently validated as correct predictions by revaluation of the source literature. Moreover, XenoSite output is interpretable as a probability, which reflects both the confidence of the model that a particular atom is metabolized and the statistical likelihood that its prediction for that atom is correct.

MULTI-SITE EVALUATIONS OF CANDIDATE METHODOLOGIES FOR DETERMINING COARSE PARTICULATE (PM 10-2.5) CONCENTRATIONS: AUGUST 2005 UPDATED REPORT REGARDING SECOND-GENERATION AND NEW PM 10-2.5 SAMPLERS

EPA Science Inventory

Multi-site field studies were conducted to evaluate the performance of sampling methods for measuring the coarse fraction of PM10 (PM10 2.5) in ambient air. The field studies involved the use of both time-integrated filter-based and direct continuous methods. Despite operationa...

A comparison of two collection methods for estimating abundance and parity of Anopheles albimanus in breeding sites and villages of southern Mexico.

PubMed

Ulloa, A; Rodríguez, M H; Rodríguez, A D; Roberts, D R

1997-09-01

The abundance and age structure of Anopheles albimanus populations were estimated by UV updraft light traps and human landing catches within villages and in nearby breeding sites of southern México. Four villages and 5 breeding sites were selected for the study. Light trap and human landing catches were simultaneously carried out in each breeding site and each village. Anopheles albimanus was the most abundant malaria vector caught in breeding sites and in villages. Significant differences in overall An. albimanus abundance among villages and among breeding sites were detected only by human landing catches. In both villages and breeding sites, more mosquitoes were captured by 1 human bait (34.3 +/- 6.3 and 14.6 +/- 2.9, respectively) than by one light trap (15.9 +/- 3.3 and 2.4 +/- 0.3 respectively) collection. After pooling, no significant differences were detected in the abundance estimated by each method in breeding sites and villages. A significant correlation of numbers of specimens between methods was detected. Age structure was different between samples from breeding sites and villages, with more gravid females collected in breeding sites, whereas more nulipars were collected in villages. By collection method, age structure was also different both in breeding sites and in villages. In breeding sites, the percentage of parous females was significantly higher in human landing catches, whereas the percentage of gravid females was significantly higher in light traps. In villages, only the percentage of gravid females was significantly higher in light traps. Our results suggests that UV light traps could be used to measure several entomological parameters of An. albimanus populations because both abundance variations and parity rates were similarly detected by both methods.

Methods for identifying high collision concentration locations (HCCL) for potential safety improvements : phase II, Evaluation of alternative methods for identifying HCCL.

DOT National Transportation Integrated Search

2011-01-01

The objective of network screening should ideally be to not only identify sites for safety : investigation but also to prioritize those sites efficiently. Using roadway, intersection, and : collision data from California, this study compared the perf...

A Mixed Methods Sampling Methodology for a Multisite Case Study

ERIC Educational Resources Information Center

Sharp, Julia L.; Mobley, Catherine; Hammond, Cathy; Withington, Cairen; Drew, Sam; Stringfield, Sam; Stipanovic, Natalie

2012-01-01

The flexibility of mixed methods research strategies makes such approaches especially suitable for multisite case studies. Yet the utilization of mixed methods to select sites for these studies is rarely reported. The authors describe their pragmatic mixed methods approach to select a sample for their multisite mixed methods case study of a…

Clinical accuracy of non-contact infrared thermometer from umbilical region in children: A new side.

PubMed

Apa, Hurşit; Gözmen, Salih; Keskin-Gözmen, Şükran; Aslan, Fatma; Bayram, Nuri; Devrim, İlker

2016-01-01

Measurement from axillary site with digital thermometer has been accepted as the most accurate method. But this method is time consuming. Tympanic and forehead measurements are often used but don't always seem to be more appropriate. Another site, umbilical region, could be an alternative site. This study aims to compare the measurements with axillary digital thermometer and non-contact infrared thermometers at sites from umbilicus and forehead to determine whether umbilical site could be used accurately in children. For each method, 2,048 measurements in total were performed. Using axillary method as gold standard, with a cut-off temperature of 38oC, the sensitivities and specificities, positive and negative predictive values of umbilical and forehead temperatures and area under the ROC curve were determined in non obese children. There was a significant positive correlation between axillary and umbilical temperatures with a correlation coefficient of 0.78. The average difference between the mean of both axillary and umbilical temperatures was -0.47 ± 0.65°C. The Bland-Altman plot showed good accuracy with only 2.5 % of the readings falling outside the 95% level of confidence. Umbilical measurements showed sensitivity of 71.7% and specificity of 95.8%. The area under the ROC curve was 0.93. The easy application may lead noncontact measurements from umbilicus site to be the preferable method for health care providers, but agreement limits mentioned in this study should be considered.

Spatial distribution of source locations for particulate nitrate and sulfate in the upper-midwestern United States

NASA Astrophysics Data System (ADS)

Zhao, Weixiang; Hopke, Philip K.; Zhou, Liming

Two back-trajectory analysis methods designed to be used with multiple site data, simplified quantitative transport bias analysis (SQTBA) and residence time weighted concentration (RTWC), were applied to nitrate and sulfate concentration data from two rural sites (the Mammoth Cave National Park and the Great Smoky Mountain National Park) and five urban sites (Chicago, Cleveland, Detroit, Indianapolis, and St. Louis) for an intensive investigation on the spatial patterns of origins for these two species in the upper-midwestern area. The study was made by dividing the data into five categories: all sites and all seasons, rural sites in summer, rural sites in winter, urban sites in summer, and urban sites in winter. A general conclusion was that the origins of the nitrate in these seven sites were mainly in the upper-midwestern areas, while the sulfate in these seven sites were mainly from the Ohio and Tennessee River Valley areas. The upper-midwestern areas are regions of high ammonia emissions rather than high NO x emissions. In the winter, metropolitan areas showed the highest nitrate emission potential suggesting the importance of local NO x emissions. In the summer, ammonia emissions from fertilizer application in the lower midwestern area made a significant contribution to nitrate in the rural sites of this study. The impact of the wind direction prevalence on the source spatial patterns was observed by comparing the urban and rural patterns of the summer. The differences between the results of two methods are discussed and suggestions for applying these methods are also provided.

Systematic data ingratiation of clinical trial recruitment locations for geographic-based query and visualization.

PubMed

Luo, Jake; Chen, Weiheng; Wu, Min; Weng, Chunhua

2017-12-01

Prior studies of clinical trial planning indicate that it is crucial to search and screen recruitment sites before starting to enroll participants. However, currently there is no systematic method developed to support clinical investigators to search candidate recruitment sites according to their interested clinical trial factors. In this study, we aim at developing a new approach to integrating the location data of over one million heterogeneous recruitment sites that are stored in clinical trial documents. The integrated recruitment location data can be searched and visualized using a map-based information retrieval method. The method enables systematic search and analysis of recruitment sites across a large amount of clinical trials. The location data of more than 1.4 million recruitment sites of over 183,000 clinical trials was normalized and integrated using a geocoding method. The integrated data can be used to support geographic information retrieval of recruitment sites. Additionally, the information of over 6000 clinical trial target disease conditions and close to 4000 interventions was also integrated into the system and linked to the recruitment locations. Such data integration enabled the construction of a novel map-based query system. The system will allow clinical investigators to search and visualize candidate recruitment sites for clinical trials based on target conditions and interventions. The evaluation results showed that the coverage of the geographic location mapping for the 1.4 million recruitment sites was 99.8%. The evaluation of 200 randomly retrieved recruitment sites showed that the correctness of geographic information mapping was 96.5%. The recruitment intensities of the top 30 countries were also retrieved and analyzed. The data analysis results indicated that the recruitment intensity varied significantly across different countries and geographic areas. This study contributed a new data processing framework to extract and integrate the location data of heterogeneous recruitment sites from clinical trial documents. The developed system can support effective retrieval and analysis of potential recruitment sites using target clinical trial factors. Copyright © 2017 Elsevier B.V. All rights reserved.

Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes.

PubMed

Cockburn, Darrell; Wilkens, Casper; Dilokpimol, Adiphol; Nakai, Hiroyuki; Lewińska, Anna; Abou Hachem, Maher; Svensson, Birte

2016-01-01

Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data.

Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes

PubMed Central

Wilkens, Casper; Dilokpimol, Adiphol; Nakai, Hiroyuki; Lewińska, Anna; Abou Hachem, Maher; Svensson, Birte

2016-01-01

Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data. PMID:27504624

Local Site Characterization Using HVSR, ReMi, and SPAC, Study Case: Soccer Field At Autonomous University of Santo Domingo, Dominican Republic

NASA Astrophysics Data System (ADS)

Upegui Botero, F. M.; Rojas Mercedes, N.; Huerta-Lopez, C.; Martinez-Cruzado, J. A.; Suárez, L.; Lopez, A. M.; Huerfano Moreno, V.

2013-12-01

Earthquake effects are frequently quantified by the energy liberated at the source, and the degree of damage produced in urban areas. The damage of historic events such as the Mw=8.3, September 19, 1985 Mexico City Earthquake was dominated by the amplification of seismic waves due to local site conditions. The assessment of local site effects can be carried out with site response analyses in order to determine the properties of the subsoil such as the dominant period, and the Vs30. The evaluation of the aforementioned properties is through the analysis of ground motion. However, in locations with low seismicity, the most convenient method to assess the site effect is the analysis of ambient vibration measurements. The Spatial Auto Correlation method (SPAC) can be used to determine a Vs30 model from ambient vibration measurements using a triangular array of sensors. Refraction Microtremor (ReMi) considers the phase velocity of the Rayleigh waves can be separated of apparent velocities; the aim of the ReMI method is to obtain the Vs30 model. The HVSR technique or Nakamura's method has been adopted to obtain the resonant frequency of the site from the calculation of ratio between the Fourier amplitude spectra or PSD spectrum of the horizontal and vertical components of ambient vibration. The aim of this work is to compare the results using different techniques to assess local site conditions in the urban area of Santo Domingo, Dominican Republic. The data used was collected during the Pan-American Advance Studies Institute (PASI), Workshop held in Santo Domingo, Dominican Republic from July 14 to 25, 2013. The PASI was sponsored by IRIS Consortium, NSF and DOE. Results obtained using SPAC, and ReMi, show a comparable model of surface waves velocities. In addition to the above, the HVSR method is combined with the stiffness matrices method for layered soils to calculate a model of velocities and the predominant period on the site. As part of this work a comparison with geological and geotechnical data on the studied sites was carried out. The advantages and limitations of each procedure are discussed in detail. HVSR Results

Methods for using clinical laboratory test results as baseline confounders in multi-site observational database studies when missing data are expected.

PubMed

Raebel, Marsha A; Shetterly, Susan; Lu, Christine Y; Flory, James; Gagne, Joshua J; Harrell, Frank E; Haynes, Kevin; Herrinton, Lisa J; Patorno, Elisabetta; Popovic, Jennifer; Selvan, Mano; Shoaibi, Azadeh; Wang, Xingmei; Roy, Jason

2016-07-01

Our purpose was to quantify missing baseline laboratory results, assess predictors of missingness, and examine performance of missing data methods. Using the Mini-Sentinel Distributed Database from three sites, we selected three exposure-outcome scenarios with laboratory results as baseline confounders. We compared hazard ratios (HRs) or risk differences (RDs) and 95% confidence intervals (CIs) from models that omitted laboratory results, included only available results (complete cases), and included results after applying missing data methods (multiple imputation [MI] regression, MI predictive mean matching [PMM] indicator). Scenario 1 considered glucose among second-generation antipsychotic users and diabetes. Across sites, glucose was available for 27.7-58.9%. Results differed between complete case and missing data models (e.g., olanzapine: HR 0.92 [CI 0.73, 1.12] vs 1.02 [0.90, 1.16]). Across-site models employing different MI approaches provided similar HR and CI; site-specific models provided differing estimates. Scenario 2 evaluated creatinine among individuals starting high versus low dose lisinopril and hyperkalemia. Creatinine availability: 44.5-79.0%. Results differed between complete case and missing data models (e.g., HR 0.84 [CI 0.77, 0.92] vs. 0.88 [0.83, 0.94]). HR and CI were identical across MI methods. Scenario 3 examined international normalized ratio (INR) among warfarin users starting interacting versus noninteracting antimicrobials and bleeding. INR availability: 20.0-92.9%. Results differed between ignoring INR versus including INR using missing data methods (e.g., RD 0.05 [CI -0.03, 0.13] vs 0.09 [0.00, 0.18]). Indicator and PMM methods gave similar estimates. Multi-site studies must consider site variability in missing data. Different missing data methods performed similarly. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Health technology assessment: Off-site sterilization

PubMed Central

Dehnavieh, Reza; Mirshekari, Nadia; Ghasemi, Sara; Goudarzi, Reza; Haghdoost, AliAkbar; Mehrolhassani, Mohammad Hossain; Moshkani, Zahra; Noori Hekmat, Somayeh

2016-01-01

Background: Every year millions of dollars are expended to equip and maintain the hospital sterilization centers, and our country is not an exception of this matter. According to this, it is important to use more effective technologies and methods in health system in order to reach more effectiveness and saving in costs. This study was conducted with the aim of evaluating the technology of regional sterilization centers. Methods: This study was done in four steps. At the first step, safety and effectiveness of technology was studied via systematic study of evidence. The next step was done to evaluate the economical aspect of off-site sterilization technology using gathered data from systematic review of the texts which were related to the technology and costs of off-site and in-site hospital sterilization. Third step was conducted to collect experiences of using technology in some selected hospitals around the world. And in the last step different aspects of acceptance and use of this technology in Iran were evaluated. Results: Review of the selected articles indicated that efficacy and effectiveness of this technology is Confirmed. The results also showed that using this method is not economical in Iran. Conclusion: According to the revealed evidences and also cost analysis, due to shortage of necessary substructures and economical aspect, installing the off-site sterilization health technology in hospitals is not possible currently. But this method can be used to provide sterilization services for clinics and outpatients centers. PMID:27390714

Electron microscopy methods in studies of cultural heritage sites

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

Vasiliev, A. L., E-mail: a.vasiliev56@gmail.com; Kovalchuk, M. V.; Yatsishina, E. B.

The history of the development and application of scanning electron microscopy (SEM), transmission electron microscopy (TEM), and energy-dispersive X-ray microanalysis (EDXMA) in studies of cultural heritage sites is considered. In fact, investigations based on these methods began when electron microscopes became a commercial product. Currently, these methods, being developed and improved, help solve many historical enigmas. To date, electron microscopy combined with microanalysis makes it possible to investigate any object, from parchment and wooden articles to pigments, tools, and objects of art. Studies by these methods have revealed that some articles were made by ancient masters using ancient “nanotechnologies”; hence,more » their comprehensive analysis calls for the latest achievements in the corresponding instrumental methods and sample preparation techniques.« less

Electron microscopy methods in studies of cultural heritage sites

NASA Astrophysics Data System (ADS)

Vasiliev, A. L.; Kovalchuk, M. V.; Yatsishina, E. B.

2016-11-01

The history of the development and application of scanning electron microscopy (SEM), transmission electron microscopy (TEM), and energy-dispersive X-ray microanalysis (EDXMA) in studies of cultural heritage sites is considered. In fact, investigations based on these methods began when electron microscopes became a commercial product. Currently, these methods, being developed and improved, help solve many historical enigmas. To date, electron microscopy combined with microanalysis makes it possible to investigate any object, from parchment and wooden articles to pigments, tools, and objects of art. Studies by these methods have revealed that some articles were made by ancient masters using ancient "nanotechnologies"; hence, their comprehensive analysis calls for the latest achievements in the corresponding instrumental methods and sample preparation techniques.

An X-ray absorption spectroscopic study of the metal site preference in Al1-xGaxFeO3

NASA Astrophysics Data System (ADS)

Walker, James D. S.; Grosvenor, Andrew P.

2013-01-01

Magnetoelectric materials have potential for being introduced into next generation technologies, especially memory devices. The AFeO3 (Pna21; A=Al, Ga) system has received attention to better understand the origins of magnetoelectric coupling. The magnetoelectric properties this system exhibits depend on the amount of anti-site disorder present, which is affected by the composition and the method of synthesis. In this study, Al1-xGaxFeO3 was synthesized by the ceramic method and studied by X-ray absorption spectroscopy. Al L2,3-, Ga K-, and Fe K-edge spectra were collected to examine how the average metal coordination number changes with composition. Examination of XANES spectra from Al1-xGaxFeO3 indicate that with increasing Ga content, Al increasingly occupies octahedral sites while Ga displays a preference for occupying the tetrahedral site. The Fe K-edge spectra indicate that more Fe is present in the tetrahedral site in AlFeO3 than in GaFeO3, implying more anti-site disorder is present in AlFeO3.

Application of Geographic Information System and Remotesensing in effective solid waste disposal sites selection in Wukro town, Tigray, Ethiopia

NASA Astrophysics Data System (ADS)

Mohammedshum, A. A.; Gebresilassie, M. A.; Rulinda, C. M.; Kahsay, G. H.; Tesfay, M. S.

2014-11-01

Identifying solid waste disposal sites and appropriately managing them is a challenging task to many developing countries. This is a critical problem too in Ethiopia in general and in Wukro town in particular. The existing site for Wukro town is not sufficient in its capacity and it is damaging the environment due to its location, and the type of waste dumped, while the surrounding area is being irrigated. Due to the swift expansion and urbanization developments in Wukro town, it badly needs to develop controlled solid waste dumping site to prevent several contamination problems. This study was conducted first, to assess the existing waste management strategies in Wukro town; and second, to find out the potential waste disposal sites for the town, using GIS and Remote Sensing techniques. The study exploited the Multi-Criteria Evaluation (MCE) methods to combine necessary factors considered for dumping site selection. The selected method also uses various geographical data including remote sensing data, with GIS spatial analysis tools. Accordingly, site suitability maps for each of the factors were developed in a GIS environment. Results indicate that 12 dumping sites were appropriate and they were further ranked against their suitability in terms of wind direction, proximity to settlement area and distance from the center of the town. Finally, two sites are the best suitable for dumping site. This study indicated that the application of Geographic Information System and Remote Sensing techniques are efficient and low cost tools to study and select appropriate dumping site so as to facilitate decision making processes.

Examining differences in types and location of recruitment venues for young males and females from urban neighborhoods: findings from a multi-site HIV prevention study.

PubMed

Chutuape, Kate S; Ziff, Mauri; Auerswald, Colette; Castillo, Marné; McFadden, Antionette; Ellen, Jonathan

2009-01-01

Finding and accessing members of youth subpopulations, such as young men who have sex with men (YMSM) of color or young females of color, for behavioral or disease surveillance or study recruitment, pose particular challenges. Venue-based sampling strategies--which hinge on where individuals congregate or "hang out" rather than where they live--appear to be effective alternatives. Methods used to identify venues focus on engaging members of social networks to learn where targeted populations congregate. However, it is not always clear if and how these methods differ according to gender, whether the youth accessed at a venue are actually from neighborhoods in which the venues are found, and whether the location of venues relative to neighborhoods of residence is different for young men and young women. This study illustrates the gender differences in venue type and venue location where eligible youth study participants from high-risk neighborhoods could be accessed for HIV research across 15 research sites (sites). The findings indicate that the study's method led to identifying venues where one quarter or more of the youth were eligible study participants and from the high-risk neighborhoods. Sites targeting young women of color had a higher proportion of eligible study participants who were also from the high-risk neighborhoods than sites targeting YMSM. Clubs were most commonly identified by sites targeting YMSM as recruitment venues, whereas neighborhood-based service or commercial centers were more common venues for young women of color. This study reveals how venue-based recruitment strategies can be tailored and resources maximized by understanding the key differences in the types of venues preferred by males and females and by recognizing that female-preferred venues are more likely to be closer to home.

Predict and Analyze Protein Glycation Sites with the mRMR and IFS Methods

PubMed Central

Gu, Wenxiang; Zhang, Wenyi; Wang, Jianan

2015-01-01

Glycation is a nonenzymatic process in which proteins react with reducing sugar molecules. The identification of glycation sites in protein may provide guidelines to understand the biological function of protein glycation. In this study, we developed a computational method to predict protein glycation sites by using the support vector machine classifier. The experimental results showed that the prediction accuracy was 85.51% and an overall MCC was 0.70. Feature analysis indicated that the composition of k-spaced amino acid pairs feature contributed the most for glycation sites prediction. PMID:25961025

FIELD OPERATIONS AND METHODS FOR MEASURING THE ECOLOGICAL CONDITION OF NON-WADEABLE RIVERS AND STREAMS

EPA Science Inventory

The methods and instructions for field operations presented in this manual for surveys of non-wadeable streams and rivers were developed and tested based on 55 sample sites in the Mid-Atlantic region and 53 sites in an Oregon study during two years of pilot and demonstration proj...

College Students' Uses and Perceptions of Social Networking Sites for Health and Wellness Information

ERIC Educational Resources Information Center

Zhang, Yan

2012-01-01

Introduction: This study explores college students' use of social networking sites for health and wellness information and their perceptions of this use. Method: Thirty-eight college students were interviewed. Analysis: The interview transcripts were analysed using the qualitative content analysis method. Results: Those who had experience using…

A method of selecting forest sites for air pollution study

Treesearch

Sreedevi K. Bringi; Thomas A. Seliga; Leon S. Dochinger

1981-01-01

Presents a method of selecting suitable forested areas for meaningful assessments of air pollution effects. The approach is based on the premise that environmental influences can significantly affect the forest-air pollution relationship, and that it is, therefore, desirable to equalize such influences at different sites. From existing data on environmental factors and...

Comparison of CyTOF assays across sites: Results of a six-center pilot study.

PubMed

Leipold, Michael D; Obermoser, Gerlinde; Fenwick, Craig; Kleinstuber, Katja; Rashidi, Narges; McNevin, John P; Nau, Allison N; Wagar, Lisa E; Rozot, Virginie; Davis, Mark M; DeRosa, Stephen; Pantaleo, Giuseppe; Scriba, Thomas J; Walker, Bruce D; Olsen, Lars R; Maecker, Holden T

2018-02-01

For more than five years, high-dimensional mass cytometry has been employed to study immunology. However, these studies have typically been performed in one laboratory on one or few instruments. We present the results of a six-center study using healthy control human peripheral blood mononuclear cells (PBMCs) and commercially available reagents to test the intra-site and inter-site variation of mass cytometers and operators. We used prestained controls generated by the primary center as a reference to compare against samples stained at each individual center. Data were analyzed at the primary center, including investigating the effects of two normalization methods. All six sites performed similarly, with CVs for both Frequency of Parent and median signal intensity (MSI) values<30%. Increased background was seen when using the premixed antibody cocktail aliquots at each site, suggesting that cocktails are best made fresh. Both normalization methods tested performed adequately for normalizing MSI values between centers. Clustering algorithms revealed slight differences between the prestained and the sites-stained samples, due mostly to the increased background of a few antibodies. Therefore, we believe that multicenter mass cytometry assays are feasible. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

[Identification of meeting places of sexual partners in 2 cities of the Southern Mexican borders, using the PLACE method].

PubMed

Negroni-Belén, Mirka; Vargas-Guadarrama, Galileo; Rueda-Neria, Celina Magally; Bassett-Hileman, Sarah; Weir, Sharon; Bronfman, Mario

2003-01-01

To identify the meeting sites of new sexual partners in two Southern border cities in Mexico. A descriptive epidemiologic study was carried out in May 2001, by surveying key informants in two border cities. Each reported site was visited to interview a resident subject. Subjects socializing in a subsample of sites were also interviewed. The key informants of the community reported 134 meeting sites in Chetumal and 111 in Ciudad Hidalgo. Both sites had scarce HIV/AIDS prevention activities. Characteristics were obtained for 89 sites in Chetumal and 42 in Ciudad Hidalgo. Almost 21% of interviewees reportedly met a new sexual partner in these sites in the past four weeks. Preventive actions are needed in meeting sites of new sexual partners. This method may provide information to plan for future interventions. The English version of this paper is available too at:http://www.insp.mx/salud/index.html.

Combining stakeholder analysis and spatial multicriteria evaluation to select and rank inert landfill sites.

PubMed

Geneletti, Davide

2010-02-01

This paper presents a method based on the combination of stakeholder analysis and spatial multicriteria evaluation (SMCE) to first design possible sites for an inert landfill, and then rank them according to their suitability. The method was tested for the siting of an inert landfill in the Sarca's Plain, located in south-western Trentino, an alpine region in northern Italy. Firstly, stakeholder analysis was conducted to identify a set of criteria to be satisfied by new inert landfill sites. SMCE techniques were then applied to combine the criteria, and obtain a suitability map of the study region. Subsequently, the most suitable sites were extracted by taking into account also thresholds based on size and shape. These sites were then compared and ranked according to their visibility, accessibility and dust pollution. All these criteria were assessed through GIS modelling. Sensitivity analyses were performed on the results to assess the stability of the ranking with respect to variations in the input (criterion scores and weights). The study concluded that the three top-ranking sites are located close to each other, in the northernmost sector of the study area. A more general finding was that the use of different criteria in the different stages of the analysis allowed to better differentiate the suitability of the potential landfill sites.

SUPERFUND TREATABILITY CLEARINGHOUSE: FINAL REPORT, PHASE I - IMMEDIATE ASSESSMENT, ACME SOLVENTS SITE

EPA Science Inventory

This is a site assessment and feasibility study of incineration alternatives at the ACME Solvents Site at Rockford, Illinois. The document contains laboratory results that are reported to simulate incineration conditions but no details on test methods were provided. The d...

ASSESSMENT OF LARGE RIVER BENTHIC MACROINVERTEBRATE ASSEMBLAGES

EPA Science Inventory

During the summer of 2001, twelve sites were sampled for macroinvertebrates, six each on the Great Miami and Kentucky Rivers. Sites were chosen in each river from those sampled in the 1999 methods comparison study to reflect a disturbance gradient. At each site, a total distanc...

ASSESSMENT OF LARGE RIVER MACROINVERTEBRATE ASSEMBLAGES

EPA Science Inventory

During the summer of 2001, twelve sites were sampled for macroinvertebrates, six each on the Great Miami and Kentucky Rivers. Sites were chosen in each river from those sampled in the 1999 methods comparison study to reflect a disturbance gradient. At each site, a total distanc...

ASSESSMENT OF LARGE RIVER MACROINVERTEBRATES: HOW FAR IS ENOUGH?

EPA Science Inventory

During the summer of 2001, twelve sites were sampled for macroinvertebrates, six each on the Great Miami and Kentucky Rivers. Sites were chosen to reflect a disturbance gradient in each river using sites sampled in a 1999 methods comparison study. Our sampling protocol improves...

Methods for preventing ASR in new construction: results of field exposure sites.

DOT National Transportation Integrated Search

2013-12-01

As part of the FHWA ASR Development and Deployment Program, two sites were built to study ASR in new concrete construction. Concrete blocks were produced with a range of aggregates and cementitious materials and placed on outdoor exposure sites at th...

Evaluation of Cone Penetrometer Data for Permeability Correlation at the Savannah River Site

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

Harris, M.K.

1997-02-01

This report documents the results of an assessment of cone penetrometer technology (CPT) use at the Savannah River Site. The study is intended to provide valuable insight into methods of increasing the utility of CPT data for site characterization.

Verification of chemistry reference ranges using a simple method in sub-Saharan Africa.

PubMed

De Baetselier, Irith; Taylor, Douglas; Mandala, Justin; Nanda, Kavita; Van Campenhout, Christel; Agingu, Walter; Madurai, Lorna; Barsch, Eva-Maria; Deese, Jennifer; Van Damme, Lut; Crucitti, Tania

2016-01-01

Chemistry safety assessments are interpreted by using chemistry reference ranges (CRRs). Verification of CRRs is time consuming and often requires a statistical background. We report on an easy and cost-saving method to verify CRRs. Using a former method introduced by Sigma Diagnostics, three study sites in sub-Saharan Africa, Bondo, Kenya, and Pretoria and Bloemfontein, South Africa, verified the CRRs for hepatic and renal biochemistry assays performed during a clinical trial of HIV antiretroviral pre-exposure prophylaxis. The aspartate aminotransferase/alanine aminotransferase, creatinine and phosphorus results from 10 clinically-healthy participants at the screening visit were used. In the event the CRRs did not pass the verification, new CRRs had to be calculated based on 40 clinically-healthy participants. Within a few weeks, the study sites accomplished verification of the CRRs without additional costs. The aspartate aminotransferase reference ranges for the Bondo, Kenya site and the alanine aminotransferase reference ranges for the Pretoria, South Africa site required adjustment. The phosphorus CRR passed verification and the creatinine CRR required adjustment at every site. The newly-established CRR intervals were narrower than the CRRs used previously at these study sites due to decreases in the upper limits of the reference ranges. As a result, more toxicities were detected. To ensure the safety of clinical trial participants, verification of CRRs should be standard practice in clinical trials conducted in settings where the CRR has not been validated for the local population. This verification method is simple, inexpensive, and can be performed by any medical laboratory.

Time and space in the middle paleolithic: Spatial structure and occupation dynamics of seven open-air sites.

PubMed

Clark, Amy E

2016-05-06

The spatial structure of archeological sites can help reconstruct the settlement dynamics of hunter-gatherers by providing information on the number and length of occupations. This study seeks to access this information through a comparison of seven sites. These sites are open-air and were all excavated over large spatial areas, up to 2,000 m(2) , and are therefore ideal for spatial analysis, which was done using two complementary methods, lithic refitting and density zones. Both methods were assessed statistically using confidence intervals. The statistically significant results from each site were then compiled to evaluate trends that occur across the seven sites. These results were used to assess the "spatial consistency" of each assemblage and, through that, the number and duration of occupations. This study demonstrates that spatial analysis can be a powerful tool in research on occupation dynamics and can help disentangle the many occupations that often make up an archeological assemblage. © 2016 Wiley Periodicals, Inc.

Assessing Non-Technical Site Suitability Criteria for Stormwater Capture, Treatment and Recharge

NASA Astrophysics Data System (ADS)

Eisenstein, W.

2016-12-01

This presentation will describe a new method for assessing non-technical site suitability criteria for the siting of stormwater capture, treatment and recharge (or stormwater CTR) facilities in Sonoma County, California, USA. "Non-technical site suitability criteria" include issues such as community acceptance, aesthetics, nuisances and hazards, and compatibility with neighboring land uses, and are distinguished from "technical criteria" such as hydrology and soil characteristics that are the traditional subject of suitability analyses. Non-technical criteria are rarely, if ever, considered in formal siting suitability studies conducted by agencies and municipalities, yet can be fatal to the prospects of a given project's construction if not identified and mitigated. The researchers developed a new method for identifying and spatially characterizing relevant non-technical criteria through interviews and questionnaires with community stakeholders, and introducing those criteria into a spatial multi-criteria decision analysis framework that assesses site suitabilty across a study watershed (the Upper Petaluma River watershed in Sonoma County).

Multi-site precipitation downscaling using a stochastic weather generator

NASA Astrophysics Data System (ADS)

Chen, Jie; Chen, Hua; Guo, Shenglian

2018-03-01

Statistical downscaling is an efficient way to solve the spatiotemporal mismatch between climate model outputs and the data requirements of hydrological models. However, the most commonly-used downscaling method only produces climate change scenarios for a specific site or watershed average, which is unable to drive distributed hydrological models to study the spatial variability of climate change impacts. By coupling a single-site downscaling method and a multi-site weather generator, this study proposes a multi-site downscaling approach for hydrological climate change impact studies. Multi-site downscaling is done in two stages. The first stage involves spatially downscaling climate model-simulated monthly precipitation from grid scale to a specific site using a quantile mapping method, and the second stage involves the temporal disaggregating of monthly precipitation to daily values by adjusting the parameters of a multi-site weather generator. The inter-station correlation is specifically considered using a distribution-free approach along with an iterative algorithm. The performance of the downscaling approach is illustrated using a 10-station watershed as an example. The precipitation time series derived from the National Centers for Environment Prediction (NCEP) reanalysis dataset is used as the climate model simulation. The precipitation time series of each station is divided into 30 odd years for calibration and 29 even years for validation. Several metrics, including the frequencies of wet and dry spells and statistics of the daily, monthly and annual precipitation are used as criteria to evaluate the multi-site downscaling approach. The results show that the frequencies of wet and dry spells are well reproduced for all stations. In addition, the multi-site downscaling approach performs well with respect to reproducing precipitation statistics, especially at monthly and annual timescales. The remaining biases mainly result from the non-stationarity of NCEP precipitation. Overall, the proposed approach is efficient for generating multi-site climate change scenarios that can be used to investigate the spatial variability of climate change impacts on hydrology.

Comparison of shear-wave slowness profiles at 10 strong-motion sites from noninvasive SASW measurements and measurements made in boreholes

USGS Publications Warehouse

Brown, L.T.; Boore, D.M.; Stokoe, K.H.

2002-01-01

The spectral-analysis-of-surface-waves (SASW) method is a relatively new in situ method for determining shear-wave slownesses. All measurements are made on the ground surface, making it much less costly than methods that require boreholes. The SASW method uses a number of active sources (ranging from a commercial Vibroseis truck to a small handheld hammer for the study conducted here) and different receiver spacings to map a curve of apparent phase velocity versus frequency. With the simplifying assumption that the phase velocities correspond to fundamental mode surface waves, forward modeling yields an estimate of the sub-surface shear-wave slownesses. To establish the reliability of this indirect technique, we conducted a blind evaluation of the SASW method. SASW testing was performed at 10 strong-motion stations at which borehole seismic measurements were previously or subsequently made; if previously made, the borehole results were not used for the interpretation of the SASW data, and vice-versa. Comparisons of the shear-wave slownesses from the SASW and borehole measurements are generally very good. The differences in predicted ground-motion amplifications are less than about 15% for most frequencies. In addition, both methods gave the same NEHRP site classification for seven of the sites. For the other three sites the average velocities from the downhole measurements were only 5-13 m/sec larger than the velocity defining the class C/D boundary. This study demonstrates that in many situations the SASW method can provide subsurface information suitable for site response predictions.

Subepidermal moisture surrounding pressure ulcers in persons with a spinal cord injury: A pilot study

PubMed Central

Harrow, Jeffrey John; Mayrovitz, Harvey N.

2014-01-01

Objective Characterization of a non-invasive method of quantifying subepidermal moisture (SEM) surrounding stages III and IV pressure ulcers (PrUs) in spinal cord injury (SCI). Design Prospective, single-visit, single-rater, observational study, using repeated-measures analysis. Method Setting-inpatient units of one VA SCI Center. Participants Convenience sample of 16 subjects with SCI with stage III or IV PrUs over sacrum or ischium. Interventions Measurement with the MoistureMeter-D, a hand-held device using 300 MHz electromagnetic waves. Outcome measures Dielectric constant, a dimensionless number which increases with the moisture content. Each subject had a PrU site and a control site. Measurements were made at each site, on intact skin, at four points spaced angularly around the site, in triplicate. Results (1) Short-term, single-rater relative error was 2.5%. (2) Order effect: first readings were higher than second readings in 55 of 64 measurement sets. Order effect was significant for control sites (P < 0.0001) but not for PrU sites. (3) Angular effect: SEM varied by angle at the PrU sites (P < 0.01); 12 o'clock position the highest and 6 o'clock the lowest. (4) Ability to differentiate PrUs from intact skin: SEM at PrU sites was greater by 9.0% than control sites (P < 0.05). (5) Site effect: SEM was higher at sacral locations than ischial at control sites by 20% (P < 0.005). Conclusions SEM differentiates PrUs from intact skin. Future study designs must take into account order, angular, and site effects on this measure. This information will inform designers of future studies of SEM in healing of PrUs. PMID:25398030

Methods to characterize environmental settings of stream and groundwater sampling sites for National Water-Quality Assessment

USGS Publications Warehouse

Nakagaki, Naomi; Hitt, Kerie J.; Price, Curtis V.; Falcone, James A.

2012-01-01

Characterization of natural and anthropogenic features that define the environmental settings of sampling sites for streams and groundwater, including drainage basins and groundwater study areas, is an essential component of water-quality and ecological investigations being conducted as part of the U.S. Geological Survey's National Water-Quality Assessment program. Quantitative characterization of environmental settings, combined with physical, chemical, and biological data collected at sampling sites, contributes to understanding the status of, and influences on, water-quality and ecological conditions. To support studies for the National Water-Quality Assessment program, a geographic information system (GIS) was used to develop a standard set of methods to consistently characterize the sites, drainage basins, and groundwater study areas across the nation. This report describes three methods used for characterization-simple overlay, area-weighted areal interpolation, and land-cover-weighted areal interpolation-and their appropriate applications to geographic analyses that have different objectives and data constraints. In addition, this document records the GIS thematic datasets that are used for the Program's national design and data analyses.

Computational Prediction of Protein Epsilon Lysine Acetylation Sites Based on a Feature Selection Method.

PubMed

Gao, JianZhao; Tao, Xue-Wen; Zhao, Jia; Feng, Yuan-Ming; Cai, Yu-Dong; Zhang, Ning

2017-01-01

Lysine acetylation, as one type of post-translational modifications (PTM), plays key roles in cellular regulations and can be involved in a variety of human diseases. However, it is often high-cost and time-consuming to use traditional experimental approaches to identify the lysine acetylation sites. Therefore, effective computational methods should be developed to predict the acetylation sites. In this study, we developed a position-specific method for epsilon lysine acetylation site prediction. Sequences of acetylated proteins were retrieved from the UniProt database. Various kinds of features such as position specific scoring matrix (PSSM), amino acid factors (AAF), and disorders were incorporated. A feature selection method based on mRMR (Maximum Relevance Minimum Redundancy) and IFS (Incremental Feature Selection) was employed. Finally, 319 optimal features were selected from total 541 features. Using the 319 optimal features to encode peptides, a predictor was constructed based on dagging. As a result, an accuracy of 69.56% with MCC of 0.2792 was achieved. We analyzed the optimal features, which suggested some important factors determining the lysine acetylation sites. We developed a position-specific method for epsilon lysine acetylation site prediction. A set of optimal features was selected. Analysis of the optimal features provided insights into the mechanism of lysine acetylation sites, providing guidance of experimental validation. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Between Site Reliability of Startle Prepulse Inhibition Across Two Early Psychosis Consortia

PubMed Central

Addington, Jean; Cannon, Tyrone D.; Cornblatt, Barbara A.; de la Fuente-Sandoval, Camilo; Mathalon, Dan H.; Perkins, Diana O.; Seidman, Larry J.; Tsuang, Ming; Walker, Elaine F.; Woods, Scott W.; Bachman, Peter; Belger, Ayse; Carrión, Ricardo E.; Donkers, Franc C.L.; Duncan, Erica; Johannesen, Jason; León-Ortiz, Pablo; Light, Gregory; Mondragón, Alejandra; Niznikiewicz, Margaret; Nunag, Jason; Roach, Brian J.; Solís-Vivanco, Rodolfo

2014-01-01

Prepulse inhibition (PPI) and reactivity of the acoustic startle response are widely used biobehavioral markers in psychopathology research. Previous studies have demonstrated that PPI and startle reactivity exhibit substantial within-site stability; between-site stability, however, has not been established. In two separate consortia investigating biomarkers of early psychosis, traveling subjects studies were performed as part of quality assurance procedures in order to assess the fidelity of data across sites. In the North American Prodromal Longitudinal Studies (NAPLS) Consortium, 8 normal subjects traveled to each of the 8 NAPLS sites and were tested twice at each site on the startle PPI paradigm. In preparation for a binational study, 10 healthy subjects were assessed twice in both San Diego and Mexico City. Intraclass correlations between and within sites were significant for PPI and startle response parameters, confirming the reliability of startle measures across sites in both consortia. There were between site differences in startle magnitude in the NAPLS study that did not appear to be related to methods or equipment. In planning multi-site studies, it is essential to institute quality assurance procedures early and establish between site reliability to assure comparable data across sites. PMID:23799460

Immobilization of alkaline phosphatase on solid surface through self-assembled monolayer and by active-site protection.

PubMed

Gao, En-Feng; Kang, Kyung Lhi; Kim, Jeong Hee

2014-06-01

Retaining biological activity of a protein after immobilization is an important issue and many studies reported to enhance the activity of proteins after immobilization. We recently developed a new immobilization method of enzyme using active-site protection and minimization of the cross-links between enzyme and surface with a DNA polymerase as a model system. In this study, we extended the new method to an enzyme with a small mono-substrate using alkaline phosphatase (AP) as another model system. A condition to apply the new method is that masking agents, in this case its own substrate needs to stay at the active-site of the enzyme to be immobilized in order to protect the active-site during the harsh immobilization process. This could be achieved by removal of essential divalent ion, Zn2+ that is required for full enzyme activity of AP from the masking solution while active-site of AP was protected with p-nitrophenyl phosphate (pNPP). Approximately 40% of the solution-phase activity was acquired with active-site protected immobilized AP. In addition to protection active-site of AP, the number of immobilization links was kinetically controlled. When the mole fraction of the activated carboxyl group of the linker molecule in self-assembled monolayer (SAM) of 12-mercaptododecanoic acid and 6-mercapto-1-ethanol was varied, 10% of 12-mercaptododecanoic acid gave the maximum enzyme activity. Approximately 51% increase in enzyme activity of the active-site protected AP was observed compared to that of the unprotected group. It was shown that the concept of active-site protection and kinetic control of the number of covalent immobilization bonds can be extended to enzymes with small mono-substrates. It opens the possibility of further extension of the new methods of active-site protection and kinetic control of immobilization bond to important enzymes used in research and industrial fields.

A Simplified 4-Site Economical Intradermal Post-Exposure Rabies Vaccine Regimen: A Randomised Controlled Comparison with Standard Methods

PubMed Central

Warrell, Mary J.; Riddell, Anna; Yu, Ly-Mee; Phipps, Judith; Diggle, Linda; Bourhy, Hervé; Deeks, Jonathan J.; Fooks, Anthony R.; Audry, Laurent; Brookes, Sharon M.; Meslin, François-Xavier; Moxon, Richard; Pollard, Andrew J.; Warrell, David A.

2008-01-01

Background The need for economical rabies post-exposure prophylaxis (PEP) is increasing in developing countries. Implementation of the two currently approved economical intradermal (ID) vaccine regimens is restricted due to confusion over different vaccines, regimens and dosages, lack of confidence in intradermal technique, and pharmaceutical regulations. We therefore compared a simplified 4-site economical PEP regimen with standard methods. Methods Two hundred and fifty-four volunteers were randomly allocated to a single blind controlled trial. Each received purified vero cell rabies vaccine by one of four PEP regimens: the currently accepted 2-site ID; the 8-site regimen using 0.05 ml per ID site; a new 4-site ID regimen (on day 0, approximately 0.1 ml at 4 ID sites, using the whole 0.5 ml ampoule of vaccine; on day 7, 0.1 ml ID at 2 sites and at one site on days 28 and 90); or the standard 5-dose intramuscular regimen. All ID regimens required the same total amount of vaccine, 60% less than the intramuscular method. Neutralising antibody responses were measured five times over a year in 229 people, for whom complete data were available. Findings All ID regimens showed similar immunogenicity. The intramuscular regimen gave the lowest geometric mean antibody titres. Using the rapid fluorescent focus inhibition test, some sera had unexpectedly high antibody levels that were not attributable to previous vaccination. The results were confirmed using the fluorescent antibody virus neutralisation method. Conclusions This 4-site PEP regimen proved as immunogenic as current regimens, and has the advantages of requiring fewer clinic visits, being more practicable, and having a wider margin of safety, especially in inexperienced hands, than the 2-site regimen. It is more convenient than the 8-site method, and can be used economically with vaccines formulated in 1.0 or 0.5 ml ampoules. The 4-site regimen now meets all requirements of immunogenicity for PEP and can be introduced without further studies. Trial Registration Controlled-Trials.com ISRCTN 30087513 PMID:18431444

Evaluation of acidity estimation methods for mine drainage, Pennsylvania, USA.

PubMed

Park, Daeryong; Park, Byungtae; Mendinsky, Justin J; Paksuchon, Benjaphon; Suhataikul, Ratda; Dempsey, Brian A; Cho, Yunchul

2015-01-01

Eighteen sites impacted by abandoned mine drainage (AMD) in Pennsylvania were sampled and measured for pH, acidity, alkalinity, metal ions, and sulfate. This study compared the accuracy of four acidity calculation methods with measured hot peroxide acidity and identified the most accurate calculation method for each site as a function of pH and sulfate concentration. Method E1 was the sum of proton and acidity based on total metal concentrations; method E2 added alkalinity; method E3 also accounted for aluminum speciation and temperature effects; and method E4 accounted for sulfate speciation. To evaluate errors between measured and predicted acidity, the Nash-Sutcliffe efficiency (NSE), the coefficient of determination (R (2)), and the root mean square error to standard deviation ratio (RSR) methods were applied. The error evaluation results show that E1, E2, E3, and E4 sites were most accurate at 0, 9, 4, and 5 of the sites, respectively. Sites where E2 was most accurate had pH greater than 4.0 and less than 400 mg/L of sulfate. Sites where E3 was most accurate had pH greater than 4.0 and sulfate greater than 400 mg/L with two exceptions. Sites where E4 was most accurate had pH less than 4.0 and more than 400 mg/L sulfate with one exception. The results indicate that acidity in AMD-affected streams can be accurately predicted by using pH, alkalinity, sulfate, Fe(II), Mn(II), and Al(III) concentrations in one or more of the identified equations, and that the appropriate equation for prediction can be selected based on pH and sulfate concentration.

A prospective study evaluating duration of swine breeding herd PRRS virus-free status and its relationship with measured risk.

PubMed

Holtkamp, Derald J; Yeske, Paul E; Polson, Dale D; Melody, Jamie L; Philips, Reid C

2010-09-01

A variety of methods for eliminating the PRRS virus from pig production sites have been successfully applied. However, success in maintaining a PRRS virus-free status for extended periods of time following elimination has been inconsistent and unpredictable. The objective of this study was to evaluate whether risks measured using version 1 of the American Association of Swine Veterinarians (AASV) PRRS Risk Assessment for the Breeding Herd, season of year and method by which swine breeding herd sites were established PRRS virus-free were associated with how long they retained their virus-free status. Thirty-three swine farrow-to-wean breeding herd sites that were established as PRRS virus-free by either populating a new site with virus-free breeding animals or by completely depopulating the site and repopulating with PRRS virus-free breeding animals were enrolled in this study. Survival analysis, using the Cox proportional hazards model and Kaplan-Meier survival curves, was performed where the outcome was the duration of time PRRS virus-free breeding herd sites remained virus-free ("survived"). Covariates evaluated included the internal and external risk scores measured by the PRRS Risk Assessment for the Breeding Herd as well as the season and the method by which the site was established free of the PRRS virus. All but 5 (15%) of the 33 sites became positive to the PRRS virus during the course of the study and approximately 40% became positive within 1 year from when they were established free of the PRRS virus. A higher external risk score was associated with a greater risk of becoming positive to the PRRS virus and shorter survival times. The internal risk score was not significantly associated with survival. Establishing breeding herd sites free of the PRRS virus in winter months (November through February) was associated with a greater risk of becoming positive to the PRRS virus and shorter survival times compared to those established in non-winter months. The association between the risk of becoming positive to the PRRS virus and the external risk score was confounded by the method the site was established PRRS virus-free. 2010 Elsevier B.V. All rights reserved.

A Profilometry-Based Dentifrice Abrasion Method for V8 Brushing Machines Part III: Multi-Laboratory Validation Testing of RDA-PE.

PubMed

Schneiderman, Eva; Colón, Ellen L; White, Donald J; Schemehorn, Bruce; Ganovsky, Tara; Haider, Amir; Garcia-Godoy, Franklin; Morrow, Brian R; Srimaneepong, Viritpon; Chumprasert, Sujin

2017-09-01

We have previously reported on progress toward the refinement of profilometry-based abrasivity testing of dentifrices using a V8 brushing machine and tactile or optical measurement of dentin wear. The general application of this technique may be advanced by demonstration of successful inter-laboratory confirmation of the method. The objective of this study was to explore the capability of different laboratories in the assessment of dentifrice abrasivity using a profilometry-based evaluation technique developed in our Mason laboratories. In addition, we wanted to assess the interchangeability of human and bovine specimens. Participating laboratories were instructed in methods associated with Radioactive Dentin Abrasivity-Profilometry Equivalent (RDA-PE) evaluation, including site visits to discuss critical elements of specimen preparation, masking, profilometry scanning, and procedures. Laboratories were likewise instructed on the requirement for demonstration of proportional linearity as a key condition for validation of the technique. Laboratories were provided with four test dentifrices, blinded for testing, with a broad range of abrasivity. In each laboratory, a calibration curve was developed for varying V8 brushing strokes (0, 4,000, and 10,000 strokes) with the ISO abrasive standard. Proportional linearity was determined as the ratio of standard abrasion mean depths created with 4,000 and 10,000 strokes (2.5 fold differences). Criteria for successful calibration within the method (established in our Mason laboratory) was set at proportional linearity = 2.5 ± 0.3. RDA-PE was compared to Radiotracer RDA for the four test dentifrices, with the latter obtained by averages from three independent Radiotracer RDA sites. Individual laboratories and their results were compared by 1) proportional linearity and 2) acquired RDA-PE values for test pastes. Five sites participated in the study. One site did not pass proportional linearity objectives. Data for this site are not reported at the request of the researchers. Three of the remaining four sites reported herein tested human dentin and all three met proportional linearity objectives for human dentin. Three of four sites participated in testing bovine dentin and all three met the proportional linearity objectives for bovine dentin. RDA-PE values for test dentifrices were similar between sites. All four sites that met proportional linearity requirement successfully identified the dentifrice formulated above the industry standard 250 RDA (as RDA-PE). The profilometry method showed at least as good reproducibility and differentiation as Radiotracer assessments. It was demonstrated that human and bovine specimens could be used interchangeably. The standardized RDA-PE method was reproduced in multiple laboratories in this inter-laboratory study. Evidence supports that this method is a suitable technique for ISO method 11609 Annex B.

Timing of nest vegetation measurement may obscure adaptive significance of nest-site characteristics: A simulation study.

PubMed

McConnell, Mark D; Monroe, Adrian P; Burger, Loren Wes; Martin, James A

2017-02-01

Advances in understanding avian nesting ecology are hindered by a prevalent lack of agreement between nest-site characteristics and fitness metrics such as nest success. We posit this is a result of inconsistent and improper timing of nest-site vegetation measurements. Therefore, we evaluated how the timing of nest vegetation measurement influences the estimated effects of vegetation structure on nest survival. We simulated phenological changes in nest-site vegetation growth over a typical nesting season and modeled how the timing of measuring that vegetation, relative to nest fate, creates bias in conclusions regarding its influence on nest survival. We modeled the bias associated with four methods of measuring nest-site vegetation: Method 1-measuring at nest initiation, Method 2-measuring at nest termination regardless of fate, Method 3-measuring at nest termination for successful nests and at estimated completion for unsuccessful nests, and Method 4-measuring at nest termination regardless of fate while also accounting for initiation date. We quantified and compared bias for each method for varying simulated effects, ranked models for each method using AIC, and calculated the proportion of simulations in which each model (measurement method) was selected as the best model. Our results indicate that the risk of drawing an erroneous or spurious conclusion was present in all methods but greater with Method 2 which is the most common method reported in the literature. Methods 1 and 3 were similarly less biased. Method 4 provided no additional value as bias was similar to Method 2 for all scenarios. While Method 1 is seldom practical to collect in the field, Method 3 is logistically practical and minimizes inherent bias. Implementation of Method 3 will facilitate estimating the effect of nest-site vegetation on survival, in the least biased way, and allow reliable conclusions to be drawn.

Slope stability and bearing capacity of landfills and simple on-site test methods.

PubMed

Yamawaki, Atsushi; Doi, Yoichi; Omine, Kiyoshi

2017-07-01

This study discusses strength characteristics (slope stability, bearing capacity, etc.) of waste landfills through on-site tests that were carried out at 29 locations in 19 sites in Japan and three other countries, and proposes simple methods to test and assess the mechanical strength of landfills on site. Also, the possibility of using a landfill site was investigated by a full-scale eccentric loading test. As a result of this, landfills containing more than about 10 cm long plastics or other fibrous materials were found to be resilient and hard to yield. An on-site full scale test proved that no differential settlement occurs. The repose angle test proposed as a simple on-site test method has been confirmed to be a good indicator for slope stability assessment. The repose angle test suggested that landfills which have high, near-saturation water content have considerably poorer slope stability. The results of our repose angle test and the impact acceleration test were related to the internal friction angle and the cohesion, respectively. In addition to this, it was found that the air pore volume ratio measured by an on-site air pore volume ratio test is likely to be related to various strength parameters.

Multi-Site Ethnography, Hypermedia and the Productive Hazards of Digital Methods: A Struggle for Liveness

ERIC Educational Resources Information Center

Gallagher, Kathleen; Freeman, Barry

2011-01-01

This article explores the possibilities and frustrations of using digital methods in a multi-sited ethnographic research project. The project, "Urban School Performances: The interplay, through live and digital drama, of local-global knowledge about student engagement", is a study of youth and teachers in drama classrooms in contexts of…

Recruiting Research Participants at Community Education Sites

PubMed Central

SADLER, GEORGIA ROBINS; PETERSON, MELANIE; WASSERMAN, LINDA; MILLS, PAUL L.; MALCARNE, VANESSA L.; ROCK, CHERYL; ANCOLI-ISRAEL, SONIA; MOORE, AMANDA; WELDON, RAI-NESHA; GARCIA, TENISHA; KOLODNER, RICHARD D.

2006-01-01

Background Minority groups are underrepresented in research, making it difficult to apply medical advances with confidence. In this study, we explored whether community-based cancer education sites and educators serving the African American community could be used to recruit minority participants to research. Methods We invited Individuals at community education sites to provide buccal scrapings, saliva samples, psychometric data, and personal information anonymously. Results Culturally aligned community sites (100%) collaborated in the research recruitment, as did 83% of the individuals at those sites. Conclusion Community-based education sites offer exceptional promise for teaching about research benefits and recruiting members of minority groups to research studies. PMID:16497136

Human Splice-Site Prediction with Deep Neural Networks.

PubMed

Naito, Tatsuhiko

2018-04-18

Accurate splice-site prediction is essential to delineate gene structures from sequence data. Several computational techniques have been applied to create a system to predict canonical splice sites. For classification tasks, deep neural networks (DNNs) have achieved record-breaking results and often outperformed other supervised learning techniques. In this study, a new method of splice-site prediction using DNNs was proposed. The proposed system receives an input sequence data and returns an answer as to whether it is splice site. The length of input is 140 nucleotides, with the consensus sequence (i.e., "GT" and "AG" for the donor and acceptor sites, respectively) in the middle. Each input sequence model is applied to the pretrained DNN model that determines the probability that an input is a splice site. The model consists of convolutional layers and bidirectional long short-term memory network layers. The pretraining and validation were conducted using the data set tested in previously reported methods. The performance evaluation results showed that the proposed method can outperform the previous methods. In addition, the pattern learned by the DNNs was visualized as position frequency matrices (PFMs). Some of PFMs were very similar to the consensus sequence. The trained DNN model and the brief source code for the prediction system are uploaded. Further improvement will be achieved following the further development of DNNs.

The performance of various palaeointensity techniques as a function of rock magnetic behaviour - A case study for La Palma

NASA Astrophysics Data System (ADS)

Monster, Marilyn W. L.; de Groot, Lennart V.; Biggin, Andrew J.; Dekkers, Mark J.

2015-05-01

Three different palaeointensity methods were applied to six historical and three carbon-dated flows from the island of La Palma (Spain); in total fifteen sites were processed. The two 20th-century flows were sampled at multiple locations as their obtained directions and intensities can be compared directly to those from the International Geomagnetic Reference Field (IGRF). After determination of the declinations and inclinations of the natural remanent magnetisation (NRM) by thermal and alternating-field demagnetisation, the samples were subjected to standard rock magnetic analyses to determine their Curie and alteration temperatures. Based on these characteristics, the sites were allocated to one of four rock magnetic groups labelled L∗, L, C, and H, a division primarily based on the temperature-dependent behaviour of the low-field susceptibility that has been used in studies of other volcanic edifices. Scanning electron microscope (SEM) observations revealed little oxidation and exsolution (oxidation classes I to III). Palaeointensities were determined using the classic Thellier-Thellier method (Aitken and IZZI protocols), the microwave method and the domain-state-corrected multispecimen method. Thellier-Thellier and microwave results were analysed using the ThellierTool A and B sets of selection criteria as modified by Paterson et al. (2014). Their combined success rate was around 40%. Of the eight IGRF sites, two yielded average intensities within 10% of the IGRF value. For the microwave method, three sites reproduced the IGRF intensity within 10%. In the domain-state-corrected multispecimen protocol, just one site (site 9, 1971) passed the 'ARM-test' (applied in retrospect) and showed less than 3% progressive alteration. Its multispecimen result reproduced the palaeofield within error. The other IGRF sites over- or underestimated the palaeofield by up to 50%. The seven older sites produced plausible palaeointensities, generally within a few μT of model data, and if multiple methods were successful, the results were within error of each other. For all three PI methods, it seems that sites with low Curie temperatures (<150 °C; group L∗), are more likely to pass all selection criteria while substantially over- or underestimating the palaeofield. It is hypothesised that time-dependent processes after cooling of the lava would be a prime reason for this discrepancy: PI experiments with a laboratory thermoremanent magnetisation (TRM), imparted at a temperature above the site's dominant Curie temperature but below its alteration temperature, yielded the correct intensity of the laboratory-imparted TRM. When two or three methods agree to within a few μT, the obtained palaeointensity is close to the palaeofield. Multi-method consistency provides an additional palaeointensity reliability check.

A rapid and reliable PCR method for genotyping the ABO blood group.

PubMed

O'Keefe, D S; Dobrovic, A

1993-01-01

The ABO blood group has been used extensively as a marker in population studies, epidemiology, and forensic work. However, until the cloning of the gene, it was not possible to determine the genotype of group A and B individuals without recourse to family studies. We have developed a method to determine the ABO genotype directly from human DNA using multiplex PCR and restriction enzyme analysis. Two PCR fragments spanning positions 258 and 700 of the cDNA sequence are amplified. The site at position 258 allows us to differentiate the O allele from the A and B alleles. The site at position 700 allows us to distinguish the B allele from the A and O alleles. Analysis at the two sites thus allows us to distinguish the three alleles. The multiplex PCR product is digested separately with four enzymes, two for each of the sites. The pair of enzymes for each site cut in a reciprocal fashion. Whereas one enzyme for each site is theoretically sufficient for genotyping, the use of complementary pairs of enzymes prevents the assignment of a false genotype as a result of false negative or partial digestion. This method is fast and reliable, does not rely on probing of blots, and should be widely applicable.

Geophysical studies of the Syncline Ridge area, Nevada Test Site, Nye County, Nevada

USGS Publications Warehouse

Hoover, D.B.; Hanna, W.F.; Anderson, L.A.; Flanigan, V.J.; Pankratz, L.W.

1982-01-01

A wide variety of geophysical methods were employed to study a proposed nuclear waste site at Syncline Ridge on the Nevada Test Site, Nev. The proposed site was believed to be a relatively undisturbed synclinal structure containing a thick argillite unit of Misslsslppian age, the Eleana Formation unit J, which would be the emplacement medium. Data acquisition for the geophysical studies was constrained because of rugged topography in a block of Tipplpah Limestone overlying the central part of the proposed site. This study employed gravity, magnetic, seismic refraction and reflection, and four distinct electrical methods to try and define the structural integrity and shape of the proposed repository medium. Detailed and regional gravity work revealed complex structure at the site. Magnetics helped only in identifying small areas of Tertiary volcanic rocks because of low magnetization of the rocks. Seismic refraction assisted in identifying near surface faulting and bedrock structure. Difficulty was experienced in obtaining good quality reflection data. This implied significant structural complexity but also revealed the principal features that were supported by other data. Electrical methods were used for fault identification and for mapping of a thick argillaceous unit of the Eleana Formation in which nuclear waste was to be emplaced. The geophysical studies indicate that major faults along the axis of Syncline Ridge and on both margins have large vertical offsets displacing units so as not only to make mining difficult, but also providing potential paths for waste migration to underlying carbonate aquifers. The Eleana Formation appeared heterogeneous, which was inferred to be due to structural complexity. Only a small region in the northwest part of the study area was found to contain a thick and relatively undisturbed volume of host rock.

A Study of Ziegler–Natta Propylene Polymerization Catalysts by Spectroscopic Methods

PubMed Central

Tkachenko, Olga P.; Kucherov, Alexey V.; Kustov, Leonid M.; Virkkunen, Ville; Leinonen, Timo; Denifl, Peter

2017-01-01

Ziegler–Natta polymerization catalysts were characterized by a complex of surface- and bulk-sensitive methods (DRIFTS, XPS, ESR, and XAS = XANES + EXAFS). A diffuse-reflectance Fourier-transform IR spectroscopy (DRIFTS) study showed the presence of strong Lewis acid sites in different concentrations and absence of strong basic sites in the polymerization catalysts. X-ray photoelectron spectroscopy (XPS), electron-spin resonance (ESR), and (X-ray absorption near-edge structure (XANES) analysis revealed the presence of Ti4+, Ti3+, Ti2+, and Ti1+ species in the surface layers and in the bulk of catalysts. The samples under study differ drastically in terms of the number of ESR-visible paramagnetic sites. The EXAFS study shows the presence of a Cl atom as a nearest neighbor of the absorbing Ti atom. PMID:28772850

Stratigraphy Identification with Emphasis to Shells Layer using 2-D Electrical Resistivity Method at Guar Kepah, Penang

NASA Astrophysics Data System (ADS)

Rosli, Najmiah; Mansor, Hafizuddin; Ismail, N. A.; Masnan, S. S. K.; Saidin, M.

2018-04-01

2-D electrical resistivity method was done at an archaeological site in Guar Kepah, Penang, to determine its stratigraphy with emphasis to shells layer. This study aims to guide the archaeological studies where many prehistoric findings are related to shells and also for engineering purposes as an archaeological gallery is to be built there. Results show that the area is composed of three unconsolidated soil strata where the uppermost layer is sandy-clay, followed by shells layer, and lastly sandy layer. The shells layer is undulating with similar thickness throughout the site, but thickens at the northern part of the study area. The depth of the shells layer however, is different at different parts of the site.

ASSESSMENT OF LARGE RIVER MACROINVERTEBRATE ASSEMBLAGES: HOW FAR IS ENOUGH?

EPA Science Inventory

During the summer of 2001, twelve sites were sampled for macroinvertebrates, six each on the Great Miami and Kentucky Rivers. Sites were chosen in each river from those sampled in the 1999 methods comparison study to reflect a disturbance gradient. At each site, a total distanc...

Applying site-index curves to northern hardwoods in New Hampshire

Treesearch

Dale S. Solomon

1968-01-01

Describes a new method for testing site-index curves. Study results indicate that Vermont site-index curves for yellow birch, paper birch, white ash, and sugar maple, and New York-Connecticut curves for red maple, can be applied satisfactorily in New Hampshire when used with certain precautions and corrections.

Efficiency of Fiscal Allocations in Site-Based Empowered Schools

ERIC Educational Resources Information Center

Meyer, Jerome Jay

2011-01-01

This study implemented a two phase concurrent mixed-methods design to generate a greater understanding of how elementary schools with increased autonomy in fiscal decision making allocated their money, how their site-based decisions affected allocative efficiency, and how increased autonomy affected site-based decision making when compared with a…

A combined source and site-effect study of ground motions generated by an earthquake in Port au Prince (Haiti)

NASA Astrophysics Data System (ADS)

St Fleur, Sadrac; Courboulex, Francoise; Bertrand, Etienne; Deschamps, Anne; Mercier de Lepinay, Bernard; Prepetit, Claude; Hough, Suzan

2013-04-01

We present the preliminary results of a study with the aim of understanding how some combinations of source and site effects can generate extreme ground motions in the city of Port au Prince. For this study, we have used the recordings of several tens of earthquakes with magnitude larger than 3.0 at 3 to 14 stations from three networks: 3 stations of the Canadian Broad-band network (RNCan), 2 stations of the educational French network (SaE) and 9 stations of the accelerometric network (Bureau des Mines et de l'Energie of Port au Prince and US Geological survey). In order to estimate site effects under each station, we have applied classical spectral ratio methods: The H/V (Horizontal/Vertical) method was first used to select a reference station, which was itself used in a site/reference method. Because a true reference station was not available, we have used successively stations HCEA, then station PAPH, then an average value of 3 stations. In the frequency range studied (0.5 - 20 Hz), we found a site-to-reference ratio up to 3 to 8. However, these values present a large variability, depending on the earthquake recordings. This may indicate that the observed amplification from one station to the other depends not only from the local site effect but also from the source. We then used the same earthquake recordings as Empirical Green's Functions (EGF) in order to simulate the ground motions generated by a virtual earthquake. For this simulation, we have used a stochastic EGF summation method. We have worked on the simulation of a magnitude Mw=6.8 using successively 2 smaller events that occurred on the Leogane fault as EGF. The results obtained using the two events are surprisingly very different. Using the first EGF, we obtained almost the same ground motion values at each station in Port au Prince, whereas with the second EGF, the results highlight large differences. The large variability obtained in the results indicates that a particular combination of site and source effects may be responsible of large ground motions, especially at some given sites.

Microtremors study applying the SPAC method in Colima state, Mexico.

NASA Astrophysics Data System (ADS)

Vázquez Rosas, R.; Aguirre González, J.; Mijares Arellano, H.

2007-05-01

One of the main parts of seismic risk studies is to determine the site effect. This can be estimated by means of the microtremors measurements. From the H/V spectral ratio (Nakamura, 1989), the predominant period of the site can be estimated. Although the predominant period by itself can not represent the site effect in a wide range of frequencies and doesn't provide information of the stratigraphy. The SPAC method (Spatial Auto-Correlation Method, Aki 1957), on the other hand, is useful to estimate the stratigraphy of the site. It is based on the simultaneous recording of microtremors in several stations deployed in an instrumental array. Through the spatial autocorrelation coefficient computation, the Rayleigh wave dispersion curve can be cleared. Finally the stratigraphy model (thickness, S and P wave velocity, and density of each layer) is estimated by fitting the theoretical dispersion curve with the observed one. The theoretical dispersion curve is initially computed using a proposed model. That model is modified several times until the theoretical curve fit the observations. This method requires of a minimum of three stations where the microtremors are observed simultaneously in all the stations. We applied the SPAC method to six sites in Colima state, Mexico. Those sites are Santa Barbara, Cerro de Ortega, Tecoman, Manzanillo and two in Colima city. Totally 16 arrays were carried out using equilateral triangles with different apertures with a minimum of 5 m and a maximum of 60 m. For recording microtremors we used short period (5 seconds) velocity type vertical sensors connected to a K2 (Kinemetrics) acquisition system. We could estimate the velocities of the most superficial layers reaching different depths in each site. For Santa Bárbara site the exploration depth was about 30 m, for Tecoman 12 m, for Manzanillo 35 m, for Cerro de Ortega 68 m, and the deepest site exploration was obtained in Colima city with a depth of around 73 m. The S wave velocities fluctuate between 230 m/s and 420 m/s for the most superficial layer. It means that, in general, the most superficial layers are quite competent. The superficial layer with smaller S wave velocity was observed in Tecoman, while that of largest S wave velocity was observed in Cerro de Ortega. Our estimations are consistent with down-hole velocity records obtained in Santa Barbara by previous studies.

Nonlethal laparoscopic detection of intersex (testicular oocytes) in largemouthbass (Micropterus salmoides) and smallmouth bass (Micropterus dolomieu)

USGS Publications Warehouse

Blazer, Vicki S.; Macleod, Alexander H; Matsche, Mark A; Yonkos, Lance T

2017-01-01

Intersex in wild fish populations has received considerable attention in the scientific literature and public media. Conventional detection of testicular oocytes (TO), the presence of immature oocytes within testis of male fish, employs transverse sectioning of excised testis and is lethal. This present study used a non-lethal laparoscopic technique to collect biopsies of testis from black bass, entering the body cavity via the genital pore. Detection of TO was compared between biopsy and conventional methods using 79 smallmouth bass (SMB) Micropterus dolomieu from 8 sites and 68 largemouth bass (LMB) M. salmoides from 4 sites. Both methods performed similarly at sites where TO severity was moderate or high (6 of 8 SMB sites) while transverse sectioning resulted in superior TO detection at sites where severity was low (2 of 8 SMB sites and all 4 LMB sites). In SMB, TO prevalence by transverse and biopsy methods was strongly correlated across sites (r2 = 0.81) and severity reported by enumeration of TO was moderately correlated across sites (r2 = 0.59). Survival of a subset of LMB (n = 20) to 28-d after laparoscopic surgery was 90%. This research indicates that laparoscopy may be useful for monitoring the prevalence and severity of TO in Micropterus species, particularly when lethal sampling is precluded.

Acceleration of Binding Site Comparisons by Graph Partitioning.

PubMed

Krotzky, Timo; Klebe, Gerhard

2015-08-01

The comparison of protein binding sites is a prominent task in computational chemistry and has been studied in many different ways. For the automatic detection and comparison of putative binding cavities the Cavbase system has been developed which uses a coarse-grained set of pseudocenters to represent the physicochemical properties of a binding site and employs a graph-based procedure to calculate similarities between two binding sites. However, the comparison of two graphs is computationally quite demanding which makes large-scale studies such as the rapid screening of entire databases hardly feasible. In a recent work, we proposed the method Local Cliques (LC) for the efficient comparison of Cavbase binding sites. It employs a clique heuristic to detect the maximum common subgraph of two binding sites and an extended graph model to additionally compare the shape of individual surface patches. In this study, we present an alternative to further accelerate the LC method by partitioning the binding-site graphs into disjoint components prior to their comparisons. The pseudocenter sets are split with regard to their assigned phyiscochemical type, which leads to seven much smaller graphs than the original one. Applying this approach on the same test scenarios as in the former comprehensive way results in a significant speed-up without sacrificing accuracy. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

MDD-carb: a combinatorial model for the identification of protein carbonylation sites with substrate motifs.

PubMed

Kao, Hui-Ju; Weng, Shun-Long; Huang, Kai-Yao; Kaunang, Fergie Joanda; Hsu, Justin Bo-Kai; Huang, Chien-Hsun; Lee, Tzong-Yi

2017-12-21

Carbonylation, which takes place through oxidation of reactive oxygen species (ROS) on specific residues, is an irreversibly oxidative modification of proteins. It has been reported that the carbonylation is related to a number of metabolic or aging diseases including diabetes, chronic lung disease, Parkinson's disease, and Alzheimer's disease. Due to the lack of computational methods dedicated to exploring motif signatures of protein carbonylation sites, we were motivated to exploit an iterative statistical method to characterize and identify carbonylated sites with motif signatures. By manually curating experimental data from research articles, we obtained 332, 144, 135, and 140 verified substrate sites for K (lysine), R (arginine), T (threonine), and P (proline) residues, respectively, from 241 carbonylated proteins. In order to examine the informative attributes for classifying between carbonylated and non-carbonylated sites, multifarious features including composition of twenty amino acids (AAC), composition of amino acid pairs (AAPC), position-specific scoring matrix (PSSM), and positional weighted matrix (PWM) were investigated in this study. Additionally, in an attempt to explore the motif signatures of carbonylation sites, an iterative statistical method was adopted to detect statistically significant dependencies of amino acid compositions between specific positions around substrate sites. Profile hidden Markov model (HMM) was then utilized to train a predictive model from each motif signature. Moreover, based on the method of support vector machine (SVM), we adopted it to construct an integrative model by combining the values of bit scores obtained from profile HMMs. The combinatorial model could provide an enhanced performance with evenly predictive sensitivity and specificity in the evaluation of cross-validation and independent testing. This study provides a new scheme for exploring potential motif signatures at substrate sites of protein carbonylation. The usefulness of the revealed motifs in the identification of carbonylated sites is demonstrated by their effective performance in cross-validation and independent testing. Finally, these substrate motifs were adopted to build an available online resource (MDD-Carb, http://csb.cse.yzu.edu.tw/MDDCarb/ ) and are also anticipated to facilitate the study of large-scale carbonylated proteomes.

Rapid-estimation method for assessing scour at highway bridges

USGS Publications Warehouse

Holnbeck, Stephen R.

1998-01-01

A method was developed by the U.S. Geological Survey for rapid estimation of scour at highway bridges using limited site data and analytical procedures to estimate pier, abutment, and contraction scour depths. The basis for the method was a procedure recommended by the Federal Highway Administration for conducting detailed scour investigations, commonly referred to as the Level 2 method. Using pier, abutment, and contraction scour results obtained from Level 2 investigations at 122 sites in 10 States, envelope curves and graphical relations were developed that enable determination of scour-depth estimates at most bridge sites in a matter of a few hours. Rather than using complex hydraulic variables, surrogate variables more easily obtained in the field were related to calculated scour-depth data from Level 2 studies. The method was tested by having several experienced individuals apply the method in the field, and results were compared among the individuals and with previous detailed analyses performed for the sites. Results indicated that the variability in predicted scour depth among individuals applying the method generally was within an acceptable range, and that conservatively greater scour depths generally were obtained by the rapid-estimation method compared to the Level 2 method. The rapid-estimation method is considered most applicable for conducting limited-detail scour assessments and as a screening tool to determine those bridge sites that may require more detailed analysis. The method is designed to be applied only by a qualified professional possessing knowledge and experience in the fields of bridge scour, hydraulics, and flood hydrology, and having specific expertise with the Level 2 method.

Predicting protein amidation sites by orchestrating amino acid sequence features

NASA Astrophysics Data System (ADS)

Zhao, Shuqiu; Yu, Hua; Gong, Xiujun

2017-08-01

Amidation is the fourth major category of post-translational modifications, which plays an important role in physiological and pathological processes. Identifying amidation sites can help us understanding the amidation and recognizing the original reason of many kinds of diseases. But the traditional experimental methods for predicting amidation sites are often time-consuming and expensive. In this study, we propose a computational method for predicting amidation sites by orchestrating amino acid sequence features. Three kinds of feature extraction methods are used to build a feature vector enabling to capture not only the physicochemical properties but also position related information of the amino acids. An extremely randomized trees algorithm is applied to choose the optimal features to remove redundancy and dependence among components of the feature vector by a supervised fashion. Finally the support vector machine classifier is used to label the amidation sites. When tested on an independent data set, it shows that the proposed method performs better than all the previous ones with the prediction accuracy of 0.962 at the Matthew's correlation coefficient of 0.89 and area under curve of 0.964.

Relationship between the components of on-site training and emotional intelligence in the librarians of Isfahan University of Medical Sciences and Isfahan University with moderating role of personality characteristics

PubMed Central

Sayadi, Saeed; Safdarian, Ali; Khayeri, Behnaz

2015-01-01

Introduction: Training the man power is an inevitable necessity that the organizations need in order to survive and develop in today changing world. Aims: The aim of the present study is to identify the relationship between the components of on-site training and emotional intelligence in librarians of Isfahan University of Medical Sciences and Isfahan University with moderating role of personality characteristics. Settings and Design: Descriptive correlation method was used in the present study. The statistical population of the study was all of the 157 librarians of Isfahan University of Medical Sciences and Isfahan University from whom the appointed individuals were selected through random sampling method. Subjects and Methods: The research tools included the researcher-made questionnaire of investigating the effectiveness of on-site training system and two other standard questionnaires of Shrink emotional intelligence, and NEO personality questionnaire, which all of them had the needed reliability and validity. Statistical Analysis: The descriptive indices (distribution and mean) and also the inferential methods (Pearson correlation, regression analysis and analysis of variance) were used through applying version 20 of SPSS software to analyze the obtained data. Results: There was a significant relationship with certainty level of 95% between the components of on-site training with emotional intelligence in those who obtained low grades in the features of being extrovert and between the individual aspects of on-site training with emotional intelligence in those who got higher grades in the characteristic of being extrovert. Conclusion: The emotional intelligence is a promotable skill and considering the existence of a significant relationship between some components of emotional intelligence and on-site training, these skills can be institutionalized through conducting mentioned educational courses. PMID:27462631

Assessment of multiple geophysical techniques for the characterization of municipal waste deposit sites

NASA Astrophysics Data System (ADS)

Gaël, Dumont; Tanguy, Robert; Nicolas, Marck; Frédéric, Nguyen

2017-10-01

In this study, we tested the ability of geophysical methods to characterize a large technical landfill installed in a former sand quarry. The geophysical surveys specifically aimed at delimitating the deposit site horizontal extension, at estimating its thickness and at characterizing the waste material composition (the moisture content in the present case). The site delimitation was conducted with electromagnetic (in-phase and out-of-phase) and magnetic (vertical gradient and total field) methods that clearly showed the transition between the waste deposit and the host formation. Regarding waste deposit thickness evaluation, electrical resistivity tomography appeared inefficient on this particularly thick deposit site. Thus, we propose a combination of horizontal to vertical noise spectral ratio (HVNSR) and multichannel analysis of the surface waves (MASW), which successfully determined the approximate waste deposit thickness in our test landfill. However, ERT appeared to be an appropriate tool to characterize the moisture content of the waste, which is of prior information for the organic waste biodegradation process. The global multi-scale and multi-method geophysical survey offers precious information for site rehabilitation studies, water content mitigation processes for enhanced biodegradation or landfill mining operation planning.

Testing the efficiency of rover science protocols for robotic sample selection: A GeoHeuristic Operational Strategies Test

NASA Astrophysics Data System (ADS)

Yingst, R. A.; Bartley, J. K.; Chidsey, T. C.; Cohen, B. A.; Gilleaudeau, G. J.; Hynek, B. M.; Kah, L. C.; Minitti, M. E.; Williams, R. M. E.; Black, S.; Gemperline, J.; Schaufler, R.; Thomas, R. J.

2018-05-01

The GHOST field tests are designed to isolate and test science-driven rover operations protocols, to determine best practices. During a recent field test at a potential Mars 2020 landing site analog, we tested two Mars Science Laboratory data-acquisition and decision-making methods to assess resulting science return and sample quality: a linear method, where sites of interest are studied in the order encountered, and a "walkabout-first" method, where sites of interest are examined remotely before down-selecting to a subset of sites that are interrogated with more resource-intensive instruments. The walkabout method cost less time and fewer resources, while increasing confidence in interpretations. Contextual data critical to evaluating site geology was acquired earlier than for the linear method, and given a higher priority, which resulted in development of more mature hypotheses earlier in the analysis process. Combined, this saved time and energy in the collection of data with more limited spatial coverage. Based on these results, we suggest that the walkabout method be used where doing so would provide early context and time for the science team to develop hypotheses-critical tests; and that in gathering context, coverage may be more important than higher resolution.

Prospects for Problems Associated with Integrative and Inter-comparative Analysis of Eddy Flux Data Sets

NASA Astrophysics Data System (ADS)

Kobayashi, Y.; Miyata, A.; Nagai, H.; Mano, M.; Yamamoto, S.

2005-12-01

In last decade, numerous long-term eddy flux measurements have been conducted worldwide to assess annual/seasonal energy, water and carbon exchanges between terrestrial ecosystem and the atmosphere. And FLUXNET communities now seem to come into a next phase with the objectives: integration of flux data observed at various ecosystems and/or inter-sites comparative studies. For example, a big research project "S-1" is ongoing in Japan and other eastern Asian region to set up terrestrial carbon management of Asia in the 21st century. One of the highlights of S-1 project is to provide a carbon budget map of all over Asia based on integrated and inter-compared eddy flux data collected at 15 sites of S-1 membership. FLUXNET communities including S-1 project have recognized that integration and inter-comparison of eddy flux data are the key issues to understand aspects of energy, water and carbon budgets at regional scale. However, the issues have difficulties to be settled because each flux site applies own data processing methods and gap-filling methods with site-specified classification and threshold values. In order to conduct appropriate integrative and inter-comparative analysis for eddy flux data effectively, we made it clear that how the differences in the data processing method affect the obtained flux values and searched for suitable and common gap-filling methodology. The differences in the data processing methods affect the obtained flux data in the present study was discussed based on a comparative experiment in S-1 project. We prepared one-month common test data sets, which consisted of 10 Hz eddy covariance raw data and related half-hourly meteorological data obtained at a larch forest site and a paddy site, in the comparative experiment. The 15 sites of S-1 memberships processed the test data by using their own processing methods. The results indicated that combined influences of coordinate rotation, detrending and frequency response correction brought about up to 10% of flux discrepancy, and that the forest sites were more sensitive to differences in the data processing methods than the non-forest sites. Multiple imputation method (MI), one of the statistical operations for analyzing incomplete multivariate data set, is likely to be an easy-to-use and objective gap-filling method to account for missing eddy flux data. We also discussed validity of application of MI to fill missing flux data by comparing a gap-filled complete eddy flux data set obtained by MI with that by nonlinear regression method and look-up table method. It was revealed that, with suitable separation of the periods to be filled and proper selection of reference variables, MI has potential to be applied commonly to gap-filling missing flux data, and that MI can be a useful tool for FLUXNET communities to make inter-site comparison of long-term flux data.

Comparing regeneration techniques for afforesting previously farmed bottomland hardwood sites in the Lower Mississippi Alluvial Valley, USA

Treesearch

Brian Roy Lockhart; Bob Keeland; John McCoy; Thomas J. Dean

2003-01-01

A study was implemented to test site preparation methods and artificial regeneration of three oak (Quercus spp.) species on four agricultural fields in the Lower Mississippi Alluvial Valley in Louisiana, USA. Six years after establishment, few consistent differences were found in oak density between sowing acorn methods (seed drill versus broadcast...

Impacts of heterogeneous organic matter on phenanthrene sorption--Different soil and sediment samples

USGS Publications Warehouse

Karapanagioti, Hrissi K.; Childs, Jeffrey; Sabatini, David A.

2001-01-01

Organic petrography has been proposed as a tool for characterizing the heterogeneous organic matter present in soil and sediment samples. A new simplified method is proposed as a quantitative means of interpreting observed sorption behavior for phenanthrene and different soils and sediments based on their organic petrographical characterization. This method is tested under singe solute conditions and at phenanthrene concentration of 1 μg/L. Since the opaque organic matter fraction dominates the sorption process, we propose that by quantifying this fraction one can interpret organic content normalized sorption distribution coefficient (Koc) values for a sample. While this method was developed and tested for various samples within the same aquifer, in the current study the method is validated for soil and sediment samples from different sites that cover a wide range of organic matter origin, age, and organic content. All 10 soil and sediment samples studied had log Koc values for the opaque particles between 5.6 and 6.8. This range of Koc values illustrates the heterogeneity of opaque particles between sites and geological formations and thus the need to characterize the opaque fraction of materials on a site-by-site basis.

A greater number of somatic pain sites is associated with poor mental health in adolescents: a cross-sectional study

PubMed Central

2013-01-01

Background Identifying indicators of poor mental health during adolescence is a significant public health issue. Previous studies which suggested an association between the number of somatic pains and depression have mainly focused on adults or have employed samples with a narrow age range. To date, results from previous studies have been inconsistent regarding the association between somatic pain and academic impairment. Therefore, the main aims of the present study were to 1) investigate the association between the number of somatic pain sites and poor mental health using a community sample of adolescents aged 12 to 18 years and employing a simple method of assessment, and 2) examine the association between the number of somatic pain sites and perceived academic impairment. Methods Data analysis was conducted using a large cross-sectional survey of adolescents in grades 7 to 12. The one-month prevalence rates for three sites of somatic pain including head, neck and shoulders, and abdomen were examined. Poor mental health was evaluated using the General Health Questionnaire, and perceived academic impairment was measured using a self-report questionnaire. Results A total of 18,104 adolescents participated in the survey. A greater number of pain sites was associated with poor mental health, and this association was consistent across age and gender. There was no difference in effect on mental health between any of the pain sites. Although there was an association between the number of somatic pain sites and perceived academic impairment, the results suggested that the association was mediated by poor mental health. Conclusions Simple reporting methods for assessing the number of pain sites may be a feasible indicator of poor mental health in adolescents. Professionals working with adolescents should consider the possibility of poor mental health, especially when students report multiple somatic pains. PMID:23327684

a Hyperspectral Based Method to Detect Cannabis Plantation in Inaccessible Areas

NASA Astrophysics Data System (ADS)

Houmi, M.; Mohamadi, B.; Balz, T.

2018-04-01

The increase in drug use worldwide has led to sophisticated illegal planting methods. Most countries depend on helicopters, and local knowledge to identify such illegal plantations. However, remote sensing techniques can provide special advantages for monitoring the extent of illegal drug production. This paper sought to assess the ability of the Satellite remote sensing to detect Cannabis plantations. This was achieved in two stages: 1- Preprocessing of Hyperspectral data EO-1, and testing the capability to collect the spectral signature of Cannabis in different sites of the study area (Morocco) from well-known Cannabis plantation fields. 2- Applying the method of Spectral Angle Mapper (SAM) based on a specific angle threshold on Hyperion data EO-1 in well-known Cannabis plantation sites, and other sites with negative Cannabis plantation in another study area (Algeria), to avoid any false Cannabis detection using these spectra. This study emphasizes the benefits of using hyperspectral remote sensing data as an effective detection tool for illegal Cannabis plantation in inaccessible areas based on SAM classification method with a maximum angle (radians) less than 0.03.

PROPOSED STANDARDIZED ASSESSMENT METHODS (SAMS) FOR ELECTROFISHING LARGE RIVERS

EPA Science Inventory

The effects of electrofishing design and sampling distance were studied at 49 sites across four boatable rivers ranging in drainage area from 13,947 to 23,041 km2 in the Ohio River basin. Two general types of sites were sampled: Run-of-the-River (Free-flowing sites or with smal...

Sulfometuron methyl: Its use in forestry and potential phytotoxicity

Treesearch

Nathan D. Robertson; Anthony S. Davis

2010-01-01

Planting site preparation is a common practice used to enhance seedling establishment success. Site preparations include herbicide, fire, and mechanical methods. Studies designed to explore the use of herbicides as site preparation and release tools are common, and herbicides have shown their use in forestry to be logistically, economically, and ecologically...

Under What Assumptions Do Site-by-Treatment Instruments Identify Average Causal Effects?

ERIC Educational Resources Information Center

Reardon, Sean F.; Raudenbush, Stephen W.

2013-01-01

The increasing availability of data from multi-site randomized trials provides a potential opportunity to use instrumental variables methods to study the effects of multiple hypothesized mediators of the effect of a treatment. We derive nine assumptions needed to identify the effects of multiple mediators when using site-by-treatment interactions…

Estimation of Velocity Structure Using Microtremor Recordings from Arrays: Comparison of Results from the SPAC and the F-K Analysis Methods

NASA Astrophysics Data System (ADS)

Flores-Estrella, H.; Aguirre, J.; Boore, D.; Yussim, S.

2001-12-01

Microtremor recordings have become a useful tool for microzonation studies in countries with low to moderate seismicity and also in countries where there are few seismographs or the recurrence time for an earthquake is quite long. Microtremor recordings can be made at almost any time and any place without needing to wait for an earthquake. The measurements can be made using one station or an array of stations. Microtremor recordings can be used to estimate site response directly (e.g. by using Nakamura's technique), or they can be used to estimate shear-wave velocities, from which site response can be calculated. A number of studies have found that the direct estimation of site response may be unreliable, except for identifying the fundamental resonant period of a site. Obtaining shear-wave velocities requires inverting measurements of Rayleigh wave phase velocities from microtremors, which are obtained by using the Spatial Autocorrelation (SPAC) (Aki, 1957) or the Frequency-Wave Number (F-K) (Horike, 1985) methods. Estimating shear-wave velocities from microtremor recordings is a cheaper alternative than direct methods, such as the logging of boreholes. In this work we use simultaneous microtremor recordings from triangular arrays located at two sites in Mexico City, Mexico, one ("Texcoco") with a lacustrine sediment layer of about 200 m depth, and the other one ("Ciudad Universitaria") underlain by 2,000 year old basaltic flows from Xitle volcano. The data are analyzed using both the SPAC method and by the standard F-K method. The results obtained from the SPAC method are more consistent with expectations from the geological conditions and an empirical transfer function (Montalvo et al., 2001) than those from F-K method. We also analyze data from the Hollister Municipal Airport in California. The triangular array at this site is located near a borehole from which seismic velocities have been obtained using a downhole logging method (Liu et al., 2000). We compare results from the microtremor recordings analyzed using both the SPAC and F-K methods with those obtained from the downhole logging.

Web vulnerability study of online pharmacy sites.

PubMed

Kuzma, Joanne

2011-01-01

Consumers are increasingly using online pharmacies, but these sites may not provide an adequate level of security with the consumers' personal data. There is a gap in this research addressing the problems of security vulnerabilities in this industry. The objective is to identify the level of web application security vulnerabilities in online pharmacies and the common types of flaws, thus expanding on prior studies. Technical, managerial and legal recommendations on how to mitigate security issues are presented. The proposed four-step method first consists of choosing an online testing tool. The next steps involve choosing a list of 60 online pharmacy sites to test, and then running the software analysis to compile a list of flaws. Finally, an in-depth analysis is performed on the types of web application vulnerabilities. The majority of sites had serious vulnerabilities, with the majority of flaws being cross-site scripting or old versions of software that have not been updated. A method is proposed for the securing of web pharmacy sites, using a multi-phased approach of technical and managerial techniques together with a thorough understanding of national legal requirements for securing systems.

Limitation and applicability of microtremor records for site-response estimation

NASA Astrophysics Data System (ADS)

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 meaning in real cases, results obtained using the microtremor method were compared with results from a field test, a spectral inversion method, and the reference station method for sites of strong motion stations in the southern Korean Peninsula.

Studying modification of aminoglycoside antibiotics by resistance-causing enzymes via microarray.

PubMed

Disney, Matthew D

2012-01-01

Widespread bacterial resistance to antibiotics is a significant public health concern. To remain a step ahead of evolving bacteria, new methods to study resistance to antibacterials and to uncover novel antibiotics that evade resistance are urgently needed. Herein, microarray-based methods that have been developed to study aminoglycoside modification by resistance-causing enzymes are reviewed. These arrays can also be used to study the binding of aminoglycoside antibiotics to a mimic of their therapeutic target, the rRNA aminoacyl site (A-site), and how modification by resistance-causing enzymes affects their abilities to bind RNA.

Predicting lysine glycation sites using bi-profile bayes feature extraction.

PubMed

Ju, Zhe; Sun, Juhe; Li, Yanjie; Wang, Li

2017-12-01

Glycation is a nonenzymatic post-translational modification which has been found to be involved in various biological processes and closely associated with many metabolic diseases. The accurate identification of glycation sites is important to understand the underlying molecular mechanisms of glycation. As the traditional experimental methods are often labor-intensive and time-consuming, it is desired to develop computational methods to predict glycation sites. In this study, a novel predictor named BPB_GlySite is proposed to predict lysine glycation sites by using bi-profile bayes feature extraction and support vector machine algorithm. As illustrated by 10-fold cross-validation, BPB_GlySite achieves a satisfactory performance with a Sensitivity of 63.68%, a Specificity of 72.60%, an Accuracy of 69.63% and a Matthew's correlation coefficient of 0.3499. Experimental results also indicate that BPB_GlySite significantly outperforms three existing glycation sites predictors: NetGlycate, PreGly and Gly-PseAAC. Therefore, BPB_GlySite can be a useful bioinformatics tool for the prediction of glycation sites. A user-friendly web-server for BPB_GlySite is established at 123.206.31.171/BPB_GlySite/. Copyright © 2017 Elsevier Ltd. All rights reserved.

Shared worlds: multi-sited ethnography and nursing research.

PubMed

Molloy, Luke; Walker, Kim; Lakeman, Richard

2017-03-22

Background Ethnography, originally developed for the study of supposedly small-scale societies, is now faced with an increasingly mobile, changing and globalised world. Cultural identities can exist without reference to a specific location and extend beyond regional and national boundaries. It is therefore no longer imperative that the sole object of the ethnographer's practice should be a geographically bounded site. Aim To present a critical methodological review of multi-sited ethnography. Discussion Understanding that it can no longer be taken with any certainty that location alone determines culture, multi-sited ethnography provides a method of contextualising multi-sited social phenomena. The method enables researchers to examine social phenomena that are simultaneously produced in different locations. It has been used to undertake cultural analysis of diverse areas such as organ trafficking, global organisations, technologies and anorexia. Conclusion The authors contend that multi-sited ethnography is particularly suited to nursing research as it provides researchers with an ethnographic method that is more relevant to the interconnected world of health and healthcare services. Implications for practice Multi-sited ethnography provides nurse researchers with an approach to cultural analysis in areas such as the social determinants of health, healthcare services and the effects of health policies across multiple locations.

Kinetics and mechanism of hydroxyapatite crystal dissolution in weak acid buffers using the rotating disk method.

PubMed

Wu, M S; Higuchi, W I; Fox, J L; Friedman, M

1976-01-01

The model given in this report and the rotating disk method provide a useful combination in the study of dental enamel and hydroxyapatite dissolution kinetics. The present approach is a significant improvement over earlier studies, and both the ionic activity product that governs the dissolution reaction and the apparent surface dissolution reaction rate constant may be simultaneously obtained. Thus, these investigations have established the baseline for the dissolution rate studies under sink conditions. Concurrent studies, under conditions where the acidic buffer mediums are partially saturated with respect to hydroxyapatite have shown another dissolution site for hydroxyapatite that operates at a higher ionic activity product but has a much smaller apparent surface reaction rate constant. This has raised the question of whether the presence of this second site may interfere with the proper theoretical analysis of the experimental results obtained under sink conditions. A preliminary analysis of the two-site model has shown that the dissolution kinetics of hydroxyapatite under sink conditions is almost completely governed by the sink condition site (KHAP = 10(-124.5), k' = 174) established in this report. The difference between the predicted dissolution rate for the one-site model and the two-site model are generally of the order of 4 to 5% where the experiments are conducted under sink conditions and over the range of variables covered in the present study.

Reconciling PM10 analyses by different sampling methods for Iron King Mine tailings dust.

PubMed

Li, Xu; Félix, Omar I; Gonzales, Patricia; Sáez, Avelino Eduardo; Ela, Wendell P

2016-03-01

The overall project objective at the Iron King Mine Superfund site is to determine the level and potential risk associated with heavy metal exposure of the proximate population emanating from the site's tailings pile. To provide sufficient size-fractioned dust for multi-discipline research studies, a dust generator was built and is now being used to generate size-fractioned dust samples for toxicity investigations using in vitro cell culture and animal exposure experiments as well as studies on geochemical characterization and bioassay solubilization with simulated lung and gastric fluid extractants. The objective of this study is to provide a robust method for source identification by comparing the tailing sample produced by dust generator and that collected by MOUDI sampler. As and Pb concentrations of the PM10 fraction in the MOUDI sample were much lower than in tailing samples produced by the dust generator, indicating a dilution of Iron King tailing dust by dust from other sources. For source apportionment purposes, single element concentration method was used based on the assumption that the PM10 fraction comes from a background source plus the Iron King tailing source. The method's conclusion that nearly all arsenic and lead in the PM10 dust fraction originated from the tailings substantiates our previous Pb and Sr isotope study conclusion. As and Pb showed a similar mass fraction from Iron King for all sites suggesting that As and Pb have the same major emission source. Further validation of this simple source apportionment method is needed based on other elements and sites.

RESULTS OF A METHOD VERIFICATION STUDY FOR ANALYSES OF PCP IN SOIL

EPA Science Inventory

As a prelude to a field demonstration of the fungal treatment technology by the SITE Program, a field treatability study was performed to select optimal fungal species and loading rates.using the site-specific soil matrix contaminated with Wood preserving wastes: PCP and PAHS. ur...

A simplified 4-site economical intradermal post-exposure rabies vaccine regimen: a randomised controlled comparison with standard methods.

PubMed

Warrell, Mary J; Riddell, Anna; Yu, Ly-Mee; Phipps, Judith; Diggle, Linda; Bourhy, Hervé; Deeks, Jonathan J; Fooks, Anthony R; Audry, Laurent; Brookes, Sharon M; Meslin, François-Xavier; Moxon, Richard; Pollard, Andrew J; Warrell, David A

2008-04-23

The need for economical rabies post-exposure prophylaxis (PEP) is increasing in developing countries. Implementation of the two currently approved economical intradermal (ID) vaccine regimens is restricted due to confusion over different vaccines, regimens and dosages, lack of confidence in intradermal technique, and pharmaceutical regulations. We therefore compared a simplified 4-site economical PEP regimen with standard methods. Two hundred and fifty-four volunteers were randomly allocated to a single blind controlled trial. Each received purified vero cell rabies vaccine by one of four PEP regimens: the currently accepted 2-site ID; the 8-site regimen using 0.05 ml per ID site; a new 4-site ID regimen (on day 0, approximately 0.1 ml at 4 ID sites, using the whole 0.5 ml ampoule of vaccine; on day 7, 0.1 ml ID at 2 sites and at one site on days 28 and 90); or the standard 5-dose intramuscular regimen. All ID regimens required the same total amount of vaccine, 60% less than the intramuscular method. Neutralising antibody responses were measured five times over a year in 229 people, for whom complete data were available. All ID regimens showed similar immunogenicity. The intramuscular regimen gave the lowest geometric mean antibody titres. Using the rapid fluorescent focus inhibition test, some sera had unexpectedly high antibody levels that were not attributable to previous vaccination. The results were confirmed using the fluorescent antibody virus neutralisation method. This 4-site PEP regimen proved as immunogenic as current regimens, and has the advantages of requiring fewer clinic visits, being more practicable, and having a wider margin of safety, especially in inexperienced hands, than the 2-site regimen. It is more convenient than the 8-site method, and can be used economically with vaccines formulated in 1.0 or 0.5 ml ampoules. The 4-site regimen now meets all requirements of immunogenicity for PEP and can be introduced without further studies. Controlled-Trials.com ISRCTN 30087513.

Applications of the JARS method to study levee sites in southern Texas and southern New Mexico

USGS Publications Warehouse

Ivanov, J.; Miller, R.D.; Xia, J.; Dunbar, J.B.

2007-01-01

We apply the joint analysis of refractions with surface waves (JARS) method to several sites and compare its results to traditional refraction-tomography methods in efforts of finding a more realistic solution to the inverse refraction-traveltime problem. The JARS method uses a reference model, derived from surface-wave shear-wave velocity estimates, as a constraint. In all of the cases JARS estimates appear more realistic than those from the conventional refraction-tomography methods. As a result, we consider, the JARS algorithm as the preferred method for finding solutions to the inverse refraction-tomography problems. ?? 2007 Society of Exploration Geophysicists.

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

NASA Astrophysics Data System (ADS)

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.

Probability-based estimates of site-specific copper water quality criteria for the Chesapeake Bay, USA.

PubMed

Arnold, W Ray; Warren-Hicks, William J

2007-01-01

The object of this study was to estimate site- and region-specific dissolved copper criteria for a large embayment, the Chesapeake Bay, USA. The intent is to show the utility of 2 copper saltwater quality site-specific criteria estimation models and associated region-specific criteria selection methods. The criteria estimation models and selection methods are simple, efficient, and cost-effective tools for resource managers. The methods are proposed as potential substitutes for the US Environmental Protection Agency's water effect ratio methods. Dissolved organic carbon data and the copper criteria models were used to produce probability-based estimates of site-specific copper saltwater quality criteria. Site- and date-specific criteria estimations were made for 88 sites (n = 5,296) in the Chesapeake Bay. The average and range of estimated site-specific chronic dissolved copper criteria for the Chesapeake Bay were 7.5 and 5.3 to 16.9 microg Cu/L. The average and range of estimated site-specific acute dissolved copper criteria for the Chesapeake Bay were 11.7 and 8.3 to 26.4 microg Cu/L. The results suggest that applicable national and state copper criteria can increase in much of the Chesapeake Bay and remain protective. Virginia Department of Environmental Quality copper criteria near the mouth of the Chesapeake Bay, however, need to decrease to protect species of equal or greater sensitivity to that of the marine mussel, Mytilus sp.

Influence of the Redundant Verification and the Non-Redundant Verification on the Hydraulic Tomography

NASA Astrophysics Data System (ADS)

Wei, T. B.; Chen, Y. L.; Lin, H. R.; Huang, S. Y.; Yeh, T. C. J.; Wen, J. C.

2016-12-01

In the groundwater study, it estimated the heterogeneous spatial distribution of hydraulic Properties, there were many scholars use to hydraulic tomography (HT) from field site pumping tests to estimate inverse of heterogeneous spatial distribution of hydraulic Properties, to prove the most of most field site aquifer was heterogeneous hydrogeological parameters spatial distribution field. Many scholars had proposed a method of hydraulic tomography to estimate heterogeneous spatial distribution of hydraulic Properties of aquifer, the Huang et al. [2011] was used the non-redundant verification analysis of pumping wells changed, observation wells fixed on the inverse and the forward, to reflect the feasibility of the heterogeneous spatial distribution of hydraulic Properties of field site aquifer of the non-redundant verification analysis on steady-state model.From post literature, finding only in steady state, non-redundant verification analysis of pumping well changed location and observation wells fixed location for inverse and forward. But the studies had not yet pumping wells fixed or changed location, and observation wells fixed location for redundant verification or observation wells change location for non-redundant verification of the various combinations may to explore of influences of hydraulic tomography method. In this study, it carried out redundant verification method and non-redundant verification method for forward to influences of hydraulic tomography method in transient. And it discuss above mentioned in NYUST campus sites the actual case, to prove the effectiveness of hydraulic tomography methods, and confirmed the feasibility on inverse and forward analysis from analysis results.Keywords: Hydraulic Tomography, Redundant Verification, Heterogeneous, Inverse, Forward

The Fall River Long-Term Site Productivity study in coastal Washington: site characteristics, methods, and biomass and carbon and nitrogen stores before and after harvest.

Treesearch

Adrian Ares; Thomas A. Terry; Kathryn B. Piatek; Robert B. Harrison; Richard E. Miller; Barry L. Flaming; ChristopherW Licata; Brian D. Strahm; Constance A. Harrington; Rodney Meade; Harry W. Anderson; Leslie C. Brodie; Joseph M. Kraft

2007-01-01

The Fall River research site in coastal Washington is an affiliate installation of the North American Long-Term Soil Productivity (LTSP) network, which constitutes one of the world’s largest coordinated research programs addressing forest management impacts on sustained productivity. Overall goals of the Fall River study are to assess effects of biomass removals, soil...

Assessment of the Effects of Holding Time and Temperature on Escherichia coli Densities in Surface Water Samples

PubMed Central

Pope, Misty L.; Bussen, Michelle; Feige, Mary Ann; Shadix, Lois; Gonder, Sharon; Rodgers, Crystal; Chambers, Yildiz; Pulz, Jessica; Miller, Ken; Connell, Kevin; Standridge, Jon

2003-01-01

Escherichia coli is a routinely used microbiological indicator of water quality. To determine whether holding time and storage conditions had an effect on E. coli densities in surface water, studies were conducted in three phases, encompassing 24 sites across the United States and four commonly used monitoring methods. During all three phases of the study, E. coli samples were analyzed at time 0 and at 8, 24, 30, and 48 h after sample collection. During phase 1, when 4°C samples were evaluated by Colilert or by placing a membrane onto mFC medium followed by transfer to nutrient agar containing 4-methylumbelliferyl-β-d-glucuronide (mFC/NA-MUG), three of four sites showed no significant differences throughout the 48-h study. During phase 2, five of seven sites showed no significant difference between time 0 and 24 h by membrane filtration (mFC/NA-MUG). When evaluated by the Colilert method, five of seven sites showed no significant difference in E. coli density between time 0 and 48 h. During phase 3, 8 of 13 sites showed no significant differences in E. coli densities between time 0 and the 48-h holding time, regardless of method. Based on the results of these studies, it appears that if samples are held below 10°C and are not allowed to freeze, most surface water E. coli samples analyzed by commonly used methods beyond 8 h after sample collection can generate E. coli data comparable to those generated within 8 h of sample collection. Notwithstanding this conclusion, E. coli samples collected from surface waters should always be analyzed as soon as possible. PMID:14532081

Clustering and Bayesian hierarchical modeling for the definition of informative prior distributions in hydrogeology

NASA Astrophysics Data System (ADS)

Cucchi, K.; Kawa, N.; Hesse, F.; Rubin, Y.

2017-12-01

In order to reduce uncertainty in the prediction of subsurface flow and transport processes, practitioners should use all data available. However, classic inverse modeling frameworks typically only make use of information contained in in-situ field measurements to provide estimates of hydrogeological parameters. Such hydrogeological information about an aquifer is difficult and costly to acquire. In this data-scarce context, the transfer of ex-situ information coming from previously investigated sites can be critical for improving predictions by better constraining the estimation procedure. Bayesian inverse modeling provides a coherent framework to represent such ex-situ information by virtue of the prior distribution and combine them with in-situ information from the target site. In this study, we present an innovative data-driven approach for defining such informative priors for hydrogeological parameters at the target site. Our approach consists in two steps, both relying on statistical and machine learning methods. The first step is data selection; it consists in selecting sites similar to the target site. We use clustering methods for selecting similar sites based on observable hydrogeological features. The second step is data assimilation; it consists in assimilating data from the selected similar sites into the informative prior. We use a Bayesian hierarchical model to account for inter-site variability and to allow for the assimilation of multiple types of site-specific data. We present the application and validation of the presented methods on an established database of hydrogeological parameters. Data and methods are implemented in the form of an open-source R-package and therefore facilitate easy use by other practitioners.

Selection of remedial alternatives for mine sites: a multicriteria decision analysis approach.

PubMed

Betrie, Getnet D; Sadiq, Rehan; Morin, Kevin A; Tesfamariam, Solomon

2013-04-15

The selection of remedial alternatives for mine sites is a complex task because it involves multiple criteria and often with conflicting objectives. However, an existing framework used to select remedial alternatives lacks multicriteria decision analysis (MCDA) aids and does not consider uncertainty in the selection of alternatives. The objective of this paper is to improve the existing framework by introducing deterministic and probabilistic MCDA methods. The Preference Ranking Organization Method for Enrichment Evaluation (PROMETHEE) methods have been implemented in this study. The MCDA analysis involves processing inputs to the PROMETHEE methods that are identifying the alternatives, defining the criteria, defining the criteria weights using analytical hierarchical process (AHP), defining the probability distribution of criteria weights, and conducting Monte Carlo Simulation (MCS); running the PROMETHEE methods using these inputs; and conducting a sensitivity analysis. A case study was presented to demonstrate the improved framework at a mine site. The results showed that the improved framework provides a reliable way of selecting remedial alternatives as well as quantifying the impact of different criteria on selecting alternatives. Copyright © 2013 Elsevier Ltd. All rights reserved.

The impacts of speed cameras on road accidents: an application of propensity score matching methods.

PubMed

Li, Haojie; Graham, Daniel J; Majumdar, Arnab

2013-11-01

This paper aims to evaluate the impacts of speed limit enforcement cameras on reducing road accidents in the UK by accounting for both confounding factors and the selection of proper reference groups. The propensity score matching (PSM) method is employed to do this. A naïve before and after approach and the empirical Bayes (EB) method are compared with the PSM method. A total of 771 sites and 4787 sites for the treatment and the potential reference groups respectively are observed for a period of 9 years in England. Both the PSM and the EB methods show similar results that there are significant reductions in the number of accidents of all severities at speed camera sites. It is suggested that the propensity score can be used as the criteria for selecting the reference group in before-after control studies. Speed cameras were found to be most effective in reducing accidents up to 200 meters from camera sites and no evidence of accident migration was found. Copyright © 2013 Elsevier Ltd. All rights reserved.

A machine-learning approach for predicting palmitoylation sites from integrated sequence-based features.

PubMed

Li, Liqi; Luo, Qifa; Xiao, Weidong; Li, Jinhui; Zhou, Shiwen; Li, Yongsheng; Zheng, Xiaoqi; Yang, Hua

2017-02-01

Palmitoylation is the covalent attachment of lipids to amino acid residues in proteins. As an important form of protein posttranslational modification, it increases the hydrophobicity of proteins, which contributes to the protein transportation, organelle localization, and functions, therefore plays an important role in a variety of cell biological processes. Identification of palmitoylation sites is necessary for understanding protein-protein interaction, protein stability, and activity. Since conventional experimental techniques to determine palmitoylation sites in proteins are both labor intensive and costly, a fast and accurate computational approach to predict palmitoylation sites from protein sequences is in urgent need. In this study, a support vector machine (SVM)-based method was proposed through integrating PSI-BLAST profile, physicochemical properties, [Formula: see text]-mer amino acid compositions (AACs), and [Formula: see text]-mer pseudo AACs into the principal feature vector. A recursive feature selection scheme was subsequently implemented to single out the most discriminative features. Finally, an SVM method was implemented to predict palmitoylation sites in proteins based on the optimal features. The proposed method achieved an accuracy of 99.41% and Matthews Correlation Coefficient of 0.9773 for a benchmark dataset. The result indicates the efficiency and accuracy of our method in prediction of palmitoylation sites based on protein sequences.

Effects of site preparation on timber and non-timber values of loblolly pine plantations

Treesearch

Jianbang Gan; Stephen H. Kolison; James H. Miller; Tasha M. Hargrove

1998-01-01

This study evaluated the timber and non-timber values of the forest stands generated by four site preparation methods tested in the Tuskegee National Forest 15 yr earlier. The timber values of the forest stands were assessed with the timber yields predicted by the SE TWIGS model. Non-timber benefits were evaluated through the Contingent Valuation Method. Two hundred...

Suicide by Jumping and Accessibility of Bridges: Results from a National Survey in Switzerland

ERIC Educational Resources Information Center

Reisch, Thomas; Schuster, Ursula; Michel, Konrad

2007-01-01

Rates of suicide by jumping show large regional differences. Barriers on bridges may prevent suicides but also may lead to a substitution of jumping site or method. The aim of our study was to compare suicide data from regions with and without suicide bridges and to estimate the effects on method and site substitution if bridges were to be…

A method for locating potential tree-planting sites in urban areas: a case study of Los Angeles, USA

Treesearch

Chunxia Wua; Qingfu Xiaoa; Gregory E. McPherson

2008-01-01

A GIS-based method for locating potential tree-planting sites based on land cover data is introduced. Criteria were developed to identify locations that are spatially available for potential tree planting based on land cover, sufficient distance from impervious surfaces, a minimum amount of pervious surface, and no crown overlap with other trees. In an ArcGIS...

Case-control analysis in highway safety: Accounting for sites with multiple crashes.

PubMed

Gross, Frank

2013-12-01

There is an increased interest in the use of epidemiological methods in highway safety analysis. The case-control and cohort methods are commonly used in the epidemiological field to identify risk factors and quantify the risk or odds of disease given certain characteristics and factors related to an individual. This same concept can be applied to highway safety where the entity of interest is a roadway segment or intersection (rather than a person) and the risk factors of interest are the operational and geometric characteristics of a given roadway. One criticism of the use of these methods in highway safety is that they have not accounted for the difference between sites with single and multiple crashes. In the medical field, a disease either occurs or it does not; multiple occurrences are generally not an issue. In the highway safety field, it is necessary to evaluate the safety of a given site while accounting for multiple crashes. Otherwise, the analysis may underestimate the safety effects of a given factor. This paper explores the use of the case-control method in highway safety and two variations to account for sites with multiple crashes. Specifically, the paper presents two alternative methods for defining cases in a case-control study and compares the results in a case study. The first alternative defines a separate case for each crash in a given study period, thereby increasing the weight of the associated roadway characteristics in the analysis. The second alternative defines entire crash categories as cases (sites with one crash, sites with two crashes, etc.) and analyzes each group separately in comparison to sites with no crashes. The results are also compared to a "typical" case-control application, where the cases are simply defined as any entity that experiences at least one crash and controls are those entities without a crash in a given period. In a "typical" case-control design, the attributes associated with single-crash segments are weighted the same as the attributes of segments with multiple crashes. The results support the hypothesis that the "typical" case-control design may underestimate the safety effects of a given factor compared to methods that account for sites with multiple crashes. Compared to the first alternative case definition (where multiple crash segments represent multiple cases) the results from the "typical" case-control design are less pronounced (i.e., closer to unity). The second alternative (where case definitions are constructed for various crash categories and analyzed separately) provides further evidence that sites with single and multiple crashes should not be grouped together in a case-control analysis. This paper indicates a clear need to differentiate sites with single and multiple crashes in a case-control analysis. While the results suggest that sites with multiple crashes can be accounted for using a case-control design, further research is needed to determine the optimal method for addressing this issue. This paper provides a starting point for that research. Copyright © 2012 Elsevier Ltd. All rights reserved.

Interactions of cephalexin with bovine serum albumin: displacement reaction and molecular docking.

PubMed

Hamishehkar, Hamed; Hosseini, Soheila; Naseri, Abdolhossein; Safarnejad, Azam; Rasoulzadeh, Farzaneh

2016-01-01

Introduction: The drug-plasma protein interaction is a fundamental issue in guessing and checking the serious drug side effects related with other drugs. The purpose of this research was to study the interaction of cephalexin with bovine serum albumin (BSA) and displacement reaction using site probes. Methods: The interaction mechanism concerning cephalexin (CPL) with BSA was investigated using various spectroscopic methods and molecular modeling method. The binding sites number, n, apparent binding constant, K, and thermodynamic parameters, ΔG 0 , ΔH 0 , and ΔS 0 were considered at different temperatures. To evaluate the experimental results, molecular docking modeling was calculated. Results: The distance, r=1.156 nm between BSA and CPL were found in accordance with the Forster theory of non-radiation energy transfer (FRET) indicating energy transfer occurs between BSA and CPL. According to the binding parameters and ΔG 0 = negative values and ΔS 0 = 28.275 j mol -1 K -1 , a static quenching process is effective in the CPL-BSA interaction spontaneously. ΔG 0 for the CPL-BSA complex obtained from the docking simulation is -28.99 kj mol -1 , which is close to experimental ΔG of binding, -21.349 kj mol -1 that indicates a good agreement between the results of docking methods and experimental data. Conclusion: The outcomes of spectroscopic methods revealed that the conformation of BSA changed during drug-BSA interaction. The results of FRET propose that CPL quenches the fluorescence of BSA by static quenching and FRET. The displacement study showed that phenylbutazon and ketoprofen displaced CPL, indicating that its binding site on albumin is site I and Gentamicin cannot be displaced from the binding site of CPL. All results of molecular docking method agreed with the results of experimental data.

A Methodology to Evaluate Ecological Resources and Risk Using Two Case Studies at the Department of Energy's Hanford Site

NASA Astrophysics Data System (ADS)

Burger, Joanna; Gochfeld, Michael; Bunn, Amoret; Downs, Janelle; Jeitner, Christian; Pittfield, Taryn; Salisbury, Jennifer; Kosson, David

2017-03-01

An assessment of the potential risks to ecological resources from remediation activities or other perturbations should involve a quantitative evaluation of resources on the remediation site and in the surrounding environment. We developed a risk methodology to rapidly evaluate potential impact on ecological resources for the U.S. Department of Energy's Hanford Site in southcentral Washington State. We describe the application of the risk evaluation for two case studies to illustrate its applicability. The ecological assessment involves examining previous sources of information for the site, defining different resource levels from 0 to 5. We also developed a risk rating scale from non-discernable to very high. Field assessment is the critical step to determine resource levels or to determine if current conditions are the same as previously evaluated. We provide a rapid assessment method for current ecological conditions that can be compared to previous site-specific data, or that can be used to assess resource value on other sites where ecological information is not generally available. The method is applicable to other Department of Energy's sites, where its development may involve a range of state regulators, resource trustees, Tribes and other stakeholders. Achieving consistency across Department of Energy's sites for valuation of ecological resources on remediation sites will assure Congress and the public that funds and personnel are being deployed appropriately.

A Methodology to Evaluate Ecological Resources and Risk Using Two Case Studies at the Department of Energy's Hanford Site.

PubMed

Burger, Joanna; Gochfeld, Michael; Bunn, Amoret; Downs, Janelle; Jeitner, Christian; Pittfield, Taryn; Salisbury, Jennifer; Kosson, David

2017-03-01

An assessment of the potential risks to ecological resources from remediation activities or other perturbations should involve a quantitative evaluation of resources on the remediation site and in the surrounding environment. We developed a risk methodology to rapidly evaluate potential impact on ecological resources for the U.S. Department of Energy's Hanford Site in southcentral Washington State. We describe the application of the risk evaluation for two case studies to illustrate its applicability. The ecological assessment involves examining previous sources of information for the site, defining different resource levels from 0 to 5. We also developed a risk rating scale from non-discernable to very high. Field assessment is the critical step to determine resource levels or to determine if current conditions are the same as previously evaluated. We provide a rapid assessment method for current ecological conditions that can be compared to previous site-specific data, or that can be used to assess resource value on other sites where ecological information is not generally available. The method is applicable to other Department of Energy's sites, where its development may involve a range of state regulators, resource trustees, Tribes and other stakeholders. Achieving consistency across Department of Energy's sites for valuation of ecological resources on remediation sites will assure Congress and the public that funds and personnel are being deployed appropriately.

Child/Adolescent Anxiety Multimodal Study (CAMS): rationale, design, and methods

PubMed Central

2010-01-01

Objective To present the design, methods, and rationale of the Child/Adolescent Anxiety Multimodal Study (CAMS), a recently completed federally-funded, multi-site, randomized placebo-controlled trial that examined the relative efficacy of cognitive-behavior therapy (CBT), sertraline (SRT), and their combination (COMB) against pill placebo (PBO) for the treatment of separation anxiety disorder (SAD), generalized anxiety disorder (GAD) and social phobia (SoP) in children and adolescents. Methods Following a brief review of the acute outcomes of the CAMS trial, as well as the psychosocial and pharmacologic treatment literature for pediatric anxiety disorders, the design and methods of the CAMS trial are described. Results CAMS was a six-year, six-site, randomized controlled trial. Four hundred eighty-eight (N = 488) children and adolescents (ages 7-17 years) with DSM-IV-TR diagnoses of SAD, GAD, or SoP were randomly assigned to one of four treatment conditions: CBT, SRT, COMB, or PBO. Assessments of anxiety symptoms, safety, and functional outcomes, as well as putative mediators and moderators of treatment response were completed in a multi-measure, multi-informant fashion. Manual-based therapies, trained clinicians and independent evaluators were used to ensure treatment and assessment fidelity. A multi-layered administrative structure with representation from all sites facilitated cross-site coordination of the entire trial, study protocols and quality assurance. Conclusions CAMS offers a model for clinical trials methods applicable to psychosocial and psychopharmacological comparative treatment trials by using state-of-the-art methods and rigorous cross-site quality controls. CAMS also provided a large-scale examination of the relative and combined efficacy and safety of the best evidenced-based psychosocial (CBT) and pharmacologic (SSRI) treatments to date for the most commonly occurring pediatric anxiety disorders. Primary and secondary results of CAMS will hold important implications for informing practice-relevant decisions regarding the initial treatment of youth with anxiety disorders. Trial registration ClinicalTrials.gov NCT00052078. PMID:20051130

When felids and hominins ruled at Olduvai Gorge: A machine learning analysis of the skeletal profiles of the non-anthropogenic Bed I sites

NASA Astrophysics Data System (ADS)

Arriaza, Mari Carmen; Domínguez-Rodrigo, Manuel

2016-05-01

In the past twenty years, skeletal part profiles, which are prone to equifinality, have not occupied a prominent role in the interpretation of early Pleistocene sites on Africa. Alternatively, taphonomic studies on bone surface modifications and bone breakage patterns, have provided heuristic interpretations of some of the best preserved archaeological record of this period; namely, the Olduvai Bed I sites. The most recent and comprehensive taphonomic study of these sites (Domínguez-Rodrigo et al., 2007a) showed that FLK Zinj was an anthropogenic assemblage in which hominins acquired carcasses via primary access. That study also showed that the other sites were palimpsests with minimal or no intervention by hominins. The FLK N, FLK NN and DK sequence seemed to be dominated by single-agent (mostly, felid) or multiple-agent (mostly, felid-hyenid) processes. The present study re-analyzes the Bed I sites focusing on skeletal part profiles. Machine learning methods, which incorporate complex algorithms, are powerful predictive and classification methods and have the potential to better extract information from skeletal part representation than past approaches. Here, multiple algorithms (via decision trees, neural networks, random forests and support vector machines) are combined to produce a solid interpretation of bone accumulation agency at the Olduvai Bed I sites. This new approach virtually coincides with previous taphonomic interpretations on a site by site basis and shows that felids were dominant accumulating agents over hyenas during Bed I times. The recent discovery of possibly a modern lion-accumulated assemblage at Olduvai Gorge (Arriaza et al., submitted) provides a very timely analog for this interpretation.

Remediation of petroleum hydrocarbon-contaminated sites by DNA diagnosis-based bioslurping technology.

PubMed

Kim, Seungjin; Krajmalnik-Brown, Rosa; Kim, Jong-Oh; Chung, Jinwook

2014-11-01

The application of effective remediation technologies can benefit from adequate preliminary testing, such as in lab-scale and Pilot-scale systems. Bioremediation technologies have demonstrated tremendous potential with regards to cost, but they cannot be used for all contaminated sites due to limitations in biological activity. The purpose of this study was to develop a DNA diagnostic method that reduces the time to select contaminated sites that are good candidates for bioremediation. We applied an oligonucleotide microarray method to detect and monitor genes that lead to aliphatic and aromatic degradation. Further, the bioremediation of a contaminated site, selected based on the results of the genetic diagnostic method, was achieved successfully by applying bioslurping in field tests. This gene-based diagnostic technique is a powerful tool to evaluate the potential for bioremediation in petroleum hydrocarbon contaminated soil. Copyright © 2014 Elsevier B.V. All rights reserved.

Variable context Markov chains for HIV protease cleavage site prediction.

PubMed

Oğul, Hasan

2009-06-01

Deciphering the knowledge of HIV protease specificity and developing computational tools for detecting its cleavage sites in protein polypeptide chain are very desirable for designing efficient and specific chemical inhibitors to prevent acquired immunodeficiency syndrome. In this study, we developed a generative model based on a generalization of variable order Markov chains (VOMC) for peptide sequences and adapted the model for prediction of their cleavability by certain proteases. The new method, called variable context Markov chains (VCMC), attempts to identify the context equivalence based on the evolutionary similarities between individual amino acids. It was applied for HIV-1 protease cleavage site prediction problem and shown to outperform existing methods in terms of prediction accuracy on a common dataset. In general, the method is a promising tool for prediction of cleavage sites of all proteases and encouraged to be used for any kind of peptide classification problem as well.

Characterization and forensic analysis of soil samples using laser-induced breakdown spectroscopy (LIBS).

PubMed

Jantzi, Sarah C; Almirall, José R

2011-07-01

A method for the quantitative elemental analysis of surface soil samples using laser-induced breakdown spectroscopy (LIBS) was developed and applied to the analysis of bulk soil samples for discrimination between specimens. The use of a 266 nm laser for LIBS analysis is reported for the first time in forensic soil analysis. Optimization of the LIBS method is discussed, and the results compared favorably to a laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) method previously developed. Precision for both methods was <10% for most elements. LIBS limits of detection were <33 ppm and bias <40% for most elements. In a proof of principle study, the LIBS method successfully discriminated samples from two different sites in Dade County, FL. Analysis of variance, Tukey's post hoc test and Student's t test resulted in 100% discrimination with no type I or type II errors. Principal components analysis (PCA) resulted in clear groupings of the two sites. A correct classification rate of 99.4% was obtained with linear discriminant analysis using leave-one-out validation. Similar results were obtained when the same samples were analyzed by LA-ICP-MS, showing that LIBS can provide similar information to LA-ICP-MS. In a forensic sampling/spatial heterogeneity study, the variation between sites, between sub-plots, between samples and within samples was examined on three similar Dade sites. The closer the sampling locations, the closer the grouping on a PCA plot and the higher the misclassification rate. These results underscore the importance of careful sampling for geographic site characterization.

A case study of alternative site response explanatory variables in Parkfield, California

USGS Publications Warehouse

Thompson, E.M.; Baise, L.G.; Kayen, R.E.; Morgan, E.C.; Kaklamanos, J.

2011-01-01

The combination of densely-spaced strong-motion stations in Parkfield, California, and spectral analysis of surface waves (SASW) profiles provides an ideal dataset for assessing the accuracy of different site response explanatory variables. We judge accuracy in terms of spatial coverage and correlation with observations. The performance of the alternative models is period-dependent, but generally we observe that: (1) where a profile is available, the square-root-of-impedance method outperforms VS30 (average S-wave velocity to 30 m depth), and (2) where a profile is unavailable, the topographic-slope method outperforms surficial geology. The fundamental site frequency is a valuable site response explanatory variable, though less valuable than VS30. However, given the expense and difficulty of obtaining reliable estimates of VS30 and the relative ease with which the fundamental site frequency can be computed, the fundamental site frequency may prove to be a valuable site response explanatory variable for many applications. ?? 2011 ASCE.

Comparing horizontal-to-vertical spectral ratios with sediment-to-bedrock spectral ratios in a region with a thin layer of unconsolidated sediments

NASA Astrophysics Data System (ADS)

Schleicher, L.; Pratt, T. L.

2017-12-01

Underlying sediment can amplify ground motions during earthquakes, making site response estimates key components in seismic evaluations for building infrastructure. The horizontal-to-vertical spectral ratio (HVSR) method, using either earthquake signals or ambient noise as input, is an appealing method for estimating site response because it uses only a single seismic station rather than requiring two or more seismometers traditionally used to compute a horizontal sediment-to-bedrock spectral ratio (SBSR). A number of studies have had mixed results when comparing the accuracy of the HVSR versus SBSR methods for identifying the frequencies and amplitudes of the primary resonance peaks. Many of these studies have been carried out in areas of complex geology, such as basins with structures that can introduce 3D effects. Here we assess the effectiveness of the HVSR method by a comparison with the SBSR method and models of transfer functions in an area dominated by a flat and thin, unconsolidated sediment layer over bedrock, which should be an ideal setting for using the HVSR method. In this preliminary study, we analyze teleseismic and regional earthquake recordings from a temporary seismometer array deployed throughout Washington, DC, which is underlain by a wedge of 0 to 270 m thick layer of unconsolidated Atlantic Coastal Plain sedimentary strata. At most sites, we find a close match in the amplitudes and frequencies of large resonance peaks in horizontal ground motions at frequencies of 0.7 to 5 Hz in site response estimates using the HVSR and SBSR methods. Amplitudes of the HVSRs tend to be slightly lower than SBSRs at 3 Hz and less, but the amplitudes of the fundamental resonance peaks often match closely. The results suggest that the HVSR method could be a successful approach to consider for computing site response estimates in areas of simple shallow geology consisting of thin sedimentary layers with a strong reflector at the underlying bedrock surface. [This publication represents the views of the authors and does not necessarily represent the views of the Defense Nuclear Facilities Safety Board.

Protocol for a mixed-methods study on leader-based interventions in construction contractors' safety commitments.

PubMed

Pedersen, Betina Holbaek; Dyreborg, Johnny; Kines, Pete; Mikkelsen, Kim Lyngby; Hannerz, Harald; Andersen, Dorte Raaby; Spangenberg, Søren

2010-06-01

Owing to high injury rates, safety interventions are needed in the construction industry. Evidence-based interventions tailored to this industry are, however, scarce. Leader-based safety interventions have proven more effective than worker-based interventions in other industries. To test a leader-based safety intervention for construction sites. The intervention consists of encouraging safety coordinators to provide feedback on work safety to the client and line management. The intention is to increase communication and interactions regarding safety within the line management and between the client and the senior management. It is hypothesised that this, in turn, will lead to increased communication and interaction about safety between management and coworkers as well as an increased on-site safety level. A group-randomised double-blinded case study of six Danish construction sites (three intervention sites and three control sites). The recruitment of the construction sites is performed continuously from January 2010 to June 2010. The investigation of each site lasts 20 continuous weeks. Confirmatory statistical analysis is used to test if the safety level increased, and if the probability of safety communications between management and coworkers increases as a consequence of the intervention. The data collection will be blinded. Qualitative methods are used to evaluate if communication and interactions about safety at all managerial levels, including the client, increase. (1) The proportion of safety-related communications out of all studied communications between management and coworkers. (2) The safety level index of the construction sites.

LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length.

PubMed

Bao, Yu; Hayashida, Morihiro; Akutsu, Tatsuya

2016-11-25

Dicer is necessary for the process of mature microRNA (miRNA) formation because the Dicer enzyme cleaves pre-miRNA correctly to generate miRNA with correct seed regions. Nonetheless, the mechanism underlying the selection of a Dicer cleavage site is still not fully understood. To date, several studies have been conducted to solve this problem, for example, a recent discovery indicates that the loop/bulge structure plays a central role in the selection of Dicer cleavage sites. In accordance with this breakthrough, a support vector machine (SVM)-based method called PHDCleav was developed to predict Dicer cleavage sites which outperforms other methods based on random forest and naive Bayes. PHDCleav, however, tests only whether a position in the shift window belongs to a loop/bulge structure. In this paper, we used the length of loop/bulge structures (in addition to their presence or absence) to develop an improved method, LBSizeCleav, for predicting Dicer cleavage sites. To evaluate our method, we used 810 empirically validated sequences of human pre-miRNAs and performed fivefold cross-validation. In both 5p and 3p arms of pre-miRNAs, LBSizeCleav showed greater prediction accuracy than PHDCleav did. This result suggests that the length of loop/bulge structures is useful for prediction of Dicer cleavage sites. We developed a novel algorithm for feature space mapping based on the length of a loop/bulge for predicting Dicer cleavage sites. The better performance of our method indicates the usefulness of the length of loop/bulge structures for such predictions.

Evaluation of subcutaneous and alveolar implantation surgical sites in the study of the biological properties of root-end filling endodontic materials

PubMed Central

CINTRA, Luciano Tavares Angelo; BERNABÉ, Pedro Felício Estrada; de MORAES, Ivaldo Gomes; GOMES-FILHO, João Eduardo; OKAMOTO, Tetuo; CONSOLARO, Alberto; PINHEIRO, Tiago Novaes

2010-01-01

Objective The aim of this study was to compare two methodologies used in the evaluation of tissue response to root-end filling materials in rats. Material and Methods Forty rats were divided into 4 groups: in Groups I and II (control groups), empty polyethylene tubes were implanted in the extraction site and in the subcutaneous tissue, respectively; in Groups III and IV, polyethylene tubes filled with ProRoot MTA were implanted in the extraction site and in the subcutaneous tissue, respectively. The animals were killed 7 and 30 days after tube implantation, and the hemi-maxillas and the capsular subcutaneous tissue, both with the tubes, were removed. Specimens were processed and evaluated histomorphologicaly under light microscopy. The scores obtained were analyzed statistically by the Kruskal-Wallis test (p<0.05). Results There were no statistically significant differences between the implantation methods (p=0.78033, p=0.72039). It was observed that the 30-day groups presented a more mature healing process due to smaller number of inflammatory cells. Conclusion The present study showed no differences in tissue responses as far as the implantation site and the studied period were concerned. Alveolar socket implantation methodology represents an interesting method in the study of the biological properties of root-end filling endodontic materials due to the opportunity to evaluate bone tissue response. PMID:20379685

Shared Opportunities on Institutional Lands: On-Site Food Production, Its Benefits, Barriers, and Opportunities.

PubMed

Knezevic, Irena; Mount, Phil; Clement, Chantal

2016-10-01

This article outlines preliminary findings of a 3-year project that explored on-site food production on institutional properties, primarily healthcare facilities. There are growing pressures on healthcare facilities to improve their food offerings and incorporate food gardens into their health programs. While several healthcare facilities produce food on-site, there are few studies that explore opportunities, capacities, and institutional barriers related to on-site food production. The study employed mixed methods including historical review, case studies, surveys, interviews, pilot garden projects, and Geographic Information System mapping. The number of participating institutions varied by method. Benefits associated with on-site food production can be health, economic, environmental, and social. There are also institutional barriers including administrative roadblocks, perceived obstacles, and the difficulty in quantitatively, measuring the qualitatively documented benefits. The benefits of food gardens far outweigh the challenges. On-site food production has tremendous potential to improve nutrition for staff and patients, offer healing spaces, better connect institutions with the communities in which they are located, and provide the long-professed benefits of gardening for all involved-from therapeutic benefits and outdoor physical activities to developing skills and social relationships in ways that few other activities do. © The Author(s) 2016.

Analysis strategies for longitudinal attachment loss data.

PubMed

Beck, J D; Elter, J R

2000-02-01

The purpose of this invited review is to describe and discuss methods currently in use to quantify the progression of attachment loss in epidemiological studies of periodontal disease, and to make recommendations for specific analytic methods based upon the particular design of the study and structure of the data. The review concentrates on the definition of incident attachment loss (ALOSS) and its component parts; measurement issues including thresholds and regression to the mean; methods of accounting for longitudinal change, including changes in means, changes in proportions of affected sites, incidence density, the effect of tooth loss and reversals, and repeated events; statistical models of longitudinal change, including the incorporation of the time element, use of linear, logistic or Poisson regression or survival analysis, and statistical tests; site vs person level of analysis, including statistical adjustment for correlated data; the strengths and limitations of ALOSS data. Examples from the Piedmont 65+ Dental Study are used to illustrate specific concepts. We conclude that incidence density is the preferred methodology to use for periodontal studies with more than one period of follow-up and that the use of studies not employing methods for dealing with complex samples, correlated data, and repeated measures does not take advantage of our current understanding of the site- and person-level variables important in periodontal disease and may generate biased results.

Characterization of Leachate at Simpang Renggam Landfill Site, Johor, Malaysia

NASA Astrophysics Data System (ADS)

Zailani, L. W. M.; Amdan, N. S. M.; Zin, N. S. M.

2018-04-01

Nowadays, the world facing a major problem in managed solid waste due to the increasing of solid waste. Malaysia, one of the country also involves in this matter which is 296 landfills are open to overcome this problem. Currently, the best alternative option to manage solid waste is by using landfilling method because it has low costing advantages. The disadvantage of landfill method, it might cause a pollution by producing leachate that will give an effect to the ground and surface water resources. This study focuses on analysing the leachate composition at Simpang Renggam Landfill(SRL) site for seven parameters such as COD, BOD, SS, turbidity, pH, BOD5/COD, and ammonia (NH3-N). All the data obtained were compared with previous researcher and Malaysia Environmental Quality Act 1974. From the result, SRL site was categorized as partially stabilized leachate with the parameter of BOD5/COD > 0.1. The SRL site is recommended to use a physical-chemical method for a better treatment because the leachate composition is classified as old leachate and aerated lagoon method are not satisfied to be used in treating the aging leachate at SRL site.

Site-specific mouth rinsing can improve oral odor by altering bacterial counts. Blind crossover clinical study.

PubMed

Alqumber, Mohammed A; Arafa, Khaled A

2014-11-01

To determine whether site-specific mouth rinsing with oral disinfectants can improve oral odor beyond the traditional panoral mouth disinfection with mouth rinses by targeting specifically oral malodor implicated anaerobic bacteria. Twenty healthy fasting subjects volunteered for a blinded prospective, descriptive correlational crossover cross-section clinical trial conducted during the month of Ramadan between July and August 2013 in Albaha province in Saudi Arabia involving the application of Listerine Cool Mint mouth rinse by either the traditional panoral rinsing method, or a site-specific disinfection method targeting the subgingival and supragingival plaque and the posterior third of the tongue dorsum, while avoiding the remaining locations within the oral cavity. The viable anaerobic and aerobic bacterial counts, volatile sulfur compounds (VSCs) levels, organoleptic assessment of oral odor, and the tongue-coating index were compared at baseline, one, 5, and 9 hours after the treatment. The site-specific disinfection method reduced the VSCs and anaerobic bacterial loads while keeping the aerobic bacterial numbers higher than the traditional panoral rinsing method. Site-specific disinfection can more effectively maintain a healthy oral cavity by predominantly disinfecting the niches of anaerobic bacteria within the oral cavity.

Core Binding Site of a Thioflavin-T-Derived Imaging Probe on Amyloid β Fibrils Predicted by Computational Methods.

PubMed

Kawai, Ryoko; Araki, Mitsugu; Yoshimura, Masashi; Kamiya, Narutoshi; Ono, Masahiro; Saji, Hideo; Okuno, Yasushi

2018-05-16

Development of new diagnostic imaging probes for Alzheimer's disease, such as positron emission tomography (PET) and single photon emission computed tomography (SPECT) probes, has been strongly desired. In this study, we investigated the most accessible amyloid β (Aβ) binding site of [ 123 I]IMPY, a Thioflavin-T-derived SPECT probe, using experimental and computational methods. First, we performed a competitive inhibition assay with Orange-G, which recognizes the KLVFFA region in Aβ fibrils, suggesting that IMPY and Orange-G bind to different sites in Aβ fibrils. Next, we precisely predicted the IMPY binding site on a multiple-protofilament Aβ fibril model using computational approaches, consisting of molecular dynamics and docking simulations. We generated possible IMPY-binding structures using docking simulations to identify candidates for probe-binding sites. The binding free energy of IMPY with the Aβ fibril was calculated by a free energy simulation method, MP-CAFEE. These computational results suggest that IMPY preferentially binds to an interfacial pocket located between two protofilaments and is stabilized mainly through hydrophobic interactions. Finally, our computational approach was validated by comparing it with the experimental results. The present study demonstrates the possibility of computational approaches to screen new PET/SPECT probes for Aβ imaging.

Soil properties and root biomass responses to prescribed burning in young Corsican pine (Pinus nigra Arn.) stands.

PubMed

Tufekcioglu, Aydin; Kucuk, Mehmet; Saglam, Bulent; Bilgili, Ertugrul; Altun, Lokman

2010-05-01

Fire is an important tool in the management of forest ecosystems. Although both prescribed and wildland fires are common in Turkey, few studies have addressed the influence of such disturbances on soil properties and root biomass dynamics. In this study, soil properties and root biomass responses to prescribed fire were investigated in 25-year-old corsican pine (Pinus nigra Arn.) stands in Kastamonu, Turkey. The stands were established by planting and were subjected to prescribed burning in July 2003. Soil respiration rates were determined every two months using soda-lime method over a two-year period. Fine (0-2 mm diameter) and small root (2-5 mm diameter) biomass were sampled approximately bimonthly using sequential coring method. Mean daily soil respiration ranged from 0.65 to 2.19 g Cm(-2) d(-1) among all sites. Soil respiration rates were significantly higher in burned sites than in controls. Soil respiration rates were correlated significantly with soil moisture and soil temperature. Fine root biomass was significantly lower in burned sites than in control sites. Mean fine root biomass values were 4940 kg ha(-1) for burned and 5450 kg ha(-1) for control sites. Soil pH was significantly higher in burned sites than in control sites in 15-35 cm soil depth. Soil organic matter content did not differ significantly between control and burned sites. Our results indicate that, depending on site conditions, fire could be used successfully as a tool in the management of forest stands in the study area.

Studies on rock characteristics and timing of creep at selected landslide sites in Taiwan

Treesearch

Cheng-Yi Lee

2000-01-01

A study was conducted to investigate the causes of and rock characteristics at three landslide sites in the Tesngwen Reservoir watershed of southern Taiwan. Research methods used included the petrographic microscope, X-ray diffraction (XRD), scanning electron microscope (SEM), inductively coupled plasma spectroscope (ICP), constant head permeameter in triaxial...

A Multi-Site Study on Medical School Selection, Performance, Motivation and Engagement

ERIC Educational Resources Information Center

Wouters, A.; Croiset, G.; Schripsema, N. R.; Cohen-Schotanus, J.; Spaai, G. W.; Hulsman, R. L.; Kusurkar, R. A.

2017-01-01

Medical schools seek ways to improve their admissions strategies, since the available methods prove to be suboptimal for selecting the best and most motivated students. In this multi-site cross-sectional questionnaire study, we examined the value of (different) selection procedures compared to a weighted lottery procedure, which includes direct…

INVESTIGATING THE EFFICACY OF CLINICAL TRIAL MONITORING STRATEGIES: Design and Implementation of the Cluster Randomized START Monitoring Substudy

PubMed Central

Hullsiek, Katherine Huppler; Kagan, Jonathan M; Engen, Nicole; Grarup, Jesper; Hudson, Fleur; Denning, Eileen T; Carey, Catherine; Courtney-Rodgers, David; Finley, Elizabeth B; Jansson, Per O; Pearson, Mary T; Peavy, Dwight E; Belloso, Waldo H

2014-01-01

Background Trial monitoring protects participant safety and study integrity. While monitors commonly go on-site to verify source data, there is little evidence that this practice is efficient or effective. An ongoing international HIV treatment trial (START) provides an opportunity to explore the usefulness of different monitoring approaches. Methods All START sites are centrally monitored and required to follow a local monitoring plan requiring specific quality assurance activities. Additionally, sites were randomized (1:1) to receive, or not receive, annual on-site monitoring. The study will determine if on-site monitoring increases the identification of major protocol deviations (eligibility or consent violations, improper study drug use, primary or serious event underreporting, data alteration or fraud). Results The START study completed enrollment in December 2013, with planned follow-up through December 2016. The monitoring study is ongoing at 196 sites in 34 countries. Results are expected when the START study concludes in December 2016. PMID:25973346

Ultimate pier and contraction scour prediction in cohesive soils at selected bridges in Illinois

USGS Publications Warehouse

Straub, Timothy D.; Over, Thomas M.; Domanski, Marian M.

2013-01-01

The Scour Rate In COhesive Soils-Erosion Function Apparatus (SRICOS-EFA) method includes an ultimate scour prediction that is the equilibrium maximum pier and contraction scour of cohesive soils over time. The purpose of this report is to present the results of testing the ultimate pier and contraction scour methods for cohesive soils on 30 bridge sites in Illinois. Comparison of the ultimate cohesive and noncohesive methods, along with the Illinois Department of Transportation (IDOT) cohesive soil reduction-factor method and measured scour are presented. Also, results of the comparison of historic IDOT laboratory and field values of unconfined compressive strength of soils (Qu) are presented. The unconfined compressive strength is used in both ultimate cohesive and reduction-factor methods, and knowing how the values from field methods compare to the laboratory methods is critical to the informed application of the methods. On average, the non-cohesive method results predict the highest amount of scour, followed by the reduction-factor method results; and the ultimate cohesive method results predict the lowest amount of scour. The 100-year scour predicted for the ultimate cohesive, noncohesive, and reduction-factor methods for each bridge site and soil are always larger than observed scour in this study, except 12% of predicted values that are all within 0.4 ft of the observed scour. The ultimate cohesive scour prediction is smaller than the non-cohesive scour prediction method for 78% of bridge sites and soils. Seventy-six percent of the ultimate cohesive predictions show a 45% or greater reduction from the non-cohesive predictions that are over 10 ft. Comparing the ultimate cohesive and reduction-factor 100-year scour predictions methods for each bridge site and soil, the scour predicted by the ultimate cohesive scour prediction method is less than the reduction-factor 100-year scour prediction method for 51% of bridge sites and soils. Critical shear stress remains a needed parameter in the ultimate scour prediction for cohesive soils. The unconfined soil compressive strength measured by IDOT in the laboratory was found to provide a good prediction of critical shear stress, as measured by using the erosion function apparatus in a previous study. Because laboratory Qu analyses are time-consuming and expensive, the ability of field-measured Rimac data to estimate unconfined soil strength in the critical shear–soil strength relation was tested. A regression analysis was completed using a historic IDOT dataset containing 366 data pairs of laboratory Qu and field Rimac measurements from common sites with cohesive soils. The resulting equations provide a point prediction of Qu, given any Rimac value with the 90% confidence interval. The prediction equations are not significantly different from the identity Qu = Rimac. The alternative predictions of ultimate cohesive scour presented in this study assume Qu will be estimated using Rimac measurements that include computed uncertainty. In particular, the ultimate cohesive predicted scour is greater than observed scour for the entire 90% confidence interval range for predicting Qu at the bridges and soils used in this study, with the exception of the six predicted values that are all within 0.6 ft of the observed scour.

Microbiologic tests in epidemiologic studies: are they reproducible?

PubMed

Aass, A M; Preus, H R; Zambon, J J; Gjermo, P

1994-12-01

Microbiologic assessments are often included in longitudinal studies to elucidate the significance of the association of certain Gram-negative bacteria and the development of periodontal diseases. In such studies, the reliability of methods is crucial. There are several methods to identify putative pathogens, and some of them are commercially available. The purpose of the present study was to compare the reproducibility of four different methods for detecting Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, and Prevotella intermedia in order to evaluate their usefulness in epidemiologic studies. The test panel consisted of 10 young subjects and 10 adult periodontitis patients. Subgingival plaque was sampled from sites showing bone loss and "healthy" control sites. The four different methods for detecting the target bacteria were 1) cultivation, 2) Evalusite (a chair-side kit based on ELISA), 3) OmniGene, Inc, based on DNA probes, and 4) indirect immunofluorescence (IIF). The test procedure was repeated after a 1-wk interval and was performed by one examiner. Sites reported to be positive for a microorganism by any of the four methods at one or both examinations were considered to be positive for that organism and included in the analysis. The reproducibility of the four methods was low. The IIF and the cultivation methods showed somewhat higher reproducibility than did the commercial systems. A second test was done for Evalusite, three paper points for sampling being used instead of one as described in the manual. The reproducibility of the second test was improved, indicating that the detection level of the system may influence the reliability.

TarPmiR: a new approach for microRNA target site prediction.

PubMed

Ding, Jun; Li, Xiaoman; Hu, Haiyan

2016-09-15

The identification of microRNA (miRNA) target sites is fundamentally important for studying gene regulation. There are dozens of computational methods available for miRNA target site prediction. Despite their existence, we still cannot reliably identify miRNA target sites, partially due to our limited understanding of the characteristics of miRNA target sites. The recently published CLASH (crosslinking ligation and sequencing of hybrids) data provide an unprecedented opportunity to study the characteristics of miRNA target sites and improve miRNA target site prediction methods. Applying four different machine learning approaches to the CLASH data, we identified seven new features of miRNA target sites. Combining these new features with those commonly used by existing miRNA target prediction algorithms, we developed an approach called TarPmiR for miRNA target site prediction. Testing on two human and one mouse non-CLASH datasets, we showed that TarPmiR predicted more than 74.2% of true miRNA target sites in each dataset. Compared with three existing approaches, we demonstrated that TarPmiR is superior to these existing approaches in terms of better recall and better precision. The TarPmiR software is freely available at http://hulab.ucf.edu/research/projects/miRNA/TarPmiR/ CONTACTS: haihu@cs.ucf.edu or xiaoman@mail.ucf.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Seismic velocity site characterization of 10 Arizona strong-motion recording stations by spectral analysis of surface wave dispersion

USGS Publications Warehouse

Kayen, Robert E.; Carkin, Brad A.; Corbett, Skye C.

2017-10-19

Vertical one-dimensional shear wave velocity (VS) profiles are presented for strong-motion sites in Arizona for a suite of stations surrounding the Palo Verde Nuclear Generating Station. The purpose of the study is to determine the detailed site velocity profile, the average velocity in the upper 30 meters of the profile (VS30), the average velocity for the entire profile (VSZ), and the National Earthquake Hazards Reduction Program (NEHRP) site classification. The VS profiles are estimated using a non-invasive continuous-sine-wave method for gathering the dispersion characteristics of surface waves. Shear wave velocity profiles were inverted from the averaged dispersion curves using three independent methods for comparison, and the root-mean-square combined coefficient of variation (COV) of the dispersion and inversion calculations are estimated for each site.

Easier operation and similar power of 10 g monofilament test for screening diabetic peripheral neuropathy.

PubMed

Zhang, Qi; Yi, Na; Liu, Siying; Zheng, Hangping; Qiao, Xiaona; Xiong, Qian; Liu, Xiaoxia; Zhang, Shuo; Wen, Jie; Ye, Hongying; Zhou, Linuo; Li, Yiming; Hu, Renming; Lu, Bin

2018-01-01

Objective The 10 g Semmes-Weinstein monofilament evaluation (SWME) of 4 sites on each foot is recommended for distal symmetric polyneuropathy screening and diagnosis. A similar method has been proposed to diagnose 'high-risk' (for ulceration) feet, using 3 sites per foot. This study compared the effectiveness of SWME for testing 3, 4 and 10 sites per foot to identify patients with diabetic neuropathy. Methods We included 3497 subjects in a SWME of 10 sites; records from the 10-site SWME were used for a SWME of 3 and 4 sites. Neuropathy symptom scores and neuropathy deficit scores were evaluated to identify patients with diabetic peripheral neuropathy. Results The sensitivities of the 10 g SWME for 3, 4 and 10 sites were 17.8%, 19.0% and 22.4%, respectively. The Kappa coefficients for the SWME tests of 3, 4 and 10 sites were high (range: 0.78-0.93). Conclusions There were no significant differences in the effectiveness of 3-, 4- and 10-site SWME testing for diabetic peripheral neuropathy screening. SWME testing of 3 sites on each foot may be sufficient to screen for diabetic neuropathy.

Subsurface profiling using integrated geophysical methods for 2D site response analysis in Bangalore city, India: a new approach

NASA Astrophysics Data System (ADS)

Chandran, Deepu; Anbazhagan, P.

2017-10-01

Recently, site response analysis has become a mandatory step for the design of important structures. Subsurface investigation is an essential step, from where the input parameters for the site response study like density, shear wave velocity (Vs), thickness and damping characteristics, etc, are obtained. Most site response studies at shallow bedrock sites are one-dimensional (1D) and are usually carried out by using Vs from multi-channel analysis of surface waves (MASW) or a standard penetration test (SPT) for N values with assumptions that soil layers are horizontal, uniform and homogeneous. These assumptions are not completely true in shallow bedrock regions as soil deposits are heterogeneous. The objective of this study is to generate the actual subsurface profiles in two-dimensions at shallow bedrock regions using integrated subsurface investigation testing. The study area selected for this work is Bangalore, India. Three survey lines were selected in Bangalore at two different locations; one at the Indian Institute of Science (IISc) Campus and the other at Whitefield. Geophysical surveys like ground penetrating radar (GPR) and 2D MASW were carried out at these survey lines. Geophysical test results are compared and validated with a conventional geotechnical SPT. At the IISc site, the soil profile is obtained from a trench excavated for a proposed pipeline used to compare the geophysical test results. Test results show that GPR is very useful to delineate subsurface layers, especially for shallow depths at both sites (IISc Campus and Whitefield). MASW survey results show variation of Vs values and layer thickness comparatively at deeper depths for both sites. They also show higher density soil strata with high Vs value obtained at the IISc Campus site, whereas at the Whitefield site weaker soil with low shear velocity is observed. Combining these two geophysical methods helped to generate representative 2D subsurface profiles. These subsurface profiles can be further used to understand the difference between 1D and 2D site response.

A method for coupling a parameterization of the planetary boundary layer with a hydrologic model

NASA Technical Reports Server (NTRS)

Lin, J. D.; Sun, Shu Fen

1986-01-01

Deardorff's parameterization of the planetary boundary layer is adapted to drive a hydrologic model. The method converts the atmospheric conditions measured at the anemometer height at one site to the mean values in the planetary boundary layer; it then uses the planetary boundary layer parameterization and the hydrologic variables to calculate the fluxes of momentum, heat and moisture at the atmosphere-land interface for a different site. A simplified hydrologic model is used for a simulation study of soil moisture and ground temperature on three different land surface covers. The results indicate that this method can be used to drive a spatially distributed hydrologic model by using observed data available at a meteorological station located on or nearby the site.

Aquatic environmental assessment of Lake Balaton in the light of physical-chemical water parameters.

PubMed

Sebestyén, Vitkor; Németh, József; Juzsakova, Tatjana; Domokos, Endre; Kovács, Zsófia; Rédey, Ákos

2017-11-01

One of the issues of the Hungarian Water Management Strategy is the improvement and upgrading of the water of Lake Balaton. The Water Framework Directive (WFD) specifies and sets forth the achievement of the good ecological status. However, the assessment of the water quality of the lake as a complex system requires a comprehensive monitoring and evaluation procedure. Measurements were carried out around the Lake Balaton at ten different locations/sites and 13 physical-chemical parameters were monitored at each measurement site.For the interpretation of the water chemistry parameters the Aquatic Environmental Assessment (AEA) method devised by authors was used for the water body of the Lake Balaton. The AEA method can be used for all types of the water bodies since it is flexible and using individual weighting procedure for the water chemistry parameters comprehensive information can be obtain. The AEA method was compared with existing EIA methods according to a predefined criterion system and proved to be the most suitable tool for evaluating the environmental impacts in our study.On the basis of the results it can be concluded that the status of the quality of studied area on the Lake Balaton can be categorized as proper quality (from the outcome of the ten measurement sites this conclusion was reached at seven sites).

Deciphering the functions of O-GlcNAc glycosylation in the brain: The role of site-specific quantitative O-GlcNAcomics.

PubMed

Thompson, John W; Sorum, Alexander W; Hsieh-Wilson, Linda C

2018-06-23

The dynamic posttranslational modification O-linked β-N-acetylglucosamine glycosylation (O-GlcNAcylation) is present on thousands of intracellular proteins in the brain. Like phosphorylation, O-GlcNAcylation is inducible and plays important functional roles in both physiology and disease. Recent advances in mass spectrometry (MS) and bioconjugation methods are now enabling the mapping of O-GlcNAcylation events to individual sites in proteins. However, our understanding of which glycosylation events are necessary for regulating protein function and controlling specific processes, phenotypes, or diseases remains in its infancy. Given the sheer number of O-GlcNAc sites, methods are greatly needed to identify promising sites and prioritize them for time- and resource-intensive functional studies. Revealing sites that are dynamically altered by different stimuli or disease states will likely to go a long way in this regard. Here, we describe advanced methods for identifying O-GlcNAc sites on individual proteins and across the proteome, and for determining their stoichiometry in vivo. We also highlight emerging technologies for quantitative, site-specific MS-based O-GlcNAc proteomics (O-GlcNAcomics), which allow proteome-wide tracking of O-GlcNAcylation dynamics at individual sites. These cutting-edge technologies are beginning to bridge the gap between the high-throughput cataloging of O-GlcNAcylated proteins and the relatively low-throughput study of individual proteins. By uncovering the O-GlcNAcylation events that change in specific physiological and disease contexts, these new approaches are providing key insights into the regulatory functions of O-GlcNAc in the brain, including their roles in neuroprotection, neuronal signaling, learning and memory, and neurodegenerative diseases.

D Model Generation from Uav: Historical Mosque (masjid LAMA Nilai)

NASA Astrophysics Data System (ADS)

Nasir, N. H. Mohd; Tahar, K. N.

2017-08-01

Preserving cultural heritage and historic sites is an important issue. These sites are subjected to erosion and vandalism, and, as long-lived artifacts, they have gone through many phases of construction, damage and repair. It is important to keep an accurate record of these sites using the 3-D model building technology as they currently are, so that preservationists can track changes, foresee structural problems, and allow a wider audience to "virtually" see and tour these sites. Due to the complexity of these sites, building 3-D models is time consuming and difficult, usually involving much manual effort. This study discusses new methods that can reduce the time to build a model using the Unmanned Aerial Vehicle method. This study aims to develop a 3D model of a historical mosque using UAV photogrammetry. In order to achieve this, the data acquisition set of Masjid Lama Nilai, Negeri Sembilan was captured by using an Unmanned Aerial Vehicle. In addition, accuracy assessment between the actual and measured values is made. Besides that, a comparison between the rendering 3D model and texturing 3D model is also carried out through this study.

Mapping of RNA accessible sites by extension of random oligonucleotide libraries with reverse transcriptase.

PubMed Central

Allawi, H T; Dong, F; Ip, H S; Neri, B P; Lyamichev, V I

2001-01-01

A rapid and simple method for determining accessible sites in RNA that is independent of the length of target RNA and does not require RNA labeling is described. In this method, target RNA is allowed to hybridize with sequence-randomized libraries of DNA oligonucleotides linked to a common tag sequence at their 5'-end. Annealed oligonucleotides are extended with reverse transcriptase and the extended products are then amplified by using PCR with a primer corresponding to the tag sequence and a second primer specific to the target RNA sequence. We used the combination of both the lengths of the RT-PCR products and the location of the binding site of the RNA-specific primer to determine which regions of the RNA molecules were RNA extendible sites, that is, sites available for oligonucleotide binding and extension. We then employed this reverse transcription with the random oligonucleotide libraries (RT-ROL) method to determine the accessible sites on four mRNA targets, human activated ras (ha-ras), human intercellular adhesion molecule-1 (ICAM-1), rabbit beta-globin, and human interferon-gamma (IFN-gamma). Our results were concordant with those of other researchers who had used RNase H cleavage or hybridization with arrays of oligonucleotides to identify accessible sites on some of these targets. Further, we found good correlation between sites when we compared the location of extendible sites identified by RT-ROL with hybridization sites of effective antisense oligonucleotides on ICAM-1 mRNA in antisense inhibition studies. Finally, we discuss the relationship between RNA extendible sites and RNA accessibility. PMID:11233988

Development of a local-scale urban stream assessment method using benthic macroinvertebrates: An example from the Santa Clara Basin, California

USGS Publications Warehouse

Carter, J.L.; Purcell, A.H.; Fend, S.V.; Resh, V.H.

2009-01-01

Research that explores the biological response to urbanization on a site-specific scale is necessary for management of urban basins. Recent studies have proposed a method to characterize the biological response of benthic macroinvertebrates along an urban gradient for several climatic regions in the USA. Our study demonstrates how this general framework can be refined and applied on a smaller scale to an urbanized basin, the Santa Clara Basin (surrounding San Jose, California, USA). Eighty-four sampling sites on 14 streams in the Santa Clara Basin were used for assessing local stream conditions. First, an urban index composed of human population density, road density, and urban land cover was used to determine the extent of urbanization upstream from each sampling site. Second, a multimetric biological index was developed to characterize the response of macroinvertebrate assemblages along the urban gradient. The resulting biological index included metrics from 3 ecological categories: taxonomic composition ( Ephemeroptera, Plecoptera, and Trichoptera), functional feeding group (shredder richness), and habit ( clingers). The 90th-quantile regression line was used to define the best available biological conditions along the urban gradient, which we define as the predicted biological potential. This descriptor was then used to determine the relative condition of sites throughout the basin. Hierarchical partitioning of variance revealed that several site-specific variables (dissolved O2 and temperature) were significantly related to a site's deviation from its predicted biological potential. Spatial analysis of each site's deviation from its biological potential indicated geographic heterogeneity in the distribution of impaired sites. The presence and operation of local dams optimize water use, but modify natural flow regimes, which in turn influence stream habitat, dissolved O2, and temperature. Current dissolved O2 and temperature regimes deviate from natural conditions and appear to affect benthic macroinvertebrate assemblages. The assessment methods presented in our study provide finer-scale assessment tools for managers in urban basins. ?? North American Benthological Society.

Repeat 24-hour recalls and locally developed food composition databases: a feasible method to estimate dietary adequacy in a multi-site preconception maternal nutrition RCT.

PubMed

Lander, Rebecca L; Hambidge, K Michael; Krebs, Nancy F; Westcott, Jamie E; Garces, Ana; Figueroa, Lester; Tejeda, Gabriela; Lokangaka, Adrien; Diba, Tshilenge S; Somannavar, Manjunath S; Honnayya, Ranjitha; Ali, Sumera A; Khan, Umber S; McClure, Elizabeth M; Thorsten, Vanessa R; Stolka, Kristen B

2017-01-01

Background : Our aim was to utilize a feasible quantitative methodology to estimate the dietary adequacy of >900 first-trimester pregnant women in poor rural areas of the Democratic Republic of the Congo, Guatemala, India and Pakistan. This paper outlines the dietary methods used. Methods : Local nutritionists were trained at the sites by the lead study nutritionist and received ongoing mentoring throughout the study. Training topics focused on the standardized conduct of repeat multiple-pass 24-hr dietary recalls, including interview techniques, estimation of portion sizes, and construction of a unique site-specific food composition database (FCDB). Each FCDB was based on 13 food groups and included values for moisture, energy, 20 nutrients (i.e. macro- and micronutrients), and phytate (an anti-nutrient). Nutrient values for individual foods or beverages were taken from recently developed FAO-supported regional food composition tables or the USDA national nutrient database. Appropriate adjustments for differences in moisture and application of nutrient retention and yield factors after cooking were applied, as needed. Generic recipes for mixed dishes consumed by the study population were compiled at each site, followed by calculation of a median recipe per 100 g. Each recipe's nutrient values were included in the FCDB. Final site FCDB checks were planned according to FAO/INFOODS guidelines. Discussion : This dietary strategy provides the opportunity to assess estimated mean group usual energy and nutrient intakes and estimated prevalence of the population 'at risk' of inadequate intakes in first-trimester pregnant women living in four low- and middle-income countries. While challenges and limitations exist, this methodology demonstrates the practical application of a quantitative dietary strategy for a large international multi-site nutrition trial, providing within- and between-site comparisons. Moreover, it provides an excellent opportunity for local capacity building and each site FCDB can be easily modified for additional research activities conducted in other populations living in the same area.

Screening of groundwater remedial alternatives for brownfield sites: a comprehensive method integrated MCDA with numerical simulation.

PubMed

Li, Wei; Zhang, Min; Wang, Mingyu; Han, Zhantao; Liu, Jiankai; Chen, Zhezhou; Liu, Bo; Yan, Yan; Liu, Zhu

2018-06-01

Brownfield sites pollution and remediation is an urgent environmental issue worldwide. The screening and assessment of remedial alternatives is especially complex owing to its multiple criteria that involves technique, economy, and policy. To help the decision-makers selecting the remedial alternatives efficiently, the criteria framework conducted by the U.S. EPA is improved and a comprehensive method that integrates multiple criteria decision analysis (MCDA) with numerical simulation is conducted in this paper. The criteria framework is modified and classified into three categories: qualitative, semi-quantitative, and quantitative criteria, MCDA method, AHP-PROMETHEE (analytical hierarchy process-preference ranking organization method for enrichment evaluation) is used to determine the priority ranking of the remedial alternatives and the solute transport simulation is conducted to assess the remedial efficiency. A case study was present to demonstrate the screening method in a brownfield site in Cangzhou, northern China. The results show that the systematic method provides a reliable way to quantify the priority of the remedial alternatives.

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

Taylor, B.B.; Ripp, J.; Sims, R.C.

The Electric Power Research Institute (EPRI) is studying the environmental impact of preservatives associated with in-service utility poles. As part of this endeavor, two EPRI contractors, META Environmental, Inc. (META) and Atlantic Environmental Services, Inc. (Atlantic), have collected soil samples from around wood utility poles nationwide, for various chemical and physical analyses. This report covers the results for 107 pole sites in the US. These pole sites included a range of preservative types, soil types, wood types, pole sizes, and in-service ages. The poles in this study were preserved with one of two types of preservative: pentachlorophenol (PCP) or creosote.more » Approximately 40 to 50 soil samples were collected from each wood pole site in this study. The soil samples collected from the pole sites were analyzed for chlorinated phenols and total petroleum hydrocarbons (TPH) if the pole was preserved with PCP, or for polycyclic aromatic hydrocarbons (PAHs) if the pole was preserved with creosote. The soil samples were also analyzed for physical/chemical parameters, such as pH, total organic carbon (TOC), and cationic exchange capacity (CEC). Additional samples were used in studies to determine biological degradation rates, and soil-water distribution and retardation coefficients of PCP in site soils. Methods of analysis followed standard EPA and ASTM methods, with some modifications in the chemical analyses to enable the efficient processing of many samples with sufficiently low detection limits for this study. All chemical, physical, and site-specific data were stored in a relational computer database.« less

Effects of grazing on leaf area index, fractional cover and evapotranspiration by a desert phreatophyte community at a former uranium mill site on the Colorado Plateau

USGS Publications Warehouse

Bresloff, Cynthia J.; Nguyen, Uyen; Glenn, Edward P.; Waugh, Jody; Nagler, Pamela L.

2013-01-01

This study employed ground and remote sensing methods to monitor the effects of grazing on leaf area index (LAI), fractional cover (fc) and evapotranspiration (ET) of a desert phreatophyte community over an 11 year period at a former uranium mill site on the Colorado Plateau, U.S. Nitrate, ammonium and sulfate are migrating away from the mill site in a shallow alluvial aquifer. The phreatophyte community, consisting of Atriplex canescens (ATCA) and Sarcobatus vermiculatus (SAVE) shrubs, intercepts groundwater and could potentially slow the movement of the contaminant plume through evapotranspiration (ET). However, the site has been heavily grazed by livestock, reducing plant cover and LAI. We used livestock exclosures and revegetation plots to determine the effects of grazing on LAI, fc and ET, then projected the findings over the whole site using multi-platform remote sensing methods. We show that ET is approximately equal to annual precipitation at the site, but when ATCA and SAVE are protected from grazing they can develop high fc and LAI values, and ET can exceed annual precipitation, with the excess coming from groundwater discharge. Therefore, control of grazing could be an effective method to slow migration of contaminants at this and similar sites in the western U.S.

Clinical evaluation of near-infrared light transillumination in approximal dentin caries detection.

PubMed

Ozkan, Gokhan; Guzel, Kadriye Gorkem Ulu

2017-08-01

The objective of this clinical study was to compare conventional caries detection techniques, pen-type laser fluorescence device, and near-infrared light transillumination method in approximal dentin caries lesions. The study included 157 patients, aged 12-18, without any cavity in the posterior teeth. Two calibrated examiners carried out the assessments of selected approximal caries sites independently. After the assessments, the unopened sites were excluded and a total of 161 approximal sites were included in the study. When both the examiners arrived at a consensus regarding the presence of dentin caries, the detected lesions were opened with a conical diamond burr, the cavity extent was examined and validated (gold standard). Sensitivity, specificity, negative predictive value, positive predictive value, accuracy, and area under the ROC curve (Az) values among the caries detection methods were calculated. Bitewing radiography and near-infrared (NIR) light transillumination methods showed the highest sensitivity (0.83-0.82) and accuracy (0.82-0.80) among the methods. Visual inspection showed the lowest sensitivity (0.54). Laser fluorescence device and visual inspection showed nearly equal performance. Near-infrared light transillumination can be used as an alternative method to approximal dentin caries detection. Visual inspection and laser fluorescence device alone should not be used for approximal dentin caries.

Site disturbances associated with alternative prescriptions in an upland hardwood forest of northern Alabama

Treesearch

Emily Carter; Robert B. Rummer; Bryce Stokes

1997-01-01

A study was installed in an upland hardwood forest to evaluate the site impacts associated with three alternative prescriptions --- clearcut, deferment cut, and strip cut. Two methods of site impact assessment were employed: 1) assignment of disturbance classes to selected points within each treatment area; and 2) measurement of soil bulk density, gravimetric water...

Public preferences for nontimber benefits of loblolly pine (Pinus taeda) stands regenerated by different site preparation methods

Treesearch

Jianbang Gan; Stephen H. Kolison; James Miller

2000-01-01

This study assesses public preferences for nontimber benefits of loblolly pine (Pinus taeda L.)stands regenerated 1.5 yr earlier using different site preparation treatments at national forest and industrial forestry sites. Treatments tested on the Tuskegee National Forest were none, chainsaw felling, tree injection, and soil-active herbicide. At the...

Site index curves for white fir in the southwestern United States developed using a guide curve method

Treesearch

Robert L. Mathiasen; William K. Olsen; Carleton B. Edminster

2006-01-01

Site index curves for white fir (Abies concolor) in Arizona, New Mexico, and southwestern Colorado were developed using height-age measurements and an estimated guide curve and 95% confidence intervals for individual predictions. The curves were developed using height-age data for 1,048 white firs from 263 study sites distributed across eight...

Seismic site characterization of an urban dedimentary basin, Livermore Valley, California: Site tesponse, basin-edge-induced surface waves, and 3D simulations

USGS Publications Warehouse

Hartzell, Stephen; Leeds, Alena L.; Ramirez-Guzman, Leonardo; Allen, James P.; Schmitt, Robert G.

2016-01-01

Thirty‐two accelerometers were deployed in the Livermore Valley, California, for approximately one year to study sedimentary basin effects. Many local and near‐regional earthquakes were recorded, including the 24 August 2014 Mw 6.0 Napa, California, earthquake. The resulting ground‐motion data set is used to quantify the seismic response of the Livermore basin, a major structural depression in the California Coast Range Province bounded by active faults. Site response is calculated by two methods: the reference‐site spectral ratio method and a source‐site spectral inversion method. Longer‐period (≥1  s) amplification factors follow the same general pattern as Bouguer gravity anomaly contours. Site response spectra are inverted for shallow shear‐wave velocity profiles, which are consistent with independent information. Frequency–wavenumber analysis is used to analyze plane‐wave propagation across the Livermore Valley and to identify basin‐edge‐induced surface waves with back azimuths different from the source back azimuth. Finite‐element simulations in a 3D velocity model of the region illustrate the generation of basin‐edge‐induced surface waves and point out strips of elevated ground velocities along the margins of the basin.

Comparative assessment of GIS-based methods and metrics for estimating long-term exposures to air pollution

NASA Astrophysics Data System (ADS)

Gulliver, John; de Hoogh, Kees; Fecht, Daniela; Vienneau, Danielle; Briggs, David

2011-12-01

The development of geographical information system techniques has opened up a wide array of methods for air pollution exposure assessment. The extent to which these provide reliable estimates of air pollution concentrations is nevertheless not clearly established. Nor is it clear which methods or metrics should be preferred in epidemiological studies. This paper compares the performance of ten different methods and metrics in terms of their ability to predict mean annual PM 10 concentrations across 52 monitoring sites in London, UK. Metrics analysed include indicators (distance to nearest road, traffic volume on nearest road, heavy duty vehicle (HDV) volume on nearest road, road density within 150 m, traffic volume within 150 m and HDV volume within 150 m) and four modelling approaches: based on the nearest monitoring site, kriging, dispersion modelling and land use regression (LUR). Measures were computed in a GIS, and resulting metrics calibrated and validated against monitoring data using a form of grouped jack-knife analysis. The results show that PM 10 concentrations across London show little spatial variation. As a consequence, most methods can predict the average without serious bias. Few of the approaches, however, show good correlations with monitored PM 10 concentrations, and most predict no better than a simple classification based on site type. Only land use regression reaches acceptable levels of correlation ( R2 = 0.47), though this can be improved by also including information on site type. This might therefore be taken as a recommended approach in many studies, though care is needed in developing meaningful land use regression models, and like any method they need to be validated against local data before their application as part of epidemiological studies.

Study on Site Conditions Based on Topographic Slope

NASA Astrophysics Data System (ADS)

Wu, X.; Wang, X.; Yuan, X.; Chen, M.; Dou, A.

2018-04-01

The travel-time averaged shear-wave velocity to a depth of 30m (Vs30) below the Earth's surface is widely used to classify sites in many building codes. Vs30 is also used to estimate site classification in recent ground-motion prediction equations (GMPEs), and the distribution of Vs30 has been mapped in a region or country. An alternative method has recently been proposed for evaluating global seismic site conditions or Vs30, from the SRTM (Shuttle Radar Topography Mission) DEMs (digital elevation models). The basic premise of the method is that the topographic slope can be used as a reliable proxy for Vs30 in the absence of geologically and geotechnically based site-condition maps through correlations between Vs30 measurements and topographic gradient. Here, we use different resolutions (3 arcsec, 30 arcsec) DEM data to get Vs30 data separately, analyze and compare the difference of Vs30 data and site conditions obtained from different resolution DEM data. Shandong Province in eastern China and Sichuan Province in Western China are studied respectively. It is found that the higher resolution data is better at defining spatial topographic features than the 30c data, but less improvement in its correlation with Vs30.

Soil respiration and root biomass responses to burning in calabrian pine (Pinus brutia) stands in Edirne, Turkey.

PubMed

Tufekcioglu, Aydin; Kucuk, Mehmet; Bilmis, Tuncay; Altun, Lokman; Yilmaz, Murat

2010-01-01

In this study soil properties and root biomass responses to prescribed fire were investigated in 25-30 year-old calabrian pine (Pinus brutia Ten.) stands in Edirne, Turkey. The stands were established by planting and were subjected to prescribed burning in July 2005. Soil respiration rates were determined every two months using the soda-lime method over a two-year period. Fine (> or = 2 mm diameter) and small root (> 2-5 mm diameter) biomass were sampled approximately bimonthly using the sequential coring method. Soil respiration rates in burned sites were significantly higher than in control sites during the summer season but there was no significant difference in the other seasons. Soil respiration rates were correlated significantly with soil moisture and soil temperature. Fine and small root biomass were significantly lower in burned sites than in control sites. Mean fine root biomass values were 3204 kg ha(-1) for burned and 3772 kg ha(-1) for control sites. Annual soil CO2 releases totaled 515 g Cm(-2) for burned and 418 g C m(-2) for control sites. Our results indicate that, depending on site conditions, fire could be used successfully as a tool in the management of calabrian pine stands in the study area.

Benthic macroinvertebrate field sampling effort required to ...

EPA Pesticide Factsheets

This multi-year pilot study evaluated a proposed field method for its effectiveness in the collection of a benthic macroinvertebrate sample adequate for use in the condition assessment of streams and rivers in the Neuquén Province, Argentina. A total of 13 sites, distributed across three rivers, were sampled. At each site, benthic macroinvertebrates were collected at 11 transects. Each sample was processed independently in the field and laboratory. Based on a literature review and resource considerations, the collection of 300 organisms (minimum) at each site was determined to be necessary to support a robust condition assessment, and therefore, selected as the criterion for judging the adequacy of the method. This targeted number of organisms was collected at all sites, at a minimum, when collections from all 11 transects were combined. Subsequent bootstrapping analysis of data was used to estimate whether collecting at fewer transects would reach the minimum target number of organisms for all sites. In a subset of sites, the total number of organisms frequently fell below the target when fewer than 11 transects collections were combined.Site conditions where <300 organisms might be collected are discussed. These preliminary results suggest that the proposed field method results in a sample that is adequate for robust condition assessment of the rivers and streams of interest. When data become available from a broader range of sites, the adequacy of the field

Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities.

PubMed

Nguyen, Van-Nui; Huang, Kai-Yao; Huang, Chien-Hsun; Chang, Tzu-Hao; Bretaña, Neil; Lai, K; Weng, Julia; Lee, Tzong-Yi

2015-01-01

In eukaryotes, ubiquitin-conjugation is an important mechanism underlying proteasome-mediated degradation of proteins, and as such, plays an essential role in the regulation of many cellular processes. In the ubiquitin-proteasome pathway, E3 ligases play important roles by recognizing a specific protein substrate and catalyzing the attachment of ubiquitin to a lysine (K) residue. As more and more experimental data on ubiquitin conjugation sites become available, it becomes possible to develop prediction models that can be scaled to big data. However, no development that focuses on the investigation of ubiquitinated substrate specificities has existed. Herein, we present an approach that exploits an iteratively statistical method to identify ubiquitin conjugation sites with substrate site specificities. In this investigation, totally 6259 experimentally validated ubiquitinated proteins were obtained from dbPTM. After having filtered out homologous fragments with 40% sequence identity, the training data set contained 2658 ubiquitination sites (positive data) and 5532 non-ubiquitinated sites (negative data). Due to the difficulty in characterizing the substrate site specificities of E3 ligases by conventional sequence logo analysis, a recursively statistical method has been applied to obtain significant conserved motifs. The profile hidden Markov model (profile HMM) was adopted to construct the predictive models learned from the identified substrate motifs. A five-fold cross validation was then used to evaluate the predictive model, achieving sensitivity, specificity, and accuracy of 73.07%, 65.46%, and 67.93%, respectively. Additionally, an independent testing set, completely blind to the training data of the predictive model, was used to demonstrate that the proposed method could provide a promising accuracy (76.13%) and outperform other ubiquitination site prediction tool. A case study demonstrated the effectiveness of the characterized substrate motifs for identifying ubiquitination sites. The proposed method presents a practical means of preliminary analysis and greatly diminishes the total number of potential targets required for further experimental confirmation. This method may help unravel their mechanisms and roles in E3 recognition and ubiquitin-mediated protein degradation.

Laboratory and clinical evaluation of on-site urine drug testing.

PubMed

Beck, Olof; Carlsson, Sten; Tusic, Marinela; Olsson, Robert; Franzen, Lisa; Hulten, Peter

2014-11-01

Products for on-site urine drug testing offer the possibility to perform screening for drugs of abuse directly at the point-of-care. This is a well-established routine in emergency and dependency clinics but further evaluation of performance is needed due to inherent limitations with the available products. Urine drug testing by an on-site product was compared with routine laboratory methods. First, on-site testing was performed at the laboratory in addition to the routine method. Second, the on-site testing was performed at a dependency clinic and urine samples were subsequently sent to the laboratory for additional analytical investigation. The on-site testing products did not perform with assigned cut-off levels. The subjective reading between the presence of a spot (i.e. negative test result) being present or no spot (positive result) was difficult in 3.2% of the cases, and occurred for all parameters. The tests performed more accurately in drug negative samples (specificity 96%) but less accurately for detecting positives (sensitivity 79%). Of all incorrect results by the on-site test the proportion of false negatives was 42%. The overall agreement between on-site and laboratory testing was 95% in the laboratory study and 98% in the clinical study. Although a high degree of agreement was observed between on-site and routine laboratory urine drug testing, the performance of on-site testing was not acceptable due to significant number of false negative results. The limited sensitivity of on-site testing compared to laboratory testing reduces the applicability of these tests.

Clear-water abutment and contraction scour in the Coastal Plain and Piedmont Provinces of South Carolina, 1996-99

USGS Publications Warehouse

Benedict, Stephen T.

2016-01-01

Data from this study have been compiled into a database that includes photographs, figures, observed scour depths, theoretical scour depths, limited basin characteristics, limited soil data, and theoretical hydraulic data. The database can be used to compare studied sites with unstudied sites to assess the potential for scour at the unstudied sites. In addition, the database can be used to assess the performance of various theoretical methods for predicting clear-water abutment and contraction scour.

Space-time clusters for early detection of grizzly bear predation.

PubMed

Kermish-Wells, Joseph; Massolo, Alessandro; Stenhouse, Gordon B; Larsen, Terrence A; Musiani, Marco

2018-01-01

Accurate detection and classification of predation events is important to determine predation and consumption rates by predators. However, obtaining this information for large predators is constrained by the speed at which carcasses disappear and the cost of field data collection. To accurately detect predation events, researchers have used GPS collar technology combined with targeted site visits. However, kill sites are often investigated well after the predation event due to limited data retrieval options on GPS collars (VHF or UHF downloading) and to ensure crew safety when working with large predators. This can lead to missing information from small-prey (including young ungulates) kill sites due to scavenging and general site deterioration (e.g., vegetation growth). We used a space-time permutation scan statistic (STPSS) clustering method (SaTScan) to detect predation events of grizzly bears ( Ursus arctos ) fitted with satellite transmitting GPS collars. We used generalized linear mixed models to verify predation events and the size of carcasses using spatiotemporal characteristics as predictors. STPSS uses a probability model to compare expected cluster size (space and time) with the observed size. We applied this method retrospectively to data from 2006 to 2007 to compare our method to random GPS site selection. In 2013-2014, we applied our detection method to visit sites one week after their occupation. Both datasets were collected in the same study area. Our approach detected 23 of 27 predation sites verified by visiting 464 random grizzly bear locations in 2006-2007, 187 of which were within space-time clusters and 277 outside. Predation site detection increased by 2.75 times (54 predation events of 335 visited clusters) using 2013-2014 data. Our GLMMs showed that cluster size and duration predicted predation events and carcass size with high sensitivity (0.72 and 0.94, respectively). Coupling GPS satellite technology with clusters using a program based on space-time probability models allows for prompt visits to predation sites. This enables accurate identification of the carcass size and increases fieldwork efficiency in predation studies.

Random Decrement Method and Modeling H/V Spectral Ratios: An Application for Soft Shallow Layers Characterization

NASA Astrophysics Data System (ADS)

Song, H.; Huerta-Lopez, C. I.; Martinez-Cruzado, J. A.; Rodriguez-Lozoya, H. E.; Espinoza-Barreras, F.

2009-05-01

Results of an ongoing study to estimate the ground response upon weak and moderate earthquake excitations are presented. A reliable site characterization in terms of its soil properties and sub-soil layer configuration are parameters required in order to do a trustworthy estimation of the ground response upon dynamic loads. This study can be described by the following four steps: (1) Ambient noise measurements were collected at the study site where a bridge was under construction between the cities of Tijuana and Ensenada in Mexico. The time series were collected using a six channels recorder with an ADC converter of 16 bits within a maximum voltage range of ± 2.5 V, the recorder has an optional settings of: Butterworth/Bessel filters, gain and sampling rate. The sensors were a three orthogonal component (X, Y, Z) accelerometers with a sensitivity of 20 V/g, flat frequency response between DC to 200 Hz, and total full range of ±0.25 of g, (2) experimental H/V Spectral Ratios were computed to estimate the fundamental vibration frequency at the site, (3) using the time domain experimental H/V spectral ratios as well as the original recorded time series, the random decrement method was applied to estimate the fundamental frequency and damping of the site (system), and (4) finally the theoretical H/V spectral ratios were obtained by means of the stiffness matrix wave propagation method.. The interpretation of the obtained results was then finally compared with a geotechnical study available at the site.

Design of a Multisite Study Assessing the Impact of Tic Disorders on Individuals, Families, and Communities.

PubMed

Augustine, E F; Adams, H R; Bitsko, R H; van Wijngaarden, E; Claussen, A H; Thatcher, A; Hanks, C E; Lewin, A B; O'Connor, T G; Vierhile, A; Danielson, M L; Kurlan, R; Murphy, T K; Mink, J W

2017-03-01

Tic disorders, including Tourette syndrome, are complex, multisymptom diseases, yet the impact of these disorders on affected children, families, and communities is not well understood. To improve the understanding of the impacts of Tourette syndrome, two research groups conducted independent cross-sectional studies using qualitative and quantitative measures. They focused on similar themes, but distinct scientific objectives, and the sites collaborated to align methods of independent research proposals with the aim of increasing the analyzable sample size. Site 1 (University of Rochester) was a Pediatric Neurology referral center. Site 2 (University of South Florida) was a Child Psychiatry referral center. A total of 205 children with tic disorders were enrolled from both studies. The University of Rochester also enrolled 100 control children in order to clearly isolate impacts of Tourette syndrome distinct from those occurring in the general population. The majority of children with tic disorders (n = 191, 93.1%) had Tourette syndrome, the primary population targeted for these studies. Children with Tourette syndrome were similar across sites in terms of tic severity and the occurrence of comorbid conditions. The occurrence of psychiatric comorbidities in the control group was comparable with that in the general pediatric population of the United States, making this a well-justified comparison group. Through collaboration, two sites conducting independent research developed convergent research methods to enable pooling of data, and by extension increased power, for future analyses. This method of collaboration is a novel model for future epidemiological research of tic disorders. Copyright © 2016 Elsevier Inc. All rights reserved.

APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data.

PubMed

Ye, Congting; Long, Yuqi; Ji, Guoli; Li, Qingshun Quinn; Wu, Xiaohui

2018-06-01

Alternative polyadenylation (APA) has been increasingly recognized as a crucial mechanism that contributes to transcriptome diversity and gene expression regulation. As RNA-seq has become a routine protocol for transcriptome analysis, it is of great interest to leverage such unprecedented collection of RNA-seq data by new computational methods to extract and quantify APA dynamics in these transcriptomes. However, research progress in this area has been relatively limited. Conventional methods rely on either transcript assembly to determine transcript 3' ends or annotated poly(A) sites. Moreover, they can neither identify more than two poly(A) sites in a gene nor detect dynamic APA site usage considering more than two poly(A) sites. We developed an approach called APAtrap based on the mean squared error model to identify and quantify APA sites from RNA-seq data. APAtrap is capable of identifying novel 3' UTRs and 3' UTR extensions, which contributes to locating potential poly(A) sites in previously overlooked regions and improving genome annotations. APAtrap also aims to tally all potential poly(A) sites and detect genes with differential APA site usages between conditions. Extensive comparisons of APAtrap with two other latest methods, ChangePoint and DaPars, using various RNA-seq datasets from simulation studies, human and Arabidopsis demonstrate the efficacy and flexibility of APAtrap for any organisms with an annotated genome. Freely available for download at https://apatrap.sourceforge.io. liqq@xmu.edu.cn or xhuister@xmu.edu.cn. Supplementary data are available at Bioinformatics online.

Multimodality language mapping in patients with left-hemispheric language dominance on Wada test

PubMed Central

Kojima, Katsuaki; Brown, Erik C.; Rothermel, Robert; Carlson, Alanna; Matsuzaki, Naoyuki; Shah, Aashit; Atkinson, Marie; Mittal, Sandeep; Fuerst, Darren; Sood, Sandeep; Asano, Eishi

2012-01-01

Objective We determined the utility of electrocorticography (ECoG) and stimulation for detecting language-related sites in patients with left-hemispheric language-dominance on Wada test. Methods We studied 13 epileptic patients who underwent language mapping using event-related gamma-oscillations on ECoG and stimulation via subdural electrodes. Sites showing significant gamma-augmentation during an auditory-naming task were defined as language-related ECoG sites. Sites at which stimulation resulted in auditory perceptual changes, failure to verbalize a correct answer, or sensorimotor symptoms involving the mouth were defined as language-related stimulation sites. We determined how frequently these methods revealed language-related sites in the superior-temporal, inferior-frontal, dorsolateral-premotor, and inferior-Rolandic regions. Results Language-related sites in the superior-temporal and inferior-frontal gyri were detected by ECoG more frequently than stimulation (p < 0.05), while those in the dorsolateral-premotor and inferior-Rolandic regions were detected by both methods equally. Stimulation of language-related ECoG sites, compared to the others, more frequently elicited language symptoms (p < 0.00001). One patient developed dysphasia requiring in-patient speech therapy following resection of the dorsolateral-premotor and inferior-Rolandic regions containing language-related ECoG sites not otherwise detected by stimulation. Conclusions Language-related gamma-oscillations may serve as an alternative biomarker of underlying language function in patients with left-hemispheric language-dominance. Significance Measurement of language-related gamma-oscillations is warranted in presurgical evaluation of epileptic patients. PMID:22503906

The effect of synthetic method and annealing temperature on metal site preference in Al(1-x)Ga(x)FeO3.

PubMed

Walker, James D S; Grosvenor, Andrew P

2013-08-05

Magnetoelectric materials couple both magnetic and electronic properties, making them attractive for use in multifunctional devices. The magnetoelectric AFeO3 compounds (Pna2(1); A = Al, Ga) have received attention as the properties of the system depend on composition as well as the synthetic method used. Al(1-x)Ga(x)FeO3. (0 ≤ x ≤ 1) was synthesized by the sol-gel and coprecipitation methods and studied by X-ray absorption near-edge spectroscopy (XANES). Al L(2,3-), Ga K-, and Fe K-edge XANES spectra were collected to examine how the average metal coordination number (CN) changes with the synthetic method. Al and Fe were found to prefer octahedral sites, while Ga prefers the tetrahedral site. It was found that composition played a larger role in determining site occupancies than synthetic method. Samples made by the sol-gel or ceramic methods (reported previously; Walker, J. D. S.; Grosvenor, A. P. J. Solid State Chem. 2013, 197, 147-153) showed smaller spectral changes than samples made via the coprecipitation method. This is attributed to greater ion mobility in samples synthesized via coprecipitation as the reactants do not have a long-range polymeric or oxide network during synthesis like samples synthesized via the sol-gel or ceramic method. Increasing annealing temperature increases the average coordination number of Al, and to a lesser extent Ga, while the average coordination number of Fe decreases. This study indicates that greater disorder is observed when the Al(1-x)Ga(x)FeO3. compounds have high Al content, and when annealed at higher temperatures.

Evaluation of different approaches for identifying optimal sites to predict mean hillslope soil moisture content

NASA Astrophysics Data System (ADS)

Liao, Kaihua; Zhou, Zhiwen; Lai, Xiaoming; Zhu, Qing; Feng, Huihui

2017-04-01

The identification of representative soil moisture sampling sites is important for the validation of remotely sensed mean soil moisture in a certain area and ground-based soil moisture measurements in catchment or hillslope hydrological studies. Numerous approaches have been developed to identify optimal sites for predicting mean soil moisture. Each method has certain advantages and disadvantages, but they have rarely been evaluated and compared. In our study, surface (0-20 cm) soil moisture data from January 2013 to March 2016 (a total of 43 sampling days) were collected at 77 sampling sites on a mixed land-use (tea and bamboo) hillslope in the hilly area of Taihu Lake Basin, China. A total of 10 methods (temporal stability (TS) analyses based on 2 indices, K-means clustering based on 6 kinds of inputs and 2 random sampling strategies) were evaluated for determining optimal sampling sites for mean soil moisture estimation. They were TS analyses based on the smallest index of temporal stability (ITS, a combination of the mean relative difference and standard deviation of relative difference (SDRD)) and based on the smallest SDRD, K-means clustering based on soil properties and terrain indices (EFs), repeated soil moisture measurements (Theta), EFs plus one-time soil moisture data (EFsTheta), and the principal components derived from EFs (EFs-PCA), Theta (Theta-PCA), and EFsTheta (EFsTheta-PCA), and global and stratified random sampling strategies. Results showed that the TS based on the smallest ITS was better (RMSE = 0.023 m3 m-3) than that based on the smallest SDRD (RMSE = 0.034 m3 m-3). The K-means clustering based on EFsTheta (-PCA) was better (RMSE <0.020 m3 m-3) than these based on EFs (-PCA) and Theta (-PCA). The sampling design stratified by the land use was more efficient than the global random method. Forty and 60 sampling sites are needed for stratified sampling and global sampling respectively to make their performances comparable to the best K-means method (EFsTheta-PCA). Overall, TS required only one site, but its accuracy was limited. The best K-means method required <8 sites and yielded high accuracy, but extra soil and terrain information is necessary when using this method. The stratified sampling strategy can only be used if no pre-knowledge about soil moisture variation is available. This information will help in selecting the optimal methods for estimation the area mean soil moisture.

Identifying N6-methyladenosine sites using multi-interval nucleotide pair position specificity and support vector machine

NASA Astrophysics Data System (ADS)

Xing, Pengwei; Su, Ran; Guo, Fei; Wei, Leyi

2017-04-01

N6-methyladenosine (m6A) refers to methylation of the adenosine nucleotide acid at the nitrogen-6 position. It plays an important role in a series of biological processes, such as splicing events, mRNA exporting, nascent mRNA synthesis, nuclear translocation and translation process. Numerous experiments have been done to successfully characterize m6A sites within sequences since high-resolution mapping of m6A sites was established. However, as the explosive growth of genomic sequences, using experimental methods to identify m6A sites are time-consuming and expensive. Thus, it is highly desirable to develop fast and accurate computational identification methods. In this study, we propose a sequence-based predictor called RAM-NPPS for identifying m6A sites within RNA sequences, in which we present a novel feature representation algorithm based on multi-interval nucleotide pair position specificity, and use support vector machine classifier to construct the prediction model. Comparison results show that our proposed method outperforms the state-of-the-art predictors on three benchmark datasets across the three species, indicating the effectiveness and robustness of our method. Moreover, an online webserver implementing the proposed predictor has been established at http://server.malab.cn/RAM-NPPS/. It is anticipated to be a useful prediction tool to assist biologists to reveal the mechanisms of m6A site functions.

Step-By-Step In Vitro Mutagenesis: Lessons From Fucose-Binding Lectin PA-IIL.

PubMed

Mrázková, Jana; Malinovská, Lenka; Wimmerová, Michaela

2017-01-01

Site-directed mutagenesis is a powerful technique which is used to understand the basis of interactions between proteins and their binding partners, as well as to modify these interactions. Methods of rational design that are based on detailed knowledge of the structure of a protein of interest are often used for preliminary investigations of the possible outcomes which can result from the practical application of site-directed mutagenesis. Also, random mutagenesis can be used in tandem with site-directed mutagenesis for an examination of amino acid "hotspots."Lectins are sugar-binding proteins which, among other functions, mediate the recognition of host cells by a pathogen and its adhesion to the host cell surface. Hence, lectins and their binding properties are studied and engineered using site-directed mutagenesis.In this chapter, we describe a site-directed mutagenesis method used for investigating the sugar binding pattern of the PA-IIL lectin from the pathogenic bacterium Pseudomonas aeruginosa. Moreover, procedures for the production and purification of PA-IIL mutants are described, and several basic methods for characterizing the mutants are discussed.

Maternal Opioid Treatment: Human Experimental Research (MOTHER) – Approach, Issues, and Lessons Learned

PubMed Central

Jones, Hendrée E.; Fischer, Gabriele; Heil, Sarah H.; Kaltenbach, Karol; Martin, Peter R.; Coyle, Mara G.; Selby, Peter; Stine, Susan M.; O’Grady, Kevin E.; Arria, Amelia M.

2015-01-01

Aims The Maternal Opioid Treatment: Human Experimental Research (MOTHER) project, an eight-site randomized, double-blind, double-dummy, flexible-dosing, parallel-group clinical trial is described. This study is the most current – and single most comprehensive – research effort to investigate the safety and efficacy of maternal and prenatal exposure to methadone and buprenorphine. Methods The MOTHER study design is outlined, and its basic features are presented. Conclusions At least seven important lessons have been learned from the MOTHER study: (1) an interdisciplinary focus improves the design and methods of a randomized clinical trial; (2) multiple sites in a clinical trial present continuing challenges to the investigative team due to variations in recruitment goals, patient populations, and hospital practices that in turn differentially impact recruitment rates, treatment compliance, and attrition; (3) study design and protocols must be flexible in order to meet the unforeseen demands of both research and clinical management; (4) staff turnover needs to be addressed with a proactive focus on both hiring and training; (5) the implementation of a protocol for the treatment of a particular disorder may identify important ancillary clinical issues worthy of investigation; (6) timely tracking of data in a multi-site trial is both demanding and unforgiving; and, (7) complex multi-site trials pose unanticipated challenges that complicate the choice of statistical methods, thereby placing added demands on investigators to effectively communicate their results. PMID:23106924

A Method to Recognize Anatomical Site and Image Acquisition View in X-ray Images.

PubMed

Chang, Xiao; Mazur, Thomas; Li, H Harold; Yang, Deshan

2017-12-01

A method was developed to recognize anatomical site and image acquisition view automatically in 2D X-ray images that are used in image-guided radiation therapy. The purpose is to enable site and view dependent automation and optimization in the image processing tasks including 2D-2D image registration, 2D image contrast enhancement, and independent treatment site confirmation. The X-ray images for 180 patients of six disease sites (the brain, head-neck, breast, lung, abdomen, and pelvis) were included in this study with 30 patients each site and two images of orthogonal views each patient. A hierarchical multiclass recognition model was developed to recognize general site first and then specific site. Each node of the hierarchical model recognized the images using a feature extraction step based on principal component analysis followed by a binary classification step based on support vector machine. Given two images in known orthogonal views, the site recognition model achieved a 99% average F1 score across the six sites. If the views were unknown in the images, the average F1 score was 97%. If only one image was taken either with or without view information, the average F1 score was 94%. The accuracy of the site-specific view recognition models was 100%.

Remote sensing for site characterization

USGS Publications Warehouse

Kuehn, Friedrich; King, Trude V.; Hoerig, Bernhard; Peters, Douglas C.; Kuehn, Friedrich; King, Trude V.; Hoerig, Bernhard; Peters, Douglas C.

2000-01-01

This volume, Remote Sensing for Site Characterization, describes the feasibility of aircraft- and satellite-based methods of revealing environmental-geological problems. A balanced ratio between explanations of the methodological/technical side and presentations of case studies is maintained. The comparison of case studies from North America and Germany show how the respective territorial conditions lead to distinct methodological approaches.

Web Log Analysis: A Study of Instructor Evaluations Done Online

ERIC Educational Resources Information Center

Klassen, Kenneth J.; Smith, Wayne

2004-01-01

This paper focuses on developing a relatively simple method for analyzing web-logs. It also explores the challenges and benefits of web-log analysis. The study of student behavior on this site provides insights into website design and the effectiveness of this site in particular. Another benefit realized from the paper is the ease with which these…

A study on the application of topic models to motif finding algorithms.

PubMed

Basha Gutierrez, Josep; Nakai, Kenta

2016-12-22

Topic models are statistical algorithms which try to discover the structure of a set of documents according to the abstract topics contained in them. Here we try to apply this approach to the discovery of the structure of the transcription factor binding sites (TFBS) contained in a set of biological sequences, which is a fundamental problem in molecular biology research for the understanding of transcriptional regulation. Here we present two methods that make use of topic models for motif finding. First, we developed an algorithm in which first a set of biological sequences are treated as text documents, and the k-mers contained in them as words, to then build a correlated topic model (CTM) and iteratively reduce its perplexity. We also used the perplexity measurement of CTMs to improve our previous algorithm based on a genetic algorithm and several statistical coefficients. The algorithms were tested with 56 data sets from four different species and compared to 14 other methods by the use of several coefficients both at nucleotide and site level. The results of our first approach showed a performance comparable to the other methods studied, especially at site level and in sensitivity scores, in which it scored better than any of the 14 existing tools. In the case of our previous algorithm, the new approach with the addition of the perplexity measurement clearly outperformed all of the other methods in sensitivity, both at nucleotide and site level, and in overall performance at site level. The statistics obtained show that the performance of a motif finding method based on the use of a CTM is satisfying enough to conclude that the application of topic models is a valid method for developing motif finding algorithms. Moreover, the addition of topic models to a previously developed method dramatically increased its performance, suggesting that this combined algorithm can be a useful tool to successfully predict motifs in different kinds of sets of DNA sequences.

Preceptor Perceptions of Virtual Quality Assurance Experiential Site Visits.

PubMed

Clarke, Cheryl L; Schott, Kathryn A; Arnold, Austin D

2018-05-01

Objective. To determine preceptor perceptions of the value of experiential quality assurance site visits between virtual and onsite visits, and to gauge preceptor opinions of the optimal method of site visits based on the type of visit received. Methods. Site visits (12 virtual and 17 onsite) were conducted with 29 APPE sites located at least 200 miles from campus. Participating preceptors were invited to complete an online post-visit survey adapted from a previously validated and published survey tool measuring preceptor perceptions of the value of traditional onsite visits. Results. Likert-type score averages for survey questions ranged from 4.2 to 4.6 in the virtual group and from 4.3 to 4.7 in the onsite group. No statistically significant difference was found between the two groups. Preceptors were more inclined to prefer the type of visit they received. Preceptors receiving onsite visits were also more likely to indicate no visit type preference. Conclusion. Preceptors perceived value from both onsite and virtual site visits. Preceptors who experienced virtual site visits highly preferred that methodology. This study suggests that virtual site visits may be a viable alternative for providing experiential quality assurance site visits from a preceptor's perspective.

Community level patterns in diverse systems: A case study of litter fauna in a Mexican pine-oak forest using higher taxa surrogates and re-sampling methods

NASA Astrophysics Data System (ADS)

Moreno, Claudia E.; Guevara, Roger; Sánchez-Rojas, Gerardo; Téllez, Dianeis; Verdú, José R.

2008-01-01

Environmental assessment at the community level in highly diverse ecosystems is limited by taxonomic constraints and statistical methods requiring true replicates. Our objective was to show how diverse systems can be studied at the community level using higher taxa as biodiversity surrogates, and re-sampling methods to allow comparisons. To illustrate this we compared the abundance, richness, evenness and diversity of the litter fauna in a pine-oak forest in central Mexico among seasons, sites and collecting methods. We also assessed changes in the abundance of trophic guilds and evaluated the relationships between community parameters and litter attributes. With the direct search method we observed differences in the rate of taxa accumulation between sites. Bootstrap analysis showed that abundance varied significantly between seasons and sampling methods, but not between sites. In contrast, diversity and evenness were significantly higher at the managed than at the non-managed site. Tree regression models show that abundance varied mainly between seasons, whereas taxa richness was affected by litter attributes (composition and moisture content). The abundance of trophic guilds varied among methods and seasons, but overall we found that parasitoids, predators and detrivores decreased under management. Therefore, although our results suggest that management has positive effects on the richness and diversity of litter fauna, the analysis of trophic guilds revealed a contrasting story. Our results indicate that functional groups and re-sampling methods may be used as tools for describing community patterns in highly diverse systems. Also, the higher taxa surrogacy could be seen as a preliminary approach when it is not possible to identify the specimens at a low taxonomic level in a reasonable period of time and in a context of limited financial resources, but further studies are needed to test whether the results are specific to a system or whether they are general with regards to land management.

A Methodology to Evaluate Ecological Resources and Risk Using Two Case Studies at the Department of Energy’s Hanford Site

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

Burger, Joanna; Gochfeld, Michael; Bunn, Amoret

An assessment of the potential risks to ecological resources from remediation activities or other perturbations should involve a quantitative evaluation of resources on the remediation site and in the surrounding environment. We developed a risk methodology to rapidly evaluate potential impact on ecological resources for the U.S. Department of Energy’s Hanford Site in southcentral Washington State. We describe the application of the risk evaluation for two case studies to illustrate its applicability. The ecological assessment involves examining previous sources of information for the site, defining different resource levels from 0 to 5. We also developed a risk rating scale frommore » nondiscernable to very high. Field assessment is the critical step to determine resource levels or to determine if current conditions are the same as previously evaluated. We provide a rapid assessment method for current ecological conditions that can be compared to previous site-specific data, or that can be used to assess resource value on other sites where ecological information is not generally available. The method is applicable to other Department of Energy’s sites, where its development may involve a range of state regulators, resource trustees, Tribes and other stakeholders. Achieving consistency across Department of Energy’s sites for valuation of ecological resources on remediation sites will assure Congress and the public that funds and personnel are being deployed appropriately.« less

Hotspot Identification for Shanghai Expressways Using the Quantitative Risk Assessment Method

PubMed Central

Chen, Can; Li, Tienan; Sun, Jian; Chen, Feng

2016-01-01

Hotspot identification (HSID) is the first and key step of the expressway safety management process. This study presents a new HSID method using the quantitative risk assessment (QRA) technique. Crashes that are likely to happen for a specific site are treated as the risk. The aggregation of the crash occurrence probability for all exposure vehicles is estimated based on the empirical Bayesian method. As for the consequences of crashes, crashes may not only cause direct losses (e.g., occupant injuries and property damages) but also result in indirect losses. The indirect losses are expressed by the extra delays calculated using the deterministic queuing diagram method. The direct losses and indirect losses are uniformly monetized to be considered as the consequences of this risk. The potential costs of crashes, as a criterion to rank high-risk sites, can be explicitly expressed as the sum of the crash probability for all passing vehicles and the corresponding consequences of crashes. A case study on the urban expressways of Shanghai is presented. The results show that the new QRA method for HSID enables the identification of a set of high-risk sites that truly reveal the potential crash costs to society. PMID:28036009

Site selection for managed aquifer recharge using fuzzy rules: integrating geographical information system (GIS) tools and multi-criteria decision making

NASA Astrophysics Data System (ADS)

Malekmohammadi, Bahram; Ramezani Mehrian, Majid; Jafari, Hamid Reza

2012-11-01

One of the most important water-resources management strategies for arid lands is managed aquifer recharge (MAR). In establishing a MAR scheme, site selection is the prime prerequisite that can be assisted by geographic information system (GIS) tools. One of the most important uncertainties in the site-selection process using GIS is finite ranges or intervals resulting from data classification. In order to reduce these uncertainties, a novel method has been developed involving the integration of multi-criteria decision making (MCDM), GIS, and a fuzzy inference system (FIS). The Shemil-Ashkara plain in the Hormozgan Province of Iran was selected as the case study; slope, geology, groundwater depth, potential for runoff, land use, and groundwater electrical conductivity have been considered as site-selection factors. By defining fuzzy membership functions for the input layers and the output layer, and by constructing fuzzy rules, a FIS has been developed. Comparison of the results produced by the proposed method and the traditional simple additive weighted (SAW) method shows that the proposed method yields more precise results. In conclusion, fuzzy-set theory can be an effective method to overcome associated uncertainties in classification of geographic information data.

Site Selection in School District Research: A Measure of Effectiveness Using Hierarchical Longitudinal Growth Models of Performance

ERIC Educational Resources Information Center

Bowers, Alex J.

2015-01-01

School districts in the USA are an active area of study in education research as findings have shown that some districts find success in certain contexts while others struggle. However, the research domain has had few actionable methods for site selection for in-depth qualitative studies. This study analyses all districts in the state of Ohio (n =…

A randomized comparative prospective study of platelet-rich plasma, platelet-rich fibrin, and hydroxyapatite as a graft material for mandibular third molar extraction socket healing

PubMed Central

Dutta, Shubha Ranjan; Passi, Deepak; Singh, Purnima; Sharma, Sarang; Singh, Mahinder; Srivastava, Dhirendra

2016-01-01

Aim: The purpose of this study was to compare the efficacy of platelet-rich plasma (PRP), platelet-rich fibrin (PRF), and hydroxyapatite (HA) for reduction of pain and swelling, absence of dry socket, soft tissue healing, and bone regeneration after mandibular third molar extraction in human patients. Materials and Methods: Forty patients requiring extraction of mandibular third molars were randomly grouped as control, PRP, PRF, and HA-treated. The patients were assessed for postoperative pain, swelling, dry socket, and soft tissue healing on the 3rd, 7th, and 14th day of postoperative periods depending on the standard methods. Radiological assessment of the extraction site was done at 1, 2, and 6 months interval to compare the change in bone density in the sockets in control and treated patients. Results: Pain and swelling were less on PRP and PRF site when compared to HA and control site. PRP and PRF site showed better soft tissue healing when compared to HA and control site. Radiographic assessment showed comparatively lesser bone density values in PRP, PRF, and control site at 1, 2, and 6 months than HA site. Conclusion: Our study showed that PRP and PRF are better graft materials than HA regarding pain, swelling, dry socket, and soft tissue healing. Bone regeneration is induced promptly by HA as compared to other graft materials. However, a more elaborate study with a larger number of clinical cases is very much essential to be more conclusive regarding the efficacy of the graft materials. PMID:28163478

Landfill site selection by using geographic information systems

NASA Astrophysics Data System (ADS)

Şener, Başak; Süzen, M. Lütfi; Doyuran, Vedat

2006-01-01

One of the serious and growing potential problems in most large urban areas is the shortage of land for waste disposal. Although there are some efforts to reduce and recover the waste, disposal in landfills is still the most common method for waste destination. An inappropriate landfill site may have negative environmental, economic and ecological impacts. Therefore, it should be selected carefully by considering both regulations and constraints on other sources. In this study, candidate sites for an appropriate landfill area in the vicinity of Ankara are determined by using the integration of geographic information systems and multicriteria decision analysis (MCDA). For this purpose, 16 input map layers including topography, settlements (urban centers and villages), roads (Highway E90 and village roads), railways, airport, wetlands, infrastructures (pipelines and power lines), slope, geology, land use, floodplains, aquifers and surface water are prepared and two different MCDA methods (simple additive weighting and analytic hierarchy process) are implemented to a geographical information system. Comparison of the maps produced by these two different methods shows that both methods yield conformable results. Field checks also confirm that the candidate sites agree well with the selected criteria.

Virtual Diving in the Underwater Archaeological Site of Cala Minnola

NASA Astrophysics Data System (ADS)

Bruno, F.; Lagudi, A.; Barbieri, L.; Muzzupappa, M.; Mangeruga, M.; Pupo, F.; Cozza, M.; Cozza, A.; Ritacco, G.; Peluso, R.; Tusa, S.

2017-02-01

The paper presents the application of the technologies and methods defined in the VISAS project for the case study of the underwater archaeological site of Cala Minnola located in the island of Levanzo, in the archipelago of the Aegadian Islands (Sicily, Italy). The VISAS project (http://visas-project.eu) aims to improve the responsible and sustainable exploitation of the Underwater Cultural Heritage by means the development of new methods and technologies including an innovative virtual tour of the submerged archaeological sites. In particular, the paper describes the 3D reconstruction of the underwater archaeological site of Cala Minnola and focus on the development of the virtual scene for its visualization and exploitation. The virtual dive of the underwater archaeological site allows users to live a recreational and educational experience by receiving historical, archaeological and biological information about the submerged exhibits, the flora and fauna of the place.

Documentation of archaeological sites in northern iraq using remote sensing methods

NASA Astrophysics Data System (ADS)

Matoušková, E.; Pavelka, K.; Nováček, K.; Starková, L.

2015-08-01

The MULINEM (The Medieval Urban Landscape in Northeastern Mesopotamia) project is aiming to investigate a Late Sasanian and Islamic urban network in the land of Erbil, historic province of Hidyab (Adiabene) that is located in the northern Iraq. The research of the hierarchical urban network in a defined area belongs to approaches rarely used in the study of the Islamic urbanism. The project focuses on the cluster of urban sites of the 6th-17th centuries A.D. This paper focuses on remote sensing analysis of historical sites with special interest of FORMOSAT-2 data that have been gained through a research announcement: Free FORMOSAT-2 satellite Imagery. Documentation of two archaeological sites (Makhmúr al-Qadima and Kushaf) are introduced. FORMOSAT-2 data results have been compared to historic CORONA satellite data of mentioned historical sites purchased earlier by the University of West Bohemia. Remote sensing methods were completed using in-situ measurements.

Analysis of the site-specific carbon isotope composition of propane by gas source isotope ratio mass spectrometer

NASA Astrophysics Data System (ADS)

Piasecki, Alison; Sessions, Alex; Lawson, Michael; Ferreira, A. A.; Neto, E. V. Santos; Eiler, John M.

2016-09-01

Site-specific isotope ratio measurements potentially provide valuable information about the formation and degradation of complex molecules-information that is lost in conventional bulk isotopic measurements. Here we discuss the background and possible applications of such measurements, and present a technique for studying the site-specific carbon isotope composition of propane at natural abundance based on mass spectrometric analysis of the intact propane molecule and its fragment ions. We demonstrate the feasibility of this approach through measurements of mixtures of natural propane and propane synthesized with site-specific 13C enrichment, and we document the limits of precision of our technique. We show that mass balance calculations of the bulk δ13C of propane based on our site-specific measurements is generally consistent with independent constraints on bulk δ13C. We further demonstrate the accuracy of the technique, and illustrate one of its simpler applications by documenting the site-specific carbon isotope signature associated with gas phase diffusion of propane, confirming that our measurements conform to the predictions of the kinetic theory of gases. This method can be applied to propane samples of moderate size (tens of micromoles) isolated from natural gases. Thus, it provides a means of studying the site-specific stable isotope systematics of propane at natural isotope abundances on sample sizes that are readily recovered from many natural environments. This method may also serve as a model for future techniques that apply high-resolution mass spectrometry to study the site-specific isotopic distributions of larger organic molecules, with potential applications to biosynthesis, forensics and other geochemical subjects.

Do regional methods really help reduce uncertainties in flood frequency analyses?

NASA Astrophysics Data System (ADS)

Cong Nguyen, Chi; Payrastre, Olivier; Gaume, Eric

2013-04-01

Flood frequency analyses are often based on continuous measured series at gauge sites. However, the length of the available data sets is usually too short to provide reliable estimates of extreme design floods. To reduce the estimation uncertainties, the analyzed data sets have to be extended either in time, making use of historical and paleoflood data, or in space, merging data sets considered as statistically homogeneous to build large regional data samples. Nevertheless, the advantage of the regional analyses, the important increase of the size of the studied data sets, may be counterbalanced by the possible heterogeneities of the merged sets. The application and comparison of four different flood frequency analysis methods to two regions affected by flash floods in the south of France (Ardèche and Var) illustrates how this balance between the number of records and possible heterogeneities plays in real-world applications. The four tested methods are: (1) a local statistical analysis based on the existing series of measured discharges, (2) a local analysis valuating the existing information on historical floods, (3) a standard regional flood frequency analysis based on existing measured series at gauged sites and (4) a modified regional analysis including estimated extreme peak discharges at ungauged sites. Monte Carlo simulations are conducted to simulate a large number of discharge series with characteristics similar to the observed ones (type of statistical distributions, number of sites and records) to evaluate to which extent the results obtained on these case studies can be generalized. These two case studies indicate that even small statistical heterogeneities, which are not detected by the standard homogeneity tests implemented in regional flood frequency studies, may drastically limit the usefulness of such approaches. On the other hand, these result show that the valuation of information on extreme events, either historical flood events at gauged sites or estimated extremes at ungauged sites in the considered region, is an efficient way to reduce uncertainties in flood frequency studies.

Real-Time Safety Risk Assessment Based on a Real-Time Location System for Hydropower Construction Sites

PubMed Central

Fan, Qixiang; Qiang, Maoshan

2014-01-01

The concern for workers' safety in construction industry is reflected in many studies focusing on static safety risk identification and assessment. However, studies on real-time safety risk assessment aimed at reducing uncertainty and supporting quick response are rare. A method for real-time safety risk assessment (RTSRA) to implement a dynamic evaluation of worker safety states on construction site has been proposed in this paper. The method provides construction managers who are in charge of safety with more abundant information to reduce the uncertainty of the site. A quantitative calculation formula, integrating the influence of static and dynamic hazards and that of safety supervisors, is established to link the safety risk of workers with the locations of on-site assets. By employing the hidden Markov model (HMM), the RTSRA provides a mechanism for processing location data provided by the real-time location system (RTLS) and analyzing the probability distributions of different states in terms of false positives and negatives. Simulation analysis demonstrated the logic of the proposed method and how it works. Application case shows that the proposed RTSRA is both feasible and effective in managing construction project safety concerns. PMID:25114958

Real-time safety risk assessment based on a real-time location system for hydropower construction sites.

PubMed

Jiang, Hanchen; Lin, Peng; Fan, Qixiang; Qiang, Maoshan

2014-01-01

The concern for workers' safety in construction industry is reflected in many studies focusing on static safety risk identification and assessment. However, studies on real-time safety risk assessment aimed at reducing uncertainty and supporting quick response are rare. A method for real-time safety risk assessment (RTSRA) to implement a dynamic evaluation of worker safety states on construction site has been proposed in this paper. The method provides construction managers who are in charge of safety with more abundant information to reduce the uncertainty of the site. A quantitative calculation formula, integrating the influence of static and dynamic hazards and that of safety supervisors, is established to link the safety risk of workers with the locations of on-site assets. By employing the hidden Markov model (HMM), the RTSRA provides a mechanism for processing location data provided by the real-time location system (RTLS) and analyzing the probability distributions of different states in terms of false positives and negatives. Simulation analysis demonstrated the logic of the proposed method and how it works. Application case shows that the proposed RTSRA is both feasible and effective in managing construction project safety concerns.

Measurement of Light Pollution of Iranian National Observatory

NASA Astrophysics Data System (ADS)

Son Hosseini, S.; Nasiri, S.

2006-08-01

The problem of Light pollution became important mainly since 1960, by growth of urban development and using more artificial lights and lamps at the nighttimes. Optical telescopes share the same range of wavelengths as are used to provide illumination of roadways, buildings and automobiles. The light glow that emanates from man made pollution will scatter off the atmosphere and affects the images taken by the observatory instruments. A method of estimating the night sky brightness produced by a city of known population and distance is useful in site testing of the new observatories, as well as in studying the likely future deterioration of existing sites. Now with planning the Iranian National Observatory that will house a 2-meter telescope and on the way of the site selection project, studying the light pollution is propounded in Iran. Thus, we need a site with the least light pollution, beside other parameters, i.e. seeing, meteorological, geophysical and local parameters. The seeing parameter is being measured in our 4 preliminary selected sites at Qom, Kashan, Kerman and Birjand since 2 years ago using an out of focus Differential Image Motion Monitor. These sites are selected among 33 candidate sites by studying the meteorological data obtained from the local synoptic stations and the Meteosat. We use the Walker's law to estimate the Sky glow of these sites having the population and the distances of the nearby regions. The results are corrected by the methods introduced by Treanor and Berry using the atmospheric extinction coefficients. The data obtained using an 11 inch telescope with a ST7 CCD camera for above sites are consistent with the estimated values of the light pollution mentioned above.

Impact of enumeration method on diversity of Escherichia coli genotypes isolated from surface water.

PubMed

Martin, E C; Gentry, T J

2016-11-01

There are numerous regulatory-approved Escherichia coli enumeration methods, but it is not known whether differences in media composition and incubation conditions impact the diversity of E. coli populations detected by these methods. A study was conducted to determine if three standard water quality assessments, Colilert ® , USEPA Method 1603, (modified mTEC) and USEPA Method 1604 (MI), detect different populations of E. coli. Samples were collected from six watersheds and analysed using the three enumeration approaches followed by E. coli isolation and genotyping. Results indicated that the three methods generally produced similar enumeration data across the sites, although there were some differences on a site-by-site basis. The Colilert ® method consistently generated the least diverse collection of E. coli genotypes as compared to modified mTEC and MI, with those two methods being roughly equal to each other. Although the three media assessed in this study were designed to enumerate E. coli, the differences in the media composition, incubation temperature, and growth platform appear to have a strong selective influence on the populations of E. coli isolated. This study suggests that standardized methods of enumeration and isolation may be warranted if researchers intend to obtain individual E. coli isolates for further characterization. This study characterized the impact of three USEPA-approved Escherichia coli enumeration methods on observed E. coli population diversity in surface water samples. Results indicated that these methods produced similar E. coli enumeration data but were more variable in the diversity of E. coli genotypes observed. Although the three methods enumerate the same species, differences in media composition, growth platform, and incubation temperature likely contribute to the selection of different cultivable populations of E. coli, and thus caution should be used when implementing these methods interchangeably for downstream applications which require cultivated isolates. © 2016 The Society for Applied Microbiology.

Improving LiDAR Data Post-Processing Techniques for Archaeological Site Management and Analysis: A Case Study from Canaveral National Seashore Park

NASA Astrophysics Data System (ADS)

Griesbach, Christopher

Methods used to process raw Light Detection and Ranging (LiDAR) data can sometimes obscure the digital signatures indicative of an archaeological site. This thesis explains the negative effects that certain LiDAR data processing procedures can have on the preservation of an archaeological site. This thesis also presents methods for effectively integrating LiDAR with other forms of mapping data in a Geographic Information Systems (GIS) environment in order to improve LiDAR archaeological signatures by examining several pre-Columbian Native American shell middens located in Canaveral National Seashore Park (CANA).

Methylated site display (MSD)-AFLP, a sensitive and affordable method for analysis of CpG methylation profiles.

PubMed

Aiba, Toshiki; Saito, Toshiyuki; Hayashi, Akiko; Sato, Shinji; Yunokawa, Harunobu; Maruyama, Toru; Fujibuchi, Wataru; Kurita, Hisaka; Tohyama, Chiharu; Ohsako, Seiichiroh

2017-03-09

It has been pointed out that environmental factors or chemicals can cause diseases that are developmental in origin. To detect abnormal epigenetic alterations in DNA methylation, convenient and cost-effective methods are required for such research, in which multiple samples are processed simultaneously. We here present methylated site display (MSD), a unique technique for the preparation of DNA libraries. By combining it with amplified fragment length polymorphism (AFLP) analysis, we developed a new method, MSD-AFLP. Methylated site display libraries consist of only DNAs derived from DNA fragments that are CpG methylated at the 5' end in the original genomic DNA sample. To test the effectiveness of this method, CpG methylation levels in liver, kidney, and hippocampal tissues of mice were compared to examine if MSD-AFLP can detect subtle differences in the levels of tissue-specific differentially methylated CpGs. As a result, many CpG sites suspected to be tissue-specific differentially methylated were detected. Nucleotide sequences adjacent to these methyl-CpG sites were identified and we determined the methylation level by methylation-sensitive restriction endonuclease (MSRE)-PCR analysis to confirm the accuracy of AFLP analysis. The differences of the methylation level among tissues were almost identical among these methods. By MSD-AFLP analysis, we detected many CpGs showing less than 5% statistically significant tissue-specific difference and less than 10% degree of variability. Additionally, MSD-AFLP analysis could be used to identify CpG methylation sites in other organisms including humans. MSD-AFLP analysis can potentially be used to measure slight changes in CpG methylation level. Regarding the remarkable precision, sensitivity, and throughput of MSD-AFLP analysis studies, this method will be advantageous in a variety of epigenetics-based research.

Multidimensional Programming Methods for Energy Facility Siting: Alternative Approaches

NASA Technical Reports Server (NTRS)

Solomon, B. D.; Haynes, K. E.

1982-01-01

The use of multidimensional optimization methods in solving power plant siting problems, which are characterized by several conflicting, noncommensurable objectives is addressed. After a discussion of data requirements and exclusionary site screening methods for bounding the decision space, classes of multiobjective and goal programming models are discussed in the context of finite site selection. Advantages and limitations of these approaches are highlighted and the linkage of multidimensional methods with the subjective, behavioral components of the power plant siting process is emphasized.

Multiple site receptor modeling with a minimal spanning tree combined with a Kohonen neural network

NASA Astrophysics Data System (ADS)

Hopke, Philip K.

1999-12-01

A combination of two pattern recognition methods has been developed that allows the generation of geographical emission maps form multivariate environmental data. In such a projection into a visually interpretable subspace by a Kohonen Self-Organizing Feature Map, the topology of the higher dimensional variables space can be preserved, but parts of the information about the correct neighborhood among the sample vectors will be lost. This can partly be compensated for by an additional projection of Prim's Minimal Spanning Tree into the trained neural network. This new environmental receptor modeling technique has been adapted for multiple sampling sites. The behavior of the method has been studied using simulated data. Subsequently, the method has been applied to mapping data sets from the Southern California Air Quality Study. The projection of a 17 chemical variables measured at up to 8 sampling sites provided a 2D, visually interpretable, geometrically reasonable arrangement of air pollution source sin the South Coast Air Basin.

Modification site localization scoring integrated into a search engine.

PubMed

Baker, Peter R; Trinidad, Jonathan C; Chalkley, Robert J

2011-07-01

Large proteomic data sets identifying hundreds or thousands of modified peptides are becoming increasingly common in the literature. Several methods for assessing the reliability of peptide identifications both at the individual peptide or data set level have become established. However, tools for measuring the confidence of modification site assignments are sparse and are not often employed. A few tools for estimating phosphorylation site assignment reliabilities have been developed, but these are not integral to a search engine, so require a particular search engine output for a second step of processing. They may also require use of a particular fragmentation method and are mostly only applicable for phosphorylation analysis, rather than post-translational modifications analysis in general. In this study, we present the performance of site assignment scoring that is directly integrated into the search engine Protein Prospector, which allows site assignment reliability to be automatically reported for all modifications present in an identified peptide. It clearly indicates when a site assignment is ambiguous (and if so, between which residues), and reports an assignment score that can be translated into a reliability measure for individual site assignments.

Estimates of evapotranspiration in alkaline scrub and meadow communities of Owens Valley, California, using the Bowen-ratio, eddy-correlation, and Penman-combination methods

USGS Publications Warehouse

Duell, L. F. W.

1988-01-01

In Owens Valley, evapotranspiration (ET) is one of the largest components of outflow in the hydrologic budget and the least understood. ET estimates for December 1983 through October 1985 were made for seven representative locations selected on the basis of geohydrology and the characteristics of phreatophytic alkaline scrub and meadow communities. The Bowen-ratio, eddy-correlation, and Penman-combination methods were used to estimate ET. The results of the analyses appear satisfactory when compared to other estimates of ET. Results by the eddy-correlation method are for a direct and a residual latent-heat flux that is based on sensible-heat flux and energy budget measurements. Penman-combination potential ET estimates were determined to be unusable because they overestimated actual ET. Modification in the psychrometer constant of this method to account for differences between heat-diffusion resistance and vapor-diffusion resistance permitted actual ET to be estimated. The methods may be used for studies in similar semiarid and arid rangeland areas in the Western United States. Meteorological data for three field sites are included in the appendix. Simple linear regression analysis indicates that ET estimates are correlated to air temperature, vapor-density deficit, and net radiation. Estimates of annual ET range from 300 mm at a low-density scrub site to 1,100 mm at a high-density meadow site. The monthly percentage of annual ET was determined to be similar for all sites studied. (Author 's abstract)

(PRESENTED NAQC SAN FRANCISCO, CA) COARSE PM METHODS STUDY: STUDY DESIGN AND RESULTS

EPA Science Inventory

Comprehensive field studies were conducted to evaluate the performance of sampling methods for measuring the coarse fraction of PM10 in ambient air. Five separate sampling approaches were evaluated at each of three sampling sites. As the primary basis of comparison, a discrete ...

A multi-method assessment of bone maintenance and loss in an Imperial Roman population: Implications for future studies of age-related bone loss in the past.

PubMed

Beauchesne, Patrick; Agarwal, Sabrina C

2017-09-01

One of the hallmarks of contemporary osteoporosis and bone loss is dramatically higher prevalence of loss and fragility in females post-menopause. In contrast, bioarchaeological studies of bone loss have found a greater diversity of age- and sex-related patterns of bone loss in past populations. We argue that the differing findings may relate to the fact that most studies use only a single methodology to quantify bone loss and do not account for the heterogeneity and complexity of bone maintenance across the skeleton and over the life course. We test the hypothesis that bone mass and maintenance in trabecular bone sites versus cortical bone sites will show differing patterns of age-related bone loss, with cortical bone sites showing sex difference in bone loss that are similar to contemporary Western populations, and trabecular bone loss at earlier ages. We investigated this hypothesis in the Imperial Roman population of Velia using three methods: radiogrammetry of the second metacarpal (N = 71), bone histology of ribs (N = 70), and computerized tomography of trabecular bone architecture (N = 47). All three methods were used to explore sex and age differences in patterns of bone loss. The suite of methods utilized reveal differences in the timing of bone loss with age, but all methods found no statistically significant differences in age-related bone loss. We argue that a multi-method approach reduces the influence of confounding factors by building a reconstruction of bone turnover over the life cycle that a limited single-method project cannot provide. The implications of using multiple methods beyond studies of bone loss are also discussed. © 2017 Wiley Periodicals, Inc.

A full-potential approach to the relativistic single-site Green's function

DOE PAGES

Liu, Xianglin; Wang, Yang; Eisenbach, Markus; ...

2016-07-07

One major purpose of studying the single-site scattering problem is to obtain the scattering matrices and differential equation solutions indispensable to multiple scattering theory (MST) calculations. On the other hand, the single-site scattering itself is also appealing because it reveals the physical environment experienced by electrons around the scattering center. In this study, we demonstrate a new formalism to calculate the relativistic full-potential single-site Green's function. We implement this method to calculate the single-site density of states and electron charge densities. Lastly, the code is rigorously tested and with the help of Krein's theorem, the relativistic effects and full potentialmore » effects in group V elements and noble metals are thoroughly investigated.« less

CHARACTERIZATION OF HAZARDOUS WASTE SITES, A METHODS MANUAL. VOLUME 2. AVAILABLE SAMPLING METHODS (SECOND EDITION)

EPA Science Inventory

Investigations at hazardous waste sites and sites of chemical spills often require on-site measurements and sampling activities to assess the type and extent of contamination. This document is a compilation of sampling methods and materials suitable to address most needs that ari...

Integration of paleoseismic data from multiple sites to develop an objective earthquake chronology: Application to the Weber segment of the Wasatch fault zone, Utah

USGS Publications Warehouse

DuRoss, Christopher B.; Personius, Stephen F.; Crone, Anthony J.; Olig, Susan S.; Lund, William R.

2011-01-01

We present a method to evaluate and integrate paleoseismic data from multiple sites into a single, objective measure of earthquake timing and recurrence on discrete segments of active faults. We apply this method to the Weber segment (WS) of the Wasatch fault zone using data from four fault-trench studies completed between 1981 and 2009. After systematically reevaluating the stratigraphic and chronologic data from each trench site, we constructed time-stratigraphic OxCal models that yield site probability density functions (PDFs) of the times of individual earthquakes. We next qualitatively correlated the site PDFs into a segment-wide earthquake chronology, which is supported by overlapping site PDFs, large per-event displacements, and prominent segment boundaries. For each segment-wide earthquake, we computed the product of the site PDF probabilities in common time bins, which emphasizes the overlap in the site earthquake times, and gives more weight to the narrowest, best-defined PDFs. The product method yields smaller earthquake-timing uncertainties compared to taking the mean of the site PDFs, but is best suited to earthquakes constrained by broad, overlapping site PDFs. We calculated segment-wide earthquake recurrence intervals and uncertainties using a Monte Carlo model. Five surface-faulting earthquakes occurred on the WS at about 5.9, 4.5, 3.1, 1.1, and 0.6 ka. With the exception of the 1.1-ka event, we used the product method to define the earthquake times. The revised WS chronology yields a mean recurrence interval of 1.3 kyr (0.7–1.9-kyr estimated two-sigma [2δ] range based on interevent recurrence). These data help clarify the paleoearthquake history of the WS, including the important question of the timing and rupture extent of the most recent earthquake, and are essential to the improvement of earthquake-probability assessments for the Wasatch Front region.

Integration of paleoseismic data from multiple sites to develop an objective earthquake chronology: Application to the Weber segment of the Wasatch fault zone, Utah

USGS Publications Warehouse

DuRoss, C.B.; Personius, S.F.; Crone, A.J.; Olig, S.S.; Lund, W.R.

2011-01-01

We present a method to evaluate and integrate paleoseismic data from multiple sites into a single, objective measure of earthquake timing and recurrence on discrete segments of active faults. We apply this method to the Weber segment (WS) of the Wasatch fault zone using data from four fault-trench studies completed between 1981 and 2009. After systematically reevaluating the stratigraphic and chronologic data from each trench site, we constructed time-stratigraphic OxCal models that yield site probability density functions (PDFs) of the times of individual earthquakes. We next qualitatively correlated the site PDFs into a segment-wide earthquake chronology, which is supported by overlapping site PDFs, large per-event displacements, and prominent segment boundaries. For each segment-wide earthquake, we computed the product of the site PDF probabilities in common time bins, which emphasizes the overlap in the site earthquake times, and gives more weight to the narrowest, best-defined PDFs. The product method yields smaller earthquake-timing uncertainties compared to taking the mean of the site PDFs, but is best suited to earthquakes constrained by broad, overlapping site PDFs. We calculated segment-wide earthquake recurrence intervals and uncertainties using a Monte Carlo model. Five surface-faulting earthquakes occurred on the WS at about 5.9, 4.5, 3.1, 1.1, and 0.6 ka. With the exception of the 1.1-ka event, we used the product method to define the earthquake times. The revised WS chronology yields a mean recurrence interval of 1.3 kyr (0.7-1.9-kyr estimated two-sigma [2??] range based on interevent recurrence). These data help clarify the paleoearthquake history of the WS, including the important question of the timing and rupture extent of the most recent earthquake, and are essential to the improvement of earthquake-probability assessments for the Wasatch Front region.

Estimated flow-duration curves for selected ungaged sites in Kansas

USGS Publications Warehouse

Studley, S.E.

2001-01-01

Flow-duration curves for 1968-98 were estimated for 32 ungaged sites in the Missouri, Smoky Hill-Saline, Solomon, Marais des Cygnes, Walnut, Verdigris, and Neosho River Basins in Kansas. Also included from a previous report are estimated flow-duration curves for 16 ungaged sites in the Cimarron and lower Arkansas River Basins in Kansas. The method of estimation used six unique factors of flow duration: (1) mean streamflow and percentage duration of mean streamflow, (2) ratio of 1-percent-duration streamflow to mean streamflow, (3) ratio of 0.1-percent-duration streamflow to 1-percent-duration streamflow, (4) ratio of 50-percent-duration streamflow to mean streamflow, (5) percentage duration of appreciable streamflow (0.10 cubic foot per second), and (6) average slope of the flow-duration curve. These factors were previously developed from a regionalized study of flow-duration curves using streamflow data for 1921-76 from streamflow-gaging stations with drainage areas of 100 to 3,000 square miles. The method was tested on a currently (2001) measured, continuous-record streamflow-gaging station on Salt Creek near Lyndon, Kansas, with a drainage area of 111 square miles and was found to adequately estimate the computed flow-duration curve for the station. The method also was tested on a currently (2001) measured, continuous-record, streamflow-gaging station on Soldier Creek near Circleville, Kansas, with a drainage area of 49.3 square miles. The results of the test on Soldier Creek near Circleville indicated that the method could adequately estimate flow-duration curves for sites with drainage areas of less than 100 square miles. The low-flow parts of the estimated flow-duration curves were verified or revised using 137 base-flow discharge measurements made during 1999-2000 at the 32 ungaged sites that were correlated with base-flow measurements and flow-duration analyses performed at nearby, long-term, continuous-record, streamflow-gaging stations (index stations). The method did not adequately estimate the flow-duration curves for two sites in the western one-third of the State because of substantial changes in farming practices (terracing and intensive ground-water withdrawal) that were not accounted for in the two previous studies (Furness, 1959; Jordan, 1983). For these two sites, there was enough historic, continuous-streamflow record available to perform record-extension techniques correlated to their respective index stations for the development of the estimated flow-duration curves. The estimated flow-duration curves at the ungaged sites can be used for projecting future flow frequencies for assessment of total maximum daily loads (TMDLs) or other water-quality constituents, water-availability studies, and for basin-characteristic studies.

Temporary site selection and decision-making methods: a case study of Tehran, Iran.

PubMed

Omidvar, Babak; Baradaran-Shoraka, Mohammad; Nojavan, Mehdi

2013-07-01

Decisions on selecting an appropriate site for temporary shelter used to be taken in a limited amount of time after a disaster. The need for a systematic method in this area inspired the MADM (multi-attribute decision making) for complex disaster management decisions. This research proposes a model for appropriate and systematic site selection for temporary shelters, before an earthquake, using a geographical information system and MADM based on an earthquake damage assessment. After the effective criteria for site selection of temporary shelters are determined, the geographical layers of these criteria are prepared for Municipal District No.1 of Greater Tehran, the capital of Iran. Given these attributes and the required shelter area (415-610 hectares), 14 zones are proposed initially. Various MADM methods are used for the final selection. The mean of the aggregated ranking results are determined, and 10 of the 14 initial zones are ranked. © 2013 The Author(s). Journal compilation © Overseas Development Institute, 2013.

A biomonitoring plan for assessing potential radionuclide exposure using Amchitka Island in the Aleutian chain of Alaska as a case study.

PubMed

Burger, Joanna; Gochfeld, Michael; Kosson, D S; Powers, Charles W

2007-01-01

With the ending of the Cold War, the US and other nations were faced with a legacy of nuclear wastes. For some sites where hazardous nuclear wastes will remain in place, methods must be developed to protect human health and the environment. Biomonitoring is one method of assessing the status and trends of potential radionuclide exposure from nuclear waste sites, and of providing the public with early warning of any potential harmful exposure. Amchitka Island (51 degrees N lat, 179 degrees E long) was the site of three underground nuclear tests from 1965 to 1971. Following a substantive study of radionuclide levels in biota from the marine environment around Amchitka and a reference site, we developed a suite of bioindicators (with suggested isotopes) that can serve as a model for other sites contaminated with radionuclides. Although the species selection was site-specific, the methods can provide a framework for other sites. We selected bioindicators using five criteria: (1) occurrence at all three test shots (and reference site), (2) receptor groups (subsistence foods, commercial species, and food chain nodes), (3) species groups (plants, invertebrates, fish, and birds), (4) trophic levels, and (5) an accumulator of one or several radionuclides. Our major objective was to identify bioindicators that could serve for both human health and the ecosystem, and were abundant enough to collect adjacent to the three test sites and at the reference site. Site-specific information on both biota availability and isotope levels was essential in the final selection of bioindicators. Actinides bioaccumulated in algae and invertebrates, while radiocesium accumulated in higher trophic level birds and fish. Thus, unlike biomonitoring schemes developed for heavy metals or other contaminants, top-level predators are not sufficient to evaluate potential radionuclide exposure at Amchitka. The process described in this paper resulted in the selection of Fucus, Alaria fistulosa, blue mussel (Mytilus trossulus), dolly varden (Salvelinus malma), black rockfish (Sebastes melanops), Pacific cod (Gadus macrocephalus), Pacific halibut (Hippoglossus stenolepis), and glaucous-winged gull (Larus glaucescens) as bioindicators. This combination of species included mainly subsistence foods, commercial fish, and nodes on different food chains.

Using Geographic Information Systems to Determine Site Suitability for a Low-Level Radioactive Waste Storage Facility.

PubMed

Wilson, Charles A; Matthews, Kennith; Pulsipher, Allan; Wang, Wei-Hsung

2016-02-01

Radioactive waste is an inevitable product of using radioactive material in education and research activities, medical applications, energy generation, and weapons production. Low-level radioactive waste (LLW) makes up a majority of the radioactive waste produced in the United States. In 2010, over two million cubic feet of LLW were shipped to disposal sites. Despite efforts from several states and compacts as well as from private industry, the options for proper disposal of LLW remain limited. New methods for quickly identifying potential storage locations could alleviate current challenges and eventually provide additional sites and allow for adequate regional disposal of LLW. Furthermore, these methods need to be designed so that they are easily communicated to the public. A Geographic Information Systems (GIS) based method was developed to determine suitability of potential LLW disposal (or storage) sites. Criteria and other parameters of suitability were based on the Code of Federal Regulation (CFR) requirements as well as supporting literature and reports. The resultant method was used to assess areas suitable for further evaluation as prospective disposal sites in Louisiana. Criteria were derived from the 10 minimum requirements in 10 CFR Part 61.50, the Nuclear Regulatory Commission's Regulatory Guide 0902, and studies at existing disposal sites. A suitability formula was developed permitting the use of weighting factors and normalization of all criteria. Data were compiled into GIS data sets and analyzed on a cell grid of approximately 14,000 cells (covering 181,300 square kilometers) using the suitability formula. Requirements were analyzed for each cell using multiple criteria/sub-criteria as well as surrogates for unavailable datasets. Additional criteria were also added when appropriate. The method designed in this project proved to be sufficient for initial screening tests in determining the most suitable areas for prospective disposal (or storage) sites. Cells above 90%, 95%, and 99% suitability include respectively 404, 88, and 4 cells suitable for further analysis. With these areas identified, the next step in siting a LLW storage facility would be on-site analysis using additional requirements as specified by relevant regulatory guidelines. The GIS based method provides an easy, economic, efficient and effective means in evaluating potential sites for LLW storage facilities where sufficient GIS data exist.

Modelling a suitable location for Urban Solid Waste Management using AHP method and GIS -A geospatial approach and MCDM Model

NASA Astrophysics Data System (ADS)

Iqbal, M.; Islam, A.; Hossain, A.; Mustaque, S.

2016-12-01

Multi-Criteria Decision Making(MCDM) is advanced analytical method to evaluate appropriate result or decision from multiple criterion environment. Present time in advanced research, MCDM technique is progressive analytical process to evaluate a logical decision from various conflict. In addition, Present day Geospatial approach (e.g. Remote sensing and GIS) also another advanced technical approach in a research to collect, process and analyze various spatial data at a time. GIS and Remote sensing together with the MCDM technique could be the best platform to solve a complex decision making process. These two latest process combined very effectively used in site selection for solid waste management in urban policy. The most popular MCDM technique is Weighted Linear Method (WLC) where Analytical Hierarchy Process (AHP) is another popular and consistent techniques used in worldwide as dependable decision making. Consequently, the main objective of this study is improving a AHP model as MCDM technique with Geographic Information System (GIS) to select a suitable landfill site for urban solid waste management. Here AHP technique used as a MCDM tool to select the best suitable landfill location for urban solid waste management. To protect the urban environment in a sustainable way municipal waste needs an appropriate landfill site considering environmental, geological, social and technical aspect of the region. A MCDM model generate from five class related which related to environmental, geological, social and technical using AHP method and input the result set in GIS for final model location for urban solid waste management. The final suitable location comes out that 12.2% of the area corresponds to 22.89 km2 considering the total study area. In this study, Keraniganj sub-district of Dhaka district in Bangladesh is consider as study area which is densely populated city currently undergoes an unmanaged waste management system especially the suitable landfill sites for waste dumping site.

Comparison of American Fisheries Society (AFS) standard fish sampling techniques and environmental DNA for characterizing fish communities in a large reservoir

USGS Publications Warehouse

Perez, Christina R.; Bonar, Scott A.; Amberg, Jon J.; Ladell, Bridget; Rees, Christopher B.; Stewart, William T.; Gill, Curtis J.; Cantrell, Chris; Robinson, Anthony

2017-01-01

Recently, methods involving examination of environmental DNA (eDNA) have shown promise for characterizing fish species presence and distribution in waterbodies. We evaluated the use of eDNA for standard fish monitoring surveys in a large reservoir. Specifically, we compared the presence, relative abundance, biomass, and relative percent composition of Largemouth Bass Micropterus salmoides and Gizzard Shad Dorosoma cepedianum measured through eDNA methods and established American Fisheries Society standard sampling methods for Theodore Roosevelt Lake, Arizona. Catches at electrofishing and gillnetting sites were compared with eDNA water samples at sites, within spatial strata, and over the entire reservoir. Gizzard Shad were detected at a higher percentage of sites with eDNA methods than with boat electrofishing in both spring and fall. In contrast, spring and fall gillnetting detected Gizzard Shad at more sites than eDNA. Boat electrofishing and gillnetting detected Largemouth Bass at more sites than eDNA; the exception was fall gillnetting, for which the number of sites of Largemouth Bass detection was equal to that for eDNA. We observed no relationship between relative abundance and biomass of Largemouth Bass and Gizzard Shad measured by established methods and eDNA copies at individual sites or lake sections. Reservoirwide catch composition for Largemouth Bass and Gizzard Shad (numbers and total weight [g] of fish) as determined through a combination of gear types (boat electrofishing plus gillnetting) was similar to the proportion of total eDNA copies from each species in spring and fall field sampling. However, no similarity existed between proportions of fish caught via spring and fall boat electrofishing and the proportion of total eDNA copies from each species. Our study suggests that eDNA field sampling protocols, filtration, DNA extraction, primer design, and DNA sequencing methods need further refinement and testing before incorporation into standard fish sampling surveys.

PS2-06: Best Practices for Advancing Multi-site Chart Abstraction Research

PubMed Central

Blick, Noelle; Cole, Deanna; King, Colleen; Riordan, Rick; Von Worley, Ann; Yarbro, Patty

2012-01-01

Background/Aims Multi-site chart abstraction studies are becoming increasingly common within the HMORN. Differences in systems among HMORN sites can pose significant obstacles to the success of these studies. It is therefore crucial to standardize abstraction activities by following best practices for multi-site chart abstraction, as consistency of processes across sites will increase efficiencies and enhance data quality. Methods Over the past few months the authors have been meeting to identify obstacles to multi-site chart abstraction and to address ways in which multi-site chart abstraction processes can be systemized and standardized. The aim of this workgroup is to create a best practice guide for multi-site chart abstraction studies. Focus areas include: abstractor training, format for chart abstraction (database, paper, etc), data quality, redaction, mechanism for transferring data, site specific access to medical records, IRB/HIPAA concerns, and budgetary issues. Results The results of the workgroup’s efforts (the best practice guide) will be presented by a panel of experts at the 2012 HMORN conference. The presentation format will also focus on discussion among attendees to elicit further input and to identify areas that need to be further addressed. Subsequently, the best practice guide will be posted on the HMORN website. Discussion The best practice guide for multi-site chart abstraction studies will establish sound guidelines and serve as an aid to researchers embarking on multi-site chart abstraction studies. Efficiencies and data quality will be further enhanced with standardized multi-site chart abstraction practices.

Evaluating the uncertainties of thermal catalytic conversion in measuring atmospheric nitrogen dioxide at four differently polluted sites in China

NASA Astrophysics Data System (ADS)

Xu, Zheng; Wang, Tao; Xue, L. K.; Louie, Peter K. K.; Luk, Connie W. Y.; Gao, J.; Wang, S. L.; Chai, F. H.; Wang, W. X.

2013-09-01

A widely used method for measuring nitrogen dioxide (NO2) in the atmosphere is the conversion of NO2 to nitric oxide (NO) on the hot surface of a molybdenum oxide (MoO) catalyst followed by the chemiluminescence detection of NO. Although it has long been recognized that this type of conversion may suffer from the positive interference of other oxidized nitrogen compounds, evaluations of such interference in the atmosphere are scarce, thus rendering it difficult to make use of a large portion of the NO2 or NOx data obtained via this method (often denoted as NO2* or NOx*). In the present study, we compared the MoO converter with a selective, more accurate photolytic approach at four differently polluted sites in China. The converter worked well at the urban site, which was greatly affected by fresh emissions, but, on average, overestimated NO2 by 30%-50% at the two suburban sites and by more than 130% at the mountain-top site during afternoon hours, with a much larger positive bias seen during the top 10% of ozone events. The degree of overestimation depended on both air-parcel age and the composition of the oxidation products/intermediates of NOx (NOz). We attempted to derive an empirical formula to correct for this overestimation using concurrently measured O3, NO, and NO2* at the two suburban sites. Although the formula worked well at each individual site, the different NOz partitions at the sites made it difficult to obtain a universal formula. In view of the difficulty of assessing the uncertainties of the conventional conversion method, thus limiting the usability of data obtained via this method in atmospheric research, we suggest that, in areas away from fresh NOx emission sources, either a more selective NO2 measurement method or a NOy (NOx and its reaction products and intermediates) instrument should be adopted.

Biodiversity Sampling Using a Global Acoustic Approach: Contrasting Sites with Microendemics in New Caledonia

PubMed Central

Gasc, Amandine; Sueur, Jérôme; Pavoine, Sandrine; Pellens, Roseli; Grandcolas, Philippe

2013-01-01

New Caledonia is a Pacific island with a unique biodiversity showing an extreme microendemism. Many species distributions observed on this island are extremely restricted, localized to mountains or rivers making biodiversity evaluation and conservation a difficult task. A rapid biodiversity assessment method based on acoustics was recently proposed. This method could help to document the unique spatial structure observed in New Caledonia. Here, this method was applied in an attempt to reveal differences among three mountain sites (Mandjélia, Koghis and Aoupinié) with similar ecological features and species richness level, but with high beta diversity according to different microendemic assemblages. In each site, several local acoustic communities were sampled with audio recorders. An automatic acoustic sampling was run on these three sites for a period of 82 successive days. Acoustic properties of animal communities were analysed without any species identification. A frequency spectral complexity index (NP) was used as an estimate of the level of acoustic activity and a frequency spectral dissimilarity index (Df) assessed acoustic differences between pairs of recordings. As expected, the index NP did not reveal significant differences in the acoustic activity level between the three sites. However, the acoustic variability estimated by the index Df, could first be explained by changes in the acoustic communities along the 24-hour cycle and second by acoustic dissimilarities between the three sites. The results support the hypothesis that global acoustic analyses can detect acoustic differences between sites with similar species richness and similar ecological context, but with different species assemblages. This study also demonstrates that global acoustic methods applied at broad spatial and temporal scales could help to assess local biodiversity in the challenging context of microendemism. The method could be deployed over large areas, and could help to compare different sites and determine conservation priorities. PMID:23734245

Biodiversity sampling using a global acoustic approach: contrasting sites with microendemics in New Caledonia.

PubMed

Gasc, Amandine; Sueur, Jérôme; Pavoine, Sandrine; Pellens, Roseli; Grandcolas, Philippe

2013-01-01

New Caledonia is a Pacific island with a unique biodiversity showing an extreme microendemism. Many species distributions observed on this island are extremely restricted, localized to mountains or rivers making biodiversity evaluation and conservation a difficult task. A rapid biodiversity assessment method based on acoustics was recently proposed. This method could help to document the unique spatial structure observed in New Caledonia. Here, this method was applied in an attempt to reveal differences among three mountain sites (Mandjélia, Koghis and Aoupinié) with similar ecological features and species richness level, but with high beta diversity according to different microendemic assemblages. In each site, several local acoustic communities were sampled with audio recorders. An automatic acoustic sampling was run on these three sites for a period of 82 successive days. Acoustic properties of animal communities were analysed without any species identification. A frequency spectral complexity index (NP) was used as an estimate of the level of acoustic activity and a frequency spectral dissimilarity index (Df ) assessed acoustic differences between pairs of recordings. As expected, the index NP did not reveal significant differences in the acoustic activity level between the three sites. However, the acoustic variability estimated by the index Df , could first be explained by changes in the acoustic communities along the 24-hour cycle and second by acoustic dissimilarities between the three sites. The results support the hypothesis that global acoustic analyses can detect acoustic differences between sites with similar species richness and similar ecological context, but with different species assemblages. This study also demonstrates that global acoustic methods applied at broad spatial and temporal scales could help to assess local biodiversity in the challenging context of microendemism. The method could be deployed over large areas, and could help to compare different sites and determine conservation priorities.

Effects of grazing on leaf area index, fractional cover and evapotranspiration by a desert phreatophyte community at a former uranium mill site on the Colorado Plateau.

PubMed

Bresloff, Cynthia J; Nguyen, Uyen; Glenn, Edward P; Waugh, Jody; Nagler, Pamela L

2013-01-15

This study employed ground and remote sensing methods to monitor the effects of grazing on leaf area index (LAI), fractional cover (f(c)) and evapotranspiration (ET) of a desert phreatophyte community over an 11 year period at a former uranium mill site on the Colorado Plateau, U.S. Nitrate, ammonium and sulfate are migrating away from the mill site in a shallow alluvial aquifer. The phreatophyte community, consisting of Atriplex canescens (ATCA) and Sarcobatus vermiculatus (SAVE) shrubs, intercepts groundwater and could potentially slow the movement of the contaminant plume through evapotranspiration (ET). However, the site has been heavily grazed by livestock, reducing plant cover and LAI. We used livestock exclosures and revegetation plots to determine the effects of grazing on LAI, f(c) and ET, then projected the findings over the whole site using multi-platform remote sensing methods. We show that ET is approximately equal to annual precipitation at the site, but when ATCA and SAVE are protected from grazing they can develop high f(c) and LAI values, and ET can exceed annual precipitation, with the excess coming from groundwater discharge. Therefore, control of grazing could be an effective method to slow migration of contaminants at this and similar sites in the western U.S. Copyright © 2012 Elsevier Ltd. All rights reserved.

Scaffold-Based Delivery of Autologous Mesenchymal Stem Cells for Mandibular Distraction Osteogenesis: Preliminary Studies in a Porcine Model

PubMed Central

Sun, Zongyang; Tee, Boon Ching; Kennedy, Kelly S.; Kennedy, Patrick M.; Kim, Do-Gyoon; Mallery, Susan R.; Fields, Henry W.

2013-01-01

Purpose Bone regeneration through distraction osteogenesis (DO) is promising but remarkably slow. To accelerate it, autologous mesenchymal stem cells have been directly injected to the distraction site in a few recent studies. Compared to direct injection, a scaffold-based method can provide earlier cell delivery with potentially better controlled cell distribution and retention. This pilot project investigated a scaffold-based cell-delivery approach in a porcine mandibular DO model. Materials and Methods Eleven adolescent domestic pigs were used for two major sets of studies. The in-vitro set established methodologies to: aspirate bone marrow from the tibia; isolate, characterize and expand bone marrow-derived mesenchymal stem cells (BM-MSCs); enhance BM-MSC osteogenic differentiation using FGF-2; and confirm cell integration with a gelatin-based Gelfoam scaffold. The in-vivo set transplanted autologous stem cells into the mandibular distraction sites using Gelfoam scaffolds; completed a standard DO-course and assessed bone regeneration by macroscopic, radiographic and histological methods. Repeated-measure ANOVAs and t-tests were used for statistical analyses. Results From aspirated bone marrow, multi-potent, heterogeneous BM-MSCs purified from hematopoietic stem cell contamination were obtained. FGF-2 significantly enhanced pig BM-MSC osteogenic differentiation and proliferation, with 5 ng/ml determined as the optimal dosage. Pig BM-MSCs integrated readily with Gelfoam and maintained viability and proliferative ability. After integration with Gelfoam scaffolds, 2.4–5.8×107 autologous BM-MSCs (undifferentiated or differentiated) were transplanted to each experimental DO site. Among 8 evaluable DO sites included in the final analyses, the experimental DO sites demonstrated less interfragmentary mobility, more advanced gap obliteration, higher mineral content and faster mineral apposition than the control sites, and all transplanted scaffolds were completely degraded. Conclusion It is technically feasible and biologically sound to deliver autologous BM-MSCs to the distraction site immediately after osteotomy using a Gelfoam scaffold to enhance mandibular DO. PMID:24040314

Fish communities of benchmark streams in agricultural areas of eastern Wisconsin

USGS Publications Warehouse

Sullivan, D.J.; Peterson, E.M.

1997-01-01

Fish communities were surveyed at 20 stream sites in agricultural areas in eastern Wisconsin in 1993 and 1995 as part of the National Water-Quality Assessment (NAWQA) Program. These streams, designated "benchmark streams," were selected for study because of their potential use as regional references for healthy streams in agricultural areas, based on aquatic communities, habitat, and water chemistry. The agricultural benchmark streams were selected from four physical settings, or relatively homogeneous units (RHU's), that differ in bedrock type, texture of surficial deposits, and land use. Additional data were collected along with the fish-community data, including measures of habitat, water chemistry, and population surveys of algae and benthic invertebrates. Of the 20 sites, 19 are classified as trout (salmonid) streams. Fish species that require cold or cool water were the most commonly collected. At least one species of trout was collected at 18 sites, and trout were the most abundant species at 13 sites. The species with the greatest collective abundance, and collected at 18 of the 20 sites, were mottled sculpin (Cottus bairdi), a coldwater species. The next most abundant species were brown trout (Salmo trutta), followed by brook trout (Salvelinusfontinalis), creek chub (Semotilus atromaculatus), and longnose dace (Rhinichthys cataractae). In all, 31 species of fish were collected. The number of species per stream ranged from 2 to 14, and the number of individuals collected ranged from 19 to 264. According to Index of Biotic Integrity (IBI) scores, 5 sites were rated excellent, 10 sites rated good, 4 rated fair, and 1 rated poor. The ratings of the five sites in the fair to poor range were low for various reasons. Two sites appeared to have more warmwater species than was ideal for a high-quality coldwater stream. One was sampled during high flow and the results may not be valid for periods of normal flow; the other may have been populated by migrating warmwater species. Two sites had insufficient deep-water habitat to support large numbers offish, especially top carnivores. Finally, one stream may be too cool to support enough warmwater species and too warm to support trout. In general, two methods of evaluating site habitat indicate that habitat is not a limiting factor for fish communities. However, two sites were rated as fair according to both habitat evaluation methods due to low base flow. Two sites rated below good according to one habitat evaluation method but rated good or excellent according to the other. Detrended correspondence analysis (DCA) of data for 17 sites showed three station groupings. These groupings fell along RHU divisions and each group was associated with one of three trout species. A species-richness gradient was evident on the station-ordination diagram. Intolerant species were associated with each grouping, a reflection of the generally high water quality at the sites. However, no significant differences were found between IBI scores or habitat indices among the site groupings. The DCA axis 1 and 2 scores correlated with average velocity and percent pool as well as RHU factors percent sandy surficial deposits, percent wetland, percent agriculture, and bedrock. Average velocity was highest at three sites which also had among the highest measured flow and largest drainage areas. Percent pool was generally lower at sites with smaller percentages of sandy surficial deposits, with one exception. The usefulness of ordination methods in conjunction with more traditional methods of defining biotic integrity (IB I) has been noted in previous studies. In this study, however, perhaps because of the relative homogeneity of the benchmark streams, the IBI did not correlate with the same kinds of factors as the DCA axis scores did. 

Spontaneous revegetation vs. forestry reclamation in post-mining sand pits.

PubMed

Šebelíková, Lenka; Řehounková, Klára; Prach, Karel

2016-07-01

Vegetation development of sites restored by two different methods, spontaneous revegetation and forestry reclamation, was compared in four sand pit mining complexes located in the southern part of the Czech Republic, central Europe. The space-for-time substitution method was applied to collect vegetation records in 13 differently aged and sufficiently large sites with known history. The restoration method, age (time since site abandonment/reclamation), groundwater table, slope, and aspect in all sampled plots were recorded in addition to the visual estimation of percentage cover of all present vascular plant species. Multivariate methods and GLM were used for the data elaboration. Restoration method was the major factor influencing species pattern. Both spontaneously revegetated and forestry reclaimed sites developed towards forest on a comparable timescale. Although the sites did not significantly differ in species richness (160 species in spontaneously revegetated vs. 111 in forestry reclaimed sites), spontaneously revegetated sites tended to be more diverse with more species of conservation potential (10 Red List species in spontaneous sites vs. 4 Red List species in forestry reclaimed sites). These results support the use of spontaneous revegetation as an effective and low-cost method of sand pit restoration and may contribute to implementation of this method in practice.

Lessons learned from a practice-based, multi-site intervention study with nurse participants

PubMed Central

Friese, Christopher R.; Mendelsohn-Victor, Kari; Ginex, Pamela; McMahon, Carol M.; Fauer, Alex J.; McCullagh, Marjorie C.

2016-01-01

Purpose To identify challenges and solutions to the efficient conduct of a multi-site, practice-based randomized controlled trial to improve nurses’ adherence to personal protective equipment use in ambulatory oncology settings. Design The Drug Exposure Feedback and Education for Nurses’ Safety (DEFENS) study is a clustered, randomized, controlled trial. Participating sites are randomized to web-based feedback on hazardous drug exposures in the sites plus tailored messages to address barriers versus a control intervention of a web-based continuing education video. Approach The study principal investigator, the study coordinator, and two site leaders identified challenges to study implementation and potential solutions, plus potential methods to prevent logistical challenges in future studies. Findings Noteworthy challenges included variation in human subjects protection policies, grants and contracts budgeting, infrastructure for nursing-led research, and information technology variation. Successful strategies included scheduled web conferences, site-based study champions, site visits by the principal investigator, and centrally-based document preparation. Strategies to improve efficiency in future studies include early and continued engagement with contract personnel in sites, and proposed changes to the common rule concerning human subjects. The DEFENS study successfully recruited 393 nurses across 12 sites. To date, 369 have completed surveys and 174 nurses have viewed educational materials. Conclusions Multi-site studies of nursing personnel are rare and challenging to existing infrastructure. These barriers can be overcome with strong engagement and planning. Clinical Relevance Leadership engagement, onsite staff support, and continuous communication can facilitate successful recruitment to a workplace-based randomized, controlled behavioral trial. PMID:28098951

Comparison of stool collection on site versus at home in a population-based study : feasibility and participants' preference in Pretest 2 of the German National Cohort.

PubMed

Schultze, A; Akmatov, M K; Andrzejak, M; Karras, N; Kemmling, Y; Maulhardt, A; Wieghold, S; Ahrens, W; Günther, K; Schlenz, H; Krause, G; Pessler, F

2014-11-01

For certain laboratory investigations it is necessary to obtain native stool samples and process them within a narrow time window at the point of contact or a nearby laboratory. However, it is not known whether it is feasible to obtain stool samples from asymptomatic individuals during an appointment in a study center (SC). We therefore compared participants' preference, feasibility and acceptance of stool sample collection during the appointment at the study center (on-site sampling) to collection at home after the appointment. The study was conducted at two sites in Northern Germany (Bremen, n = 156; Hannover, n = 147) during the Pretest 2 phase of the German National Cohort (GNC), drawing upon a randomly selected population supplemented by a small convenience sample. In the study center, the participants were given the choice to provide a stool sample during the appointment or to collect a sample later at home and return it by mail. In all, 303 of the 351 participants (86 %) of Pretest 2 at these sites participated in this feasibility study. Only 7.9 % (24/303) of the participants chose on-site collection, whereas 92 % (279/303) chose at-home collection. There were significant differences between the two study sites in that 14 % (21/147) of participants in Hannover and 2 % (3/156) of participants in Bremen chose on-site collection. Compliance was high in both groups, as 100 % (24/24) and 98 % (272/279) of participants in the on-site and at-home groups, respectively, provided complete samples. Both methods were highly accepted, as 92 % of the participants in each group (22/24 and 227/248) stated that stool collection at the respective site was acceptable. When given a choice, most participants in this population-based study preferred home collection of stool samples to collection in the study center. Thus, native stool samples for immediate processing in the study center may potentially be obtained only from a subpopulation of participants, which may lead to selection bias. Home collection, on the other hand, proved to be a highly feasible method for studies that do not require freshly collected native stool.

Streamflow monitoring and statistics for development of water rights claims for Wild and Scenic Rivers, Owyhee Canyonlands Wilderness, Idaho, 2012

USGS Publications Warehouse

Wood, Molly S.; Fosness, Ryan L.

2013-01-01

The U.S. Geological Survey, in cooperation with the Bureau of Land Management (BLM), collected streamflow data in 2012 and estimated streamflow statistics for stream segments designated "Wild," "Scenic," or "Recreational" under the National Wild and Scenic Rivers System in the Owyhee Canyonlands Wilderness in southwestern Idaho. The streamflow statistics were used by BLM to develop and file a draft, federal reserved water right claim in autumn 2012 to protect federally designated "outstanding remarkable values" in the stream segments. BLM determined that the daily mean streamflow equaled or exceeded 20 and 80 percent of the time during bimonthly periods (two periods per month) and the bankfull streamflow are important streamflow thresholds for maintaining outstanding remarkable values. Prior to this study, streamflow statistics estimated using available datasets and tools for the Owyhee Canyonlands Wilderness were inaccurate for use in the water rights claim. Streamflow measurements were made at varying intervals during February–September 2012 at 14 monitoring sites; 2 of the monitoring sites were equipped with telemetered streamgaging equipment. Synthetic streamflow records were created for 11 of the 14 monitoring sites using a partial‑record method or a drainage-area-ratio method. Streamflow records were obtained directly from an operating, long-term streamgage at one monitoring site, and from discontinued streamgages at two monitoring sites. For 10 sites analyzed using the partial-record method, discrete measurements were related to daily mean streamflow at a nearby, telemetered “index” streamgage. Resulting regression equations were used to estimate daily mean and annual peak streamflow at the monitoring sites during the full period of record for the index sites. A synthetic streamflow record for Sheep Creek was developed using a drainage-area-ratio method, because measured streamflows did not relate well to any index site to allow use of the partial-record method. The synthetic and actual daily mean streamflow records were used to estimate daily mean streamflow that was exceeded 80, 50, and 20 percent of the time (80-, 50-, and 20-percent exceedances) for bimonthly and annual periods. Bankfull streamflow statistics were calculated by fitting the synthetic and actual annual peak streamflow records to a log Pearson Type III distribution using Bulletin 17B guidelines in the U.S. Geological Survey PeakFQ program. The coefficients of determination (R2) for the regressions between the monitoring and index sites ranged from 0.74 for Wickahoney Creek to 0.98 for the West Fork Bruneau River and Deep Creek. Confidence in computed streamflow statistics is highest among other sites for the East Fork Owyhee River and the West Fork Bruneau River on the basis of regression statistics, visual fit of the related data, and the range and number of streamflow measurements. Streamflow statistics for sites with the greatest uncertainty included Big Jacks, Little Jacks, Cottonwood, Wickahoney, and Sheep Creeks. The uncertainty in computed streamflow statistics was due to a number of factors which included the distance of index sites relative to monitoring sites, relatively low streamflow conditions that occurred during the study, and the limited number and range of streamflow measurements. However, the computed streamflow statistics are considered the best possible estimates given available datasets in the remote study area. Streamflow measurements over a wider range of hydrologic and climatic conditions would improve the relations between streamflow characteristics at monitoring and index sites. Additionally, field surveys are needed to verify if the streamflows selected for the water rights claims are sufficient for maintaining outstanding remarkable values in the Wild and Scenic rivers included in the study.

Enhancement of alkylation catalysts for improved supercritical fluid regeneration

DOEpatents

Ginosar, Daniel M [Idaho Falls, ID; Petkovic, Lucia [Idaho Falls, ID

2009-09-22

A method of modifying an alkylation catalyst to reduce the formation of condensed hydrocarbon species thereon. The method comprises providing an alkylation catalyst comprising a plurality of active sites. The plurality of active sites on the alkylation catalyst may include a plurality of weakly acidic active sites, intermediate acidity active sites, and strongly acidic active sites. A base is adsorbed to a portion of the plurality of active sites, such as the strongly acidic active sites, selectively poisoning the strongly acidic active sites. A method of modifying the alkylation catalyst by providing an alkylation catalyst comprising a pore size distribution that sterically constrains formation of the condensed hydrocarbon species on the alkylation catalyst or by synthesizing the alkylation catalyst to comprise a decreased number of strongly acidic active sites is also disclosed, as is a method of improving a regeneration efficiency of the alkylation catalyst.

Enhancement of alkylation catalysts for improved supercritical fluid regeneration

DOEpatents

Ginosar, Daniel M.; Petkovic, Lucia M.

2010-12-28

A method of modifying an alkylation catalyst to reduce the formation of condensed hydrocarbon species thereon. The method comprises providing an alkylation catalyst comprising a plurality of active sites. The plurality of active sites on the alkylation catalyst may include a plurality of weakly acidic active sites, intermediate acidity active sites, and strongly acidic active sites. A base is adsorbed to a portion of the plurality of active sites, such as the strongly acidic active sites, selectively poisoning the strongly acidic active sites. A method of modifying the alkylation catalyst by providing an alkylation catalyst comprising a pore size distribution that sterically constrains formation of the condensed hydrocarbon species on the alkylation catalyst or by synthesizing the alkylation catalyst to comprise a decreased number of strongly acidic active sites is also disclosed, as is a method of improving a regeneration efficiency of the alkylation catalyst.

Quantitative determination of occupation sites of trace Co substituted for multiple Fe sites in M-type hexagonal ferrite using statistical beam-rocking TEM-EDXS analysis.

PubMed

Ohtsuka, Masahiro; Muto, Shunsuke; Tatsumi, Kazuyoshi; Kobayashi, Yoshinori; Kawata, Tsunehiro

2016-04-01

The occupation sites and the occupancies of trace dopants in La/Co co-doped Sr-M-type ferrite, SrFe12O19, were quantitatively and precisely determined by beam-rocking energy-dispersive X-ray spectroscopy (EDXS) on the basis of electron-channeling effects. Because the Co atoms, in particular, should be partially substituted for the five crystallographically inequivalent sites, which could be key parameters in improving the magneto-crystalline anisotropy, it is difficult yet intriguing to discover their occupation sites and occupancies without using the methods of large-scale facilities, such as neutron diffraction and synchrotron radiation. In the present study, we tackled this problem by applying an extended statistical atom location by channeling enhanced microanalysis method, using conventional transmission electron microscopy, EDXS and dynamical electron elastic/inelastic scattering theories. The results show that the key occupation sites of Co were the 2a, 4f1 and 12k sites. The quantified occupancies of Co were consistent with those of the previous study, which involved a combination of neutron diffraction and extended X-ray absorption fine structure analysis, as well as energetics considerations based on by first-principles calculations. © The Author 2015. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Regional flood probabilities

USGS Publications Warehouse

Troutman, Brent M.; Karlinger, Michael R.

2003-01-01

The T‐year annual maximum flood at a site is defined to be that streamflow, that has probability 1/T of being exceeded in any given year, and for a group of sites the corresponding regional flood probability (RFP) is the probability that at least one site will experience a T‐year flood in any given year. The RFP depends on the number of sites of interest and on the spatial correlation of flows among the sites. We present a Monte Carlo method for obtaining the RFP and demonstrate that spatial correlation estimates used in this method may be obtained with rank transformed data and therefore that knowledge of the at‐site peak flow distribution is not necessary. We examine the extent to which the estimates depend on specification of a parametric form for the spatial correlation function, which is known to be nonstationary for peak flows. It is shown in a simulation study that use of a stationary correlation function to compute RFPs yields satisfactory estimates for certain nonstationary processes. Application of asymptotic extreme value theory is examined, and a methodology for separating channel network and rainfall effects on RFPs is suggested. A case study is presented using peak flow data from the state of Washington. For 193 sites in the Puget Sound region it is estimated that a 100‐year flood will occur on the average every 4.5 years.

Microbial Profiles and Detection Techniques in Peri-Implant Diseases: a Systematic Review

PubMed Central

Padial-Molina, Miguel; López-Martínez, Jesús; O’Valle, Francisco

2016-01-01

ABSTRACT Objectives To describe the microbial profiles of peri-implant diseases and the main detection methods. Material and Methods A literature search was performed in MEDLINE via PubMed database to identify studies on microbial composition of peri-implant surfaces in humans published in the last 5 years. Studies had to have clear implant status definition for health, peri-implant mucositis and/or peri-implantitis and specifically study microbial composition of the peri-implant sulcus. Results A total of 194 studies were screened and 47 included. Peri-implant sites are reported to be different microbial ecosystems compared to periodontal sites. However, differences between periodontal and peri-implant health and disease are not consistent across all studies, possibly due to the bias introduced by the microbial detection technique. New methods non species-oriented are being used to find ‘unexpected’ microbiota not previously described in these scenarios. Conclusions Microbial profile of peri-implant diseases usually includes classic periodontopathogens. However, correlation between studies is difficult, particularly because of the use of different detection methods. New metagenomic techniques should be promoted for future studies to avoid detection bias. PMID:27833735

Plant-based FRET biosensor discriminates enviornmental zinc levels

USDA-ARS?s Scientific Manuscript database

Heavy metal accumulation in the environment poses great risks to flora and fauna. However, monitoring sites prone to accumulation poses scale and economic challenges. In this study, we present and test a method for monitoring these sites using fluorescent resonance energy transfer (FRET) change in r...

A Weighting Method for Assessing Between-Site Heterogeneity in Causal Mediation Mechanism

ERIC Educational Resources Information Center

Qin, Xu; Hong, Guanglei

2017-01-01

When a multisite randomized trial reveals between-site variation in program impact, methods are needed for further investigating heterogeneous mediation mechanisms across the sites. We conceptualize and identify a joint distribution of site-specific direct and indirect effects under the potential outcomes framework. A method-of-moments procedure…

Coordinating short-term projects into an effective research program: effects of site preparation methods on bird communities in pine plantations

Treesearch

John C. Kilgo; Karl V. Miller; William F. Moore

2000-01-01

Several short-term projects conducted at the Savannah River Site have focused on the effects on avian populations of different techniques of preparing a site for tree planting in young pine plantations. The purpose of this paper is to provide an overview of these studies, to summarize the information they provide regarding the effects of pine management on avian...

Physical-Habitat and Geomorphic Data for Selected River Reaches in Central Arizona Basins, 1995-98

DTIC Science & Technology

2000-01-01

identification purposes only and does not constitute endorsement by the U.S. Geological Survey. Information regarding research and data-collection programs of...of measurement sites for Central Arizona Basins study area [<, less than] Site number (see fig. 1) Site name Station- identification number Latitude...measurements of instream characteristics, solar contribution to the system, and identification of riparian vegetation. The methods used to measure

The Experience of Bulimic College Students Who Use "Pro-Ana/Pro-Mia" Web Sites: A Two-Phase Mixed-Method Study

ERIC Educational Resources Information Center

Davis, Blair J.

2010-01-01

Eating disorders (EDs) are a serious problem in the U.S. due to their rise in prevalence during the 20th century and high morbidity and mortality rates. A relatively new, controversial phenomenon, "pro-Ana" (pro-anorexia) and "pro-Mia" (pro-bulimia) Web sites, came to the public's attention around 2000. These sites are created by and for people…

Identification of S-glutathionylation sites in species-specific proteins by incorporating five sequence-derived features into the general pseudo-amino acid composition.

PubMed

Zhao, Xiaowei; Ning, Qiao; Ai, Meiyue; Chai, Haiting; Yang, Guifu

2016-06-07

As a selective and reversible protein post-translational modification, S-glutathionylation generates mixed disulfides between glutathione (GSH) and cysteine residues, and plays an important role in regulating protein activity, stability, and redox regulation. To fully understand S-glutathionylation mechanisms, identification of substrates and specific S-Glutathionylated sites is crucial. Experimental identification of S-glutathionylated sites is labor-intensive and time consuming, so establishing an effective computational method is much desirable due to their convenient and fast speed. Therefore, in this study, a new bioinformatics tool named SSGlu (Species-Specific identification of Protein S-glutathionylation Sites) was developed to identify species-specific protein S-glutathionylated sites, utilizing support vector machines that combine multiple sequence-derived features with a two-step feature selection. By 5-fold cross validation, the performance of SSGlu was measured with an AUC of 0.8105 and 0.8041 for Homo sapiens and Mus musculus, respectively. Additionally, SSGlu was compared with the existing methods, and the higher MCC and AUC of SSGlu demonstrated that SSGlu was very promising to predict S-glutathionylated sites. Furthermore, a site-specific analysis showed that S-glutathionylation intimately correlated with the features derived from its surrounding sites. The conclusions derived from this study might help to understand more of the S-glutathionylation mechanism and guide the related experimental validation. For public access, SSGlu is freely accessible at http://59.73.198.144:8080/SSGlu/. Copyright © 2016 Elsevier Ltd. All rights reserved.

A combinatorial feature selection approach to describe the QSAR of dual site inhibitors of acetylcholinesterase.

PubMed

Asadabadi, Ebrahim Barzegari; Abdolmaleki, Parviz; Barkooie, Seyyed Mohsen Hosseini; Jahandideh, Samad; Rezaei, Mohammad Ali

2009-12-01

Regarding the great potential of dual binding site inhibitors of acetylcholinesterase as the future potent drugs of Alzheimer's disease, this study was devoted to extraction of the most effective structural features of these inhibitors from among a large number of quantitative descriptors. To do this, we adopted a unique approach in quantitative structure-activity relationships. An efficient feature selection method was emphasized in such an approach, using the confirmative results of different routine and novel feature selection methods. The proposed methods generated quite consistent results ensuring the effectiveness of the selected structural features.

Detecting cis-regulatory binding sites for cooperatively binding proteins

PubMed Central

van Oeffelen, Liesbeth; Cornelis, Pierre; Van Delm, Wouter; De Ridder, Fedor; De Moor, Bart; Moreau, Yves

2008-01-01

Several methods are available to predict cis-regulatory modules in DNA based on position weight matrices. However, the performance of these methods generally depends on a number of additional parameters that cannot be derived from sequences and are difficult to estimate because they have no physical meaning. As the best way to detect cis-regulatory modules is the way in which the proteins recognize them, we developed a new scoring method that utilizes the underlying physical binding model. This method requires no additional parameter to account for multiple binding sites; and the only necessary parameters to model homotypic cooperative interactions are the distances between adjacent protein binding sites in basepairs, and the corresponding cooperative binding constants. The heterotypic cooperative binding model requires one more parameter per cooperatively binding protein, which is the concentration multiplied by the partition function of this protein. In a case study on the bacterial ferric uptake regulator, we show that our scoring method for homotypic cooperatively binding proteins significantly outperforms other PWM-based methods where biophysical cooperativity is not taken into account. PMID:18400778

Cavity detection and delineation research. Part 1: Microgravimetric and magnetic surveys: Medford Cave Site, Florida

NASA Astrophysics Data System (ADS)

Butler, D. K.

1982-03-01

This report reviews the scope of a research effort initiated in 1974 at the U.S. Army Engineer Waterways Experiment Station with the objectives of (a) assessing the state of the art in geophysical cavity detection and delineation methodology and (b) developing new methods and improving or adapting old methods for application to cavity detection and delineation. Two field test sites were selected: (a) the Medford Cave site with a relatively shallow (10- to 50-ft-deep) air-filled cavity system and (b) the Manatee Springs site with a deeper (approximately 100-ft-deep) water-filled cavity system. Results of field studies at the Medford Cave site are presented in this report: (a) the site geology, (b) the site topographic survey, (c) the site drilling program (boreholes for geophysical tests, for determination of a detailed geological cross section, and for verification of geophysical anomalies), (d) details of magnetic and microgravimetric surveys, and (e) correlation of geophysical results with known site geology. Qualitative interpretation guidelines using complementary geophysical techniques for site investigations in karst regions are presented. Including the results of electrical resistivity surveys conducted at the Medford Cave site, the qualitative guidelines are applied to four profile lines, and drilling locations are indicated on the profile plots of gravity, magnetic, and electrical resistivity data. Borehole logs are then presented for comparison with the predictions of the qualitative interpretation guidelines.

Quantification of Lysine Acetylation and Succinylation Stoichiometry in Proteins Using Mass Spectrometric Data-Independent Acquisitions (SWATH)

NASA Astrophysics Data System (ADS)

Meyer, Jesse G.; D'Souza, Alexandria K.; Sorensen, Dylan J.; Rardin, Matthew J.; Wolfe, Alan J.; Gibson, Bradford W.; Schilling, Birgit

2016-11-01

Post-translational modification of lysine residues by NƐ-acylation is an important regulator of protein function. Many large-scale protein acylation studies have assessed relative changes of lysine acylation sites after antibody enrichment using mass spectrometry-based proteomics. Although relative acylation fold-changes are important, this does not reveal site occupancy, or stoichiometry, of individual modification sites, which is critical to understand functional consequences. Recently, methods for determining lysine acetylation stoichiometry have been proposed based on ratiometric analysis of endogenous levels to those introduced after quantitative per-acetylation of proteins using stable isotope-labeled acetic anhydride. However, in our hands, we find that these methods can overestimate acetylation stoichiometries because of signal interferences when endogenous levels of acylation are very low, which is especially problematic when using MS1 scans for quantification. In this study, we sought to improve the accuracy of determining acylation stoichiometry using data-independent acquisition (DIA). Specifically, we use SWATH acquisition to comprehensively collect both precursor and fragment ion intensity data. The use of fragment ions for stoichiometry quantification not only reduces interferences but also allows for determination of site-level stoichiometry from peptides with multiple lysine residues. We also demonstrate the novel extension of this method to measurements of succinylation stoichiometry using deuterium-labeled succinic anhydride. Proof of principle SWATH acquisition studies were first performed using bovine serum albumin for both acetylation and succinylation occupancy measurements, followed by the analysis of more complex samples of E. coli cell lysates. Although overall site occupancy was low (<1%), some proteins contained lysines with relatively high acetylation occupancy.

Quantifying Apparent Groundwater Ages near Managed Aquifer Recharge Operations Using Radio-Sulfur ( 35S) as an Intrinsic Tracer

DOE PAGES

Clark, Jordan; Urióstegui, Stephanie; Bibby, Richard; ...

2016-10-25

The application of the cosmogenic radioisotope sulfur-35 ( 35S) as a chronometer near spreading basins is evaluated at two well-established Managed Aquifer Recharge (MAR) sites: the Atlantis facility (South Africa) and Orange County Water District’s (OCWD’s) Kraemer Basin (Northern Orange County, CA, USA). Source water for both of these sites includes recycled wastewater. Despite lying nearer to the outlet end of their respective watersheds than to the headwaters, 35S was detected in most of the water sampled, including from wells found close to the spreading ponds and in the source water. Dilution with 35S-dead continental SO 4 was minimal, amore » surprising finding given its short ~3 month half-life. The initial work at the Atlantis MAR site demonstrated that remote laboratories could be set up and that small volume samples—saline solutions collected after the resin elution step from the recently developed batch method described below—can be stored and transported to the counting laboratory. This study also showed that the batch method needed to be altered to remove unknown compounds eluted from the resin along with SO 4. Using the improved batch method, times series measurements of both source and well water from OCWD’s MAR site showed significant temporal variations. Finally, this result indicates that during future studies, monthly to semi-monthly sampling should be conducted. Nevertheless, both of these initial studies suggest the 35S chronometer may become a valuable tool for managing MAR sites where regulations require minimum retention times.« less

Quantifying Apparent Groundwater Ages near Managed Aquifer Recharge Operations Using Radio-Sulfur ( 35S) as an Intrinsic Tracer

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

Clark, Jordan; Urióstegui, Stephanie; Bibby, Richard

The application of the cosmogenic radioisotope sulfur-35 ( 35S) as a chronometer near spreading basins is evaluated at two well-established Managed Aquifer Recharge (MAR) sites: the Atlantis facility (South Africa) and Orange County Water District’s (OCWD’s) Kraemer Basin (Northern Orange County, CA, USA). Source water for both of these sites includes recycled wastewater. Despite lying nearer to the outlet end of their respective watersheds than to the headwaters, 35S was detected in most of the water sampled, including from wells found close to the spreading ponds and in the source water. Dilution with 35S-dead continental SO 4 was minimal, amore » surprising finding given its short ~3 month half-life. The initial work at the Atlantis MAR site demonstrated that remote laboratories could be set up and that small volume samples—saline solutions collected after the resin elution step from the recently developed batch method described below—can be stored and transported to the counting laboratory. This study also showed that the batch method needed to be altered to remove unknown compounds eluted from the resin along with SO 4. Using the improved batch method, times series measurements of both source and well water from OCWD’s MAR site showed significant temporal variations. Finally, this result indicates that during future studies, monthly to semi-monthly sampling should be conducted. Nevertheless, both of these initial studies suggest the 35S chronometer may become a valuable tool for managing MAR sites where regulations require minimum retention times.« less

Planning for the closure of uncontrolled landfills in Turkey to reduce environmental impacts.

PubMed

Ergene Şentürk, Didar; Alp, Emre

2016-11-01

Landfilling is the most preferred solid waste disposal method in Turkey owing to both economic and technical reasons. However, beside the sanitary landfills there are also hundreds of uncontrolled waste sites located throughout Turkey, which are often left either abandoned or burning. Because there is a lack of legislative guidelines governing the closure and rehabilitation of these dumpsites, the municipalities that are responsible for waste management do not initiate the proactive strategies required for the closure of these sites. In this study, a method based on a multi-criteria analysis is conducted for different dumpsites in Turkey to evaluate the level of negative impacts on the environment. This method is based on the use of environmental indices for a quantitative assessment of the landfills, such as environmental interaction between the source and the receptors, environmental values of the receptors, and operational conditions. It was possible to assess the robustness of the proposed methodology since the pre- and post-groundwater quality monitoring data was available from the study sites that were closed and rehabilitated in 2014. The results of this study show that the method based on a multi-criteria analysis is an effective tool while in the preliminary planning stages of closure and rehabilitation activities of uncontrolled waste landfills. © The Author(s) 2016.

Environmental impact assessment of Gonabad municipal waste landfill site using Leopold Matrix

PubMed Central

Sajjadi, Seyed Ali; Aliakbari, Zohreh; Matlabi, Mohammad; Biglari, Hamed; Rasouli, Seyedeh Samira

2017-01-01

Introduction An environmental impact assessment (EIA) before embarking on any project is a useful tool to reduce the potential effects of each project, including landfill, if possible. The main objective of this study was to assess the environmental impact of the current municipal solid waste disposal site of Gonabad by using the Iranian Leopold matrix method. Methods This cross-sectional study was conducted to assess the environmental impacts of a landfill site in Gonabad in 2015 by an Iranian matrix (modified Leopold matrix). This study was conducted based on field visits of the landfill, and collected information from various sources and analyzing and comparing between five available options, including the continuation of the current disposal practices, construction of new sanitary landfills, recycling plans, composting, and incineration plants was examined. The best option was proposed to replace the existing landfill. Results The current approach has a score of 2.35, the construction of new sanitary landfill has a score of 1.59, a score of 1.57 for the compost plant, and recycling and incineration plant, respectively, have scores of 1.68 and 2.3. Conclusion Results showed that continuation of the current method of disposal, due to severe environmental damage and health problems, is rejected. A compost plant with the lowest negative score is the best option for the waste disposal site of Gonabad City and has priority over the other four options. PMID:28465797

Site correction of stochastic simulation in southwestern Taiwan

NASA Astrophysics Data System (ADS)

Lun Huang, Cong; Wen, Kuo Liang; Huang, Jyun Yan

2014-05-01

Peak ground acceleration (PGA) of a disastrous earthquake, is concerned both in civil engineering and seismology study. Presently, the ground motion prediction equation is widely used for PGA estimation study by engineers. However, the local site effect is another important factor participates in strong motion prediction. For example, in 1985 the Mexico City, 400km far from the epicenter, suffered massive damage due to the seismic wave amplification from the local alluvial layers. (Anderson et al., 1986) In past studies, the use of stochastic method had been done and showed well performance on the simulation of ground-motion at rock site (Beresnev and Atkinson, 1998a ; Roumelioti and Beresnev, 2003). In this study, the site correction was conducted by the empirical transfer function compared with the rock site response from stochastic point-source (Boore, 2005) and finite-fault (Boore, 2009) methods. The error between the simulated and observed Fourier spectrum and PGA are calculated. Further we compared the estimated PGA to the result calculated from ground motion prediction equation. The earthquake data used in this study is recorded by Taiwan Strong Motion Instrumentation Program (TSMIP) from 1991 to 2012; the study area is located at south-western Taiwan. The empirical transfer function was generated by calculating the spectrum ratio between alluvial site and rock site (Borcheret, 1970). Due to the lack of reference rock site station in this area, the rock site ground motion was generated through stochastic point-source model instead. Several target events were then chosen for stochastic point-source simulating to the halfspace. Then, the empirical transfer function for each station was multiplied to the simulated halfspace response. Finally, we focused on two target events: the 1999 Chi-Chi earthquake (Mw=7.6) and the 2010 Jiashian earthquake (Mw=6.4). Considering the large event may contain with complex rupture mechanism, the asperity and delay time for each sub-fault is to be concerned. Both the stochastic point-source and the finite-fault model were used to check the result of our correction.

Using pre-screening methods for an effective and reliable site characterization at megasites.

PubMed

Algreen, Mette; Kalisz, Mariusz; Stalder, Marcel; Martac, Eugeniu; Krupanek, Janusz; Trapp, Stefan; Bartke, Stephan

2015-10-01

This paper illustrates the usefulness of pre-screening methods for an effective characterization of polluted sites. We applied a sequence of site characterization methods to a former Soviet military airbase with likely fuel and benzene, toluene, ethylbenzene, and xylene (BTEX) contamination in shallow groundwater and subsoil. The methods were (i) phytoscreening with tree cores; (ii) soil gas measurements for CH4, O2, and photoionization detector (PID); (iii) direct-push with membrane interface probe (MIP) and laser-induced fluorescence (LIF) sensors; (iv) direct-push sampling; and (v) sampling from soil and from groundwater monitoring wells. Phytoscreening and soil gas measurements are rapid and inexpensive pre-screening methods. Both indicated subsurface pollution and hot spots successfully. The direct-push sensors yielded 3D information about the extension and the volume of the subsurface plume. This study also expanded the applicability of tree coring to BTEX compounds and tested the use of high-resolution direct-push sensors for light hydrocarbons. Comparison of screening results to results from conventional soil and groundwater sampling yielded in most cases high rank correlation and confirmed the findings. The large-scale application of non- or low-invasive pre-screening can be of help in directing and focusing the subsequent, more expensive investigation methods. The rapid pre-screening methods also yielded useful information about potential remediation methods. Overall, we see several benefits of a stepwise screening and site characterization scheme, which we propose in conclusion.

Missing Data and Influential Sites: Choice of Sites for Phylogenetic Analysis Can Be As Important As Taxon Sampling and Model Choice

PubMed Central

Shavit Grievink, Liat; Penny, David; Holland, Barbara R.

2013-01-01

Phylogenetic studies based on molecular sequence alignments are expected to become more accurate as the number of sites in the alignments increases. With the advent of genomic-scale data, where alignments have very large numbers of sites, bootstrap values close to 100% and posterior probabilities close to 1 are the norm, suggesting that the number of sites is now seldom a limiting factor on phylogenetic accuracy. This provokes the question, should we be fussy about the sites we choose to include in a genomic-scale phylogenetic analysis? If some sites contain missing data, ambiguous character states, or gaps, then why not just throw them away before conducting the phylogenetic analysis? Indeed, this is exactly the approach taken in many phylogenetic studies. Here, we present an example where the decision on how to treat sites with missing data is of equal importance to decisions on taxon sampling and model choice, and we introduce a graphical method for illustrating this. PMID:23471508

Water quality and habitat conditions in upper Midwest streams relative to riparian vegetation and soil characteristics, August 1997 : study design, methods, and data

USGS Publications Warehouse

Sorenson, S.K.; Porter, S.D.; Akers, K.B.; Harris, M.A.; Kalkhoff, S.J.; Lee, K.E.; Roberts, L.; Terrio, P.J.

1999-01-01

Water-chemistry, biological, and habitat data were collected from 70 sites on Midwestern streams during August 1997 as part of an integrated, regional water-quality assessment by the U.S. Geological Survey National Water-Quality Assessment (NAWQA) Program. The study area includes the Corn Belt region of southern Minnesota, eastern Iowa, and west-central Illinois, one of the most intensive and productive agricultural regions of the world. The focus of the study was to evaluate the condition of woodedriparian zones and the influence of basin soildrainage characteristics on water quality and biological-community responses. This report includes a description of the study design and site-characterization process, sample-collection and processing methods, laboratory methods, quality-assurance procedures, and summaries of data on nutrients, herbicides and metabolites, stream productivity and respiration, biological communities, habitat conditions, and agriculturalchemical and land-use information.

Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods.

PubMed

Bate, Paul; Warwicker, Jim

2004-07-02

Calculations of charge interactions complement analysis of a characterised active site, rationalising pH-dependence of activity and transition state stabilisation. Prediction of active site location through large DeltapK(a)s or electrostatic strain is relevant for structural genomics. We report a study of ionisable groups in a set of 20 enzymes, finding that false positives obscure predictive potential. In a larger set of 156 enzymes, peaks in solvent-space electrostatic properties are calculated. Both electric field and potential match well to active site location. The best correlation is found with electrostatic potential calculated from uniform charge density over enzyme volume, rather than from assignment of a standard atom-specific charge set. Studying a shell around each molecule, for 77% of enzymes the potential peak is within that 5% of the shell closest to the active site centre, and 86% within 10%. Active site identification by largest cleft, also with projection onto a shell, gives 58% of enzymes for which the centre of the largest cleft lies within 5% of the active site, and 70% within 10%. Dielectric boundary conditions emphasise clefts in the uniform charge density method, which is suited to recognition of binding pockets embedded within larger clefts. The variation of peak potential with distance from active site, and comparison between enzyme and non-enzyme sets, gives an optimal threshold distinguishing enzyme from non-enzyme. We find that 87% of the enzyme set exceeds the threshold as compared to 29% of the non-enzyme set. Enzyme/non-enzyme homologues, "structural genomics" annotated proteins and catalytic/non-catalytic RNAs are studied in this context.

Determination of slope failure using 2-D resistivity method

NASA Astrophysics Data System (ADS)

Muztaza, Nordiana Mohd; Saad, Rosli; Ismail, Nur Azwin; Bery, Andy Anderson

2017-07-01

Landslides and slope failure may give negative economic effects including the cost to repair structures, loss of property value and medical costs in the event of injury. To avoid landslide, slope failure and disturbance of the ecosystem, good and detailed planning must be done when developing hilly area. Slope failure classification and various factors contributing to the instability using 2-D resistivity survey conducted in Selangor, Malaysia are described. The study on landslide and slope failure was conducted at Site A and Site B, Selangor using 2-D resistivity method. The implications of the anticipated ground conditions as well as the field observation of the actual conditions are discussed. Nine 2-D resistivity survey lines were conducted in Site A and six 2-D resistivity survey lines with 5 m minimum electrode spacing using Pole-dipole array were performed in Site B. The data were processed using Res2Dinv and Surfer10 software to evaluate the subsurface characteristics. 2-D resistivity results from both locations show that the study areas consist of two main zones. The first zone is alluvium or highly weathered with the resistivity of 100-1000 Ωm at 20-70 m depth. This zone consists of saturated area (1-100 Ωm) and boulders with resistivity value of 1200-3000 Ωm. The second zone with resistivity values of > 3000 Ωm was interpreted as granitic bedrock. The study area was characterized by saturated zones, highly weathered zone, highly contain of sand and boulders that will trigger slope failure in the survey area. Based on the results obtained from the study findings, it can be concluded that 2-D resistivity method is useful method in determination of slope failure.

Evaluating non-equilibrium solute transport in small soil columns

NASA Astrophysics Data System (ADS)

Kamra, S. K.; Lennartz, B.; Van Genuchten, M. Th; Widmoser, P.

2001-04-01

Displacement studies on leaching of bromide and two pesticides (atrazine and isoproturon) were conducted under unsaturated steady state flow conditions in 24 small undisturbed soil columns (5.7 cm in diameter and 10 cm long) each collected from two sites differing in soil structure and organic carbon content in North Germany. There were large and irregular variabilities in the characteristics of both soils, as well as in the shapes of breakthrough curves (BTCs) of different columns, including some with early breakthrough and increased tailing, qualitatively indicating the presence of preferential flow. It was estimated that one preferential flow column (PFC) at site A, and four at site B, contributed, respectively to 11% and 58% of the accumulated leached fraction and to more than 80% of the maximum observed standard deviation (SD) in the field-scale concentration and mass flux of pesticides at two sites. The bromide BTCs of two sites were analyzed with the equilibrium convection-dispersion equation (CDE) and a non-equilibrium two-region/mobile-immobile model. Transport parameters of these models for individual BTCs were determined using a curve fitting program, CXTFIT, and by the time moment method. For the CDE based equilibrium model, the mean values of retardation factor, R, considered separately for all columns, PFCs or non-preferential flow columns (NPFCs) were comparable for the two methods; significant differences were observed in the values of dispersion coefficients of two sites using the two estimation methods. It was inferred from the estimated parameters of non-equilibrium model that 5-12% of water at site A, and 12% at site B, was immobile during displacement in NPFCs. The corresponding values for PFCs of two sites were much larger, ranging from 25% to 51% by CXTFIT and from 24% to 72% by the moment method, suggesting the role of certain mechanisms other than immobile water in higher degrees of non-equilibrium in these columns. Peclet numbers in PFCs of both sites were consistently smaller than five, indicating the inadequacy of the non-equilibrium model to incorporate the effect of all forms of non-equilibrium in PFCs. Overall, the BTCs of individual NPFCs, PFCs and of field average concentration at the two sites were better reproduced with parameters obtained from CXTFIT than by the moment method. The moment method failed to capture the peak concentrations in PFCs, but tended to describe the desorption and tail branches of BTCs better than the curve fitting approach.

Prospective analysis of the quality of Spanish health information web sites after 3 years.

PubMed

Conesa-Fuentes, Maria C; Hernandez-Morante, Juan J

2016-12-01

Although the Internet has become an essential source of health information, our study conducted 3 years ago provided evidence of the low quality of Spanish health web sites. The objective of the present study was to evaluate the quality of Spanish health information web sites now, and to compare these results with those obtained 3 years ago. For the original study, the most visited health information web sites were selected through the PageRank® (Google®) system. The present study evaluated the quality of the same web sites from February to May 2013, using the method developed by Bermúdez-Tamayo et al. and HONCode® criteria. The mean quality of the selected web sites was low and has deteriorated since the previous evaluation, especially in regional health services and institutions' web sites. The quality of private web sites remained broadly similar. Compliance with privacy and update criteria also improved in the intervening period. The results indicate that, even in the case of health web sites, design or appearance is more relevant to developers than quality of information. It is recommended that responsible institutions should increase their efforts to eliminate low-quality health information that may further contribute to health problems.

ALTERNATIVE REMEDIATION TECHNOLOGY STUDY FOR GROUNDWATER TREATMENT AT 200-PO-1 OPERABLE UNIT AT HANFORD SITE

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

DADO MA

2008-07-31

This study focuses on the remediation methods and technologies applicable for use at 200-PO-I Groundwater Operable Unit (OU) at the Hanford Site. The 200-PO-I Groundwater au requires groundwater remediation because of the existence of contaminants of potential concern (COPC). A screening was conducted on alternative technologies and methods of remediation to determine which show the most potential for remediation of groundwater contaminants. The possible technologies were screened to determine which would be suggested for further study and which were not applicable for groundwater remediation. COPCs determined by the Hanford Site groundwater monitoring were grouped into categories based on properties linkingmore » them by remediation methods applicable to each COPC group. The screening considered the following criteria. (1) Determine if the suggested method or technology can be used for the specific contaminants found in groundwater and if the technology can be applied at the 200-PO-I Groundwater au, based on physical characteristics such as geology and depth to groundwater. (2) Evaluate screened technologies based on testing and development stages, effectiveness, implementability, cost, and time. This report documents the results of an intern research project conducted by Mathew Dado for Central Plateau Remediation in the Soil and Groundwater Remediation Project. The study was conducted under the technical supervision of Gloria Cummins and management supervision of Theresa Bergman and Becky Austin.« less

MULTI-SITE PERFORMANCE EVALUATIONS OF CANDIDATE METHODOLOGIES FOR DETERMINING COARSE PARTICULATE MATTER (PMC) CONCENTRATIONS

EPA Science Inventory

Comprehensive field studies were conducted to evaluate the performance of sampling methods for measuring the coarse fraction of PM10 in ambient air. Five separate sampling approaches were evaluated at each of three sampling sites. As the primary basis of comparison, a discret...

MULTI-SITE EVALUATIONS OF CANDIDATE METHODOLOGIES FOR DETERMINING COARSE PARTICULATE MATTER (PMC) CONCENTRATIONS

EPA Science Inventory

Comprehensive field studies were conducted to evaluate the performance of sampling methods for measuring the coarse fraction of PM10 in ambient air. Five separate sampling approaches were evaluated at each of three sampling sites. As the primary basis of comparison, a discret...

MULTI-SITE EVALUATIONS OF CANDIDATE METHODOLOGIES FOR DETERMINING COARSE PARTICULATE MATTER (PMC) CONCENTRATIONS

EPA Science Inventory

Comprehensive field studies were conducted to evaluate the performance of sampling methods for measuring the coarse fraction of PM10 in ambient air. Five separate sampling approaches were evaluated at each of three sampling sites. As the primary basis of comparison, a discrete ...

MusiteDeep: a deep-learning framework for general and kinase-specific phosphorylation site prediction.

PubMed

Wang, Duolin; Zeng, Shuai; Xu, Chunhui; Qiu, Wangren; Liang, Yanchun; Joshi, Trupti; Xu, Dong

2017-12-15

Computational methods for phosphorylation site prediction play important roles in protein function studies and experimental design. Most existing methods are based on feature extraction, which may result in incomplete or biased features. Deep learning as the cutting-edge machine learning method has the ability to automatically discover complex representations of phosphorylation patterns from the raw sequences, and hence it provides a powerful tool for improvement of phosphorylation site prediction. We present MusiteDeep, the first deep-learning framework for predicting general and kinase-specific phosphorylation sites. MusiteDeep takes raw sequence data as input and uses convolutional neural networks with a novel two-dimensional attention mechanism. It achieves over a 50% relative improvement in the area under the precision-recall curve in general phosphorylation site prediction and obtains competitive results in kinase-specific prediction compared to other well-known tools on the benchmark data. MusiteDeep is provided as an open-source tool available at https://github.com/duolinwang/MusiteDeep. xudong@missouri.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Integrated use of surface geophysical methods for site characterization — A case study in North Kingstown, Rhode Island

USGS Publications Warehouse

Johnson, Carole D.; Lane, John W.; Brandon, William C.; Williams, Christine A.P.; White, Eric A.

2010-01-01

A suite of complementary, non‐invasive surface geophysical methods was used to assess their utility for site characterization in a pilot investigation at a former defense site in North Kingstown, Rhode Island. The methods included frequency‐domain electromagnetics (FDEM), ground‐penetrating radar (GPR), electrical resistivity tomography (ERT), and multi‐channel analysis of surface‐wave (MASW) seismic. The results of each method were compared to each other and to drive‐point data from the site. FDEM was used as a reconnaissance method to assess buried utilities and anthropogenic structures; to identify near‐surface changes in water chemistry related to conductive leachate from road‐salt storage; and to investigate a resistive signature possibly caused by groundwater discharge. Shallow anomalies observed in the GPR and ERT data were caused by near‐surface infrastructure and were consistent with anomalies observed in the FDEM data. Several parabolic reflectors were observed in the upper part of the GPR profiles, and a fairly continuous reflector that was interpreted as bedrock could be traced across the lower part of the profiles. MASW seismic data showed a sharp break in shear wave velocity at depth, which was interpreted as the overburden/bedrock interface. The MASW profile indicates the presence of a trough in the bedrock surface in the same location where the ERT data indicate lateral variations in resistivity. Depths to bedrock interpreted from the ERT, MASW, and GPR profiles were similar and consistent with the depths of refusal identified in the direct‐push wells. The interpretations of data collected using the individual methods yielded non‐unique solutions with considerable uncertainty. Integrated interpretation of the electrical, electromagnetic, and seismic geophysical profiles produced a more consistent and unique estimation of depth to bedrock that is consistent with ground‐truth data at the site. This test case shows that using complementary techniques that measure different properties can be more effective for site characterization than a single‐method investigation.

Analysis of four recruitment methods for obtaining normative data through a Web-based questionnaire: a pilot study.

PubMed

Nolte, Michael T; Shauver, Melissa J; Chung, Kevin C

2015-09-01

Quality normative data requires a diverse sample of participants and plays an important role in the appropriate use of health outcomes. Using social media and other online resources for survey recruitment is a tempting prospect, but the effectiveness of these methods in collecting a diverse sample is unknown. The purpose of this study is to pilot test four methods of recruitment to determine their ability to produce a sample representative of the general US population. This project is part of a larger study to gather normative data for the Michigan Hand Outcomes Questionnaire (MHQ). We used flyers, e-mail, Facebook, and an institution-specific clinical research recruitment Web site to direct participants to complete an online version of the MHQ. Participants also provided comorbidity and demographic information. The institution-specific recruitment Web site yielded the greatest number of respondents in an age distribution that mirrored the US population. Facebook was effective for recruiting young adults, and e-mail was successful for recruiting the older adults. None of the methods was successful in reaching an ethnically diverse sample. Obtaining normative data that is truly representative of the US population is a difficult task. The use of any one recruitment method is unlikely to result in a representative sample, but a greater understanding of these methods will empower researchers to use them to target specific populations. This pilot analysis provides support for the use of Facebook and clinical research sites in addition to traditional methods of e-mail and paper flyers.

Improving safety climate through a communication and recognition program for construction: a mixed-methods study

PubMed Central

Sparer, Emily H; Catalano, Paul J; Herrick, Robert F; Dennerlein, Jack T

2016-01-01

Objectives This study aimed to evaluate the efficacy of a safety communication and recognition program (B-SAFE), designed to encourage improvement of physical working conditions and hazard reduction in construction. Methods A matched pair cluster randomized controlled trial was conducted on eight worksites (four received the B-SAFE intervention, four served as control sites) for approximately five months per site. Pre- and post-exposure worker surveys were collected at all sites (N=615, pre-exposure response rate of 74%, post-exposure response rate of 88%). Multi-level mixed-effect regression models evaluated the effect of B-SAFE on safety climate as assessed from surveys. Focus groups (N=6–8 workers/site) were conducted following data collection. Transcripts were coded and analyzed for thematic content using Atlas.ti (version 6). Results The mean safety climate score at intervention sites, as measured on a 0–50 point scale, increased 0.5 points (1%) between pre- and post-B-SAFE exposure, compared to control sites that decreased 0.8 points (1.6%). The intervention effect size was 1.64 (3.28%) (P-value=0.01) when adjusted for month the worker started on-site, total length of time on-site, as well as individual characteristics (trade, title, age, and race/ethnicity). At intervention sites, workers noted increased levels of safety awareness, communication, and teamwork compared to control sites. Conclusions B-SAFE led to many positive changes, including an improvement in safety climate, awareness, teambuilding, and communication. B-SAFE was a simple intervention that engaged workers through effective communication infrastructures and had a significant, positive effect on worksite safety. PMID:27158914

Comparison of Bowen-ratio, eddy-correlation, and weighing-lysimeter evapotranspiration for two sparse-canopy sites in eastern Washington

USGS Publications Warehouse

Tomlinson, S.A.

1996-01-01

This report compares evapotranspiration estimated with the Bowen-ratio and eddy-correlation methods with evapotranspiration measured by weighing lysimeters for two sparse-canopy sites in eastern Washington. The sites are located in a grassland area (grass lysimeter site) and a sagbrush- covered area (sage lysimeter site) on the Arid Lands Ecology Reserve in Benton County, Washington. Lysimeter data were collected at the sites from August 1990 to November 1994. Bowen-ratio data were collected for varying periods from May 1993 to November 1994. Additional Bowen-ratio data without interchanging air- temperature and vapor-pressure sensors to remove sensor bias (fixed-sensor system) were collected from October 1993 to June 1994. Eddy-correlation data were collected at the grass lysimeter site from March to April 1994, and at the sage lysimeter site from April to May 1994. The comparisons of evapotranspiration determined by the various methods differed considerably, depending on the periods of record being compared and the sites being analyzed. The year 1993 was very wet, with about 50 percent more precipitation than average; 1994 was a very dry year, with only about half the average precipitation. The study showed that on an annual basis, at least in 1994, Bowen-ratio evapotranspiration closely matched lysimeter evapotranspiration. In 1993, Bowen-ratio and lysimeter evapotranspiration comparisons were variable. Evapotranspiration estimated with the Bowen-ratio method averaged 5 percent more than evapotranspiration measured by lysimeters at the grass lysimeter site from October 1993 to November 1994, and 3 percent less than lysimeters at the sage lysimeter site from November 1993 to October 1994. From March 24 to April 5, 1994, at the grass lysimeter site, the Bowen-ratio method estimated 11 percent less, the Bowen-ratio method utilizing the fixed sensor system about 7 percent more, and the eddy-correlation method about 28 percent less evapotranspiration than the lysimeters measured. From May 7 to June 18, 1993, however, the Bowen-ratio method estimated only 54 percent of the evapotranspiration measured by lysimeters at the grass lysimeter site. This large difference possibly may be attributed to Bowen-ratio instrument variability or error, to the density of grasses in the lysimeters being greater than in the surrounding area, or to heating effects on the lysimeters. From September 1 to October 31, 1993, the Bowen-ratio method estimated more than 450 percent more evapotranspiration than was measured by lysimeters at the sage lysimeter site. This difference may have been due to conditions in the lysimeters at the sage lysimeter site that were unrepresentative of natural conditions. The Bowen-ratio instruments measured evapotrans- piration over sagebrush plants outside the lysimeters, which were blooming very heavily, possibly using supplemental ground water or spring water from nearby upslope areas. The sagebrush plants contained by the lysimeters showed very little evapotranspiration, possibly because they were root-bound and had already used all available water. Also, plants in the lysimeters would not have been able to access any supplemental water available to plants outside the confines of the lysimeters. Earlier in 1993, from June 17 to July 12, the Bowen-ratio method estimated only 1 percent less evapotranspiration than determined for the lysimeters at the sage lysimeter site. On the basis of lysimeter measurements from August 1990 to November 1994, cumulative evapotrans- piration ranged from about 97 to 103 percent of the annual precipitation each year. The evapotranspiration measurements made at the grass and sage lysimeter sites, which were based on weight changes in the lysimeters, showed that storage changes became nearly zero each year some time between August and November as average surface soil moisture decreased to about 2 percent and evapotranspiration rates decreased to less than 0.1 millimeter per day.

Repeat 24-hour recalls and locally developed food composition databases: a feasible method to estimate dietary adequacy in a multi-site preconception maternal nutrition RCT

PubMed Central

Lander, Rebecca L.; Hambidge, K. Michael; Krebs, Nancy F.; Westcott, Jamie E.; Garces, Ana; Figueroa, Lester; Tejeda, Gabriela; Lokangaka, Adrien; Diba, Tshilenge S.; Somannavar, Manjunath S.; Honnayya, Ranjitha; Ali, Sumera A.; Khan, Umber S.; McClure, Elizabeth M.; Thorsten, Vanessa R.; Stolka, Kristen B.

2017-01-01

ABSTRACT Background: Our aim was to utilize a feasible quantitative methodology to estimate the dietary adequacy of >900 first-trimester pregnant women in poor rural areas of the Democratic Republic of the Congo, Guatemala, India and Pakistan. This paper outlines the dietary methods used. Methods: Local nutritionists were trained at the sites by the lead study nutritionist and received ongoing mentoring throughout the study. Training topics focused on the standardized conduct of repeat multiple-pass 24-hr dietary recalls, including interview techniques, estimation of portion sizes, and construction of a unique site-specific food composition database (FCDB). Each FCDB was based on 13 food groups and included values for moisture, energy, 20 nutrients (i.e. macro- and micronutrients), and phytate (an anti-nutrient). Nutrient values for individual foods or beverages were taken from recently developed FAO-supported regional food composition tables or the USDA national nutrient database. Appropriate adjustments for differences in moisture and application of nutrient retention and yield factors after cooking were applied, as needed. Generic recipes for mixed dishes consumed by the study population were compiled at each site, followed by calculation of a median recipe per 100 g. Each recipe’s nutrient values were included in the FCDB. Final site FCDB checks were planned according to FAO/INFOODS guidelines. Discussion: This dietary strategy provides the opportunity to assess estimated mean group usual energy and nutrient intakes and estimated prevalence of the population ‘at risk’ of inadequate intakes in first-trimester pregnant women living in four low- and middle-income countries. While challenges and limitations exist, this methodology demonstrates the practical application of a quantitative dietary strategy for a large international multi-site nutrition trial, providing within- and between-site comparisons. Moreover, it provides an excellent opportunity for local capacity building and each site FCDB can be easily modified for additional research activities conducted in other populations living in the same area. PMID:28469549

Assessing technical performance at diverse ambulatory care sites.

PubMed

Osterweis, M; Bryant, E

1978-01-01

The purpose of the large study reported here was to develop and test methods for assessing the quality of health care that would be broadly applicable to diverse ambulatory care organizations for periodic comparative review. Methodological features included the use of an age-sex stratified random sampling scheme, dependence on medical records as the source of data, a fixed study period year, use of Kessner's tracer methodology (including not only acute and chronic diseases but also screening and immunization rates as indicators), and a fixed tracer matrix at all test sites. This combination of methods proved more efficacious in estimating certain parameters for the total patient populations at each site (including utilization patterns, screening, and immunization rates) and the process of care for acute conditions than it did in examining the process of care for the selected chronic condition. It was found that the actual process of care at all three sites for the three acute conditions (streptococcal pharyngitis, urinary tract infection, and iron deficiency anemia) often differed from the expected process in terms of both diagnostic procedures and treatment. For hypertension, the chronic disease tracer, medical records were frequently a deficient data source from which to draw conclusions about the adequacy of treatment. Several aspects of the study methodology were found to be detrimental to between-site comparisons of the process of care for chronic disease management. The use of an age-sex stratified random sampling scheme resulted in the identification of too few cases of hypertension at some sites for analytic purposes, thereby necessitating supplementary sampling by diagnosis. The use of a fixed study period year resulted in an arbitrary starting point in the course of the disease. Furthermore, in light of the diverse sociodemographic characteristics of the patient populations, the use of a fixed matrix of tracer conditions for all test sites is questionable. The discussion centers on these and other problems encountered in attempting to compare technical performance within diverse ambulatory care organizations and provides some guidelines as to the utility of alternative methods for assessing the quality of health care.

Patterns of macromycete community assemblage along an elevation gradient: options for fungal gradient and metacommunity analyse

Treesearch

Marko Gómez-Hernández; Guadalupe Williams-Linera; Roger Guevara; D. Jean Lodge

2012-01-01

Gradient analysis is rarely used in studies of fungal communities. Data on macromycetes from eight sites along an elevation gradient in central Veracruz, Mexico, were used to demonstrate methods for gradient analysis that can be applied to studies of communities of fungi. Selected sites from 100 to 3,500 m altitude represent tropical dry forest, tropical montane cloud...

Method of draining water through a solid waste site without leaching

DOEpatents

Treat, Russell L.; Gee, Glendon W.; Whyatt, Greg A.

1993-01-01

The present invention is a method of preventing water from leaching solid waste sites by preventing atmospheric precipitation from contacting waste as the water flows through a solid waste site. The method comprises placing at least one drain hole through the solid waste site. The drain hole is seated to prevent waste material from entering the drain hole, and the solid waste site cover material is layered and graded to direct water to flow toward the drain hole and to soil beneath the waste site.

Method of draining water through a solid waste site without leaching

DOEpatents

Treat, R.L.; Gee, G.W.; Whyatt, G.A.

1993-02-02

The present invention is a method of preventing water from leaching solid waste sites by preventing atmospheric precipitation from contacting waste as the water flows through a solid waste site. The method comprises placing at least one drain hole through the solid waste site. The drain hole is seated to prevent waste material from entering the drain hole, and the solid waste site cover material is layered and graded to direct water to flow toward the drain hole and to soil beneath the waste site.

UNDERSTANDING AND APPLYING ENVIRONMENTAL RELATIVE MOLDINESS INDEX - ERMI

EPA Science Inventory

This study compared two binary classification methods to evaluate the mold condition in 271 homes of infants, 144 of which later developed symptoms of respiratory illness. A method using on-site visual mold inspection was compared to another method using a quantitative index of ...

Methodological comparison of alpine meadow evapotranspiration on the Tibetan Plateau, China.

PubMed

Chang, Yaping; Wang, Jie; Qin, Dahe; Ding, Yongjian; Zhao, Qiudong; Liu, Fengjing; Zhang, Shiqiang

2017-01-01

Estimation of evapotranspiration (ET) for alpine meadow areas in the Tibetan Plateau (TP) is essential for water resource management. However, observation data has been limited due to the extreme climates and complex terrain of this region. To address these issues, four representative methods, Penman-Monteith (PM), Priestley-Taylor (PT), Hargreaves-Samani (HS), and Mahringer (MG) methods, were adopted to estimate ET, which were then compared with ET measured using Eddy Covariance (EC) for five alpine meadow sites during the growing seasons from 2010 to 2014. And each site was measured for one growing season during this period. The results demonstrate that the PT method outperformed at all sites with a coefficient of determination (R2) ranging from 0.76 to 0.94 and root mean square error (RMSE) ranging from 0.41 to 0.62 mm d-1. The PM method showed better performance than HS and MG methods, and the HS method produced relatively acceptable results with higher R2 (0.46) and lower RMSE (0.89 mm d-1) compared to MG method with R2 of 0.16 and RMSE of 1.62 mm d-1, while MG underestimated ET at all alpine meadow sites. Therefore, the PT method, being the simpler approach and less data dependent, is recommended to estimate ET for alpine meadow areas in the Tibetan Plateau. The PM method produced reliable results when available data were sufficient, and the HS method proved to be a complementary method when variables were insufficient. On the contrary, the MG method always underestimated ET and is, thus, not suitable for alpine meadows. These results provide a basis for estimating ET on the Tibetan Plateau for annual data collection, analysis, and future studies.

Methodological comparison of alpine meadow evapotranspiration on the Tibetan Plateau, China

PubMed Central

Chang, Yaping; Wang, Jie; Qin, Dahe; Ding, Yongjian; Zhao, Qiudong; Liu, Fengjing

2017-01-01

Estimation of evapotranspiration (ET) for alpine meadow areas in the Tibetan Plateau (TP) is essential for water resource management. However, observation data has been limited due to the extreme climates and complex terrain of this region. To address these issues, four representative methods, Penman-Monteith (PM), Priestley-Taylor (PT), Hargreaves-Samani (HS), and Mahringer (MG) methods, were adopted to estimate ET, which were then compared with ET measured using Eddy Covariance (EC) for five alpine meadow sites during the growing seasons from 2010 to 2014. And each site was measured for one growing season during this period. The results demonstrate that the PT method outperformed at all sites with a coefficient of determination (R2) ranging from 0.76 to 0.94 and root mean square error (RMSE) ranging from 0.41 to 0.62 mm d-1. The PM method showed better performance than HS and MG methods, and the HS method produced relatively acceptable results with higher R2 (0.46) and lower RMSE (0.89 mm d-1) compared to MG method with R2 of 0.16 and RMSE of 1.62 mm d-1, while MG underestimated ET at all alpine meadow sites. Therefore, the PT method, being the simpler approach and less data dependent, is recommended to estimate ET for alpine meadow areas in the Tibetan Plateau. The PM method produced reliable results when available data were sufficient, and the HS method proved to be a complementary method when variables were insufficient. On the contrary, the MG method always underestimated ET and is, thus, not suitable for alpine meadows. These results provide a basis for estimating ET on the Tibetan Plateau for annual data collection, analysis, and future studies. PMID:29236754

Formulation and evaluation of controlled release antibiotic biodegradable implants for post operative site delivery.

PubMed

Mathur, Vijay; Mudnaik, Rajesh; Barde, Laxmikant; Roy, Arghya; Shivhare, Umesh; Bhusari, Kishore

2010-03-01

Biodegradable implants of ciprofloxacin hydrochloride for post operative site delivery were prepared using glyceryl monostearate and different concentrations of polyethylene glycol (PEG 6000), glycerol and Tween 80 as erosion enhancers by compression and molding technique. Formulations were subjected to in vitro drug release by the USP dissolution method, while promising formulations were subjected to in vitro drug release by the agar gel method and also to stability studies. It was observed that glyceryl monostearate formed hydrophobic matrix and delayed the drug delivery. Antibiotic release profile was controlled by using different combinations of erosion enhancers. The formulation prepared by the compression method showed more delayed release compared to formulations prepared by the molding method.

Time-of-travel data for Nebraska streams, 1968 to 1977

USGS Publications Warehouse

Petri, L.R.

1984-01-01

This report documents the results of 10 time-of-travel studies, using ' dye-tracer ' methods, conducted on five streams in Nebraska during the period 1968 to 1977. Streams involved in the studies were the North Platte, North Loup, Elkhorn, and Big Blue Rivers and Salt Creek. Rhodamine WT dye in a 20 percent solution was used as the tracer for all 10 time-of-travel studies. Water samples were collected at several points below each injection site. Concentrations of dye in the samples were measured by determining fluorescence of the sample and comparing that value to fluorescence-concentration curves. Stream discharges were measured before and during each study. Results of each time-by-travel study are shown on two tables and on graph. The first table shows water discharge at injection and sampling sites, distance between sites, and time and rate of travel of the dye between sites. The second table provides descriptions of study sites, amounts of dye injected in the streams, actual sampling times, and actual concentrations of dye detected. The graphs for each time-of-travel study provide indications of changing travel rates between sampling sites, information on length of dye clouds, and times for dye passage past given points. (USGS)

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

Liu, Xianglin; Wang, Yang; Eisenbach, Markus

One major purpose of studying the single-site scattering problem is to obtain the scattering matrices and differential equation solutions indispensable to multiple scattering theory (MST) calculations. On the other hand, the single-site scattering itself is also appealing because it reveals the physical environment experienced by electrons around the scattering center. In this study, we demonstrate a new formalism to calculate the relativistic full-potential single-site Green's function. We implement this method to calculate the single-site density of states and electron charge densities. Lastly, the code is rigorously tested and with the help of Krein's theorem, the relativistic effects and full potentialmore » effects in group V elements and noble metals are thoroughly investigated.« less

Healing at the interface between recipient sites and autologous block bone grafts affixed by either position or lag screw methods: a histomorphometric study in rabbits.

PubMed

Caneva, Marco; Botticelli, Daniele; Carneiro Martins, Evandro Neto; Caneva, Martina; Lang, Niklaus P; Xavier, Samuel P

2017-12-01

To compare the sequential healing at the interface gap occurring between autologous bone grafts and recipient sites using two types of fixation techniques. Twenty-four adult male New Zealand white rabbits were used. Two bone grafts were collected from the calvaria and secured to the lateral aspect of the angle of mandible in each animal. Cortical perforations at the recipient sites were performed. However, no modifications were applied to the graft for its adaptation to the recipient site. Two types of fixation techniques by position or lag screws were applied. This was done by preparing osteotomy holes smaller or larger than the screw diameter, respectively. The animals were sacrificed after 3, 7, 20, and 40 days. After 3 days, the distance between the graft and the recipient site was similar between the two different fixations. Due to the anatomical shapes of the recipient sites and grafts, the distance between the two parts was lower in the central region (<0.1 mm) compared to the external regions of the graft (0.5-0.6 mm). The first evidence of small amounts of new (woven) bone was seen after 7 days, forming from the parent bone. The percentage increased after 20 and 40 days. After 40 days, the grafts were well incorporated within the recipient sites in both groups without any statistically significant difference. The present study did not show superiority of one method over another. A fixation to a recipient site with perforations may be sufficient for incorporating an autologous bone graft even if its adaptation is not perfect and irrespectively of the fixation method. Distances of approximately half millimeter were bridged with newly formed bone. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Optimal river monitoring network using optimal partition analysis: a case study of Hun River, Northeast China.

PubMed

Wang, Hui; Liu, Chunyue; Rong, Luge; Wang, Xiaoxu; Sun, Lina; Luo, Qing; Wu, Hao

2018-01-09

River monitoring networks play an important role in water environmental management and assessment, and it is critical to develop an appropriate method to optimize the monitoring network. In this study, an effective method was proposed based on the attainment rate of National Grade III water quality, optimal partition analysis and Euclidean distance, and Hun River was taken as a method validation case. There were 7 sampling sites in the monitoring network of the Hun River, and 17 monitoring items were analyzed once a month during January 2009 to December 2010. The results showed that the main monitoring items in the surface water of Hun River were ammonia nitrogen (NH 4 + -N), chemical oxygen demand, and biochemical oxygen demand. After optimization, the required number of monitoring sites was reduced from seven to three, and 57% of the cost was saved. In addition, there were no significant differences between non-optimized and optimized monitoring networks, and the optimized monitoring networks could correctly represent the original monitoring network. The duplicate setting degree of monitoring sites decreased after optimization, and the rationality of the monitoring network was improved. Therefore, the optimal method was identified as feasible, efficient, and economic.

An improved cost-effective, reproducible method for evaluation of bone loss in a rodent model.

PubMed

Fine, Daniel H; Schreiner, Helen; Nasri-Heir, Cibele; Greenberg, Barbara; Jiang, Shuying; Markowitz, Kenneth; Furgang, David

2009-02-01

This study was designed to investigate the utility of two "new" definitions for assessment of bone loss in a rodent model of periodontitis. Eighteen rats were divided into three groups. Group 1 was infected by Aggregatibacter actinomycetemcomitans (Aa), group 2 was infected with an Aa leukotoxin knock-out, and group 3 received no Aa (controls). Microbial sampling and antibody titres were determined. Initially, two examiners measured the distance from the cemento-enamel-junction to alveolar bone crest using the three following methods; (1) total area of bone loss by radiograph, (2) linear bone loss by radiograph, (3) a direct visual measurement (DVM) of horizontal bone loss. Two "new" definitions were adopted; (1) any site in infected animals showing bone loss >2 standard deviations above the mean seen at that site in control animals was recorded as bone loss, (2) any animal with two or more sites in any quadrant affected by bone loss was considered as diseased. Using the "new" definitions both evaluators independently found that infected animals had significantly more disease than controls (DVM system; p<0.05). The DVM method provides a simple, cost effective, and reproducible method for studying periodontal disease in rodents.

AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis.

PubMed

Greener, Joe G; Sternberg, Michael J E

2015-10-23

Despite being hugely important in biological processes, allostery is poorly understood and no universal mechanism has been discovered. Allosteric drugs are a largely unexplored prospect with many potential advantages over orthosteric drugs. Computational methods to predict allosteric sites on proteins are needed to aid the discovery of allosteric drugs, as well as to advance our fundamental understanding of allostery. AlloPred, a novel method to predict allosteric pockets on proteins, was developed. AlloPred uses perturbation of normal modes alongside pocket descriptors in a machine learning approach that ranks the pockets on a protein. AlloPred ranked an allosteric pocket top for 23 out of 40 known allosteric proteins, showing comparable and complementary performance to two existing methods. In 28 of 40 cases an allosteric pocket was ranked first or second. The AlloPred web server, freely available at http://www.sbg.bio.ic.ac.uk/allopred/home, allows visualisation and analysis of predictions. The source code and dataset information are also available from this site. Perturbation of normal modes can enhance our ability to predict allosteric sites on proteins. Computational methods such as AlloPred assist drug discovery efforts by suggesting sites on proteins for further experimental study.

Candidate muon-probe sites in oxide superconductors

NASA Astrophysics Data System (ADS)

Dawson, W. K.; Tibbs, K.; Weathersby, S. P.; Boekema, C.; Chan, K.-C. B.

1988-11-01

Two independent search methods (potential-energy and magnetic-dipole-field calculations) are used to determine muon stop sites in the RBa2Cu3O(x) (x equal to about 7) superconductors. Possible sites, located about 1 A away from oxygen ions, have been found and are prime candidates as muon-probe locations. The results are discussed in light of existing muon-spin-relaxation data of these exciting oxides, and are compared to H-oxide and positron-oxide superconductor studies. Further work is in progress to establish in detail the muon-probe sites.

Performance and Specificity of the Covalently Linked Immunomagnetic Separation-ATP Method for Rapid Detection and Enumeration of Enterococci in Coastal Environments

PubMed Central

Zimmer-Faust, Amity G.; Thulsiraj, Vanessa; Ferguson, Donna

2014-01-01

The performance and specificity of the covalently linked immunomagnetic separation-ATP (Cov-IMS/ATP) method for the detection and enumeration of enterococci was evaluated in recreational waters. Cov-IMS/ATP performance was compared with standard methods: defined substrate technology (Enterolert; IDEXX Laboratories), membrane filtration (EPA Method 1600), and an Enterococcus-specific quantitative PCR (qPCR) assay (EPA Method A). We extend previous studies by (i) analyzing the stability of the relationship between the Cov-IMS/ATP method and culture-based methods at different field sites, (ii) evaluating specificity of the assay for seven ATCC Enterococcus species, (iii) identifying cross-reacting organisms binding the antibody-bead complexes with 16S rRNA gene sequencing and evaluating specificity of the assay to five nonenterococcus species, and (iv) conducting preliminary tests of preabsorption as a means of improving the assay. Cov-IMS/ATP was found to perform consistently and with strong agreement rates (based on exceedance/compliance with regulatory limits) of between 83% and 100% compared to the culture-based Enterolert method at a variety of sites with complex inputs. The Cov-IMS/ATP method is specific to five of seven different Enterococcus spp. tested. However, there is potential for nontarget bacteria to bind the antibody, which may be reduced by purification of the IgG serum with preabsorption at problematic sites. The findings of this study help to validate the Cov-IMS/ATP method, suggesting a predictable relationship between the Cov-IMS/ATP method and traditional culture-based methods, which will allow for more widespread application of this rapid and field-portable method for coastal water quality assessment. PMID:24561583

Orthodontic extrusion for pre-implant site enhancement: Principles and clinical guidelines.

PubMed

Alsahhaf, Abdulaziz; Att, Wael

2016-07-01

The aim of this paper is to provide a concise overview about the principles of pre-implant orthodontic extrusion, describe methods and techniques available and provide the clinicians with guidelines about its application. A number of reports describe orthodontic extrusion as a reliable method for pre-implant site enhancement. However, no standard protocols have been provided about the application of this technique. The literature database was searched for studies involving implant site enhancement by means of orthodontic extrusion. Information about the principles, indications and contraindications of this method, type of anchorage, force and time were obtained from the literature. Despite that the scarce data is largely limited to case reports and case series, implant site enhancement by means of orthodontic extrusion seems to be a promising option to improve soft and hard tissue conditions prior to implant placement. Orthodontic extrusion is being implemented as a treatment alternative to enhance hard and soft tissue prior to implant placement. While the current literature does not provide clear guidelines, the decision making for a specific approach seems to be based on the clinician's preferences. Clinical studies are needed to verify the validity of this treatment option. Copyright © 2016 Japan Prosthodontic Society. Published by Elsevier Ltd. All rights reserved.

Recruitment and accrual of women in a placebo-controlled clinical pilot study on manual therapy.

PubMed

Cambron, Jerrilyn A; Hawk, Cheryl; Evans, Roni; Long, Cynthia R

2004-06-01

To investigate the accrual rates and recruitment processes among 3 Midwestern sites during a pilot study on manual therapy for chronic pelvic pain. Multisite pilot study for a randomized, placebo-controlled clinical trial. Three chiropractic institutions in or near major metropolitan cities in the Midwestern United States. Thirty-nine women aged 18 to 45 with chronic pelvic pain of at least 6 months duration, diagnosed by a board certified gynecologist. The method of recruitment was collected for each individual who responded to an advertisement and completed an interviewer-administered telephone screen. Participants who were willing and eligible after 3 baseline visits were entered into a randomized clinical trial. The number of responses and accrual rates were determined for the overall study, each of the 3 treatment sites, and each of the 5 recruitment efforts. In this study, 355 women were screened over the telephone and 39 were randomized, making the rate of randomization approximately 10%. The most effective recruitment methods leading to randomization were direct mail (38%) and radio advertisements (34%). However, success of the recruitment process differed by site. Based on the accrual of this multisite pilot study, a full-scale trial would not be feasible using this study's parameters. However, useful information was gained on recruitment effectiveness, eligibility criteria, and screening protocols among the 3 metropolitan sites.

Region of interest methylation analysis: a comparison of MSP with MS-HRM and direct BSP.

PubMed

Akika, Reem; Awada, Zainab; Mogharbil, Nahed; Zgheib, Nathalie K

2017-07-01

The aim of this study was to compare and contrast three DNA methylation methods of a specific region of interest (ROI): methylation-specific PCR (MSP), methylation-sensitive high resolution melting (MS-HRM) and direct bisulfite sequencing (BSP). The methylation of a CpG area in the promoter region of Estrogen receptor alpha (ESR1) was evaluated by these three methods with samples and standards of different methylation percentages. MSP data were neither reproducible nor sensitive, and the assay was not specific due to non-specific binding of primers. MS-HRM was highly reproducible and a step forward into categorizing the methylation status of the samples as percent ranges. Direct BSP was the most informative method regarding methylation percentage of each CpG site. Though not perfect, it was reproducible and sensitive. We recommend the use of either method depending on the research question and target amplicon, and provided that the designed primers and expected amplicons are within recommendations. If the research question targets a limited number of CpG sites and simple yes/no results are enough, MSP may be attempted. For short amplicons that are crowded with CpG sites and of single melting domain, MS-HRM may be the method of choice though it only indicates the overall methylation percentage of the entire amplicon. Although the assay is highly reproducible, being semi-quantitative makes it of lesser interest to study ROI methylation of samples with little methylation differences. Direct BSP is a step forward as it gives information about the methylation percentage at each CpG site.

Estimates of evapotranspiration in alkaline scrub and meadow communities of Owens Valley, California, using the Bowen-ratio, eddy-correlation, and penman-combination methods

USGS Publications Warehouse

Duell, Lowell F. W.

1990-01-01

In Owens Valley, evapotranspiration (ET) is one of the largest components of outflow in the hydrologic budget and the least understood. ET estimates for December 1983 through October 1985 were made for seven representative locations selected on the basis of geohydrology and the characteristics of phreatophytic alkaline scrub and meadow communities. The Bowen-ratio, eddy-correlation, and Penman-combination methods were used to estimate ET. The results of the analyses appear satisfactory when compared with other estimates of ET. Results by the eddy-correlation method are for a direct and a residual latent-heat flux that is based on sensible-heat flux and energy-budget measurements. Penman-combination potential-ET estimates were determined to be unusable because they overestimated actual ET. Modification of the psychrometer constant of this method to account for differences between heat-diffusion resistance and vapor-diffusion resistance permitted actual ET to be estimated. The methods described in this report may be used for studies in similar semiarid and arid rangeland areas in the Western United States. Meteorological data for three field sites are included in the appendix of this report. Simple linear regression analysis indicates that ET estimates are correlated to air temperature, vapor-density deficit, and net radiation. Estimates of annual ET range from 301 millimeters at a low-density scrub site to 1,137 millimeters at a high-density meadow site. The monthly percentage of annual ET was determined to be similar for all sites studied.

DDT Analysis of Wetland Sediments in Upper Escambia Bay, Florida

NASA Astrophysics Data System (ADS)

Hopko, M. N.; Wright, J.; Liebens, J.; Vaughan, P.

2017-12-01

Dichlorodiphenyltrichloroethane (DDT) was a commonly used pesticide from World War II through the 1960's. DDT is generally used to control mosquito populations and as an agricultural insecticide. The pesticide and its degradation products (DDD and DDE) can bioaccumulate within ecosystems having negative implications for animal and human health. Consequently, DDT usage was banned in the United States in 1973. In a contaminant study performed in Escambia Bay, Florida, in 2009, DDT was present in 25% of study sites, most of which were located in the upper bay wetlands. Concentrations were well above the Florida Department of Environmental Protection's (FDEP) Probable Effect Level (PEL) and ratios of DDT and its metabolites indicated a recent introduction to the system. A follow-up study performed in 2016 found no DDT, but did show DDE at several sites. The current study repeated sampling in May 2017 at sites from the 2009 and 2016 studies. Sediment samples were collected in triplicate using a ponar sampler and DDT, DDD and DDE were extracted using EPA methods 3540c and 3620c. Extracts were analyzed using a gas chromatograph with electron capture detection (GC-ECD) as per EPA method 8081c. Sediment was also analyzed for organic carbon and particle size using an elemental NC analyzer and a laser diffraction particle sizer. Results show the presence of breakdown products DDE and DDD at multiple sites, but no detectable levels of DDT at any site. Sampling sites with high levels of DDT contamination in 2009 show only breakdown products in both 2016 and 2017. Particle size has little influence on DDD or DDE concentrations but OC is a controlling factor as indicated for contaminated sites by Pearson correlations between OC and DDE and DDD of 0.82 and 0.92, respectively. The presence of only DDD and/or DDE in the 2016 and 2017 studies indicates that the parent, DDT, has not been re-introduced into the watershed since 2009 but is degrading in the environment.

Methane and other hydrocarbon gases in sediment from the southeastern North American continental margin

USGS Publications Warehouse

Kvenvolden, K.A.; Lorenson, T.D.

2000-01-01

Residual concentrations and distributions of hydrocarbon gases from methane to n-heptane were measured in sediments at seven sites on Ocean Drilling Program (ODP) Leg 164. Three sites were drilled at the Cape Fear Diapir of the Carolina Rise, and one site was drilled on the Blake Ridge Diapir. Methane concentrations at these sites result from microbial generation which is influenced by the amount of pore-water sulfate and possible methane oxidation. Methane hydrate was found at the Blake Ridge Diapir site. The other hydrocarbon gases at these sites are likely the produce of early microbial processes. Three sites were drilled on a transect of holes across the crest of the Blake Ridge. The base of the zone of gas-hydrate occurrence was penetrated at all three sites. Trends in hydrocarbon gas distributions suggest that methane is microbial in origin and that the hydrocarbon gas mixture is affected by diagenesis, outgassing, and, near the surface, by microbial oxidation. Methane hydrate was recovered at two of these three sites, although gas hydrate is likely present at all three sites. The method used here for determining amounts of residual hydrocarbon gases has its limitations and provides poor assessment of gas distributions, particularly in the stratigraphic interval below about ~ 100 mbsf. One advantage of the method, however, is that it yields sufficient quantities of gas for other studies such as isotopic determinations.

Comparison of soil sampling and analytical methods for asbestos at the Sumas Mountain Asbestos Site-Working towards a toolbox for better assessment.

PubMed

Wroble, Julie; Frederick, Timothy; Frame, Alicia; Vallero, Daniel

2017-01-01

Established soil sampling methods for asbestos are inadequate to support risk assessment and risk-based decision making at Superfund sites due to difficulties in detecting asbestos at low concentrations and difficulty in extrapolating soil concentrations to air concentrations. Environmental Protection Agency (EPA)'s Office of Land and Emergency Management (OLEM) currently recommends the rigorous process of Activity Based Sampling (ABS) to characterize site exposures. The purpose of this study was to compare three soil analytical methods and two soil sampling methods to determine whether one method, or combination of methods, would yield more reliable soil asbestos data than other methods. Samples were collected using both traditional discrete ("grab") samples and incremental sampling methodology (ISM). Analyses were conducted using polarized light microscopy (PLM), transmission electron microscopy (TEM) methods or a combination of these two methods. Data show that the fluidized bed asbestos segregator (FBAS) followed by TEM analysis could detect asbestos at locations that were not detected using other analytical methods; however, this method exhibited high relative standard deviations, indicating the results may be more variable than other soil asbestos methods. The comparison of samples collected using ISM versus discrete techniques for asbestos resulted in no clear conclusions regarding preferred sampling method. However, analytical results for metals clearly showed that measured concentrations in ISM samples were less variable than discrete samples.

Comparison of micrometeorological methods using open-path optical instruments for measuring methane emission from agricultural sites

USDA-ARS?s Scientific Manuscript database

In this study, we evaluated the accuracies of two relatively new micrometeorological methods using open-path tunable diode laser absorption spectrometers: vertical radial plume mapping method (US EPA OTM-10) and the backward Lagragian stochastic method (Wintrax®). We have evaluated the accuracy of t...

Water-quality assessment of part of the upper Mississippi River basin, Minnesota and Wisconsin: Design and implementation of water-quality studies, 1995-98

USGS Publications Warehouse

Stark, James R.; Fallon, J.D.; Fong, A.L.; Goldstein, R.M.; Hanson, P.E.; Kroening, S.E.; Lee, K.E.

1999-01-01

This report describes the design, site-selection, and implementation of the study. Methods used to collect, process, and analyze samples; characterize sites; and assess habitat are described. A comprehensive list of sample sites is provided. Sample analyses for water-quality studies included chlorophyll a, major inorganic constituents, nutrients, trace elements, tritium, radon, environmental isotopes, organic carbon, pesticides, volatile organic compounds, and other synthetic and naturallyoccurring organic compounds. Aquatic-biological samples included fish, benthic macroinvertebrates, and algal enumeration and identification, as well as synthetic-organic compounds and trace elements in fish tissue.

Spatio-temporal characteristics of the extreme precipitation by L-moment-based index-flood method in the Yangtze River Delta region, China

NASA Astrophysics Data System (ADS)

Yin, Yixing; Chen, Haishan; Xu, Chong-Yu; Xu, Wucheng; Chen, Changchun; Sun, Shanlei

2016-05-01

The regionalization methods, which "trade space for time" by pooling information from different locations in the frequency analysis, are efficient tools to enhance the reliability of extreme quantile estimates. This paper aims at improving the understanding of the regional frequency of extreme precipitation by using regionalization methods, and providing scientific background and practical assistance in formulating the regional development strategies for water resources management in one of the most developed and flood-prone regions in China, the Yangtze River Delta (YRD) region. To achieve the main goals, L-moment-based index-flood (LMIF) method, one of the most popular regionalization methods, is used in the regional frequency analysis of extreme precipitation with special attention paid to inter-site dependence and its influence on the accuracy of quantile estimates, which has not been considered by most of the studies using LMIF method. Extensive data screening of stationarity, serial dependence, and inter-site dependence was carried out first. The entire YRD region was then categorized into four homogeneous regions through cluster analysis and homogenous analysis. Based on goodness-of-fit statistic and L-moment ratio diagrams, generalized extreme-value (GEV) and generalized normal (GNO) distributions were identified as the best fitted distributions for most of the sub-regions, and estimated quantiles for each region were obtained. Monte Carlo simulation was used to evaluate the accuracy of the quantile estimates taking inter-site dependence into consideration. The results showed that the root-mean-square errors (RMSEs) were bigger and the 90 % error bounds were wider with inter-site dependence than those without inter-site dependence for both the regional growth curve and quantile curve. The spatial patterns of extreme precipitation with a return period of 100 years were finally obtained which indicated that there are two regions with highest precipitation extremes and a large region with low precipitation extremes. However, the regions with low precipitation extremes are the most developed and densely populated regions of the country, and floods will cause great loss of human life and property damage due to the high vulnerability. The study methods and procedure demonstrated in this paper will provide useful reference for frequency analysis of precipitation extremes in large regions, and the findings of the paper will be beneficial in flood control and management in the study area.

Probabilistic analysis of tsunami hazards

USGS Publications Warehouse

Geist, E.L.; Parsons, T.

2006-01-01

Determining the likelihood of a disaster is a key component of any comprehensive hazard assessment. This is particularly true for tsunamis, even though most tsunami hazard assessments have in the past relied on scenario or deterministic type models. We discuss probabilistic tsunami hazard analysis (PTHA) from the standpoint of integrating computational methods with empirical analysis of past tsunami runup. PTHA is derived from probabilistic seismic hazard analysis (PSHA), with the main difference being that PTHA must account for far-field sources. The computational methods rely on numerical tsunami propagation models rather than empirical attenuation relationships as in PSHA in determining ground motions. Because a number of source parameters affect local tsunami runup height, PTHA can become complex and computationally intensive. Empirical analysis can function in one of two ways, depending on the length and completeness of the tsunami catalog. For site-specific studies where there is sufficient tsunami runup data available, hazard curves can primarily be derived from empirical analysis, with computational methods used to highlight deficiencies in the tsunami catalog. For region-wide analyses and sites where there are little to no tsunami data, a computationally based method such as Monte Carlo simulation is the primary method to establish tsunami hazards. Two case studies that describe how computational and empirical methods can be integrated are presented for Acapulco, Mexico (site-specific) and the U.S. Pacific Northwest coastline (region-wide analysis).

Computational active site analysis of molecular pathways to improve functional classification of enzymes.

PubMed

Ozyurt, A Sinem; Selby, Thomas L

2008-07-01

This study describes a method to computationally assess the function of homologous enzymes through small molecule binding interaction energy. Three experimentally determined X-ray structures and four enzyme models from ornithine cyclo-deaminase, alanine dehydrogenase, and mu-crystallin were used in combination with nine small molecules to derive a function score (FS) for each enzyme-model combination. While energy values varied for a single molecule-enzyme combination due to differences in the active sites, we observe that the binding energies for the entire pathway were proportional for each set of small molecules investigated. This proportionality of energies for a reaction pathway appears to be dependent on the amino acids in the active site and their direct interactions with the small molecules, which allows a function score (FS) to be calculated to assess the specificity of each enzyme. Potential of mean force (PMF) calculations were used to obtain the energies, and the resulting FS values demonstrate that a measurement of function may be obtained using differences between these PMF values. Additionally, limitations of this method are discussed based on: (a) larger substrates with significant conformational flexibility; (b) low homology enzymes; and (c) open active sites. This method should be useful in accurately predicting specificity for single enzymes that have multiple steps in their reactions and in high throughput computational methods to accurately annotate uncharacterized proteins based on active site interaction analysis. 2008 Wiley-Liss, Inc.

A simple method for calculating growth rates of petroleum hydrocarbon plumes

USGS Publications Warehouse

Bekins, B.A.; Cozzarelli, I.M.; Curtis, G.P.

2005-01-01

Consumption of aquifer Fe(III) during biodegradation of ground water contaminants may result in expansion of a contaminant plume, changing the outlook for monitored natural attenuation. Data from two research sites contaminated with petroleum hydrocarbons show that toluene and xylenes degrade under methanogenic conditions, but the benzene and ethylbenzene plumes grow as aquifer Fe(III) supplies are depleted. By considering a one-dimensional reaction front in a constant unidirectional flow field, it is possible to derive a simple expression for the growth rate of a benzene plume. The method balances the mass flux of benzene with the Fe(III) content of the aquifer, assuming that the biodegradation reaction is instantaneous. The resulting expression shows that the benzene front migration is retarded relative to the ground water velocity by a factor that depends on the concentrations of hydrocarbon and bioavailable Fe(III). The method provides good agreement with benzene plumes at a crude oil study site in Minnesota and a gasoline site in South Carolina. Compared to the South Carolina site, the Minnesota site has 25% higher benzene flux but eight times the Fe(III), leading to about one-sixth the expansion rate. Although it was developed for benzene, toluene, ethylbenzene, and xylenes, the growth-rate estimation method may have applications to contaminant plumes from other persistent contaminant sources. Copyright ?? 2005 National Ground Water Association.

Ground beetles (Coleoptera, Carabidae) of the Hanford Nuclear Site in south-central Washington State.

PubMed

Looney, Chris; Zack, Richard S; Labonte, James R

2014-01-01

Carabidae) collected from the Hanford Nuclear Reservation and Hanford National Monument (together the Hanford Site), which is located in south-central Washington State. The Site is a relatively undisturbed relict of the shrub-steppe habitat present throughout much of the western Columbia Basin before the westward expansion of the United States. Species, localities, months of capture, and capture method are reported for field work conducted between 1994 and 2002. Most species were collected using pitfall traps, although other capture methods were employed. Trapping results indicate the Hanford Site supports a diverse ground beetle community, with over 90% of the 92 species captured native to North America. Four species collected during the study period are newly recorded for Washington State: Bembidion diligens Casey, Calosoma obsoletum Say, Pseudaptinus rufulus (LeConte), and Stenolophus lineola (Fabricius). Based on these data, the Site maintains a diverse ground beetle fauna and, due to its size and diversity of habitats, is an important repository of shrub-steppe biodiversity.

A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water

PubMed Central

Wu, Xiongwu; Brooks, Bernard R.

2015-01-01

Chemical and thermodynamic equilibrium of multiple states is a fundamental phenomenon in biology systems and has been the focus of many experimental and computational studies. This work presents a simulation method to directly study the equilibrium of multiple states. This method constructs a virtual mixture of multiple states (VMMS) to sample the conformational space of all chemical states simultaneously. The VMMS system consists of multiple subsystems, one for each state. The subsystem contains a solute and a solvent environment. The solute molecules in all subsystems share the same conformation but have their own solvent environments. Transition between states is implicated by the change of their molar fractions. Simulation of a VMMS system allows efficient calculation of relative free energies of all states, which in turn determine their equilibrium molar fractions. For systems with a large number of state transition sites, an implicit site approximation is introduced to minimize the cost of simulation. A direct application of the VMMS method is for constant pH simulation to study protonation equilibrium. Applying the VMMS method to a heptapeptide of 3 ionizable residues, we calculated the pKas of those residues both with all explicit states and with implicit sites and obtained consistent results. For mouse epidermal growth factor of 9 ionizable groups, our VMMS simulations with implicit sites produced pKas of all 9 ionizable groups and the results agree qualitatively with NMR measurement. This example demonstrates the VMMS method can be applied to systems of a large number of ionizable groups and the computational cost scales linearly with the number of ionizable groups. For one of the most challenging systems in constant pH calculation, SNase Δ+PHS/V66K, our VMMS simulation shows that it is the state-dependent water penetration that causes the large deviation in lysine66’s pKa. PMID:26506245

A Muskingum-based methodology for river discharge estimation and rating curve development under significant lateral inflow conditions

NASA Astrophysics Data System (ADS)

Barbetta, Silvia; Moramarco, Tommaso; Perumal, Muthiah

2017-11-01

Quite often the discharge at a site is estimated using the rating curve developed for that site and its development requires river flow measurements, which are costly, tedious and dangerous during severe floods. To circumvent the conventional rating curve development approach, Perumal et al. in 2007 and 2010 applied the Variable Parameter Muskingum Stage-hydrograph (VPMS) routing method for developing stage-discharge relationships especially at those ungauged river sites where stage measurements and details of section geometry are available, but discharge measurements are not made. The VPMS method enables to estimate rating curves at ungauged river sites with acceptable accuracy. But the application of the method is subjected to the limitation of negligible presence of lateral flow within the routing reach. To overcome this limitation, this study proposes an extension of the VPMS method, henceforth, known herein as the VPMS-Lin method, for enabling the streamflow assessment even when significant lateral inflow occurs along the river reach considered for routing. The lateral inflow is estimated through the continuity equation expressed in the characteristic form as advocated by Barbetta et al. in 2012. The VPMS-Lin, is tested on two rivers characterized by different geometric and hydraulic properties: 1) a 50 km reach of the Tiber River in (central Italy) and 2) a 73 km reach of the Godavari River in the peninsular India. The study demonstrates that both the upstream and downstream discharge hydrographs are well reproduced, with a root mean square error equal on average to about 35 and 1700 m3 s-1 for the Tiber River and the Godavari River case studies, respectively. Moreover, simulation studies carried out on a river stretch of the Tiber River using the one-dimensional hydraulic model MIKE11 and the VPMS-Lin models demonstrate the accuracy of the VMPS-Lin model, which besides enabling the estimation of streamflow, also enables the estimation of reach averaged optimal roughness coefficients for the considered routing events.

A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water.

PubMed

Wu, Xiongwu; Brooks, Bernard R

2015-10-01

Chemical and thermodynamic equilibrium of multiple states is a fundamental phenomenon in biology systems and has been the focus of many experimental and computational studies. This work presents a simulation method to directly study the equilibrium of multiple states. This method constructs a virtual mixture of multiple states (VMMS) to sample the conformational space of all chemical states simultaneously. The VMMS system consists of multiple subsystems, one for each state. The subsystem contains a solute and a solvent environment. The solute molecules in all subsystems share the same conformation but have their own solvent environments. Transition between states is implicated by the change of their molar fractions. Simulation of a VMMS system allows efficient calculation of relative free energies of all states, which in turn determine their equilibrium molar fractions. For systems with a large number of state transition sites, an implicit site approximation is introduced to minimize the cost of simulation. A direct application of the VMMS method is for constant pH simulation to study protonation equilibrium. Applying the VMMS method to a heptapeptide of 3 ionizable residues, we calculated the pKas of those residues both with all explicit states and with implicit sites and obtained consistent results. For mouse epidermal growth factor of 9 ionizable groups, our VMMS simulations with implicit sites produced pKas of all 9 ionizable groups and the results agree qualitatively with NMR measurement. This example demonstrates the VMMS method can be applied to systems of a large number of ionizable groups and the computational cost scales linearly with the number of ionizable groups. For one of the most challenging systems in constant pH calculation, SNase Δ+PHS/V66K, our VMMS simulation shows that it is the state-dependent water penetration that causes the large deviation in lysine66's pKa.

Inversely Estimating the Vertical Profile of the Soil CO2 Production Rate in a Deciduous Broadleaf Forest Using a Particle Filtering Method

PubMed Central

Sakurai, Gen; Yonemura, Seiichiro; Kishimoto-Mo, Ayaka W.; Murayama, Shohei; Ohtsuka, Toshiyuki; Yokozawa, Masayuki

2015-01-01

Carbon dioxide (CO2) efflux from the soil surface, which is a major source of CO2 from terrestrial ecosystems, represents the total CO2 production at all soil depths. Although many studies have estimated the vertical profile of the CO2 production rate, one of the difficulties in estimating the vertical profile is measuring diffusion coefficients of CO2 at all soil depths in a nondestructive manner. In this study, we estimated the temporal variation in the vertical profile of the CO2 production rate using a data assimilation method, the particle filtering method, in which the diffusion coefficients of CO2 were simultaneously estimated. The CO2 concentrations at several soil depths and CO2 efflux from the soil surface (only during the snow-free period) were measured at two points in a broadleaf forest in Japan, and the data were assimilated into a simple model including a diffusion equation. We found that there were large variations in the pattern of the vertical profile of the CO2 production rate between experiment sites: the peak CO2 production rate was at soil depths around 10 cm during the snow-free period at one site, but the peak was at the soil surface at the other site. Using this method to estimate the CO2 production rate during snow-cover periods allowed us to estimate CO2 efflux during that period as well. We estimated that the CO2 efflux during the snow-cover period (about half the year) accounted for around 13% of the annual CO2 efflux at this site. Although the method proposed in this study does not ensure the validity of the estimated diffusion coefficients and CO2 production rates, the method enables us to more closely approach the “actual” values by decreasing the variance of the posterior distribution of the values. PMID:25793387

Estimation of design floods in ungauged catchments using a regional index flood method. A case study of Lake Victoria Basin in Kenya

NASA Astrophysics Data System (ADS)

Nobert, Joel; Mugo, Margaret; Gadain, Hussein

Reliable estimation of flood magnitudes corresponding to required return periods, vital for structural design purposes, is impacted by lack of hydrological data in the study area of Lake Victoria Basin in Kenya. Use of regional information, derived from data at gauged sites and regionalized for use at any location within a homogenous region, would improve the reliability of the design flood estimation. Therefore, the regional index flood method has been applied. Based on data from 14 gauged sites, a delineation of the basin into two homogenous regions was achieved using elevation variation (90-m DEM), spatial annual rainfall pattern and Principal Component Analysis of seasonal rainfall patterns (from 94 rainfall stations). At site annual maximum series were modelled using the Log normal (LN) (3P), Log Logistic Distribution (LLG), Generalized Extreme Value (GEV) and Log Pearson Type 3 (LP3) distributions. The parameters of the distributions were estimated using the method of probability weighted moments. Goodness of fit tests were applied and the GEV was identified as the most appropriate model for each site. Based on the GEV model, flood quantiles were estimated and regional frequency curves derived from the averaged at site growth curves. Using the least squares regression method, relationships were developed between the index flood, which is defined as the Mean Annual Flood (MAF) and catchment characteristics. The relationships indicated area, mean annual rainfall and altitude were the three significant variables that greatly influence the index flood. Thereafter, estimates of flood magnitudes in ungauged catchments within a homogenous region were estimated from the derived equations for index flood and quantiles from the regional curves. These estimates will improve flood risk estimation and to support water management and engineering decisions and actions.

Investigating temporal field sampling strategies for site-specific calibration of three soil moisture-neutron intensity parameterisation methods

NASA Astrophysics Data System (ADS)

Iwema, J.; Rosolem, R.; Baatz, R.; Wagener, T.; Bogena, H. R.

2015-07-01

The Cosmic-Ray Neutron Sensor (CRNS) can provide soil moisture information at scales relevant to hydrometeorological modelling applications. Site-specific calibration is needed to translate CRNS neutron intensities into sensor footprint average soil moisture contents. We investigated temporal sampling strategies for calibration of three CRNS parameterisations (modified N0, HMF, and COSMIC) by assessing the effects of the number of sampling days and soil wetness conditions on the performance of the calibration results while investigating actual neutron intensity measurements, for three sites with distinct climate and land use: a semi-arid site, a temperate grassland, and a temperate forest. When calibrated with 1 year of data, both COSMIC and the modified N0 method performed better than HMF. The performance of COSMIC was remarkably good at the semi-arid site in the USA, while the N0mod performed best at the two temperate sites in Germany. The successful performance of COSMIC at all three sites can be attributed to the benefits of explicitly resolving individual soil layers (which is not accounted for in the other two parameterisations). To better calibrate these parameterisations, we recommend in situ soil sampled to be collected on more than a single day. However, little improvement is observed for sampling on more than 6 days. At the semi-arid site, the N0mod method was calibrated better under site-specific average wetness conditions, whereas HMF and COSMIC were calibrated better under drier conditions. Average soil wetness condition gave better calibration results at the two humid sites. The calibration results for the HMF method were better when calibrated with combinations of days with similar soil wetness conditions, opposed to N0mod and COSMIC, which profited from using days with distinct wetness conditions. Errors in actual neutron intensities were translated to average errors specifically to each site. At the semi-arid site, these errors were below the typical measurement uncertainties from in situ point-scale sensors and satellite remote sensing products. Nevertheless, at the two humid sites, reduction in uncertainty with increasing sampling days only reached typical errors associated with satellite remote sensing products. The outcomes of this study can be used by researchers as a CRNS calibration strategy guideline.

Multiple external hazards compound level 3 PSA methods research of nuclear power plant

NASA Astrophysics Data System (ADS)

Wang, Handing; Liang, Xiaoyu; Zhang, Xiaoming; Yang, Jianfeng; Liu, Weidong; Lei, Dina

2017-01-01

2011 Fukushima nuclear power plant severe accident was caused by both earthquake and tsunami, which results in large amount of radioactive nuclides release. That accident has caused the radioactive contamination on the surrounding environment. Although this accident probability is extremely small, once such an accident happens that is likely to release a lot of radioactive materials into the environment, and cause radiation contamination. Therefore, studying accidents consequences is important and essential to improve nuclear power plant design and management. Level 3 PSA methods of nuclear power plant can be used to analyze radiological consequences, and quantify risk to the public health effects around nuclear power plants. Based on multiple external hazards compound level 3 PSA methods studies of nuclear power plant, and the description of the multiple external hazards compound level 3 PSA technology roadmap and important technical elements, as well as taking a coastal nuclear power plant as the reference site, we analyzed the impact of off-site consequences of nuclear power plant severe accidents caused by multiple external hazards. At last we discussed the impact of off-site consequences probabilistic risk studies and its applications under multiple external hazards compound conditions, and explained feasibility and reasonableness of emergency plans implementation.

Empirical studies assessing the quality of health information for consumers on the world wide web: a systematic review.

PubMed

Eysenbach, Gunther; Powell, John; Kuss, Oliver; Sa, Eun-Ryoung

The quality of consumer health information on the World Wide Web is an important issue for medicine, but to date no systematic and comprehensive synthesis of the methods and evidence has been performed. To establish a methodological framework on how quality on the Web is evaluated in practice, to determine the heterogeneity of the results and conclusions, and to compare the methodological rigor of these studies, to determine to what extent the conclusions depend on the methodology used, and to suggest future directions for research. We searched MEDLINE and PREMEDLINE (1966 through September 2001), Science Citation Index (1997 through September 2001), Social Sciences Citation Index (1997 through September 2001), Arts and Humanities Citation Index (1997 through September 2001), LISA (1969 through July 2001), CINAHL (1982 through July 2001), PsychINFO (1988 through September 2001), EMBASE (1988 through June 2001), and SIGLE (1980 through June 2001). We also conducted hand searches, general Internet searches, and a personal bibliographic database search. We included published and unpublished empirical studies in any language in which investigators searched the Web systematically for specific health information, evaluated the quality of Web sites or pages, and reported quantitative results. We screened 7830 citations and retrieved 170 potentially eligible full articles. A total of 79 distinct studies met the inclusion criteria, evaluating 5941 health Web sites and 1329 Web pages, and reporting 408 evaluation results for 86 different quality criteria. Two reviewers independently extracted study characteristics, medical domains, search strategies used, methods and criteria of quality assessment, results (percentage of sites or pages rated as inadequate pertaining to a quality criterion), and quality and rigor of study methods and reporting. Most frequently used quality criteria used include accuracy, completeness, readability, design, disclosures, and references provided. Fifty-five studies (70%) concluded that quality is a problem on the Web, 17 (22%) remained neutral, and 7 studies (9%) came to a positive conclusion. Positive studies scored significantly lower in search (P =.02) and evaluation (P =.04) methods. Due to differences in study methods and rigor, quality criteria, study population, and topic chosen, study results and conclusions on health-related Web sites vary widely. Operational definitions of quality criteria are needed.

Evaluating dengue burden in Africa in passive fever surveillance and seroprevalence studies: protocol of field studies of the Dengue Vaccine Initiative

PubMed Central

Lim, Jacqueline Kyungah; Carabali, Mabel; Lee, Jung-Seok; Lee, Kang-Sung; Namkung, Suk; Lim, Sl-Ki; Ridde, Valéry; Fernandes, Jose; Lell, Bertrand; Matendechero, Sultani Hadley; Esen, Meral; Andia, Esther; Oyembo, Noah; Barro, Ahmed; Bonnet, Emmanuel; Njenga, Sammy M; Agnandji, Selidji Todagbe; Yaro, Seydou; Alexander, Neal; Yoon, In-Kyu

2018-01-01

Introduction Dengue is an important and well-documented public health problem in the Asia-Pacific and Latin American regions. However, in Africa, information on disease burden is limited to case reports and reports of sporadic outbreaks, thus hindering the implementation of public health actions for disease control. To gather evidence on the undocumented burden of dengue in Africa, epidemiological studies with standardised methods were launched in three locations in Africa. Methods and analysis In 2014–2017, the Dengue Vaccine Initiative initiated field studies at three sites in Ouagadougou, Burkina Faso; Lambaréné, Gabon and Mombasa, Kenya to obtain comparable incidence data on dengue and assess its burden through standardised hospital-based surveillance and community-based serological methods. Multidisciplinary measurements of the burden of dengue were obtained through field studies that included passive facility-based fever surveillance, cost-of-illness surveys, serological surveys and healthcare utilisation surveys. All three sites conducted case detection using standardised procedures with uniform laboratory assays to diagnose dengue. Healthcare utilisation surveys were conducted to adjust population denominators in incidence calculations for differing healthcare seeking patterns. The fever surveillance data will allow calculation of age-specific incidence rates and comparison of symptomatic presentation between patients with dengue and non-dengue using multivariable logistic regression. Serological surveys assessed changes in immune status of cohorts of approximately 3000 randomly selected residents at each site at 6-month intervals. The age-stratified serosurvey data will allow calculation of seroprevalence and force of infection of dengue. Cost-of-illness evaluations were conducted among patients with acute dengue by Rapid Diagnostic Test. Ethics and dissemination By standardising methods to evaluate dengue burden across several sites in Africa, these studies will generate evidence for dengue burden in Africa and data will be disseminated as publication in peer-review journals in 2018. PMID:29358421

A Survey of Health-Related Activities on Second Life

PubMed Central

Beard, Leslie; Wilson, Kumanan; Morra, Dante

2009-01-01

Background Increasingly, governments, health care agencies, companies, and private groups have chosen Second Life as part of their Web 2.0 communication strategies. Second Life offers unique design features for disseminating health information, training health professionals, and enabling patient education for both academic and commercial health behavior research. Objectives This study aimed to survey and categorize the range of health-related activities on Second Life; to examine the design attributes of the most innovative and popular sites; and to assess the potential utility of Second Life for the dissemination of health information and for health behavior change. Methods We used three separate search strategies to identify health-related sites on Second Life. The first used the application’s search engine, entering both generic and select illness-specific keywords, to seek out sites. The second identified sites through a comprehensive review of print, blog, and media sources discussing health activities on Second Life. We then visited each site and used a snowball method to identify other health sites until we reached saturation (no new health sites were identified). The content, user experience, and chief purpose of each site were tabulated as well as basic site information, including user traffic data and site size. Results We found a wide range of health-related activities on Second Life, and a diverse group of users, including organizations, groups, and individuals. For many users, Second Life activities are a part of their Web 2.0 communication strategy. The most common type of health-related site in our sample (n = 68) were those whose principle aim was patient education or to increase awareness about health issues. The second most common type of site were support sites, followed by training sites, and marketing sites. Finally, a few sites were purpose-built to conduct research in SL or to recruit participants for real-life research. Conclusions Studies show that behaviors from virtual worlds can translate to the real world. Our survey suggests that users are engaged in a range of health-related activities in Second Life which are potentially impacting real-life behaviors. Further research evaluating the impact of health-related activities on Second Life is warranted. PMID:19632971

FuncPatch: a web server for the fast Bayesian inference of conserved functional patches in protein 3D structures.

PubMed

Huang, Yi-Fei; Golding, G Brian

2015-02-15

A number of statistical phylogenetic methods have been developed to infer conserved functional sites or regions in proteins. Many methods, e.g. Rate4Site, apply the standard phylogenetic models to infer site-specific substitution rates and totally ignore the spatial correlation of substitution rates in protein tertiary structures, which may reduce their power to identify conserved functional patches in protein tertiary structures when the sequences used in the analysis are highly similar. The 3D sliding window method has been proposed to infer conserved functional patches in protein tertiary structures, but the window size, which reflects the strength of the spatial correlation, must be predefined and is not inferred from data. We recently developed GP4Rate to solve these problems under the Bayesian framework. Unfortunately, GP4Rate is computationally slow. Here, we present an intuitive web server, FuncPatch, to perform a fast approximate Bayesian inference of conserved functional patches in protein tertiary structures. Both simulations and four case studies based on empirical data suggest that FuncPatch is a good approximation to GP4Rate. However, FuncPatch is orders of magnitudes faster than GP4Rate. In addition, simulations suggest that FuncPatch is potentially a useful tool complementary to Rate4Site, but the 3D sliding window method is less powerful than FuncPatch and Rate4Site. The functional patches predicted by FuncPatch in the four case studies are supported by experimental evidence, which corroborates the usefulness of FuncPatch. The software FuncPatch is freely available at the web site, http://info.mcmaster.ca/yifei/FuncPatch golding@mcmaster.ca Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

In Cell Footprinting Coupled with Mass Spectrometry for the Structural Analysis of Proteins in Live Cells.

PubMed

Espino, Jessica A; Mali, Vishaal S; Jones, Lisa M

2015-08-04

Protein footprinting coupled with mass spectrometry has become a widely used tool for the study of protein-protein and protein-ligand interactions and protein conformational change. These methods provide residue-level analysis on protein interaction sites and have been successful in studying proteins in vitro. The extension of these methods for in cell footprinting would open an avenue to study proteins that are not amenable for in vitro studies and would probe proteins in their native environment. Here we describe the application of an oxidative-based footprinting approach inside cells in which hydroxyl radicals are used to oxidatively modify proteins. Mass spectrometry is used to detect modification sites and to calculate modification levels. The method is probing biologically relevant proteins in live cells, and proteins in various cellular compartments can be oxdiatively modified. Several different amino acid residues are modified making the method a general labeling strategy for the study of a variety of proteins. Further, comparison of the extent of oxidative modification with solvent accessible surface area reveals the method successfully probes solvent accessibility. This marks the first time protein footprinting has been performed in live cells.

Isolation of anticancer drug TAXOL from Pestalotiopsis breviseta with apoptosis and B-Cell lymphoma protein docking studies

PubMed Central

Kathiravan, G.; Sureban, Sripathi M.; Sree, Harsha N.; Bhuvaneshwari, V.; Kramony, Evelin

2012-01-01

Background: Extraction and investigation of TAXOL from Pestalotiopsis breviseta (Sacc.) using protein docking, which is a computational technique that samples conformations of small molecules in protein-binding sites. Scoring functions are used to assess which of these conformations best complements the protein binding site and active site prediction. Materials and Methods: Coelomycetous fungi P. breviseta (Sacc.) Steyaert was screened for the production of TAXOL, an anticancer drug. Results: TAXOL production was confirmed by the following methods: Ultraviolet (UV) spectroscopic analysis, Infrared analysis, High performance liquid chromatography analysis (HPLC), and Liquid chromatography mass spectrum (LC-MASS). TAXOL produced by the fungi was compared with authentic TAXOL, and protein docking studies were performed. Conclusion: The BCL2 protein of human origin showed a higher affinity toward the compound paclitaxel. It has the binding energy value of −13.0061 (KJ/Mol) with four hydrogen bonds. PMID:24808664

Skin hydration in nursing home residents using disposable bed baths.

PubMed

Gillis, Katrin; Tency, Inge; Roelant, Ella; Laureys, Sarina; Devriendt, Hendrik; Lips, Dirk

2016-01-01

The objective of this study was to evaluate a new way for applying bed baths and reducing the risk for dry skin by comparing the effect of two washing methods on skin hydration. A cluster randomized trial was conducted. Skin hydration was measured before and after implementation of disposable wash gloves, using a MoistureMeter SC at three skin sites. Total skin hydration did not differ between residents at the start of the study in both groups. After implementation, the post minus pre hydration scores were higher for the intervention group than the control group at all skin sites. However, the difference was only significant at cheek site. The use of disposable wash gloves does not increase the risk for dry skin in comparison with traditional washing methods. These results may encourage the introduction of disposable wash gloves as an innovation in daily skin care practice. Copyright © 2016 Elsevier Inc. All rights reserved.

Geostatistics and GIS: tools for characterizing environmental contamination.

PubMed

Henshaw, Shannon L; Curriero, Frank C; Shields, Timothy M; Glass, Gregory E; Strickland, Paul T; Breysse, Patrick N

2004-08-01

Geostatistics is a set of statistical techniques used in the analysis of georeferenced data that can be applied to environmental contamination and remediation studies. In this study, the 1,1-dichloro-2,2-bis(p-chlorophenyl)ethylene (DDE) contamination at a Superfund site in western Maryland is evaluated. Concern about the site and its future clean up has triggered interest within the community because residential development surrounds the area. Spatial statistical methods, of which geostatistics is a subset, are becoming increasingly popular, in part due to the availability of geographic information system (GIS) software in a variety of application packages. In this article, the joint use of ArcGIS software and the R statistical computing environment are demonstrated as an approach for comprehensive geostatistical analyses. The spatial regression method, kriging, is used to provide predictions of DDE levels at unsampled locations both within the site and the surrounding areas where residential development is ongoing.

A method for assessing the physical recovery of Antarctic desert pavements following human-induced disturbances: a case study in the Ross Sea region of Antarctica.

PubMed

O'Neill, Tanya A; Balks, Megan R; López-Martínez, Jerónimo; McWhirter, Judi L

2012-12-15

With increasing visitor numbers an understanding of the impacts of human activities in Antarctic terrestrial environments has become important. The objective of this study was to develop a means for assessing recovery of the ground surface desert pavement following physical disturbance. A set of 11 criteria were identified to assess desert pavement recovery. Assessed criteria were: embeddedness of surface clasts; impressions of removed clasts; degree of clast surface weathering; % overturned clasts; salt on underside of clasts; development of salt coatings; armouring per m(2); colour contrast; evidence of subsidence/melt out; accumulation of salt on cut surfaces; and evidence of patterned ground development. Recovery criteria were assigned a severity/extent rating on a scale from zero to four, zero being highly disturbed, and four being undisturbed. A relative % recovery for each criteria was calculated for each site by comparison with a nearby undisturbed control area, and an overall Mean Recovery Index (MRI) was assigned to each pavement surface. To test the method, 54 sites in the Ross Sea region of Antarctica were investigated including areas disturbed by: bulldozer scraping for road-fill, contouring for infrastructure, geotechnical investigations, and experimental treading trial sites. Disturbances had occurred at timescales ranging from one week to 50 years prior to assessment. The extent of desert pavement recovery at the sites investigated in this study was higher than anticipated. Fifty of the 54 sites investigated were in an intermediate, or higher, stage of desert pavement recovery, 30 sites were in an advanced stage of recovery, and four sites were indistinguishable from adjacent control sites (MRI = 100%). It was found that active surfaces, such as the gravel beach deposits at the Greenpeace World Park Base site at Cape Evans, the aeolian sand deposits at Bull Pass, and the alluvial fan deposits of the Loop Moraine field campsite, recovered relatively quickly, whereas less active sites, such as the bulldozed tracks at Marble Point, and Williams Field to McMurdo Station pipeline site on Ross Island, showed only intermediate recovery 20-30 years after disturbance. The slabby grano-diorite surface material at the former Vanda Station site, meant that the impacts that had occurred were hard to detect following decommissioning of the station and site remediation. Desert pavements disturbed by randomly dispersed footprints, temporary field campsites at the Loop Moraine and VXE6 Pond in the Wright Valley, recovered to be undetectable (MRI = 100%) within five years, whereas track formation from repeated trampling, particularly the concentration of larger clasts along the margin of a confined track, persisted for over 15 years (MRI = 82%). The recovery assessment method developed in this study has environmental management applications and potential to advance our ability to predict the recovery of desert pavement following human impacts from activities in Antarctica. Copyright © 2012 Elsevier Ltd. All rights reserved.

Methods to Identify Changes in Background Water-Quality Conditions Using Dissolved-Solids Concentrations and Loads as Indicators, Arkansas River and Fountain Creek, in the Vicinity of Pueblo, Colorado

USGS Publications Warehouse

Ortiz, Roderick F.

2004-01-01

Effective management of existing water-storage capacity in the Arkansas River Basin is anticipated to help satisfy the need for water in southeastern Colorado. A strategy to meet these needs has been developed, but implementation could affect the water quality of the Arkansas River and Fountain Creek in the vicinity of Pueblo, Colorado. Because no known methods are available to determine what effects future changes in operations will have on water quality, the U.S. Geological Survey, in cooperation with the Southeastern Colorado Water Activity Enterprise, began a study in 2002 to develop methods that could identify if future water-quality conditions have changed significantly from background (preexisting) water-quality conditions. A method was developed to identify when significant departures from background (preexisting) water-quality conditions occur in the lower Arkansas River and Fountain Creek in the vicinity of Pueblo, Colorado. Additionally, the methods described in this report provide information that can be used by various water-resource agencies for an internet-based decision-support tool. Estimated dissolved-solids concentrations at five sites in the study area were evaluated to designate historical background conditions and to calculate tolerance limits used to identify statistical departures from background conditions. This method provided a tool that could be applied with defined statistical probabilities associated with specific tolerance limits. Drought data from 2002 were used to test the method. Dissolved-solids concentrations exceeded the tolerance limits at all four sites on the Arkansas River at some point during 2002. The number of exceedances was particularly evident when streamflow from Pueblo Reservoir was reduced, and return flows and ground-water influences to the river were more prevalent. No exceedances were observed at the site on Fountain Creek. These comparisons illustrated the need to adjust the concentration data to account for varying streamflow. As such, similar comparisons between flow-adjusted data were done. At the site Arkansas River near Avondale, nearly all the 2002 flow-adjusted concentration data were less than the flow-adjusted tolerance limit which illustrated the effects of using flow-adjusted concentrations. Numerous exceedances of the flow-adjusted tolerance limits, however, were observed at the sites Arkansas River above Pueblo and Arkansas River at Pueblo. These results indicated that the method was able to identify a change in the ratio of source waters under drought conditions. Additionally, tolerance limits were calculated for daily dissolved-solids load and evaluated in a similar manner. Several other mass-load approaches were presented to help identify long-term changes in water quality. These included comparisons of cumulative mass load at selected sites and comparisons of mass load contributed at the Arkansas River near Avondale site by measured and unmeasured sources.

DNA methylation markers in combination with skeletal and dental ages to improve age estimation in children.

PubMed

Shi, Lei; Jiang, Fan; Ouyang, Fengxiu; Zhang, Jun; Wang, Zhimin; Shen, Xiaoming

2018-03-01

Age estimation is critical in forensic science, in competitive sports and games and in other age-related fields, but the current methods are suboptimal. The combination of age-associated DNA methylation markers with skeletal age (SA) and dental age (DA) may improve the accuracy and precision of age estimation, but no study has examined this topic. In the current study, we measured SA (GP, TW3-RUS, and TW3-Carpal methods) and DA (Demirjian and Willems methods) by X-ray examination in 124 Chinese children (78 boys and 46 girls) aged 6-15 years. To identify age-associated CpG sites, we analyzed methylome-wide DNA methylation profiling by using the Illumina HumanMethylation450 BeadChip system in 48 randomly selected children. Five CpG sites were identified as associated with chronologic age (CA), with an absolute value of Pearson's correlation coefficient (r)>0.5 (p<0.01) and a false discovery rate<0.01. The validation of age-associated CpG sites was performed using droplet digital PCR techniques in all 124 children. After validation, four CpG sites for boys and five CpG sites for girls were further adopted to build the age estimation model with SA and DA using multivariate linear stepwise regressions. These CpG sites were located at 4 known genes: DDO, PRPH2, DHX8, and ITGA2B and at one unknown gene with the Illumina ID number of 22398226. The accuracy of age estimation methods was compared according to the mean absolute error (MAE) and root mean square error (RMSE). The best single measure for SA was the TW3-RUS method (MAE=0.69years, RMSE=0.95years) in boys, and the GP method (MAE=0.74years, RMSE=0.94years) in girls. For DA, the Willems method was the best single measure for both boys (MAE=0.63years, RMSE=0.78years) and girls (MAE=0.54years, RMSE=0.68years). The models that incorporated SA and DA with the methylation levels of age-associated CpG sites provided the highest accuracy of age estimation in both boys (MAE=0.47years, R 2 =0.886) and girls (MAE=0.33years, R 2 =0.941). Cross validation of the results confirmed the reliability and validity of the models. In conclusion, age-associated DNA methylation markers in combination with SA and DA greatly improve the accuracy of age estimation in Chinese children. This method may be applied in forensic science, in competitive sports and games and in other age-related fields. Copyright © 2017. Published by Elsevier B.V.

Searching for transcription factor binding sites in vector spaces

PubMed Central

2012-01-01

Background Computational approaches to transcription factor binding site identification have been actively researched in the past decade. Learning from known binding sites, new binding sites of a transcription factor in unannotated sequences can be identified. A number of search methods have been introduced over the years. However, one can rarely find one single method that performs the best on all the transcription factors. Instead, to identify the best method for a particular transcription factor, one usually has to compare a handful of methods. Hence, it is highly desirable for a method to perform automatic optimization for individual transcription factors. Results We proposed to search for transcription factor binding sites in vector spaces. This framework allows us to identify the best method for each individual transcription factor. We further introduced two novel methods, the negative-to-positive vector (NPV) and optimal discriminating vector (ODV) methods, to construct query vectors to search for binding sites in vector spaces. Extensive cross-validation experiments showed that the proposed methods significantly outperformed the ungapped likelihood under positional background method, a state-of-the-art method, and the widely-used position-specific scoring matrix method. We further demonstrated that motif subtypes of a TF can be readily identified in this framework and two variants called the k NPV and k ODV methods benefited significantly from motif subtype identification. Finally, independent validation on ChIP-seq data showed that the ODV and NPV methods significantly outperformed the other compared methods. Conclusions We conclude that the proposed framework is highly flexible. It enables the two novel methods to automatically identify a TF-specific subspace to search for binding sites. Implementations are available as source code at: http://biogrid.engr.uconn.edu/tfbs_search/. PMID:23244338

The VA Ostomy Health-Related Quality of Life Study: objectives, methods, and patient sample.

PubMed

Krouse, Robert S; Mohler, M Jane; Wendel, Christopher S; Grant, Marcia; Baldwin, Carol M; Rawl, Susan M; McCorkle, Ruth; Rosenfeld, Kenneth E; Ko, Clifford Y; Schmidt, C Max; Coons, Stephen Joel

2006-04-01

To present the design and methods of a multisite study of health-related quality of life (HR-QOL) in veterans living with ostomies. Veterans from Tucson, Indianapolis, and Los Angeles VA Medical Centers were surveyed using the validated City of Hope ostomy-specific tool (mCOH-QOL-Ostomy) and the SF-36V. Cases (ostomates) had a major gastrointestinal procedure that required an intestinal stoma, while controls had similar procedures for which an ostomy was not required. Ostomy subjects were recruited for four focus groups in each of two sites divided by ostomy type (colostomy versus ileostomy) and overall mCOH-QOL-Ostomy HR-QOL score (highest versus lowest quartile). The focus groups further evaluated barriers, concerns, and adaptation methods and skills. This report presents recruitment results, reliability of survey instruments, and demographic characteristics of the sample. The overall response (i.e., recruitment) rate across all sites was 48% and by site was 53%, 57%, and 37%, respectively (p < 0.001). Internal consistency reliability estimates indicated that both instruments remain reliable in this population (Cronbach's alpha for HR-QOL domains/scales: 0.71-0.96). Cases and controls were similar in demographic characteristics. Proportions of minority subjects matched projections from the site patient populations. Subjects with ostomies had significantly longer time since surgery than controls (p < 0.001). Focus groups were comprised of two to six subjects per group and demonstrated racial diversity at the Los Angeles site. The unique design of our study of VA patients with ostomies is an illustration of a successful mixed methods approach to HR-QOL research. We collected meaningful quantitative and qualitative data that will be used in the development of new approaches to care that will lead to improved functioning and well-being in persons living with ostomies. Subsequent reports will provide the results of this research project.

A method for the quantitative site-specific study of the biochemistry within dental plaque biofilms formed in vivo.

PubMed

Robinson, C; Kirkham, J; Percival, R; Shore, R C; Bonass, W A; Brookes, S J; Kusa, L; Nakagaki, H; Kato, K; Nattress, B

1997-01-01

The study of plaque biofilms in the oral cavity is difficult as plaque removal inevitably disrupts biofilm integrity precluding kinetic studies involving the penetration of components and metabolism of substrates in situ. A method is described here in which plaque is formed in vivo under normal (or experimental) conditions using a collection device which can be removed from the mouth after a specified time without physical disturbance to the plaque biofilm, permitting site-specific analysis or exposure of the undisturbed plaque to experimental conditions in vitro. Microbiological analysis revealed plaque flora which was similar to that reported from many natural sources. Analytical data can be related to plaque volume rather than weight. Using this device, plaque fluoride concentrations have been shown to vary with plaque depth and in vitro short-term exposure to radiolabelled components may be carried out, permitting important conclusions to be drawn regarding the site-specific composition and dynamics of dental plaque.

Evaluation of permeable fractures in rock aquifers

NASA Astrophysics Data System (ADS)

Bok Lee, Hang

2015-04-01

In this study, the practical usefulness and fundamental applicability of a self-potential (SP) method for identifying the permeable fractures were evaluated by a comparison of SP methods with other geophysical logging methods and hydraulic tests. At a 10 m-shallow borehole in the study site, the candidates of permeable fractures crossing the borehole were first determined by conventional geophysical methods such as an acoustic borehole televiwer, temperature, electrical conductivity and gamma-gamma loggings, which was compared to the analysis by the SP method. Constant pressure injection and recovery tests were conducted for verification of the hydraulic properties of the fractures identified by various logging methods. The acoustic borehole televiwer and gamma-gamma loggings detected the open space or weathering zone within the borehole, but they cannot prove the possibility of a groundwater flow through the detected fractures. The temperature and electrical conductivity loggings had limitations to detect the fractured zones where groundwater in the borehole flows out to the surrounding rock aquifers. Comparison of results from different methods showed that there is a best correlation between the distribution of hydraulic conductivity and the variation of the SP signals, and the SP logging can estimate accurately the hydraulic activity as well as the location of permeable fractures. Based on the results, the SP method is recommended for determining the hydraulically-active fractures rather than other conventional geophysical loggings. This self-potential method can be effectively applied in the initial stage of a site investigation which selects the optimal location and evaluates the hydrogeological property of fractures in target sites for the underground structure including the geothermal reservoir and radioactive waste disposal.

MO-F-CAMPUS-J-02: Automatic Recognition of Patient Treatment Site in Portal Images Using Machine Learning

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

Chang, X; Yang, D

Purpose: To investigate the method to automatically recognize the treatment site in the X-Ray portal images. It could be useful to detect potential treatment errors, and to provide guidance to sequential tasks, e.g. automatically verify the patient daily setup. Methods: The portal images were exported from MOSAIQ as DICOM files, and were 1) processed with a threshold based intensity transformation algorithm to enhance contrast, and 2) where then down-sampled (from 1024×768 to 128×96) by using bi-cubic interpolation algorithm. An appearance-based vector space model (VSM) was used to rearrange the images into vectors. A principal component analysis (PCA) method was usedmore » to reduce the vector dimensions. A multi-class support vector machine (SVM), with radial basis function kernel, was used to build the treatment site recognition models. These models were then used to recognize the treatment sites in the portal image. Portal images of 120 patients were included in the study. The images were selected to cover six treatment sites: brain, head and neck, breast, lung, abdomen and pelvis. Each site had images of the twenty patients. Cross-validation experiments were performed to evaluate the performance. Results: MATLAB image processing Toolbox and scikit-learn (a machine learning library in python) were used to implement the proposed method. The average accuracies using the AP and RT images separately were 95% and 94% respectively. The average accuracy using AP and RT images together was 98%. Computation time was ∼0.16 seconds per patient with AP or RT image, ∼0.33 seconds per patient with both of AP and RT images. Conclusion: The proposed method of treatment site recognition is efficient and accurate. It is not sensitive to the differences of image intensity, size and positions of patients in the portal images. It could be useful for the patient safety assurance. The work was partially supported by a research grant from Varian Medical System.« less

A grammar inference approach for predicting kinase specific phosphorylation sites.

PubMed

Datta, Sutapa; Mukhopadhyay, Subhasis

2015-01-01

Kinase mediated phosphorylation site detection is the key mechanism of post translational mechanism that plays an important role in regulating various cellular processes and phenotypes. Many diseases, like cancer are related with the signaling defects which are associated with protein phosphorylation. Characterizing the protein kinases and their substrates enhances our ability to understand the mechanism of protein phosphorylation and extends our knowledge of signaling network; thereby helping us to treat such diseases. Experimental methods for predicting phosphorylation sites are labour intensive and expensive. Also, manifold increase of protein sequences in the databanks over the years necessitates the improvement of high speed and accurate computational methods for predicting phosphorylation sites in protein sequences. Till date, a number of computational methods have been proposed by various researchers in predicting phosphorylation sites, but there remains much scope of improvement. In this communication, we present a simple and novel method based on Grammatical Inference (GI) approach to automate the prediction of kinase specific phosphorylation sites. In this regard, we have used a popular GI algorithm Alergia to infer Deterministic Stochastic Finite State Automata (DSFA) which equally represents the regular grammar corresponding to the phosphorylation sites. Extensive experiments on several datasets generated by us reveal that, our inferred grammar successfully predicts phosphorylation sites in a kinase specific manner. It performs significantly better when compared with the other existing phosphorylation site prediction methods. We have also compared our inferred DSFA with two other GI inference algorithms. The DSFA generated by our method performs superior which indicates that our method is robust and has a potential for predicting the phosphorylation sites in a kinase specific manner.

Elimination of the Reaction Rate "Scale Effect": Application of the Lagrangian Reactive Particle-Tracking Method to Simulate Mixing-Limited, Field-Scale Biodegradation at the Schoolcraft (MI, USA) Site

NASA Astrophysics Data System (ADS)

Ding, Dong; Benson, David A.; Fernández-Garcia, Daniel; Henri, Christopher V.; Hyndman, David W.; Phanikumar, Mantha S.; Bolster, Diogo

2017-12-01

Measured (or empirically fitted) reaction rates at groundwater remediation sites are typically much lower than those found in the same material at the batch or laboratory scale. The reduced rates are commonly attributed to poorer mixing at the larger scales. A variety of methods have been proposed to account for this scaling effect in reactive transport. In this study, we use the Lagrangian particle-tracking and reaction (PTR) method to simulate a field bioremediation experiment at the Schoolcraft, MI site. A denitrifying bacterium, Pseudomonas Stutzeri strain KC (KC), was injected to the aquifer, along with sufficient substrate, to degrade the contaminant, carbon tetrachloride (CT), under anaerobic conditions. The PTR method simulates chemical reactions through probabilistic rules of particle collisions, interactions, and transformations to address the scale effect (lower apparent reaction rates for each level of upscaling, from batch to column to field scale). In contrast to a prior Eulerian reaction model, the PTR method is able to match the field-scale experiment using the rate coefficients obtained from batch experiments.

Checklist and "Pollard Walk" butterfly survey methods on public lands

USGS Publications Warehouse

Royer, Ronald A.; Austin, Jane E.; Newton, Wesley E.

1998-01-01

Checklist and “Pollard Walk” butterfly survey methods were contemporaneously applied to seven public sites in North Dakota during the summer of 1995. Results were compared for effect of method and site on total number of butterflies and total number of species detected per hour. Checklist searching produced significantly more butterfly detections per hour than Pollard Walks at all sites. Number of species detected per hour did not differ significantly either among sites or between methods. Many species were detected by only one method, and at most sites generalist and invader species were more likely to be observed during checklist searches than during Pollard Walks. Results indicate that checklist surveys are a more efficient means for initial determination of a species list for a site, whereas for long-term monitoring the Pollard Walk is more practical and statistically manageable. Pollard Walk transects are thus recommended once a prairie butterfly fauna has been defined for a site by checklist surveys.

Prediction of Protein-Protein Interaction Sites by Random Forest Algorithm with mRMR and IFS

PubMed Central

Li, Bi-Qing; Feng, Kai-Yan; Chen, Lei; Huang, Tao; Cai, Yu-Dong

2012-01-01

Prediction of protein-protein interaction (PPI) sites is one of the most challenging problems in computational biology. Although great progress has been made by employing various machine learning approaches with numerous characteristic features, the problem is still far from being solved. In this study, we developed a novel predictor based on Random Forest (RF) algorithm with the Minimum Redundancy Maximal Relevance (mRMR) method followed by incremental feature selection (IFS). We incorporated features of physicochemical/biochemical properties, sequence conservation, residual disorder, secondary structure and solvent accessibility. We also included five 3D structural features to predict protein-protein interaction sites and achieved an overall accuracy of 0.672997 and MCC of 0.347977. Feature analysis showed that 3D structural features such as Depth Index (DPX) and surface curvature (SC) contributed most to the prediction of protein-protein interaction sites. It was also shown via site-specific feature analysis that the features of individual residues from PPI sites contribute most to the determination of protein-protein interaction sites. It is anticipated that our prediction method will become a useful tool for identifying PPI sites, and that the feature analysis described in this paper will provide useful insights into the mechanisms of interaction. PMID:22937126

Bioaccumulation Using Surrogate Samplers (Bass): Evaluation Of A Passive Sampler As An Alternative Monitoring Tool For Environmental Contaminants At The Savannah River Site

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

Paller, M.; Knox, A.; Kuhne, W.

2015-10-15

DOE sites conduct traditional environmental monitoring programs that require collecting, processing, and analyzing water, sediment, and fish samples. However, recently developed passive sampling technologies, such as Diffusive Gradient in Thin films (DGT), may measure the chemical phases that are available and toxic to organisms (the bioavailable fraction), thereby producing more accurate and economical results than traditional methods.  Our laboratory study showed that dissolved copper concentrations measured by DGT probes were strongly correlated with the uptake of copper by Lumbriculus variegatus, an aquatic worm, and with concentrations of copper measured by conventional methods.  Dissolved copper concentrations in DGT probes increased with timemore » of exposure, paralleling the increase in copper with time that ocurred in Lumbriculus.  Additional studies with a combination of seven dissolved metals showed similar results.  These findings support the use of DGT as a biomimetic monitoring tool and provide a basis for refinement of these methods for cost-effective environmental monitoring at DOE sites.« less

Current perspective on assessing site of digestion in ruminants.

PubMed

Merchen, N R; Elizalde, J C; Drackley, J K

1997-08-01

The site of nutrient digestion in the gastrointestinal tract of ruminants affects nutrient availability and the nature of digestive end-products supplied to the host animal. Methods to study site of digestion in vivo provide a tool to obtain data that enhance the ability to interpret or predict animal responses to some feeding practices. Examples are discussed for which site of digestion data provided insights that might not have been evident from other approaches. The use of site of digestion techniques may provide interpretation regarding digestion of N by ruminants different from those derived from measurement of total tract N digestion. Site of digestion measurements have been particularly important in studying effects of heat processing of protein sources and in understanding the nature of digestion of N in high-quality, fresh forages. Moreover, site of digestion techniques have been instrumental in interpreting the influences of supplemental fat sources on ruminal digestion and ruminal biohydrogenation and small intestinal digestion of long-chain fatty acids.

Using MCDA and GIS for hazardous waste landfill siting considering land scarcity for waste disposal.

PubMed

De Feo, Giovanni; De Gisi, Sabino

2014-11-01

The main aim of this study was to develop a procedure that minimizes the wasting of space for the siting of hazardous waste landfills as part of a solid waste management system. We wanted to tackle the shortage of land for waste disposal that is a serious and growing problem in most large urban regions. The procedure combines a multi-criteria decision analysis (MCDA) approach with a geographical information system (GIS). The GIS was utilised to obtain an initial screening in order to eliminate unsuitable areas, whereas the MCDA was developed to select the most suitable sites. The novelty of the proposed siting procedure is the introduction of a new screening phase before the macro-siting step aimed at producing a "land use map of potentially suitable areas" for the siting of solid waste facilities which simultaneously takes into consideration all plant types. The issue of obtaining sites evaluations of a specific facility was coupled with the issue of not wasting land appropriate to facilitate other types of waste management options. In the developed case study, the use of an innovative criteria weighting tool (the "Priority Scale") in combination with the Analytic Hierarchy Process was useful to easier define the priorities of the evaluation criteria in comparison with other classic methods such as the Paired Comparison Technique in combination with the Simple Additive Weighting method. Copyright © 2014 Elsevier Ltd. All rights reserved.

Estimating site index from tree species composition in mixed stands of upland eastern hardwoods: Should shrubs be included?

Treesearch

W. Henry McNab

2010-01-01

Site index is the most widely used method for site quality assessment in hardwood forests of the eastern United States. Its application in most oak (Quercus sp. L.) dominated stands is often problematic, however, because available sample trees usually do not meet important underlying assumptions of the method. A prototype method for predicting site index from tree...

Effects of site preparation on seedling, growth: a preliminary comparison of broadcast burning and pile burning.

Treesearch

Don Minore

1986-01-01

Site preparation is often necessary to obtain adequate forest regeneration, but inappropriate treatment may reduce subsequent growth. Broadcast-burned and piled-and-burned plantations were studied in southwestern Oregon to determine if burning method affected the growth of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco var. menziesii...

Assessment of Uinta Basin Oil and Natural Gas Well Pad Pneumatic Controller Emissions

EPA Science Inventory

In the fall of 2016, a field study was conducted in the Uinta Basin Utah to improve information on oil and natural gas well pad pneumatic controllers (PCs) and emission measurement methods. A total of 80 PC systems at five oil sites (supporting six wells) and three gas sites (sup...

Health effects and water quality at marine sites: Results from the National Epidemiologic and Environmental Assessment of Recreational Water

EPA Science Inventory

Since 2003, we have conducted a series of epidemiological studies at beach sites impacted by treated sewage discharge. The goal was to evaluate the association between swimming-associated illness and novel and faster methods of measuring water quality. In 2005 and 2007, we expand...

Pine growth and plant community response to chemical vs. mechanical site preparation for establishing loblolly and slash pine

Treesearch

James H. Miller; Zhijuan Qiu

1995-01-01

Chemical and mechanical site preparation methods were studied for establishing loblolly (Pinus taeda L) and slash (P. elliottii var. elliottii Engelm.) pine following both integrated fuelwood-pulpwood harvesting and conventional whole-tree harvesting of pines and hardwoods in southem Alabama's Middle Coastal...

Development and Validation of Rapid Assessment Indices for Condition of Coastal Wetlands in Southern New England USA

EPA Science Inventory

The goals of this study were to develop and validate a Rapid Assessment Method (RAM) for assessing the condition of coastal wetlands in New England, USA. Eighty-one coastal wetland sites were assessed; nested within these were ten reference sites which were previously assessed us...

Comparison of different methods of estimating the mean radiant temperature in outdoor thermal comfort studies.

PubMed

Krüger, E L; Minella, F O; Matzarakis, A

2014-10-01

Correlations between outdoor thermal indices and the calculated or measured mean radiant temperature T(mrt) are in general of high importance because of the combined effect on human energy balance in outdoor spaces. The most accurate way to determine T(mrt) is by means of integral radiation measurements, i.e. measuring the short- and long-wave radiation from six directions using pyranometers and pyrgeometers, an expensive and not always an easily available procedure. Some studies use globe thermometers combined with air temperature and wind speed sensors. An alternative way to determine T(mrt) is based on output from the RayMan model from measured data of incoming global radiation and morphological features of the monitoring site in particular sky view factor (SVF) data. The purpose of this paper is to compare different methods to assess the mean radiant temperature T(mrt) in terms of differences to a reference condition (T(mrt) calculated from field measurements) and to resulting outdoor comfort levels expressed as PET and UTCI values. The T(mrt) obtained from field measurements is a combination of air temperature, wind speed and globe temperature data according to the forced ventilation formula of ISO 7726 for data collected in Glasgow, UK. Four different methods were used in the RayMan model for T(mrt) calculations: input data consisting exclusively of data measured at urban sites; urban data excluding solar radiation, estimated SVF data and solar radiation data measured at a rural site; urban data excluding solar radiation with SVF data for each site; urban data excluding solar radiation and including solar radiation at the rural site taking no account of SVF information. Results show that all methods overestimate T(mrt) when compared to ISO calculations. Correlations were found to be significant for the first method and lower for the other three. Results in terms of comfort (PET, UTCI) suggest that reasonable estimates could be made based on global radiation data measured at the urban site or as a surrogate of missing SR data or globe temperature data recorded at the urban area on global radiation data measured at a rural location.

A Coupled model for ERT monitoring of contaminated sites

NASA Astrophysics Data System (ADS)

Wang, Yuling; Zhang, Bo; Gong, Shulan; Xu, Ya

2018-02-01

The performance of electrical resistivity tomography (ERT) system is usually investigated using a fixed resistivity distribution model in numerical simulation study. In this paper, a method to construct a time-varying resistivity model by coupling water transport, solute transport and constant current field is proposed for ERT monitoring of contaminated sites. Using the proposed method, a monitoring model is constructed for a contaminated site with a pollution region on the surface and ERT monitoring results at different time is calculated by the finite element method. The results show that ERT monitoring profiles can effectively reflect the increase of the pollution area caused by the diffusion of pollutants, but the extent of the pollution is not exactly the same as the actual situation. The model can be extended to any other case and can be used to scheme design and results analysis for ERT monitoring.

3D Documentation and BIM Modeling of Cultural Heritage Structures Using UAVs: The Case of the Foinikaria Church

NASA Astrophysics Data System (ADS)

Themistocleous, K.; Agapiou, A.; Hadjimitsis, D.

2016-10-01

The documentation of architectural cultural heritage sites has traditionally been expensive and labor-intensive. New innovative technologies, such as Unmanned Aerial Vehicles (UAVs), provide an affordable, reliable and straightforward method of capturing cultural heritage sites, thereby providing a more efficient and sustainable approach to documentation of cultural heritage structures. In this study, hundreds of images of the Panagia Chryseleousa church in Foinikaria, Cyprus were taken using a UAV with an attached high resolution camera. The images were processed to generate an accurate digital 3D model by using Structure in Motion techniques. Building Information Model (BIM) was then used to generate drawings of the church. The methodology described in the paper provides an accurate, simple and cost-effective method of documenting cultural heritage sites and generating digital 3D models using novel techniques and innovative methods.

Using Formative Research to Develop Environmental and Ecological Interventions to Address Overweight and Obesity

PubMed Central

Wilson, Mark G.; Goetzel, Ron Z.; Ozminkowski, Ronald J.; DeJoy, Dave M.; Della, Lindsay; Roemer, Enid Chung; Schneider, Jennifer; Tully, Karen J.; White, John M.; Baase, Catherine M.

2010-01-01

Objective This paper presents the formative research phase of a large multi-site intervention study conducted to inform the feasibility of introducing environmental and ecological interventions. Methods Using mixed methods that included an environmental assessment, climate survey, leadership focus groups and interviews, and archival data, information was collected on employee health and job factors, the physical environment, social-organizational environment, and current health programs. Results Results show that 83% of employees at the study sites were overweight or obese. Leadership was very supportive of health initiatives and felt integrating the strategies into organizational operations would increase their likelihood of success. Environmental assessment scores ranged from 47 to 19 on a 100 point scale. Health services personnel tended to view the organizational climate for health more positively than site leadership (mean of 3.6 vs 3.0 respectively). Conclusions Intervention strategies chosen included increasing healthy food choices in vending, cafeterias, and company meetings, providing a walking path, targeting messages, developing site goals, training leaders, and establishing leaders at the work group level. PMID:18073340

Elucidating the druggable interface of protein-protein interactions using fragment docking and coevolutionary analysis.

PubMed

Bai, Fang; Morcos, Faruck; Cheng, Ryan R; Jiang, Hualiang; Onuchic, José N

2016-12-13

Protein-protein interactions play a central role in cellular function. Improving the understanding of complex formation has many practical applications, including the rational design of new therapeutic agents and the mechanisms governing signal transduction networks. The generally large, flat, and relatively featureless binding sites of protein complexes pose many challenges for drug design. Fragment docking and direct coupling analysis are used in an integrated computational method to estimate druggable protein-protein interfaces. (i) This method explores the binding of fragment-sized molecular probes on the protein surface using a molecular docking-based screen. (ii) The energetically favorable binding sites of the probes, called hot spots, are spatially clustered to map out candidate binding sites on the protein surface. (iii) A coevolution-based interface interaction score is used to discriminate between different candidate binding sites, yielding potential interfacial targets for therapeutic drug design. This approach is validated for important, well-studied disease-related proteins with known pharmaceutical targets, and also identifies targets that have yet to be studied. Moreover, therapeutic agents are proposed by chemically connecting the fragments that are strongly bound to the hot spots.

Magnesium oxide prepared via metal-chitosan complexation method: Application as catalyst for transesterification of soybean oil and catalyst deactivation studies

NASA Astrophysics Data System (ADS)

Almerindo, Gizelle I.; Probst, Luiz F. D.; Campos, Carlos E. M.; de Almeida, Rusiene M.; Meneghetti, Simoni M. P.; Meneghetti, Mario R.; Clacens, Jean-Marc; Fajardo, Humberto V.

2011-10-01

A simple method to prepare magnesium oxide catalysts for biodiesel production by transesterification reaction of soybean oil with ethanol is proposed. The method was developed using a metal-chitosan complex. Compared to the commercial oxide, the proposed catalysts displayed higher surface area and basicity values, leading to higher yield in terms of fatty acid ethyl esters (biodiesel). The deactivation of the catalyst due to contact with CO2 and H2O present in the ambient air was verified. It was confirmed that the active catalytic site is a hydrogenocarbonate adsorption site.

The method of landing sites selection for Russian lunar lander missions

NASA Astrophysics Data System (ADS)

Mitrofanov, Igor; Djachkova, Maya; Litvak, Maxim; Sanin, Anton

2016-04-01

Russian space agency is planning to launch two lunar landers in the upcoming years - Luna-Glob (2018) and Luna-Resurs (2021). Instruments installed on board the landers are designed to study volatiles and water ice, lunar exosphere, dust particles and regolith composition. As primary scientific interest is concentrated in the south polar region, the landing sites for both landers will be selected there. Since rugged terrain, conditions of solar illumination at high altitudes and necessity of direct radio communication with the Earth, it is essential to select an optimal landing site for each lander. We present the method of landing sites selection, which is based on geographical information systems (GIS) technologies to perform analysis, based on the criteria of surface suitability for landing, such as slopes, illumination conditions and Earth visibility. In addition, the estimations of hydrogen concentration in regolith based on LEND/LRO data were used to evaluate landing site candidates on possible water ice presence. The method gave us 6 canditates to land. Four of them are located in the impact craters: Simpelius D, Simpelius E, Boguslawsky C, Boussingault, and the other two are located to the north of Schomberger crater and to the north-west of Boguslawsky C crater and associated with probable basin-related materials. The main parameters of these sites will be presented with possible prioritization based on both technical requirements and scientific interest.

Genotoxicity in Atlantic killifish (Fundulus heteroclitus) from a PAH-contaminated Superfund site on the Elizabeth River, Virginia.

PubMed

Jung, Dawoon; Matson, Cole W; Collins, Leonard B; Laban, Geoff; Stapleton, Heather M; Bickham, John W; Swenberg, James A; Di Giulio, Richard T

2011-11-01

The Atlantic Wood Industries Superfund site (AWI) on the Elizabeth River in Portsmouth, VA is heavily contaminated with polycyclic aromatic hydrocarbons (PAHs) from a wood treatment facility. Atlantic killifish, or mummichog (Fundulus heteroclitus), at this Superfund site are exposed to very high concentrations of several carcinogens. In this study, we measured PAH concentrations in both fish tissues and sediments. Concurrently, we assessed different aspects of genotoxicity in the killifish exposed in situ. Both sediment and tissue PAH levels were significantly higher in AWI samples, relative to a reference site, but the chemistry profile was different between sediments and tissues. Killifish at AWI exhibited higher levels of DNA damage compared to reference fish, as measured via the flow cytometric method (FCM), and the damage was consistent with sediment PAH concentrations. Covalent binding of benzo[a]pyrene (BaP) metabolites to DNA, as measured via LC-MS/MS adduct detection methods, were also elevated and could be partially responsible for the DNA damage. Using similar LC-MS/MS methods, we found no evidence that oxidative DNA adducts had a role in observed genotoxicity.

Site-Specific RNase A Activity Was Dramatically Reduced in Serum from Multiple Types of Cancer Patients

PubMed Central

Huang, Weiyan; Zhao, Mei; Wei, Na; Wang, Xiaoxia; Cao, Huqing; Du, Quan; Liang, Zicai

2014-01-01

Potent RNase activities were found in the serum of mammals but the physiological function of the RNases was never well illustrated, largely due to the caveats in methods of RNase activity measurement. None of the existing methods can distinguish between RNases with different target specificities. A systematic study was recently carried out in our lab to investigate the site-specificity of serum RNases on double-stranded RNA substrates, and found that serum RNases cleave double-stranded RNAs predominantly at 5′-U/A-3′ and 5′-C/A-3′ dinucleotide sites, in a manner closely resembling RNase A. Based on this finding, a FRET assay was developed in the current study to measure this site-specific serum RNase activity in human samples using a double stranded RNA substrate. We demonstrated that the method has a dynamic range of 10−5 mg/ml- 10−1 mg/ml using serial dilution of RNase A. The sera of 303 cancer patients were subjected to comparison with 128 healthy controls, and it was found that serum RNase activities visualized with this site-specific double stranded probe were found to be significantly reduced in patients with gastric cancer, liver cancer, pancreatic cancer, esophageal cancer, ovary cancer, cervical cancer, bladder cancer, kidney cancer and lung cancer, while only minor changes were found in breast and colon cancer patients. This is the first report using double stranded RNA as probe to quantify site-specific activities of RNase A in a serum. The results illustrated that RNase A might be further evaluated to determine if it can serve as a new class of biomarkers for certain cancer types. PMID:24805924

Considerations for Public Health Organizations Attempting to Implement a Social Media Presence: A Qualitative Study

PubMed Central

2016-01-01

Background In the past decade, social media has become an integral part of our everyday lives, but research on how this tool is used by public health workers and organizations is still developing. Budget cuts and staff reduction in county departments have required employees to take on more responsibilities. These reductions have caused a reduction in the time for training or collaborating with others in the field. To make up for the loss, many employees are seeking collaboration through social media sites but are unable to do so because state departments block these Internet sites. Objective This study sought to highlight the key considerations and decision-making process for a public health organization deciding whether to implement a social media presence for their organization. Methods Using 3 structured interviews, 15 stakeholders were questioned on their personal experience with social media, experience within the context of public health, and their thoughts on implementation for their center. Interviews were coded using constant comparative qualitative methods. Results The following themes emerged from the interviews: (1) personal experience with technology and social networking sites, (2) use of social networking sites in public health, (3) use of social networking sites in work environments, (4) social networking sites access, (5) ways the Rural South Public Health Training Center could use social networking sites, and (6) perceived outcomes of social networking site usage for the Rural South Public Health Training Center (positive and negative). Conclusions The collective voice of the center showed a positive perceived perception of social media implementation, with the benefits outweighing the risks. Despite the benefits, there is a cautious skepticism of the importance of social networking site use. PMID:27227160

CaMELS: In silico prediction of calmodulin binding proteins and their binding sites.

PubMed

Abbasi, Wajid Arshad; Asif, Amina; Andleeb, Saiqa; Minhas, Fayyaz Ul Amir Afsar

2017-09-01

Due to Ca 2+ -dependent binding and the sequence diversity of Calmodulin (CaM) binding proteins, identifying CaM interactions and binding sites in the wet-lab is tedious and costly. Therefore, computational methods for this purpose are crucial to the design of such wet-lab experiments. We present an algorithm suite called CaMELS (CalModulin intEraction Learning System) for predicting proteins that interact with CaM as well as their binding sites using sequence information alone. CaMELS offers state of the art accuracy for both CaM interaction and binding site prediction and can aid biologists in studying CaM binding proteins. For CaM interaction prediction, CaMELS uses protein sequence features coupled with a large-margin classifier. CaMELS models the binding site prediction problem using multiple instance machine learning with a custom optimization algorithm which allows more effective learning over imprecisely annotated CaM-binding sites during training. CaMELS has been extensively benchmarked using a variety of data sets, mutagenic studies, proteome-wide Gene Ontology enrichment analyses and protein structures. Our experiments indicate that CaMELS outperforms simple motif-based search and other existing methods for interaction and binding site prediction. We have also found that the whole sequence of a protein, rather than just its binding site, is important for predicting its interaction with CaM. Using the machine learning model in CaMELS, we have identified important features of protein sequences for CaM interaction prediction as well as characteristic amino acid sub-sequences and their relative position for identifying CaM binding sites. Python code for training and evaluating CaMELS together with a webserver implementation is available at the URL: http://faculty.pieas.edu.pk/fayyaz/software.html#camels. © 2017 Wiley Periodicals, Inc.

Successful field trial of attractive toxic sugar bait (ATSB) plant-spraying methods against malaria vectors in the Anopheles gambiae complex in Mali, West Africa

PubMed Central

2010-01-01

Background Based on highly successful demonstrations in Israel that attractive toxic sugar bait (ATSB) methods can decimate local populations of mosquitoes, this study determined the effectiveness of ATSB methods for malaria vector control in the semi-arid Bandiagara District of Mali, West Africa. Methods Control and treatment sites, selected along a road that connects villages, contained man-made ponds that were the primary larval habitats of Anopheles gambiae and Anopheles arabiensis. Guava and honey melons, two local fruits shown to be attractive to An. gambiae s.l., were used to prepare solutions of Attractive Sugar Bait (ASB) and ATSB that additionally contained boric acid as an oral insecticide. Both included a color dye marker to facilitate determination of mosquitoes feeding on the solutions. The trial was conducted over a 38-day period, using CDC light traps to monitor mosquito populations. On day 8, ASB solution in the control site and ATSB solution in the treatment site were sprayed using a hand-pump on patches of vegetation. Samples of female mosquitoes were age-graded to determine the impact of ATSB treatment on vector longevity. Results Immediately after spraying ATSB in the treatment site, the relative abundance of female and male An. gambiae s.l. declined about 90% from pre-treatment levels and remained low. In the treatment site, most females remaining after ATSB treatment had not completed a single gonotrophic cycle, and only 6% had completed three or more gonotrophic cycles compared with 37% pre-treatment. In the control site sprayed with ASB (without toxin), the proportion of females completing three or more gonotrophic cycles increased from 28.5% pre-treatment to 47.5% post-treatment. In the control site, detection of dye marker in over half of the females and males provided direct evidence that the mosquitoes were feeding on the sprayed solutions. Conclusion This study in Mali shows that even a single application of ATSB can substantially decrease malaria vector population densities and longevity. It is likely that ATSB methods can be used as a new powerful tool for the control of malaria vectors, particularly since this approach is highly effective for mosquito control, technologically simple, inexpensive, and environmentally safe. PMID:20663142

Marine molluscs and fish as biomarkers of pollution stress in littoral regions of the Red Sea, Mediterranean Sea and North Sea

NASA Astrophysics Data System (ADS)

Bresler, Vladimir; Bissinger, Vera; Abelson, Avigdor; Dizer, Halim; Sturm, Armin; Kratke, Renate; Fishelson, Lev; Hansen, Peter-Diedrich

1999-12-01

The intensive development of industry and urban structures along the seashores of the world, as well as the immense increase in marine transportation and other activities, has resulted in the deposition of thousands of new chemicals and organic compounds, endangering the existence of organisms and ecosystems. The conventional single biomarker methods used in ecological assessment studies cannot provide an adequate base for environmental health assessment, management and sustainability planning. The present study uses a set of novel biochemical, physiological, cytogenetic and morphological methods to characterize the state of health of selected molluscs and fish along the shores of the German North Sea, as well as the Israeli Mediterranean and Red Sea. The methods include measurement of activity of multixenobiotic resistance-mediated transporter (MXRtr) and the system of active transport of organic anions (SATOA) as indicators of antixenobiotic defence; glutathione S-transferase (GST) activity as an indicator of biotransformation of xenobiotics; DNA unwinding as a marker of genotoxicity; micronucleus test for clastogenicity; levels of phagocytosis for immunotoxicity; cholinesterase (ChE) activity and level of catecholamines as indicators of neurotoxicity; permeability of external epithelia to anionic hydrophilic probe, intralysosomal accumulation of cationic amphiphilic probe and activity of non-specific esterases as indicators of cell/tissue viability. Complete histopathological examination was used for diagnostics of environmental pathology. The obtained data show that the activity of the defensive pumps, MXRtr and SATOA in the studied organisms was significantly higher in the surface epithelia of molluscs from a polluted site than that of the same species from control, unpolluted stations, providing clear evidence of response to stress. Enhanced frequency of DNA lesions (alkaline and acidic DNA unwinding) and micronucleus-containing cells was significantly higher in samples from polluted sites in comparison to those from the clean sites that exhibited genotoxic and clastogenic activity of the pollutants. In all the studied molluscs a negative correlation was found between the MXRtr levels of activity and the frequency of micronucleus-containing hemocytes. The expression of this was in accordance with the level of pollution. The complete histopathological examination demonstrates significantly higher frequencies of pathological alterations in organs of animals from polluted sites. A strong negative correlation was found between the frequency of these alterations and MXRtr activity in the same specimens. In addition to these parameters, a decrease in the viability was noted in molluscs from the polluted sites, but ChE activities remained similar at most sites. The methods applied in our study unmasked numerous early cryptic responses and negative alterations of health in populations of marine biota sampled from the polluted sites. This demonstrates that genotoxic, clastogenic and pathogenic xenobiotics are present and act in the studied sites and this knowledge can provide a reliable base for consideration for sustainable development.

An analytical framework for estimating aquatic species density from environmental DNA

USGS Publications Warehouse

Chambert, Thierry; Pilliod, David S.; Goldberg, Caren S.; Doi, Hideyuki; Takahara, Teruhiko

2018-01-01

Environmental DNA (eDNA) analysis of water samples is on the brink of becoming a standard monitoring method for aquatic species. This method has improved detection rates over conventional survey methods and thus has demonstrated effectiveness for estimation of site occupancy and species distribution. The frontier of eDNA applications, however, is to infer species density. Building upon previous studies, we present and assess a modeling approach that aims at inferring animal density from eDNA. The modeling combines eDNA and animal count data from a subset of sites to estimate species density (and associated uncertainties) at other sites where only eDNA data are available. As a proof of concept, we first perform a cross-validation study using experimental data on carp in mesocosms. In these data, fish densities are known without error, which allows us to test the performance of the method with known data. We then evaluate the model using field data from a study on a stream salamander species to assess the potential of this method to work in natural settings, where density can never be known with absolute certainty. Two alternative distributions (Normal and Negative Binomial) to model variability in eDNA concentration data are assessed. Assessment based on the proof of concept data (carp) revealed that the Negative Binomial model provided much more accurate estimates than the model based on a Normal distribution, likely because eDNA data tend to be overdispersed. Greater imprecision was found when we applied the method to the field data, but the Negative Binomial model still provided useful density estimates. We call for further model development in this direction, as well as further research targeted at sampling design optimization. It will be important to assess these approaches on a broad range of study systems.

Quantification of Lysine Acetylation and Succinylation Stoichiometry in Proteins Using Mass Spectrometric Data-Independent Acquisitions (SWATH)

DOE PAGES

Meyer, Jesse G.; D’Souza, Alexandria K.; Sorensen, Dylan J.; ...

2016-09-02

Post-translational modification of lysine residues by N ε-acylation is an important regulator of protein function. Many large-scale protein acylation studies have assessed relative changes of lysine acylation sites after antibody enrichment using mass spectrometry-based proteomics. Although relative acylation fold-changes are important, this does not reveal site occupancy, or stoichiometry, of individual modification sites, which is critical to understand functional consequences. Recently, methods for determining lysine acetylation stoichiometry have been proposed based on ratiometric analysis of endogenous levels to those introduced after quantitative per-acetylation of proteins using stable isotope-labeled acetic anhydride. However, in our hands, we find that these methods canmore » overestimate acetylation stoichiometries because of signal interferences when endogenous levels of acylation are very low, which is especially problematic when using MS1 scans for quantification. In this study, we sought to improve the accuracy of determining acylation stoichiometry using data-independent acquisition (DIA). Specifically, we use SWATH acquisition to comprehensively collect both precursor and fragment ion intensity data. The use of fragment ions for stoichiometry quantification not only reduces interferences but also allows for determination of site-level stoichiometry from peptides with multiple lysine residues. We also demonstrate the novel extension of this method to measurements of succinylation stoichiometry using deuterium-labeled succinic anhydride. Proof of principle SWATH acquisition studies were first performed using bovine serum albumin for both acetylation and succinylation occupancy measurements, followed by the analysis of more complex samples of E. coli cell lysates. Although overall site occupancy was low (<1%), some proteins contained lysines with relatively high acetylation occupancy.« less

Intraoperative detection of 18F-FDG-avid tissue sites using the increased probe counting efficiency of the K-alpha probe design and variance-based statistical analysis with the three-sigma criteria

PubMed Central

2013-01-01

Background Intraoperative detection of 18F-FDG-avid tissue sites during 18F-FDG-directed surgery can be very challenging when utilizing gamma detection probes that rely on a fixed target-to-background (T/B) ratio (ratiometric threshold) for determination of probe positivity. The purpose of our study was to evaluate the counting efficiency and the success rate of in situ intraoperative detection of 18F-FDG-avid tissue sites (using the three-sigma statistical threshold criteria method and the ratiometric threshold criteria method) for three different gamma detection probe systems. Methods Of 58 patients undergoing 18F-FDG-directed surgery for known or suspected malignancy using gamma detection probes, we identified nine 18F-FDG-avid tissue sites (from amongst seven patients) that were seen on same-day preoperative diagnostic PET/CT imaging, and for which each 18F-FDG-avid tissue site underwent attempted in situ intraoperative detection concurrently using three gamma detection probe systems (K-alpha probe, and two commercially-available PET-probe systems), and then were subsequently surgical excised. Results The mean relative probe counting efficiency ratio was 6.9 (± 4.4, range 2.2–15.4) for the K-alpha probe, as compared to 1.5 (± 0.3, range 1.0–2.1) and 1.0 (± 0, range 1.0–1.0), respectively, for two commercially-available PET-probe systems (P < 0.001). Successful in situ intraoperative detection of 18F-FDG-avid tissue sites was more frequently accomplished with each of the three gamma detection probes tested by using the three-sigma statistical threshold criteria method than by using the ratiometric threshold criteria method, specifically with the three-sigma statistical threshold criteria method being significantly better than the ratiometric threshold criteria method for determining probe positivity for the K-alpha probe (P = 0.05). Conclusions Our results suggest that the improved probe counting efficiency of the K-alpha probe design used in conjunction with the three-sigma statistical threshold criteria method can allow for improved detection of 18F-FDG-avid tissue sites when a low in situ T/B ratio is encountered. PMID:23496877

Quantification of amine functional groups and their influence on OM/OC in the IMPROVE network

NASA Astrophysics Data System (ADS)

Kamruzzaman, Mohammed; Takahama, Satoshi; Dillner, Ann M.

2018-01-01

Recently, we developed a method using FT-IR spectroscopy coupled with partial least squares (PLS) regression to measure the four most abundant organic functional groups, aliphatic C-H, alcohol OH, carboxylic acid OH and carbonyl C=O, in atmospheric particulate matter. These functional groups are summed to estimate organic matter (OM) while the carbon from the functional groups is summed to estimate organic carbon (OC). With this method, OM and OM/OC can be estimated for each sample rather than relying on one assumed value to convert OC measurements to OM. This study continues the development of the FT-IR and PLS method for estimating OM and OM/OC by including the amine functional group. Amines are ubiquitous in the atmosphere and come from motor vehicle exhaust, animal husbandry, biomass burning, and vegetation among other sources. In this study, calibration standards for amines are produced by aerosolizing individual amine compounds and collecting them on PTFE filters using an IMPROVE sampler, thereby mimicking the filter media and collection geometry of ambient standards. The moles of amine functional group on each standard and a narrow range of amine-specific wavenumbers in the FT-IR spectra (wavenumber range 1 550-1 500 cm-1) are used to develop a PLS calibration model. The PLS model is validated using three methods: prediction of a set of laboratory standards not included in the model, a peak height analysis and a PLS model with a broader wavenumber range. The model is then applied to the ambient samples collected throughout 2013 from 16 IMPROVE sites in the USA. Urban sites have higher amine concentrations than most rural sites, but amine functional groups account for a lower fraction of OM at urban sites. Amine concentrations, contributions to OM and seasonality vary by site and sample. Amine has a small impact on the annual average OM/OC for urban sites, but for some rural sites including amine in the OM/OC calculations increased OM/OC by 0.1 or more.

Hypothesis-driven and field-validated method to prioritize fragmentation mitigation efforts in road projects.

PubMed

Vanthomme, Hadrien; Kolowski, Joseph; Nzamba, Brave S; Alonso, Alfonso

2015-10-01

The active field of connectivity conservation has provided numerous methods to identify wildlife corridors with the aim of reducing the ecological effect of fragmentation. Nevertheless, these methods often rely on untested hypotheses of animal movements, usually fail to generate fine-scale predictions of road crossing sites, and do not allow managers to prioritize crossing sites for implementing road fragmentation mitigation measures. We propose a new method that addresses these limitations. We illustrate this method with data from southwestern Gabon (central Africa). We used stratified random transect surveys conducted in two seasons to model the distribution of African forest elephant (Loxodonta cyclotis), forest buffalo (Syncerus caffer nanus), and sitatunga (Tragelaphus spekii) in a mosaic landscape along a 38.5 km unpaved road scheduled for paving. Using a validation data set of recorded crossing locations, we evaluated the performance of three types of models (local suitability, local least-cost movement, and regional least-cost movement) in predicting actual road crossings for each species, and developed a unique and flexible scoring method for prioritizing road sections for the implementation of road fragmentation mitigation measures. With a data set collected in <10 weeks of fieldwork, the method was able to identify seasonal changes in animal movements for buffalo and sitatunga that shift from a local exploitation of the site in the wet season to movements through the study site in the dry season, whereas elephants use the entire study area in both seasons. These three species highlighted the need to use species- and season-specific modeling of movement. From these movement models, the method ranked road sections for their suitability for implementing fragmentation mitigation efforts, allowing managers to adjust priority thresholds based on budgets and management goals. The method relies on data that can be obtained in a period compatible with environmental impact assessment constraints, and is flexible enough to incorporate other potential movement models and scoring criteria. This approach improves upon available methods and can help inform prioritization of road and other linear infrastructure segments that require impact mitigation methods to ensure long-term landscape connectivity.

Electromagnetic exploration in high-salinity groundwater zones: case studies from volcanic and soft sedimentary sites in coastal Japan

NASA Astrophysics Data System (ADS)

Suzuki, Koichi; Kusano, Yukiko; Ochi, Ryota; Nishiyama, Nariaki; Tokunaga, Tomochika; Tanaka, Kazuhiro

2017-01-01

Estimating the spatial distribution of groundwater salinity in coastal plain regions is becoming increasingly important for site characterisation and the prediction of hydrogeological environmental conditions resulting from radioactive waste disposal and underground CO2 storage. In previous studies of the freshwater-saltwater interface, electromagnetic methods were used for sites characterised by unconsolidated deposits or Neocene soft sedimentary rocks. However, investigating the freshwater-saltwater interface in hard rock sites (e.g. igneous areas) is more complex, with the permeability of the rocks greatly influenced by fractures. In this study, we investigated the distribution of high-salinity groundwater at two volcanic rock sites and one sedimentary rock site, each characterised by different hydrogeological features. Our investigations included (1) applying the controlled source audio-frequency magnetotelluric (CSAMT) method and (2) conducting laboratory tests to measure the electrical properties of rock core samples. We interpreted the 2D resistivity sections by referring to previous data on geology and geochemistry of groundwater. At the Tokusa site, an area of inland volcanic rocks, low resistivity zones were detected along a fault running through volcanic rocks and shallow sediments. The results suggest that fluids rise through the Tokusa-Jifuku Fault to penetrate shallow sediments in a direction parallel to the river, and some fluids are diluted by rainwater. At the Oki site, a volcanic island on a continental shelf, four resistivity zones (in upward succession: low, high, low and high) were detected. The results suggest that these four zones were formed during a transgression-regression cycle caused by the last glacial period. At the Saijo site, located on a coastal plain composed of thick sediments, we observed a deep low resistivity zone, indicative of fossil seawater remnant from a transgression after the last glacial period. The current coastal plain formed in historical times, following which fresh water penetrated the upper parts of the fossil seawater zone to form a freshwater aquifer ~200 m in thickness.

Using MCDA and GIS for hazardous waste landfill siting considering land scarcity for waste disposal

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

Feo, Giovanni De, E-mail: g.defeo@unisa.it; Gisi, Sabino De

Highlights: • Wasting land for the siting of hazardous waste landfills must be avoided. • The siting procedure is based on a land use map of potentially suitable areas. • All the waste facilities of the management system are simultaneously considered. • A case study is developed considering two multi-criteria techniques. • An innovative criteria weighting tool (PSW) is used in combination with the AHP. - Abstract: The main aim of this study was to develop a procedure that minimizes the wasting of space for the siting of hazardous waste landfills as part of a solid waste management system. Wemore » wanted to tackle the shortage of land for waste disposal that is a serious and growing problem in most large urban regions. The procedure combines a multi-criteria decision analysis (MCDA) approach with a geographical information system (GIS). The GIS was utilised to obtain an initial screening in order to eliminate unsuitable areas, whereas the MCDA was developed to select the most suitable sites. The novelty of the proposed siting procedure is the introduction of a new screening phase before the macro-siting step aimed at producing a “land use map of potentially suitable areas” for the siting of solid waste facilities which simultaneously takes into consideration all plant types. The issue of obtaining sites evaluations of a specific facility was coupled with the issue of not wasting land appropriate to facilitate other types of waste management options. In the developed case study, the use of an innovative criteria weighting tool (the “Priority Scale”) in combination with the Analytic Hierarchy Process was useful to easier define the priorities of the evaluation criteria in comparison with other classic methods such as the Paired Comparison Technique in combination with the Simple Additive Weighting method.« less

DEVELOPMENT OF THE EPA RELATIVE MOLDINESS INDEX© AND ITS RELATIONSHIP TO HEALTH

EPA Science Inventory

This study compared two binary classification methods to evaluate the mold condition in 271 homes of infants, 144 of which later developed symptoms of respiratory illness. A method using on-site visual mold inspection was compared to another method using a quantitative index of ...

A field study of selected U.S. Geological Survey analytical methods for measuring pesticides in filtered stream water, June - September 2012

USGS Publications Warehouse

Martin, Jeffrey D.; Norman, Julia E.; Sandstrom, Mark W.; Rose, Claire E.

2017-09-06

U.S. Geological Survey monitoring programs extensively used two analytical methods, gas chromatography/mass spectrometry and liquid chromatography/mass spectrometry, to measure pesticides in filtered water samples during 1992–2012. In October 2012, the monitoring programs began using direct aqueous-injection liquid chromatography tandem mass spectrometry as a new analytical method for pesticides. The change in analytical methods, however, has the potential to inadvertently introduce bias in analysis of datasets that span the change.A field study was designed to document performance of the new method in a variety of stream-water matrices and to quantify any potential changes in measurement bias or variability that could be attributed to changes in analytical methods. The goals of the field study were to (1) summarize performance (bias and variability of pesticide recovery) of the new method in a variety of stream-water matrices; (2) compare performance of the new method in laboratory blank water (laboratory reagent spikes) to that in a variety of stream-water matrices; (3) compare performance (analytical recovery) of the new method to that of the old methods in a variety of stream-water matrices; (4) compare pesticide detections and concentrations measured by the new method to those of the old methods in a variety of stream-water matrices; (5) compare contamination measured by field blank water samples in old and new methods; (6) summarize the variability of pesticide detections and concentrations measured by the new method in field duplicate water samples; and (7) identify matrix characteristics of environmental water samples that adversely influence the performance of the new method. Stream-water samples and a variety of field quality-control samples were collected at 48 sites in the U.S. Geological Survey monitoring networks during June–September 2012. Stream sites were located across the United States and included sites in agricultural and urban land-use settings, as well as sites on major rivers.The results of the field study identified several challenges for the analysis and interpretation of data analyzed by both old and new methods, particularly when data span the change in methods and are combined for analysis of temporal trends in water quality. The main challenges identified are large (greater than 30 percent), statistically significant differences in analytical recovery, detection capability, and (or) measured concentrations for selected pesticides. These challenges are documented and discussed, but specific guidance or statistical methods to resolve these differences in methods are beyond the scope of the report. The results of the field study indicate that the implications of the change in analytical methods must be assessed individually for each pesticide and method.Understanding the possible causes of the systematic differences in concentrations between methods that remain after recovery adjustment might be necessary to determine how to account for the differences in data analysis. Because recoveries for each method are independently determined from separate reference standards and spiking solutions, the differences might be due to an error in one of the reference standards or solutions or some other basic aspect of standard procedure in the analytical process. Further investigation of the possible causes is needed, which will lead to specific decisions on how to compensate for these differences in concentrations in data analysis. In the event that further investigations do not provide insight into the causes of systematic differences in concentrations between methods, the authors recommend continuing to collect and analyze paired environmental water samples by both old and new methods. This effort should be targeted to seasons, sites, and expected concentrations to supplement those concentrations already assessed and to compare the ongoing analytical recovery of old and new methods to those observed in the summer and fall of 2012.

The role of economics in the QUERI program: QUERI Series

PubMed Central

Smith, Mark W; Barnett, Paul G

2008-01-01

Background The United States (U.S.) Department of Veterans Affairs (VA) Quality Enhancement Research Initiative (QUERI) has implemented economic analyses in single-site and multi-site clinical trials. To date, no one has reviewed whether the QUERI Centers are taking an optimal approach to doing so. Consistent with the continuous learning culture of the QUERI Program, this paper provides such a reflection. Methods We present a case study of QUERI as an example of how economic considerations can and should be integrated into implementation research within both single and multi-site studies. We review theoretical and applied cost research in implementation studies outside and within VA. We also present a critique of the use of economic research within the QUERI program. Results Economic evaluation is a key element of implementation research. QUERI has contributed many developments in the field of implementation but has only recently begun multi-site implementation trials across multiple regions within the national VA healthcare system. These trials are unusual in their emphasis on developing detailed costs of implementation, as well as in the use of business case analyses (budget impact analyses). Conclusion Economics appears to play an important role in QUERI implementation studies, only after implementation has reached the stage of multi-site trials. Economic analysis could better inform the choice of which clinical best practices to implement and the choice of implementation interventions to employ. QUERI economics also would benefit from research on costing methods and development of widely accepted international standards for implementation economics. PMID:18430199

Assessment of In-Situ Reductive Dechlorination Using Compound-Specific Stable Isotopes, Functional-Gene Pcr, and Geochemical Data

PubMed Central

Carreón-Diazconti, Concepción; Santamaría, Johanna; Berkompas, Justin; Field, James A.; Brusseau, Mark L.

2010-01-01

Isotopic analysis and molecular-based bioassay methods were used in conjunction with geochemical data to assess intrinsic reductive dechlorination processes for a chlorinated-solvent contaminated site in Tucson, Arizona. Groundwater samples were obtained from monitoring wells within a contaminant plume comprising tetrachloroethene and its metabolites trichloroethene, cis-1,2-dichloroethene, vinyl chloride, and ethene, as well as compounds associated with free-phase diesel present at the site. Compound specific isotope (CSI) analysis was performed to characterize biotransformation processes influencing the transport and fate of the chlorinated contaminants. PCR analysis was used to assess the presence of indigenous reductive dechlorinators. The target regions employed were the 16s rRNA gene sequences of Dehalococcoides sp. and Desulfuromonas sp., and DNA sequences of genes pceA, tceA, bvcA, and vcrA, which encode reductive dehalogenases. The results of the analyses indicate that relevant microbial populations are present and that reductive dechlorination is presently occurring at the site. The results further show that potential degrader populations as well as biotransformation activity is non-uniformly distributed within the site. The results of laboratory microcosm studies conducted using groundwater collected from the field site confirmed the reductive dechlorination of tetrachloroethene to dichloroethene. This study illustrates the use of an integrated, multiple-method approach for assessing natural attenuation at a complex chlorinated-solvent contaminated site. PMID:19603638

On-orbit characterization of hyperspectral imagers

NASA Astrophysics Data System (ADS)

McCorkel, Joel

Remote Sensing Group (RSG) at the University of Arizona has a long history of using ground-based test sites for the calibration of airborne- and satellite-based sensors. Often, ground-truth measurements at these tests sites are not always successful due to weather and funding availability. Therefore, RSG has also employed automated ground instrument approaches and cross-calibration methods to verify the radiometric calibration of a sensor. The goal in the cross-calibration method is to transfer the calibration of a well-known sensor to that of a different sensor. This dissertation presents a method for determining the radiometric calibration of a hyperspectral imager using multispectral imagery. The work relies on a multispectral sensor, Moderate-resolution Imaging Spectroradiometer (MODIS), as a reference for the hyperspectral sensor Hyperion. Test sites used for comparisons are Railroad Valley in Nevada and a portion of the Libyan Desert in North Africa. A method to predict hyperspectral surface reflectance using a combination of MODIS data and spectral shape information is developed and applied for the characterization of Hyperion. Spectral shape information is based on RSG's historical in situ data for the Railroad Valley test site and spectral library data for the Libyan test site. Average atmospheric parameters, also based on historical measurements, are used in reflectance prediction and transfer to space. Results of several cross-calibration scenarios that differ in image acquisition coincidence, test site, and reference sensor are found for the characterization of Hyperion. These are compared with results from the reflectance-based approach of vicarious calibration, a well-documented method developed by the RSG that serves as a baseline for calibration performance for the cross-calibration method developed here. Cross-calibration provides results that are within 2% of those of reflectance-based results in most spectral regions. Larger disagreements exist for shorter wavelengths studied in this work as well as in spectral areas that experience absorption by the atmosphere.

Validity and feasibility of a satellite imagery-based method for rapid estimation of displaced populations

PubMed Central

2013-01-01

Background Estimating the size of forcibly displaced populations is key to documenting their plight and allocating sufficient resources to their assistance, but is often not done, particularly during the acute phase of displacement, due to methodological challenges and inaccessibility. In this study, we explored the potential use of very high resolution satellite imagery to remotely estimate forcibly displaced populations. Methods Our method consisted of multiplying (i) manual counts of assumed residential structures on a satellite image and (ii) estimates of the mean number of people per structure (structure occupancy) obtained from publicly available reports. We computed population estimates for 11 sites in Bangladesh, Chad, Democratic Republic of Congo, Ethiopia, Haiti, Kenya and Mozambique (six refugee camps, three internally displaced persons’ camps and two urban neighbourhoods with a mixture of residents and displaced) ranging in population from 1,969 to 90,547, and compared these to “gold standard” reference population figures from census or other robust methods. Results Structure counts by independent analysts were reasonably consistent. Between one and 11 occupancy reports were available per site and most of these reported people per household rather than per structure. The imagery-based method had a precision relative to reference population figures of <10% in four sites and 10–30% in three sites, but severely over-estimated the population in an Ethiopian camp with implausible occupancy data and two post-earthquake Haiti sites featuring dense and complex residential layout. For each site, estimates were produced in 2–5 working person-days. Conclusions In settings with clearly distinguishable individual structures, the remote, imagery-based method had reasonable accuracy for the purposes of rapid estimation, was simple and quick to implement, and would likely perform better in more current application. However, it may have insurmountable limitations in settings featuring connected buildings or shelters, a complex pattern of roofs and multi-level buildings. Based on these results, we discuss possible ways forward for the method’s development. PMID:23343099

Validity and feasibility of a satellite imagery-based method for rapid estimation of displaced populations.

PubMed

Checchi, Francesco; Stewart, Barclay T; Palmer, Jennifer J; Grundy, Chris

2013-01-23

Estimating the size of forcibly displaced populations is key to documenting their plight and allocating sufficient resources to their assistance, but is often not done, particularly during the acute phase of displacement, due to methodological challenges and inaccessibility. In this study, we explored the potential use of very high resolution satellite imagery to remotely estimate forcibly displaced populations. Our method consisted of multiplying (i) manual counts of assumed residential structures on a satellite image and (ii) estimates of the mean number of people per structure (structure occupancy) obtained from publicly available reports. We computed population estimates for 11 sites in Bangladesh, Chad, Democratic Republic of Congo, Ethiopia, Haiti, Kenya and Mozambique (six refugee camps, three internally displaced persons' camps and two urban neighbourhoods with a mixture of residents and displaced) ranging in population from 1,969 to 90,547, and compared these to "gold standard" reference population figures from census or other robust methods. Structure counts by independent analysts were reasonably consistent. Between one and 11 occupancy reports were available per site and most of these reported people per household rather than per structure. The imagery-based method had a precision relative to reference population figures of <10% in four sites and 10-30% in three sites, but severely over-estimated the population in an Ethiopian camp with implausible occupancy data and two post-earthquake Haiti sites featuring dense and complex residential layout. For each site, estimates were produced in 2-5 working person-days. In settings with clearly distinguishable individual structures, the remote, imagery-based method had reasonable accuracy for the purposes of rapid estimation, was simple and quick to implement, and would likely perform better in more current application. However, it may have insurmountable limitations in settings featuring connected buildings or shelters, a complex pattern of roofs and multi-level buildings. Based on these results, we discuss possible ways forward for the method's development.

Utility of Penman-Monteith, Priestley-Taylor, reference evapotranspiration, and pan evaporation methods to estimate pasture evapotranspiration

USGS Publications Warehouse

Sumner, D.M.; Jacobs, J.M.

2005-01-01

Actual evapotranspiration (ETa) was measured at 30-min resolution over a 19-month period (September 28, 2000-April 23, 2002) from a nonirrigated pasture site in Florida, USA, using eddy correlation methods. The relative magnitude of measured ETa (about 66% of long-term annual precipitation at the study site) indicates the importance of accurate ET a estimates for water resources planning. The time and cost associated with direct measurements of ETa and the rarity of historical measurements of ETa make the use of methods relying on more easily obtainable data desirable. Several such methods (Penman-Monteith (PM), modified Priestley-Taylor (PT), reference evapotranspiration (ET 0), and pan evaporation (Ep)) were related to measured ETa using regression methods to estimate PM bulk surface conductance, PT ??, ET0 vegetation coefficient, and Ep pan coefficient. The PT method, where the PT ?? is a function of green-leaf area index (LAI) and solar radiation, provided the best relation with ET a (standard error (SE) for daily ETa of 0.11 mm). The PM method, in which the bulk surface conductance was a function of net radiation and vapor-pressure deficit, was slightly less effective (SE=0.15 mm) than the PT method. Vegetation coefficients for the ET0 method (SE=0.29 mm) were found to be a simple function of LAI. Pan coefficients for the Ep method (SE=0.40 mm) were found to be a function of LAI and Ep. Historical or future meteorological, LAI, and pan evaporation data from the study site could be used, along with the relations developed within this study, to provide estimates of ETa in the absence of direct measurements of ETa. Additionally, relations among PM, PT, and ET0 methods and ETa can provide estimates of ETa in other, environmentally similar, pasture settings for which meteorological and LAI data can be obtained or estimated. ?? 2004 Elsevier B.V. All rights reserved.

A Comparison of Two Sampling Strategies to Assess Discomycete Diversity in Wet Tropical Forests

Treesearch

SHARON A. CANTRELL

2004-01-01

Most of the fungal diversity studies that have used a systematic collecting scheme have not included the discomycetes, so optimal sampling methods are not available for this group. In this study, I tested two sampling methods at each sites in the Caribbean National Forest, Puerto Rico and Ebano Verde Reserve, Dominican Republic. For a plot-based sampling method, 10 ×...

Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics.

PubMed

Graham, Sarah E; Smith, Richard D; Carlson, Heather A

2018-02-26

Water molecules are an important factor in protein-ligand binding. Upon binding of a ligand with a protein's surface, waters can either be displaced by the ligand or may be conserved and possibly bridge interactions between the protein and ligand. Depending on the specific interactions made by the ligand, displacing waters can yield a gain in binding affinity. The extent to which binding affinity may increase is difficult to predict, as the favorable displacement of a water molecule is dependent on the site-specific interactions made by the water and the potential ligand. Several methods have been developed to predict the location of water sites on a protein's surface, but the majority of methods are not able to take into account both protein dynamics and the interactions made by specific functional groups. Mixed-solvent molecular dynamics (MixMD) is a cosolvent simulation technique that explicitly accounts for the interaction of both water and small molecule probes with a protein's surface, allowing for their direct competition. This method has previously been shown to identify both active and allosteric sites on a protein's surface. Using a test set of eight systems, we have developed a method using MixMD to identify conserved and displaceable water sites. Conserved sites can be determined by an occupancy-based metric to identify sites which are consistently occupied by water even in the presence of probe molecules. Conversely, displaceable water sites can be found by considering the sites which preferentially bind probe molecules. Furthermore, the inclusion of six probe types allows the MixMD method to predict which functional groups are capable of displacing which water sites. The MixMD method consistently identifies sites which are likely to be nondisplaceable and predicts the favorable displacement of water sites that are known to be displaced upon ligand binding.

Field demonstration of on-site analytical methods for TNT and RDX in ground water

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

Craig, H.; Ferguson, G.; Markos, A.

1996-12-31

A field demonstration was conducted to assess the performance of eight commercially-available and emerging colorimetric, immunoassay, and biosensor on-site analytical methods for explosives 2,4,6-trinitrotoluene (TNT) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in ground water and leachate at the Umatilla Army Depot Activity, Hermiston, Oregon and US Naval Submarine Base, Bangor, Washington, Superfund sites. Ground water samples were analyzed by each of the on-site methods and results compared to laboratory analysis using high performance liquid chromatography (HPLC) with EPA SW-846 Method 8330. The commercial methods evaluated include the EnSys, Inc., TNT and RDX colorimetric test kits (EPA SW-846 Methods 8515 and 8510) with amore » solid phase extraction (SPE) step, the DTECH/EM Science TNT and RDX immunoassay test kits (EPA SW-846 Methods 4050 and 4051), and the Ohmicron TNT immunoassay test kit. The emerging methods tested include the antibody-based Naval Research Laboratory (NRL) Continuous Flow Immunosensor (CFI) for TNT and RDX, and the Fiber Optic Biosensor (FOB) for TNT. Accuracy of the on-site methods were evaluated using linear regression analysis and relative percent difference (RPD) comparison criteria. Over the range of conditions tested, the colorimetric methods for TNT and RDX showed the highest accuracy of the emerging methods for TNT and RDX. The colorimetric method was selected for routine ground water monitoring at the Umatilla site, and further field testing on the NRL CFI and FOB biosensors will continue at both Superfund sites.« less

Machine-Learning Methods Enable Exhaustive Searches for Active Bimetallic Facets and Reveal Active Site Motifs for CO 2 Reduction

DOE PAGES

Ulissi, Zachary W.; Tang, Michael T.; Xiao, Jianping; ...

2017-07-27

Bimetallic catalysts are promising for the most difficult thermal and electrochemical reactions, but modeling the many diverse active sites on polycrystalline samples is an open challenge. Here, we present a general framework for addressing this complexity in a systematic and predictive fashion. Active sites for every stable low-index facet of a bimetallic crystal are enumerated and cataloged, yielding hundreds of possible active sites. The activity of these sites is explored in parallel using a neural-network-based surrogate model to share information between the many density functional theory (DFT) relaxations, resulting in activity estimates with an order of magnitude fewer explicit DFTmore » calculations. Sites with interesting activity were found and provide targets for follow-up calculations. This process was applied to the electrochemical reduction of CO 2 on nickel gallium bimetallics and indicated that most facets had similar activity to Ni surfaces, but a few exposed Ni sites with a very favorable on-top CO configuration. This motif emerged naturally from the predictive modeling and represents a class of intermetallic CO 2 reduction catalysts. These sites rationalize recent experimental reports of nickel gallium activity and why previous materials screens missed this exciting material. Most importantly these methods suggest that bimetallic catalysts will be discovered by studying facet reactivity and diversity of active sites more systematically.« less

Machine-Learning Methods Enable Exhaustive Searches for Active Bimetallic Facets and Reveal Active Site Motifs for CO 2 Reduction

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

Ulissi, Zachary W.; Tang, Michael T.; Xiao, Jianping

Bimetallic catalysts are promising for the most difficult thermal and electrochemical reactions, but modeling the many diverse active sites on polycrystalline samples is an open challenge. Here, we present a general framework for addressing this complexity in a systematic and predictive fashion. Active sites for every stable low-index facet of a bimetallic crystal are enumerated and cataloged, yielding hundreds of possible active sites. The activity of these sites is explored in parallel using a neural-network-based surrogate model to share information between the many density functional theory (DFT) relaxations, resulting in activity estimates with an order of magnitude fewer explicit DFTmore » calculations. Sites with interesting activity were found and provide targets for follow-up calculations. This process was applied to the electrochemical reduction of CO 2 on nickel gallium bimetallics and indicated that most facets had similar activity to Ni surfaces, but a few exposed Ni sites with a very favorable on-top CO configuration. This motif emerged naturally from the predictive modeling and represents a class of intermetallic CO 2 reduction catalysts. These sites rationalize recent experimental reports of nickel gallium activity and why previous materials screens missed this exciting material. Most importantly these methods suggest that bimetallic catalysts will be discovered by studying facet reactivity and diversity of active sites more systematically.« less

Meteorologically-adjusted trend analysis of surface observed ozone at three monitoring sites in Delhi, India: 2007-2011

NASA Astrophysics Data System (ADS)

Biswas, J.; Farooqui, Z.; Guttikunda, S. K.

2012-12-01

It is well known that meteorological parameters have significant impact on surface ozone concentrations. Therefore it is important to remove the effects of meteorology on ozone concentrations to correctly estimate long-term trends in ozone levels due to the alterations in precursor emissions. This is important for the development of effectual control strategies. In this study surface observed ozone trends in New Delhi are analyzed using Komogorov-Zurbenko (KZ) filter, US EPA ozone adjustment due to weather approach and the classification and regression tree method. The statistical models are applied to the ozone data at three observational sites in New Delhi metropolitan areas, 1) Income Tax Office (ITO) 2) Sirifort and 3) Delhi College of Engineering (DCE). The ITO site is located adjacent to a traffic crossing, Sirifort is an urban site and the DCE site is located in a residential area. The ITO site is also influenced by local industrial emissions. DCE has higher ozone levels than the other two sites. It was found that ITO has lowest ozone concentrations amongst the three sites due to ozone titrating due to industrial and on-road mobile NOx emissions. The statistical methods employed can assess ozone trends at these sites with a high degree of confidence and the results can be used to gauge the effectiveness of control strategies on surface ozone levels in New Delhi.

Videoconferencing for site initiations in clinical studies: Mixed methods evaluation of usability, acceptability, and impact on recruitment.

PubMed

Randell, Rebecca; Backhouse, Michael R; Nelson, E Andrea

2016-12-01

A critical issue for multicentre clinical studies is conducting site initiations, ensuring sites are trained in study procedures and comply with relevant governance requirements before they begin recruiting patients. How technology can support site initiations has not previously been explored. This study sought to evaluate use of off-the-shelf web-based videoconferencing to deliver site initiations for a large national multicentre study. Participants in the initiations, including podiatrists, diabetologists, trial coordinators, and research nurses, completed an online questionnaire based on the System Usability Scale (SUS) (N = 15). This was followed by semi-structured interviews, with a consultant diabetologist, a trial coordinator, and three research nurses, exploring perceived benefits and limitations of videoconferencing. The mean SUS score for the videoconferencing platform was 87.2 (SD = 13.7), suggesting a good level of usability. Interview participants perceived initiations delivered by videoconferencing as being more interactive and easier to follow than those delivered by teleconference. In comparison to face-to-face initiations, videoconferencing takes less time, easily fitting in with the work of staff at the local sites. Perceptions of impact on communication varied according to the hardware used. Off-the-shelf videoconferencing is a viable alternative to face-to-face site initiations and confers advantages over teleconferencing.

The Benchmark Farm Program : a method for estimating irrigation water use in southwest Florida

USGS Publications Warehouse

Duerr, A.D.; Trommer, J.T.

1982-01-01

Irrigation water-use data are summarized in this report for 74 farms in the Southwest Florida Water Management District. Most data are for 1978-90, but 18 farms have data extending back to the early 1970's. Data include site number and location, season and year, crop type, irrigation system, monitoring method, and inches of water applied per acre. Crop types include citrus, cucumbers, pasture, peanuts, sod, strawberries, and tropical fish farms are also included. Water-application rates per growing season ranged from 0 inches per acre for several citrus and pasture sites to 239.7 inches per acre for a nursery site. The report also includes rainfall data for 12 stations throughout the study area. (USGS)

Methods for estimating peak-flow frequencies at ungaged sites in Montana based on data through water year 2011: Chapter F in Montana StreamStats

USGS Publications Warehouse

Sando, Roy; Sando, Steven K.; McCarthy, Peter M.; Dutton, DeAnn M.

2016-04-05

The U.S. Geological Survey (USGS), in cooperation with the Montana Department of Natural Resources and Conservation, completed a study to update methods for estimating peak-flow frequencies at ungaged sites in Montana based on peak-flow data at streamflow-gaging stations through water year 2011. The methods allow estimation of peak-flow frequencies (that is, peak-flow magnitudes, in cubic feet per second, associated with annual exceedance probabilities of 66.7, 50, 42.9, 20, 10, 4, 2, 1, 0.5, and 0.2 percent) at ungaged sites. The annual exceedance probabilities correspond to 1.5-, 2-, 2.33-, 5-, 10-, 25-, 50-, 100-, 200-, and 500-year recurrence intervals, respectively.Regional regression analysis is a primary focus of Chapter F of this Scientific Investigations Report, and regression equations for estimating peak-flow frequencies at ungaged sites in eight hydrologic regions in Montana are presented. The regression equations are based on analysis of peak-flow frequencies and basin characteristics at 537 streamflow-gaging stations in or near Montana and were developed using generalized least squares regression or weighted least squares regression.All of the data used in calculating basin characteristics that were included as explanatory variables in the regression equations were developed for and are available through the USGS StreamStats application (http://water.usgs.gov/osw/streamstats/) for Montana. StreamStats is a Web-based geographic information system application that was created by the USGS to provide users with access to an assortment of analytical tools that are useful for water-resource planning and management. The primary purpose of the Montana StreamStats application is to provide estimates of basin characteristics and streamflow characteristics for user-selected ungaged sites on Montana streams. The regional regression equations presented in this report chapter can be conveniently solved using the Montana StreamStats application.Selected results from this study were compared with results of previous studies. For most hydrologic regions, the regression equations reported for this study had lower mean standard errors of prediction (in percent) than the previously reported regression equations for Montana. The equations presented for this study are considered to be an improvement on the previously reported equations primarily because this study (1) included 13 more years of peak-flow data; (2) included 35 more streamflow-gaging stations than previous studies; (3) used a detailed geographic information system (GIS)-based definition of the regulation status of streamflow-gaging stations, which allowed better determination of the unregulated peak-flow records that are appropriate for use in the regional regression analysis; (4) included advancements in GIS and remote-sensing technologies, which allowed more convenient calculation of basin characteristics and investigation of many more candidate basin characteristics; and (5) included advancements in computational and analytical methods, which allowed more thorough and consistent data analysis.This report chapter also presents other methods for estimating peak-flow frequencies at ungaged sites. Two methods for estimating peak-flow frequencies at ungaged sites located on the same streams as streamflow-gaging stations are described. Additionally, envelope curves relating maximum recorded annual peak flows to contributing drainage area for each of the eight hydrologic regions in Montana are presented and compared to a national envelope curve. In addition to providing general information on characteristics of large peak flows, the regional envelope curves can be used to assess the reasonableness of peak-flow frequency estimates determined using the regression equations.

A multisite validation of whole slide imaging for primary diagnosis using standardized data collection and analysis.

PubMed

Wack, Katy; Drogowski, Laura; Treloar, Murray; Evans, Andrew; Ho, Jonhan; Parwani, Anil; Montalto, Michael C

2016-01-01

Text-based reporting and manual arbitration for whole slide imaging (WSI) validation studies are labor intensive and do not allow for consistent, scalable, and repeatable data collection or analysis. The objective of this study was to establish a method of data capture and analysis using standardized codified checklists and predetermined synoptic discordance tables and to use these methods in a pilot multisite validation study. Fifteen case report form checklists were generated from the College of American Pathology cancer protocols. Prior to data collection, all hypothetical pairwise comparisons were generated, and a level of harm was determined for each possible discordance. Four sites with four pathologists each generated 264 independent reads of 33 cases. Preestablished discordance tables were applied to determine site by site and pooled accuracy, intrareader/intramodality, and interreader intramodality error rates. Over 10,000 hypothetical pairwise comparisons were evaluated and assigned harm in discordance tables. The average difference in error rates between WSI and glass, as compared to ground truth, was 0.75% with a lower bound of 3.23% (95% confidence interval). Major discordances occurred on challenging cases, regardless of modality. The average inter-reader agreement across sites for glass was 76.5% (weighted kappa of 0.68) and for digital it was 79.1% (weighted kappa of 0.72). These results demonstrate the feasibility and utility of employing standardized synoptic checklists and predetermined discordance tables to gather consistent, comprehensive diagnostic data for WSI validation studies. This method of data capture and analysis can be applied in large-scale multisite WSI validations.

Stream Bank Stability in Eastern Nebraska

USGS Publications Warehouse

Soenksen, Phillip J.; Turner, Mary J.; Dietsch, Benjamin J.; Simon, Andrew

2003-01-01

Dredged and straightened channels in eastern Nebraska have experienced degradation leading to channel widening by bank failure. Degradation has progressed headward and affected the drainage systems upstream from the modified reaches. This report describes a study that was undertaken to analyze bank stability at selected sites in eastern Nebraska and develop a simplified method for estimating the stability of banks at future study sites. Bank cross sections along straight reaches of channel and geotechnical data were collected at approximately 150 sites in 26 counties of eastern Nebraska. The sites were categorized into three groups based on mapped soil permeability. With increasing permeability of the soil groups, the median cohesion values decreased and the median friction angles increased. Three analytical methods were used to determine if banks were stable (should not fail even when saturated), at risk (should not fail unless saturated), or unstable (should have already failed). The Culmann and Agricultural Research Service methods were based on the Coulomb equation and planar failure; an indirect method was developed that was based on Bishop's simplified method of slices and rotational failure. The maximum angle from horizontal at which the bank would be stable for the given soil and bank height conditions also was computed with the indirect method. Because of few soil shear-strength data, all analyses were based on the assumption of homogeneous banks, which was later shown to be atypical, at least for some banks. Using the Culmann method and assuming no soil tension cracks, 67 percent of all 908 bank sections were identified as stable, 32 percent were at risk, and 1 percent were unstable; when tension cracks were assumed, the results changed to 58 percent stable, 40 percent at risk, and 1 percent unstable. Using the Agricultural Research Service method, 67 percent of all bank sections were identified as stable and 33 percent were at risk. Using the indirect method, 62 percent of all bank sections were identified as stable and 31 percent were at risk; 3 percent were unstable, and 3 percent were outside of the range of the tables developed for the method. For each of the methods that were used, the largest percentage of stable banks and the smallest percentage of at risk banks was for the soil group with the lowest soil permeability and highest median cohesion values. A comparison of the expected stable bank angles for saturated conditions and the surveyed bank angles indicated that many of the surveyed bank angles were considerably less than the maximum expected stable bank angles despite the banks being classified as at risk or unstable. For severely degraded channels along straight reaches this was not expected. It was expected that they would have angles close to the maximum stable angle as they should have been failing from an oversteepened condition. Several explanations are possible. The channel reaches of some study sites have not yet been affected to a significant degree by degradation; study sites were selected throughout individual basins and severe degradation has not yet extended to some sites along upper reaches; and some reaches have experienced aggradation as degradation progresses upstream. Another possibility is that some bank sections have been affected by lateral migration processes, which typically result in shallow bank angles on the inside bend of the channel. Another possibility is that the maximum expected stable bank angles are too steep. The stability methods used were well established and in essential agreement with each other, and there was no reason to question the geometry data. This left non-representative soil data as a probable reason for computed stable bank angles that, at least in some cases, are overly steep. Based on an examination of the cohesion data, to which the stable bank-angle calculations were most sensitive, both vertical and horizontal variability in soil properti

A comparison of single- and multi-site calibration and validation: a case study of SWAT in the Miyun Reservoir watershed, China

NASA Astrophysics Data System (ADS)

Bai, Jianwen; Shen, Zhenyao; Yan, Tiezhu

2017-09-01

An essential task in evaluating global water resource and pollution problems is to obtain the optimum set of parameters in hydrological models through calibration and validation. For a large-scale watershed, single-site calibration and validation may ignore spatial heterogeneity and may not meet the needs of the entire watershed. The goal of this study is to apply a multi-site calibration and validation of the Soil andWater Assessment Tool (SWAT), using the observed flow data at three monitoring sites within the Baihe watershed of the Miyun Reservoir watershed, China. Our results indicate that the multi-site calibration parameter values are more reasonable than those obtained from single-site calibrations. These results are mainly due to significant differences in the topographic factors over the large-scale area, human activities and climate variability. The multi-site method involves the division of the large watershed into smaller watersheds, and applying the calibrated parameters of the multi-site calibration to the entire watershed. It was anticipated that this case study could provide experience of multi-site calibration in a large-scale basin, and provide a good foundation for the simulation of other pollutants in followup work in the Miyun Reservoir watershed and other similar large areas.

U.S. Geological Survey research in radioactive waste disposal - Fiscal years 1983, 1984, and 1985

USGS Publications Warehouse

Dinwiddie, G.A.; Trask, N.J.

1986-01-01

The report summarizes progress on geologic and hydrologic research related to the disposal of radioactive wastes. The research is described according to whether it is related most directly to: (1) high-level and transuranic wastes, (2) low-level wastes, or (3) uranium mill tailings. Included is research applicable to the identification and geohydrologic characterization of waste-disposal sites, to investigations of specific sites where wastes have been stored, and to studies of regions or environments where waste-disposal sites might be located. A significant part of the activity is concerned with techniques and methods for characterizing disposal sites and studies of geologic and hydrologic processes related to the transport and (or) retention of waste radionuclides.

TargetM6A: Identifying N6-Methyladenosine Sites From RNA Sequences via Position-Specific Nucleotide Propensities and a Support Vector Machine.

PubMed

Li, Guang-Qing; Liu, Zi; Shen, Hong-Bin; Yu, Dong-Jun

2016-10-01

As one of the most ubiquitous post-transcriptional modifications of RNA, N 6 -methyladenosine ( [Formula: see text]) plays an essential role in many vital biological processes. The identification of [Formula: see text] sites in RNAs is significantly important for both basic biomedical research and practical drug development. In this study, we designed a computational-based method, called TargetM6A, to rapidly and accurately target [Formula: see text] sites solely from the primary RNA sequences. Two new features, i.e., position-specific nucleotide/dinucleotide propensities (PSNP/PSDP), are introduced and combined with the traditional nucleotide composition (NC) feature to formulate RNA sequences. The extracted features are further optimized to obtain a much more compact and discriminative feature subset by applying an incremental feature selection (IFS) procedure. Based on the optimized feature subset, we trained TargetM6A on the training dataset with a support vector machine (SVM) as the prediction engine. We compared the proposed TargetM6A method with existing methods for predicting [Formula: see text] sites by performing stringent jackknife tests and independent validation tests on benchmark datasets. The experimental results show that the proposed TargetM6A method outperformed the existing methods for predicting [Formula: see text] sites and remarkably improved the prediction performances, with MCC = 0.526 and AUC = 0.818. We also provided a user-friendly web server for TargetM6A, which is publicly accessible for academic use at http://csbio.njust.edu.cn/bioinf/TargetM6A.

Filling the gaps in meteorological continuous data measured at FLUXNET sites with ERA-Interim reanalysis

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

Vuichard, N.; Papale, D.

In this study, exchanges of carbon, water and energy between the land surface and the atmosphere are monitored by eddy covariance technique at the ecosystem level. Currently, the FLUXNET database contains more than 500 registered sites, and up to 250 of them share data (free fair-use data set). Many modelling groups use the FLUXNET data set for evaluating ecosystem models' performance, but this requires uninterrupted time series for the meteorological variables used as input. Because original in situ data often contain gaps, from very short (few hours) up to relatively long (some months) ones, we develop a new and robustmore » method for filling the gaps in meteorological data measured at site level. Our approach has the benefit of making use of continuous data available globally (ERA-Interim) and a high temporal resolution spanning from 1989 to today. These data are, however, not measured at site level, and for this reason a method to downscale and correct the ERA-Interim data is needed. We apply this method to the level 4 data (L4) from the La Thuile collection, freely available after registration under a fair-use policy. The performance of the developed method varies across sites and is also function of the meteorological variable. On average over all sites, applying the bias correction method to the ERA-Interim data reduced the mismatch with the in situ data by 10 to 36 %, depending on the meteorological variable considered. In comparison to the internal variability of the in situ data, the root mean square error (RMSE) between the in situ data and the unbiased ERA-I (ERA-Interim) data remains relatively large (on average over all sites, from 27 to 76 % of the standard deviation of in situ data, depending on the meteorological variable considered). The performance of the method remains poor for the wind speed field, in particular regarding its capacity to conserve a standard deviation similar to the one measured at FLUXNET stations.« less

Filling the gaps in meteorological continuous data measured at FLUXNET sites with ERA-Interim reanalysis

DOE PAGES

Vuichard, N.; Papale, D.

2015-07-13

In this study, exchanges of carbon, water and energy between the land surface and the atmosphere are monitored by eddy covariance technique at the ecosystem level. Currently, the FLUXNET database contains more than 500 registered sites, and up to 250 of them share data (free fair-use data set). Many modelling groups use the FLUXNET data set for evaluating ecosystem models' performance, but this requires uninterrupted time series for the meteorological variables used as input. Because original in situ data often contain gaps, from very short (few hours) up to relatively long (some months) ones, we develop a new and robustmore » method for filling the gaps in meteorological data measured at site level. Our approach has the benefit of making use of continuous data available globally (ERA-Interim) and a high temporal resolution spanning from 1989 to today. These data are, however, not measured at site level, and for this reason a method to downscale and correct the ERA-Interim data is needed. We apply this method to the level 4 data (L4) from the La Thuile collection, freely available after registration under a fair-use policy. The performance of the developed method varies across sites and is also function of the meteorological variable. On average over all sites, applying the bias correction method to the ERA-Interim data reduced the mismatch with the in situ data by 10 to 36 %, depending on the meteorological variable considered. In comparison to the internal variability of the in situ data, the root mean square error (RMSE) between the in situ data and the unbiased ERA-I (ERA-Interim) data remains relatively large (on average over all sites, from 27 to 76 % of the standard deviation of in situ data, depending on the meteorological variable considered). The performance of the method remains poor for the wind speed field, in particular regarding its capacity to conserve a standard deviation similar to the one measured at FLUXNET stations.« less

An investigation into the bedrock depth in the Eskisehir Quaternary Basin (Turkey) using the microtremor method

NASA Astrophysics Data System (ADS)

Tün, M.; Pekkan, E.; Özel, O.; Guney, Y.

2016-10-01

Amplification can occur in a graben as a result of strong earthquake-induced ground motion. Thus, in seismic hazard and seismic site response studies, it is of the utmost importance to determine the geometry of the bedrock depth. The main objectives of this study were to determine the bedrock depth and map the depth-to-bedrock ratio for use in land use planning in regard to the mitigation of earthquake hazards in the Eskişehir Basin. The fundamental resonance frequencies (fr) of 318 investigation sites in the Eskişehir Basin were determined through case studies, and the 2-D S-wave velocity structure down to the bedrock depth was explored. Single-station microtremor data were collected from the 318 sites, as well as microtremor array data from nine sites, seismic reflection data from six sites, deep-drilling log data from three sites and shallow drilling log data from ten sites in the Eskişehir Graben. The fundamental resonance frequencies of the Eskişehir Basin sites were obtained from the microtremor data using the horizontal-to vertical (H/V) spectral ratio (HVSR) method. The phase velocities of the Rayleigh waves were estimated from the microtremor data using the spatial autocorrelation (SPAC) method. The fundamental resonance frequency range at the deepest point of the Eskişehir Basin was found to be 0.23-0.35 Hz. Based on the microtremor array measurements and the 2-D S-wave velocity profiles obtained using the SPAC method, a bedrock level with an average velocity of 1300 m s-1 was accepted as the bedrock depth limit in the region. The log data from a deep borehole and a seismic reflection cross-section of the basement rocks of the Eskişehir Basin were obtained and permitted a comparison of bedrock levels. Tests carried out using a multichannel walk-away technique permitted a seismic reflection cross-section to be obtained up to a depth of 1500-2000 m using an explosive energy source. The relationship between the fundamental resonance frequency in the Eskişehir Basin and the results of deep drilling, shallow drilling, shear wave velocity measurement and sedimentary cover depth measurement obtained from the seismic reflection section was expressed in the form of a nonlinear regression equation. An empirical relationship between fr, the thickness of sediments and the bedrock depth is suggested for use in future microzonation studies of sites in the region. The results revealed a maximum basin depth of 1000 m, located in the northeast of the Eskişehir Basin, and the SPAC and HVSR results indicated that within the study area the basin is characterized by a thin local sedimentary cover with low shear wave velocity overlying stiff materials, resulting in a sharp velocity contrast. The thicknesses of the old Quaternary and Tertiary fluvial sediments within the basin serve as the primary data sources in seismic hazard and seismic site response studies, and these results add to the body of available seismic hazard data contributing to a seismic microzonation of the Eskişehir Graben in advance of the severe earthquakes expected in the Anatolian Region.

Analysis of laparoscopic port site complications: A descriptive study

PubMed Central

Karthik, Somu; Augustine, Alfred Joseph; Shibumon, Mundunadackal Madhavan; Pai, Manohar Varadaraya

2013-01-01

CONTEXT: The rate of port site complications following conventional laparoscopic surgery is about 21 per 100,000 cases. It has shown a proportional rise with increase in the size of the port site incision and trocar. Although rare, complications that occur at the port site include infection, bleeding, and port site hernia. AIMS: To determine the morbidity associated with ports at the site of their insertion in laparoscopic surgery and to identify risk factors for complications. SETTINGS AND DESIGN: Prospective descriptive study. MATERIALS AND METHODS: In the present descriptive study, a total of 570 patients who underwent laparoscopic surgeries for various ailments between August 2009 and July 2011 at our institute were observed for port site complications prospectively and the complications were reviewed. STATISTICAL ANALYSIS USED: Descriptive statistical analysis was carried out in the present study. The statistical software, namely, SPSS 15.0 was used for the analysis of the data. RESULTS: Of the 570 patients undergoing laparoscopic surgery, 17 (3%) had developed complications specifically related to the port site during a minimum follow-up of three months; port site infection (PSI) was the most frequent (n = 10, 1.8%), followed by port site bleeding (n = 4, 0.7%), omentum-related complications (n = 2; 0.35%), and port site metastasis (n = 1, 0.175%). CONCLUSIONS: Laparoscopic surgeries are associated with minimal port site complications. Complications are related to the increased number of ports. Umbilical port involvement is the commonest. Most complications are manageable with minimal morbidity, and can be further minimized with meticulous surgical technique during entry and exit. PMID:23741110

Challenges to be overcome using population-based sampling methods to recruit veterans for a study of post-traumatic stress disorder and traumatic brain injury.

PubMed

Bayley, Peter J; Kong, Jennifer Y; Helmer, Drew A; Schneiderman, Aaron; Roselli, Lauren A; Rosse, Stephanie M; Jackson, Jordan A; Baldwin, Janet; Isaac, Linda; Nolasco, Michael; Blackman, Marc R; Reinhard, Matthew J; Ashford, John Wesson; Chapman, Julie C

2014-04-08

Many investigators are interested in recruiting veterans from recent conflicts in Afghanistan and Iraq with Traumatic Brain Injury (TBI) and/or Post Traumatic Stress Disorder (PTSD). Researchers pursuing such studies may experience problems in recruiting sufficient numbers unless effective strategies are used. Currently, there is very little information on recruitment strategies for individuals with TBI and/or PTSD. It is known that groups of patients with medical conditions may be less likely to volunteer for clinical research. This study investigated the feasibility of recruiting veterans returning from recent military conflicts--Operation Enduring Freedom (OEF) and Operation Iraqi Freedom (OIF)--using a population-based sampling method. Individuals were sampled from a previous epidemiological study. Three study sites focused on recruiting survey respondents (n = 445) who lived within a 60 mile radius of one of the sites. Overall, the successful recruitment of veterans using a population-based sampling method was dependent on the ability to contact potential participants following mass mailing. Study enrollment of participants with probable TBI and/or PTSD had a recruitment yield (enrolled/total identified) of 5.4%. We were able to contact 146 individuals, representing a contact rate of 33%. Sixty-six of the individuals contacted were screened. The major reasons for not screening included a stated lack of interest in the study (n = 37), a failure to answer screening calls after initial contact (n = 30), and an unwillingness or inability to travel to a study site (n = 10). Based on the phone screening, 36 veterans were eligible for the study. Twenty-four veterans were enrolled, (recruitment yield = 5.4%) and twelve were not enrolled for a variety of reasons. Our experience with a population-based sampling method for recruitment of recent combat veterans illustrates the challenges encountered, particularly contacting and screening potential participants. The screening and enrollment data will help guide recruitment for future studies using population-based methods.

Rapid Assessment and Response Studies of Injection Drug Use: Knowledge Gain, Capacity Building, and Intervention Development in a Multisite Study

PubMed Central

Stimson, Gerry V.; Fitch, Chris; Jarlais, Don Des; Poznyak, Vladimir; Perlis, Theresa; Oppenheimer, Edna; Rhodes, Tim

2006-01-01

Objectives. We evaluated the World Health Organization’s rapid assessment and response (RAR) method of assessing injection drug use and its associated health problems, focusing on knowledge gain, capacity building, and whether RAR leads to the development of interventions reducing the health effects of injection drug use. Methods. Data were derived from RAR studies conducted in Beijing, China; Bogotá, Colombia; Greater Rosario, Argentina; Hanoi, Vietnam; Kharkiv, Ukraine; Minsk, Belarus; Nairobi, Kenya; Penang, Malaysia; St. Petersburg, Russia; and Tehran, Iran. Results. Substantial gains in knowledge and response capacity were reported at all of the study sites. Before RAR initiation, prevention and intervention programs had been absent or inadequate at most of the sites. The RARs resulted in many new or modified interventions; 7 sites reported 24 health-related interventions that were subsequently developed and influenced by the RARs. Conclusions. RARs, which require relatively little external funding, appear to be effective in linking assessment to development of appropriate interventions. The present results add to the evidence that rapid assessment is an important public health tool. PMID:16380578

A central storage facility to reduce pesticide suicides--a feasibility study from India.

PubMed

Vijayakumar, Lakshmi; Jeyaseelan, Lakshmanan; Kumar, Shuba; Mohanraj, Rani; Devika, Shanmugasundaram; Manikandan, Sarojini

2013-09-16

Pesticide suicides are considered the single most important means of suicide worldwide. Centralized pesticide storage facilities have the possible advantage of delaying access to pesticides thereby reducing suicides. We undertook this study to examine the feasibility and acceptability of a centralized pesticide storage facility as a preventive intervention strategy in reducing pesticide suicides. A community randomized controlled feasibility study using a mixed methods approach involving a household survey; focus group discussions (FGDs) and surveillance were undertaken. The study was carried out in a district in southern India. Eight villages that engaged in floriculture were identified. Using the lottery method two were randomized to be the intervention sites and two villages constituted the control site. Two centralized storage facilities were constructed with local involvement and lockable storage boxes were constructed. The household survey conducted at baseline and one and a half years later documented information on sociodemographic data, pesticide usage, storage and suicides. At baseline 4446 individuals (1097 households) in the intervention and 3307 individuals (782 households) in the control sites were recruited while at follow up there were 4308 individuals (1063 households) in the intervention and 2673 individuals (632 households) in the control sites. There were differences in baseline characteristics and imbalances in the prevalence of suicides between intervention and control sites as this was a small feasibility study.The results from the FGDs revealed that most participants found the storage facility to be both useful and acceptable. In addition to protecting against wastage, they felt that it had also helped prevent pesticide suicides as the pesticides stored here were not as easily and readily accessible. The primary analyses were done on an Intention to Treat basis. Following the intervention, the differences between sites in changes in combined, completed and attempted suicide rates per 100,000 person-years were 295 (95% CI: 154.7, 434.8; p < 0.001) for pesticide suicide and 339 (95% CI: 165.3, 513.2, p < 0.001) for suicide of all methods. Suicide by pesticides poisoning is a major public health problem and needs innovative interventions to address it. This study, the first of its kind in the world, examined the feasibility of a central storage facility as a means of limiting access to pesticides and, has provided preliminary results on its usefulness. These results need to be interpreted with caution in view of the imbalances between sites. The facility was found to be acceptable, thereby underscoring the need for larger studies for a longer duration. ISRCTN04912407.

A Potential Biofilm Metabolite Signature for Caries Activity - A Pilot Clinical Study

PubMed Central

Zandona, F; Soini, HA; Novotny, MV; Santiago, E; Eckert, GJ; Preisser, JS; Benecha, HK; Arthur, RA; Zero, DT

2016-01-01

Background This study's aim was to compare the dental biofilm metabolite-profile of caries-active (N=11) or caries-free (N=4) children by gas chromatography-mass spectrometry (GC/MS) analyses. Methods Samples collected after overnight fasting, with or without a previous glucose rinse, were combined for each child based on the caries status of the site, re-suspended in ethanol and analyzed by GC/MS. Results Biofilm from caries-active sites exhibited a different chromatographic profile compared to caries-free sites. Qualitative and quantitative analysis suggested a special cluster of branched alcohols and esters present at substantially higher intensity in biofilms of caries-active sites. Conclusions This pilot study indicates that there are metabolites present in the biofilm which have the potential to provide a characteristic metabolomics signature for caries activity. PMID:27885354

Postmortem dynamic cerebral angiography for detecting aneurysm and bleeding sites in cases of subarachnoid hemorrhage.

PubMed

Inokuchi, Go; Yajima, Daisuke; Hayakawa, Mutsumi; Motomura, Ayumi; Chiba, Fumiko; Torimitsu, Suguru; Makino, Yohsuke; Iwase, Hirotaro

2014-12-01

One of the advantages of postmortem imaging is its ability to obtain diagnostic findings in a non-destructive manner when autopsy is either difficult or may destroy forensic evidence. In recent years, efforts have been made to incorporate computed tomography (CT) based postmortem angiography into forensic pathology; however, it is not currently clear how well the modality can determine sites of bleeding in cases of subarachnoid hemorrhage. Therefore, in this study, we investigated the utility of postmortem cerebral angiography using multi-detector row CT (MDCT) by injecting a contrast medium through a catheter inserted into the internal carotid and vertebral arteries of 10 subarachnoid hemorrhage cases. While postmortem MDCT angiography (PMCTA) was capable of detecting aneurysms in a non-destructive manner, it was sometimes difficult to identify the aneurysm and bleeding sites because of a large amount of contrast medium leaking into the extravascular space. To overcome this problem, we developed the novel contrast imaging method "dynamic cerebral angiography," which involves scanning the same area multiple times while injecting contrast medium to enable real-time observation of the contrasted vasculature. Using multiphase contrast images acquired by this method, we successfully captured the moment when contrast medium leaked from the hemorrhage site. This method will be useful for identifying exact bleeding sites on PMCTA.

Curriculum renewal in child psychiatry.

PubMed

Hanson, M; Tiberius, R; Charach, A; Ulzen, T; Sackin, D; Jain, U; Reiter, S; Shomair, G

1999-11-01

To ensure uniform design and evaluation of a clerkship curriculum for child and adolescent psychiatry teaching common disorders and problems in an efficient manner across 5 teaching sites and to include structures for continuous improvement. The curriculum committee selected for course inclusion disorders and problems of child psychiatry that were commonly encountered by primary care physicians. Instruction methods that encouraged active student learning were selected. Course coordination across sites was encouraged by several methods: involving faculty, adopting a centralized examination format, and aligning teaching methods with examination format. Quantitative and qualitative methods were used to measure students' perceptions of the course's value. These evaluative results were reviewed, and course modifications were implemented and reevaluated. The average adjusted student return rate for course evaluation questionnaires for the 3-year study period was 63%. Clerks' ratings of course learning value demonstrated that the course improved significantly and continually across all sites, according to a Scheffé post-hoc analysis. Analysis of student statements from focus-group transcripts contributed to course modifications, such as the Brief Focused Interview (BFI). Our curriculum in child psychiatry, which focused on common problems and used active learning methods, was viewed as a valuable learning experience by clinical clerks. Curriculum coordination across multiple teaching sites was accomplished by including faculty in the process and by using specific teaching and examination strategies. Structures for continuous course improvement were effective.

On the use of haplotype phylogeny to detect disease susceptibility loci

PubMed Central

Bardel, Claire; Danjean, Vincent; Hugot, Jean-Pierre; Darlu, Pierre; Génin, Emmanuelle

2005-01-01

Background The cladistic approach proposed by Templeton has been presented as promising for the study of the genetic factors involved in common diseases. This approach allows the joint study of multiple markers within a gene by considering haplotypes and grouping them in nested clades. The idea is to search for clades with an excess of cases as compared to the whole sample and to identify the mutations defining these clades as potential candidate disease susceptibility sites. However, the performance of this approach for the study of the genetic factors involved in complex diseases has never been studied. Results In this paper, we propose a new method to perform such a cladistic analysis and we estimate its power through simulations. We show that under models where the susceptibility to the disease is caused by a single genetic variant, the cladistic test is neither really more powerful to detect an association nor really more efficient to localize the susceptibility site than an individual SNP testing. However, when two interacting sites are responsible for the disease, the cladistic analysis greatly improves the probability to find the two susceptibility sites. The impact of the linkage disequilibrium and of the tree characteristics on the efficiency of the cladistic analysis are also discussed. An application on a real data set concerning the CARD15 gene and Crohn disease shows that the method can successfully identify the three variant sites that are involved in the disease susceptibility. Conclusion The use of phylogenies to group haplotypes is especially interesting to pinpoint the sites that are likely to be involved in disease susceptibility among the different markers identified within a gene. PMID:15904492

Identification of new 2,5-diketopiperazine derivatives as simultaneous effective inhibitors of αβ-tubulin and BCRP proteins: Molecular docking, Structure-Activity Relationships and virtual consensus docking studies

NASA Astrophysics Data System (ADS)

Fani, Najmeh; Sattarinezhad, Elham; Bordbar, Abdol-Khalegh

2017-06-01

In the first part of this paper, docking method was employed in order to study the binding mechanism of breast cancer resistance protein (BCRP) with a group of previously synthesized TPS-A derivatives which known as potent inhibitors of this protein to get insight into drug binding site of BCRP and to explore structure-activity relationship of these compounds. Molecular docking results showed that most of these compounds bind in the binding site of BCRP at the interface between the membrane and outer environment. In the second part, a group of designed TPS-A derivatives which showed good binding energies in the binding site of αβ-tubulin in the previous study were chosen to study their binding energies in the binding site of BCRP to investigate their simultaneous inhibitory effect on both αβ-tubulin and BCRP. The results showed that all of these compounds bind to the binding site of BCRP with relatively suitable binding energies and therefore could be potential inhibitors of both αβ-tubulin and BCRP proteins. Finally, virtual consensus docking method was utilized with the aim of design of new 2,5-diketopiperazine derivatives with significant inhibitory effect on both αβ-tubulin and BCRP proteins. For this purpose binding energies of a library of 2,5-diketopiperazine derivatives in the binding sites of αβ-tubulin and BCRP was investigated by using AutoDock and AutoDock vina tools. Molecular docking results revealed that a group of 36 compounds among them exhibit strong anti-tubulin and anti-BCRP activity.

A fractured rock geophysical toolbox method selection tool

USGS Publications Warehouse

Day-Lewis, F. D.; Johnson, C.D.; Slater, L.D.; Robinson, J.L.; Williams, J.H.; Boyden, C.L.; Werkema, D.D.; Lane, J.W.

2016-01-01

Geophysical technologies have the potential to improve site characterization and monitoring in fractured rock, but the appropriate and effective application of geophysics at a particular site strongly depends on project goals (e.g., identifying discrete fractures) and site characteristics (e.g., lithology). No method works at every site or for every goal. New approaches are needed to identify a set of geophysical methods appropriate to specific project goals and site conditions while considering budget constraints. To this end, we present the Excel-based Fractured-Rock Geophysical Toolbox Method Selection Tool (FRGT-MST). We envision the FRGT-MST (1) equipping remediation professionals with a tool to understand what is likely to be realistic and cost-effective when contracting geophysical services, and (2) reducing applications of geophysics with unrealistic objectives or where methods are likely to fail.

Estimation of future flow regime for a spatially varied Himalayan watershed using improved multi-site calibration method of SWAT model.

NASA Astrophysics Data System (ADS)

Pradhanang, S. M.; Hasan, M. A.; Booth, P.; Fallatah, O.

2016-12-01

The monsoon and snow driven regime in the Himalayan region has received increasing attention in the recent decade regarding the effects of climate change on hydrologic regimes. Modeling streamflow in such spatially varied catchment requires proper calibration and validation in hydrologic modeling. While calibration and validation are time consuming and computationally intensive, an effective regionalized approach with multi-site information is crucial for flow estimation, especially in daily scale. In this study, we adopted a multi-site approach to calibration and validation of the Soil Water Assessment Tool (SWAT) model for the Karnali river catchment, which is characterized as being the most vulnerable catchment to climate change in the Himalayan region. APHRODITE's (Asian Precipitation - Highly-Resolved Observational Data Integration Towards Evaluation) daily gridded precipitation data, one of the accurate and reliable weather date over this region were utilized in this study. The model evaluation of the entire catchment divided into four sub-catchments, utilizing discharge records from 1963 to 2010. In previous studies, multi-site calibration used only a single set of calibration parameters for all sub-catchment of a large watershed. In this study, we introduced a technique that can incorporate different sets of calibration parameters for each sub-basin, which eventually ameliorate the flow of the whole watershed. Results show that the calibrated model with new method can capture almost identical pattern of flow over the region. The predicted daily streamflow matched the observed values, with a Nash-Sutcliffe coefficient of 0.73 during calibration and 0.71 during validation period. The method perfumed better than existing multi-site calibration methods. To assess the influence of continued climate change on hydrologic processes, we modified the weather inputs for the model using precipitation and temperature changes for two Representative Concentration Pathways (RCPs) scenarios, RCP 4.5 and 8.5. Climate simulation for RCP scenarios were conducted from 1981-2100, where 1981-2005 was considered as baseline and 2006-2100 was considered as the future projection. The result shows that probability of flooding will eventually increase in future years due to increased flow in both scenarios.

Detection of Influenza A viruses at migratory bird stopover sites in Michigan, USA.

PubMed

Lickfett, Todd M; Clark, Erica; Gehring, Thomas M; Alm, Elizabeth W

2018-01-01

Introduction: Influenza A viruses have the potential to cause devastating illness in humans and domestic poultry. Wild birds are the natural reservoirs of Influenza A viruses and migratory birds are implicated in their global dissemination. High concentrations of this virus are excreted in the faeces of infected birds and faecal contamination of shared aquatic habitats can lead to indirect transmission among birds via the faecal-oral route. The role of migratory birds in the spread of avian influenza has led to large-scale surveillance efforts of circulating avian influenza viruses through direct sampling of live and dead wild birds. Environmental monitoring of bird habitats using molecular detection methods may provide additional information on the persistence of influenza virus at migratory stopover sites distributed across large spatial scales. Materials and methods: In the current study, faecal and water samples were collected at migratory stopover sites and evaluated for Influenza A by real-time quantitative reverse transcriptase PCR. Results and Discussion: This study found that Influenza A was detected at 53% of the evaluated stopover sites, and 7% and 4.8% of the faecal and water samples, respectively, tested positive for Influenza A virus. Conclusion: Environmental monitoring detected Influenza A at stopover sites used by migratory birds.

Estimation of Vs30 Soil Profile Structure of Singapore from Microtremor Records

NASA Astrophysics Data System (ADS)

Walling, M. Y.; Megawati, K.; Zhu, C.

2012-04-01

Singapore lies at the southern tip of the Malay Peninsula, covering a land area of 600 km2 and with a population exceeding 5 million. Array microtremor recording were carried out in Singapore for 40 sites that encompasses the sites of all the major geological formations. The Spatial Autocorrelation (SPAC) method is employed to determine the phase velocity dispersion curves and subsequently inverted to determine the shallow shear-wave velocity (V s) and soil stratigraphy. The depth of penetration is generally about 30 m - 40 m for most of the sites. For the present study, the V s estimation is restricted to the upper 30 m of the soil (V s30), confirming with the IBC (2006). The Reclaimed Land and the young Quaternary soft soil deposit of Kallang Formation show low V s30 values ranging from 207 m/s - 247 m/s, belonging to site E and at the boundary of site E and D. The Old Alluvium formation shows higher V s30 values ranging from 362 m/s - 563 m/s and can be classified under site C. The estimated V s30 for the sedimentary sequence of Jurong Formation reveal site C classification, with the V s30 range from 317 m/s - 712 m/s. On the other hand, the Bukit Timah Granite body shows low V s30 ranging from 225 m/s - 387 m/s, with most of the sites concentrated under site D classification and few sites at the boundary of sites D and C, for the upper 30 m. This low V s30 value of the granitic body can be explained in the light of intense weathering that the granite body has undergone for the upper layer, which is also supported from borehole records. The SPAC results are compared with nearby borehole data and they show a good correlation for sites that have soft soil formation and for the weathered granite body. The correlation confirms the reliability of SPAC method that can be applied for highly populated urbanized places like Singapore. The present research finding will be useful for further studies of site response analysis, site characterization and ground motion simulation.

Using Kriging with a heterogeneous measurement error to improve the accuracy of extreme precipitation return level estimation

NASA Astrophysics Data System (ADS)

Yin, Shui-qing; Wang, Zhonglei; Zhu, Zhengyuan; Zou, Xu-kai; Wang, Wen-ting

2018-07-01

Extreme precipitation can cause flooding and may result in great economic losses and deaths. The return level is a commonly used measure of extreme precipitation events and is required for hydrological engineer designs, including those of sewerage systems, dams, reservoirs and bridges. In this paper, we propose a two-step method to estimate the return level and its uncertainty for a study region. In the first step, we use the generalized extreme value distribution, the L-moment method and the stationary bootstrap to estimate the return level and its uncertainty at the site with observations. In the second step, a spatial model incorporating the heterogeneous measurement errors and covariates is trained to estimate return levels at sites with no observations and to improve the estimates at sites with limited information. The proposed method is applied to the daily rainfall data from 273 weather stations in the Haihe river basin of North China. We compare the proposed method with two alternatives: the first one is based on the ordinary Kriging method without measurement error, and the second one smooths the estimated location and scale parameters of the generalized extreme value distribution by the universal Kriging method. Results show that the proposed method outperforms its counterparts. We also propose a novel approach to assess the two-step method by comparing it with the at-site estimation method with a series of reduced length of observations. Estimates of the 2-, 5-, 10-, 20-, 50- and 100-year return level maps and the corresponding uncertainties are provided for the Haihe river basin, and a comparison with those released by the Hydrology Bureau of Ministry of Water Resources of China is made.

Validity and reliability of a simple, low cost measure to quantify children’s dietary intake in afterschool settings

PubMed Central

Davison, Kirsten K.; Austin, S. Bryn; Giles, Catherine; Cradock, Angie L.; Lee, Rebekka M.; Gortmaker, Steven L.

2017-01-01

Interest in evaluating and improving children’s diets in afterschool settings has grown, necessitating the development of feasible yet valid measures for capturing children’s intake in such settings. This study’s purpose was to test the criterion validity and cost of three unobtrusive visual estimation methods compared to a plate-weighing method: direct on-site observation using a 4-category rating scale and off-site rating of digital photographs taken on-site using 4- and 10-category scales. Participants were 111 children in grades 1–6 attending four afterschool programs in Boston, MA in December 2011. Researchers observed and photographed 174 total snack meals consumed across two days at each program. Visual estimates of consumption were compared to weighed estimates (the criterion measure) using intra-class correlations. All three methods were highly correlated with the criterion measure, ranging from 0.92–0.94 for total calories consumed, 0.86–0.94 for consumption of pre-packaged beverages, 0.90–0.93 for consumption of fruits/vegetables, and 0.92–0.96 for consumption of grains. For water, which was not pre-portioned, coefficients ranged from 0.47–0.52. The photographic methods also demonstrated excellent inter-rater reliability: 0.84–0.92 for the 4-point and 0.92–0.95 for the 10-point scale. The costs of the methods for estimating intake ranged from $0.62 per observation for the on-site direct visual method to $0.95 per observation for the criterion measure. This study demonstrates that feasible, inexpensive methods can validly and reliably measure children’s dietary intake in afterschool settings. Improving precision in measures of children’s dietary intake can reduce the likelihood of spurious or null findings in future studies. PMID:25596895

Examination of the reliability of the crash modification factors using empirical Bayes method with resampling technique.

PubMed

Wang, Jung-Han; Abdel-Aty, Mohamed; Wang, Ling

2017-07-01

There have been plenty of studies intended to use different methods, for example, empirical Bayes before-after methods, to get accurate estimation of CMFs. All of them have different assumptions toward crash count if there was no treatment. Additionally, another major assumption is that multiple sites share the same true CMF. Under this assumption, the CMF at an individual intersection is randomly drawn from a normally distributed population of CMFs at all intersections. Since CMFs are non-zero values, the population of all CMFs might not follow normal distributions, and even if it does, the true mean of CMFs at some intersections may be different from that at others. Therefore, a bootstrap method based on before-after empirical Bayes theory was proposed to estimate CMFs, but it did not make distributional assumptions. This bootstrap procedure has the added benefit of producing a measure of CMF stability. Furthermore, based on the bootstrapped CMF, a new CMF precision rating method was proposed to evaluate the reliability of CMFs. This study chose 29 urban four-legged intersections as treated sites, and their controls were changed from stop-controlled to signal-controlled. Meanwhile, 124 urban four-legged stop-controlled intersections were selected as reference sites. At first, different safety performance functions (SPFs) were applied to five crash categories, and it was found that each crash category had different optimal SPF form. Then, the CMFs of these five crash categories were estimated using the bootstrap empirical Bayes method. The results of the bootstrapped method showed that signalization significantly decreased Angle+Left-Turn crashes, and its CMF had the highest precision. While, the CMF for Rear-End crashes was unreliable. For KABCO, KABC, and KAB crashes, their CMFs were proved to be reliable for the majority of intersections, but the estimated effect of signalization may be not accurate at some sites. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dating the Middle Paleolithic deposits of La Quina Amont (Charente, France) using luminescence methods.

PubMed

Frouin, Marine; Lahaye, Christelle; Valladas, Hélène; Higham, Thomas; Debénath, André; Delagnes, Anne; Mercier, Norbert

2017-08-01

The site of La Quina Amont, located in the Charente region, is one of the most important sites in southwestern France for studying major changes in human behaviors from the Middle Paleolithic (MP) to the Early Upper Paleolithic (EUP). Extensively excavated over the past 50 years, numerous dating studies have been focused on the Upper Paleolithic deposits using radiocarbon on bone collagen and thermoluminescence (TL) on heated flints; however, the Mousterian levels remain undated due to the scarcity of suitable materials. Our investigations aimed to provide for the first time a chronological framework for the site using luminescence dating methods on different minerals contained in the sediments. Coarse grains of quartz were dated using the optically stimulated luminescence (OSL) technique, and polymineral fine grains were dated using both infrared (IRSL) and post-infrared (pIR-IRSL) stimulated luminescence signals. OSL, IRSL and pIR-IRSL results were combined with available TL and radiocarbon data sets to propose a chronology for the site. The agreement between these methods provides key insights into the sedimentological processes involved in the site formation and into the chronology of the human occupations. In particular, it shows that the sequence spans almost ∼20,000 years (20 ka). Moreover, the new chronological framework suggests that the makers of the Quina lithic technocomplex (LTC), who were reindeer hunters, inhabited the site from the end of marine isotope stage (MIS) 4 to the beginning of MIS 3. We also show that Levallois and Discoidal industries occurred successively under temperate paleoclimatic conditions, during MIS 3 but not after ∼40 ka. Finally, we compare the Quina LTC dataset with other sites in southern France in order to shed light upon the variability in Mousterian industries of this region. Copyright © 2017 Elsevier Ltd. All rights reserved.

System and method for laser-based, non-evaporative repair of damage sites in the surfaces of fused silica optics

DOEpatents

Adams, John J.; Bolourchi, Masoud; Bude, Jeffrey D.; Guss, Gabriel M.; Jarboe, Jeffery A.; Matthews, Manyalibo J.; Nostrand, Michael C; Wegner, Paul J.

2016-09-06

A method for repairing a damage site on a surface of an optical material is disclosed. The method may involve focusing an Infrared (IR) laser beam having a predetermined wavelength, with a predetermined beam power, to a predetermined full width ("F/W") 1/e.sup.2 diameter spot on the damage site. The focused IR laser beam is maintained on the damage site for a predetermined exposure period corresponding to a predetermined acceptable level of downstream intensification. The focused IR laser beam heats the damage site to a predetermined peak temperature, which melts and reflows material at the damage site of the optical material to create a mitigated site.

Strategies to Support Recruitment of Patients with Life-limiting illness for Research: The Palliative Care Research Cooperative Group

PubMed Central

Hanson, Laura C.; Bull, Janet; Wessell, Kathryn; Massie, Lisa; Bennett, Rachael E.; Kutner, Jean S.; Aziz, Noreen M.; Abernethy, Amy

2014-01-01

Context The Palliative Care Research Cooperative group (PCRC) is the first clinical trials cooperative for palliative care in the United States. Objectives To describe barriers and strategies for recruitment during the inaugural PCRC clinical trial. Methods The parent study was a multi-site randomized controlled trial enrolling adults with life expectancy anticipated to be 1–6 months, randomized to discontinue statins (intervention) vs. to continue on statins (control). To study recruitment best practices, we conducted semi-structured interviews with 18 site Principal Investigators (PI) and Clinical Research Coordinators (CRC), and reviewed recruitment rates. Interviews covered 3 topics – 1) successful strategies for recruitment, 2) barriers to recruitment, and 3) optimal roles of the PI and CRC. Results All eligible site PIs and CRCs completed interviews and provided data on statin protocol recruitment. The parent study completed recruitment of n=381 patients. Site enrollment ranged from 1–109 participants, with an average of 25 enrolled per site. Five major barriers included difficulty locating eligible patients, severity of illness, family and provider protectiveness, seeking patients in multiple settings, and lack of resources for recruitment activities. Five effective recruitment strategies included systematic screening of patient lists, thoughtful messaging to make research relevant, flexible protocols to accommodate patients’ needs, support from clinical champions, and the additional resources of a trials cooperative group. Conclusion The recruitment experience from the multi-site PCRC yields new insights into methods for effective recruitment to palliative care clinical trials. These results will inform training materials for the PCRC and may assist other investigators in the field. PMID:24863152

Use of Telehealth for Research and Clinical Measures in Cochlear Implant Recipients: A Validation Study

ERIC Educational Resources Information Center

Hughes, Michelle L.; Goehring, Jenny L.; Baudhuin, Jacquelyn L.; Diaz, Gina R.; Sanford, Todd; Harpster, Roger; Valente, Daniel L.

2012-01-01

Purpose: The goal of this study was to compare clinical and research-based cochlear implant (CI) measures using telehealth versus traditional methods. Method: This prospective study used an ABA design (A = laboratory, B = remote site). All measures were made twice per visit for the purpose of assessing within-session variability. Twenty-nine adult…

Controlling feeding behavior by chemical or gene-directed targeting in the brain: what's so spatial about our methods?

PubMed Central

Khan, Arshad M.

2013-01-01

Intracranial chemical injection (ICI) methods have been used to identify the locations in the brain where feeding behavior can be controlled acutely. Scientists conducting ICI studies often document their injection site locations, thereby leaving kernels of valuable location data for others to use to further characterize feeding control circuits. Unfortunately, this rich dataset has not yet been formally contextualized with other published neuroanatomical data. In particular, axonal tracing studies have delineated several neural circuits originating in the same areas where ICI injection feeding-control sites have been documented, but it remains unclear whether these circuits participate in feeding control. Comparing injection sites with other types of location data would require careful anatomical registration between the datasets. Here, a conceptual framework is presented for how such anatomical registration efforts can be performed. For example, by using a simple atlas alignment tool, a hypothalamic locus sensitive to the orexigenic effects of neuropeptide Y (NPY) can be aligned accurately with the locations of neurons labeled by anterograde tracers or those known to express NPY receptors or feeding-related peptides. This approach can also be applied to those intracranial “gene-directed” injection (IGI) methods (e.g., site-specific recombinase methods, RNA expression or interference, optogenetics, and pharmacosynthetics) that involve viral injections to targeted neuronal populations. Spatial alignment efforts can be accelerated if location data from ICI/IGI methods are mapped to stereotaxic brain atlases to allow powerful neuroinformatics tools to overlay different types of data in the same reference space. Atlas-based mapping will be critical for community-based sharing of location data for feeding control circuits, and will accelerate our understanding of structure-function relationships in the brain for mammalian models of obesity and metabolic disorders. PMID:24385950

Quantitative trace analysis of polyfluorinated alkyl substances (PFAS) in ambient air samples from Mace Head (Ireland): A method intercomparison

NASA Astrophysics Data System (ADS)

Jahnke, Annika; Barber, Jonathan L.; Jones, Kevin C.; Temme, Christian

A method intercomparison study of analytical methods for the determination of neutral, volatile polyfluorinated alkyl substances (PFAS) was carried out in March, 2006. Environmental air samples were collected in triplicate at the European background site Mace Head on the west coast of Ireland, a site dominated by 'clean' westerly winds coming across the Atlantic. Extraction and analysis were performed at two laboratories active in PFAS research using their in-house methods. Airborne polyfluorinated telomer alcohols (FTOHs), fluorooctane sulfonamides and sulfonamidoethanols (FOSAs/FOSEs) as well as additional polyfluorinated compounds were investigated. Different native and isotope-labelled internal standards (IS) were applied at various steps in the analytical procedure to evaluate the different quantification strategies. Field blanks revealed no major blank problems. European background concentrations observed at Mace Head were found to be in a similar range to Arctic data reported in the literature. Due to trace-levels at the remote site, only FTOH data sets were complete and could therefore be compared between the laboratories. Additionally, FOSEs could partly be included. Data comparison revealed that despite the challenges inherent in analysis of airborne PFAS and the low concentrations, all methods applied in this study obtained similar results. However, application of isotope-labelled IS early in the analytical procedure leads to more precise results and is therefore recommended.

Natal dispersal in the cooperatively breeding Acorn Woodpecker

USGS Publications Warehouse

Koenig, Walter D.; Hooge, P.N.; Stanback, M.T.; Haydock, J.

2000-01-01

Dispersal data are inevitably biased toward short-distance events, often highly so. We illustrate this problem using our long-term study of Acorn Woodpeckers (Melanerpes formicivorus) in central coastal California. Estimating the proportion of birds disappearing from the study area and correcting for detectability within the maximum observable distance are the first steps toward achieving a realistic estimate of dispersal distributions. Unfortunately, there is generally no objective way to determine the fates of birds not accounted for by these procedures, much less estimating the distances they may have moved. Estimated mean and root-mean-square dispersal distances range from 0.22-2.90 km for males and 0.53-9.57 km for females depending on what assumptions and corrections are made. Three field methods used to help correct for bias beyond the limits of normal study areas include surveying alternative study sites, expanding the study site (super study sites), and radio-tracking dispersers within a population. All of these methods have their limitations or can only be used in special cases. New technologies may help alleviate this problem in the near future. Until then, we urge caution in interpreting observed dispersal data from all but the most isolated of avian populations.

Comparisons of shear-wave slowness in the Santa Clara Valley, California using blind interpretations of data from invasive and noninvasive methods

USGS Publications Warehouse

Boore, D.M.; Asten, M.W.

2008-01-01

Many groups contributed to a blind interpretation exercise for the determination of shear-wave slowness beneath the Santa Clara Valley. The methods included invasive methods in deep boreholes as well as noninvasive methods using active and passive sources, at six sites within the valley (with most investigations being conducted at a pair of closely spaced sites near the center of the valley). Although significant variability exists between the models, the slownesses from the various methods are similar enough that linear site amplifications estimated in several ways are generally within 20% of one another. The methods were able to derive slownesses that increase systematically with distance from the valley edge, corresponding to a tendency for the sites to be underlain by finer-grained materials away from the valley edge. This variation is in agreement with measurements made in the boreholes at the sites.

AN OBJECTIVE CLIMATOLOGY OF CAROLINA COASTAL FRONTS

EPA Science Inventory

This study describes a simple objective method to identify cases of coastal frontogenesis offshore of the Carolinas and to characterize the sensible weather associated with frontal passage at measurement sites near the coast. The identification method, based on surface hourly d...

Guide for evaluating sweetgum sites

Treesearch

W. M. Broadfoot; Roger M. Krinard

1959-01-01

Studies at the Stonevill Research Center1 have established 3 practical methods of estimating the ability of Midsouth soils to grow sweetgum (liquidambar styraciflua). The methods were developed from data collected from 104 sweetgum plots in the area mapped on the opposite page.

Cigars, youth, and the Internet link.

PubMed Central

Malone, R E; Bero, L A

2000-01-01

OBJECTIVES: This study examined the accessibility and appeal to youth of cigar marketing sites on the Internet. METHODS: Sites marketing cigars (n = 141) were examined for age restrictions, prices, health warnings, and other elements. RESULTS: Although it is illegal for minors to purchase tobacco, only 36 sites (25.5%) prohibited purchases by minors. Sites offered low prices, and 32% accepted money orders, cashier's checks, or cash-on-delivery (COD) orders. Almost 30% of the sites included elements with potential youth appeal; only 3.5% displayed health warnings. CONCLUSIONS: The unregulated promotion of cigars on the Internet has the potential to attract youth, and there are few barriers to Internet tobacco purchases by minors. PMID:10800432

Bacterial populations within copper mine tailings: long-term effects of amendment with Class A biosolids

USDA-ARS?s Scientific Manuscript database

This study evaluates the effect of surface application of dried Class A biosolids on microbial populations within copper mine tailings. Methods and Results: Mine tailing sites were established at ASARCO Mission Mine close to Sahuarita, Arizona. Site 1 (Dec. 1998) was amended with 248 tons ha-1 of C...

Integrating Monitoring and Genetic Methods To Infer Historical Risks of PCBs and DDE to Common and Roseate Terns Nesting Near the New Bedford Harbor Superfund Site (Massachusetts, USA)

EPA Science Inventory

Common and roseate terns are migratory piscivorous seabirds with major breeding colonies within feeding range of thepolychlorinated biphenyl (PCB)-contaminated New Bedford Harbor (NBH, MA, USA) Superfund site. Our longitudinal study shows that before PCB discharges into NBH cease...

LEAK AND GAS PERMEABILITY TESTING DURING SOIL-GAS SAMPLING AT HAL'S CHEVRON LUST SITE IN GREEN RIVER, UTAH

EPA Science Inventory

The results of gas permeability and leak testing during active soil-gas sampling at Hal’s Chevron LUST Site in Green River, Utah are presented. This study was conducted to support development of a passive soil-gas sampling method. Gas mixtures containing helium and methane were...

Instrumentation, methods of flood-data collection and transmission, and evaluation of streamflow-gaging network in Indiana

USGS Publications Warehouse

Glatfelter, D.R.; Butch, G.K.

1994-01-01

The study results indicate that installation of streamflow-gaging stations at 15 new sites would improve collection of flood data. Instrumenting the 15 new sites plus 26 existing streamflow-gaging stations with telemetry, preferably data-collection platforms with satellite transmitters, would improve transmission of data to users of the information.

Silviculture and multi-resource management case studies for southwestern pinyon-juniper woodlands

Treesearch

Gerald J. Gottfried

2008-01-01

Southwestern pinyon-juniper and juniper woodlands cover large areas of the Western United States. The woodlands are heterogeneous, consisting of numerous combinations of tree, shrub, and herbaceous species and stand densities that are representative of the wide range of sites and habitat types they occupy. Silvicultural methods can be employed on better sites to meet...

The effects of festival attributes upon perceptions of crowding

Treesearch

Matthew Anderson; Deborah Kerstette; Alan Graefe

1998-01-01

The primary purpose of this study was to explore the relationship between festival attributes and perceived crowding at a festival site. Visitors to the Northwest Folklife Festival in Seattle, Washington, were chosen by a systematic sampling method to complete an on-site and follow-up survey. These surveys included questions which addressed the determinate attributes...

Nursing Home Administrators' Opinions of the Nursing Home Compare Web Site

ERIC Educational Resources Information Center

Castle, Nicholas G.

2005-01-01

Purpose: In November of 2002 the Centers for Medicare and Medicaid Services publicly reported on a national basis the quality of nursing homes on the Nursing Home Compare (NHC) Web site. This study examines administrators' opinions of this initiative and whether it has fostered quality improvement. Design and Methods: Data used in this…

Hypnosis control based on the minimum concentration of anesthetic drug for maintaining appropriate hypnosis.

PubMed

Furutani, Eiko; Nishigaki, Yuki; Kanda, Chiaki; Takeda, Toshihiro; Shirakami, Gotaro

2013-01-01

This paper proposes a novel hypnosis control method using Auditory Evoked Potential Index (aepEX) as a hypnosis index. In order to avoid side effects of an anesthetic drug, it is desirable to reduce the amount of an anesthetic drug during surgery. For this purpose many studies of hypnosis control systems have been done. Most of them use Bispectral Index (BIS), another hypnosis index, but it has problems of dependence on anesthetic drugs and nonsmooth change near some particular values. On the other hand, aepEX has an ability of clear distinction between patient consciousness and unconsciousness and independence of anesthetic drugs. The control method proposed in this paper consists of two elements: estimating the minimum effect-site concentration for maintaining appropriate hypnosis and adjusting infusion rate of an anesthetic drug, propofol, using model predictive control. The minimum effect-site concentration is estimated utilizing the property of aepEX pharmacodynamics. The infusion rate of propofol is adjusted so that effect-site concentration of propofol may be kept near and always above the minimum effect-site concentration. Simulation results of hypnosis control using the proposed method show that the minimum concentration can be estimated appropriately and that the proposed control method can maintain hypnosis adequately and reduce the total infusion amount of propofol.

ON-SITE MERCURY ANALYSIS OF SOIL AT HAZARDOUS WASTE SITES BY IMMUNOASSAY AND ASV

EPA Science Inventory

Two field methods for Hg, immunoassay and anodic stripping voltammetry (ASV), that can provide onsite results for quick decisions at hazardous waste sites were evaluated. Each method was applied to samples from two Superfund sites that contain high levels of Hg; Sulphur Bank Me...

40 CFR 53.30 - General provisions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... more information about the site. Any such pre-test approval of a test site by the EPA shall indicate... Methods and Reference Methods § 53.30 General provisions. (a) Determination of comparability. The test... discretion of the Administrator. (b) Selection of test sites. (1) Each test site shall be in an area which...

40 CFR 53.30 - General provisions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... more information about the site. Any such pre-test approval of a test site by the EPA shall indicate... Methods and Reference Methods § 53.30 General provisions. (a) Determination of comparability. The test... discretion of the Administrator. (b) Selection of test sites. (1) Each test site shall be in an area which...

40 CFR 53.30 - General provisions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... more information about the site. Any such pre-test approval of a test site by the EPA shall indicate... Methods and Reference Methods § 53.30 General provisions. (a) Determination of comparability. The test... discretion of the Administrator. (b) Selection of test sites. (1) Each test site shall be in an area which...

40 CFR 53.30 - General provisions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... more information about the site. Any such pre-test approval of a test site by the EPA shall indicate... Methods and Reference Methods § 53.30 General provisions. (a) Determination of comparability. The test... discretion of the Administrator. (b) Selection of test sites. (1) Each test site shall be in an area which...

40 CFR 53.30 - General provisions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... more information about the site. Any such pre-test approval of a test site by the EPA shall indicate... Methods and Reference Methods § 53.30 General provisions. (a) Determination of comparability. The test... discretion of the Administrator. (b) Selection of test sites. (1) Each test site shall be in an area which...

Study of Physico-Chemical Characteristics of Wastewater in an Urban Agglomeration in Romania

PubMed Central

Popa, Paula; Timofti, Mihaela; Voiculescu, Mirela; Dragan, Silvia; Trif, Catalin; Georgescu, Lucian P.

2012-01-01

This study investigates the level of wastewater pollution by analyzing its chemical characteristics at five wastewater collectors. Samples are collected before they discharge into the Danube during a monitoring campaign of two weeks. Organic and inorganic compounds, heavy metals, and biogenic compounds have been analyzed using potentiometric and spectrophotometric methods. Experimental results show that the quality of wastewater varies from site to site and it greatly depends on the origin of the wastewater. Correlation analysis was used in order to identify possible relationships between concentrations of various analyzed parameters, which could be used in selecting the appropriate method for wastewater treatment to be implemented at wastewater plants. PMID:22919336

Comparison of water-quality samples collected by siphon samplers and automatic samplers in Wisconsin

USGS Publications Warehouse

Graczyk, David J.; Robertson, Dale M.; Rose, William J.; Steur, Jeffrey J.

2000-01-01

In small streams, flow and water-quality concentrations often change quickly in response to meteorological events. Hydrologists, field technicians, or locally hired stream ob- servers involved in water-data collection are often unable to reach streams quickly enough to observe or measure these rapid changes. Therefore, in hydrologic studies designed to describe changes in water quality, a combination of manual and automated sampling methods have commonly been used manual methods when flow is relatively stable and automated methods when flow is rapidly changing. Auto- mated sampling, which makes use of equipment programmed to collect samples in response to changes in stage and flow of a stream, has been shown to be an effective method of sampling to describe the rapid changes in water quality (Graczyk and others, 1993). Because of the high cost of automated sampling, however, especially for studies examining a large number of sites, alternative methods have been considered for collecting samples during rapidly changing stream conditions. One such method employs the siphon sampler (fig. 1). also referred to as the "single-stage sampler." Siphon samplers are inexpensive to build (about $25- $50 per sampler), operate, and maintain, so they are cost effective to use at a large number of sites. Their ability to collect samples representing the average quality of water passing though the entire cross section of a stream, however, has not been fully demonstrated for many types of stream sites.

School Site Visits for Community-Based Participatory Research on Healthy Eating

PubMed Central

Patel, Anisha I.; Bogart, Laura M.; Uyeda, Kimberly E.; Martinez, Homero; Knizewski, Ritamarie; Ryan, Gery W.; Schuster, Mark A.

2010-01-01

Background School nutrition policies are gaining support as a means of addressing childhood obesity. Community-based participatory research (CBPR) offers an approach for academic and community partners to collaborate to translate obesity-related school policies into practice. Site visits, in which trained observers visit settings to collect multilevel data (e.g., observation, qualitative interviews), may complement other methods that inform health promotion efforts. This paper demonstrates the utility of site visits in the development of an intervention to implement obesity-related policies in Los Angeles Unified School District (LAUSD) middle schools. Methods In 2006, trained observers visited four LAUSD middle schools. Observers mapped cafeteria layout; observed food/beverage offerings, student consumption, waste patterns, and duration of cafeteria lines; spoke with school staff and students; and collected relevant documents. Data were examined for common themes and patterns. Results Food and beverages sold in study schools met LAUSD nutritional guidelines, and nearly all observed students had time to eat most or all of their meal. Some LAUSD policies were not implemented, including posting nutritional information for cafeteria food, marketing school meals to improve student participation in the National School Lunch Program, and serving a variety of fruits and vegetables. Cafeteria understaffing and cost were obstacles to policy implementation. Conclusions Site visits were a valuable methodology for evaluating the implementation of school district obesity-related policies and contributed to the development of a CBPR intervention to translate school food policies into practice. Future CBPR studies may consider site visits in their toolbox of formative research methods. PMID:19896033

Alternative right ventricular pacing sites.

PubMed

Łuciuk, Dariusz; Łuciuk, Marek; Gajek, Jacek

2015-01-01

The main adverse effect of chronic stimulation is stimulation-induced heart failure in case of ventricular contraction dyssynchrony. Because of this fact, new techniques of stimulation should be considered to optimize electrotherapy. One of these methods is pacing from alternative right ventricular sites. The purpose of this article is to review currently accumulated data about alternative sites of cardiac pacing. Medline and PubMed bases were used to search English and Polish reports published recently. Recent studies report a deleterious effect of long term apical pacing. It is suggested that permanent apical stimulation, by omitting physiological conduction pattern with His-Purkinie network, may lead to electrical and mechanical dyssynchrony of heart muscle contraction. In the long term this pathological situation can lead to severe heart failure and death. Because of this, scientists began to search for some alternative sites of cardiac pacing to reduce the deleterious effect of stimulation. Based on current accumulated data, it is suggested that the right ventricular outflow tract, right ventricular septum, direct His-bundle or biventricular pacing are better alternatives due to more physiological electrical impulse propagation within the heart and the reduction of the dyssynchrony effect. These methods should preserve a better left ventricular function and prevent the development of heart failure in permanent paced patients. As there is still not enough, long-term, randomized, prospective, cross-over and multicenter studies, further research is required to validate the benefits of using this kind of therapy. The article should pay attention to new sites of cardiac stimulation as a better and safer method of treatment.

Oriented Immobilization of Fab Fragments by Site-Specific Biotinylation at the Conserved Nucleotide Binding Site for Enhanced Antigen Detection.

PubMed

Mustafaoglu, Nur; Alves, Nathan J; Bilgicer, Basar

2015-09-08

Oriented immobilization of antibodies and antibody fragments has become increasingly important as a result of the efforts to reduce the size of diagnostic and sensor devices to miniaturized dimensions for improved accessibility to the end-user. Reduced dimensions of sensor devices necessitate the immobilized antibodies to conserve their antigen binding activity for proper operation. Fab fragments are becoming more commonly used in small-scaled diagnostic devices due to their small size and ease of manufacture. In this study, we used the previously described UV-NBS(Biotin) method to functionalize Fab fragments with IBA-EG11-Biotin linker utilizing UV energy to initiate a photo-cross-linking reaction between the nucleotide binding site (NBS) on the Fab fragment and IBA-Biotin molecule. Our results demonstrate that immobilization of biotinylated Fab fragments via UV-NBS(Biotin) method generated the highest level of immobilized Fab on surfaces when compared to other typical immobilization methods while preserving antigen binding activity. UV-NBS(Biotin) method provided 432-fold, 114-fold, and 29-fold improved antigen detection sensitivity than physical adsorption, NHS-Biotin, and ε-NH3(+), methods, respectively. Additionally, the limit of detection (LOD) for PSA utilizing Fab fragments immobilized via UV-NBS(Biotin) method was significantly lower than that of the other immobilization methods, with an LOD of 0.4 pM PSA. In summary, site-specific biotinylation of Fab fragments without structural damage or loss in antigen binding activity provides a wide range of application potential for UV-NBS immobilization technique across numerous diagnostic devices and nanotechnologies.

Clinical attachment loss: estimation by direct and indirect methods.

PubMed

Barbosa, Viviane Leal; Angst, Patricia D Melchiors; Finger Stadler, Amanda; Oppermann, Rui V; Gomes, Sabrina Carvalho

2016-06-01

This observational study aimed to compare the estimation of clinical attachment loss (CAL) as measured by direct (CALD ) and indirect (CALI ) methods. Periodontitis patients (n = 75; mean age: 50.9 ± 8.02 years; 72.2% women; 50.6% smokers) received a periodontal examination (six sites/tooth) to determine the presence of visible plaque and calculus, the gingival bleeding index (GBI), periodontal probing depth (PPD), bleeding on probing (BOP), CALD and gingival recession (GR). CALI values resulted from the sum of PPD and GR values. Statistical analysis considered only data from sites with visible GR (e.g. the gingival margin apical to the cemento-enamel junction; n = 4,757 sites) and determined the mean difference between CALI and CALD measurements. Based on the mean difference, univariate and multivariate analyses were also performed. Mean CALD and CALI values were 3.96 ± 2.07 mm and 4.47 ± 2.03 mm, respectively. The indirect method overestimated CAL compared with the direct method (mean difference: 0.51 ± 1.23 mm; P < 0.001). On uni- and multivariate analyses, absence of GBI and BOP, PPD and proximal site location had significant influences on the overestimation of CAL by the indirect method (all P ≤ 0.01). The indirect method increased the CAL value by 0.38 mm for each additional 1 mm in PPD. To decrease the number of probing errors in daily practice it is suggested that direct examination is more appropriate than the indirect method for estimating CAL. © 2016 FDI World Dental Federation.

Spatial correlation of shear-wave velocity in the San Francisco Bay Area sediments

USGS Publications Warehouse

Thompson, E.M.; Baise, L.G.; Kayen, R.E.

2007-01-01

Ground motions recorded within sedimentary basins are variable over short distances. One important cause of the variability is that local soil properties are variable at all scales. Regional hazard maps developed for predicting site effects are generally derived from maps of surficial geology; however, recent studies have shown that mapped geologic units do not correlate well with the average shear-wave velocity of the upper 30 m, Vs(30). We model the horizontal variability of near-surface soil shear-wave velocity in the San Francisco Bay Area to estimate values in unsampled locations in order to account for site effects in a continuous manner. Previous geostatistical studies of soil properties have shown horizontal correlations at the scale of meters to tens of meters while the vertical correlations are on the order of centimeters. In this paper we analyze shear-wave velocity data over regional distances and find that surface shear-wave velocity is correlated at horizontal distances up to 4 km based on data from seismic cone penetration tests and the spectral analysis of surface waves. We propose a method to map site effects by using geostatistical methods based on the shear-wave velocity correlation structure within a sedimentary basin. If used in conjunction with densely spaced shear-wave velocity profiles in regions of high seismic risk, geostatistical methods can produce reliable continuous maps of site effects. ?? 2006 Elsevier Ltd. All rights reserved.

Occurrence of Organic Wastewater Compounds in Selected Surface-Water Supplies, Triangle Area of North Carolina, 2002-2005

USGS Publications Warehouse

Giorgino, M.J.; Rasmussen, R.B.; Pfeifle, C.M .

2007-01-01

Selected organic wastewater compounds, such as household, industrial, and agricultural-use compounds, sterols, pharmaceuticals, and antibiotics, were measured at eight sites classified as drinking-water supplies in the Triangle Area of North Carolina. From October 2002 through July 2005, seven of the sites were sampled twice, and one site was sampled 28 times, for a total of 42 sets of environmental samples. Samples were analyzed for as many as 126 compounds using three laboratory analytical methods. These methods were developed by the U.S. Geological Survey to detect low levels (generally less than or equal to 1.0 microgram per liter) of the target compounds in filtered water. Because analyses were conducted on filtered samples, the results presented in this report may not reflect the total concentration of organic wastewater compounds in the waters that were sampled. Various quality-control samples were used to quality assure the results in terms of method performance and possible laboratory or field contamination. Of the 108 organic wastewater compounds that met method performance criteria, 24 were detected in at least one sample during the study. These 24 compounds included 3 pharmaceutical compounds, 6 fire retardants and plasticizers, 3 antibiotics, 3 pesticides, 6 fragrances and flavorants, 1 disinfectant, and 2 miscellaneous-use compounds, all of which likely originated from a variety of domestic, industrial, and agricultural sources. The 10 most frequently detected compounds included acetyl-hexamethyl tetrahydronaphthalene and hexahydro-hexamethyl cyclopentabenzopyran (synthetic musks that are widely used in personal-care products and are known endocrine disruptors); tri(2-chloroethyl) phosphate, tri(dichloroisopropyl) phosphate, and tributyl phosphate (fire retardants); metolachlor (herbicide); caffeine (nonprescription stimulant); cotinine (metabolite of nicotine); acetaminophen (nonprescription analgesic); and sulfamethoxazole (prescription antibiotic). The occurrence and distribution of organic wastewater compounds varied considerably among sampling sites, but at least one compound was detected at every location. The most organic wastewater compounds (19) were detected at the Neuse River above U.S. 70 at Smithfield, where two-thirds of the total number of samples were collected. The fewest organic wastewater compounds (1) were detected at the Eno River at Hillsborough. The detection of multiple organic wastewater compounds was common, with a median of 3.5 and as many as 12 compounds observed in individual samples. Some compounds, including acetaminophen, cotinine, tri(2-chloroethyl) phosphate, and metolachlor, were detected at numerous sites and in numerous samples, indicating that they are widely distributed in the environment. Other organic wastewater compounds, including acetyl-hexamethyl tetrahydronaphthalene and hexahydro-hexamethyl cyclopentabenzopyran, were detected in numerous samples but at only one location, indicating that sources of these compounds are more site specific. Results indicate that municipal wastewater may be a source of antibiotics and synthetic musks; however, the three sites in this study that are located downstream from wastewater discharges also receive runoff from agricultural, urban, and rural residential lands. Source identification was not an objective of this study. Concentrations of individual compounds generally were less than 0.5 microgram per liter. No concentrations exceeded Federal drinking-water standards or health advisories, nor water-quality criteria established by the State of North Carolina; however, such criteria are available for only a few of the compounds that were studied. Compared with other surface waters that have been sampled across the United States, the Triangle Area water-supply sites had fewer detections of organic wastewater compounds; however, differences in study design and analytical methods used among studies must be considered when mak

Genome-Wide Analysis of A-to-I RNA Editing.

PubMed

Savva, Yiannis A; Laurent, Georges St; Reenan, Robert A

2016-01-01

Adenosine (A)-to-inosine (I) RNA editing is a fundamental posttranscriptional modification that ensures the deamination of A-to-I in double-stranded (ds) RNA molecules. Intriguingly, the A-to-I RNA editing system is particularly active in the nervous system of higher eukaryotes, altering a plethora of noncoding and coding sequences. Abnormal RNA editing is highly associated with many neurological phenotypes and neurodevelopmental disorders. However, the molecular mechanisms underlying RNA editing-mediated pathogenesis still remain enigmatic and have attracted increasing attention from researchers. Over the last decade, methods available to perform genome-wide transcriptome analysis, have evolved rapidly. Within the RNA editing field researchers have adopted next-generation sequencing technologies to identify RNA-editing sites within genomes and to elucidate the underlying process. However, technical challenges associated with editing site discovery have hindered efforts to uncover comprehensive editing site datasets, resulting in the general perception that the collections of annotated editing sites represent only a small minority of the total number of sites in a given organism, tissue, or cell type of interest. Additionally to doubts about sensitivity, existing RNA-editing site lists often contain high percentages of false positives, leading to uncertainty about their validity and usefulness in downstream studies. An accurate investigation of A-to-I editing requires properly validated datasets of editing sites with demonstrated and transparent levels of sensitivity and specificity. Here, we describe a high signal-to-noise method for RNA-editing site detection using single-molecule sequencing (SMS). With this method, authentic RNA-editing sites may be differentiated from artifacts. Machine learning approaches provide a procedure to improve upon and experimentally validate sequencing outcomes through use of computationally predicted, iterative feedback loops. Subsequent use of extensive Sanger sequencing validations can generate accurate editing site lists. This approach has broad application and accurate genome-wide editing analysis of various tissues from clinical specimens or various experimental organisms is now a possibility.

Using site-selection model to identify suitable sites for seagrass transplantation in the west coast of South Sulawesi

NASA Astrophysics Data System (ADS)

Lanuru, Mahatma; Mashoreng, S.; Amri, K.

2018-03-01

The success of seagrass transplantation is very much depending on the site selection and suitable transplantation methods. The main objective of this study is to develop and use a site-selection model to identify the suitability of sites for seagrass (Enhalus acoroides) transplantation. Model development was based on the physical and biological characteristics of the transplantation site. The site-selection process is divided into 3 phases: Phase I identifies potential seagrass habitat using available knowledge, removes unnecessary sites before the transplantation test is performed. Phase II involves field assessment and transplantation test of the best scoring areas identified in Phase I. Phase III is the final calculation of the TSI (Transplant Suitability Index), based on results from Phases I and II. The model was used to identify the suitability of sites for seagrass transplantation in the West coast of South Sulawesi (3 sites at Labakkang Coast, 3 sites at Awerange Bay, and 3 sites at Lale-Lae Island). Of the 9 sites, two sites were predicted by the site-selection model to be the most suitable sites for seagrass transplantation: Site II at Labakkang Coast and Site III at Lale-Lae Island.

Improved Environmental Life Cycle Assessment of Crop Production at the Catchment Scale via a Process-Based Nitrogen Simulation Model.

PubMed

Liao, Wenjie; van der Werf, Hayo M G; Salmon-Monviola, Jordy

2015-09-15

One of the major challenges in environmental life cycle assessment (LCA) of crop production is the nonlinearity between nitrogen (N) fertilizer inputs and on-site N emissions resulting from complex biogeochemical processes. A few studies have addressed this nonlinearity by combining process-based N simulation models with LCA, but none accounted for nitrate (NO3(-)) flows across fields. In this study, we present a new method, TNT2-LCA, that couples the topography-based simulation of nitrogen transfer and transformation (TNT2) model with LCA, and compare the new method with a current LCA method based on a French life cycle inventory database. Application of the two methods to a case study of crop production in a catchment in France showed that, compared to the current method, TNT2-LCA allows delineation of more appropriate temporal limits when developing data for on-site N emissions associated with specific crops in this catchment. It also improves estimates of NO3(-) emissions by better consideration of agricultural practices, soil-climatic conditions, and spatial interactions of NO3(-) flows across fields, and by providing predicted crop yield. The new method presented in this study provides improved LCA of crop production at the catchment scale.

A comparison of on-line and off-line bioaerosol measurements at a biowaste site.

PubMed

Feeney, Patrick; Rodríguez, Santiago Fernández; Molina, Rafael; McGillicuddy, Eoin; Hellebust, Stig; Quirke, Michael; Daly, Shane; O'Connor, David; Sodeau, John

2018-06-01

An air measurement campaign was carried out at a green-waste composting site in the South of Ireland during Spring 2016. The aim was to quantify and identify the levels of Primary Biological Aerosol Particles (PBAP) that were present using the traditional off-line, impaction/optical microscopy method alongside an on-line, spectroscopic approach termed WIBS (Wideband Integrated Bioaerosol Sensor), which can provide number concentrations, sizes and "shapes" of airborne PBAP in real-time by use of Light Induced Fluorescence (LIF). The results from the two techniques were compared in order to validate the use of the spectroscopic method for determining the releases of the wide-range of PBAP present there as a function of site activity and meteorological conditions. The seven-day monitoring period undertaken was much longer than any real-time studies that have been previously performed and allowed due comparison between weekday (working) activities at the site and weekend (closed) releases. The time-span also allowed relationships between site activities like turning, agitation or waste delivery and the WIBS data to be determined in a quantitative manner. This information cannot be obtained with the Andersen Sampling methods generally employed at green-waste management sites. Furthermore, few specific bioaerosol types other than Aspergillus fumigatus, are identified using the traditional protocols employed for site licensing purposes. Here though the co-location of WIBS with the impaction instrument made it possible to identify the real-time release behaviour of a specific plant pathogenic spore, Ustilago maydis, present after green-waste deliveries were made by a local distillery. Copyright © 2018 Elsevier Ltd. All rights reserved.

Trends in the survival of patients diagnosed with cancer in the Nordic countries 1964-2003 followed up to the end of 2006. Material and methods.

PubMed

Engholm, Gerda; Gislum, Mette; Bray, Freddie; Hakulinen, Timo

2010-06-01

Comparable data on cancer incidence and mortality in Denmark, Finland, Iceland, Norway, and Sweden are available for analysis through a collaboration of the national Cancer Registries via the NORDCAN website (http://ancr.nu). In the continued spirit of Nordic collaborative research, a number of studies examining trends in cancer survival are published in this journal. The data were divided into eight 5-year periods by sex in five Nordic countries. Age-standardised 5-year relative survival ratios and excess mortality rates in the short-term (first month and 1-3 months following diagnosis), and the long-term (2-5 years after diagnosis) were calculated, as were age-specific 5-year relative survival using cohort-survival methods. A hybrid method combining the cohort and period methods was used for the period 1999-2003 as not all patients were followed for five years. Age-standardisation used the International Cancer Survival Standard, and calculation of expected deaths used country-specific population mortality rates. The data series constitutes 3 360 397 tumours among 3 160 802 patients followed up for death through 2006 for 39 different cancer sites diagnosed in the years 1964-2003. The paper describes the data, exclusions and imputations, design and analysis, age structure and standardisation procedures, follow-up, and case-mix adjustment methods. The strengths of this study include the overall comparability and quality of the data, the national coverage, and the length of the time series. Collecting and analysing data from the five Nordic countries for 39 different cancer sites over 40 years in a systematised and comparable way is a major undertaking. A thorough description of the analyses, definitions and exclusions in the survival study, supplemented with corresponding information on cancer incidence and mortality is needed for appropriate interpretation and comparison between countries, and between and within cancer sites. This information must be made available to provide appropriate interpretation of the site-specific results.

Siting MSW landfill using weighted linear combination and analytical hierarchy process (AHP) methodology in GIS environment (case study: Karaj).

PubMed

Moeinaddini, Mazaher; Khorasani, Nematollah; Danehkar, Afshin; Darvishsefat, Ali Asghar; Zienalyan, Mehdi

2010-05-01

Selection of landfill site is a complex process and needs many diverse criteria. The purpose of this paper is to evaluate the suitability of the studied site as landfill for MSW in Karaj. Using weighted linear combination (WLC) method and spatial cluster analysis (SCA), suitable sites for allocation of landfill for a 20-year period were identified. For analyzing spatial auto-correlation of the land suitability map layer (LSML), Maron's I was used. Finally, using the analytical hierarchy process (AHP), the most preferred alternative for the landfill siting was identified. Main advantages of AHP are: relative ease of handling multiple criteria, easy to understand and effective handling of both qualitative and quantitative data. As a result, 6% of the study area is suitable for landfill siting and third alternative was identified as the most preferred for siting MSW landfill by AHP. The ranking of alternatives were obtained only by applying the WLC approach showed different results from the AHP. The WLC should be used only for the identification of alternatives and the AHP is used for prioritization. We suggest the employed procedure for other similar regions. Copyright (c) 2010 Elsevier Ltd. All rights reserved.