Adequacy of a Small Quantity Site RH-TRU Waste Program in Meeting Proposed WIPP Characterization Objectives

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

Biedscheid, J.; Stahl, S.; Devarakonda, M.

2002-02-26

The first remote-handled transuranic (RH-TRU) waste is expected to be permanently disposed of at the Waste Isolation Pilot Plant (WIPP) during Fiscal Year (FY) 2003. The first RH-TRU waste shipments are scheduled from the Battelle Columbus Laboratories (BCL) to WIPP in order to facilitate compliance with BCL Decommissioning Project (BCLDP) milestones. Milestones requiring RH-TRU waste containerization and removal from the site by 2004 in order to meet a 2006 site closure goal, established by Congress in the Defense Facilities Closure Projects account, necessitated the establishment and implementation of a site-specific program to direct the packaging of BCLDP RH-TRU waste priormore » to the finalization of WIPP RH-TRU waste characterization requirements. The program was designed to collect waste data, including audio and videotape records of waste packaging, such that upon completion of waste packaging, comprehensive data records exist from which compliance with final WIPP RH-TRU waste characterization requirements can be demonstrated. With the BCLDP data records generated to date and the development by the U.S. Department of Energy (DOE)-Carlsbad Field Office (CBFO) of preliminary documents proposing the WIPP RH-TRU waste characterization program, it is possible to evaluate the adequacy of the BCLDP program with respect to meeting proposed characterization objectives. The BCLDP characterization program uses primarily acceptable knowledge (AK) and visual examination (VE) during waste packaging to characterize RH-TRU waste. These methods are used to estimate physical waste parameters, including weight percentages of metals, cellulosics, plastics, and rubber in the waste, and to determine the absence of prohibited items, including free liquids. AK combined with computer modeling is used to estimate radiological waste parameters, including total activity on a waste container basis, for the majority of BCLDP RH-TRU waste. AK combined with direct analysis is used to characterize radiological parameters for the small populations of the RH-TRU waste generated by the BCLDP. All characterization based on AK is verified. Per its design for comprehensive waste data collection, the BCLDP characterization program using AK and waste packaging procedures, including VE during packaging, meets the proposed WIPP RH-TRU waste characterization objectives. The conservative program design implemented generates certification data that will be adequate to meet any additional program requirements that may be imposed by the CBFO.« less

Draft environmental assessment: Davis Canyon site, Utah. Nuclear Waste Policy Act (Section 112). [Contains glossary

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

Not Available

1984-12-01

In February 1983, the US Department of Energy (DOE) identified the Davis Canyon site in Utah, as one of nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Davis Canyon site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for Nuclear Waste Repositories. These evaluations are reported in this draft environmental assessment (EA), which is being issued for public review and comment. The DOE findings and determinations that are based on these evaluationsmore » are preliminary and subject to public review and comment. A final EA will be prepared after considering the comments received. On the basis of the evaluations reported in this draft EA, the DOE has found that the Davis Canyon site is not disqualified under the guidelines. The site is in the Paradox Basin, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains one other potentially acceptable site - the Lavender Canyon site. Although the Lavender Canyon site appears to be suitable for site characterization, the DOE has concluded that the Davis Canyon site is the preferred site in the Paradox Basin. Furthermore, the DOE finds that the site is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is proposing to nominate the Davis Canyon site as one of five sites suitable for characterization. Having compared the Davis Canyon site with the other four sites proposed for nomination, the DOE has determined that the Davis Canyon site is not one of the three preferred sites for recommendation to the President as candidates for characterization.« less

Environmental assessment: Davis Canyon site, Utah

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

none,

1986-05-01

In February 1983, the US Department of Energy (DOE) identified the Davis Canyon site in Utah as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Davis Canyon site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOEmore » prepared the final EA. The Davis Canyon site is in the Paradox Basin, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains one other potentially acceptable site -- the Lavender Canyon site. Although the Lavender Canyon site is suitable for site characterization, the DOE has concluded that the Davis Canyon site is the preferred site in the Paradox Basin. On the basis of the evaluations reported in this EA, the DOE has found that the Davis Canyon site is not disqualified under the guidelines. Furthermore, the DOE has fond that the site is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Davis Canyon site as one of five sites suitable for characterization. 181 figs., 175 tabs.« less

Environmental assessment: Davis Canyon site, Utah

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

none,

1986-05-01

In February 1983, the US Department of Energy (DOE) identified the Davis Canyon site in Utah as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high- level radioactive waste. To determine their suitability, the Davis Canyon site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, themore » DOE prepared the final EA. The Davis Canyon site is in the Paradox Basin, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains one other potentially acceptable site -- the Lavender Canyon site. Although the Lavender Canyon site is suitable for site characterization, the DOE has concluded that the Davis Canyon site is the preferred site in the Paradox Basin. On the basis of the evaluations reported in this EA, the DOE has found that the Davis Canyon site is not disqualified under the guidelines. Furthermore, the DOE has found that the site is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Davis Canyon site as one of the five sites suitable for characterization.« less

Innovative Field Methods for Characterizing the Hydraulic Properties of a Complex Fractured Rock Aquifer (Ploemeur, Brittany)

NASA Astrophysics Data System (ADS)

Bour, O.; Le Borgne, T.; Longuevergne, L.; Lavenant, N.; Jimenez-Martinez, J.; De Dreuzy, J. R.; Schuite, J.; Boudin, F.; Labasque, T.; Aquilina, L.

2014-12-01

Characterizing the hydraulic properties of heterogeneous and complex aquifers often requires field scale investigations at multiple space and time scales to better constrain hydraulic property estimates. Here, we present and discuss results from the site of Ploemeur (Brittany, France) where complementary hydrological and geophysical approaches have been combined to characterize the hydrogeological functioning of this highly fractured crystalline rock aquifer. In particular, we show how cross-borehole flowmeter tests, pumping tests and frequency domain analysis of groundwater levels allow quantifying the hydraulic properties of the aquifer at different scales. In complement, we used groundwater temperature as an excellent tracer for characterizing groundwater flow. At the site scale, measurements of ground surface deformation through long-base tiltmeters provide robust estimates of aquifer storage and allow identifying the active structures where groundwater pressure changes occur, including those acting during recharge process. Finally, a numerical model of the site that combines hydraulic data and groundwater ages confirms the geometry of this complex aquifer and the consistency of the different datasets. The Ploemeur site, which has been used for water supply at a rate of about 106 m3 per year since 1991, belongs to the French network of hydrogeological sites H+ and is currently used for monitoring groundwater changes and testing innovative field methods.

A Task-oriented Approach for Hydrogeological Site Characterization

NASA Astrophysics Data System (ADS)

Rubin, Y.; Nowak, W.; de Barros, F.

2010-12-01

Hydrogeological site characterization is a challenging task from several reasons: (1) the large spatial variability and scarcity of prior information render the outcome of any planned sampling campaign uncertain; (2) there are no simple tools for comparing between the many alternative measurement techniques and data acquisition strategies, and (3) physical and budgetary constraints associated with data acquisition. This paper presents several ideas on how to plan sampling campaigns in a rational manner while addressing these challenges. The first idea is to recognize that different sites and different problems require different characterization strategies. Hence the idea is to plan data acquisition according to its capability for meeting site-specific goals. For example, the characterization needs at a “research problem” site (e.g., a site intended to investigate the transport of uranium in the subsurface such as in Hanford) are different from those of a “problem” site (e.g., contaminated site associated with a health risk to human such as Camp Lejeune, or determining the safe yield of an aquifer). This distinction requires planners to define the characterization goal(s) in a quantitative manner. The second idea is to define metrics that could link specific data types and data acquisition strategies with the site-specific goals in a way that would allow planners to compare between strongly different, alternatives strategies at the design stage (even prior to data acquisition) and to modify the strategies as more data become available. To meet this goal, we developed the concept of the (comparative) information yield curve. Finally, we propose to look at site characterization from the perspective of statistical hypothesis testing, whereby data acquisition strategies could be evaluated in terms of their ability to support or refute various hypotheses made with regard to the characterization goals, and the strategies could be modified once the test is completed. Accept/reject regions for hypothesis testing can be determined based on goals determined by regulations or by agreement between the stakeholders. Hypothesis-driven design could help in minimizing the chances of making wrong decision (false positives or false negatives) with regard to the site-specific goals.

Statistical Methods and Tools for Uxo Characterization (SERDP Final Technical Report)

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

Pulsipher, Brent A.; Gilbert, Richard O.; Wilson, John E.

2004-11-15

The Strategic Environmental Research and Development Program (SERDP) issued a statement of need for FY01 titled Statistical Sampling for Unexploded Ordnance (UXO) Site Characterization that solicited proposals to develop statistically valid sampling protocols for cost-effective, practical, and reliable investigation of sites contaminated with UXO; protocols that could be validated through subsequent field demonstrations. The SERDP goal was the development of a sampling strategy for which a fraction of the site is initially surveyed by geophysical detectors to confidently identify clean areas and subsections (target areas, TAs) that had elevated densities of anomalous geophysical detector readings that could indicate the presencemore » of UXO. More detailed surveys could then be conducted to search the identified TAs for UXO. SERDP funded three projects: those proposed by the Pacific Northwest National Laboratory (PNNL) (SERDP Project No. UXO 1199), Sandia National Laboratory (SNL), and Oak Ridge National Laboratory (ORNL). The projects were closely coordinated to minimize duplication of effort and facilitate use of shared algorithms where feasible. This final report for PNNL Project 1199 describes the methods developed by PNNL to address SERDP's statement-of-need for the development of statistically-based geophysical survey methods for sites where 100% surveys are unattainable or cost prohibitive.« less

Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization.

PubMed

Beuming, Thijs; Che, Ye; Abel, Robert; Kim, Byungchan; Shanmugasundaram, Veerabahu; Sherman, Woody

2012-03-01

Water plays an essential role in determining the structure and function of all biological systems. Recent methodological advances allow for an accurate and efficient estimation of the thermodynamic properties of water molecules at the surface of proteins. In this work, we characterize these thermodynamic properties and relate them to various structural and functional characteristics of the protein. We find that high-energy hydration sites often exist near protein motifs typically characterized as hydrophilic, such as backbone amide groups. We also find that waters around alpha helices and beta sheets tend to be less stable than waters around loops. Furthermore, we find no significant correlation between the hydration site-free energy and the solvent accessible surface area of the site. In addition, we find that the distribution of high-energy hydration sites on the protein surface can be used to identify the location of binding sites and that binding sites of druggable targets tend to have a greater density of thermodynamically unstable hydration sites. Using this information, we characterize the FKBP12 protein and show good agreement between fragment screening hit rates from NMR spectroscopy and hydration site energetics. Finally, we show that water molecules observed in crystal structures are less stable on average than bulk water as a consequence of the high degree of spatial localization, thereby resulting in a significant loss in entropy. These findings should help to better understand the characteristics of waters at the surface of proteins and are expected to lead to insights that can guide structure-based drug design efforts. Copyright © 2011 Wiley Periodicals, Inc.

A continuous intrusion miniature cone penetration test system for transportation applications : final report.

DOT National Transportation Integrated Search

1999-01-01

The electronic cone penetrometer is a popular in situ investigation tool for site characterization. This research report describes the application of this proven concept of the cone penetration test (CPT) to highway design and construction control by...

(Low-level waste disposal facility siting and site characterization)

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

Mezga, L.J.; Ketelle, R.H.; Pin, F.G.

A US team consisting of representatives of Oak Ridge National Laboratory (ORNL), Savannah River Plant (SRP), Savannah river Laboratory (SRL), and the Department of Energy Office of Defense Waste and Byproducts Management participated in the fourth meeting held under the US/French Radioactive Waste Management Agreement between the US Department of Energy and the Commissariat a l'Energie Atomique. This meeting, held at Agence Nationale pour les Gestion des Dechets Radioactifs' (ANDRA's) Headquarters in Paris, was a detailed, technical topical workshop focusing on Low-Level Waste Disposal Facility Siting and Site Characterization.'' The meeting also included a visit to the Centre de lamore » Manche waste management facility operated by ANDRA to discuss and observe the French approach to low-level waste management. The final day of the meeting was spent at the offices of Societe Generale pour les Techniques Nouvelles (SGN) discussing potential areas of future cooperation and exchange. 20 figs.« less

Alveolar ridge reduction after tooth extraction in adolescents: an animal study

PubMed Central

Sun, Zongyang; Herring, Susan W.; Tee, Boon Ching; Gales, Jordan

2013-01-01

Objective The mechanism for tooth extraction induced residual alveolar ridge reduction (RRR) during adolescence is poorly understood. This study investigated the alveolar bone morphology, growth, resorption and functional loading at normal and extraction sites using an adolescent pig model. Design Sixteen 3-month-old pigs were divided into two groups – immediate post-extraction (IE) and 6-week post-extraction (SE). The IE group received an extraction of one deciduous mandibular molar, immediately followed by a final experiment to record masseter muscle EMGs and strains from the buccal surface of the extraction and contralateral non-extraction sites during function (mastication). The SE group was given the same tooth extraction, then kept for 6 weeks before the same final functional recording as the IE group. Both groups also received baseline (pre-extraction) EMGs and fluorescent vital stains 10 and 3 days before the final functional recording. Immediately after the final functional recording, animals were euthanized and alveolar bone specimens from extraction and contralateral non-extraction sites were collected and used to analyze alveolar bone morphology, apposition and resorption based on fluorescent and hematoxylin and eosin stained histological sections. Results At control sites (IE-extraction, IE-non-extraction and SE-non-extraction), the alveolar ridges grew gingivally and buccally. Bone formation characterized the buccal surface and lingual bundle bone, whereas resorption characterized the lingual surface and buccal bundle bone. The SE-extraction sites showed three major alterations: convergence of the buccal and lingual gingival crests, loss of apposition on the lingual bundle bone, and decelerated growth at the entire buccal surface. These alterations likely resulted from redirected crestal growth as part of the socket healing process, loss of tongue pressure to the lingual side of the teeth which normally provides mechanical stimulation for dental arch expansion, and masticatory underloading during the initial post-extraction period, respectively. Conclusions These data indicate that the initial phase of RRR in adolescents is a product of modified growth, not resorption, possibly because of decreased mechanical stimulation at the extraction site. PMID:23380583

United States Air Force 611th Air Support Group/Civil Engineering Squadron Elmendorf AFB, Alaska. Remedial investigation and feasibility study. Barter Island Radar Installation, Alaska. Volume 1 (includes appendices a through c). Revision 1. Final report, January 1995-January 1996

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

Karmi, S.; Madden, J.; Borsetti, R.

1996-01-05

This report presents the findings of Remedial Investigations and Feasibility Studies at sites located at the Barter Island radar installation in northern Alaska. The sites were characterized based on sampling and analyses conducted during Remedial Investigation activities performed during August and September 1993.

From the utilization point of view, the two approaches seem to United States Air Force 611th Air Support Group/Civil Engineering Squadron, Elmendorf AFB, Alaska. Remedial investigation and feasibility study Point Barrow Radar Installation, Alaska. Final report

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

Karmi, S.

1996-02-19

This report presents the findings of Remedial Investigations and Feasibility Studies at sites located at the Point Barrow radar installation in northern Alaska. The sites were characterized based on sampling and analyses conducted during Remedial Investigation activities performed during August and September 1993.

Strains, functions, and dynamics in the expanded Human Microbiome Project

PubMed Central

Lloyd-Price, Jason; Mahurkar, Anup; Rahnavard, Gholamali; Crabtree, Jonathan; Orvis, Joshua; Hall, A. Brantley; Brady, Arthur; Creasy, Heather H.; McCracken, Carrie; Giglio, Michelle G.; McDonald, Daniel; Franzosa, Eric A.; Knight, Rob; White, Owen; Huttenhower, Curtis

2018-01-01

Summary The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, microbial population diversity, biogeography, and molecular function. The NIH Human Microbiome Project (HMP) has provided one of the broadest such characterizations to date. Here, we introduce an expanded second phase of the study, abbreviated HMP1-II, comprising 1,631 new metagenomic samples (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. We applied updated profiling and assembly methods to these data to provide new characterizations of microbiome personalization. Strain identification revealed distinct subspecies clades specific to body sites; it also quantified species with phylogenetic diversity under-represented in isolate genomes. Body-wide functional profiling classified pathways into universal, human-enriched, and body site-enriched subsets. Finally, temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. This study furthers our knowledge of baseline human microbial diversity, thus enabling an understanding of personalized microbiome function and dynamics. PMID:28953883

Environmental assessment: Reference repository location, Hanford site, Washington

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

none,

1986-05-01

In February 1983, the US Department of Energy (DOE) identified a reference repository location at the Hanford Site in Washington as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. The site is in the Columbia Plateau, which is one of five distinct geohydrologic settings considered for the first repository. To determine their suitability, the Hanford Site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported inmore » draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EAs. On the basis of the evaluations reported in this EA, the DOE has found that the Hanford site is not disqualified under the guidelines. The DOE has also found that it is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Hanford site as one of five sites suitable for characterization.« less

Environmental assessment: Yucca Mountain site, Nevada research and development area, Nevada; Volume 1

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

NONE

1986-05-01

In February 1983, the US Department of Energy (DOE) identified the Yucca Mountain site in Nevada as one of nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high- level radioactive waste. The site is in the Great Basin, which is one of five distinct geohydrologic settings considered for the first repository. To determine their suitability, the Yucca Mountain site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE`s General Guideline for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessmentsmore » (EA), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EAs. On the basis of the evaluations reported in this EA, the DOE found that the Yucca Mountain site is not disqualified under the guidelines. The DOE has also found that it is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Yucca Mountain site as of five sites suitable for characterization.« less

Environmental assessment: Yucca Mountain site, Nevada research and development area, Nevada; Volume 3

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

NONE

1986-05-01

In February 1983, the US Department of Energy (DOE) identified the Yucca Mountain site in Nevada as one of nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. The site is in the Great Basin, which is one of five distinct geohydrologic settings considered for the first repository. To determine their suitability, the Yucca Mountain site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE`s General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs),more » which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EAs. On the basis of the evaluations reported in this EA, the DOE has found that the Yucca Mountain site is not disqualified under the guidelines. The DOE has also found that it is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Yucca Mountain site as one of five sites suitable for characterization.« less

CHARACTERIZATION OF ISOPRENE AND OXYGENATED VOLATILE ORGANIC CARBON COMPOUNDS AT RURAL, FORESTED SITES. (R825261)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Insights from native mass spectrometry approaches for top- and middle- level characterization of site-specific antibody-drug conjugates

PubMed Central

Botzanowski, Thomas; Erb, Stéphane; Hernandez-Alba, Oscar; Ehkirch, Anthony; Colas, Olivier; Wagner-Rousset, Elsa; Rabuka, David; Beck, Alain; Drake, Penelope M.; Cianférani, Sarah

2017-01-01

ABSTRACT Antibody-drug conjugates (ADCs) have emerged as a family of compounds with promise as efficient immunotherapies. First-generation ADCs were generated mostly via reactions on either lysine side-chain amines or cysteine thiol groups after reduction of the interchain disulfide bonds, resulting in heterogeneous populations with a variable number of drug loads per antibody. To control the position and the number of drug loads, new conjugation strategies aiming at the generation of more homogeneous site-specific conjugates have been developed. We report here the first multi-level characterization of a site-specific ADC by state-of-the-art mass spectrometry (MS) methods, including native MS and its hyphenation to ion mobility (IM-MS). We demonstrate the versatility of native MS methodologies for site-specific ADC analysis, with the unique ability to provide several critical quality attributes within one single run, along with a direct snapshot of ADC homogeneity/heterogeneity without extensive data interpretation. The capabilities of native IM-MS to directly access site-specific ADC conformational information are also highlighted. Finally, the potential of these techniques for assessing an ADC's heterogeneity/homogeneity is illustrated by comparing the analytical characterization of a site-specific DAR4 ADC to that of first-generation ADCs. Altogether, our results highlight the compatibility, versatility, and benefits of native MS approaches for the analytical characterization of all types of ADCs, including site-specific conjugates. Thus, we envision integrating native MS and IM-MS approaches, even in their latest state-of-the-art forms, into workflows that benchmark bioconjugation strategies. PMID:28406343

Agricultural areas in potentially contaminated sites: characterization, risk, management.

PubMed

Vanni, Fabiana; Scaini, Federica; Beccaloni, Eleonora

2016-01-01

In Italy, the current legislation for contaminants in soils provides two land uses: residential/public or private gardens and commercial/industrial; there are not specific reference values for agricultural soils, even if a special decree has been developed and is currently going through the legislative approval process. The topic of agricultural areas is relevant, also in consideration of their presence near potentially contaminated sites. Aim and results. In this paper, contamination sources and transport modes of contaminants from sources to the target in agricultural areas are examined and a suitable "conceptual model" to define appropriate characterization methods and risk assessment procedures is proposed. These procedures have already been used by the National Institute of Health in various Italian areas characterized by different agricultural settings. Finally, specific remediation techniques are suggested to preserve soil resources and, if possible, its particular land use.

76 FR 43319 - Record of Decision for the Continued Operation of the Y-12 National Security Complex

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-20

...; visual resources; site infrastructure; traffic and transportation; geology and soils; air quality and... excavation, soil characterization, transportation or disposal associated with the UPF. Response. The Y-12 Final SWEIS includes an analysis of the impacts of the UPF construction, including soil disturbance...

Air/Superfund national technical guidance study series, Volume 2. Estimation of baseline air emission at Superfund sites. Interim report(Final)

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

Not Available

1989-01-01

This volume is one in a series of manuals prepared for EPA to assist its Remedial Project Managers in the assessment of the air contaminant pathway and developing input data for risk assessment. The manual provides guidance on developing baseline-emission estimates from hazardous waste sites. Baseline-emission estimates (BEEs) are defined as emission rates estimated for a site in its undisturbed state. Specifically, the manual is intended to: Present a protocol for selecting the appropriate level of effort to characterize baseline air emissions; Assist site managers in designing an approach for BEEs; Describe useful technologies for developing site-specific baseline emission estimatesmore » (BEEs); Help site managers select the appropriate technologies for generating site-specific BEEs.« less

Migration and site selection of Ornithodiplostomum ptychocheilus (Trematoda: Digenea) metacercariae in the brain of fathead minnows ( Pimephales promelas).

PubMed

Matisz, Chelsea E; Goater, Cameron P; Bray, Douglas

2010-04-01

The migration of subadult parasites to preferred sites within final hosts is well characterized. In contrast, the migration of larval stages of trematodes to specific sites within their second intermediate hosts is poorly understood. We used a serial necropsy approach to characterize the migration of Ornithodiplostomum ptychocheilus diplostomules from the point of cercarial penetration, to encystment within the outermost tissues of the brain of fathead minnows. Diplostomules utilized peripheral nerves to access the central nerve cord, or they used specific cranial nerves to directly access the brain. Within 3 h of exposure to cercariae, 46% of all diplostomules were observed within the medulla of the brain. Diplostomules subsequently utilized specific neural tracts to reach lateral regions of the outermost tissue layer of the optic lobes, the stratum marginale. Diplostomules remained in this layer during their 4-week growth phase, then shifted site to the adjacent meninges for encystment. Characterization of a habitat shift for developing versus encysted metacercariae helps explain the results of previous ecological studies that document transient changes in the effects of metacercariae on the surivival, behaviour, and anti-parasite defences of infected fish.

Final Quality Assurance Plan for the Remedial Investigations and Feasibility Studies of the Helicopter Hangar Area and the Fire Training Area at Fort George G. Meade, Maryland

DTIC Science & Technology

1995-05-05

impoundment for a metal products manufacturer in Florida. During the site investigation, evidence of offsite contamination was found to be migrating onto...equipment, cross contamination through improper storage of samples) " Audit sampling documentation and procedures to ensure that samples are labeled...characterization of the occurrence and distribution of chemical contamination and site characteristics that are likely to influence human exposure or remediation

Multi-Sensor Characterization of the Boreal Forest: Initial Findings

NASA Technical Reports Server (NTRS)

Reith, Ernest; Roberts, Dar A.; Prentiss, Dylan

2001-01-01

Results are presented in an initial apriori knowledge approach toward using complementary multi-sensor multi-temporal imagery in characterizing vegetated landscapes over a site in the Boreal Ecosystem-Atmosphere Study (BOREAS). Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) and Airborne Synthetic Aperture Radar (AIRSAR) data were segmented using multiple endmember spectral mixture analysis and binary decision tree approaches. Individual date/sensor land cover maps had overall accuracies between 55.0% - 69.8%. The best eight land cover layers from all dates and sensors correctly characterized 79.3% of the cover types. An overlay approach was used to create a final land cover map. An overall accuracy of 71.3% was achieved in this multi-sensor approach, a 1.5% improvement over our most accurate single scene technique, but 8% less than the original input. Black spruce was evaluated to be particularly undermapped in the final map possibly because it was also contained within jack pine and muskeg land coverages.

Systematic Functional Analysis of Active-Site Residues in l-Threonine Dehydrogenase from Thermoplasma volcanium

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

Desjardins, Morgan; Mak, Wai Shun; O’Brien, Terrence E.

Enzymes have been through millions of years of evolution during which their active-site microenvironments are fine-tuned. Active-site residues are commonly conserved within protein families, indicating their importance for substrate recognition and catalysis. In this work, we systematically mutated active-site residues of l-threonine dehydrogenase from Thermoplasma volcanium and characterized the mutants against a panel of substrate analogs. Our results demonstrate that only a subset of these residues plays an essential role in substrate recognition and catalysis and that the native enzyme activity can be further enhanced roughly 4.6-fold by a single point mutation. Kinetic characterization of mutants on substrate analogs showsmore » that l-threonine dehydrogenase possesses promiscuous activities toward other chemically similar compounds not previously observed. Quantum chemical calculations on the hydride-donating ability of these substrates also reveal that this enzyme did not evolve to harness the intrinsic substrate reactivity for enzyme catalysis. Our analysis provides insights into connections between the details of enzyme active-site structure and specific function. Finally, these results are directly applicable to rational enzyme design and engineering.« less

Systematic Functional Analysis of Active-Site Residues in l-Threonine Dehydrogenase from Thermoplasma volcanium

DOE PAGES

Desjardins, Morgan; Mak, Wai Shun; O’Brien, Terrence E.; ...

2017-07-07

Enzymes have been through millions of years of evolution during which their active-site microenvironments are fine-tuned. Active-site residues are commonly conserved within protein families, indicating their importance for substrate recognition and catalysis. In this work, we systematically mutated active-site residues of l-threonine dehydrogenase from Thermoplasma volcanium and characterized the mutants against a panel of substrate analogs. Our results demonstrate that only a subset of these residues plays an essential role in substrate recognition and catalysis and that the native enzyme activity can be further enhanced roughly 4.6-fold by a single point mutation. Kinetic characterization of mutants on substrate analogs showsmore » that l-threonine dehydrogenase possesses promiscuous activities toward other chemically similar compounds not previously observed. Quantum chemical calculations on the hydride-donating ability of these substrates also reveal that this enzyme did not evolve to harness the intrinsic substrate reactivity for enzyme catalysis. Our analysis provides insights into connections between the details of enzyme active-site structure and specific function. Finally, these results are directly applicable to rational enzyme design and engineering.« less

Solar Technology Validation Project - USS Data, LLC: Cooperative Research and Development Final Report, CRADA Number CRD-09-367-04

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

Wilcox, S.

2013-08-01

Under this Agreement, NREL will work with Participant to improve concentrating solar power system performance characterizations. This work includes, but is not limited to, research and development of methods for acquiring renewable resource characterization information using site-specific measurements of solar radiation and meteorological conditions; collecting system performance data; and developing tools for improving the design, installation, operation, and maintenance of solar energy conversion systems. This work will be conducted at NREL and Participant facilities.

Solar Technology Validation Project - RES Americas: Cooperative Research and Development Final Report, CRADA Number CRD-09-367-11

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

Wilcox, S.

Under this Agreement, NREL will work with Participant to improve concentrating solar power system performance characterizations. This work includes, but is not limited to, research and development of methods for acquiring renewable resource characterization information using site-specific measurements of solar radiation and meteorological conditions; collecting system performance data; and developing tools for improving the design, installation, operation, and maintenance of solar energy conversion systems. This work will be conducted at NREL and Participant facilities.

Examination of the current practice of lighting in Virginia : nighttime work zones and improving safety through the development of nighttime lighting specifications : final report.

DOT National Transportation Integrated Search

2017-09-01

This project evaluated current nighttime work zone lighting practices for limited-access highways and primary routes in Virginia through (1) an on-site evaluation of lighting levels in work zones; (2) an illuminance characterization of various commer...

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.

Site Selection for the Disposal of LLW in Taiwan

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

Chuang, W.S.; Chi, L.M.; Tien, N.C.

2006-07-01

This paper presents the implementation status of the low-level radioactive waste (LLW) disposal program in Taiwan, including the disposal facility regulations, status of waste management, final disposal program, licensing procedures, waste acceptance criteria, site selection criteria and processes and preliminary disposal concepts. The first phase of site selection for low-level radioactive waste final disposal in Taiwan was implemented between 1992 and 2002. The site selection process adopted a Geographic Information System (GIS), Hierarchical Analysis System, Expert Evaluation System, and site reconnaissance. An incentive program for voluntary sites was also initiated. After a series of evaluations and discussion of 30 potentialmore » candidate sites, including 8 recommended sites, 5 qualified voluntary townships, and several remote uninhabited small islets, Hsiao-chiou islet was selected as the first priority candidate site in February 1998. The geological investigation work in Hsiao-chiou was conducted from March 1999 through October 2000. An Environmental Impact Statement Report (EIS) and the Investment Feasibility Study Report (IFS) were submitted to the Environmental Protection Agency (EPA) in November 2000 and to the Ministry of Economic Affairs (MOEA) in June 2001, respectively. Unfortunately, the site investigation was discontinued in 2002 due to political and public acceptance consideration. After years of planning, the second phase of the site selection process was launched in August 2004 and will be conducted through 2008. It is planned that a repository will be constructed in early 2009 and start to operate in 2014. The site selection process for the second phase is based on the earlier work and four potential candidate sites were selected for evaluation until 2005. A near surface disposal concept is proposed for a site located in the Taiwan strait, and cavern disposal concepts are proposed for three other sites located on the main island. This paper presents the implementation status of the LLW disposal program in Taiwan, including the disposal facility regulations, status of waste management, final disposal program, licensing procedures, waste acceptance criteria, site selection criteria and processes, and preliminary disposal concepts 'NIMBY' (Not in my backyard) is a critical problem for implementation of the final disposal project. Resistance from local communities has been continuously received during site characterization. To overcome this, an incentive program to encourage community acceptance has been approved by the Government. Programs for community promotion are being proposed and negotiations are also underway. (authors)« less

Site descriptive modeling as a part of site characterization in Sweden - Concluding the surface based investigations

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

Andersson, Johan; Winberg, Anders; Skagius, Kristina

The Swedish Nuclear Fuel and Waste Management Co., SKB, is currently finalizing its surface based site investigations for the final repository for spent nuclear fuel in the municipalities of Oestharmnar (the Forsmark area) and Oskarshamn (the Simpevar/Laxemar area). The investigation data are assessed into a Site Descriptive Model, constituting a synthesis of geology, rock mechanics, thermal properties, hydrogeology, hydro-geochemistry, transport properties and a surface system description. Site data constitute a wide range of different measurement results. These data both need to be checked for consistency and to be interpreted into a format more amenable for three-dimensional modeling. The three-dimensional modelingmore » (i.e. estimating the distribution of parameter values in space) is made in a sequence where the geometrical framework is taken from the geological models and in turn used by the rock mechanics, thermal and hydrogeological modeling. These disciplines in turn are partly interrelated, and also provide feedback to the geological modeling, especially if the geological description appears unreasonable when assessed together with the other data. Procedures for assessing the uncertainties and the confidence in the modeling have been developed during the course of the site modeling. These assessments also provide key input to the completion of the site investigation program. (authors)« less

Speciation and Attenuation of Arsenic and Selenium at Coal Combustion By-Product Management Facilities

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

K. Ladwig; B. Hensel; D. Wallschlager

2005-10-18

Following completion of contracting activities, sites were identified for the field leachate characterization study. Sampling and Analyses Plans (SAPs) and Site Access Agreements (SAAs) were developed for each site. A total of ten sites were sampled during this reporting period. Among the trace constituents, boron, silicon, and strontium were present in highest concentrations, with median values above 1 mg/L (1,000 {micro}g/L). Work on the first of three sites for the detailed arsenic and selenium adsorption studies began in 2002, prior to completion of the final DOE award. Kd values ranged from 100 to 12,000 L/kg for arsenic (V), 15 tomore » 160 L.kg for As(III), and 5 to 25 L/kg for Se(VI).« less

Remedial Action Plan and site design for stabilization of the inactive uranium mill tailings site at Durango, Colorado: Attachment 4, Water resources protection strategy. Revised final report

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

Not Available

1991-12-01

To achieve compliance with the proposed US Environmental Protection Agency (EPA) groundwater protection standards (Subpart A of 40 CFR 192), the US Department of Energy (DOE) proposes to meet background concentrations or the EPA maximum concentration limits (MCLS) for hazardous constituents in groundwater in the uppermost aquifer (Cliff House/Menefee aquifer) at the point of compliance (POC) at the Uranium Mill Tailings Remedial Action (UMTRA) Project disposal site in Bodo Canyon near Durango, Colorado (DOE, 1989). Details of hydrologic site characterization at the disposal site are provided in Attachment 3, Groundwater Hydrology Report. The principal features of the water resources protectionmore » strategy for the Bodo Canyon disposal site are presented in this document.« less

Cloning and Characterization of the Receptor for TPF (Tumor Promoting Factor), A Novel Angiogenic Factor

DTIC Science & Technology

2002-04-01

In addition, we have mapped the CKIs phosphorylation sites of Smad3 to the MH1 domain and the linker region. Furthermore, in the absence of TGF-beta...increases TGF-beta mediated transcription. Finally, CKI epsilon is capable of significantly enhancing the transcriptional activity of smad3 . Taken together

Metal–organic and covalent organic frameworks as single-site catalysts

PubMed Central

Rogge, S. M. J.; Bavykina, A.; Hajek, J.; Garcia, H.; Olivos-Suarez, A. I.; Sepúlveda-Escribano, A.; Vimont, A.; Clet, G.; Bazin, P.; Kapteijn, F.

2017-01-01

Heterogeneous single-site catalysts consist of isolated, well-defined, active sites that are spatially separated in a given solid and, ideally, structurally identical. In this review, the potential of metal–organic frameworks (MOFs) and covalent organic frameworks (COFs) as platforms for the development of heterogeneous single-site catalysts is reviewed thoroughly. In the first part of this article, synthetic strategies and progress in the implementation of such sites in these two classes of materials are discussed. Because these solids are excellent playgrounds to allow a better understanding of catalytic functions, we highlight the most important recent advances in the modelling and spectroscopic characterization of single-site catalysts based on these materials. Finally, we discuss the potential of MOFs as materials in which several single-site catalytic functions can be combined within one framework along with their potential as powerful enzyme-mimicking materials. The review is wrapped up with our personal vision on future research directions. PMID:28338128

Electron paramagnetic resonance, scanning electron microscopy with energy dispersion X-ray spectrometry, X-ray powder diffraction, and NMR characterization of iron-rich fired clays.

PubMed

Presciutti, Federica; Capitani, Donatella; Sgamellotti, Antonio; Brunetti, Brunetto Giovanni; Costantino, Ferdinando; Viel, Stéphane; Segre, Annalaura

2005-12-01

The aim of this study is to clarify the structure of an iron-rich clay and the structural changes involved in the firing process as a preliminary step to get information on ancient ceramic technology. To this purpose, illite-rich clay samples fired at different temperatures were characterized using a multitechnique approach, i.e., by electron paramagnetic resonance, scanning electron microscopy with electron dispersion X-ray spectrometry, X-ray powder diffraction, magic angle spinning and multiple quantum magic angle spinning NMR. During firing, four main reaction processes occur: dehydration, dehydroxylation, structural breakdown, and recrystallization. When the results are combined from all characterization methods, the following conclusions could be obtained. Interlayer H2O is located close to aluminum in octahedral sites and is driven off at temperatures lower than 600 degrees C. Between 600 and 700 degrees C dehydroxylation occurs whereas, between 800 and 900 degrees C, the aluminum in octahedral sites disappears, due to the breakdown of the illite structure, and all iron present is oxidized to Fe3+. In samples fired at 1000 and 1100 degrees C iron clustering was observed as well as large single crystals of iron with the occurrence of ferro- or ferrimagnetic effects. Below 900 degrees C the aluminum in octahedral sites presents a continuous distribution of chemical shift, suggesting the presence of slightly distorted sites. Finally, over the whole temperature range, the presence of at least two tetrahedral aluminum sites was revealed, characterized by different values of the quadrupolar coupling constant.

Characterizing site specific considerations for protecting aircraft during LGS operations at W. M. Keck Observatory

NASA Astrophysics Data System (ADS)

Stomski, Paul J., Jr.; Campbell, Randy; McCann, Kevin; Shimko, Steve

2010-07-01

W. M. Keck Observatory (WMKO) routinely operates laser guide star (LGS) Adaptive Optics (AO) systems at the telescope facility on the Big Island of Hawaii. One of the operational requirements for the LGS system is that a safety system to prevent nearby aircraft from being adversely affected by the laser must be provided. We will support operations in the near term with human aircraft spotters until we can successfully develop and get the appropriate approvals needed for an Automated, Integrated and Reliable System for an Aircraft Friendly Environment (AIRSAFE). This report describes some of the preliminary requirements development work at WMKO in support of the future development of AIRSAFE. We discuss the results of recent work to characterize site specific considerations that impact requirements development. The site specific considerations include the proximity of WMKO laser operations to nearby commercial airports, the implications of military operations in the area and the character of the air traffic volume and flight patterns over the telescope facility. Finally, we discuss how the design and implementation of AIRSAFE will be impacted by these site specific considerations.

MODIS. Volume 2: MODIS level 1 geolocation, characterization and calibration algorithm theoretical basis document, version 1

NASA Technical Reports Server (NTRS)

Barker, John L.; Harnden, Joann M. K.; Montgomery, Harry; Anuta, Paul; Kvaran, Geir; Knight, ED; Bryant, Tom; Mckay, AL; Smid, Jon; Knowles, Dan, Jr.

1994-01-01

The EOS Moderate Resolution Imaging Spectrometer (MODIS) is being developed by NASA for flight on the Earth Observing System (EOS) series of satellites, the first of which (EOS-AM-1) is scheduled for launch in 1998. This document describes the algorithms and their theoretical basis for the MODIS Level 1B characterization, calibration, and geolocation algorithms which must produce radiometrically, spectrally, and spatially calibrated data with sufficient accuracy so that Global change research programs can detect minute changes in biogeophysical parameters. The document first describes the geolocation algorithm which determines geodetic latitude, longitude, and elevation of each MODIS pixel and the determination of geometric parameters for each observation (satellite zenith angle, satellite azimuth, range to the satellite, solar zenith angle, and solar azimuth). Next, the utilization of the MODIS onboard calibration sources, which consist of the Spectroradiometric Calibration Assembly (SRCA), Solar Diffuser (SD), Solar Diffuser Stability Monitor (SDSM), and the Blackbody (BB), is treated. Characterization of these sources and integration of measurements into the calibration process is described. Finally, the use of external sources, including the Moon, instrumented sites on the Earth (called vicarious calibration), and unsupervised normalization sites having invariant reflectance and emissive properties is treated. Finally, algorithms for generating utility masks needed for scene-based calibration are discussed. Eight appendices are provided, covering instrument design and additional algorithm details.

Evaluation of Final Radiological Conditions at Areas of the Niagara Falls Storage Site Remediated under the Formerly Utilized Sites Remedial Action Program -12184

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

Clayton, Christopher; Kothari, Vijendra; Starr, Ken

2012-02-26

The U. S. Department of Energy (DOE) methods and protocols allow evaluation of remediation and final site conditions to determine if remediated sites remain protective. Two case studies are presented that involve the Niagara Falls Storage Site (NFSS) and associated vicinity properties (VPs), which are being remediated under the Formerly Utilized Sites Remedial Action Program (FUSRAP). These properties are a part of the former Lake Ontario Ordnance Works (LOOW). In response to stakeholders concerns about whether certain remediated NFSS VPs were putting them at risk, DOE met with stakeholders and agreed to evaluate protectiveness. Documentation in the DOE records collectionmore » adequately described assessed and final radiological conditions at the completed VPs. All FUSRAP wastes at the completed sites were cleaned up to meet DOE guidelines for unrestricted use. DOE compiled the results of the investigation in a report that was released for public comment. In conducting the review of site conditions, DOE found that stakeholders were also concerned about waste from the Separations Process Research Unit (SPRU) at the Knolls Atomic Power Laboratory (KAPL) that was handled at LOOW. DOE agreed to determine if SPRU waste remained at that needed to be remediated. DOE reviewed records of waste characterization, historical handling locations and methods, and assessment and remediation data. DOE concluded that the SPRU waste was remediated on the LOOW to levels that pose no unacceptable risk and allow unrestricted use and unlimited exposure. This work confirms the following points as tenets of an effective long-term surveillance and maintenance (LTS&M) program: Stakeholder interaction must be open and transparent, and DOE must respond promptly to stakeholder concerns. DOE, as the long-term custodian, must collect and preserve site records in order to demonstrate that remediated sites pose no unacceptable risk. DOE must continue to maintain constructive relationships with the U.S. Army Corps of Engineers and state and federal regulators.« less

Youth Corps Case Studies: The New York City Volunteer Corps Exit Report.

ERIC Educational Resources Information Center

Jaffe, Natalie; Freedman, Marc

This exit report chronicles the last 20 months of the 3-year demonstration phase of the New York City Volunteer Corps (CVC), whose members worked in teams at various sites to either provide human services or do physical work. These final months were characterized by the following factors: (1) a change in Corps leadership; (2) concern about…

Regulatory controls on the hydrogeological characterization of a mixed waste disposal site, Radioactive Waste Management Complex, Idaho National Engineering Laboratory

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

Ruebelmann, K.L.

1990-01-01

Following the detection of chlorinated volatile organic compounds in the groundwater beneath the SDA in the summer of 1987, hydrogeological characterization of the Radioactive Waste Management Complex (RWMC), Idaho National Engineering Laboratory (INEL) was required by the Resource Conservation and Recovery Act (RCRA). The waste site, the Subsurface Disposal Area (SDA), is the subject of a RCRA Corrective Action Program. Regulatory requirements for the Corrective Action Program dictate a phased approach to evaluation of the SDA. In the first phase of the program, the SDA is the subject of a RCRA Facility Investigation (RIF), which will obtain information to fullymore » characterize the physical properties of the site, determine the nature and extent of contamination, and identify pathways for migration of contaminants. If the need for corrective measures is identified during the RIF, a Corrective Measures Study (CMS) will be performed as second phase. Information generated during the RIF will be used to aid in the selection and implementation of appropriate corrective measures to correct the release. Following the CMS, the final phase is the implementation of the selected corrective measures. 4 refs., 1 fig.« less

Intergrated 3-D Ground-Penetrating Radar,Outcrop,and Boreholoe Data Applied to Reservoir Characterization and Flow Simulation.

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

McMechan et al.

2001-08-31

Existing reservoir models are based on 2-D outcrop;3-D aspects are inferred from correlation between wells,and so are inadequately constrained for reservoir simulations. To overcome these deficiencies, we initiated a multidimensional characterization of reservoir analogs in the Cretaceous Ferron Sandstone in Utah.The study was conducted at two sites(Corbula Gulch Coyote Basin); results from both sites are contained in this report. Detailed sedimentary facies maps of cliff faces define the geometry and distribution of potential reservoir flow units, barriers and baffles at the outcrop. High resolution 2-D and 3-D ground penetrating radar(GPR) images extend these reservoir characteristics into 3-D to allow developmentmore » of realistic 3-D reservoir models. Models use geometric information from the mapping and the GPR data, petrophysical data from surface and cliff-face outcrops, lab analyses of outcrop and core samples, and petrography. The measurements are all integrated into a single coordinate system using GPS and laser mapping of the main sedimentologic features and boundaries. The final step is analysis of results of 3-D fluid flow modeling to demonstrate applicability of our reservoir analog studies to well siting and reservoir engineering for maximization of hydrocarbon production. The main goals of this project are achieved. These are the construction of a deterministic 3-D reservoir analog model from a variety of geophysical and geologic measurements at the field sites, integrating these into comprehensive petrophysical models, and flow simulation through these models. This unique approach represents a significant advance in characterization and use of reservoir analogs. To data,the team has presented five papers at GSA and AAPG meetings produced a technical manual, and completed 15 technical papers. The latter are the main content of this final report. In addition,the project became part of 5 PhD dissertations, 3 MS theses,and two senior undergraduate research projects.« less

A study of the stress wave factor technique for the characterization of composite materials

NASA Technical Reports Server (NTRS)

Henneke, E. G., II; Duke, J. C., Jr.; Stinchcomb, W. W.; Govada, A.; Lemascon, A.

1983-01-01

A testing program was undertaken to provide an independent investigation and evaluation of the stress wave factor for characterizing the mechanical behavior of composite laminates. Some of the data which was obtained after performing a very large number of tests to determine the reproducibility of the SWF measurement is presented. It was determined that, with some optimizing of experimental parameters, the SWF value can be reproduced to within + or - 10%. Results are also given which show that, after careful calibration procedures, the lowest SWF value along the length of a specimen will correlate very closely to the site of final failure when the specimen is loaded in tension. Finally, using a moire interferometry technique, it was found that local regions having the highest in plane strains under tensile loading also had the lowest SWF values.

Public-health assessment for Algoma Municipal Landfill, Algoma, Kewaunee County, Wisconsin, Region 5. CERCLIS No. WID980610380. Final report

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

Not Available

1992-07-22

The Algoma Landfill Superfund Site is a former municipal landfill which accepted hazardous industrial waste from several area companies. The contaminant of concern is benzene in on-site groundwater. Samples taken from off-site private water supplies in the vicinity of the landfill did not indicate the presence of contaminants. On-site soil and sediment samples revealed low levels of inorganic chemicals. Although soil samples were not analyzed for asbestos it remains a contaminant of concern since asbestos-containing debris was reportedly buried as the site. The Algoma Landfill Superfund Site is a indeterminate public health hazard. There is insufficient data to evaluate workermore » exposure to airborne asbestos in the past when Kalo dust was deposited at the site. The public health assessment recommends that access to the site be restricted to prevent trespassing and disturbance of the soil. Additional groundwater monitoring and characterization is recommended as well as sampling of surface soil for asbestos contamination.« less

Medical devices; hematology and pathology devices; classification of early growth response 1 gene fluorescence in-situ hybridization test system for specimen characterization. Final order.

PubMed

2014-09-03

The Food and Drug Administration (FDA) is classifying early growth response 1 (EGR1) gene fluorescence in-situ hybridization (FISH) test system for specimen characterization into class II (special controls). The special controls that will apply to this device are identified in this order and will be part of the codified language for the early growth response 1 (EGR1) gene fluorescence in-site hybridization (FISH) test system for specimen characterization classification. The Agency is classifying the device into class II (special controls) in order to provide a reasonable assurance of safety and effectiveness of the device.

Technical approach to groundwater restoration. Final report

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

Not Available

1993-11-01

The Technical Approach to Groundwater Restoration (TAGR) provides general technical guidance to implement the groundwater restoration phase of the Uranium Mill Tailings Remedial Action (UMTRA) Project. The TAGR includes a brief overview of the surface remediation and groundwater restoration phases of the UMTRA Project and describes the regulatory requirements, the National Environmental Policy Act (NEPA) process, and regulatory compliance. A section on program strategy discusses program optimization, the role of risk assessment, the observational approach, strategies for meeting groundwater cleanup standards, and remedial action decision-making. A section on data requirements for groundwater restoration evaluates the data quality objectives (DQO) andmore » minimum data required to implement the options and comply with the standards. A section on sits implementation explores the development of a conceptual site model, approaches to site characterization, development of remedial action alternatives, selection of the groundwater restoration method, and remedial design and implementation in the context of site-specific documentation in the site observational work plan (SOWP) and the remedial action plan (RAP). Finally, the TAGR elaborates on groundwater monitoring necessary to evaluate compliance with the groundwater cleanup standards and protection of human health and the environment, and outlines licensing procedures.« less

Ames Laboratory site environmental report, calendar year 1988

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

Mathison, L.K.

1989-05-01

The summarized data and conclusions from the Ames Laboratory environmental monitoring program are presented in this Annual Site Environmental Report. Ames Laboratory is located on the campus of Iowa State University (ISU) and occupies several buildings owned by the Department of Energy. A study is being conducted to identify environmental sampling methods which can characterize and separate the impact of Ames Laboratory's campus activities and that of ISU. This will enable the Laboratory to determine what possible impact it's operations may be having to the environment, if any. Two Pollution Abatement projects were begun in 1988. They were: removal ofmore » thorium contaminated soil resulting from a historical release of thorium at the Laboratory, to the Ames, Iowa Water Pollution Control (sewage) Plant and demolition of a small Blockhouse'' constructed of concrete block which had been used for low level radioactive waste handling. The contaminated soil has been removed and transported to Hanford, WA for disposal. A final site radiological survey for thorium is pending. In addition, contaminated debris was transported to Hanford, WA for disposal and a final site survey is pending. 7 refs., 4 figs., 1 tab.« less

Position specific variation in the rate of evolution in transcription factor binding sites

PubMed Central

Moses, Alan M; Chiang, Derek Y; Kellis, Manolis; Lander, Eric S; Eisen, Michael B

2003-01-01

Background The binding sites of sequence specific transcription factors are an important and relatively well-understood class of functional non-coding DNAs. Although a wide variety of experimental and computational methods have been developed to characterize transcription factor binding sites, they remain difficult to identify. Comparison of non-coding DNA from related species has shown considerable promise in identifying these functional non-coding sequences, even though relatively little is known about their evolution. Results Here we analyse the genome sequences of the budding yeasts Saccharomyces cerevisiae, S. bayanus, S. paradoxus and S. mikatae to study the evolution of transcription factor binding sites. As expected, we find that both experimentally characterized and computationally predicted binding sites evolve slower than surrounding sequence, consistent with the hypothesis that they are under purifying selection. We also observe position-specific variation in the rate of evolution within binding sites. We find that the position-specific rate of evolution is positively correlated with degeneracy among binding sites within S. cerevisiae. We test theoretical predictions for the rate of evolution at positions where the base frequencies deviate from background due to purifying selection and find reasonable agreement with the observed rates of evolution. Finally, we show how the evolutionary characteristics of real binding motifs can be used to distinguish them from artefacts of computational motif finding algorithms. Conclusion As has been observed for protein sequences, the rate of evolution in transcription factor binding sites varies with position, suggesting that some regions are under stronger functional constraint than others. This variation likely reflects the varying importance of different positions in the formation of the protein-DNA complex. The characterization of the pattern of evolution in known binding sites will likely contribute to the effective use of comparative sequence data in the identification of transcription factor binding sites and is an important step toward understanding the evolution of functional non-coding DNA. PMID:12946282

Near surface geotechnical and geophysical data cross validated for site characterization applications. The cases of selected accelerometric stations in Crete island (Greece)

NASA Astrophysics Data System (ADS)

Loupasakis, Constantinos; Tsangaratos, Paraskevas; Rozos, Dimitrios; Rondoyianni, Theodora; Vafidis, Antonis; Steiakakis, Emanouil; Agioutantis, Zacharias; Savvaidis, Alexandros; Soupios, Pantelis; Papadopoulos, Ioannis; Papadopoulos, Nikos; Sarris, Apostolos; Mangriotis, Maria-Dafni; Dikmen, Unal

2015-04-01

The near surface ground conditions are highly important for the design of civil constructions. These conditions determine primarily the ability of the foundation formations to bear loads, the stress - strain relations and the corresponding deformations, as well as the soil amplification and corresponding peak ground motion in case of dynamic loading. The static and dynamic geotechnical parameters as well as the ground-type/soil-category can be determined by combining geotechnical and geophysical methods, such as engineering geological surface mapping, geotechnical drilling, in situ and laboratory testing and geophysical investigations. The above mentioned methods were combined for the site characterization in selected sites of the Hellenic Accelerometric Network (HAN) in the area of Crete Island. The combination of the geotechnical and geophysical methods in thirteen (13) sites provided sufficient information about their limitations, setting up the minimum tests requirements in relation to the type of the geological formations. The reduced accuracy of the surface mapping in urban sites, the uncertainties introduced by the geophysical survey in sites with complex geology and the 1-D data provided by the geotechnical drills are some of the causes affecting the right order and the quantity of the necessary investigation methods. Through this study the gradual improvement on the accuracy of the site characterization data in regards to the applied investigation techniques is presented by providing characteristic examples from the total number of thirteen sites. As an example of the gradual improvement of the knowledge about the ground conditions the case of AGN1 strong motion station, located at Agios Nikolaos city (Eastern Crete), is briefly presented. According to the medium scale geological map of IGME the station was supposed to be founded over limestone. The detailed geological mapping reveled that a few meters of loose alluvial deposits occupy the area, expected to lay over the Neogene marly formations and the Mesozoic limestone, identified at the surrounding area. This changes the ground type to E instead of A, based on the EC8 classification. According the geophysical survey the Neogene formations extend down several meters and the mean Vs30 is 476m/s, increasing the rank of the ground type to B. Finally, the geotechnical drill reviled that the loose alluvial deposits extend down 13m containing two clearly identified layers of liquefiable loose sand. Below the alluvial deposits a thin layer (1,5m thick) of Neogene marly formations and the karstified limestone was located, as expected. So finally it was proved that the ground type category at the site is S2, setting up the geotechnical drills as the determinant investigation technique for this site. Besides the above described case, all selected examples present sufficiently the ability, the limitations and the right order of the investigation methods aiming to the site characterization. This research has been co-financed by the European Union (European Social Fund - ESF) and Greek national funds through the Operational Program "Education and Lifelong Learning" of the National Strategic Reference Framework (NSRF) - Research Funding Program: THALES. Investing in knowledge society through the European Social Fund.

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.

Offshore Wind Guidance Document: Oceanography and Sediment Stability (Version 1) Development of a Conceptual Site Model.

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

Roberts, Jesse D.; Jason Magalen; Craig Jones

This guidance document provide s the reader with an overview of the key environmental considerations for a typical offshore wind coastal location and the tools to help guide the reader through a thoro ugh planning process. It will enable readers to identify the key coastal processes relevant to their offshore wind site and perform pertinent analysis to guide siting and layout design, with the goal of minimizing costs associated with planning, permitting , and long - ter m maintenance. The document highlight s site characterization and assessment techniques for evaluating spatial patterns of sediment dynamics in the vicinity of amore » wind farm under typical, extreme, and storm conditions. Finally, the document des cribe s the assimilation of all of this information into the conceptual site model (CSM) to aid the decision - making processes.« less

Site- and species-specific hydrolysis rates of heroin.

PubMed

Szöcs, Levente; Orgován, Gábor; Tóth, Gergő; Kraszni, Márta; Gergó, Lajos; Hosztafi, Sándor; Noszál, Béla

2016-06-30

The hydroxide-catalyzed non-enzymatic, simultaneous and consecutive hydrolyses of diacetylmorphine (DAM, heroin) are quantified in terms of 10 site- and species-specific rate constants in connection with also 10 site- and species-specific acid-base equilibrium constants, comprising all the 12 coexisting species in solution. This characterization involves the major and minor decomposition pathways via 6-acetylmorphine and 3-acetylmorphine, respectively, and morphine, the final product. Hydrolysis has been found to be 18-120 times faster at site 3 than at site 6, depending on the status of the amino group and the rest of the molecule. Nitrogen protonation accelerates the hydrolysis 5-6 times at site 3 and slightly less at site 6. Hydrolysis rate constants are interpreted in terms of intramolecular inductive effects and the concomitant local electron densities. Hydrolysis fraction, a new physico-chemical parameter is introduced and determined to quantify the contribution of the individual microspecies to the overall hydrolysis. Hydrolysis fractions are depicted as a function of pH. Copyright © 2016 Elsevier B.V. All rights reserved.

An optical method for characterizing carbon content in ceramic pot filters.

PubMed

Goodwin, J Y; Elmore, A C; Salvinelli, C; Reidmeyer, Mary R

2017-08-01

Ceramic pot filter (CPF) technology is a relatively common means of household water treatment in developing areas, and performance characteristics of CPFs have been characterized using production CPFs, experimental CPFs fabricated in research laboratories, and ceramic disks intended to be CPF surrogates. There is evidence that CPF manufacturers do not always fire their products according to best practices and the result is incomplete combustion of the pore forming material and the creation of a carbon core in the final CPFs. Researchers seldom acknowledge the existence of potential existence of carbon cores, and at least one CPF producer has postulated that the carbon may be beneficial in terms of final water quality because of the presence of activated carbon in consumer filters marketed in the Western world. An initial step in characterizing the presence and impact of carbon cores is the characterization of those cores. An optical method which may be more viable to producers relative to off-site laboratory analysis of carbon content has been developed and verified. The use of the optical method is demonstrated via preliminary disinfection and flowrate studies, and the results of these studies indicate that the method may be of use in studying production kiln operation.

Journal Article: EPA's National Dioxin Air Monitoring Network ...

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (U.S. EPA) established the National Dioxin Air Monitoring Network (NDAMN) in June of 1998, and operated it until November of 2004. The objective of NDAMN was to determine background air concentrations of polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), and dioxin-like polychlorinated biphenyls (dl-PCBs). NDAMN started with 10 sampling sites, adding more over time until the final count of 34 sites was reached by the beginning of 2003. Samples were taken quarterly, and the final sample count was 685. All samples were measured for 17 PCDD/PCDF congeners, 8 PCDD/PCDF homologue groups, and 7 dl-PCBs (note: 5 additional dl-PCBs were added for samples starting in the summer of 2002; 317 samples had measurements of 12 dl-PCBs). The overall average total toxic equivalent (TEQ) concentration in the United States was 11.2 fg TEQ m−3 with dl-PCBs contributing 0.8 fg TEQ m−3 (7%) to this total. The archetype dioxin and furan background air congener profile was seen in the survey averages and in most individual samples. This archetype profile is characterized by low and similar concentrations for tetra – through hexa PCDD/PCDF congeners, with elevations in four congeners – a hepta dioxin and furan congener, and both octa congeners. Sites were generally categorized as urban (4 sites), rural (23 sites), or remote (7 sites). The average TEQ concentrations over all sites and samples within these cat

Decision Support System For Management Of Low-Level Radioactive Waste Disposal At The Nevada Test Site

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

Shott, G.; Yucel, V.; Desotell, L.

2006-07-01

The long-term safety of U.S. Department of Energy (DOE) low-level radioactive disposal facilities is assessed by conducting a performance assessment -- a systematic analysis that compares estimated risks to the public and the environment with performance objectives contained in DOE Manual 435.1-1, Radioactive Waste Management Manual. Before site operations, facilities design features such as final inventory, waste form characteristics, and closure cover design may be uncertain. Site operators need a modeling tool that can be used throughout the operational life of the disposal site to guide decisions regarding the acceptance of problematic waste streams, new disposal cell design, environmental monitoringmore » program design, and final site closure. In response to these needs the National Nuclear Security Administration Nevada Site Office (NNSA/NSO) has developed a decision support system for the Area 5 Radioactive Waste Management Site in Frenchman Flat on the Nevada Test Site. The core of the system is a probabilistic inventory and performance assessment model implemented in the GoldSim{sup R} simulation platform. The modeling platform supports multiple graphic capabilities that allow clear documentation of the model data sources, conceptual model, mathematical implementation, and results. The combined models have the capability to estimate disposal site inventory, contaminant concentrations in environmental media, and radiological doses to members of the public engaged in various activities at multiple locations. The model allows rapid assessment and documentation of the consequences of waste management decisions using the most current site characterization information, radionuclide inventory, and conceptual model. The model is routinely used to provide annual updates of site performance, evaluate the consequences of disposal of new waste streams, develop waste concentration limits, optimize the design of new disposal cells, and assess the adequacy of environmental monitoring programs. (authors)« less

Kvichak River RISEC Project Resource Reconnaissance and Physical Characterization

DOE Data Explorer

Jarlath McEntee

2015-10-01

During the summer and fall of 2011 TerraSond Ltd. (TerraSond) completed a bathymetric survey and hydrokinetic energy assessment of the Kvichak River at Igiugig, Alaska. The purpose of this work was to characterize the initial site conditions for the design and installation of a hydrokinetic turbine to provide electric power for the village. There were six distinct phases of work for this project. The first was a literature review and investigation of prior surveys and hydrologic studies done in the area. The second, third, fourth, and fifth phases consisted of four field expeditions conducted over the summer and fall of 2011. These expeditions consisted of an initial reconnaissance, multi beam bathymetric surveys, flow velocity and discharge measurements, a survey of water levels, and detailed flow velocity studies. The final phase of the project was complete data reduction, and preparation of the final report with its accompanying map sheets and data packages. This submission contains the final report for the Kvichak River RiISEC Project in addition to weather data for Igiugig, AK, Summer 2015.

FY94 CAG trip reports, CAG memos and other products: Volume 2. Final report

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

NONE

1994-12-15

The Yucca Mountain Site Characterization Project (YMP) of the US DOE is tasked with designing, constructing, and operating an Exploratory Studies Facility (ESF) at Yucca Mountain, Nevada. The purpose of the YMP is to provide detailed characterization of the Yucca Mountain site for the potential mined geologic repository for permanent disposal of high-level radioactive waste. Detailed characterization of properties of the site are to be conducted through a wide variety of short-term and long-term in-situ tests. Testing methods require the installation of a large number of test instruments and sensors with a variety of functions. These instruments produce analog andmore » digital data that must be collected, processed, stored, and evaluated in an attempt to predict performance of the repository. The Integrated Data and Control System (IDCS) is envisioned as a distributed data acquisition that electronically acquires and stores data from these test instruments. IDCS designers are responsible for designing and overseeing the procurement of the system, IDCS Operation and Maintenance operates and maintains the installed system, and the IDCS Data Manager is responsible for distribution of IDCS data to participants. This report is a compilation of trip reports, interoffice memos, and other memos relevant to Computer Applications Group, Inc., work on this project.« less

Remedial Action Plan and site design for stabilization of the inactive uranium mill tailings site at Durango, Colorado: Attachment 2, Geology report. Revised final report

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

Not Available

1991-12-01

Detailed investigations of geologic, geomorphic, and seismic conditions at the Bodo Canyon disposal site were conducted. The purpose of these investigations was basic site characterization and identification of potential geologic hazards that could affect long-term site stability. Subsequent engineering studies, such as analyses of hydrologic and liquefaction hazards, used the data developed in these studies. The geomorphic analysis was employed in the design of effective erosion protection. Studies of the regional and local seismotectonic setting, which included a detailed search for possible capable faults within a 65 kilometer radius of the site, provided the basis for seismic design parameters. Themore » scope of work performed included the following: Compilation and analysis of previous published and unpublished geologic literature and maps; Review of historical and instrumental earthquake data; Review of site-specific subsurface geologic data, including lithologic and geophysical logs of exploratory boreholes advanced in the site area; Photogeologic interpretations of existing conventional aerial photographs; and, Ground reconnaissance and mapping of the site region.« less

Developing Hydrogeological Site Characterization Strategies based on Human Health Risk

NASA Astrophysics Data System (ADS)

de Barros, F.; Rubin, Y.; Maxwell, R. M.

2013-12-01

In order to provide better sustainable groundwater quality management and minimize the impact of contamination in humans, improved understanding and quantification of the interaction between hydrogeological models, geological site information and human health are needed. Considering the joint influence of these components in the overall human health risk assessment and the corresponding sources of uncertainty aid decision makers to better allocate resources in data acquisition campaigns. This is important to (1) achieve remediation goals in a cost-effective manner, (2) protect human health and (3) keep water supplies clean in order to keep with quality standards. Such task is challenging since a full characterization of the subsurface is unfeasible due to financial and technological constraints. In addition, human exposure and physiological response to contamination are subject to uncertainty and variability. Normally, sampling strategies are developed with the goal of reducing uncertainty, but less often they are developed in the context of their impacts on the overall system uncertainty. Therefore, quantifying the impact from each of these components (hydrogeological, behavioral and physiological) in final human health risk prediction can provide guidance for decision makers to best allocate resources towards minimal prediction uncertainty. In this presentation, a multi-component human health risk-based framework is presented which allows decision makers to set priorities through an information entropy-based visualization tool. Results highlight the role of characteristic length-scales characterizing flow and transport in determining data needs within an integrated hydrogeological-health framework. Conditions where uncertainty reduction in human health risk predictions may benefit from better understanding of the health component, as opposed to a more detailed hydrogeological characterization, are also discussed. Finally, results illustrate how different dose-response models can impact the probability of human health risk exceeding a regulatory threshold.

10 CFR 52.39 - Finality of early site permit determinations.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 2 2010-01-01 2010-01-01 false Finality of early site permit determinations. 52.39... NUCLEAR POWER PLANTS Early Site Permits § 52.39 Finality of early site permit determinations. (a) Commission finality. (1) Notwithstanding any provision in 10 CFR 50.109, while an early site permit is in...

10 CFR 52.39 - Finality of early site permit determinations.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 2 2011-01-01 2011-01-01 false Finality of early site permit determinations. 52.39... NUCLEAR POWER PLANTS Early Site Permits § 52.39 Finality of early site permit determinations. (a) Commission finality. (1) Notwithstanding any provision in 10 CFR 50.109, while an early site permit is in...

Regulatory requirements and tools for environmental assessment of hazardous wastes: Understanding tribal and stakeholder concerns using Department of Energy sites

PubMed Central

Burger, Joanna; Powers, Charles; Gochfeld, Michael

2014-01-01

Many US governmental and Tribal Nation agencies, as well as state and local entities, deal with hazardous wastes within regulatory frameworks that require specific environmental assessments. In this paper we use Department of Energy (DOE) sites as examples to examine the relationship between regulatory requirements and environmental assessments for hazardous waste sites and give special attention to how assessment tools differ. We consider federal laws associated with environmental protection include the National Environmental Policy Act (NEPA), the Resource Conservation and Recovery Act (RCRA), the Comprehensive Environmental Response Compensation and Liability Act (CERCLA), as well as regulations promulgated by the Nuclear Regulatory Commission, Tribal Nations and state agencies. These regulatory regimes require different types of environmental assessments and remedial investigations, dose assessments and contaminant pathways. The DOE case studies illustrate the following points: 1) there is often understandable confusion about what regulatory requirements apply to the site resources, and what environmental assessments are required by each, 2) the messages sent on site safety issued by different regulatory agencies are sometimes contradictory or confusing (e.g. Oak Ridge Reservation), 3) the regulatory frameworks being used to examine the same question can be different, leading to different conclusions (e.g. Brookhaven National Laboratory), 4) computer models used in support of groundwater models or risk assessments are not necessarily successful in convincing Native Americans and others that there is no possibility of risk from contaminants (e.g. Amchitka Island), 5) when given the opportunity to choose between relying on a screening risk assessments or waiting for a full site-specific analysis of contaminants in biota, the screening risk assessment option is rarely selected (e.g. Amchitka, Hanford Site), and finally, 6) there needs to be agreement on whether there has been adequate characterization to support the risk assessment (e.g. Hanford). The assessments need to be transparent and to accommodate different opinions about the relationship between characterizations and risk assessments. This paper illustrates how many of the problems at DOE sites, and potentially at other sites in the U.S. and elsewhere, derive from a lack of either understanding of, or consensus about, the regulatory process, including the timing and types of required characterizations and data in support of site characterizations and risk assessments. PMID:20719428

Site Effects, Attenuation and Signal Duration in the 1356 Basel Earthquake Area (Southern Upper Rhine Graben))

NASA Astrophysics Data System (ADS)

GRANET, M.; BOITEL, G.

2001-12-01

A field experiment has been carried out in the epicentral area of the Basel (northern Switzerland) earthquake of 18 October 1356, the largest historical earthquake in central Europe, with the aim to better characterize the spatial variability of the amplitudes of the seismic waves due to the local geology. Such site effects evaluation are needed in seismic engineering in order to establish effective building codes. In order to determine the site effects, we used a spectral ratio method, utilizing the data collected from a mobile network of 45 stations, installed from March to August 2000. As the main result, we found resonant peak amplitudes at 3, 4 and 6 Hz, which are more pronounced when the seismic stations are located on the sediments. From the same data set, attenuation laws have been calculated. They show the importance of the geometrical attenuation in this region and the influence of the local geology on the amplitude of ground velocities. Finally, we notice that the velocities are more amplified for the lower part of the observed seismic signal frequency band. The computation of relations linking the duration of the signal to the magnitude, the distance and the local geology shows a good correlation of stations characterized by long duration signals with those affected by site effects. As for ground velocities, the duration becomes also more significant at the low frequencies. Finally, we computed the quality factor QP using the spectral ratio method. Unfortunately does the limited number of available data prevent us to obtain a very detailed model. Nevertheless does QP show a very significant attenuation across the whole area, without large contrasts, and a decrease of the attenuation with increasing frequencies. To conclude, this newly collected data set from a dense array of 45 stations in this tectonically active and hazardous area shows large site effects associated with an increasing of both amplitudes and duration of the signal, especially at low frequencies.

Surface chemistry characterization of hydrodesulfurization and methanol synthesis model nanocatalysts

NASA Astrophysics Data System (ADS)

Komarneni, Mallikharjuna Rao

Surface science investigations of model catalysts have contributed significantly to heterogeneous catalysis over the past several decades. The unique properties of nanomaterials are being exploited in catalysis for the development of highly active and selective catalysts. Surface science investigations of model catalysts such as inorganic fullerene-like (IF) nanoparticles (NP), inorganic nanotubes (INT), and the oxide-supported nanoclusters are included in this dissertation. Thermal desorption spectroscopy and molecular beam scattering were respectively utilized to study the adsorption kinetics and dynamics of gas phase molecules on catalyst surfaces. In addition, ambient pressure kinetics experiments were performed to characterize the catalytic activity of hydrodesulfurization (HDS) nanocatalysts. The nanocatalysts were characterized with a variety of techniques, including Auger electron spectroscopy, x-ray photoelectron spectroscopy, electron microscopy, and x-ray diffraction. The adsorption kinetics studies of thiophene on novel HDS catalysts provided the first evidence for the presence of different adsorption sites on INT-WS2. Additionally, the adsorption sites on IF-MoS2 NP and silica-supported Mo clusters (Mo/silica) were characterized. Furthermore, the C-S bond activation energy of thiophene on Mo/silica was determined. These studies finally led to the fabrication of Ni/Co coated INT-WS2, which showed good catalytic activity towards HDS of thiophene. The studies of methanol synthesis catalysts include the adsorption kinetics and dynamics studies of CO and CO2 on Cu/silica and silica-supported EBL-fabricated Cu/CuOx nanoclusters. The adsorption dynamics of CO on Cu/silica are modeled within the frame work of the capture zone model (CZM), and the active sites of the silica-supported Au/Cu catalysts are successfully mapped. Studies on EBL model catalysts identify the rims of the CuOx nanoclusters as catalytically active sites. This observation has implications for new methanol catalyst design.

Results from Three Years of Ka-Band Propagation Characterization at Svalbard, Norway

NASA Technical Reports Server (NTRS)

Nessel, James; Zemba, Michael; Morse, Jacquelynne

2015-01-01

Over the next several years, NASA plans to launch several earth science missions which are expected to achieve data throughputs of 5-40 terabits per day transmitted from low earth orbiting spacecraft to ground stations. The current S-band and X-band frequency allocations in use by NASA, however, are incapable of supporting the data rates required to meet this demand. As such, NASA is in the planning stages to upgrade its existing Near Earth Network (NEN) polar ground stations to support Ka-band (25.5-27 GHz) operations. Consequently, it installed and operated a Ka-band radiometer at the Svalbard site. Svalbard was chosen as the appropriate site for two primary reasons: (1) Svalbard will be the first site to be upgraded to Ka-band operations within the NEN Polar Network enhancement plan, and (2) there exists a complete lack of Ka-band propagation data at this site (as opposed to the Fairbanks, AK NEN site, which has 5 years of characterization collected during the Advanced Communications Technology becomes imperative that characterization of propagation effects at these NEN sites is conducted to determine expected system Satellite (ACTS) campaign). processing and provide the Herein, we discuss the data three-year measurement results performance, particularly at low elevation angles ((is) less than 10 deg) from the ongoing Ka-band propagation characterization where spacecraft signal acquisition typically occurs. Since May 2011, NASA Glenn Research Center has installed and operated a Ka-band radiometer at the NEN site located in Svalbard, Norway. The Ka-band radiometer monitors the water vapor line, as well as 4 frequencies around 26.5 GHz at a fixed 10 deg elevation angle. Three-year data collection results indicate good campaign at Svalbard, Norway. Comparison of these results with the ITU models and existing ERA profile data indicates very good agreement when the 2010 rain maps and cloud statistics are used. Finally, the Svalbard data is used to derive the expected atmospheric margin requirements for this site agreement with models and comparable performance to necessary to maintain total system availability levels for the previously characterized northern latitude sites in the United States, i.e., Fairbanks, Alaska. The Svalbard data is used to upcoming Joint Polar Satellite System (JPSS) launch in the derive availability results for an upcoming earth-observation 2017/2022 timeframes. mission, JPSS-1, and indicate a requirement of 4 dB of atmospheric attenuation margin necessary to close the link with 99% overall system availability for the expected LEO orbital cycle, as observed from the Svalbard location.

Results from Three Years of Ka-band Propagation Characterization at Svalbard, Norway

NASA Technical Reports Server (NTRS)

Nessel, James A.; Zemba, Michael; Morse, Jacquelynne

2015-01-01

Over the next several years, NASA plans to launch several earth science missions which are expected to achieve data throughputs of 5-40 terabits per day transmitted from low earth orbiting spacecraft to ground stations. The current S-band and X-band frequency allocations in use by NASA, however, are incapable of supporting the data rates required to meet this demand. As such, NASA is in the planning stages to upgrade its existing Near Earth Network (NEN) polar ground stations to support Ka-band (25.5-27 GHz) operations. Consequently, it installed and operated a Ka-band radiometer at the Svalbard site. Svalbard was chosen as the appropriate site for two primary reasons: (1) Svalbard will be the first site to be upgraded to Ka-band operations within the NEN Polar Network enhancement plan, and (2) there exists a complete lack of Ka-band propagation data at this site (as opposed to the Fairbanks, AK NEN site, which has 5 years of characterization collected during the Advanced Communications Technology becomes imperative that characterization of propagation effects at these NEN sites is conducted to determine expected system Satellite (ACTS) campaign). processing and provide the Herein, we discuss the data three-year measurement results performance, particularly at low elevation angles ((is) less than 10 deg) from the ongoing Ka-band propagation characterization where spacecraft signal acquisition typically occurs. Since May 2011, NASA Glenn Research Center has installed and operated a Ka-band radiometer at the NEN site located in Svalbard, Norway. The Ka-band radiometer monitors the water vapor line, as well as 4 frequencies around 26.5 GHz at a fixed 10 deg elevation angle. Three-year data collection results indicate good campaign at Svalbard, Norway. Comparison of these results with the ITU models and existing ERA profile data indicates very good agreement when the 2010 rain maps and cloud statistics are used. Finally, the Svalbard data is used to derive the expected atmospheric margin requirements for this site agreement with models and comparable performance to necessary to maintain total system availability levels for the previously characterized northern latitude sites in the United States, i.e., Fairbanks, Alaska. The Svalbard data is used to upcoming Joint Polar Satellite System (JPSS) launch in the derive availability results for an upcoming earth-observation 2017/2022 timeframes. mission, JPSS-1, and indicate a requirement of 4 dB of atmospheric attenuation margin necessary to close the link with 99% overall system availability for the expected LEO orbital cycle, as observed from the Svalbard location.

Seismic Hazard and Ground Motion Characterization at the Itoiz Dam (Northern Spain)

NASA Astrophysics Data System (ADS)

Rivas-Medina, A.; Santoyo, M. A.; Luzón, F.; Benito, B.; Gaspar-Escribano, J. M.; García-Jerez, A.

2012-08-01

This paper presents a new hazard-consistent ground motion characterization of the Itoiz dam site, located in Northern Spain. Firstly, we propose a methodology with different approximation levels to the expected ground motion at the dam site. Secondly, we apply this methodology taking into account the particular characteristics of the site and of the dam. Hazard calculations were performed following the Probabilistic Seismic Hazard Assessment method using a logic tree, which accounts for different seismic source zonings and different ground-motion attenuation relationships. The study was done in terms of peak ground acceleration and several spectral accelerations of periods coinciding with the fundamental vibration periods of the dam. In order to estimate these ground motions we consider two different dam conditions: when the dam is empty ( T = 0.1 s) and when it is filled with water to its maximum capacity ( T = 0.22 s). Additionally, seismic hazard analysis is done for two return periods: 975 years, related to the project earthquake, and 4,975 years, identified with an extreme event. Soil conditions were also taken into account at the site of the dam. Through the proposed methodology we deal with different forms of characterizing ground motion at the study site. In a first step, we obtain the uniform hazard response spectra for the two return periods. In a second step, a disaggregation analysis is done in order to obtain the controlling earthquakes that can affect the dam. Subsequently, we characterize the ground motion at the dam site in terms of specific response spectra for target motions defined by the expected values SA ( T) of T = 0.1 and 0.22 s for the return periods of 975 and 4,975 years, respectively. Finally, synthetic acceleration time histories for earthquake events matching the controlling parameters are generated using the discrete wave-number method and subsequently analyzed. Because of the short relative distances between the controlling earthquakes and the dam site we considered finite sources in these computations. We conclude that directivity effects should be taken into account as an important variable in this kind of studies for ground motion characteristics.

Environmental assessment: Richton Dome Site, Mississippi

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

none,

1986-05-01

In February 1983, the US Department of Energy (DOE) identified the Richton Dome site in Mississippi as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Richton Dome site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOEmore » prepared the final EAs. The site is in the Gulf interior region, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains two other potentially acceptable sites--the Cypress Creek Dome site in Mississippi and the Vacherie Dome site in Louisiana. Although the Cypress Creek Dome and the Vacherie Dome sites are suitable for site characterization, the DOE has concluded that the Richton Dome site is the preferred site in the Gulf interior region. On the basis of the evaluations reported in this EA, the DOE has found that the Richton Dome site is not disqualified under the guidelines.« less

Structural and Biochemical Characterization of a Novel Aminopeptidase from Human Intestine

DOE PAGES

Tykvart, Jan; Bařinka, Cyril; Svoboda, Michal; ...

2015-03-09

N-acetylated α-linked acidic dipeptidase-like protein (NAALADase L), encoded by the NAALADL1 gene, is a close homolog of glutamate carboxypeptidase II, a metallopeptidase that has been intensively studied as a target for imaging and therapy of solid malignancies and neuropathologies. However, neither the physiological functions nor structural features of NAALADase L are known at present. In this paper, we report a thorough characterization of the protein product of the human NAALADL1 gene, including heterologous overexpression and purification, structural and biochemical characterization, and analysis of its expression profile. By solving the NAALADase L x-ray structure, we provide the first experimental evidence thatmore » it is a zinc-dependent metallopeptidase with a catalytic mechanism similar to that of glutamate carboxypeptidase II yet distinct substrate specificity. A proteome-based assay revealed that the NAALADL1 gene product possesses previously unrecognized aminopeptidase activity but no carboxy- or endopeptidase activity. These findings were corroborated by site-directed mutagenesis and identification of bestatin as a potent inhibitor of the enzyme. Analysis of NAALADL1 gene expression at both the mRNA and protein levels revealed the small intestine as the major site of protein expression and points toward extensive alternative splicing of the NAALADL1 gene transcript. Taken together, our data imply that the NAALADL1 gene product's primary physiological function is associated with the final stages of protein/peptide digestion and absorption in the human digestive system. Finally, based on these results, we suggest a new name for this enzyme: human ileal aminopeptidase (HILAP).« less

EPA's National Dioxin Air Monitoring Network (NDAMN): Design, implementation, and final results

NASA Astrophysics Data System (ADS)

Lorber, Matthew; Ferrario, Joseph; Byrne, Christian

2013-10-01

The U.S. Environmental Protection Agency (U.S. EPA) established the National Dioxin Air Monitoring Network (NDAMN) in June of 1998, and operated it until November of 2004. The objective of NDAMN was to determine background air concentrations of polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), and dioxin-like polychlorinated biphenyls (dl-PCBs). NDAMN started with 10 sampling sites, adding more over time until the final count of 34 sites was reached by the beginning of 2003. Samples were taken quarterly, and the final sample count was 685. All samples were measured for 17 PCDD/PCDF congeners, 8 PCDD/PCDF homologue groups, and 7 dl-PCBs (note: 5 additional dl-PCBs were added for samples starting in the summer of 2002; 317 samples had measurements of 12 dl-PCBs). The overall average total toxic equivalent (TEQ) concentration in the United States was 11.2 fg TEQ m-3 with dl-PCBs contributing 0.8 fg TEQ m-3 (7%) to this total. The archetype dioxin and furan background air congener profile was seen in the survey averages and in most individual samples. This archetype profile is characterized by low and similar concentrations for tetra - through hexa PCDD/PCDF congeners, with elevations in four congeners - a hepta dioxin and furan congener, and both octa congeners. Sites were generally categorized as urban (4 sites), rural (23 sites), or remote (7 sites). The average TEQ concentrations over all sites and samples within these categories were: urban = 15.9 fg TEQ m-3, rural = 13.9 fg TEQ m-3, and remote = 1.2 fg TEQ m-3. Rural sites showed elevations during the fall or winter months when compared to the spring or summer months, and the same might be said for urban sites, but the remote sites appear to show little variation over time. The four highest individual moment measurements were 847, 292, 241, and 132 fg TEQ m-3. For the 847 and 292 fg TEQ m-3 samples, the concentrations of all congeners were elevated over their site averages, but for the 241 and 132 fg TEQ m-3 measurements, only the PCDD congeners were elevated while PCDF and dl-PCB concentrations were similar to the site averages.

Soils, surficial geology, and geomorphology of the Bear Creek Valley Low-Level Waste Disposal Development and Demonstration Program site

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

Lietzke, D.A.; Lee, S.Y.; Lambert, R.E.

1988-04-01

An intensive soil survey was conducted on the proposed Low-Level Waste Disposal Development and Demonstration Program site (LLWDDD) in Bear Creek Valley. Soils on the site were related to the underlying residuum and to the surficial colluvium and alluvium. Within any particular geologic formation, soils were subdivided based mostly on the degree of weathering, as reflected by saprolite weathering and morphologic features of the soils. Degree of weathering was related both to slope shape and gradient and to the joint-fracture system. Erosion classes were also used to make further subdivisions of any particular soil. Deep pits were dug in eachmore » of the major Conasauga Group formations (Pumpkin Valley, Rogersville, Maryville, and Nolichucky) for soil and saprolite characterization. Because of the widespread presence of alluvium and colluvium, which are potential sources of fill and final cover material, pits and trenches were dug to characterize the properties of these soils and to try to understand the past geomorphic history of the site. The results of the soil survey investigation indicated that the deeply weathered Pumpkin Valley residuum has good potential for the construction of tumuli or other types of belowground or aboveground burial of prepackaged compacted waste. 11 refs., 30 figs., 3 tabs.« less

FY02 Final Report on Phytoremediation of Chlorinated Ethenes in Southern Sector Sediments of the Savannah River Site

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

Brigmon, R..L.

This final report details the operations and results of a 3-year Seepline Phytoremediation Project performed adjacent to Tims Branch, which is located in the Southern Sector of the Savannah River Site (SRS) A/M Area. Phytoremediation is a process where interactions between vegetation, associated microorganisms, and the host substrate combine to effectively degrade contaminated soils, sediments, and groundwater. Phytoremediation is a rapidly developing technology that shows promise for the effective and safe cleanup of certain hazardous wastes. It has the potential to remediate numerous volatile organic compounds (VOCs). Extensive characterization work has demonstrated that two VOCs, tetrachloroethylene (PCE) and trichloroethylene (TCE)more » are the major components of the VOC-contaminated groundwater that is migrating through the Southern Sector and Tims Branch seepline area (WSRC, 1999). The PCE and TCE are chlorinated ethenes (CE), and have been detected in seepline soils and ground water adjacent to the ecologically-sensitive Tims Branch seepline area.« less

Interests of long-term hydrogeological observatories for characterizing and modelling heterogeneous groundwater systems at multiple temporal and spatial scales: the example of Ploemeur, a crystalline rock aquifer (Brittany).

NASA Astrophysics Data System (ADS)

Bour, Olivier; Longuervergne, Laurent; Le Borgne, Tanguy; Lavenant, Nicolas; de Dreuzy, Jean-Raynald; Schuite, Jonathan; Labasque, Thierry; Aquilina, Luc; Davy, Philippe

2017-04-01

Characterizing groundwater flows and surface interactions in heterogeneous groundwater systems such as crystalline fractured rock is often extremely complex. In particular, hydraulic properties are highly variable while groundwater chemical properties may vary both in space and time, especially due to the impact of groundwater abstraction. Here, we show the interest of hydrological observatories and long-term monitoring for characterizing hydrological processes occurring in a crystalline rock aquifer. We present results from the site of Ploemeur (French Brittany) that belongs to the network of hydrogeological sites H+ and the research infrastructure OZCAR, and where interdisciplinary and integrated research at multiple temporal and spatial scales has been developed for almost twenty years. This outstandingly heterogeneous crystalline rock aquifer is also used for groundwater supply since 1991. In particular, we show how cross-borehole flowmeter tests, pumping tests and a frequency domain analysis of groundwater levels allow quantifying the hydraulic properties of the aquifer at different scales. In addition, groundwater temperature evolution was used as an excellent tracer for characterizing groundwater flow. At the site scale, measurements of ground surface deformation through long-base tiltmeters provide robust estimates of aquifer storage and allow identifying the active structures, including those acting during recharge process. Finally, a numerical model of the watershed scale that combines hydraulic data and groundwater ages confirms the geometry of this complex aquifer and the consistency of the different datasets. In parallel, this hydrological observatory is also used for developing hydrogeophysical methods and to characterize groundwater transport and biogeochemical reactivity in the sub-surface. The Ploemeur hydrogeological observatory is a good example of the interest of focusing research activities on a site during long-term as it provides a thorough understanding of both hydrological and biogeochemical processes that can be extended to many heterogeneous aquifers.

Remedial action plan and site design for stabilization of the inactive Uranium Mill Tailing site Maybell, Colorado. Attachment 3, ground water hydrology report, Attachment 4, water resources protection strategy. Final report

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

Not Available

1994-06-01

The U.S. Environmental Protection Agency (EPA) has established health and environmental regulations to correct and prevent ground water contamination resulting from former uranium processing activities at inactive uranium processing sites (40 CFR Part 192 (1993)) (52 FR 36000 (1978)). According to the Uranium Mill Tailings Radiation Control Act (UMTRCA) of 1978 (42 USC {section} 7901 et seq.), the U.S. Department of Energy (DOE) is responsible for assessing the inactive uranium processing sites. The DOE has decided that each assessment will include information on hydrogeologic site characterization. The water resources protection strategy that describes the proposed action compliance with the EPAmore » ground water protection standards is presented in Attachment 4, Water Resources Protection Strategy. Site characterization activities discussed in this section include the following: (1) Definition of the hydrogeologic characteristics of the environment, including hydrostratigraphy, aquifer parameters, areas of aquifer recharge and discharge, potentiometric surfaces, and ground water velocities. (2) Definition of background ground water quality and comparison with proposed EPA ground water protection standards. (3) Evaluation of the physical and chemical characteristics of the contaminant source and/or residual radioactive materials. (4) Definition of existing ground water contamination by comparison with the EPA ground water protection standards. (5) Description of the geochemical processes that affect the migration of the source contaminants at the processing site. (6) Description of water resource use, including availability, current and future use and value, and alternate water supplies.« less

Characterizing hydrology and the importance of ground-water discharge in natural and constructed wetlands

USGS Publications Warehouse

Hunt, Randall J.; Walker, John F.; Krabbenhoft, David P.

1999-01-01

Although considered the most important component for the establishment and persistence of wetlands, hydrology has been hard to characterize and linkages between hydrology and other environmental conditions are often poorly understood. In this work, methods for characterizing a wetland’s hydrology from hydrographs were developed, and the importance of ground water to the physical and geochemical conditions in the root zone was investigated. Detailed sampling of nearly continuous hydrographs showed that sites with greater ground-water discharge had higher water tables and more stable hydrographs. Subsampling of the continuous hydrograph failed to characterize the sites correctly, even though the wetland complex is located in a strong regional ground-water-discharge area. By comparing soil-moisture-potential measurements to the water-table hydrograph at one site, we noted that the amount of root-zone saturation was not necessarily driven by the water-table hydrograph but can be a result of other soil parameters (i.e., soil texture and associated capillary fringe). Ground-water discharge was not a significant determinant of maximum or average temperatures in the root zone. High ground-water discharge was associated with earliest date of thaw and shortest period of time that the root zone was frozen, however. Finally, the direction and magnitude of shallow ground-water flow was found to affect the migration and importance of a geochemical species. Areas of higher ground-water discharge had less downward penetration of CO2 generated in the root zone. In contrast, biotically derived CO2 was able to penetrate the deeper ground-water system in areas of ground-water recharge. Although ground-water flows are difficult to characterize, understanding these components is critical to the success of wetland restoration and creation efforts.

Lichens as bioindicators of air quality. Forest Service general technical report (Final)

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

Stolte, K.; Doty, R.; Mangis, D.

1993-03-01

The report is the result of a workshop held in Denver, Colorado on April 9-11, 1991. It summarizes the current literature and techniques for using lichens to monitor air quality. Experts in lichenology and ecology contributed information on lichen floristics, characterization of monitoring sites, lichen species and communities, identifying lichen species sensitive to pollutants, active monitoring with transplants, chemical analysis of lichens, and case studies as examples of lichen biomonitoring scenarios.

Incorporation of High Energy Materials Into High Density Polymers

DTIC Science & Technology

1987-09-21

and the pure graft copolymer was isolated by selective solvent extraction. 5 f. Isolation of pure Qraft copolymers. The isolation of pure EPDM -g-PS...characterized, such as EPDM -g-PST and EPDM -g-PMST. Two methods of synthesis were successful: a macromonomer (a polymer containing a polymerizab head group) was...copolymerized with ethylene and propylene to lead to the final product, and chlorination of a commercial EPDM allowed the chlorinated sites to serve as

Characterization of bacterial isolates from rubber dump site and their use in biodegradation of isoprene in batch and continuous bioreactors.

PubMed

Srivastva, Navnita; Shukla, Awadhesh Kumar; Singh, Ram Sharan; Upadhyay, Siddh Nath; Dubey, Suresh Kumar

2015-01-01

Bacterial isolates from contaminated soil of a waste rubber dumping site were isolated and characterized using biochemical and molecular approaches. Isoprene degradation kinetics in batch mode (isoprene concentration: 100-1000 ppm) revealed the degradation efficiency of isolates as: Pseudomonas sp. (83%)>Alcaligenes sp. (70%)>Klebsiella sp. (68.5%). The most efficient isolate Pseudomonas sp. was finally inoculated in a specifically designed bioreactor system comprising a bioscrubber and a biofilter packed with polyurethane foam connected in series. The bioscrubber and biofilter units when operated in a series showed more than 90% removal efficiency up to the inlet loading rate (IL) of 371.1g/m(3)/h. Maximum elimination capacity (EC) of biofilter was found to be an order of magnitude greater than that for bioscrubber. Oxidative cleavage of the double bond of isoprene has been revealed through IR spectra of the leachate. Copyright © 2015 Elsevier Ltd. All rights reserved.

West Hackberry Strategic Petroleum Reserve site brine-disposal monitoring, Year I report. Volume II. Physical and chemical oceanography. Final report

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

DeRouen, L.R.; Hann, R.W.; Casserly, D.M.

1983-02-01

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

Identification and characterization of conservative organic tracers for use as hydrologic tracers for the Yucca Mountain site characterization study. Final report

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

Stetzenbach, K.; Farnham, I.

1996-06-01

Extensive tracer testing is expected to take place at the C-well complex in the Nevada Test Site as part of the Yucca Mountain Site Characterization Project. The C-well complex consists of one pumping well, C3, and two injection wells, C1 and C2 into which tracer will be introduced. The goal of this research was to provide USGS with numerous tracers to completed these tests. Several classes of fluorinated organic acids have been evaluated. These include numerous isomers of fluorinated benzoic acids, cinnamic acids, and salicylic acids. Also several derivatives of 2-hydroxy nicotinic acid (pyridone) have been tested. The stability ofmore » these compounds was determined using batch and column tests. Ames testing (mutagenicity/carcinogenicity) was conducted on the fluorinated benzoic acids and a literature review of toxicity of the fluorobenzoates and three perfluoro aliphatic acids was prepared. Solubilities were measured and method development work was performed to optimize the detection of these compounds. A Quality Assurance (QA) Program was developed under existing DOE and USGS guidelines. The program includes QA procedures and technical standard operating procedures. A tracer test, using sodium iodide, was performed at the C-well complex. HRC chemists performed analyses on site, to provide real time data for the USGS hydrologists and in the laboratories at UNLV. Over 2,500 analyses were performed. This report provides the results of the laboratory experiments and literature reviews used to evaluate the potential tracers and reports on the results of the iodide C-well tracer test.« less

From Ground Truth to Space: Surface, Subsurface and Remote Observations Associated with Nuclear Test Detection

NASA Astrophysics Data System (ADS)

Sussman, A. J.; Anderson, D.; Burt, C.; Craven, J.; Kimblin, C.; McKenna, I.; Schultz-Fellenz, E. S.; Miller, E.; Yocky, D. A.; Haas, D.

2016-12-01

Underground nuclear explosions (UNEs) result in numerous signatures that manifest on a wide range of temporal and spatial scales. Currently, prompt signals, such as the detection of seismic waves provide only generalized locations and the timing and amplitude of non-prompt signals are difficult to predict. As such, research into improving the detection, location, and identification of suspect events has been conducted, resulting in advancement of nuclear test detection science. In this presentation, we demonstrate the scalar variably of surface and subsurface observables, briefly discuss current capabilities to locate, detect and characterize potential nuclear explosion locations, and explain how emergent technologies and amalgamation of disparate data sets will facilitate improved monitoring and verification. At the smaller scales, material and fracture characterization efforts on rock collected from legacy UNE sites and from underground experiments using chemical explosions can be incorporated into predictive modeling efforts. Spatial analyses of digital elevation models and orthoimagery of both modern conventional and legacy nuclear sites show subtle surface topographic changes and damage at nearby outcrops. Additionally, at sites where such technology cannot penetrate vegetative cover, it is possible to use the vegetation itself as both a companion signature reflecting geologic conditions and showing subsurface impacts to water, nutrients, and chemicals. Aerial systems based on RGB imagery, light detection and ranging, and hyperspectral imaging can allow for combined remote sensing modalities to perform pattern recognition and classification tasks. Finally, more remote systems such as satellite based synthetic aperture radar and satellite imagery are other techniques in development for UNE site detection, location and characterization.

Review. Neurobiology of nicotine dependence.

PubMed

Markou, Athina

2008-10-12

Nicotine is a psychoactive ingredient in tobacco that significantly contributes to the harmful tobacco smoking habit. Nicotine dependence is more prevalent than dependence on any other substance. Preclinical research in animal models of the various aspects of nicotine dependence suggests a critical role of glutamate, gamma-aminobutyric acid (GABA), cholinergic and dopamine neurotransmitter interactions in the ventral tegmental area and possibly other brain sites, such as the central nucleus of the amygdala and the prefrontal cortex, in the effects of nicotine. Specifically, decreasing glutamate transmission or increasing GABA transmission with pharmacological manipulations decreased the rewarding effects of nicotine and cue-induced reinstatement of nicotine seeking. Furthermore, early nicotine withdrawal is characterized by decreased function of presynaptic inhibitory metabotropic glutamate 2/3 receptors and increased expression of postsynaptic glutamate receptor subunits in limbic and frontal brain sites, while protracted abstinence may be associated with increased glutamate response to stimuli associated with nicotine administration. Finally, adaptations in nicotinic acetylcholine receptor function are also involved in nicotine dependence. These neuroadaptations probably develop to counteract the decreased glutamate and cholinergic transmission that is hypothesized to characterize early nicotine withdrawal. In conclusion, glutamate, GABA and cholinergic transmission in limbic and frontal brain sites are critically involved in nicotine dependence.

Structural and biochemical characterization of Xylella fastidiosa DsbA family members: new insights into the enzyme-substrate interaction.

PubMed

Rinaldi, Fábio C; Meza, Andréia N; Guimarães, Beatriz G

2009-04-21

Disulfide oxidoreductase DsbA catalyzes disulfide bond formation in proteins secreted to the periplasm and has been related to the folding process of virulence factors in many organisms. It is among the most oxidizing of the thioredoxin-like proteins, and DsbA redox power is understood in terms of the electrostatic interactions involving the active site motif CPHC. The plant pathogen Xylella fastidiosa has two chromosomal genes encoding two oxidoreductases belonging to the DsbA family, and in one of them, the canonical motif CPHC is replaced by CPAC. Biochemical assays showed that both X. fastidiosa homologues have similar redox properties and the determination of the crystal structure of XfDsbA revealed substitutions in the active site of X. fastidiosa enzymes, which are proposed to compensate for the lack of the conserved histidine in XfDsbA2. In addition, electron density maps showed a ligand bound to the XfDsbA active site, allowing the characterization of the enzyme interaction with an 8-mer peptide. Finally, surface analysis of XfDsbA and XfDsbA2 suggests that X. fastidiosa enzymes may have different substrate specificities.

Structural and Biochemical Characterization of Xylella fastidiosa DsbA Family Members: New insightsinto the Enzyme-Substrate Interaction

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

Rinaldi, F.; Meza, A; Gulmarges, B

2009-01-01

Disulfide oxidoreductase DsbA catalyzes disulfide bond formation in proteins secreted to the periplasm and has been related to the folding process of virulence factors in many organisms. It is among the most oxidizing of the thioredoxin-like proteins, and DsbA redox power is understood in terms of the electrostatic interactions involving the active site motif CPHC. The plant pathogen Xylella fastidiosa has two chromosomal genes encoding two oxidoreductases belonging to the DsbA family, and in one of them, the canonical motif CPHC is replaced by CPAC. Biochemical assays showed that both X. fastidiosa homologues have similar redox properties and the determinationmore » of the crystal structure of XfDsbA revealed substitutions in the active site of X. fastidiosa enzymes, which are proposed to compensate for the lack of the conserved histidine in XfDsbA2. In addition, electron density maps showed a ligand bound to the XfDsbA active site, allowing the characterization of the enzyme interaction with an 8-mer peptide. Finally, surface analysis of XfDsbA and XfDsbA2 suggests that X. fastidiosa enzymes may have different substrate specificities.« less

Selection and Characterization of Landing Sites for Chandrayaan-2 Lander

NASA Astrophysics Data System (ADS)

Gopala Krishna, Barla; Amitabh, Amitabh; Srinivasan, T. P.; Karidhal, Ritu; Nagesh, G.; Manjusha, N.

2016-07-01

Indian Space Research Organisation has planned the second mission to moon known as Chandrayaan-2, which consists of an Orbiter, a Lander and a Rover. This will be the first soft landing mission of India on lunar surface. The Orbiter, Lander and Rover individually will carry scientific payloads that enhance the scientific objectives of Chandrayaan-2. The Lander soft lands on the lunar surface and subsequently Lander & Rover will carry on with the payload activities on the moon surface. Landing Site identification based on the scientific and engineering constrains of lander plays an important role in success of a mission. The Lander poses some constraints because of its engineering design for the selection of the landing site and on the other hand the landing site / region imparts some constrain on the Lander. The various constraints that have to be considered for the study of the landing site are Local slope, Sun illumination during mission life, Radio communication with the Earth, Global slope towards equator, Boulders size, Crater density and boulder distribution. This paper describes the characterization activities of the different landing locations which have been studied for Chandrayaan-2 Lander. The sites have been studied both in the South Polar and North Polar regions of the moon on the near side. The Engineering Constraints at the sites due to the Lander, Factors that affect mission life (i.e. illumination at the location), Factors influencing communication to earth (i.e. RF visibility) & Shadow movements have been studied at these locations and zones that are favourable for landing have been short listed. This paper gives methodology of these studies along with the results of the characteristics of all the sites and the recommendations for further action in finalizing the landing area.

Environmental impacts on the evapotranspiration of an water limited and heterogeneous Mediterranean ecosystem.

NASA Astrophysics Data System (ADS)

Mackay, D. S.; Ewers, B. E.; Sperry, J. S.; Frank, J. M.; Reed, D. E.

2014-12-01

Mediterranean water limited ecosystems are characterized by an heterogeneous spatial distribution of different plant functional types (PFT), such as grass and trees, competing for water use. Typically, during the dry summers, these ecosystems are characterized by a simple dual PFTs system with strong-resistant woody vegetation and bare soil, since grass died. The coupled use of sap flow measurements and eddy covariance technique is essential to estimate Evapotransiration (ET) in an heterogeneous ecosystem. An eddy covariance - micrometeorological tower has been installed since 2003 and 33 thermo-dissipation probes based on the Granier technique have installed at the Orroli site in Sardinia (Italy). The site landscape is a mixture of Mediterranean patchy vegetation types: wild olives, different shrubs and herbaceous species, which died during the summer. The sensors have been installed at the Orroli site into 15 wild olives clumps with different characteristics in terms of tree size, exposition to wind and solar radiation and soil depth. A network of 30 soil moisture sensors has also been installed for monitoring soil moisture spatial and temporal dynamics and their correlation with trees. Sap flow measurements show the significantly impacts on ET of soil moisture, radiation, vapor pressure deficit (VPD) and interestingly of tree position into the clump, showing double rates for the trees inside the wild olive clumps. The sap flow sensor outputs are analyzed for estimating innovative allometric relationships between sapwood area, diameter, canopy cover area, which are needed for the correct upscale of the local tree measurements to the site plot larger scale. Finally using an innovative scaling procedure, the sap-flow transpiration at field scale have been compared to the eddy covariance ET, showing the approximation of the eddy covariance technique. Finally the impact of environmental factors on ET for different soil depth and tree position is demonstrated.

Environmental impacts on the evapotranspiration of an water limited and heterogeneous Mediterranean ecosystem.

NASA Astrophysics Data System (ADS)

Montaldo, N.; Curreli, M.; Corona, R.; Oren, R.

2015-12-01

Mediterranean water limited ecosystems are characterized by an heterogeneous spatial distribution of different plant functional types (PFT), such as grass and trees, competing for water use. Typically, during the dry summers, these ecosystems are characterized by a simple dual PFTs system with strong-resistant woody vegetation and bare soil, since grass died. The coupled use of sap flow measurements and eddy covariance technique is essential to estimate Evapotransiration (ET) in an heterogeneous ecosystem. An eddy covariance - micrometeorological tower has been installed since 2003 and 33 thermo-dissipation probes based on the Granier technique have installed at the Orroli site in Sardinia (Italy). The site landscape is a mixture of Mediterranean patchy vegetation types: wild olives, different shrubs and herbaceous species, which died during the summer. The sensors have been installed at the Orroli site into 15 wild olives clumps with different characteristics in terms of tree size, exposition to wind and solar radiation and soil depth. A network of 30 soil moisture sensors has also been installed for monitoring soil moisture spatial and temporal dynamics and their correlation with trees. Sap flow measurements show the significantly impacts on ET of soil moisture, radiation, vapor pressure deficit (VPD) and interestingly of tree position into the clump, showing double rates for the trees inside the wild olive clumps. The sap flow sensor outputs are analyzed for estimating innovative allometric relationships between sapwood area, diameter, canopy cover area, which are needed for the correct upscale of the local tree measurements to the site plot larger scale. Finally using an innovative scaling procedure, the sap-flow transpiration at field scale have been compared to the eddy covariance ET, showing the approximation of the eddy covariance technique. Finally the impact of environmental factors on ET for different soil depth and tree position is demonstrated.

40 CFR 228.15 - Dumping sites designated on a final basis.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 25 2014-07-01 2014-07-01 false Dumping sites designated on a final basis. 228.15 Section 228.15 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) OCEAN DUMPING CRITERIA FOR THE MANAGEMENT OF DISPOSAL SITES FOR OCEAN DUMPING § 228.15 Dumping sites designated on a final basis. (a)(1) The sites...

40 CFR 228.15 - Dumping sites designated on a final basis.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 26 2013-07-01 2013-07-01 false Dumping sites designated on a final basis. 228.15 Section 228.15 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) OCEAN DUMPING CRITERIA FOR THE MANAGEMENT OF DISPOSAL SITES FOR OCEAN DUMPING § 228.15 Dumping sites designated on a final basis. (a)(1) The sites...

40 CFR 228.15 - Dumping sites designated on a final basis.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 24 2010-07-01 2010-07-01 false Dumping sites designated on a final basis. 228.15 Section 228.15 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) OCEAN DUMPING CRITERIA FOR THE MANAGEMENT OF DISPOSAL SITES FOR OCEAN DUMPING § 228.15 Dumping sites designated on a final basis. (a)(1) The sites...

40 CFR 228.15 - Dumping sites designated on a final basis.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 26 2012-07-01 2011-07-01 true Dumping sites designated on a final basis. 228.15 Section 228.15 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) OCEAN DUMPING CRITERIA FOR THE MANAGEMENT OF DISPOSAL SITES FOR OCEAN DUMPING § 228.15 Dumping sites designated on a final basis. (a)(1) The sites...

Study of the ambient air metallic elements Cr, Cu, Zn, Cd and Pb at HAF sampling sites.

PubMed

Fang, Guor-Cheng; Kuo, Yu-Chen; Zhuang, Yuan-Jie; Tsai, Kai-Hsiang; Huang, Wen-Chuan

2017-08-01

This study characterized diurnal variations in the compositions of total suspended particulates (TSP) and dry deposits of particulates from ambient air, and the metallic elements that are contained in them at harbor, airport and farmland (HAF) sampling sites from August, 2013 to July, 2014. Two-way ANOVA of the amounts of metallic elements in the TSP and dry deposits was carried out in all four seasons at the HAF sampling sites. The metallic elements Cr and Cu originated in local emission sources at the airport. Metallic elements Zn and Pb originated in local emission sources at the harbor. Finally, metallic element Cd originated in local emissions form farmland. The following results were also obtained. (1) The metallic composition of the TSP differed significantly from that of the dry deposits in all four seasons at the harbor and farmland sampling sites, but not at the airport sampling site. (2) High correlations coefficients were found between the amounts of metallic elements Cr and Cu in the TSP and those in the dry deposits at the airport sampling site. (3) Pb was present in the TSP and the dry deposits at the harbor sampling site.

Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) identifies immune-selected HIV variants

DOE PAGES

Hraber, Peter; Korber, Bette; Wagh, Kshitij; ...

2015-10-21

Within-host genetic sequencing from samples collected over time provides a dynamic view of how viruses evade host immunity. Immune-driven mutations might stimulate neutralization breadth by selecting antibodies adapted to cycles of immune escape that generate within-subject epitope diversity. Comprehensive identification of immune-escape mutations is experimentally and computationally challenging. With current technology, many more viral sequences can readily be obtained than can be tested for binding and neutralization, making down-selection necessary. Typically, this is done manually, by picking variants that represent different time-points and branches on a phylogenetic tree. Such strategies are likely to miss many relevant mutations and combinations ofmore » mutations, and to be redundant for other mutations. Longitudinal Antigenic Sequences and Sites from Intrahost Evolution (LASSIE) uses transmitted founder loss to identify virus “hot-spots” under putative immune selection and chooses sequences that represent recurrent mutations in selected sites. LASSIE favors earliest sequences in which mutations arise. Here, with well-characterized longitudinal Env sequences, we confirmed selected sites were concentrated in antibody contacts and selected sequences represented diverse antigenic phenotypes. Finally, practical applications include rapidly identifying immune targets under selective pressure within a subject, selecting minimal sets of reagents for immunological assays that characterize evolving antibody responses, and for immunogens in polyvalent “cocktail” vaccines.« less

Biological and functional relevance of CASP predictions

PubMed Central

Liu, Tianyun; Ish‐Shalom, Shirbi; Torng, Wen; Lafita, Aleix; Bock, Christian; Mort, Matthew; Cooper, David N; Bliven, Spencer; Capitani, Guido; Mooney, Sean D.

2017-01-01

Abstract Our goal is to answer the question: compared with experimental structures, how useful are predicted models for functional annotation? We assessed the functional utility of predicted models by comparing the performances of a suite of methods for functional characterization on the predictions and the experimental structures. We identified 28 sites in 25 protein targets to perform functional assessment. These 28 sites included nine sites with known ligand binding (holo‐sites), nine sites that are expected or suggested by experimental authors for small molecule binding (apo‐sites), and Ten sites containing important motifs, loops, or key residues with important disease‐associated mutations. We evaluated the utility of the predictions by comparing their microenvironments to the experimental structures. Overall structural quality correlates with functional utility. However, the best‐ranked predictions (global) may not have the best functional quality (local). Our assessment provides an ability to discriminate between predictions with high structural quality. When assessing ligand‐binding sites, most prediction methods have higher performance on apo‐sites than holo‐sites. Some servers show consistently high performance for certain types of functional sites. Finally, many functional sites are associated with protein‐protein interaction. We also analyzed biologically relevant features from the protein assemblies of two targets where the active site spanned the protein‐protein interface. For the assembly targets, we find that the features in the models are mainly determined by the choice of template. PMID:28975675

SITE CHARACTERIZATION LIBRARY VERSION 3.0

EPA Science Inventory

The Site Characterization Library is a CD that provides a centralized, field-portable source for site characterization information. Version 3 of the Site Characterization Library contains additional (from earlier versions) electronic documents and computer programs related to th...

REAL-TIME IN SITU DETECTION OF ORGANIC CONTAMINANTS BY LASER-INDUCED FLUORESCENCE SYSTEM. Final tropical report (Task 1.3).

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

Daniel J. Stepan; James A. Sorensen; Jaroslav Solc

This report summarizes the results of the field demonstration of a laser-induced fluorescence (LIF) method for characterization of brownfields and other contaminated sites. The technology was provided and demonstrated by Dakota Technologies, Inc. (DTI), of Fargo, North Dakota. LIF generates continuous data on the distribution of polycyclic aromatic hydrocarbons (PAHs) within the soil profile. The sensor used to record real-time data is deployed into the soil using a modified truck-mounted Geoprobe percussion soil probing device. The summary of observations described in the following text represents an independent evaluation of the performance, usefulness, and economics of the demonstrated technology for characterizationmore » at PAH-contaminated sites.« less

Human health exposure assessment for Rocky Mountain Arsenal study area evaluations. Volume 6-E. Central study area exposure assessment. Version 4. 1(volume 6-E). Final report

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

Not Available

The objectives of the Human Health Exposure Assessment include: (1) estimate the type and magnitude of exposures to contaminants; (2) Identify contaminants of concern; (3) Identify sites for remedial action; (4) Recommend sites for the no action remedial alternative; and (5) Provide a basis for detailed characterization of the risk associated with all sites. This document consists of the following: An executive summary. Vol I - Land use and exposed population evaluations. Vol. II III - Toxicity assessment (includes army and shell toxicity profiles). Vol. IV - PPLV Methodology. Vol. V - PPLV Calculations. Vol. VI - Study area exposuremore » analysis A introduction, B Western study ares, C Southern study area, D northern Central study area, E Central study area, F Eastern study area, G South plants study area, and H North plants study area. Vol. VII - Summary exposure assessment.« less

Study area evaluations. Volume 6-H. North plants study area exposure assessment version 4. 1. Final report

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

Not Available

The objectives of the Human Health Exposure Assessment include: (1) estimate the type and magnitude of exposures to contaminants; (2) Identify contaminants of concern; (3) Identify sites for remedial action; (4) Recommend sites for the no action remedial alternative; and (5) Provide a basis for detailed characterization of the risk associated with all sites. This document consists of the following: An executive summary. Vol I - Land use and exposed population evaluations. Vol. II III - Toxicity assessment (includes army and shell toxicity profiles). Vol. IV - PPLV Methodology. Vol. V - PPLV Calculations. Vol. VI - Study area exposuremore » analysis A introduction, B Western study ares, C Southern study area, D northern Central study area, E Central study area, F Eastern study area, G South plants study area, and H North plants study area. Vol. VII - Summary exposure assessment.« less

Human health exposure assessment for Rocky Mountain Arsenal. Volume 7. Summary exposure assessment version 4. 1. Final report

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

Not Available

The objectives of the Human Health Exposure Assessment include: (1) estimate the type and magnitude of exposures to contaminants; (2) Identify contaminants of concern; (3) Identify sites for remedial action; (4) Recommend sites for the no action remedial alternative; and (5) Provide a basis for detailed characterization of the risk associated with all sites. This document consists of the following: An executive summary. Vol I - Land use and exposed population evaluations. Vol. II III - Toxicity assessment (includes army and shell toxicity profiles). Vol. IV - PPLV Methodology. Vol. V - PPLV Calculations. Vol. VI - Study area exposuremore » analysis A introduction, B Western study ares, C Southern study area, D northern Central study area, E Central study area, F Eastern study area, G South plants study area, and H North plants study area. Vol. VII - Summary exposure assessment.« less

Human health exposure assessment for Rocky Mountain Arsenal study area evaluations. Volume 6-F. Eastern study area exposure assessment. Version 4. 1(volume 6-F). Final report

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

Not Available

The objectives of the Human Health Exposure Assessment include: (1) estimate the type and magnitude of exposures to contaminants; (2) Identify contaminants of concern; (3) Identify sites for remedial action; (4) Recommend sites for the no action remedial alternative; and (5) Provide a basis for detailed characterization of the risk associated with all sites. This document consists of the following: An executive summary. Vol I - Land use and exposed population evaluations. Vol. II III - Toxicity assessment (includes army and shell toxicity profiles). Vol. IV - PPLV Methodology. Vol. V - PPLV Calculations. Vol. VI - Study area exposuremore » analysis A introduction, B Western study ares, C Southern study area, D northern Central study area, E Central study area, F Eastern study area, G South plants study area, and H North plants study area. Vol. VII - Summary exposure assessment.« less

Human health exposure assessment for Rocky Mountain Arsenal. Volume 8. Response to comments on the draft exposure assessment version 4. 1. Final report

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

Not Available

The objectives of the Human Health Exposure Assessment include: (1) estimate the type and magnitude of exposures to contaminants; (2) Identify contaminants of concern; (3) Identify sites for remedial action; (4) Recommend sites for the no action remedial alternative; and (5) Provide a basis for detailed characterization of the risk associated with all sites. This document consists of the following: An executive summary. Vol I - Land use and exposed population evaluations. Vol. II III - Toxicity assessment (includes army and shell toxicity profiles). Vol. IV - PPLV Methodology. Vol. V - PPLV Calculations. Vol. VI - Study area exposuremore » analysis A introduction, B Western study ares, C Southern study area, D northern Central study area, E Central study area, F Eastern study area, G South plants study area, and H North plants study area. Vol. VII - Summary exposure assessment.« less

Human health exposure assessment for Rocky Mountain Arsenal. Volume 2-A. Toxicity assessment. Version 4. 1. Final report

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

Not Available

The objectives of the Human Health Exposure Assessment include: (1) estimate the type and magnitude of exposures to contaminants; (2) Identify contaminants of concern; (3) Identify sites for remedial action; (4) Recommend sites for the no action remedial alternative; and (5) Provide a basis for detailed characterization of the risk associated with all sites. This document consists of the following: An executive summary. Vol I - Land use and exposed population evaluations. Vol. II III - Toxicity assessment (includes army and shell toxicity profiles). Vol. IV - PPLV Methodology. Vol. V - PPLV Calculations. Vol. VI - Study area exposuremore » analysis a introduction, B Western study ares, C Southern study area, D northern Central study area, E Central study area, F Eastern study area, G South plants study area, and H North plants study area. Vol. VII - Summary exposure assessment.« less

Human health exposure assessment for Rocky Mountain Arsenal. Volume 3. Toxicity assessment version 4. 1. Final report

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

Not Available

The objectives of the Human Health Exposure Assessment include: (1) estimate the type and magnitude of exposures to contaminants; (2) Identify contaminants of concern; (3) Identify sites for remedial action; (4) Recommend sites for the no action remedial alternative; and (5) Provide a basis for detailed characterization of the risk associated with all sites. This document consists of the following: An executive summary. Vol I - Land use and exposed population evaluations. Vol. II III - Toxicity assessment (includes army and shell toxicity profiles). Vol. IV - PPLV Methodology. Vol. V - PPLV Calculations. Vol. VI - Study area exposuremore » analysis A introduction, B Western study ares, C Southern study area, D northern Central study area, E Central study area, F Eastern study area, G South plants study area, and H North plants study area. Vol. VII - Summary exposure assessment.« less

Human health exposure assessment for Rocky Mountain Arsenal. Volume 1. Land use and exposed population evaluations version 4. 1. Final report

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

Not Available

The objectives of the Human Health Exposure Assessment include: (1) estimate the type and magnitude of exposures to contaminants; (2) Identify contaminants of concern; (3) Identify sites for remedial action; (4) Recommend sites for the no action remedial alternative; and (5) Provide a basis for detailed characterization of the risk associated with all sites. This document consists of the following: An executive summary. Vol I - Land use and exposed population evaluations. Vol. II III - Toxicity assessment (includes army and shell toxicity profiles). Vol. IV - PPLV Methodology. Vol. V - PPLV Calculations. Vol. VI - Study area exposuremore » analysis A introduction, B Western study ares, C Southern study area, D northern Central study area, E Central study area, F Eastern study area, G South plants study area, and H North plants study area. Vol. VII - Summary exposure assessment.« less

Human health exposure assessment for Rocky Mountain Arsenal study area evaluations. Volume 6-C. Southern study area exposure assessment version 4. 1. Final report

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

Not Available

The objectives of the Human Health Exposure Assessment include: (1) estimate the type and magnitude of exposures to contaminants; (2) Identify contaminants of concern; (3) Identify sites for remedial action; (4) Recommend sites for the no action remedial alternative; and (5) Provide a basis for detailed characterization of the risk associated with all sites. This document consists of the following: An executive summary. Vol I - Land use and exposed population evaluations. Vol. II III - Toxicity assessment (includes army and shell toxicity profiles). Vol. IV - PPLV Methodology. Vol. V - PPLV Calculations. Vol. VI - Study area exposuremore » analysis A introduction, B Western study ares, C Southern study area, D northern Central study area, E Central study area, F Eastern study area, G South plants study area, and H North plants study area. Vol. VII - Summary exposure assessment.« less

Location Capability and Site Characterization Installing a Borehole VBB Seismometer: the OGS Experience in Ferrara (Italy)

NASA Astrophysics Data System (ADS)

Pesaresi, D.; Barnaba, C.

2014-12-01

The Centro di Ricerche Sismologiche (CRS, Seismological Research Centre) of the Istituto Nazionale di Oceanografia e di Geofisica Sperimentale (OGS, Italian National Institute for Oceanography and Experimental Geophysics) in Udine (Italy) after the strong earthquake of magnitude M=6.4 occurred in 1976 in the Italian Friuli-Venezia Giulia region, started to operate the Northeastern Italy Seismic Network: it currently consists of 19 very sensitive broad band and 17 simpler short period seismic stations, all telemetered to and acquired in real time at the OGS CRS data centre in Udine. The southwestern edge of the OGS seismic network stands on the Po alluvial basin: earthquake localization and characterization in this area is affected by the presence of soft alluvial deposits. Following the ML=5.9 earthquake that struck the Emilia region around Ferrara in Northern Italy on May 20, 2012, a cooperation of Istituto Nazionale di Geofisica e Vulcanologia, OGS, the Comune di Ferrara and the University of Ferrara lead to the reinstallation of a previously existing very broad band (VBB) borehole seismic station in Ferrara and to the deployment of a temporary seismographic network consisting of eight portable seismological stations, to record the local earthquakes that occurred during the seismic sequence. The aim of the OGS intervention was on one hand to extend its real time seismic monitoring capabilities toward South-West, including Ferrara and its surroundings, and on the other hand to evaluate seismic site responses in the area. We will introduce details of the Ferrara VBB borehole station and the OGS temporary seismographic network configuration and installation. We will then illustrate the location capability performances, and finally we will shortly describe seismic site characterization with surface/borehole comparisons in terms of seismic noise, site amplification and resonance frequencies.

Synthesis, spectroscopic, biological activity and thermal characterization of ceftazidime with transition metals

NASA Astrophysics Data System (ADS)

Masoud, Mamdouh S.; Ali, Alaa E.; Elasala, Gehan S.; Kolkaila, Sherif A.

2018-03-01

Synthesis, physicochemical characterization and thermal analysis of ceftazidime complexes with transition metals (Cr(III), Mn(II), Fe(III), Co(II), Ni(II), Cu(II), Zn(II), Cd(II) and Hg(II)) were discussed. It's obtained that ceftazidime act as bidentate ligand. From magnetic measurement and spectral data, octahedral structures were proposed for all complexes except for cobalt, nickel and mercury had tetrahedral structural. Hyper chemistry program confirmed binding sites of ceftazidime. Ceftazidime complexes show higher activity than ceftazidime for some strains. From TG and DTA curves the thermal decomposition mechanisms of ceftazidime and their metal complexes were suggested. The thermal decomposition of the complexes ended with the formation of metal oxides as a final product except in case of Hg complex.

Characterization and remediation of 91B radioactive waste sites under performance based contracts at Lackland Air Force Base, San Antonio, Texas

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

Trujillo, P.A.; Anderson, K.D.

2007-07-01

This paper describes the challenges behind the implementation of the characterization, remediation, and the Site Closure for three 91b Radioactive Wastes under a Performance Based Contract at Lackland Air Force Base, San Antonio, Texas. The Defense Environmental Restoration Program (DERP) was established by Section 211 of the Superfund Amendments and Reauthorization Act of 1986 (SARA). A part of the DERP provides for the cleanup of hazardous substances associated with past Department of Defense (DoD) activities and is consistent with the provisions of the Comprehensive Environmental Response, Compensation and Liability Act (CERCLA). It is the Air Force Installation Restoration Program (IRP)more » that has responsibility for the cleanup activities associated with CERCLA. Under contract to the Air Force Center for Environmental Excellence (AFCEE), the ECC Project Team, that included ECC, Cabrera Services, and Malcolm Pirnie, was responsible for the implementation of the actions at three sites. The three IRP (91b) sites included RW015, a 0.02 square kilometer (5.5 acre) site, RW017 a 0.003 square kilometer (0.9 acre) site, and RW033 an 0.356 square kilometer (88 acre) site. Adding to the complexities of the project were issues of archaeological areas of interest, jurisdictional wetlands, land open to hunting, issues of security as well as compliance to the myriad of air force base rules, regulations, and Air Force Instructions (AFI). The award of the project task order was July of 2005, the project plan phase started in July of 2005 followed by the remedy implementation that included characterization and remediation as required reached completion in June of 2006. The project closure including the development and approval final status survey reports, proposed plans, and decision documents that parallel the CERCLA process was initiated in June of 2006 and is expected to reach completion in August of 2007. This paper will focus on the issues of working to achieve radiological and chemical closure under a performance based contract vehicle and the challenges encountered while reaching this goal. (authors)« less

Genome-wide mapping reveals single-origin chromosome replication in Leishmania, a eukaryotic microbe.

PubMed

Marques, Catarina A; Dickens, Nicholas J; Paape, Daniel; Campbell, Samantha J; McCulloch, Richard

2015-10-19

DNA replication initiates on defined genome sites, termed origins. Origin usage appears to follow common rules in the eukaryotic organisms examined to date: all chromosomes are replicated from multiple origins, which display variations in firing efficiency and are selected from a larger pool of potential origins. To ask if these features of DNA replication are true of all eukaryotes, we describe genome-wide origin mapping in the parasite Leishmania. Origin mapping in Leishmania suggests a striking divergence in origin usage relative to characterized eukaryotes, since each chromosome appears to be replicated from a single origin. By comparing two species of Leishmania, we find evidence that such origin singularity is maintained in the face of chromosome fusion or fission events during evolution. Mapping Leishmania origins suggests that all origins fire with equal efficiency, and that the genomic sites occupied by origins differ from related non-origins sites. Finally, we provide evidence that origin location in Leishmania displays striking conservation with Trypanosoma brucei, despite the latter parasite replicating its chromosomes from multiple, variable strength origins. The demonstration of chromosome replication for a single origin in Leishmania, a microbial eukaryote, has implications for the evolution of origin multiplicity and associated controls, and may explain the pervasive aneuploidy that characterizes Leishmania chromosome architecture.

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

Hraber, Peter; Korber, Bette; Wagh, Kshitij

Within-host genetic sequencing from samples collected over time provides a dynamic view of how viruses evade host immunity. Immune-driven mutations might stimulate neutralization breadth by selecting antibodies adapted to cycles of immune escape that generate within-subject epitope diversity. Comprehensive identification of immune-escape mutations is experimentally and computationally challenging. With current technology, many more viral sequences can readily be obtained than can be tested for binding and neutralization, making down-selection necessary. Typically, this is done manually, by picking variants that represent different time-points and branches on a phylogenetic tree. Such strategies are likely to miss many relevant mutations and combinations ofmore » mutations, and to be redundant for other mutations. Longitudinal Antigenic Sequences and Sites from Intrahost Evolution (LASSIE) uses transmitted founder loss to identify virus “hot-spots” under putative immune selection and chooses sequences that represent recurrent mutations in selected sites. LASSIE favors earliest sequences in which mutations arise. Here, with well-characterized longitudinal Env sequences, we confirmed selected sites were concentrated in antibody contacts and selected sequences represented diverse antigenic phenotypes. Finally, practical applications include rapidly identifying immune targets under selective pressure within a subject, selecting minimal sets of reagents for immunological assays that characterize evolving antibody responses, and for immunogens in polyvalent “cocktail” vaccines.« less

DESIGNING AN OPPORTUNITY FUEL WITH BIOMASS AND TIRE-DERIVED FUEL FOR COFIRING AT WILLOW ISLAND GENERATING STATION

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

K. Payette; D. Tillman

During the period January 1, 2001-March 31, 2001, Allegheny Energy Supply Co., LLC (Allegheny) finalized the engineering of the Willow Island cofiring project, completed the fuel characterizations for both the Willow Island and Albright Generating Station projects, and initiated construction of both projects. Allegheny and its contractor, Foster Wheeler, selected appropriate fuel blends and issued purchase orders for all processing and mechanical equipment to be installed at both sites. This report summarizes the activities associated with the Designer Opportunity Fuel program, and demonstrations at Willow Island and Albright Generating Stations. The third quarter of the project involved completing the detailedmore » designs for the Willow Island Designer Fuel project. It also included complete characterization of the coal and biomass fuels being burned, focusing upon the following characteristics: proximate and ultimate analysis; higher heating value; carbon 13 nuclear magnetic resonance testing for aromaticity, number of aromatic carbons per cluster, and the structural characteristics of oxygen in the fuel; drop tube reactor testing for high temperature devolatilization kinetics and generation of fuel chars; thermogravimetric analyses (TGA) for char oxidation kinetics; and related testing. The construction at both sites commenced during this quarter, and was largely completed at the Albright Generating Station site.« less

N- and O-Glycosylation in the Murine Synaptosome*

PubMed Central

Trinidad, Jonathan C.; Schoepfer, Ralf; Burlingame, Alma L.; Medzihradszky, Katalin F.

2013-01-01

We present the first large scale study characterizing both N- and O-linked glycosylation in a site-specific manner on hundreds of proteins. We demonstrate that a lectin-affinity fractionation step using wheat germ agglutinin enriches not only peptides carrying intracellular O-GlcNAc, but also those bearing ER/Golgi-derived N- and O-linked carbohydrate structures. Liquid chromatography-MS (LC/MS) analysis with high accuracy precursor mass measurements and high sensitivity ion trap electron-transfer dissociation (ETD) were utilized for structural characterization of glycopeptides. Our results reveal both the identity of the precise sites of glycosylation and information on the oligosaccharide structures possible on these proteins. We report a novel iterative approach that allowed us to interpret the ETD data set directly without making prior assumptions about the nature and distribution of oligosaccharides present in our glycopeptide mixture. Over 2500 unique N- and O-linked glycopeptides were identified on 453 proteins. The extent of microheterogeneity varied extensively, and up to 19 different oligosaccharides were attached at a given site. We describe the presence of the well-known mucin-type structures for O-glycosylation, an EGF-domain-specific fucosylation and a rare O-mannosylation on the transmembrane phosphatase Ptprz1. Finally, we identified three examples of O-glycosylation on tyrosine residues. PMID:23816992

N- and O-glycosylation in the murine synaptosome.

PubMed

Trinidad, Jonathan C; Schoepfer, Ralf; Burlingame, Alma L; Medzihradszky, Katalin F

2013-12-01

We present the first large scale study characterizing both N- and O-linked glycosylation in a site-specific manner on hundreds of proteins. We demonstrate that a lectin-affinity fractionation step using wheat germ agglutinin enriches not only peptides carrying intracellular O-GlcNAc, but also those bearing ER/Golgi-derived N- and O-linked carbohydrate structures. Liquid chromatography-MS (LC/MS) analysis with high accuracy precursor mass measurements and high sensitivity ion trap electron-transfer dissociation (ETD) were utilized for structural characterization of glycopeptides. Our results reveal both the identity of the precise sites of glycosylation and information on the oligosaccharide structures possible on these proteins. We report a novel iterative approach that allowed us to interpret the ETD data set directly without making prior assumptions about the nature and distribution of oligosaccharides present in our glycopeptide mixture. Over 2500 unique N- and O-linked glycopeptides were identified on 453 proteins. The extent of microheterogeneity varied extensively, and up to 19 different oligosaccharides were attached at a given site. We describe the presence of the well-known mucin-type structures for O-glycosylation, an EGF-domain-specific fucosylation and a rare O-mannosylation on the transmembrane phosphatase Ptprz1. Finally, we identified three examples of O-glycosylation on tyrosine residues.

SMARTe Site Characterization Tool. In: SMARTe20ll, EPA/600/C-10/007

EPA Science Inventory

The purpose of the Site Characterization Tool is to: (1) develop a sample design for collecting site characterization data and (2) perform data analysis on uploaded data. The sample design part helps to determine how many samples should be collected to characterize a site with ...

Environmental Analysis of Endocrine Disrupting Effects from Hydrocarbon Contaminants in the Ecosystem - Final Report - 09/15/1996 - 09/14/2000

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

McLachlan, John A.

The three major components of the research included: (a) a biotechnology based screening system to identify potential hormone mimics and antagonists (b) an animal screening system to identify biomarkers of endocrine effects and (c) a literature review to identify compounds at various DOE sites that are potential endocrine disruptors. Species of particular interest in this study were those that can serve as sentinel species (e.g., amphibians) and thus provide early warning signals for more widespread impacts on an ecosystem and its wildlife and human inhabitants. The objective of this basic research is to characterize the potential of common hydrocarbon contaminantsmore » in ecosystems to act as endocrine disruptors. Although the endocrine disrupting effects of contaminants such as dioxin and PCBs have been well characterized in both animals and humans, little is known about the capacities of other hydrocarbon contaminants to act as endocrine disruptors. Results obtained from this research project have provided information on endocrine disrupting contaminants for consideration in DOE's risk analyses for determining clean-up levels and priorities at contaminated DOE sites.« less

West Hackberry Strategic Petroleum Reserve site brine-disposal monitoring, Year I report. Volume IV. Bibliography and supporting data for physical oceanography. Final report. [421 references

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

DeRouen, L.R.; Hann, R.W.; Casserly, D.M.

This project centers around the Strategic Petroleum Site (SPR) known as the West Hackberry salt dome which is located in southwestern Louisiana and which is designed to store 241 million barrels of crude oil. Oil storage caverns are formed by injecting water into salt deposits, and pumping out the resulting brine. Studies described in this report were designed as follow-on studies to three months of pre-discharge characterization work, and include data collected during the first year of brine leaching operations. The objectives were to: (1) characterize the environment in terms of physical, chemical and biological attributes; (2) determine if significantmore » adverse changes in ecosystem productivity and stability of the biological community are occurring as a result of brine discharge; and (3) determine the magnitude of any change observed. Volume IV contains the following: bibliography; appendices for supporting data for physical oceanography, and summary of the physical oceanography along the western Louisiana coast.« less

Argonne National Laboratory Expedited Site Characterization: First International Symposium on Integrated Technical Approaches to Site Characterization - Proceedings Volume

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

NONE

1998-06-08

Laboratory applications for the analysis of PCBS (polychlorinated biphenyls) in environmental matrices such as soil/sediment/sludge and oil/waste oil were evaluated for potential reduction in waste, source reduction, and alternative techniques for final determination. As a consequence, new procedures were studied for solvent substitution, miniaturization of extraction and cleanups, minimization of reagent consumption, reduction of cost per analysis, and reduction of time. These new procedures provide adequate data that meet all the performance requirements for the determination of PCBS. Use of the new procedures reduced costs for all sample preparation techniques. Time and cost were also reduced by combining the newmore » sample preparation procedures with the power of fast gas chromatography. Separation of Aroclor 1254 was achieved in less than 6 min by using DB-1 and SPB-608 columns. With the greatly shortened run times, reproducibility can be tested quickly and consequently with low cost. With performance-based methodology, the applications presented here can be applied now, without waiting for regulatory approval.« less

Analysis of Substrate Access to Active Sites in Bacterial Multicomponent Monooxygenase Hydroxylases: X-ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase from Pseudomonas sp. OX1†,‡

PubMed Central

McCormick, Michael S.; Lippard, Stephen J.

2011-01-01

In all structurally characterized bacterial multicomponent monooxygenase (BMM) hydroxylase proteins, a series of hydrophobic cavities in the α-subunit trace a conserved path from the protein exterior to the carboxylate-bridged diiron active site. The present study examines these cavities as a potential route for dioxygen transport to the active site by crystallographic characterization of a xenon-pressurized sample of the hydroxylase component of phenol hydroxylase from Pseudomonas sp. OX1. Computational analyses of the hydrophobic cavities in the hydroxylase α-subunits of phenol hydroxylase (PHH), toluene/o-xylene monooxygenase (ToMOH), and soluble methane monooxygenase (sMMOH) are also presented. The results, together with previous findings from crystallographic studies of xenon-pressurized sMMO hydroxylase, clearly identify the propensity for these cavities to bind hydrophobic gas molecules in the protein interior. This proposed functional role is supported by recent stopped flow kinetic studies of ToMOH variants (Song, et al., 2011). In addition to information about the Xe sites, the structure determination revealed significantly reduced regulatory protein binding to the hydroxylase in comparison to the previously reported structure of PHH, as well as the presence of a newly identified metal binding site in the α-subunit that adopts a linear coordination environment consistent with Cu(I), and a glycerol molecule bound to Fe1 in a fashion that is unique among hydrocarbon-diiron site adducts reported to date in BMM hydroxylase structures. Finally, a comparative analysis of the α-subunit structures of MMOH, ToMOH, and PHH details proposed routes for the other three BMM substrates, the hydrocarbon, electrons, and protons, comprising cavities, channels, hydrogen-bonding networks, and pores in the structures of their α-subunits. PMID:22136180

Monomolecular Siloxane Film as a Model of Single Site Catalysts

DOE PAGES

Martynowycz, Michael W.; Hu, Bo; Kuzmenko, Ivan; ...

2016-09-06

Achieving structurally well-defined catalytic species requires a fundamental understanding of surface chemistry. Detailed structural characterization of the catalyst binding sites in situ, such as single site catalysts on silica supports, is technically challenging or even unattainable. Octadecyltrioxysilane (OTOS) monolayers formed from octadecyltrimethoxysilane (OTMS) at the air-liquid interface after hydrolysis and condensation at low pH were chosen as a model system of surface binding sites in silica-supported Zn 2+ catalysts. We characterize the system by grazing incidence X-ray diffraction, X-ray reflectivity (XR), and X-ray fluorescence spectroscopy (XFS). Previous X-ray and infrared surface studies of OTMS/OTOS films at the airliquid interface proposedmore » the formation of polymer OTOS structures. According to our analysis, polymer formation is inconsistent with the X-ray observations and structural properties of siloxanes; it is energetically unfavorable and thus highly unlikely. We suggest an alternative mechanism of hydrolysis/condensation in OTMS leading to the formation of structurally allowed cyclic trimers with the six-membered siloxane rings, which explain well both the X-ray and infrared results. XR and XFS consistently demonstrate that tetrahedral [Zn(NH 3) 4] 2+ ions bind to hydroxyl groups of the film at a stoichiometric ratio of OTOS:Zn ~ 2:1. The high binding affinity of zinc ions to OTOS trimers suggests that the six-membered siloxane rings are binding locations for single site Zn/SiO 2 catalysts. Finally, our results show that OTOS monolayers may serve as a platform for studying silica surface chemistry or hydroxyl-mediated reactions.« less

Smallpox Inhibitor of Complement Enzymes (SPICE): Dissecting Functional Sites and Abrogating Activity1

PubMed Central

Liszewski, M. Kathryn; Leung, Marilyn K.; Hauhart, Richard; Fang, Celia J.; Bertram, Paula; Atkinson, John P.

2010-01-01

Although smallpox was eradicated as a global illness more than 30 years ago, variola virus and other related pathogenic poxviruses, such as monkeypox, remain potential bioterrorist weapons or could re-emerge as natural infections. Poxviruses express virulence factors that down-modulate the host’s immune system. We previously compared functional profiles of the poxviral complement inhibitors of smallpox, vaccinia, and monkeypox known as SPICE, VCP (or VICE), and MOPICE, respectively. SPICE was the most potent regulator of human complement and attached to cells via glycosaminoglycans. The major goals of the present study were to further characterize the complement regulatory and heparin binding sites of SPICE and to evaluate a mAb that abrogates its function. Using substitution mutagenesis, we established that (1) elimination of the three heparin binding sites severely decreases but does not eliminate glycosaminoglycan binding, (2) there is a hierarchy of activity for heparin binding among the three sites, and (3) complement regulatory sites overlap with each of the three heparin binding motifs. By creating chimeras with interchanges of SPICE and VCP residues, a combination of two SPICE amino acids (H77 plus K120) enhances VCP activity ~200-fold. Also, SPICE residue L131 is critical for both complement regulatory function and accounts for the electrophoretic differences between SPICE and VCP. An evolutionary history for these structure-function adaptations of SPICE is proposed. Finally, we identified and characterized a mAb that inhibits the complement regulatory activity of SPICE, MOPICE, and VCP and thus could be used as a therapeutic agent. PMID:19667083

Study site characterization. Chapter 2

Treesearch

Chris Potter; Richard Birdsey

2008-01-01

This chapter is an overview of the main site characterization requirements at landscape-scale sampling locations. The overview is organized according to multiple "Site Attribute" headings that require descriptions throughout a given study site area, leading ultimately to a sufficient overall site characterization. Guidance is provided to describe the major...

Biological and functional relevance of CASP predictions.

PubMed

Liu, Tianyun; Ish-Shalom, Shirbi; Torng, Wen; Lafita, Aleix; Bock, Christian; Mort, Matthew; Cooper, David N; Bliven, Spencer; Capitani, Guido; Mooney, Sean D; Altman, Russ B

2018-03-01

Our goal is to answer the question: compared with experimental structures, how useful are predicted models for functional annotation? We assessed the functional utility of predicted models by comparing the performances of a suite of methods for functional characterization on the predictions and the experimental structures. We identified 28 sites in 25 protein targets to perform functional assessment. These 28 sites included nine sites with known ligand binding (holo-sites), nine sites that are expected or suggested by experimental authors for small molecule binding (apo-sites), and Ten sites containing important motifs, loops, or key residues with important disease-associated mutations. We evaluated the utility of the predictions by comparing their microenvironments to the experimental structures. Overall structural quality correlates with functional utility. However, the best-ranked predictions (global) may not have the best functional quality (local). Our assessment provides an ability to discriminate between predictions with high structural quality. When assessing ligand-binding sites, most prediction methods have higher performance on apo-sites than holo-sites. Some servers show consistently high performance for certain types of functional sites. Finally, many functional sites are associated with protein-protein interaction. We also analyzed biologically relevant features from the protein assemblies of two targets where the active site spanned the protein-protein interface. For the assembly targets, we find that the features in the models are mainly determined by the choice of template. © 2017 The Authors Proteins: Structure, Function and Bioinformatics Published by Wiley Periodicals, Inc.

Characterization and classification of South American land cover types using satellite data

NASA Technical Reports Server (NTRS)

Townshend, J. R. G.; Justice, C. O.; Kalb, V.

1987-01-01

Various methods are compared for carrying out land cover classifications of South America using multitemporal Advanced Very High Resolution Radiometer data. Fifty-two images of the normalized difference vegetation index (NDVI) from a 1-year period are used to generate multitemporal data sets. Three main approaches to land cover classification are considered, namely the use of the principal components transformed images, the use of a characteristic curves procedure based on NDVI values plotted against time, and finally application of the maximum likelihood rule to multitemporal data sets. Comparison of results from training sites indicates that the last approach yields the most accurate results. Despite the reliance on training site figures for performance assessment, the results are nevertheless extremely encouraging, with accuracies for several cover types exceeding 90 per cent.

Installation-restoration program. Phase 2. Confirmation/quantification. Stage 1 for Shaw Air Force Base, South Carolina. Final report, January 1984-October 1986

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

Alexander, W.J.; Liddle, S.K.

1986-09-01

The primary objectives of this project were to collect and analyze groundwater, surface water, and sediment samples and to perform an initial characterization of the hydrogeochemical regime at potential contamination sites on Shaw Air Force Base near Sumter, South Carolina. This study constituted Phase II of the U.S. Air Force Installation Restoration Program (IRP). Five potential sources of groundwater pollution were studied. The evaluation primarily included the drilling of soil test borings, the installation, development, and sampling of groundwater monitoring wells, and the analyses of soil, surface water, and groundwater samples. Also used in the study were field measurements ofmore » water quality, water-level measurements site observations, published hydrogeologic data and Shaw AFB documents.« less

Enhancing the reactivity of gold: Nanostructured Au(111) adsorbs CO

DOE PAGES

Hoffmann, F. M.; Hrbek, J.; Ma, S.; ...

2015-12-02

Low-coordinated sites are surface defects whose presence can transform a surface of inert or noble metal such as Au into an active catalyst. We prepared gold surfaces modified by pits, starting with a well-ordered Au(111) surface; we then used microscopy (STM) for their structural characterization and CO spectroscopy (IRAS and NEXAFS) for probing reactivity of surface defects. In contrast to the Au(111) surface CO adsorbs readily on the pitted surfaces bonding to low-coordinated sites identified as step atoms forming {111} and {100} microfacets. Finally, pitted nanostructured surfaces can serve as interesting and easily prepared models of catalytic surfaces with definedmore » defects that offer an attractive alternative to vicinal surfaces or nanoparticles commonly employed in catalysis science.« less

Report of sampling and analysis results, Addison Army housing units, Addison, Illinois. Final report

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

Not Available

1990-09-01

The objectives of this sampling and analysis effort include further characterization of environmental contamination identified in an enhanced preliminary assessment carried out in 1989. The specific activities performed at this site were identification, evaluation of the condition, and collection of samples from specific suspected asbestos-containing materials, including floor tiles, pipe run and pipe fitting insulation, dust in the ductwork, and exterior siding, where present. These evaluation were necessary to clarify potential environmental issues identified in the earlier report, prior to the sale or realignment of the property.

Pyrrole and Fused Pyrrole Compounds with Bioactivity against Inflammatory Mediators.

PubMed

Said Fatahala, Samar; Hasabelnaby, Sherifa; Goudah, Ayman; Mahmoud, Ghada I; Helmy Abd-El Hameed, Rania

2017-03-17

A new series of pyrrolopyridines and pyrrolopyridopyrimidines have been synthesized from aminocyanopyrroles. The synthesized compounds have been characterized by FTIR, ¹H-NMR and mass spectroscopy. The final compounds have been screened for in vitro pro-inflammatory cytokine inhibitory and in vivo anti-inflammatory activity. The biological results revealed that among all tested compounds some fused pyrroles, namely the pyrrolopyridines 3i and 3l , show promising activity. A docking study of the active synthesized molecules confirmed the biological results and revealed a new binding pose in the COX-2 binding site.

M3 Status and Science Discussion

NASA Technical Reports Server (NTRS)

Pieters, Carle

2007-01-01

Members of the M3 Science Team will attend the Chandrayaan-I Science Team Meeting in Bangalore, India to present a brief summary of instrument status and the near-term milestones (e.g., final I&T, pre-ship review). The principal purpose of the meeting is to interact with other members of the Chandrayaan-I Science Team to prepare for successful science return. The objectives are: 1) Characterize the diversity and extent of different types of basaltic volcanism; 2) Constrain evolution over time; and 3) Examine high priority regional sites.

An assessment of health risks associated with arsenic exposure via consumption of homegrown vegetables near contaminated glassworks sites.

PubMed

Uddh-Söderberg, Terese E; Gunnarsson, Sara J; Hogmalm, K Johan; Lindegård, M I Boel G; Augustsson, Anna L M

2015-12-01

The health risk posed by arsenic in vegetables grown in private gardens near 22 contaminated glassworks sites was investigated in this study. Firstly, vegetable (lettuce and potato) and soil samples were collected and arsenic concentrations measured to characterize the arsenic uptake in the selected crops. Secondly, a probabilistic exposure assessment was conducted to estimate the average daily intake (ADIveg), which was then evaluated against toxicological reference values by the calculation of hazard quotients (HQs) and cancer risks (CRs). The results show that elevated arsenic concentrations in residential garden soils are mirrored by elevated concentrations in vegetables, and that consumption of these vegetables alone may result in an unacceptable cancer risk; the calculated reasonable maximum exposure, for example, corresponded to a cancer incidence 20 times higher than the stated tolerance limit. However, the characterization of risk depends to a great extent on which toxicological reference value is used for comparison, as well as how the exposure is determined. Based on the assumptions made in the present study, the threshold levels for chronic non-carcinogenic or acute effects were not exceeded, but the cancer risks indicated highlight the need for further exposure studies, as dietary intake involves more than just homegrown vegetables and total exposure is a function of more than just one exposure pathway. In addition, glassworks sites--and contaminated sites in general--contain multiple contaminants, affecting the final and total risk. Copyright © 2015. Published by Elsevier B.V.

Public health assessment for USAF Langley Air Force Base and NASA-Langley Research Center, Hampton, York County, Virginia, Region 3. CERCLIS Number VA4570024477 and CERCLIS Number VA2800005033; Final report

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

NONE

1998-12-29

Langley Air Force Base (Langley AFB) and the National Aeronautics and Space Administration Langley Research Center (NASA LaRC) are located adjacent to each other on a small coastal basin of the Back River, a tidal estuary of the Chesapeake Bay. The Agency for Toxic Substances and Disease Registry (ATSDR) visited the sites in 1994 and 1997. During the 1994 visit, several potential public health concerns were raised. (1) the potential for contaminants to migrate to fish and shellfish (which might be ingested by local residents) in the adjoining estuary, (2) surface soil contamination at a former playground at Langley AFBmore » Site OT-06, (3) surface soil contamination and physical hazards at Langley AFB Sites OT-25 and FT-41, where children or youths might trespass, (4) the use of Langley AFB Site LF-12 for storing fill material, and (5) lead-contaminated soil in the housing areas at Langley AFB. ATSDR made recommendations for several of these sites. During the 1997 visit, ATSDR identified one additional potential concern at NASA LaRC Site 4, an open storage site where surface soil has not been characterized.« less

Molecular Characterization of Monoclonal Antibodies that Inhibit Acetylcholinesterase by Targeting the Peripheral Site and Backdoor Region

PubMed Central

Essono, Sosthène; Mondielli, Grégoire; Lamourette, Patricia; Boquet, Didier; Grassi, Jacques; Marchot, Pascale

2013-01-01

The inhibition properties and target sites of monoclonal antibodies (mAbs) Elec403, Elec408 and Elec410, generated against Electrophorus electricus acetylcholinesterase (AChE), have been defined previously using biochemical and mutagenesis approaches. Elec403 and Elec410, which bind competitively with each other and with the peptidic toxin inhibitor fasciculin, are directed toward distinctive albeit overlapping epitopes located at the AChE peripheral anionic site, which surrounds the entrance of the active site gorge. Elec408, which is not competitive with the other two mAbs nor fasciculin, targets a second epitope located in the backdoor region, distant from the gorge entrance. To characterize the molecular determinants dictating their binding site specificity, we cloned and sequenced the mAbs; generated antigen-binding fragments (Fab) retaining the parental inhibition properties; and explored their structure-function relationships using complementary x-ray crystallography, homology modeling and flexible docking approaches. Hypermutation of one Elec403 complementarity-determining region suggests occurrence of antigen-driven selection towards recognition of the AChE peripheral site. Comparative analysis of the 1.9Å-resolution structure of Fab408 and of theoretical models of its Fab403 and Fab410 congeners evidences distinctive surface topographies and anisotropic repartitions of charges, consistent with their respective target sites and inhibition properties. Finally, a validated, data-driven docking model of the Fab403-AChE complex suggests a mode of binding at the PAS that fully correlates with the functional data. This comprehensive study documents the molecular peculiarities of Fab403 and Fab410, as the largest peptidic inhibitors directed towards the peripheral site, and those of Fab408, as the first inhibitor directed toward the backdoor region of an AChE and a unique template for the design of new, specific modulators of AChE catalysis. PMID:24146971

Quantitative characterization of the regressive ecological succession by fractal analysis of plant spatial patterns

USGS Publications Warehouse

Alados, C.L.; Pueyo, Y.; Giner, M.L.; Navarro, T.; Escos, J.; Barroso, F.; Cabezudo, B.; Emlen, J.M.

2003-01-01

We studied the effect of grazing on the degree of regression of successional vegetation dynamic in a semi-arid Mediterranean matorral. We quantified the spatial distribution patterns of the vegetation by fractal analyses, using the fractal information dimension and spatial autocorrelation measured by detrended fluctuation analyses (DFA). It is the first time that fractal analysis of plant spatial patterns has been used to characterize the regressive ecological succession. Plant spatial patterns were compared over a long-term grazing gradient (low, medium and heavy grazing pressure) and on ungrazed sites for two different plant communities: A middle dense matorral of Chamaerops and Periploca at Sabinar-Romeral and a middle dense matorral of Chamaerops, Rhamnus and Ulex at Requena-Montano. The two communities differed also in the microclimatic characteristics (sea oriented at the Sabinar-Romeral site and inland oriented at the Requena-Montano site). The information fractal dimension increased as we moved from a middle dense matorral to discontinuous and scattered matorral and, finally to the late regressive succession, at Stipa steppe stage. At this stage a drastic change in the fractal dimension revealed a change in the vegetation structure, accurately indicating end successional vegetation stages. Long-term correlation analysis (DFA) revealed that an increase in grazing pressure leads to unpredictability (randomness) in species distributions, a reduction in diversity, and an increase in cover of the regressive successional species, e.g. Stipa tenacissima L. These comparisons provide a quantitative characterization of the successional dynamic of plant spatial patterns in response to grazing perturbation gradient. ?? 2002 Elsevier Science B.V. All rights reserved.

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

de Ruiter, Graham; Carsch, Kurtis M.; Gul, Sheraz

In this paper, we report the synthesis, characterization, and reactivity of [LFe 3(PhPz) 3OMn( sPhIO)][OTf] x (3: x=2; 4: x=3), where 4 is one of very few examples of iodosobenzene–metal adducts characterized by X-ray crystallography. Access to these rare heterometallic clusters enabled differentiation of the metal centers involved in oxygen atom transfer (Mn) or redox modulation (Fe). Specifically, 57Fe Mössbauer and X-ray absorption spectroscopy provided unique insights into how changes in oxidation state (Fe III 2Fe IIMn II vs. Fe III 3Mn II) influence oxygen atom transfer in tetranuclear Fe 3Mn clusters. Finally, in particular, a one-electron redox change atmore » a distal metal site leads to a change in oxygen atom transfer reactivity by ca. two orders of magnitude.« less

“Metallic burn paper” used for in situ characterization of laser beam properties

DOE PAGES

Bass, Isaac L.; Negres, Raluca A.; Stanion, Ken; ...

2016-04-12

In situ ablation of thin metal films on fused silica substrates by picosecond class lasers was investigated in this paper as a method of characterizing the beam at the sample plane. The technique involved plotting the areas enclosed by constant fluence contours identified in optical microscope images of the ablation sites versus the logs of the pulse energies. Inconel films on commercially available neutral density filters as well as magnetron sputtered gold films were used. It was also shown that this technique could be used to calibrate real-time beam profile diagnostics against the beam at the sample plane. Finally, themore » contours were shown to correspond to the boundary where part or all of the film was ablated.« less

10 CFR 960.3-2-3 - Recommendation of sites for characterization.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 4 2011-01-01 2011-01-01 false Recommendation of sites for characterization. 960.3-2-3... POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-2-3 Recommendation of sites... President not less than three candidate sites for such characterization. The recommendation decision shall...

10 CFR 960.3-1-4-3 - Site recommendation for characterization.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 4 2011-01-01 2011-01-01 false Site recommendation for characterization. 960.3-1-4-3... POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-1-4-3 Site recommendation for characterization. The evidence required to support the recommendation of a site as a candidate...

The 100-C-7 Remediation Project. An Overview of One of DOE's Largest Remediation Projects - 13260

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

Post, Thomas C.; Strom, Dean; Beulow, Laura

The U.S. Department of Energy Richland Operations Office (RL), U.S. Environmental Protection Agency (EPA) and Washington Closure Hanford LLC (WCH) completed remediation of one of the largest waste sites in the U.S. Department of Energy complex. The waste site, 100-C-7, covers approximately 15 football fields and was excavated to a depth of 85 feet (groundwater). The project team removed a total of 2.3 million tons of clean and contaminated soil, concrete debris, and scrap metal. 100-C-7 lies in Hanford's 100 B/C Area, home to historic B and C Reactors. The waste site was excavated in two parts as 100-C-7 andmore » 100-C-7:1. The pair of excavations appear like pit mines. Mining engineers were hired to design their tiered sides, with safety benches every 17 feet and service ramps which allowed equipment access to the bottom of the excavations. The overall cleanup project was conducted over a span of almost 10 years. A variety of site characterization, excavation, load-out and sampling methodologies were employed at various stages of remediation. Alternative technologies were screened and evaluated during the project. A new method for cost effectively treating soils was implemented - resulting in significant cost savings. Additional opportunities for minimizing waste streams and recycling were identified and effectively implemented by the project team. During the final phase of cleanup the project team applied lessons learned throughout the entire project to address the final, remaining source of chromium contamination. The C-7 cleanup now serves as a model for remediating extensive deep zone contamination sites at Hanford. (authors)« less

75 FR 77229 - Federal Requirements Under the Underground Injection Control (UIC) Program for Carbon Dioxide (CO2

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-10

...This action finalizes minimum Federal requirements under the Safe Drinking Water Act (SDWA) for underground injection of carbon dioxide (CO2) for the purpose of geologic sequestration (GS). GS is one of a portfolio of options that could be deployed to reduce CO2 emissions to the atmosphere and help to mitigate climate change. This final rule applies to owners or operators of wells that will be used to inject CO2 into the subsurface for the purpose of long-term storage. It establishes a new class of well, Class VI, and sets minimum technical criteria for the permitting, geologic site characterization, area of review (AoR) and corrective action, financial responsibility, well construction, operation, mechanical integrity testing (MIT), monitoring, well plugging, post-injection site care (PISC), and site closure of Class VI wells for the purposes of protecting underground sources of drinking water (USDWs). The elements of this rulemaking are based on the existing Underground Injection Control (UIC) regulatory framework, with modifications to address the unique nature of CO2 injection for GS. This rule will help ensure consistency in permitting underground injection of CO2 at GS operations across the United States and provide requirements to prevent endangerment of USDWs in anticipation of the eventual use of GS to reduce CO2 emissions to the atmosphere and to mitigate climate change.

Distribution of genetic markers of fecal pollution on a freshwater sandy shoreline in proximity to wastewater effluent

PubMed Central

Eichmiller, Jessica J.; Hicks, Randall E.; Sadowsky, Michael J.

2013-01-01

Water, sand, and sediment from a Lake Superior harbor site continuously receiving wastewater effluent was sampled monthly for June to October 2010 and from May to September 2011. Understanding the dynamics of genetic markers of fecal bacteria in these matrices is essential to accurately characterizing health risks. Genetic markers for enterococci, total Bacteroides, and human-associated Bacteroides were measured in site-water, sand, and sediment and in final effluent by quantitative PCR. The similarity between the quantity of molecular markers in the water column and effluent indicated that the abundance of genetic markers in the water column was likely controlled by effluent inputs. Effluent turbidity was positively correlated (p ≤ 0.05) with AllBac and HF183 in final effluent and AllBac in the water column. In sand and sediment, Entero1 and AllBac were most abundant in the upper 1– 3 cm depths, whereas HF183 was most abundant in the upper 1 cm of sand and at 7 cm in sediment. The AllBac and Entero1 markers were 1- and 2-orders of magnitude more abundant in sand and sediment relative to the water column per unit mass. These results indicate that sand and sediment may act as reservoirs for genetic markers of fecal pollution at some freshwater sites. PMID:23473470

Strategy for Ranking the Science Value of the Surface of Asteroid 101955 Bennu for Sample Site Selection for Osiris-REx

NASA Technical Reports Server (NTRS)

Nakamura-Messenger, K.; Connolly, H. C., Jr.; Lauretta, D. S.

2014-01-01

OSRIS-REx is NASA's New Frontiers 3 sample return mission that will return at least 60 g of pristine surface material from near-Earth asteroid 101955 Bennu in September 2023. The scientific value of the sample increases enormously with the amount of knowledge captured about the geological context from which the sample is collected. The OSIRIS-REx spacecraft is highly maneuverable and capable of investigating the surface of Bennu at scales down to the sub-cm. The OSIRIS-REx instruments will characterize the overall surface geology including spectral properties, microtexture, and geochemistry of the regolith at the sampling site in exquisite detail for up to 505 days after encountering Bennu in August 2018. The mission requires at the very minimum one acceptable location on the asteroid where a touch-and-go (TAG) sample collection maneuver can be successfully per-formed. Sample site selection requires that the follow-ing maps be produced: Safety, Deliverability, Sampleability, and finally Science Value. If areas on the surface are designated as safe, navigation can fly to them, and they have ingestible regolith, then the scientific value of one site over another will guide site selection.

HMG-D is an architecture-specific protein that preferentially binds to DNA containing the dinucleotide TG.

PubMed Central

Churchill, M E; Jones, D N; Glaser, T; Hefner, H; Searles, M A; Travers, A A

1995-01-01

The high mobility group (HMG) protein HMG-D from Drosophila melanogaster is a highly abundant chromosomal protein that is closely related to the vertebrate HMG domain proteins HMG1 and HMG2. In general, chromosomal HMG domain proteins lack sequence specificity. However, using both NMR spectroscopy and standard biochemical techniques we show that binding of HMG-D to a single DNA site is sequence selective. The preferred duplex DNA binding site comprises at least 5 bp and contains the deformable dinucleotide TG embedded in A/T-rich sequences. The TG motif constitutes a common core element in the binding sites of the well-characterized sequence-specific HMG domain proteins. We show that a conserved aromatic residue in helix 1 of the HMG domain may be involved in recognition of this core sequence. In common with other HMG domain proteins HMG-D binds preferentially to DNA sites that are stably bent and underwound, therefore HMG-D can be considered an architecture-specific protein. Finally, we show that HMG-D bends DNA and may confer a superhelical DNA conformation at a natural DNA binding site in the Drosophila fushi tarazu scaffold-associated region. Images PMID:7720717

Closure Report for Corrective Action Unit 412: Clean Slate I Plutonium Dispersion (TTR) Tonopah Test Range, Nevada, Revision 0

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

Matthews, Patrick

This Closure Report (CR) presents information supporting the clean closure of Corrective Action Unit (CAU) 412: Clean Slate I Plutonium Dispersion (TTR), located on the Tonopah Test Range, Nevada. CAU 412 consists of a release of radionuclides to the surrounding soil from a storage–transportation test conducted on May 25, 1963. Corrective action investigation (CAI) activities were performed in April and May 2015, as set forth in the Streamlined Approach for Environmental Restoration (SAFER) Plan for Corrective Action Unit 412: Clean Slate I Plutonium Dispersion (TTR), Tonopah Test Range, Nevada; and in accordance with the Soils Activity Quality Assurance Plan. Themore » purpose of the CAI was to fulfill data needs as defined during the data quality objectives process. The CAU 412 dataset of investigation results was evaluated based on a data quality assessment. This assessment demonstrated the dataset is complete and acceptable for use in fulfilling the data needs identified by the data quality objectives process. This CR provides documentation and justification for the clean closure of CAU 412 under the FFACO without further corrective action. This justification is based on historical knowledge of the site, previous site investigations, implementation of the 1997 interim corrective action, and the results of the CAI. The corrective action of clean closure was confirmed as appropriate for closure of CAU 412 based on achievement of the following closure objectives: Radiological contamination at the site is less than the final action level using the ground troops exposure scenario (i.e., the radiological dose is less than the final action level): Removable alpha contamination is less than the high contamination area criterion: No potential source material is present at the site, and any impacted soil associated with potential source material has been removed so that remaining soil contains contaminants at concentrations less than the final action levels: and There is sufficient information to characterize investigation and remediation waste for disposal.« less

Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor

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

Brosey, Chris A.; Ho, Chris; Long, Winnie Z.

Apoptosis-inducing factor (AIF) is critical for mitochondrial respiratory complex biogenesis and for mediating necroptotic parthanatos; these functions are seemingly regulated by enigmatic allosteric switching driven by NADH charge-transfer complex (CTC) formation. In this paper, we define molecular pathways linking AIF's active site to allosteric switching regions by characterizing dimer-permissive mutants using small-angle X-ray scattering (SAXS) and crystallography and by probing AIF-CTC communication networks using molecular dynamics simulations. Collective results identify two pathways propagating allostery from the CTC active site: (1) active-site H454 links to S480 of AIF's central β-strand to modulate a hydrophobic border at the dimerization interface, and (2)more » an interaction network links AIF's FAD cofactor, central β-strand, and Cβ-clasp whereby R529 reorientation initiates C-loop release during CTC formation. Finally, this knowledge of AIF allostery and its flavoswitch mechanism provides a foundation for biologically understanding and biomedically controlling its participation in mitochondrial homeostasis and cell death.« less

Lower Columbia River and Estuary Ecosystem Restoration Program Reference Site Study: 2011 Restoration Analysis - FINAL REPORT

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

Borde, Amy B.; Cullinan, Valerie I.; Diefenderfer, Heida L.

The Reference Site (RS) study is part of the research, monitoring, and evaluation (RME) effort developed by the Action Agencies (Bonneville Power Administration [BPA], U.S. Army Corps of Engineers, Portland District [USACE], and U.S. Bureau of Reclamation) in response to Federal Columbia River Power System (FCRPS) Biological Opinions (BiOp). While the RS study was initiated in 2007, data have been collected at relatively undisturbed reference wetland sites in the LCRE by PNNL and collaborators since 2005. These data on habitat structural metrics were previously summarized to provide baseline characterization of 51 wetlands throughout the estuarine and tidal freshwater portions ofmore » the 235-km LCRE; however, further analysis of these data has been limited. Therefore, in 2011, we conducted additional analyses of existing field data previously collected for the Columbia Estuary Ecosystem Restoration Program (CEERP) - including data collected by PNNL and others - to help inform the multi-agency restoration planning and ecosystem management work underway in the LCRE.« less

Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor

DOE PAGES

Brosey, Chris A.; Ho, Chris; Long, Winnie Z.; ...

2016-11-03

Apoptosis-inducing factor (AIF) is critical for mitochondrial respiratory complex biogenesis and for mediating necroptotic parthanatos; these functions are seemingly regulated by enigmatic allosteric switching driven by NADH charge-transfer complex (CTC) formation. In this paper, we define molecular pathways linking AIF's active site to allosteric switching regions by characterizing dimer-permissive mutants using small-angle X-ray scattering (SAXS) and crystallography and by probing AIF-CTC communication networks using molecular dynamics simulations. Collective results identify two pathways propagating allostery from the CTC active site: (1) active-site H454 links to S480 of AIF's central β-strand to modulate a hydrophobic border at the dimerization interface, and (2)more » an interaction network links AIF's FAD cofactor, central β-strand, and Cβ-clasp whereby R529 reorientation initiates C-loop release during CTC formation. Finally, this knowledge of AIF allostery and its flavoswitch mechanism provides a foundation for biologically understanding and biomedically controlling its participation in mitochondrial homeostasis and cell death.« less

Arecibo radar observations of Mars surface characteristics in the Northern Hemisphere

NASA Technical Reports Server (NTRS)

Simpson, R. A.; Tyler, G. L.; Campbell, D. B.

1978-01-01

Mars surface characteristics at and near the Viking Chryse and Tritonis Lacus landing areas were determined by radio scatter using the 12.6-cm radar at the Arecibo Observatory during 1975-76. Interpretation of each power spectrum suggests rms surface tilts of 4 deg at the final A1WNW (47.9 deg W, 22.5 deg N) site, 5 deg near the original A1 site, and 6 deg between the two. At the back-up site (A2) surface-roughness estimates were about 4 deg. Striking changes in surface texture have been found near the eastern bases of Tharsis Montes and Albor Tholus, each volcanic feature marking the western boundary of very smooth surface units. The roughness sensed at 1- to 100-m scales by radar appears to be relatively independent of the surface units defined at large scale lengths by photogeologists. Radar properties thus provide an additional means by which planetary surfaces may be characterized.

A New Approach to Standardize Multicenter Studies: Mobile Lab Technology for the German Environmental Specimen Bank

PubMed Central

Lermen, Dominik; Schmitt, Daniel; Bartel-Steinbach, Martina; Schröter-Kermani, Christa; Kolossa-Gehring, Marike; von Briesen, Hagen; Zimmermann, Heiko

2014-01-01

Technical progress has simplified tasks in lab diagnosis and improved quality of test results. Errors occurring during the pre-analytical phase have more negative impact on the quality of test results than errors encountered during the total analytical process. Different infrastructures of sampling sites can highly influence the quality of samples and therewith of analytical results. Annually the German Environmental Specimen Bank (ESB) collects, characterizes, and stores blood, plasma, and urine samples of 120–150 volunteers each on four different sampling sites in Germany. Overarching goal is to investigate the exposure to environmental pollutants of non-occupational exposed young adults combining human biomonitoring with questionnaire data. We investigated the requirements of the study and the possibility to realize a highly standardized sampling procedure on a mobile platform in order to increase the required quality of the pre-analytical phase. The results lead to the development of a mobile epidemiologic laboratory (epiLab) in the project “Labor der Zukunft” (future’s lab technology). This laboratory includes a 14.7 m2 reception area to record medical history and exposure-relevant behavior, a 21.1 m2 examination room to record dental fillings and for blood withdrawal, a 15.5 m2 biological safety level 2 laboratory to process and analyze samples on site including a 2.8 m2 personnel lock and a 3.6 m2 cryofacility to immediately freeze samples. Frozen samples can be transferred to their final destination within the vehicle without breaking the cold chain. To our knowledge, we herewith describe for the first time the implementation of a biological safety laboratory (BSL) 2 lab and an epidemiologic unit on a single mobile platform. Since 2013 we have been collecting up to 15.000 individual human samples annually under highly standardized conditions using the mobile laboratory. Characterized and free of alterations they are kept ready for retrospective analyses in their final archive, the German ESB. PMID:25141120

A new approach to standardize multicenter studies: mobile lab technology for the German Environmental Specimen Bank.

PubMed

Lermen, Dominik; Schmitt, Daniel; Bartel-Steinbach, Martina; Schröter-Kermani, Christa; Kolossa-Gehring, Marike; von Briesen, Hagen; Zimmermann, Heiko

2014-01-01

Technical progress has simplified tasks in lab diagnosis and improved quality of test results. Errors occurring during the pre-analytical phase have more negative impact on the quality of test results than errors encountered during the total analytical process. Different infrastructures of sampling sites can highly influence the quality of samples and therewith of analytical results. Annually the German Environmental Specimen Bank (ESB) collects, characterizes, and stores blood, plasma, and urine samples of 120-150 volunteers each on four different sampling sites in Germany. Overarching goal is to investigate the exposure to environmental pollutants of non-occupational exposed young adults combining human biomonitoring with questionnaire data. We investigated the requirements of the study and the possibility to realize a highly standardized sampling procedure on a mobile platform in order to increase the required quality of the pre-analytical phase. The results lead to the development of a mobile epidemiologic laboratory (epiLab) in the project "Labor der Zukunft" (future's lab technology). This laboratory includes a 14.7 m(2) reception area to record medical history and exposure-relevant behavior, a 21.1 m(2) examination room to record dental fillings and for blood withdrawal, a 15.5 m(2) biological safety level 2 laboratory to process and analyze samples on site including a 2.8 m(2) personnel lock and a 3.6 m2 cryofacility to immediately freeze samples. Frozen samples can be transferred to their final destination within the vehicle without breaking the cold chain. To our knowledge, we herewith describe for the first time the implementation of a biological safety laboratory (BSL) 2 lab and an epidemiologic unit on a single mobile platform. Since 2013 we have been collecting up to 15.000 individual human samples annually under highly standardized conditions using the mobile laboratory. Characterized and free of alterations they are kept ready for retrospective analyses in their final archive, the German ESB.

10 CFR 60.18 - Review of site characterization activities. 2

Code of Federal Regulations, 2011 CFR

2011-01-01

... developed, and on the progress of waste form and waste package research and development. The semiannual... of site characterization will be established. Other topics related to site characterization shall...

10 CFR 60.18 - Review of site characterization activities. 2

Code of Federal Regulations, 2012 CFR

2012-01-01

... developed, and on the progress of waste form and waste package research and development. The semiannual... of site characterization will be established. Other topics related to site characterization shall...

10 CFR 60.18 - Review of site characterization activities. 2

Code of Federal Regulations, 2013 CFR

2013-01-01

... developed, and on the progress of waste form and waste package research and development. The semiannual... of site characterization will be established. Other topics related to site characterization shall...

10 CFR 60.18 - Review of site characterization activities. 2

Code of Federal Regulations, 2014 CFR

2014-01-01

... developed, and on the progress of waste form and waste package research and development. The semiannual... of site characterization will be established. Other topics related to site characterization shall...

Superfund record of decision (EPA Region 5): Skinner Landfill, West Chester, OH, June 1993

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

Not Available

1993-06-04

The decision document presents the selected final remedial action for the Skinner Landfill site in West Chester, Ohio. The remedy is the second and final of two operable units for this site. The first operable unit addressed immediate site concerns, through the construction of a fence around the contaminated area, and by offering an alternate supply of drinking water to the potentially affected users of groundwater. This final operable unit addresses potential future migration of site contaminants into the groundwater and will limit the potential for direct exposure of site contaminants to humans through source control measures.

Electrochemical Processes for In-Situ Treatment of Contaminated Soils - Final Report - 09/15/1996 - 01/31/2001

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

Huang, Chin-Pao

2001-05-31

This project will study electrochemical processes for the in situ treatment of soils contaminated by mixed wastes, i.e., organic and inorganic. Soil samples collected form selected DOE waste sites will be characterized for specific organic and metal contaminants and hydraulic permeability. The soil samples are then subject to desorption experiments under various physical-chemical conditions such as pH and the presence of surfactants. Batch electro-osmosis experiments will be conducted to study the transport of contaminants in the soil-water systems. Organic contaminants that are released from the soil substrate will be treated by an advanced oxidation process, i.e., electron-Fantan. Finally, laboratory reactormore » integrating the elector-osmosis and elector-Fantan processes will be used to study the treatment of contaminated soil in situ.« less

78 FR 1143 - Explosive Siting Requirements; Correction

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-08

... launch site operators in site planning for the storage and handling of energetic liquids and explosives...: For technical questions concerning this final rule, contact Yvonne Tran, Commercial Space... this final rule, contact Laura Montgomery, AGC 200, [[Page 1144

SMARTE'S SITE CHARACTERIZATION TOOL

EPA Science Inventory

Site Characterization involves collecting environmental data to evaluate the nature and extent of contamination. Environmental data could consist of chemical analyses of soil, sediment, water or air samples. Typically site characterization data are statistically evaluated for thr...

Sources of Listeria monocytogenes Contamination in a Cold-Smoked Rainbow Trout Processing Plant Detected by Pulsed-Field Gel Electrophoresis Typing

PubMed Central

Autio, Tiina; Hielm, Sebastian; Miettinen, Maria; Sjöberg, Anna-Maija; Aarnisalo, Kaarina; Björkroth, Johanna; Mattila-Sandholm, Tiina; Korkeala, Hannu

1999-01-01

Sites of Listeria monocytogenes contamination in a cold-smoked rainbow trout (Oncorhynchus mykiss) processing plant were detected by sampling the production line, environment, and fish at different production stages. Two lots were monitored. The frequency of raw fish samples containing L. monocytogenes was low. During processing, the frequency of fish contaminated with L. monocytogenes clearly rose after brining, and the most contaminated sites of the processing plant were the brining and postbrining areas. A total of 303 isolates from the raw fish, product, and the environment were characterized by pulsed-field gel electrophoresis (PFGE). PFGE yielded nine pulsotypes, which formed four clusters. The predominating L. monocytogenes pulsotypes of the final product were associated with brining and slicing, whereas contaminants of raw fish were not detected in the final product. Air-mediated contamination in the plant could not be proved. In accordance with these results, an L. monocytogenes eradication program was planned. The use of hot steam, hot air, and hot water seemed to be useful in eliminating L. monocytogenes. None of the control samples taken in the 5 months after the eradication program was implemented contained L. monocytogenes. PMID:9872773

40 CFR 280.63 - Initial site characterization.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 26 2010-07-01 2010-07-01 false Initial site characterization. 280.63... Hazardous Substances § 280.63 Initial site characterization. (a) Unless directed to do otherwise by the implementing agency, owners and operators must assemble information about the site and the nature of the...

Characterising an intense PM pollution episode in March 2015 in France from multi-site approach and near real time data: Climatology, variabilities, geographical origins and model evaluation

NASA Astrophysics Data System (ADS)

Petit, J.-E.; Amodeo, T.; Meleux, F.; Bessagnet, B.; Menut, L.; Grenier, D.; Pellan, Y.; Ockler, A.; Rocq, B.; Gros, V.; Sciare, J.; Favez, O.

2017-04-01

During March 2015, a severe and large-scale particulate matter (PM) pollution episode occurred in France. Measurements in near real-time of the major chemical composition at four different urban background sites across the country (Paris, Creil, Metz and Lyon) allowed the investigation of spatiotemporal variabilities during this episode. A climatology approach showed that all sites experienced clear unusual rain shortage, a pattern that is also found on a longer timescale, highlighting the role of synoptic conditions over Wester-Europe. This episode is characterized by a strong predominance of secondary pollution, and more particularly of ammonium nitrate, which accounted for more than 50% of submicron aerosols at all sites during the most intense period of the episode. Pollution advection is illustrated by similar variabilities in Paris and Creil (distant of around 100 km), as well as trajectory analyses applied on nitrate and sulphate. Local sources, especially wood burning, are however found to contribute to local/regional sub-episodes, notably in Metz. Finally, simulated concentrations from Chemistry-Transport model CHIMERE were compared to observed ones. Results highlighted different patterns depending on the chemical components and the measuring site, reinforcing the need of such exercises over other pollution episodes and sites.

Using a Consensus Conference to Characterize Regulatory Concerns Regarding Bioremediation of Radionuclides and Heavy Metals in Mixed Waste at DOE Sites

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

Denise Lach; Stephanie Sanford

2006-09-01

A consensus workshop was developed and convened with ten state regulators to characterize concerns regarding emerging bioremediation technology to be used to clean-up radionuclides and heavy metals in mixed wastes at US DOE sites. Two questions were explored: integrated questions: (1) What impact does participation in a consensus workshop have on the knowledge, attitudes, and practices of state regulators regarding bioremediation technology? (2) How effective is a consensus workshop as a strategy for eliciting and articulating regulators’ concerns regarding the use of bioremediation to clean up radionuclides and heavy metals in mixed wastes at U.S. Department of Energy Sites aroundmore » the county? State regulators met together for five days over two months to learn about bioremediation technology and develop a consensus report of their recommendations regarding state regulatory concerns. In summary we found that panel members: - quickly grasped the science related to bioremediation and were able to effectively interact with scientists working on complicated issues related to the development and implementation of the technology; - are generally accepting of in situ bioremediation, but concerned about costs, implementation (e.g., institutional controls), and long-term effectiveness of the technology; - are concerned equally about technological and implementation issues; and - believed that the consensus workshop approach to learning about bioremediation was appropriate and useful. Finally, regulators wanted decision makers at US DOE to know they are willing to work with DOE regarding innovative approaches to clean-up at their sites, and consider a strong relationship between states and the DOE as critical to any effective clean-up. They do not want perceive themselves to be and do not want others to perceive them as barriers to successful clean-up at their sites.« less

Contaminant source identification using semi-supervised machine learning

DOE PAGES

Vesselinov, Velimir Valentinov; Alexandrov, Boian S.; O’Malley, Dan

2017-11-08

Identification of the original groundwater types present in geochemical mixtures observed in an aquifer is a challenging but very important task. Frequently, some of the groundwater types are related to different infiltration and/or contamination sources associated with various geochemical signatures and origins. The characterization of groundwater mixing processes typically requires solving complex inverse models representing groundwater flow and geochemical transport in the aquifer, where the inverse analysis accounts for available site data. Usually, the model is calibrated against the available data characterizing the spatial and temporal distribution of the observed geochemical types. Numerous different geochemical constituents and processes may needmore » to be simulated in these models which further complicates the analyses. In this paper, we propose a new contaminant source identification approach that performs decomposition of the observation mixtures based on Non-negative Matrix Factorization (NMF) method for Blind Source Separation (BSS), coupled with a custom semi-supervised clustering algorithm. Our methodology, called NMFk, is capable of identifying (a) the unknown number of groundwater types and (b) the original geochemical concentration of the contaminant sources from measured geochemical mixtures with unknown mixing ratios without any additional site information. NMFk is tested on synthetic and real-world site data. Finally, the NMFk algorithm works with geochemical data represented in the form of concentrations, ratios (of two constituents; for example, isotope ratios), and delta notations (standard normalized stable isotope ratios).« less

Contaminant source identification using semi-supervised machine learning

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

Vesselinov, Velimir Valentinov; Alexandrov, Boian S.; O’Malley, Dan

Identification of the original groundwater types present in geochemical mixtures observed in an aquifer is a challenging but very important task. Frequently, some of the groundwater types are related to different infiltration and/or contamination sources associated with various geochemical signatures and origins. The characterization of groundwater mixing processes typically requires solving complex inverse models representing groundwater flow and geochemical transport in the aquifer, where the inverse analysis accounts for available site data. Usually, the model is calibrated against the available data characterizing the spatial and temporal distribution of the observed geochemical types. Numerous different geochemical constituents and processes may needmore » to be simulated in these models which further complicates the analyses. In this paper, we propose a new contaminant source identification approach that performs decomposition of the observation mixtures based on Non-negative Matrix Factorization (NMF) method for Blind Source Separation (BSS), coupled with a custom semi-supervised clustering algorithm. Our methodology, called NMFk, is capable of identifying (a) the unknown number of groundwater types and (b) the original geochemical concentration of the contaminant sources from measured geochemical mixtures with unknown mixing ratios without any additional site information. NMFk is tested on synthetic and real-world site data. Finally, the NMFk algorithm works with geochemical data represented in the form of concentrations, ratios (of two constituents; for example, isotope ratios), and delta notations (standard normalized stable isotope ratios).« less

Remote geologic structural analysis of Yucca Flat

NASA Astrophysics Data System (ADS)

Foley, M. G.; Heasler, P. G.; Hoover, K. A.; Rynes, N. J.; Thiessen, R. L.; Alfaro, J. L.

1991-12-01

The Remote Geologic Analysis (RGA) system was developed by Pacific Northwest Laboratory (PNL) to identify crustal structures that may affect seismic wave propagation from nuclear tests. Using automated methods, the RGA system identifies all valleys in a digital elevation model (DEM), fits three-dimensional vectors to valley bottoms, and catalogs all potential fracture or fault planes defined by coplanar pairs of valley vectors. The system generates a cluster hierarchy of planar features having greater-than-random density that may represent areas of anomalous topography manifesting structural control of erosional drainage development. Because RGA uses computer methods to identify zones of hypothesized control of topography, ground truth using a well-characterized test site was critical in our evaluation of RGA's characterization of inaccessible test sites for seismic verification studies. Therefore, we applied RGA to a study area centered on Yucca Flat at the Nevada Test Site (NTS) and compared our results with both mapped geology and geologic structures and with seismic yield-magnitude models. This is the final report of PNL's RGA development project for peer review within the U.S. Department of Energy Office of Arms Control (OAC) seismic-verification community. In this report, we discuss the Yucca Flat study area, the analytical basis of the RGA system and its application to Yucca Flat, the results of the analysis, and the relation of the analytical results to known topography, geology, and geologic structures.

Tackling the Challenge of Deep Vadose Zone Remediation at the Hanford Site

NASA Astrophysics Data System (ADS)

Morse, J. G.; Wellman, D. M.; Gephart, R.

2010-12-01

The Central Plateau of the Hanford Site in Washington State contains some 800 waste disposal sites where 1.7 trillion liters of contaminated water was once discharged into the subsurface. Most of these sites received liquids from the chemical reprocessing of spent uranium fuel to recover plutonium. In addition, 67 single shell tanks have leaked or are suspected to have leaked 3.8 million liters of high alkali and aluminate rich cesium-contaminated liquids into the sediment. Today, this inventory of subsurface contamination contains an estimated 550,000 curies of radioactivity and 150 million kg (165,000 tons) of metals and hazardous chemicals. Radionuclides range from mobile 99Tc to more immobilized 137Cs, 241Am, uranium, and plutonium. A significant fraction of these contaminants likely remain within the deep vadose zone. Plumes of groundwater containing tritium, nitrate, 129I and other contaminants have migrated through the vadose zone and now extend outward from the Central Plateau to the Columbia River. During most of Hanford Site history, subsurface studies focused on groundwater monitoring and characterization to support waste management decisions. Deep vadose zone studies were not a priority because waste practices relied upon that zone to buffer contaminant releases into the underlying aquifer. Remediation of the deep vadose zone is now central to Hanford Site cleanup because these sediments can provide an ongoing source of contamination to the aquifer and therefore to the Columbia River. However, characterization and remediation of the deep vadose zone pose some unique challenges. These include sediment thickness; contaminant depth; coupled geohydrologic, geochemical, and microbial processes controlling contaminant spread; limited availability and effectiveness of traditional characterization tools and cleanup remedies; and predicting contaminant behavior and remediation performance over long time periods and across molecular to field scales. The U.S Department of Energy recognizes these challenges and is committed to a sustained, focused effort of continuing to apply existing technologies where feasible while investing and developing in new innovative, field-demonstrated capabilities supporting longer-term basic and applied research to establish the technical underpinning for solving intractable deep vadose zone problems and implementing final remedies. This approach will rely upon Multi-Project Teams focusing on coordinated projects across multiple DOE offices, programs, and site contractors plus the facilitation of basic and applied research investments through implementing a Deep Vadose Zone Applied Field Research Center and other scientific studies.

GPR impedance inversion for imaging and characterization of buried archaeological remains: A case study at Mudu city cite in Suzhou, China

NASA Astrophysics Data System (ADS)

Liu, Yu; Shi, Zhanjie; Wang, Bangbing; Yu, Tianxiang

2018-01-01

As a method with high resolution, GPR has been extensively used in archaeological surveys. However, conventional GPR profile can only provide limited geometry information, such as the shape or location of the interface, but can't give the distribution of physical properties which could help identify the historical remains more directly. A common way for GPR to map parameter distribution is the common-midpoint velocity analysis, but it provides limited resolution. Another research hotspot, the full-waveform inversion, is unstable and relatively dependent on the initial model. Coring method could give direct information in drilling site, while the accurate result is only limited in several boreholes. In this paper, we propose a new scheme to enhance imaging and characterization of archaeological targets by fusion of GPR and coring data. The scheme mainly involves the impedance inversion of conventional common-offset GPR data, which uses well log to compensate GPR data and finally obtains a high-resolution estimation of permittivity. The core analysis result also contributes to interpretation of the inversion result. To test this method, we did a case study at Mudu city site in Suzhou, China. The results provide clear images of the ancient city's moat and wall subsurface and improve the characterization of archaeological targets. It is shown that this method is effective and feasible for archaeological exploration.

Site characterization of the Romanian Seismic Network stations: a national initiative and its first preliminary results

NASA Astrophysics Data System (ADS)

Grecu, Bogdan; Zahria, Bogdan; Manea, Elena; Neagoe, Cristian; Borleanu, Felix; Diaconescu, Mihai; Constantinescu, Eduard; Bala, Andrei

2017-04-01

The seismic activity in Romania is dominated by the intermediate-depth earthquakes occurring in Vrancea region, although weak to moderate crustal earthquakes are produced regularly in different areas of the country. The National Institute for Earth Physics (NIEP) built in the last years an impressive infrastructure for monitoring this activity, known as the Romanian Seismic Network (RSN). At present, RSN consists of 122 seismic stations, of which 70 have broadband velocity sensors and 42 short period sensors. One hundred and eleven stations out of 122 have accelerometer sensors collocated with velocity sensors and only 10 stations have only accelerometers. All the stations record continuously the ground motion and the data are transmitted in real-time to the Romanian National Data Center (RoNDC), in Magurele. Last year, NIEP has started a national project that addresses the characterization of all real-time seismic stations that constitute the RSN. We present here the steps that were undertaken and the preliminary results obtained since the beginning the project. The first two activities consisted of collecting all the existent technical and geological data, with emphasize on the latter. Then, we performed station noise investigations and analyses in order to characterize the noise level and estimate the resonances of the sites. The computed H/V ratios showed clear resonant peaks at different frequencies which correlate relatively well with the thickness of the sedimentary package beneath the stations. The polarization analysis of the H/V ratios indicates for some stations a strong directivity of the resonance peak which suggests possible topographic effects at the stations. At the same time, special attention was given to the estimation of the site amplification from earthquake data. The spectral ratios obtained from the analysis of more than 50 earthquakes with magnitudes (Mw) larger than 4.1 are characterized by similar resonance peaks as those obtained from noise H/V ratios in case of the stations with strong site effects. On the contrary, the spectral curves are flat for some stations located on hard rock or show amplifications around two on wide frequency band for stations located on deep sediments. Finally, both active (MASW) and passive (ReMi) surface waves surveys were performed at several sites to estimate the shallow velocity structure beneath the stations.

SEMINAR PUBLICATION: SITE CHARACTERIZATION FOR SUBSURFACE REMEDIATION

EPA Science Inventory

This seminar publication provides a comprehensive approach to site characterization for subsurface remediation. Chapter 1 describes a methodology for integrating site characterization with subsurface remediation. The rest of the handbook is divided into three parts. Part I covers...

Demonstration of innovative monitoring technologies at the Savannah River Integrated Demonstration Site

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

Rossabi, J.; Jenkins, R.A.; Wise, M.B.

1993-12-31

The Department of Energy`s Office of Technology Development initiated an Integrated Demonstration Program at the Savannah River Site in 1989. The objective of this program is to develop, demonstrate, and evaluate innovative technologies that can improve present-day environmental restoration methods. The Integrated Demonstration Program at SRS is entitled ``Cleanup of Organics in Soils and Groundwater at Non-Arid Sites.`` New technologies in the areas of drilling, characterization, monitoring, and remediation are being demonstrated and evaluated for their technical performance and cost effectiveness in comparison with baseline technologies. Present site characterization and monitoring methods are costly, time-consuming, overly invasive, and often imprecise.more » Better technologies are required to accurately describe the subsurface geophysical and geochemical features of a site and the nature and extent of contamination. More efficient, nonintrusive characterization and monitoring techniques are necessary for understanding and predicting subsurface transport. More reliable procedures are also needed for interpreting monitoring and characterization data. Site characterization and monitoring are key elements in preventing, identifying, and restoring contaminated sites. The remediation of a site cannot be determined without characterization data, and monitoring may be required for 30 years after site closure.« less

Evaluation and Optimization of MTBE Biodegradation in Aquifers, Final Report

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

Legler, T; Balser, L; Koester, C

This study was focused on meeting the following objectives concerning the process of methyl tertiary butyl ether (MTBE) biodegradation, with the goal of optimizing this process in situ: 1. Assess whether intrinsic bioattenuation of MTBE is feasible under aerobic conditions across several contaminated sites. 2. Determine the effect of co-contaminants, specifically water-soluble gasoline components (most notably benzene, toluene, ethylbenzene and xylenes [BTEX]) on MTBE biodegradation. 3. Determine whether microbial and/or chemical factors contribute to different MTBE degradative activities. 4. Isolate and characterize MTBE-degrading microorganisms from sediments in which MTBE biodegradation was observed.

Emerging behavior in electronic bidding.

PubMed

Yang, I; Jeong, H; Kahng, B; Barabási, A-L

2003-07-01

We characterize the statistical properties of a large number of agents on two major online auction sites. The measurements indicate that the total number of bids placed in a single category and the number of distinct auctions frequented by a given agent follow power-law distributions, implying that a few agents are responsible for a significant fraction of the total bidding activity on the online market. We find that these agents exert an unproportional influence on the final price of the auctioned items. This domination of online auctions by an unusually active minority may be a generic feature of all online mercantile processes.

Emerging behavior in electronic bidding

NASA Astrophysics Data System (ADS)

Yang, I.; Jeong, H.; Kahng, B.; Barabási, A.-L.

2003-07-01

We characterize the statistical properties of a large number of agents on two major online auction sites. The measurements indicate that the total number of bids placed in a single category and the number of distinct auctions frequented by a given agent follow power-law distributions, implying that a few agents are responsible for a significant fraction of the total bidding activity on the online market. We find that these agents exert an unproportional influence on the final price of the auctioned items. This domination of online auctions by an unusually active minority may be a generic feature of all online mercantile processes.

Afraid to Start Because the Outcome is Uncertain?: Social Site Characterization as a Tool for Informing Public Engagement Efforts

USGS Publications Warehouse

Wade, S.; Greenberg, S.

2009-01-01

This paper introduces the concept of social site characterization as a parallel effort to technical site characterization to be used in evaluating and planning carbon dioxides capture and storage (CCS) projects. Social site characterization, much like technical site characterization, relies on a series of iterative investigations into public attitudes towards a CCS project and the factors that will shape those views. This paper also suggests ways it can be used to design approaches for actively engaging stakeholders and communities in the deployment of CCS projects. This work is informed by observing the site selection process for FutureGen and the implementation of research projects under the Regional Carbon Sequestration Partnership Program. ?? 2009 Elsevier Ltd. All rights reserved.

Iron loading site on the Fe-S cluster assembly scaffold protein is distinct from the active site.

PubMed

Rodrigues, Andria V; Kandegedara, Ashoka; Rotondo, John A; Dancis, Andrew; Stemmler, Timothy L

2015-06-01

Iron-sulfur (Fe-S) cluster containing proteins are utilized in almost every biochemical pathway. The unique redox and coordination chemistry associated with the cofactor allows these proteins to participate in a diverse set of reactions, including electron transfer, enzyme catalysis, DNA synthesis and signaling within several pathways. Due to the high reactivity of the metal, it is not surprising that biological Fe-S cluster assembly is tightly regulated within cells. In yeast, the major assembly pathway for Fe-S clusters is the mitochondrial ISC pathway. Yeast Fe-S cluster assembly is accomplished using the scaffold protein (Isu1) as the molecular foundation, with assistance from the cysteine desulfurase (Nfs1) to provide sulfur, the accessory protein (Isd11) to regulate Nfs1 activity, the yeast frataxin homologue (Yfh1) to regulate Nfs1 activity and participate in Isu1 Fe loading possibly as a chaperone, and the ferredoxin (Yah1) to provide reducing equivalents for assembly. In this report, we utilize calorimetric and spectroscopic methods to provide molecular insight into how wt-Isu1 from S. cerevisiae becomes loaded with iron. Isothermal titration calorimetry and an iron competition binding assay were developed to characterize the energetics of protein Fe(II) binding. Differential scanning calorimetry was used to identify thermodynamic characteristics of the protein in the apo state or under iron loaded conditions. Finally, X-ray absorption spectroscopy was used to characterize the electronic and structural properties of Fe(II) bound to Isu1. Current data are compared to our previous characterization of the D37A Isu1 mutant, and these suggest that when Isu1 binds Fe(II) in a manner not perturbed by the D37A substitution, and that metal binding occurs at a site distinct from the cysteine rich active site in the protein.

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

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

DeRouen, L.R.; Hann, R.W.; Casserly, D.M.

1983-02-01

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

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

dos Reis, Roberto; Yang, Hao; Ophus, Colin

A key to the unique combination of electronic and optical properties in halide perovskite materials lies in their rich structural complexity. However, their radiation sensitive nature limits nanoscale structural characterization requiring dose efficient microscopic techniques in order to determine their structures precisely. In this work, we determine the space-group and directly image the Br halide sites of CsPbBr 3, a promising material for optoelectronic applications. Based on the symmetry of high-order Laue zone reflections of convergent-beam electron diffraction, we identify the tetragonal (I4/mcm) structural phase of CsPbBr 3 at cryogenic temperature. Electron ptychography provides a highly sensitive phase contrast measurementmore » of the halide positions under low electron-dose conditions, enabling imaging of the elongated Br sites originating from the out-of-phase octahedral rotation viewed along the [001] direction of I4/mcm persisting at room temperature. The measurement of these features and comparison with simulations yield an octahedral rotation angle of 6.5°(±1.5°). Finally, the approach demonstrated here opens up opportunities for understanding the atomic scale structural phenomena applying advanced characterization tools on a wide range of radiation sensitive halide-based all-inorganic and hybrid organic-inorganic perovskites.« less

Characterization of Human Papillomavirus Type 154 and Tissue Tropism of Gammapapillomaviruses

PubMed Central

Ure, Agustín Enrique; Forslund, Ola

2014-01-01

The novel human papillomavirus type 154 (HPV154) was characterized from a wart on the crena ani of a three-year-old boy. It was previously designated as the putative HPV type FADI3 by sequencing of a subgenomic FAP amplicon. We obtained the complete genome by combined methods including rolling circle amplification (RCA), genome walking through an adapted method for detection of integrated papillomavirus sequences by ligation-mediated PCR (DIPS-PCR), long-range PCR, and finally by cloning of four overlapping amplicons. Phylogenetically, the HPV154 genome clustered together with members of the proposed species Gammapapillomavirus 11, and demonstrated the highest identity in L1 to HPV136 (68.6%). The HPV154 was detected in 3% (2/62) of forehead skin swabs from healthy children. In addition, the different detection sites of 62 gammapapillomaviruses were summarized in order to analyze their tissue tropism. Several of these HPV types have been detected from multiple sources such as skin, oral, nasal, and genital sites, suggesting that the gammapapillomaviruses are generalists with a broader tissue tropism than previously appreciated. The study expands current knowledge concerning genetic diversity and tropism among HPV types in the rapidly growing gammapapillomavirus genus. PMID:24551244

A step forward in understanding step-overs: the case of the Dead Sea Fault in northern Israel

NASA Astrophysics Data System (ADS)

Dembo, Neta; Granot, Roi; Hamiel, Yariv

2017-04-01

The rotational deformation field around step-overs between segments of strike-slip faults is poorly resolved. Vertical-axis paleomagnetic rotations can be used to characterize the deformation field, and together with mechanical modeling, can provide constraints on the characteristics of the adjacent fault segments. The northern Dead Sea Fault, a major segmented sinistral transform fault that straddles the boundary between the Arabian Plate and Sinai Subplate, offers an appropriate tectonic setting for our detailed mechanical and paleomagnetic investigation. We examine the paleomagnetic vertical-axis rotations of Neogene-Pleistocene basalt outcrops surrounding a right step-over between two prominent segments of the fault: the Jordan Gorge section and the Hula East Boundary Fault. Results from 20 new paleomagnetic sites reveal significant (>20˚) counterclockwise rotations within the step-over and small clockwise rotations in the vicinity. Sites located further (>2.5 km) away from the step-over generally experience negligible to minor rotations. Finally, we construct a mechanical model guided by the observed rotational field that allows us to characterize the structural, mechanical and kinematic behavior of the Dead Sea Fault in northern Israel.

A new metal binding domain involved in cadmium, cobalt and zinc transport

DOE PAGES

Smith, Aaron T.; Barupala, Dulmini; Stemmler, Timothy L.; ...

2015-07-20

The P 1B-ATPases, which couple cation transport across membranes to ATP hydrolysis, are central to metal homeostasis in all organisms. An important feature of P 1B-ATPases is the presence of soluble metal binding domains (MBDs) that regulate transport activity. Only one type of MBD has been characterized extensively, but bioinformatics analyses indicate that a diversity of MBDs may exist in nature. In this paper, we report the biochemical, structural and functional characterization of a new MBD from the Cupriavidus metallidurans P 1B-4-ATPase CzcP (CzcP MBD). The CzcP MBD binds two Cd 2+, Co 2+ or Zn 2+ ions in distinctmore » and unique sites and adopts an unexpected fold consisting of two fused ferredoxin-like domains. Both in vitro and in vivo activity assays using full-length CzcP, truncated CzcP and several variants indicate a regulatory role for the MBD and distinct functions for the two metal binding sites. Finally, taken together, these findings elucidate a previously unknown MBD and suggest new regulatory mechanisms for metal transport by P 1B-ATPases.« less

Cell-free synthesis of functional human epidermal growth factor receptor: Investigation of ligand-independent dimerization in Sf21 microsomal membranes using non-canonical amino acids

PubMed Central

Quast, Robert B.; Ballion, Biljana; Stech, Marlitt; Sonnabend, Andrei; Varga, Balázs R.; Wüstenhagen, Doreen A.; Kele, Péter; Schiller, Stefan M.; Kubick, Stefan

2016-01-01

Cell-free protein synthesis systems represent versatile tools for the synthesis and modification of human membrane proteins. In particular, eukaryotic cell-free systems provide a promising platform for their structural and functional characterization. Here, we present the cell-free synthesis of functional human epidermal growth factor receptor and its vIII deletion mutant in a microsome-containing system derived from cultured Sf21 cells. We provide evidence for embedment of cell-free synthesized receptors into microsomal membranes and asparagine-linked glycosylation. Using the cricket paralysis virus internal ribosome entry site and a repetitive synthesis approach enrichment of receptors inside the microsomal fractions was facilitated thereby providing analytical amounts of functional protein. Receptor tyrosine kinase activation was demonstrated by monitoring receptor phosphorylation. Furthermore, an orthogonal cell-free translation system that provides the site-directed incorporation of p-azido-L-phenylalanine is characterized and applied to investigate receptor dimerization in the absence of a ligand by photo-affinity cross-linking. Finally, incorporated azides are used to generate stable covalently linked receptor dimers by strain-promoted cycloaddition using a novel linker system. PMID:27670253

Stressor Identification (Si) at Contaminated Sites: Upper Arkansas River, Colorado (Final)

EPA Science Inventory

EPA announced the availability of the final report, Stressor Identification (SI) at Contaminated Sites: Upper Arkansas River, Colorado. This report describes a causal assessment for impairments of plant growth and plant species richness at a terrestrial contaminated site ...

Characterization of the Inner Knot of the Crab: the Site of the Gamma-ray Flares?

NASA Technical Reports Server (NTRS)

Weisskopf, Martin C.

2015-01-01

One of the most intriguing recent discoveries has been the detection of powerful gamma-ray flares from the Crab Nebula. Such events, with a recurrence time of about once per year, can be so dramatic to make the system the brightest source in the gamma-ray sky as occurred, e.g. in April 2011. These flares challenge our understanding of how pulsar wind nebulae work and defy current astrophysical models for particle acceleration. We present here our study of the inner knot located within a fraction of an arcsecond from the pulsar with the aim of characterizing the feature and asking if this might be the site of the origin of the gamma-ray flares. We took data using Keck, HST, and Chandra obtained as part of our multi-wavelength campaign to identify the source of the enigmatic flares. We set an upper limit as to the gamma-ray flux from the knot. We also find that the dimensions, surface brightness, flux, etc. of the optical and infrared knot are all correlated with distance from the pulsar. This distance, in turn, varies with time. In addition to this most thorough characterization of the inner knot's properties, we examine the hypothesis that the knot may be the site of the flares by examining the knot separation versus the Fermi/LAT gamma-ray flux. Finally, as part of this research, we make use of a new approach employing singular value decomposition (SVD) for analyzing time series of images and compare the approach to more traditional methods. Our conclusions are only refined but not impacted by using the new approach.

Methane emissions from the global oil and gas supply chain: recent advances and next steps

NASA Astrophysics Data System (ADS)

Zavala Araiza, D.; Herndon, S. C.; Roscioli, J. R.; Yacovitch, T. I.; Knighton, W. B.; Johnson, M.; Tyner, D. R.; Hamburg, S.

2017-12-01

A wide body of research has characterized methane emissions from the oil and gas system in the US. In contrast, empirical data is limited for other significant oil and gas producing regions across the world. As a consequence, measuring and characterizing methane emissions across global oil and gas operations will be crucial to the design of effective mitigation strategies. Several countries have announced pledges to reduce methane emissions from this system (e.g., North America, Climate and Clean Air Coalition [CCAC] ministers). In the case of Canada, the federal government recently announced regulations supporting a 40-45% reduction of methane emissions from the oil and gas production systems. For these regulations to be effective, it is critical to understand the current methane emission patterns. We present results from a coordinated multiscale (i.e., airborne-based, ground-based) measurement campaign in Alberta, Canada. We use empirically derived emission estimates to characterize site-level emissions and derive an emissions distribution. Our work shows that many major sources of emissions are unmeasured or underreported. Consistent with previous studies in the US, a small fraction of sites disproportionately account for the majority of emissions: roughly 20% of sites accounted for 75% of emissions. An independent airborne-based regional estimate was 40% lower than the ground-based regional estimate, but not statistically different. Finally, we summarize next steps as part of the CCAC Oil and Gas Methane Study: ongoing work that is targeting oil and gas sectors/production regions with limited empirical data on methane emissions. This work builds on the approach deployed in quantifying methane emissions from the oil and gas supply chain in the US, underscoring the commitment to transparency of the collected data, external review, deployment of multiple methodologies, and publication of results in peer-reviewed journals.

Radiogenic isotopic approaches for quantifying radionuclide transport (Invited)

NASA Astrophysics Data System (ADS)

Maher, K.; Depaolo, D. J.; Singleton, M. J.; Christensen, J. N.; Conrad, M. E.

2009-12-01

Naturally occurring variations in the isotopic compositions of U and Sr provide unique opportunities for assessing the fate and transport of radionuclides at field-scale conditions. When coupled with reactive transport models, U and Sr isotopes may also provide additional constraints on the rates of sediment-fluid or sediment-waste interactions. Such isotopic approaches can be useful for sites where subsurface characterization is complicated by a lack of accessibility or the presence of substantial heterogeneity. In addition, a variety of quantitative modeling approaches of different complexity can be used to evaluate experimentally determined parameters for radionuclide mobility at the field-scale. At the Hanford Site in eastern Washington, 87Sr/86Sr and 234U/238U ratios have been used to quantify the residence time of Sr and U in the unsaturated zone, the long-term background infiltration rate through the unsaturated zone, and to assess the influence of enhanced wastewater discharge on the regional unconfined aquifer. As a result of different processing techniques or due to interactions between caustic waste and the natural sediment, waste plumes may also inherit isotopic fingerprints (e.g. 234U/238U, 235U/238U, 236U/238U; δ15N & δ18O of nitrate) that can be used to resolve multiple sources of contamination. Finally, enriched isotopic tracers can be applied to experimental manipulations to assess the retardation of a variety of contaminants. Collectively this isotopic data contributes unique perspectives on both the hydrologic conditions across the site and the mobility of key radionuclides. Predicting the long-term fate and transport of radionuclides in the environment is often challenging due to natural heterogeneity and incomplete characterization of the subsurface, however detailed analysis of isotopic variations can provide one additional means of characterizing the subsurface.

SITE CHARACTERIZATION LIBRARY: VOLUMN 1 (RELEASE 2.5)

EPA Science Inventory

This CD-ROM, Volume 1, Release 2.5, of EPA's National Exposure Research Laboratory (NERL - Las Vegas) Site Characterization Library, contains additional electronic documents and computer programs related to the characterization of hazardous waste sites. EPA has produced this libr...

Site Selection for Hvdc Ground Electrodes

NASA Astrophysics Data System (ADS)

Freire, P. F.; Pereira, S. Y.

2014-12-01

High-Voltage Direct Current (HVDC) transmission systems are composed of a bipole transmission line with a converter substation at each end. Each substation may be equipped with a HVDC ground electrode, which is a wide area (up to 1 km Ø) and deep (from 3 to 100m) electrical grounding. When in normal operation, the ground electrode will dissipate in the soil the unbalance of the bipole (~1.5% of the rated current). When in monopolar operation with ground return, the HVDC electrode will inject in the soil the nominal pole continuous current, of about 2000 to 3000 Amperes, continuously for a period up to a few hours. HVDC ground electrodes site selection is a work based on extensive geophysical and geological surveys, in order to attend the desired design requirements established for the electrodes, considering both its operational conditions (maximum soil temperature, working life, local soil voltage gradients etc.) and the interference effects on the installations located up to 50 km away. This poster presents the geophysical investigations conducted primarily for the electrodes site selection, and subsequently for the development of the crust resistivity model, which will be used for the interference studies. A preliminary site selection is conducted, based on general geographical and geological criteria. Subsequently, the geology of each chosen area is surveyed in detail, by means of electromagnetic/electrical geophysical techniques, such as magnetotelluric (deep), TDEM (near-surface) and electroresistivity (shallow). Other complementary geologic and geotechnical surveys are conducted, such as wells drilling (for geotechnical characterization, measurement of the water table depth and water flow, and electromagnetic profiling), and soil and water sampling (for measurement of thermal parameters and evaluation of electrosmosis risk). The site evaluation is a dynamic process along the surveys, and some sites will be discarded. For the two or three final sites, the inversion of the combined deep, near-surface and shallow apparent resistivity curves, results in the layered crust resistivity models. These models will allow for the preliminary interference studies, that will result on the selection of the final electrode site (one for each converter substation).

Measurement Sets and Sites Commonly Used for Characterization

NASA Technical Reports Server (NTRS)

Pagnutti, Mary; Holekamp, Kara; Ryan, Robert; Sellers, Richard; Davis, Bruce; Zanoni, Vicki

2002-01-01

Scientists at NASA's Earth Science Applications Directorate are creating a well-characterized Verification & Validation (V&V) site at the Stennis Space Center. This site enables the in-flight characterization of remote sensing systems and the data they acquire. The data are predominantly acquired by commercial, high spatial resolution satellite systems, such as IKONOS and QuickBird 2, and airborne systems. The smaller scale of these newer high resolution remote sensing systems allows scientists to characterize the geometric, spatial, and radiometric data properties using a single V&V site. The targets and techniques used to characterize data from these newer systems can differ significantly from the techniques used to characterize data from the earlier, coarser spatial resolution systems. Scientists are also using the SSC V&V site to characterize thermal infrared systems and active LIDAR systems. SSC employs geodetic targets, edge targets, radiometric tarps, and thermal calibration ponds to characterize remote sensing data products. This paper presents a proposed set of required measurements for visible through long-wave infrared remote sensing systems and a description of the Stennis characterization. Other topics discussed include: 1) The use of ancillary atmospheric and solar measurements taken at SSC that support various characterizations; 2) Additional sites used for radiometric, geometric, and spatial characterization in the continental United States; 3) The need for a standardized technique to be adopted by CEOS and other organizations.

77 FR 16558 - General Management Plan/Final Environmental Impact Statement, Hampton National Historic Site...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-21

... Management Plan/Final Environmental Impact Statement, Hampton National Historic Site, Maryland AGENCY...) announces the availability of the Final Environmental Impact Statement for the General Management Plan.../Baltimore County Library, 320 York Avenue, Towson, Maryland 21204. Baltimore County Tourism Office and...

EPA Region 2 SEMS_CERCLIS Sites All [R2] and SEMS_CERCLIS Sites NPL [R2] GIS Layers

EPA Pesticide Factsheets

The Region 2 SEMS_CERCLIS Sites All [R2] GIS layer contains unique Superfund Enterprise Management System (SEMS) site records. These records have the following NPL_STATUS designations: CURRENTLY ON FINAL NPL, DELETED FROM FINAL NPL, NOT ON NPL, PROPOSED FOR NPL, REMOVED FROM PROPOSED NPL, and SITE IS PART OF NPL SITE. The Region 2 SEMS_CERCLIS NPL Sites [R2] GIS layer only has SEMS records with the following NPL_STATUS designations: 'CURRENTLY ON FINAL NPL', 'DELETED FROM FINAL NPL', 'PROPOSED FOR NPL'.The Superfund Enterprise Management System (SEMS) is EPA's official record for tracking hazardous waste sites, potentially hazardous waste sites, and remedial activities performed in support of the Superfund Program across the nation. This includes sites that are on the National Priorities List (NPL) or are being considered for the NPL. SEMS represents a joint development and ongoing collaboration between Superfund's Remedial, Removal, Federal Facilities, Enforcement, and Emergency Response programs. It provides its wide audience base with a means of ongoing analysis of Superfund Program activities and informational needs at the site, regional management, and national management levels. The customers of SEMS or SEMS data are five EPA Headquarters offices and regional staff, citizens, the regulated community, other Federal agencies, States, Tribes, local agencies, and industry. SEMS stakeholders are States, Congress, other Federal agencies, industry groups, and cit

Click-coated, heparinized, decellularized vascular grafts

PubMed Central

Dimitrievska, Sashka; Cai, Chao; Weyers, Amanda; Balestrini, Jenna L.; Lin, Tylee; Sundaram, Sumati; Hatachi, Go; Spiegel, David A.; Kyriakides, Themis R.; Miao, Jianjun; Li, Guoyun; Niklason, Laura; Linhardt, Robert J.

2014-01-01

A novel method enabling the engineering of a dense and appropriately oriented heparin-containing layer on decellularized aortas has been developed. Amino groups of decellularized aortas were first modified to azido groups using 3-azidobenzoic acid. Azide-clickable dendrons were attached onto the azido groups through “alkyne-azide” click chemistry, affording a ten-fold amplification of adhesions sites. Dendron end groups were finally decorated with end-on modified heparin chains. Heparin chains were oriented like heparan sulfate groups on native endothelial cells surface. XPS, NMR, MS and FTIR were used to characterize the synthesis steps, building the final heparin layered coatings. Continuity of the heparin coating was verified using fluorescent microscopy and histological analysis. Efficacy of heparin linkage was demonstrated with factor Xa antithrombogenic assay and platelet adhesion studies. The results suggest that oriented heparin immobilization to decellularized aortas may improve the in vivo blood compatibility of decellularized aortas and vessels. PMID:25463496

FIELD EVALUATION OF IN-SITU BIODEGRADATION OF CHLORINATED ETHENES: PART I, METHODOLOGY AND FIELD SITE CHARACTERIZATION

EPA Science Inventory

Careful site characterization and implementation of quantitative monitoring methods are prerequisites for a convincing evaluation of enhanced biostimulation for aquifer restoration. his paper describes the characterization of a site at Moffett Naval Air Station, Mountain View, Ca...

SITE CHARACTERIZATION AND ANALYSIS PENETROMETER SYSTEM(SCAPS) LAZER-INDUCED FLUORESCENCE (LIF) SENSOR AND SUPPORT SYSTEM

EPA Science Inventory

The Consortium for Site Characterization Technology (CSCT) has established a formal program to accelerate acceptance and application of innovative monitoring and site characterization technologies that improve the way the nation manages its environmental problems. In 1995 the CS...

Molecular simulations and Markov state modeling reveal the structural diversity and dynamics of a theophylline-binding RNA aptamer in its unbound state

PubMed Central

Warfield, Becka M.

2017-01-01

RNA aptamers are oligonucleotides that bind with high specificity and affinity to target ligands. In the absence of bound ligand, secondary structures of RNA aptamers are generally stable, but single-stranded and loop regions, including ligand binding sites, lack defined structures and exist as ensembles of conformations. For example, the well-characterized theophylline-binding aptamer forms a highly stable binding site when bound to theophylline, but the binding site is unstable and disordered when theophylline is absent. Experimental methods have not revealed at atomic resolution the conformations that the theophylline aptamer explores in its unbound state. Consequently, in the present study we applied 21 microseconds of molecular dynamics simulations to structurally characterize the ensemble of conformations that the aptamer adopts in the absence of theophylline. Moreover, we apply Markov state modeling to predict the kinetics of transitions between unbound conformational states. Our simulation results agree with experimental observations that the theophylline binding site is found in many distinct binding-incompetent states and show that these states lack a binding pocket that can accommodate theophylline. The binding-incompetent states interconvert with binding-competent states through structural rearrangement of the binding site on the nanosecond to microsecond timescale. Moreover, we have simulated the complete theophylline binding pathway. Our binding simulations supplement prior experimental observations of slow theophylline binding kinetics by showing that the binding site must undergo a large conformational rearrangement after the aptamer and theophylline form an initial complex, most notably, a major rearrangement of the C27 base from a buried to solvent-exposed orientation. Theophylline appears to bind by a combination of conformational selection and induced fit mechanisms. Finally, our modeling indicates that when Mg2+ ions are present the population of binding-competent aptamer states increases more than twofold. This population change, rather than direct interactions between Mg2+ and theophylline, accounts for altered theophylline binding kinetics. PMID:28437473

Importance of geologic characterization of potential low-level radioactive waste disposal sites

USGS Publications Warehouse

Weibel, C.P.; Berg, R.C.

1991-01-01

Using the example of the Geff Alternative Site in Wayne County, Illinois, for the disposal of low-level radioactive waste, this paper demonstrates, from a policy and public opinion perspective, the importance of accurately determining site stratigraphy. Complete and accurate characterization of geologic materials and determination of site stratigraphy at potential low-level waste disposal sites provides the frame-work for subsequent hydrologic and geochemical investigations. Proper geologic characterization is critical to determine the long-term site stability and the extent of interactions of groundwater between the site and its surroundings. Failure to adequately characterize site stratigraphy can lead to the incorrect evaluation of the geology of a site, which in turn may result in a lack of public confidence. A potential problem of lack of public confidence was alleviated as a result of the resolution and proper definition of the Geff Alternative Site stratigraphy. The integrity of the investigation was not questioned and public perception was not compromised. ?? 1991 Springer-Verlag New York Inc.

Characterization of Martian Rock Shape for MER Airbag Drop Tests

NASA Astrophysics Data System (ADS)

Dimaggio, E. N.; Schroeder, R.; Castle, N.; Golombek, M.

2002-12-01

Rock distributions for the final platforms used in airbag drop tests are currently being designed for the Mars Exploration Rovers (MER) scheduled to launch in 2003. Like Mars Pathfinder (MPF), launched in 1996, MER will use a series of airbags to cushion its landing on the surface of Mars. Previous MER airbag drop tests have shown that sharp, angular (triangular) rocks >20 cm high may be hazardous. To aid in defining the rock distributions for the final airbag tests, images from the Viking Landers 1 and 2 and MPF were used to identify rocks that are >20 cm high, and characterize them as triangular, square or round. Approximately 33% of all rocks analyzed are triangular. Of the rocks analyzed that are ~20-60 cm high, ~14% are triangular. Most of these triangular rocks are small, ~20-30 cm high. Rock distributions of previous airbag platforms were similarly classified and show a greater percentage of triangular and square rocks that are ~20-60 cm high than at the landing sites. The burial of a rock (perched, partially buried or buried) was also considered because perched rocks may pose less of a threat to the airbags than those buried because perched rocks can be dislodged and roll during impact. Approximately 19% of all rocks analyzed, and ~19% of rocks that are ~20-60 cm high, are triangular and partially buried or buried. These data suggest that the platform rock distributions appropriately represented the risks to the airbags associated with triangular rocks. A similar percentage of >20 cm high triangular rocks will be added to the drop test platforms to represent landing site rock distributions.

Emissions from cold heavy oil production with sands (CHOPS) facilities in Alberta, Canada

NASA Astrophysics Data System (ADS)

Roscioli, J. R.; Herndon, S. C.; Yacovitch, T. I.; Knighton, W. B.; Zavala-Araiza, D.; Johnson, M. R.; Tyner, D. R.

2017-12-01

Cold heavy oil production with sands (CHOPS) is generally characterized as a pump driven oil extraction method producing a mixture of sand, water, and heavy oil to heated liquid storage tanks. In addition to fluids, CHOPS sites also produce solution gas, primarily composed of methane, through the well annulus. Depending on formation and well production characteristics, large volumes of this solution gas are frequently vented to the atmosphere without flaring or conservation. To better understand these emission we present measurements of methane, ethane, propane and aromatic emission rates from CHOPS sites using dual tracer flux ratio methodology. The use of two tracers allowed on-site emission sources to be accurately identified and in one instance indicated that the annular vent was responsible for >75% of emissions at the facility. Overall, a measurement survey of five CHOPS sites finds that the methane emissions are in general significantly under-reported by operators. This under-reporting may arise from uncertainties associated with measured gas-to-oil ratios upon which the reported vent volume is based. Finally, measurements of ethane, propane and aromatics from these facilities indicates surprisingly low non-methane hydrocarbon content.

Estimates of projection overlap and zones of convergence within frontal-striatal circuits.

PubMed

Averbeck, Bruno B; Lehman, Julia; Jacobson, Moriah; Haber, Suzanne N

2014-07-16

Frontal-striatal circuits underlie important decision processes, and pathology in these circuits is implicated in many psychiatric disorders. Studies have shown a topographic organization of cortical projections into the striatum. However, work has also shown that there is considerable overlap in the striatal projection zones of nearby cortical regions. To characterize this in detail, we quantified the complete striatal projection zones from 34 cortical injection locations in rhesus monkeys. We first fit a statistical model that showed that the projection zone of a cortical injection site could be predicted with considerable accuracy using a cross-validated model estimated on only the other injection sites. We then examined the fraction of overlap in striatal projection zones as a function of distance between cortical injection sites, and found that there was a highly regular relationship. Specifically, nearby cortical locations had as much as 80% overlap, and the amount of overlap decayed exponentially as a function of distance between the cortical injection sites. Finally, we found that some portions of the striatum received inputs from all the prefrontal regions, making these striatal zones candidates as information-processing hubs. Thus, the striatum is a site of convergence that allows integration of information spread across diverse prefrontal cortical areas. Copyright © 2014 the authors 0270-6474/14/339497-09$15.00/0.

Exobiological exploration of Mars.

PubMed

Klein, H P; DeVincenzi, D L

1995-03-01

Of all the other planets in the solar system, Mars remains the most promising for further elucidating concepts about chemical evolution and the origin of life. Strategies were developed to pursue three exobiological objectives for Mars exploration: determining the abundance and distribution of the biogenic elements and organic compounds, detecting evidence of an ancient biota on Mars, and determining whether indigenous organisms exist anywhere on the planet. The three strategies are quite similar and, in fact, share the same sequence of phases. In the first phase, each requires global reconnaissance and remote sensing by orbiters to select sites of interest for detailed in situ analyses. In the second phase, lander missions are conducted to characterize the chemical and physical properties of the selected sites. The third phase involves conducting "critical" experiments at sites whose properties make them particularly attractive for exobiology. These critical experiments would include, for example, identification of organics, detection of fossils, and detection of extant life. The fourth phase is the detailed analysis of samples returned from these sites in Earth-based laboratories to confirm and extend previous discoveries. Finally, in the fifth phase, human exploration is needed to establish the geological settings for the earlier findings or to discover and explore sites that are not accessible to robotic spacecraft.

Characterizing dry deposition of mercury in urban runoff

USGS Publications Warehouse

Fulkerson, M.; Nnadi, F.N.; Chasar, L.S.

2007-01-01

Stormwater runoff from urban surfaces often contains elevated levels of toxic metals. When discharged directly into water bodies, these pollutants degrade water quality and impact aquatic life and human health. In this study, the composition of impervious surface runoff and associated rainfall was investigated for several storm events at an urban site in Orlando, Florida. Total mercury in runoff consisted of 58% particulate and 42% filtered forms. Concentration comparisons at the start and end of runoff events indicate that about 85% of particulate total mercury and 93% of particulate methylmercury were removed from the surface before runoff ended. Filtered mercury concentrations showed less than 50% reduction of both total and methylmercury from first flush to final flush. Direct comparison between rainfall and runoff at this urban site indicates dry deposition accounted for 22% of total inorganic mercury in runoff. ?? 2007 Springer Science+Business Media B.V.

Binding interaction between rice glutelin and amylose: Hydrophobic interaction and conformational changes.

PubMed

Xu, Xingfeng; Liu, Wei; Zhong, Junzhen; Luo, Liping; Liu, Chengmei; Luo, Shunjing; Chen, Lin

2015-11-01

The interaction of rice glutelin (RG) with amylose was characterized by spectroscopic and molecular docking studies. The intrinsic fluorescence of RG increased upon the addition of amylose. The binding sites, binding constant and thermodynamic features indicated that binding process was spontaneous and the main driving force of the interaction was hydrophobic interaction. The surface hydrophobicity of RG decreased with increasing amount of amylose. Furthermore, synchronous fluorescence and circular dichroism (CD) spectra provided data concerning conformational and micro-environmental changes of RG. With the concentration of amylose increasing, the polarity around the tyrosine residues increased while the hydrophobicity decreased. Alteration of protein conformation was observed with increasing of α-helix and reducing of β-sheet. Finally, a visual representation of two binding sites located in the amorphous area of RG was presented by molecular modeling studies. Copyright © 2015 Elsevier B.V. All rights reserved.

Remote identification of polar bear maternal den habitat in northern Alaska

USGS Publications Warehouse

Durner, George M.; Amstrup, Steven C.; Ambrosius, Ken J.

2001-01-01

Polar bears (Ursus maritimus) give birth in dens of ice and snow to protect their altricial young. During the snow-free season, we visited 25 den sites located previously by radiotelemetry and characterized the den site physiognomy. Seven dens occurred in habitats with minimal relief. Eighteen dens (72%) were in coastal and river banks. These "banks" were identifiable on aerial photographs. We then searched high-resolution aerial photographs (n = 3000) for habitats similar to those of the 18 dens. On aerial photos, we mapped 1782 km of bank habitats suitable for denning. Bank habitats comprised 0.18% of our study area between the Colville River and the Tamayariak River in northern Alaska. The final map, which correctly identified 88% of bank denning habitat in this region, will help minimize the potential for disruptions of maternal dens by winter petroleum exploration activities.

A FIELD EVALUATION OF IN-SITU BIODEGRADATION OF CHLORINATED ETHENES: PART I, METHODOLOGY AND FIELD SITE CHARACTERIZATION

EPA Science Inventory

Careful site characterization and implementation of quantitative monitoring methods are prerequisites for a convincing evaluation of enhanced biostimulation for aquifer restoration. This paper describes the characterization of a site at Moffett Naval Air Station, Mountain View, C...

10 CFR 60.16 - Site characterization plan required.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 2 2010-01-01 2010-01-01 false Site characterization plan required. 60.16 Section 60.16 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES IN GEOLOGIC REPOSITORIES Licenses Preapplication Review § 60.16 Site characterization plan required. Before proceeding to...

Measurement Sets and Sites Commonly used for Characterizations

NASA Technical Reports Server (NTRS)

Pagnutti, Mary; Holekamp, Kara; Ryan, Robert; Blonski, Slawomir; Sellers, Richard; Davis, Bruce; Zanoni, Vicki

2002-01-01

Scientists with NASA's Earth Science Applications Directorate are creating a well-characterized Verification & Validation (V&V) site at the Stennis Space Center (SSC). This site enables the in-flight characterization of remote sensing systems and the data that they require. The data are predominantly acquired by commercial, high-spatial resolution satellite systems, such as IKONOS and QuickBird 2, and airborne systems. The smaller scale of these newer high-resolution remote sensing systems allows scientists to characterize the geometric, spatial, and radiometric data properties using a single V&V site. The targets and techniques used to characterize data from these newer systems can differ significantly from the earlier, coarser spatial resolution systems. Scientists are also using the SSC V&V site to characterize thermal infrared systems and active Light Detection and Ranging (LIDAR) systems. SSC employs geodetic targets, edge targets, radiometric tarps, and thermal calibration ponds to characterize remote sensing data products. This paper presents a proposed set of required measurements for visible-through-longwave infrared remote sensing systems, and a description of the Stennis characterization. Other topics discussed inslude: 1) use of ancillary atmospheric and solar measurements taken at SSC that support various characterizations, 2) other sites used for radiometric, geometric, and spatial characterization in the continental United States,a nd 3) the need for a standardized technique to be adopted by the Committee on Earth Observation Satellites (CEOS) and other organizations.

Predicting DNAPL Source Zone and Plume Response Using Site-Measured Characteristics

DTIC Science & Technology

2017-05-19

FINAL REPORT Predicting DNAPL Source Zone and Plume Response Using Site- Measured Characteristics SERDP Project ER-1613 MAY 2017...Final Report 3. DATES COVERED (From - To) 2007 - 2017 4. TITLE AND SUBTITLE PREDICTING DNAPL SOURCE ZONE AND PLUME RESPONSE USING SITE- MEASURED ...historical record of concentration and head measurements , particularly in the near-source region. For each site considered, currently available data

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2012 CFR

2012-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2011 CFR

2011-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2013 CFR

2013-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2010 CFR

2010-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2014 CFR

2014-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

SH-wave refraction/reflection and site characterization

USGS Publications Warehouse

Wang, Z.; Street, R.L.; Woolery, E.W.; Madin, I.P.

2000-01-01

Traditionally, nonintrusive techniques used to characterize soils have been based on P-wave refraction/reflection methods. However, near-surface unconsolidated soils are oftentimes water-saturated, and when groundwater is present at a site, the velocity of the P-waves is more related to the compressibility of the pore water than to the matrix of the unconsolidated soils. Conversely, SH-waves are directly relatable to the soil matrix. This makes SH-wave refraction/reflection methods effective in site characterizations where groundwater is present. SH-wave methods have been used extensively in site characterization and subsurface imaging for earthquake hazard assessments in the central United States and western Oregon. Comparison of SH-wave investigations with geotechnical investigations shows that SH-wave refraction/reflection techniques are viable and cost-effective for engineering site characterization.

HS3D, A Dataset of Homo Sapiens Splice Regions, and its Extraction Procedure from a Major Public Database

NASA Astrophysics Data System (ADS)

Pollastro, Pasquale; Rampone, Salvatore

The aim of this work is to describe a cleaning procedure of GenBank data, producing material to train and to assess the prediction accuracy of computational approaches for gene characterization. A procedure (GenBank2HS3D) has been defined, producing a dataset (HS3D - Homo Sapiens Splice Sites Dataset) of Homo Sapiens Splice regions extracted from GenBank (Rel.123 at this time). It selects, from the complete GenBank Primate Division, entries of Human Nuclear DNA according with several assessed criteria; then it extracts exons and introns from these entries (actually 4523 + 3802). Donor and acceptor sites are then extracted as windows of 140 nucleotides around each splice site (3799 + 3799). After discarding windows not including canonical GT-AG junctions (65 + 74), including insufficient data (not enough material for a 140 nucleotide window) (686 + 589), including not AGCT bases (29 + 30), and redundant (218 + 226), the remaining windows (2796 + 2880) are reported in the dataset. Finally, windows of false splice sites are selected by searching canonical GT-AG pairs in not splicing positions (271 937 + 332 296). The false sites in a range +/- 60 from a true splice site are marked as proximal. HS3D, release 1.2 at this time, is available at the Web server of the University of Sannio: http://www.sci.unisannio.it/docenti/rampone/.

Innovations in Site Characterization Case Study: The Role of a Conceptual Site Model for Expedited Site Characterization Using the Triad Approach at the Poudre River Site, Fort Collins, Colorado

EPA Pesticide Factsheets

This case study examines how systematic planning, an evolving conceptual site model (CSM), dynamic work strategies, and real time measurement technologies can be used to unravel complex contaminant distribution patterns...

Development of Next Generation Synthetic Biology Tools for Use in Streptomyces venezuelae

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

Phelan, Ryan M.; Sachs, Daniel; Petkiewicz, Shayne J.

Streptomyces have a rich history as producers of important natural products and this genus of bacteria has recently garnered attention for its potential applications in the broader context of synthetic biology. However, the dearth of genetic tools available to control and monitor protein production precludes rapid and predictable metabolic engineering that is possible in hosts such as Escherichia coli or Saccharomyces cerevisiae. In an effort to improve genetic tools for Streptomyces venezuelae, we developed a suite of standardized, orthogonal integration vectors and an improved method to monitor protein production in this host. These tools were applied to characterize heterologous promotersmore » and various attB chromosomal integration sites. A final study leveraged the characterized toolset to demonstrate its use in producing the biofuel precursor bisabolene using a chromosomally integrated expression system. In conclusion, these tools advance S. venezuelae to be a practical host for future metabolic engineering efforts.« less

Legacy sample disposition project. Volume 2: Final report

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

Gurley, R.N.; Shifty, K.L.

1998-02-01

This report describes the legacy sample disposition project at the Idaho Engineering and Environmental Laboratory (INEEL), which assessed Site-wide facilities/areas to locate legacy samples and owner organizations and then characterized and dispositioned these samples. This project resulted from an Idaho Department of Environmental Quality inspection of selected areas of the INEEL in January 1996, which identified some samples at the Test Reactor Area and Idaho Chemical Processing Plant that had not been characterized and dispositioned according to Resource Conservation and Recovery Act (RCRA) requirements. The objective of the project was to manage legacy samples in accordance with all applicable environmentalmore » and safety requirements. A systems engineering approach was used throughout the project, which included collecting the legacy sample information and developing a system for amending and retrieving the information. All legacy samples were dispositioned by the end of 1997. Closure of the legacy sample issue was achieved through these actions.« less

Synthesis and characterization of mesoporous hydrocracking catalysts

NASA Astrophysics Data System (ADS)

Munir, D.; Usman, M. R.

2016-08-01

Mesoporous catalysts have shown great prospective for catalytic reactions due to their high surface area that aids better distribution of impregnated metal. They have been found to contain more adsorption sites and controlled pore diameter. Hydrocracking, in the presence of mesoporous catalyst is considered more efficient and higher conversion of larger molecules is observed as compared to the cracking reactions in smaller microporous cavities of traditional zeolites. In the present study, a number of silica-alumina based mesoporous catalysts are synthesized in the laboratory. The concentration and type of surfactants and quantities of silica and alumina sources are the variables studied in the preparation of catalyst supports. The supports prepared are well characterized using SEM, EDX, and N2-BET techniques. Finally, the catalysts are tested in a high pressure autoclave reactor to study the activity and selectivity of the catalysts for the hydrocracking of a model mixture of plastics comprising of LDPE, HDPE, PP, and PS.

Accelerated Oxygen Atom Transfer and C-H Bond Oxygenation by Remote Redox Changes in Fe 3Mn-Iodosobenzene Adducts

DOE PAGES

de Ruiter, Graham; Carsch, Kurtis M.; Gul, Sheraz; ...

2017-03-24

In this paper, we report the synthesis, characterization, and reactivity of [LFe 3(PhPz) 3OMn( sPhIO)][OTf] x (3: x=2; 4: x=3), where 4 is one of very few examples of iodosobenzene–metal adducts characterized by X-ray crystallography. Access to these rare heterometallic clusters enabled differentiation of the metal centers involved in oxygen atom transfer (Mn) or redox modulation (Fe). Specifically, 57Fe Mössbauer and X-ray absorption spectroscopy provided unique insights into how changes in oxidation state (Fe III 2Fe IIMn II vs. Fe III 3Mn II) influence oxygen atom transfer in tetranuclear Fe 3Mn clusters. Finally, in particular, a one-electron redox change atmore » a distal metal site leads to a change in oxygen atom transfer reactivity by ca. two orders of magnitude.« less

78 FR 23837 - Cranes and Derricks in Construction: Underground Construction and Demolition

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-23

... report here the results for the entire heavy-and-civil engineering sector and the entire site... in this final rule because employers included in the heavy-and-civil engineering sector, or the site... final rule. This final rule affects two construction sectors: NAICS 237990 (Other Heavy and Civil...

Final Report Feasibility Study for the California Wave Energy Test Center (CalWavesm)

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

Blakeslee, Samuel Norman; Toman, William I.; Williams, Richard B.

The California Wave Energy Test Center (CalWave) Feasibility Study project was funded over multiple phases by the Department of Energy to perform an interdisciplinary feasibility assessment to analyze the engineering, permitting, and stakeholder requirements to establish an open water, fully energetic, grid connected, wave energy test center off the coast of California for the purposes of advancing U.S. wave energy research, development, and testing capabilities. Work under this grant included wave energy resource characterization, grid impact and interconnection requirements, port infrastructure and maritime industry capability/suitability to accommodate the industry at research, demonstration and commercial scale, and macro and micro sitingmore » considerations. CalWave Phase I performed a macro-siting and down-selection process focusing on two potential test sites in California: Humboldt Bay and Vandenberg Air Force Base. This work resulted in the Vandenberg Air Force Base site being chosen as the most favorable site based on a peer reviewed criteria matrix. CalWave Phase II focused on four siting location alternatives along the Vandenberg Air Force Base coastline and culminated with a final siting down-selection. Key outcomes from this work include completion of preliminary engineering and systems integration work, a robust turnkey cost estimate, shoreside and subsea hazards assessment, storm wave analysis, lessons learned reports from several maritime disciplines, test center benchmarking as compared to existing international test sites, analysis of existing applicable environmental literature, the completion of a preliminary regulatory, permitting and licensing roadmap, robust interaction and engagement with state and federal regulatory agency personnel and local stakeholders, and the population of a Draft Federal Energy Regulatory Commission (FERC) Preliminary Application Document (PAD). Analysis of existing offshore oil and gas infrastructure was also performed to assess the potential value and re-use scenarios of offshore platform infrastructure and associated subsea power cables and shoreside substations. The CalWave project team was well balanced and was comprised of experts from industry, academia, state and federal regulatory agencies. The result of the CalWave feasibility study finds that the CalWave Test Center has the potential to provide the most viable path to commercialization for wave energy in the United States.« less

Model Validation and Site Characterization for Early Deployment MHK Sites and Establishment of Wave Classification Scheme

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

Kilcher, Levi F

Model Validation and Site Characterization for Early Deployment Marine and Hydrokinetic Energy Sites and Establishment of Wave Classification Scheme presentation from from Water Power Technologies Office Peer Review, FY14-FY16.

Recent Experience Using Active Love Wave Techniques to Characterize Seismographic Station Sites

NASA Astrophysics Data System (ADS)

Martin, A. J.; Yong, A.; Salomone, L.

2014-12-01

Active-source Love waves recorded by the multi-channel analysis of surface wave (MASLW) technique were recently analyzed in two site characterization projects. Between 2010 and 2011, the 2009 American Recovery and Reinvestment Act (ARRA) funded GEOVision to conduct geophysical investigations at 189 seismographic stations—185 in California and 4 in the Central Eastern U.S. (CEUS). The original project plan was to utilize active and passive Rayleigh wave-based techniques to obtain shear-wave velocity (VS) profiles to a minimum depth of 30 m and the time-averaged VS of the upper 30 meters (VS30). Early in the investigation it became evident that Rayleigh wave techniques, such as multi-channel analysis of surface waves (MASRW), were not effective at characterizing all sites. Shear-wave seismic refraction and MASLW techniques were therefore applied. The MASLW technique was deployed at a total of 38 sites, in addition to other methods, and used as the primary technique to characterize 22 sites, 5 of which were also characterized using Rayleigh wave techniques. In 2012, the Electric Power Research Institute funded characterization of 33 CEUS station sites. Based on experience from the ARRA investigation, both MASRW and MASLW data were acquired by GEOVision at 24 CEUS sites—the remaining 9 sites and 2 overlapping sites were characterized by University of Texas, Austin. Of the 24 sites characterized by GEOVision, 16 were characterized using MASLW data, 4 using both MASLW and MASRW data and 4 using MASRW data. Love wave techniques were often found to perform better, or at least yield phase velocity data that could be more readily modeled using the fundamental mode assumption, at shallow rock sites, sites with steep velocity gradients, and, sites with a thin, low velocity, surficial soil layer overlying stiffer sediments. These types of velocity structure often excite dominant higher modes in Rayleigh wave data, but not in Love wave data. At such sites, it may be possible to model Rayleigh wave data using multi- or effective-mode techniques; however, in many cases extraction of adequate Rayleigh wave dispersion data for modeling was difficult. These results imply that field procedures should include careful scrutiny of Rayleigh wave-based dispersion data in order to collect Love wave data when warranted.

Soil contamination by heavy metals: measurements from a closed unlined landfill.

PubMed

Kasassi, A; Rakimbei, P; Karagiannidis, A; Zabaniotou, A; Tsiouvaras, K; Nastis, A; Tzafeiropoulou, K

2008-12-01

The aim of the present study was the characterization of soil samples of a closed unlined landfill located northwest of Thessaloniki, North Greece, in relation to heavy metals values. Samples were obtained by drilling in different depths (2.5-17.5m). Then they were analyzed by atomic absorption spectrophotometry for Cd, Cr, Cu, Ni, Pb and Zn investigation. The chemical analysis showed that the metal values varied over a wide range: from 0.50 to 18.75mg/kg for Cd, 3.88-171.88mg/kg for Cr, 8.13-356.25mg/kg for Cu, 5.63-63.75mg/kg for Ni, 2.50-92.50mg/kg for Pb and 6.38-343.75mg/kg for Zn. The highest values found in three of the six drillings, in depths over 2.5m. Although the area is heavily industrialized, the presented results indicated that local industries have not constituted an extensive metal pollution source for the site. Finally, after all necessary preparatory operations of site cleaning and flattening, surface planting selected and applied as a phytoremediation rehabilitation method of the site.

Spice In Martian Soil

NASA Astrophysics Data System (ADS)

Seiferlin, K.; Spohn, T.; Spice Team

The Netlander mission offers a unique opportunity to study the surface and the inte- rior of Mars at four different locations at the same time. In addition to real "network"- science, where the presence of four stations is a 'must' to address global science as- pects, local, landing site-related instruments can more than double our knowledge of the surface of Mars, compared to the three landing sites (Viking 1 and 2, Pathfinder) we are currently familiar with. The SPICE instrument will characterize the soil at the landing sites. Force sensors integrated into the seismometer legs (three per station) will determine the mechanical strength of the soil. Thermal sensors will measure the local soil temperature, the thermal inertia and the thermal diffusivity independently, thus allowing us to determine the thermal conductivity and the volumetric heat capac- ity of the soil. These properties will tell us about (1) soil cementation ("duricrust"), (2) volatile exchange with the atmosphere, (3) grain size, (4) near-surface stratigra- phy, and (5) will finally provide ground truth for remote sensing data such as that from Mars Global Surveyor's thermal emission spectrometer.

Engineered Proteins Program Mammalian Cells to Target Inflammatory Disease Sites.

PubMed

Qudrat, Anam; Mosabbir, Abdullah Al; Truong, Kevin

2017-06-22

Disease sites in atherosclerosis and cancer feature cell masses (e.g., plaques/tumors), a low pH extracellular microenvironment, and various pro-inflammatory cytokines such as tumor necrosis factor α (TNFα). The ability to engineer a cell to seek TNFα sources allows for targeted therapeutic delivery. To accomplish this, here we introduced a system of proteins: an engineered TNFα chimeric receptor (named TNFR1chi), a previously engineered Ca 2+ -activated RhoA (named CaRQ), vesicular stomatitis virus glycoprotein G (VSVG), and thymidine kinase. Upon binding TNFα, TNFR1chi generates a Ca 2+ signal that in turn activates CaRQ-mediated non-apoptotic blebs that allow migration toward the TNFα source. Next, the addition of VSVG, upon low pH induction, causes membrane fusion of the engineered and TNFα source cells. Finally, after ganciclovir treatment cells undergo death via the thymidine kinase suicide mechanism. Hence, we assembled a system of proteins that forms the basis of engineering a cell to target inflammatory disease sites characterized by TNFα secretion and a low-pH microenvironment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Tricyclic Covalent Inhibitors Selectively Target Jak3 through an Active Site Thiol

DOE PAGES

Goedken, Eric R.; Argiriadi, Maria A.; Banach, David L.; ...

2014-12-31

The action of Janus kinases (JAKs) is required for multiple cytokine signaling pathways, and as such, JAK inhibitors hold promise for treatment of autoimmune disorders, including rheumatoid arthritis, inflammatory bowel disease, and psoriasis. However, due to high similarity in the active sites of the four members (Jak1, Jak2, Jak3, and Tyk2), developing selective inhibitors within this family is challenging. In this paper, we have designed and characterized substituted, tricyclic Jak3 inhibitors that selectively avoid inhibition of the other JAKs. This is accomplished through a covalent interaction between an inhibitor containing a terminal electrophile and an active site cysteine (Cys-909). Wemore » found that these ATP competitive compounds are irreversible inhibitors of Jak3 enzyme activity in vitro. They possess high selectivity against other kinases and can potently (IC 50 < 100 nM) inhibit Jak3 activity in cell-based assays. Finally, these results suggest irreversible inhibitors of this class may be useful selective agents, both as tools to probe Jak3 biology and potentially as therapies for autoimmune diseases.« less

Tricyclic Covalent Inhibitors Selectively Target Jak3 through an Active Site Thiol

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

Goedken, Eric R.; Argiriadi, Maria A.; Banach, David L.

The action of Janus kinases (JAKs) is required for multiple cytokine signaling pathways, and as such, JAK inhibitors hold promise for treatment of autoimmune disorders, including rheumatoid arthritis, inflammatory bowel disease, and psoriasis. However, due to high similarity in the active sites of the four members (Jak1, Jak2, Jak3, and Tyk2), developing selective inhibitors within this family is challenging. In this paper, we have designed and characterized substituted, tricyclic Jak3 inhibitors that selectively avoid inhibition of the other JAKs. This is accomplished through a covalent interaction between an inhibitor containing a terminal electrophile and an active site cysteine (Cys-909). Wemore » found that these ATP competitive compounds are irreversible inhibitors of Jak3 enzyme activity in vitro. They possess high selectivity against other kinases and can potently (IC 50 < 100 nM) inhibit Jak3 activity in cell-based assays. Finally, these results suggest irreversible inhibitors of this class may be useful selective agents, both as tools to probe Jak3 biology and potentially as therapies for autoimmune diseases.« less

On-site GC/MS analysis of Chapman gasification separator liquor. Final report Jul 80-Mar 81

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

Thielen, C.J.; Magee, R.A.; Collins, R.V.

1981-08-01

The report gives results of a characterization of a wastewater stream from a coal gasification plant, using on-site extraction and GC/MS analysis. Extractable material in the wastewater was primarily phenols and alkylphenols, accounting for about 99% of the total mass identified. Several polynuclear aromatic compounds were also identified. The composition of the sample deteriorated even though the water was held in amber bottles at 4C: this was most evident in the concentration of dimethylphenols which dropped about 75% during 2 weeks of refrigerated storage. Ambient sample storage produced a greater decrease in the concentration of phenol, but did not appearmore » to affect the alkylphenols or the base/neutral compounds as much. The observed changes in composition should hamper any off-site wastewater treatbility studies with waters of this type. Diisopropyl ether (DIPE) extraction confirmed the 99-plus % removal efficiency of phenol which had been demonstrated in previous studies. Wet oxidation removed organics almost as efficiently as DIPE extraction, but may have limited use because of its high operating cost.« less

10 CFR 960.3-2-2 - Nomination of sites as suitable for characterization.

Code of Federal Regulations, 2010 CFR

2010-01-01

... OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-2-2 Nomination of... of each repository site. For the second repository, at least three of the sites shall not have been nominated previously. Any site nominated as suitable for characterization for the first repository, but not...

Meta-analysis of radiocesium contamination data in Japanese forest trees over the period 2011-2013.

PubMed

Gonze, M-A; Calmon, P

2017-12-01

The fate and dispersion of radiocesium in forests affected by the Fukushima atmospheric fallouts have been efficiently characterized by Japanese scientists thanks to monitoring surveys of radioactive contents in contaminated soil, water, and vegetation samples at numerous sites. In this paper, we carry out a meta-analysis of the field surveys conducted over the period 2011-2013 in evergreen coniferous and deciduous broadleaf forests of Fukushima or neighboring prefectures. The review focuses on contamination data acquired in tree vegetation - about 1500 spatio-temporal measurements of concentrations, inventories and depuration fluxes - with a particular interest for organs that were directly exposed to the atmospheric fallouts and subjected to depuration mechanisms (foliage, branches and outer bark). To reduce the spatial variability between the sites, radioactive data were normalized by the total deposit estimated at each site. Our analysis highlights the overall consistency of field observations despite the variety of experimental protocols, disparate sampling periods, differences in the forest stand characteristics and variability of the atmospheric deposition conditions. Assuming that the sites conformed to the same dynamics (within the range of residual variability), we then derive, discuss, and compare the mean representative evolutions of radiocesium contamination in the two categories of forest. Thanks to a simple mass balance approach, we finally demonstrate that: (i) about 90% of the radiocesium deposit was intercepted by evergreen coniferous vegetation, (ii) 80% of the deposit was gradually transferred to the forest floor in 3years, according to a well characterized depuration kinetics, and (iii) about 4% was readily absorbed by the foliage and translocated to internal organs (inner bark, stem wood and roots) at a rate of about 10 -4 d -1 . Copyright © 2017 Elsevier B.V. All rights reserved.

Use of airborne lidar data to improve plant species richness and diversity monitoring in lowland and mountain forests

PubMed Central

Durrieu, Sylvie; Gosselin, Frédéric; Herpigny, Basile

2017-01-01

We explored the potential of airborne laser scanner (ALS) data to improve Bayesian models linking biodiversity indicators of the understory vegetation to environmental factors. Biodiversity was studied at plot level and models were built to investigate species abundance for the most abundant plants found on each study site, and for ecological group richness based on light preference. The usual abiotic explanatory factors related to climate, topography and soil properties were used in the models. ALS data, available for two contrasting study sites, were used to provide biotic factors related to forest structure, which was assumed to be a key driver of understory biodiversity. Several ALS variables were found to have significant effects on biodiversity indicators. However, the responses of biodiversity indicators to forest structure variables, as revealed by the Bayesian model outputs, were shown to be dependent on the abiotic environmental conditions characterizing the study areas. Lower responses were observed on the lowland site than on the mountainous site. In the latter, shade-tolerant and heliophilous species richness was impacted by vegetation structure indicators linked to light penetration through the canopy. However, to reveal the full effects of forest structure on biodiversity indicators, forest structure would need to be measured over much wider areas than the plot we assessed. It seems obvious that the forest structure surrounding the field plots can impact biodiversity indicators measured at plot level. Various scales were found to be relevant depending on: the biodiversity indicators that were modelled, and the ALS variable. Finally, our results underline the utility of lidar data in abundance and richness models to characterize forest structure with variables that are difficult to measure in the field, either due to their nature or to the size of the area they relate to. PMID:28902920

A case of thymic Langerhans cell histiocytosis with diabetes insipidus as the first presentation.

PubMed

Chen, Xiaoyan; Huang, Xiaochun; Qiu, Yuan; Chen, Hanzhang; Fu, Yingyu; Li, Xinchun

2013-03-01

Langerhans cell histiocytosis (LCH) is an idiopathic group of reactive proliferative diseases linked to aberrant immunity, pathologically characterized by clonal proliferation of Langerhans cells. LCH rarely involves the thymus. We report a case of thymic LCH with diabetes insipidus as the first presentation, without evidence of myasthenia gravis and without evidenced involvement of the skin, liver, spleen, bones, lungs and superficial lymph nodes. This present case may have important clinical implications. In screening for LCH lesions, attention should be attached to rarely involved sites in addition to commonly involved organs. Follow-up and imageological examination are very important to a final diagnosis.

N-Glycopeptide Profiling in Arabidopsis Inflorescence

DOE PAGES

Xu, Shou-Ling; Medzihradszky, Katalin F.; Wang, Zhi-Yong; ...

2016-04-11

This study presents the first large scale analysis of plant intact glycopeptides. Using wheat germ agglutinin lectin weak affinity chromatography to enrich modified peptides, followed by ETD fragmentation tandem mass spectrometry, glycan compositions on over 1100 glycopeptides from 270 proteins found in Arabidopsis inflorescence tissue were characterized. While some sites were only detected with a single glycan attached, others displayed up to 16 different glycoforms. Among the identified glycopeptides were four modified in non-consensus glycosylation motifs. Finally, while most of the modified proteins are secreted, membrane, ER or Golgi localized proteins, surprisingly N-linked sugars were detected on a protein predictedmore » to be cytosolic or nuclear.« less

Ames expedited site characterization demonstration at the former manufactured gas plant site, Marshalltown, Iowa

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

Bevolo, A.J.; Kjartanson, B.H.; Wonder, J.D.

1996-03-01

The goal of the Ames Expedited Site Characterization (ESC) project is to evaluate and promote both innovative technologies (IT) and state-of-the-practice technologies (SOPT) for site characterization and monitoring. In April and May 1994, the ESC project conducted site characterization, technology comparison, and stakeholder demonstration activities at a former manufactured gas plant (FMGP) owned by Iowa Electric Services (IES) Utilities, Inc., in Marshalltown, Iowa. Three areas of technology were fielded at the Marshalltown FMGP site: geophysical, analytical and data integration. The geophysical technologies are designed to assess the subsurface geological conditions so that the location, fate and transport of the targetmore » contaminants may be assessed and forecasted. The analytical technologies/methods are designed to detect and quantify the target contaminants. The data integration technology area consists of hardware and software systems designed to integrate all the site information compiled and collected into a conceptual site model on a daily basis at the site; this conceptual model then becomes the decision-support tool. Simultaneous fielding of different methods within each of the three areas of technology provided data for direct comparison of the technologies fielded, both SOPT and IT. This document reports the results of the site characterization, technology comparison, and ESC demonstration activities associated with the Marshalltown FMGP site. 124 figs., 27 tabs.« less

Sequential analysis of hydrochemical data for watershed characterization.

PubMed

Thyne, Geoffrey; Güler, Cüneyt; Poeter, Eileen

2004-01-01

A methodology for characterizing the hydrogeology of watersheds using hydrochemical data that combine statistical, geochemical, and spatial techniques is presented. Surface water and ground water base flow and spring runoff samples (180 total) from a single watershed are first classified using hierarchical cluster analysis. The statistical clusters are analyzed for spatial coherence confirming that the clusters have a geological basis corresponding to topographic flowpaths and showing that the fractured rock aquifer behaves as an equivalent porous medium on the watershed scale. Then principal component analysis (PCA) is used to determine the sources of variation between parameters. PCA analysis shows that the variations within the dataset are related to variations in calcium, magnesium, SO4, and HCO3, which are derived from natural weathering reactions, and pH, NO3, and chlorine, which indicate anthropogenic impact. PHREEQC modeling is used to quantitatively describe the natural hydrochemical evolution for the watershed and aid in discrimination of samples that have an anthropogenic component. Finally, the seasonal changes in the water chemistry of individual sites were analyzed to better characterize the spatial variability of vertical hydraulic conductivity. The integrated result provides a method to characterize the hydrogeology of the watershed that fully utilizes traditional data.

Thermodynamic Characterization of Hydration Sites from Integral Equation-Derived Free Energy Densities: Application to Protein Binding Sites and Ligand Series.

PubMed

Güssregen, Stefan; Matter, Hans; Hessler, Gerhard; Lionta, Evanthia; Heil, Jochen; Kast, Stefan M

2017-07-24

Water molecules play an essential role for mediating interactions between ligands and protein binding sites. Displacement of specific water molecules can favorably modulate the free energy of binding of protein-ligand complexes. Here, the nature of water interactions in protein binding sites is investigated by 3D RISM (three-dimensional reference interaction site model) integral equation theory to understand and exploit local thermodynamic features of water molecules by ranking their possible displacement in structure-based design. Unlike molecular dynamics-based approaches, 3D RISM theory allows for fast and noise-free calculations using the same detailed level of solute-solvent interaction description. Here we correlate molecular water entities instead of mere site density maxima with local contributions to the solvation free energy using novel algorithms. Distinct water molecules and hydration sites are investigated in multiple protein-ligand X-ray structures, namely streptavidin, factor Xa, and factor VIIa, based on 3D RISM-derived free energy density fields. Our approach allows the semiquantitative assessment of whether a given structural water molecule can potentially be targeted for replacement in structure-based design. Finally, PLS-based regression models from free energy density fields used within a 3D-QSAR approach (CARMa - comparative analysis of 3D RISM Maps) are shown to be able to extract relevant information for the interpretation of structure-activity relationship (SAR) trends, as demonstrated for a series of serine protease inhibitors.

Prediction of Protein-Protein Interaction Sites Using Electrostatic Desolvation Profiles

PubMed Central

Fiorucci, Sébastien; Zacharias, Martin

2010-01-01

Abstract Protein-protein complex formation involves removal of water from the interface region. Surface regions with a small free energy penalty for water removal or desolvation may correspond to preferred interaction sites. A method to calculate the electrostatic free energy of placing a neutral low-dielectric probe at various protein surface positions has been designed and applied to characterize putative interaction sites. Based on solutions of the finite-difference Poisson equation, this method also includes long-range electrostatic contributions and the protein solvent boundary shape in contrast to accessible-surface-area-based solvation energies. Calculations on a large set of proteins indicate that in many cases (>90%), the known binding site overlaps with one of the six regions of lowest electrostatic desolvation penalty (overlap with the lowest desolvation region for 48% of proteins). Since the onset of electrostatic desolvation occurs even before direct protein-protein contact formation, it may help guide proteins toward the binding region in the final stage of complex formation. It is interesting that the probe desolvation properties associated with residue types were found to depend to some degree on whether the residue was outside of or part of a binding site. The probe desolvation penalty was on average smaller if the residue was part of a binding site compared to other surface locations. Applications to several antigen-antibody complexes demonstrated that the approach might be useful not only to predict protein interaction sites in general but to map potential antigenic epitopes on protein surfaces. PMID:20441756

The Role and Specificity of the Catalytic and Regulatory Cation-binding Sites of the Na+-pumping NADH:Quinone Oxidoreductase from Vibrio cholerae*

PubMed Central

Juárez, Oscar; Shea, Michael E.; Makhatadze, George I.; Barquera, Blanca

2011-01-01

The Na+-translocating NADH:quinone oxidoreductase is the entry site for electrons into the respiratory chain and the main sodium pump in Vibrio cholerae and many other pathogenic bacteria. In this work, we have employed steady-state and transient kinetics, together with equilibrium binding measurements to define the number of cation-binding sites and characterize their roles in the enzyme. Our results show that sodium and lithium ions stimulate enzyme activity, and that Na+-NQR enables pumping of Li+, as well as Na+ across the membrane. We also confirm that the enzyme is not able to translocate other monovalent cations, such as potassium or rubidium. Although potassium is not used as a substrate, Na+-NQR contains a regulatory site for this ion, which acts as a nonessential activator, increasing the activity and affinity for sodium. Rubidium can bind to the same site as potassium, but instead of being activated, enzyme turnover is inhibited. Activity measurements in the presence of both sodium and lithium indicate that the enzyme contains at least two functional sodium-binding sites. We also show that the binding sites are not exclusively responsible for ion selectivity, and other steps downstream in the mechanism also play a role. Finally, equilibrium-binding measurements with 22Na+ show that, in both its oxidized and reduced states, Na+-NQR binds three sodium ions, and that the affinity for sodium is the same for both of these states. PMID:21652714

Structural Insights into the Assembly of the Adeno-associated Virus Type 2 Rep68 Protein on the Integration Site AAVS1*

PubMed Central

Musayev, Faik N.; Zarate-Perez, Francisco; Bishop, Clayton; Burgner, John W.; Escalante, Carlos R.

2015-01-01

Adeno-associated virus (AAV) is the only eukaryotic virus with the property of establishing latency by integrating site-specifically into the human genome. The integration site known as AAVS1 is located in chromosome 19 and contains multiple GCTC repeats that are recognized by the AAV non-structural Rep proteins. These proteins are multifunctional, with an N-terminal origin-binding domain (OBD) and a helicase domain joined together by a short linker. As a first step to understand the process of site-specific integration, we proceeded to characterize the recognition and assembly of Rep68 onto the AAVS1 site. We first determined the x-ray structure of AAV-2 Rep68 OBD in complex with the AAVS1 DNA site. Specificity is achieved through the interaction of a glycine-rich loop that binds the major groove and an α-helix that interacts with a downstream minor groove on the same face of the DNA. Although the structure shows a complex with three OBD molecules bound to the AAVS1 site, we show by using analytical centrifugation and electron microscopy that the full-length Rep68 forms a heptameric complex. Moreover, we determined that a minimum of two direct repeats is required to form a stable complex and to melt DNA. Finally, we show that although the individual domains bind DNA poorly, complex assembly requires oligomerization and cooperation between its OBD, helicase, and the linker domains. PMID:26370092

Site-conditions map for Portugal based on VS measurements: methodology and final model

NASA Astrophysics Data System (ADS)

Vilanova, Susana; Narciso, João; Carvalho, João; Lopes, Isabel; Quinta Ferreira, Mario; Moura, Rui; Borges, José; Nemser, Eliza; Pinto, carlos

2017-04-01

In this paper we present a statistically significant site-condition model for Portugal based on shear-wave velocity (VS) data and surface geology. We also evaluate the performance of commonly used Vs30 proxies based on exogenous data and analyze the implications of using those proxies for calculating site amplification in seismic hazard assessment. The dataset contains 161 Vs profiles acquired in Portugal in the context of research projects, technical reports, academic thesis and academic papers. The methodologies involved in characterizing the Vs structure at the sites in the database include seismic refraction, multichannel analysis of seismic waves and refraction microtremor. Invasive measurements were performed in selected locations in order to compare the Vs profiles obtained from both invasive and non-invasive techniques. In general there was good agreement in the subsurface structure of Vs30 obtained from the different methodologies. The database flat-file includes information on Vs30, surface geology at 1:50.000 and 1:500.000 scales, elevation and topographic slope and based on SRTM30 topographic dataset. The procedure used to develop the site-conditions map is based on a three-step process that includes defining a preliminary set of geological units based on the literature, performing statistical tests to assess whether or not the differences in the distributions of Vs30 are statistically significant, and merging of the geological units accordingly. The dataset was, to some extent, affected by clustering and/or preferential sampling and therefore a declustering algorithm was applied. The final model includes three geological units: 1) Igneous, metamorphic and old (Paleogene and Mesozoic) sedimentary rocks; 2) Neogene and Pleistocene formations, and 3) Holocene formations. The evaluation of proxies indicates that although geological analogues and topographic slope are in general unbiased, the latter shows significant bias for particular geological units and subsequently for some geographical regions.

Characterization of the clustered regularly interspaced short palindromic repeats sites in Streptococcus mutans isolated from early childhood caries patients.

PubMed

Chen, Jing; Li, Tiancheng; Zhou, Xuedong; Cheng, Lei; Huo, Yuanyuan; Zou, Jing; Li, Yuqing

2017-11-01

The aim of this study was to analyze the characteristics of the clustered regularly interspaced short palindromic repeats (CRISPR) sites in 45 clinical Streptococcus mutans strains and their relationship to the clinical manifestations of early childhood caries (ECC). Forty-five S. mutans strains were isolated from the plaque samples taken from sixty-three children. CRISPR sites were sequenced and BLAST was used to compare these sites to those in the CRISPRTarget database. The association between the distribution of CRISPR sites and the manifestation of caries was analyzed by Chi-Square test. Further, biofilm formation (by crystal violet staining) and the synthesis of polysaccharide (by anthrone-sulfuric method) of all clinical isolated S. mutans strains with both CRISPR sites and no CRISPR site were comapared. Finally, acidogenicity and acidurity of two typical strains were determined using pH drop and acid tolerance assays. Biofilm formation and EPS synthesis by two typical strains were compared by 3D CLSM (Confocal Laser Scanning Microscope) assays and the expression of gtf genes were evaluated using qPCR. We found that most of the spacers in the clinical S. mutans strains were derived from Streptococcus phages APCM01 and M102. The number of CRISPR sites in these strains was associated with the clinical manifestations of ECC. Moreover, we found that the biofilm formation and EPS synthesis ability of the S. mutans strains with both CRISPR sites was significant improved. An association was found between the distribution of CRISPR sites and the clinical manifestations of caries. The CRISPR sites might contribute to the cariogenic potential of S. mutans. Copyright © 2017 Elsevier Ltd. All rights reserved.

Site Characterization Technologies for DNAPL Investigations

EPA Pesticide Factsheets

This document is intended to help managers at sites with potential or confirmed DNAPL contamination identify suitable characterization technologies, screen the technologies for potential application, learn about applications at similar sites, and...

Structural and functional characterization of cargo-binding sites on the μ4-subunit of adaptor protein complex 4.

PubMed

Ross, Breyan H; Lin, Yimo; Corales, Esteban A; Burgos, Patricia V; Mardones, Gonzalo A

2014-01-01

Adaptor protein (AP) complexes facilitate protein trafficking by playing key roles in the selection of cargo molecules to be sorted in post-Golgi compartments. Four AP complexes (AP-1 to AP-4) contain a medium-sized subunit (μ1-μ4) that recognizes YXXØ-sequences (Ø is a bulky hydrophobic residue), which are sorting signals in transmembrane proteins. A conserved, canonical region in μ subunits mediates recognition of YXXØ-signals by means of a critical aspartic acid. Recently we found that a non-canonical YXXØ-signal on the cytosolic tail of the Alzheimer's disease amyloid precursor protein (APP) binds to a distinct region of the μ4 subunit of the AP-4 complex. In this study we aimed to determine the functionality of both binding sites of μ4 on the recognition of the non-canonical YXXØ-signal of APP. We found that substitutions in either binding site abrogated the interaction with the APP-tail in yeast-two hybrid experiments. Further characterization by isothermal titration calorimetry showed instead loss of binding to the APP signal with only the substitution R283D at the non-canonical site, in contrast to a decrease in binding affinity with the substitution D190A at the canonical site. We solved the crystal structure of the C-terminal domain of the D190A mutant bound to this non-canonical YXXØ-signal. This structure showed no significant difference compared to that of wild-type μ4. Both differential scanning fluorimetry and limited proteolysis analyses demonstrated that the D190A substitution rendered μ4 less stable, suggesting an explanation for its lower binding affinity to the APP signal. Finally, in contrast to overexpression of the D190A mutant, and acting in a dominant-negative manner, overexpression of μ4 with either a F255A or a R283D substitution at the non-canonical site halted APP transport at the Golgi apparatus. Together, our analyses support that the functional recognition of the non-canonical YXXØ-signal of APP is limited to the non-canonical site of μ4.

Structural and Functional Characterization of Cargo-Binding Sites on the μ4-Subunit of Adaptor Protein Complex 4

PubMed Central

Ross, Breyan H.; Lin, Yimo; Corales, Esteban A.; Burgos, Patricia V.; Mardones, Gonzalo A.

2014-01-01

Adaptor protein (AP) complexes facilitate protein trafficking by playing key roles in the selection of cargo molecules to be sorted in post-Golgi compartments. Four AP complexes (AP-1 to AP-4) contain a medium-sized subunit (μ1-μ4) that recognizes YXXØ-sequences (Ø is a bulky hydrophobic residue), which are sorting signals in transmembrane proteins. A conserved, canonical region in μ subunits mediates recognition of YXXØ-signals by means of a critical aspartic acid. Recently we found that a non-canonical YXXØ-signal on the cytosolic tail of the Alzheimer's disease amyloid precursor protein (APP) binds to a distinct region of the μ4 subunit of the AP-4 complex. In this study we aimed to determine the functionality of both binding sites of μ4 on the recognition of the non-canonical YXXØ-signal of APP. We found that substitutions in either binding site abrogated the interaction with the APP-tail in yeast-two hybrid experiments. Further characterization by isothermal titration calorimetry showed instead loss of binding to the APP signal with only the substitution R283D at the non-canonical site, in contrast to a decrease in binding affinity with the substitution D190A at the canonical site. We solved the crystal structure of the C-terminal domain of the D190A mutant bound to this non-canonical YXXØ-signal. This structure showed no significant difference compared to that of wild-type μ4. Both differential scanning fluorimetry and limited proteolysis analyses demonstrated that the D190A substitution rendered μ4 less stable, suggesting an explanation for its lower binding affinity to the APP signal. Finally, in contrast to overexpression of the D190A mutant, and acting in a dominant-negative manner, overexpression of μ4 with either a F255A or a R283D substitution at the non-canonical site halted APP transport at the Golgi apparatus. Together, our analyses support that the functional recognition of the non-canonical YXXØ-signal of APP is limited to the non-canonical site of μ4. PMID:24498434

Framework for Site Characterization for Monitored Natural Attenuation of Volatile Organic Compounds in Ground Water

EPA Science Inventory

Monitored Natural Attenuation (MNA) is unique among remedial technologies in relying entirely on natural processes to achieve site-specific objectives. Site characterization is essential to provide site-specific data and interpretations for the decision-making process (i.e., to ...

Effects of the synthesis temperature on the crystalline structure and the magnetic properties of cobalt ferrite nanoparticles prepared via coprecipitation

NASA Astrophysics Data System (ADS)

Hutamaningtyas, Evangelin; Utari; Suharyana; Purnama, Budi; Wijayanta, Agung Tri

2016-08-01

The effects of the synthesis temperature on the crystalline structure and the magnetic properties of cobalt ferrite (CoFe2O4) nanoparticles prepared via coprecipitation are discussed. The synthesis was conducted at temperatures of 75 °C, 85 °C and 95 °C. Fourier transform infrared spectroscopy characterization related to a stretching vibration at a wavenumber of 590 cm-1 indicated the formation of a CoFe2O4 metal oxide. In addition, powder X ray diffraction (XRD) characterization proved that the metal oxide was CoFe2O4. Crystallite sizes calculated using the Scherer formula at the strongest peak of the XRD spectra of the samples synthesized at 75 °C, 85 °C and 95 °C were 32 nm, 43 nm and 50.4 nm, respectively. Finally, the results of the vibrating sample magnetometer characterization showed that the saturation magnetization decreased with increasing synthesis temperature, which is related to the dominant preference of Co2+ over Fe3+ cations at the octahedral sites.

Slug Test Characterization Results for Multi-Test/Depth Intervals Conducted During the Drilling of CERCLA Operable Unit OU UP-1 Wells 299-W19-48, 699-30-66, and 699-36-70B

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

Spane, Frank A.; Newcomer, Darrell R.

2010-06-15

This report presents test descriptions and analysis results for multiple, stress-level slug tests that were performed at selected test/depth intervals within three Operable Unit (OU) UP-1 wells: 299-W19-48 (C4300/Well K), 699-30-66 (C4298/Well R), and 699-36-70B (C4299/Well P). These wells are located within, adjacent to, and to the southeast of the Hanford Site 200-West Area. The test intervals were characterized as the individual boreholes were advanced to their final drill depths. The primary objective of the hydrologic tests was to provide information pertaining to the areal variability and vertical distribution of hydraulic conductivity with depth at these locations within the OUmore » UP-1 area. This type of characterization information is important for predicting/simulating contaminant migration (i.e., numerical flow/transport modeling) and designing proper monitor well strategies for OU and Waste Management Area locations.« less

Slug Test Characterization Results for Multi-Test/Depth Intervals Conducted During the Drilling of CERCLA Operable Unit OU ZP-1 Wells 299-W11-43, 299-W15-50, and 299-W18-16

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

Spane, Frank A.; Newcomer, Darrell R.

2010-06-21

The following report presents test descriptions and analysis results for multiple, stress level slug tests that were performed at selected test/depth intervals within three Operable Unit (OU) ZP-1 wells: 299-W11-43 (C4694/Well H), 299-W15-50 (C4302/Well E), and 299-W18-16 (C4303/Well D). These wells are located within south-central region of the Hanford Site 200-West Area (Figure 1.1). The test intervals were characterized as the individual boreholes were advanced to their final drill depths. The primary objective of the hydrologic tests was to provide information pertaining to the areal variability and vertical distribution of hydraulic conductivity with depth at these locations within the OUmore » ZP-1 area. This type of characterization information is important for predicting/simulating contaminant migration (i.e., numerical flow/transport modeling) and designing proper monitor well strategies for OU and Waste Management Area locations.« less

Determination of the structural phase and octahedral rotation angle in halide perovskites

DOE PAGES

dos Reis, Roberto; Yang, Hao; Ophus, Colin; ...

2018-02-12

A key to the unique combination of electronic and optical properties in halide perovskite materials lies in their rich structural complexity. However, their radiation sensitive nature limits nanoscale structural characterization requiring dose efficient microscopic techniques in order to determine their structures precisely. In this work, we determine the space-group and directly image the Br halide sites of CsPbBr 3, a promising material for optoelectronic applications. Based on the symmetry of high-order Laue zone reflections of convergent-beam electron diffraction, we identify the tetragonal (I4/mcm) structural phase of CsPbBr 3 at cryogenic temperature. Electron ptychography provides a highly sensitive phase contrast measurementmore » of the halide positions under low electron-dose conditions, enabling imaging of the elongated Br sites originating from the out-of-phase octahedral rotation viewed along the [001] direction of I4/mcm persisting at room temperature. The measurement of these features and comparison with simulations yield an octahedral rotation angle of 6.5°(±1.5°). Finally, the approach demonstrated here opens up opportunities for understanding the atomic scale structural phenomena applying advanced characterization tools on a wide range of radiation sensitive halide-based all-inorganic and hybrid organic-inorganic perovskites.« less

Contribution of soil fauna to soil functioning in degraded environments: a multidisciplinary approach

NASA Astrophysics Data System (ADS)

Gargiulo, Laura; Mele, Giacomo; Moradi, Jabbar; Kukla, Jaroslav; Jandová, Kateřina; Frouz, Jan

2016-04-01

The restoration of the soil functions is essential for the recovery of highly degraded sites and, consequently, the study of the soil fauna role in the soil development in such environments has great potential from a practical point of view. The soils of the post-mining sites represent unique models for the study of the natural ecological succession because mining creates similar environments characterized by the same substrate, but by different ages according to the year of closure of mines. The aim of this work was to assess the contribution of different species of macrofauna on the evolution of soil structure and on the composition and activity of the microbial community in soil samples subjected to ecological restoration or characterized by spontaneous ecological succession. For this purpose, an experimental test was carried out in two sites characterized by different post-mining conditions: 1) natural succession, 2) reclamation with planting trees. These sites are located in the post-mining area of Sokolov (Czech Republic). For the experimental test repacked soil cores were prepared in laboratory with sieved soil sampled from the two sites. The soil cores were prepared maintaining the sequence of soil horizons present in the field. These samples were inoculated separately with two genera of earthworms (Lumbricus and Aporrectodea) and two of centipedes (Julida and Polydesmus). In particular, based on their body size, were inoculated for each cylinder 2 individuals of millipedes, 1 individual of Lumbricus and 4 individuals of Aporrectodea. For each treatment and for control samples 5 replicates were prepared and all samples were incubated in field for 1 month in the two original sampling sites. After the incubation the samples were removed from the field and transported in laboratory in order to perform the analysis of microbial respiration, of PLFA (phospholipid-derived fatty acids) and ergosterol contents and finally for the characterization of soil structure. All replicates were subjected to soil respiration measurement by means of chemical titration method. Then some replicates were destructively analyzed for PLFA and ergosterol and others were used for the 3D soil image analysis of the soil pore system. The soil cores were imaged using X-ray microtomography and three-dimensional image processing was performed in order to obtain 3D reconstructions and preliminary analysis of the identified biopores. The experimental approach used in this multidisciplinary study showed a promising potential to provide new useful information about the widely differentiated contribution of many types of macrofauna to the formation of the soil pore system and to the development of the soil microbial functions in different types of environments.

10 CFR 960.3-4 - Environmental impacts.

Code of Federal Regulations, 2010 CFR

2010-01-01

... REPOSITORY Implementation Guidelines § 960.3-4 Environmental impacts. Environmental impacts shall be considered by the DOE throughout the site characterization, site selection, and repository development..., during site characterization and repository construction, operation, closure, and decommissioning. ...

Strong ground motion in the Kathmandu Valley during the 2015 Gorkha, Nepal, earthquake

NASA Astrophysics Data System (ADS)

Takai, Nobuo; Shigefuji, Michiko; Rajaure, Sudhir; Bijukchhen, Subeg; Ichiyanagi, Masayoshi; Dhital, Megh Raj; Sasatani, Tsutomu

2016-01-01

On 25 April 2015, a large earthquake of Mw 7.8 occurred along the Main Himalayan Thrust fault in central Nepal. It was caused by a collision of the Indian Plate beneath the Eurasian Plate. The epicenter was near the Gorkha region, 80 km northwest of Kathmandu, and the rupture propagated toward east from the epicentral region passing through the sediment-filled Kathmandu Valley. This event resulted in over 8000 fatalities, mostly in Kathmandu and the adjacent districts. We succeeded in observing strong ground motions at our four observation sites (one rock site and three sedimentary sites) in the Kathmandu Valley during this devastating earthquake. While the observed peak ground acceleration values were smaller than the predicted ones that were derived from the use of a ground motion prediction equation, the observed peak ground velocity values were slightly larger than the predicted ones. The ground velocities observed at the rock site (KTP) showed a simple velocity pulse, resulting in monotonic-step displacements associated with the permanent tectonic offset. The vertical ground velocities observed at the sedimentary sites had the same pulse motions that were observed at the rock site. In contrast, the horizontal ground velocities as well as accelerations observed at three sedimentary sites showed long duration with conspicuous long-period oscillations, due to the valley response. The horizontal valley response was characterized by large amplification (about 10) and prolonged oscillations. However, the predominant period and envelope shape of their oscillations differed from site to site, indicating a complicated basin structure. Finally, on the basis of the velocity response spectra, we show that the horizontal long-period oscillations on the sedimentary sites had enough destructive power to damage high-rise buildings with natural periods of 3 to 5 s.

Construction of armored RNA containing long-size chimeric RNA by increasing the number and affinity of the pac site in exogenous rna and sequence coding coat protein of the MS2 bacteriophage.

PubMed

Wei, Baojun; Wei, Yuxiang; Zhang, Kuo; Yang, Changmei; Wang, Jing; Xu, Ruihuan; Zhan, Sien; Lin, Guigao; Wang, Wei; Liu, Min; Wang, Lunan; Zhang, Rui; Li, Jinming

2008-01-01

To construct a one-plasmid expression system of the armored RNA containing long chimeric RNA by increasing the number and affinity of the pac site. The plasmid pET-MS2-pac was constructed with one C-variant pac site, and then the plasmid pM-CR-2C containing 1,891-bp chimeric sequences and two C-variant pac sites was produced. Meanwhile, three plasmids (pM-CR-C, pM-CR-2W and pM-CR-W) were obtained as parallel controls with a different number and affinity of the pac site. Finally, the armored RNA was expressed and purified. The armored RNA with 1,891 bases target RNA was expressed successfully by the one-plasmid expression system with two C-variant pac sites, while for one pac site, no matter whether the affinity was changed or not, only the 1,200 bases target RNA was packaged. It was also found that the C-variant pac site could increase the expression efficiency of the armored RNA. The armored RNA with 1,891-bp exogenous RNA in our study showed the characterization of ribonuclease resistance and stability at different time points and temperature conditions. The armored RNA with 1,891 bases exogenous RNA was constructed and the expression system can be used as a platform for preparation of the armored RNA containing long RNA sequences. Copyright 2008 S. Karger AG, Basel.

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-...

Modeling the intraurban variation in nitrogen dioxide in urban areas in Kathmandu Valley, Nepal.

PubMed

Gurung, Anobha; Levy, Jonathan I; Bell, Michelle L

2017-05-01

With growing urbanization, traffic has become one of the main sources of air pollution in Nepal. Understanding the impact of air pollution on health requires estimation of exposure. Land use regression (LUR) modeling is widely used to investigate intraurban variation in air pollution for Western cities, but LUR models are relatively scarce in developing countries. In this study, we developed LUR models to characterize intraurban variation of nitrogen dioxide (NO 2 ) in urban areas of Kathmandu Valley, Nepal, one of the fastest urbanizing areas in South Asia. Over the study area, 135 monitoring sites were selected using stratified random sampling based on building density and road density along with purposeful sampling. In 2014, four sampling campaigns were performed, one per season, for two weeks each. NO 2 was measured using duplicate Palmes tubes at 135 sites, with additional information on nitric oxide (NO), NO 2 , and nitrogen oxide (NOx) concentrations derived from Ogawa badges at 28 sites. Geographical variables (e.g., road network, land use, built area) were used as predictor variables in LUR modeling, considering buffers 25-400m around each monitoring site. Annual average NO 2 by site ranged from 5.7 to 120ppb for the study area, with higher concentrations in the Village Development Committees (VDCs) of Kathmandu and Lalitpur than in Kirtipur, Thimi, and Bhaktapur, and with variability present within each VDC. In the final LUR model, length of major road, built area, and industrial area were positively associated with NO 2 concentration while normalized difference vegetation index (NDVI) was negatively associated with NO 2 concentration (R 2 =0.51). Cross-validation of the results confirmed the reliability of the model. The combination of passive NO 2 sampling and LUR modeling techniques allowed for characterization of nitrogen dioxide patterns in a developing country setting, demonstrating spatial variability and high pollution levels. Copyright © 2017 Elsevier Inc. All rights reserved.

45 CFR 154.230 - Submission and posting of Final Justifications for unreasonable rate increases.

Code of Federal Regulations, 2011 CFR

2011-10-01

... information available to the public on its Web site for at least three years. (d) CMS will post all Final Justifications on the CMS Web site. This information will remain available to the public on the CMS Web site for... submitted in the Preliminary Justification supporting the rate increase; and (2) Prominently post on its Web...

10 CFR 52.83 - Finality of referenced NRC approvals; partial initial decision on site suitability.

Code of Federal Regulations, 2010 CFR

2010-01-01

....145, and 52.171. (b) While a partial decision on site suitability is in effect under 10 CFR 2.617(b)(2... decision on site suitability. 52.83 Section 52.83 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS Combined Licenses § 52.83 Finality of referenced NRC...

10 CFR 52.83 - Finality of referenced NRC approvals; partial initial decision on site suitability.

Code of Federal Regulations, 2012 CFR

2012-01-01

....145, and 52.171. (b) While a partial decision on site suitability is in effect under 10 CFR 2.617(b)(2... decision on site suitability. 52.83 Section 52.83 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS Combined Licenses § 52.83 Finality of referenced NRC...

EPIC'S PRODUCTS AND SERVICES

EPA Science Inventory

EPIC completes approximately 150 site characterizations annually using current and historical aerial photographs. This work is done in support of EPA Regional and Program
offices. Site characterization provides detailed information about a site and its history, often going ba...

Conformational and thermodynamic hallmarks of DNA operator site specificity in the copper sensitive operon repressor from Streptomyces lividans

PubMed Central

Tan, Benedict G.; Vijgenboom, Erik; Worrall, Jonathan A. R.

2014-01-01

Metal ion homeostasis in bacteria relies on metalloregulatory proteins to upregulate metal resistance genes and enable the organism to preclude metal toxicity. The copper sensitive operon repressor (CsoR) family is widely distributed in bacteria and controls the expression of copper efflux systems. CsoR operator sites consist of G-tract containing pseudopalindromes of which the mechanism of operator binding is poorly understood. Here, we use a structurally characterized CsoR from Streptomyces lividans (CsoRSl) together with three specific operator targets to reveal the salient features pertaining to the mechanism of DNA binding. We reveal that CsoRSl binds to its operator site through a 2-fold axis of symmetry centred on a conserved 5′-TAC/GTA-3′ inverted repeat. Operator recognition is stringently dependent not only on electropositive residues but also on a conserved polar glutamine residue. Thermodynamic and circular dichroic signatures of the CsoRSl–DNA interaction suggest selectivity towards the A-DNA-like topology of the G-tracts at the operator site. Such properties are enhanced on protein binding thus enabling the symmetrical binding of two CsoRSl tetramers. Finally, differential binding modes may exist in operator sites having more than one 5′-TAC/GTA-3′ inverted repeat with implications in vivo for a mechanism of modular control. PMID:24121681

Human cancer tissues exhibit reduced A-to-I editing of miRNAs coupled with elevated editing of their targets

PubMed Central

Pinto, Yishay; Buchumenski, Ilana

2018-01-01

Abstract A-to-I RNA editing is an important post-transcriptional modification, known to be altered in tumors. It targets dozens of sites within miRNAs, some of which impact miRNA biogenesis and function, as well as many miRNA recognition sites. However, the full extent of the effect of editing on regulation by miRNAs and its behavior in human cancers is still unknown. Here we systematically characterized miRNA editing in 10 593 human samples across 32 cancer types and normal controls. We find that the majority of previously reported sites show little to no evidence for editing in this dataset, compile a list of 58 reliable miRNA editing sites, and study them across normal and cancer samples. Edited miRNA versions tend to suppress expression of known oncogenes, and, consistently, we observe a clear global tendency for hypo-editing in tumors, in strike contrast to the behavior for mRNA editing, allowing an accurate classification of normal/tumor samples based on their miRNA editing profile. In many cancers this profile correlates with patients' survival. Finally, thousands of miRNA binding sites are differentially edited in cancer. Our study thus establishes the important effect of RNA editing on miRNA-regulation in the tumor cell, with prospects for diagnostic and prognostic applications. PMID:29165639

The 28S–18S rDNA intergenic spacer from Crithidia fasciculata: repeated sequences, length heterogeneity, putative processing sites and potential interactions between U3 small nucleolar RNA and the ribosomal RNA precursor

PubMed Central

Schnare, Murray N.; Collings, James C.; Spencer, David F.; Gray, Michael W.

2000-01-01

In Crithidia fasciculata, the ribosomal RNA (rRNA) gene repeats range in size from ∼11 to 12 kb. This length heterogeneity is localized to a region of the intergenic spacer (IGS) that contains tandemly repeated copies of a 19mer sequence. The IGS also contains four copies of an ∼55 nt repeat that has an internal inverted repeat and is also present in the IGS of Leishmania species. We have mapped the C.fasciculata transcription initiation site as well as two other reverse transcriptase stop sites that may be analogous to the A0 and A′ pre-rRNA processing sites within the 5′ external transcribed spacer (ETS) of other eukaryotes. Features that could influence processing at these sites include two stretches of conserved primary sequence and three secondary structure elements present in the 5′ ETS. We also characterized the C.fasciculata U3 snoRNA, which has the potential for base-pairing with pre-rRNA sequences. Finally, we demonstrate that biosynthesis of large subunit rRNA in both C.fasciculata and Trypanosoma brucei involves 3′-terminal addition of three A residues that are not present in the corresponding DNA sequences. PMID:10982863

Preparing Nursing Home Data from Multiple Sites for Clinical Research – A Case Study Using Observational Health Data Sciences and Informatics

PubMed Central

Boyce, Richard D.; Handler, Steven M.; Karp, Jordan F.; Perera, Subashan; Reynolds, Charles F.

2016-01-01

Introduction: A potential barrier to nursing home research is the limited availability of research quality data in electronic form. We describe a case study of converting electronic health data from five skilled nursing facilities to a research quality longitudinal dataset by means of open-source tools produced by the Observational Health Data Sciences and Informatics (OHDSI) collaborative. Methods: The Long-Term Care Minimum Data Set (MDS), drug dispensing, and fall incident data from five SNFs were extracted, translated, and loaded into version 4 of the OHDSI common data model. Quality assurance involved identifying errors using the Achilles data characterization tool and comparing both quality measures and drug exposures in the new database for concordance with externally available sources. Findings: Records for a total 4,519 patients (95.1%) made it into the final database. Achilles identified 10 different types of errors that were addressed in the final dataset. Drug exposures based on dispensing were generally accurate when compared with medication administration data from the pharmacy services provider. Quality measures were generally concordant between the new database and Nursing Home Compare for measures with a prevalence ≥ 10%. Fall data recorded in MDS was found to be more complete than data from fall incident reports. Conclusions: The new dataset is ready to support observational research on topics of clinical importance in the nursing home including patient-level prediction of falls. The extraction, translation, and loading process enabled the use of OHDSI data characterization tools that improved the quality of the final dataset. PMID:27891528

10 CFR 960.3-2-2-4 - The environmental assessment.

Code of Federal Regulations, 2011 CFR

2011-01-01

... the site-characterization activities at the site on public health and safety and the environment; a discussion of alternative activities related to site characterization that may be taken to avoid such impact; and an assessment of the regional and local impacts of locating a repository at the site. The draft...

10 CFR 960.3-2-3 - Recommendation of sites for characterization.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 4 2014-01-01 2014-01-01 false Recommendation of sites for characterization. 960.3-2-3 Section 960.3-2-3 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-2-3 Recommendation of sites...

10 CFR 960.3-2-3 - Recommendation of sites for characterization.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 4 2013-01-01 2013-01-01 false Recommendation of sites for characterization. 960.3-2-3 Section 960.3-2-3 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-2-3 Recommendation of sites...

10 CFR 960.3-2-3 - Recommendation of sites for characterization.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 4 2012-01-01 2012-01-01 false Recommendation of sites for characterization. 960.3-2-3 Section 960.3-2-3 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-2-3 Recommendation of sites...

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

EPA Science Inventory

At many of the sites where we have been asked to assist in site characterization, we have discovered severe discrepancies that new technologies may be able to prevent. This presentation is designed to illustrate these new technologies or unique uses of existing technology and the...

Tracing Cytoplasmic Ca2+ Ion and Water Access Points in the Ca2+-ATPase

PubMed Central

Musgaard, Maria; Thøgersen, Lea; Schiøtt, Birgit; Tajkhorshid, Emad

2012-01-01

Sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) transports two Ca2+ ions across the membrane of the sarco(endo)plasmic reticulum against the concentration gradient, harvesting the required energy by hydrolyzing one ATP molecule during each transport cycle. Although SERCA is one of the best structurally characterized membrane transporters, it is still largely unknown how the transported Ca2+ ions reach their transmembrane binding sites in SERCA from the cytoplasmic side. Here, we performed extended all-atom molecular dynamics simulations of SERCA. The calculated electrostatic potential of the protein reveals a putative mechanism by which cations may be attracted to and bind to the Ca2+-free state of the transporter. Additional molecular dynamics simulations performed on a Ca2+-bound state of SERCA reveal a water-filled pathway that may be used by the Ca2+ ions to reach their buried binding sites from the cytoplasm. Finally, several residues that are involved in attracting and guiding the cations toward the possible entry channel are identified. The results point to a single Ca2+ entry site close to the kinked part of the first transmembrane helix, in a region loaded with negatively charged residues. From this point, a water pathway outlines a putative Ca2+ translocation pathway toward the transmembrane ion-binding sites. PMID:22339863

Public Outreach of the South Texas Health Physic Society and Texas A&M University Nuclear Engineering Department

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

Berry, R. O.

In a cooperative effort of the members of the South Texas Chapter of the Heath Physics Society (STC-HPS) and the Texas A&M University Nuclear Engineering Department, great efforts have been made to reach out and provide educational opportunities to members of the general public, school age children, and specifically teachers. These efforts have taken the form of Science Teacher Workshops (STW), visits to schools all over the state of Texas, public forums, and many other educational arenas. A major motivational factor for these most recent efforts can be directly tied to the attempt of the State of Texas to sitemore » a low-level radioactive waste facility near Sierra Blanca in West Texas. When the State of Texas first proposed to site a low level radioactive waste site after the Low-Level Radioactive Waste Policy Act of 1980 was passed, many years of political struggle ensued. Finally, a site at Sierra Blanca in far West Texas was selected for study and characterization for a disposal site for waste generated in the Texas Compact states of Maine, Vermont and Texas. During this process, the outreach to and education of the local public became a paramount issue.« less

Characterization of the microbial community in a lotic environment to assess the effect of pollution on nitrifying and potentially pathogenic bacteria.

PubMed

Medeiros, J D; Araújo, L X; da Silva, V L; Diniz, C G; Cesar, D E; Del'Duca, A; Coelho, C M

2014-08-01

This study aimed to investigate microbes involved in the nitrogen cycle and potentially pathogenic bacteria from urban and rural sites of the São Pedro stream. Water samples were collected from two sites. A seasonal survey of bacterial abundance was conducted. The dissolved nutrient content was analysed. PCR and FISH analysis were performed to identify and quantify microbes involved in the nitrogen cycle and potentially pathogenic bacteria. The seasonal survey revealed that the bacterial abundance was similar along the year on the rural area but varied on the urban site. Higher concentration of dissolved nutrients in the urban area indicated a eutrophic system. Considering the nitrifying microbes, the genus Nitrobacter was found, especially in the urban area, and may act as the principal bacteria in converting nitrite into nitrate at this site. The molecular markers napA, amoA, and nfrA were more accumulated at the urban site, justifying the higher content of nutrients metabolised by these enzymes. Finally, high intensity of amplicons from Enterococcus, Streptococcus, Bacteroides/Prevotella/Porphyromonas, Salmonella, S. aureus, P. aeruginosa and the diarrheagenic lineages of E. coli were observed at the urban site. These results indicate a change in the structure of the microbial community imposed by anthrophic actions. The incidence of pathogenic bacteria in aquatic environments is of particular importance to public health, emphasising the need for sewage treatment to minimise the environmental impacts associated with urbanisation.

Rehabilitation of El Yahoudia dumping site, Tunisia.

PubMed

Zaïri, M; Ferchichi, M; Ismaïl, A; Jenayeh, M; Hammami, H

2004-01-01

As in all developing countries, cities in Tunisia face serious problems of environmental pollution caused mainly by the inadequate and inefficient final disposal of their generated solid wastes. The Tunisian government launched a development program including the construction of landfills in the main cities and the closure of the contaminated sites issued from solid wastes landrising practice. The project of the Henchir El Yahoudia landfill restoration is the first experience in this programme. It has been suggested to convert the site to a green park and to implement an ornamental plant nursery. The whole surface of the landfill is approximately 100 ha from which 30 ha have been already transformed to an urban recreational area and the remaining 70 ha have to be characterized for the project extension. A field investigation by boring was conducted in order to define the geological and the hydrogeological conditions, the vertical and horizontal wastes layer extension, content and degree of decomposition and the composition and quantities of leachate and landfill gas. Representative samples of waste, soil, groundwater and leachate were collected for laboratory analyses. Several of these borings were converted to piezometers to define the flow regime in the site. The results showed that the biogas (CH4, H2S, and CO2), leachate and waste, distribution in the site is mainly affected by the temporal variation of the site operating method. The underlying fissured clay layer facilitated leachate infiltration into the groundwater where high BOD, COD and nitrogen concentrations were registered.

U.S. Department of Energy's site screening, site selection, and initial characterization for storage of CO2 in deep geological formations

USGS Publications Warehouse

Rodosta, T.D.; Litynski, J.T.; Plasynski, S.I.; Hickman, S.; Frailey, S.; Myer, L.

2011-01-01

The U.S. Department of Energy (DOE) is the lead Federal agency for the development and deployment of carbon sequestration technologies. As part of its mission to facilitate technology transfer and develop guidelines from lessons learned, DOE is developing a series of best practice manuals (BPMs) for carbon capture and storage (CCS). The "Site Screening, Site Selection, and Initial Characterization for Storage of CO2 in Deep Geological Formations" BPM is a compilation of best practices and includes flowchart diagrams illustrating the general decision making process for Site Screening, Site Selection, and Initial Characterization. The BPM integrates the knowledge gained from various programmatic efforts, with particular emphasis on the Characterization Phase through pilot-scale CO2 injection testing of the Validation Phase of the Regional Carbon Sequestration Partnership (RCSP) Initiative. Key geologic and surface elements that suitable candidate storage sites should possess are identified, along with example Site Screening, Site Selection, and Initial Characterization protocols for large-scale geologic storage projects located across diverse geologic and regional settings. This manual has been written as a working document, establishing a framework and methodology for proper site selection for CO2 geologic storage. This will be useful for future CO2 emitters, transporters, and storage providers. It will also be of use in informing local, regional, state, and national governmental agencies of best practices in proper sequestration site selection. Furthermore, it will educate the inquisitive general public on options and processes for geologic CO2 storage. In addition to providing best practices, the manual presents a geologic storage resource and capacity classification system. The system provides a "standard" to communicate storage and capacity estimates, uncertainty and project development risk, data guidelines and analyses for adequate site characterization, and guidelines for reporting estimates within the classification based on each project's status. 

Involvement of two classes of binding sites in the interactions of cyclophilin B with peripheral blood T-lymphocytes.

PubMed

Denys, A; Allain, F; Carpentier, M; Spik, G

1998-12-15

Cyclophilin B (CyPB) is a cyclosporin A (CsA)-binding protein, mainly associated with the secretory pathway, and is released in biological fluids. We recently reported that CyPB specifically binds to T-lymphocytes and promotes enhanced incorporation of CsA. The interactions with cellular binding sites involved, at least in part, the specific N-terminal extension of the protein. In this study, we intended to specify further the nature of the CyPB-binding sites on peripheral blood T-lymphocytes. We first provide evidence that the CyPB binding to heparin-Sepharose is prevented by soluble sulphated glycosaminoglycans (GAG), raising the interesting possibility that such interactions may occur on the T-cell surface. We then characterized CyPB binding to T-cell surface GAG and found that these interactions involved the N-terminal extension of CyPB, but not its conserved CsA-binding domain. In addition, we determined the presence of a second CyPB binding site, which we termed a type I site, in contrast with type II for GAG interactions. The two binding sites exhibit a similar affinity but the expression of the type I site was 3-fold lower. The conclusion that CyPB binding to the type I site is distinct from the interactions with GAG was based on the findings that it was (1) resistant to NaCl wash and GAG-degrading enzyme treatments, (2) reduced in the presence of CsA or cyclophilin C, and (3) unmodified in the presence of either the N-terminal peptide of CyPB or protamine. Finally, we showed that the type I binding sites were involved in an endocytosis process, supporting the hypothesis that they may correspond to a functional receptor for CyPB.

iss012e16633

NASA Image and Video Library

2006-01-28

ISS012-E-16633 (28 Jan. 2006) --- Savannah River Site, South Carolina is featured in this image photographed by an Expedition 12 crew member on the International Space Station. Situated between the South Carolina piedmont and the Atlantic Ocean, the Savannah River Site is an important part of the US Department of Energy’s nuclear program. Construction of the site – originally called the Savannah River Plant – began in 1951 for the purpose of generating radioactive materials, primarily the hydrogen isotope tritium and plutonium-239, necessary for nuclear weapons production during the Cold War. A total of five nuclear reactors occupy the central portion of the site and operated throughout 1953-1992. Following the end of the Cold War in 1991 activities at the Savannah River Site are now focused on disposal of nuclear wastes, environmental cleanup of the site itself, and development of advanced remediation technologies. The Savannah River Site is located in the Sand Hills region of South Carolina and includes an area of 800 square kilometers (300 square miles). The southern half of the Site (building clusters with reflective white rooftops) is shown. The nearby Savannah River and its tributary creeks provided a ready source of water for the nuclear reactors; to this end, two artificial lakes (“L” Lake and Par Pond) were constructed. The meandering channel of the River and its floodplain, characterized by grey-brown sediments, extends from northwest to southeast across the left portion of the image. The proximity of the River, and the permeable nature of the geological materials under laying the site (sand, clay, gravel, and carbonate rocks), necessitate extensive and ongoing environmental monitoring and cleanup efforts to reduce potential contamination of local water sources. According to NASA scientists, final remediation of wastes posing threats to surface and groundwater is scheduled to occur by 2025.

Stennis Space Center Verification & Validation Capabilities

NASA Technical Reports Server (NTRS)

Pagnutti, Mary; Ryan, Robert E.; Holekamp, Kara; ONeal, Duane; Knowlton, Kelly; Ross, Kenton; Blonski, Slawomir

2005-01-01

Scientists within NASA s Applied Sciences Directorate have developed a well-characterized remote sensing Verification & Validation (V&V) site at the John C. Stennis Space Center (SSC). This site enables the in-flight characterization of satellite and airborne high spatial and moderate resolution remote sensing systems and their products. The smaller scale of the newer high resolution remote sensing systems allows scientists to characterize geometric, spatial, and radiometric data properties using a single V&V site. The targets and techniques used to characterize data from these newer systems can differ significantly from the techniques used to characterize data from the earlier, coarser spatial resolution systems. Scientists are also using the SSC V&V site to characterize thermal infrared systems and active lidar systems. SSC employs geodetic targets, edge targets, radiometric tarps, atmospheric monitoring equipment, and thermal calibration ponds to characterize remote sensing data products. The SSC Instrument Validation Lab is a key component of the V&V capability and is used to calibrate field instrumentation and to provide National Institute of Standards and Technology traceability. This poster presents a description of the SSC characterization capabilities and examples of calibration data.

History, rare, and multiple events of mechanical unfolding of repeat proteins

NASA Astrophysics Data System (ADS)

Sumbul, Fidan; Marchesi, Arin; Rico, Felix

2018-03-01

Mechanical unfolding of proteins consisting of repeat domains is an excellent tool to obtain large statistics. Force spectroscopy experiments using atomic force microscopy on proteins presenting multiple domains have revealed that unfolding forces depend on the number of folded domains (history) and have reported intermediate states and rare events. However, the common use of unspecific attachment approaches to pull the protein of interest holds important limitations to study unfolding history and may lead to discarding rare and multiple probing events due to the presence of unspecific adhesion and uncertainty on the pulling site. Site-specific methods that have recently emerged minimize this uncertainty and would be excellent tools to probe unfolding history and rare events. However, detailed characterization of these approaches is required to identify their advantages and limitations. Here, we characterize a site-specific binding approach based on the ultrastable complex dockerin/cohesin III revealing its advantages and limitations to assess the unfolding history and to investigate rare and multiple events during the unfolding of repeated domains. We show that this approach is more robust, reproducible, and provides larger statistics than conventional unspecific methods. We show that the method is optimal to reveal the history of unfolding from the very first domain and to detect rare events, while being more limited to assess intermediate states. Finally, we quantify the forces required to unfold two molecules pulled in parallel, difficult when using unspecific approaches. The proposed method represents a step forward toward more reproducible measurements to probe protein unfolding history and opens the door to systematic probing of rare and multiple molecule unfolding mechanisms.

Final Status Survey Report for Corrective Action Unit 117 - Pluto Disassembly Facility, Building 2201, Nevada National Security Site, Nevada

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

Jeremy Gwin and Douglas Frenette

This document contains the process knowledge, radiological data and subsequent statistical methodology and analysis to support approval for the radiological release of Corrective Action Unit (CAU) 117 – Pluto Disassembly Facility, Building 2201 located in Area 26 of the Nevada National Security Site (NNSS). Preparations for release of the building began in 2009 and followed the methodology described in the Multi-Agency Radiation Survey and Site Investigation Manual (MARSSIM). MARSSIM is the DOE approved process for release of Real Property (buildings and landmasses) to a set of established criteria or authorized limits. The pre-approved authorized limits for surface contamination values andmore » corresponding assumptions were established by DOE O 5400.5. The release criteria coincide with the acceptance criteria of the U10C landfill permit. The U10C landfill is the proposed location to dispose of the radiologically non-impacted, or “clean,” building rubble following demolition. However, other disposition options that include the building and/or waste remaining at the NNSS may be considered providing that the same release limits apply. The Final Status Survey was designed following MARSSIM guidance by reviewing historical documentation and radiological survey data. Following this review a formal radiological characterization survey was performed in two phases. The characterization revealed multiple areas of residual radioactivity above the release criteria. These locations were remediated (decontaminated) and then the surface activity was verified to be less than the release criteria. Once remediation efforts had been successfully completed, a Final Status Survey Plan (10-015, “Final Status Survey Plan for Corrective Action Unit 117 – Pluto Disassembly Facility, Building 2201”) was developed and implemented to complete the final step in the MARSSIM process, the Final Status Survey. The Final Status Survey Plan consisted of categorizing each individual room into one of three categories: Class 1, Class 2 or Class 3 (a fourth category is a “Non-Impacted Class” which in the case of Building 2201 only pertained to exterior surfaces of the building.) The majority of the rooms were determined to fall in the less restrictive Class 3 category, however, Rooms 102, 104, 106, and 107 were identified as containing Class 1 and 2 areas. Building 2201 was divided into “survey units” and surveyed following the requirements of the Final Status Survey Plan for each particular class. As each survey unit was completed and documented, the survey results were evaluated. Each sample (static measurement) with units of counts per minute (cpm) was corrected for the appropriate background and converted to a value with units of dpm/100 cm2. With a surface contamination value in the appropriate units, it was compared to the surface contamination limits, or in this case the derived concentration guideline level (DCGLw). The appropriate statistical test (sign test) was then performed. If the survey unit was statistically determined to be below the DCGLw, then the survey unit passed and the null hypothesis (that the survey unit is above limits) was rejected. If the survey unit was equal to or below the critical value in the sign test, the null hypothesis was not rejected. This process was performed for all survey units within Building 2201. A total of thirty-three “Class 1,” four “Class 2,” and one “Class 3” survey units were developed, surveyed, and evaluated. All survey units successfully passed the statistical test. Building 2201 meets the release criteria commensurate with the Waste Acceptance Criteria (for radiological purposes) of the U10C landfill permit residing within NNSS boundaries. Based on the thorough statistical sampling and scanning of the building’s interior, Building 2201 may be considered radiologically “clean,” or free of contamination.« less

Partial Updating of TSCA Inventory DataBase; Production and Site Reports; Final Rule

EPA Pesticide Factsheets

A partial updating of the TSCA inventory database. The final rule requires manufacturers and importers of certain chemical substances included on the TSCA Chemical Substances Inventory to report current data on the production volume, plant site, etc.

10 CFR 960.3-1-4-3 - Site recommendation for characterization.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 4 2013-01-01 2013-01-01 false Site recommendation for characterization. 960.3-1-4-3 Section 960.3-1-4-3 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-1-4-3 Site recommendation...

10 CFR 960.3-1-4-3 - Site recommendation for characterization.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 4 2014-01-01 2014-01-01 false Site recommendation for characterization. 960.3-1-4-3 Section 960.3-1-4-3 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-1-4-3 Site recommendation...

10 CFR 960.3-1-4-3 - Site recommendation for characterization.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 4 2012-01-01 2012-01-01 false Site recommendation for characterization. 960.3-1-4-3 Section 960.3-1-4-3 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-1-4-3 Site recommendation...

10 CFR 960.3-1-4-3 - Site recommendation for characterization.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 4 2010-01-01 2010-01-01 false Site recommendation for characterization. 960.3-1-4-3 Section 960.3-1-4-3 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-1-4-3 Site recommendation...

Characterization and Disposition of Legacy Low-Level Waste at the Y-12 National Security Complex - 12133

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

Tharp, Tim; Donnelly, Jim

2012-07-01

The Y-12 National Security Complex (Y-12) is concluding a multi-year program to characterize and dispose of all legacy low-level waste (LLW). The inventory of legacy waste at Y-12 has been reduced from over 3500 containers in Fiscal Year (FY) 2000 to 6 containers at the end of FY2011. In addition, the site recently eliminated the inventory of other low-level waste that is greater than 365 days old (i.e., >365-Day LLW), to be in full compliance with DOE Order 435.1. A consistent technical characterization approach emerged for both of these populations of backlogged waste: (1) compile existing historical data and processmore » knowledge and conduct interviews with site personnel; (2) inspect the containers and any tags, labels, or other markings to confirm or glean additional data; (3) with appropriate monitoring, open the container, visually inspect and photograph the contents while obtaining preliminary radiological surveys; (4) obtain gross weight and field non-destructive assay (NDA) data as needed; (5) use the non-public Oak Ridge Reservation Haul Road to ship the container to a local offsite vendor for waste sorting and segregation; (6) sort, drain, sample, and remove prohibited items; and (7) compile final data and prepare for shipment to disposal. After disposing of this backlog, the focus has now turned to avoiding the recurrence of this situation by maintaining low inventories of low-level waste and shortening the duration between waste generation and disposal. An enhanced waste tracking system and monthly metric charts are used to monitor and report progress to contractor and federal site office management. During the past 2 years, the average age of LLW onsite at Y-12 has decreased from more than 180 days to less than 60 days. (authors)« less

Measuring the Impact of Wildfire on Active Layer Thickness in a Discontinuous Permafrost region using Interferometric Synthetic Aperture Radar (InSAR)

NASA Astrophysics Data System (ADS)

Michaelides, R. J.; Schaefer, K. M.; Zebker, H. A.; Liu, L.; Chen, J.; Parsekian, A.

2017-12-01

In permafrost regions, the active layer is defined as the uppermost portion of the permafrost table that is subject to annual freeze/thaw cycles. The active layer plays a crucial role in surface processes, surface hydrology, and vegetation succession; furthermore, trapped methane, carbon dioxide, and other greenhouse gases in permafrost are released into the atmosphere as permafrost thaws. A detailed understanding of active layer dynamics is therefore critical towards understanding the interactions between permafrost surface processes, freeze/thaw cycles, and climate-especially in regions across the Arctic subject to long-term permafrost degradation. The Yukon-Kuskokwim (YK) delta in southwestern Alaska is a region of discontinuous permafrost characterized by surface lakes, wetlands, and thermokarst depressions. Furthermore, extensive wildfires have burned across the YK delta in 2006, 2007, and 2015, impacting vegetation cover, surface soil moisture, and the active layer. Using data from the ALOS PALSAR, ALOS-2 PALSAR-2, and Sentinel-1A/B space borne synthetic aperture radar (SAR) systems, we generate a series of interferograms over a study site in the YK delta spanning 2007-2011, and 2014-present. Using the ReSALT (Remotely-Sensed Active Layer Thickness) technique, we demonstrate that active layer can be characterized over most of the site from the relative interferometric phase difference due to ground subsidence and rebound associated with the seasonal active layer freeze/thaw cycle. Additionally, we show that this technique successfully discriminates between burned and unburned regions, and can resolve increases in active layer thickness in burned regions on the order of 10's of cms. We use the time series of interferograms to discuss permafrost recovery following wildfire burn, and compare our InSAR observations with GPR and active layer probing data from a 2016 summer field campaign to the study site. Finally, we compare the advantages and disadvantages of the ALOS, ALOS-2, and Sentinel systems for characterizing permafrost dynamics.

An improved segmentation method for defects inspection on steel roller surface

NASA Astrophysics Data System (ADS)

Xu, Jirui; Li, Xuekun; Cao, Yuzhong; Shi, Depeng; Yang, Jun; Jiang, Sheng; Rong, Yiming

2018-05-01

In the field of metal rolling, the quality of the steel roller's surface is significant for the final rolling products, e.g. metal sheets or foils. Besides the dimensional accuracy and surface roughness, the optical uniformity of the roller surface is also required for high quality rolling application. The typical optical defects of rollers after finish grinding include speckles, chatter marks, feed traces, and combination of all above. Unlike surface roughness, the optical defects can hardly be characterized by the topography or scanning electrical microscope measurement. Only the inspection by bared eyes of experienced engineers appears to be the effective manner for surface optical defects examination for large steel rollers. In this paper, an on-site machine vision system is designed to add on to the roller grinding machine to capture the surface image, and then an improved optical defects segmentation algorithm is developed based on the active contour model. Finally, experiments are carried out to verify the efficacy of the improved model.

Human herpes virus type 6 can cause skin lesions at the BCG inoculation site similar to Kawasaki Disease.

PubMed

Kakisaka, Yosuke; Ohara, Tomoichiro; Katayama, Saori; Suzuki, Tasuku; Sasai, Shu; Hino-Fukuyo, Naomi; Kure, Shigeo

2012-12-01

Kawasaki Disease (KD) is acute, febrile, multisystem vasculitis of early childhood, the detailed mechanism of which is still unclear. Skin symptoms occur in KD, such as edema of the hands and feet with subsequent desquamation and redness at the inoculation site of bacillus Calmette-Guerin (BCG). The change at the BCG inoculation site has been considered as a specific feature of KD, although its mechanism is not fully understood. We present an 11-month-old boy who developed fever with redness of the BCG site due to infection with human herpes virus type 6 (HHV6). At the age of 3 months, the patient received BCG. His fever remitted 7 days after the onset of skin redness, with sequential desquamation at the BCG site and extremities, which is not a common feature of HHV6 infection that typically lasts for 3 days. The final diagnosis was exanthema subitum. Characteristically, the HHV6 infection in our patient appeared to be associated with the invigoration of the T cell system, as represented by the elevated serum levels of soluble interleukin-2 receptor (3,490 U/ml vs. normal range 145-519 U/ml). This patient clearly showed redness and crusting at the BCG inoculation site, suggesting that HHV6 infection might cause skin changes similar to those of KD via an unknown mechanism. In addition, we suggest that the activation of the T cell system may account for the skin lesions in KD, characterized by redness and subsequent crusting of the BCG inoculation site and desquamation of the extremities.

Characterizing the diversity of coral reef habitats and fish communities found in a UNESCO World Heritage Site: the strategy developed for Lagoons of New Caledonia.

PubMed

Andréfouët, S; Wantiez, L

2010-01-01

Since 1972, the UNESCO "World Heritage Convention" offers an international canvas for conservation and management that targets areas of high cultural and environmental significance. To support the designation of areas within the 36.000 km(2) of New Caledonia coral reefs and lagoons as a World Heritage Site, the natural value and diversity of the proposed zones needed to be demonstrated. To exhaustively identify each configuration of shallow habitats, high resolution remote sensing images were used to select the sampling sites. This optimal scheme resulted in the selection of nearly 1300 sampling sites, and was then simplified to render its application realistic. In the final sampling plan, only the most common or the most remarkable coral zones were selected. Following this selection, in situ habitat and fish surveys were conducted in 2006-2008 in five large areas spanning a 600 km-long latitudinal gradient. Habitats were described using line-intercept transects in parallel with underwater visual census of indicator and commercial coral reef fish species. We report here on the results achieved in terms of: (i) the actual diversity of coral habitats captured by the remote sensing based sampling strategy, (ii) the different reef fish communities captured from the different sites, and (iii) how well they represent New Caledonia diversity. We discuss the possible generalization of this scheme to other sites, in the context of World Heritage Site selection and for other large-scale conservation planning activities. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Prediction of protein-protein interaction sites using electrostatic desolvation profiles.

PubMed

Fiorucci, Sébastien; Zacharias, Martin

2010-05-19

Protein-protein complex formation involves removal of water from the interface region. Surface regions with a small free energy penalty for water removal or desolvation may correspond to preferred interaction sites. A method to calculate the electrostatic free energy of placing a neutral low-dielectric probe at various protein surface positions has been designed and applied to characterize putative interaction sites. Based on solutions of the finite-difference Poisson equation, this method also includes long-range electrostatic contributions and the protein solvent boundary shape in contrast to accessible-surface-area-based solvation energies. Calculations on a large set of proteins indicate that in many cases (>90%), the known binding site overlaps with one of the six regions of lowest electrostatic desolvation penalty (overlap with the lowest desolvation region for 48% of proteins). Since the onset of electrostatic desolvation occurs even before direct protein-protein contact formation, it may help guide proteins toward the binding region in the final stage of complex formation. It is interesting that the probe desolvation properties associated with residue types were found to depend to some degree on whether the residue was outside of or part of a binding site. The probe desolvation penalty was on average smaller if the residue was part of a binding site compared to other surface locations. Applications to several antigen-antibody complexes demonstrated that the approach might be useful not only to predict protein interaction sites in general but to map potential antigenic epitopes on protein surfaces. Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

A Four Lake Latitudinal Comparison Along Coastal Southern to Central California: A Late-Holocene Perspective on the Western US Precipitation Dipole.

NASA Astrophysics Data System (ADS)

Kirby, M.; Nichols, K. E.; Ramezan, R.; Palermo, J. A.; Hiner, C.; Bonuso, N.; Patterson, W. P.; Silveira, E.

2016-12-01

One of the dominant hydroclimatic features of the western United States is the winter season precipitation dipole. The dipole is characterized by a N-S antiphased precipitation regime presently centered on 40° N latitude (Cayan et al., 1998; Dettinger et al., 1998; Wise, 2010). For example, the position of the dipole dictates where CA receives its winter precipitation; thus, it is critical to understand the dipole from a paleoperspective, which at present is poorly known. Here, we present four lake sites spanning 33°-36° N latitude along coastal CA. These sites include: Lake Elsinore, Crystal Lake, Zaca Lake, and Abbott Lake. All four of these sites are located south of the dipole's average historic (since 1950 AD) latitude. The predominant hydroclimatic indicator is similar for each basin (i.e., grain size); although, several other indicators are used for independent verification/assessment of the grain size interpretation. Notably, these lakes contain varied age control, which limits site-to-site correlation without consideration of age model dependence. Following a Bayesian framework, MCMC algorithms in conjuction with radiocarbon dating will be used to estimate timestamps of sediment deposits with a degree of statistical uncertainty. Samples from the posterior distribution will be used to correlate hydroclimatic features between sites. Included in this analysis are tree ring records from the region to assess the similarities and differences as recorded in annually resolved tree ring drought reconstructions and decadally resolved lake sediment hydroclimatic records. Finally, the four sites are assessed in the context of tropical and north Pacific SST forcing.

MX Siting Investigation. Prime Characterization Sites Central High Plains Candidate Siting Province.

DTIC Science & Technology

1979-02-15

information obtained from these studies , in combination with data obtained in the Screen- ing studies , has been used for geotechnical ranking (FN-TR-25). I...Plains Candi- date Siting Province (CSP), one of six provinces included in the geotechnical Characterization studies . The location of the sites within...remaining after Intermediate Screening were divided into CSPs based on similar geotechnical characteristics. Intermediate Screening studies (FN-TR-17

Optical Assembly and Characterization System for Nano-Photonics Research

DTIC Science & Technology

2016-03-01

Unlimited Final Report: Optical Assembly and Characterization System for Nano -Photonics Research The views, opinions and/or findings contained in this...reviewed journals: Final Report: Optical Assembly and Characterization System for Nano -Photonics Research Report Title With this equipment funding support...Assembly and Characterization System for Nano -Photonics Research PI: Prof. Weidong Zhou, University of Texas at Arlington (UTA) 500 S. Cooper St

Site Characterization in the Urban Area of Tijuana, B. C., Mexico by Means of: H/V Spectral Ratios, Spectral Analysis of Surface Waves, and Random Decrement Method

NASA Astrophysics Data System (ADS)

Tapia-Herrera, R.; Huerta-Lopez, C. I.; Martinez-Cruzado, J. A.

2009-05-01

Results of site characterization for an experimental site in the metropolitan area of Tijuana, B. C., Mexico are presented as part of the on-going research in which time series of earthquakes, ambient noise, and induced vibrations were processed with three different methods: H/V spectral ratios, Spectral Analysis of Surface Waves (SASW), and the Random Decrement Method, (RDM). Forward modeling using the wave propagation stiffness matrix method (Roësset and Kausel, 1981) was used to compute the theoretical SH/P, SV/P spectral ratios, and the experimental H/V spectral ratios were computed following the conventional concepts of Fourier analysis. The modeling/comparison between the theoretical and experimental H/V spectral ratios was carried out. For the SASW method the theoretical dispersion curves were also computed and compared with the experimental one, and finally the theoretical free vibration decay curve was compared with the experimental one obtained with the RDM. All three methods were tested with ambient noise, induced vibrations, and earthquake signals. Both experimental spectral ratios obtained with ambient noise as well as earthquake signals agree quite well with the theoretical spectral ratios, particularly at the fundamental vibration frequency of the recording site. Differences between the fundamental vibration frequencies are evident for sites located at alluvial fill (~0.6 Hz) and at sites located at conglomerate/sandstones fill (0.75 Hz). Shear wave velocities for the soft soil layers of the 4-layer discrete soil model ranges as low as 100 m/s and up to 280 m/s. The results with the SASW provided information that allows to identify low velocity layers, not seen before with the traditional seismic methods. The damping estimations obtained with the RDM are within the expected values, and the dominant frequency of the system also obtained with the RDM correlates within the range of plus-minus 20 % with the one obtained by means of the H/V spectral ratio.

Instability dynamics and breather formation in a horizontally shaken pendulum chain.

PubMed

Xu, Y; Alexander, T J; Sidhu, H; Kevrekidis, P G

2014-10-01

Inspired by the experimental results of Cuevas et al. [Phys. Rev. Lett. 102, 224101 (2009)], we consider theoretically the behavior of a chain of planar rigid pendulums suspended in a uniform gravitational field and subjected to a horizontal periodic driving force applied to the pendulum pivots. We characterize the motion of a single pendulum, finding bistability near the fundamental resonance and near the period-3 subharmonic resonance. We examine the development of modulational instability in a driven pendulum chain and find both a critical chain length and a critical frequency for the appearance of the instability. We study the breather solutions and show their connection to the single-pendulum dynamics and extend our analysis to consider multifrequency breathers connected to the period-3 periodic solution, showing also the possibility of stability in these breather states. Finally we examine the problem of breather generation and demonstrate a robust scheme for generation of on-site and off-site breathers.

Crystallographic and spectroscopic snapshots reveal a dehydrogenase in action

DOE PAGES

Huo, Lu; Davis, Ian; Liu, Fange; ...

2015-01-07

Aldehydes are ubiquitous intermediates in metabolic pathways and their innate reactivity can often make them quite unstable. There are several aldehydic intermediates in the metabolic pathway for tryptophan degradation that can decay into neuroactive compounds that have been associated with numerous neurological diseases. An enzyme of this pathway, 2-aminomuconate-6-semialdehyde dehydrogenase, is responsible for ‘disarming’ the final aldehydic intermediate. Here we show the crystal structures of a bacterial analogue enzyme in five catalytically relevant forms: resting state, one binary and two ternary complexes, and a covalent, thioacyl intermediate. We also report the crystal structures of a tetrahedral, thiohemiacetal intermediate, a thioacylmore » intermediate and an NAD +-bound complex from an active site mutant. These covalent intermediates are characterized by single-crystal and solution-state electronic absorption spectroscopy. The crystal structures reveal that the substrate undergoes an E/Z isomerization at the enzyme active site before an sp 3-to-sp 2 transition during enzyme-mediated oxidation.« less

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

Wolfe, M.; Norman, D.

Birds and mammals exposed to waterborne mercury (Hg) and methylmercury (MeHg) were collected and/or sampled at Clear Lake, California, USA, to field test the predictive wildlife criteria model developed for the Great Lakes Water Quality Initiative (GLWQI). Tissue samples collected from sampled animals were analyzed for Hg and organochlorine residues, and for selected physiologic parameters known to be affected by Hg. All mammalian organ tissues analyzed contained less than 12 ppm total Hg, wet weight. All avian tissue samples analyzed contained less than 3 ppm total Hg, wet weight. No evidence of Hg-associated health effects was found. Tissue Hg residuesmore » were compared with water, sediment, and animal food samples to characterize bioaccumulation of mercury in the Clear Lake food web. Total Hg bioaccumulation factors for the Clear Lake site closest to the Hg source were: TL-2: 11,100; TL-3: 31,200; TL-4, 190,000. The results support the final wildlife criterion and suggest that the GLWQI model, with site-specific modifications, is predictive for other Hg-bearing aquatic systems.« less

Constructing and Representing: a New Project for 3d Surveying of Yazilikaya - HATTUŠA

NASA Astrophysics Data System (ADS)

Repola, L.; Marazzi, M.; Tilia, S.

2017-05-01

Within the cooperation project between the University Suor Orsola Benincasa of Naples and the archaeological mission in Hattuša of the German Archaeological Institute of Istanbul, directed by Andreas Schachner, in agreement with the Turkish Ministry of Culture and Tourism, the workgroup of the University of Naples, has carried out, in September 2015, a first survey campaign of the whole rocky site of Yazılıkaya. The experimentation has been finalized at constructing a global 3D territorial and monumental model of the site, capable that is, through the application of differing scanning procedures, according to the different components (topography, rocky complex, the cultural spaces therein, complex of sculptural reliefs, inscriptions accompanying the divine representations), of virtually reproducing in detail, for safegaurd, exhibition and study purposes (in particular from an epigraphical and historic-artistic point of view) all the aspects characterizing the artefact and not completely visible to the naked eye today.

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

French, Jarrod B.; Ealick, Steven E.

The stereospecific oxidative degradation of uric acid to (S)-allantoin was recently shown to proceed via three enzymatic steps. The final conversion is a decarboxylation of the unstable intermediate 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) and is catalyzed by OHCU decarboxylase. Here we present the structures of Klebsiella pneumoniae OHCU decarboxylase in unliganded form and with bound allantoin. These structures provide evidence that ligand binding organizes the active site residues for catalysis. Modeling of the substrate and intermediates provides additional support for this hypothesis. In addition we characterize the steady state kinetics of this enzyme and report the first OHCU decarboxylase inhibitor, allopurinol, a structuralmore » isomer of hypoxanthine. This molecule is a competitive inhibitor of K. pneumoniae OHCU decarboxylase with a K{sub i} of 30 {+-} 2 {micro}m. Circular dichroism measurements confirm structural observations that this inhibitor disrupts the necessary organization of the active site. Our structural and biochemical studies also provide further insights into the mechanism of catalysis of OHCU decarboxylation.« less

Using synthetic bacterial enhancers to reveal a looping-based mechanism for quenching-like repression

PubMed Central

Brunwasser-Meirom, Michal; Pollak, Yaroslav; Goldberg, Sarah; Levy, Lior; Atar, Orna; Amit, Roee

2016-01-01

We explore a model for ‘quenching-like' repression by studying synthetic bacterial enhancers, each characterized by a different binding site architecture. To do so, we take a three-pronged approach: first, we compute the probability that a protein-bound dsDNA molecule will loop. Second, we use hundreds of synthetic enhancers to test the model's predictions in bacteria. Finally, we verify the mechanism bioinformatically in native genomes. Here we show that excluded volume effects generated by DNA-bound proteins can generate substantial quenching. Moreover, the type and extent of the regulatory effect depend strongly on the relative arrangement of the binding sites. The implications of these results are that enhancers should be insensitive to 10–11 bp insertions or deletions (INDELs) and sensitive to 5–6 bp INDELs. We test this prediction on 61 σ54-regulated qrr genes from the Vibrio genus and confirm the tolerance of these enhancers' sequences to the DNA's helical repeat. PMID:26832446

Using synthetic bacterial enhancers to reveal a looping-based mechanism for quenching-like repression.

PubMed

Brunwasser-Meirom, Michal; Pollak, Yaroslav; Goldberg, Sarah; Levy, Lior; Atar, Orna; Amit, Roee

2016-02-02

We explore a model for 'quenching-like' repression by studying synthetic bacterial enhancers, each characterized by a different binding site architecture. To do so, we take a three-pronged approach: first, we compute the probability that a protein-bound dsDNA molecule will loop. Second, we use hundreds of synthetic enhancers to test the model's predictions in bacteria. Finally, we verify the mechanism bioinformatically in native genomes. Here we show that excluded volume effects generated by DNA-bound proteins can generate substantial quenching. Moreover, the type and extent of the regulatory effect depend strongly on the relative arrangement of the binding sites. The implications of these results are that enhancers should be insensitive to 10-11 bp insertions or deletions (INDELs) and sensitive to 5-6 bp INDELs. We test this prediction on 61 σ(54)-regulated qrr genes from the Vibrio genus and confirm the tolerance of these enhancers' sequences to the DNA's helical repeat.

Evaluation of the pollution load discharged at an upstream industry--Egypt--and methods for its reduction.

PubMed

El-Dars, F M S E; Mohammed, H A; Farag, A B

2011-01-01

Oil exploration in Egypt is a major contributor to the national Gross Domestic Product (GDP). With 50-65% of the oil resources located in the Gulf of Suez (GoS) region, the impact of such activity upon the region's water environment and its quality cannot be overlooked because of the volume of effluent generated. The objective of this study (September 2000-September 2001) was to assess the impact of a 650,000 barrels/day (bl/d) (100,000 m3/d) effluent arising from a major oil exploration site located south of GoS upon the local water environment. Another objective was to identify the pollutant contents amenable for reduction relative to the new Egyptian regulations. This was achieved by the characterization of the main contributing streams and the identification of the final effluent parameter constraints relative to the type of injection waters used. Subsequent investigations for the reduction of these contents were conducted on site and the results obtained are reviewed herewith.

Analytical methods for characterization of explosives-contaminated sites on U.S. Army installations

NASA Astrophysics Data System (ADS)

Jenkins, Thomas F.; Walsh, Marianne E.; Thorne, Philip G.

1995-10-01

The U.S. Army manufactures munitions at facilities throughout the United States. Many of these facilities are contaminated with residues of explosives from production, disposal of off- specification, and out-of-data munitions. The first step in remediating these sites is careful characterization. Currently sites are being characterized using a combination of on-site field screening and off-site laboratory analysis. Most of the contamination is associated with TNT (2,4,6-trinitrotoluene) and RDX (hexahydro-1,3,5-tri-nitro-1,3,5-triazine) and their manufacturing impurities and environmental transformation products. Both colorimetric and enzyme immunoassay-based field screening methods have been used successfully for on-site characterization. These methods have similar detection capabilities but differ in their selectivity. Although field screening is very cost-effective, laboratory analysis is still required to fully characterize a site. Laboratory analysis for explosives residues in the United States is generally conducted using high-performance liquid chromatography equipped with a UV detector. Air-dried soils are extracted with acetonitrile in an ultrasonic bath. Water is analyzed directly if detection limits in the range of 10 - 20 (mu) g/L are acceptable, or preconcentrated using either salting-out solvent extraction with acetonitrile or solid phase extraction.

Site Characterization and Monitoring Technical Support Center FY16 Report

EPA Science Inventory

SCMTSC’s primary goal is to provide technical assistance to regional programs on complex hazardous waste site characterization issues. This annual report illustrates the range and extent of projects that SCMTSC supported in FY 2016. Our principal audiences are site project manage...

Stennis Space Center Verification & Validation Capabilities

NASA Technical Reports Server (NTRS)

Pagnutti, Mary; Ryan, Robert E.; Holekamp, Kara; O'Neal, Duane; Knowlton, Kelly; Ross, Kenton; Blonski, Slawomir

2007-01-01

Scientists within NASA#s Applied Research & Technology Project Office (formerly the Applied Sciences Directorate) have developed a well-characterized remote sensing Verification & Validation (V&V) site at the John C. Stennis Space Center (SSC). This site enables the in-flight characterization of satellite and airborne high spatial resolution remote sensing systems and their products. The smaller scale of the newer high resolution remote sensing systems allows scientists to characterize geometric, spatial, and radiometric data properties using a single V&V site. The targets and techniques used to characterize data from these newer systems can differ significantly from the techniques used to characterize data from the earlier, coarser spatial resolution systems. Scientists have used the SSC V&V site to characterize thermal infrared systems. Enhancements are being considered to characterize active lidar systems. SSC employs geodetic targets, edge targets, radiometric tarps, atmospheric monitoring equipment, and thermal calibration ponds to characterize remote sensing data products. Similar techniques are used to characterize moderate spatial resolution sensing systems at selected nearby locations. The SSC Instrument Validation Lab is a key component of the V&V capability and is used to calibrate field instrumentation and to provide National Institute of Standards and Technology traceability. This poster presents a description of the SSC characterization capabilities and examples of calibration data.

Computational Optimization and Characterization of Molecularly Imprinted Polymers

NASA Astrophysics Data System (ADS)

Terracina, Jacob J.

Molecularly imprinted polymers (MIPs) are a class of materials containing sites capable of selectively binding to the imprinted target molecule. Computational chemistry techniques were used to study the effect of different fabrication parameters (the monomer-to-target ratios, pre-polymerization solvent, temperature, and pH) on the formation of the MIP binding sites. Imprinted binding sites were built in silico for the purposes of better characterizing the receptor - ligand interactions. Chiefly, the sites were characterized with respect to their selectivities and the heterogeneity between sites. First, a series of two-step molecular mechanics (MM) and quantum mechanics (QM) computational optimizations of monomer -- target systems was used to determine optimal monomer-to-target ratios for the MIPs. Imidazole- and xanthine-derived target molecules were studied. The investigation included both small-scale models (one-target) and larger scale models (five-targets). The optimal ratios differed between the small and larger scales. For the larger models containing multiple targets, binding-site surface area analysis was used to evaluate the heterogeneity of the sites. The more fully surrounded sites had greater binding energies. Molecular docking was then used to measure the selectivities of the QM-optimized binding sites by comparing the binding energies of the imprinted target to that of a structural analogue. Selectivity was also shown to improve as binding sites become more fully encased by the monomers. For internal sites, docking consistently showed selectivity favoring the molecules that had been imprinted via QM geometry optimizations. The computationally imprinted sites were shown to exhibit size-, shape-, and polarity-based selectivity. This represented a novel approach to investigate the selectivity and heterogeneity of imprinted polymer binding sites, by applying the rapid orientation screening of MM docking to the highly accurate QM-optimized geometries. Next, we sought to computationally construct and investigate binding sites for their enantioselectivity. Again, a two-step MM [special characters removed] QM optimization scheme was used to "computationally imprint" chiral molecules. Using docking techniques, the imprinted binding sites were shown to exhibit an enantioselective preference for the imprinted molecule over its enantiomer. Docking of structurally similar chiral molecules showed that the sites computationally imprinted with R- or S-tBOC-tyrosine were able to differentiate between R- and S-forms of other tyrosine derivatives. The cross-enantioselectivity did not hold for chiral molecules that did not share the tyrosine H-bonding functional group orientations. Further analysis of the individual monomer - target interactions within the binding site led us to conclude that H-bonding functional groups that are located immediately next to the target's chiral center, and therefore spatially fixed relative to the chiral center, will have a stronger contribution to the enantioselectivity of the site than those groups separated from the chiral center by two or more rotatable bonds. These models were the first computationally imprinted binding sites to exhibit this enantioselective preference for the imprinted target molecules. Finally, molecular dynamics (MD) was used to quantify H-bonding interactions between target molecules, monomers, and solvents representative of the pre-polymerization matrix. It was found that both target dimerization and solvent interference decrease the number of monomer - target H-bonds present. Systems were optimized via simulated annealing to create binding sites that were then subjected to molecular docking analysis. Docking showed that the presence of solvent had a detrimental effect on the sensitivity and selectivity of the sites, and that solvents with more H-bonding capabilities were more disruptive to the binding properties of the site. Dynamic simulations also showed that increasing the temperature of the solution can significantly decrease the number of H-bonds formed between the targets and monomers. It is believed that the monomer - target complexes formed within the pre-polymerization matrix are translated into the selective binding cavities formed during polymerization. Elucidating the nature of these interactions in silico improves our understanding of MIPs, ultimately allowing for more optimized sensing materials.

Accumulation of dechlorination daughter products: A valid metric of chloroethene biodegradation

USGS Publications Warehouse

Bradley, Paul M.; Chapelle, Frank H.

2007-01-01

In situ reductive dechlorination of perchloroethene (PCE) and trichloroethene (TCE) generates characteristic chlorinated (cis-dichloroethene [cis-DCE] and vinyl chloride [VC]) and nonchlorinated (ethene and ethane) products. The accumulation of these daughter products is commonly used as a metric for ongoing biodegradation at field sites. However, this interpretation assumes that reductive dechlorination is the only chloroethene degradation process of any significance in situ and that the characteristic daughter products of chloroethene reductive dechlorination persist in the environment. Laboratory microcosms, prepared with aquifer and surface-water sediments from hydrologically diverse sites throughout the United States and amended with [1,2-14C] TCE, [1,2-14C] DCE, [1,2-14C] DCA, or [1,2-14C] VC, demonstrated widely variable patterns of intermediate and final product accumulation. In predominantly methanogenic sediment treatments, accumulation of 14C-DCE, 14C-VC, 14C-ethene, and 14C-ethane predominated. Treatments characterized by significant Fe(III) and/or Mn(IV) reduction, on the other hand, demonstrated substantial, and in some cases exclusive, accumulation of 14CO2and 14CH4. These results suggest that relying on the accumulation of cis-DCE, VC, ethene, and ethane may substantially underestimate overall chloroethene biodegradation at many sites.

Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe[superscript 2+] metal-ion preference

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

Jackson, Colin J.; Hadler, Kieran S.; Carr, Paul D.

2011-09-28

The structure of a malonate-bound form of the glycerophosphodiesterase from Enterobacter aerogenes, GpdQ, has been refined at a resolution of 2.2 {angstrom} to a final R factor of 17.1%. The structure was originally solved to 2.9 {angstrom} resolution using SAD phases from Zn{sup 2+} metal ions introduced into the active site of the apoenzyme [Jackson et al. (2007), J. Mol. Biol. 367, 1047-1062]. However, the 2.9 {angstrom} resolution was insufficient to discern significant details of the architecture of the binuclear metal centre that constitutes the active site. Furthermore, kinetic analysis revealed that the enzyme lost a significant amount of activitymore » in the presence of Zn2+, suggesting that it is unlikely to be a catalytically relevant metal ion. In this communication, a higher resolution structure of GpdQ is presented in which malonate is visibly coordinated in the active site and analysis of the native metal-ion preference is presented using atomic absorption spectroscopy and anomalous scattering. Catalytic implications of the structure and its Fe{sup 2+} metal-ion preference are discussed.« less

Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe[supscript 2+] metal-ion preference

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

Jackson, Colin J.; Hadler, Kieran S.; Carr, Paul D.

2010-09-20

The structure of a malonate-bound form of the glycerophosphodiesterase from Enterobacter aerogenes, GpdQ, has been refined at a resolution of 2.2 {angstrom} to a final R factor of 17.1%. The structure was originally solved to 2.9 {angstrom} resolution using SAD phases from Zn{sup 2+} metal ions introduced into the active site of the apoenzyme [Jackson et al. (2007), J. Mol. Biol. 367, 1047-1062]. However, the 2.9 {angstrom} resolution was insufficient to discern significant details of the architecture of the binuclear metal centre that constitutes the active site. Furthermore, kinetic analysis revealed that the enzyme lost a significant amount of activitymore » in the presence of Zn{sup 2+}, suggesting that it is unlikely to be a catalytically relevant metal ion. In this communication, a higher resolution structure of GpdQ is presented in which malonate is visibly coordinated in the active site and analysis of the native metal-ion preference is presented using atomic absorption spectroscopy and anomalous scattering. Catalytic implications of the structure and its Fe{sup 2+} metal-ion preference are discussed.« less

Ka-Band Atmospheric Phase Stability Measurements in Goldstone, CA; White Sands, NM; and Guam

NASA Technical Reports Server (NTRS)

Zemba, Michael J.; Morse, Jacquelynne Rose; Nessel, James A.

2014-01-01

As spacecraft communication links are driven to higher frequencies (e.g. Ka-band) both by spectrum congestion and the appeal of higher data rates, the propagation phenomena at these frequencies must be well characterized for effective system design. In particular, the phase stability of a site at a given frequency will govern whether or not the site is a practical location for an antenna array, particularly if uplink capabilities are desired. Propagation studies to characterize such phenomena must be done on a site-by-site basis due to the wide variety of climates and weather conditions at each ground terminal. Accordingly, in order to statistically characterize the atmospheric effects on Ka-Band links, site test interferometers (STIs) have been deployed at three of NASA's operational sites to directly measure each site's tropospheric phase stability. Using three years of results from these experiments, this paper will statistically characterize the simultaneous atmospheric phase noise measurements recorded by the STIs deployed at the following ground station sites: the Goldstone Deep Space Communications Complex near Barstow, CA; the White Sands Ground Terminal near Las Cruces, NM; and the Guam Remote Ground Terminal on the island of Guam.

Environmental waste site characterization utilizing aerial photographs and satellite imagery: Three sites in New Mexico, USA

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

Van Eeckhout, E.; Pope, P.; Becker, N.

1996-04-01

The proper handling and characterization of past hazardous waste sites is becoming more and more important as world population extends into areas previously deemed undesirable. Historical photographs, past records, current aerial satellite imagery can play an important role in characterizing these sites. These data provide clear insight into defining problem areas which can be surface samples for further detail. Three such areas are discussed in this paper: (1) nuclear wastes buried in trenches at Los Alamos National Laboratory, (2) surface dumping at one site at Los Alamos National Laboratory, and (3) the historical development of a municipal landfill near Lasmore » Cruces, New Mexico.« less

CO{sub 2} Sequestration Capacity and Associated Aspects of the Most Promising Geologic Formations in the Rocky Mountain Region: Local-Scale Analyses

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

Laes, Denise; Eisinger, Chris; Morgan, Craig

2013-07-30

The purpose of this report is to provide a summary of individual local-­scale CCS site characterization studies conducted in Colorado, New Mexico and Utah. These site-­ specific characterization analyses were performed as part of the “Characterization of Most Promising Sequestration Formations in the Rocky Mountain Region” (RMCCS) project. The primary objective of these local-­scale analyses is to provide a basis for regional-­scale characterization efforts within each state. Specifically, limits on time and funding will typically inhibit CCS projects from conducting high-­ resolution characterization of a state-­sized region, but smaller (< 10,000 km{sup 2}) site analyses are usually possible, and suchmore » can provide insight regarding limiting factors for the regional-­scale geology. For the RMCCS project, the outcomes of these local-­scale studies provide a starting point for future local-­scale site characterization efforts in the Rocky Mountain region.« less

Technical support for geopressured-geothermal activities in Louisiana. Final geological report, 1 November 1981-31 October 1982

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

Pilger, R.H.

1984-06-25

This report contains the component Site-Specific Studies-Geophysics, Diagenesis, Geochemistry. Work for Site-Specific Studies is finished, and the results presented in this report are final. Individual studies have been entered separately into the data base. (ACR)

Multiscale Structure of UXO Site Characterization: Spatial Estimation and Uncertainty Quantification

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

Ostrouchov, George; Doll, William E.; Beard, Les P.

2009-01-01

Unexploded ordnance (UXO) site characterization must consider both how the contamination is generated and how we observe that contamination. Within the generation and observation processes, dependence structures can be exploited at multiple scales. We describe a conceptual site characterization process, the dependence structures available at several scales, and consider their statistical estimation aspects. It is evident that most of the statistical methods that are needed to address the estimation problems are known but their application-specific implementation may not be available. We demonstrate estimation at one scale and propose a representation for site contamination intensity that takes full account of uncertainty,more » is flexible enough to answer regulatory requirements, and is a practical tool for managing detailed spatial site characterization and remediation. The representation is based on point process spatial estimation methods that require modern computational resources for practical application. These methods have provisions for including prior and covariate information.« less

Exposure to fall hazards and safety climate in the aircraft maintenance industry.

PubMed

Neitzel, Richard L; Seixas, Noah S; Harris, Michael J; Camp, Janice

2008-01-01

Falls represent a significant occupational hazard, particularly in industries with dynamic work environments. This paper describes rates of noncompliance with fall hazard prevention requirements, perceived safety climate and worker knowledge and beliefs, and the association between fall exposure and safety climate measures in commercial aircraft maintenance activities. Walkthrough observations were conducted on aircraft mechanics at two participating facilities (Sites A and B) to ascertain the degree of noncompliance. Mechanics at each site completed questionnaires concerning fall hazard knowledge, personal safety beliefs, and safety climate. Questionnaire results were summarized into safety climate and belief scores by workgroup and site. Noncompliance rates observed during walkthroughs were compared to the climate-belief scores, and were expected to be inversely associated. Important differences were seen in fall safety performance between the sites. The study provided a characterization of aircraft maintenance fall hazards, and also demonstrated the effectiveness of an objective hazard assessment methodology. Noncompliance varied by height, equipment used, location of work on the aircraft, shift, and by safety system. Although the expected relationship between safety climate and noncompliance was seen for site-average climate scores, workgroups with higher safety climate scores had greater observed noncompliance within Site A. Overall, use of engineered safety systems had a significant impact on working safely, while safety beliefs and climate also contributed, though inconsistently. The results of this study indicate that safety systems are very important in reducing noncompliance with fall protection requirements in aircraft maintenance facilities. Site-level fall safety compliance was found to be related to safety climate, although an unexpected relationship between compliance and safety climate was seen at the workgroup level within site. Finally, observed fall safety compliance was found to differ from self-reported compliance.

Final Report Feasibility Study for the California Wave Energy Test Center (CalWavesm) - Volume #2 - Appendices #16-17

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

Dooher, Brendan; Toman, William I.; Davy, Doug M.

The California Wave Energy Test Center (CalWave) Feasibility Study project was funded over multiple phases by the Department of Energy to perform an interdisciplinary feasibility assessment to analyze the engineering, permitting, and stakeholder requirements to establish an open water, fully energetic, grid connected, wave energy test center off the coast of California for the purposes of advancing U.S. wave energy research, development, and testing capabilities. Work under this grant included wave energy resource characterization, grid impact and interconnection requirements, port infrastructure and maritime industry capability/suitability to accommodate the industry at research, demonstration and commercial scale, and macro and micro sitingmore » considerations. CalWave Phase I performed a macro-siting and down-selection process focusing on two potential test sites in California: Humboldt Bay and Vandenberg Air Force Base. This work resulted in the Vandenberg Air Force Base site being chosen as the most favorable site based on a peer reviewed criteria matrix. CalWave Phase II focused on four siting location alternatives along the Vandenberg Air Force Base coastline and culminated with a final siting down-selection. Key outcomes from this work include completion of preliminary engineering and systems integration work, a robust turnkey cost estimate, shoreside and subsea hazards assessment, storm wave analysis, lessons learned reports from several maritime disciplines, test center benchmarking as compared to existing international test sites, analysis of existing applicable environmental literature, the completion of a preliminary regulatory, permitting and licensing roadmap, robust interaction and engagement with state and federal regulatory agency personnel and local stakeholders, and the population of a Draft Federal Energy Regulatory Commission (FERC) Preliminary Application Document (PAD). Analysis of existing offshore oil and gas infrastructure was also performed to assess the potential value and re-use scenarios of offshore platform infrastructure and associated subsea power cables and shoreside substations. The CalWave project team was well balanced and was comprised of experts from industry, academia, state and federal regulatory agencies. The result of the CalWave feasibility study finds that the CalWave Test Center has the potential to provide the most viable path to commercialization for wave energy in the United States.« less

FATE AND TRANSPORT MODELING OF CONTAMINANTS OF CONCERN FROM A CAFO IN AN AGRICULTURAL WATERSHED

EPA Science Inventory

The groundwater flow and transport modeling effort will require hydrogeological site characterization and the development of a conceptual flow model for the site. Site characterization will involve an assessment of both the surface and subsurface and be accomplished through joint...

Airborne and Ground-Based Optical Characterization of Legacy Underground Nuclear Test Sites

NASA Astrophysics Data System (ADS)

Vigil, S.; Craven, J.; Anderson, D.; Dzur, R.; Schultz-Fellenz, E. S.; Sussman, A. J.

2015-12-01

Detecting, locating, and characterizing suspected underground nuclear test sites is a U.S. security priority. Currently, global underground nuclear explosion monitoring relies on seismic and infrasound sensor networks to provide rapid initial detection of potential underground nuclear tests. While seismic and infrasound might be able to generally locate potential underground nuclear tests, additional sensing methods might be required to further pinpoint test site locations. Optical remote sensing is a robust approach for site location and characterization due to the ability it provides to search large areas relatively quickly, resolve surface features in fine detail, and perform these tasks non-intrusively. Optical remote sensing provides both cultural and surface geological information about a site, for example, operational infrastructure, surface fractures. Surface geological information, when combined with known or estimated subsurface geologic information, could provide clues concerning test parameters. We have characterized two legacy nuclear test sites on the Nevada National Security Site (NNSS), U20ak and U20az using helicopter-, ground- and unmanned aerial system-based RGB imagery and light detection and ranging (lidar) systems. The multi-faceted information garnered from these different sensing modalities has allowed us to build a knowledge base of how a nuclear test site might look when sensed remotely, and the standoff distances required to resolve important site characteristics.

Measurement Sets and Sites Commonly Used for High Spatial Resolution Image Product Characterization

NASA Technical Reports Server (NTRS)

Pagnutti, Mary

2006-01-01

Scientists within NASA's Applied Sciences Directorate have developed a well-characterized remote sensing Verification & Validation (V&V) site at the John C. Stennis Space Center (SSC). This site has enabled the in-flight characterization of satellite high spatial resolution remote sensing system products form Space Imaging IKONOS, Digital Globe QuickBird, and ORBIMAGE OrbView, as well as advanced multispectral airborne digital camera products. SSC utilizes engineered geodetic targets, edge targets, radiometric tarps, atmospheric monitoring equipment and their Instrument Validation Laboratory to characterize high spatial resolution remote sensing data products. This presentation describes the SSC characterization capabilities and techniques in the visible through near infrared spectrum and examples of calibration results.

Computer-based prediction of mitochondria-targeting peptides.

PubMed

Martelli, Pier Luigi; Savojardo, Castrense; Fariselli, Piero; Tasco, Gianluca; Casadio, Rita

2015-01-01

Computational methods are invaluable when protein sequences, directly derived from genomic data, need functional and structural annotation. Subcellular localization is a feature necessary for understanding the protein role and the compartment where the mature protein is active and very difficult to characterize experimentally. Mitochondrial proteins encoded on the cytosolic ribosomes carry specific patterns in the precursor sequence from where it is possible to recognize a peptide targeting the protein to its final destination. Here we discuss to which extent it is feasible to develop computational methods for detecting mitochondrial targeting peptides in the precursor sequences and benchmark our and other methods on the human mitochondrial proteins endowed with experimentally characterized targeting peptides. Furthermore, we illustrate our newly implemented web server and its usage on the whole human proteome in order to infer mitochondrial targeting peptides, their cleavage sites, and whether the targeting peptide regions contain or not arginine-rich recurrent motifs. By this, we add some other 2,800 human proteins to the 124 ones already experimentally annotated with a mitochondrial targeting peptide.

Molecular Imprinting of Silica Nanoparticle Surfaces via Reversible Addition-Fragmentation Polymerization for Optical Biosensing Applications

NASA Astrophysics Data System (ADS)

Oluz, Zehra; Nayab, Sana; Kursun, Talya Tugana; Caykara, Tuncer; Yameen, Basit; Duran, Hatice

Azo initiator modified surface of silica nanoparticles were coated via reversible addition-fragmentation polymerization (RAFT) of methacrylic acid and ethylene glycol dimethacrylate using 2-phenylprop 2-yl dithobenzoate as chain transfer agent. Using L-phenylalanine anilide as template during polymerization led molecularly imprinted nanoparticles. RAFT polymerization offers an efficient control of grafting process, while molecularly imprinted polymers shows enhanced capacity as sensor. L-phenylalanine anilide imprinted silica particles were characterized by X-Ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM). Performances of the particles were followed by surface plasmon resonance spectroscopy (SPR) after coating the final product on gold deposited glass substrate against four different analogous of analyte molecules: D-henylalanine anilide, L-tyrosine, L-tryptophan and L-phenylalanine. Characterizations indicated that silica particles coated with polymer layer do contain binding sites for L-phenylalanine anilide, and are highly selective for the molecule of interest. This project was supported by TUBITAK (Project No:112M804).

Impact of Distributed Energy Resources on the Reliability of Critical Telecommunications Facilities: Preprint

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

Robinson, D. G.; Arent, D. J.; Johnson, L.

2006-06-01

This paper documents a probabilistic risk assessment of existing and alternative power supply systems at a large telecommunications office. The analysis characterizes the increase in the reliability of power supply through the use of two alternative power configurations. Failures in the power systems supporting major telecommunications service nodes are a main contributor to significant telecommunications outages. A logical approach to improving the robustness of telecommunication facilities is to increase the depth and breadth of technologies available to restore power during power outages. Distributed energy resources such as fuel cells and gas turbines could provide additional on-site electric power sources tomore » provide backup power, if batteries and diesel generators fail. The analysis is based on a hierarchical Bayesian approach and focuses on the failure probability associated with each of three possible facility configurations, along with assessment of the uncertainty or confidence level in the probability of failure. A risk-based characterization of final best configuration is presented.« less

Evolution of the Corrosion Morphology on AZ31B Tracked Electrochemically and by In Situ Microscopy in Chloride-Containing Media

NASA Astrophysics Data System (ADS)

Melia, M. A.; Cain, T. W.; Briglia, B. F.; Scully, J. R.; Fitz-Gerald, J. M.

2017-11-01

The evolution of open-circuit corrosion morphology as a function of immersion time for Mg alloy AZ31B in 0.6-M NaCl solution was investigated. Real-time optical microscopy accompanied by simultaneous electrochemical characterization was used to characterize the filiform corrosion (FFC) of AZ31B. Specifically, the behavior of propagating corrosion filaments on the metal surface was observed, and correlations among polarization resistance, filament propagation rates, open-circuit potential, and active coverage of local corrosion sites were revealed. Three distinct stages of corrosion were observed in 0.6-M NaCl. An initial passive region, during which a slow potential rise occurred (termed stage I), a second FFC region (termed stage II) with shallow penetrating, distinct filaments, and a final FFC region (termed stage III) with deeper penetrating filaments, aligned to form a linear front. The electrochemical properties of each stage are discussed, providing insights into the penetration rates and corrosion model.

Site Characterization for a Deep Borehole Field Test

NASA Astrophysics Data System (ADS)

Kuhlman, K. L.; Hardin, E. L.; Freeze, G. A.; Sassani, D.; Brady, P. V.

2015-12-01

The US Department of Energy Office of Nuclear Energy is at the beginning of 5-year Deep Borehole Field Test (DBFT) to investigate the feasibility of constructing and characterizing two boreholes in crystalline basement rock to a depth of 5 km (16,400 ft). The concept of deep borehole disposal for radioactive waste has some advantages over mined repositories, including incremental construction and loading, the enhanced natural barriers provided by deep continental crystalline basement, and reduced site characterization. Site characterization efforts need to determine an eligible site that does not have the following disqualifying characteristics: greater than 2 km to crystalline basement, upward vertical fluid potential gradients, presence of economically exploitable natural resources, presence of high permeability connection to the shallow subsurface, and significant probability of future seismic or volcanic activity. Site characterization activities for the DBFT will include geomechanical (i.e., rock in situ stress state, and fluid pressure), geological (i.e., rock and fracture infill lithology), hydrological (i.e., quantity of fluid, fluid convection properties, and solute transport mechanisms), and geochemical (i.e., rock-water interaction and natural tracers) aspects. Both direct (i.e., sampling and in situ testing) and indirect (i.e., borehole geophysical) methods are planned for efficient and effective characterization of these site aspects and physical processes. Borehole-based characterization will be used to determine the variability of system state (i.e., stress, pressure, temperature, and chemistry) with depth, and interpretation of material and system parameters relevant to numerical site simulation. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Evaluating Ecological Risk to Invertebrate Receptors from PAHs in Sediments at Hazardous Waste Sites (Final Report)

EPA Science Inventory

EPA's Ecological Risk Assessment Support Center (ERASC) announced the release of the final report, Evaluating Ecological Risk to Invertebrate Receptors from PAHs in Sediments at Hazardous Waste Sites. The report provides an overview of an approach for assessing risk to ...

Presence of pro-tobacco messages on the Web.

PubMed

Hong, Traci; Cody, Michael J

2002-01-01

Ignored in the finalized Master Settlement Agreement (National Association of Attorneys General, 1998), the unmonitored, unregulated World Wide Web (Web) can operate as a major vehicle for delivering pro-tobacco messages, images, and products to millions of young consumers. A content analysis of 318 randomly sampled pro-tobacco Web sites revealed that tobacco has a pervasive presence on the Web, especially on e-commerce sites and sites featuring hobbies, recreation, and "fetishes." Products can be ordered online on nearly 50% of the sites, but only 23% of the sites included underage verification. Further, only 11% of these sites contain health warnings. Instead, pro-tobacco sites frequently associate smoking with "glamorous" and "alternative" lifestyles, and with images of young males and young (thin, attractive) females. Finally, many of the Web sites offered interactive site features that are potentially appealing to young Web users. Recommendations for future research and counterstrategies are discussed.

Isolation and characterization of NBS–LRR resistance gene analogues from mango

PubMed Central

Lei, Xintao; Yao, Quansheng; Xu, Xuerong; Liu, Yang

2014-01-01

The nucleotide-binding site (NBS)–leucine-rich repeat (LRR) gene family is a class of R genes in plants. NBS genes play a very important role in disease defence. To further study the variation and homology of mango NBS–LRR genes, 16 resistance gene analogues (RGAs) (GenBank accession number HM446507-22) were isolated from the polymerase chain reaction fragments and sequenced by using two degenerate primer sets. The total nucleotide diversity index Pi was 0.362, and 236 variation sites were found among 16 RGAs. The degree of homology between the RGAs varied from 44.4% to 98.5%. Sixteen RGAs could be translated into amino sequences. The high level of this homology in the protein sequences of the P-loop and kinase-2 of the NBS domain between the RGAs isolated in this study and previously characterized R genes indicated that these cloned sequences belonged to the NBS–LRR gene family. Moreover, these 16 RGAs could be classified into the non-TIR–NBS–LRR gene family because only tryptophan (W) could be claimed as the final residual of the kinase-2 domain of all RGAs isolated here. From our results, we concluded that our mango NBS–LRR genes possessed a high level of variation from the mango genome, which may allow mango to recognize many different pathogenic virulence factors. PMID:26740762

Techniques for Large-Scale Bacterial Genome Manipulation and Characterization of the Mutants with Respect to In Silico Metabolic Reconstructions.

PubMed

diCenzo, George C; Finan, Turlough M

2018-01-01

The rate at which all genes within a bacterial genome can be identified far exceeds the ability to characterize these genes. To assist in associating genes with cellular functions, a large-scale bacterial genome deletion approach can be employed to rapidly screen tens to thousands of genes for desired phenotypes. Here, we provide a detailed protocol for the generation of deletions of large segments of bacterial genomes that relies on the activity of a site-specific recombinase. In this procedure, two recombinase recognition target sequences are introduced into known positions of a bacterial genome through single cross-over plasmid integration. Subsequent expression of the site-specific recombinase mediates recombination between the two target sequences, resulting in the excision of the intervening region and its loss from the genome. We further illustrate how this deletion system can be readily adapted to function as a large-scale in vivo cloning procedure, in which the region excised from the genome is captured as a replicative plasmid. We next provide a procedure for the metabolic analysis of bacterial large-scale genome deletion mutants using the Biolog Phenotype MicroArray™ system. Finally, a pipeline is described, and a sample Matlab script is provided, for the integration of the obtained data with a draft metabolic reconstruction for the refinement of the reactions and gene-protein-reaction relationships in a metabolic reconstruction.

Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq

PubMed Central

Shepard, Peter J.; Choi, Eun-A; Lu, Jente; Flanagan, Lisa A.; Hertel, Klemens J.; Shi, Yongsheng

2011-01-01

Alternative polyadenylation (APA) of mRNAs has emerged as an important mechanism for post-transcriptional gene regulation in higher eukaryotes. Although microarrays have recently been used to characterize APA globally, they have a number of serious limitations that prevents comprehensive and highly quantitative analysis. To better characterize APA and its regulation, we have developed a deep sequencing-based method called Poly(A) Site Sequencing (PAS-Seq) for quantitatively profiling RNA polyadenylation at the transcriptome level. PAS-Seq not only accurately and comprehensively identifies poly(A) junctions in mRNAs and noncoding RNAs, but also provides quantitative information on the relative abundance of polyadenylated RNAs. PAS-Seq analyses of human and mouse transcriptomes showed that 40%–50% of all expressed genes produce alternatively polyadenylated mRNAs. Furthermore, our study detected evolutionarily conserved polyadenylation of histone mRNAs and revealed novel features of mitochondrial RNA polyadenylation. Finally, PAS-Seq analyses of mouse embryonic stem (ES) cells, neural stem/progenitor (NSP) cells, and neurons not only identified more poly(A) sites than what was found in the entire mouse EST database, but also detected significant changes in the global APA profile that lead to lengthening of 3′ untranslated regions (UTR) in many mRNAs during stem cell differentiation. Together, our PAS-Seq analyses revealed a complex landscape of RNA polyadenylation in mammalian cells and the dynamic regulation of APA during stem cell differentiation. PMID:21343387

Long-term characterization, lagoon treatment and migration potential of landfill leachate: a case study in an active Italian landfill.

PubMed

Frascari, D; Bronzini, F; Giordano, G; Tedioli, G; Nocentini, M

2004-01-01

The elaboration of 10 years of monitoring of leachate quality and quantity, leachate treatment and degree of contamination of soil and surface waters at the Tre Monti site--an active, 4-million-m(3) landfill in Northern Italy--is presented in this study. A hydrological model of leachate production is applied, with a good match of the experimental data. The concentrations of all leachate components except sulfate are characterized by fluctuations over a constant or increasing value. Different ways of interpreting leachate quality data are discussed; the elaboration indicates that the pollutant load on the leachate treatment facility will remain basically constant as long as waste will be added to the landfill. The analysis of the data relative to 10 years of leachate pre-treatment in the adjoining, non-aerated lagoon system indicates that a significant removal is achieved for most leachate components; the operational conditions of the plant are described, and the removal mechanisms are discussed. Finally, the potential for contamination of soil and surface waters is examined by analyzing long-term quality trends of the sub-superficial waters sampled near the lagoons and by means of an analytical campaign conducted on clay cores sampled near and underneath the treatment ponds. The experimental values indicate that the clay layer located under the entire site offers an effective barrier to the migration of leachate contaminants.

Applications of multi-season hyperspectral remote sensing for acid mine water characterization and mapping of secondary iron minerals associated with acid mine drainage

NASA Astrophysics Data System (ADS)

Davies, Gwendolyn E.

Acid mine drainage (AMD) resulting from the oxidation of sulfides in mine waste is a major environmental issue facing the mining industry today. Open pit mines, tailings ponds, ore stockpiles, and waste rock dumps can all be significant sources of pollution, primarily heavy metals. These large mining-induced footprints are often located across vast geographic expanses and are difficult to access. With the continuing advancement of imaging satellites, remote sensing may provide a useful monitoring tool for pit lake water quality and the rapid assessment of abandoned mine sites. This study explored the applications of laboratory spectroscopy and multi-season hyperspectral remote sensing for environmental monitoring of mine waste environments. Laboratory spectral experiments were first performed on acid mine waters and synthetic ferric iron solutions to identify and isolate the unique spectral properties of mine waters. These spectral characterizations were then applied to airborne hyperspectral imagery for identification of poor water quality in AMD ponds at the Leviathan Mine Superfund site, CA. Finally, imagery varying in temporal and spatial resolutions were used to identify changes in mineralogy over weathering overburden piles and on dry AMD pond liner surfaces at the Leviathan Mine. Results show the utility of hyperspectral remote sensing for monitoring a diverse range of surfaces associated with AMD.

Conformational exchange in pseudoazurin: different kinds of microsecond to millisecond dynamics characterized by their pH and buffer dependence using 15N NMR relaxation.

PubMed

Hass, Mathias A S; Vlasie, Monica D; Ubbink, Marcellus; Led, Jens J

2009-01-13

The dynamics of the reduced form of the blue copper protein pseudoazurin from Alcaligenes faecalis S-6 was investigated using (15)N relaxation measurements with a focus on the dynamics of the micro- to millisecond time scale. Different types of conformational exchange processes are observed in the protein on this time scale. At low pH, the protonation of the C-terminal copper-ligated histidine, His81, is observed. A comparison of the exchange rates in the presence and absence of added buffers shows that the protonation is the rate-limiting step at low buffer concentrations. This finding agrees with previous observations for other blue copper proteins, e.g., amicyanin and plastocyanin. However, in contrast to plastocyanin but similar to amicyanin, a second conformational exchange between different conformations of the protonated copper site is observed at low pH, most likely triggered by the protonation of His81. This process has been further characterized using CPMG dispersion methods and is found to occur with a rate of a few thousands per second. Finally, micro- to millisecond motions are observed in one of the loop regions and in the alpha-helical regions. These motions are unaffected by pH and are unrelated to the conformational changes in the active site of pseudoazurin.

Use of Electrical Conductivity Logging to Characterize the Geological Context of Releases at UST Sites

EPA Science Inventory

Risk is the combination of hazard and exposure. Risk characterization at UST release sites has traditionally emphasized hazard (presence of residual fuel) with little attention to exposure. Exposure characterization often limited to a one-dimensional model such as the RBCA equa...

Fiscal Year 2012 Revegetation Assessment

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

Jenifer Nordstrom

2012-11-01

This report summarizes the Fiscal Year 2012 Revegetation Assessment by Battelle Energy Alliance, LLC. This assessment was conducted to supplement documentation related to the Storm Water Pollution Prevention Plan for Construction Activities and to ensure that disturbed vegetation and soil at various locations are being restored. This report provides the following information for each site being monitored by the Idaho National Laboratory Environmental Support and Services: • Summary of each site • Assessment of vegetation status and site stabilization at each location • Actions and Resolutions for each site. Ten disturbed sites were evaluated for this assessment. Six have achievedmore » final stabilization. The remaining four sites not meeting the criteria for final stabilization will be evaluated again in the next fiscal year.« less

Lunar site characterization and mining

NASA Technical Reports Server (NTRS)

Glass, Charles E.

1992-01-01

Lunar mining requirements do not appear to be excessively demanding in terms of volume of material processed. It seems clear, however, that the labor-intensive practices that characterize terrestrial mining will not suffice at the low-gravity, hard-vacuum, and inaccessible sites on the Moon. New research efforts are needed in three important areas: (1) to develop high-speed, high-resolution through-rock vision systems that will permit more detailed and efficient mine site investigation and characterization; (2) to investigate the impact of lunar conditions on our ability to convert conventional mining and exploration equipment to lunar prototypes; and (3) to develop telerobotic or fully robotic mining systems for operations on the Moon and other bodies in the inner solar system. Other aspects of lunar site characterization and mining are discussed.

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

Characterization of a Multi-element Clinical HIFU System Using Acoustic Holography and Nonlinear Modeling

PubMed Central

Kreider, Wayne; Yuldashev, Petr V.; Sapozhnikov, Oleg A.; Farr, Navid; Partanen, Ari; Bailey, Michael R.; Khokhlova, Vera A.

2014-01-01

High-intensity focused ultrasound (HIFU) is a treatment modality that relies on the delivery of acoustic energy to remote tissue sites to induce thermal and/or mechanical tissue ablation. To ensure the safety and efficacy of this medical technology, standard approaches are needed for accurately characterizing the acoustic pressures generated by clinical ultrasound sources under operating conditions. Characterization of HIFU fields is complicated by nonlinear wave propagation and the complexity of phased-array transducers. Previous work has described aspects of an approach that combines measurements and modeling, and here we demonstrate this approach for a clinical phased array transducer. First, low-amplitude hydrophone measurements were performed in water over a scan plane between the array and the focus. Second, these measurements were used to holographically reconstruct the surface vibrations of the transducer and to set a boundary condition for a 3-D acoustic propagation model. Finally, nonlinear simulations of the acoustic field were carried out over a range of source power levels. Simulation results were compared to pressure waveforms measured directly by hydrophone at both low and high power levels, demonstrating that details of the acoustic field including shock formation are quantitatively predicted. PMID:25004539

Chromatin Accessibility Mapping Identifies Mediators of Basal Transcription and Retinoid-Induced Repression of OTX2 in Medulloblastoma

PubMed Central

Zhang, Monica; Song, Lingyun; Lee, Bum-Kyu; Iyer, Vishwanath R.; Furey, Terrence S.; Crawford, Gregory E.; Yan, Hai; He, Yiping

2014-01-01

Despite an emerging understanding of the genetic alterations giving rise to various tumors, the mechanisms whereby most oncogenes are overexpressed remain unclear. Here we have utilized an integrated approach of genomewide regulatory element mapping via DNase-seq followed by conventional reporter assays and transcription factor binding site discovery to characterize the transcriptional regulation of the medulloblastoma oncogene Orthodenticle Homeobox 2 (OTX2). Through these studies we have revealed that OTX2 is differentially regulated in medulloblastoma at the level of chromatin accessibility, which is in part mediated by DNA methylation. In cell lines exhibiting chromatin accessibility of OTX2 regulatory regions, we found that autoregulation maintains OTX2 expression. Comparison of medulloblastoma regulatory elements with those of the developing brain reveals that these tumors engage a developmental regulatory program to drive OTX2 transcription. Finally, we have identified a transcriptional regulatory element mediating retinoid-induced OTX2 repression in these tumors. This work characterizes for the first time the mechanisms of OTX2 overexpression in medulloblastoma. Furthermore, this study establishes proof of principle for applying ENCODE datasets towards the characterization of upstream trans-acting factors mediating expression of individual genes. PMID:25198066

Seven functional classes of Barth syndrome mutation.

PubMed

Whited, Kevin; Baile, Matthew G; Currier, Pamela; Claypool, Steven M

2013-02-01

Patients with Barth syndrome (BTHS), a rare X-linked disease, suffer from skeletal and cardiomyopathy and bouts of cyclic neutropenia. The causative gene encodes tafazzin, a transacylase, which is the major determinant of the final acyl chain composition of the mitochondrial-specific phospholipid, CL. In addition to numerous frame shift and splice-site mutations, 36 missense mutations have been associated with BTHS. Previously, we established a BTHS-mutant panel in the yeast Saccharomyces cerevisiae that successfully models 18/21 conserved pathogenic missense mutations and defined the loss-of-function mechanism associated with a subset of the mutant tafazzins. Here, we report the biochemical and cell biological characterization of the rest of the yeast BTHS-mutant panel and in so doing identify three additional modes of tafazzin dysfunction. The largest group of mutant tafazzins is catalytically null, two mutants encode hypomorphic alleles, and another two mutants are temperature sensitive. Additionally, we have expanded the defects associated with previously characterized matrix-mislocalized-mutant tafazzins to include the rapid degradation of aggregation-prone polypeptides that correctly localize to the mitochondrial IMS. In sum, our in-depth characterization of the yeast BTHS-mutant panel has identified seven functional classes of BTHS mutation.

Waste-water characterization survey, Whiteman Air Force Base, Missouri. Final report, 28 Oct-7 Nov 91

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

Fields, M.K.; Davis, R.P.

1992-08-01

A wastewater characterization survey was conducted by members of the Armstrong Laboratory Occupational and Environmental Health directorate Water Quality Function from 28 Oct 91 - 7 Nov 91 at Whiteman AFB, MO. The purpose of the survey was to identify and characterize the wastewater, determine the appropriateness of present disposal methods, determine the need for routine sampling or monitoring and recommend parameters for wastewater analysis. Results of the sampling showed metals and volatile organic discharge in varying concentrations throughout the base. Recommendations are: (1) evaluation of industrial operations and chemical disposal procedures at designated sites; (2) routine monitoring of themore » discharge from the Hospital and Audiovisual for silver; (3) excavation and sediment disposal at the Transportation Washrack and WWTP Effluent discharge point; (4) collection and analyses of sludge at oil water separators, to include the oil and water side; (5) evaluation of the sanitary sewer system for corrosion and sediment buildup by a mobile Reveal and Seal Unit; (6) background soil sample collection and analyses; and (7) pretreatment of Aqueous Film Forming Foam discharge and notification of the Base Bioenvironmental Engineer, Environmental Coordinator, and WWTP personnel when discharge occurs.« less

Final Hanford Comprehensive Land-Use Plan Environmental Impact Statement, Hanford Site, Richland, Washington

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

N /A

This Final ''Hanford Comprehensive Land-Use Plan Environmental Impact Statement'' (HCP EIS) is being used by the Department of Energy (DOE) and its nine cooperating and consulting agencies to develop a comprehensive land-use plan (CLUP) for the Hanford Site. The DOE will use the Final HCP EIS as a basis for a Record of Decision (ROD) on a CLUP for the Hanford Site. While development of the CLUP will be complete with release of the HCP EIS ROD, full implementation of the CLUP is expected to take at least 50 years. Implementation of the CLUP would begin a more detailed planningmore » process for land-use and facility-use decisions at the Hanford Site. The DOE would use the CLUP to screen proposals. Eventually, management of Hanford Site areas would move toward the CLUP land-use goals. This CLUP process could take more than 50 years to fully achieve the land-use goals.« less

Pretest information for a test to validate plume simulation procedures (FA-17)

NASA Technical Reports Server (NTRS)

Hair, L. M.

1978-01-01

The results of an effort to plan a final verification wind tunnel test to validate the recommended correlation parameters and application techniques were presented. The test planning effort was complete except for test site finalization and the associated coordination. Two suitable test sites were identified. Desired test conditions were shown. Subsequent sections of this report present the selected model and test site, instrumentation of this model, planned test operations, and some concluding remarks.

Assessment of remote sensing technologies to discover and characterize waste sites

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

NONE

1992-03-11

This report presents details about waste management practices that are being developed using remote sensing techniques to characterize DOE waste sites. Once the sites and problems have been located and characterized and an achievable restoration and remediation program have been established, efforts to reclaim the environment will begin. Special problems to be considered are: concentrated waste forms in tanks and pits; soil and ground water contamination; ground safety hazards for workers; and requirement for long-term monitoring.

Cleanups In My Community (CIMC) - Superfund National Priority List (NPL) Sites, National Layer

EPA Pesticide Factsheets

This data layer provides access to Superfund National Priority List Sites as part of the CIMC web service. Superfund is a program administered by the EPA to locate, investigate, and clean up worst hazardous waste sites throughout the United States. EPA administers the Superfund program in cooperation with individual states and tribal governments. These sites include abandoned warehouses, manufacturing facilities, processing plants, and landfills - the key word here being abandoned.Only NPL sites have been included in Cleanups in My Community thus far. EPA maintains the NPL, which identifies for the States and the public those sites or other releases that appear to warrant remedial (long term) actions. These NPL sites fall into the following categories:Proposed: Sites may be proposed for the NPL and then may be placed on the NPL as final or be removed from the Proposed NPL.Final: Those sites placed on the NPL are called final, and for these sites, a cleanup remedy is selected and implemented. However, it may be several years after construction of the remedy is completed before the hazardous substances are completely cleaned up or controlled in place.Deleted: After the clean up process is complete, and appropriate reviews confirm the area is cleaned up or the hazards are controlled, sites can be deleted from the NPL.For more information on the data provided through this web service, please see the processing steps below, and see more information here: https://www.

10 CFR 60.18 - Review of site characterization activities. 2

Code of Federal Regulations, 2010 CFR

2010-01-01

... IN GEOLOGIC REPOSITORIES Licenses Preapplication Review § 60.18 Review of site characterization... its progress in developing the design of a geologic repository operations area appropriate for the...

SITE CHARACTERIZATION TO SUPPORT DEVELOPMENT OF CONCEPTUAL SITE MODELS AND TRANSPORT MODELS FOR MONITORING CONTAMINANTS IN GROUND WATER

EPA Science Inventory

The development of conceptual and predictive models is an important tool to guide site characterization in support of monitoring contaminants in ground water. The accuracy of predictive models is limited by the adequacy of the input data and the assumptions made to constrain mod...

New methods to characterize site amplification

USGS Publications Warehouse

Safak, Erdal

1993-01-01

Methods alternative to spectral ratios are introduced to characterize site amplification. The methods are developed by using a range of models, from the simple constant amplification model to the time-varying filter model. Examples are given for each model by using a pair of rock- and soil-site recordings from the Loma Prieta earthquake.

OBSERVATIONAL STUDY OF FINAL CLEANING AND AHERA CLEARANCE SAMPLING AT ASBESTOS-ABATEMENT SITES IN NEW JERSEY

EPA Science Inventory

A study was conducted during the summer of 1988 to document final cleaning procedures and evaluate Asbestos Hazard Emergency Response Act (AHERA) clearance air sampling practices used at 20 asbestos-abatement sites in New Jersey. Each abatement took place in a school building and...

Magnetic Characterization of Organic Materials

DTIC Science & Technology

2016-12-12

measurements. Magnetic shielding of nearby optical components was achieved for reliable experimental results. Magnetic -field applied ultrafast broadband...AFRL-AFOSR-JP-TR-2017-0005 Magnetic Characterization of Organic Materials Dongho Kim YONSEI UNIVERSITY UNIVERSITY-INDUSTRY FOUNDATION Final Report 12...Final 3. DATES COVERED (From - To) 10 Sep 2015 to 09 Sep 2016 4. TITLE AND SUBTITLE Magnetic Characterization of Organic Materials 5a.  CONTRACT

Limited Pollen Dispersal Contributes to Population Genetic Structure but Not Local Adaptation in Quercus oleoides Forests of Costa Rica.

PubMed

Deacon, Nicholas John; Cavender-Bares, Jeannine

2015-01-01

Quercus oleoides Cham. and Schlect., tropical live oak, is a species of conservation importance in its southern range limit of northwestern Costa Rica. It occurs in high-density stands across a fragmented landscape spanning a contrasting elevation and precipitation gradient. We examined genetic diversity and spatial genetic structure in this geographically isolated and genetically distinct population. We characterized population genetic diversity at 11 nuclear microsatellite loci in 260 individuals from 13 sites. We monitored flowering time at 10 sites, and characterized the local environment in order to compare observed spatial genetic structure to hypotheses of isolation-by-distance and isolation-by-environment. Finally, we quantified pollen dispersal distances and tested for local adaptation through a reciprocal transplant experiment in order to experimentally address these hypotheses. High genetic diversity is maintained in the population and the genetic variation is significantly structured among sampled sites. We identified 5 distinct genetic clusters and average pollen dispersal predominately occurred over short distances. Differences among sites in flowering phenology and environmental factors, however, were not strictly associated with genetic differentiation. Growth and survival of upland and lowland progeny in their native and foreign environments was expected to exhibit evidence of local adaptation due to the more extreme dry season in the lowlands. Seedlings planted in the lowland garden experienced much higher mortality than seedlings in the upland garden, but we did not identify evidence for local adaptation. Overall, this study indicates that the Costa Rican Q. oleoides population has a rich population genetic history. Despite environmental heterogeneity and habitat fragmentation, isolation-by-distance and isolation-by-environment alone do not explain spatial genetic structure. These results add to studies of genetic structure by examining a common, tropical tree over multiple habitats and provide information for managers of a successional forest in a protected area.

Genome-wide activity of unliganded estrogen receptor-α in breast cancer cells

PubMed Central

Caizzi, Livia; Ferrero, Giulio; Cutrupi, Santina; Cordero, Francesca; Ballaré, Cecilia; Miano, Valentina; Reineri, Stefania; Ricci, Laura; Friard, Olivier; Testori, Alessandro; Corà, Davide; Caselle, Michele; Di Croce, Luciano; De Bortoli, Michele

2014-01-01

Estrogen receptor-α (ERα) has central role in hormone-dependent breast cancer and its ligand-induced functions have been extensively characterized. However, evidence exists that ERα has functions that are independent of ligands. In the present work, we investigated the binding of ERα to chromatin in the absence of ligands and its functions on gene regulation. We demonstrated that in MCF7 breast cancer cells unliganded ERα binds to more than 4,000 chromatin sites. Unexpectedly, although almost entirely comprised in the larger group of estrogen-induced binding sites, we found that unliganded-ERα binding is specifically linked to genes with developmental functions, compared with estrogen-induced binding. Moreover, we found that siRNA-mediated down-regulation of ERα in absence of estrogen is accompanied by changes in the expression levels of hundreds of coding and noncoding RNAs. Down-regulated mRNAs showed enrichment in genes related to epithelial cell growth and development. Stable ERα down-regulation using shRNA, which caused cell growth arrest, was accompanied by increased H3K27me3 at ERα binding sites. Finally, we found that FOXA1 and AP2γ binding to several sites is decreased upon ERα silencing, suggesting that unliganded ERα participates, together with other factors, in the maintenance of the luminal-specific cistrome in breast cancer cells. PMID:24639548

Computational analysis of EBNA1 ``druggability'' suggests novel insights for Epstein-Barr virus inhibitor design

NASA Astrophysics Data System (ADS)

Gianti, Eleonora; Messick, Troy E.; Lieberman, Paul M.; Zauhar, Randy J.

2016-04-01

The Epstein-Barr Nuclear Antigen 1 (EBNA1) is a critical protein encoded by the Epstein-Barr Virus (EBV). During latent infection, EBNA1 is essential for DNA replication and transcription initiation of viral and cellular genes and is necessary to immortalize primary B-lymphocytes. Nonetheless, the concept of EBNA1 as drug target is novel. Two EBNA1 crystal structures are publicly available and the first small-molecule EBNA1 inhibitors were recently discovered. However, no systematic studies have been reported on the structural details of EBNA1 "druggable" binding sites. We conducted computational identification and structural characterization of EBNA1 binding pockets, likely to accommodate ligand molecules (i.e. "druggable" binding sites). Then, we validated our predictions by docking against a set of compounds previously tested in vitro for EBNA1 inhibition (PubChem AID-2381). Finally, we supported assessments of pocket druggability by performing induced fit docking and molecular dynamics simulations paired with binding affinity predictions by Molecular Mechanics Generalized Born Surface Area calculations for a number of hits belonging to druggable binding sites. Our results establish EBNA1 as a target for drug discovery, and provide the computational evidence that active AID-2381 hits disrupt EBNA1:DNA binding upon interacting at individual sites. Lastly, structural properties of top scoring hits are proposed to support the rational design of the next generation of EBNA1 inhibitors.

SITE CHARACTERIZATION OF AREA 6, DOVER AIR FORCE BASE, IN SUPPORT OF NATURAL ATTENUATION AND ENHANCED ANAEROBIC BIOREMEDIATION PROJECTS

EPA Science Inventory

A field program for site characterization of targeted study areas at the Dover Air Force Base was conducted between January 16, 1995, and March 9, 1995. The stated objectives of the investigation, "to characterize the stratigraphy, depth to groundwater, groundwater flow directio...

Nanosecond Dynamics at Protein Metal Sites: An Application of Perturbed Angular Correlation (PAC) of γ-Rays Spectroscopy.

PubMed

Chakraborty, Saumen; Pallada, Stavroula; Pedersen, Jeppe T; Jancso, Attila; Correia, Joao G; Hemmingsen, Lars

2017-09-19

Metalloproteins are essential to numerous reactions in nature, and constitute approximately one-third of all known proteins. Molecular dynamics of proteins has been elucidated with great success both by experimental and theoretical methods, revealing atomic level details of function involving the organic constituents on a broad spectrum of time scales. However, the characterization of dynamics at biomolecular metal sites on nanosecond time scales is scarce in the literature. The aqua ions of many biologically relevant metal ions exhibit exchange of water molecules on the nanosecond time scale or faster, often defining their reactivity in aqueous solution, and this is presumably also a relevant time scale for the making and breaking of coordination bonds between metal ions and ligands at protein metal sites. Ligand exchange dynamics is critical for a variety of elementary steps of reactions in metallobiochemistry, for example, association and dissociation of metal bound water, association of substrate and dissociation of product in the catalytic cycle of metalloenzymes, at regulatory metal sites which require binding and dissociation of metal ions, as well as in the transport of metal ions across cell membranes or between proteins involved in metal ion homeostasis. In Perturbed Angular Correlation of γ-rays (PAC) spectroscopy, the correlation in time and space of two γ-rays emitted successively in a nuclear decay is recorded, reflecting the hyperfine interactions of the PAC probe nucleus with the surroundings. This allows for characterization of molecular and electronic structure as well as nanosecond dynamics at the PAC probe binding site. Herein, selected examples describing the application of PAC spectroscopy in probing the dynamics at protein metal sites are presented, including (1) exchange of Cd 2+ bound water in de novo designed synthetic proteins, and the effect of remote mutations on metal site dynamics; (2) dynamics at the β-lactamase active site, where the metal ion appears to jump between the two adjacent sites; (3) structural relaxation in small blue copper proteins upon 111 Ag + to 111 Cd 2+ transformation in radioactive nuclear decay; (4) metal ion transfer between two HAH1 proteins with change in coordination number; and (5) metal ion sensor proteins with two coexisting metal site structures. With this Account, we hope to make our modest contribution to the field and perhaps spur additional interest in dynamics at protein metal sites, which we consider to be severely underexplored. Relatively little is known about detailed atomic motions at metal sites, for example, how ligand exchange processes affect protein function, and how the amino acid composition of the protein may control this facet of metal site characteristics. We also aim to provide the reader with a qualitative impression of the possibilities offered by PAC spectroscopy in bioinorganic chemistry, especially when elucidating dynamics at protein metal sites, and finally present data that may serve as benchmarks on a relevant time scale for development and tests of theoretical molecular dynamics methods applied to biomolecular metal sites.

Carbinolamine Formation and Dehydration in a DNA Repair Enzyme Active Site

PubMed Central

Dodson, M. L.; Walker, Ross C.; Lloyd, R. Stephen

2012-01-01

In order to suggest detailed mechanistic hypotheses for the formation and dehydration of a key carbinolamine intermediate in the T4 pyrimidine dimer glycosylase (T4PDG) reaction, we have investigated these reactions using steered molecular dynamics with a coupled quantum mechanics–molecular mechanics potential (QM/MM). We carried out simulations of DNA abasic site carbinolamine formation with and without a water molecule restrained to remain within the active site quantum region. We recovered potentials of mean force (PMF) from thirty replicate reaction trajectories using Jarzynski averaging. We demonstrated feasible pathways involving water, as well as those independent of water participation. The water–independent enzyme–catalyzed reaction had a bias–corrected Jarzynski–average barrier height of approximately for the carbinolamine formation reaction and ) for the reverse reaction at this level of representation. When the proton transfer was facilitated with an intrinsic quantum water, the barrier height was approximately in the forward (formation) reaction and for the reverse. In addition, two modes of unsteered (free dynamics) carbinolamine dehydration were observed: in one, the quantum water participated as an intermediate proton transfer species, and in the other, the active site protonated glutamate hydrogen was directly transferred to the carbinolamine oxygen. Water–independent unforced proton transfer from the protonated active site glutamate carboxyl to the unprotonated N–terminal amine was also observed. In summary, complex proton transfer events, some involving water intermediates, were studied in QM/MM simulations of T4PDG bound to a DNA abasic site. Imine carbinolamine formation was characterized using steered QM/MM molecular dynamics. Dehydration of the carbinolamine intermediate to form the final imine product was observed in free, unsteered, QM/MM dynamics simulations, as was unforced acid-base transfer between the active site carboxylate and the N–terminal amine. PMID:22384015

PM2.5 and volatile organic compounds (VOCs) in ambient air: a focus on the effect of meteorology.

PubMed

Giakoumi, A; Maggos, Th; Michopoulos, J; Helmis, C; Vasilakos, Ch

2009-05-01

PM(2.5) and VOCs (benzene, toluene, m-p-o-xylenes) concentrations were measured in an urban and a suburban site in Athens, Greece, during the period between April and November 2004. This period, which is considered to be the warmer period in Greece, is characterized by the development of sea-breeze over the Attica Basin. Additionally strong Northern, North-eastern winds called "The Etesians", predominate during the summer months (July-August), acting positively to the dispersion of pollutants. In this campaign, 24 days with sea-breeze development were observed, 15 days with northern winds, 6 days with southern winds while the rest of the days presented no specific wind profile. Maximum concentrations of PM(2.5), VOCs and nitrogen oxides, were detected during the days with sea-breeze, while minimum concentrations during the days with northern winds. Ozone was the only pollutant that appeared to have higher concentrations in the background site and not in the city centre, where benzene presented strong negative correlation with ozone, indicating the photochemical reaction of hydrocarbons that lead to the ozone formation. The BTX ratios were similar for both sites and wind profiles, indicating common sources for those pollutants. T/B ratio ranged in low levels, between 3-5 for site A and 2-5 for site B, suggesting vehicles emissions as the main sources of volatile compounds. Finally, the strong correlations of PM(2.5) and benzene concentrations, between the two sampling sites, indicate that both the city centre and the background site, are affected by the same sources, under common meteorological conditions (sea-breeze, northern winds).

North Slope (Wahluke Slope) expedited response action cleanup plan

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

Not Available

The purpose of this action is to mitigate any threat to public health and the environment from hazards on the North Slope and meet the expedited response action (ERA) objective of cleanup to a degree requiring no further action. The ERA may be the final remediation of the 100-I-3 Operable Unit. A No Action record of decision (ROD) may be issued after remediation completion. The US Department of Energy (DOE) currently owns or administers approximately 140 mi{sup 2} (about 90,000 acres) of land north and east of the Columbia River (referred to as the North Slope) that is part ofmore » the Hanford Site. The North Slope, also commonly known as the Wahluke Slope, was not used for plutonium production or support facilities; it was used for military air defense of the Hanford Site and vicinity. The North Slope contained seven antiaircraft gun emplacements and three Nike-Ajax missile positions. These military positions were vacated in 1960--1961 as the defense requirements at Hanford changed. They were demolished in 1974. Prior to government control in 1943, the North Slope was homesteaded. Since the initiation of this ERA in the summer of 1992, DOE signed the modified Hanford Federal Agreement and Consent Order (Tri-Party Agreement) with the Washington Department of Ecology (Ecology) and the US Environmental Protection Agency (EPA), in which a milestone was set to complete remediation activities and a draft closeout report by October 1994. Remediation activities will make the North Slope area available for future non-DOE uses. Thirty-nine sites have undergone limited characterization to determine if significant environmental hazards exist. This plan documents the results of that characterization and evaluates the potential remediation alternatives.« less

Dimensional and chemical characterization of particles at a downwind receptor site of a waste-to-energy plant

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

Buonanno, G., E-mail: buonanno@unicas.i; Stabile, L.; Avino, P.

2010-07-15

In the last years numerous epidemiological studies were carried out to evaluate the effects of particulate matter on human health. In industrialized areas, anthropogenic activities highly contribute to the fine and ultrafine particle concentrations. Then, it is important to characterize the evolution of particle size distribution and chemical composition near these emission points. Waste incineration represents a favorable technique for reducing the waste volume. However, in the past, municipal waste incinerators (MWIs) had a bad reputation due to the emission of toxic combustion byproducts. Consequently, the risk perception of the people living near MWIs is very high even if inmore » Western countries waste incineration has nowadays to be considered a relatively clean process from a technical point of view. The study here presented has an exemplary meaning for developing appropriate management and control strategies for air quality in the surrounding of MWIs and to perform exposure assessment for populations involved. Environment particles were continuously measured through a SMPS/APS system over 12 months. The monitoring site represents a downwind receptor of a typical MWI. Furthermore, elements and organic fractions were measured by means of the Instrumental Neutron Activation Analysis and using dichotomous and high volume samplers. Annual mean values of 8.6 x 10{sup 3} +- 3.7 x 10{sup 2} part. cm{sup -3} and 31.1 +- 9.0 mug m{sup -3} were found for number and mass concentration, typical of a rural site. Most of the elements can be attributed to long-range transport from other natural and/or anthropogenic sources. Finally, the Polycyclic Aromatic Hydrocarbons present low concentrations with a mean value of 24.6 ng m{sup -3}.« less

Mechanism of Intramembrane Cleavage of Alcadeins by γ-Secretase

PubMed Central

Piao, Yi; Kimura, Ayano; Urano, Satomi; Saito, Yuhki; Taru, Hidenori; Yamamoto, Tohru; Hata, Saori; Suzuki, Toshiharu

2013-01-01

Background Alcadein proteins (Alcs; Alcα, Alcβand Alcγ) are predominantly expressed in neurons, as is Alzheimer's β-amyloid (Aβ) precursor protein (APP). Both Alcs and APP are cleaved by primary α- or β-secretase to generate membrane-associated C-terminal fragments (CTFs). Alc CTFs are further cleaved by γ-secretase to secrete p3-Alc peptide along with the release of intracellular domain fragment (Alc ICD) from the membrane. In the case of APP, APP CTFβ is initially cleaved at the ε-site to release the intracellular domain fragment (AICD) and consequently the γ-site is determined, by which Aβ generates. The initial ε-site is thought to define the final γ-site position, which determines whether Aβ40/43 or Aβ42 is generated. However, initial intracellular ε-cleavage sites of Alc CTF to generate Alc ICD and the molecular mechanism that final γ-site position is determined remains unclear in Alcs. Methodology Using HEK293 cells expressing Alcs plus presenilin 1 (PS1, a catalytic unit of γ-secretase) and the membrane fractions of these cells, the generation of p3-Alc possessing C-terminal γ-cleavage site and Alc ICD possessing N-terminal ε-cleavage site were analysed with MALDI-TOF/MS. We determined the initial ε-site position of all Alcα, Alcβ and Alcγ, and analyzed the relationship between the initially determined ε-site position and the final γ-cleavage position. Conclusions The initial ε-site position does not always determine the final γ-cleavage position in Alcs, which differed from APP. No additional γ-cleavage sites are generated from artificial/non-physiological positions of ε-cleavage for Alcs, while the artificial ε-cleavage positions can influence in selection of physiological γ-site positions. Because alteration of γ-secretase activity is thought to be a pathogenesis of sporadic Alzheimer's disease, Alcs are useful and sensitive substrate to detect the altered cleavage of substrates by γ-secretase, which may be induced by malfunction of γ-secretase itself or changes of membrane environment for enzymatic reaction. PMID:23658629

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

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

10 CFR 60.7 - License not required for certain preliminary activities.

Code of Federal Regulations, 2010 CFR

2010-01-01

... WASTES IN GEOLOGIC REPOSITORIES General Provisions § 60.7 License not required for certain preliminary... repository: (a) For purposes of site characterization; or (b) For use, during site characterization or...

Analysis and interpretation of the 1985 Sequoia transport experiment. Final report

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

Myrup, L.; Flocchini, R.

1987-10-01

An analysis and interpretation is presented of the 1985 Aerosol Transport and Characterization Program at Sequoia National Park, sponsored by the California Air Resources Board. Overall, it was found that the Program produced unique data sets and interesting new results relating particulate air quality and meteorology in the context of complex terrain. The major conclusion is that the meso-scale wind field, as modulated by synoptic-scale fluctuations, is the chief factor acting to cause variation in particulate concentrations in the Park. Areas for future work are discussed. In addition, it was recommended that in future measurement programs, greater effort be mademore » to locate sites completely unaffected by local sources of pollutants.« less

Solar Spectral Radiative Forcing Due to Dust Aerosol During the Puerto Rico Dust Experiment

NASA Technical Reports Server (NTRS)

Pilewskie, P.; Bergstrom, R.; Rabbette, M.; Livingston, J.; Russell, P.; Gore, Warren J. (Technical Monitor)

2000-01-01

During the Puerto Rico Dust Experiment (PRIDE) upwelling and downwelling solar spectral irradiance was measured on board the SPAWAR Navajo and downwelling solar spectral flux was measured at a surface site using the NASA Ames Solar Spectral Flux Radiometer. These data will be used to determine the net solar radiative forcing of dust aerosol and to quantify the solar spectral radiative energy budget in the presence of elevated aerosol loading. We will assess the variability in spectral irradiance using formal principal component analysis procedures and relate the radiative variability to aerosol microphysical properties. Finally, we will characterize the sea surface reflectance to improve aerosol optical depth retrievals from the AVHRR satellite and to validate SeaWiFS ocean color products.

Characterization And Evaluation Of A Prototype Forward-Looking Automotive Radar (Flar), Final Report

DOT National Transportation Integrated Search

1997-03-01

This is the final report for a three-year Discretionary Cooperative Agreement with the National Highway Traffic Safety Administration (NHTSA Grant DTNH22-94-Y-17016), Characterization and Evaluation of a Forward-Looking automotive Radar Sensor....

Yucca Mountain Biological Resources Monitoring Program. Progress report, January 1994--December 1994

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

NONE

1995-07-01

The US Department of Energy (DOE) is required by the Nuclear Waste Policy Act of 1982 (as amended in 1987) to study and characterize the suitability of Yucca Mountain as a potential geological repository for high-level nuclear waste. During site characterization, the DOE will conduct a variety of geotechnical, geochemical, geological, and hydrological studies to determine the suitability of Yucca Mountain as a potential repository. To ensure that site characterization activities do not adversely affect the environment at Yucca Mountain, a program has been implemented to monitor and mitigate potential impacts and ensure activities comply with applicable environmental regulations. Thismore » report describes the activities and accomplishments of EG and G Energy Measurements, Inc. (EG and G/EM) from January 1994 through December 1994 for six program areas within the Terrestrial Ecosystem component of the environmental program for the Yucca Mountain Site Characterization Project (YMP): Site Characterization Effects, Desert Tortoises (Gopherus agassizii), Habitat Reclamation, Monitoring and Mitigation, Radiological Monitoring, and Biological Support.« less

Resolution of Novel Pancreatic Ductal Adenocarcinoma Subtypes by Global Phosphotyrosine Profiling*

PubMed Central

Humphrey, Emily S.; Su, Shih-Ping; Nagrial, Adnan M.; Hochgräfe, Falko; Pajic, Marina; Lehrbach, Gillian M.; Parton, Robert G.; Yap, Alpha S.; Horvath, Lisa G.; Chang, David K.; Biankin, Andrew V.; Wu, Jianmin; Daly, Roger J.

2016-01-01

Comprehensive characterization of signaling in pancreatic ductal adenocarcinoma (PDAC) promises to enhance our understanding of the molecular aberrations driving this devastating disease, and may identify novel therapeutic targets as well as biomarkers that enable stratification of patients for optimal therapy. Here, we use immunoaffinity-coupled high-resolution mass spectrometry to characterize global tyrosine phosphorylation patterns across two large panels of human PDAC cell lines: the ATCC series (19 cell lines) and TKCC series (17 cell lines). This resulted in the identification and quantification of over 1800 class 1 tyrosine phosphorylation sites and the consistent segregation of both PDAC cell line series into three subtypes with distinct tyrosine phosphorylation profiles. Subtype-selective signaling networks were characterized by identification of subtype-enriched phosphosites together with pathway and network analyses. This revealed that the three subtypes characteristic of the ATCC series were associated with perturbations in signaling networks associated with cell-cell adhesion and epithelial-mesenchyme transition, mRNA metabolism, and receptor tyrosine kinase (RTK) signaling, respectively. Specifically, the third subtype exhibited enhanced tyrosine phosphorylation of multiple RTKs including the EGFR, ERBB3 and MET. Interestingly, a similar RTK-enriched subtype was identified in the TKCC series, and 'classifier' sites for each series identified using Random Forest models were able to predict the subtypes of the alternate series with high accuracy, highlighting the conservation of the three subtypes across the two series. Finally, RTK-enriched cell lines from both series exhibited enhanced sensitivity to the small molecule EGFR inhibitor erlotinib, indicating that their phosphosignature may provide a predictive biomarker for response to this targeted therapy. These studies highlight how resolution of subtype-selective signaling networks can provide a novel taxonomy for particular cancers, and provide insights into PDAC biology that can be exploited for improved patient management. PMID:27259358

Acid–base catalysis over perovskites: a review

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

Polo-Garzon, Felipe; Wu, Zili

We present that perovskite catalysts have been extensively studied for reduction–oxidation (redox) reactions; however, their acid–base catalytic properties are still under-explored. This review collects work aiming to study the acid–base catalytic properties of perovskites. Reports regarding combined acid–base/redox catalysis over perovskites lie beyond the scope of the present review. For the characterization of acid–base properties, researchers have studied the interaction of probe molecules with perovskite surfaces by means of multiple techniques that provide information about the density, strength and type of adsorption sites. The top-surface composition of perovskites, which relates to the abundance of the acid–base sites, has been studiedmore » by means of low energy ion scattering (LEIS), and, the less surface sensitive, conventional X-ray photoelectron spectroscopy (XPS). Probe reactions, with the conversion of 2-propanol as the common choice, have also been employed for characterizing the acid–base catalytic properties of perovskites. The complex nature of perovskite surfaces, which explains the still absent fundamental relations between the structure of the catalyst and reaction rates/selectivity, encounters a great challenge due to the surface reconstruction of these materials. In this review, we devote a special section to highlight recent publications that report the impact of surface reconstruction and particle shape on acid–base catalysis over perovskites. In addition, we review promising catalytic performances of perovskite catalysts for other reactions of interest. Challenges in acid–base catalysis over perovskites focus on the development of time-resolved monolayer-sensitive characterization of surfaces under operando conditions and the discernment of combined acid–base/redox reaction mechanisms. Finally, opportunities lay on tuning the acid–base characteristics of perovskites with computation-based catalytic descriptors to achieve desired selectivities and enhanced rates.« less

Purification of an alpha amylase from Aspergillus flavus NSH9 and molecular characterization of its nucleotide gene sequence.

PubMed

Karim, Kazi Muhammad Rezaul; Husaini, Ahmad; Sing, Ngieng Ngui; Sinang, Fazia Mohd; Roslan, Hairul Azman; Hussain, Hasnain

2018-04-01

In this study, an alpha-amylase enzyme from a locally isolated Aspergillus flavus NSH9 was purified and characterized. The extracellular α-amylase was purified by ammonium sulfate precipitation and anion-exchange chromatography at a final yield of 2.55-fold and recovery of 11.73%. The molecular mass of the purified α-amylase was estimated to be 54 kDa using SDS-PAGE and the enzyme exhibited optimal catalytic activity at pH 5.0 and temperature of 50 °C. The enzyme was also thermally stable at 50 °C, with 87% residual activity after 60 min. As a metalloenzymes containing calcium, the purified α-amylase showed significantly increased enzyme activity in the presence of Ca 2+ ions. Further gene isolation and characterization shows that the α-amylase gene of A. flavus NSH9 contained eight introns and an open reading frame that encodes for 499 amino acids with the first 21 amino acids presumed to be a signal peptide. Analysis of the deduced peptide sequence showed the presence of three conserved catalytic residues of α-amylase, two Ca 2+ -binding sites, seven conserved peptide sequences, and several other properties that indicates the protein belongs to glycosyl hydrolase family 13 capable of acting on α-1,4-bonds only. Based on sequence similarity, the deduced peptide sequence of A. flavus NSH9 α-amylase was also found to carry two potential surface/secondary-binding site (SBS) residues (Trp 237 and Tyr 409) that might be playing crucial roles in both the enzyme activity and also the binding of starch granules.

The topology and dynamics of complex networks

NASA Astrophysics Data System (ADS)

Dezso, Zoltan

We start with a brief introduction about the topological properties of real networks. Most real networks are scale-free, being characterized by a power-law degree distribution. The scale-free nature of real networks leads to unexpected properties such as the vanishing epidemic threshold. Traditional methods aiming to reduce the spreading rate of viruses cannot succeed on eradicating the epidemic on a scale-free network. We demonstrate that policies that discriminate between the nodes, curing mostly the highly connected nodes, can restore a finite epidemic threshold and potentially eradicate the virus. We find that the more biased a policy is towards the hubs, the more chance it has to bring the epidemic threshold above the virus' spreading rate. We continue by studying a large Web portal as a model system for a rapidly evolving network. We find that the visitation pattern of a news document decays as a power law, in contrast with the exponential prediction provided by simple models of site visitation. This is rooted in the inhomogeneous nature of the browsing pattern characterizing individual users: the time interval between consecutive visits by the same user to the site follows a power law distribution, in contrast with the exponential expected for Poisson processes. We show that the exponent characterizing the individual user's browsing patterns determines the power-law decay in a document's visitation. Finally, we turn our attention to biological networks and demonstrate quantitatively that protein complexes in the yeast, Saccharomyces cerevisiae, are comprised of a core in which subunits are highly coexpressed, display the same deletion phenotype (essential or non-essential) and share identical functional classification and cellular localization. The results allow us to define the deletion phenotype and cellular task of most known complexes, and to identify with high confidence the biochemical role of hundreds of proteins with yet unassigned functionality.

Acid–base catalysis over perovskites: a review

DOE PAGES

Polo-Garzon, Felipe; Wu, Zili

2018-01-15

We present that perovskite catalysts have been extensively studied for reduction–oxidation (redox) reactions; however, their acid–base catalytic properties are still under-explored. This review collects work aiming to study the acid–base catalytic properties of perovskites. Reports regarding combined acid–base/redox catalysis over perovskites lie beyond the scope of the present review. For the characterization of acid–base properties, researchers have studied the interaction of probe molecules with perovskite surfaces by means of multiple techniques that provide information about the density, strength and type of adsorption sites. The top-surface composition of perovskites, which relates to the abundance of the acid–base sites, has been studiedmore » by means of low energy ion scattering (LEIS), and, the less surface sensitive, conventional X-ray photoelectron spectroscopy (XPS). Probe reactions, with the conversion of 2-propanol as the common choice, have also been employed for characterizing the acid–base catalytic properties of perovskites. The complex nature of perovskite surfaces, which explains the still absent fundamental relations between the structure of the catalyst and reaction rates/selectivity, encounters a great challenge due to the surface reconstruction of these materials. In this review, we devote a special section to highlight recent publications that report the impact of surface reconstruction and particle shape on acid–base catalysis over perovskites. In addition, we review promising catalytic performances of perovskite catalysts for other reactions of interest. Challenges in acid–base catalysis over perovskites focus on the development of time-resolved monolayer-sensitive characterization of surfaces under operando conditions and the discernment of combined acid–base/redox reaction mechanisms. Finally, opportunities lay on tuning the acid–base characteristics of perovskites with computation-based catalytic descriptors to achieve desired selectivities and enhanced rates.« less

10 CFR 960.3-2-3 - Recommendation of sites for characterization.

Code of Federal Regulations, 2010 CFR

2010-01-01

... POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-2-3 Recommendation of sites... characterization for the selection of the first repository, the Secretary shall recommend in writing to the..., and, after the first repository, consideration of regionality in §§ 960.3-1-1, 960.3-1-2, and 960.3-1...

Characterization of a backbone cleavage product of BMS-196854 (Oncostatin M), a recombinant anti-inflammatory cytokine.

PubMed

Zhao, F; Stein, D J; Paborji, M; Cash, P W; Root, B J; Wei, Z; Knupp, C J

2001-01-01

BMS-196843 (Oncostatin M) is a therapeutic recombinant protein in development. Scale-up process changes led to unexpected instability of the bulk drug substance solution during storage. A product with an apparent higher MW than the parent protein was observed by the size-exclusion chromatography (SEC). This study was aimed to fully characterize the product and to identify a solution to stabilize the protein. SEC, SDS-PAGE, tryptic mapping, and N-terminal sequencing were performed to characterize the unknown product. The effect of pH, temperature, bulk concentration, and immobilized trypsin inhibitor on the degradation rate was studied to elucidate the mechanism and to identify stabilization strategies. Despite the apparent high MW indicated initially by SEC, the unknown was characterized to be a degradation product resulted from a backbone cleavage between residues Arg145-Gly146. The resulting fragments from the backbone cleavage were, however, still linked through an intramolecular disulfide bond. Thus, the final product had a more open structure with an increased hydrodynamic radius compared to the parent protein, which explains the initial SEC results. The site-specific backbone cleavage was suspected to be catalyzed by trypsin-like protease impurities in the bulk solution. The bulk drug substance solution was subsequently treated with immobilized soybean trypsin inhibitor, and the degradation rate was significantly reduced. Furthermore, increasing the solution pH from 5 to 8 led to an increase in the degradation rate, which was consistent with the expected pH dependency of trypsin activity. In addition, the effect of bulk concentration also supported the involvement of protease impurities rather than a spontaneous peptide bond hydrolysis reaction. Trace trypsin-like protease impurities led to an unusual site-specific backbone cleavage of BMS-196854. The proteolytic degradation can be minimized by treating the bulk solution with immobilized soybean trypsin inhibitor and/or controlling the solution pH and storage temperature.

CHARACTERIZING SITE HYDROLOGY (REGION 5)

EPA Science Inventory

Hydrogeology is the foundation of subsurface site characterization for evaluations of monitored natural attenuation (MNA). Three case studies are presented. Examples of the potentially detrimental effects of drilling additives on ground-water samples from monitoring wells are d...

Challenges with Final Status Surveys at a Large Decommissioning Site - 13417

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

Downey, Heath; Collopy, Peter; Shephard, Eugene

2013-07-01

As part of decommissioning a former nuclear fuel manufacturing site, one of the crucial final steps is to conduct Final Status Surveys (FSS) in order to demonstrate compliance with the release criteria. At this decommissioning site, the area for FSS was about 100 hectares (248 acres) and included varying terrain, wooded areas, ponds, excavations, buildings and a brook. The challenges in performing the FSS included determining location, identifying FSS units, logging gamma walkover survey data, determining sample locations, managing water in excavations, and diverting water in the brook. The approaches taken to overcome these challenges will be presented in themore » paper. The paper will present and discuss lessons learned that will aid others in the FSS process. (authors)« less

Cone penetrometer testing and discrete-depth ground water sampling techniques: A cost-effective method of site characterization in a multiple-aquifer setting

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

Zemo, D.A.; Pierce, Y.G.; Gallinatti, J.D.

Cone penetrometer testing (CPT), combined with discrete-depth ground water sampling methods, can significantly reduce the time and expense required to characterize large sites that have multiple aquifers. Results from the screening site characterization can then be used to design and install a cost-effective monitoring well network. At a site in northern California, it was necessary to characterize the stratigraphy and the distribution of volatile organic compounds (VOCs). To expedite characterization, a five-week field screening program was implemented that consisted of a shallow ground water survey, CPT soundings and pore-pressure measurements, and discrete-depth ground water sampling. Based on continuous lithologic informationmore » provided by the CPT soundings, four predominantly coarse-grained, water yielding stratigraphic packages were identified. Seventy-nine discrete-depth ground water samples were collected using either shallow ground water survey techniques, the BAT Enviroprobe, or the QED HydroPunch I, depending on subsurface conditions. Using results from these efforts, a 20-well monitoring network was designed and installed to monitor critical points within each stratigraphic package. Good correlation was found for hydraulic head and chemical results between discrete-depth screening data and monitoring well data. Understanding the vertical VOC distribution and concentrations produced substantial time and cost savings by minimizing the number of permanent monitoring wells and reducing the number of costly conductor casings that had to be installed. Additionally, significant long-term cost savings will result from reduced sampling costs, because fewer wells comprise the monitoring network. The authors estimate these savings to be 50% for site characterization costs, 65% for site characterization time, and 60% for long-term monitoring costs.« less

Development of a Comprehensive Plan for Scientific Research, Exploration, and Design: Creation of an Undergroung Radioactive Waste Isloation Facility at the Nizhnekansky Rock Massif

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

Jardine, L J

2005-06-15

ISTC Partner Project No.2377, ''Development of a General Research and Survey Plan to Create an Underground RW Isolation Facility in Nizhnekansky Massif'', funded a group of key Russian experts in geologic disposal, primarily at Federal State Unitary Enterprise All-Russian Design and Research Institute of Engineering Production (VNIPIPT) and Mining Chemical Combine Krasnoyarsk-26 (MCC K-26) (Reference 1). The activities under the ISTC Partner Project were targeted to the creation of an underground research laboratory which was to justify the acceptability of the geologic conditions for ultimate isolation of high-level waste in Russia. In parallel to this project work was also undermore » way with Minatom's financial support to characterize alternative sections of the Nizhnekansky granitoid rock massif near the MCC K-26 site to justify the possibility of creating an underground facility for long-term or ultimate isolation of radioactive waste (RW) and spent nuclear fuel (SNF). (Reference 2) The result was a synergistic, integrated set of activities several years that advanced the geologic repository site characterization and development of a proposed underground research laboratory better than could have been expected with only the limited funds from ISTC Partner Project No.2377 funded by the U.S. DOE-RW. There were four objectives of this ISTC Partner Project 2377 geologic disposal work: (1) Generalize and analyze all research work done previously at the Nizhnekansky granitoid massif by various organizations; (2) Prepare and issue a declaration of intent (DOI) for proceeding with an underground research laboratory in a granite massif near the MCC K-26 site. (The DOI is similar to a Record of Decision in U.S. terminology). (3) Proceeding from the data obtained as a result of scientific research and exploration and design activities, prepare a justification of investment (JOI) for an underground research laboratory in as much detail as the available site characterization data allow. Consider the possibility of the substantiated selection of a specific site for the underground laboratory at this stage. (The JOI is similar to an advanced conceptual design or preliminary design in U.S. terminology). (4) Perform a preliminary safety assessment of the geologic isolation of radioactive waste and unreprocessable spent nuclear fuel (SNF) in the Nizhnekansky massif. Significant progress has been made toward fulfilling the joint project objectives. The results were documented in a series of quarterly reports and one final report over a period of {approx}2 3/4 years.« less

Seismic site coefficients and acceleration design response spectra based on conditions in South Carolina : final report.

DOT National Transportation Integrated Search

2014-11-15

The simplified procedure in design codes for determining earthquake response spectra involves : estimating site coefficients to adjust available rock accelerations to site accelerations. Several : investigators have noted concerns with the site coeff...

A GIS-BASED MULTI-CRITERIA EVALUATION SYSTEM FOR SELECTION OF LANDFILL SITES: a case study from Abu Dhabi, United Arab Emirates

NASA Astrophysics Data System (ADS)

Issa, S. M.; Shehhi, B. Al

2012-07-01

Landfill sites receive 92% of total annual solid waste produced by municipalities in the emirate of Abu Dhabi. In this study, candidate sites for an appropriate landfill location for the Abu Dhabi municipal area are determined by integrating geographic information systems (GIS) and multi-criteria evaluation (MCE) analysis. To identify appropriate landfill sites, eight input map layers including proximity to urban areas, proximity to wells and water table depth, geology and topography, proximity to touristic and archeological sites, distance from roads network, distance from drainage networks, and land slope are used in constraint mapping. A final map was generated which identified potential areas showing suitability for the location of the landfill site. Results revealed that 30% of the study area was identified as highly suitable, 25% as suitable, and 45% as unsuitable. The selection of the final landfill site, however, requires further field research.

CHARACTERIZING SITE HYDROLOGY (WORKSHOP MSA PRESENTATION)

EPA Science Inventory

Hydrogeology is the foundation of subsurface site characterization for evaluations of monitored natural attenuation (MNA). Three case studies are presented. Examples of the potentially detrimental effects of drilling additives on ground-water samples from monitoring wells are d...

Characterizing Site Hydrology (Region 10, Seattle, WA)

EPA Science Inventory

Hydrogeology is the foundation of subsurface site characterization for evaluations of monitored natural attenuation (MNA). Three case studies are presented. Examples of the potentially detrimental effects of drilling additives on ground-water samples from monitoring wells are d...

CHARACTERIZING SITE HYDROLOGY (REGION 8 WORKSHOP)

EPA Science Inventory

Hydrogeology is the foundation of subsurface site characterization for evaluations of monitored natural attenuation (MNA). Three case studies are presented. Examples of the potentially detrimental effects of drilling additives on ground-water samples from monitoring wells are d...

Yucca Mountain Biological Resources Monitoring Program; Annual report, FY91

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

NONE

1992-01-01

The US Department of Energy (DOE) is required by the Nuclear Waste Policy Act of 1982 (as amended in 1987) to study and characterize Yucca Mountain as a possible site for a geologic repository for high-level nuclear waste. During site characterization, the DOE will conduct a variety of geotechnical, geochemical, geological, and hydrological studies to determine the suitability of Yucca Mountain as a repository. To ensure that site characterization activities (SCA) do not adversely affect the Yucca Mountain area, an environmental program has been implemented to monitor and mitigate potential impacts and to ensure that activities comply with applicable environmentalmore » regulations. This report describes the activities and accomplishments during fiscal year 1991 (FY91) for six program areas within the Terrestrial Ecosystem component of the YMP environmental program. The six program areas are Site Characterization Activities Effects, Desert Tortoises, Habitat Reclamation, Monitoring and Mitigation, Radiological Monitoring, and Biological Support.« less

Adaptive Sampling approach to environmental site characterization at Joliet Army Ammunition Plant: Phase 2 demonstration

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

Bujewski, G.E.; Johnson, R.L.

1996-04-01

Adaptive sampling programs provide real opportunities to save considerable time and money when characterizing hazardous waste sites. This Strategic Environmental Research and Development Program (SERDP) project demonstrated two decision-support technologies, SitePlanner{trademark} and Plume{trademark}, that can facilitate the design and deployment of an adaptive sampling program. A demonstration took place at Joliet Army Ammunition Plant (JAAP), and was unique in that it was tightly coupled with ongoing Army characterization work at the facility, with close scrutiny by both state and federal regulators. The demonstration was conducted in partnership with the Army Environmental Center`s (AEC) Installation Restoration Program and AEC`s Technology Developmentmore » Program. AEC supported researchers from Tufts University who demonstrated innovative field analytical techniques for the analysis of TNT and DNT. SitePlanner{trademark} is an object-oriented database specifically designed for site characterization that provides an effective way to compile, integrate, manage and display site characterization data as it is being generated. Plume{trademark} uses a combination of Bayesian analysis and geostatistics to provide technical staff with the ability to quantitatively merge soft and hard information for an estimate of the extent of contamination. Plume{trademark} provides an estimate of contamination extent, measures the uncertainty associated with the estimate, determines the value of additional sampling, and locates additional samples so that their value is maximized.« less

Molecular Characterization of Transgene Integration by Next-Generation Sequencing in Transgenic Cattle

PubMed Central

Zhang, Ran; Yin, Yinliang; Zhang, Yujun; Li, Kexin; Zhu, Hongxia; Gong, Qin; Wang, Jianwu; Hu, Xiaoxiang; Li, Ning

2012-01-01

As the number of transgenic livestock increases, reliable detection and molecular characterization of transgene integration sites and copy number are crucial not only for interpreting the relationship between the integration site and the specific phenotype but also for commercial and economic demands. However, the ability of conventional PCR techniques to detect incomplete and multiple integration events is limited, making it technically challenging to characterize transgenes. Next-generation sequencing has enabled cost-effective, routine and widespread high-throughput genomic analysis. Here, we demonstrate the use of next-generation sequencing to extensively characterize cattle harboring a 150-kb human lactoferrin transgene that was initially analyzed by chromosome walking without success. Using this approach, the sites upstream and downstream of the target gene integration site in the host genome were identified at the single nucleotide level. The sequencing result was verified by event-specific PCR for the integration sites and FISH for the chromosomal location. Sequencing depth analysis revealed that multiple copies of the incomplete target gene and the vector backbone were present in the host genome. Upon integration, complex recombination was also observed between the target gene and the vector backbone. These findings indicate that next-generation sequencing is a reliable and accurate approach for the molecular characterization of the transgene sequence, integration sites and copy number in transgenic species. PMID:23185606

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

Link, P.K.

A total of 48 papers were presented at the Engineering Geology and Geotechnical Engineering 30th Symposium. These papers are presented in this proceedings under the following headings: site characterization--Pocatello area; site characterization--Boise Area; site assessment; Idaho National Engineering Laboratory; geophysical methods; remediation; geotechnical engineering; and hydrogeology, northern and western Idaho. Individual papers have been processed separately for inclusion in the Energy Science and Technology Database.

Targeted Single-Site MOF Node Modification: Trivalent Metal Loading via Atomic Layer Deposition

DOE PAGES

Kim, In Soo; Borycz, Joshua; Platero-Prats, Ana E.; ...

2015-07-02

Postsynthetic functionalization of metal organic frameworks (MOFs) enables the controlled, high-density incorporation of new atoms on a crystallographically precise framework. Leveraging the broad palette of known atomic layer deposition (ALD) chemistries, ALD in MOFs (AIM) is one such targeted approach to construct diverse, highly functional, few-atom clusters. In this paper, we demonstrate the saturating reaction of trimethylindium (InMe 3) with the node hydroxyls and ligated water of NU-1000, which takes place without significant loss of MOF crystallinity or internal surface area. We computationally identify the elementary steps by which trimethylated trivalent metal compounds (ALD precursors) react with this Zr-based MOFmore » node to generate a uniform and well characterized new surface layer on the node itself, and we predict a final structure that is fully consistent with experimental X-ray pair distribution function (PDF) analysis. Finally, we further demonstrate tunable metal loading through controlled number density of the reactive handles (–OH and –OH 2) achieved through node dehydration at elevated temperatures.« less

Targeted Single-Site MOF Node Modification: Trivalent Metal Loading via Atomic Layer Deposition

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

Kim, In Soo; Borycz, Joshua; Platero-Prats, Ana E.

Postsynthetic functionalization of metal organic frameworks (MOFs) enables the controlled, high-density incorporation of new atoms on a crystallographically precise framework. Leveraging the broad palette of known atomic layer deposition (ALD) chemistries, ALD in MOFs (AIM) is one such targeted approach to construct diverse, highly functional, few-atom clusters. In this paper, we demonstrate the saturating reaction of trimethylindium (InMe 3) with the node hydroxyls and ligated water of NU-1000, which takes place without significant loss of MOF crystallinity or internal surface area. We computationally identify the elementary steps by which trimethylated trivalent metal compounds (ALD precursors) react with this Zr-based MOFmore » node to generate a uniform and well characterized new surface layer on the node itself, and we predict a final structure that is fully consistent with experimental X-ray pair distribution function (PDF) analysis. Finally, we further demonstrate tunable metal loading through controlled number density of the reactive handles (–OH and –OH 2) achieved through node dehydration at elevated temperatures.« less

Engineering synthetic TAL effectors with orthogonal target sites

PubMed Central

Garg, Abhishek; Lohmueller, Jason J.; Silver, Pamela A.; Armel, Thomas Z.

2012-01-01

The ability to engineer biological circuits that process and respond to complex cellular signals has the potential to impact many areas of biology and medicine. Transcriptional activator-like effectors (TALEs) have emerged as an attractive component for engineering these circuits, as TALEs can be designed de novo to target a given DNA sequence. Currently, however, the use of TALEs is limited by degeneracy in the site-specific manner by which they recognize DNA. Here, we propose an algorithm to computationally address this problem. We apply our algorithm to design 180 TALEs targeting 20 bp cognate binding sites that are at least 3 nt mismatches away from all 20 bp sequences in putative 2 kb human promoter regions. We generated eight of these synthetic TALE activators and showed that each is able to activate transcription from a targeted reporter. Importantly, we show that these proteins do not activate synthetic reporters containing mismatches similar to those present in the genome nor a set of endogenous genes predicted to be the most likely targets in vivo. Finally, we generated and characterized TALE repressors comprised of our orthogonal DNA binding domains and further combined them with shRNAs to accomplish near complete repression of target gene expression. PMID:22581776

The BCube Crawler: Web Scale Data and Service Discovery for EarthCube.

NASA Astrophysics Data System (ADS)

Lopez, L. A.; Khalsa, S. J. S.; Duerr, R.; Tayachow, A.; Mingo, E.

2014-12-01

Web-crawling, a core component of the NSF-funded BCube project, is researching and applying the use of big data technologies to find and characterize different types of web services, catalog interfaces, and data feeds such as the ESIP OpenSearch, OGC W*S, THREDDS, and OAI-PMH that describe or provide access to scientific datasets. Given the scale of the Internet, which challenges even large search providers such as Google, the BCube plan for discovering these web accessible services is to subdivide the problem into three smaller, more tractable issues. The first, to be able to discover likely sites where relevant data and data services might be found, the second, to be able to deeply crawl the sites discovered to find any data and services which might be present. Lastly, to leverage the use of semantic technologies to characterize the services and data found, and to filter out everything but those relevant to the geosciences. To address the first two challenges BCube uses an adapted version of Apache Nutch (which originated Hadoop), a web scale crawler, and Amazon's ElasticMapReduce service for flexibility and cost effectiveness. For characterization of the services found, BCube is examining existing web service ontologies for their applicability to our needs and will re-use and/or extend these in order to query for services with specific well-defined characteristics in scientific datasets such as the use of geospatial namespaces. The original proposal for the crawler won a grant from Amazon's academic program, which allowed us to become operational; we successfully tested the Bcube Crawler at web scale obtaining a significant corpus, sizeable enough to enable work on characterization of the services and data found. There is still plenty of work to be done, doing "smart crawls" by managing the frontier, developing and enhancing our scoring algorithms and fully implementing the semantic characterization technologies. We describe the current status of the project, our successes and issues encountered. The final goal of the BCube crawler project is to provide relevant data services to other projects on the EarthCube stack and third party partners so they can be brokered and used by a wider scientific community.

Environmental Technology Verification (ETV) Program: Site Characterization and Monitoring Technologies Center

EPA Pesticide Factsheets

The ETV Site Characterization and Monitoring Technology Pilot is composed of EPA, DoD, DOE, other Federal agencies, state regulators, technology evaluation and verification entities, and potential end users of these technologies to facilitate independent..

Role of Imaging Specrometer Data for Model-based Cross-calibration of Imaging Sensors

NASA Technical Reports Server (NTRS)

Thome, Kurtis John

2014-01-01

Site characterization benefits from imaging spectrometry to determine spectral bi-directional reflectance of a well-understood surface. Cross calibration approaches, uncertainties, role of imaging spectrometry, model-based site characterization, and application to product validation.

10 CFR 2.629 - Finality of partial decision on site suitability issues in a combined license proceeding.

Code of Federal Regulations, 2014 CFR

2014-01-01

...), the Director of the Office of New Reactors or the Director of the Office of Nuclear Reactor Regulation... 10 Energy 1 2014-01-01 2014-01-01 false Finality of partial decision on site suitability issues in a combined license proceeding. 2.629 Section 2.629 Energy NUCLEAR REGULATORY COMMISSION AGENCY RULES...

10 CFR 2.629 - Finality of partial decision on site suitability issues in a combined license proceeding.

Code of Federal Regulations, 2013 CFR

2013-01-01

...), the Director of the Office of New Reactors or the Director of the Office of Nuclear Reactor Regulation... 10 Energy 1 2013-01-01 2013-01-01 false Finality of partial decision on site suitability issues in a combined license proceeding. 2.629 Section 2.629 Energy NUCLEAR REGULATORY COMMISSION AGENCY RULES...

Drilling and geophysical logs of the tophole at an oil-and-gas well site, Central Venango County, Pennsylvania

USGS Publications Warehouse

Williams, John H.; Bird, Philip H.; Conger, Randall W.; Anderson, J. Alton

2014-01-01

Collection and integrated analysis of drilling and geophysical logs provided an efficient and effective means for characterizing the geohydrologic framework and conditions penetrated by the tophole at the selected oil-and-gas well site. The logging methods and lessons learned at this well site could be applied at other oil-and-gas drilling sites to better characterize the shallow subsurface with the overall goal of protecting freshwater aquifers during hydrocarbon development.

Polyadenylation site prediction using PolyA-iEP method.

PubMed

Kavakiotis, Ioannis; Tzanis, George; Vlahavas, Ioannis

2014-01-01

This chapter presents a method called PolyA-iEP that has been developed for the prediction of polyadenylation sites. More precisely, PolyA-iEP is a method that recognizes mRNA 3'ends which contain polyadenylation sites. It is a modular system which consists of two main components. The first exploits the advantages of emerging patterns and the second is a distance-based scoring method. The outputs of the two components are finally combined by a classifier. The final results reach very high scores of sensitivity and specificity.

Knowledge-based systems in Japan

NASA Technical Reports Server (NTRS)

Feigenbaum, Edward; Engelmore, Robert S.; Friedland, Peter E.; Johnson, Bruce B.; Nii, H. Penny; Schorr, Herbert; Shrobe, Howard

1994-01-01

This report summarizes a study of the state-of-the-art in knowledge-based systems technology in Japan, organized by the Japanese Technology Evaluation Center (JTEC) under the sponsorship of the National Science Foundation and the Advanced Research Projects Agency. The panel visited 19 Japanese sites in March 1992. Based on these site visits plus other interactions with Japanese organizations, both before and after the site visits, the panel prepared a draft final report. JTEC sent the draft to the host organizations for their review. The final report was published in May 1993.

Discovery and characterization of a photo-oxidative histidine-histidine cross-link in IgG1 antibody utilizing ¹⁸O-labeling and mass spectrometry.

PubMed

Liu, Min; Zhang, Zhongqi; Cheetham, Janet; Ren, Da; Zhou, Zhaohui Sunny

2014-05-20

A novel photo-oxidative cross-linking between two histidines (His-His) has been discovered and characterized in an IgG1 antibody via the workflow of XChem-Finder, (18)O labeling and mass spectrometry (Anal. Chem. 2013, 85, 5900-5908). Its structure was elucidated by peptide mapping with multiple proteases with various specificities (e.g., trypsin, Asp-N, and GluC combined with trypsin or Asp-N) and mass spectrometry with complementary fragmentation modes (e.g., collision-induced dissociation (CID) and electron-transfer dissociation (ETD)). Our data indicated that cross-linking occurred across two identical conserved histidine residues on two separate heavy chains in the hinge region, which is highly flexible and solvent accessible. On the basis of model studies with short peptides, it has been proposed that singlet oxygen reacts with the histidyl imidazole ring to form an endoperoxide and then converted to the 2-oxo-histidine (2-oxo-His) and His+32 intermediates, the latter is subject to a nucleophilic attack by the unmodified histidine; and finally, elimination of a water molecule leads to the final adduct with a net mass increase of 14 Da. Our findings are consistent with this mechanism. Successful discovery of cross-linked His-His again demonstrates the broad applicability and utility of our XChem-Finder approach in the discovery and elucidation of protein cross-linking, particularly without a priori knowledge of the chemical nature and site of cross-linking.

Principles on Radiological Characterization of the Unit 1 at Ignalina NPP for Decommissioning Purposes

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

Poskas, P.; Zujus, R.; Drumstas, G.

There is only one nuclear power plant in Lithuania - Ignalina NPP (INPP). The INPP operated two similar units with installed capacity of 1500 MW(each). They were commissioned in 12/1983 and 08/1987, and the original design lifetime was projected out to 2010 and 2015 respectively. But the first Unit of Ignalina NPP was shutdown December 31, 2004, and second Unit will be closed down before 2010 taking into consideration substantial long-term financial assistance from the EU, G7 and other states as well as international institutions. Implementation of dismantling activities requires detailed knowledge of the radiological situation at the Unit 1.more » General Programme of Radiological Survey for Ignalina NPP Unit 1 based on NUREG-1575 was prepared in 2005- 2006 by Consortium led by Lithuanian Energy Institute and approved by Regulatory Bodies. It includes such main steps as historical site assessment, scoping, characterization, remedial actions/decontamination support surveys and final status surveys. General Programme of Radiological Survey defines content and principles of the surveys, and preliminary survey considerations, including identification of the contaminants, establishment of the free release levels, principles on areas classification depending on contamination potential, identification of the final survey units, criteria for selection survey instrumentation, techniques and methods etc. So, in the paper information on these principles and the content of the different stages in General Programme of Radiological Survey is presented. (authors)« less

Mobile laboratories: An innovative and efficient solution for radiological characterization of sites under or after decommissioning.

PubMed

Goudeau, V; Daniel, B; Dubot, D

2017-04-21

During the operation and the decommissioning of a nuclear site the operator must assure the protection of the workers and the environment. It must furthermore identify and classify the various wastes, while optimizing the associated costs. At all stages of the decommissioning radiological measurements are performed to determine the initial situation, to monitor the demolition and clean-up, and to verify the final situation. Radiochemical analysis is crucial for the radiological evaluation process to optimize the clean-up operations and to the respect limits defined with the authorities. Even though these types of analysis are omnipresent in activities such as the exploitation, the monitoring, and the cleaning up of nuclear plants, some nuclear sites do not have their own radiochemical analysis laboratory. Mobile facilities can overcome this lack when nuclear facilities are dismantled, when contaminated sites are cleaned-up, or in a post-accident situation. The current operations for the characterization of radiological soils of CEA nuclear facilities, lead to a large increase of radiochemical analysis. To manage this high throughput of samples in a timely manner, the CEA has developed a new mobile laboratory for the clean-up of its soils, called SMaRT (Shelter for Monitoring and nucleAR chemisTry). This laboratory is dedicated to the preparation and the radiochemical analysis (alpha, beta, and gamma) of potentially contaminated samples. In this framework, CEA and Eichrom laboratories has signed a partnership agreement to extend the analytical capacities and bring on site optimized and validated methods for different problematic. Gamma-emitting radionuclides can usually be measured in situ as little or no sample preparation is required. Alpha and beta-emitting radionuclides are a different matter. Analytical chemistry laboratory facilities are required. Mobile and transportable laboratories equipped with the necessary tools can provide all that is needed. The main advantage of a mobile laboratory is its portability; the shelter can be placed in the vicinity of nuclear facilities under decommissioning, or of contaminated sites with infrastructures unsuitable for the reception and treatment of radioactive samples. Radiological analysis can then be performed without the disadvantages of radioactive material transport. This paper describes how this solution allows a fast response and control of costs, with a high analytical capacity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Middlesex FUSRAP Site - A Path to Site-Wide Closure - 13416

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

Miller, David M.; Edge, Helen

2013-07-01

The road-map to obtaining closure of the Middlesex Sampling Plant FUSRAP site in Middlesex, New Jersey (NJ) has required a multi-faceted approach, following the CERCLA Process. Since 1998, the US ACE, ECC, and other contractors have completed much of the work required for regulatory acceptance of site closure with unrestricted use. To date, three buildings have been decontaminated, demolished, and disposed of. Two interim storage piles have been removed and disposed of, followed by the additional removal and disposal of over 87,000 tons of radiologically and chemically-impacted subsurface soils by the summer of 2008. The US ACE received a determinationmore » from the EPA for the soils Operable Unit, (OU)-1, in September 2010 that the remedial excavations were acceptable, and meet the criteria for unrestricted use as required by the 2004 Record of Decision (ROD) for OU-1. Following the completion of OU-1, the project delivery team performed additional field investigation of the final Operable Unit for Middlesex, OU-2, Groundwater. As of December 2012, the project delivery team has completed a Supplemental Remedial Investigation, which will be followed with a streamlined Feasibility Study, Proposed Plan, and ROD. Several years of historical groundwater data was available from previous investigations and the FUSRAP Environmental Surveillance Program. Historical data indicated sporadic detections of Volatile Organic Compounds (VOCs), primarily trichloroethylene (TCE), carbon tetrachloride (CT), and methyl tert-butyl ether (MTBE), with no apparent trend or pattern indicating extent or source of the VOC impact. In 2008, the project delivery team initiated efforts to re-assess the Conceptual Site Model (CSM) for groundwater. The bedrock was re-evaluated as a leaky multi-unit aquifer, and a plan was developed for additional investigations for adequate bedrock characterization and delineation of groundwater contaminated primarily by CT, TCE, and tetrachloroethene (PCE). The investigation was designed to accumulate multiple lines of evidence to determine the source and to delineate the extent of contamination, as required to complete the CERCLA Process and gain regulatory acceptance. Investigative techniques included in-well vertical flow tracing, borehole geophysics and packer testing of temporary test holes to characterize contamination in the bedrock fractures beneath the site, and to delineate likely source areas. (authors)« less

Study of electron transport in the functionalized nanotubes and their impact on the electron transfer in the active site of horseradish peroxidase

NASA Astrophysics Data System (ADS)

Feizabadi, Mina; Ajloo, Davood; Soleymanpour, Ahmad; Faridnouri, Hassan

2018-05-01

Electrochemical characterization of functionalized carbon nanotubes (f-CNT) including carboxyl (CNT-COOH), amine (CNT-NH2) and hydroxyl (CNT-OH) functional groups were studied using differential pulse voltammetry (DPV). The current-voltage (I-V) curves were obtained from each system and the effect of f-CNT on redox interaction of horseradish peroxidase (HRP) immobilized on the electrode surface was investigated. The non-equilibrium Green's function (NEGF) combined with density functional theory (DFT) were used to study the transport properties of f-CNT. Additionally, the effect of the number of functional groups on transport properties of CNT, I-V characteristics, electronic transmission coefficients and spatial distribution of f-CNTs have been calculated and analyzed. The results showed that the carboxyl derivative has larger transmission coefficients and current value than other f-CNTs. Then, the effect of functional groups on the electron transport in heme group of HRP is discussed. Finally, the effect of a covalent bond between active site amino acids and amine functional group of CNT was investigated and discussed.

Characterization of Cu(II)-reconstituted ACC Oxidase using experimental and theoretical approaches.

PubMed

El Bakkali-Tahéri, Nadia; Tachon, Sybille; Orio, Maylis; Bertaina, Sylvain; Martinho, Marlène; Robert, Viviane; Réglier, Marius; Tron, Thierry; Dorlet, Pierre; Simaan, A Jalila

2017-06-01

1-Aminocyclopropane-1-carboxylic acid oxidase (ACCO) is a non heme iron(II) containing enzyme that catalyzes the final step of the ethylene biosynthesis in plants. The iron(II) ion is bound in a facial triad composed of two histidines and one aspartate (H177, D179 and H234). Several active site variants were generated to provide alternate binding motifs and the enzymes were reconstituted with copper(II). Continuous wave (cw) and pulsed Electron Paramagnetic Resonance (EPR) spectroscopies as well as Density Functional Theory (DFT) calculations were performed and models for the copper(II) binding sites were deduced. In all investigated enzymes, the copper ion is equatorially coordinated by the two histidine residues (H177 and H234) and probably two water molecules. The copper-containing enzymes are inactive, even when hydrogen peroxide is used in peroxide shunt approach. EPR experiments and DFT calculations were undertaken to investigate substrate's (ACC) binding on the copper ion and the results were used to rationalize the lack of copper-mediated activity. Copyright © 2017 Elsevier Inc. All rights reserved.

New insights into replication origin characteristics in metazoans

PubMed Central

Puy, Aurore; Rialle, Stéphanie; Kaplan, Noam; Segal, Eran

2012-01-01

We recently reported the identification and characterization of DNA replication origins (Oris) in metazoan cell lines. Here, we describe additional bioinformatic analyses showing that the previously identified GC-rich sequence elements form origin G-rich repeated elements (OGREs) that are present in 67% to 90% of the DNA replication origins from Drosophila to human cells, respectively. Our analyses also show that initiation of DNA synthesis takes place precisely at 160 bp (Drosophila) and 280 bp (mouse) from the OGRE. We also found that in most CpG islands, an OGRE is positioned in opposite orientation on each of the two DNA strands and detected two sites of initiation of DNA synthesis upstream or downstream of each OGRE. Conversely, Oris not associated with CpG islands have a single initiation site. OGRE density along chromosomes correlated with previously published replication timing data. Ori sequences centered on the OGRE are also predicted to have high intrinsic nucleosome occupancy. Finally, OGREs predict G-quadruplex structures at Oris that might be structural elements controlling the choice or activation of replication origins. PMID:22373526

Identifying Autism from Resting-State fMRI Using Long Short-Term Memory Networks.

PubMed

Dvornek, Nicha C; Ventola, Pamela; Pelphrey, Kevin A; Duncan, James S

2017-09-01

Functional magnetic resonance imaging (fMRI) has helped characterize the pathophysiology of autism spectrum disorders (ASD) and carries promise for producing objective biomarkers for ASD. Recent work has focused on deriving ASD biomarkers from resting-state functional connectivity measures. However, current efforts that have identified ASD with high accuracy were limited to homogeneous, small datasets, while classification results for heterogeneous, multi-site data have shown much lower accuracy. In this paper, we propose the use of recurrent neural networks with long short-term memory (LSTMs) for classification of individuals with ASD and typical controls directly from the resting-state fMRI time-series. We used the entire large, multi-site Autism Brain Imaging Data Exchange (ABIDE) I dataset for training and testing the LSTM models. Under a cross-validation framework, we achieved classification accuracy of 68.5%, which is 9% higher than previously reported methods that used fMRI data from the whole ABIDE cohort. Finally, we presented interpretation of the trained LSTM weights, which highlight potential functional networks and regions that are known to be implicated in ASD.

Oxime amides as a novel zinc binding group in histone deacetylase inhibitors: synthesis, biological activity, and computational evaluation.

PubMed

Botta, Cinzia B; Cabri, Walter; Cini, Elena; De Cesare, Lucia; Fattorusso, Caterina; Giannini, Giuseppe; Persico, Marco; Petrella, Antonello; Rondinelli, Francesca; Rodriquez, Manuela; Russo, Adele; Taddei, Maurizio

2011-04-14

Several oxime containing molecules, characterized by a SAHA-like structure, were explored to select a potentially new biasing binding element for the zinc in HDAC catalytic site. All compounds were evaluated for their in vitro inhibitory activity against the 11 human HDACs isoforms. After identification of a "hit" molecule, a programmed variation at the cap group and at the linker was carried out in order to increase HDAC inhibition and/or paralogue selectivity. Some of the new derivatives showed increased activity against a number of HDAC isoforms, even if their overall activity range is still far from the inhibition values reported for SAHA. Moreover, different from what was reported for their hydroxamic acid analogues the new α-oxime amide derivatives do not select between class I and class II HDACs; rather they target specific isoforms in each class. These somehow contradictory results were finally rationalized by a computational assisted SAR, which gave us the chance to understand how the oxime derivatives interact with the catalytic site and justify the observed activity profile.

Enhanced MALDI-TOF MS Analysis of Phosphopeptides Using an Optimized DHAP/DAHC Matrix

PubMed Central

Hou, Junjie; Xie, Zhensheng; Xue, Peng; Cui, Ziyou; Chen, Xiulan; Li, Jing; Cai, Tanxi; Wu, Peng; Yang, Fuquan

2010-01-01

Selecting an appropriate matrix solution is one of the most effective means of increasing the ionization efficiency of phosphopeptides in matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). In this study, we systematically assessed matrix combinations of 2, 6-dihydroxyacetophenone (DHAP) and diammonium hydrogen citrate (DAHC), and demonstrated that the low ratio DHAP/DAHC matrix was more effective in enhancing the ionization of phosphopeptides. Low femtomole level of phosphopeptides from the tryptic digests of α-casein and β-casein was readily detected by MALDI-TOF-MS in both positive and negative ion mode without desalination or phosphopeptide enrichment. Compared with the DHB/PA matrix, the optimized DHAP/DAHC matrix yielded superior sample homogeneity and higher phosphopeptide measurement sensitivity, particularly when multiple phosphorylated peptides were assessed. Finally, the DHAP/DAHC matrix was applied to identify phosphorylation sites from α-casein and β-casein and to characterize two phosphorylation sites from the human histone H1 treated with Cyclin-Dependent Kinase-1 (CDK1) by MALDI-TOF/TOF MS. PMID:20339515

Identifying Autism from Resting-State fMRI Using Long Short-Term Memory Networks

PubMed Central

Dvornek, Nicha C.; Ventola, Pamela; Pelphrey, Kevin A.; Duncan, James S.

2017-01-01

Functional magnetic resonance imaging (fMRI) has helped characterize the pathophysiology of autism spectrum disorders (ASD) and carries promise for producing objective biomarkers for ASD. Recent work has focused on deriving ASD biomarkers from resting-state functional connectivity measures. However, current efforts that have identified ASD with high accuracy were limited to homogeneous, small datasets, while classification results for heterogeneous, multi-site data have shown much lower accuracy. In this paper, we propose the use of recurrent neural networks with long short-term memory (LSTMs) for classification of individuals with ASD and typical controls directly from the resting-state fMRI time-series. We used the entire large, multi-site Autism Brain Imaging Data Exchange (ABIDE) I dataset for training and testing the LSTM models. Under a cross-validation framework, we achieved classification accuracy of 68.5%, which is 9% higher than previously reported methods that used fMRI data from the whole ABIDE cohort. Finally, we presented interpretation of the trained LSTM weights, which highlight potential functional networks and regions that are known to be implicated in ASD. PMID:29104967

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

Not Available

The Nuclear Waste Policy Act of 1982 (42 USC sections 10101-10226) requires the environmental assessment of a proposed site to include a statement of the basis for nominating a site as suitable for characterization. Volume 2 provides a detailed statement evaluating the site suitability of the Deaf Smith County Site under DOE siting guidelines, as well as a comparison of the Deaf Smith County Site to the other sites under consideration. The evaluation of the Deaf Smith County Site is based on the impacts associated with the reference repository design, but the evaluation will not change if based on themore » Mission Plan repository concept. The second part of this document compares the Deaf Smith County Site to Davis Canyon, Hanford, Richton Dome and Yucca Mountain. This comparison is required under DOE guidelines and is not intended to directly support subsequent recommendation of three sites for characterization as candidate sites. 259 refs., 29 figs., 66 refs. (MHB)« less

Disposal site quality team final report

DOT National Transportation Integrated Search

2001-09-01

The disposal site quality team was formed in July 2000 to address Caltrans (Department) and Federal Highway Administration (FHWA) policies on disposal, staging, and borrow areas (DSB), including plant sites, contractor yards, and access roads. Caltra...

Environmental characterization of two potential locations at Hanford for a new production reactor

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

Watson, E.C.; Becker, C.D.; Fitzner, R.E.

This report describes various environmental aspects of two areas on the Hanford Site that are potential locations for a New Production Reactor (NPR). The area known as the Skagit Hanford Site is considered the primary or reference site. The second area, termed the Firehouse Site, is considered the alternate site. The report encompasses an environmental characterization of these two potential NPR locations. Eight subject areas are covered: geography and demography; ecology; meteorology; hydrology; geology; cultural resources assessment; economic and social effects of station construction and operation; and environmental monitoring. 80 refs., 68 figs., 109 tabs.

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.

The "fossilized" mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate.

PubMed

Richardson, Aaron O; Rice, Danny W; Young, Gregory J; Alverson, Andrew J; Palmer, Jeffrey D

2013-04-15

The mitochondrial genomes of flowering plants vary greatly in size, gene content, gene order, mutation rate and level of RNA editing. However, the narrow phylogenetic breadth of available genomic data has limited our ability to reconstruct these traits in the ancestral flowering plant and, therefore, to infer subsequent patterns of evolution across angiosperms. We sequenced the mitochondrial genome of Liriodendron tulipifera, the first from outside the monocots or eudicots. This 553,721 bp mitochondrial genome has evolved remarkably slowly in virtually all respects, with an extraordinarily low genome-wide silent substitution rate, retention of genes frequently lost in other angiosperm lineages, and conservation of ancestral gene clusters. The mitochondrial protein genes in Liriodendron are the most heavily edited of any angiosperm characterized to date. Most of these sites are also edited in various other lineages, which allowed us to polarize losses of editing sites in other parts of the angiosperm phylogeny. Finally, we added comprehensive gene sequence data for two other magnoliids, Magnolia stellata and the more distantly related Calycanthus floridus, to measure rates of sequence evolution in Liriodendron with greater accuracy. The Magnolia genome has evolved at an even lower rate, revealing a roughly 5,000-fold range of synonymous-site divergence among angiosperms whose mitochondrial gene space has been comprehensively sequenced. Using Liriodendron as a guide, we estimate that the ancestral flowering plant mitochondrial genome contained 41 protein genes, 14 tRNA genes of mitochondrial origin, as many as 7 tRNA genes of chloroplast origin, >700 sites of RNA editing, and some 14 colinear gene clusters. Many of these gene clusters, genes and RNA editing sites have been variously lost in different lineages over the course of the ensuing ∽200 million years of angiosperm evolution.

A membrane-embedded pathway delivers general anesthetics to two interacting binding sites in the Gloeobacter violaceus ion channel.

PubMed

Arcario, Mark J; Mayne, Christopher G; Tajkhorshid, Emad

2017-06-09

General anesthetics exert their effects on the central nervous system by acting on ion channels, most notably pentameric ligand-gated ion channels. Although numerous studies have focused on pentameric ligand-gated ion channels, the details of anesthetic binding and channel modulation are still debated. A better understanding of the anesthetic mechanism of action is necessary for the development of safer and more efficacious drugs. Herein, we present a computational study identifying two anesthetic binding sites in the transmembrane domain of the Gloeobacter violaceus ligand-gated ion channel (GLIC) channel, characterize the putative binding pathway, and observe structural changes associated with channel function. Molecular simulations of desflurane reveal a binding pathway to GLIC via a membrane-embedded tunnel using an intrasubunit protein lumen as the conduit, an observation that explains the Meyer-Overton hypothesis, or why the lipophilicity of an anesthetic and its potency are generally proportional. Moreover, employing high concentrations of ligand led to the identification of a second transmembrane site (TM2) that inhibits dissociation of anesthetic from the TM1 site and is consistent with the high concentrations of anesthetics required to achieve clinical effects. Finally, asymmetric binding patterns of anesthetic to the channel were found to promote an iris-like conformational change that constricts and dehydrates the ion pore, creating a 13.5 kcal/mol barrier to ion translocation. Together with previous studies, the simulations presented herein demonstrate a novel anesthetic binding site in GLIC that is accessed through a membrane-embedded tunnel and interacts with a previously known site, resulting in conformational changes that produce a non-conductive state of the channel. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Digital mapping of the Mars Pathfinder landing site: Design, acquisition, and derivation of cartographic products for science applications

USGS Publications Warehouse

Gaddis, L.R.; Kirk, R.L.; Johnson, J. R.; Soderblom, L.A.; Ward, A.W.; Barrett, J.; Becker, K.; Decker, T.; Blue, J.; Cook, D.; Eliason, E.; Hare, T.; Howington-Kraus, E.; Isbell, C.; Lee, E.M.; Redding, B.; Sucharski, R.; Sucharski, T.; Smith, P.H.; Britt, D.T.

1999-01-01

The Imager for Mars Pathfinder (IMP) acquired more than 16,000 images and provided panoramic views of the surface of Mars at the Mars Pathfinder landing site in Ares Vallis. This paper describes the stereoscopic, multispectral IMP imaging sequences and focuses on their use for digital mapping of the landing site and for deriving cartographic products to support science applications of these data. Two-dimensional cartographic processing of IMP data, as performed via techniques and specialized software developed for ISIS (the U.S.Geological Survey image processing software package), is emphasized. Cartographic processing of IMP data includes ingestion, radiometric correction, establishment of geometric control, coregistration of multiple bands, reprojection, and mosaicking. Photogrammetric processing, an integral part of this cartographic work which utilizes the three-dimensional character of the IMP data, supplements standard processing with geometric control and topographic information [Kirk et al., this issue]. Both cartographic and photogrammetric processing are required for producing seamless image mosaics and for coregistering the multispectral IMP data. Final, controlled IMP cartographic products include spectral cubes, panoramic (360?? azimuthal coverage) and planimetric (top view) maps, and topographic data, to be archived on four CD-ROM volumes. Uncontrolled and semicontrolled versions of these products were used to support geologic characterization of the landing site during the nominal and extended missions. Controlled products have allowed determination of the topography of the landing site and environs out to ???60 m, and these data have been used to unravel the history of large- and small-scale geologic processes which shaped the observed landing site. We conclude by summarizing several lessons learned from cartographic processing of IMP data. Copyright 1999 by the American Geophysical Union.

Highway runoff stormwater management potential (HRSMP) site characterization using NASA public domain imagery.

DOT National Transportation Integrated Search

2016-04-01

The focus of this research project was the development of geospatial technology (GST) methodology to : characterize and evaluate highway runoff stormwater management potential (HRSMP) sites in order to : reduce their impact on properties, save lives ...

An intensive monitoring campaign of PAHs for assessing the impact of a steel plant.

PubMed

Di Gilio, A; Ventrella, G; Giungato, P; Tutino, M; Giua, R; Assennato, G; de Gennaro, G

2017-02-01

This study provided a useful approach for assessing the impact of industrial sources on surrounding, especially in a sensitive industrial area as Taranto (South of Italy). Taranto is one of the most industrialized Italian towns, where several emission sources operate simultaneously in proximity to the urban settlement. An intensive monitoring campaign of PAHs was carried out from January 28th to July 30th, 2011, in seven sites located in residential settlement around the industrial area and in the city center. The collected data were integrated with the information about wind direction and speed by means bivariate polarplot in order to characterize and localize the industrial sources. High BaP concentrations were detected especially when Benzene to Toluene ratio (B/T ratio) values excedeed 1 and all receptor sites were downwind to the steel plant. Moreover, in order to discriminate among PAH sources and quantify their contributions, a source apportionment analysis of the collected data was provided by means Principal component Analysis (PCA) and Positive Matrix Factorization (PMF) methods. Finally, the processing of PMF5.0 output by bivariate polar plot, confirmed the impact of steel plant on both industrial sites downwind the steel plant and the city center. B[a]P apportionment was quite similar for industrial and urban sites: the traffic source contributed only 11% and 24% to B[a]P measured at two sites, respectively. Therefore, the proximity of Taranto downtown to industrial pole makes negligible all other source contributions to PAH concentrations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Towards a mechanistic and physiological understanding of a ferredoxin disulfide reductase from the domains Archaea and Bacteria.

PubMed

Prakash, Divya; Walters, Karim A; Martinie, Ryan J; McCarver, Addison C; Kumar, Adepu K; Lessner, Daniel J; Krebs, Carsten; Golbeck, John H; Ferry, James G

2018-05-02

Disulfide reductases reduce other proteins and are critically important for cellular redox signaling and homeostasis. Methanosarcina acetivorans is a methane-producing microbe from the domain Archaea that produces a ferredoxin:disulfide reductase (FDR) for which the crystal structure has been reported, yet its biochemical mechanism and physiological substrates are unknown. FDR and the extensively characterized plant-type ferredoxin:thioredoxin reductase (FTR) belong to a distinct class of disulfide reductases that contain a unique active-site [4Fe-4S] cluster. The results reported here support a mechanism for FDR similar to that reported for FTR with notable exceptions. Unlike FTR, FDR contains a rubredoxin [1Fe-0S] center postulated to mediate electron transfer from ferredoxin to the active-site [4Fe-4S] cluster.  UV-Vis, EPR and Mӧssbauer spectroscopic data indicated that two-electron reduction of the active-site disulfide in FDR involves a one-electron-reduced [4Fe-4S]1+ intermediate previously hypothesized for FTR. Our results support a role for an active-site tyrosine in FDR that occupies the equivalent position of an essential histidine in the active-site of FTR. Of note, one of seven Trxs encoded in the genome (Trx5) and methanoredoxin, a glutaredoxin-like enzyme from M. acetivorans, were reduced by FDR advancing the physiological understanding of FDRs role in the redox metabolism of methanoarchaea. Finally, bioinformatics analyses show FDR homologs are widespread in diverse microbes from the domain Bacteria. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Ebola virus RNA editing depends on the primary editing site sequence and an upstream secondary structure.

PubMed

Mehedi, Masfique; Hoenen, Thomas; Robertson, Shelly; Ricklefs, Stacy; Dolan, Michael A; Taylor, Travis; Falzarano, Darryl; Ebihara, Hideki; Porcella, Stephen F; Feldmann, Heinz

2013-01-01

Ebolavirus (EBOV), the causative agent of a severe hemorrhagic fever and a biosafety level 4 pathogen, increases its genome coding capacity by producing multiple transcripts encoding for structural and nonstructural glycoproteins from a single gene. This is achieved through RNA editing, during which non-template adenosine residues are incorporated into the EBOV mRNAs at an editing site encoding for 7 adenosine residues. However, the mechanism of EBOV RNA editing is currently not understood. In this study, we report for the first time that minigenomes containing the glycoprotein gene editing site can undergo RNA editing, thereby eliminating the requirement for a biosafety level 4 laboratory to study EBOV RNA editing. Using a newly developed dual-reporter minigenome, we have characterized the mechanism of EBOV RNA editing, and have identified cis-acting sequences that are required for editing, located between 9 nt upstream and 9 nt downstream of the editing site. Moreover, we show that a secondary structure in the upstream cis-acting sequence plays an important role in RNA editing. EBOV RNA editing is glycoprotein gene-specific, as a stretch encoding for 7 adenosine residues located in the viral polymerase gene did not serve as an editing site, most likely due to an absence of the necessary cis-acting sequences. Finally, the EBOV protein VP30 was identified as a trans-acting factor for RNA editing, constituting a novel function for this protein. Overall, our results provide novel insights into the RNA editing mechanism of EBOV, further understanding of which might result in novel intervention strategies against this viral pathogen.

Site characterization plan: Yucca Mountain Site, Nevada Research and Development Area, Nevada: Volume 8, Part B: Chapter 8, Sections 8.3.5 through 8.3.5.20

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

NONE

1988-12-01

This site characterization plan (SCP) has been developed for the candidate repository site at Yucca Mountain in the State of Nevada. The SCP includes a description of the Yucca Mountain site (Chapters 1-5), a conceptual design for the repository (Chapter 6), a description of the packaging to be used for the waste to be emplaced in the repository (Chapter 7), and a description of the planned site characterization activities (Chapter 8). The schedules and milestones presented in Sections 8.3 and 8.5 of the SCP were developed to be consistent with the June 1988 draft Amendment to the DOE`s Mission Planmore » for the Civilian Radioactive Waste Management Program. The five month delay in the scheduled start of exploratory shaft construction that was announced recently is not reflected in these schedules. 68 figs., 102 tabs.« less

Carbohydrate recognition by the antiviral lectin cyanovirin-N

PubMed Central

Fujimoto, Yukiji K.; Green, David F.

2012-01-01

Cyanovirin-N is a cyanobacterial lectin with potent antiviral activity, and has been the focus of extensive pre-clinical investigation as a potential prophylactic for the prevention of the sexual transmission of the human immunodeficiency virus (HIV). Here we present a detailed analysis of carbohydrate recognition by this important protein, using a combination of computational methods, including extensive molecular dynamics simulations and Molecular-Mechanics/ Poisson–Boltzmann/Surface-Area (MM/PBSA) energetic analysis. The simulation results strongly suggest that the observed tendency of wildtype CVN to form domain-swapped dimers is the result of a previously unidentified cis-peptide bond present in the monomeric state. The energetic analysis additionally indicates that the highest-affinity ligand for CVN characterized to date (α-Man-(1,2)-α-Man-(1,2)-α-Man) is recognized asymmetrically by the two binding sites. Finally, we are able to provide a detailed map of the role of all binding site functional groups (both backbone and side chain) to various aspects of molecular recognition: general affinity for cognate ligands, specificity for distinct oligosaccharide targets and the asymmetric recognition of α-Man-(1,2)-α-Man-(1,2)-α-Man. Taken as a whole, these results complement past experimental characterization (both structural and thermodynamic) to provide the most complete understanding of carbohydrate recognition by CVN to date. The results also provide strong support for the application of similar approaches to the understanding of other protein–carbohydrate complexes. PMID:23057413

Electrical characterization of 6H crystalline silicon carbide. M.S. Thesis Final Report

NASA Technical Reports Server (NTRS)

Lempner, Stephen E.

1994-01-01

Crystalline silicon carbide (SiC) substrates and epilayers, undoped as well as n- and p-doped, have been electrically characterized by performing Hall effect and resistivity measurements (van der Pauw) over the temperature range of approximately 85 K to 650 K (200 K to 500 K for p-type sample). By fitting the measured temperature dependent carrier concentration data to the single activation energy theoretical model: (1) the activation energy for the nitrogen donor ranged from 0.078 eV to 0.101 eV for a doping concentration range of 10(exp 17) cm(exp -3) to 10(exp 18) cm(exp -3) and (2) the activation energy for the aluminum acceptor was 0.252 eV for a doping concentration of 4.6 x 10(exp 18) cm(exp -3). By fitting the measured temperature dependent carrier concentration data to the double activation energy level theoretical model for the nitrogen donor: (1) the activation energy for the hexagonal site was 0.056 eV and 0.093 eV corresponding to doping concentrations of 3.33 x 10 (exp 17) cm(exp -3) and 1.6 x 10(exp 18) cm(exp -3) and (2) the activation energy for the cubic site was 0.113 and 0.126 eV corresponding to doping concentrations of 4.2 x 10(exp 17) cm(exp -3) and 5.4 x 10(exp 18) cm(exp -3).

SINGLE HEATER TEST FINAL REPORT

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

J.B. Cho

The Single Heater Test is the first of the in-situ thermal tests conducted by the U.S. Department of Energy as part of its program of characterizing Yucca Mountain in Nevada as the potential site for a proposed deep geologic repository for the disposal of spent nuclear fuel and high-level nuclear waste. The Site Characterization Plan (DOE 1988) contained an extensive plan of in-situ thermal tests aimed at understanding specific aspects of the response of the local rock-mass around the potential repository to the heat from the radioactive decay of the emplaced waste. With the refocusing of the Site Characterization Planmore » by the ''Civilian Radioactive Waste Management Program Plan'' (DOE 1994), a consolidated thermal testing program emerged by 1995 as documented in the reports ''In-Situ Thermal Testing Program Strategy'' (DOE 1995) and ''Updated In-Situ Thermal Testing Program Strategy'' (CRWMS M&O 1997a). The concept of the Single Heater Test took shape in the summer of 1995 and detailed planning and design of the test started with the beginning fiscal year 1996. The overall objective of the Single Heater Test was to gain an understanding of the coupled thermal, mechanical, hydrological, and chemical processes that are anticipated to occur in the local rock-mass in the potential repository as a result of heat from radioactive decay of the emplaced waste. This included making a priori predictions of the test results using existing models and subsequently refining or modifying the models, on the basis of comparative and interpretive analyses of the measurements and predictions. A second, no less important, objective was to try out, in a full-scale field setting, the various instruments and equipment to be employed in the future on a much larger, more complex, thermal test of longer duration, such as the Drift Scale Test. This ''shake down'' or trial aspect of the Single Heater Test applied not just to the hardware, but also to the teamwork and cooperation between multiple organizations performing their part in the test.« less

75 FR 65558 - Final Supplemental Environmental Impact Statement, Single Nuclear Unit at the Bellefonte Plant...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-25

... TENNESSEE VALLEY AUTHORITY Final Supplemental Environmental Impact Statement, Single Nuclear Unit... Environmental Impact Statement for a Single Nuclear Unit at the Bellefonte Plant Site (final SEIS) on September... the ROD. TVA prepared the final SEIS to update the extensive environmental information and analyses...

VS30 – A site-characterization parameter for use in building Codes, simplified earthquake resistant design, GMPEs, and ShakeMaps

USGS Publications Warehouse

Borcherdt, Roger D.

2012-01-01

VS30, defined as the average seismic shear-wave velocity from the surface to a depth of 30 meters, has found wide-spread use as a parameter to characterize site response for simplified earthquake resistant design as implemented in building codes worldwide. VS30 , as initially introduced by the author for the US 1994 NEHRP Building Code, provides unambiguous definitions of site classes and site coefficients for site-dependent response spectra based on correlations derived from extensive borehole logging and comparative ground-motion measurement programs in California. Subsequent use of VS30 for development of strong ground motion prediction equations (GMPEs) and measurement of extensive sets of VS borehole data have confirmed the previous empirical correlations and established correlations of SVS30 with VSZ at other depths. These correlations provide closed form expressions to predict S30 V at a large number of additional sites and further justify S30 V as a parameter to characterize site response for simplified building codes, GMPEs, ShakeMap, and seismic hazard mapping.

Superfund Record of Decision (EPA Region 5): Novaco Industries, MI. (First remedial action), (Amendment), September 1991. Final report

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

Not Available

The 2.6-acre Novaco Industries site is a one building site in Temperance, Michigan. Land use in the area is predominantly residential and agricultural. The estimated 85 residences located within 1/2 mile of the site use the underlying sand/gravel and limestone aquifer as their drinking water supply. A 1986 Record of Decision (ROD) addressed a final remedy for ground water contamination and provided for ground water pumping and treatment using electrochemical reduction/ion exchange polishing, followed by onsite discharge to surface water. The ROD amends the 1986 ROD. The amended remedial action for the site is no further action.

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.

Statistical Profiling of One Promiscuous Protein Binding Site: Illustrated by Urokinase Catalytic Domain.

PubMed

Cerisier, Natacha; Regad, Leslie; Triki, Dhoha; Petitjean, Michel; Flatters, Delphine; Camproux, Anne-Claude

2017-10-01

While recent literature focuses on drug promiscuity, the characterization of promiscuous binding sites (ability to bind several ligands) remains to be explored. Here, we present a proteochemometric modeling approach to analyze diverse ligands and corresponding multiple binding sub-pockets associated with one promiscuous binding site to characterize protein-ligand recognition. We analyze both geometrical and physicochemical profile correspondences. This approach was applied to examine the well-studied druggable urokinase catalytic domain inhibitor binding site, which results in a large number of complex structures bound to various ligands. This approach emphasizes the importance of jointly characterizing pocket and ligand spaces to explore the impact of ligand diversity on sub-pocket properties and to establish their main profile correspondences. This work supports an interest in mining available 3D holo structures associated with a promiscuous binding site to explore its main protein-ligand recognition tendency. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Final Report: Technical Assistance for the Kearsarge Metallurgical Corporation Superfund Site, Conway, New Hampshire, EPA Region 1

EPA Pesticide Factsheets

This report reviews and provides recommendations for a long-term groundwater monitoring network for the Kearsarge Metallurgical Corporation Superfund site (KMC site). The KMC site is a former foundry and metal fabrication facility in Conway, New Hampshire.

Myth and Reality in Hydrogeological Site Characterization at DD and R Sites

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

Rubin, Yoram

2008-01-15

The science of hydrogeological site characterization has made significant progress over the last twenty years. Progress has been made in modeling of flow and transport in the heterogeneous subsurface, in understanding of the complex patterns of geological heterogeneity and in measurement technologies. Modeling of uncertainty has also advanced significantly, in recognition of the inherent limitations of subsurface characterization. Much less progress has been made in transforming this progress into practice, where characterization is determined to a large extent by regulations. Environmental regulations have not progressed as much as the science, for example, in recognizing uncertainty. As such, practitioners are lessmore » inclined to adopt advanced, science-based solutions, this opening the door for myths and conflicts. Myths develop where the science base is perceived to be weak, whereas conflicts arise in the face of a disconnect between the science and the regulations. Myths translate to ad-hoc solutions and misplaced empiricism, as well as to unjustified reliance on field experience, to the detriment of D and DR. This paper explores the roots for this situation and identifies ideas that may help in bridging the gap between research and applications. A rational approach for DD and R is needed that will encourage innovation in site characterization, reduce costs and accelerate completion. Such an approach needs to include several elements. DD and R regulations need to recognize the various aspects of uncertainty inherent to site characterization, and as such, should be formulated using probabilistic concepts. One of the immediate benefits will be in allowing a gradual approach for data acquisition in DD and R sites: decisions can be made even under the most severe data limitations, and can be modified as additional data become available. The definition of risk is another major element. There is no universal definition of risk or of a methodology to define risk. Different sites justify different definitions, depending on many environmental, economical and social factors. Despite the lack of consensus, it seems that a good place to start is in fact to recognize that there is a room for all these factors, and a need to balance between them. As experience is gained, through research and discussions among DD and R stakeholders, this may become less of a challenge. Regulations need to recognize the possibility of developing alternative, site-specific characterization strategies based on the various length and time scales that define specific environmental problems, including length scales of heterogeneity, source dimensions and distance to environmental targets. For example, point and distributed sources justify different characterization strategies. Development of problem- or site-specific strategies will create the context for defining innovative efficient DD and R strategies. Innovation in characterization can will also follow from recognizing the specific physiological aspects of the toxins and the related uncertainty. This will open the door for improving risk characterization not only from the hydrologic perspective, but also form the physiologic one.« less

Endobronchial ultrasound-guided transbronchial needle aspiration: performance of biomedical scientists on rapid on-site evaluation and preliminary diagnosis.

PubMed

Schacht, M J; Toustrup, C B; Madsen, L B; Martiny, M S; Larsen, B B; Simonsen, J T

2016-10-01

Rapid on-site evaluation (ROSE) of endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) followed by a subsequent preliminary adequacy assessment and a preliminary diagnosis, was performed at Aarhus University Hospital by biomedical scientists (BMS). The aim of this study was to evaluate the BMS accuracy of ROSE adequacy assessment, the preliminary adequacy assessment and the preliminary diagnosis as compared with the cytopathologist-rendered final adequacy assessment and final diagnosis. The BMS-rendered assessments for 717 sites from 319 consecutive patients over a 4-month period were compared with the cytopathologist-rendered assessments. Comparisons of adequacy and preliminary diagnoses were based on inter-observer Cohen's Kappa coefficient with a 95% confidence interval (CI). Strong correlations between ROSE and final adequacy assessments [Kappa coefficient of 0.90 (CI: 0.85-0.96)] and between the preliminary and final adequacy assessments [Kappa coefficient of 0.93 (CI: 0.87-0.99)] were found. As for the correlation between the preliminary and final diagnoses, the Kappa coefficient was 0.99 (CI: 0.98-1). Both ROSE and preliminary adequacy assessments as well as preliminary diagnoses, all performed by BMS, were highly accurate when compared with the final assessment by the cytopathologist. © 2016 John Wiley & Sons Ltd.

An overview of geophysical technologies appropriate for characterization and monitoring at fractured-rock sites

EPA Science Inventory

Geophysical methods are used increasingly for characterization and monitoring at remediation sites in fractured-rock aquifers. The complex heterogeneity of fractured rock poses enormous challenges to groundwater remediation professionals, and new methods are needed to cost-effect...

Anisotropic polaron localization and spontaneous symmetry breaking: Comparison of cation-site acceptors in GaN and ZnO

NASA Astrophysics Data System (ADS)

Sun, Y. Y.; Abtew, Tesfaye A.; Zhang, Peihong; Zhang, S. B.

2014-10-01

The behavior of cation substitutional hole doping in GaN and ZnO is investigated using hybrid density functional calculations. Our results reveal that Mg substitution for Ga (MgGa) in GaN can assume three different configurations. Two of the configurations are characterized by the formation of defect-bound small polaron (i.e., a large structural distortion accompanied by hole localization on one of the neighboring N atoms). The third one has a relatively small but significant distortion that is characterized by highly anisotropic polaron localization. In this third configuration, MgGa exhibits both effective-mass-like and noneffective-mass-like characters. In contrast, a similar defect in ZnO, LiZn, cannot sustain the anisotropic polaron in the hybrid functional calculation, but undergoes spontaneous breaking of a mirror symmetry through a mechanism driven by the hole localization. Finally, using NaZn in ZnO as an example, we show that the deep acceptor levels of the small-polaron defects could be made shallower by applying compressive strain to the material.

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

Hoban, Matty J.; Department of Computer Science, University of Oxford, Wolfson Building, Parks Road, Oxford OX1 3QD; Wallman, Joel J.

We consider general settings of Bell inequality experiments with many parties, where each party chooses from a finite number of measurement settings each with a finite number of outcomes. We investigate the constraints that Bell inequalities place upon the correlations possible in local hidden variable theories using a geometrical picture of correlations. We show that local hidden variable theories can be characterized in terms of limited computational expressiveness, which allows us to characterize families of Bell inequalities. The limited computational expressiveness for many settings (each with many outcomes) generalizes previous results about the many-party situation each with a choice ofmore » two possible measurements (each with two outcomes). Using this computational picture we present generalizations of the Popescu-Rohrlich nonlocal box for many parties and nonbinary inputs and outputs at each site. Finally, we comment on the effect of preprocessing on measurement data in our generalized setting and show that it becomes problematic outside of the binary setting, in that it allows local hidden variable theories to simulate maximally nonlocal correlations such as those of these generalized Popescu-Rohrlich nonlocal boxes.« less

Cluster model studies of anion and molecular specificities via electrospray ionization photoelectron spectroscopy

DOE PAGES

Wang, Xue -Bin

2017-01-06

Ion specificity, a widely observed macroscopic phenomenon in condensed phases and at interfaces, is essentially a fundamental chemical physical issue. We have been investigating such effects using cluster models in an “atom-by-atom” and “molecule-by-molecule” fashion not possible with condensed-phase methods. We use electrospray ionization (ESI) to generate molecular and ionic clusters to simulate key molecular entities involved in local binding regions, and characterize them employing negative ion photoelectron spectroscopy (NIPES). Inter- and intramolecular interactions and binding configurations are directly obtained as functions of cluster size and composition, providing insightful molecular-level description and characterization over the local active sites that playmore » crucial roles in determining solution chemistry and condensed phase phenomena. Finally, the topics covered in this article are relevant to a wide scope of research fields ranging from ion specific effects in electrolyte solutions, ion selectivity/recognition in normal functioning of life, to molecular specificity in aerosol particle formation, as well as in rational material design and synthesis.« less

Self-assembled nanocages based on the coiled coil bundle motif

NASA Astrophysics Data System (ADS)

Sinha, Nairiti; Villegas, Jose; Saven, Jeffery; Kiick, Kristi; Pochan, Darrin

Computational design of coiled coil peptide bundles that undergo solution phase self-assembly presents a diverse toolbox for engineering new materials with tunable and pre-determined nanostructures that can have various end applications such as in drug delivery, biomineralization and electronics. Self-assembled cages are especially advantageous as the cage geometry provides three distinct functional sites: the interior, the exterior and the solvent-cage interface. In this poster, syntheses and characterization of a peptide cage based on computationally designed homotetrameric coiled coil bundles as building blocks is discussed. Techniques such as Transmission Electron Microscopy (TEM), Small-Angle Neutron Scattering (SANS) and Analytical Ultracentrifugation (AUC) are employed to characterize the size, shape and molecular weight of the self-assembled peptide cages under different pH and temperature conditions. Various self-assembly pathways such as dialysis and thermal quenching are shown to have a significant impact on the final structure of these peptides in solution. Comparison of results with the target cage design can be used to iteratively improve the peptide design and provide greater understanding of its interactions and folding.

Natural separation of the acyl-CoA ligase reaction results in a non-adenylating enzyme.

PubMed

Wang, Nan; Rudolf, Jeffrey D; Dong, Liao-Bin; Osipiuk, Jerzy; Hatzos-Skintges, Catherine; Endres, Michael; Chang, Chin-Yuan; Babnigg, Gyorgy; Joachimiak, Andrzej; Phillips, George N; Shen, Ben

2018-06-04

Acyl-coenzyme A (CoA) ligases catalyze the activation of carboxylic acids via a two-step reaction of adenylation followed by thioesterification. Here, we report the discovery of a non-adenylating acyl-CoA ligase PtmA2 and the functional separation of an acyl-CoA ligase reaction. Both PtmA1 and PtmA2, two acyl-CoA ligases from the biosynthetic pathway of platensimycin and platencin, are necessary for the two steps of CoA activation. Gene inactivation of ptmA1 and ptmA2 resulted in the accumulation of free acid and adenylate intermediates, respectively. Enzymatic and structural characterization of PtmA2 confirmed its ability to only catalyze thioesterification. Structural characterization of PtmA2 revealed it binds both free acid and adenylate substrates and undergoes the established mechanism of domain alternation. Finally, site-directed mutagenesis restored both the adenylation and complete CoA activation reactions. This study challenges the currently accepted paradigm of adenylating enzymes and inspires future investigations on functionally separated acyl-CoA ligases and their ramifications in biology.

Studies of proteoglycan involvement in CPP-mediated delivery.

PubMed

Wittrup, Anders; Zhang, Si-He; Belting, Mattias

2011-01-01

Cell-penetrating peptides (CPPs) are widely used to deliver macromolecular cargoes to intracellular sites of action. Many CPPs have been demonstrated to rely on cell surface heparan sulfate proteoglycans (HSPGs) for efficient cellular entry and delivery. In this chapter, we describe methods for the study of PG involvement in CPP uptake. We provide descriptions of how to determine whether uptake of a CPP of interest is dependent on PGs. We also provide detailed protocols for the purification of PGs by anion-exchange chromatography as well as the characterization of the HSPG core protein composition of a cell line of interest. Finally, we present methods for modulating the expression level of specific HSPG core proteins as a means to determine the core protein specificity in the uptake of a particular CPP.

CELFish ways to modulate mRNA decay

PubMed Central

St. Louis, Irina Vlasova; Dickson, Alexa M.; Bohjanen, Paul R.; Wilusz, Carol J.

2013-01-01

The CELF family of RNA-binding proteins regulates many steps of mRNA metabolism. Although their best characterized function is in pre-mRNA splice site choice, CELF family members are also powerful modulators of mRNA decay. In this review we focus on the different modes of regulation that CELF proteins employ to mediate mRNA decay by binding to GU-rich elements. After starting with an overview of the importance of CELF proteins during development and disease pathogenesis, we then review the mRNA networks and cellular pathways these proteins regulate and the mechanisms by which they influence mRNA decay. Finally, we discuss how CELF protein activity is modulated during development and in response to cellular signals. We conclude by highlighting the priorities for new experiments in this field. PMID:23328451

75 FR 26131 - National Oil and Hazardous Substance Pollution Contingency Plan; National Priorities List

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-11

... publishing a direct final Notice of Deletion of the Asbestos Dump Superfund Site (Site), located in Long Hill... Deletion of the Asbestos Dump Superfund site (Site), from the National Priorities List (NPL). The NPL... discusses the Asbestos Dump Superfund Site and demonstrates how it meets the deletion criteria. Section V...

Technical Analysis and Characterization of Southern Cayo, Belize for Tropical Testing and Evaluation of Foliage Penetration Remote Sensing Systems

DTIC Science & Technology

2011-05-01

Characterization of Test Sites 57 Appendix 4 – Interactive Maps and Images...issued by the tropical test study panel, reporting the results of work conducted at 24 sites. The evolution of tropical testing to the suite of sites...macrophylla, Terminalia amazonia, Virola brachycarpa, and the palm Astrocaryum mexicanum. The mangrove and littoral forest are ecologically important to the

Active Site Detection by Spatial Conformity and Electrostatic Analysis—Unravelling a Proteolytic Function in Shrimp Alkaline Phosphatase

PubMed Central

Chakraborty, Sandeep; Minda, Renu; Salaye, Lipika; Bhattacharjee, Swapan K.; Rao, Basuthkar J.

2011-01-01

Computational methods are increasingly gaining importance as an aid in identifying active sites. Mostly these methods tend to have structural information that supplement sequence conservation based analyses. Development of tools that compute electrostatic potentials has further improved our ability to better characterize the active site residues in proteins. We have described a computational methodology for detecting active sites based on structural and electrostatic conformity - C ata L ytic A ctive S ite P rediction (CLASP). In our pipelined model, physical 3D signature of any particular enzymatic function as defined by its active sites is used to obtain spatially congruent matches. While previous work has revealed that catalytic residues have large pKa deviations from standard values, we show that for a given enzymatic activity, electrostatic potential difference (PD) between analogous residue pairs in an active site taken from different proteins of the same family are similar. False positives in spatially congruent matches are further pruned by PD analysis where cognate pairs with large deviations are rejected. We first present the results of active site prediction by CLASP for two enzymatic activities - β-lactamases and serine proteases, two of the most extensively investigated enzymes. The results of CLASP analysis on motifs extracted from Catalytic Site Atlas (CSA) are also presented in order to demonstrate its ability to accurately classify any protein, putative or otherwise, with known structure. The source code and database is made available at www.sanchak.com/clasp/. Subsequently, we probed alkaline phosphatases (AP), one of the well known promiscuous enzymes, for additional activities. Such a search has led us to predict a hitherto unknown function of shrimp alkaline phosphatase (SAP), where the protein acts as a protease. Finally, we present experimental evidence of the prediction by CLASP by showing that SAP indeed has protease activity in vitro. PMID:22174814

Magnetic fluctuations and superconducting properties of CaKFe 4 As 4 studied by As 75 NMR

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

Cui, J.; Ding, Q. -P.; Meier, W. R.

In this paper, we report 75As nuclear magnetic resonance (NMR) studies on a new iron-based superconductor, CaKFe 4As 4, with T c = 35 K. 75As NMR spectra show two distinct lines corresponding to the As(1) and As(2) sites close to the K and Ca layers, respectively, revealing that K and Ca layers are well ordered without site inversions. We found that nuclear quadrupole frequencies ν Q of the As(1) and As(2) sites show an opposite temperature T dependence. Nearly T independent behavior of the Knight shifts K is observed in the normal state, and a sudden decrease in Kmore » in the superconducting (SC) state suggests spin-singlet Cooper pairs. 75As spin-lattice relaxation rates 1/T 1 show a power-law T dependence with different exponents for the two As sites. The isotropic antiferromagnetic spin fluctuations characterized by the wave vector q = (π, 0) or (0, π) in the single-iron Brillouin zone notation are revealed by 1/T 1T and K measurements. Such magnetic fluctuations are necessary to explain the observed temperature dependence of the 75As quadrupole frequencies, as evidenced by our first-principles calculations. Finally, in the SC state, 1/T 1 shows a rapid decrease below T c without a Hebel-Slichter peak and decreases exponentially at low T, consistent with an s ± nodeless two-gap superconductor.« less

A human brain network derived from coma-causing brainstem lesions.

PubMed

Fischer, David B; Boes, Aaron D; Demertzi, Athena; Evrard, Henry C; Laureys, Steven; Edlow, Brian L; Liu, Hesheng; Saper, Clifford B; Pascual-Leone, Alvaro; Fox, Michael D; Geerling, Joel C

2016-12-06

To characterize a brainstem location specific to coma-causing lesions, and its functional connectivity network. We compared 12 coma-causing brainstem lesions to 24 control brainstem lesions using voxel-based lesion-symptom mapping in a case-control design to identify a site significantly associated with coma. We next used resting-state functional connectivity from a healthy cohort to identify a network of regions functionally connected to this brainstem site. We further investigated the cortical regions of this network by comparing their spatial topography to that of known networks and by evaluating their functional connectivity in patients with disorders of consciousness. A small region in the rostral dorsolateral pontine tegmentum was significantly associated with coma-causing lesions. In healthy adults, this brainstem site was functionally connected to the ventral anterior insula (AI) and pregenual anterior cingulate cortex (pACC). These cortical areas aligned poorly with previously defined resting-state networks, better matching the distribution of von Economo neurons. Finally, connectivity between the AI and pACC was disrupted in patients with disorders of consciousness, and to a greater degree than other brain networks. Injury to a small region in the pontine tegmentum is significantly associated with coma. This brainstem site is functionally connected to 2 cortical regions, the AI and pACC, which become disconnected in disorders of consciousness. This network of brain regions may have a role in the maintenance of human consciousness. © 2016 American Academy of Neurology.

Bioaccumulation and metabolomics responses in oysters Crassostrea hongkongensis impacted by different levels of metal pollution.

PubMed

Cao, Chen; Wang, Wen-Xiong

2016-09-01

Jiulong River Estuary, located in southern China, was heavily contaminated by metal pollution. In this study, the estuarine oysters Crassostrea hongkongensis were transplanted to two sites with similar hydrological conditions but different levels of metal pollution in Jiulong River Estuary over a six-month period. We characterized the time-series change of metal bioaccumulation and final metabolomics responses of oysters. Following transplantation, all metals (Cd, Cu, Cr, Ni, Pb, and Zn) in the oyster digestive glands had elevated concentrations over time. By the end of six-month exposure, Cu, Zn and Cd were the main metals significantly differentiating the two sites. Using (1)H NMR metabolite approach, we further demonstrated the disturbance in osmotic regulation, energy metabolism, and glycerophospholipid metabolism induced by metal contaminations. Six months later, the oysters transplanted in the two sites showed a similar metabolite variation pattern when compared with the initial oysters regardless of different metal levels in the tissues. Interestingly, by comparing the oysters from two sites, the more severely polluted oysters accumulated significantly higher amounts of osmolytes (betaine and homarine) and lower energy storage compounds (glycogen) than the less polluted oysters; these changes could be the potential biomarkers for different levels of metal pollution. Our study demonstrated the complexity of biological effects under field conditions, and NMR metabolomics provides an important approach to detect sensitive variation of oyster inner status. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Geomatics Contribution for the Valorisation Project in the Rocca of San Silvestro Landscape Site

NASA Astrophysics Data System (ADS)

Brocchini, D.; Chiabrando, F.; Colucci, E.; Sammartano, G.; Spanò, A.; Teppati Losè, L.; Villa, A.

2017-05-01

This paper proposes an emblematic project where several multi-sensor strategies for spatial data acquisition and management, range based and image based, were combined to create a series of integrated territorial and architectural scale products characterized by a rich multi-content nature. The work presented here was finalized in a test site that is composed by an ensemble of diversified cultural deposits; the objects that were surveyed and modelled range from the landscape with its widespread mining sites, the main tower with its defensive role, the urban configuration of the settlement, the building systems and techniques, a medieval mine. For this reason, the Rocca of San Silvestro represented a perfect test case, due to its complex and multi-stratified character. This archaeological site is a medieval fortified village near the municipality of Campiglia Marittima (LI), Italy. The Rocca is part of an Archaeological Mines Park and is included in the Parchi della Val di Cornia (a system of archaeological parks, natural parks and museums in the south-west of Tuscany). The fundamental role of a deep knowledge about a cultural artefact before the planning of a restoration and valorisation project is globally recognized; the qualitative and quantitative knowledge provided by geomatics techniques is part of this process. The paper will present the different techniques that were used, the products that were obtained and will focus on some mapping and WEB GIS applications and analyses that were performed and considerations that were made.

Magnetic fluctuations and superconducting properties of CaKFe 4 As 4 studied by As 75 NMR

DOE PAGES

Cui, J.; Ding, Q. -P.; Meier, W. R.; ...

2017-09-25

In this paper, we report 75As nuclear magnetic resonance (NMR) studies on a new iron-based superconductor, CaKFe 4As 4, with T c = 35 K. 75As NMR spectra show two distinct lines corresponding to the As(1) and As(2) sites close to the K and Ca layers, respectively, revealing that K and Ca layers are well ordered without site inversions. We found that nuclear quadrupole frequencies ν Q of the As(1) and As(2) sites show an opposite temperature T dependence. Nearly T independent behavior of the Knight shifts K is observed in the normal state, and a sudden decrease in Kmore » in the superconducting (SC) state suggests spin-singlet Cooper pairs. 75As spin-lattice relaxation rates 1/T 1 show a power-law T dependence with different exponents for the two As sites. The isotropic antiferromagnetic spin fluctuations characterized by the wave vector q = (π, 0) or (0, π) in the single-iron Brillouin zone notation are revealed by 1/T 1T and K measurements. Such magnetic fluctuations are necessary to explain the observed temperature dependence of the 75As quadrupole frequencies, as evidenced by our first-principles calculations. Finally, in the SC state, 1/T 1 shows a rapid decrease below T c without a Hebel-Slichter peak and decreases exponentially at low T, consistent with an s ± nodeless two-gap superconductor.« less

A human brain network derived from coma-causing brainstem lesions

PubMed Central

Boes, Aaron D.; Demertzi, Athena; Evrard, Henry C.; Laureys, Steven; Edlow, Brian L.; Liu, Hesheng; Saper, Clifford B.; Pascual-Leone, Alvaro; Geerling, Joel C.

2016-01-01

Objective: To characterize a brainstem location specific to coma-causing lesions, and its functional connectivity network. Methods: We compared 12 coma-causing brainstem lesions to 24 control brainstem lesions using voxel-based lesion-symptom mapping in a case-control design to identify a site significantly associated with coma. We next used resting-state functional connectivity from a healthy cohort to identify a network of regions functionally connected to this brainstem site. We further investigated the cortical regions of this network by comparing their spatial topography to that of known networks and by evaluating their functional connectivity in patients with disorders of consciousness. Results: A small region in the rostral dorsolateral pontine tegmentum was significantly associated with coma-causing lesions. In healthy adults, this brainstem site was functionally connected to the ventral anterior insula (AI) and pregenual anterior cingulate cortex (pACC). These cortical areas aligned poorly with previously defined resting-state networks, better matching the distribution of von Economo neurons. Finally, connectivity between the AI and pACC was disrupted in patients with disorders of consciousness, and to a greater degree than other brain networks. Conclusions: Injury to a small region in the pontine tegmentum is significantly associated with coma. This brainstem site is functionally connected to 2 cortical regions, the AI and pACC, which become disconnected in disorders of consciousness. This network of brain regions may have a role in the maintenance of human consciousness. PMID:27815400

Development of a Methodology for Hydrogeological Characterization of Faults: Progress of the Project in Berkeley, California

NASA Astrophysics Data System (ADS)

Goto, J.; Moriya, T.; Yoshimura, K.; Tsuchi, H.; Karasaki, K.; Onishi, T.; Ueta, K.; Tanaka, S.; Kiho, K.

2010-12-01

The Nuclear Waste Management Organization of Japan (NUMO), in collaboration with Lawrence Berkeley National Laboratory (LBNL), has carried out a project to develop an efficient and practical methodology to characterize hydrologic property of faults since 2007, exclusively for the early stage of siting a deep underground repository. A preliminary flowchart of the characterization program and a classification scheme of fault hydrology based on the geological feature have been proposed. These have been tested through the field characterization program on the Wildcat Fault in Berkeley, California. The Wildcat Fault is a relatively large non-active strike-slip fault which is believed to be a subsidiary of the active Hayward Fault. Our classification scheme assumes the contrasting hydrologic features between the linear northern part and the split/spread southern part of the Wildcat Fault. The field characterization program to date has been concentrated in and around the LBNL site on the southern part of the fault. Several lines of electrical and reflection seismic surveys, and subsequent trench investigations, have revealed the approximate distribution and near-surface features of the Wildcat Fault (see also Onishi, et al. and Ueta, et al.). Three 150m deep boreholes, WF-1 to WF-3, have been drilled on a line normal to the trace of the fault in the LBNL site. Two vertical holes were placed to characterize the undisturbed Miocene sedimentary formations at the eastern and western sides of the fault (WF-1 and WF-2 respectively). WF-2 on the western side intersected the rock formation, which was expected only in WF-1, and several of various intensities. Therefore, WF-3, originally planned as inclined to penetrate the fault, was replaced by the vertical hole further to the west. It again encountered unexpected rocks and faults. Preliminary results of in-situ hydraulic tests suggested that the transmissivity of WF-1 is ten to one hundred times higher than WF-2. The monitoring of hydraulic pressure displayed different head distribution patterns between WF-1 and WF-2 (see also Karasaki, et al.). Based on these results, three hypotheses on the distribution of the Wildcat Fault were proposed: (a) a vertical fault in between WF-1 and WF-2, (b) a more gently dipping fault intersected in WF-2 and WF-3, and (c) a wide zone of faults extending between WF-1 and WF-3. At present, WF-4, an inclined hole to penetrate the possible (eastern?) master fault, is ongoing to test these hypotheses. After the WF-4 investigation, hydrologic and geochemical analyses and modeling of the southern part of the fault will be carried out. A simpler field characterization program will also be carried out in the northern part of the fault. Finally, all the results will be synthesized to improve the comprehensive methodology.

Geothermal well site restoration and plug and abandonment of wells, DOE Gladys McCall test site, Cameron Parish, Louisiana and DOE Willis Hulin test site, Vermillion Parish, Louisiana

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

Rinehart, Ben N.

1994-08-01

A report is presented on the final phase of an energy research program conducted by the U.S. Department of Energy (DOE) involving two geothermal well sites in the State of Louisiana--the Gladys McCall site and the Willis Hulin site. The research program was intended to improve geothermal technology and to determine the efficacy of producing electricity commercially from geopressured resource sites. The final phase of the program consisted of plug and abandonment (P&A) of the wells and restoration of the well sites. Restoration involved (a) initial soil and water sampling and analysis; (b) removal and disposal of well pads, concrete,more » utility poles, and trash; (c) plugging of monitor and freshwater wells; and (d) site leveling and general cleanup. Restoration of the McCall site required removal of naturally occurring radioactive material (NORM), which was costly and time-consuming. Exhibits are included that provide copies of work permits and authorizations, P&A reports, and cost and salvage reports. Site locations, grid maps, and photographs are provided.« less

Beyond the Ivory Tower: A Comparison of Grades Across Academic and Community OB/GYN Clerkship Sites.

PubMed

Fay, Emily E; Schiff, Melissa A; Mendiratta, Vicki; Benedetti, Thomas J; Debiec, Kate

2016-01-01

CONSTRUCT: Decentralized clinical education is the use of community facilities and community physicians to educate medical students. The theory behind decentralized clinical education is that academic and community sites will provide educational equivalency as determined by objective and subjective performance measures, while training more medical students and exposing students to rural or underserved communities. One of the major challenges of decentralized clinical education is ensuring site comparability in both learning opportunities and evaluation of students. Previous research has examined objective measures of student performance, but less is known about subjective performance measures, particularly in the field of obstetrics and gynecology (OB/GYN). This study explores the implications of clinical site on the adequacy of subjective and objective performance measures. This was a retrospective cohort study of 801 students in the University of Washington School of Medicine OB/GYN clerkship from 2008 to 2012. Academic sites included those with OB/GYN residency programs (n = 2) and community sites included those without residency programs (n = 29). The association between clerkship site and National Board of Medical Examiners (NBME) grade was assessed using linear regression and clinical and final grade using multinomial regression, estimating β coefficient and relative risks (RR), respectively, and 95% confidence intervals (CIs), adjusting for gender, academic quarter of clerkship, and year of clerkship. There were no differences in NBME exam grades of students at academic sites (76.4 (7.3) versus 74.6 (8.0), β = -0.11, 95% CI [1.35, 1.12] compared to community sites. For clinical grade, students at community sites were 2.4 times more likely to receive honors relative to high pass (RR 2.45), 95% CI [1.72, 3.50], and for final grade, students at community sites were 1.9 times more likely to receive honors relative to pass (RR 1.98), 95% CI [1.27, 3.09], and 1.6 times more likely to receive honors relative to high pass (RR 1.62), 95% CI [1.05, 2.50], compared to those at academic sites. Students at community sites receive higher clinical and final grades in the OB/GYN clerkship. This highlights a significant challenge in decentralized clinical education-ensuring site comparability in clinical grading, Further work should examine the differences in sites, as well as improve standardization of clinical grading. This also underscores an important consideration, as the final grade can influence medical school rank, nomination into honor societies, and ranking of residency applicants.

Site Characterization To Support Use Of Monitored Natural Attentuation For Remediation Of Inorganic Contaminants In Groundwater

EPA Science Inventory

Technical recommendations have recently been published by the U.S. Environmental Protection Agency to address site characterization needed to support selection of Monitored Natural Attenuation (MNA) for cleanup of inorganic contaminant plumes in groundwater. Immobilization onto ...

Integrated Pore-Water and Geophysical Investigations StreamlineCharacterization of Ground-Water Discharges to Surface Water

EPA Science Inventory

This issue of Technology News and Trends highlights strategies and tools for characterizing or monitoring remediation of sites with contaminated sediment. Addressing these sites often relies upon dynamic workplans that involve more efficient, cost-effective, and practical methods...

10 CFR 60.17 - Contents of site characterization plan.

Code of Federal Regulations, 2010 CFR

2010-01-01

... GEOLOGIC REPOSITORIES Licenses Preapplication Review § 60.17 Contents of site characterization plan. The... construction authorization for a geologic repository operations area; (4) Criteria, developed pursuant to... area for the location of a geologic repository; and (5) Any other information which the Commission, by...

SITE CHARACTERIZATION AND MONITORING TECHNOLOGY VERIFICATION: PROGRESS AND RESULTS

EPA Science Inventory

The Site Characterization and Monitoring Technology Pilot of the U.S. Environmental Protection Agency's Environmental Technology Verification Program (ETV) has been engaged in verification activities since the fall of 1994 (U.S. EPA, 1997). The purpose of the ETV is to promote th...

A CASE STUDY ILLUSTRATING THE IMPORTANCE OF ACCURATE SITE CHARACTERIZATION

EPA Science Inventory

Too frequently, researchers rely on incomplete site characterization data to determine the placement of the sampling wells. They forget that it is these sampling wells that will be used to evaluate the effectiveness of their research efforts. This case study illustrates the eff...

Yucca Mountain biological resources monitoring program; Annual report FY92

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

NONE

1993-02-01

The US Department of Energy (DOE) is required by the Nuclear Waste Policy Act of 1982 (as amended in 1987) to study and characterize Yucca Mountain as a potential site for a geologic repository for high-level nuclear waste. During site characterization, the DOE will conduct a variety of geotechnical, geochemical, geological, and hydrological studies to determine the suitability of Yucca Mountain as a potential repository. To ensure that site characterization activities (SCA) do not adversely affect the environment at Yucca Mountain, an environmental program has been implemented to monitor and mitigate potential impacts and ensure activities comply with applicable environmentalmore » regulations. This report describes the activities and accomplishments of EG&G Energy Measurements, Inc. (EG&G/EM) during fiscal year 1992 (FY92) for six program areas within the Terrestrial Ecosystem component of the YMP environmental program. The six program areas are Site Characterization Effects, Desert Tortoises, Habitat Reclamation, Monitoring and Mitigation, Radiological Monitoring, and Biological Support.« less

Four Finalist Landing Site Candidates for Mars Science Laboratory

NASA Image and Video Library

2008-11-19

Out of more than 30 sites considered as possible landing targets for NASA Mars Science Laboratory mission, by November 2008 four of the most intriguing places on Mars rose to the final round of the site-selection process.

Site selection for MSFC operational tests of solar heating and cooling systems

NASA Technical Reports Server (NTRS)

1978-01-01

The criteria, methodology, and sequence aspects of the site selection process are presented. This report organized the logical thought process that should be applied to the site selection process, but final decisions are highly selective.

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

R. L. VanHorn; N. L. Hampton; R. C. Morris

This document presents reference material for conducting screening level ecological risk assessments (SLERAs)for the waste area groups (WAGs) at the Idaho National Engineering Laboratory. Included in this document are discussions of the objectives of and processes for conducting SLERAs. The Environmental Protection Agency ecological risk assessment framework is closely followed. Guidance for site characterization, stressor characterization, ecological effects, pathways of contaminant migration, the conceptual site model, assessment endpoints, measurement endpoints, analysis guidance, and risk characterization are included.

Multi-Scale Particle Size Distributions of Mars, Moon and Itokawa based on a time-maturation dependent fragmentation model

NASA Astrophysics Data System (ADS)

Charalambous, C. A.; Pike, W. T.

2013-12-01

We present the development of a soil evolution framework and multiscale modelling of the surface of Mars, Moon and Itokawa thus providing an atlas of extra-terrestrial Particle Size Distributions (PSD). These PSDs are profoundly based on a tailoring method which interconnects several datasets from different sites captured by the various missions. The final integrated product is then fully justified through a soil evolution analysis model mathematically constructed via fundamental physical principles (Charalambous, 2013). The construction of the PSD takes into account the macroscale fresh primary impacts and their products, the mesoscale distributions obtained by the in-situ data of surface missions (Golombek et al., 1997, 2012) and finally the microscopic scale distributions provided by Curiosity and Phoenix Lander (Pike, 2011). The distribution naturally extends at the magnitudinal scales at which current data does not exist due to the lack of scientific instruments capturing the populations at these data absent scales. The extension is based on the model distribution (Charalambous, 2013) which takes as parameters known values of material specific probabilities of fragmentation and grinding limits. Additionally, the establishment of a closed-form statistical distribution provides a quantitative description of the soil's structure. Consequently, reverse engineering of the model distribution allows the synthesis of soil that faithfully represents the particle population at the studied sites (Charalambous, 2011). Such representation essentially delivers a virtual soil environment to work with for numerous applications. A specific application demonstrated here will be the information that can directly be extracted for the successful drilling probability as a function of distance in an effort to aid the HP3 instrument of the 2016 Insight Mission to Mars. Pike, W. T., et al. "Quantification of the dry history of the Martian soil inferred from in situ microscopy." Geophysical Research Letters 38.24 (2011). C. A. Charalambous and W. T. Pike (2013). 'Evolution of Particle Size Distributions in Fragmentation Over Time' Abstract Submitted to the AGU 46th Fall Meeting. Charalambous, C., Pike, W. T., Goetz, W., Hecht, M. H., & Staufer, U. (2011, December). 'A Digital Martian Soil based on In-Situ Data.' In AGU Fall Meeting Abstracts (Vol. 1, p. 1669). Golombek, M., & Rapp, D. (1997). 'Size-frequency distributions of rocks on Mars and Earth analog sites: Implications for future landed missions.' Journal of Geophysical Research, 102(E2), 4117-4129. Golombek, M., Huertas, A., Kipp, D., & Calef, F. (2012). 'Detection and characterization of rocks and rock size-frequency distributions at the final four Mars Science Laboratory landing sites.' Mars, 7, 1-22.

Integrated Remote Sensing Modalities for Classification at a Legacy Test Site

NASA Astrophysics Data System (ADS)

Lee, D. J.; Anderson, D.; Craven, J.

2016-12-01

Detecting, locating, and characterizing suspected underground nuclear test sites is of interest to the worldwide nonproliferation monitoring community. Remote sensing provides both cultural and surface geological information over a large search area in a non-intrusive manner. We have characterized a legacy nuclear test site at the Nevada National Security Site (NNSS) using an aerial system based on RGB imagery, light detection and ranging, and hyperspectral imaging. We integrate these different remote sensing modalities to perform pattern recognition and classification tasks on the test site. These tasks include detecting cultural artifacts and exotic materials. We evaluate if the integration of different remote sensing modalities improves classification performance.

Choosing a Field: How Graduate Student Choices of Field Sites Reflect Different Ideas of "Real" Anthropology in Colombia and the United States

ERIC Educational Resources Information Center

Macia, Laura

2012-01-01

This paper examines the decisions and motivations of graduate students in cultural anthropology when defining the field sites and topics of their final projects. The decisions among students at the Universidad de los Andes in Colombia are contrasted with those at the University of Pittsburgh in the United States. A review of recent final projects…

Remedial Investigation Report Area of Contamination (AOC) 43G. Volume 1

DTIC Science & Technology

1996-02-01

FORT DEVENS FINAL REMEDIAL INVESTIGATION FOR GROUP 2 & 7 SITES FINAL REMEDIAL INVESTIGATION REPORT AREA OF CONTAMINATION ( AOC ) 43G VOLUME I OF II...Liability Act for environmental investigations and remedial actions at Fort Devens . The agreement required that Site Investigations be undertaken at each... Remedial Investigation (RI) Report on Area of Contamination ( AOC ) 43G at the Fort Devens U.S. Army Installation, Massachusetts (

THE RAPID OPTICAL TOOL (TM) LASER-INDUCED FLUORESCENCE SYSTEM FOR SCREENING OF PETROLEUM HYDROCARBONS IN SUBSURFACE SOILS

EPA Science Inventory

The Consortium for Site Characterization Technology (CSCT) has established a formal program to accelerate acceptance and application of innovative monitoring and site characterization technologies that improve the way the nation manages its environmental problems. In 1995 the CS...

SITE CHARACTERIZATION TO SUPPORT MODEL DEVELOPMENT FOR CONTAMINANTS IN GROUND WATER

EPA Science Inventory

The development of conceptual and predictive models is an important tool to guide site characterization in support of monitoring contaminants in ground water. The accuracy of predictive models is limited by the adequacy of the input data and the assumptions made to constrain mod...

TECHNICAL APPROACHES TO CHARACTERIZING AND CLEANING UP BROWNFIELDS SITES: GUIDANCE DOCUMENT

EPA Science Inventory

NRMRL-CIN-1741 SAIC. Technical Approaches to Characterizing and Cleaning up Brownfields Sites. EPA/625/R/00/009 (NTIS PB2002-105021) , Available: 68-C7-0011. The guidance document gives assistance to communities, decision-makers, states and municipalities, academia, and the p...

Innovations in Site Characterization: Streamlining Cleanup at Vapor Intrusion and Product Removal Sites Using the Triad Approach: Hartford Plume Site, Hartford, Illinois

EPA Pesticide Factsheets

The Hartford Plume Site case study provides a detailed example of the strategies and technologies used at the site that are available to environmental practitioners to use at large and small hydrocarbon sites.

Geoscientific Characterization of the Bruce Site, Tiverton, Ontario

NASA Astrophysics Data System (ADS)

Raven, K.; Jackson, R.; Avis, J.; Clark, I.; Jensen, M.

2009-05-01

Ontario Power Generation is proposing a Deep Geologic Repository (DGR) for the long-term management of its Low and Intermediate Level Radioactive Waste (L&ILW) within a Paleozoic-age sedimentary sequence beneath the Bruce site near Tiverton, Ontario, Canada. The concept envisions that the DGR would be excavated at a depth of approximately 680 m within the Ordovician Cobourg Formation, a massive, dense, low- permeability, argillaceous limestone. Characterization of the Bruce site for waste disposal is being conducted in accordance with a four year multi-phase Geoscientific Site Characterization Plan (GSCP). The GSCP, initially developed in 2006 and later revised in 2008 to account for acquired site knowledge based on successful completion of Phase I investigations, describes the tools and methods selected for geological, hydrogeological and geomechanical site characterization. The GSCP was developed, in part, on an assessment of geoscience data needs and collection methods, review of the results of detailed geoscientific studies completed in the same bedrock formations found off the Bruce site, and recent international experience in geoscientific characterization of similar sedimentary rocks for long-term radioactive waste management purposes. Field and laboratory work related to Phase 1 and Phase 2A are nearing completion and have focused on the drilling, testing and monitoring of four continuously cored vertical boreholes through Devonian, Silurian, Ordovician and Cambrian bedrock to depths of about 860 mBGS. Work in 2009 will focus on drilling and testing of inclined boreholes to assess presence of vertical structure. The available geological, hydrogeological and hydrogeochemical data indicate the presence of remarkably uniform and predictable geology, physical hydrogeologic and geochemical properties over well separation distances exceeding 1 km. The current data set including 2-D seismic reflection surveys, field and lab hydraulic testing, lab petrophysical and diffusion testing, lab porewater and field groundwater characterization, and field head monitoring confirm the anticipated favourable characteristics of the Bruce site for long-term waste management. These favourable characteristics include a tight geomechanically stable host formation that is overlain and underlain by thick, massive, very low permeability shale and argillaceous limestone formations where radionuclide transport appears to be very limited and dominated by diffusion.

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.

DNAPL SITE EVALUATION - Project Summary

EPA Science Inventory

Dense nonaqueous-phase liquids (DNAPLs), especially chlorinated solvents, are among the most prevalent subsurface contaminants identified in ground-water supplies and at waste disposal sites. There are several site-characterization issues specific to DNAPL sites including (a) the...

Environmental Site Characterization for the Wide Area Mine Sensor Demonstration, Aberdeen Proving Ground, October 1988

DTIC Science & Technology

1991-05-01

AD-A237 045 MP I ENVIRONMENTAL SITE CHARACTERIZATION of EFOR THE WIDE AREA MINE SENSOR DEMONSTRATION, ABERDEEN PROVING GROUND , OCTOBER 1988 T- by...Wide Area Mine Sensor Demonstration, Aberdeen Proving Ground , October 1988 6. AUTHOR(S) Bruce M. Sabol, Thomas E. Berry, Ben L. Garnes 7. PERFORMING... Proving Ground (APG), Maryland. This report presents data that characterize terrain and environmental factors expected to affect WAN sensor performance

Chemical Decontamination at Browns Ferry Unit 1

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

Hartwig, Ed; Reid, Richard

2003-09-01

In May, 2002, the Tennessee Valley Authority's (TVA) Board of Directors approved the recovery and restart of Unit 1 at Browns Ferry Nuclear Station. As an initial step in the site characterization and restart feasibility review, a majority of the primary reactor circuit was chemically decontaminated. Close cooperation between TVA and vendor personnel resulted in project completion ahead of schedule with outstanding results. The final average decontamination factors were excellent, and the final dose rates were very low, with contact readings on most points between one and three mRem/hr. In addition to allowing TVA to do a complete and thoroughmore » job of determining the feasibility of the Unit 1 restart, the decontamination effort will greatly reduce personnel exposure during plant recovery, both whole body exposure to gamma radiation and airborne exposure during pipe replacement efforts. The implementation of lessons learned from previous decontamination work performed at Browns Ferry, as well as decontamination efforts at other plants aided greatly in the success. Specific items of note are: (1) The initial leak check of the temporary decontamination system should include ancillary systems such as the spent resin system, as well as the main circulation loop. This could save time and dose exposure if leaks are discovered before the use of such systems is required. (2) Due to the quick turnaround time from the award of contract, a vendor representative was onsite early in the project to help with engineering efforts and procedures. This aided greatly in completing preparations for the decontamination. (3) The work was performed under a single maintenance activity. This resulted in great craft and plant support. (4) The constant coverage by the site's decontamination flush directors provided timely plant support and interface. (5) The FPC system isolation and back flushing to prevent residual chemicals from being left in the FPC system should have been addressed in more detail in the pre-engineering study to prevent delays during the final system cleanup.« less

In situ radiological surveying at the Double Tracks site, Nellis Air Force Range, Tonopah, Nevada

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

Riedhauser, S.R.; Tipton, W.J.

1996-04-01

A team from the Remote Sensing Laboratory conducted a series of in situ radiological measurements at the Double Tracks site on the Nellis Air Force Range just east of Goldfield, Nevada, during the periods of April 10-13 and June 5-9, 1995. The survey team measured the terrestrial gamma radiation at the site to determine the levels of natural and man-made radiation. This site includes the areas covered by previous surveys conducted from 1962 through 1993. The main purpose of the first expedition was to assess several new techniques for characterizing sites with dispersed plutonium. The two purposes of the secondmore » expedition were to characterize the distribution of transuranic contamination (primarily plutonium) at the site by measuring the gamma rays from americium-241 and to assess the performance of the two new detector platforms. Both of the new platforms performed well, and the characterization of the americium-241 activity at the site was completed. Several plots compare these ground-based system measurements and the 1993 aerial data. The agreement is good considering the systems are characterized and calibrated through independent means. During the April expedition, several methods for measuring the depth distribution of americium-241 in the field were conducted as a way of quickly and reliably obtaining depth profiles without the need to wait for laboratory analysis. Two of the methods were not very effective, but the results of the third method appear very promising.« less

Pharmacological characterization of CCKB receptors in human brain: no evidence for receptor heterogeneity.

PubMed

Kinze, S; Schöneberg, T; Meyer, R; Martin, H; Kaufmann, R

1996-10-11

In this paper, cholecystokinin (CCK) B-type binding sites were characterized with receptor binding studies in different human brain regions (various parts of cerebral cortex, basal ganglia, hippocampus, thalamus, cerebellar cortex) collected from 22 human postmortem brains. With the exception of the thalamus, where no specific CCK binding sites were found, a pharmacological characterization demonstrated a single class of high affinity CCK sites in all brain areas investigated. Receptor densities ranged from 0.5 fmol/mg protein (hippocampus) to 8.4 fmol/mg protein (nucleus caudatus). These CCK binding sites displayed a typical CCKA binding profile as shown in competition studies by using different CCK-related compounds and non peptide CCK antagonists discriminating between CCKA and CCKB sites. The rank order of agonist or antagonist potency in inhibiting specific sulphated [propionyl-3H]cholecystokinin octapeptide binding was similar and highly correlated for the brain regions investigated as demonstrated by a computer-assisted analysis. Therefore it is concluded that CCKB binding sites in human cerebral cortex, basal ganglia, cerebellar cortex share identical ligand binding characteristics.

GRAND PLAZA SITE INVESTIGATION USING THE TRIAD APPROACH AND EVALUATION OF VAPOR INTRUSION - (ITER)

EPA Science Inventory

This document provides a detailed report about a field study conducted by EQM/URS on behalf of EPA/NRMRL to characterize the subsurface contamination of volatile organic compounds (VOCs) at a Brownfield commercial site. The TRIAD approach was implemented to characterize the exten...

Time-resolved single-turnover of caa(3) oxidase from Thermus thermophilus. Fifth electron of the fully reduced enzyme converts O(H) into E(H) state.

PubMed

Siletsky, Sergey A; Belevich, Ilya; Belevich, Nikolai P; Soulimane, Tewfik; Verkhovsky, Michael I

2011-09-01

The oxidative part of the catalytic cycle of the caa(3)-type cytochrome c oxidase from Thermus thermophilus was followed by time-resolved optical spectroscopy. Rate constants, chemical nature and the spectral properties of the catalytic cycle intermediates (Compounds A, P, F) reproduce generally the features typical for the aa(3)-type oxidases with some distinctive peculiarities caused by the presence of an additional 5-th redox-center-a heme center of the covalently bound cytochrome c. Compound A was formed with significantly smaller yield compared to aa(3) oxidases in general and to ba(3) oxidase from the same organism. Two electrons, equilibrated between three input redox-centers: heme a, Cu(A) and heme c are transferred in a single transition to the binuclear center during reduction of the compound F, converting the binuclear center through the highly reactive O(H) state into the final product of the reaction-E(H) (one-electron reduced) state of the catalytic site. In contrast to previous works on the caa(3)-type enzymes, we concluded that the finally produced E(H) state of caa(3) oxidase is characterized by the localization of the fifth electron in the binuclear center, similar to the O(H)→E(H) transition of the aa(3)-type oxidases. So, the fully-reduced caa(3) oxidase is competent in rapid electron transfer from the input redox-centers into the catalytic heme-copper site. 2011 Elsevier B.V. All rights reserved.

Machine cataloging of impact craters on Mars

NASA Astrophysics Data System (ADS)

Stepinski, Tomasz F.; Mendenhall, Michael P.; Bue, Brian D.

2009-09-01

This study presents an automated system for cataloging impact craters using the MOLA 128 pixels/degree digital elevation model of Mars. Craters are detected by a two-step algorithm that first identifies round and symmetric topographic depressions as crater candidates and then selects craters using a machine-learning technique. The system is robust with respect to surface types; craters are identified with similar accuracy from all different types of martian surfaces without adjusting input parameters. By using a large training set in its final selection step, the system produces virtually no false detections. Finally, the system provides a seamless integration of crater detection with its characterization. Of particular interest is the ability of our algorithm to calculate crater depths. The system is described and its application is demonstrated on eight large sites representing all major types of martian surfaces. An evaluation of its performance and prospects for its utilization for global surveys are given by means of detailed comparison of obtained results to the manually-derived Catalog of Large Martian Impact Craters. We use the results from the test sites to construct local depth-diameter relationships based on a large number of craters. In general, obtained relationships are in agreement with what was inferred on the basis of manual measurements. However, we have found that, in Terra Cimmeria, the depth/diameter ratio has an abrupt decrease at ˜38°S regardless of crater size. If shallowing of craters is attributed to presence of sub-surface ice, a sudden change in its spatial distribution is suggested by our findings.

SVM-Based Prediction of Propeptide Cleavage Sites in Spider Toxins Identifies Toxin Innovation in an Australian Tarantula

PubMed Central

Wong, Emily S. W.; Hardy, Margaret C.; Wood, David; Bailey, Timothy; King, Glenn F.

2013-01-01

Spider neurotoxins are commonly used as pharmacological tools and are a popular source of novel compounds with therapeutic and agrochemical potential. Since venom peptides are inherently toxic, the host spider must employ strategies to avoid adverse effects prior to venom use. It is partly for this reason that most spider toxins encode a protective proregion that upon enzymatic cleavage is excised from the mature peptide. In order to identify the mature toxin sequence directly from toxin transcripts, without resorting to protein sequencing, the propeptide cleavage site in the toxin precursor must be predicted bioinformatically. We evaluated different machine learning strategies (support vector machines, hidden Markov model and decision tree) and developed an algorithm (SpiderP) for prediction of propeptide cleavage sites in spider toxins. Our strategy uses a support vector machine (SVM) framework that combines both local and global sequence information. Our method is superior or comparable to current tools for prediction of propeptide sequences in spider toxins. Evaluation of the SVM method on an independent test set of known toxin sequences yielded 96% sensitivity and 100% specificity. Furthermore, we sequenced five novel peptides (not used to train the final predictor) from the venom of the Australian tarantula Selenotypus plumipes to test the accuracy of the predictor and found 80% sensitivity and 99.6% 8-mer specificity. Finally, we used the predictor together with homology information to predict and characterize seven groups of novel toxins from the deeply sequenced venom gland transcriptome of S. plumipes, which revealed structural complexity and innovations in the evolution of the toxins. The precursor prediction tool (SpiderP) is freely available on ArachnoServer (http://www.arachnoserver.org/spiderP.html), a web portal to a comprehensive relational database of spider toxins. All training data, test data, and scripts used are available from the SpiderP website. PMID:23894279

Initial Characterization of the Pf-Int Recombinase from the Malaria Parasite Plasmodium falciparum

PubMed Central

Ghorbal, Mehdi; Scheidig-Benatar, Christine; Bouizem, Salma; Thomas, Christophe; Paisley, Genevieve; Faltermeier, Claire; Liu, Melanie; Scherf, Artur; Lopez-Rubio, Jose-Juan; Gopaul, Deshmukh N.

2012-01-01

Background Genetic variation is an essential means of evolution and adaptation in many organisms in response to environmental change. Certain DNA alterations can be carried out by site-specific recombinases (SSRs) that fall into two families: the serine and the tyrosine recombinases. SSRs are seldom found in eukaryotes. A gene homologous to a tyrosine site-specific recombinase has been identified in the genome of Plasmodium falciparum. The sequence is highly conserved among five other members of Plasmodia. Methodology/Principal Findings The predicted open reading frame encodes for a ∼57 kDa protein containing a C-terminal domain including the putative tyrosine recombinase conserved active site residues R-H-R-(H/W)-Y. The N-terminus has the typical alpha-helical bundle and potentially a mixed alpha-beta domain resembling that of λ-Int. Pf-Int mRNA is expressed differentially during the P. falciparum erythrocytic life stages, peaking in the schizont stage. Recombinant Pf-Int and affinity chromatography of DNA from genomic or synthetic origin were used to identify potential DNA targets after sequencing or micro-array hybridization. Interestingly, the sequences captured also included highly variable subtelomeric genes such as var, rif, and stevor sequences. Electrophoretic mobility shift assays with DNA were carried out to verify Pf-Int/DNA binding. Finally, Pf-Int knock-out parasites were created in order to investigate the biological role of Pf-Int. Conclusions/Significance Our data identify for the first time a malaria parasite gene with structural and functional features of recombinases. Pf-Int may bind to and alter DNA, either in a sequence specific or in a non-specific fashion, and may contribute to programmed or random DNA rearrangements. Pf-Int is the first molecular player identified with a potential role in genome plasticity in this pathogen. Finally, Pf-Int knock-out parasite is viable showing no detectable impact on blood stage development, which is compatible with such function. PMID:23056326

Investigation and demonstration of turbidity reduction in stormwater runoff for Oklahoma highway construction sites : final report.

DOT National Transportation Integrated Search

2013-12-01

The Environmental protection Agency (USEPA) has issued new requirements on the construction industry to control the discharge of pollutants from the sites. The construction effluent guidelines or ELGs require construction sites to reduce the pollu...

Contractor for geopressured-geothermal sites: Final contract report, Volume 1, fiscal years 1986--1990 (5 years), testing of wells through October 1990. Appendix A, Volume 2, Gladys McCall Site (Cameron Parish LA); Appendix B-1, Volume 3, Pleasant Bayou Site; Appendix B-2, Volume 4, Pleasant Bayou Site; Appendix C, Volume 5, Willis Hulin Site

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

Not Available

1992-09-01

Field tests and studies were conducted to determine the production behavior of geopressured-geothermal reservoirs and their potential as future energy sources. Results are presented for Gladys McCall Site, Pleasant Bayou Site, and Hulin Site.