Tightly integrated single- and multi-crystal data collection strategy calculation and parallelized data processing in JBluIce beamline control system

PubMed Central

Pothineni, Sudhir Babu; Venugopalan, Nagarajan; Ogata, Craig M.; Hilgart, Mark C.; Stepanov, Sergey; Sanishvili, Ruslan; Becker, Michael; Winter, Graeme; Sauter, Nicholas K.; Smith, Janet L.; Fischetti, Robert F.

2014-01-01

The calculation of single- and multi-crystal data collection strategies and a data processing pipeline have been tightly integrated into the macromolecular crystallographic data acquisition and beamline control software JBluIce. Both tasks employ wrapper scripts around existing crystallographic software. JBluIce executes scripts through a distributed resource management system to make efficient use of all available computing resources through parallel processing. The JBluIce single-crystal data collection strategy feature uses a choice of strategy programs to help users rank sample crystals and collect data. The strategy results can be conveniently exported to a data collection run. The JBluIce multi-crystal strategy feature calculates a collection strategy to optimize coverage of reciprocal space in cases where incomplete data are available from previous samples. The JBluIce data processing runs simultaneously with data collection using a choice of data reduction wrappers for integration and scaling of newly collected data, with an option for merging with pre-existing data. Data are processed separately if collected from multiple sites on a crystal or from multiple crystals, then scaled and merged. Results from all strategy and processing calculations are displayed in relevant tabs of JBluIce. PMID:25484844

Tightly integrated single- and multi-crystal data collection strategy calculation and parallelized data processing in JBluIce beamline control system

DOE PAGES

Pothineni, Sudhir Babu; Venugopalan, Nagarajan; Ogata, Craig M.; ...

2014-11-18

The calculation of single- and multi-crystal data collection strategies and a data processing pipeline have been tightly integrated into the macromolecular crystallographic data acquisition and beamline control software JBluIce. Both tasks employ wrapper scripts around existing crystallographic software. JBluIce executes scripts through a distributed resource management system to make efficient use of all available computing resources through parallel processing. The JBluIce single-crystal data collection strategy feature uses a choice of strategy programs to help users rank sample crystals and collect data. The strategy results can be conveniently exported to a data collection run. The JBluIce multi-crystal strategy feature calculates amore » collection strategy to optimize coverage of reciprocal space in cases where incomplete data are available from previous samples. The JBluIce data processing runs simultaneously with data collection using a choice of data reduction wrappers for integration and scaling of newly collected data, with an option for merging with pre-existing data. Data are processed separately if collected from multiple sites on a crystal or from multiple crystals, then scaled and merged. Results from all strategy and processing calculations are displayed in relevant tabs of JBluIce.« less

System and method for measuring fluorescence of a sample

DOEpatents

Riot, Vincent J

2015-03-24

The present disclosure provides a system and a method for measuring fluorescence of a sample. The sample may be a polymerase-chain-reaction (PCR) array, a loop-mediated-isothermal amplification array, etc. LEDs are used to excite the sample, and a photodiode is used to collect the sample's fluorescence. An electronic offset signal is used to reduce the effects of background fluorescence and the noises from the measurement system. An integrator integrates the difference between the output of the photodiode and the electronic offset signal over a given period of time. The resulting integral is then converted into digital domain for further processing and storage.

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

Riot, Vincent J.

The present disclosure provides a system and a method for measuring fluorescence of a sample. The sample may be a polymerase-chain-reaction (PCR) array, a loop-mediated-isothermal amplification array, etc. LEDs are used to excite the sample, and a photodiode is used to collect the sample's fluorescence. An electronic offset signal is used to reduce the effects of background fluorescence and the noises from the measurement system. An integrator integrates the difference between the output of the photodiode and the electronic offset signal over a given period of time. The resulting integral is then converted into digital domain for further processing andmore » storage.« less

Fit for purpose frozen tissue collections by RNA integrity number-based quality control assurance at the Erasmus MC tissue bank.

PubMed

Kap, Marcel; Oomen, Monique; Arshad, Shazia; de Jong, Bas; Riegman, Peter

2014-04-01

About 5000 frozen tissue samples are collected each year by the Erasmus Medical Center tissue bank. Two percent of these samples are randomly selected annually for RNA isolation and RNA Integrity Number (RIN) measurement. A similar quality assessment was conducted during centralization of a 20-year-old tissue collection from the cancer institute, a 15-year-old liver sample archive (-80°C), and a 13-year-old clinical pathology frozen biopsy archive (Liquid Nitrogen). Samples were divided into either high-quality (RIN ≥6.5) or low-quality overall categories, or into four "fit-for-purpose" quality groups: RIN <5: not reliable for demanding downstream analysis; 5 ≤RIN <6: suitable for RT-qPCR; 6 ≤RIN <8: suitable for gene array analysis; and RIN ≥8: suitable for all downstream techniques. In general, low RIN values were correlated with fatty, fibrous, pancreatic, or necrotic tissue. When the percentage of samples with RIN ≥6.5 is higher than 90%, the tissue bank performance is adequate. The annual 2011 quality control assessment showed that 90.3% (n=93) of all samples had acceptable RIN values; 97.4% (n=39) of the cancer institute collection had RIN values above 6.5; and 88.6% (n=123) of samples from the liver sample archive collection had RIN values higher than 6.5. As the clinical pathology biopsy collection contained only 58.8% (n=24) acceptable samples, the procurement protocols used for these samples needed immediate evaluation. When the distribution of RIN values of the different collections were compared, no significant differences were found, despite differences in average storage time and temperature. According to the principle of "fit-for-purpose" distribution, the vast majority of samples are considered good enough for most downstream techniques. In conclusion, an annual tissue bank quality control procedure provides useful information on tissue sample quality and sheds light on where and if improvements need to be made.

Comparison of U.S. Geological Survey and Ohio Environmental Protection Agency fish-collection methods using the index of biotic integrity and modified index of well-being, 1996-97

USGS Publications Warehouse

Covert, S. Alex

2001-01-01

The U.S. Geological Survey (USGS) and Ohio Environmental Protection Agency (OEPA) collected data on fish from 10 stream sites in 1996 and 3 stream sites in 1997 as part of a comparative study of fish community assessment methods. The sites sampled represent a wide range of basin sizes (ranging from 132?6,330 square kilometers) and surrounding land-use types (urban, agricultural, and mixed). Each agency used its own fish-sampling protocol. Using the Index of Biotic Integrity and Modified Index of Well-Being, differences between data sets were tested for significance by means of the Wilcoxon signed-ranks test (a = 0.05). Results showed that the median of Index of Biotic Integrity differences between data sets was not significantly different from zero (p = 0.2521); however, the same statistical test showed the median differences in the Modified Index of Well-Being scores to be significantly different from zero (p = 0.0158). The differences observed in the Index of Biotic Integrity scores are likely due to natural variability, increased variability at sites with degraded water quality, differences in sampling methods, and low-end adjustments in the Index of Biotic Integrity calculation when fewer than 50 fish were collected. The Modified Index of Well-Being scores calculated by OEPA were significantly higher than those calculated by the USGS. This finding was attributed to the comparatively large numbers and biomass of fish collected by the OEPA. By combining the two indices and viewing them in terms of the percentage attainment of Ohio Warmwater Habitat criteria, the two agencies? data seemed comparable, although the Index of Biotic Integrity scores were more similar than the Modified Index of Well-Being scores.

Effects of RNA integrity on transcript quantification by total RNA sequencing of clinically collected human placental samples.

PubMed

Reiman, Mario; Laan, Maris; Rull, Kristiina; Sõber, Siim

2017-08-01

RNA degradation is a ubiquitous process that occurs in living and dead cells, as well as during handling and storage of extracted RNA. Reduced RNA quality caused by degradation is an established source of uncertainty for all RNA-based gene expression quantification techniques. RNA sequencing is an increasingly preferred method for transcriptome analyses, and dependence of its results on input RNA integrity is of significant practical importance. This study aimed to characterize the effects of varying input RNA integrity [estimated as RNA integrity number (RIN)] on transcript level estimates and delineate the characteristic differences between transcripts that differ in degradation rate. The study used ribodepleted total RNA sequencing data from a real-life clinically collected set ( n = 32) of human solid tissue (placenta) samples. RIN-dependent alterations in gene expression profiles were quantified by using DESeq2 software. Our results indicate that small differences in RNA integrity affect gene expression quantification by introducing a moderate and pervasive bias in expression level estimates that significantly affected 8.1% of studied genes. The rapidly degrading transcript pool was enriched in pseudogenes, short noncoding RNAs, and transcripts with extended 3' untranslated regions. Typical slowly degrading transcripts (median length, 2389 nt) represented protein coding genes with 4-10 exons and high guanine-cytosine content.-Reiman, M., Laan, M., Rull, K., Sõber, S. Effects of RNA integrity on transcript quantification by total RNA sequencing of clinically collected human placental samples. © FASEB.

Characterizing the distribution of particles in urban stormwater: advancements through improved sampling technology

USGS Publications Warehouse

Selbig, William R.

2014-01-01

A new sample collection system was developed to improve the representation of sediment in stormwater by integrating the entire water column. The depth-integrated sampler arm (DISA) was able to mitigate sediment stratification bias in storm water, thereby improving the characterization of particle size distribution from urban source areas. Collector streets had the lowest median particle diameter of 8 μm, followed by parking lots, arterial streets, feeder streets, and residential and mixed land use (32, 43, 50, 80 and 95 μm, respectively). Results from this study suggest there is no single distribution of particles that can be applied uniformly to runoff in urban environments; however, integrating more of the entire water column during the sample collection can address some of the shortcomings of a fixed-point sampler by reducing variability and bias caused by the stratification of solids in a water column.

Introduction to Field Water-Quality Methods for the Collection of Metals - 2007 Project Summary

USGS Publications Warehouse

Allen, Monica L.

2008-01-01

The U.S. Geological Survey (USGS), Region VI of the U.S. Environmental Protection Agency (USEPA), and the Osage Nation presented three 3-day workshops, in June-August 2007, entitled ?Introduction to Field Water-Quality Methods for the Collection of Metals.? The purpose of the workshops was to provide instruction to tribes within USEPA Region VI on various USGS surface-water measurement methods and water-quality sampling protocols for the collection of surface-water samples for metals analysis. Workshop attendees included members from over 22 tribes and pueblos. USGS instructors came from Oklahoma, New Mexico, and Georgia. Workshops were held in eastern and south-central Oklahoma and New Mexico and covered many topics including presampling preparation, water-quality monitors, and sampling for metals in surface water. Attendees spent one full classroom day learning the field methods used by the USGS Water Resources Discipline and learning about the complexity of obtaining valid water-quality and quality-assurance data. Lectures included (1) a description of metal contamination sources in surface water; (2) introduction on how to select field sites, equipment, and laboratories for sample analysis; (3) collection of sediment in surface water; and (4) utilization of proper protocol and methodology for sampling metals in surface water. Attendees also were provided USGS sampling equipment for use during the field portion of the class so they had actual ?hands-on? experience to take back to their own organizations. The final 2 days of the workshop consisted of field demonstrations of current USGS water-quality sample-collection methods. The hands-on training ensured that attendees were exposed to and experienced proper sampling procedures. Attendees learned integrated-flow techniques during sample collection, field-property documentation, and discharge measurements and calculations. They also used enclosed chambers for sample processing and collected quality-assurance samples to verify their techniques. Benefits of integrated water-quality sample-collection methods are varied. Tribal environmental programs now have the ability to collect data that are comparable across watersheds. The use of consistent sample collection, manipulation, and storage techniques will provide consistent quality data that will enhance the understanding of local water resources. The improved data quality also will help the USEPA better document the condition of the region?s water. Ultimately, these workshops equipped tribes to use uniform sampling methods and to provide consistent quality data that are comparable across the region.

Development of a depth-integrated sample arm (DISA) to reduce solids stratification bias in stormwater sampling

USGS Publications Warehouse

Selbig, William R.; ,; Roger T. Bannerman,

2011-01-01

A new depth-integrated sample arm (DISA) was developed to improve the representation of solids in stormwater, both organic and inorganic, by collecting a water quality sample from multiple points in the water column. Data from this study demonstrate the idea of vertical stratification of solids in storm sewer runoff. Concentrations of suspended sediment in runoff were statistically greater using a fixed rather than multipoint collection system. Median suspended sediment concentrations measured at the fixed location (near the pipe invert) were approximately double those collected using the DISA. In general, concentrations and size distributions of suspended sediment decreased with increasing vertical distance from the storm sewer invert. Coarser particles tended to dominate the distribution of solids near the storm sewer invert as discharge increased. In contrast to concentration and particle size, organic material, to some extent, was distributed homogenously throughout the water column, likely the result of its low specific density, which allows for thorough mixing in less turbulent water.

Development of a depth-integrated sample arm to reduce solids stratification bias in stormwater sampling.

PubMed

Selbig, William R; Bannerman, Roger T

2011-04-01

A new depth-integrated sample arm (DISA) was developed to improve the representation of solids in stormwater, both organic and inorganic, by collecting a water quality sample from multiple points in the water column. Data from this study demonstrate the idea of vertical stratification of solids in storm sewer runoff. Concentrations of suspended sediment in runoff were statistically greater using a fixed rather than multipoint collection system. Median suspended sediment concentrations measured at the fixed location (near the pipe invert) were approximately double those collected using the DISA. In general, concentrations and size distributions of suspended sediment decreased with increasing vertical distance from the storm sewer invert. Coarser particles tended to dominate the distribution of solids near the storm sewer invert as discharge increased. In contrast to concentration and particle size, organic material, to some extent, was distributed homogenously throughout the water column, likely the result of its low specific density, which allows for thorough mixing in less turbulent water.

Development of a depth-integrated sample arm to reduce solids stratification bias in stormwater sampling

USGS Publications Warehouse

Selbig, W.R.; Bannerman, R.T.

2011-01-01

A new depth-integrated sample arm (DISA) was developed to improve the representation of solids in stormwater, both organic and inorganic, by collecting a water quality sample from multiple points in the water column. Data from this study demonstrate the idea of vertical stratification of solids in storm sewer runoff. Concentrations of suspended sediment in runoff were statistically greater using a fixed rather than multipoint collection system. Median suspended sediment concentrations measured at the fixed location (near the pipe invert) were approximately double those collected using the DISA. In general, concentrations and size distributions of suspended sediment decreased with increasing vertical distance from the storm sewer invert. Coarser particles tended to dominate the distribution of solids near the storm sewer invert as discharge increased. In contrast to concentration and particle size, organic material, to some extent, was distributed homogenously throughout the water column, likely the result of its low specific density, which allows for thorough mixing in less turbulent water. ?? 2010 Publishing Technology.

Sampling device with a capped body and detachable handle

DOEpatents

Jezek, Gerd-Rainer

2000-01-01

The apparatus is a sampling device having a pad for sample collection, a body which supports the pad, a detachable handle connected to the body and a cap which encloses and retains the pad and body to protect the integrity of the sample.

Using regression methods to estimate stream phosphorus loads at the Illinois River, Arkansas

USGS Publications Warehouse

Haggard, B.E.; Soerens, T.S.; Green, W.R.; Richards, R.P.

2003-01-01

The development of total maximum daily loads (TMDLs) requires evaluating existing constituent loads in streams. Accurate estimates of constituent loads are needed to calibrate watershed and reservoir models for TMDL development. The best approach to estimate constituent loads is high frequency sampling, particularly during storm events, and mass integration of constituents passing a point in a stream. Most often, resources are limited and discrete water quality samples are collected on fixed intervals and sometimes supplemented with directed sampling during storm events. When resources are limited, mass integration is not an accurate means to determine constituent loads and other load estimation techniques such as regression models are used. The objective of this work was to determine a minimum number of water-quality samples needed to provide constituent concentration data adequate to estimate constituent loads at a large stream. Twenty sets of water quality samples with and without supplemental storm samples were randomly selected at various fixed intervals from a database at the Illinois River, northwest Arkansas. The random sets were used to estimate total phosphorus (TP) loads using regression models. The regression-based annual TP loads were compared to the integrated annual TP load estimated using all the data. At a minimum, monthly sampling plus supplemental storm samples (six samples per year) was needed to produce a root mean square error of less than 15%. Water quality samples should be collected at least semi-monthly (every 15 days) in studies less than two years if seasonal time factors are to be used in the regression models. Annual TP loads estimated from independently collected discrete water quality samples further demonstrated the utility of using regression models to estimate annual TP loads in this stream system.

SAIL--a software system for sample and phenotype availability across biobanks and cohorts.

PubMed

Gostev, Mikhail; Fernandez-Banet, Julio; Rung, Johan; Dietrich, Joern; Prokopenko, Inga; Ripatti, Samuli; McCarthy, Mark I; Brazma, Alvis; Krestyaninova, Maria

2011-02-15

The Sample avAILability system-SAIL-is a web based application for searching, browsing and annotating biological sample collections or biobank entries. By providing individual-level information on the availability of specific data types (phenotypes, genetic or genomic data) and samples within a collection, rather than the actual measurement data, resource integration can be facilitated. A flexible data structure enables the collection owners to provide descriptive information on their samples using existing or custom vocabularies. Users can query for the available samples by various parameters combining them via logical expressions. The system can be scaled to hold data from millions of samples with thousands of variables. SAIL is available under Aferro-GPL open source license: https://github.com/sail.

A microfluidic platform for precision small-volume sample processing and its use to size separate biological particles with an acoustic microdevice [Precision size separation of biological particles in small-volume samples by an acoustic microfluidic system

DOE PAGES

Fong, Erika J.; Huang, Chao; Hamilton, Julie; ...

2015-11-23

Here, a major advantage of microfluidic devices is the ability to manipulate small sample volumes, thus reducing reagent waste and preserving precious sample. However, to achieve robust sample manipulation it is necessary to address device integration with the macroscale environment. To realize repeatable, sensitive particle separation with microfluidic devices, this protocol presents a complete automated and integrated microfluidic platform that enables precise processing of 0.15–1.5 ml samples using microfluidic devices. Important aspects of this system include modular device layout and robust fixtures resulting in reliable and flexible world to chip connections, and fully-automated fluid handling which accomplishes closed-loop sample collection,more » system cleaning and priming steps to ensure repeatable operation. Different microfluidic devices can be used interchangeably with this architecture. Here we incorporate an acoustofluidic device, detail its characterization, performance optimization, and demonstrate its use for size-separation of biological samples. By using real-time feedback during separation experiments, sample collection is optimized to conserve and concentrate sample. Although requiring the integration of multiple pieces of equipment, advantages of this architecture include the ability to process unknown samples with no additional system optimization, ease of device replacement, and precise, robust sample processing.« less

Relationship of 24-hour urinary free cortisol to 4-hour salivary morning and afternoon cortisol and cortisone as measured by a time-integrated oral diffusion sink.

PubMed

Kathol, R G; Poland, R E; Stokes, P E; Wade, S

1995-05-01

The relationship between salivary corticosteroids integrated over 4-hour periods and urinary free cortisol collected over 24 hours was investigated in normal controls. Twenty-one normal volunteers wore "oral diffusion sink" sampling devices in their mouths for two 4-hour periods (08:00-12:00 hours and 13:00-17:00 hours) and on the same day collected a 24-hour urine specimen. Time-integrated salivary corticosteroid concentrations were determined from the sample devices and urinary free cortisol was measured. Salivary corticosteroids were not consistently higher in the morning than in the afternoon period and did not differ between men and women. Urinary free cortisol levels were higher in women. No salivary corticosteroids measure was significantly correlated with urinary free cortisol. We conclude that time-integrated salivary corticosteroids do not reflect urinary free cortisol levels in normal controls.

Evaluation of environmental sampling methods for detection of Salmonella enterica in a large animal veterinary hospital.

PubMed

Goeman, Valerie R; Tinkler, Stacy H; Hammac, G Kenitra; Ruple, Audrey

2018-04-01

Environmental surveillance for Salmonella enterica can be used for early detection of contamination; thus routine sampling is an integral component of infection control programs in hospital environments. At the Purdue University Veterinary Teaching Hospital (PUVTH), the technique regularly employed in the large animal hospital for sample collection uses sterile gauze sponges for environmental sampling, which has proven labor-intensive and time-consuming. Alternative sampling methods use Swiffer brand electrostatic wipes for environmental sample collection, which are reportedly effective and efficient. It was hypothesized that use of Swiffer wipes for sample collection would be more efficient and less costly than the use of gauze sponges. A head-to-head comparison between the 2 sampling methods was conducted in the PUVTH large animal hospital and relative agreement, cost-effectiveness, and sampling efficiency were compared. There was fair agreement in culture results between the 2 sampling methods, but Swiffer wipes required less time and less physical effort to collect samples and were more cost-effective.

Integration of Apollo Lunar Sample Data into Google Moon

NASA Technical Reports Server (NTRS)

Dawson, Melissa D.; Todd, Nancy S.; Lofgren, Gary

2010-01-01

The Google Moon Apollo Lunar Sample Data Integration project is a continuation of the Apollo 15 Google Moon Add-On project, which provides a scientific and educational tool for the study of the Moon and its geologic features. The main goal of this project is to provide a user-friendly interface for an interactive and educational outreach and learning tool for the Apollo missions. Specifically, this project?s focus is the dissemination of information about the lunar samples collected during the Apollo missions by providing any additional information needed to enhance the Apollo mission data on Google Moon. Apollo missions 15 and 16 were chosen to be completed first due to the availability of digitized lunar sample photographs and the amount of media associated with these missions. The user will be able to learn about the lunar samples collected in these Apollo missions, as well as see videos, pictures, and 360 degree panoramas of the lunar surface depicting the lunar samples in their natural state, following collection and during processing at NASA. Once completed, these interactive data layers will be submitted for inclusion into the Apollo 15 and 16 missions on Google Moon.

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

Marutzky, Sam; Farnham, Irene

The purpose of the Nevada National Security Site (NNSS) Integrated Sampling Plan (referred to herein as the Plan) is to provide a comprehensive, integrated approach for collecting and analyzing groundwater samples to meet the needs and objectives of the U.S. Department of Energy (DOE), National Nuclear Security Administration Nevada Field Office (NNSA/NFO) Underground Test Area (UGTA) Activity. Implementation of this Plan will provide high-quality data required by the UGTA Activity for ensuring public protection in an efficient and cost-effective manner. The Plan is designed to ensure compliance with the UGTA Quality Assurance Plan (QAP). The Plan’s scope comprises sample collectionmore » and analysis requirements relevant to assessing the extent of groundwater contamination from underground nuclear testing. This Plan identifies locations to be sampled by corrective action unit (CAU) and location type, sampling frequencies, sample collection methodologies, and the constituents to be analyzed. In addition, the Plan defines data collection criteria such as well-purging requirements, detection levels, and accuracy requirements; identifies reporting and data management requirements; and provides a process to ensure coordination between NNSS groundwater sampling programs for sampling of interest to UGTA. This Plan does not address compliance with requirements for wells that supply the NNSS public water system or wells involved in a permitted activity.« less

Ethanol and sodium acetate as a preservation method to delay degradation of environmental DNA

USGS Publications Warehouse

Ladell, Bridget A.; Walleser, Liza R.; McCalla, S. Grace; Erickson, Richard A.; Amberg, Jon J.

2018-01-01

Environmental DNA (eDNA) samples that are collected from remote locations depend on rapid stabilization of the DNA. The degradation of eDNA in water samples is minimized when samples are stored at ≤ 4 °C. Developing a preservation technique to maintain eDNA integrity at room temperature would allow a wider range of locations to be sampled. We evaluated an ethanol and sodium acetate solution to maintain the integrity of the DNA samples for the time between collection and lab testing. For this evaluation, replicate water samples taken from a tank housing Asian carp were placed on ice or held at room temperature. At both temperatures, water samples were left untreated or were preserved with an ethanol and sodium acetate solution (EtOH–NaAc). Every day for 6 days following collection, a subset of the samples was removed from each preservation method and DNA was extracted and nuclear and mitochondrial markers were assayed with qPCR. Results showed comparable persistence of DNA between iced samples without the EtOH–NaAc treatment and samples that received EtOH–NaAc treatment that were kept at room temperature. We found that DNA can be amplified from preserved samples using an EtOH–NaAc solution after up to 7 days at room temperature.

Apollo Lunar Sample Integration into Google Moon: A New Approach to Digitization

NASA Technical Reports Server (NTRS)

Dawson, Melissa D.; Todd, nancy S.; Lofgren, Gary E.

2011-01-01

The Google Moon Apollo Lunar Sample Data Integration project is part of a larger, LASER-funded 4-year lunar rock photo restoration project by NASA s Acquisition and Curation Office [1]. The objective of this project is to enhance the Apollo mission data already available on Google Moon with information about the lunar samples collected during the Apollo missions. To this end, we have combined rock sample data from various sources, including Curation databases, mission documentation and lunar sample catalogs, with newly available digital photography of rock samples to create a user-friendly, interactive tool for learning about the Apollo Moon samples

DITTY - a computer program for calculating population dose integrated over ten thousand years

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

Napier, B.A.; Peloquin, R.A.; Strenge, D.L.

The computer program DITTY (Dose Integrated Over Ten Thousand Years) was developed to determine the collective dose from long term nuclear waste disposal sites resulting from the ground-water pathways. DITTY estimates the time integral of collective dose over a ten-thousand-year period for time-variant radionuclide releases to surface waters, wells, or the atmosphere. This document includes the following information on DITTY: a description of the mathematical models, program designs, data file requirements, input preparation, output interpretations, sample problems, and program-generated diagnostic messages.

Migration, Adjustment, and Integration of the Indian Into the Urban Environment.

ERIC Educational Resources Information Center

McCaskill, Donald N.

The migration, adjustment, and integration patterns of Canadian Indian and Metis families in an urban setting were studied. Data were collected in 1968 via a 64-item interview schedule administered to a sample of 71 families moving into the city of Winnepeg, Canada. Addressing the problems of migration, adjustment, and integration, analysis…

Preserving Samples and Their Scientific Integrity — Insights into MSR from the Astromaterials Acquisition and Curation Office at NASA Johnson Space Center

NASA Astrophysics Data System (ADS)

Calaway, M. J.; Regberg, A. B.; Mitchell, J. L.; Fries, M. D.; Zeigler, R. A.; McCubbin, F. M.; Harrington, A. D.

2018-04-01

Rigorous collection of samples for contamination knowledge, the information gained from the characterization of reference materials and witness plates in concurrence with sample return, is essential for MSR mission success.

Integrated global background monitoring network. Preliminary results from Torres del Paine and Olympic National Parks

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

Wiersma, G.B.; Kohler, A.; Boelcke, C.

1985-10-01

During 1984, a pilot project was initiated for monitoring pollution at Torres del Paine National Park in southern Chile and Olympic National Park in the United States. These are two of three initial sites that are to be established as part of an integrated global backgound monitoring network. Eventually, the plan is to establish a world-wide system of such sites. We collected and analyzed samples of the soil, water, air, and two species of plants (moss and lichen). We also collected and analyzed samples of the forest litter. We compared the samples of soil and vegetation against reference samples. Wemore » also compared samples of soil, vegetation, and of organic material from Torres del Paine against similar samples from Olympic and Sequoia-Kings Canyon National Parks in the United States. Although the data is preliminary, it is in agreement with out initial hypothesis that Torres del Paine and Olympic National Parks are not a polluted sites.« less

Integrating quantitative PCR and Bayesian statistics in quantifying human adenoviruses in small volumes of source water.

PubMed

Wu, Jianyong; Gronewold, Andrew D; Rodriguez, Roberto A; Stewart, Jill R; Sobsey, Mark D

2014-02-01

Rapid quantification of viral pathogens in drinking and recreational water can help reduce waterborne disease risks. For this purpose, samples in small volume (e.g. 1L) are favored because of the convenience of collection, transportation and processing. However, the results of viral analysis are often subject to uncertainty. To overcome this limitation, we propose an approach that integrates Bayesian statistics, efficient concentration methods, and quantitative PCR (qPCR) to quantify viral pathogens in water. Using this approach, we quantified human adenoviruses (HAdVs) in eighteen samples of source water collected from six drinking water treatment plants. HAdVs were found in seven samples. In the other eleven samples, HAdVs were not detected by qPCR, but might have existed based on Bayesian inference. Our integrated approach that quantifies uncertainty provides a better understanding than conventional assessments of potential risks to public health, particularly in cases when pathogens may present a threat but cannot be detected by traditional methods. © 2013 Elsevier B.V. All rights reserved.

Environmental Factors Related to a Semiarid Climate Influence the Freezability of Sperm from Collared Peccaries (Pecari tajacu Linnaeus, 1758).

PubMed

Maia, Keilla M; Souza, Ana L P; Praxedes, Erica C G; Bezerra, Luana G P; Silva, Andreia M; Campos, Livia B; Moreira, Samara S J; Apolinário, Carlos A C; Souza, João B F; Silva, Alexandre R

2018-04-30

The influence of environmental factors in a semiarid climate on characteristics of fresh and frozen/thawed sperm collected from collared peccaries (Pecari tajacu) was assessed. Semen from 11 male collared peccaries was collected by electroejaculation during the peaks of the dry and rainy periods while rainfall indices, air temperatures, relative humidity levels, and wind speeds were measured. The number, motility, morphology, osmotic response, and membrane integrity of sperm in the collected ejaculates were assessed. Samples were then frozen in liquid nitrogen, thawed, and reassessed. The rainfall index of the rainy period (73.2 mm) was significantly higher than that of the dry period (13.6 mm) and the relative humidity was significantly higher during the rainy period (74.6%) than it was during the dry period (66.8%). Air temperature and wind speed did not differ between the two periods. Characteristics of sperm in the fresh samples were not affected by environmental parameters. In contrast, computerized analysis revealed that sperm in samples frozen during the rainy period exhibited better post-thaw membrane integrity (28.6 ± 6%), motility (29.5 ± 7.7%), and rapid sperm population (13.7 ± 6.2%) than did sperm in samples frozen during the dry period (23.4 ± 3% membrane integrity, 14.6 ± 4.1% motility, and 4.1 ± 1.2% rapid sperm; p < 0.05). Other characteristics of the frozen/thawed sperm did not differ depending on the period in which they were collected. We demonstrated that environmental parameters did not affect the quality of fresh sperm, but could influence the freezability of sperm collected from collared peccaries raised under a semiarid climate.

40 CFR 63.997 - Performance test and compliance assessment requirements for control devices.

Code of Federal Regulations, 2012 CFR

2012-07-01

... regulated materials are loaded, and samples shall be collected using integrated sampling or grab samples... material concentration and percent reduction may be measured as either total organic regulated material or... regulated material or TOC, sampling sites shall be located as specified in paragraphs (e)(2)(i)(A)(1) and (e...

40 CFR 63.997 - Performance test and compliance assessment requirements for control devices.

Code of Federal Regulations, 2013 CFR

2013-07-01

... regulated materials are loaded, and samples shall be collected using integrated sampling or grab samples... material concentration and percent reduction may be measured as either total organic regulated material or... regulated material or TOC, sampling sites shall be located as specified in paragraphs (e)(2)(i)(A)(1) and (e...

40 CFR 63.997 - Performance test and compliance assessment requirements for control devices.

Code of Federal Regulations, 2014 CFR

2014-07-01

... regulated materials are loaded, and samples shall be collected using integrated sampling or grab samples... material concentration and percent reduction may be measured as either total organic regulated material or... regulated material or TOC, sampling sites shall be located as specified in paragraphs (e)(2)(i)(A)(1) and (e...

Regression modeling of particle size distributions in urban storm water: advancements through improved sample collection methods

USGS Publications Warehouse

Fienen, Michael N.; Selbig, William R.

2012-01-01

A new sample collection system was developed to improve the representation of sediment entrained in urban storm water by integrating water quality samples from the entire water column. The depth-integrated sampler arm (DISA) was able to mitigate sediment stratification bias in storm water, thereby improving the characterization of suspended-sediment concentration and particle size distribution at three independent study locations. Use of the DISA decreased variability, which improved statistical regression to predict particle size distribution using surrogate environmental parameters, such as precipitation depth and intensity. The performance of this statistical modeling technique was compared to results using traditional fixed-point sampling methods and was found to perform better. When environmental parameters can be used to predict particle size distributions, environmental managers have more options when characterizing concentrations, loads, and particle size distributions in urban runoff.

Evaluation of epididymis storage temperature and cryopreservation conditions for improved mitochondrial membrane potential, membrane integrity, sperm motility and in vitro fertilization in bovine epididymal sperm.

PubMed

Nichi, M; Rijsselaere, T; Losano, Jda; Angrimani, Dsr; Kawai, Gkv; Goovaerts, Igf; Van Soom, A; Barnabe, V H; De Clercq, Jbp; Bols, Pej

2017-04-01

The maintaining of the epididymis at lower temperatures during storage and transport improves sperm quality. Our study aimed to test whether epididymis storage temperature (post-mortem) and sperm cryopreservation affect sperm kinetics, membrane integrity, mitochondrial potential and fertility capacity. Thirty-six epididymides were collected from 18 bulls after slaughter and divided into two groups: at 4 or 34°C for 2-3 hr. The sperm was collected from the epididymis cauda. The evaluation consisted of computer-assisted sperm analysis (CASA), SYBR14/PI/JC1 to evaluate membrane integrity, mitochondrial membrane potential (MMP) and measurement of lipid peroxidation (TBARS). The sperm was then frozen using an automatic device. After thawing, sperm samples were evaluated by the same variables and further in vitro fertilization rates. Cryopreservation negatively affected sperm motility in samples stored at 4 and 34°C. Nevertheless, the 4°C samples yielded higher rates of blastocyst formation. Pre-freeze sperm motility, progressive motility and velocity were higher in sperm from epididymis stored at 4°C while post-thaw sperm motility, progressive motility and velocity remained the same among samples from epididymis stored at 4 or 34°C. However, with regard to the kinetic patterns, samples collected from epididymis stored at 34°C had lower values when compared to those stored at 4°C prior the cryopreservation process. Our results indicate that epididymis handling conditions after cryopreservation may affect sperm quality after thawing, especially due to compromised MMP in sperm collected from epididymis stored at higher temperatures. © 2016 Blackwell Verlag GmbH.

ESDA®-Lite collection of DNA from latent fingerprints on documents.

PubMed

Plaza, Dane T; Mealy, Jamia L; Lane, J Nicholas; Parsons, M Neal; Bathrick, Abigail S; Slack, Donia P

2015-05-01

The ability to detect and non-destructively collect biological samples for DNA processing would benefit the forensic community by preserving the physical integrity of evidentiary items for more thorough evaluations by other forensic disciplines. The Electrostatic Detection Apparatus (ESDA®) was systemically evaluated for its ability to non-destructively collect DNA from latent fingerprints deposited on various paper substrates for short tandem repeat (STR) DNA profiling. Fingerprints were deposited on a variety of paper substrates that included resume paper, cotton paper, magazine paper, currency, copy paper, and newspaper. Three DNA collection techniques were performed: ESDA collection, dry swabbing, and substrate cutting. Efficacy of each collection technique was evaluated by the quantity of DNA present in each sample and the percent profile generated by each sample. Both the ESDA and dry swabbing non-destructive sampling techniques outperformed the destructive methodology of substrate cutting. A greater number of full profiles were generated from samples collected with the non-destructive dry swabbing collection technique than were generated from samples collected with the ESDA; however, the ESDA also allowed the user to visualize the area of interest while non-destructively collecting the biological material. The ability to visualize the biological material made sampling straightforward and eliminated the need for numerous, random swabbings/cuttings. Based on these results, the evaluated non-destructive ESDA collection technique has great potential for real-world forensic implementation. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Sampling of suspended particulate matter using particle traps in the Rhône River: Relevance and representativeness for the monitoring of contaminants.

PubMed

Masson, M; Angot, H; Le Bescond, C; Launay, M; Dabrin, A; Miège, C; Le Coz, J; Coquery, M

2018-05-10

Monitoring hydrophobic contaminants in surface freshwaters requires measuring contaminant concentrations in the particulate fraction (sediment or suspended particulate matter, SPM) of the water column. Particle traps (PTs) have been recently developed to sample SPM as cost-efficient, easy to operate and time-integrative tools. But the representativeness of SPM collected with PTs is not fully understood, notably in terms of grain size distribution and particulate organic carbon (POC) content, which could both skew particulate contaminant concentrations. The aim of this study was to evaluate the representativeness of SPM characteristics (i.e. grain size distribution and POC content) and associated contaminants (i.e. polychlorinated biphenyls, PCBs; mercury, Hg) in samples collected in a large river using PTs for differing hydrological conditions. Samples collected using PTs (n = 74) were compared with samples collected during the same time period by continuous flow centrifugation (CFC). The grain size distribution of PT samples shifted with increasing water discharge: the proportion of very fine silts (2-6 μm) decreased while that of coarse silts (27-74 μm) increased. Regardless of water discharge, POC contents were different likely due to integration by PT of high POC-content phytoplankton blooms or low POC-content flood events. Differences in PCBs and Hg concentrations were usually within the range of analytical uncertainties and could not be related to grain size or POC content shifts. Occasional Hg-enriched inputs may have led to higher Hg concentrations in a few PT samples (n = 4) which highlights the time-integrative capacity of the PTs. The differences of annual Hg and PCB fluxes calculated either from PT samples or CFC samples were generally below 20%. Despite some inherent limitations (e.g. grain size distribution bias), our findings suggest that PT sampling is a valuable technique to assess reliable spatial and temporal trends of particulate contaminants such as PCBs and Hg within a river monitoring network. Copyright © 2018 Elsevier B.V. All rights reserved.

Automated biowaste sampling system improved feces collection, mass measurement and sampling. [by use of a breadboard model

NASA Technical Reports Server (NTRS)

Fogal, G. L.; Mangialardi, J. K.; Young, R.

1974-01-01

The capability of the basic automated Biowaste Sampling System (ABSS) hardware was extended and improved through the design, fabrication and test of breadboard hardware. A preliminary system design effort established the feasibility of integrating the breadboard concepts into the ABSS.

The "Anatomy" of a Performance-Enhancing Drug Test in Sports

ERIC Educational Resources Information Center

Werner, T. C.

2012-01-01

The components of a performance-enhancing drug (PED) test in sports include sample selection, collection, establishing sample integrity, sample pretreatment, analyte detection, data evaluation, reporting results, and action taken based on the result. Undergraduate curricula generally focus on the detection and evaluation steps of an analytical…

Digital Curation of Marine Physical Samples at Ocean Networks Canada

NASA Astrophysics Data System (ADS)

Jenkyns, R.; Tomlin, M. C.; Timmerman, R.

2015-12-01

Ocean Networks Canada (ONC) has collected hundreds of geological, biological and fluid samples from the water column and seafloor during its maintenance expeditions. These samples have been collected by Remotely Operated Vehicles (ROVs), divers, networked and autonomously deployed instruments, and rosettes. Subsequent measurements are used for scientific experiments, calibration of in-situ and remote sensors, monitoring of Marine Protected Areas, and environment characterization. Tracking the life cycles of these samples from collection to dissemination of results with all the pertinent documents (e.g., protocols, imagery, reports), metadata (e.g., location, identifiers, purpose, method) and data (e.g., measurements, taxonomic classification) is a challenge. The initial collection of samples is normally documented in SeaScribe (an ROV dive logging tool within ONC's Oceans 2.0 software) for which ONC has defined semantics and syntax. Next, samples are often sent to individual scientists and institutions (e.g., Royal BC Museum) for processing and storage, making acquisition of results and life cycle metadata difficult. Finally, this information needs to be retrieved and collated such that multiple user scenarios can be addressed. ONC aims to improve and extend its digital infrastructure for physical samples to support this complex array of samples, workflows and applications. However, in order to promote effective data discovery and exchange, interoperability and community standards must be an integral part of the design. Thus, integrating recommendations and outcomes of initiatives like the EarthCube iSamples working groups are essential. Use cases, existing tools, schemas and identifiers are reviewed, while remaining gaps and challenges are identified. The current status, selected approaches and possible future directions to enhance ONC's digital infrastructure for each sample type are presented.

SPRUCE Deep Peat Heat (DPH) Metagenomes for Peat Samples Collected June 2015

DOE Data Explorer

Klumber, Laurel A. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Yang, Zamin K. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Schadt, Christopher W. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.

2015-01-01

This data set provides links to the results of metagenomic analyses of 38 peat core samples collected on 16 June 2015 from SPRUCE experiment treatment plots after approximately one year of belowground heating. These metagenomes are archived in the U.S. Department of Energy Joint Genome Institute (DOE JGI) Integrated Microbial Genomes (IMG) system and are available at the accession numbers provided in the accompanying inventory file.

An integratable microfluidic cartridge for forensic swab samples lysis.

PubMed

Yang, Jianing; Brooks, Carla; Estes, Matthew D; Hurth, Cedric M; Zenhausern, Frederic

2014-01-01

Fully automated rapid forensic DNA analysis requires integrating several multistep processes onto a single microfluidic platform, including substrate lysis, extraction of DNA from the released lysate solution, multiplexed PCR amplification of STR loci, separation of PCR products by capillary electrophoresis, and analysis for allelic peak calling. Over the past several years, most of the rapid DNA analysis systems developed started with the reference swab sample lysate and involved an off-chip lysis of collected substrates. As a result of advancement in technology and chemistry, addition of a microfluidic module for swab sample lysis has been achieved in a few of the rapid DNA analysis systems. However, recent reports on integrated rapid DNA analysis systems with swab-in and answer-out capability lack any quantitative and qualitative characterization of the swab-in sample lysis module, which is important for downstream forensic sample processing. Maximal collection and subsequent recovery of the biological material from the crime scene is one of the first and critical steps in forensic DNA technology. Herein we present the design, fabrication and characterization of an integratable swab lysis cartridge module and the test results obtained from different types of commonly used forensic swab samples, including buccal, saliva, and blood swab samples, demonstrating the compatibility with different downstream DNA extraction chemistries. This swab lysis cartridge module is easy to operate, compatible with both forensic and microfluidic requirements, and ready to be integrated with our existing automated rapid forensic DNA analysis system. Following the characterization of the swab lysis module, an integrated run from buccal swab sample-in to the microchip CE electropherogram-out was demonstrated on the integrated prototype instrument. Therefore, in this study, we demonstrate that this swab lysis cartridge module is: (1) functionally, comparable with routine benchtop lysis, (2) compatible with various types of swab samples and chemistries, and (3) integratable to achieve a micro total analysis system (μTAS) for rapid DNA analysis. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Collecting a better water-quality sample: Reducing vertical stratification bias in open and closed channels

USGS Publications Warehouse

Selbig, William R.

2017-01-01

Collection of water-quality samples that accurately characterize average particle concentrations and distributions in channels can be complicated by large sources of variability. The U.S. Geological Survey (USGS) developed a fully automated Depth-Integrated Sample Arm (DISA) as a way to reduce bias and improve accuracy in water-quality concentration data. The DISA was designed to integrate with existing autosampler configurations commonly used for the collection of water-quality samples in vertical profile thereby providing a better representation of average suspended sediment and sediment-associated pollutant concentrations and distributions than traditional fixed-point samplers. In controlled laboratory experiments, known concentrations of suspended sediment ranging from 596 to 1,189 mg/L were injected into a 3 foot diameter closed channel (circular pipe) with regulated flows ranging from 1.4 to 27.8 ft3 /s. Median suspended sediment concentrations in water-quality samples collected using the DISA were within 7 percent of the known, injected value compared to 96 percent for traditional fixed-point samplers. Field evaluation of this technology in open channel fluvial systems showed median differences between paired DISA and fixed-point samples to be within 3 percent. The range of particle size measured in the open channel was generally that of clay and silt. Differences between the concentration and distribution measured between the two sampler configurations could potentially be much larger in open channels that transport larger particles, such as sand.

Preliminary assessment of an economical fugitive road dust sampler for the collection of bulk samples for geochemical analysis.

PubMed

Witt, Emitt C; Wronkiewicz, David J; Shi, Honglan

2013-01-01

Fugitive road dust collection for chemical analysis and interpretation has been limited by the quantity and representativeness of samples. Traditional methods of fugitive dust collection generally focus on point-collections that limit data interpretation to a small area or require the investigator to make gross assumptions about the origin of the sample collected. These collection methods often produce a limited quantity of sample that may hinder efforts to characterize the samples by multiple geochemical techniques, preserve a reference archive, and provide a spatially integrated characterization of the road dust health hazard. To achieve a "better sampling" for fugitive road dust studies, a cyclonic fugitive dust (CFD) sampler was constructed and tested. Through repeated and identical sample collection routes at two collection heights (50.8 and 88.9 cm above the road surface), the products of the CFD sampler were characterized using particle size and chemical analysis. The average particle size collected by the cyclone was 17.9 μm, whereas particles collected by a secondary filter were 0.625 μm. No significant difference was observed between the two sample heights tested and duplicates collected at the same height; however, greater sample quantity was achieved at 50.8 cm above the road surface than at 88.9 cm. The cyclone effectively removed 94% of the particles >1 μm, which substantially reduced the loading on the secondary filter used to collect the finer particles; therefore, suction is maintained for longer periods of time, allowing for an average sample collection rate of about 2 g mi. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

The Importance of Contamination Knowledge in Curation - Insights into Mars Sample Return

NASA Technical Reports Server (NTRS)

Harrington, A. D.; Calaway, M. J.; Regberg, A. B.; Mitchell, J. L.; Fries, M. D.; Zeigler, R. A.; McCubbin, F. M.

2018-01-01

The Astromaterials Acquisition and Curation Office at NASA Johnson Space Center (JSC), in Houston, TX (henceforth Curation Office) manages the curation of extraterrestrial samples returned by NASA missions and shared collections from international partners, preserving their integrity for future scientific study while providing the samples to the international community in a fair and unbiased way. The Curation Office also curates flight and non-flight reference materials and other materials from spacecraft assembly (e.g., lubricants, paints and gases) of sample return missions that would have the potential to cross-contaminate a present or future NASA astromaterials collection.

Methotrexate Reduces DNA Integrity in Sperm From Men With Inflammatory Bowel Disease.

PubMed

Ley, Dana; Jones, Jeffrey; Parrish, John; Salih, Sana; Caldera, Freddy; Tirado, Edna; Leader, Benjamin; Saha, Sumona

2018-06-01

There are few data on the effects of methotrexate on reproductive capacity in men with inflammatory bowel diseases (IBDs). We performed a case-control study to determine the effects of methotrexate on sperm quality and genetic integrity. We compared sperm samples from 7 men with IBD who had been exposed to methotrexate for at least 3 months with sperm samples collected from 1912 age-matched men at fertility centers (controls) where sperm parameters would be expected to be worse than those of the general population. Sperm were evaluated by basic semen analysis and advanced sperm integrity testing. In samples from men with IBD, all basic semen analysis parameters were within normal limits. However, these samples had reduced sperm integrity, based on significant increases in levels of DNA fragmentation and damage from oxidative stress compared with controls. Our findings indicate that methotrexate can reduce DNA integrity in sperm and cause damage via oxidative stress. Copyright © 2018 AGA Institute. Published by Elsevier Inc. All rights reserved.

SAIL—a software system for sample and phenotype availability across biobanks and cohorts

PubMed Central

Gostev, Mikhail; Fernandez-Banet, Julio; Rung, Johan; Dietrich, Joern; Prokopenko, Inga; Ripatti, Samuli; McCarthy, Mark I.; Brazma, Alvis; Krestyaninova, Maria

2011-01-01

Summary: The Sample avAILability system—SAIL—is a web based application for searching, browsing and annotating biological sample collections or biobank entries. By providing individual-level information on the availability of specific data types (phenotypes, genetic or genomic data) and samples within a collection, rather than the actual measurement data, resource integration can be facilitated. A flexible data structure enables the collection owners to provide descriptive information on their samples using existing or custom vocabularies. Users can query for the available samples by various parameters combining them via logical expressions. The system can be scaled to hold data from millions of samples with thousands of variables. Availability: SAIL is available under Aferro-GPL open source license: https://github.com/sail. Contact: gostev@ebi.ac.uk, support@simbioms.org Supplementary information: Supplementary data are available at Bioinformatics online and from http://www.simbioms.org. PMID:21169373

Electrofishing effort required to estimate biotic condition in southern Idaho Rivers

USGS Publications Warehouse

Maret, Terry R.; Ott, Douglas S.; Herlihy, Alan T.

2007-01-01

An important issue surrounding biomonitoring in large rivers is the minimum sampling effort required to collect an adequate number of fish for accurate and precise determinations of biotic condition. During the summer of 2002, we sampled 15 randomly selected large-river sites in southern Idaho to evaluate the effects of sampling effort on an index of biotic integrity (IBI). Boat electrofishing was used to collect sample populations of fish in river reaches representing 40 and 100 times the mean channel width (MCW; wetted channel) at base flow. Minimum sampling effort was assessed by comparing the relation between reach length sampled and change in IBI score. Thirty-two species of fish in the families Catostomidae, Centrarchidae, Cottidae, Cyprinidae, Ictaluridae, Percidae, and Salmonidae were collected. Of these, 12 alien species were collected at 80% (12 of 15) of the sample sites; alien species represented about 38% of all species (N = 32) collected during the study. A total of 60% (9 of 15) of the sample sites had poor IBI scores. A minimum reach length of about 36 times MCW was determined to be sufficient for collecting an adequate number of fish for estimating biotic condition based on an IBI score. For most sites, this equates to collecting 275 fish at a site. Results may be applicable to other semiarid, fifth-order through seventh-order rivers sampled during summer low-flow conditions.

40 CFR 60.51b - Definitions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... gases, liquids, or solids through the heating of municipal solid waste, and the gases, liquids, or... diluent gas) for subsequent on-or off-site analysis; integrated sample(s) collected are representative of... arithmetic average flue gas temperature measured at the particulate matter control device inlet during four...

40 CFR 60.51b - Definitions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... gases, liquids, or solids through the heating of municipal solid waste, and the gases, liquids, or... diluent gas) for subsequent on-or off-site analysis; integrated sample(s) collected are representative of... arithmetic average flue gas temperature measured at the particulate matter control device inlet during four...

40 CFR 60.51b - Definitions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... gases, liquids, or solids through the heating of municipal solid waste, and the gases, liquids, or... diluent gas) for subsequent on-or off-site analysis; integrated sample(s) collected are representative of... arithmetic average flue gas temperature measured at the particulate matter control device inlet during four...

Integration of Multiplex Bead Assays for Parasitic Diseases into a National, Population-Based Serosurvey of Women 15-39 Years of Age in Cambodia

PubMed Central

Priest, Jeffrey W.; Jenks, M. Harley; Moss, Delynn M.; Mao, Bunsoth; Buth, Sokhal; Wannemuehler, Kathleen; Soeung, Sann Chan; Lucchi, Naomi W.; Udhayakumar, Venkatachalam; Gregory, Christopher J.; Huy, Rekol; Muth, Sinuon; Lammie, Patrick J.

2016-01-01

Collection of surveillance data is essential for monitoring and evaluation of public health programs. Integrated collection of household-based health data, now routinely carried out in many countries through demographic health surveys and multiple indicator surveys, provides critical measures of progress in health delivery. In contrast, biomarker surveys typically focus on single or related measures of malaria infection, HIV status, vaccination coverage, or immunity status for vaccine-preventable diseases (VPD). Here we describe an integrated biomarker survey based on use of a multiplex bead assay (MBA) to simultaneously measure antibody responses to multiple parasitic diseases of public health importance as part of a VPD serological survey in Cambodia. A nationally-representative cluster-based survey was used to collect serum samples from women of child-bearing age. Samples were tested by MBA for immunoglobulin G antibodies recognizing recombinant antigens from Plasmodium falciparum and P. vivax, Wuchereria bancrofti, Toxoplasma gondii, Taenia solium, and Strongyloides stercoralis. Serologic IgG antibody results were useful both for generating national prevalence estimates for the parasitic diseases of interest and for confirming the highly focal distributions of some of these infections. Integrated surveys offer an opportunity to systematically assess the status of multiple public health programs and measure progress toward Millennium Development Goals. PMID:27136913

Contract-Based Integration of Cyber-Physical Analyses

DTIC Science & Technology

2014-10-14

for cyber-physical systems , 2013 [3] Torngren et al. Integrating viewpoints in the development of mechatronic products, 2013 [4] Rajhans et al...Conference on Embedded Software Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection of information is...failures 5 Analytic aspect of integration Sensor Sampling PID Controller Actuator Controller Communication bus Sensor board CPU Actuator board System Bin

Uncertainties in stormwater runoff data collection from a small urban catchment, Southeast China.

PubMed

Huang, Jinliang; Tu, Zhenshun; Du, Pengfei; Lin, Jie; Li, Qingsheng

2010-01-01

Monitoring data are often used to identify stormwater runoff characteristics and in stormwater runoff modelling without consideration of their inherent uncertainties. Integrated with discrete sample analysis and error propagation analysis, this study attempted to quantify the uncertainties of discrete chemical oxygen demand (COD), total suspended solids (TSS) concentration, stormwater flowrate, stormwater event volumes, COD event mean concentration (EMC), and COD event loads in terms of flow measurement, sample collection, storage and laboratory analysis. The results showed that the uncertainties due to sample collection, storage and laboratory analysis of COD from stormwater runoff are 13.99%, 19.48% and 12.28%. Meanwhile, flow measurement uncertainty was 12.82%, and the sample collection uncertainty of TSS from stormwater runoff was 31.63%. Based on the law of propagation of uncertainties, the uncertainties regarding event flow volume, COD EMC and COD event loads were quantified as 7.03%, 10.26% and 18.47%.

Integrated fiducial sample mount and software for correlated microscopy

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

Timothy R McJunkin; Jill R. Scott; Tammy L. Trowbridge

2014-02-01

A novel design sample mount with integrated fiducials and software for assisting operators in easily and efficiently locating points of interest established in previous analytical sessions is described. The sample holder and software were evaluated with experiments to demonstrate the utility and ease of finding the same points of interest in two different microscopy instruments. Also, numerical analysis of expected errors in determining the same position with errors unbiased by a human operator was performed. Based on the results, issues related to acquiring reproducibility and best practices for using the sample mount and software were identified. Overall, the sample mountmore » methodology allows data to be efficiently and easily collected on different instruments for the same sample location.« less

Determining the sources of suspended sediment in a Mediterranean groundwater-dominated river: the Na Borges basin (Mallorca, Spain).

NASA Astrophysics Data System (ADS)

Estrany, Joan; Martinez-Carreras, Nuria

2013-04-01

Tracers have been acknowledged as a useful tool to identify sediment sources, based upon a variety of techniques and chemical and physical sediment properties. Sediment fingerprinting supports the notion that changes in sedimentation rates are not just related to increased/reduced erosion and transport in the same areas, but also to the establishment of different pathways increasing sediment connectivity. The Na Borges is a Mediterranean lowland agricultural river basin (319 km2) where traditional soil and water conservation practices have been applied over millennia to provide effective protection of cultivated land. During the twentieth century, industrialisation and pressure from tourism activities have increased urbanised surfaces, which have impacts on the processes that control streamflow. Within this context, source material sampling was focused in Na Borges on obtaining representative samples from potential sediment sources (comprised topsoil; i.e., 0-2 cm) susceptible to mobilisation by water and subsequent routing to the river channel network, while those representing channel bank sources were collected from actively eroding channel margins and ditches. Samples of road dust and of solids from sewage treatment plants were also collected. During two hydrological years (2004-2006), representative suspended sediment samples for use in source fingerprinting studies were collected at four flow gauging stations and at eight secondary sampling points using time-integrating sampling samplers. Likewise, representative bed-channel sediment samples were obtained using the resuspension approach at eight sampling points in the main stem of the Na Borges River. These deposits represent the fine sediment temporarily stored in the bed-channel and were also used for tracing source contributions. A total of 102 individual time-integrated sediment samples, 40 bulk samples and 48 bed-sediment samples were collected. Upon return to the laboratory, source material samples were oven-dried at 40° C, disaggregated using a pestle and mortar, and dry sieved to

A Collection of Papers on Self-Study and Institutional Improvement, 1996.

ERIC Educational Resources Information Center

Van Kollenburg, Susan E., Ed.

This collection presents 68 papers or summaries presented at a 1996 conference on self-study and institutional improvement for institutions of higher education. Papers are grouped in the following 10 chapters (with sample topics in parentheses): (1) "Integrity and Accreditation: Current Issues" (intercollegiate athletics, nontraditional students,…

A new method of snowmelt sampling for water stable isotopes

USGS Publications Warehouse

Penna, D.; Ahmad, M.; Birks, S. J.; Bouchaou, L.; Brencic, M.; Butt, S.; Holko, L.; Jeelani, G.; Martinez, D. E.; Melikadze, G.; Shanley, J.B.; Sokratov, S. A.; Stadnyk, T.; Sugimoto, A.; Vreca, P.

2014-01-01

We modified a passive capillary sampler (PCS) to collect snowmelt water for isotopic analysis. Past applications of PCSs have been to sample soil water, but the novel aspect of this study was the placement of the PCSs at the ground-snowpack interface to collect snowmelt. We deployed arrays of PCSs at 11 sites in ten partner countries on five continents representing a range of climate and snow cover worldwide. The PCS reliably collected snowmelt at all sites and caused negligible evaporative fractionation effects in the samples. PCS is low-cost, easy to install, and collects a representative integrated snowmelt sample throughout the melt season or at the melt event scale. Unlike snow cores, the PCS collects the water that would actually infiltrate the soil; thus, its isotopic composition is appropriate to use for tracing snowmelt water through the hydrologic cycle. The purpose of this Briefing is to show the potential advantages of PCSs and recommend guidelines for constructing and installing them based on our preliminary results from two snowmelt seasons.

Integration of georeferencing, habitat, sampling, and genetic data for documentation of wild plant genetic resources

USDA-ARS?s Scientific Manuscript database

Plant genetic resource collections provide novel materials to the breeding and research communities. Availability of detailed documentation of passport, phenotypic, and genetic data increases the value of the genebank accessions. Inclusion of georeferenced sources, habitats, and sampling data in co...

Determining Source Impacts Near Roadways using Wind Regression and Organic Source Markers

EPA Science Inventory

Concentrations of 13 organic source markers (10 polycyclic aromatic hydrocarbons and 3 hopanes) are reported from time-integrated samples (24-hr and sub-daily) collected near an highway in Las Vegas, NV. Sample selection for assessing source impacts from the roadway was complete...

A novel method for sampling the suspended sediment load in the tidal environment using bi-directional time-integrated mass-flux sediment (TIMS) samplers

NASA Astrophysics Data System (ADS)

Elliott, Emily A.; Monbureau, Elaine; Walters, Glenn W.; Elliott, Mark A.; McKee, Brent A.; Rodriguez, Antonio B.

2017-12-01

Identifying the source and abundance of sediment transported within tidal creeks is essential for studying the connectivity between coastal watersheds and estuaries. The fine-grained suspended sediment load (SSL) makes up a substantial portion of the total sediment load carried within an estuarine system and efficient sampling of the SSL is critical to our understanding of nutrient and contaminant transport, anthropogenic influence, and the effects of climate. Unfortunately, traditional methods of sampling the SSL, including instantaneous measurements and automatic samplers, can be labor intensive, expensive and often yield insufficient mass for comprehensive geochemical analysis. In estuaries this issue is even more pronounced due to bi-directional tidal flow. This study tests the efficacy of a time-integrated mass sediment sampler (TIMS) design, originally developed for uni-directional flow within the fluvial environment, modified in this work for implementation the tidal environment under bi-directional flow conditions. Our new TIMS design utilizes an 'L' shaped outflow tube to prevent backflow, and when deployed in mirrored pairs, each sampler collects sediment uniquely in one direction of tidal flow. Laboratory flume experiments using dye and particle image velocimetry (PIV) were used to characterize the flow within the sampler, specifically, to quantify the settling velocities and identify stagnation points. Further laboratory tests of sediment indicate that bidirectional TIMS capture up to 96% of incoming SSL across a range of flow velocities (0.3-0.6 m s-1). The modified TIMS design was tested in the field at two distinct sampling locations within the tidal zone. Single-time point suspended sediment samples were collected at high and low tide and compared to time-integrated suspended sediment samples collected by the bi-directional TIMS over the same four-day period. Particle-size composition from the bi-directional TIMS were representative of the array of single time point samples, but yielded greater mass, representative of flow and sediment-concentration conditions at the site throughout the deployment period. This work proves the efficacy of the modified bi-directional TIMS design, offering a novel tool for collection of suspended sediment in the tidally-dominated portion of the watershed.

Bridging Professional Teacher Knowledge for Science and Literary Integration via Design-Based Research

ERIC Educational Resources Information Center

Fazio, Xavier; Gallagher, Tiffany L.

2018-01-01

We offer insights for using design-based research (DBR) as a model for constructing professional development that supports curriculum and instructional knowledge regarding science and literacy integration. We spotlight experiences in the DBR process from data collected from a sample of four elementary teachers. Findings from interviews, focus…

Evaluation of the lake macroinvertebrate integrity index (LMII) and alternate indices for eastern U.S. lakes and reservoirs

EPA Science Inventory

We applied the Lake Macroinvertebrate Integrity Index (LMII) to 69 lakes and reservoirs across the eastern United States. Genus-level sub-littoral benthos samples, collected by EPA Regions 2 and 3 in 2007, were used to calcualte LMII scores for each lake. We investigated relation...

Strategies and equipment for sampling suspended sediment and associated toxic chemicals in large rivers - with emphasis on the Mississippi River

USGS Publications Warehouse

Meade, R.H.; Stevens, H.H.

1990-01-01

A Lagrangian strategy for sampling large rivers, which was developed and tested in the Orinoco and Amazon Rivers of South America during the early 1980s, is now being applied to the study of toxic chemicals in the Mississippi River. A series of 15-20 cross-sections of the Mississippi mainstem and its principal tributaries is sampled by boat in downstream sequence, beginning upriver of St. Louis and concluding downriver of New Orleans 3 weeks later. The timing of the downstream sampling sequence approximates the travel time of the river water. Samples at each cross-section are discharge-weighted to provide concentrations of dissolved and suspended constituents that are converted to fluxes. Water-sediment mixtures are collected from 10-40 equally spaced points across the river width by sequential depth integration at a uniform vertical transit rate. Essential equipment includes (i) a hydraulic winch, for sensitive control of vertical transit rates, and (ii) a collapsible-bag sampler, which allows integrated samples to be collected at all depths in the river. A section is usually sampled in 4-8 h, for a total sample recovery of 100-120 l. Sampled concentrations of suspended silt and clay are reproducible within 3%.

Perceived leader integrity and employee job satisfaction: A quantitative study of U.S. aerospace engineers

NASA Astrophysics Data System (ADS)

Harper, Kay E.

The goal of this quantitative study was to determine if there is a significant relationship between perceived leader integrity and employee job satisfaction. The population selected to be analyzed was U.S. Aerospace engineers. Two existing valid and reliable survey instruments were used to collect data. One of the surveys was the Perceived Leader Integrity Scale developed by Craig and Gustafson. The second survey was the Minnesota Satisfaction Questionnaire created by Weiss, Dawis, England, and Lofquist. The public professional networking site LinkedIn was used to invite U.S. Aerospace engineers to participate. The survey results were monitored by Survey Monkey and the sample data was analyzed using SPSS software. 184 responses were collected and of those, 96 were incomplete. 91 usable survey responses were left to be analyzed. When the results were plotted on an x-y plot, the data line had a slight negative slope. The plotted data showed a very small negative relationship between perceived leader integrity and employee job satisfaction. This relationship could be interpreted to mean that as perceived leader integrity improved, employee job satisfaction decreased only slightly. One explanation for this result could be that employees focused on their negative feelings about their current job assignment when they did not have to be concerned about the level of integrity with which their leader acted. The findings of this study reinforce the importance of employee's perception of a critical leader quality - integrity. For future research, a longitudinal study utilizing another sampling method other than convenience sampling may better statistically capture the relationship between perceived leader integrity and employee job satisfaction for U.S. aerospace engineers.

Retrovirus Integration Database (RID): a public database for retroviral insertion sites into host genomes.

PubMed

Shao, Wei; Shan, Jigui; Kearney, Mary F; Wu, Xiaolin; Maldarelli, Frank; Mellors, John W; Luke, Brian; Coffin, John M; Hughes, Stephen H

2016-07-04

The NCI Retrovirus Integration Database is a MySql-based relational database created for storing and retrieving comprehensive information about retroviral integration sites, primarily, but not exclusively, HIV-1. The database is accessible to the public for submission or extraction of data originating from experiments aimed at collecting information related to retroviral integration sites including: the site of integration into the host genome, the virus family and subtype, the origin of the sample, gene exons/introns associated with integration, and proviral orientation. Information about the references from which the data were collected is also stored in the database. Tools are built into the website that can be used to map the integration sites to UCSC genome browser, to plot the integration site patterns on a chromosome, and to display provirus LTRs in their inserted genome sequence. The website is robust, user friendly, and allows users to query the database and analyze the data dynamically. https://rid.ncifcrf.gov ; or http://home.ncifcrf.gov/hivdrp/resources.htm .

What can one sample tell us? Stable isotopes can assess complex processes in national assessments of lakes, rivers and streams.

EPA Science Inventory

Stable isotopes can be very useful in large-scale monitoring programs because samples for isotopic analysis are easy to collect, and isotopes integrate information about complex processes such as evaporation from water isotopes and denitrification from nitrogen isotopes. Traditi...

Large-scale atlas of microarray data reveals biological landscape of gene expression in Arabidopsis

USDA-ARS?s Scientific Manuscript database

Transcriptome datasets from thousands of samples of the model plant Arabidopsis thaliana have been collectively generated by multiple individual labs. Although integration and meta-analysis of these samples has become routine in the plant research community, it is often hampered by the lack of metad...

The focus on sample quality: Influence of colon tissue collection on reliability of qPCR data

PubMed Central

Korenkova, Vlasta; Slyskova, Jana; Novosadova, Vendula; Pizzamiglio, Sara; Langerova, Lucie; Bjorkman, Jens; Vycital, Ondrej; Liska, Vaclav; Levy, Miroslav; Veskrna, Karel; Vodicka, Pavel; Vodickova, Ludmila; Kubista, Mikael; Verderio, Paolo

2016-01-01

Successful molecular analyses of human solid tissues require intact biological material with well-preserved nucleic acids, proteins, and other cell structures. Pre-analytical handling, comprising of the collection of material at the operating theatre, is among the first critical steps that influence sample quality. The aim of this study was to compare the experimental outcomes obtained from samples collected and stored by the conventional means of snap freezing and by PAXgene Tissue System (Qiagen). These approaches were evaluated by measuring rRNA and mRNA integrity of the samples (RNA Quality Indicator and Differential Amplification Method) and by gene expression profiling. The collection procedures of the biological material were implemented in two hospitals during colon cancer surgery in order to identify the impact of the collection method on the experimental outcome. Our study shows that the pre-analytical sample handling has a significant effect on the quality of RNA and on the variability of qPCR data. PAXgene collection mode proved to be more easily implemented in the operating room and moreover the quality of RNA obtained from human colon tissues by this method is superior to the one obtained by snap freezing. PMID:27383461

Towards Making Data Bases Practical for use in the Field

NASA Astrophysics Data System (ADS)

Fischer, T. P.; Lehnert, K. A.; Chiodini, G.; McCormick, B.; Cardellini, C.; Clor, L. E.; Cottrell, E.

2014-12-01

Geological, geochemical, and geophysical research is often field based with travel to remote areas and collection of samples and data under challenging environmental conditions. Cross-disciplinary investigations would greatly benefit from near real-time data access and visualisation within the existing framework of databases and GIS tools. An example of complex, interdisciplinary field-based and data intensive investigations is that of volcanologists and gas geochemists, who sample gases from fumaroles, hot springs, dry gas vents, hydrothermal vents and wells. Compositions of volcanic gas plumes are measured directly or by remote sensing. Soil gas fluxes from volcanic areas are measured by accumulation chamber and involve hundreds of measurements to calculate the total emission of a region. Many investigators also collect rock samples from recent or ancient volcanic eruptions. Structural, geochronological, and geophysical data collected during the same or related field campaigns complement these emissions data. All samples and data collected in the field require a set of metadata including date, time, location, sample or measurement id, and descriptive comments. Currently, most of these metadata are written in field notebooks and later transferred into a digital format. Final results such as laboratory analyses of samples and calculated flux data are tabulated for plotting, correlation with other types of data, modeling and finally publication and presentation. Data handling, organization and interpretation could be greatly streamlined by using digital tools available in the field to record metadata, assign an International Geo Sample Number (IGSN), upload measurements directly from field instruments, and arrange sample curation. Available data display tools such as GeoMapApp and existing data sets (PetDB, IRIS, UNAVCO) could be integrated to direct locations for additional measurements during a field campaign. Nearly live display of sampling locations, pictures, and comments could be used as an educational and outreach tool during sampling expeditions. Achieving these goals requires the integration of existing online data resources, with common access through a dedicated web portal.

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering.

PubMed

Gil-Ley, Alejandro; Bussi, Giovanni

2015-03-10

The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strengths of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide.

Effect of an isotonic lubricant on sperm collection and sperm quality.

PubMed

Agarwal, Ashok; Malvezzi, Helena; Sharma, Rakesh

2013-05-01

To assess the influence of an isotonic lubricant used during sperm sample collection on [1] ease of collection and [2] resultant sperm quality. Paired randomized cross-over design. Tertiary hospital. Healthy men over 18 years old with normal semen analysis as per World Health Organization 2010 guidelines. Collection of semen sample from 22 subjects by masturbation with or without the use of Pre-Seed personal lubricant. Qualitative survey results and quantitative sperm function outcomes were measured to determine resultant sperm quality and collection experience with and without Pre-Seed lubricant. The qualitative questionnaire results showed that 73% of donors prefer the semen collection process with the isotonic lubricant and 55% recommended the use of lubricant in their everyday collection. The motility, viability, membrane integrity, levels of reactive oxygen species, total antioxidant capacity, and percentage of DNA damage in collected semen samples were not affected by the use of the lubricant. More donors prefer, and find it easier, to collect semen samples with the use of the lubricant. The isotonic lubricant Pre-Seed did not compromise sperm quality as evaluated in an array of sperm assays, suggesting its safe use in fertility patients as required during sperm collection. Copyright © 2013 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Effect of different procedures of ejaculate collection, extenders and packages on DNA integrity of boar spermatozoa following freezing-thawing.

PubMed

Fraser, L; Strzezek, J

2007-06-01

Whole ejaculate or sperm-rich fraction, collected from four sexually mature boars, was frozen in an extender containing lactose-hen egg yolk with glycerol (lactose-HEY-G) or extender containing lactose, lyophilized lipoprotein fractions isolated from ostrich egg yolk and glycerol (lactose-LPFo-G), and Orvus Es Paste, respectively. The sperm samples were also frozen in a standard boar semen extender (Kortowo-3), without the addition of cryoprotective substances. Sperm DNA integrity was assessed using a modified neutral comet assay. Sperm characteristics such as motility, plasma membrane integrity (SYBR-14/PI), mitochondrial function (rhodamine 123) and acrosome integrity were monitored. Freezing-thawing caused a significant increase (P<0.05) in sperm DNA fragmentation, irrespective of the procedures of ejaculate collection and extender type. Sperm DNA fragmentation was significantly lower (P<0.05) in the whole ejaculate compared with the sperm-rich fraction, indicating that spermatozoa maintained in the whole seminal plasma prior to its removal for freezing-thawing procedure were less vulnerable to cryo-induced DNA fragmentation. Furthermore, spermatozoa frozen in lactose-HEY-G or lactose-LPFo-G extender exhibited lower (P<0.05) DNA fragmentation than those frozen in the absence of cryoprotective substances. The levels of sperm DNA damage, as expressed by comet tail length and tail moment values, were significantly higher (P<0.05) in sperm samples frozen in the absence of cryoprotective substances. The deterioration in post-thaw sperm DNA integrity was concurrent with reduced sperm characteristics. It can be suggested that evaluation of DNA integrity, coupled with different sperm characteristics such as motility, plasma membrane integrity and mitochondrial function, may aid in determining the quality of frozen-thawed boar semen.

Evaluation of passive samplers for the collection of dissolved organic matter in streams.

PubMed

Warner, Daniel L; Oviedo-Vargas, Diana; Royer, Todd V

2015-01-01

Traditional sampling methods for dissolved organic matter (DOM) in streams limit opportunities for long-term studies due to time and cost constraints. Passive DOM samplers were constructed following a design proposed previously which utilizes diethylaminoethyl (DEAE) cellulose as a sampling medium, and they were deployed throughout a temperate stream network in Indiana. Two deployments of the passive samplers were conducted, during which grab samples were frequently collected for comparison. Differences in DOM quality between sites and sampling methods were assessed using several common optical analyses. The analyses revealed significant differences in optical properties between sampling methods, with the passive samplers preferentially collecting terrestrial, humic-like DOM. We assert that the differences in DOM composition from each sampling method were caused by preferential binding of complex humic compounds to the DEAE cellulose in the passive samplers. Nonetheless, the passive samplers may provide a cost-effective, integrated sample of DOM in situations where the bulk DOM pool is composed mainly of terrestrial, humic-like compounds.

[Donors' personal profile in Tuscany's network of milk banks].

PubMed

Strambi, M; Anselmi, A; Coppi, S

2012-10-01

An investigation on human milk donors among the milk banks of Tuscany's network was carried out. Milk banks select, collect, check, process, store and deliver human milk, whose donors should have certain physical and psychological well-being features. The aim of the study was to describe a personal and social profile of milk donors. The study included a sample of 100 milk donors and a sample of 100 non-milk donor mothers; a questionnaire that collected data about mothers' general information, clinical history, pregnancy and delivery, weight variations, state of health, lifestyle, breastfeeding and knowledge about milk banks was administered to all of them. Then information about food history of mothers has also been collected. First the samples of donors were analysed for all variables considered. Subsequently the samples of donors were compared with the samples of non-donors: statistical analysis was carried out with χ2 test and documented significant differences between donors and non-donors for the majority of variables considered in the questionnaire and for food history. Milk donors have a good state of health, and the integration in milk donation initiative headed towards a healthier lifestyle. It is necessary to promote an advertising campaign to integrate social and sanitary politics, fitting to local socio-economical contest. Furthermore, the improvement of milk banks of public hospitals is necessary, as hospitals are places of major stream both of potential donors and newborns.

Impact of collection container material and holding times on sample integrity for mercury and methylmercury in water

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

Riscassi, Ami L; Miller, Carrie L; Brooks, Scott C

Mercury (Hg) and methylmercury (MeHg) concentrations in streamwater can vary on short timescales (hourly or less) during storm flow and on a diel cycle; the frequency and timing of sampling required to accurately characterize these dynamics may be difficult to accomplish manually. Automated sampling can assist in sample collection; however use has been limited for Hg and MeHg analysis due to stability concerns of trace concentrations during extended storage times. We examined the viability of using automated samplers with disposable low-density polyethylene (LDPE) sample bags to collect industrially contaminated streamwater for unfiltered and filtered Hg and MeHg analysis. Specifically wemore » investigated the effect of holding times ranging from hours to days on streamwater collected during baseflow and storm flow. Unfiltered and filtered Hg and MeHg concentrations decreased with increases in time prior to sample processing; holding times of 24 hours or less resulted in concentration changes (mean 11 7% different) similar to variability in duplicates collected manually during analogous field conditions (mean 7 10% different). Comparisons of samples collected with manual and automated techniques throughout a year for a wide range of stream conditions were also found to be similar to differences observed between duplicate grab samples. These results demonstrate automated sampling into LDPE bags with holding times of 24 hours or less can be effectively used to collect streamwater for Hg and MeHg analysis, and encourage the testing of these materials and methods for implementation in other aqueous systems where high-frequency sampling is warranted.« less

Flipping the Audience Script: An Activity That Integrates Research and Audience Analysis

ERIC Educational Resources Information Center

Lam, Chris; Hannah, Mark A.

2016-01-01

This article describes a flipped classroom activity that requires students to integrate research and audience analysis. The activity uses Twitter as a data source. In the activity, students identify a sample, collect customer tweets, and analyze the language of the tweets in an effort to construct knowledge about an audience's values, needs, and…

Go Digital! Making Physical Samples a Valued Part of the Online Record of Science

NASA Astrophysics Data System (ADS)

Klump, J. F.; Lehnert, K.

2016-12-01

Physical samples, at first glance, seem to be the opposite to the virtual world of the internet. Yet, as anything not natively digital, physical samples can have a digital representation that is accessible through the internet. Most museums and other institutions have many more objects in their collections than they could ever put on display and many samples exist outside of formal curation workflows. Nevertheless, these objects can be of importance to science, maybe because this particular fossil is a holotype that defines an extinct animal species, or it is a mineral sample that was used to derive a reference optical reflectance spectrum that is used in the interpretation of remote sensing data from satellites. As these examples show, the value of a scientific collection lies not only in its objects but also in how these objects are integrated into the record of science. Fundamental to this are, of course, catalogues of the samples held in a collection. Significant value can be added to a collection if its catalogue is web accessible, and even better if its catalogue can be harvested into disciplinary portals to aid the discovery of samples. Sample curation in the digital age, however, must go beyond simply labeling and cataloguing. In the same way that publications and datasets can now be identified and accessed over the web, steps are now being made to do the same for physical samples. Globally unique, resolvable identifiers of samples, datasets and literature can serve as nodes to link these resources together and in this way, then cross-link between scientific interpretation in the literature, data interpreted in these works, and samples from which these data were derived. These linkages must not only be recorded in the metadata but must also be machine actionable to allow integration of these digital assets into the ever growing body and richness of the scientific record. This presentation will discuss cyberinfrastructures for samples and sample curation through case studies that illustrate how the life cycle of a sample relates to other digital objects in literature and data, and how added value is generated through these linkages.

Achieving Integration in Mixed Methods Designs—Principles and Practices

PubMed Central

Fetters, Michael D; Curry, Leslie A; Creswell, John W

2013-01-01

Mixed methods research offers powerful tools for investigating complex processes and systems in health and health care. This article describes integration principles and practices at three levels in mixed methods research and provides illustrative examples. Integration at the study design level occurs through three basic mixed method designs—exploratory sequential, explanatory sequential, and convergent—and through four advanced frameworks—multistage, intervention, case study, and participatory. Integration at the methods level occurs through four approaches. In connecting, one database links to the other through sampling. With building, one database informs the data collection approach of the other. When merging, the two databases are brought together for analysis. With embedding, data collection and analysis link at multiple points. Integration at the interpretation and reporting level occurs through narrative, data transformation, and joint display. The fit of integration describes the extent the qualitative and quantitative findings cohere. Understanding these principles and practices of integration can help health services researchers leverage the strengths of mixed methods. PMID:24279835

Achieving integration in mixed methods designs-principles and practices.

PubMed

Fetters, Michael D; Curry, Leslie A; Creswell, John W

2013-12-01

Mixed methods research offers powerful tools for investigating complex processes and systems in health and health care. This article describes integration principles and practices at three levels in mixed methods research and provides illustrative examples. Integration at the study design level occurs through three basic mixed method designs-exploratory sequential, explanatory sequential, and convergent-and through four advanced frameworks-multistage, intervention, case study, and participatory. Integration at the methods level occurs through four approaches. In connecting, one database links to the other through sampling. With building, one database informs the data collection approach of the other. When merging, the two databases are brought together for analysis. With embedding, data collection and analysis link at multiple points. Integration at the interpretation and reporting level occurs through narrative, data transformation, and joint display. The fit of integration describes the extent the qualitative and quantitative findings cohere. Understanding these principles and practices of integration can help health services researchers leverage the strengths of mixed methods. © Health Research and Educational Trust.

Geosamples.org: Shared Cyberinfrastructure for Geoscience Samples

NASA Astrophysics Data System (ADS)

Lehnert, Kerstin; Allison, Lee; Arctur, David; Klump, Jens; Lenhardt, Christopher

2014-05-01

Many scientific domains, specifically in the geosciences, rely on physical samples as basic elements for study and experimentation. Samples are collected to analyze properties of natural materials and features that are key to our knowledge of Earth's dynamical systems and evolution, and to preserve a record of our environment over time. Huge volumes of samples have been acquired over decades or even centuries and stored in a large number and variety of institutions including museums, universities and colleges, state geological surveys, federal agencies, and industry. All of these collections represent highly valuable, often irreplaceable records of nature that need to be accessible so that they can be re-used in future research and for educational purposes. Many sample repositories are keen to use cyberinfrastructure capabilities to enhance access to their collections on the internet and to support and streamline collection management (accessioning of new samples, labeling, handling sample requests, etc.), but encounter substantial challenges and barriers to integrate digital sample management into their daily routine. They lack the resources (staff, funding) and infrastructure (hardware, software, IT support) to develop and operate web-enabled databases, to migrate analog sample records into digital data management systems, and to transfer paper- or spreadsheet-based workflows to electronic systems. Use of commercial software is often not an option as it incurs high costs for licenses, requires IT expertise for installation and maintenance, and often does not match the needs of the smaller repositories, being designed for large museums or different types of collections (art, archeological, biological). Geosamples.org is an alliance of sample repositories (academic, US federal and state surveys, industry) and data facilities that aims to develop a cyberinfrastructure that will dramatically advance access to physical samples for the research community, government agencies, students, educators, and the general public, while supporting, simplifying, and standardizing the work of curators in repositories, museums, and universities, and even for individual investigators who manage personal or project-based sample collections in their lab. Geosamples.org builds upon best practices and cyberinfrastructure for sample identification, registration, and documentation developed by the IGSN e.V., an international organization that governs the International Geosample Number, a persistent unique identifier for physical samples. Geosamples.org will develop a Digital Environment for Sample Curation (DESC) that will facilitate the creation, identification, and registration of 'virtual samples' and network them into an 'Internet of Samples' that will allow to discover, access, and track online physical samples, the data derived by their study, and the publications that contain these data. DESC will provide easy-to-use software tools for curators to maintain digital catalogs of their collections, to provide online access to the catalog to search for and request samples, manage sample requests and users, track collection usage and impact. Geosamples.org will also work toward joint practices for the recognition of intellectual property, build mechanisms to create sustainable business models for continuing maintenance and evolution of managing sample resources, and integrate the sample management life-cycle into professional and cultural practice of science.

Isotopic (d18O/d2H) integrity of water samples collected and stored by automatic samplers

USDA-ARS?s Scientific Manuscript database

Stable water isotopes are increasingly becoming part of routine monitoring programs that utilize automatic samplers. The objectives of this study were to quantify the uncertainty in isotope signatures due to the length of sample storage (1-24 d) inside autosamplers over a range of air temperatures (...

Screening for microplastic particles in plankton samples: How to integrate marine litter assessment into existing monitoring programs?

PubMed

Gorokhova, Elena

2015-10-15

Microplastics (MPs) are a newly recognized type of environmental pollution in aquatic systems; however no monitoring of these contaminants is conducted, mostly due to the lack of routine quantification. In the net samples collected with a 90-μm WP2 net, pelagic MP abundance was quantified by light microscopy and evaluated as a function of inshore-offshore gradient, depth, and season; the same samples were used for zooplankton analysis. The MP abundance was ∼10(2)-10(4)particlesm(-3), with no significant inshore-offshore gradient during summer but increasing offshore in winter. MP abundance in deeper layers was positively affected by zooplankton abundance in the upper layers and significantly lower during winter compared to summer. These findings indicate heterogeneity of MP distribution due to biotic and abiotic factors and suggest that samples collected for other purposes can be used for quantification of MPs in the Baltic Sea, thus facilitating integration of MP assessment into existing monitoring schemes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Integrated Verification Experiment data collected as part of the Los Alamos National Laboratory's Source Region Program

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

Fitzgerald, T.J.; Carlos, R.C.; Argo, P.E.

As part of the integrated verification experiment (IVE), we deployed a network of hf ionospheric sounders to detect the effects of acoustic waves generated by surface ground motion following underground nuclear tests at the Nevada Test Site. The network sampled up to four geographic locations in the ionosphere from almost directly overhead of the surface ground zero out to a horizontal range of 60 km. We present sample results for four of the IVEs: Misty Echo, Texarkana, Mineral Quarry, and Bexar.

Nevada National Security Site Integrated Groundwater Sampling Plan, Revision 1

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

Wilborn, Bill R.; Boehlecke, Robert F.

The purpose is to provide a comprehensive, integrated approach for collecting and analyzing groundwater samples to meet the needs and objectives of the DOE/EM Nevada Program’s UGTA Activity. Implementation of this Plan will provide high-quality data required by the UGTA Activity for ensuring public protection in an efficient and cost-effective manner. The Plan is designed to ensure compliance with the UGTA Quality Assurance Plan (QAP) (NNSA/NFO, 2015); Federal Facility Agreement and Consent Order (FFACO) (1996, as amended); and DOE Order 458.1, Radiation Protection of the Public and the Environment (DOE, 2013). The Plan’s scope comprises sample collection and analysis requirementsmore » relevant to assessing both the extent of groundwater contamination from underground nuclear testing and impact of testing on water quality in downgradient communities. This Plan identifies locations to be sampled by CAU and location type, sampling frequencies, sample collection methodologies, and the constituents to be analyzed. In addition, the Plan defines data collection criteria such as well purging, detection levels, and accuracy requirements/recommendations; identifies reporting and data management requirements; and provides a process to ensure coordination between NNSS groundwater sampling programs for sampling analytes of interest to UGTA. Information used in the Plan development—including the rationale for selection of wells, sampling frequency, and the analytical suite—is discussed under separate cover (N-I, 2014) and is not reproduced herein. This Plan does not address compliance for those wells involved in a permitted activity. Sampling and analysis requirements associated with these wells are described in their respective permits and are discussed in NNSS environmental reports (see Section 5.2). In addition, sampling for UGTA CAUs that are in the Closure Report (CR) stage are not included in this Plan. Sampling requirements for these CAUs are described in the CR. Frenchman Flat is currently the only UGTA CAU in the CR stage. Sampling requirements for this CAU are described in Underground Test Area (UGTA) Closure Report for Corrective Action Unit 98: Frenchman Flat Nevada National Security Site, Nevada (NNSA/NFO, 2016).« less

[MicroRNA Target Prediction Based on Support Vector Machine Ensemble Classification Algorithm of Under-sampling Technique].

PubMed

Chen, Zhiru; Hong, Wenxue

2016-02-01

Considering the low accuracy of prediction in the positive samples and poor overall classification effects caused by unbalanced sample data of MicroRNA (miRNA) target, we proposes a support vector machine (SVM)-integration of under-sampling and weight (IUSM) algorithm in this paper, an under-sampling based on the ensemble learning algorithm. The algorithm adopts SVM as learning algorithm and AdaBoost as integration framework, and embeds clustering-based under-sampling into the iterative process, aiming at reducing the degree of unbalanced distribution of positive and negative samples. Meanwhile, in the process of adaptive weight adjustment of the samples, the SVM-IUSM algorithm eliminates the abnormal ones in negative samples with robust sample weights smoothing mechanism so as to avoid over-learning. Finally, the prediction of miRNA target integrated classifier is achieved with the combination of multiple weak classifiers through the voting mechanism. The experiment revealed that the SVM-IUSW, compared with other algorithms on unbalanced dataset collection, could not only improve the accuracy of positive targets and the overall effect of classification, but also enhance the generalization ability of miRNA target classifier.

DISCUSSION AND EVALUATION OF THE VOLATILITY TEST FOR EQUIVALENCY OF OTHER METHODS TO THE FEDERAL REFERENCE METHOD FOR FINE PARTICULATE MATTER

EPA Science Inventory

In July 1997, EPA promulgated a new National Ambient Air Quality Standard (NAAQS) for fine particulate matter (PM2.5). This new standard was based on collection of an integrated mass sample on a filter. Field studies have demonstrated that the collection of semivolatile compoun...

DEVELOPMENT OF A TAMPER RESISTANT/INDICATING AEROSOL COLLECTION SYSTEM FOR ENVIRONMENTAL SAMPLING AT BULK HANDLING FACILITIES

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

Sexton, L.

2012-06-06

Environmental sampling has become a key component of International Atomic Energy Agency (IAEA) safeguards approaches since its approval for use in 1996. Environmental sampling supports the IAEA's mission of drawing conclusions concerning the absence of undeclared nuclear material or nuclear activities in a Nation State. Swipe sampling is the most commonly used method for the collection of environmental samples from bulk handling facilities. However, augmenting swipe samples with an air monitoring system, which could continuously draw samples from the environment of bulk handling facilities, could improve the possibility of the detection of undeclared activities. Continuous sampling offers the opportunity tomore » collect airborne materials before they settle onto surfaces which can be decontaminated, taken into existing duct work, filtered by plant ventilation, or escape via alternate pathways (i.e. drains, doors). Researchers at the Savannah River National Laboratory and Oak Ridge National Laboratory have been working to further develop an aerosol collection technology that could be installed at IAEA safeguarded bulk handling facilities. The addition of this technology may reduce the number of IAEA inspector visits required to effectively collect samples. The principal sample collection device is a patented Aerosol Contaminant Extractor (ACE) which utilizes electrostatic precipitation principles to deposit particulates onto selected substrates. Recent work has focused on comparing traditional swipe sampling to samples collected via an ACE system, and incorporating tamper resistant and tamper indicating (TRI) technologies into the ACE system. Development of a TRI-ACE system would allow collection of samples at uranium/plutonium bulk handling facilities in a manner that ensures sample integrity and could be an important addition to the international nuclear safeguards inspector's toolkit. This work was supported by the Next Generation Safeguards Initiative (NGSI), Office of Nonproliferation and International Security (NIS), National Nuclear Security Administration (NNSA).« less

Metabolomics study of Populus type propolis.

PubMed

Anđelković, Boban; Vujisić, Ljubodrag; Vučković, Ivan; Tešević, Vele; Vajs, Vlatka; Gođevac, Dejan

2017-02-20

Herein, we propose rapid and simple spectroscopic methods to determine the chemical composition of propolis derived from various Populus species using a metabolomics approach. In order to correlate variability in Populus type propolis composition with the altitude of its collection, NMR, IR, and UV spectroscopy followed by OPLS was conducted. The botanical origin of propolis was established by comparing propolis spectral data to those of buds of various Populus species. An O2PLS method was utilized to integrate two blocks of data. According to OPLS and O2PLS, the major compounds in propolis samples, collected from temperate continental climate above 500m, were phenolic glycerides originating from P. tremula buds. Flavonoids were predominant in propolis samples collected below 400m, originating from P. nigra and P. x euramericana buds. Samples collected at 400-500m were of mixed origin, with variable amounts of all detected metabolites. Copyright © 2016 Elsevier B.V. All rights reserved.

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering

PubMed Central

2015-01-01

The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strengths of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide. PMID:25838811

Transition to collective oscillations in finite Kuramoto ensembles

NASA Astrophysics Data System (ADS)

Peter, Franziska; Pikovsky, Arkady

2018-03-01

We present an alternative approach to finite-size effects around the synchronization transition in the standard Kuramoto model. Our main focus lies on the conditions under which a collective oscillatory mode is well defined. For this purpose, the minimal value of the amplitude of the complex Kuramoto order parameter appears as a proper indicator. The dependence of this minimum on coupling strength varies due to sampling variations and correlates with the sample kurtosis of the natural frequency distribution. The skewness of the frequency sample determines the frequency of the resulting collective mode. The effects of kurtosis and skewness hold in the thermodynamic limit of infinite ensembles. We prove this by integrating a self-consistency equation for the complex Kuramoto order parameter for two families of distributions with controlled kurtosis and skewness, respectively.

An electronic specimen collection protocol schema (eSCPS). Document architecture for specimen management and the exchange of specimen collection protocols between biobanking information systems.

PubMed

Eminaga, O; Semjonow, A; Oezguer, E; Herden, J; Akbarov, I; Tok, A; Engelmann, U; Wille, S

2014-01-01

The integrity of collection protocols in biobanking is essential for a high-quality sample preparation process. However, there is not currently a well-defined universal method for integrating collection protocols in the biobanking information system (BIMS). Therefore, an electronic schema of the collection protocol that is based on Extensible Markup Language (XML) is required to maintain the integrity and enable the exchange of collection protocols. The development and implementation of an electronic specimen collection protocol schema (eSCPS) was performed at two institutions (Muenster and Cologne) in three stages. First, we analyzed the infrastructure that was already established at both the biorepository and the hospital information systems of these institutions and determined the requirements for the sufficient preparation of specimens and documentation. Second, we designed an eSCPS according to these requirements. Finally, a prospective study was conducted to implement and evaluate the novel schema in the current BIMS. We designed an eSCPS that provides all of the relevant information about collection protocols. Ten electronic collection protocols were generated using the supplementary Protocol Editor tool, and these protocols were successfully implemented in the existing BIMS. Moreover, an electronic list of collection protocols for the current studies being performed at each institution was included, new collection protocols were added, and the existing protocols were redesigned to be modifiable. The documentation time was significantly reduced after implementing the eSCPS (5 ± 2 min vs. 7 ± 3 min; p = 0.0002). The eSCPS improves the integrity and facilitates the exchange of specimen collection protocols in the existing open-source BIMS.

Assessment of fish assemblages and minimum sampling effort required to determine botic integrity of large rivers in southern Idaho, 2002

USGS Publications Warehouse

Maret, Terry R.; Ott, D.S.

2004-01-01

width was determined to be sufficient for collecting an adequate number of fish to estimate species richness and evaluate biotic integrity. At most sites, about 250 fish were needed to effectively represent 95 percent of the species present. Fifty-three percent of the sites assessed, using an IBI developed specifically for large Idaho rivers, received scores of less than 50, indicating poor biotic integrity.

Factors influencing moisture analysis in the 3013 destructive examination surveillance program

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

Scogin, J. H.

Thermogravimetric analysis of a solid sample with mass spectrometry (TGA-MS) of the evolved gas is used in the destructive examination (DE) portion of the Integrated Surveillance Program to quantify the moisture content of the material stored in a 3013 container. As with any measurement determined from a small sample, the collection, storage, transportation, and handling of the sample can affect its ability to represent the properties of the bulk material. During the course of the DE program, questions have periodically arisen concerning the ability of the moisture sample to reflect reliably the actual moisture content of the entire material storedmore » in the 3013 container. Most concerns are related to the ability to collect a representative sample and to preserve the moisture content of the sample between collection and analysis. Recent delays in analysis caused by maintenance issues with the TGA-MS instrument presented a unique opportunity to document and quantify the effects various factors have on the TGA-MS moisture measurement. This report will use recent data to document the effects that current sample collection and handling practices have on the TGA-MS moisture measurement. Some suggestions will be made which could improve the current sample collection and handling practices for the TGA-MS moisture measurement so that the analytical results more accurately reflect the moisture content of the material stored in the 3013 container.« less

Methods for collecting algal samples as part of the National Water-Quality Assessment Program

USGS Publications Warehouse

Porter, Stephen D.; Cuffney, Thomas F.; Gurtz, Martin E.; Meador, Michael R.

1993-01-01

Benthic algae (periphyton) and phytoplankton communities are characterized in the U.S. Geological Survey's National Water-Quality Assessment Program as part of an integrated physical, chemical, and biological assessment of the Nation's water quality. This multidisciplinary approach provides multiple lines of evidence for evaluating water-quality status and trends, and for refining an understanding of the factors that affect water-quality conditions locally, regionally, and nationally. Water quality can be characterized by evaluating the results of qualitative and quantitative measurements of the algal community. Qualitative periphyton samples are collected to develop of list of taxa present in the sampling reach. Quantitative periphyton samples are collected to measure algal community structure within selected habitats. These samples of benthic algal communities are collected from natural substrates, using the sampling methods that are most appropriate for the habitat conditions. Phytoplankton samples may be collected in large nonwadeable streams and rivers to meet specific program objectives. Estimates of algal biomass (chlorophyll content and ash-free dry mass) also are optional measures that may be useful for interpreting water-quality conditions. A nationally consistent approach provides guidance on site, reach, and habitat selection, as well as information on methods and equipment for qualitative and quantitative sampling. Appropriate quality-assurance and quality-control guidelines are used to maximize the ability to analyze data locally, regionally, and nationally.

a Comparison of Morphological Taxonomy and Next Generation DNA Sequencing for the Assessment of Zooplankton Diversity

NASA Astrophysics Data System (ADS)

Harvey, J.; Fisher, J. L.; Johnson, S.; Morgan, S.; Peterson, W. T.; Satterthwaite, E. V.; Vrijenhoek, R. C.

2016-02-01

Our ability to accurately characterize the diversity of planktonic organisms is affected by both the methods we use to collect water samples and our approaches to assessing sample contents. Plankton nets collect organisms from high volumes of water, but integrate sample contents along the net's path. In contrast, plankton pumps collect water from discrete depths. Autonomous underwater vehicles (AUVs) can collect water samples with pinpoint accuracy from physical features such as upwelling fronts or biological features such as phytoplankton blooms, but sample volumes are necessarily much smaller than those possible with nets. Characterization of plankton diversity and abundances in water samples may also vary with the assessment method we apply. Morphological taxonomy provides visual identification and enumeration of organisms via microscopy, but is labor intensive. Next generation DNA sequencing (NGS) shows great promise for assessing plankton diversity in water samples but accurate assessment of relative abundances may not be possible in all cases. Comparison of morphological taxonomy to molecular approaches is necessary to identify areas of overlap and also areas of disagreement between these methods. We have compared morphological taxonomic assessments to mitochondrial COI and nuclear 28S ribosomal RNA NGS results for plankton net samples collected in Monterey bay, California. We have made a similar comparison for plankton pump samples, and have also applied our NGS methods to targeted, small volume water samples collected by an AUV. Our goal is to communicate current results and lessons learned regarding application of traditional taxonomy and novel molecular approaches to the study of plankton diversity in spatially and temporally variable, coastal marine environments.

Sampling protocol for post-landfall Deepwater Horizon oil release, Gulf of Mexico, 2010

USGS Publications Warehouse

Wilde, F.D.; Skrobialowski, S.C.; Hart, J.S.

2010-01-01

The protocols and procedures described in this report are designed to be used by U.S. Geological Survey (USGS) field teams for the collection of environmental data and samples in coastal areas affected by the 2010 Deepwater Horizon oil spill in the Gulf of Mexico. This sampling protocol focuses specifically on sampling for water, sediments, benthic invertebrates, and microorganisms (ambient bacterial populations) after shoreline arrival of petroleum-associated product on beach, barrier island, and wetland environments of the Gulf of Mexico coastal states. Deployment to sampling sites, site setup, and sample collection in these environments necessitates modifications to standard USGS sampling procedures in order to address the regulatory, logistical, and legal requirements associated with samples collected in oil-impacted coastal areas. This document, therefore, has been written as an addendum to the USGS National Field Manual for the Collection of Water-Quality Data (NFM) (http://pubs.water.usgs.gov/twri9A/), which provides the basis for training personnel in the use of standard USGS sampling protocols. The topics covered in this Gulf of Mexico oil-spill sampling protocol augment NFM protocols for field-deployment preparations, health and safety precautions, sampling and quality-assurance procedures, and decontamination requirements under potentially hazardous environmental conditions. Documentation procedures and maintenance of sample integrity by use of chain-of-custody procedures also are described in this protocol.

Fluid transport container

DOEpatents

DeRoos, Bradley G.; Downing, Jr., John P.; Neal, Michael P.

1995-01-01

An improved fluid container for the transport, collection, and dispensing of a sample fluid that maintains the fluid integrity relative to the conditions of the location at which it is taken. More specifically, the invention is a fluid sample transport container that utilizes a fitment for both penetrating and sealing a storage container under controlled conditions. Additionally, the invention allows for the periodic withdrawal of portions of the sample fluid without contamination or intermixing from the environment surrounding the sample container.

Comparing and Combining Data across Multiple Sources via Integration of Paired-sample Data to Correct for Measurement Error

PubMed Central

Huang, Yunda; Huang, Ying; Moodie, Zoe; Li, Sue; Self, Steve

2014-01-01

Summary In biomedical research such as the development of vaccines for infectious diseases or cancer, measures from the same assay are often collected from multiple sources or laboratories. Measurement error that may vary between laboratories needs to be adjusted for when combining samples across laboratories. We incorporate such adjustment in comparing and combining independent samples from different labs via integration of external data, collected on paired samples from the same two laboratories. We propose: 1) normalization of individual level data from two laboratories to the same scale via the expectation of true measurements conditioning on the observed; 2) comparison of mean assay values between two independent samples in the Main study accounting for inter-source measurement error; and 3) sample size calculations of the paired-sample study so that hypothesis testing error rates are appropriately controlled in the Main study comparison. Because the goal is not to estimate the true underlying measurements but to combine data on the same scale, our proposed methods do not require that the true values for the errorprone measurements are known in the external data. Simulation results under a variety of scenarios demonstrate satisfactory finite sample performance of our proposed methods when measurement errors vary. We illustrate our methods using real ELISpot assay data generated by two HIV vaccine laboratories. PMID:22764070

DETERMINATION OF SULFUR DIOXIDE, NITROGEN OXIDES, AND CARBON DIOXIDE IN EMISSIONS FROM ELECTRIC UTILITY PLANTS BY ALKALINE PERMANGANATE SAMPLING AND ION CHROMATOGRAPHY

EPA Science Inventory

A manual 24-h integrated method for determining SO2, NOx, and CO2 in emissions from electric utility plants was developed and field tested downstream from an SO2 control system. Samples were collected in alkaline potassium permanganate solution contained in restricted-orifice imp...

Integrated nonlinear optical imaging microscope for on-axis crystal detection and centering at a synchrotron beamline

PubMed Central

Madden, Jeremy T.; Toth, Scott J.; Dettmar, Christopher M.; Newman, Justin A.; Oglesbee, Robert A.; Hedderich, Hartmut G.; Everly, R. Michael; Becker, Michael; Ronau, Judith A.; Buchanan, Susan K.; Cherezov, Vadim; Morrow, Marie E.; Xu, Shenglan; Ferguson, Dale; Makarov, Oleg; Das, Chittaranjan; Fischetti, Robert; Simpson, Garth J.

2013-01-01

Nonlinear optical (NLO) instrumentation has been integrated with synchrotron X-ray diffraction (XRD) for combined single-platform analysis, initially targeting applications for automated crystal centering. Second-harmonic-generation microscopy and two-photon-excited ultraviolet fluorescence microscopy were evaluated for crystal detection and assessed by X-ray raster scanning. Two optical designs were constructed and characterized; one positioned downstream of the sample and one integrated into the upstream optical path of the diffractometer. Both instruments enabled protein crystal identification with integration times between 80 and 150 µs per pixel, representing a ∼103–104-fold reduction in the per-pixel exposure time relative to X-ray raster scanning. Quantitative centering and analysis of phenylalanine hydroxylase from Chromobacterium violaceum cPAH, Trichinella spiralis deubiquitinating enzyme TsUCH37, human κ-opioid receptor complex kOR-T4L produced in lipidic cubic phase (LCP), intimin prepared in LCP, and α-cellulose samples were performed by collecting multiple NLO images. The crystalline samples were characterized by single-crystal diffraction patterns, while α-cellulose was characterized by fiber diffraction. Good agreement was observed between the sample positions identified by NLO and XRD raster measurements for all samples studied. PMID:23765294

BioData: a national aquatic bioassessment database

USGS Publications Warehouse

MacCoy, Dorene

2011-01-01

BioData is a U.S. Geological Survey (USGS) web-enabled database that for the first time provides for the capture, curation, integration, and delivery of bioassessment data collected by local, regional, and national USGS projects. BioData offers field biologists advanced capabilities for entering, editing, and reviewing the macroinvertebrate, algae, fish, and supporting habitat data from rivers and streams. It offers data archival and curation capabilities that protect and maintain data for the long term. BioData provides the Federal, State, and local governments, as well as the scientific community, resource managers, the private sector, and the public with easy access to tens of thousands of samples collected nationwide from thousands of stream and river sites. BioData also provides the USGS with centralized data storage for delivering data to other systems and applications through automated web services. BioData allows users to combine data sets of known quality from different projects in various locations over time. It provides a nationally aggregated database for users to leverage data from many independent projects that, until now, was not feasible at this scale. For example, from 1991 to 2011, the USGS Idaho Water Science Center collected more than 816 bioassessment samples from 63 sites for the National Water Quality Assessment (NAWQA) Program and more than 477 samples from 39 sites for a cooperative USGS and State of Idaho Statewide Water Quality Network (fig. 1). Using BioData, 20 years of samples collected for both of these projects can be combined for analysis. BioData delivers all of the data using current taxonomic nomenclature, thus relieving users of the difficult and time-consuming task of harmonizing taxonomy among samples collected during different time periods. Fish data are reported using the Integrated Taxonomic Information Service (ITIS) Taxonomic Serial Numbers (TSN's). A simple web-data input interface and self-guided, public data-retrieval web site provides access to bioassessment data. BioData currently accepts data collected using two national protocols: (1) NAWQA and (2) U.S. Environmental Protection Agency (USEPA) National Rivers and Streams Assessment (NRSA). Additional collection protocols are planned for future versions.

Integration of DNA sample collection into a multi-site birth defects case-control study.

PubMed

Rasmussen, Sonja A; Lammer, Edward J; Shaw, Gary M; Finnell, Richard H; McGehee, Robert E; Gallagher, Margaret; Romitti, Paul A; Murray, Jeffrey C

2002-10-01

Advances in quantitative analysis and molecular genotyping have provided unprecedented opportunities to add biological sampling and genetic information to epidemiologic studies. The purpose of this article is to describe the incorporation of DNA sample collection into the National Birth Defects Prevention Study (NBDPS), an ongoing case-control study in an eight-state consortium with a primary goal to identify risk factors for birth defects. Babies with birth defects are identified through birth defects surveillance systems in the eight participating centers. Cases are infants with one or more of over 30 major birth defects. Controls are infants without defects from the same geographic area. Epidemiologic information is collected through an hour-long interview with mothers of both cases and controls. We added the collection of buccal cytobrush DNA samples for case-infants, control-infants, and their parents to this study. We describe here the methods by which the samples have been collected and processed, establishment of a centralized resource for DNA banking, and quality control, database management, access, informed consent, and confidentiality issues. Biological sampling and genetic analyses are important components to epidemiologic studies of birth defects aimed at identifying risk factors. The DNA specimens collected in this study can be used for detection of mutations, study of polymorphic variants that confer differential susceptibility to teratogens, and examination of interactions among genetic risk factors. Information on the methods used and issues faced by the NBDPS may be of value to others considering the addition of DNA sampling to epidemiologic studies.

Application of the high throughput Attagene Factorial TM ...

EPA Pesticide Factsheets

Bioassays can be employed to evaluate the integrated effects of complex mixtures of both known and unidentified contaminants present in environmental samples. However, such methods have typically focused on one or a few pathways despite the fact that the chemicals in a mixture may exhibit a wide range of activities. High throughput toxicology approaches that can rapidly screen samples for a broad diversity of biological activities offer a means to provide a more comprehensive characterization of complex mixtures. To test this concept, twenty-four ambient water samples were collected, extracted, and screened for their ability to interact with or modulate over 80 different transcription factors using the Attagene FactorialTM platform utilized by the US EPA’s ToxCast Program. Samples evaluated included 10 water samples collected in varying proximity to a wastewater discharge into the St. Louis River, MN; water collected at five sites along a gradient centered on a wastewater discharge into the Maumee River, Ohio, USA; and eight samples collected in association with a nation-wide USGS surface streams study. For samples collected along the St. Louis River, the greatest number of biological activities were observed at locations closest to wastewater discharge with up to 13 endpoints responding. The Maumee River showed a gradient response in the number of observed activities, ranging from three positive responses observed far upstream of a wastewater discharge to 10

Information Requirements for Integrating Spatially Discrete, Feature-Based Earth Observations

NASA Astrophysics Data System (ADS)

Horsburgh, J. S.; Aufdenkampe, A. K.; Lehnert, K. A.; Mayorga, E.; Hsu, L.; Song, L.; Zaslavsky, I.; Valentine, D. L.

2014-12-01

Several cyberinfrastructures have emerged for sharing observational data collected at densely sampled and/or highly instrumented field sites. These include the CUAHSI Hydrologic Information System (HIS), the Critical Zone Observatory Integrated Data Management System (CZOData), the Integrated Earth Data Applications (IEDA) and EarthChem system, and the Integrated Ocean Observing System (IOOS). These systems rely on standard data encodings and, in some cases, standard semantics for classes of geoscience data. Their focus is on sharing data on the Internet via web services in domain specific encodings or markup languages. While they have made progress in making data available, it still takes investigators significant effort to discover and access datasets from multiple repositories because of inconsistencies in the way domain systems describe, encode, and share data. Yet, there are many scenarios that require efficient integration of these data types across different domains. For example, understanding a soil profile's geochemical response to extreme weather events requires integration of hydrologic and atmospheric time series with geochemical data from soil samples collected over various depth intervals from soil cores or pits at different positions on a landscape. Integrated access to and analysis of data for such studies are hindered because common characteristics of data, including time, location, provenance, methods, and units are described differently within different systems. Integration requires syntactic and semantic translations that can be manual, error-prone, and lossy. We report information requirements identified as part of our work to define an information model for a broad class of earth science data - i.e., spatially-discrete, feature-based earth observations resulting from in-situ sensors and environmental samples. We sought to answer the question: "What information must accompany observational data for them to be archivable and discoverable within a publication system as well as interpretable once retrieved from such a system for analysis and (re)use?" We also describe development of multiple functional schemas (i.e., physical implementations for data storage, transfer, and archival) for the information model that capture the requirements reported here.

Water-quality sampling by the U.S. Geological Survey-Standard protocols and procedures

USGS Publications Warehouse

Wilde, Franceska D.

2010-01-01

Thumbnail of and link to report PDF (1.0 MB) The U.S. Geological Survey (USGS) develops the sampling procedures and collects the data necessary for the accurate assessment and wise management of our Nation's surface-water and groundwater resources. Federal and State agencies, water-resource regulators and managers, and many organizations and interested parties in the public and private sectors depend on the reliability, timeliness, and integrity of the data we collect and the scientific soundness and impartiality of our data assessments and analysis. The standard data-collection methods uniformly used by USGS water-quality personnel are peer reviewed, kept up-to-date, and published in the National Field Manual for the Collection of Water-Quality Data (http://pubs.water.usgs.gov/twri9A/).

The Level of Satisfaction of Female Learning Disabilities' Parents with Their Kids' Integration in Regular Schools in Riyadh, Saudi Arabia

ERIC Educational Resources Information Center

Abahusain, Wedad A.

2016-01-01

This study aims at finding out the parents' level of satisfaction with the integration of their daughters with learning disabilities in regular schools in Riyadh, Saudi Arabia. The study sample consisted of 283 parents of female students. The instrument of data collection was a questionnaire consisting of 59 items for 10 domains. The study results…

The Effects of Integrating Theatre-Arts Strategies and Traditional Strategies on Student Performance in an English Classroom at a Selected High School

ERIC Educational Resources Information Center

Kariuki, Patrick N.; Black, Lacie N.

2016-01-01

The purpose of this study was to examine the effects of integrating theatre-arts strategies and traditional strategies in high school English classrooms. The sample consisted of one eleventh grade English class of twenty-one students. Data were collected from students' cumulative grades. The study was conducted throughout an eighteen-week term,…

Integrated Verification Experiment data collected as part of the Los Alamos National Laboratory`s Source Region Program. Appendix D: Ionospheric measurements for IVEs

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

Fitzgerald, T.J.; Carlos, R.C.; Argo, P.E.

As part of the integrated verification experiment (IVE), we deployed a network of hf ionospheric sounders to detect the effects of acoustic waves generated by surface ground motion following underground nuclear tests at the Nevada Test Site. The network sampled up to four geographic locations in the ionosphere from almost directly overhead of the surface ground zero out to a horizontal range of 60 km. We present sample results for four of the IVEs: Misty Echo, Texarkana, Mineral Quarry, and Bexar.

Digital Management and Curation of the National Rock and Ore Collections at NMNH, Smithsonian

NASA Astrophysics Data System (ADS)

Cottrell, E.; Andrews, B.; Sorensen, S. S.; Hale, L. J.

2011-12-01

The National Museum of Natural History, Smithsonian Institution, is home to the world's largest curated rock collection. The collection houses 160,680 physical rock and ore specimen lots ("samples"), all of which already have a digital record that can be accessed by the public through a searchable web interface (http://collections.mnh.si.edu/search/ms/). In addition, there are 66 accessions pending that when catalogued will add approximately 60,000 specimen lots. NMNH's collections are digitally managed on the KE EMu° platform which has emerged as the premier system for managing collections in natural history museums worldwide. In 2010 the Smithsonian released an ambitious 5 year Digitization Strategic Plan. In Mineral Sciences, new digitization efforts in the next five years will focus on integrating various digital resources for volcanic specimens. EMu sample records will link to the corresponding records for physical eruption information housed within the database of Smithsonian's Global Volcanism Program (GVP). Linkages are also planned between our digital records and geochemical databases (like EarthChem or PetDB) maintained by third parties. We anticipate that these linkages will increase the use of NMNH collections as well as engender new scholarly directions for research. Another large project the museum is currently undertaking involves the integration of the functionality of in-house designed Transaction Management software with the EMu database. This will allow access to the details (borrower, quantity, date, and purpose) of all loans of a given specimen through its catalogue record. We hope this will enable cross-referencing and fertilization of research ideas while avoiding duplicate efforts. While these digitization efforts are critical, we propose that the greatest challenge to sample curation is not posed by digitization and that a global sample registry alone will not ensure that samples are available for reuse. We suggest instead that the ability of the Earth science community to identify and preserve important collections and make them available for future study is limited by personnel and space resources from the level of the individual PI to the level of national facilities. Moreover, when it comes to specimen "estate planning," the cultural attitudes of scientists, institutions, and funding agencies are often inadequate to provide for long-term specimen curation - even if specimen discovery is enabled by digital registry. Timely access to curated samples requires that adequate resources be devoted to the physical care of specimens (facilities) and to the personnel costs associated with curation - from the conservation, storage, and inventory management of specimens, to the dispersal of samples for research, education, and exhibition.

Cross-Cultural Validation of the Patient Perception of Integrated Care Survey.

PubMed

Tietschert, Maike V; Angeli, Federica; van Raak, Arno J A; Ruwaard, Dirk; Singer, Sara J

2017-07-20

To test the cross-cultural validity of the U.S. Patient Perception of Integrated Care (PPIC) Survey in a Dutch sample using a standardized procedure. Primary data collected from patients of five primary care centers in the south of the Netherlands, through survey research from 2014 to 2015. Cross-sectional data collected from patients who saw multiple health care providers during 6 months preceding data collection. The PPIC survey includes 59 questions that measure patient perceived care integration across providers, settings, and time. Data analysis followed a standardized procedure guiding data preparation, psychometric analysis, and included invariance testing with the U.S. dataset. Latent scale structures of the Dutch and U.S. survey were highly comparable. Factor "Integration with specialist" had lower reliability scores and noninvariance. For the remaining factors, internal consistency and invariance estimates were strong. The standardized cross-cultural validation procedure produced strong support for comparable psychometric characteristics of the Dutch and U.S. surveys. Future research should examine the usability of the proposed procedure for contexts with greater cultural differences. © Health Research and Educational Trust.

Integrated Blood Barcode Chips

PubMed Central

Fan, Rong; Vermesh, Ophir; Srivastava, Alok; Yen, Brian K.H.; Qin, Lidong; Ahmad, Habib; Kwong, Gabriel A.; Liu, Chao-Chao; Gould, Juliane; Hood, Leroy; Heath, James R.

2008-01-01

Blood comprises the largest version of the human proteome1. Changes of plasma protein profiles can reflect physiological or pathological conditions associated with many human diseases, making blood the most important fluid for clinical diagnostics2-4. Nevertheless, only a handful of plasma proteins are utilized in routine clinical tests. This is due to a host of reasons, including the intrinsic complexity of the plasma proteome1, the heterogeneity of human diseases and the fast kinetics associated with protein degradation in sampled blood5. Simple technologies that can sensitively sample large numbers of proteins over broad concentration ranges, from small amounts of blood, and within minutes of sample collection, would assist in solving these problems. Herein, we report on an integrated microfluidic system, called the Integrated Blood Barcode Chip (IBBC). It enables on-chip blood separation and the rapid measurement of a panel of plasma proteins from small quantities of blood samples including a fingerprick of whole blood. This platform holds potential for inexpensive, non-invasive, and informative clinical diagnoses, particularly, for point-of-care. PMID:19029914

Use of Persistent Identifiers to link Heterogeneous Data Systems in the Integrated Earth Data Applications (IEDA) Facility

NASA Astrophysics Data System (ADS)

Hsu, L.; Lehnert, K. A.; Carbotte, S. M.; Arko, R. A.; Ferrini, V.; O'hara, S. H.; Walker, J. D.

2012-12-01

The Integrated Earth Data Applications (IEDA) facility maintains multiple data systems with a wide range of solid earth data types from the marine, terrestrial, and polar environments. Examples of the different data types include syntheses of ultra-high resolution seafloor bathymetry collected on large collaborative cruises and analytical geochemistry measurements collected by single investigators in small, unique projects. These different data types have historically been channeled into separate, discipline-specific databases with search and retrieval tailored for the specific data type. However, a current major goal is to integrate data from different systems to allow interdisciplinary data discovery and scientific analysis. To increase discovery and access across these heterogeneous systems, IEDA employs several unique IDs, including sample IDs (International Geo Sample Number, IGSN), person IDs (GeoPass ID), funding award IDs (NSF Award Number), cruise IDs (from the Marine Geoscience Data System Expedition Metadata Catalog), dataset IDs (DOIs), and publication IDs (DOIs). These IDs allow linking of a sample registry (System for Earth SAmple Registration), data libraries and repositories (e.g. Geochemical Research Library, Marine Geoscience Data System), integrated synthesis databases (e.g. EarthChem Portal, PetDB), and investigator services (IEDA Data Compliance Tool). The linked systems allow efficient discovery of related data across different levels of granularity. In addition, IEDA data systems maintain links with several external data systems, including digital journal publishers. Links have been established between the EarthChem Portal and ScienceDirect through publication DOIs, returning sample-level objects and geochemical analyses for a particular publication. Linking IEDA-hosted data to digital publications with IGSNs at the sample level and with IEDA-allocated dataset DOIs are under development. As an example, an individual investigator could sign up for a GeoPass account ID, write a proposal to NSF and create a data plan using the IEDA Data Management Plan Tool. Having received the grant, the investigator then collects rock samples on a scientific cruise from dredges and registers the samples with IGSNs. The investigator then performs analytical geochemistry on the samples, and submits the full dataset to the Geochemical Resource Library for a dataset DOI. Finally, the investigator writes an article that is published in Science Direct. Knowing any of the following IDs: Investigator GeoPass ID, NSF Award Number, Cruise ID, Sample IGSNs, dataset DOI, or publication DOI, a user would be able to navigate to all samples, datasets, and publications in IEDA and external systems. Use of persistent identifiers to link heterogeneous data systems in IEDA thus increases access, discovery, and proper citation of hard-earned investigator datasets.

Explosive vapor detection payload for small robots

NASA Astrophysics Data System (ADS)

Stimac, Phil J.; Pettit, Michael; Wetzel, John P.; Haas, John W.

2013-05-01

Detection of explosive hazards is a critical component of enabling and improving operational mobility and protection of US Forces. The Autonomous Mine Detection System (AMDS) developed by the US Army RDECOM CERDEC Night Vision and Electronic Sensors Directorate (NVESD) is addressing this challenge for dismounted soldiers. Under the AMDS program, ARA has developed a vapor sampling system that enhances the detection of explosive residues using commercial-off-the-shelf (COTS) sensors. The Explosives Hazard Trace Detection (EHTD) payload is designed for plug-and-play installation and operation on small robotic platforms, addressing critical Army needs for more safely detecting concealed or exposed explosives in areas such as culverts, walls and vehicles. In this paper, we describe the development, robotic integration and performance of the explosive vapor sampling system, which consists of a sampling "head," a vapor transport tube and an extendable "boom." The sampling head and transport tube are integrated with the boom, allowing samples to be collected from targeted surfaces up to 7-ft away from the robotic platform. During sample collection, an IR lamp in the sampling head is used to heat a suspected object/surface and the vapors are drawn through the heated vapor transport tube to an ion mobility spectrometer (IMS) for detection. The EHTD payload is capable of quickly (less than 30 seconds) detecting explosives such as TNT, PETN, and RDX at nanogram levels on common surfaces (brick, concrete, wood, glass, etc.).

The Internet of Samples in the Earth Sciences: Providing Access to Uncurated Collections

NASA Astrophysics Data System (ADS)

Carter, M. R.; Lehnert, K. A.

2014-12-01

Vast amounts of physical samples have been collected in the Earth Sciences for studies that address a wide range of scientific questions. Only a fraction of these samples are well curated and preserved long-term in sample repositories and museums. Many samples and collections are stored in the offices and labs of investigators, or in basements and sheds of institutions and investigators' homes. These 'uncurated' collections often contain samples that have been well studied, or are unique and irreplaceable. They may also include samples that could reveal new insights if re-analyzed using new techniques, or specimens that could have unanticipated relevance to research being conducted in fields other than the one for which they were collected. Currently, these samples cannot be accessed or discovered online by the broader science community. Investigators and departments often lack the resources to properly catalog and curate the samples and respond to requests for splits. Long-term preservation of and access to these samples is usually not provided for. iSamplES, a recently-funded EarthCube Research Coordination Network (RCN), seeks to integrate scientific samples, including 'uncurated' samples, into digital data and information infrastructure in the Earth Sciences and to facilitate their curation, discovery, access, sharing, and analysis. The RCN seeks to develop and implement best practices that increase digital access to samples with the goal of establishing a comprehensive infrastructure not only for the digital, but also physical curation of samples. The RCN will engage a broad group of individuals from domain scientists to curators to publishers to computer scientists to define, articulate, and address the needs and challenges of digital sample management and recommend community-endorsed best practices and standards for registering, describing, identifying, and citing physical specimens, drawing upon other initiatives and existing or emerging software tools for digital sample and collection management. Community engagement will include surveys, in-person workshops and outreach events, the creation of the iSamplES knowledge hub (semantic wiki) and a registry of collections. iSamplES will specifically engage early career scientists to encourage that no samples go uncurated.

Human blood RNA stabilization in samples collected and transported for a large biobank

PubMed Central

2012-01-01

Background The Norwegian Mother and Child Cohort Study (MoBa) is a nation-wide population-based pregnancy cohort initiated in 1999, comprising more than 108.000 pregnancies recruited between 1999 and 2008. In this study we evaluated the feasibility of integrating RNA analyses into existing MoBa protocols. We compared two different blood RNA collection tube systems – the PAXgene™ Blood RNA system and the Tempus™ Blood RNA system - and assessed the effects of suboptimal blood volumes in collection tubes and of transportation of blood samples by standard mail. Endpoints to characterize the samples were RNA quality and yield, and the RNA transcript stability of selected genes. Findings High-quality RNA could be extracted from blood samples stabilized with both PAXgene and Tempus tubes. The RNA yields obtained from the blood samples collected in Tempus tubes were consistently higher than from PAXgene tubes. Higher RNA yields were obtained from cord blood (3 – 4 times) compared to adult blood with both types of tubes. Transportation of samples by standard mail had moderate effects on RNA quality and RNA transcript stability; the overall RNA quality of the transported samples was high. Some unexplained changes in gene expression were noted, which seemed to correlate with suboptimal blood volumes collected in the tubes. Temperature variations during transportation may also be of some importance. Conclusions Our results strongly suggest that special collection tubes are necessary for RNA stabilization and they should be used for establishing new biobanks. We also show that the 50,000 samples collected in the MoBa biobank provide RNA of high quality and in sufficient amounts to allow gene expression analyses for studying the association of disease with altered patterns of gene expression. PMID:22988904

An Integrated Curriculum at an Islamic University: Perceptions of Students and Lecturers

ERIC Educational Resources Information Center

Suraydi, Bambang; Ekayanti, Fika; Amalia, Euis

2018-01-01

Methods: A descriptive quantitative research study was conducted with 670 students and 90 lecturers from 11 faculties at UIN Jakarta. The student samples consisted of 270 men and 400 women, while lecturer samples consisted of 44 men and 46 women. Data were collected via interviews and a perceptual questionnaire consisting of 54 items scored on a…

NHEXAS PHASE I ARIZONA STUDY--STANDARD OPERATING PROCEDURE FOR COLLECTION OF FIXED SITE INDOOR AND OUTDOOR FORMALDEHYDE PASSIVE SAMPLES (UA-F-13.1)

EPA Science Inventory

The purpose of this SOP is to describe the methods used to sample residential indoor and outdoor atmospheres for the presence of formaldehyde using the PF-1 passive formaldehyde sampler. The PF-1 passive sampler is used as a fixed location monitor to determine time integrated ex...

Biopolymers for sample collection, protection, and preservation.

PubMed

Sorokulova, Iryna; Olsen, Eric; Vodyanoy, Vitaly

2015-07-01

One of the principal challenges in the collection of biological samples from air, water, and soil matrices is that the target agents are not stable enough to be transferred from the collection point to the laboratory of choice without experiencing significant degradation and loss of viability. At present, there is no method to transport biological samples over considerable distances safely, efficiently, and cost-effectively without the use of ice or refrigeration. Current techniques of protection and preservation of biological materials have serious drawbacks. Many known techniques of preservation cause structural damages, so that biological materials lose their structural integrity and viability. We review applications of a novel bacterial preservation process, which is nontoxic and water soluble and allows for the storage of samples without refrigeration. The method is capable of protecting the biological sample from the effects of environment for extended periods of time and then allows for the easy release of these collected biological materials from the protective medium without structural or DNA damage. Strategies for sample collection, preservation, and shipment of bacterial, viral samples are described. The water-soluble polymer is used to immobilize the biological material by replacing the water molecules within the sample with molecules of the biopolymer. The cured polymer results in a solid protective film that is stable to many organic solvents, but quickly removed by the application of the water-based solution. The process of immobilization does not require the use of any additives, accelerators, or plastifiers and does not involve high temperature or radiation to promote polymerization.

The Astromaterials X-Ray Computed Tomography Laboratory at Johnson Space Center

NASA Technical Reports Server (NTRS)

Zeigler, R. A.; Coleff, D. M.; McCubbin, F. M.

2017-01-01

The Astromaterials Acquisition and Curation Office at NASA's Johnson Space Center (hereafter JSC curation) is the past, present, and future home of all of NASA's astromaterials sample collections. JSC curation currently houses all or part of nine different sample collections: (1) Apollo samples (1969), (2) Lunar samples (1972), (3) Antarctic meteorites (1976), (4) Cosmic Dust particles (1981), (5) Microparticle Impact Collection (1985), (6) Genesis solar wind atoms (2004); (7) Stardust comet Wild-2 particles (2006), (8) Stardust interstellar particles (2006), and (9) Hayabusa asteroid Itokawa particles (2010). Each sample collection is housed in a dedicated clean room, or suite of clean rooms, that is tailored to the requirements of that sample collection. Our primary goals are to maintain the long-term integrity of the samples and ensure that the samples are distributed for scientific study in a fair, timely, and responsible manner, thus maximizing the return on each sample. Part of the curation process is planning for the future, and we also perform fundamental research in advanced curation initiatives. Advanced Curation is tasked with developing procedures, technology, and data sets necessary for curating new types of sample collections, or getting new results from existing sample collections [2]. We are (and have been) planning for future curation, including cold curation, extended curation of ices and volatiles, curation of samples with special chemical considerations such as perchlorate-rich samples, and curation of organically- and biologically-sensitive samples. As part of these advanced curation efforts we are augmenting our analytical facilities as well. A micro X-Ray computed tomography (micro-XCT) laboratory dedicated to the study of astromaterials will be coming online this spring within the JSC Curation office, and we plan to add additional facilities that will enable nondestructive (or minimally-destructive) analyses of astromaterials in the near future (micro-XRF, confocal imaging Raman Spectroscopy). These facilities will be available to: (1) develop sample handling and storage techniques for future sample return missions; (2) be utilized by PET for future sample return missions; (3) be used for retroactive PET (Positron Emission Tomography)-style analyses of our existing collections; and (4) for periodic assessments of the existing sample collections. Here we describe the new micro-XCT system, as well as some of the ongoing or anticipated applications of the instrument.

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

Madden, Jeremy T.; Toth, Scott J.; Dettmar, Christopher M.

Nonlinear optical (NLO) instrumentation has been integrated with synchrotron X-ray diffraction (XRD) for combined single-platform analysis, initially targeting applications for automated crystal centering. Second-harmonic-generation microscopy and two-photon-excited ultraviolet fluorescence microscopy were evaluated for crystal detection and assessed by X-ray raster scanning. Two optical designs were constructed and characterized; one positioned downstream of the sample and one integrated into the upstream optical path of the diffractometer. Both instruments enabled protein crystal identification with integration times between 80 and 150 µs per pixel, representing a ~10 3–10 4-fold reduction in the per-pixel exposure time relative to X-ray raster scanning. Quantitative centering andmore » analysis of phenylalanine hydroxylase fromChromobacterium violaceumcPAH,Trichinella spiralisdeubiquitinating enzyme TsUCH37, human κ-opioid receptor complex kOR-T4L produced in lipidic cubic phase (LCP), intimin prepared in LCP, and α-cellulose samples were performed by collecting multiple NLO images. The crystalline samples were characterized by single-crystal diffraction patterns, while α-cellulose was characterized by fiber diffraction. Good agreement was observed between the sample positions identified by NLO and XRD raster measurements for all samples studied.« less

Variance of discharge estimates sampled using acoustic Doppler current profilers from moving boats

USGS Publications Warehouse

Garcia, Carlos M.; Tarrab, Leticia; Oberg, Kevin; Szupiany, Ricardo; Cantero, Mariano I.

2012-01-01

This paper presents a model for quantifying the random errors (i.e., variance) of acoustic Doppler current profiler (ADCP) discharge measurements from moving boats for different sampling times. The model focuses on the random processes in the sampled flow field and has been developed using statistical methods currently available for uncertainty analysis of velocity time series. Analysis of field data collected using ADCP from moving boats from three natural rivers of varying sizes and flow conditions shows that, even though the estimate of the integral time scale of the actual turbulent flow field is larger than the sampling interval, the integral time scale of the sampled flow field is on the order of the sampling interval. Thus, an equation for computing the variance error in discharge measurements associated with different sampling times, assuming uncorrelated flow fields is appropriate. The approach is used to help define optimal sampling strategies by choosing the exposure time required for ADCPs to accurately measure flow discharge.

Publishing Linked Open Data for Physical Samples - Lessons Learned

NASA Astrophysics Data System (ADS)

Ji, P.; Arko, R. A.; Lehnert, K.; Bristol, S.

2016-12-01

Most data and information about physical samples and associated sampling features currently reside in relational databases. Integrating common concepts from various databases has motivated us to publish Linked Open Data for collections of physical samples, using Semantic Web technologies including the Resource Description Framework (RDF), RDF Query Language (SPARQL), and Web Ontology Language (OWL). The goal of our work is threefold: To evaluate and select ontologies in different granularities for common concepts; to establish best practices and develop a generic methodology for publishing physical sample data stored in relational database as Linked Open Data; and to reuse standard community vocabularies from the International Commission on Stratigraphy (ICS), Global Volcanism Program (GVP), General Bathymetric Chart of the Oceans (GEBCO), and others. Our work leverages developments in the EarthCube GeoLink project and the Interdisciplinary Earth Data Alliance (IEDA) facility for modeling and extracting physical sample data stored in relational databases. Reusing ontologies developed by GeoLink and IEDA has facilitated discovery and integration of data and information across multiple collections including the USGS National Geochemical Database (NGDB), System for Earth Sample Registration (SESAR), and Index to Marine & Lacustrine Geological Samples (IMLGS). We have evaluated, tested, and deployed Linked Open Data tools including Morph, Virtuoso Server, LodView, LodLive, and YASGUI for converting, storing, representing, and querying data in a knowledge base (RDF triplestore). Using persistent identifiers such as Open Researcher & Contributor IDs (ORCIDs) and International Geo Sample Numbers (IGSNs) at the record level makes it possible for other repositories to link related resources such as persons, datasets, documents, expeditions, awards, etc. to samples, features, and collections. This work is supported by the EarthCube "GeoLink" project (NSF# ICER14-40221 and others) and the "USGS-IEDA Partnership to Support a Data Lifecycle Framework and Tools" project (USGS# G13AC00381).

A benthic-macroinvertebrate index of biotic integrity and assessment of conditions in selected streams in Chester County, Pennsylvania, 1998-2009

USGS Publications Warehouse

Reif, Andrew G.

2012-01-01

The Stream Conditions of Chester County Biological Monitoring Network (Network) was established by the U.S. Geological Survey and the Chester County Water Resources Authority in 1969. Chester County encompasses 760 square miles in southeastern Pennsylvania and has a rapidly expanding population. Land-use change has occurred in response to this continual growth, as open space, agricultural lands, and wooded lands have been converted to residential and commercial lands. In 1998, the Network was modified to include 18 fixed-location sites and 9 flexible-location sites. Sites were sampled annually in the fall (October-November) during base-flow conditions for water chemistry, instream habitat, and benthic macroinvertebrates. A new set of 9 flexible-location sites was selected each year. From 1998 to 2009, 213 samples were collected from the 18 fixed-location sites and 107 samples were collected from the 84 flexible-location sites. Eighteen flexible-location sites were sampled more than once over the 12-year period; 66 sites were sampled only once. Benthic-macroinvertebrate data from samples collected during 1998-2009 were used to establish the Chester County Index of Biotic Integrity (CC-IBI). The CC-IBI was based on the methods and metrics outlined in the Pennsylvania Department of Environmental Protection's "A Benthic Index of Biotic Integrity for Wadeable Freestone Streams in Pennsylvania." The resulting CC-IBI consists of scores for benthic-macroinvertebrate samples collected from sites in the Network that related to reference conditions in Chester County. Mean CC-IBI scores for 18 fixed-location sites ranged from 37.21 to 88.92. Thirty-nine percent of the 213 samples collected at the 18 fixed-location sites had a CC-IBI score less than 50; 33 percent, 50 to 70; 28 percent, greater than 70. CC-IBI scores from the 107 flexible-location samples ranged from 23.48 to 99.96. Twenty-five percent of the 107 samples collected at the flexible-location sites had a CC-IBI score less than 50; 33 percent, 50 to 70; and 42 percent, greater than 70. Factors that were found to affect CC-IBI scores are nutrient concentrations, habitat conditions, and percent of wooded and urban land use. A positive relation was determined between mean CC-IBI scores and mean total habitat scores for the 18 fixed-location sites. CC-IBI scores were most strongly affected by stream bank vegetative protection, embeddedness, riparian zone width, and sediment deposition. The highest CC-IBI scores were associated with sites that had greater than 28 percent wooded-wetland-water land use, less than 5 percent urban land use, and no municipal wastewater discharges within 10 miles upstream from the sampling site. The lowest CC-IBI scores were associated with sites where urban land use was greater than 15 percent or a municipal wastewater discharge was within 10 miles upstream from the sampling reach. The Mann Kendall test for trends was used to determine trends in CC-IBI scores and concentrations of nitrate, orthophosphate, and chloride for the 18 fixed-location sites. A positive trend in CC-IBI was determined for six sites, and a negative trend was determined for one site. Positive trends in nitrate concentrations were determined for 4 of the 18 fixed-location sites, and a negative trend in orthophosphate concentrations was determined for 1 of the 18 fixed-location sites. Positive trends in chloride concentrations were determined for 16 of the 18 fixed-location sites.

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

PubMed Central

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

2016-01-01

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

A Comparison of Burnout Levels of Preschool Teachers in Terms of Having Integration Students in Their Classes or Not

ERIC Educational Resources Information Center

Sahbaz, Ümit; Koyutürk Koçer, Nazife

2017-01-01

The aim of the present study is to compare burnout levels of preschool teachers who have integration students in their classes and those who do not. The sample of the study consists of 185 preschool teachers working in Isparta city and town centers. The data of the study were collected using the Burnout Inventory developed by Maslach and Jackson…

Perspectives of teachers regarding the integration of mathematics and science at the secondary school level

NASA Astrophysics Data System (ADS)

Zolnierczyk, Joanna Asia

The integration of mathematics and science in secondary schools in the 21st century continues to be an important topic of practice and research. The purpose of my research study, which builds on studies by Frykholm and Glasson (2005) and Berlin and White (2010), is to explore the potential constraints and benefits of integrating mathematics and science in Ontario secondary schools based on the perspectives of in-service and pre-service teachers with various math and/or science backgrounds. A qualitative and quantitative research design with an exploratory approach was used. The qualitative data was collected from a sample of 12 in-service teachers with various math and/or science backgrounds recruited from two school boards in Eastern Ontario. The quantitative and some qualitative data was collected from a sample of 81 pre-service teachers from the Queen's University Bachelor of Education (B.Ed) program. Semi-structured interviews were conducted with the in-service teachers while a survey and a focus group was conducted with the pre-service teachers. Once the data was collected, the qualitative data were abductively analyzed. For the quantitative data, descriptive and inferential statistics (one-way ANOVAs and Pearson Chi Square analyses) were calculated to examine perspectives of teachers regardless of teaching background and to compare groups of teachers based on teaching background. The findings of this study suggest that in-service and pre-service teachers have a positive attitude towards the integration of math and science and view it as valuable to student learning and success. The pre-service teachers viewed the integration as easy and did not express concerns to this integration. On the other hand, the in-service teachers highlighted concerns and challenges such as resources, scheduling, and time constraints. My results illustrate when teachers perceive it is valuable to integrate math and science and which aspects of the classroom benefit best from the integration. Furthermore, the results highlight barriers and possible solutions to better the integration of math and science. In addition to the benefits and constraints of integration, my results illustrate why some teachers may opt out of integrating math and science and the different strategies teachers have incorporated to integrate math and science in their classroom.

Cryopreservation of human spermatozoa. I. Effects of holding procedure and seeding on motility, fertilizability, and acrosome reaction.

PubMed

Critser, J K; Huse-Benda, A R; Aaker, D V; Arneson, B W; Ball, G D

1987-04-01

Three experiments were conducted to evaluate effects of holding semen at +5.0 degrees C for 30 minutes or -5.0 degrees C for 10 minutes and ice crystal induction (seeding) on frozen-thawed human spermatozoa. In experiment 1, spermatozoa were frozen, and postthaw motility was evaluated immediately (0 hour) and 24 hours later. At both 0 and 24 hours, nonfrozen control samples had higher motility than all other treatment groups. At 0 hour postthaw, motility was higher in samples held at -5.0 degrees C for 10 minutes with no significant effect of seeding. At 24 hours, samples held at -5.0 degrees C for 10 minutes and seeded, but not samples held at -5.0 degrees C and not seeded, had higher motility than samples held at +5.0 degrees C. In experiment 2, semen samples were frozen, and fertilizability was evaluated in a zona-free hamster egg penetration assay. Seeded samples had a higher frequency of sperm penetration than either nonfrozen or nonseeded samples. In experiment 3, nonfrozen controls and frozen treatment groups were evaluated for the frequency of survival and acrosomal integrity. Seeded samples had higher frequencies of survival and loss of acrosomal integrity than nonseeded samples. All frozen-thawed samples had a lower frequency of survival and a higher frequency of loss of acrosomal integrity than nonfrozen controls. Although altered patterns of fertilizability and acrosomal integrity are induced, collectively these data suggest that incorporating a holding temperature of -5.0 degrees C for 10 minutes and seeding may result in a superior protocol for freezing human spermatozoa.

The UK Biobank sample handling and storage protocol for the collection, processing and archiving of human blood and urine.

PubMed

Elliott, Paul; Peakman, Tim C

2008-04-01

UK Biobank is a large prospective study in the UK to investigate the role of genetic factors, environmental exposures and lifestyle in the causes of major diseases of late and middle age. Extensive data and biological samples are being collected from 500,000 participants aged between 40 and 69 years. The biological samples that are collected and how they are processed and stored will have a major impact on the future scientific usefulness of the UK Biobank resource. The aim of the UK Biobank sample handling and storage protocol is to specify methods for the collection and storage of participant samples that give maximum scientific return within the available budget. Processing or storage methods that, as far as can be predicted, will preclude current or future assays have been avoided. The protocol was developed through a review of the literature on sample handling and processing, wide consultation within the academic community and peer review. Protocol development addressed which samples should be collected, how and when they should be processed and how the processed samples should be stored to ensure their long-term integrity. The recommended protocol was extensively tested in a series of validation studies. UK Biobank collects about 45 ml blood and 9 ml of urine with minimal local processing from each participant using the vacutainer system. A variety of preservatives, anti-coagulants and clot accelerators is used appropriate to the expected end use of the samples. Collection of other material (hair, nails, saliva and faeces) was also considered but rejected for the full cohort. Blood and urine samples from participants are transported overnight by commercial courier to a central laboratory where they are processed and aliquots of urine, plasma, serum, white cells and red cells stored in ultra-low temperature archives. Aliquots of whole blood are also stored for potential future production of immortalized cell lines. A standard panel of haematology assays is completed on whole blood from all participants, since such assays need to be conducted on fresh samples (whereas other assays can be done on stored samples). By the end of the recruitment phase, 15 million sample aliquots will be stored in two geographically separate archives: 9.5 million in a -80 degrees C automated archive and 5.5 million in a manual liquid nitrogen archive at -180 degrees C. Because of the size of the study and the numbers of samples obtained from participants, the protocol stipulates a highly automated approach for the processing and storage of samples. Implementation of the processes, technology, systems and facilities has followed best practices used in manufacturing industry to reduce project risk and to build in quality and robustness. The data produced from sample collection, processing and storage are highly complex and are managed by a commercially available LIMS system fully integrated with the entire process. The sample handling and storage protocol adopted by UK Biobank provides quality assured and validated methods that are feasible within the available funding and reflect the size and aims of the project. Experience from recruiting and processing the first 40,000 participants to the study demonstrates that the adopted methods and technologies are fit-for-purpose and robust.

The Use of Handheld X-Ray Fluorescence (XRF) Technology in Unraveling the Eruptive History of the San Francisco Volcanic Field, Arizona

NASA Technical Reports Server (NTRS)

Young, Kelsey E.; Evans, C. A.; Hodges, K. V.

2012-01-01

While traditional geologic mapping includes the examination of structural relationships between rock units in the field, more advanced technology now enables us to simultaneously collect and combine analytical datasets with field observations. Information about tectonomagmatic processes can be gleaned from these combined data products. Historically, construction of multi-layered field maps that include sample data has been accomplished serially (first map and collect samples, analyze samples, combine data, and finally, readjust maps and conclusions about geologic history based on combined data sets). New instruments that can be used in the field, such as a handheld xray fluorescence (XRF) unit, are now available. Targeted use of such instruments enables geologists to collect preliminary geochemical data while in the field so that they can optimize scientific data return from each field traverse. Our study tests the application of this technology and projects the benefits gained by real-time geochemical data in the field. The integrated data set produces a richer geologic map and facilitates a stronger contextual picture for field geologists when collecting field observations and samples for future laboratory work. Real-time geochemical data on samples also provide valuable insight regarding sampling decisions by the field geologist

Source apportion of atmospheric particulate matter: a joint Eulerian/Lagrangian approach.

PubMed

Riccio, A; Chianese, E; Agrillo, G; Esposito, C; Ferrara, L; Tirimberio, G

2014-12-01

PM2.5 samples were collected during an annual monitoring campaign (January 2012-January 2013) in the urban area of Naples, one of the major cities in Southern Italy. Samples were collected by means of a standard gravimetric sampler (Tecora Echo model) and characterized from a chemical point of view by ion chromatography. As a result, 143 samples together with their ionic composition have been collected. We extend traditional source apportionment techniques, usually based on multivariate factor analysis, interpreting the chemical analysis results within a Lagrangian framework. The Hybrid Single-Particle Lagrangian Integrated Trajectory Model (HYSPLIT) model was used, providing linkages to the source regions in the upwind areas. Results were analyzed in order to quantify the relative weight of different source types/areas. Model results suggested that PM concentrations are strongly affected not only by local emissions but also by transboundary emissions, especially from the Eastern and Northern European countries and African Saharan dust episodes.

International Space Station Urine Monitoring System Functional Integration and Science Testing

NASA Technical Reports Server (NTRS)

Rodriquez, Branelle R.; Broyan, James Lee, Jr.

2011-01-01

Exposure to microgravity during human spaceflight needs to be better understood as the human exploration of space requires longer duration missions. It is known that long term exposure to microgravity causes bone loss. Measuring the calcium and other metabolic byproducts in a crew member s urine can evaluate the effectiveness of bone loss countermeasures. The International Space Station (ISS) Urine Monitoring System (UMS) is an automated urine collection device designed to collect urine, separate the urine and air, measure the void volume, and allow for syringe sampling. Accurate measuring and minimal cross-contamination is essential to determine bone loss and the effectiveness of countermeasures. The ISS UMS provides minimal cross-contamination (<0.7 mL urine) and has volume accuracy of 2% between 100 to 1000 mL urine voids. Designed to provide a non-invasive means to collect urine samples from crew members, the ISS UMS operates in-line with the Node 3 Waste and Hygiene Compartment (WHC). The ISS UMS has undergone modifications required to interface with the WHC, including material changes, science algorithm improvements, and software platform revisions. Integrated functional testing was performed to determine the pressure drop, air flow rate, and the maximum amount of fluid capable of being discharged from the UMS to the WHC. This paper will detail the results of the science and the functional integration tests.

USE OF AN INTEGRATED APPROACH TO EVALUATE YOUNG CHILDREN'S ACTIVITIES

EPA Science Inventory

Linking a young child's activity pattern data with the environmental, biological, and personal samples that are collected during an exposure assessment is important in evaluating potential exposures and dose associated with environmental contaminants. A number of different appro...

An Intervention to Reduce Residential Insecticide Exposure during Pregnancy among an Inner-City Cohort

PubMed Central

Williams, Megan K.; Barr, Dana B.; Camann, David E.; Cruz, Linda A.; Carlton, Elizabeth J.; Borjas, Mejico; Reyes, Andria; Evans, Dave; Kinney, Patrick L.; Whitehead, Ralph D.; Perera, Frederica P.; Matsoanne, Stephen; Whyatt, Robin M.

2006-01-01

Background We previously reported widespread insecticide exposure during pregnancy among inner-city women from New York City. Here we report on a pilot intervention using integrated pest management (IPM) to reduce pest infestations and residential insecticide exposures among pregnant New York City African-American and Latina women (25 intervention and 27 control homes). Methods The IPM consisted of professional cleaning, sealing of pest entry points, application of low-toxicity pesticides, and education. Cockroach infestation levels and 2-week integrated indoor air samples were collected at baseline and one month postintervention. The insecticides detected in the indoor air samples were also measured in maternal and umbilical cord blood collected at delivery. Results Cockroach infestations decreased significantly (p = 0.016) after the intervention among intervention cases but not control households. Among the intervention group, levels of piperonyl butoxide (a pyrethroid synergist) were significantly lower in indoor air samples after the intervention (p = 0.016). Insecticides were detected in maternal blood samples collected at delivery from controls but not from the intervention group. The difference was significant for trans-permethrin (p = 0.008) and of borderline significance (p = 0.1) for cis-permethrin and 2-isopropoxyphenol (a propoxur metabolite). Conclusion To our knowledge, this is the first study to use biologic dosimeters of prenatal pesticide exposure for assessing effectiveness of IPM. These pilot data suggest that IPM is an effective strategy for reducing pest infestation levels and the internal dose of insecticides during pregnancy. PMID:17107853

The EuPA Biobank Initiative: Meeting the future challenges of biobanking in proteomics & systems medicine.

PubMed

Wheelock, Åsa M; Paulson, Linda; Litton, Jan-Eric

2015-09-08

In this News & Reviews Discussion, the recently launched EuPA (European Proteomics Association) Biobank Initiative is introduced in the context of current and future challenges in biobanking. The purpose of the initiative is to provide a forumand knowledge platform for integrating the extensive experiences collected by the EuPA community, and link it to the European and international biobanking communities at large. The specific impact of providing a forum and easy access to this type of information to the EuPA community is the potential of improving the quality of future sample collections and biobanks, the quality of the research produced from these sample collections, as well as the output and productivity from existing biobanks. The underutilization of biobanks has recently been identified as an emerging issue of biobankingworldwide. Measures to improve our ability to locate and access appropriate sample collections for a wide range of research purposes may enhance both the scientific quality and biobank sustainability, thereby contributing to the important task of moving our research beyond basic findings and mere publications, into clinical practice. This manuscript is intended as a Discussion piece, and represents a recollection of the presentation under the “EuPA Initiative” session at HUPO/EuPA 2014 in Madrid. The launch of the EuPA (European Proteomics Association) Biobank Initiative in the context of current and future challenges in biobanking is discussed. The purpose of the initiative is to provide a forum and knowledge base for integrating the extensive experiences collected by the EuPA community, and link it to the European and international biobanking communities at large. The specific impact of providing a forumand easy access to this type of information to the EuPA community is the potential of improving the quality of future sample collections and biobanks, the quality of the research produced from these sample collections, aswell as the output and productivity fromexisting biobanks. The underutilization of biobanks has recently been identified as a challenge to the well-being and economic sustainability of biobanking worldwide. Measures to improve our ability to localize and access appropriate sample collections for validation studies and other research purposes is thus of benefit bothto scientific quality and biobank sustainability, thereby contributing to the important task of moving our research beyond basic findings and mere publications, into clinical practice. This article is part of a Special Issue entitled: HUPO 2014.

GeoLab 2011: New Instruments and Operations Tested at Desert RATS

NASA Technical Reports Server (NTRS)

Evans, Cindy A.; Calaway, M. J.; Bell, M. S.

2012-01-01

GeoLab is a geological laboratory and testbed designed for supporting geoscience activities during NASA's analog demonstrations. Scientists at NASA's Johnson Space Center built GeoLab as part of a technology project to aid the development of science operational concepts for future planetary surface missions [1, 2, 3]. It is integrated into NASA's Habitat Demonstration Unit, a first generation exploration habitat test article. As a prototype workstation, GeoLab provides a high fidelity working space for analog mission crewmembers to perform in-situ characterization of geologic samples and communicate their findings with supporting scientists. GeoLab analog operations can provide valuable data for assessing the operational and scientific considerations of surface-based geologic analyses such as preliminary examination of samples collected by astronaut crews [4, 5]. Our analog tests also feed into sample handling and advanced curation operational concepts and procedures that will, ultimately, help ensure that the most critical samples are collected during future exploration on a planetary surface, and aid decisions about sample prioritization, sample handling and return. Data from GeoLab operations also supports science planning during a mission by providing additional detailed geologic information to supporting scientists, helping them make informed decisions about strategies for subsequent sample collection opportunities.

Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.

PubMed

Walls, Ramona L; Deck, John; Guralnick, Robert; Baskauf, Steve; Beaman, Reed; Blum, Stanley; Bowers, Shawn; Buttigieg, Pier Luigi; Davies, Neil; Endresen, Dag; Gandolfo, Maria Alejandra; Hanner, Robert; Janning, Alyssa; Krishtalka, Leonard; Matsunaga, Andréa; Midford, Peter; Morrison, Norman; Ó Tuama, Éamonn; Schildhauer, Mark; Smith, Barry; Stucky, Brian J; Thomer, Andrea; Wieczorek, John; Whitacre, Jamie; Wooley, John

2014-01-01

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.

Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies

PubMed Central

Baskauf, Steve; Blum, Stanley; Bowers, Shawn; Davies, Neil; Endresen, Dag; Gandolfo, Maria Alejandra; Hanner, Robert; Janning, Alyssa; Krishtalka, Leonard; Matsunaga, Andréa; Midford, Peter; Tuama, Éamonn Ó.; Schildhauer, Mark; Smith, Barry; Stucky, Brian J.; Thomer, Andrea; Wieczorek, John; Whitacre, Jamie; Wooley, John

2014-01-01

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. PMID:24595056

Measuring Concentrations of Particulate 140La in the Air

DOE PAGES

Okada, Colin E.; Kernan, Warnick J.; Keillor, Martin E.; ...

2016-05-01

Air sampling systems were deployed to measure the concentration of radioactive material in the air during the Full-Scale Radiological Dispersal Device experiments. The air samplers were positioned 100-600 meters downwind of the release point. The filters were collected immediately and analyzed in the field. Quantities for total activity collected on the air filters are reported along with additional information to compute the average or integrated air concentrations.

Urban Air Toxics Monitoring Program, 1989

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

McAllister, R.A.; Moore, W.H.; Rice, J.

1990-10-01

From January 1989 through January 1990 samples of ambient air were collected at 14 sites in the eastern part of the U.S. Every 12 days, air was integrated over 24-hour periods into passivated stainless steel canisters. Simultaneously, air was drawn through cartridges containing dinitrophenylhydrazine to collect carbonyl compounds. The samples were analyzed at a central laboratory for a total of 37 halogenated and aromatic hydrocarbons, formaldehyde, acetaldehyde, and other oxygenated species. The hydrocarbon species were analyzed by gas chromatography/multiple detectors and gas chromatography/mass spectrometry, while the carbonyl species were analyzed by liquid chromatography. An extensive quality assurance program was carriedmore » on to secure high quality data. Complete data for all the carbonyl samples are presented in the report.« less

Shedding light on the Global Ocean microbiome with algorithms and data collection

NASA Astrophysics Data System (ADS)

Lauro, F.; Ostrowski, M.; Chénard, C.; Acerbi, E.; Paulsen, I.; Jensen, R.

2016-02-01

In the Global Oceans, the marine microbiome plays a critical role in biogeochemical cycling of nutrients, but surveying marine microbial communities requires ship time for sample collection, economically constraining the number of samples collected. An integrative understanding of the microbiome's activity and performance requires the collection of high-density data, both temporally and spatially in a cost-effective way. We have overcome this bottleneck by crowdsourcing the data collection to vessels of opportunity, including bluewater sailing yachts. Sailors know the oceans, and experience first-hand the declines in ocean productivity and the effects of pollution and climate change. Moreover, simply the ability to sample a microbial community during anomalous or inclement weather conditions is a major advance in sampling strategy. Our approach inherently incorporates the benefit of outreach and participation of people in scientific research, gaining positive media attention for sailors, scientists and concerned citizens alike. We have tested the basic methods during a 2013 Indian Ocean Concept Cruise, from Cape Town to Singapore, performing experimental work and reaching sampling locations inaccessible to traditional Oceanographic Vessels. At the same time we developed a small, yacht-adapted automated sampling device that takes a variety of biological and chemical measurements. In 2015 our first beta-cruisers sampled the Pacific Ocean in the first ever citizen-oceanography transect at high and low latitudes in both hemispheres. The collected samples were characterized with next-gen sequencing technology and analysed with a combination of novel algorithmic approaches. With big data management, machine learning algorithms and agent-based models we show that it is possible to deconvolute the complexity of the Ocean Microbiome for the scientific management of fisheries, marine protected areas and preservation of the oceans and seas for generations to come.

Pre-analytic evaluation of volumetric absorptive microsampling and integration in a mass spectrometry-based metabolomics workflow.

PubMed

Volani, Chiara; Caprioli, Giulia; Calderisi, Giovanni; Sigurdsson, Baldur B; Rainer, Johannes; Gentilini, Ivo; Hicks, Andrew A; Pramstaller, Peter P; Weiss, Guenter; Smarason, Sigurdur V; Paglia, Giuseppe

2017-10-01

Volumetric absorptive microsampling (VAMS) is a novel approach that allows single-drop (10 μL) blood collection. Integration of VAMS with mass spectrometry (MS)-based untargeted metabolomics is an attractive solution for both human and animal studies. However, to boost the use of VAMS in metabolomics, key pre-analytical questions need to be addressed. Therefore, in this work, we integrated VAMS in a MS-based untargeted metabolomics workflow and investigated pre-analytical strategies such as sample extraction procedures and metabolome stability at different storage conditions. We first evaluated the best extraction procedure for the polar metabolome and found that the highest number and amount of metabolites were recovered upon extraction with acetonitrile/water (70:30). In contrast, basic conditions (pH 9) resulted in divergent metabolite profiles mainly resulting from the extraction of intracellular metabolites originating from red blood cells. In addition, the prolonged storage of blood samples at room temperature caused significant changes in metabolome composition, but once the VAMS devices were stored at - 80 °C, the metabolome remained stable for up to 6 months. The time used for drying the sample did also affect the metabolome. In fact, some metabolites were rapidly degraded or accumulated in the sample during the first 48 h at room temperature, indicating that a longer drying step will significantly change the concentration in the sample. Graphical abstract Volumetric absorptive microsampling (VAMS) is a novel technology that allows single-drop blood collection and, in combination with mass spectrometry (MS)-based untargeted metabolomics, represents an attractive solution for both human and animal studies. In this work, we integrated VAMS in a MS-based untargeted metabolomics workflow and investigated pre-analytical strategies such as sample extraction procedures and metabolome stability at different storage conditions. The latter revealed that prolonged storage of blood samples at room temperature caused significant changes in metabolome composition, but if VAMS devices were stored at - 80 °C, the metabolome remained stable for up to 6 months.

Characterizing the bioactivity of complex environmental ...

EPA Pesticide Factsheets

Bioassays can be employed to evaluate the integrated effects of complex mixtures of both known and unidentified contaminants present in environmental samples. However, such methods have typically focused on one or a few bioactivities despite the fact that the chemicals in a mixture may exhibit a wide range of activities. High throughput toxicology approaches that can rapidly screen samples for a broad diversity of biological activities offer a means to provide a more comprehensive characterization. To test this concept, twenty-four ambient water samples were collected, extracted, and screened for their ability to interact with or modulate over 80 different transcription factors using the Attagene subset of assays utilized by the US EPA’s ToxCast Program. Samples evaluated included water collected at five sites along a spatial gradient centered around a wastewater discharge into the Maumee River, Ohio, USA; 10 samples were collected in varying proximity to a wastewater discharge within the St. Louis River Area of Concern (AOC), MN; and eight samples were associated with a nation-wide US Geological Survey Mixture Study. Samples collected along the Maumee River showed a gradient response in the number of observed activities, ranging from three positive assay responses observed far upstream of discharge to seven positive responses in water from the mixing zone. TGFb signaling and the aryl hydrocarbon receptor (AhR) activation were the biological activities obser

A passive integrative sampler for mercury vapor in air and neutral mercury species in water

USGS Publications Warehouse

Brumbaugh, W.G.; Petty, J.D.; May, T.W.; Huckins, J.N.

2000-01-01

A passive integrative mercury sampler (PIMS) based on a sealed polymeric membrane was effective for the collection and preconcentration of Hg0. Because the Hg is both oxidized and stabilized in the PIMS, sampling intervals of weeks to months are possible. The effective air sampling rate for a 15 x 2.5 cm device was about 21-equivalents/day (0.002 m3/day) and the detection limit for 4-week sampling was about 2 ng/m3 for conventional ICP-MS determination without clean-room preparation. Sampling precision was ??? 5% RSD for laboratory exposures, and 5-10% RSD for field exposures. These results suggest that the PIMS could be useful for screening assessments of Hg contamination and exposure in the environment, the laboratory, and the workplace. The PIMS approach may be particularly useful for applications requiring unattended sampling for extended periods at remote locations. Preliminary results indicate that sampling for dissolved gaseous mercury (DGM) and potentially other neutral mercury species from water is also feasible. Rigorous validation of the sampler performance is currently in progress. (C) 1999 Elsevier Science Ltd.A passive integrative mercury sampler (PIMS) based on a sealed polymeric membrane was effective for the collection and preconcentration of Hg0. Because the Hg is both oxidized and stabilized in the PIMS, sampling intervals of weeks to months are possible. The effective air sampling rate for a 15??2.5 cm device was about 21-equivalents/day (0.002 m3/day) and the detection limit for 4-week sampling was about 2 ng/m3 for conventional ICP-MS determination without clean-room preparation. Sampling precision was ???5% RSD for laboratory exposures, and 5-10% RSD for field exposures. These results suggest that the PIMS could be useful for screening assessments of Hg contamination and exposure in the environment, the laboratory, and the workplace. The PIMS approach may be particularly useful for applications requiring unattended sampling for extended periods at remote locations. Preliminary results indicate that sampling for dissolved gaseous mercury (DGM) and potentially other neutral mercury species from water is also feasible. Rigorous validation of the sampler performance is currently in progress.

Strategies for monitoring the emerging polar organic contaminants in water with emphasis on integrative passive sampling.

PubMed

Söderström, Hanna; Lindberg, Richard H; Fick, Jerker

2009-01-16

Although polar organic contaminants (POCs) such as pharmaceuticals are considered as some of today's most emerging contaminants few of them are regulated or included in on-going monitoring programs. However, the growing concern among the public and researchers together with the new legislature within the European Union, the registration, evaluation and authorisation of chemicals (REACH) system will increase the future need of simple, low cost strategies for monitoring and risk assessment of POCs in aquatic environments. In this article, we overview the advantages and shortcomings of traditional and novel sampling techniques available for monitoring the emerging POCs in water. The benefits and drawbacks of using active and biological sampling were discussed and the principles of organic passive samplers (PS) presented. A detailed overview of type of polar organic PS available, and their classes of target compounds and field of applications were given, and the considerations involved in using them such as environmental effects and quality control were discussed. The usefulness of biological sampling of POCs in water was found to be limited. Polar organic PS was considered to be the only available, but nevertheless, an efficient alternative to active water sampling due to its simplicity, low cost, no need of power supply or maintenance, and the ability of collecting time-integrative samples with one sample collection. However, the polar organic PS need to be further developed before they can be used as standard in water quality monitoring programs.

Prevention of Organ Injury in Exertional Heat Stroke: Preclinical Evaluation of a New Class of NSAIDs

DTIC Science & Technology

2017-10-01

and integration of data from 3 centers. PROGRESS: All of year one goals were completed except for completion of the manuscripts, which are...samples from mice, integrate data collection from the 3 laboratories and prepare final reports and manuscripts of experimental outcomes. PROGRESS...the later recovery period. These data suggest some abnormalities in glucose metabolism, particularly in male mice, during the recovery from EHS

Considerations for Integrating Women into Closed Occupations in the U.S. Special Operations Forces

DTIC Science & Technology

2015-05-01

effectiveness of integration. Ideally, studies adopting an experimental design (using both test and control groups ) would be preferred, but sample sizes may...data -- a survey of SOF personnel and a series of focus group discussions -- collected by the research team regarding the potential challenges to... controlled positions. This report summarizes our research , analysis, and conclusions. We used a mixed-methods approach. We reviewed the current state of

ANALYSIS OF NHEXAS DATA FROM THE CHILDREN'S PESTICIDE EXPOSURE STUDY IN MINNESOTA

EPA Science Inventory

The "Minnesota Children's Pesticide Exposure Study" (MNCPES) evaluated the feasibility of conducting a multipathway exposure monitoring study with a sample of children, and implemented a strategy for collection and integration of survey information (e.g., pesticide usage and act...

Study of Z production in PbPb and pp collisions at TeV in the dimuon and dielectron decay channels

NASA Astrophysics Data System (ADS)

Chatrchyan, S.; Khachatryan, V.; Sirunyan, A. M.; Adam, W.; Bergauer, T.; Dragicevic, M.; Erö, J.; Fabjan, C.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hartl, C.; Hörmann, N.; Hrubec, J.; Jeitler, M.; Kiesenhofer, W.; Knünz, V.; Krammer, M.; Krätschmer, I.; Liko, D.; Mikulec, I.; Rabady, D.; Rahbaran, B.; Rohringer, H.; Schöfbeck, R.; Strauss, J.; Taurok, A.; Treberer-Treberspurg, W.; Waltenberger, W.; Wulz, C.-E.; Mossolov, V.; Shumeiko, N.; Suarez Gonzalez, J.; Alderweireldt, S.; Bansal, M.; Bansal, S.; Cornelis, T.; De Wolf, E. A.; Janssen, X.; Knutsson, A.; Luyckx, S.; Ochesanu, S.; Roland, B.; Rougny, R.; Van De Klundert, M.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Van Spilbeeck, A.; Blekman, F.; Blyweert, S.; D'Hondt, J.; Daci, N.; Heracleous, N.; Keaveney, J.; Lowette, S.; Maes, M.; Olbrechts, A.; Python, Q.; Strom, D.; Tavernier, S.; Van Doninck, W.; Van Mulders, P.; Van Onsem, G. P.; Villella, I.; Caillol, C.; Clerbaux, B.; De Lentdecker, G.; Dobur, D.; Favart, L.; Gay, A. P. R.; Grebenyuk, A.; Léonard, A.; Mohammadi, A.; Perniè, L.; Reis, T.; Seva, T.; Thomas, L.; Vander Velde, C.; Vanlaer, P.; Wang, J.; Adler, V.; Beernaert, K.; Benucci, L.; Cimmino, A.; Costantini, S.; Crucy, S.; Dildick, S.; Fagot, A.; Garcia, G.; Mccartin, J.; Ocampo Rios, A. A.; Ryckbosch, D.; Salva Diblen, S.; Sigamani, M.; Strobbe, N.; Thyssen, F.; Tytgat, M.; Yazgan, E.; Zaganidis, N.; Basegmez, S.; Beluffi, C.; Bruno, G.; Castello, R.; Caudron, A.; Ceard, L.; Da Silveira, G. G.; Delaere, C.; du Pree, T.; Favart, D.; Forthomme, L.; Giammanco, A.; Hollar, J.; Jez, P.; Komm, M.; Lemaitre, V.; Nuttens, C.; Pagano, D.; Perrini, L.; Pin, A.; Piotrzkowski, K.; Popov, A.; Quertenmont, L.; Selvaggi, M.; Vidal Marono, M.; Vizan Garcia, J. M.; Beliy, N.; Caebergs, T.; Daubie, E.; Hammad, G. H.; Aldá Júnior, W. L.; Alves, G. A.; Brito, L.; Correa Martins Junior, M.; Pol, M. E.; Carvalho, W.; Chinellato, J.; Custódio, A.; Da Costa, E. M.; De Jesus Damiao, D.; De Oliveira Martins, C.; Fonseca De Souza, S.; Malbouisson, H.; Matos Figueiredo, D.; Mundim, L.; Nogima, H.; Prado Da Silva, W. L.; Santaolalla, J.; Santoro, A.; Sznajder, A.; Tonelli Manganote, E. J.; Vilela Pereira, A.; Bernardes, C. A.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Mercadante, P. G.; Novaes, S. F.; Padula, Sandra S.; Aleksandrov, A.; Genchev, V.; Iaydjiev, P.; Marinov, A.; Piperov, S.; Rodozov, M.; Sultanov, G.; Vutova, M.; Dimitrov, A.; Glushkov, I.; Hadjiiska, R.; Kozhuharov, V.; Litov, L.; Pavlov, B.; Petkov, P.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Du, R.; Jiang, C. H.; Liang, D.; Liang, S.; Plestina, R.; Tao, J.; Wang, X.; Wang, Z.; Asawatangtrakuldee, C.; Ban, Y.; Guo, Y.; Li, Q.; Li, W.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Zhang, L.; Zou, W.; Avila, C.; Sierra, L. F.; Florez, C.; Gomez, J. P.; Gomez Moreno, B.; Sanabria, J. C.; Godinovic, N.; Lelas, D.; Polic, D.; Puljak, I.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Kadija, K.; Luetic, J.; Mekterovic, D.; Sudic, L.; Attikis, A.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Bodlak, M.; Finger, M.; Finger, M.; Assran, Y.; Ellithi Kamel, A.; Mahmoud, M. A.; Radi, A.; Kadastik, M.; Murumaa, M.; Raidal, M.; Tiko, A.; Eerola, P.; Fedi, G.; Voutilainen, M.; Härkönen, J.; Karimäki, V.; Kinnunen, R.; Kortelainen, M. J.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Mäenpää, T.; Peltola, T.; Tuominen, E.; Tuominiemi, J.; Tuovinen, E.; Wendland, L.; Tuuva, T.; Besancon, M.; Couderc, F.; Dejardin, M.; Denegri, D.; Fabbro, B.; Faure, J. L.; Favaro, C.; Ferri, F.; Ganjour, S.; Givernaud, A.; Gras, P.; Hamel de Monchenault, G.; Jarry, P.; Locci, E.; Malcles, J.; Rander, J.; Rosowsky, A.; Titov, M.; Baffioni, S.; Beaudette, F.; Busson, P.; Charlot, C.; Dahms, T.; Dalchenko, M.; Dobrzynski, L.; Filipovic, N.; Florent, A.; Granier de Cassagnac, R.; Mastrolorenzo, L.; Miné, P.; Mironov, C.; Naranjo, I. N.; Nguyen, M.; Ochando, C.; Paganini, P.; Salerno, R.; Sauvan, J. B.; Sirois, Y.; Veelken, C.; Yilmaz, Y.; Zabi, A.; Agram, J.-L.; Andrea, J.; Aubin, A.; Bloch, D.; Brom, J.-M.; Chabert, E. C.; Collard, C.; Conte, E.; Fontaine, J.-C.; Gelé, D.; Goerlach, U.; Goetzmann, C.; Le Bihan, A.-C.; Van Hove, P.; Gadrat, S.; Beauceron, S.; Beaupere, N.; Boudoul, G.; Brochet, S.; Carrillo Montoya, C. A.; Chasserat, J.; Chierici, R.; Contardo, D.; Depasse, P.; El Mamouni, H.; Fan, J.; Fay, J.; Gascon, S.; Gouzevitch, M.; Ille, B.; Kurca, T.; Lethuillier, M.; Mirabito, L.; Perries, S.; Ruiz Alvarez, J. D.; Sabes, D.; Sgandurra, L.; Sordini, V.; Vander Donckt, M.; Verdier, P.; Viret, S.; Xiao, H.; Bagaturia, I.; Autermann, C.; Beranek, S.; Bontenackels, M.; Edelhoff, M.; Feld, L.; Hindrichs, O.; Klein, K.; Ostapchuk, A.; Perieanu, A.; Raupach, F.; Sammet, J.; Schael, S.; Weber, H.; Wittmer, B.; Zhukov, V.; Ata, M.; Dietz-Laursonn, E.; Duchardt, D.; Erdmann, M.; Fischer, R.; Güth, A.; Hebbeker, T.; Heidemann, C.; Hoepfner, K.; Klingebiel, D.; Knutzen, S.; Kreuzer, P.; Merschmeyer, M.; Meyer, A.; Olschewski, M.; Padeken, K.; Papacz, P.; Reithler, H.; Schmitz, S. A.; Sonnenschein, L.; Teyssier, D.; Thüer, S.; Weber, M.; Cherepanov, V.; Erdogan, Y.; Flügge, G.; Geenen, H.; Geisler, M.; Haj Ahmad, W.; Hoehle, F.; Kargoll, B.; Kress, T.; Kuessel, Y.; Lingemann, J.; Nowack, A.; Nugent, I. M.; Perchalla, L.; Pooth, O.; Stahl, A.; Asin, I.; Bartosik, N.; Behr, J.; Behrenhoff, W.; Behrens, U.; Bell, A. J.; Bergholz, M.; Bethani, A.; Borras, K.; Burgmeier, A.; Cakir, A.; Calligaris, L.; Campbell, A.; Choudhury, S.; Costanza, F.; Diez Pardos, C.; Dooling, S.; Dorland, T.; Eckerlin, G.; Eckstein, D.; Eichhorn, T.; Flucke, G.; Garay Garcia, J.; Geiser, A.; Gunnellini, P.; Hauk, J.; Hempel, M.; Horton, D.; Jung, H.; Kalogeropoulos, A.; Kasemann, M.; Katsas, P.; Kieseler, J.; Kleinwort, C.; Krücker, D.; Lange, W.; Leonard, J.; Lipka, K.; Lobanov, A.; Lohmann, W.; Lutz, B.; Mankel, R.; Marfin, I.; Melzer-Pellmann, I.-A.; Meyer, A. B.; Mittag, G.; Mnich, J.; Mussgiller, A.; Naumann-Emme, S.; Nayak, A.; Novgorodova, O.; Nowak, F.; Ntomari, E.; Perrey, H.; Pitzl, D.; Placakyte, R.; Raspereza, A.; Ribeiro Cipriano, P. M.; Ron, E.; Sahin, M. Ö.; Salfeld-Nebgen, J.; Saxena, P.; Schmidt, R.; Schoerner-Sadenius, T.; Schröder, M.; Seitz, C.; Spannagel, S.; Vargas Trevino, A. D. R.; Walsh, R.; Wissing, C.; Aldaya Martin, M.; Blobel, V.; Centis Vignali, M.; Draeger, A. R.; Erfle, J.; Garutti, E.; Goebel, K.; Görner, M.; Haller, J.; Hoffmann, M.; Höing, R. S.; Kirschenmann, H.; Klanner, R.; Kogler, R.; Lange, J.; Lapsien, T.; Lenz, T.; Marchesini, I.; Ott, J.; Peiffer, T.; Pietsch, N.; Poehlsen, J.; Rathjens, D.; Sander, C.; Schettler, H.; Schleper, P.; Schlieckau, E.; Schmidt, A.; Seidel, M.; Sola, V.; Stadie, H.; Steinbrück, G.; Troendle, D.; Usai, E.; Vanelderen, L.; Barth, C.; Baus, C.; Berger, J.; Böser, C.; Butz, E.; Chwalek, T.; De Boer, W.; Descroix, A.; Dierlamm, A.; Feindt, M.; Frensch, F.; Giffels, M.; Hartmann, F.; Hauth, T.; Husemann, U.; Katkov, I.; Kornmayer, A.; Kuznetsova, E.; Lobelle Pardo, P.; Mozer, M. U.; Müller, Th.; Nürnberg, A.; Quast, G.; Rabbertz, K.; Ratnikov, F.; Röcker, S.; Simonis, H. J.; Stober, F. M.; Ulrich, R.; Wagner-Kuhr, J.; Wayand, S.; Weiler, T.; Wolf, R.; Anagnostou, G.; Daskalakis, G.; Geralis, T.; Giakoumopoulou, V. A.; Kyriakis, A.; Loukas, D.; Markou, A.; Markou, C.; Psallidas, A.; Topsis-Giotis, I.; Agapitos, A.; Panagiotou, A.; Saoulidou, N.; Stiliaris, E.; Aslanoglou, X.; Evangelou, I.; Flouris, G.; Foudas, C.; Kokkas, P.; Manthos, N.; Papadopoulos, I.; Paradas, E.; Bencze, G.; Hajdu, C.; Hidas, P.; Horvath, D.; Sikler, F.; Veszpremi, V.; Vesztergombi, G.; Zsigmond, A. J.; Beni, N.; Czellar, S.; Karancsi, J.; Molnar, J.; Palinkas, J.; Szillasi, Z.; Raics, P.; Trocsanyi, Z. L.; Ujvari, B.; Swain, S. K.; Beri, S. B.; Bhatnagar, V.; Dhingra, N.; Gupta, R.; Bhawandeep, U.; Kalsi, A. K.; Kaur, M.; Mittal, M.; Nishu, N.; Singh, J. B.; Kumar, Ashok; Kumar, Arun; Ahuja, S.; Bhardwaj, A.; Choudhary, B. C.; Kumar, A.; Malhotra, S.; Naimuddin, M.; Ranjan, K.; Sharma, V.; Banerjee, S.; Bhattacharya, S.; Chatterjee, K.; Dutta, S.; Gomber, B.; Jain, Sa.; Jain, Sh.; Khurana, R.; Modak, A.; Mukherjee, S.; Roy, D.; Sarkar, S.; Sharan, M.; Abdulsalam, A.; Dutta, D.; Kailas, S.; Kumar, V.; Mohanty, A. K.; Pant, L. M.; Shukla, P.; Topkar, A.; Aziz, T.; Banerjee, S.; Bhowmik, S.; Chatterjee, R. M.; Dewanjee, R. K.; Dugad, S.; Ganguly, S.; Ghosh, S.; Guchait, M.; Gurtu, A.; Kole, G.; Kumar, S.; Maity, M.; Majumder, G.; Mazumdar, K.; Mohanty, G. B.; Parida, B.; Sudhakar, K.; Wickramage, N.; Bakhshiansohi, H.; Behnamian, H.; Etesami, S. M.; Fahim, A.; Goldouzian, R.; Jafari, A.; Khakzad, M.; Najafabadi, M.; Naseri, M.; Paktinat Mehdiabadi, S.; Safarzadeh, B.; Zeinali, M.; Felcini, M.; Grunewald, M.; Abbrescia, M.; Barbone, L.; Calabria, C.; Chhibra, S. S.; Colaleo, A.; Creanza, D.; De Filippis, N.; De Palma, M.; Fiore, L.; Iaselli, G.; Maggi, G.; Maggi, M.; My, S.; Nuzzo, S.; Pompili, A.; Pugliese, G.; Radogna, R.; Selvaggi, G.; Silvestris, L.; Singh, G.; Venditti, R.; Verwilligen, P.; Zito, G.; Abbiendi, G.; Benvenuti, A. C.; Bonacorsi, D.; Braibant-Giacomelli, S.; Brigliadori, L.; Campanini, R.; Capiluppi, P.; Castro, A.; Cavallo, F. R.; Codispoti, G.; Cuffiani, M.; Dallavalle, G. M.; Fabbri, F.; Fanfani, A.; Fasanella, D.; Giacomelli, P.; Grandi, C.; Guiducci, L.; Marcellini, S.; Masetti, G.; Montanari, A.; Navarria, F. L.; Perrotta, A.; Primavera, F.; Rossi, A. M.; Rovelli, T.; Siroli, G. P.; Tosi, N.; Travaglini, R.; Albergo, S.; Cappello, G.; Chiorboli, M.; Costa, S.; Giordano, F.; Potenza, R.; Tricomi, A.; Tuve, C.; Barbagli, G.; Ciulli, V.; Civinini, C.; D'Alessandro, R.; Focardi, E.; Gallo, E.; Gonzi, S.; Gori, V.; Lenzi, P.; Meschini, M.; Paoletti, S.; Sguazzoni, G.; Tropiano, A.; Benussi, L.; Bianco, S.; Fabbri, F.; Piccolo, D.; Ferro, F.; Lo Vetere, M.; Robutti, E.; Tosi, S.; Dinardo, M. E.; Fiorendi, S.; Gennai, S.; Gerosa, R.; Ghezzi, A.; Govoni, P.; Lucchini, M. T.; Malvezzi, S.; Manzoni, R. A.; Martelli, A.; Marzocchi, B.; Menasce, D.; Moroni, L.; Paganoni, M.; Pedrini, D.; Ragazzi, S.; Redaelli, N.; Tabarelli de Fatis, T.; Buontempo, S.; Cavallo, N.; Di Guida, S.; Fabozzi, F.; Iorio, A. O. M.; Lista, L.; Meola, S.; Merola, M.; Paolucci, P.; Azzi, P.; Bacchetta, N.; Bisello, D.; Branca, A.; Carlin, R.; Checchia, P.; Dall'Osso, M.; Dorigo, T.; Galanti, M.; Gasparini, F.; Gasparini, U.; Giubilato, P.; Gozzelino, A.; Kanishchev, K.; Lacaprara, S.; Margoni, M.; Meneguzzo, A. T.; Passaseo, M.; Pazzini, J.; Pegoraro, M.; Pozzobon, N.; Ronchese, P.; Torassa, E.; Tosi, M.; Zotto, P.; Zucchetta, A.; Zumerle, G.; Gabusi, M.; Ratti, S. P.; Riccardi, C.; Salvini, P.; Vitulo, P.; Biasini, M.; Bilei, G. M.; Ciangottini, D.; Fanò, L.; Lariccia, P.; Mantovani, G.; Menichelli, M.; Romeo, F.; Saha, A.; Santocchia, A.; Spiezia, A.; Androsov, K.; Azzurri, P.; Bagliesi, G.; Bernardini, J.; Boccali, T.; Broccolo, G.; Castaldi, R.; Ciocci, M. A.; Dell'Orso, R.; Donato, S.; Fiori, F.; Foà, L.; Giassi, A.; Grippo, M. T.; Ligabue, F.; Lomtadze, T.; Martini, L.; Messineo, A.; Moon, C. S.; Palla, F.; Rizzi, A.; Savoy-Navarro, A.; Serban, A. T.; Spagnolo, P.; Squillacioti, P.; Tenchini, R.; Tonelli, G.; Venturi, A.; Verdini, P. G.; Vernieri, C.; Barone, L.; Cavallari, F.; Del Re, D.; Diemoz, M.; Grassi, M.; Jorda, C.; Longo, E.; Margaroli, F.; Meridiani, P.; Micheli, F.; Nourbakhsh, S.; Organtini, G.; Paramatti, R.; Rahatlou, S.; Rovelli, C.; Santanastasio, F.; Soffi, L.; Traczyk, P.; Amapane, N.; Arcidiacono, R.; Argiro, S.; Arneodo, M.; Bellan, R.; Biino, C.; Cartiglia, N.; Casasso, S.; Costa, M.; Degano, A.; Demaria, N.; Finco, L.; Mariotti, C.; Maselli, S.; Migliore, E.; Monaco, V.; Musich, M.; Obertino, M. M.; Ortona, G.; Pacher, L.; Pastrone, N.; Pelliccioni, M.; Pinna Angioni, G. L.; Potenza, A.; Romero, A.; Ruspa, M.; Sacchi, R.; Solano, A.; Staiano, A.; Tamponi, U.; Belforte, S.; Candelise, V.; Casarsa, M.; Cossutti, F.; Della Ricca, G.; Gobbo, B.; La Licata, C.; Marone, M.; Montanino, D.; Schizzi, A.; Umer, T.; Zanetti, A.; Chang, S.; Kropivnitskaya, A.; Nam, S. K.; Kim, D. H.; Kim, G. N.; Kim, M. S.; Kong, D. J.; Lee, S.; Oh, Y. D.; Park, H.; Sakharov, A.; Son, D. C.; Kim, T. J.; Kim, J. Y.; Song, S.; Choi, S.; Gyun, D.; Hong, B.; Jo, M.; Kim, H.; Kim, Y.; Lee, B.; Lee, K. S.; Park, S. K.; Roh, Y.; Choi, M.; Kim, J. H.; Park, I. C.; Park, S.; Ryu, G.; Ryu, M. S.; Choi, Y.; Choi, Y. K.; Goh, J.; Kim, D.; Kwon, E.; Lee, J.; Seo, H.; Yu, I.; Juodagalvis, A.; Komaragiri, J. R.; Ali, M. A. B. Md; Castilla-Valdez, H.; De La Cruz-Burelo, E.; Heredia-de La Cruz, I.; Lopez-Fernandez, R.; Sanchez-Hernandez, A.; Carrillo Moreno, S.; Vazquez Valencia, F.; Pedraza, I.; Salazar Ibarguen, H. A.; Casimiro Linares, E.; Morelos Pineda, A.; Krofcheck, D.; Butler, P. H.; Reucroft, S.; Ahmad, A.; Ahmad, M.; Hassan, Q.; Hoorani, H. R.; Khalid, S.; Khan, W. A.; Khurshid, T.; Shah, M. A.; Shoaib, M.; Bialkowska, H.; Bluj, M.; Boimska, B.; Frueboes, T.; Górski, M.; Kazana, M.; Nawrocki, K.; Romanowska-Rybinska, K.; Szleper, M.; Zalewski, P.; Brona, G.; Bunkowski, K.; Cwiok, M.; Dominik, W.; Doroba, K.; Kalinowski, A.; Konecki, M.; Krolikowski, J.; Misiura, M.; Olszewski, M.; Wolszczak, W.; Bargassa, P.; Beirão Da Cruz E Silva, C.; Faccioli, P.; Ferreira Parracho, P. G.; Gallinaro, M.; Nguyen, F.; Rodrigues Antunes, J.; Seixas, J.; Varela, J.; Vischia, P.; Afanasiev, S.; Golutvin, I.; Karjavin, V.; Konoplyanikov, V.; Korenkov, V.; Kozlov, G.; Lanev, A.; Malakhov, A.; Matveev, V.; Mitsyn, V. V.; Moisenz, P.; Palichik, V.; Perelygin, V.; Shmatov, S.; Skatchkov, N.; Smirnov, V.; Tikhonenko, E.; Zarubin, A.; Golovtsov, V.; Ivanov, Y.; Kim, V.; Levchenko, P.; Murzin, V.; Oreshkin, V.; Smirnov, I.; Sulimov, V.; Uvarov, L.; Vavilov, S.; Vorobyev, A.; Vorobyev, An.; Andreev, Yu.; Dermenev, A.; Gninenko, S.; Golubev, N.; Kirsanov, M.; Krasnikov, N.; Pashenkov, A.; Tlisov, D.; Toropin, A.; Epshteyn, V.; Gavrilov, V.; Lychkovskaya, N.; Popov, V.; Safronov, G.; Semenov, S.; Spiridonov, A.; Stolin, V.; Vlasov, E.; Zhokin, A.; Andreev, V.; Azarkin, M.; Dremin, I.; Kirakosyan, M.; Leonidov, A.; Mesyats, G.; Rusakov, S. V.; Vinogradov, A.; Belyaev, A.; Boos, E.; Ershov, A.; Gribushin, A.; Kaminskiy, A.; Kodolova, O.; Korotkikh, V.; Lokhtin, I.; Obraztsov, S.; Petrushanko, S.; Savrin, V.; Snigirev, A.; Vardanyan, I.; Azhgirey, I.; Bayshev, I.; Bitioukov, S.; Kachanov, V.; Kalinin, A.; Konstantinov, D.; Krychkine, V.; Petrov, V.; Ryutin, R.; Sobol, A.; Tourtchanovitch, L.; Troshin, S.; Tyurin, N.; Uzunian, A.; Volkov, A.; Adzic, P.; Ekmedzic, M.; Milosevic, J.; Rekovic, V.; Alcaraz Maestre, J.; Battilana, C.; Calvo, E.; Cerrada, M.; Chamizo Llatas, M.; Colino, N.; De La Cruz, B.; Delgado Peris, A.; Domínguez Vázquez, D.; Escalante Del Valle, A.; Fernandez Bedoya, C.; Fernández Ramos, J. P.; Flix, J.; Fouz, M. C.; Garcia-Abia, P.; Gonzalez Lopez, O.; Goy Lopez, S.; Hernandez, J. M.; Josa, M. I.; Merino, G.; Navarro De Martino, E.; Pérez-Calero Yzquierdo, A.; Puerta Pelayo, J.; Quintario Olmeda, A.; Redondo, I.; Romero, L.; Soares, M. S.; Albajar, C.; de Trocóniz, J. F.; Missiroli, M.; Moran, D.; Brun, H.; Cuevas, J.; Fernandez Menendez, J.; Folgueras, S.; Gonzalez Caballero, I.; Lloret Iglesias, L.; Brochero Cifuentes, J. A.; Cabrillo, I. J.; Calderon, A.; Duarte Campderros, J.; Fernandez, M.; Gomez, G.; Graziano, A.; Lopez Virto, A.; Marco, J.; Marco, R.; Martinez Rivero, C.; Matorras, F.; Munoz Sanchez, F. J.; Piedra Gomez, J.; Rodrigo, T.; Rodríguez-Marrero, A. Y.; Ruiz-Jimeno, A.; Scodellaro, L.; Vila, I.; Vilar Cortabitarte, R.; Abbaneo, D.; Auffray, E.; Auzinger, G.; Bachtis, M.; Baillon, P.; Ball, A. H.; Barney, D.; Benaglia, A.; Bendavid, J.; Benhabib, L.; Benitez, J. F.; Bernet, C.; Bianchi, G.; Bloch, P.; Bocci, A.; Bonato, A.; Bondu, O.; Botta, C.; Breuker, H.; Camporesi, T.; Cerminara, G.; Colafranceschi, S.; D'Alfonso, M.; d'Enterria, D.; Dabrowski, A.; David, A.; De Guio, F.; De Roeck, A.; De Visscher, S.; Dobson, M.; Dordevic, M.; Dupont-Sagorin, N.; Elliott-Peisert, A.; Eugster, J.; Franzoni, G.; Funk, W.; Gigi, D.; Gill, K.; Giordano, D.; Girone, M.; Glege, F.; Guida, R.; Gundacker, S.; Guthoff, M.; Hammer, J.; Hansen, M.; Harris, P.; Hegeman, J.; Innocente, V.; Janot, P.; Kousouris, K.; Krajczar, K.; Lecoq, P.; Lourenço, C.; Magini, N.; Malgeri, L.; Mannelli, M.; Marrouche, J.; Masetti, L.; Meijers, F.; Mersi, S.; Meschi, E.; Moortgat, F.; Morovic, S.; Mulders, M.; Musella, P.; Orsini, L.; Pape, L.; Perez, E.; Perrozzi, L.; Petrilli, A.; Petrucciani, G.; Pfeiffer, A.; Pierini, M.; Pimiä, M.; Piparo, D.; Plagge, M.; Racz, A.; Rolandi, G.; Rovere, M.; Sakulin, H.; Schäfer, C.; Schwick, C.; Sharma, A.; Siegrist, P.; Silva, P.; Simon, M.; Sphicas, P.; Spiga, D.; Steggemann, J.; Stieger, B.; Stoye, M.; Treille, D.; Tsirou, A.; Veres, G. I.; Vlimant, J. R.; Wardle, N.; Wöhri, H. K.; Wollny, H.; Zeuner, W. D.; Bertl, W.; Deiters, K.; Erdmann, W.; Horisberger, R.; Ingram, Q.; Kaestli, H. C.; König, S.; Kotlinski, D.; Langenegger, U.; Renker, D.; Rohe, T.; Bachmair, F.; Bäni, L.; Bianchini, L.; Bortignon, P.; Buchmann, M. A.; Casal, B.; Chanon, N.; Deisher, A.; Dissertori, G.; Dittmar, M.; Donegà, M.; Dünser, M.; Eller, P.; Grab, C.; Hits, D.; Lustermann, W.; Mangano, B.; Marini, A. C.; Martinez Ruiz del Arbol, P.; Meister, D.; Mohr, N.; Nägeli, C.; Nessi-Tedaldi, F.; Pandolfi, F.; Pauss, F.; Peruzzi, M.; Quittnat, M.; Rebane, L.; Rossini, M.; Starodumov, A.; Takahashi, M.; Theofilatos, K.; Wallny, R.; Weber, H. A.; Amsler, C.; Canelli, M. F.; Chiochia, V.; De Cosa, A.; Hinzmann, A.; Hreus, T.; Kilminster, B.; Millan Mejias, B.; Ngadiuba, J.; Robmann, P.; Ronga, F. J.; Taroni, S.; Verzetti, M.; Yang, Y.; Cardaci, M.; Chen, K. H.; Ferro, C.; Kuo, C. M.; Lin, W.; Lu, Y. J.; Volpe, R.; Yu, S. S.; Chang, P.; Chang, Y. 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D.; Symonds, P.; Teodorescu, L.; Turner, M.; Dittmann, J.; Hatakeyama, K.; Kasmi, A.; Liu, H.; Scarborough, T.; Charaf, O.; Cooper, S. I.; Henderson, C.; Rumerio, P.; Avetisyan, A.; Bose, T.; Fantasia, C.; Heister, A.; Lawson, P.; Richardson, C.; Rohlf, J.; Sperka, D.; St. John, J.; Sulak, L.; Alimena, J.; Berry, E.; Bhattacharya, S.; Christopher, G.; Cutts, D.; Demiragli, Z.; Ferapontov, A.; Garabedian, A.; Heintz, U.; Kukartsev, G.; Laird, E.; Landsberg, G.; Luk, M.; Narain, M.; Segala, M.; Sinthuprasith, T.; Speer, T.; Swanson, J.; Breedon, R.; Breto, G.; Calderon De La Barca Sanchez, M.; Chauhan, S.; Chertok, M.; Conway, J.; Conway, R.; Cox, P. T.; Erbacher, R.; Gardner, M.; Ko, W.; Lander, R.; Miceli, T.; Mulhearn, M.; Pellett, D.; Pilot, J.; Ricci-Tam, F.; Searle, M.; Shalhout, S.; Smith, J.; Squires, M.; Stolp, D.; Tripathi, M.; Wilbur, S.; Yohay, R.; Cousins, R.; Everaerts, P.; Farrell, C.; Hauser, J.; Ignatenko, M.; Rakness, G.; Takasugi, E.; Valuev, V.; Weber, M.; Babb, J.; Burt, K.; Clare, R.; Ellison, J.; Gary, J. W.; Hanson, G.; Heilman, J.; Ivova Rikova, M.; Jandir, P.; Kennedy, E.; Lacroix, F.; Liu, H.; Long, O. R.; Luthra, A.; Malberti, M.; Nguyen, H.; Olmedo Negrete, M.; Shrinivas, A.; Sumowidagdo, S.; Wimpenny, S.; Andrews, W.; Branson, J. G.; Cerati, G. B.; Cittolin, S.; D'Agnolo, R. T.; Evans, D.; Holzner, A.; Kelley, R.; Klein, D.; Lebourgeois, M.; Letts, J.; Macneill, I.; Olivito, D.; Padhi, S.; Palmer, C.; Pieri, M.; Sani, M.; Sharma, V.; Simon, S.; Sudano, E.; Tadel, M.; Tu, Y.; Vartak, A.; Welke, C.; Würthwein, F.; Yagil, A.; Yoo, J.; Barge, D.; Bradmiller-Feld, J.; Campagnari, C.; Danielson, T.; Dishaw, A.; Flowers, K.; Franco Sevilla, M.; Geffert, P.; George, C.; Golf, F.; Gouskos, L.; Incandela, J.; Justus, C.; Mccoll, N.; Richman, J.; Stuart, D.; To, W.; West, C.; Apresyan, A.; Bornheim, A.; Bunn, J.; Chen, Y.; Di Marco, E.; Duarte, J.; Mott, A.; Newman, H. B.; Pena, C.; Rogan, C.; Spiropulu, M.; Timciuc, V.; Wilkinson, R.; Xie, S.; Zhu, R. Y.; Azzolini, V.; Calamba, A.; Ferguson, T.; Iiyama, Y.; Paulini, M.; Russ, J.; Vogel, H.; Vorobiev, I.; Cumalat, J. P.; Ford, W. T.; Gaz, A.; Luiggi Lopez, E.; Nauenberg, U.; Smith, J. G.; Stenson, K.; Ulmer, K. A.; Wagner, S. R.; Alexander, J.; Chatterjee, A.; Chu, J.; Dittmer, S.; Eggert, N.; Mirman, N.; Nicolas Kaufman, G.; Patterson, J. R.; Ryd, A.; Salvati, E.; Skinnari, L.; Sun, W.; Teo, W. D.; Thom, J.; Thompson, J.; Tucker, J.; Weng, Y.; Winstrom, L.; Wittich, P.; Winn, D.; Abdullin, S.; Albrow, M.; Anderson, J.; Apollinari, G.; Bauerdick, L. A. T.; Beretvas, A.; Berryhill, J.; Bhat, P. C.; Burkett, K.; Butler, J. N.; Cheung, H. W. K.; Chlebana, F.; Cihangir, S.; Elvira, V. D.; Fisk, I.; Freeman, J.; Gao, Y.; Gottschalk, E.; Gray, L.; Green, D.; Grünendahl, S.; Gutsche, O.; Hanlon, J.; Hare, D.; Harris, R. M.; Hirschauer, J.; Hooberman, B.; Jindariani, S.; Johnson, M.; Joshi, U.; Kaadze, K.; Klima, B.; Kreis, B.; Kwan, S.; Linacre, J.; Lincoln, D.; Lipton, R.; Liu, T.; Lykken, J.; Maeshima, K.; Marraffino, J. M.; Martinez Outschoorn, V. I.; Maruyama, S.; Mason, D.; McBride, P.; Mishra, K.; Mrenna, S.; Musienko, Y.; Nahn, S.; Newman-Holmes, C.; O'Dell, V.; Prokofyev, O.; Sexton-Kennedy, E.; Sharma, S.; Soha, A.; Spalding, W. J.; Spiegel, L.; Taylor, L.; Tkaczyk, S.; Tran, N. V.; Uplegger, L.; Vaandering, E. W.; Vidal, R.; Whitbeck, A.; Whitmore, J.; Yang, F.; Acosta, D.; Avery, P.; Bourilkov, D.; Carver, M.; Cheng, T.; Curry, D.; Das, S.; De Gruttola, M.; Di Giovanni, G. P.; Field, R. D.; Fisher, M.; Furic, I. K.; Hugon, J.; Konigsberg, J.; Korytov, A.; Kypreos, T.; Low, J. F.; Matchev, K.; Milenovic, P.; Mitselmakher, G.; Muniz, L.; Rinkevicius, A.; Shchutska, L.; Skhirtladze, N.; Snowball, M.; Yelton, J.; Zakaria, M.; Hewamanage, S.; Linn, S.; Markowitz, P.; Martinez, G.; Rodriguez, J. L.; Adams, T.; Askew, A.; Bochenek, J.; Diamond, B.; Haas, J.; Hagopian, S.; Hagopian, V.; Johnson, K. F.; Prosper, H.; Veeraraghavan, V.; Weinberg, M.; Baarmand, M. M.; Hohlmann, M.; Kalakhety, H.; Yumiceva, F.; Adams, M. R.; Apanasevich, L.; Bazterra, V. E.; Berry, D.; Betts, R. R.; Bucinskaite, I.; Cavanaugh, R.; Evdokimov, O.; Gauthier, L.; Gerber, C. E.; Hofman, D. J.; Khalatyan, S.; Kurt, P.; Moon, D. H.; O'Brien, C.; Silkworth, C.; Turner, P.; Varelas, N.; Albayrak, E. A.; Bilki, B.; Clarida, W.; Dilsiz, K.; Duru, F.; Haytmyradov, M.; Merlo, J.-P.; Mermerkaya, H.; Mestvirishvili, A.; Moeller, A.; Nachtman, J.; Ogul, H.; Onel, Y.; Ozok, F.; Penzo, A.; Rahmat, R.; Sen, S.; Tan, P.; Tiras, E.; Wetzel, J.; Yetkin, T.; Yi, K.; Barnett, B. A.; Blumenfeld, B.; Bolognesi, S.; Fehling, D.; Gritsan, A. V.; Maksimovic, P.; Martin, C.; Swartz, M.; Baringer, P.; Bean, A.; Benelli, G.; Bruner, C.; Gray, J.; Kenny, R. P.; Malek, M.; Murray, M.; Noonan, D.; Sanders, S.; Sekaric, J.; Stringer, R.; Wang, Q.; Wood, J. S.; Barfuss, A. F.; Chakaberia, I.; Ivanov, A.; Khalil, S.; Makouski, M.; Maravin, Y.; Saini, L. K.; Shrestha, S.; Svintradze, I.; Gronberg, J.; Lange, D.; Rebassoo, F.; Wright, D.; Baden, A.; Belloni, A.; Calvert, B.; Eno, S. C.; Gomez, J. A.; Hadley, N. J.; Kellogg, R. G.; Kolberg, T.; Lu, Y.; Marionneau, M.; Mignerey, A. C.; Pedro, K.; Skuja, A.; Tonjes, M. B.; Tonwar, S. C.; Apyan, A.; Barbieri, R.; Bauer, G.; Busza, W.; Cali, I. A.; Chan, M.; Di Matteo, L.; Dutta, V.; Gomez Ceballos, G.; Goncharov, M.; Gulhan, D.; Klute, M.; Lai, Y. S.; Lee, Y.-J.; Levin, A.; Luckey, P. D.; Ma, T.; Paus, C.; Ralph, D.; Roland, C.; Roland, G.; Stephans, G. S. F.; Stöckli, F.; Sumorok, K.; Velicanu, D.; Veverka, J.; Wyslouch, B.; Yang, M.; Zanetti, M.; Zhukova, V.; Dahmes, B.; Gude, A.; Kao, S. C.; Klapoetke, K.; Kubota, Y.; Mans, J.; Pastika, N.; Rusack, R.; Singovsky, A.; Tambe, N.; Turkewitz, J.; Acosta, J. G.; Oliveros, S.; Avdeeva, E.; Bloom, K.; Bose, S.; Claes, D. R.; Dominguez, A.; Gonzalez Suarez, R.; Keller, J.; Knowlton, D.; Kravchenko, I.; Lazo-Flores, J.; Malik, S.; Meier, F.; Snow, G. R.; Dolen, J.; Godshalk, A.; Iashvili, I.; Kharchilava, A.; Kumar, A.; Rappoccio, S.; Alverson, G.; Barberis, E.; Baumgartel, D.; Chasco, M.; Haley, J.; Massironi, A.; Morse, D. M.; Nash, D.; Orimoto, T.; Trocino, D.; Wang, R.-J.; Wood, D.; Zhang, J.; Hahn, K. A.; Kubik, A.; Mucia, N.; Odell, N.; Pollack, B.; Pozdnyakov, A.; Schmitt, M.; Stoynev, S.; Sung, K.; Velasco, M.; Won, S.; Brinkerhoff, A.; Chan, K. M.; Drozdetskiy, A.; Hildreth, M.; Jessop, C.; Karmgard, D. J.; Kellams, N.; Lannon, K.; Luo, W.; Lynch, S.; Marinelli, N.; Pearson, T.; Planer, M.; Ruchti, R.; Valls, N.; Wayne, M.; Wolf, M.; Woodard, A.; Antonelli, L.; Brinson, J.; Bylsma, B.; Durkin, L. S.; Flowers, S.; Hill, C.; Hughes, R.; Kotov, K.; Ling, T. Y.; Puigh, D.; Rodenburg, M.; Smith, G.; Vuosalo, C.; Winer, B. L.; Wolfe, H.; Wulsin, H. W.; Driga, O.; Elmer, P.; Hebda, P.; Hunt, A.; Koay, S. A.; Lujan, P.; Marlow, D.; Medvedeva, T.; Mooney, M.; Olsen, J.; Piroué, P.; Quan, X.; Saka, H.; Stickland, D.; Tully, C.; Werner, J. S.; Zenz, S. C.; Zuranski, A.; Brownson, E.; Mendez, H.; Ramirez Vargas, J. E.; Alagoz, E.; Barnes, V. E.; Benedetti, D.; Bolla, G.; Bortoletto, D.; De Mattia, M.; Hu, Z.; Jha, M. K.; Jones, M.; Jung, K.; Kress, M.; Leonardo, N.; Lopes Pegna, D.; Maroussov, V.; Merkel, P.; Miller, D. H.; Neumeister, N.; Radburn-Smith, B. C.; Shi, X.; Shipsey, I.; Silvers, D.; Svyatkovskiy, A.; Wang, F.; Xie, W.; Xu, L.; Yoo, H. D.; Zablocki, J.; Zheng, Y.; Parashar, N.; Stupak, J.; Adair, A.; Akgun, B.; Ecklund, K. M.; Geurts, F. J. M.; Li, W.; Michlin, B.; Padley, B. P.; Redjimi, R.; Roberts, J.; Zabel, J.; Betchart, B.; Bodek, A.; Covarelli, R.; de Barbaro, P.; Demina, R.; Eshaq, Y.; Ferbel, T.; Garcia-Bellido, A.; Goldenzweig, P.; Han, J.; Harel, A.; Khukhunaishvili, A.; Petrillo, G.; Vishnevskiy, D.; Ciesielski, R.; Demortier, L.; Goulianos, K.; Lungu, G.; Mesropian, C.; Arora, S.; Barker, A.; Chou, J. P.; Contreras-Campana, C.; Contreras-Campana, E.; Duggan, D.; Ferencek, D.; Gershtein, Y.; Gray, R.; Halkiadakis, E.; Hidas, D.; Lath, A.; Panwalkar, S.; Park, M.; Patel, R.; Salur, S.; Schnetzer, S.; Somalwar, S.; Stone, R.; Thomas, S.; Thomassen, P.; Walker, M.; Rose, K.; Spanier, S.; York, A.; Bouhali, O.; Eusebi, R.; Flanagan, W.; Gilmore, J.; Kamon, T.; Khotilovich, V.; Krutelyov, V.; Montalvo, R.; Osipenkov, I.; Pakhotin, Y.; Perloff, A.; Roe, J.; Rose, A.; Safonov, A.; Sakuma, T.; Suarez, I.; Tatarinov, A.; Akchurin, N.; Cowden, C.; Damgov, J.; Dragoiu, C.; Dudero, P. R.; Faulkner, J.; Kovitanggoon, K.; Kunori, S.; Lee, S. W.; Libeiro, T.; Volobouev, I.; Appelt, E.; Delannoy, A. G.; Greene, S.; Gurrola, A.; Johns, W.; Maguire, C.; Mao, Y.; Melo, A.; Sharma, M.; Sheldon, P.; Snook, B.; Tuo, S.; Velkovska, J.; Arenton, M. W.; Boutle, S.; Cox, B.; Francis, B.; Goodell, J.; Hirosky, R.; Ledovskoy, A.; Li, H.; Lin, C.; Neu, C.; Wood, J.; Harr, R.; Karchin, P. E.; Kottachchi Kankanamge Don, C.; Lamichhane, P.; Sturdy, J.; Belknap, D. A.; Carlsmith, D.; Cepeda, M.; Dasu, S.; Duric, S.; Friis, E.; Hall-Wilton, R.; Herndon, M.; Hervé, A.; Klabbers, P.; Lanaro, A.; Lazaridis, C.; Levine, A.; Loveless, R.; Mohapatra, A.; Ojalvo, I.; Perry, T.; Pierro, G. A.; Polese, G.; Ross, I.; Sarangi, T.; Savin, A.; Smith, W. H.; Woods, N.

2015-03-01

The production of Z bosons is studied in the dimuon and dielectron decay channels in PbPb and pp collisions at TeV, using data collected by the CMS experiment at the LHC. The PbPb data sample corresponds to an integrated luminosity of about 166 μb-1, while the pp data sample collected in 2013 at the same nucleon-nucleon centre-of-mass energy has an integrated luminosity of 5.4 pb-1. The Z boson yield is measured as a function of rapidity, transverse momentum, and collision centrality. The ratio of PbPb to pp yields, scaled by the number of inelastic nucleon-nucleon collisions, is found to be 1.06 ± 0.05 (stat) ± 0.08 (syst) in the dimuon channel and 1.02 ± 0.08 (stat) ± 0.15 (syst) in the dielectron channel, for centrality-integrated Z boson production. This binary collision scaling is seen to hold in the entire kinematic region studied, as expected for a colourless probe that is unaffected by the hot and dense QCD medium produced in heavy ion collisions. [Figure not available: see fulltext.

Integrated preservation and sample clean up procedures for studying water ingestion by recreational swimmers via urinary biomarker determination.

PubMed

Cantú, Ricardo; Shoemaker, Jody A; Kelty, Catherine A; Wymer, Larry J; Behymer, Thomas D; Dufour, Alfred P; Magnuson, Matthew L

2017-08-22

The use of cyanuric acid as a biomarker for ingestion of swimming pool water may lead to quantitative knowledge of the volume of water ingested during swimming, contributing to a better understanding of disease resulting from ingestion of environmental contaminants. When swimming pool water containing chlorinated cyanurates is inadvertently ingested, cyanuric acid is excreted quantitatively within 24 h as a urinary biomarker of ingestion. Because the volume of water ingested can be quantitatively estimated by calculation from the concentration of cyanuric acid in 24 h urine samples, a procedure for preservation, cleanup, and analysis of cyanuric acid was developed to meet the logistical demands of large scale studies. From a practical stand point, urine collected from swimmers cannot be analyzed immediately, given requirements of sample collection, shipping, handling, etc. Thus, to maintain quality control to allow confidence in the results, it is necessary to preserve the samples in a manner that ensures as quantitative analysis as possible. The preservation and clean-up of cyanuric acid in urine is complicated because typical approaches often are incompatible with the keto-enol tautomerization of cyanuric acid, interfering with cyanuric acid sample preparation, chromatography, and detection. Therefore, this paper presents a novel integration of sample preservation, clean-up, chromatography, and detection to determine cyanuric acid in 24 h urine samples. Fortification of urine with cyanuric acid (0.3-3.0 mg/L) demonstrated accuracy (86-93% recovery) and high reproducibility (RSD < 7%). Holding time studies in unpreserved urine suggested sufficient cyanuric acid stability for sample collection procedures, while longer holding times suggested instability of the unpreserved urine. Preserved urine exhibited a loss of around 0.5% after 22 days at refrigerated storage conditions of 4 °C. Published by Elsevier B.V.

Integrated indicators are important metrics of catchment biogeochemical function

NASA Astrophysics Data System (ADS)

Howden, N. J. K.; Birgand, F.; Burt, T.; Worrall, F.

2017-12-01

There are many ways to characterise catchment biogeochemical behaviour, but most rely on sporadic measurements that capture transient, rather than steady-state behaviour and function. This is because the ongoing collection of water samples and flow data can be labour intensive and thus costly both in terms of money and time. We propose that key aspects of catchment biogeochemical function can only be determined by the collation of impacts of water quality and flow integrated over time. In this paper we will illustrate how spot sample data may be useful, but also how the integration of sample data over time begins to elucidate catchment functions that may not be apparent from sparse timeslices of information. We use a number of high-resolution time series of water quality and flow data to illustrate the utility of this approach for different determinands and suggest key priorities for both sampling and analysis in small to medium-sized catchments. Clearly it is impractical for high-frequency measurements to form the basis of a wide-ranging approach, due to the prevalence of infrequent sampling as a regulatory preference across much of the world. In order to make our results relevant to this wider perspective, we also consider how infrequent sampling regimes may be used to derive our preferred integrated metrics, and the uncertainties that will be propagated due to the lower timescales of sampling. We use data from Brittany (France), North Carolina (US) and Plynlimmon (UK) to consider how our results translate to different catchments.

Four studies on effects of environmental factors on the quality of National Atmospheric Deposition Program measurements

USGS Publications Warehouse

Wetherbee, Gregory A.; Latysh, Natalie E.; Lehmann, Christopher M.B.; Rhodes, Mark F.

2011-01-01

Selected aspects of National Atmospheric Deposition Program / National Trends Network (NADP/NTN) protocols are evaluated in four studies. Meteorological conditions have minor impacts on the error in NADP/NTN sampling. Efficiency of frozen precipitation sample collection is lower than for liquid precipitation samples. Variability of NTN measurements is higher for relatively low-intensity deposition of frozen precipitation than for higher-intensity deposition of liquid precipitation. Urbanization of the landscape surrounding NADP/NTN sites is not affecting trends in wet-deposition chemistry data to a measureable degree. Five NADP siting criteria intended to preserve wet-deposition sample integrity have varying degrees of effectiveness. NADP siting criteria for objects within the 90 degrees cones and trees within the 120 degrees cones projected from the collector bucket to sky are important for protecting sample integrity. Tall vegetation, fences, and other objects located within 5 meters of the collectors are related to the frequency of visible sample contamination, indicating the importance of these factors in NADP siting criteria.

The use of FTA cards for preserving unfixed cytological material for high-throughput molecular analysis.

PubMed

Saieg, Mauro Ajaj; Geddie, William R; Boerner, Scott L; Liu, Ni; Tsao, Ming; Zhang, Tong; Kamel-Reid, Suzanne; da Cunha Santos, Gilda

2012-06-25

Novel high-throughput molecular technologies have made the collection and storage of cells and small tissue specimens a critical issue. The FTA card provides an alternative to cryopreservation for biobanking fresh unfixed cells. The current study compared the quality and integrity of the DNA obtained from 2 types of FTA cards (Classic and Elute) using 2 different extraction protocols ("Classic" and "Elute") and assessed the feasibility of performing multiplex mutational screening using fine-needle aspiration (FNA) biopsy samples. Residual material from 42 FNA biopsies was collected in the cards (21 Classic and 21 Elute cards). DNA was extracted using the Classic protocol for Classic cards and both protocols for Elute cards. Polymerase chain reaction for p53 (1.5 kilobase) and CARD11 (500 base pair) was performed to assess DNA integrity. Successful p53 amplification was achieved in 95.2% of the samples from the Classic cards and in 80.9% of the samples from the Elute cards using the Classic protocol and 28.5% using the Elute protocol (P = .001). All samples (both cards) could be amplified for CARD11. There was no significant difference in the DNA concentration or 260/280 purity ratio when the 2 types of cards were compared. Five samples were also successfully analyzed by multiplex MassARRAY spectrometry, with a mutation in KRAS found in 1 case. High molecular weight DNA was extracted from the cards in sufficient amounts and quality to perform high-throughput multiplex mutation assays. The results of the current study also suggest that FTA Classic cards preserve better DNA integrity for molecular applications compared with the FTA Elute cards. Copyright © 2012 American Cancer Society.

Thermal probe design for Europa sample acquisition

NASA Astrophysics Data System (ADS)

Horne, Mera F.

2018-01-01

The planned lander missions to the surface of Europa will access samples from the subsurface of the ice in a search for signs of life. A small thermal drill (probe) is proposed to meet the sample requirement of the Science Definition Team's (SDT) report for the Europa mission. The probe is 2 cm in diameter and 16 cm in length and is designed to access the subsurface to 10 cm deep and to collect five ice samples of 7 cm3 each, approximately. The energy required to penetrate the top 10 cm of ice in a vacuum is 26 Wh, approximately, and to melt 7 cm3 of ice is 1.2 Wh, approximately. The requirement stated in the SDT report of collecting samples from five different sites can be accommodated with repeated use of the same thermal drill. For smaller sample sizes, a smaller probe of 1.0 cm in diameter with the same length of 16 cm could be utilized that would require approximately 6.4 Wh to penetrate the top 10 cm of ice, and 0.02 Wh to collect 0.1 g of sample. The thermal drill has the advantage of simplicity of design and operations and the ability to penetrate ice over a range of densities and hardness while maintaining sample integrity.

On-chip collection of particles and cells by AC electroosmotic pumping and dielectrophoresis using asymmetric microelectrodes.

PubMed

Melvin, Elizabeth M; Moore, Brandon R; Gilchrist, Kristin H; Grego, Sonia; Velev, Orlin D

2011-09-01

The recent development of microfluidic "lab on a chip" devices requiring sample sizes <100 μL has given rise to the need to concentrate dilute samples and trap analytes, especially for surface-based detection techniques. We demonstrate a particle collection device capable of concentrating micron-sized particles in a predetermined area by combining AC electroosmosis (ACEO) and dielectrophoresis (DEP). The planar asymmetric electrode pattern uses ACEO pumping to induce equal, quadrilateral flow directed towards a stagnant region in the center of the device. A number of system parameters affecting particle collection efficiency were investigated including electrode and gap width, chamber height, applied potential and frequency, and number of repeating electrode pairs and electrode geometry. The robustness of the on-chip collection design was evaluated against varying electrolyte concentrations, particle types, and particle sizes. These devices are amenable to integration with a variety of detection techniques such as optical evanescent waveguide sensing.

Implementation of Biotic Integrity Metrics to Identify the Effects of Land Use on the Diversity of Wetlands

NASA Astrophysics Data System (ADS)

Mills, L. D.; Hamilton, S. W.; Schiller, J. R.

2005-05-01

To identify critical biological measures of wetland health, we studied twelve wetlands in north-central Tennessee and south-central Kentucky, six impacted by row crop agriculture and six unimpacted. Aquatic macroinvertebrate were collected using 10.2 cm clear PVC pipe funnel traps and wire minnow traps. Seven samples were collected from each site between May 19 and August 8, 2004. Qualitative samples (one person-hour) were collected with dip nets from each wetland to correspond with the early July trap samples. Water quality parameters measured included dissolved oxygen, pH, temperature, specific conductance, and turbidity with multiparameter aquatic probe and nephlometer. Macroinvertebrates from three sets of samples for each site were identified, when possible, to genus. The number of organism collected per trap-period per site ranged from 43 to 2224. Fifty-six taxa were identified. Generally, natural areas showed greater species richness, diversity and evenness than agricultural sites. Dipterans, primarily chironomids, were the most dominant assemblages. The three most abundant predatory orders, Coleoptera, Odonata and Hemiptera, showed alternating patterns of dominance. Habitat stability and greater vegetative complexity, which are impacted by surrounding agricultural practices, appear to be strongly related to higher species diversity.

Automated data collection based on RoboDiff at the ESRF beamline MASSIF-1

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

Nurizzo, Didier, E-mail: Didier.nurizzo@esrf.fr; Guichard, Nicolas; McSweeney, Sean

2016-07-27

The European Synchrotron Radiation Facility has a long standing history in the automation of experiments in Macromolecular Crystallography. MASSIF-1 (Massively Automated Sample Screening and evaluation Integrated Facility), a beamline constructed as part of the ESRF Upgrade Phase I program, has been open to the external user community since July 2014 and offers a unique completely automated data collection service to both academic and industrial structural biologists.

Structure determination of an integral membrane protein at room temperature from crystals in situ

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

Axford, Danny; Foadi, James; Imperial College London, London SW7 2AZ

2015-05-14

The X-ray structure determination of an integral membrane protein using synchrotron diffraction data measured in situ at room temperature is demonstrated. The structure determination of an integral membrane protein using synchrotron X-ray diffraction data collected at room temperature directly in vapour-diffusion crystallization plates (in situ) is demonstrated. Exposing the crystals in situ eliminates manual sample handling and, since it is performed at room temperature, removes the complication of cryoprotection and potential structural anomalies induced by sample cryocooling. Essential to the method is the ability to limit radiation damage by recording a small amount of data per sample from many samplesmore » and subsequently assembling the resulting data sets using specialized software. The validity of this procedure is established by the structure determination of Haemophilus influenza TehA at 2.3 Å resolution. The method presented offers an effective protocol for the fast and efficient determination of membrane-protein structures at room temperature using third-generation synchrotron beamlines.« less

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

Bustraan, M.; Coehoorn, J.; Veenema, J.J.

This report is a collection of separate contributions on some aspects of the work done on STEK up to February 1970. A description is given of STEK together with the philosophy of its design, i.e. integral measurements of fission product cross sections by a sample oscillator technique in fast reactor spectra. The influences fission products may have on fast breeder reactors are briefly demonstrated by an example. A description of the facility and of the sample oscillator and sample exchange mechanism is given. Some preliminary results of measurements of reactor parameters and the neutron spectrum in the first fast zonemore » in STEK are given. For the use of lead as material for the buffer an argumentation is given. The proposed program for the measurements of the integral fission product cross sections is outlined. The procurement of some, highly active, samples of actual fission products is briefly sketched. (auth)« less

Data on surface-water, streambed-interstitial water, and bed-sediment quality for selected locations in the small arms impact area of central Fort Gordon, Georgia, September 4-6, 2001

USGS Publications Warehouse

Priest, Sheryln; Stamey, Timothy C.; Lawrence, Stephen J.

2002-01-01

In September 2001, the U.S. Geological Survey, in cooperation with the Environmental and Natural Resources Management Office of the U.S. Army Signal Center and Fort Gordon (U.S. Department of the Army), conducted a chemical assessment of surface water, streambed-interstitial water, and bed sediments within the small arms impact area of Fort Gordon Military Installation. The study was conducted in support of the development of an Integrated Natural Resources Management Plan (INRMP) for Fort Gordon, Georgia. An effective INRMP ensures that natural resources conservation measures and U.S. Army activities on the military base are integrated and consistent with Federal requirements to manage military installations on an ecosystem basis. Filtered water samples were collected from five sites along South Prong Creek and three sites along Marcum Branch Creek for chemical analyses of major ions, nutrients, and selected trace elements. On-site measurements of pH, temperature, specific conductance, and dissolved oxygen were made at the eight sites. Filtered water collected showed varying concentrations in both surface- and streambed-interstitial water. Bed-sediment samples collected from South Prong Creek contain elevated levels of arsenic, barium, beryllium, cadmium, chromium, cobalt, copper, iron, lead, manganese, nickel, selenium, vanadium, and total organic carbon relative to previous concentrations (McConnell and others, 2000). Bed-sediment samples collected from Marcum Branch Creek contain elevated levels of beryllium, copper, lead, manganese, mercury, selenium, and total organic carbon relative to previous concentrations (McConnell and others, 2000).

IMOS National Reference Stations: a continental-wide physical, chemical and biological coastal observing system.

PubMed

Lynch, Tim P; Morello, Elisabetta B; Evans, Karen; Richardson, Anthony J; Rochester, Wayne; Steinberg, Craig R; Roughan, Moninya; Thompson, Peter; Middleton, John F; Feng, Ming; Sherrington, Robert; Brando, Vittorio; Tilbrook, Bronte; Ridgway, Ken; Allen, Simon; Doherty, Peter; Hill, Katherine; Moltmann, Tim C

2014-01-01

Sustained observations allow for the tracking of change in oceanography and ecosystems, however, these are rare, particularly for the Southern Hemisphere. To address this in part, the Australian Integrated Marine Observing System (IMOS) implemented a network of nine National Reference Stations (NRS). The network builds on one long-term location, where monthly water sampling has been sustained since the 1940s and two others that commenced in the 1950s. In-situ continuously moored sensors and an enhanced monthly water sampling regime now collect more than 50 data streams. Building on sampling for temperature, salinity and nutrients, the network now observes dissolved oxygen, carbon, turbidity, currents, chlorophyll a and both phytoplankton and zooplankton. Additional parameters for studies of ocean acidification and bio-optics are collected at a sub-set of sites and all data is made freely and publically available. Our preliminary results demonstrate increased utility to observe extreme events, such as marine heat waves and coastal flooding; rare events, such as plankton blooms; and have, for the first time, allowed for consistent continental scale sampling and analysis of coastal zooplankton and phytoplankton communities. Independent water sampling allows for cross validation of the deployed sensors for quality control of data that now continuously tracks daily, seasonal and annual variation. The NRS will provide multi-decadal time series, against which more spatially replicated short-term studies can be referenced, models and remote sensing products validated, and improvements made to our understanding of how large-scale, long-term change and variability in the global ocean are affecting Australia's coastal seas and ecosystems. The NRS network provides an example of how a continental scaled observing systems can be developed to collect observations that integrate across physics, chemistry and biology.

IMOS National Reference Stations: A Continental-Wide Physical, Chemical and Biological Coastal Observing System

PubMed Central

Lynch, Tim P.; Morello, Elisabetta B.; Evans, Karen; Richardson, Anthony J.; Rochester, Wayne; Steinberg, Craig R.; Roughan, Moninya; Thompson, Peter; Middleton, John F.; Feng, Ming; Sherrington, Robert; Brando, Vittorio; Tilbrook, Bronte; Ridgway, Ken; Allen, Simon; Doherty, Peter; Hill, Katherine; Moltmann, Tim C.

2014-01-01

Sustained observations allow for the tracking of change in oceanography and ecosystems, however, these are rare, particularly for the Southern Hemisphere. To address this in part, the Australian Integrated Marine Observing System (IMOS) implemented a network of nine National Reference Stations (NRS). The network builds on one long-term location, where monthly water sampling has been sustained since the 1940s and two others that commenced in the 1950s. In-situ continuously moored sensors and an enhanced monthly water sampling regime now collect more than 50 data streams. Building on sampling for temperature, salinity and nutrients, the network now observes dissolved oxygen, carbon, turbidity, currents, chlorophyll a and both phytoplankton and zooplankton. Additional parameters for studies of ocean acidification and bio-optics are collected at a sub-set of sites and all data is made freely and publically available. Our preliminary results demonstrate increased utility to observe extreme events, such as marine heat waves and coastal flooding; rare events, such as plankton blooms; and have, for the first time, allowed for consistent continental scale sampling and analysis of coastal zooplankton and phytoplankton communities. Independent water sampling allows for cross validation of the deployed sensors for quality control of data that now continuously tracks daily, seasonal and annual variation. The NRS will provide multi-decadal time series, against which more spatially replicated short-term studies can be referenced, models and remote sensing products validated, and improvements made to our understanding of how large-scale, long-term change and variability in the global ocean are affecting Australia's coastal seas and ecosystems. The NRS network provides an example of how a continental scaled observing systems can be developed to collect observations that integrate across physics, chemistry and biology. PMID:25517905

Early infant diagnosis of HIV in Myanmar: call for innovative interventions to improve uptake and reduce turnaround time.

PubMed

Thiha, Soe; Shewade, Hemant Deepak; Philip, Sairu; Aung, Thet Ko; Kyaw, Nang Thu Thu; Oo, Myo Minn; Kyaw, Khine Wut Yee; War, May Wint; Oo, Htun Nyunt

2017-01-01

In collaboration with the national AIDS program, early infant diagnosis (EID) is implemented by Integrated HIV Care (IHC) program through its anti-retroviral therapy (ART) centers across 10 cities in five states and regions of Myanmar. Blood samples from the ART centers are sent using public transport to a centralized PCR facility. Among HIV-exposed babies <9 months at enrolment into IHC program (2013-15), to describe the EID cascade (enrolment, sample collection for PCR, result receipt by mother, HIV diagnosis and ART initiation) and factors associated with delayed (>8 weeks of age) or no blood sample collection for EID. Retrospective cohort study involving record review. A predictive poisson regression model with robust variance estimates was fitted for risk factors of delayed or no sample collection. Of 1349 babies, 523 (39%) of the babies' mothers were on ART before pregnancy. Timely uptake of EID (<8 weeks of age) was 47% (633/1349); sample collection was delayed in 27% (367/1349) and not done in 26% (349/1349) babies. Among samples collected (n = 1000), 667 results were received by the mother; 52 (5%) were HIV-infected; among them 42 (81%) were initiated on ART. Median (IQR) turnaround time from sample collection to result receipt by mother and time to initiate ART from result receipt by mother was 7 (4,12) and 8.5 (6,16) weeks, respectively. Mothers not on ART before pregnancy and distance of ART center from PCR facility (more than 128 km) were the risk factors of delayed or no sample collection. Improving provision of ART to mothers (through universal 'test and treat') is urgently required, which has the potential to improve the timely uptake of EID as well. Interventions to reduce turnaround times, like point of care EID testing and/or systematic use of mobile technology to communicate results, are needed.

Nonmethane organic compound monitoring program. Final report 1988. Volume 2. Urban air toxics monitoring program

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

McAllister, R.A.; Moore, W.H.; Rice, J.

1989-04-01

From October, 1987 to October, 1988 samples of ambient air were collected at 19 sites in the eastern part of the U.S. Every 12 days, air was integrated over 24-hour periods into passivated stainless steel canisters. Simultaneously, air was drawn through cartridges containing dinitrophenylhydrazine to collect carbonyl compounds. The samples were analyzed at a central laboratory for a total of 37 halogenated and aromatic hydrocarbons, formaldehyde, acetaldehyde, and other oxygenated species. The hydrocarbon species were analyzed by gas chromatography/multiple detectors and gas chromatography/mass spectrometry, while the carbonyl species were analyzed by liquid chromatography. An extensive quality assurance program was carriedmore » on to secure high quality data. Complete data for all the hydrocarbon samples are presented in the report.« less

An analysis of the intake of iodine-131 by a dairy herd post-Fukushima and the subsequent excretion in milk.

PubMed

Treinen, Richard M

2015-11-01

This study focuses on iodine-131 detected in milk samples from the Dairy Science Unit at Cal Poly, San Luis Obispo, California following events at the Fukushima Dai-ichi Nuclear Power Plant in March of 2011. The milk samples, collected between March 21 and April 11, 2011, were part of the Diablo Canyon Nuclear Power Plant Radiological Environmental Monitoring Program. A correlation is made between the integrated activity of iodine-131 found in milk and the integrated activities of iodine-131 of rainwater, vegetation and air samples that were collected from March 19 to April 18, 2011. A comparison is then made to previous studies conducted on dairy cattle that were administered controlled amounts of iodine-131 through ingestion. The comparison shows good agreement to the model which states that generally 1 percent of the activity of iodine-131 ingested by dairy cattle will be detected in harvested milk. Considering the environmental factors and the uncertainties involved, these data and calculated results derived from a real world situation provide an excellent application and confirmation of studies done under controlled settings. Copyright © 2015 Elsevier Ltd. All rights reserved.

Integrated field lysimetry and porewater sampling for evaluation of chemical mobility in soils and established vegetation.

PubMed

Matteson, Audrey R; Mahoney, Denis J; Gannon, Travis W; Polizzotto, Matthew L

2014-07-04

Potentially toxic chemicals are routinely applied to land to meet growing demands on waste management and food production, but the fate of these chemicals is often not well understood. Here we demonstrate an integrated field lysimetry and porewater sampling method for evaluating the mobility of chemicals applied to soils and established vegetation. Lysimeters, open columns made of metal or plastic, are driven into bareground or vegetated soils. Porewater samplers, which are commercially available and use vacuum to collect percolating soil water, are installed at predetermined depths within the lysimeters. At prearranged times following chemical application to experimental plots, porewater is collected, and lysimeters, containing soil and vegetation, are exhumed. By analyzing chemical concentrations in the lysimeter soil, vegetation, and porewater, downward leaching rates, soil retention capacities, and plant uptake for the chemical of interest may be quantified. Because field lysimetry and porewater sampling are conducted under natural environmental conditions and with minimal soil disturbance, derived results project real-case scenarios and provide valuable information for chemical management. As chemicals are increasingly applied to land worldwide, the described techniques may be utilized to determine whether applied chemicals pose adverse effects to human health or the environment.

Integrated Field Lysimetry and Porewater Sampling for Evaluation of Chemical Mobility in Soils and Established Vegetation

PubMed Central

Gannon, Travis W.; Polizzotto, Matthew L.

2014-01-01

Potentially toxic chemicals are routinely applied to land to meet growing demands on waste management and food production, but the fate of these chemicals is often not well understood. Here we demonstrate an integrated field lysimetry and porewater sampling method for evaluating the mobility of chemicals applied to soils and established vegetation. Lysimeters, open columns made of metal or plastic, are driven into bareground or vegetated soils. Porewater samplers, which are commercially available and use vacuum to collect percolating soil water, are installed at predetermined depths within the lysimeters. At prearranged times following chemical application to experimental plots, porewater is collected, and lysimeters, containing soil and vegetation, are exhumed. By analyzing chemical concentrations in the lysimeter soil, vegetation, and porewater, downward leaching rates, soil retention capacities, and plant uptake for the chemical of interest may be quantified. Because field lysimetry and porewater sampling are conducted under natural environmental conditions and with minimal soil disturbance, derived results project real-case scenarios and provide valuable information for chemical management. As chemicals are increasingly applied to land worldwide, the described techniques may be utilized to determine whether applied chemicals pose adverse effects to human health or the environment. PMID:25045915

Eutrophication monitoring for Lake Superior’s Chequamegon Bay before and after large summer storms

EPA Science Inventory

A priority for the Lake Superior CSMI was to identify susceptible nearshore eutrophication areas. We developed an integrated sampling design to collect baseline data for Lake Superior’s Chequamegon Bay to understand how nearshore physical processes and tributary loading rel...

An integrated bioanalytical method development and validation approach: case studies.

PubMed

Xue, Y-J; Melo, Brian; Vallejo, Martha; Zhao, Yuwen; Tang, Lina; Chen, Yuan-Shek; Keller, Karin M

2012-10-01

We proposed an integrated bioanalytical method development and validation approach: (1) method screening based on analyte's physicochemical properties and metabolism information to determine the most appropriate extraction/analysis conditions; (2) preliminary stability evaluation using both quality control and incurred samples to establish sample collection, storage and processing conditions; (3) mock validation to examine method accuracy and precision and incurred sample reproducibility; and (4) method validation to confirm the results obtained during method development. This integrated approach was applied to the determination of compound I in rat plasma and compound II in rat and dog plasma. The effectiveness of the approach was demonstrated by the superior quality of three method validations: (1) a zero run failure rate; (2) >93% of quality control results within 10% of nominal values; and (3) 99% incurred sample within 9.2% of the original values. In addition, rat and dog plasma methods for compound II were successfully applied to analyze more than 900 plasma samples obtained from Investigational New Drug (IND) toxicology studies in rats and dogs with near perfect results: (1) a zero run failure rate; (2) excellent accuracy and precision for standards and quality controls; and (3) 98% incurred samples within 15% of the original values. Copyright © 2011 John Wiley & Sons, Ltd.

Autonomous water sampling for long-term monitoring of trace metals in remote environments.

PubMed

Kim, Hyojin; Bishop, James K B; Wood, Todd J; Fung, Inez Y

2012-10-16

A remotely controlled autonomous method for long-term high-frequency sampling of environmental waters in remote locations is described. The method which preserves sample integrity of dissolved trace metals and major ions for month-long periods employs a gravitational filtration system (GFS) that separates dissolved and particulate phases as samples are collected. The key elements of GFS are (1) a modified "air-outlet" filter holder to maximize filtration rate and thus minimize filtration artifacts; and (2) the direct delivery of filtrate to dedicated bottle sets for specific analytes. Depth and screen filter types were evaluated with depth filters showing best performance. GFS performance is validated using ground, stream, and estuary waters. Over 30 days of storage, samples with GFS treatment had average recoveries of 95 ± 19% and 105 ± 7% of Fe and Mn, respectively; without GFS treatment, average recoveries were only 16% and 18%. Dissolved major cations K, Mg, and Na were stable independent of collection methodology, whereas Ca in some groundwater samples decreased up to 42% without GFS due to CaCO(3) precipitation. In-field performance of GFS equipped autosamplers is demonstrated using ground and streamwater samples collected at the Angelo Coast Range Reserve, California from October 3 to November 4 2011.

Service-Learning General Chemistry: Lead Paint Analyses

NASA Astrophysics Data System (ADS)

Kesner, Laya; Eyring, Edward M.

1999-07-01

Houses painted with lead-based paints are ubiquitous in the United States because the houses and the paint have not worn out two decades after federal regulations prohibited inclusion of lead in paint. Remodeling older homes thus poses a health threat for infants and small children living in those homes. In a service-learning general chemistry class, students disseminate information about this health threat in an older neighborhood. At some of the homes they collect paint samples that they analyze for lead both qualitatively and quantitatively. This service-learning experience generates enthusiasm for general chemistry through the process of working on a "real" problem. Sample collection familiarizes the students with the concept of "representative" sampling. The sample preparation for atomic absorption spectroscopic (AAS) analysis enhances their laboratory skills. The focus of this paper is on the mechanics of integrating this particular service project into the first-term of the normal general chemistry course.

[Playful strategies for data collection with child cancer patients: an integrative review].

PubMed

Sposito, Amanda Mota Pacciulio; de Sparapani, Valéria Cássia; Pfeifer, Luzia Iara; de Lima, Regina Aparecida Garcia; Nascimento, Lucila Castanheira

2013-09-01

Children are the best sources of information on their experiences and opinions, and qualitative studies have favored the development and application of techniques that facilitate their self-expression and approaching the researcher. Through an integrative literature review, the objective of this research was to identify playful resources used in qualitative research data collection with child cancer patients, and their forms of application. Systemized searches of electronic databases and a virtual library were undertaken, which, combined with a non-systemized sample, totaled 15 studies spanning the period from 2000 and 2010. Drawing, toys, puppets, photography and creativity and sensitivity dynamics were identified which, in association with interviews or not, were shown to directly or indirectly facilitate data collection, thereby broadening the interaction with the children, and permitting further expression of their feelings. The advantages and limitations of using these resources are presented thus contributing to planning research with children.

The occurrence and distribution of trace metals in the Mississippi River and its tributaries

USGS Publications Warehouse

Taylor, Howard E.; Garbarino, J.R.; Brinton, T.I.

1990-01-01

Quantitative and semiquantitative analyses of dissolved trace metals are reported for designated sampling sites on the Mississippi River and its main tributaries utilizing depth-integrated and width-integrated sampling technology to collect statistically representative samples. Data are reported for three sampling periods, including: July-August 1987, November-December 1987, and May-June 1988. Concentrations of Al, As, Ba, Be, Cd, Co, Cr, Cu, Fe, Li, Mn, Mo, Pb, Sr, Tl, U, V, and Zn are reported quantitatively, with the remainder of the stable metals in the periodic table reported semiquantitatively. Correlations between As and V, Ba and U, Cu and Zn, Li and Ba, and Li and U are significant at the 99% confidence level for each of the sampling trips. Comparison of the results of this study for selected metals with other published data show generally good agreement for Cr, Cu, Fe, and Zn, moderate agreement for Mo, and poor agreement for Cd and V.

The Influence of Social Conditions Across the Life Course on the Human Gut Microbiota: A Pilot Project With the Wisconsin Longitudinal Study.

PubMed

Herd, Pamela; Schaeffer, Nora Cate; DiLoreto, Kerryann; Jacques, Karen; Stevenson, John; Rey, Federico; Roan, Carol

2017-12-15

To test the feasibility of collecting and integrating data on the gut microbiome into one of the most comprehensive longitudinal studies of aging and health, the Wisconsin Longitudinal Study (WLS). The long-term goal of this integration is to clarify the contribution of social conditions in shaping the composition of the gut microbiota late in life. Research on the microbiome, which is considered to be of parallel importance to human health as the human genome, has been hindered by human studies with nonrandomly selected samples and with limited data on social conditions over the life course. No existing population-based longitudinal study had collected fecal specimens. Consequently, we created an in-person protocol to collect stool specimens from a subgroup of WLS participants. We collected 429 stool specimens, yielding a 74% response rate and one of the largest human samples to date. The addition of data on the gut microbiome to the WLS-and to other population based longitudinal studies of aging-is feasible, under the right conditions, and can generate innovative research on the relationship between social conditions and the gut microbiome. © The Author 2017. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Fluidics platform and method for sample preparation

DOEpatents

Benner, Henry W.; Dzenitis, John M.

2016-06-21

Provided herein are fluidics platforms and related methods for performing integrated sample collection and solid-phase extraction of a target component of the sample all in one tube. The fluidics platform comprises a pump, particles for solid-phase extraction and a particle-holding means. The method comprises contacting the sample with one or more reagents in a pump, coupling a particle-holding means to the pump and expelling the waste out of the pump while the particle-holding means retains the particles inside the pump. The fluidics platform and methods herein described allow solid-phase extraction without pipetting and centrifugation.

INTEGRATION OF FACILITY MODELING CAPABILITIES FOR NUCLEAR NONPROLIFERATION ANALYSIS

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

Gorensek, M.; Hamm, L.; Garcia, H.

2011-07-18

Developing automated methods for data collection and analysis that can facilitate nuclear nonproliferation assessment is an important research area with significant consequences for the effective global deployment of nuclear energy. Facility modeling that can integrate and interpret observations collected from monitored facilities in order to ascertain their functional details will be a critical element of these methods. Although improvements are continually sought, existing facility modeling tools can characterize all aspects of reactor operations and the majority of nuclear fuel cycle processing steps, and include algorithms for data processing and interpretation. Assessing nonproliferation status is challenging because observations can come frommore » many sources, including local and remote sensors that monitor facility operations, as well as open sources that provide specific business information about the monitored facilities, and can be of many different types. Although many current facility models are capable of analyzing large amounts of information, they have not been integrated in an analyst-friendly manner. This paper addresses some of these facility modeling capabilities and illustrates how they could be integrated and utilized for nonproliferation analysis. The inverse problem of inferring facility conditions based on collected observations is described, along with a proposed architecture and computer framework for utilizing facility modeling tools. After considering a representative sampling of key facility modeling capabilities, the proposed integration framework is illustrated with several examples.« less

Monitoring the Quality of Medicines: Results from Africa, Asia, and South America

PubMed Central

Hajjou, Mustapha; Krech, Laura; Lane-Barlow, Christi; Roth, Lukas; Pribluda, Victor S.; Phanouvong, Souly; El-Hadri, Latifa; Evans, Lawrence; Raymond, Christopher; Yuan, Elaine; Siv, Lang; Vuong, Tuan-Anh; Boateng, Kwasi Poku; Okafor, Regina; Chibwe, Kennedy M.; Lukulay, Patrick H.

2015-01-01

Monitoring the quality of medicines plays a crucial role in an integrated medicines quality assurance system. In a publicly available medicines quality database (MQDB), the U.S. Pharmacopeial Convention (USP) reports results of data collected from medicines quality monitoring (MQM) activities spanning the period of 2003–2013 in 17 countries of Africa, Asia, and South America. The MQDB contains information on 15,063 samples collected and tested using Minilab® screening methods and/or pharmacopeial methods. Approximately 71% of the samples reported came from Asia, 23% from Africa, and 6% from South America. The samples collected and tested include mainly antibiotic, antimalarial, and antituberculosis medicines. A total of 848 samples, representing 5.6% of total samples, failed the quality test. The failure proportion per region was 11.5%, 10.4%, and 2.9% for South America, Africa, and Asia, respectively. Eighty-one counterfeit medicines were reported, 86.4% of which were found in Asia and 13.6% in Africa. Additional analysis of the data shows the distribution of poor-quality medicines per region and by therapeutic indication as well as possible trends of counterfeit medicines. PMID:25897073

Diurnal patterns of salivary cortisol and DHEA using a novel collection device: electronic monitoring confirms accurate recording of collection time using this device.

PubMed

Laudenslager, Mark L; Calderone, Jacqueline; Philips, Sam; Natvig, Crystal; Carlson, Nichole E

2013-09-01

The accurate indication of saliva collection time is important for defining the diurnal decline in salivary cortisol as well as characterizing the cortisol awakening response. We tested a convenient and novel collection device for collecting saliva on strips of filter paper in a specially constructed booklet for determination of both cortisol and DHEA. In the present study, 31 healthy adults (mean age 43.5 years) collected saliva samples four times a day on three consecutive days using filter paper collection devices (Saliva Procurement and Integrated Testing (SPIT) booklet) which were maintained during the collection period in a large plastic bottle with an electronic monitoring cap. Subjects were asked to collect saliva samples at awakening, 30 min after awakening, before lunch and 600 min after awakening. The time of awakening and the time of collection before lunch were allowed to vary by each subjects' schedule. A reliable relationship was observed between the time recorded by the subject directly on the booklet and the time recorded by electronic collection device (n=286 observations; r(2)=0.98). However, subjects did not consistently collect the saliva samples at the two specific times requested, 30 and 600 min after awakening. Both cortisol and DHEA revealed diurnal declines. In spite of variance in collection times at 30 min and 600 min after awakening, the slope of the diurnal decline in both salivary cortisol and DHEA was similar when we compared collection tolerances of ±7.5 and ±15 min for each steroid. These unique collection booklets proved to be a reliable method for recording collection times by subjects as well as for estimating diurnal salivary cortisol and DHEA patterns. Copyright © 2013 Elsevier Ltd. All rights reserved.

Diurnal patterns of salivary cortisol and DHEA using a novel collection device: Electronic monitoring confirms accurate recording of collection time using this device

PubMed Central

Laudenslager, Mark L.; Calderone, Jacqueline; Philips, Sam; Natvig, Crystal; Carlson, Nichole E.

2013-01-01

The accurate indication of saliva collection time is important for defining the diurnal decline in salivary cortisol as well as characterizing the cortisol awakening response.. We tested a convenient and novel collection device for collecting saliva on strips of filter paper in a specially constructed booklet for determination of both cortisol and DHEA. In the present study, 31 healthy adults (mean age 43.5 yrs.) collected saliva samples four times a day on three consecutive days using filter paper collection devices (Saliva Procurement and Integrated Testing (SPIT) booklet) which were maintained during the collection period in a large plastic bottle with an electronic monitoring cap. Subjects were asked to collect saliva samples at awakening, 30 min. after awakening, before lunch and 600 min. after awakening. The time of awakening and the time of collection before lunch were allowed to vary by each subjects’ schedule. A reliable relationship was observed between the time recorded by the subject directly on the booklet and the time recorded by electronic collection device (n = 286 observations; r2 = 0.98). However, subjects did not consistently collect the saliva samples at the two specific times requested, 30 and 600 min. after awakening. Both cortisol and DHEA revealed diurnal declines.. In spite of variance in collection times at 30 min. and 600 min. after awakening, the slope of the diurnal decline in both salivary cortisol and DHEA were similar when we compared collection tolerances of ± 7.5 and ± 15 min. for each steroid.. These unique collection booklets proved to be a reliable method for recording collection times by subjects as well as for estimating diurnal salivary cortisol and DHEA patterns. PMID:23490073

Field evidence of reproduction impairment through sperm DNA damage in the fish nase (Chondrostoma nasus) in anthropized hydrosystems.

PubMed

Devaux, Alain; Bony, Sylvie; Plenet, Sandrine; Sagnes, Pierre; Segura, Samuel; Suaire, Rémi; Novak, Morgane; Gilles, André; Olivier, Jean-Michel

2015-12-01

This work aims to explore in the field the relationship between the integrity of sperm DNA and the quality of offspring as a possible cause of the decline of a feral fish population through reproduction impairment. Mature nase (Chondrostoma nasus) were caught during the breeding season in three locations (A-C) of the Rhône River basin and gametes collected by stripping. Sampling locations were chosen according to the following gradient of contamination due to human activities on the watershed: A≤B

Contamination Knowledge Strategy for the Mars 2020 Sample-Collecting Rover

NASA Technical Reports Server (NTRS)

Farley, K. A.; Williford, K.; Beaty, D W.; McSween, H. Y.; Czaja, A. D.; Goreva, Y. S.; Hausrath, E.; Herd, C. D. K.; Humayun, M.; McCubbin, F. M.;

DEVELOPMENT OF AN INDEX OF BIOTIC INTEGRITY FOR THE MID-ATLANTIC HIGHLANDS REGION

EPA Science Inventory

From 1993 to 1996, fish assemblage data were collected from 309 wadeable streams in the U.S. Mid-Atlantic Highlands region as part of the U.S. Environmental Protection Agency's Environmental Monitoring and Assessment Program. Stream sites were selected with a probabilistic sampl...

An integrated approach utilizing chemometrics and GC/MS for classification of chamomile flowers, essential oils and commerical products

USDA-ARS?s Scientific Manuscript database

As part of an ongoing research program on authentication, safety and biological evaluation of phytochemicals and dietary supplements, an in-depth chemical investigation of different types of chamomile was performed. A collection of chamomile samples including authenticated plants, commercial product...

Digital Learning Compass: Distance Education State Almanac 2017. Delaware

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Delaware. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Kansas

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Kansas. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Minnesota

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Minnesota. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Utah

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Utah. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Connecticut

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Connecticut. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Wyoming

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Wyoming. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Montana

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Montana. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Iowa

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Iowa. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Alabama

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Alabama. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Nevada

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Nevada. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Mississippi

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Mississippi. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Kentucky

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Kentucky. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Ohio

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Ohio. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Oklahoma

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Oklahoma. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Texas

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Texas. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Vermont

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Vermont. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Colorado

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Colorado. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Arizona

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Arizona . The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Missouri

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Missouri. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Idaho

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Idaho. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Massachusetts

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Massachusetts. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Tennessee

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Tennessee. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Virginia

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Virginia. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Indiana

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Indiana. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Alaska

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Alaska. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Louisiana

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Louisiana. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Nebraska

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Nebraska. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Maine

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Maine. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Wisconsin

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Wisconsin. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Michigan

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Michigan. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Arkansas

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Arkansas . The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Illinois

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Illinois. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Florida

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Florida. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Maryland

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Maryland. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Oregon

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Oregon. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Washington

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Washington. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Hawaii

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Hawaii. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. California

ERIC Educational Resources Information Center

Seaman, Julia A.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of California. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Georgia

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Georgia. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Pennsylvania

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Pennsylvania. The sample for this analysis is comprised of all active, degree-granting…

DIATOM INDICES OF STREAM ECOSYSTEM CONDITIONS: COMPARISON OF GENUS VS. SPECIES LEVEL IDENTIFICATIONS

EPA Science Inventory

Diatom assemblage data collected between 1993 and 1995 from 233 Mid-Appalachian streams were used to compare indices of biotic integrity based on genus vs. species level taxonomy. Thirty-seven genera and 197 species of diatoms were identified from these samples. Metrics included...

Urban-air-toxics Monitoring Program, 1990

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

Not Available

1991-06-01

From March 1990 through February 1991 samples of ambient air were collected at 12 sites in the eastern part of the U.S. Every 12 days, air was integrated over 24-hour periods into passivated stainless steel canisters. Simultaneously, air was drawn through cartridges containing dinitrophenylhydrazine to collect carbonyl compounds. The samples were analyzed at a central laboratory for a total of 37 halogenated and aromatic hydrocarbons, formaldehyde, acetaldehyde, and other oxygenated species. The hydrocarbon species were analyzed by gas chromatography/multiple detectors and gas chromatography/mass spectrometry, while the carbonyl species were analyzed by liquid chromatography. Complete data for all the hydrocarbon samplesmore » are presented in the report.« less

Flexible Plasmonic Sensors

PubMed Central

Shir, Daniel; Ballard, Zachary S.; Ozcan, Aydogan

2016-01-01

Mechanical flexibility and the advent of scalable, low-cost, and high-throughput fabrication techniques have enabled numerous potential applications for plasmonic sensors. Sensitive and sophisticated biochemical measurements can now be performed through the use of flexible plasmonic sensors integrated into existing medical and industrial devices or sample collection units. More robust sensing schemes and practical techniques must be further investigated to fully realize the potentials of flexible plasmonics as a framework for designing low-cost, embedded and integrated sensors for medical, environmental, and industrial applications. PMID:27547023

Volatile organic compound measurements in the California/Mexico border region during SCOS97

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

Zielinska, B.; Sagebiel, J.; Uberna, E.

1999-07-01

Measurements of volatile organic compounds (VOC) were carried out in the California/Mexico border region during the Southern California Ozone study in the Summer of 1997 (SCOS97). Integrated 3-hr samples were collected in Rosarito (south of Tijuana, Mexico) and in Mexicali during Intensive Operational Periods (IOP), twice per IOP day. VOC were collected using stainless-steel 6 L canisters; carbonyl compounds were collected using 2,4-dinitrophenylhydrazine (DNPH) impregnated C{sub 18} SepPak cartridges. The canister samples were analyzed for speciated volatile hydrocarbons (C{sub 2}-C{sub 12}), CO, CO{sub 2}, CH{sub 4}, MTBE, and halogenated hydrocarbons. DNPH-impregnated cartridges were analyzed for fourteen C{sub 1}-C{sub 7} carbonylmore » compounds. The results of these measurements will be discussed.« less

Advances in Astromaterials Curation: Supporting Future Sample Return Missions

NASA Technical Reports Server (NTRS)

Evans, C. A.; Zeigler, R. A.; Fries, M. D..; Righter, K.; Allton, J. H.; Zolensky, M. E.; Calaway, M. J.; Bell, M. S.

2015-01-01

NASA's Astromaterials, curated at the Johnson Space Center in Houston, are the most extensive, best-documented, and leastcontaminated extraterrestrial samples that are provided to the worldwide research community. These samples include lunar samples from the Apollo missions, meteorites collected over nearly 40 years of expeditions to Antarctica (providing samples of dozens of asteroid bodies, the Moon, and Mars), Genesis solar wind samples, cosmic dust collected by NASA's high altitude airplanes, Comet Wild 2 and interstellar dust samples from the Stardust mission, and asteroid samples from JAXA's Hayabusa mission. A full account of NASA's curation efforts for these collections is provided by Allen, et al [1]. On average, we annually allocate about 1500 individual samples from NASA's astromaterials collections to hundreds of researchers from around the world, including graduate students and post-doctoral scientists; our allocation rate has roughly doubled over the past 10 years. The curation protocols developed for the lunar samples returned from the Apollo missions remain relevant and are adapted to new and future missions. Several lessons from the Apollo missions, including the need for early involvement of curation scientists in mission planning [1], have been applied to all subsequent sample return campaigns. From the 2013 National Academy of Sciences report [2]: "Curation is the critical interface between sample return missions and laboratory research. Proper curation has maintained the scientific integrity and utility of the Apollo, Antarctic meteorite, and cosmic dust collections for decades. Each of these collections continues to yield important new science. In the past decade, new state-of-the-art curatorial facilities for the Genesis and Stardust missions were key to the scientific breakthroughs provided by these missions." The results speak for themselves: research on NASA's astromaterials result in hundreds of papers annually, yield fundamental discoveries about the evolution of the solar system (e.g. [3] and references contained therein), and serve the global scientific community as ground truth for current and planned missions such as NASA's Dawn mission to Vesta and Ceres, and the future OSIRIS REx mission to asteroid Bennu [1,3

Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis

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

He, Fei; Maslov, Sergei; Yoo, Shinjae

Here, transcriptome datasets from thousands of samples of the model plant Arabidopsis thaliana have been collectively generated by multiple individual labs. Although integration and meta-analysis of these samples has become routine in the plant research community, it is often hampered by the lack of metadata or differences in annotation styles by different labs. In this study, we carefully selected and integrated 6,057 Arabidopsis microarray expression samples from 304 experiments deposited to NCBI GEO. Metadata such as tissue type, growth condition, and developmental stage were manually curated for each sample. We then studied global expression landscape of the integrated dataset andmore » found that samples of the same tissue tend to be more similar to each other than to samples of other tissues, even in different growth conditions or developmental stages. Root has the most distinct transcriptome compared to aerial tissues, but the transcriptome of cultured root is more similar to those of aerial tissues as the former samples lost their cellular identity. Using a simple computational classification method, we showed that the tissue type of a sample can be successfully predicted based on its expression profile, opening the door for automatic metadata extraction and facilitating re-use of plant transcriptome data. As a proof of principle we applied our automated annotation pipeline to 708 RNA-seq samples from public repositories and verified accuracy of our predictions with samples’ metadata provided by authors.« less

Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis

DOE PAGES

He, Fei; Maslov, Sergei; Yoo, Shinjae; ...

2016-05-25

Here, transcriptome datasets from thousands of samples of the model plant Arabidopsis thaliana have been collectively generated by multiple individual labs. Although integration and meta-analysis of these samples has become routine in the plant research community, it is often hampered by the lack of metadata or differences in annotation styles by different labs. In this study, we carefully selected and integrated 6,057 Arabidopsis microarray expression samples from 304 experiments deposited to NCBI GEO. Metadata such as tissue type, growth condition, and developmental stage were manually curated for each sample. We then studied global expression landscape of the integrated dataset andmore » found that samples of the same tissue tend to be more similar to each other than to samples of other tissues, even in different growth conditions or developmental stages. Root has the most distinct transcriptome compared to aerial tissues, but the transcriptome of cultured root is more similar to those of aerial tissues as the former samples lost their cellular identity. Using a simple computational classification method, we showed that the tissue type of a sample can be successfully predicted based on its expression profile, opening the door for automatic metadata extraction and facilitating re-use of plant transcriptome data. As a proof of principle we applied our automated annotation pipeline to 708 RNA-seq samples from public repositories and verified accuracy of our predictions with samples’ metadata provided by authors.« less

Evaluation of a solid matrix for collection and ambient storage of RNA from whole blood

PubMed Central

2014-01-01

Background Whole blood gene expression-based molecular diagnostic tests are becoming increasingly available. Conventional tube-based methods for obtaining RNA from whole blood can be limited by phlebotomy, volume requirements, and RNA stability during transport and storage. A dried blood spot matrix for collecting high-quality RNA, called RNA Stabilizing Matrix (RSM), was evaluated against PAXgene® blood collection tubes. Methods Whole blood was collected from 25 individuals and subjected to 3 sample storage conditions: 18 hours at either room temperature (baseline arm) or 37°C, and 6 days at room temperature. RNA was extracted and assessed for integrity by Agilent Bioanalyzer, and gene expression was compared by RT-qPCR across 23 mRNAs comprising a clinical test for obstructive coronary artery disease. Results RSM produced RNA of relatively high integrity across the various tested conditions (mean RIN ± 95% CI: baseline arm, 6.92 ± 0.24; 37°C arm, 5.98 ± 0.48; 6-day arm, 6.72 ± 0.23). PAXgene samples showed comparable RNA integrity in both baseline and 37°C arms (8.42 ± 0.17; 7.92 ± 0.1 respectively) however significant degradation was observed in the 6-day arm (3.19 ± 1.32). Gene expression scores on RSM were highly correlated between the baseline and 37°C and 6-day study arms (median r = 0.96, 0.95 respectively), as was the correlation to PAXgene tubes (median r = 0.95, p < 0.001). Conclusion RNA obtained from RSM shows little degradation and comparable RT-qPCR performance to PAXgene RNA for the 23 genes analyzed. Further development of this technology may provide a convenient method for collecting, shipping, and storing RNA for gene expression assays. PMID:24855452

A Prototype Ice-Melting Probe for Collecting Biological Samples from Cryogenic Ice at Low Pressure

NASA Astrophysics Data System (ADS)

Davis, Ashley

2017-08-01

In the Solar System, the surface of an icy moon is composed of irregular ice formations at cryogenic temperatures (<200 K), with an oxidized surface layer and a tenuous atmosphere at very low pressure (<10-6 atm). A lander mission, whose aim is to collect and analyze biological samples from the surface ice, must contain a device that collects samples without refreezing liquid and without sublimation of ice. In addition, if the samples are biological in nature, then precautions must be taken to ensure the samples do not overheat or mix with the oxidized layer. To achieve these conditions, the collector must maintain temperatures close to maintenance or growth conditions of the organism (<293 K), and it must separate or neutralize the oxidized layer and be physically gentle. Here, we describe a device that addresses these requirements and is compatible with low atmospheric pressure while using no pumps. The device contains a heated conical probe with a central orifice, which is forced into surface ice and directs the meltwater upward into a reservoir. The force on the probe is proportional to the height of meltwater (pressure) obtained in the system and allows regulation of the melt rate and temperature of the sample. The device can collect 5-50 mL of meltwater from the surface of an ice block at 233-208 K with an environmental pressure of less than 10-2 atm while maintaining a sample temperature between 273 and 293 K. These conditions maintain most biological samples in a pristine state and maintain the integrity of most organisms' structure and function.

Induced Environment Contamination Monitor (IECM), air sampler - Results from the Space Transport System (STS-2) flight

NASA Technical Reports Server (NTRS)

Peters, P. N.; Hester, H. B.; Bertsch, W.; Mayfield, H.; Zatko, D.

1983-01-01

An investigation involving sampling the rapidly changing environment of the Shuttle cargo bay is considered. Four time-integrated samples and one rapid acquisition sample were collected to determine the types and quantities of contaminants present during ascent and descent of the Shuttle. The sampling times for the various bottles were controlled by valves operated by the Data Acquisition and Control System (DACS) of the IECM. Many of the observed species were found to be common solvents used in cleaning surfaces. When the actual volume sampled is taken into account, the relative mass of organics sampled during descent is about 20 percent less than during ascent.

Current Research at the Endeavour Ridge 2000 Integrated Studies Site

NASA Astrophysics Data System (ADS)

Butterfield, D. A.; Kelley, D. S.; Ridge 2000 Community, R.

2004-12-01

Integrated geophysical, geological, chemical, and biological studies are being conducted on the Endeavour segment with primary support from NSF, the W.M. Keck Foundation, and NSERC (Canada). The research includes a seismic network, physical and chemical sensors, high-precision mapping and time-series sampling. Several research expeditions have taken place at the Endeavour ISS in the past year. In June 2003, an NSF-sponsored cruise with R.V. al T.G.Thompson/ROV al Jason2 installed microbial incubators in drill-holes in the sides of active sulfide chimneys and sampled rocks, fluids, and microbes in the Mothra and Main Endeavour Field (MEF). In July 2003, with al Thompson/Jason2, an NSF-LEXEN project at Baby Bare on Endeavour east flank conducted sampling through seafloor-penetrating probes, plus time-series sampling of fluids, microbes, and rocks at the MEF. In September 2003, with al Thompson/ROV al ROPOS, the Keck Proto-Neptune project installed a seismic network consisting of 1 broadband and 7 short-period seismometers, installation of chemical/physical sensors and time-series samplers for chemistry and microbiology in the MEF and Clam Bed sites, collection of rocks, fluids, animals, and microbes. In May/June 2004, an NSF-sponsored al Atlantis/Alvin cruise recovered sulfide incubators installed in 2003, redeployed a sulfide incubator, mapped MEF and Mothra vent fields with high-resolution Imagenix sonar, sampled fluids from MEF, Mothra, and Clam Bed, recovered year-long time-series fluid and microbial samplers from MEF and Clam Bed, recovered and installed hot vent temperature-resistivity monitors, cleaned up the MEF and deployed new markers at major sulfide structures. In August 2004, there were two MBARI/Keck-sponsored cruises with R.V. al Western Flyer/ROV al Tiburon. The first cruise completed the seismic network with addition of two more broadband seismometers and serviced all 7 short-period seismometers. al Tiburon then performed microbial and chemical investigations at MEF, Mothra, Sasquatch, and Middle Valley, collecting fluid, particle, and animal samples for culture and phylogenetic analysis. al Tiburon continued in late August/September with detailed petrological sampling. A Keck-sponsored al Thompson/ROPOS cruise in September continued work on chemical/physical sensor deployments and time-series chemical and microbial sampling. A graduate student workshop at Friday Harbor beginning October 2004 will analyze the first year of data from the seismic network and begin to correlate seismic activity with hydrothermal activity. The Endeavour ISS is still in a phase of data collection and sensor development, but moving toward data integration.

Study of Z production in PbPb and pp collisions at $$ \\sqrt{s_{\\mathrm{NN}}}=2.76 $$ TeV in the dimuon and dielectron decay channels

DOE PAGES

Chatrchyan, Serguei

2015-03-04

We found that the production of Z bosons is studied in the dimuon and dielectron decay channels in PbPb and pp collisions at √s NN=2.76 TeV, using data collected by the CMS experiment at the LHC. The PbPb data sample corresponds to an integrated luminosity of about 166 μb -1, while the pp data sample collected in 2013 at the same nucleon-nucleon centre-of-mass energy has an integrated luminosity of 5.4 pb -1. The Z boson yield is measured as a function of rapidity, transverse momentum, and collision centrality. The ratio of PbPb to pp yields, scaled by the number ofmore » inelastic nucleon-nucleon collisions, is found to be 1.06 ± 0.05 (stat) ± 0.08 (syst) in the dimuon channel and 1.02 ± 0.08 (stat) ± 0.15 (syst) in the dielectron channel, for centrality-integrated Z boson production. Finally, this binary collision scaling is seen to hold in the entire kinematic region studied, as expected for a colourless probe that is unaffected by the hot and dense QCD medium produced in heavy ion collisions.« less

An integrated approach to identify the origin of PM10 exceedances.

PubMed

Amodio, M; Andriani, E; de Gennaro, G; Demarinis Loiotile, A; Di Gilio, A; Placentino, M C

2012-09-01

This study was aimed to the development of an integrated approach for the characterization of particulate matter (PM) pollution events in the South of Italy. PM(10) and PM(2.5) daily samples were collected from June to November 2008 at an urban background site located in Bari (Puglia Region, South of Italy). Meteorological data, particle size distributions and atmospheric dispersion conditions were also monitored in order to provide information concerning the different features of PM sources. The collected data allowed suggesting four indicators to characterize different PM(10) exceedances. PM(2.5)/PM(10) ratio, natural radioactivity, aerosol maps and back-trajectory analysis and particle distributions were considered in order to evaluate the contribution of local anthropogenic sources and to determine the different origins of intrusive air mass coming from long-range transport, such as African dust outbreaks and aerosol particles from Central and Eastern Europe. The obtained results were confirmed by applying principal component analysis to the number particle concentration dataset and by the chemical characterization of the samples (PM(10) and PM(2.5)). The integrated approach for PM study suggested in this paper can be useful to support the air quality managers for the development of cost-effective control strategies and the application of more suitable risk management approaches.

Lagrangian sampling of wastewater treatment plant effluent in Boulder Creek, Colorado, and Fourmile Creek, Iowa, during the summer of 2003 and spring of 2005--Hydrological and chemical data

USGS Publications Warehouse

Barber, Larry B.; Keefe, Steffanie H.; Kolpin, Dana W.; Schnoebelen, Douglas J.; Flynn, Jennifer L.; Brown, Gregory K.; Furlong, Edward T.; Glassmeyer, Susan T.; Gray, James L.; Meyer, Michael T.; Sandstrom, Mark W.; Taylor, Howard E.; Zaugg, Steven D.

2011-01-01

This report presents methods and data for a Lagrangian sampling investigation into chemical loading and in-stream attenuation of inorganic and organic contaminants in two wastewater treatment-plant effluent-dominated streams: Boulder Creek, Colorado, and Fourmile Creek, Iowa. Water-quality sampling was timed to coincide with low-flow conditions when dilution of the wastewater treatment-plant effluent by stream water was at a minimum. Sample-collection times corresponded to estimated travel times (based on tracer tests) to allow the same "parcel" of water to reach downstream sampling locations. The water-quality data are linked directly to stream discharge using flow- and depth-integrated composite sampling protocols. A range of chemical analyses was made for nutrients, carbon, major elements, trace elements, biological components, acidic and neutral organic wastewater compounds, antibiotic compounds, pharmaceutical compounds, steroid and steroidal-hormone compounds, and pesticide compounds. Physical measurements were made for field conditions, stream discharge, and time-of-travel studies. Two Lagrangian water samplings were conducted in each stream, one in the summer of 2003 and the other in the spring of 2005. Water samples were collected from five sites in Boulder Creek: upstream from the wastewater treatment plant, the treatment-plant effluent, and three downstream sites. Fourmile Creek had seven sampling sites: upstream from the wastewater treatment plant, the treatment-plant effluent, four downstream sites, and a tributary. At each site, stream discharge was measured, and equal width-integrated composite water samples were collected and split for subsequent chemical, physical, and biological analyses. During the summer of 2003 sampling, Boulder Creek downstream from the wastewater treatment plant consisted of 36 percent effluent, and Fourmile Creek downstream from the respective wastewater treatment plant was 81 percent effluent. During the spring of 2005 samplings, Boulder Creek downstream from the wastewater treatment plant was 40 percent effluent, and Fourmile Creek downstream from that wastewater treatment plant was 28 percent effluent. At each site, 300 individual constituents were determined to characterize the water. Most of the inorganic constituents were detected in all of the stream and treatment-plant effluent samples, whereas detection of synthetic organic compounds was more limited and contaminants typically occurred only in wastewater treatment-plant effluents and at downstream sites. Concentrations ranged from nanograms per liter to milligrams per liter.

Morphological integration of anatomical, developmental, and functional postcranial modules in the crab-eating macaque (Macaca fascicularis).

PubMed

Conaway, Mark A; Schroeder, Lauren; von Cramon-Taubadel, Noreen

2018-03-22

Integration and modularity reflect the coordinated action of past evolutionary processes and, in turn, constrain or facilitate phenotypic evolvability. Here, we analyze magnitudes of integration in the macaque postcranium to test whether 20 a priori defined modules are (1) more tightly integrated than random sets of postcranial traits, and (2) are differentiated based on mode of definition, with developmental modules expected to be more integrated than functional or anatomical modules. The 3D morphometric data collected for eight limb and girdle bones for 60 macaques were collated into anatomical, developmental, and functional modules. A resampling technique was used to create random samples of integration values for each module for statistical comparison. Our results found that not all a priori defined modules were more strongly integrated than random samples of postcranial traits and that specific types of modules did not present consistent patterns of integration. Rather, girdle and joint modules were consistently less integrated than limb modules, and forelimb elements were less integrated than hindlimbs. The results suggest that morphometrically complex modules tend to be less integrated than simple limb bones, irrespective of the number of available traits. However, differences in integration of the fore- and hindlimb more likely reflects the multitude of locomotory, feeding, and social functions involved. It remains to be tested whether patterns of integration identified here are primate universals, and to what extent they vary depending on phylogenetic or functional factors. © 2018 Wiley Periodicals, Inc.

GeoLab's First Field Trials, 2010 Desert RATS: Evaluating Tools for Early Sample Characterization

NASA Technical Reports Server (NTRS)

Evans, Cindy A.; Bell, M. S.; Calaway, M. J.; Graff, Trevor; Young, Kelsey

2011-01-01

As part of an accelerated prototyping project to support science operations tests for future exploration missions, we designed and built a geological laboratory, GeoLab, that was integrated into NASA's first generation Habitat Demonstration Unit-1/Pressurized Excursion Module (HDU1-PEM). GeoLab includes a pressurized glovebox for transferring and handling samples collected on geological traverses, and a suite of instruments for collecting preliminary data to help characterize those samples. The GeoLab and the HDU1-PEM were tested for the first time as part of the 2010 Desert Research and Technology Studies (DRATS), NASA's analog field exercise for testing mission technologies. The HDU1- PEM and GeoLab participated in two weeks of joint operations in northern Arizona with two crewed rovers and the DRATS science team.

Turkish and Moroccan Young Adults in the Netherlands: The Relationship Between Acculturation and Psychological Problems.

PubMed

Özbek, Emel; Bongers, Ilja L; Lobbestael, Jill; van Nieuwenhuizen, Chijs

2015-12-01

This study investigated the relationship between acculturation and psychological problems in Turkish and Moroccan young adults living in the Netherlands. A sample of 131 healthy young adults aged between 18 and 24 years old, with a Turkish or Moroccan background was recruited using snowball sampling. Data on acculturation, internalizing and externalizing problems, beliefs about psychological problems, attributions of psychological problems and barriers to care were collected and analyzed using Latent Class Analysis and multinomial logistic regression. Three acculturation classes were identified in moderately to highly educated, healthy Turkish or Moroccan young adults: integration, separation and diffusion. None of the participants in the sample were marginalized or assimilated. Young adults reporting diffuse acculturation reported more internalizing and externalizing problems than those who were integrated or separated. Separated young adults reported experiencing more practical barriers to care than integrated young adults. Further research with a larger sample, including young adult migrants using mental health services, is required to improve our understanding of acculturation, psychological problems and barriers to care in this population. Including experiences of discrimination in the model might improve our understanding of the relationship between different forms of acculturation and psychological problems.

Associations of benthic macroinvertebrate assemblages with environmental variables in the upper Clear Creek watershed, California

USGS Publications Warehouse

Brown, Larry R.; May, Jason T.; Wulff, Marissa

2012-01-01

Benthic macroinvertebrates are integral components of stream ecosystems and are often used to assess the ecological integrity of streams. We sampled streams in the upper Clear Creek drainage in the Klamath—Siskiyou Ecoregion of northwestern California in fall 2004 (17 sites) and 2005 (original 17 plus 4 new sites) with the objectives of documenting the benthic macroinvertebrate assemblages supported by the streams in the area, determining how those assemblages respond to environmental variables, assessing the biological condition of the streams using a benthic index of biotic integrity (IBI), and understanding the assemblages in the context of biodiversity of the ecoregion. We collected both reach-wide (RW) and targeted-riffle (TR) macroinvertebrate samples at each site. The macroinvertebrate assemblages were diverse, with over 150 genera collected for each sampling protocol. The macroinvertebrate assemblages appeared to be most responsive to a general habitat gradient based on stream size, gradient, flow, and dominance of riffles. A second important habitat gradient was based on elevation and dominance of riffles. A gradient in water quality based on concentrations of dissolved ions and metals was also important. Models based on these 3 gradients had Spearman's rank correlations with macroinvertebrate taxonomic composition of 0.60 and 0.50 for the TR and RW samples, respectively. The majority (>50%) of the sites were in good or very good biological condition based on IBI scores. The diversity of macroinvertebrate assemblages is associated with the diversity of habitats available in the Klamath—Siskiyou Ecoregion. Maintaining the aquatic habitats in good condition is important in itself but is also vital to maintaining biodiversity in this diverse and unique ecoregion.

Analysis of pesticide residues in strawberries and soils by GC-MS/MS, LC-MS/MS and two-dimensional GC-time-of-flight MS comparing organic and integrated pest management farming.

PubMed

Fernandes, Virgínia C; Lehotay, Steven J; Geis-Asteggiante, Lucía; Kwon, Hyeyoung; Mol, Hans G J; van der Kamp, Henk; Mateus, Nuno; Domingues, Valentina F; Delerue-Matos, Cristina

2014-01-01

This study analysed 22 strawberry and soil samples after their collection over the course of 2 years to compare the residue profiles from organic farming with integrated pest management practices in Portugal. For sample preparation, we used the citrate-buffered version of the quick, easy, cheap, effective, rugged, and safe (QuEChERS) method. We applied three different methods for analysis: (1) 27 pesticides were targeted using LC-MS/MS; (2) 143 were targeted using low pressure GC-tandem mass spectrometry (LP-GC-MS/MS); and (3) more than 600 pesticides were screened in a targeted and untargeted approach using comprehensive, two-dimensional gas chromatography time-of-flight mass spectrometry (GC × GC-TOF-MS). Comparison was made of the analyses using the different methods for the shared samples. The results were similar, thereby providing satisfactory confirmation of both similarly positive and negative findings. No pesticides were found in the organic-farmed samples. In samples from integrated pest management practices, nine pesticides were determined and confirmed to be present, ranging from 2 µg kg(-1) for fluazifop-p-butyl to 50 µg kg(-1) for fenpropathrin. Concentrations of residues in strawberries were less than European maximum residue limits.

Use of FTA sampling cards for molecular detection of avian influenza virus in wild birds.

PubMed

Keeler, Shamus P; Ferro, Pamela J; Brown, Justin D; Fang, Xingwang; El-Attrache, John; Poulson, Rebecca; Jackwood, Mark W; Stallknecht, David E

2012-03-01

Current avian influenza (AI) virus surveillance programs involving wild birds rely on sample collection methods that require refrigeration or low temperature freezing to maintain sample integrity for virus isolation and/or reverse-transcriptase (RT) PCR. Maintaining the cold chain is critical for the success of these diagnostic assays but is not always possible under field conditions. The aim of this study was to test the utility of Finders Technology Associates (FTA) cards for reliable detection of AI virus from cloacal and oropharyngeal swabs of wild birds. The minimum detectable titer was determined, and the effect of room temperature storage was evaluated experimentally using multiple egg-propagated stock viruses (n = 6). Using real time RT-PCR, we compared results from paired cloacal swab and samples collected on FTA cards from both experimentally infected mallards (Anasplatyrhynchos) and hunter-harvested waterfowl sampled along the Texas Gulf Coast. Based on the laboratory trials, the average minimal detectable viral titer was determined to be 1 x 10(4.7) median embryo infectious dose (EID50)/ml (range: 1 x 10(4.3) to 1 x 10(5.4) EID50/ml), and viral RNA was consistently detectable on the FTA cards for a minimum of 20 days and up to 30 days for most subtypes at room temperature (23 C) storage. Real-time RT-PCR of samples collected using the FTA cards showed fair to good agreement in live birds when compared with both real-time RT-PCR and virus isolation of swabs. AI virus detection rates in samples from several wild bird species were higher when samples were collected using the FTA cards compared with cloacal swabs. These results suggest that FTA cards can be used as an alternative sample collection method when traditional surveillance methods are not possible, especially in avian populations that have historically received limited testing or situations in which field conditions limit the ability to properly store or ship swab samples.

Design and development of a highly sensitive, field portable plasma source instrument for on-line liquid stream monitoring and real-time sample analysis

NASA Astrophysics Data System (ADS)

Duan, Yixiang; Su, Yongxuan; Jin, Zhe; Abeln, Stephen P.

2000-03-01

The development of a highly sensitive, field portable, low-powered instrument for on-site, real-time liquid waste stream monitoring is described in this article. A series of factors such as system sensitivity and portability, plasma source, sample introduction, desolvation system, power supply, and the instrument configuration, were carefully considered in the design of the portable instrument. A newly designed, miniature, modified microwave plasma source was selected as the emission source for spectroscopy measurement, and an integrated small spectrometer with a charge-coupled device detector was installed for signal processing and detection. An innovative beam collection system with optical fibers was designed and used for emission signal collection. Microwave plasma can be sustained with various gases at relatively low power, and it possesses high detection capabilities for both metal and nonmetal pollutants, making it desirable to use for on-site, real-time, liquid waste stream monitoring. An effective in situ sampling system was coupled with a high efficiency desolvation device for direct-sampling liquid samples into the plasma. A portable computer control system is used for data processing. The new, integrated instrument can be easily used for on-site, real-time monitoring in the field. The system possesses a series of advantages, including high sensitivity for metal and nonmetal elements; in situ sampling; compact structure; low cost; and ease of operation and handling. These advantages will significantly overcome the limitations of previous monitoring techniques and make great contributions to environmental restoration and monitoring.

Influence of various water quality sampling strategies on load estimates for small streams

USGS Publications Warehouse

Robertson, Dale M.; Roerish, Eric D.

1999-01-01

Extensive streamflow and water quality data from eight small streams were systematically subsampled to represent various water‐quality sampling strategies. The subsampled data were then used to determine the accuracy and precision of annual load estimates generated by means of a regression approach (typically used for big rivers) and to determine the most effective sampling strategy for small streams. Estimation of annual loads by regression was imprecise regardless of the sampling strategy used; for the most effective strategy, median absolute errors were ∼30% based on the load estimated with an integration method and all available data, if a regression approach is used with daily average streamflow. The most effective sampling strategy depends on the length of the study. For 1‐year studies, fixed‐period monthly sampling supplemented by storm chasing was the most effective strategy. For studies of 2 or more years, fixed‐period semimonthly sampling resulted in not only the least biased but also the most precise loads. Additional high‐flow samples, typically collected to help define the relation between high streamflow and high loads, result in imprecise, overestimated annual loads if these samples are consistently collected early in high‐flow events.

On-chip collection of particles and cells by AC electroosmotic pumping and dielectrophoresis using asymmetric microelectrodes

PubMed Central

Melvin, Elizabeth M.; Moore, Brandon R.; Gilchrist, Kristin H.; Grego, Sonia; Velev, Orlin D.

2011-01-01

The recent development of microfluidic “lab on a chip” devices requiring sample sizes <100 μL has given rise to the need to concentrate dilute samples and trap analytes, especially for surface-based detection techniques. We demonstrate a particle collection device capable of concentrating micron-sized particles in a predetermined area by combining AC electroosmosis (ACEO) and dielectrophoresis (DEP). The planar asymmetric electrode pattern uses ACEO pumping to induce equal, quadrilateral flow directed towards a stagnant region in the center of the device. A number of system parameters affecting particle collection efficiency were investigated including electrode and gap width, chamber height, applied potential and frequency, and number of repeating electrode pairs and electrode geometry. The robustness of the on-chip collection design was evaluated against varying electrolyte concentrations, particle types, and particle sizes. These devices are amenable to integration with a variety of detection techniques such as optical evanescent waveguide sensing. PMID:22662040

Relating Optical Properties of Dusts to their Mineralogical and Physical Interrelationships

NASA Astrophysics Data System (ADS)

Engelbrecht, J. P.; Moosmuller, H.; Jayanty, R. K. M.; Casuccio, G.; Pincock, S. L.

2015-12-01

The purpose of the project was to provide information on the mineralogical, chemical and physical interrelationships of re-suspended mineral dust samples collected as grab samples from global dust sources. Surface soil samples were collected from about 65 desert sites, including the southwestern USA (12), Mali (3), Chad (3), Morocco (1), Canary Islands (8), Cape Verde (1), Djibouti (1), Afghanistan (3), Iraq (6), Kuwait (5), Qatar (1), UAE (1), Serbia (3), China (5), Namibia (3), Botswana (4), Australia (3), and Chile (1). The < 38 μm sieved fraction of each sample was re-suspended in an entrainment chamber, from which the airborne mineral dust could be monitored, sampled and analyzed. Instruments integrated into the entrainment facility included two PM10 and two PM2.5 filter samplers, a beta attenuation gauge for the continuous measurement of PM10 and PM2.5particulate mass fractions, an aerodynamic particle size (APS) analyzer, and a three wavelength (405, 532, 781nm) photoacoustic resonator with integrating reciprocal nephelometer for monitoring absorption and scattering coefficients during the dust re-suspension process. Filter sample media included Teflon® membrane and quartz fiber filters for chemical analysis (71 species), and Nuclepore® filters for individual particle analysis by Scanning Electron Microscopy (SEM). The < 38 μm sieved fractions were also analyzed by X-ray diffraction for their mineral content while the > 38 μm, < 125 μm soil fractions were mineralogically characterized by optical microscopy. We will be presenting results on the optical measurements, also showing the relationship between single scattering albedo (SSA) at three different wavelengths, and chemical as well as mineralogical content and interdependencies of the entrained dust samples. Examples showing the relationships between the single scattering albedos of airborne dusts, and iron (Fe) in hematite, goethite, and clay minerals (montmorillonite, illite, palygorskite), will be discussed. Our goal is to establish a database of the optical, mineralogical, and chemical properties of dust samples collected at multiple global dust sources. These data can be for applications in climate modeling, remote sensing, visibility, health (medical geology), ocean fertilization, and damage to equipment.

Digital Learning Compass: Distance Education State Almanac 2017. North Dakota

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of North Dakota. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. West Virginia

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of West Virginia. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. South Dakota

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of South Dakota. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. North Carolina

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of North Carolina. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. Rhode Island

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Rhode Island. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. New Hampshire

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of New Hampshire. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. New Jersey

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of New Jersey. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. New Mexico

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of New Mexico. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. New York

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of New York. The sample for this analysis is comprised of all active, degree-granting…

Digital Learning Compass: Distance Education State Almanac 2017. South Carolina

ERIC Educational Resources Information Center

Seaman, Julia E.; Seaman, Jeff

2017-01-01

This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of South Carolina. The sample for this analysis is comprised of all active, degree-granting…

EVALUATION OF MACROINVERTEBRATE TRENDS IN STREAMS VULNERABLE TO ACID DEPOSITION IN THE MID-ATLANTIC HIGHLANDS REGION OF THE U.S.A.

EPA Science Inventory

Benthic macroinvertebrate and water chemistry samples were collected from wadeable stream sites in the Mid-Atlantic Highlands region of the U.S. during 1993-1995 and 2001 in support of USEPA's TIME (Temporally Integrated Monitoring of Ecosystems) Progam. This study was designed ...

High frequency signal acquisition and control system based on DSP+FPGA

NASA Astrophysics Data System (ADS)

Liu, Xiao-qi; Zhang, Da-zhi; Yin, Ya-dong

2017-10-01

This paper introduces a design and implementation of high frequency signal acquisition and control system based on DSP + FPGA. The system supports internal/external clock and internal/external trigger sampling. It has a maximum sampling rate of 400MBPS and has a 1.4GHz input bandwidth for the ADC. Data can be collected continuously or periodically in systems and they are stored in DDR2. At the same time, the system also supports real-time acquisition, the collected data after digital frequency conversion and Cascaded Integrator-Comb (CIC) filtering, which then be sent to the CPCI bus through the high-speed DSP, can be assigned to the fiber board for subsequent processing. The system integrates signal acquisition and pre-processing functions, which uses high-speed A/D, high-speed DSP and FPGA mixed technology and has a wide range of uses in data acquisition and recording. In the signal processing, the system can be seamlessly connected to the dedicated processor board. The system has the advantages of multi-selectivity, good scalability and so on, which satisfies the different requirements of different signals in different projects.

The 2015-2016 SEPMAP Program at NASA JSC: Science, Engineering, and Program Management Training

NASA Technical Reports Server (NTRS)

Graham, L.; Archer, D.; Bakalyar, J.; Berger, E.; Blome, E.; Brown, R.; Cox, S.; Curiel, P.; Eid, R.; Eppler, D.;

Metal pollution (Cd, Pb, Zn, and As) in agricultural soils and soybean, Glycine max, in southern China.

PubMed

Zhao, Yunyun; Fang, Xiaolong; Mu, Yinghui; Cheng, Yanbo; Ma, Qibin; Nian, Hai; Yang, Cunyi

2014-04-01

Crops produced on metal-polluted agricultural soils may lead to chronic toxicity to humans via the food chain. To assess metal pollution in agricultural soils and soybean in southern China, 30 soybean grain samples and 17 soybean-field soil samples were collected from 17 sites in southern China, and metal concentrations of samples were analyzed by graphite furnace atomic absorption spectrophotometer. The integrated pollution index was used to evaluate if the samples were contaminated by Cd, Pb, Zn and As. Results showed that Cd concentration of 12 samples, Pb concentration of 2 samples, Zn concentration of 2 samples, and As concentrations of 2 samples were above the maximum permissible levels in soils. The integrated pollution index indicated that 11 of 17 soil samples were polluted by metals. Metal concentrations in soybean grain samples ranged from 0.11 to 0.91 mg kg(-1) for Cd; 0.34 to 2.83 mg kg(-1) for Pb; 42 to 88 mg kg(-1) for Zn; and 0.26 to 5.07 mg kg(-1) for As, which means all 30 soybean grain samples were polluted by Pb, Pb/Cd, Cd/Pb/As or Pb/As. Taken together, our study provides evidence that metal pollution is an important concern in agricultural soils and soybeans in southern China.

Systems Perspective of Amazon Mechanical Turk for Organizational Research: Review and Recommendations

PubMed Central

Keith, Melissa G.; Tay, Louis; Harms, Peter D.

2017-01-01

Amazon Mechanical Turk (MTurk) is becoming a prevalent source of quick and cost effective data for organizational research, but there are questions about the appropriateness of the platform for organizational research. To answer these questions, we conducted an integrative review based on 75 papers evaluating the MTurk platform and 250 MTurk samples used in organizational research. This integrative review provides four contributions: (1) we analyze the trends associated with the use of MTurk samples in organizational research; (2) we develop a systems perspective (recruitment system, selection system, and work management system) to synthesize and organize the key factors influencing data collected on MTurk that may affect generalizability and data quality; (3) within each factor, we also use available MTurk samples from the organizational literature to analyze key issues (e.g., sample characteristics, use of attention checks, payment); and (4) based on our review, we provide specific recommendations and a checklist for data reporting in order to improve data transparency and enable further research on this issue. PMID:28848474

Misbehaviors of Front-Line Research Personnel and the Integrity of Community-Based Research

PubMed Central

True, Gala; Alexander, Leslie B.; Richman, Kenneth A.

2012-01-01

There has been little empirical research into misconduct and misbehavior among community research workers who recruit and collect data in vulnerable and marginalized health populations and are also members of those same communities. We conducted qualitative interviews with community research workers and traditional research assistants to understand the context and consequences of misbehaviors that pose a threat to research ethics and data integrity. In our sample, more community research workers acknowledged engaging in research wrongdoing than did traditional research assistants. These behaviors were most prevalent among community research workers who were not well-integrated into the research team. We suggest best practices for investigators to promote an environment that supports research integrity in research projects that employ community research workers. PMID:21680972

Characterization of Dust on Solar Devices in Southern Nevada =

NASA Astrophysics Data System (ADS)

Sylva, Jason R.

Dust can impact the efficiency of solar energy collection devices, and in some arid environments, dust can reduce solar energy efficiency up to 30%. Reducing the impact of dust is therefore critical in the expansion of solar technology throughout regions where solar energy is utilized. Characterization of suspended and settled particulate matter can assist in developing strategies for dust mitigation. With the characterization of suspended and settled particulate in remote, rural, and urban environments, more informed decisions can be made regarding the selection of coating material on solar panels as well as developing cleaning and maintenance procedures. Particulate matter that deposits on a solar surface can potentially interact with solar radiation, precipitation, or even directly with the surface material itself. These interactions could lead to the formation of coatings that reduce/block radiation and/or degrade the integrity of the surface. When you extrapolate these possibilities to a larger scale preliminary characterization of dust will play a vital role when planning the construction of a solar energy facility. A variety of sampling techniques were employed to obtain particulate matter for characterization. These included direct collection of particulates from solar surfaces: via vacuum and wipe sample collection on panels, tacky dot adhesive slides and plain slides that were exposed at different intervals, desert vugs that are natural particulate collectors, as well as high volume air sampling for collection of suspended particulates. High volume air sampling was performed using glass fiber filters and 2 micron stainless steel screens. Direct collection of settled particulates was performed by sampling from solar surfaces, vugs, and by collection on exposed glass surfaces. Collection onto glass surfaces was achieved by setting up a plain microscope slide, tacky dot slides, and panes of glass. The sampling methodology allowed for the collection of samples for analyses using various analytical methods that included Raman microspectroscopy, pyrolysis gas chromatography mass spectrometry, ion chromatography and inductively coupled plasma mass spectrometry. These various methods allow for identification of organic and inorganic components as well the mineral distribution of suspended and settled particulate material. None None None None None

ADVANCING SITE CHARACTERIZATION AND MONITORING ...

EPA Pesticide Factsheets

There is no astract available for htis product. If further information is requested, please refer to the bibliogaphic citation and contact the person listed under Contract field. The overall objective of this task is to provide the Agency with improved state-of-the-science guidance, strategies, and techniques to more accurately and effectively collect environmental samples. Under this umbrella objective, research is being conducted to: (a) reduce/minimize the loss of VOCs during sample collection, handling, and preservation, (b) collect undisturbed surface sediments so that the effects of recent depositional events (e.g., flooding or dredging) can clearly be delineated as to their influence on the contamination concentrations present downstream (or where the sediments are deposited), and (c) to determine an effective method to effectively and efficiently separate asbestos in soils from the rest of the soil matrix while maintaining the integrity (i.e, no fiber size reduction) of the asbestos fibers.

Comparison of Techniques for Sampling Adult Necrophilous Insects From Pig Carcasses.

PubMed

Cruise, Angela; Hatano, Eduardo; Watson, David W; Schal, Coby

2018-02-06

Studies of the pre-colonization interval and mechanisms driving necrophilous insect ecological succession depend on effective sampling of adult insects and knowledge of their diel and successional activity patterns. The number of insects trapped, their diversity, and diel periodicity were compared with four sampling methods on neonate pigs. Sampling method, time of day and decomposition age of the pigs significantly affected the number of insects sampled from pigs. We also found significant interactions of sampling method and decomposition day, time of sampling and decomposition day. No single method was superior to the other methods during all three decomposition days. Sampling times after noon yielded the largest samples during the first 2 d of decomposition. On day 3 of decomposition however, all sampling times were equally effective. Therefore, to maximize insect collections from neonate pigs, the method used to sample must vary by decomposition day. The suction trap collected the most species-rich samples, but sticky trap samples were the most diverse, when both species richness and evenness were factored into a Shannon diversity index. Repeated sampling during the noon to 18:00 hours period was most effective to obtain the maximum diversity of trapped insects. The integration of multiple sampling techniques would most effectively sample the necrophilous insect community. However, because all four tested methods were deficient at sampling beetle species, future work should focus on optimizing the most promising methods, alone or in combinations, and incorporate hand-collections of beetles. © The Author(s) 2018. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Investigating the effect of landfill leachates on the characteristics of dissolved organic matter in groundwater using excitation-emission matrix fluorescence spectra coupled with fluorescence regional integration and self-organizing map.

PubMed

He, Xiao-Song; Fan, Qin-Dong

2016-11-01

For the purpose of investigating the effect of landfill leachate on the characteristics of organic matter in groundwater, groundwater samples were collected near and in a landfill site, and dissolved organic matter (DOM) was extracted from the groundwater samples and characterized by excitation-emission matrix (EEM) fluorescence spectra combined with fluorescence regional integration (FRI) and self-organizing map (SOM). The results showed that the groundwater DOM comprised humic-, fulvic-, and protein-like substances. The concentration of humic-like matter showed no obvious variation for all groundwater except the sample collected in the landfill site. Fulvic-like substance content decreased when the groundwater was polluted by landfill leachates. There were two kinds of protein-like matter in the groundwater. One kind was bound to humic-like substances, and its content did not change along with groundwater pollution. However, the other kind was present as "free" molecules or else bound in proteins, and its concentration increased significantly when the groundwater was polluted by landfill leachates. The FRI and SOM methods both can characterize the composition and evolution of DOM in the groundwater. However, the SOM analysis can identify whether protein-like moieties was bound to humic-like matter.

Endocrine disrupting chemicals in Minnesota lakes - Water-quality and hydrological data from 2008 and 2010

USGS Publications Warehouse

Barber, Larry B.; Writer, Jeffrey H.; Keefe, Steffanie K.; Brown, Greg K.; Ferrey, Mark L.; Jahns, Nathan D.; Kiesling, Richard L.; Lundy, James R.; Poganski, Beth H.; Rosenberry, Donald O.; Taylor, Howard E.; Woodruff, Olivia P.; Schoenfuss, Heiko L.

2012-01-01

Understanding the sources, fate, and effects of endocrine disrupting chemicals in aquatic ecosystems is important for water-resource management. This study was conducted during 2008 and 2010 to establish a framework for assessing endocrine disrupting chemicals, and involved a statewide survey of their occurrence in 14 Minnesota lakes and a targeted study of different microhabitats on a single lake. The lakes ranged in size from about 0.1 to 100 square kilometers, varied in trophic status from oligotrophic to eutrophic, and spanned a range of land-uses from wetlands and forest to agricultural and urban use. Water and sediment samples were collected from the near-shore littoral environment and analyzed for endocrine disrupting chemicals, including trace elements, acidic organic compounds, neutral organic compounds, and steroidal hormones. In addition, polar organic compound integrative samplers were deployed for 21 days and analyzed for the same organic compounds. One lake was selected for a detailed microhabitat study of multiple near-shore environments. This report compiles the results from the field measurements and laboratory chemical analysis of water, sediment, and polar organic compound integrative sampler samples collected during 2008 and 2010. Most of the organic compounds measured were not detected in any of the water samples, although a few compounds were detected in several of the lakes.

A sampling procedure to guide the collection of narrow-band, high-resolution spatially and spectrally representative reflectance data. [satellite imagery of earth resources

NASA Technical Reports Server (NTRS)

Brand, R. R.; Barker, J. L.

1983-01-01

A multistage sampling procedure using image processing, geographical information systems, and analytical photogrammetry is presented which can be used to guide the collection of representative, high-resolution spectra and discrete reflectance targets for future satellite sensors. The procedure is general and can be adapted to characterize areas as small as minor watersheds and as large as multistate regions. Beginning with a user-determined study area, successive reductions in size and spectral variation are performed using image analysis techniques on data from the Multispectral Scanner, orbital and simulated Thematic Mapper, low altitude photography synchronized with the simulator, and associated digital data. An integrated image-based geographical information system supports processing requirements.

Apparatus to collect, classify, concentrate, and characterize gas-borne particles

DOEpatents

Rader, Daniel J.; Torczynski, John R.; Wally, Karl; Brockmann, John E.

2003-12-16

An aerosol lab-on-a-chip (ALOC) integrates one or more of a variety of particle collection, classification, concentration (enrichment), an characterization processes onto a single substrate or layered stack of such substrates. By mounting a UV laser diode laser light source on the substrate, or substrates tack, so that it is located down-stream of the sample inlet port and at right angle the sample particle stream, the UV light source can illuminate individual particles in the stream to induce a fluorescence response in those particles having a fluorescent signature such as biological particles, some of said particles. An illuminated particle having a fluorescent signal above a threshold signal would trigger a sorter module that would separate that particle from the particle stream.

Analysis of the contaminants released from municipal solid waste landfill site: A case study.

PubMed

Samadder, S R; Prabhakar, R; Khan, D; Kishan, D; Chauhan, M S

2017-02-15

Release and transport of leachate from municipal solid waste landfills pose a potential hazard to both surrounding ecosystems and human populations. In the present study, soil, groundwater, and surface water samples were collected from the periphery of a municipal solid waste landfill (located at Ranital of Jabalpur, Madhya Pradesh, India) for laboratory analysis to understand the release of contaminants. The landfill does not receive any solid wastes for dumping now as the same is under a landfill closure plan. Groundwater and soil samples were collected from the bore holes of 15m deep drilled along the periphery of the landfill and the surface water samples were collected from the existing surface water courses near the landfill. The landfill had neither any bottom liner nor any leachate collection and treatment system. Thus the leachate generated from the landfills finds paths into the groundwater and surrounding surface water courses. Concentrations of various physico-chemical parameters including some toxic metals (in collected groundwater, soil, and surface water samples) and microbiological parameters (in surface water samples) were determined. The analyzed data were integrated into ArcGIS environment and the spatial distribution of the metals and other physic- chemical parameter across the landfill was extrapolated to observe the distribution. The statistical analysis and spatial variations indicated the leaching of metals from the landfill to the groundwater aquifer system. The study will help the readers and the municipal engineers to understand the release of contaminants from landfills for better management of municipal solid wastes. Copyright © 2016 Elsevier B.V. All rights reserved.

Measurement of the production cross section of a W boson in association with two b jets in pp collisions at $$\\sqrt{s}$$ = 8 TeV

DOE PAGES

Khacahtryan, V.

2017-02-11

The production cross section of a W boson in association with two b jets is measured using a sample of proton-proton collisions atmore » $$ \\sqrt{s} = $$ 8 TeV collected by the CMS experiment at the CERN LHC. The data sample corresponds to an integrated luminosity of 19.8 fb$$^{-1}$$. The W bosons are reconstructed via their leptonic decays, $$ \\mathrm{ W }\\to\\ell\

Eutrophication monitoring for Lake Superior's Chequamegon ...

EPA Pesticide Factsheets

A priority for the Lake Superior CSMI was to identify susceptible nearshore eutrophication areas. We developed an integrated sampling design to collect baseline data for Lake Superior’s Chequamegon Bay to understand how nearshore physical processes and tributary loading relate to observed chlorophyll concentrations. Sampling included ship-based water samples combined with vertical CTD casts, continuous in situ towing and data collected from an autonomous underwater glider. Sampling was conducted during June, July and September. The glider collected regional data as part of three extended missions in Lake Superior over the same periods. During the study, two significant storm events impacted the western end of Lake Superior; the first occurred during July 11-12, with 8-10 inches of rain in 24hrs, and the second on July 21 with winds in excess of 161 km/h. Using GIS software, we organized these diverse temporal data sets along a continuous time line with temporally coincident Modis Satellite data to visualize surface sediment plumes in relation to water quality measurements. Preliminary results suggest that both events impacted regional water quality, and that nearshore physical forces (upwelling and currents) influenced the spatial variability. Results comparing in situ measures with remotely sensed images will be discussed. not applicable

Data Flow Infrastructure Initiative (DFII): Coupling Inventory Practices and Data collection Technology to Enhance Research Productivity and Information Access

NASA Astrophysics Data System (ADS)

Meyer, K.; Malin, R.; Rich, R. L.; Pierce, S. A.

2011-12-01

Shortening the cycle from data collection to research publications is a competitive advantage for researchers. Existing technologies for inventory systems such as UPC barcoding systems can be coupled with flexible mobile or handheld devices to advance efficiency, productivity, automation, and integrity in data flows, from data collection to sample processing to database management and analysis, and finally publication. At the University of Texas, the Data Flow Infrastructure Initiative (DFII) has introduced handheld devices with integrated barcode scanners as a mechanism to enhance research productivity and information access. These devices are established technology and provide a flexible but consistent platform for research data collection and data management. They are not in widespread use yet in the research community. Additional application benefits will accrue by using handheld devices to deliver data on demand in teaching applications. Introducing research scientists, graduate students, and the UT community to the merits and flexibility of these data collection technologies will provide avenues for innovation as well as improving efficiency. The objective of this project is to bring the technology and expertise with handheld systems to a diverse set of pilot projects and establish proficiency at The University of Texas at Austin necessary for widespread application. We have implemented a pilot project in three research labs covering the fields of microbial ecology, water resources decision support, and biogeochemistry to introduce these technologies. We used NautizX5 handheld devices that feature: barcode scanning, bluetooth, stylus, and keypad data inputs coupled with Pendragon Forms Software, a program that allows users to create custom data collection forms structured into an SQL or Access platform thus allowing concurrent data management, data collection and analysis in field and lab settings. Results include the elimination of most manual data entry, reducing data entry error, tracking effectiveness at data collection, and increased sampling efficiency and consistency over multi-year experiments.

Questa baseline and pre-mining ground-water quality investigation. 2. Low-flow (2001) and snowmelt (2002) synoptic/tracer water chemistry for the Red River, New Mexico

USGS Publications Warehouse

McCleskey, R. Blaine; Nordstrom, D. Kirk; Steiger, Judy I.; Kimball, Briant A.; Verplanck, Philip L.

2003-01-01

Water analyses are reported for 259 samples collected from the Red River, New Mexico, and its tributaries during low-flow(2001) and spring snowmelt (2002) tracer studies. Water samples were collected along a 20-kilometer reach of the Red River beginning just east of the town of Red River and ending at the U.S. Geological Survey streamflow-gaging station located east of Questa, New Mexico. The study area was divided into three sections where separate injections and synoptic sampling events were performed during the low-flow tracer study. During the spring snowmelt tracer study, three tracer injections and synoptic sampling events were performed bracketing the areas with the greatest metal loading into the Red River as determined from the low-flow tracer study. The lowflow tracer synoptic sampling events were August 17, 20, and 24, 2001. The synoptic sampling events for the spring snowmelt tracer were March 30, 31, and April 1, 2002. Stream and large inflow water samples were sampled using equal-width and depth-integrated sampling methods and composited into half-gallon bottles. Grab water samples were collected from smaller inflows. Stream temperatures were measured at the time of sample collection. Samples were transported to a nearby central processing location where pH and specific conductance were measured and the samples processed for chemical analyses. Cations, trace metals, iron redox species, and fluoride were analyzed at the U.S. Geological Survey laboratory in Boulder, Colorado. Cations and trace metal concentrations were determined using inductively coupled plasma-optical emission spectrometry and graphite furnace atomic absorption spectrometry. Arsenic concentrations were determined using hydride generation atomic absorption spectrometry, iron redox species were measured using ultraviolet-visible spectrometry, and fluoride concentrations were determined using an ion-selective electrode. Alkalinity was measured by automated titration, and sulfate, chloride, and bromide were analyzed by ion chromatography at the U.S. Geological Survey laboratory in Salt Lake City, Utah.

Molecular characterization of avipoxviruses circulating in Mozambique, 2016-2018.

PubMed

Mapaco, Lourenço P; Lacerda, Zeiss; Monjane, Iolanda V A; Sussuro, Afonso; Viljoen, Gerrit J; Cattoli, Giovanni; Dundon, William G; Achá, Sara J

2018-05-08

Samples from 45 chickens, two turkeys, one peacock and one quail with symptoms of fowlpox were collected in Mozambique between November 2016 and January 2018. Phylogenetic analysis revealed that the samples contained avipoxviruses belonging to both clade A1 and clade A2. In addition, all of the Clade A1 viruses were positive by PCR for the integration of reticuloendotheliosis virus, while the clade A2 avipoxvirus samples were negative. This study confirms the circulation of clade A1 avipoxviruses in Mozambique in addition to identifying clade A2 for the first time in the country.

The effect of Curcuma longa extracted (curcumin) on the quality of cryopreserved boar semen.

PubMed

Chanapiwat, Panida; Kaeoket, Kampon

2015-09-01

The aim of this study was to determine the optimal concentration of curcumin needed for cryopreservation of boar semen. Semen samples (n = 9) were collected from nine Duroc boars which having proven fertility were used for routine artificial insemination. Semen samples were collected and divided into six groups (groups A-F) according to various concentrations of curcumin in freezing extender (i.e. 0, 0.125, 0.25, 0.50, 0.75 and 1.0 mmol/L, respectively). The semen was frozen by traditional liquid nitrogen vapor method and stored at -196°C in the liquid nitrogen tank. After storage, frozen semen samples were thawed at 50°C for 12 s and evaluated for progressive motility, viability and acrosome integrity. The present results indicated that the addition of curcumin at 0.25 (group C) or 0.50 mmol/L curcumin (group D) yielded the higher percentage of progressive motility (33.3 and 36.1%, respectively) (P < 0.001). A significantly higher percentage of acrosome integrity was found in groups B (29.7%), C (31.1%) and D (30.2%) than in the other groups (P < 0.01). However, there was no significant difference in percentage of viability among groups. In conclusion, addition to the freezing extender of curcumin during cryopreservation at a concentration of 0.25 or 0.50 mmol/L is the optimal concentration of curcumin for improving the quality (i.e. increased progressive motility and acrosome integrity) of cryopreserved boar semen. © 2015 Japanese Society of Animal Science.

Cell-free DNA detected by "liquid biopsy" as a potential prognostic biomarker in early breast cancer.

PubMed

Maltoni, Roberta; Casadio, Valentina; Ravaioli, Sara; Foca, Flavia; Tumedei, Maria Maddalena; Salvi, Samanta; Martignano, Filippo; Calistri, Daniele; Rocca, Andrea; Schirone, Alessio; Amadori, Dino; Bravaccini, Sara

2017-03-07

As conventional biomarkers for defining breast cancer (BC) subtypes are not always capable of predicting prognosis, search for new biomarkers which can be easily detected by liquid biopsy is ongoing. It has long been known that cell-free DNA (CF-DNA) could be a promising diagnostic and prognostic marker in different tumor types, although its prognostic value in BC is yet to be confirmed. This retrospective study evaluated the prognostic role of CF-DNA quantity and integrity of HER2, MYC, BCAS1 and PI3KCA, which are frequently altered in BC. We collected 79 serum samples before surgery from women at first diagnosis of BC at Forlì Hospital (Italy) from 2002 to 2010. Twenty-one relapsed and 58 non-relapsed patients were matched by subtype and age. Blood samples were also collected from 10 healthy donors. All samples were analyzed by Real Time PCR for CF-DNA quantity and integrity of all oncogenes. Except for MYC, BC patients showed significantly higher median values of CF-DNA quantity (ng) than healthy controls, who had higher integrity and lower apoptotic index. A difference nearing statistical significance was observed for HER2 short CF-DNA (p = 0.078, AUC value: 0.6305). HER2 short CF-DNA showed an odds ratio of 1.39 for disease recurrence with p = 0.056 (95% CI 0.991-1.973). Our study suggests that CF-DNA detected as liquid biopsy could have great potential in clinical practice once demonstration of its clinical validity and utility has been provided by prospective studies with robust assays.

Polyphyly and hidden species among Hawaiʻi’s dominant mesophotic coral genera, Leptoseris and Pavona (Scleractinia: Agariciidae)

PubMed Central

Forsman, Zac H.; Toonen, Robert J.; Leicht, Sarah J.; Kahng, Samuel E.

2013-01-01

Widespread polyphyly in stony corals (order Scleractinia) has prompted efforts to revise their systematics through approaches that integrate molecular and micromorphological evidence. To date, these approaches have not been comprehensively applied to the dominant genera in mesophotic coral ecosystems (MCEs) because several species in these genera occur primarily at depths that are poorly explored and from which sample collections are limited. This study is the first integrated morphological and molecular systematic analysis of the genera Leptoseris and Pavona to examine material both from shallow-water reefs (<30 m) and from mid- to lower-MCEs (>60 m). Skeletal and tissue samples were collected throughout the Hawaiian Archipelago between 2–127 m. A novel mitochondrial marker (cox1-1-rRNA intron) was sequenced for 70 colonies, and the micromorphologies of 94 skeletons, plus selected type material, were analyzed. The cox1-1-rRNA intron resolved 8 clades, yet Leptoseris and Pavona were polyphyletic. Skeletal micromorphology, especially costal ornamentation, showed strong correspondence and discrete differences between mitochondrial groups. One putative new Leptoseris species was identified and the global depth range of the genus Pavona was extended to 89 m, suggesting that the diversity of mesophotic scleractinians has been underestimated. Examination of species’ depth distributions revealed a pattern of depth zonation: Species common in shallow-water were absent or rare >40 m, whereas others occurred only >60 m. These patterns emphasize the importance of integrated systematic analyses and more comprehensive sampling by depth in assessing the connectivity and diversity of MCEs. PMID:24032091

Autonomous microfluidic sample preparation system for protein profile-based detection of aerosolized bacterial cells and spores.

PubMed

Stachowiak, Jeanne C; Shugard, Erin E; Mosier, Bruce P; Renzi, Ronald F; Caton, Pamela F; Ferko, Scott M; Van de Vreugde, James L; Yee, Daniel D; Haroldsen, Brent L; VanderNoot, Victoria A

2007-08-01

For domestic and military security, an autonomous system capable of continuously monitoring for airborne biothreat agents is necessary. At present, no system meets the requirements for size, speed, sensitivity, and selectivity to warn against and lead to the prevention of infection in field settings. We present a fully automated system for the detection of aerosolized bacterial biothreat agents such as Bacillus subtilis (surrogate for Bacillus anthracis) based on protein profiling by chip gel electrophoresis coupled with a microfluidic sample preparation system. Protein profiling has previously been demonstrated to differentiate between bacterial organisms. With the goal of reducing response time, multiple microfluidic component modules, including aerosol collection via a commercially available collector, concentration, thermochemical lysis, size exclusion chromatography, fluorescent labeling, and chip gel electrophoresis were integrated together to create an autonomous collection/sample preparation/analysis system. The cycle time for sample preparation was approximately 5 min, while total cycle time, including chip gel electrophoresis, was approximately 10 min. Sensitivity of the coupled system for the detection of B. subtilis spores was 16 agent-containing particles per liter of air, based on samples that were prepared to simulate those collected by wetted cyclone aerosol collector of approximately 80% efficiency operating for 7 min.

Multiplexed Quantitation of Endogenous Proteins in Dried Blood Spots by Multiple Reaction Monitoring - Mass Spectrometry

PubMed Central

Chambers, Andrew G.; Percy, Andrew J.; Yang, Juncong; Camenzind, Alexander G.; Borchers, Christoph H.

2013-01-01

Dried blood spot (DBS) sampling, coupled with multiple reaction monitoring mass spectrometry (MRM-MS), is a well-established approach for quantifying a wide range of small molecule biomarkers and drugs. This sampling procedure is simpler and less-invasive than those required for traditional plasma or serum samples enabling collection by minimally trained personnel. Many analytes are stable in the DBS format without refrigeration, which reduces the cost and logistical challenges of sample collection in remote locations. These advantages make DBS sample collection desirable for advancing personalized medicine through population-wide biomarker screening. Here we expand this technology by demonstrating the first multiplexed method for the quantitation of endogenous proteins in DBS samples. A panel of 60 abundant proteins in human blood was targeted by monitoring proteotypic tryptic peptides and their stable isotope-labeled analogs by MRM. Linear calibration curves were obtained for 40 of the 65 peptide targets demonstrating multiple proteins can be quantitatively extracted from DBS collection cards. The method was also highly reproducible with a coefficient of variation of <15% for all 40 peptides. Overall, this assay quantified 37 proteins spanning a range of more than four orders of magnitude in concentration within a single 25 min LC/MRM-MS analysis. The protein abundances of the 33 proteins quantified in matching DBS and whole blood samples showed an excellent correlation, with a slope of 0.96 and an R2 value of 0.97. Furthermore, the measured concentrations for 80% of the proteins were stable for at least 10 days when stored at −20 °C, 4 °C and 37 °C. This work represents an important first step in evaluating the integration of DBS sampling with highly-multiplexed MRM for quantitation of endogenous proteins. PMID:23221968

Trace element and Nd, Sr, Pb isotope geochemistry of Kilauea Volcano, Hawai'i, near-vent eruptive products: 1983-2001

USGS Publications Warehouse

Thornber, Carl R.; Budahn, James R.; Ridley, W. Ian; Unruh, Daniel M.

2003-01-01

This open-file report serves as a repository for geochemical data referred to in U.S. Geological Survey Professional Paper 1676 (Heliker, Swanson, and Takahashi, eds., 2003), which includes multidisciplinary research papers pertaining to the first twenty years of Puu Oo Kupaianaha eruption activity. Details of eruption characteristics and nomenclature are provided in the introductory chapter of that volume (Heliker and Mattox, 2003). Geochemical relations of this data are depicted and interpreted by Thornber (2003), Thornber and others (2003a) and Thornber (2001). This report supplements Thornber and others (2003b) in which whole-rock and glass major-element data on ~1000 near-vent lava samples collected during the 1983 to 2001 eruptive interval of Kilauea Volcano, Hawai'i, are presented. Herein, we present whole-rock trace element compositions of 85 representative samples collected from January 1983 to May 2001; glass trace-element compositions of 39 Pele’s Tear (tephra) samples collected from September 1995 to September 1996, and whole-rock Nd, Sr and Pb isotopic analyses of 10 representative samples collected from September 1983 to September 1993. Thornber and others (2003b) provide a specific record of sample characteristics, location, etc., for each of the samples reported here. Spreadsheets of both reports may be integrated and sorted based upon time of formation or sample numbers. General information pertaining to the selectivity and petrologic significance of this sample suite is presented by Thornber and others (2003b). As justified in that report, this select suite of time-constrained geochemical data is suitable for constructing petrologic models of pre-eruptive magmatic processes associated with prolonged rift zone eruption of Hawaiian shield volcanoes.

A Prototype Ice-Melting Probe for Collecting Biological Samples from Cryogenic Ice at Low Pressure.

PubMed

Davis, Ashley

2017-08-01

In the Solar System, the surface of an icy moon is composed of irregular ice formations at cryogenic temperatures (<200 K), with an oxidized surface layer and a tenuous atmosphere at very low pressure (<10 -6 atm). A lander mission, whose aim is to collect and analyze biological samples from the surface ice, must contain a device that collects samples without refreezing liquid and without sublimation of ice. In addition, if the samples are biological in nature, then precautions must be taken to ensure the samples do not overheat or mix with the oxidized layer. To achieve these conditions, the collector must maintain temperatures close to maintenance or growth conditions of the organism (<293 K), and it must separate or neutralize the oxidized layer and be physically gentle. Here, we describe a device that addresses these requirements and is compatible with low atmospheric pressure while using no pumps. The device contains a heated conical probe with a central orifice, which is forced into surface ice and directs the meltwater upward into a reservoir. The force on the probe is proportional to the height of meltwater (pressure) obtained in the system and allows regulation of the melt rate and temperature of the sample. The device can collect 5-50 mL of meltwater from the surface of an ice block at 233-208 K with an environmental pressure of less than 10 -2 atm while maintaining a sample temperature between 273 and 293 K. These conditions maintain most biological samples in a pristine state and maintain the integrity of most organisms' structure and function. Key Words: Europa-Icy moon-Microbe-Eukaryote-Spacecraft. Astrobiology 17, 709-720.

Development and Testing of a USM High Altitude Balloon

NASA Astrophysics Data System (ADS)

Thaheer, A. S. Mohamed; Ismail, N. A.; Yusoff, S. H. Md.; Nasirudin, M. A.

2018-04-01

This paper discusses on tests conducted on the component and subsystem level during development of the USM High Altitude Balloon (HAB). The tests conducted by selecting initial components then tested individually based on several case studies such as reliability test, camera viewing, power consumption, thermal capability, and parachute performance. Then, the component is integrated into sub-system level for integration and functionality test. The preliminary result is utilized to tune the components and sub-systems and trial launch is conducted where the sample images are recorded and atmospheric data successfully collected.

Label-free single-cell separation and imaging of cancer cells using an integrated microfluidic system

PubMed Central

Antfolk, Maria; Kim, Soo Hyeon; Koizumi, Saori; Fujii, Teruo; Laurell, Thomas

2017-01-01

The incidence of cancer is increasing worldwide and metastatic disease, through the spread of circulating tumor cells (CTCs), is responsible for the majority of the cancer deaths. Accurate monitoring of CTC levels in blood provides clinical information supporting therapeutic decision making, and improved methods for CTC enumeration are asked for. Microfluidics has been extensively used for this purpose but most methods require several post-separation processing steps including concentration of the sample before analysis. This induces a high risk of sample loss of the collected rare cells. Here, an integrated system is presented that efficiently eliminates this risk by integrating label-free separation with single cell arraying of the target cell population, enabling direct on-chip tumor cell identification and enumeration. Prostate cancer cells (DU145) spiked into a sample with whole blood concentration of the peripheral blood mononuclear cell (PBMC) fraction were efficiently separated and trapped at a recovery of 76.2 ± 5.9% of the cancer cells and a minute contamination of 0.12 ± 0.04% PBMCs while simultaneously enabling a 20x volumetric concentration. This constitutes a first step towards a fully integrated system for rapid label-free separation and on-chip phenotypic characterization of circulating tumor cells from peripheral venous blood in clinical practice. PMID:28425472

Label-free single-cell separation and imaging of cancer cells using an integrated microfluidic system.

PubMed

Antfolk, Maria; Kim, Soo Hyeon; Koizumi, Saori; Fujii, Teruo; Laurell, Thomas

2017-04-20

The incidence of cancer is increasing worldwide and metastatic disease, through the spread of circulating tumor cells (CTCs), is responsible for the majority of the cancer deaths. Accurate monitoring of CTC levels in blood provides clinical information supporting therapeutic decision making, and improved methods for CTC enumeration are asked for. Microfluidics has been extensively used for this purpose but most methods require several post-separation processing steps including concentration of the sample before analysis. This induces a high risk of sample loss of the collected rare cells. Here, an integrated system is presented that efficiently eliminates this risk by integrating label-free separation with single cell arraying of the target cell population, enabling direct on-chip tumor cell identification and enumeration. Prostate cancer cells (DU145) spiked into a sample with whole blood concentration of the peripheral blood mononuclear cell (PBMC) fraction were efficiently separated and trapped at a recovery of 76.2 ± 5.9% of the cancer cells and a minute contamination of 0.12 ± 0.04% PBMCs while simultaneously enabling a 20x volumetric concentration. This constitutes a first step towards a fully integrated system for rapid label-free separation and on-chip phenotypic characterization of circulating tumor cells from peripheral venous blood in clinical practice.

BioDry: An Inexpensive, Low-Power Method to Preserve Aquatic Microbial Biomass at Room Temperature.

PubMed

Tuorto, Steven J; Brown, Chris M; Bidle, Kay D; McGuinness, Lora R; Kerkhof, Lee J

2015-01-01

This report describes BioDry (patent pending), a method for reliably preserving the biomolecules associated with aquatic microbial biomass samples, without the need of hazardous materials (e.g. liquid nitrogen, preservatives, etc.), freezing, or bulky storage/sampling equipment. Gel electrophoresis analysis of nucleic acid extracts from samples treated in the lab with the BioDry method indicated that molecular integrity was protected in samples stored at room temperature for up to 30 days. Analysis of 16S/18S rRNA genes for presence/absence and relative abundance of microorganisms using both 454-pyrosequencing and TRFLP profiling revealed statistically indistinguishable communities from control samples that were frozen in liquid nitrogen immediately after collection. Seawater and river water biomass samples collected with a portable BioDry "field unit", constructed from off-the-shelf materials and a battery-operated pumping system, also displayed high levels of community rRNA preservation, despite a slight decrease in nucleic acid recovery over the course of storage for 30 days. Functional mRNA and protein pools from the field samples were also effectively conserved with BioDry, as assessed by respective RT-PCR amplification and western blot of ribulose-1-5-bisphosphate carboxylase/oxygenase. Collectively, these results demonstrate that BioDry can adequately preserve a suite of biomolecules from aquatic biomass at ambient temperatures for up to a month, giving it great potential for high resolution sampling in remote locations or on autonomous platforms where space and power are limited.

BioDry: An Inexpensive, Low-Power Method to Preserve Aquatic Microbial Biomass at Room Temperature

PubMed Central

Tuorto, Steven J.; Brown, Chris M.; Bidle, Kay D.; McGuinness, Lora R.; Kerkhof, Lee J.

2015-01-01

This report describes BioDry (patent pending), a method for reliably preserving the biomolecules associated with aquatic microbial biomass samples, without the need of hazardous materials (e.g. liquid nitrogen, preservatives, etc.), freezing, or bulky storage/sampling equipment. Gel electrophoresis analysis of nucleic acid extracts from samples treated in the lab with the BioDry method indicated that molecular integrity was protected in samples stored at room temperature for up to 30 days. Analysis of 16S/18S rRNA genes for presence/absence and relative abundance of microorganisms using both 454-pyrosequencing and TRFLP profiling revealed statistically indistinguishable communities from control samples that were frozen in liquid nitrogen immediately after collection. Seawater and river water biomass samples collected with a portable BioDry “field unit", constructed from off-the-shelf materials and a battery-operated pumping system, also displayed high levels of community rRNA preservation, despite a slight decrease in nucleic acid recovery over the course of storage for 30 days. Functional mRNA and protein pools from the field samples were also effectively conserved with BioDry, as assessed by respective RT-PCR amplification and western blot of ribulose-1-5-bisphosphate carboxylase/oxygenase. Collectively, these results demonstrate that BioDry can adequately preserve a suite of biomolecules from aquatic biomass at ambient temperatures for up to a month, giving it great potential for high resolution sampling in remote locations or on autonomous platforms where space and power are limited. PMID:26710122

The influence of nursing care integration services on nurses' work satisfaction and quality of nursing care.

PubMed

Ryu, Jeong-Im; Kim, Kisook

2018-06-20

To investigate differences in work satisfaction and quality of nursing services between nurses from the nursing care integration service and general nursing units in Korea. The nursing care integration service was recently introduced in Korea to improve patient health outcomes through the provision of high quality nursing services and to relieve the caregiving burden of patients' families. In this cross-sectional study, data were collected from a convenience sample of 116 and 156 nurses working in nursing care integration service and general units, respectively. The data were analysed using descriptive statistics, t tests and one-way analysis of variance. Regarding work satisfaction, nursing care integration service nurses scored higher than general unit nurses on professional status, autonomy and task requirements, but the overall scores showed no significant differences. Scores on overall quality of nursing services, responsiveness and assurance were higher for nursing care integration service nurses than for general unit nurses. Nursing care integration service nurses scored higher than general unit nurses on some aspects of work satisfaction and quality of nursing services. Further studies with larger sample sizes will contribute to improving the quality of nursing care integration service units. These findings can help to establish strategies for the implementation and efficient operation of the nursing care integration service system, for the improvement of the quality of nursing services, and for successfully implementing and expanding nursing care integration service services in other countries. © 2018 John Wiley & Sons Ltd.

Integrating clicker technology at nursing conferences: an innovative approach to research data collection.

PubMed

Solecki, Susan; Cornelius, Frances; Draper, Judy; Fisher, Kathleen

2010-06-01

A pilot demonstration of integrating an audience response system, that is, 'clickers' at a nursing education conference as an engaging tool for using the research process for learning through immediate research results is presented. A convenience sample of nursing conference attendees were surveyed using clicker technology before a panel presentation on the 'Impaired Health Professional'. The 208 subjects who used the clickers were mostly women (93%) and were nurse educators (81%) with at least 20 years of nursing experience (75%). The ease of data collection, real-time analysis, the active engagement of both participant and presenter were all findings of this study. The utility of this tool as a stimulus for discussion and learning was also reported. Pilot testing the clicker at an education conference for data collection and educational purposes was an important goal and positive outcome of this study. Researchers and educators are advised on the planning steps required to make this a successful experience.

Feasibility of semen collection in red-winged tinamou (Rhynchotus rufescens) by manual stimulation and sazonality implications.

PubMed

Paranzini, Cristiane Sella; Correia, Luiz Eduardo Cruz Dos Santos; de Camargo, Laiza Sartori; Silva, Kelry Mayara; de França, Tatyana Mendes; Silva, Josineudson Augusto de Vasconcelos; Veiga, Nabor; de Souza, Fabiana Ferreira

2018-02-01

This study aimed to report in detail, the technique and challenges of cloacal massage, to collect and evaluate semen from red-winged tinamou (Rhynchotus rufescens) keep in captivity, performed by only one technician. Sixty-four semen collection attempts, from 16 adult males, during breeding season and 16 attempts form these same 16 males in non-breeding season, were performed. Prior to collection, all animals were conditioned to cloacal massage for 6 weeks and the ejaculates were succeed with viable spermatozoa and then, evaluated for feces, urine and mucus contamination, volume, concentration, sperm vigor, motility, morphological defects and acrosome integrity. Semen collection success rate was 63% in breeding season and 2 (5%) samples were discarded by grade 5 contamination. Only 3 ejaculates from 16 tinamou were obtained in non-breeding season. Sperm concentration and acrosome integrity was higher (p = 0.00) in breeding season, and the percentage of total sperm morphological defects, were high in both in breeding and out breeding season. Overall, we concluded that the red-winged tinamou breeding season, is linked to photoperiod (spring and summer), and at this period time, semen can be obtained by cloacal massage collection satisfactorily, allowing its use in reproduction biotechnologies and sperm cryopreservation. Copyright © 2017 Elsevier Inc. All rights reserved.

When is success not satisfying? Integrating regulatory focus and approach/avoidance motivation theories to explain the relation between core self-evaluation and job satisfaction.

PubMed

Ferris, D Lance; Johnson, Russell E; Rosen, Christopher C; Djurdjevic, Emilija; Chang, Chu-Hsiang Daisy; Tan, James A

2013-03-01

Integrating implications from regulatory focus and approach/avoidance motivation theories, we present a framework wherein motivational orientations toward positive (approach motivation orientation) or negative (avoidance motivation orientation) stimuli interact with workplace success to mediate the relation of core self-evaluation (CSE) with job satisfaction. Using data collected from supervisor-subordinate dyads (Sample 1) and time-lagged data (Sample 2), we found that the results from two studies indicated that the interaction of workplace success and avoidance motivation orientation mediated relations of CSE with job satisfaction. Although approach motivation orientation did not interact with workplace success, it did mediate the CSE-job satisfaction relation on its own. Implications for the CSE and approach/avoidance literatures are discussed.

User-driven integrated software lives: ``Paleomag'' paleomagnetics analysis on the Macintosh

NASA Astrophysics Data System (ADS)

Jones, Craig H.

2002-12-01

"PaleoMag," a paleomagnetics analysis package originally developed for the Macintosh operating system in 1988, allows examination of demagnetization of individual samples and analysis of directional data from collections of samples. Prior to recent reinvigorated development of the software for both Macintosh and Windows, it was widely used despite not running properly on machines and operating systems sold after 1995. This somewhat surprising situation demonstrates that there is a continued need for integrated analysis software within the earth sciences, in addition to well-developed scripting and batch-mode software. One distinct advantage of software like PaleoMag is in the ability to combine quality control with analysis within a unique graphical environment. Because such demands are frequent within the earth sciences, means of nurturing the development of similar software should be found.

Seasonal and diurnal analysis of NO2 concentrations from a long-duration study conducted in Las Vegas, Nevada

EPA Science Inventory

A study, conducted in Las Vegas, NV from mid-December 2008 to mid-December 2009 along an interstate highway, collected continuous and integrated ambient air quality samples for a wide variety of species including NO2 and NOX. Previous near-road studies have been short duration, ...

PREDICTING BENTHIC STRESS IN RELATION TO SEDIMENT CONTAMINATION FROM INTEGRATED ASSESSMENTS ALONG THE U.S. ATLANTIC AND GULF OF MEXICO COASTS

EPA Science Inventory

Matching data on sediment contaminants and macroinfauna from 1,349 samples collected in estuaries along the U.S. Atlantic and Gulf of Mexico coasts were used to estimate risks of bioeffects from multiple-contaminant exposure. Sediment contamination was expressed as the mean ratio...

Analysis of the Integration of Skill Standards into Community College Curriculum

ERIC Educational Resources Information Center

Aragon, Steven R.; Woo, Hui-Jeong; Marvel, Matthew R.

2005-01-01

The utilization of skill standards in the curriculum development process has become an increasingly prominent aspect of the reform movement in career and technical education (CTE) over the past 10 years. Data were collected across 10 CTE program areas from a nationally representative sample of community colleges. The authors discuss the extent to…

Integrating Factors of Grit in School Culture: Case Studies of Two Freshman Academies

ERIC Educational Resources Information Center

Coates, Margaret Marie

2017-01-01

The purpose of this qualitative case study is to explore the cultural manifestation of grit in two freshman academy environments and describe factors of grit that support student success. This study used purposeful sampling to select sites and participants. Data were collected through: administration of Douglas' (1982) grid and group 24-question…

Understanding Employee Wellness among Non-Supervisory, Front-Line Employees in Three Maryland Industries: A Focus Group Study

ERIC Educational Resources Information Center

Russell, Mia B.

2017-01-01

Organizations are increasingly interested in improving the personal wellness of employees. The purpose of this qualitative study was to explore perceptions of wellness and workplace influences among a diverse sample of employees (n = 22) in three Maryland industries. Data were collected using focus group methodology and integrating human needs…

Using water stable isotopes to assess evaporation and water residence time of lakes in EPA’s National Lakes Assessment.

EPA Science Inventory

Stable isotopes of water (18O and 2H) can be very useful in large-scale monitoring programs because water samples are easy to collect and water isotopes integrate information about basic hydrological processes such as evaporation as a percentage of inflow (E/I), w...

A Qualitative Phenomenological Study of Emotional and Cultural Intelligence of International Students in the United States of America

ERIC Educational Resources Information Center

Thompson, Rohan

2018-01-01

This phenomenological study examined the role of emotional and cultural intelligence in the social integration of international students. The study included nine participants who were selected using purposeful sampling. The researcher used five main interview questions to guide the data-collection process. The questions were designed to help…

Chemistry and biology data

EPA Pesticide Factsheets

Chemical monitoring data and biological data from field collected samples.This dataset is associated with the following publication:Biales , A., D. Denton , D. Riordan, R. Breuer, A. Batt , D. Crane, and H. Schoenfuss. Complex watersheds, collaborative teams: Assessing pollutant presence and effects in the San Francisco Delta. Integrated Environmental Assessment and Management. Allen Press, Inc., Lawrence, KS, USA, 11(4): 674-688, (2015).

Proposed BioRepository platform solution for the ALS research community.

PubMed

Sherman, Alex; Bowser, Robert; Grasso, Daniela; Power, Breen; Milligan, Carol; Jaffa, Matthew; Cudkowicz, Merit

2011-01-01

ALS is a rare disorder whose cause and pathogenesis is largely unknown ( 1 ). There is a recognized need to develop biomarkers for ALS to better understand the disease, expedite diagnosis and to facilitate therapy development. Collaboration is essential to obtain a sufficient number of samples to allow statistically meaningful studies. The availability of high quality biological specimens for research purposes requires the development of standardized methods for collection, long-term storage, retrieval and distribution of specimens. The value of biological samples to scientists and clinicians correlates with the completeness and relevance of phenotypical and clinical information associated with the samples ( 2 , 3 ). While developing a secure Web-based system to manage an inventory of multi-site BioRepositories, algorithms were implemented to facilitate ad hoc parametric searches across heterogeneous data sources that contain data from clinical trials and research studies. A flexible schema for a barcode label was introduced to allow association of samples to these data. The ALSBank™ BioRepository platform solution for managing biological samples and associated data is currently deployed by the Northeast ALS Consortium (NEALS). The NEALS Consortium and the Massachusetts General Hospital (MGH) Neurology Clinical Trials Unit (NCTU) support a network of multiple BioBanks, thus allowing researchers to take advantage of a larger specimen collection than they might have at an individual institution. Standard operating procedures are utilized at all collection sites to promote common practices for biological sample integrity, quality control and associated clinical data. Utilizing this platform, we have created one of the largest virtual collections of ALS-related specimens available to investigators studying ALS.

Aerosol Angstrom Absorption Coefficient Comparisons during MILAGRO.

NASA Astrophysics Data System (ADS)

Marley, N. A.; Marchany-Rivera, A.; Kelley, K. L.; Mangu, A.; Gaffney, J. S.

2007-12-01

Measurements of aerosol absorption were obtained as part of the MAX-Mex component of the MILAGRO field campaign at site T0 (Instituto Mexicano de Petroleo in Mexico City) by using a 7-channel aethalometer (Thermo- Anderson) during the month of March, 2006. The absorption measurements obtained in the field at 370, 470, 520, 590, 660, 880, and 950 nm were used to determine the aerosol Angstrom absorption exponents by linear regression. Since, unlike other absorbing aerosol species (e.g. humic like substances, nitrated PAHs), black carbon absorption is relatively constant from the ultraviolet to the infrared with an Angstrom absorption exponent of -1 (1), a comparison of the Angstrom exponents can indicate the presence of aerosol components with an enhanced UV absorption over that expected from BC content alone. The Angstrom exponents determined from the aerosol absorption measurements obtained in the field varied from - 0.7 to - 1.3 during the study and was generally lower in the afternoon than the morning hours, indicating an increase in secondary aerosol formation and photochemically generated UV absorbing species in the afternoon. Twelve-hour integrated samples of fine atmospheric aerosols (<0.1micron) were also collected at site T0 and T1 (Universidad Technologica de Tecamac, State of Mexico) from 5 am to 5 pm (day) and from 5 pm to 5 am (night) during the month of March 2006. Samples were collected on quartz fiber filters with high volume impactor samplers. Continuous absorption spectra of these aerosol samples have been obtained in the laboratory from 280 to 900nm with the use of an integrating sphere coupled to a UV spectrometer (Beckman DU with a Labsphere accessory). The integrating sphere allows the detector to collect and spatially integrate the total radiant flux reflected from the sample and therefore allows for the measurement of absorption on highly reflective or diffusely scattering samples. These continuous spectra have also been used to obtain the aerosol Angstrom absorption exponents by linear regression over the entire UV-visible spectral range. These results are compared to results obtained from the absorbance measurements obtained in the field. The differences in calculated Angstrom absorption exponents between the field and laboratory measurements are attributed partly to the differences in time resolution of the sample collection resulting in heavier particle pileup on the filter surface of the 12-hour samples. Some differences in calculated results can also be attributed to the presence of narrow band absorbers below 400 nm that do not fall in the wavelengths covered by the 7 wavelengths of the aethalometer. 1. Marley, N.A., J.S. Gaffney, J.C. Baird, C.A. Blazer, P.J. Drayton, and J.E. Frederick, "The determination of scattering and absorption coefficients of size-fractionated aerosols for radiative transfer calculations." Aerosol Sci. Technol., 34, 535-549, (2001). This work was conducted as part of the Department of Energy's Atmospheric Science Program as part of the Megacity Aerosol Experiment - Mexico City during MILAGRO. This research was supported by the Office of Science (BER), U.S. Department of Energy Grant No. DE-FG02-07ER64329. We also wish to thank Mexican Scientists and students for their assistance from the Instituto Mexicano de Petroleo (IMP) and CENICA.

Multislice imaging of integrated circuits by precession X-ray ptychography.

PubMed

Shimomura, Kei; Hirose, Makoto; Takahashi, Yukio

2018-01-01

A method for nondestructively visualizing multisection nanostructures of integrated circuits by X-ray ptychography with a multislice approach is proposed. In this study, tilt-series ptychographic diffraction data sets of a two-layered circuit with a ∼1.4 µm gap at nine incident angles are collected in a wide Q range and then artifact-reduced phase images of each layer are successfully reconstructed at ∼10 nm resolution. The present method has great potential for the three-dimensional observation of flat specimens with thickness on the order of 100 µm, such as three-dimensional stacked integrated circuits based on through-silicon vias, without laborious sample preparation.

An assessment of the isotopic (2H/18O) integrity of water samples collected and stored by unattended precipitation totalizers

NASA Astrophysics Data System (ADS)

Terzer, Stefan; Wassenaar, Leonard I.; Douence, Cedric; Araguas-Araguas, Luis

2016-04-01

The IAEA-WMO Global Network of Isotopes in Precipitation (GNIP) provides worldwide δ18O and δ2H data for numerous hydrological and climatological studies. The traditional GNIP sample collection method relies on weather station operators to accumulate precipitation obtained from manual rain gauges. Over the past decades, widespread weather station automatization resulted in the increased use of unattended precipitation totalizers that accumulate and store the rainwater in the field for up to one month. Several low-tech measures were adopted to prevent in situ secondary evaporative isotopic enrichment (SEE) of totalized water samples (i.e. disequilibrium isotopic fractionation after precipitation is stored in the collection device). These include: (a) adding a 0.5-1 cm floating layer of paraffin oil to the totalizer bottle, (b) using an intake tube leading from the collection funnel and submerged to the bottom of the totalizer bottle, or (c) placing a table tennis ball in the funnel aiming to reduce evaporation of the collected water from the receiving bottle to the atmosphere. We assessed the isotopic integrity of stored rainwater samples for three totalizers under controlled settings: each aforementioned totalizer was filled with a 100 or 500 mL of isotopically known water and installed in the field with the intake funnels sheltered to prevent rainwater collection. Potential evapotranspiration (PET) was obtained from on-site meteorological recordings. Stored evaporative loss from each totalizer was evaluated on a monthly basis; gravimetrically and by analysing δ18O and δ2H of the stored water, for a period of 6 months and a cumulative PET of ˜500 mm. The gravimetric and isotope results revealed that for smaller water volumes (100 ml, corresponding to ca. 5 mm of monthly precipitation), negligible isotope enrichment (δ18O) was observed in the paraffin-oil based totalizer, whereas unacceptable evaporative isotope effects were observed for the ball-in-funnel collector. For the submerged-tube sampler, the evaporative effect depended on the amount of stored water: 100 ml showed unacceptable isotopic enrichment, whereas the SEE of 500 ml stored water was acceptable. These data allowed us to estimate the impact of secondary evaporative enrichment on a device-specific basis as a function of PET. Based on global PET grids (e.g. CGIAR data), and benchmarking the expected SEE against the reasonable uncertainty of isotope spectrometry (< ±0.1‰ for δ18O), these findings reveal the most suitable totalizer device for any given climatic condition. Under extreme conditions (e.g. high aridity, little precipitation vs. high PET), a paraffin-oil based rain totalizer is most appropriate for monthly collections. Submerged-tube samplers may be considered if either a higher frequency of collection were possible, or monthly under pluvial/temperate climate conditions. The use of ball-in-funnel type totalizers are not recommended at all, unless samples could be collected on a daily basis.

Cesium isotope ratios as indicators of nuclear power plant operations.

PubMed

Delmore, James E; Snyder, Darin C; Tranter, Troy; Mann, Nick R

2011-11-01

There are multiple paths by which radioactive cesium can reach the effluent from reactor operations. The radioactive (135)Cs/(137)Cs ratios are controlled by these paths. In an effort to better understand the origin of this radiation, these (135)Cs/(137)Cs ratios in effluents from three power reactor sites have been measured in offsite samples. These ratios are different from global fallout by up to six fold and as such cannot have a significant component from this source. A cesium ratio for a sample collected outside of the plant boundary provides integration over the operating life of the reactor. A sample collected inside the plant at any given time can be much different from this lifetime ratio. The measured cesium ratios vary significantly for the three reactors and indicate that the multiple paths have widely varying levels of contributions. There are too many ways these isotopes can fractionate to be useful for quantitative evaluations of operating parameters in an offsite sample, although it may be possible to obtain limited qualitative information for an onsite sample. Copyright © 2011 Elsevier Ltd. All rights reserved.

Bayesian Integration and Classification of Composition C-4 Plastic Explosives Based on Time-of-Flight-Secondary Ion Mass Spectrometry and Laser Ablation-Inductively Coupled Plasma Mass Spectrometry.

PubMed

Mahoney, Christine M; Kelly, Ryan T; Alexander, Liz; Newburn, Matt; Bader, Sydney; Ewing, Robert G; Fahey, Albert J; Atkinson, David A; Beagley, Nathaniel

2016-04-05

Time-of-flight-secondary ion mass spectrometry (TOF-SIMS) and laser ablation-inductively coupled plasma mass spectrometry (LA-ICPMS) were used for characterization and identification of unique signatures from a series of 18 Composition C-4 plastic explosives. The samples were obtained from various commercial and military sources around the country. Positive and negative ion TOF-SIMS data were acquired directly from the C-4 residue on Si surfaces, where the positive ion mass spectra obtained were consistent with the major composition of organic additives, and the negative ion mass spectra were more consistent with explosive content in the C-4 samples. Each series of mass spectra was subjected to partial least squares-discriminant analysis (PLS-DA), a multivariate statistical analysis approach which serves to first find the areas of maximum variance within different classes of C-4 and subsequently to classify unknown samples based on correlations between the unknown data set and the original data set (often referred to as a training data set). This method was able to successfully classify test samples of C-4, though with a limited degree of certainty. The classification accuracy of the method was further improved by integrating the positive and negative ion data using a Bayesian approach. The TOF-SIMS data was combined with a second analytical method, LA-ICPMS, which was used to analyze elemental signatures in the C-4. The integrated data were able to classify test samples with a high degree of certainty. Results indicate that this Bayesian integrated approach constitutes a robust classification method that should be employable even in dirty samples collected in the field.

Mineralogical, chemical, and optical interrelationships of mineral dusts from desert source regions

NASA Astrophysics Data System (ADS)

Engelbrecht, J. P.; Moosmüller, H.; Pincock, S.; Jayanty, J.; Casuccio, G.

2013-12-01

The goal of the project was to provide information on the mineralogical, chemical and physical interrelationships of re-suspended mineral dust samples collected from global dust sources. Surface soil samples were previously collected from more than 64 desert sites, including the southwestern USA (12), Mali (3), Chad (3), Morocco (1), Canary Islands (8), Cape Verde (1), Djibouti (1), Afghanistan (3), Iraq (6), Kuwait (5), Qatar (1), UAE (1), Serbia (3), China (5), Namibia (3), Botswana (4), Australia (3), and Chile (1). The < 38 μm sieved fraction of each sample was re-suspended in an entrainment facility, from which the airborne mineral dust could be sampled and analyzed. Instruments integrated into the entrainment facility included two PM10 and two PM2.5 filter samplers, a beta attenuation gauge for the continuous measurement of PM10 and PM2.5 particulate mass fractions, an aerodynamic particle size (APS) analyzer, and a three wavelength (405, 532, 781nm) photoacoustic instrument with integrating reciprocal nephelometer for monitoring aerosol absorption and scattering coefficients during the re-suspension process. Filter sample media included Teflon membrane and quartz fiber filters for chemical analysis (71 species), and Nuclepore filters for individual particle analysis by Scanning Electron Microscopy (SEM). The < 38 μm sieved fractions were also analyzed by X-ray diffraction for their mineral content while the > 38 μm, < 125 μm fractions were further mineralogically characterized by optical microscopy. We will be presenting results on the optical measurements, showing the relationship between single scattering albedo (SSA) at three different wavelengths, and chemical as well as mineralogical content and interrelationships, of the entrained dust samples. Information from this data base will be available for research in global climate, remote sensing, visibility, and health (medical geology).

Some thoughts on problems associated with various sampling media used for environmental monitoring

USGS Publications Warehouse

Horowitz, A.J.

1997-01-01

Modern analytical instrumentation is capable of measuring a variety of trace elements at concentrations down into the single or double digit parts-per-trillion (ng l-1) range. This holds for the three most common sample media currently used in environmental monitoring programs: filtered water, whole-water and separated suspended sediment. Unfortunately, current analytical capabilities have exceeded the current capacity to collect both uncontaminated and representative environmental samples. The success of any trace element monitoring program requires that this issue be both understood and addressed. The environmental monitoring of trace elements requires the collection of calendar- and event-based dissolved and suspended sediment samples. There are unique problems associated with the collection and chemical analyses of both types of sample media. Over the past 10 years, reported ambient dissolved trace element concentrations have declined. Generally, these decreases do not reflect better water quality, but rather improvements in the procedures used to collect, process, preserve and analyze these samples without contaminating them during these steps. Further, recent studies have shown that the currently accepted operational definition of dissolved constituents (material passing a 0.45 ??m membrane filter) is inadequat owing to sampling and processing artifacts. The existence of these artifacts raises questions about the generation of accurate, precise and comparable 'dissolved' trace element data. Suspended sediment and associated trace elements can display marked short- and long-term spatial and temporal variability. This implies that spatially representative samples only can be obtained by generating composites using depth- and width-integrated sampling techniques. Additionally, temporal variations have led to the view that the determination of annual trace element fluxes may require nearly constant (e.g., high-frequency) sampling and subsequent chemical analyses. Ultimately, sampling frequency for flux estimates becomes dependent on the time period of concern (daily, weekly, monthly, yearly) and the amount of acceptable error associated with these estimates.

Water-Quality and Biological Assessment of the Iowa River and Tributaries Within and Contiguous to the Meskwaki Settlement of the Sac and Fox Tribe of the Mississippi in Iowa, 2006-07

USGS Publications Warehouse

Littin, Gregory R.; McVay, Jason C.

2009-01-01

In cooperation with the Sac and Fox Tribe of the Mississippi in Iowa (Meskwaki Nation), the U.S. Geological Survey conducted a 2-year baseline assessment of the chemical and biological quality of streams within the Meskwaki Settlement in central Iowa. The Meskwaki Nation is a federally recognized tribe that wishes to establish water-quality standards to safeguard the integrity of surface waters and aquatic biota within the settlement for the health and welfare of the tribal community. The settlement is drained by the Iowa River and four tributaries (Onion, Cattail, Raven, and Bennett Creeks). Water-quality samples were collected at three sites on the Iowa River, two sites on Onion Creek, and one site each on Cattail, Raven, and Bennett Creeks from April 2006 through July 2007. Biological and habitat assessments were conducted at all three sites on the Iowa River and the downstream-most site on Onion Creek from June through August 2007. Analysis of physical properties, major ions, nutrients, trace compounds, bacteria, and total suspended solids in water, and trace metals and organic compounds in streambed sediment provided information about the effects of anthropogenic (human related) activities on the water quality of settlement streams. Analysis of biological samples collected during the summer of 2007, including fish community, benthic macroinvertebrates, and periphyton samples, as well as physical habitat characteristics, provided information on the effects of water quality on the condition of the aquatic environment. The majority of surface water sampled within the settlement was predominately a calcium bicarbonate type. Nitrates (nitrate plus nitrite as nitrogen) exceeded the U.S. Environmental Protection Agency's (USEPA) primary drinking-water Maximum Contaminant Level of 10 ug/L in 19 of 36 samples from sites on the Iowa River and Raven and Bennett Creeks but not in samples from Onion and Cattail Creeks. None of the samples analyzed for pesticides, trace metals, wastewater, or fuel contaminants were found to exceed drinking-water regulations for the USEPA or State of Iowa targeted constituents. Bacteria densities for Escherichia coli (E. coli) ranged from less than 10 to more than 600,000 colony-forming units per 100 milliliters of water and were largest following intense rainfall runoff. The largest densities were recorded in samples collected from the tributaries, most notably from Cattail Creek downstream from the tribal headquarters area and Onion Creek downstream from the sewage lagoons. Arsenic and nickel concentrations in bottom sediment from Onion Creek exceeded the USEPA threshold effects level in a composite sample collected during the habitat assessment in July 2007. Suspended-sediment concentration was estimated in terms of total suspended solids. Overall, Onion and Bennett Creeks were the least turbid, whereas the ephemeral Cattail Creek had the most turbid samples. Aquatic-community data were collected at four sites on the Meskwaki Settlement during the summer of 2007 to provide a baseline biological assessment of stream conditions. This assessment was based on sampling of the fish, benthic macroinvertebrate, and periphyton communities along with physical habitat characteristics. Individual biological metrics were derived from the data collected during the community surveys. These metrics were used to calculate Indexes of Biological Integrity (IBIs). The calculated values from the IBIs provided a numerical value that was used to provide an assessment of the biological condition at each biological sampling site. The fish community samples indicated that all of the sampling sites would be considered in fair condition, with one exception being a collection site on the Iowa River at Highway 49 near Tama, Iowa, which was classified in poor condition. The benthic macroinvertebrate IBI indicated a classification of good for three of the four biological sampling sites, with the Iowa River near Montour, Iowa,

Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling.

PubMed

Yang, Y Isaac; Zhang, Jun; Che, Xing; Yang, Lijiang; Gao, Yi Qin

2016-03-07

In order to efficiently overcome high free energy barriers embedded in a complex energy landscape and calculate overall thermodynamics properties using molecular dynamics simulations, we developed and implemented a sampling strategy by combining the metadynamics with (selective) integrated tempering sampling (ITS/SITS) method. The dominant local minima on the potential energy surface (PES) are partially exalted by accumulating history-dependent potentials as in metadynamics, and the sampling over the entire PES is further enhanced by ITS/SITS. With this hybrid method, the simulated system can be rapidly driven across the dominant barrier along selected collective coordinates. Then, ITS/SITS ensures a fast convergence of the sampling over the entire PES and an efficient calculation of the overall thermodynamic properties of the simulation system. To test the accuracy and efficiency of this method, we first benchmarked this method in the calculation of ϕ - ψ distribution of alanine dipeptide in explicit solvent. We further applied it to examine the design of template molecules for aromatic meta-C-H activation in solutions and investigate solution conformations of the nonapeptide Bradykinin involving slow cis-trans isomerizations of three proline residues.

Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling

NASA Astrophysics Data System (ADS)

Yang, Y. Isaac; Zhang, Jun; Che, Xing; Yang, Lijiang; Gao, Yi Qin

2016-03-01

In order to efficiently overcome high free energy barriers embedded in a complex energy landscape and calculate overall thermodynamics properties using molecular dynamics simulations, we developed and implemented a sampling strategy by combining the metadynamics with (selective) integrated tempering sampling (ITS/SITS) method. The dominant local minima on the potential energy surface (PES) are partially exalted by accumulating history-dependent potentials as in metadynamics, and the sampling over the entire PES is further enhanced by ITS/SITS. With this hybrid method, the simulated system can be rapidly driven across the dominant barrier along selected collective coordinates. Then, ITS/SITS ensures a fast convergence of the sampling over the entire PES and an efficient calculation of the overall thermodynamic properties of the simulation system. To test the accuracy and efficiency of this method, we first benchmarked this method in the calculation of ϕ - ψ distribution of alanine dipeptide in explicit solvent. We further applied it to examine the design of template molecules for aromatic meta-C—H activation in solutions and investigate solution conformations of the nonapeptide Bradykinin involving slow cis-trans isomerizations of three proline residues.

Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling

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

Yang, Y. Isaac; Zhang, Jun; Che, Xing

2016-03-07

In order to efficiently overcome high free energy barriers embedded in a complex energy landscape and calculate overall thermodynamics properties using molecular dynamics simulations, we developed and implemented a sampling strategy by combining the metadynamics with (selective) integrated tempering sampling (ITS/SITS) method. The dominant local minima on the potential energy surface (PES) are partially exalted by accumulating history-dependent potentials as in metadynamics, and the sampling over the entire PES is further enhanced by ITS/SITS. With this hybrid method, the simulated system can be rapidly driven across the dominant barrier along selected collective coordinates. Then, ITS/SITS ensures a fast convergence ofmore » the sampling over the entire PES and an efficient calculation of the overall thermodynamic properties of the simulation system. To test the accuracy and efficiency of this method, we first benchmarked this method in the calculation of ϕ − ψ distribution of alanine dipeptide in explicit solvent. We further applied it to examine the design of template molecules for aromatic meta-C—H activation in solutions and investigate solution conformations of the nonapeptide Bradykinin involving slow cis-trans isomerizations of three proline residues.« less

Methodology for estimating nutrient loads discharged from the east coast canals to Biscayne Bay, Miami-Dade County, Florida

USGS Publications Warehouse

Lietz, Arthur C.

1999-01-01

Biscayne Bay is an oligotrophic, subtropical estuary located along the southeastern coast of Florida that provides habitat for a variety of plant and animal life. Concern has arisen with regard to the ecological health of Biscayne Bay because of the presence of nutrient-laden discharges from the east coast canals that drain into the bay. This concern, as well as planned diversion of discharges for ecosystem restoration from the urban and agricultural corridors of Miami-Dade County to Everglades National Park, served as the impetus for a study conducted during the 1996 and 1997 water years to estimate nutrient loads discharged from the east coast canals into Biscayne Bay. Analytical results indicated that the highest concentration of any individual nutrient sampled for in the study was 4.38 mg/L (milligrams per liter) for nitrate at one site, and the lowest concentrations determined were below the detection limits for orthophosphate at six sites and nitrite at four sites. Median concentrations for all the sites were 0.75 mg/L for total organic nitrogen, 0.10 mg/L for ammonia, 0.02 mg/L for nitrite, 0.18 mg/L for nitrate, 0.20 mg/L for nitrite plus nitrate nitrogen, 0.02 mg/L for total phosphorus, and 0.005 mg/L for orthophosphate. The maximum total phosphorus concentration of 0.31 mg/L was the only nutrient concentration to exceed U.S. Environmental Protection Agency (1986) water-quality criteria. High concentrations of total phosphorus usually reflect contamination as a result of human activities. Five sites exceeded the fresh-water quality standard of 0.5 mg/L for ammonia concentration as determined by the Miami-Dade County Department of Environmental Resources Management. Median total organic nitrogen concentrations were higher in urban and forested/wetland areas than in agricultural areas; median concentrations of nitrite, nitrate, and nitrite plus nitrate nitrogen were higher in agricultural areas than in urban and forested/wetland areas; and ammonia, total phosphorus, and orthophosphate concentrations were higher in urban areas than in agricultural and forested/wetland areas. These results coincide with expected differences in nutrient concentrations based on knowledge of point and nonpoint source influences and nutrient cycling. The Wilcoxon signed ranks test (WSRT) was used to compare differences between point (grab) samples and depth-integrated samples for total nitrogen and total phosphorus concentrations at 12 east coast canal sites. Statistically significant differences (alpha level of 0.025) in total phosphorus concentrations between point (grab) samples collected 1.0 meter deep and depth-integrated samples were detected at three sites. One site also showed statistically significant differences in total phosphorus concentrations between point (grab) samples collected 0.5 meter deep and depth-integrated samples. There were no statistically significant differences in total nitrogen and total phosphorus concentrations between point (grab) samples collected 0.5 meter deep and 1.0 meter deep for all the sites. Results of the line of organic correlation, a fitting procedure used to compare point (grab) and depth-integrated samples where statistically significant differences exist as defined by the WSRT, indicated that point (grab) samples underestimate total phosphorus concentrations when compared to depth-integrated samples. This underestimation probably can be attributed to the reduced suspended-sediment concentrations near the surface during periods of flow as compared to those near the streambed. Predictive models were developed to estimate total nitrogen and total phosphorus loads by means of an ordinary least-squares regression technique. Instantaneous discharge was used as the independent variable, and total phosphorus load or total nitrogen load represented the dependent variable. A software program called Estimator was used to develop the regression models and to compute total nitrogen and total phosphorus loads

ultraLM and miniLM: Locator tools for smart tracking of fluorescent cells in correlative light and electron microscopy.

PubMed

Brama, Elisabeth; Peddie, Christopher J; Wilkes, Gary; Gu, Yan; Collinson, Lucy M; Jones, Martin L

2016-12-13

In-resin fluorescence (IRF) protocols preserve fluorescent proteins in resin-embedded cells and tissues for correlative light and electron microscopy, aiding interpretation of macromolecular function within the complex cellular landscape. Dual-contrast IRF samples can be imaged in separate fluorescence and electron microscopes, or in dual-modality integrated microscopes for high resolution correlation of fluorophore to organelle. IRF samples also offer a unique opportunity to automate correlative imaging workflows. Here we present two new locator tools for finding and following fluorescent cells in IRF blocks, enabling future automation of correlative imaging. The ultraLM is a fluorescence microscope that integrates with an ultramicrotome, which enables 'smart collection' of ultrathin sections containing fluorescent cells or tissues for subsequent transmission electron microscopy or array tomography. The miniLM is a fluorescence microscope that integrates with serial block face scanning electron microscopes, which enables 'smart tracking' of fluorescent structures during automated serial electron image acquisition from large cell and tissue volumes.

A chemodynamic approach for estimating losses of target organic chemicals from water during sample holding time

USGS Publications Warehouse

Capel, P.D.; Larson, S.J.

1995-01-01

Minimizing the loss of target organic chemicals from environmental water samples between the time of sample collection and isolation is important to the integrity of an investigation. During this sample holding time, there is a potential for analyte loss through volatilization from the water to the headspace, sorption to the walls and cap of the sample bottle; and transformation through biotic and/or abiotic reactions. This paper presents a chemodynamic-based, generalized approach to estimate the most probable loss processes for individual target organic chemicals. The basic premise is that the investigator must know which loss process(es) are important for a particular analyte, based on its chemodynamic properties, when choosing the appropriate method(s) to prevent loss.

Concordant integrative gene set enrichment analysis of multiple large-scale two-sample expression data sets.

PubMed

Lai, Yinglei; Zhang, Fanni; Nayak, Tapan K; Modarres, Reza; Lee, Norman H; McCaffrey, Timothy A

2014-01-01

Gene set enrichment analysis (GSEA) is an important approach to the analysis of coordinate expression changes at a pathway level. Although many statistical and computational methods have been proposed for GSEA, the issue of a concordant integrative GSEA of multiple expression data sets has not been well addressed. Among different related data sets collected for the same or similar study purposes, it is important to identify pathways or gene sets with concordant enrichment. We categorize the underlying true states of differential expression into three representative categories: no change, positive change and negative change. Due to data noise, what we observe from experiments may not indicate the underlying truth. Although these categories are not observed in practice, they can be considered in a mixture model framework. Then, we define the mathematical concept of concordant gene set enrichment and calculate its related probability based on a three-component multivariate normal mixture model. The related false discovery rate can be calculated and used to rank different gene sets. We used three published lung cancer microarray gene expression data sets to illustrate our proposed method. One analysis based on the first two data sets was conducted to compare our result with a previous published result based on a GSEA conducted separately for each individual data set. This comparison illustrates the advantage of our proposed concordant integrative gene set enrichment analysis. Then, with a relatively new and larger pathway collection, we used our method to conduct an integrative analysis of the first two data sets and also all three data sets. Both results showed that many gene sets could be identified with low false discovery rates. A consistency between both results was also observed. A further exploration based on the KEGG cancer pathway collection showed that a majority of these pathways could be identified by our proposed method. This study illustrates that we can improve detection power and discovery consistency through a concordant integrative analysis of multiple large-scale two-sample gene expression data sets.

Modeling abundance effects in distance sampling

USGS Publications Warehouse

Royle, J. Andrew; Dawson, D.K.; Bates, S.

2004-01-01

Distance-sampling methods are commonly used in studies of animal populations to estimate population density. A common objective of such studies is to evaluate the relationship between abundance or density and covariates that describe animal habitat or other environmental influences. However, little attention has been focused on methods of modeling abundance covariate effects in conventional distance-sampling models. In this paper we propose a distance-sampling model that accommodates covariate effects on abundance. The model is based on specification of the distance-sampling likelihood at the level of the sample unit in terms of local abundance (for each sampling unit). This model is augmented with a Poisson regression model for local abundance that is parameterized in terms of available covariates. Maximum-likelihood estimation of detection and density parameters is based on the integrated likelihood, wherein local abundance is removed from the likelihood by integration. We provide an example using avian point-transect data of Ovenbirds (Seiurus aurocapillus) collected using a distance-sampling protocol and two measures of habitat structure (understory cover and basal area of overstory trees). The model yields a sensible description (positive effect of understory cover, negative effect on basal area) of the relationship between habitat and Ovenbird density that can be used to evaluate the effects of habitat management on Ovenbird populations.

Standardization and utilization of biobank resources in clinical protein science with examples of emerging applications.

PubMed

Marko-Varga, György; Végvári, Ákos; Welinder, Charlotte; Lindberg, Henrik; Rezeli, Melinda; Edula, Goutham; Svensson, Katrin J; Belting, Mattias; Laurell, Thomas; Fehniger, Thomas E

2012-11-02

Biobanks are a major resource to access and measure biological constituents that can be used to monitor the status of health and disease, both in unique individual samples and within populations. Most "omic" activities rely on access to these collections of stored samples to provide the basis for establishing the ranges and frequencies of expression. Furthermore, information about the relative abundance and form of protein constituents found in stored samples provides an important historical index for comparative studies of inherited, epidemic, and developing disease. Standardizations of sample quality, form, and analysis are an important unmet need and requirement for gaining the full benefit from collected samples. Coupled to this standard is the provision of annotation describing clinical status and metadata of measurements of clinical phenotype that characterizes the sample. Today we have not yet achieved consensus on how to collect, manage, and build biobank archives in order to reach goals where these efforts are translated into value for the patient. Several initiatives (OBBR, ISBER, BBMRI) that disseminate best practice examples for biobanking are expected to play an important role in ensuring the need to preserve the sample integrity of biosamples stored for periods that reach one or several decades. These developments will be of great value and importance to programs such as the Chromosome Human Protein Project (C-HPP) that will associate protein expression in healthy and disease states with genetic foci along of each of the human chromosomes.

Uncertainty in monitoring E. coli concentrations in streams and stormwater runoff

NASA Astrophysics Data System (ADS)

Harmel, R. D.; Hathaway, J. M.; Wagner, K. L.; Wolfe, J. E.; Karthikeyan, R.; Francesconi, W.; McCarthy, D. T.

2016-03-01

Microbial contamination of surface waters, a substantial public health concern throughout the world, is typically identified by fecal indicator bacteria such as Escherichia coli. Thus, monitoring E. coli concentrations is critical to evaluate current conditions, determine restoration effectiveness, and inform model development and calibration. An often overlooked component of these monitoring and modeling activities is understanding the inherent random and systematic uncertainty present in measured data. In this research, a review and subsequent analysis was performed to identify, document, and analyze measurement uncertainty of E. coli data collected in stream flow and stormwater runoff as individual discrete samples or throughout a single runoff event. Data on the uncertainty contributed by sample collection, sample preservation/storage, and laboratory analysis in measured E. coli concentrations were compiled and analyzed, and differences in sampling method and data quality scenarios were compared. The analysis showed that: (1) manual integrated sampling produced the lowest random and systematic uncertainty in individual samples, but automated sampling typically produced the lowest uncertainty when sampling throughout runoff events; (2) sample collection procedures often contributed the highest amount of uncertainty, although laboratory analysis introduced substantial random uncertainty and preservation/storage introduced substantial systematic uncertainty under some scenarios; and (3) the uncertainty in measured E. coli concentrations was greater than that of sediment and nutrients, but the difference was not as great as may be assumed. This comprehensive analysis of uncertainty in E. coli concentrations measured in streamflow and runoff should provide valuable insight for designing E. coli monitoring projects, reducing uncertainty in quality assurance efforts, regulatory and policy decision making, and fate and transport modeling.

THE NEW YORK CITY URBAN DISPERSION PROGRAM MARCH 2005 FIELD STUDY: TRACER METHODS AND RESULTS.

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

WATSON, T.B.; HEISER, J.; KALB, P.

The Urban Dispersion Program March 2005 Field Study tracer releases, sampling, and analytical methods are described in detail. There were two days where tracer releases and sampling were conducted. A total of 16.0 g of six tracers were released during the first test day or Intensive Observation Period (IOP) 1 and 15.7 g during IOP 2. Three types of sampling instruments were used in this study. Sequential air samplers, or SAS, collected six-minute samples, while Brookhaven atmospheric tracer samplers (BATS) and personal air samplers (PAS) collected thirty-minute samples. There were a total of 1300 samples resulting from the two IOPs.more » Confidence limits in the sampling and analysis method were 20% as determined from 100 duplicate samples. The sample recovery rate was 84%. The integrally averaged 6-minute samples were compared to the 30-minute samples. The agreement was found to be good in most cases. The validity of using a background tracer to calculate sample volumes was examined and also found to have a confidence level of 20%. Methods for improving sampling and analysis are discussed. The data described in this report are available as Excel files. An additional Excel file of quality assured tracer data for use in model validation efforts is also available. The file consists of extensively quality assured BATS tracer data with background concentrations subtracted.« less

A comparative analysis of double-crested cormorant diets from stomachs and pellets from two Lake Ontario colonies

USGS Publications Warehouse

Johnson, James H.; Ross, Robert M.; McCullough, Russell D.; Mathers, Alastair

2010-01-01

Double-crested cormorant (Phalacrocorax auritus) diets were compared with evidence from the stomachs of shot birds and from regurgitated pellets at High Bluff Island and Little Galloo Island, Lake Ontario. The highest similarity in diets determined by stomach and pellet analyses occurred when both samples were collected on the same day. Diet overlap dropped substantially between the two methods when collection periods were seven to ten days apart, which suggested differences in prey availability between the two periods. Since the average number of fish recovered in pellets was significantly higher than that in stomachs, use of pellets to determine fish consumption of double-crested cormorants may be more valid than stomach analysis because pellet content represent an integrated sampling of food consumed over approximately 24 hours.

Diffractometer data collecting method and apparatus

DOEpatents

Steinmeyer, P.A.

1991-04-16

Diffractometer data is collected without the use of a movable receiver. A scanning device, positioned in the diffractometer between a sample and detector, varies the amount of the beam diffracted from the sample that is received by the detector in such a manner that the beam is detected in an integrated form. In one embodiment, a variable diameter beam stop is used which comprises a drop of mercury captured between a pair of spaced sheets and disposed in the path of the diffracted beam. By varying the spacing between the sheets, the diameter of the mercury drop is varied. In another embodiment, an adjustable iris diaphragm is positioned in the path of the diffracted beam and the iris opening is adjusted to control the amount of the beam reaching the detector. 5 figures.

Diffractometer data collecting method and apparatus

DOEpatents

Steinmeyer, Peter A.

1991-04-16

Diffractometer data is collected without the use of a movable receiving s. A scanning device, positioned in the diffractometer between a sample and detector, varies the amount of the beam diffracted from the sample that is received by the detector in such a manner that the beam is detected in an integrated form. In one embodiment, a variable diameter beam stop is used which comprises a drop of mercury captured between a pair of spaced sheets and disposed in the path of the diffracted beam. By varying the spacing between the sheets, the diameter of the mercury drop is varied. In another embodiment, an adjustable iris diaphragm is positioned in the path of the diffracted beam and the iris opening is adjusted to control the amount of the beam reaching the detector.

A digital repository with an extensible data model for biobanking and genomic analysis management.

PubMed

Izzo, Massimiliano; Mortola, Francesco; Arnulfo, Gabriele; Fato, Marco M; Varesio, Luigi

2014-01-01

Molecular biology laboratories require extensive metadata to improve data collection and analysis. The heterogeneity of the collected metadata grows as research is evolving in to international multi-disciplinary collaborations and increasing data sharing among institutions. Single standardization is not feasible and it becomes crucial to develop digital repositories with flexible and extensible data models, as in the case of modern integrated biobanks management. We developed a novel data model in JSON format to describe heterogeneous data in a generic biomedical science scenario. The model is built on two hierarchical entities: processes and events, roughly corresponding to research studies and analysis steps within a single study. A number of sequential events can be grouped in a process building up a hierarchical structure to track patient and sample history. Each event can produce new data. Data is described by a set of user-defined metadata, and may have one or more associated files. We integrated the model in a web based digital repository with a data grid storage to manage large data sets located in geographically distinct areas. We built a graphical interface that allows authorized users to define new data types dynamically, according to their requirements. Operators compose queries on metadata fields using a flexible search interface and run them on the database and on the grid. We applied the digital repository to the integrated management of samples, patients and medical history in the BIT-Gaslini biobank. The platform currently manages 1800 samples of over 900 patients. Microarray data from 150 analyses are stored on the grid storage and replicated on two physical resources for preservation. The system is equipped with data integration capabilities with other biobanks for worldwide information sharing. Our data model enables users to continuously define flexible, ad hoc, and loosely structured metadata, for information sharing in specific research projects and purposes. This approach can improve sensitively interdisciplinary research collaboration and allows to track patients' clinical records, sample management information, and genomic data. The web interface allows the operators to easily manage, query, and annotate the files, without dealing with the technicalities of the data grid.

A digital repository with an extensible data model for biobanking and genomic analysis management

PubMed Central

2014-01-01

Motivation Molecular biology laboratories require extensive metadata to improve data collection and analysis. The heterogeneity of the collected metadata grows as research is evolving in to international multi-disciplinary collaborations and increasing data sharing among institutions. Single standardization is not feasible and it becomes crucial to develop digital repositories with flexible and extensible data models, as in the case of modern integrated biobanks management. Results We developed a novel data model in JSON format to describe heterogeneous data in a generic biomedical science scenario. The model is built on two hierarchical entities: processes and events, roughly corresponding to research studies and analysis steps within a single study. A number of sequential events can be grouped in a process building up a hierarchical structure to track patient and sample history. Each event can produce new data. Data is described by a set of user-defined metadata, and may have one or more associated files. We integrated the model in a web based digital repository with a data grid storage to manage large data sets located in geographically distinct areas. We built a graphical interface that allows authorized users to define new data types dynamically, according to their requirements. Operators compose queries on metadata fields using a flexible search interface and run them on the database and on the grid. We applied the digital repository to the integrated management of samples, patients and medical history in the BIT-Gaslini biobank. The platform currently manages 1800 samples of over 900 patients. Microarray data from 150 analyses are stored on the grid storage and replicated on two physical resources for preservation. The system is equipped with data integration capabilities with other biobanks for worldwide information sharing. Conclusions Our data model enables users to continuously define flexible, ad hoc, and loosely structured metadata, for information sharing in specific research projects and purposes. This approach can improve sensitively interdisciplinary research collaboration and allows to track patients' clinical records, sample management information, and genomic data. The web interface allows the operators to easily manage, query, and annotate the files, without dealing with the technicalities of the data grid. PMID:25077808

Next Generation Offline Approaches to Trace Gas-Phase Organic Compound Speciation: Sample Collection and Analysis

NASA Astrophysics Data System (ADS)

Sheu, R.; Marcotte, A.; Khare, P.; Ditto, J.; Charan, S.; Gentner, D. R.

2017-12-01

Intermediate-volatility and semi-volatile organic compounds (I/SVOCs) are major precursors to secondary organic aerosol, and contribute to tropospheric ozone formation. Their wide volatility range, chemical complexity, behavior in analytical systems, and trace concentrations present numerous hurdles to characterization. We present an integrated sampling-to-analysis system for the collection and offline analysis of trace gas-phase organic compounds with the goal of preserving and recovering analytes throughout sample collection, transport, storage, and thermal desorption for accurate analysis. Custom multi-bed adsorbent tubes are used to collect samples for offline analysis by advanced analytical detectors. The analytical instrumentation comprises an automated thermal desorption system that introduces analytes from the adsorbent tubes into a gas chromatograph, which is coupled with an electron ionization mass spectrometer (GC-EIMS) and other detectors. In order to optimize the collection and recovery for a wide range of analyte volatility and functionalization, we evaluated a variety of commercially-available materials, including Res-Sil beads, quartz wool, glass beads, Tenax TA, and silica gel. Key properties for optimization include inertness, versatile chemical capture, minimal affinity for water, and minimal artifacts or degradation byproducts; these properties were assessed with a diverse mix of traditionally-measured and functionalized analytes. Along with a focus on material selection, we provide recommendations spanning the entire sampling-and-analysis process to improve the accuracy of future comprehensive I/SVOC measurements, including oxygenated and other functionalized I/SVOCs. We demonstrate the performance of our system by providing results on speciated VOCs-SVOCs from indoor, outdoor, and chamber studies that establish the utility of our protocols and pave the way for precise laboratory characterization via a mix of detection methods.

BIOTIC INTEGRITY OF STREAMS IN THE SAVANNAH RIVER SITE INTEGRATOR OPERABLE UNITS, 1996 TO 2003

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

Paller, M; Susan Dyer, S

2004-11-08

The Savannah River Site (SRS) has been divided into six Integrator Operable Units (IOUs) that correspond to the watersheds of the five major streams on the SRS (Upper Three Runs, Fourmile Branch, Pen Branch, Steel Creek, and Lower Three Runs) and the portions of the Savannah River and Savannah River Swamp associated with the SRS. The streams are the primary integrators within each IOU because they potentially receive, through surface or subsurface drainage, soluble contaminants from all waste sites within their watersheds. If these contaminants reach biologically significant levels, they would be expected to effect the numbers, types, and healthmore » of stream organisms. In this study, biological sampling was conducted within each IOU as a measure of the cumulative ecological effects of the waste sites within the IOUs. The use of information from biological sampling to assess environmental quality is often termed bioassessment. The IOU bioassessment program included 38 sites in SRS streams and nine sites in the Savannah River. Sampling was conducted in 1996 to 1998, 2000, and 2003. Four bioassessment methods were used to evaluate ecological conditions in the IOU streams: the Index of Biotic Integrity, the Fish Health Assessment Index, measurement of fish tissue contaminant levels, and two benthic macroinvertebrate indices. The Index of Biotic Integrity (IBI) is an EPA supported method based on comparison of ecologically important and sensitive fish assemblage variables between potentially disturbed and reference (i.e., undisturbed) sites. It is designed to assess the ability of a stream to support a self-sustaining biological community and ecological processes typical of undisturbed, natural conditions. Since many types of contaminants can bioaccumulate, fish tissue contaminant data were used to determine the types of chemicals fish were exposed to and their relative magnitudes among IOUs. The Fish Health Assessment Index (HAI) is an EPA supported method for assessing the health and condition of individual fish based on dissection and internal examination. It helped to determine whether contaminant concentrations were high enough to adversely affect the health of individual fish. The benthic macroinvertebrate multimetric index (HDMI), used in 1997 to 2000, is a method for assessing stream health based on macroinvertebrate data collected with Hester-Dendy artificial substrates. In 2003 it was replaced with the Multiple Habitat Sampling protocol, a SCDHEC method for collecting and analyzing benthic macroinvertebrate data from natural substrate. These two macroinvertebrate based methods were used in conjunction with the fish based IBI to provide a more comprehensive assessment of ecological conditions. Lastly, habitat data were collected from each stream to assist in determining whether ecological integrity was compromised by physical factors (e.g., erosion) or chemical factors (e.g., discharge of toxic materials). Fish from many SRS streams exhibited evidence of contamination as a result of current or former SRS operations. The most prevalent radiological contaminants were cesium-137 (highest in fish from Lower Three Runs followed by Steel Creek and Fourmile Branch), tritium (highest in fish from Fourmile Branch followed by Pen Branch, and the Savannah River swamp), and strontium (highest in fish from Fourmile Branch followed by Pen Branch). Radiological contaminants were also found in fish collected from the Savannah River near the mouths of contaminated SRS streams; however, contaminant levels were substantially lower than in fish from the streams themselves. Mercury levels were moderately elevated in fish from some streams, particularly Lower Three Runs, and in fish from the Savannah River. Despite the occurrence of contaminants, most SRS streams exhibited comparatively high biotic integrity (based on IBI, HDMI, and MHSP scores) and minimal levels of pathology among individual fish (e.g., presence of tumors or extreme thinness), indicating that contaminant levels were generally insufficient to cause significant ecological degradation.« less

Radiation damage in room-temperature data acquisition with the PILATUS 6M pixel detector.

PubMed

Rajendran, Chitra; Dworkowski, Florian S N; Wang, Meitian; Schulze-Briese, Clemens

2011-05-01

The first study of room-temperature macromolecular crystallography data acquisition with a silicon pixel detector is presented, where the data are collected in continuous sample rotation mode, with millisecond read-out time and no read-out noise. Several successive datasets were collected sequentially from single test crystals of thaumatin and insulin. The dose rate ranged between ∼ 1320 Gy s(-1) and ∼ 8420 Gy s(-1) with corresponding frame rates between 1.565 Hz and 12.5 Hz. The data were analysed for global radiation damage. A previously unreported negative dose-rate effect is observed in the indicators of global radiation damage, which showed an approximately 75% decrease in D(1/2) at sixfold higher dose rate. The integrated intensity decreases in an exponential manner. Sample heating that could give rise to the enhanced radiation sensitivity at higher dose rate is investigated by collecting data between crystal temperatures of 298 K and 353 K. UV-Vis spectroscopy is used to demonstrate that disulfide radicals and trapped electrons do not accumulate at high dose rates in continuous data collection.

Spatial inventory integrating raster databases and point sample data. [Geographic Information System for timber inventory

NASA Technical Reports Server (NTRS)

Strahler, A. H.; Woodcock, C. E.; Logan, T. L.

1983-01-01

A timber inventory of the Eldorado National Forest, located in east-central California, provides an example of the use of a Geographic Information System (GIS) to stratify large areas of land for sampling and the collection of statistical data. The raster-based GIS format of the VICAR/IBIS software system allows simple and rapid tabulation of areas, and facilitates the selection of random locations for ground sampling. Algorithms that simplify the complex spatial pattern of raster-based information, and convert raster format data to strings of coordinate vectors, provide a link to conventional vector-based geographic information systems.

Mechanistic and Technical Challenges in Studying the Human Microbiome and Cancer Epidemiology.

PubMed

Verma, Mukesh

2017-04-01

This article reviews the significance of the microbiome in cancer epidemiology, mechanistic and technical challenges in the field, and characterization of the microbiome in different tumor types to identify biomarkers of risk, progression, and prognosis. Publications on the microbiome and cancer epidemiology were reviewed to analyze sample collection and processing, microbiome taxa characterization by 16S ribosomal RNA sequencing, and microbiome metabolite characterization (metabotyping) by nuclear magnetic resonance and mass spectrometry. The analysis identified methodology types, research design, sample types, and issues in integrating data from different platforms. Aerodigestive cancer epidemiology studies conducted by different groups demonstrated the significance of microbiome information in developing approaches to improve health. Challenges exist in sample preparation and processing (eg, standardization of methods for collection and analysis). These challenges relate to technology, data integration from "omics" studies, inherent bias in primer selection during 16S ribosomal RNA sequencing, the need for large consortia with well-characterized biospecimens, cause and effect issues, resilience of microbiota to exposure events (requires longitudinal studies), and expanding studies for fungal and viral diversity (most studies used bacterial 16S ribosomal RNA sequencing for microbiota characterization). Despite these challenges, microbiome and cancer epidemiology studies are significant and may facilitate cancer risk assessment, diagnosis, and prognosis. In the future, clinical trials likely will use microbiota modifications to improve the efficacy of existing treatments.

Mechanistic and Technical Challenges in Studying the Human Microbiome and Cancer Epidemiology

PubMed Central

2016-01-01

This article reviews the significance of the microbiome in cancer epidemiology, mechanistic and technical challenges in the field, and characterization of the microbiome in different tumor types to identify biomarkers of risk, progression, and prognosis. Publications on the microbiome and cancer epidemiology were reviewed to analyze sample collection and processing, microbiome taxa characterization by 16S ribosomal RNA sequencing, and microbiome metabolite characterization (metabotyping) by nuclear magnetic resonance and mass spectrometry. The analysis identified methodology types, research design, sample types, and issues in integrating data from different platforms. Aerodigestive cancer epidemiology studies conducted by different groups demonstrated the significance of microbiome information in developing approaches to improve health. Challenges exist in sample preparation and processing (eg, standardization of methods for collection and analysis). These challenges relate to technology, data integration from “omics” studies, inherent bias in primer selection during 16S ribosomal RNA sequencing, the need for large consortia with well-characterized biospecimens, cause and effect issues, resilience of microbiota to exposure events (requires longitudinal studies), and expanding studies for fungal and viral diversity (most studies used bacterial 16S ribosomal RNA sequencing for microbiota characterization). Despite these challenges, microbiome and cancer epidemiology studies are significant and may facilitate cancer risk assessment, diagnosis, and prognosis. In the future, clinical trials likely will use microbiota modifications to improve the efficacy of existing treatments. PMID:27121074

Automation of high-frequency sampling of environmental waters for reactive species

NASA Astrophysics Data System (ADS)

Kim, H.; Bishop, J. K.; Wood, T.; Fung, I.; Fong, M.

2011-12-01

Trace metals, particularly iron and manganese, play a critical role in some ecosystems as a limiting factor to determine primary productivity, in geochemistry, especially redox chemistry as important electron donors and acceptors, and in aquatic environments as carriers of contaminant transport. Dynamics of trace metals are closely related to various hydrologic events such as rainfall. Storm flow triggers dramatic changes of both dissolved and particulate trace metals concentrations and affects other important environmental parameters linked to trace metal behavior such as dissolved organic carbon (DOC). To improve our understanding of behaviors of trace metals and underlying processes, water chemistry information must be collected for an adequately long period of time at higher frequency than conventional manual sampling (e.g. weekly, biweekly). In this study, we developed an automated sampling system to document the dynamics of trace metals, focusing on Fe and Mn, and DOC for a multiple-year high-frequency geochemistry time series in a small catchment, called Rivendell located at Angelo Coast Range Reserve, California. We are sampling ground and streamwater using the automated sampling system in daily-frequency and the condition of the site is substantially variable from season to season. The ranges of pH of ground and streamwater are pH 5 - 7 and pH 7.8 - 8.3, respectively. DOC is usually sub-ppm, but during rain events, it increases by an order of magnitude. The automated sampling system focuses on two aspects- 1) a modified design of sampler to improve sample integrity for trace metals and DOC and 2) remote controlling system to update sampling volume and timing according to hydrological conditions. To maintain sample integrity, the developed method employed gravity filtering using large volume syringes (140mL) and syringe filters connected to a set of polypropylene bottles and a borosilicate bottle via Teflon tubing. Without filtration, in a few days, the dissolved concentration of Fe and Mn in the ground and streamwater samples stored in low density polyethylene (LDPE) sample bags decreased by 89% and 97%, respectively. In some cases of groundwater, the concentration of Ca decreased by 25%, due to degassing of CO2. However, DOC of the samples in LDPE bags without filtration increased up to 50% in 2 weeks, suggesting contamination from the bag. Performance of the new design was evaluated using the Fe-Mn-spiked Rivendell samples and environmental water samples collected from 1) Rivendell, 2) the Strawberry Creek located at the University of California, Berkeley campus, and 3) the San Francisco Bay. The samples were filtered using the developed method and stored in room temperature in 2 - 3 weeks without further treatment. The method improved the sample integrity significantly; the average recovery rates of Fe, Mn, DOC, and Ca were 92%, 98%, 90%, and 97%, respectively.

Cyanotoxins in inland lakes of the continental United States: Photic Zone Occurrence and potential recreational health risks in the 2007 Survey of the Nation's lakes

EPA Science Inventory

The largest spatial survey of cylindrospermosins, microcystins, and saxitoxins in the United States was conducted as part of the 2007 U.S. Survey of the Nation’s Lakes. Integrated photic zone samples were collected from 1,161 lakes during May-September 2007. Cyanotoxin, cya...

Integrating DNA-based data into bioassessments improves ...

EPA Pesticide Factsheets

The integration of DNA-based identification methods into bioassessments could result in more accurate representations of species distributions and species-habitat relationships. DNA-based approaches may be particularly informative for tracking the distributions of rare and/or invasive species that can comprise a small proportion of samples or are difficult to identify morphologically. In 2012 and 2013, we used a combination of morphological and DNA-based methods (meta-barcoding) to identify fish eggs and larvae collected in the St. Louis River estuary area, Minnesota. We found a large proportion of cases where a lack of agreement occurred between species identified at a site using morphological versus DNA identification, prompting a discussion of how to best reconcile these differences. Choices made during sampling collection, DNA amplification/extraction, and bioinformatics processing influence the DNA-morphology match. The distribution of some species (including several invasives) and their relationships to habitat changed after DNA-data was incorporated. Results highlight how incorporating of DNA-data may get us closer to the “truth”, which has large ramifications in the search for rare species and when understanding the environmental drivers of species distributions is important for management. not applicable

Comparison of a real-time PCR method with a culture method for the detection of Salmonella enterica serotype enteritidis in naturally contaminated environmental samples from integrated poultry houses.

PubMed

Lungu, Bwalya; Waltman, W Douglas; Berghaus, Roy D; Hofacre, Charles L

2012-04-01

Conventional culture methods have traditionally been considered the "gold standard" for the isolation and identification of foodborne bacterial pathogens. However, culture methods are labor-intensive and time-consuming. A Salmonella enterica serotype Enteritidis-specific real-time PCR assay that recently received interim approval by the National Poultry Improvement Plan for the detection of Salmonella Enteritidis was evaluated against a culture method that had also received interim National Poultry Improvement Plan approval for the analysis of environmental samples from integrated poultry houses. The method was validated with 422 field samples collected by either the boot sock or drag swab method. The samples were cultured by selective enrichment in tetrathionate broth followed by transfer onto a modified semisolid Rappaport-Vassiliadis medium and then plating onto brilliant green with novobiocin and xylose lysine brilliant Tergitol 4 plates. One-milliliter aliquots of the selective enrichment broths from each sample were collected for DNA extraction by the commercial PrepSEQ nucleic acid extraction assay and analysis by the Salmonella Enteritidis-specific real-time PCR assay. The real-time PCR assay detected no significant differences between the boot sock and drag swab samples. In contrast, the culture method detected a significantly higher number of positive samples from boot socks. The diagnostic sensitivity of the real-time PCR assay for the field samples was significantly higher than that of the culture method. The kappa value obtained was 0.46, indicating moderate agreement between the real-time PCR assay and the culture method. In addition, the real-time PCR method had a turnaround time of 2 days compared with 4 to 8 days for the culture method. The higher sensitivity as well as the reduction in time and labor makes this real-time PCR assay an excellent alternative to conventional culture methods for diagnostic purposes, surveillance, and research studies to improve food safety.

Mean carrier transport properties and charge collection dynamics of single-crystal, natural type IIa diamonds from ion-induced conductivity measurements

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

Han, Sung Su

1993-09-01

Ion-induced conductivity has been used to investigate the detector characteristics of diamond detectors. Both integrated-charge, and time-resolved current measurements were performed to examine the mean carrier transport properties of diamond and the dynamics of charge collection under highly-localized and high-density excitation conditions. The integrated-charge measurements were conducted with a standard pulse-counting system with 241Am radioactivity as the excitation source for the detectors. The time-resolved current measurements were performed using a 70 GHz random sampling oscilloscope with the detectors incorporated into high-speed microstrip transmission lines and the excitation source for these measurements was an ion beam of either 5-MeV He +more » or 10-MeV Si 3+. The detectors used in both experiments can be described as metal-semiconductor-metal (MSM) devices where a volume of the detector material is sandwiched between two metal plates. A charge collection model was developed to interpret the integrated-charge measurements which enabled estimation of the energy required to produce an electron-hole pair (ϵ di) and the mean carrier transport properties in diamond, such as carrier mobility and lifetime, and the behavior of the electrical contacts to diamond.« less

Measurement of B0, Bs0, B+ and Λb0 production asymmetries in 7 and 8 TeV proton-proton collisions

NASA Astrophysics Data System (ADS)

Aaij, R.; Adeva, B.; Adinolfi, M.; Ajaltouni, Z.; Akar, S.; Albrecht, J.; Alessio, F.; Alexander, M.; Ali, S.; Alkhazov, G.; Alvarez Cartelle, P.; Alves, A. A.; Amato, S.; Amerio, S.; Amhis, Y.; An, L.; Anderlini, L.; Andreassi, G.; Andreotti, M.; Andrews, J. E.; Appleby, R. B.; Archilli, F.; d'Argent, P.; Arnau Romeu, J.; Artamonov, A.; Artuso, M.; Aslanides, E.; Auriemma, G.; Baalouch, M.; Babuschkin, I.; Bachmann, S.; Back, J. J.; Badalov, A.; Baesso, C.; Baker, S.; Balagura, V.; Baldini, W.; Barlow, R. J.; Barschel, C.; Barsuk, S.; Barter, W.; Baryshnikov, F.; Baszczyk, M.; Batozskaya, V.; Batsukh, B.; Battista, V.; Bay, A.; Beaucourt, L.; Beddow, J.; Bedeschi, F.; Bediaga, I.; Beiter, A.; Bel, L. J.; Bellee, V.; Belloli, N.; Belous, K.; Belyaev, I.; Ben-Haim, E.; Bencivenni, G.; Benson, S.; Berezhnoy, A.; Bernet, R.; Bertolin, A.; Betancourt, C.; Betti, F.; Bettler, M.-O.; van Beuzekom, M.; Bezshyiko, Ia.; Bifani, S.; Billoir, P.; Bird, T.; Birnkraut, A.; Bitadze, A.; Bizzeti, A.; Blake, T.; Blanc, F.; Blouw, J.; Blusk, S.; Bocci, V.; Boettcher, T.; Bondar, A.; Bondar, N.; Bonivento, W.; Bordyuzhin, I.; Borgheresi, A.; Borghi, S.; Borisyak, M.; Borsato, M.; Bossu, F.; Boubdir, M.; Bowcock, T. J. V.; Bowen, E.; Bozzi, C.; Braun, S.; Britsch, M.; Britton, T.; Brodzicka, J.; Buchanan, E.; Burr, C.; Bursche, A.; Buytaert, J.; Cadeddu, S.; Calabrese, R.; Calvi, M.; Calvo Gomez, M.; Camboni, A.; Campana, P.; Campora Perez, D. H.; Capriotti, L.; Carbone, A.; Carboni, G.; Cardinale, R.; Cardini, A.; Carniti, P.; Carson, L.; Carvalho Akiba, K.; Casse, G.; Cassina, L.; Castillo Garcia, L.; Cattaneo, M.; Cavallero, G.; Cenci, R.; Chamont, D.; Charles, M.; Charpentier, Ph.; Chatzikonstantinidis, G.; Chefdeville, M.; Chen, S.; Cheung, S. F.; Chobanova, V.; Chrzaszcz, M.; Cid Vidal, X.; Ciezarek, G.; Clarke, P. E. L.; Clemencic, M.; Cliff, H. V.; Closier, J.; Coco, V.; Cogan, J.; Cogneras, E.; Cogoni, V.; Cojocariu, L.; Collins, P.; Comerma-Montells, A.; Contu, A.; Cook, A.; Coombs, G.; Coquereau, S.; Corti, G.; Corvo, M.; Costa Sobral, C. M.; Couturier, B.; Cowan, G. A.; Craik, D. C.; Crocombe, A.; Cruz Torres, M.; Cunliffe, S.; Currie, R.; D'Ambrosio, C.; Da Cunha Marinho, F.; Dall'Occo, E.; Dalseno, J.; David, P. N. Y.; Davis, A.; De Bruyn, K.; De Capua, S.; De Cian, M.; De Miranda, J. M.; De Paula, L.; De Serio, M.; De Simone, P.; Dean, C. T.; Decamp, D.; Deckenhoff, M.; Del Buono, L.; Demmer, M.; Dendek, A.; Derkach, D.; Deschamps, O.; Dettori, F.; Dey, B.; Di Canto, A.; Dijkstra, H.; Dordei, F.; Dorigo, M.; Dosil Suárez, A.; Dovbnya, A.; Dreimanis, K.; Dufour, L.; Dujany, G.; Dungs, K.; Durante, P.; Dzhelyadin, R.; Dziurda, A.; Dzyuba, A.; Déléage, N.; Easo, S.; Ebert, M.; Egede, U.; Egorychev, V.; Eidelman, S.; Eisenhardt, S.; Eitschberger, U.; Ekelhof, R.; Eklund, L.; Ely, S.; Esen, S.; Evans, H. M.; Evans, T.; Falabella, A.; Farley, N.; Farry, S.; Fay, R.; Fazzini, D.; Ferguson, D.; Fernandez Prieto, A.; Ferrari, F.; Ferreira Rodrigues, F.; Ferro-Luzzi, M.; Filippov, S.; Fini, R. A.; Fiore, M.; Fiorini, M.; Firlej, M.; Fitzpatrick, C.; Fiutowski, T.; Fleuret, F.; Fohl, K.; Fontana, M.; Fontanelli, F.; Forshaw, D. C.; Forty, R.; Franco Lima, V.; Frank, M.; Frei, C.; Fu, J.; Funk, W.; Furfaro, E.; Färber, C.; Gallas Torreira, A.; Galli, D.; Gallorini, S.; Gambetta, S.; Gandelman, M.; Gandini, P.; Gao, Y.; Garcia Martin, L. M.; García Pardiñas, J.; Garra Tico, J.; Garrido, L.; Garsed, P. J.; Gascon, D.; Gaspar, C.; Gavardi, L.; Gazzoni, G.; Gerick, D.; Gersabeck, E.; Gersabeck, M.; Gershon, T.; Ghez, Ph.; Gianì, S.; Gibson, V.; Girard, O. G.; Giubega, L.; Gizdov, K.; Gligorov, V. V.; Golubkov, D.; Golutvin, A.; Gomes, A.; Gorelov, I. V.; Gotti, C.; Graciani Diaz, R.; Granado Cardoso, L. A.; Graugés, E.; Graverini, E.; Graziani, G.; Grecu, A.; Greim, R.; Griffith, P.; Grillo, L.; Gruberg Cazon, B. R.; Grünberg, O.; Gushchin, E.; Guz, Yu.; Gys, T.; Göbel, C.; Hadavizadeh, T.; Hadjivasiliou, C.; Haefeli, G.; Haen, C.; Haines, S. C.; Hamilton, B.; Han, X.; Hansmann-Menzemer, S.; Harnew, N.; Harnew, S. T.; Harrison, J.; Hatch, M.; He, J.; Head, T.; Heister, A.; Hennessy, K.; Henrard, P.; Henry, L.; van Herwijnen, E.; Heß, M.; Hicheur, A.; Hill, D.; Hombach, C.; Hopchev, P. H.; Hulsbergen, W.; Humair, T.; Hushchyn, M.; Hutchcroft, D.; Idzik, M.; Ilten, P.; Jacobsson, R.; Jaeger, A.; Jalocha, J.; Jans, E.; Jawahery, A.; Jiang, F.; John, M.; Johnson, D.; Jones, C. R.; Joram, C.; Jost, B.; Jurik, N.; Kandybei, S.; Karacson, M.; Kariuki, J. M.; Karodia, S.; Kecke, M.; Kelsey, M.; Kenzie, M.; Ketel, T.; Khairullin, E.; Khanji, B.; Khurewathanakul, C.; Kirn, T.; Klaver, S.; Klimaszewski, K.; Koliiev, S.; Kolpin, M.; Komarov, I.; Koopman, R. F.; Koppenburg, P.; Kosmyntseva, A.; Kozeiha, M.; Kravchuk, L.; Kreplin, K.; Kreps, M.; Krokovny, P.; Kruse, F.; Krzemien, W.; Kucewicz, W.; Kucharczyk, M.; Kudryavtsev, V.; Kuonen, A. K.; Kurek, K.; Kvaratskheliya, T.; Lacarrere, D.; Lafferty, G.; Lai, A.; Lanfranchi, G.; Langenbruch, C.; Latham, T.; Lazzeroni, C.; Le Gac, R.; van Leerdam, J.; Leflat, A.; Lefrançois, J.; Lefèvre, R.; Lemaitre, F.; Lemos Cid, E.; Leroy, O.; Lesiak, T.; Leverington, B.; Li, T.; Li, Y.; Likhomanenko, T.; Lindner, R.; Linn, C.; Lionetto, F.; Liu, X.; Loh, D.; Longstaff, I.; Lopes, J. H.; Lucchesi, D.; Lucio Martinez, M.; Luo, H.; Lupato, A.; Luppi, E.; Lupton, O.; Lusiani, A.; Lyu, X.; Machefert, F.; Maciuc, F.; Maev, O.; Maguire, K.; Malde, S.; Malinin, A.; Maltsev, T.; Manca, G.; Mancinelli, G.; Manning, P.; Maratas, J.; Marchand, J. F.; Marconi, U.; Marin Benito, C.; Marinangeli, M.; Marino, P.; Marks, J.; Martellotti, G.; Martin, M.; Martinelli, M.; Martinez Santos, D.; Martinez Vidal, F.; Martins Tostes, D.; Massacrier, L. M.; Massafferri, A.; Matev, R.; Mathad, A.; Mathe, Z.; Matteuzzi, C.; Mauri, A.; Maurice, E.; Maurin, B.; Mazurov, A.; McCann, M.; McNab, A.; McNulty, R.; Meadows, B.; Meier, F.; Meissner, M.; Melnychuk, D.; Merk, M.; Merli, A.; Michielin, E.; Milanes, D. A.; Minard, M.-N.; Mitzel, D. S.; Mogini, A.; Molina Rodriguez, J.; Monroy, I. A.; Monteil, S.; Morandin, M.; Morawski, P.; Mordà, A.; Morello, M. J.; Morgunova, O.; Moron, J.; Morris, A. B.; Mountain, R.; Muheim, F.; Mulder, M.; Mussini, M.; Müller, D.; Müller, J.; Müller, K.; Müller, V.; Naik, P.; Nakada, T.; Nandakumar, R.; Nandi, A.; Nasteva, I.; Needham, M.; Neri, N.; Neubert, S.; Neufeld, N.; Neuner, M.; Nguyen, T. D.; Nguyen-Mau, C.; Nieswand, S.; Niet, R.; Nikitin, N.; Nikodem, T.; Nogay, A.; Novoselov, A.; O'Hanlon, D. P.; Oblakowska-Mucha, A.; Obraztsov, V.; Ogilvy, S.; Oldeman, R.; Onderwater, C. J. G.; Otalora Goicochea, J. M.; Otto, A.; Owen, P.; Oyanguren, A.; Pais, P. R.; Palano, A.; Palutan, M.; Papanestis, A.; Pappagallo, M.; Pappalardo, L. L.; Parker, W.; Parkes, C.; Passaleva, G.; Pastore, A.; Patel, G. D.; Patel, M.; Patrignani, C.; Pearce, A.; Pellegrino, A.; Penso, G.; Pepe Altarelli, M.; Perazzini, S.; Perret, P.; Pescatore, L.; Petridis, K.; Petrolini, A.; Petrov, A.; Petruzzo, M.; Picatoste Olloqui, E.; Pietrzyk, B.; Pikies, M.; Pinci, D.; Pistone, A.; Piucci, A.; Placinta, V.; Playfer, S.; Plo Casasus, M.; Poikela, T.; Polci, F.; Poluektov, A.; Polyakov, I.; Polycarpo, E.; Pomery, G. J.; Popov, A.; Popov, D.; Popovici, B.; Poslavskii, S.; Potterat, C.; Price, E.; Price, J. D.; Prisciandaro, J.; Pritchard, A.; Prouve, C.; Pugatch, V.; Puig Navarro, A.; Punzi, G.; Qian, W.; Quagliani, R.; Rachwal, B.; Rademacker, J. H.; Rama, M.; Ramos Pernas, M.; Rangel, M. S.; Raniuk, I.; Ratnikov, F.; Raven, G.; Redi, F.; Reichert, S.; dos Reis, A. C.; Remon Alepuz, C.; Renaudin, V.; Ricciardi, S.; Richards, S.; Rihl, M.; Rinnert, K.; Rives Molina, V.; Robbe, P.; Rodrigues, A. B.; Rodrigues, E.; Rodriguez Lopez, J. A.; Rodriguez Perez, P.; Rogozhnikov, A.; Roiser, S.; Rollings, A.; Romanovskiy, V.; Romero Vidal, A.; Ronayne, J. W.; Rotondo, M.; Rudolph, M. S.; Ruf, T.; Ruiz Valls, P.; Saborido Silva, J. J.; Sadykhov, E.; Sagidova, N.; Saitta, B.; Salustino Guimaraes, V.; Sanchez Mayordomo, C.; Sanmartin Sedes, B.; Santacesaria, R.; Santamarina Rios, C.; Santimaria, M.; Santovetti, E.; Sarti, A.; Satriano, C.; Satta, A.; Saunders, D. M.; Savrina, D.; Schael, S.; Schellenberg, M.; Schiller, M.; Schindler, H.; Schlupp, M.; Schmelling, M.; Schmelzer, T.; Schmidt, B.; Schneider, O.; Schopper, A.; Schubert, K.; Schubiger, M.; Schune, M.-H.; Schwemmer, R.; Sciascia, B.; Sciubba, A.; Semennikov, A.; Sergi, A.; Serra, N.; Serrano, J.; Sestini, L.; Seyfert, P.; Shapkin, M.; Shapoval, I.; Shcheglov, Y.; Shears, T.; Shekhtman, L.; Shevchenko, V.; Siddi, B. G.; Silva Coutinho, R.; Silva de Oliveira, L.; Simi, G.; Simone, S.; Sirendi, M.; Skidmore, N.; Skwarnicki, T.; Smith, E.; Smith, I. T.; Smith, J.; Smith, M.; Snoek, H.; Soares Lavra, l.; Sokoloff, M. D.; Soler, F. J. P.; Souza De Paula, B.; Spaan, B.; Spradlin, P.; Sridharan, S.; Stagni, F.; Stahl, M.; Stahl, S.; Stefko, P.; Stefkova, S.; Steinkamp, O.; Stemmle, S.; Stenyakin, O.; Stevens, H.; Stevenson, S.; Stoica, S.; Stone, S.; Storaci, B.; Stracka, S.; Straticiuc, M.; Straumann, U.; Sun, L.; Sutcliffe, W.; Swientek, K.; Syropoulos, V.; Szczekowski, M.; Szumlak, T.; T'Jampens, S.; Tayduganov, A.; Tekampe, T.; Tellarini, G.; Teubert, F.; Thomas, E.; van Tilburg, J.; Tilley, M. J.; Tisserand, V.; Tobin, M.; Tolk, S.; Tomassetti, L.; Tonelli, D.; Topp-Joergensen, S.; Toriello, F.; Tournefier, E.; Tourneur, S.; Trabelsi, K.; Traill, M.; Tran, M. T.; Tresch, M.; Trisovic, A.; Tsaregorodtsev, A.; Tsopelas, P.; Tully, A.; Tuning, N.; Ukleja, A.; Ustyuzhanin, A.; Uwer, U.; Vacca, C.; Vagnoni, V.; Valassi, A.; Valat, S.; Valenti, G.; Vazquez Gomez, R.; Vazquez Regueiro, P.; Vecchi, S.; van Veghel, M.; Velthuis, J. J.; Veltri, M.; Veneziano, G.; Venkateswaran, A.; Vernet, M.; Vesterinen, M.; Viana Barbosa, J. V.; Viaud, B.; Vieira, D.; Vieites Diaz, M.; Viemann, H.; Vilasis-Cardona, X.; Vitti, M.; Volkov, V.; Vollhardt, A.; Voneki, B.; Vorobyev, A.; Vorobyev, V.; Voß, C.; de Vries, J. A.; Vázquez Sierra, C.; Waldi, R.; Wallace, C.; Wallace, R.; Walsh, J.; Wang, J.; Ward, D. R.; Wark, H. M.; Watson, N. K.; Websdale, D.; Weiden, A.; Whitehead, M.; Wicht, J.; Wilkinson, G.; Wilkinson, M.; Williams, M.; Williams, M. P.; Williams, M.; Williams, T.; Wilson, F. F.; Wimberley, J.; Wishahi, J.; Wislicki, W.; Witek, M.; Wormser, G.; Wotton, S. A.; Wraight, K.; Wyllie, K.; Xie, Y.; Xing, Z.; Xu, Z.; Yang, Z.; Yao, Y.; Yin, H.; Yu, J.; Yuan, X.; Yushchenko, O.; Zarebski, K. A.; Zavertyaev, M.; Zhang, L.; Zhang, Y.; Zhelezov, A.; Zheng, Y.; Zhu, X.; Zhukov, V.; Zucchelli, S.; LHCb Collaboration

2017-11-01

The B0, Bs0, B+ and Λb0 hadron production asymmetries are measured using a data sample corresponding to an integrated luminosity of 3.0 fb-1, collected by the LHCb experiment in proton-proton collisions at centre-of-mass energies of 7 and 8 TeV. The measurements are performed as a function of transverse momentum and rapidity of the b hadrons within the LHCb detector acceptance. The overall production asymmetries, integrated over transverse momentum and rapidity, are also determined.

Preliminary performance assessment of biotoxin detection for UWS applications using a MicroChemLab device.

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

VanderNoot, Victoria A.; Haroldsen, Brent L.; Renzi, Ronald F.

2010-03-01

In a multiyear research agreement with Tenix Investments Pty. Ltd., Sandia has been developing field deployable technologies for detection of biotoxins in water supply systems. The unattended water sensor or UWS employs microfluidic chip based gel electrophoresis for monitoring biological analytes in a small integrated sensor platform. This instrument collects, prepares, and analyzes water samples in an automated manner. Sample analysis is done using the {mu}ChemLab{trademark} analysis module. This report uses analysis results of two datasets collected using the UWS to estimate performance of the device. The first dataset is made up of samples containing ricin at varying concentrations andmore » is used for assessing instrument response and detection probability. The second dataset is comprised of analyses of water samples collected at a water utility which are used to assess the false positive probability. The analyses of the two sets are used to estimate the Receiver Operating Characteristic or ROC curves for the device at one set of operational and detection algorithm parameters. For these parameters and based on a statistical estimate, the ricin probability of detection is about 0.9 at a concentration of 5 nM for a false positive probability of 1 x 10{sup -6}.« less

A geochemical sampling technique for use in areas of active alpine glaciation: an application from the central Alaska Range

USGS Publications Warehouse

Stephens, G.C.; Evenson, E.B.; Detra, D.E.

1990-01-01

In mountainous regions containing extensive glacier systems there is a lack of suitable material for conventional geochemical sampling. As a result, in most geochemical sampling programs a few stream-sediment samples collected at, or near, the terminus of valley glaciers are used to evaluate the mineral potential of the glaciated area. We have developed and tested a technique which utilizes the medial moraines of valley glaciers for systematic geochemical exploration of the glacial catchment area. Moraine sampling provides geochemical information that is site-specific in that geochemical anomalies can be traced directly up-ice to bedrock sources. Traverses were made across the Trident and Susitna glaciers in the central Alaska Range where fine-grained (clay to sand size) samples were collected from each medial moraine. These samples were prepared and chemically analyzed to determine the concentration of specific elements. Fifty pebbles were collected at each moraine for archival purposes and for subsequent lithologic identification. Additionally, fifty cobbles and fifty boulders were examined and described at each sample site to determine the nature and abundance of lithologies present in the catchment area, the extent and nature of visible mineralization, the presence and intensity of hydrothermal alteration and the existence of veins, dikes and other minor structural features. Results from the central Alaska Range have delineated four distinct multi-element anomalies which are a response to potential mineralization up-ice from the medial moraine traverse. By integrating the lithologic, mineralogical and geochemical data the probable geological setting of the geochemical anomalies is determined. ?? 1990.

Collection of biological samples in forensic toxicology.

PubMed

Dinis-Oliveira, R J; Carvalho, F; Duarte, J A; Remião, F; Marques, A; Santos, A; Magalhães, T

2010-09-01

Forensic toxicology is the study and practice of the application of toxicology to the purposes of the law. The relevance of any finding is determined, in the first instance, by the nature and integrity of the specimen(s) submitted for analysis. This means that there are several specific challenges to select and collect specimens for ante-mortem and post-mortem toxicology investigation. Post-mortem specimens may be numerous and can endow some special difficulties compared to clinical specimens, namely those resulting from autolytic and putrefactive changes. Storage stability is also an important issue to be considered during the pre-analytic phase, since its consideration should facilitate the assessment of sample quality and the analytical result obtained from that sample. The knowledge on degradation mechanisms and methods to increase storage stability may enable the forensic toxicologist to circumvent possible difficulties. Therefore, advantages and limitations of specimen preservation procedures are thoroughfully discussed in this review. Presently, harmonized protocols for sampling in suspected intoxications would have obvious utility. In the present article an overview is given on sampling procedures for routinely collected specimens as well as on alternative specimens that may provide additional information on the route and timing of exposure to a specific xenobiotic. Last, but not least, a discussion on possible bias that can influence the interpretation of toxicological results is provided. This comprehensive review article is intented as a significant help for forensic toxicologists to accomplish their frequently overwhelming mission.

Comparison of a novel passive sampler to standard water-column sampling for organic contaminants associated with wastewater effluents entering a New Jersey stream

USGS Publications Warehouse

Alvarez, D.A.; Stackelberg, P.E.; Petty, J.D.; Huckins, J.N.; Furlong, E.T.; Zaugg, S.D.; Meyer, M.T.

2005-01-01

Four water samples collected using standard depth and width water-column sampling methodology were compared to an innovative passive, in situ, sampler (the polar organic chemical integrative sampler or POCIS) for the detection of 96 organic wastewater-related contaminants (OWCs) in a stream that receives agricultural, municipal, and industrial wastewaters. Thirty-two OWCs were identified in POCIS extracts whereas 9-24 were identified in individual water-column samples demonstrating the utility of POCIS for identifying contaminants whose occurrence are transient or whose concentrations are below routine analytical detection limits. Overall, 10 OWCs were identified exclusively in the POCIS extracts and only six solely identified in the water-column samples, however, repetitive water samples taken using the standard method during the POCIS deployment period required multiple trips to the sampling site and an increased number of samples to store, process, and analyze. Due to the greater number of OWCs detected in the POCIS extracts as compared to individual water-column samples, the ease of performing a single deployment as compared to collecting and processing multiple water samples, the greater mass of chemical residues sequestered, and the ability to detect chemicals which dissipate quickly, the passive sampling technique offers an efficient and effective alternative for detecting OWCs in our waterways for wastewater contaminants.

Integrated hollow microneedle-optofluidic biosensor for therapeutic drug monitoring in sub-nanoliter volumes

NASA Astrophysics Data System (ADS)

Ranamukhaarachchi, Sahan A.; Padeste, Celestino; Dübner, Matthias; Häfeli, Urs O.; Stoeber, Boris; Cadarso, Victor J.

2016-07-01

Therapeutic drug monitoring (TDM) typically requires painful blood drawn from patients. We propose a painless and minimally-invasive alternative for TDM using hollow microneedles suitable to extract extremely small volumes (<1 nL) of interstitial fluid to measure drug concentrations. The inner lumen of a microneedle is functionalized to be used as a micro-reactor during sample collection to trap and bind target drug candidates during extraction, without requirements of sample transfer. An optofluidic device is integrated with this microneedle to rapidly quantify drug analytes with high sensitivity using a straightforward absorbance scheme. Vancomycin is currently detected by using volumes ranging between 50-100 μL with a limit of detection (LoD) of 1.35 μM. The proposed microneedle-optofluidic biosensor can detect vancomycin with a sample volume of 0.6 nL and a LoD of <100 nM, validating this painless point of care system with significant potential to reduce healthcare costs and patients suffering.

Integrated magnetic, gravity, and GPR surveys to locate the probable source of hydrocarbon contamination in Sharm El-Sheikh area, south Sinai, Egypt

NASA Astrophysics Data System (ADS)

Morsy, Mona; Rashed, Mohamed

2013-01-01

Sharm El-Sheikh waters were suddenly hit by hydrocarbon spills which created a serious threat to the prosperous tourism industry in and around the city. Analysis of soil samples, water samples, and seabed samples collected in and around the contaminated bay area showed anomalous levels of hydrocarbons. An integrated geophysical investigation, using magnetic, gravity, and ground penetrating radar geophysical tools, was conducted in the headland overlooking the contaminated bay in order to delineate the possible subsurface source of contamination. The results of the geophysical investigations revealed three underground manmade reinforced concrete tanks and a complicated network of buried steel pipes in addition to other unidentified buried objects. The depths and dimensions of the discovered objects were determined. Geophysical investigations also revealed the presence of a north-south oblique slip fault running through the eastern part of the studied area. Excavations, conducted later on, confirmed the presence of one of the tanks delineated by the geophysical surveys.

Integrated hollow microneedle-optofluidic biosensor for therapeutic drug monitoring in sub-nanoliter volumes

PubMed Central

Ranamukhaarachchi, Sahan A.; Padeste, Celestino; Dübner, Matthias; Häfeli, Urs O.; Stoeber, Boris; Cadarso, Victor J.

2016-01-01

Therapeutic drug monitoring (TDM) typically requires painful blood drawn from patients. We propose a painless and minimally-invasive alternative for TDM using hollow microneedles suitable to extract extremely small volumes (<1 nL) of interstitial fluid to measure drug concentrations. The inner lumen of a microneedle is functionalized to be used as a micro-reactor during sample collection to trap and bind target drug candidates during extraction, without requirements of sample transfer. An optofluidic device is integrated with this microneedle to rapidly quantify drug analytes with high sensitivity using a straightforward absorbance scheme. Vancomycin is currently detected by using volumes ranging between 50–100 μL with a limit of detection (LoD) of 1.35 μM. The proposed microneedle-optofluidic biosensor can detect vancomycin with a sample volume of 0.6 nL and a LoD of <100 nM, validating this painless point of care system with significant potential to reduce healthcare costs and patients suffering. PMID:27380889

Rapid DNA analysis for automated processing and interpretation of low DNA content samples.

PubMed

Turingan, Rosemary S; Vasantgadkar, Sameer; Palombo, Luke; Hogan, Catherine; Jiang, Hua; Tan, Eugene; Selden, Richard F

2016-01-01

Short tandem repeat (STR) analysis of casework samples with low DNA content include those resulting from the transfer of epithelial cells from the skin to an object (e.g., cells on a water bottle, or brim of a cap), blood spatter stains, and small bone and tissue fragments. Low DNA content (LDC) samples are important in a wide range of settings, including disaster response teams to assist in victim identification and family reunification, military operations to identify friend or foe, criminal forensics to identify suspects and exonerate the innocent, and medical examiner and coroner offices to identify missing persons. Processing LDC samples requires experienced laboratory personnel, isolated workstations, and sophisticated equipment, requires transport time, and involves complex procedures. We present a rapid DNA analysis system designed specifically to generate STR profiles from LDC samples in field-forward settings by non-technical operators. By performing STR in the field, close to the site of collection, rapid DNA analysis has the potential to increase throughput and to provide actionable information in real time. A Low DNA Content BioChipSet (LDC BCS) was developed and manufactured by injection molding. It was designed to function in the fully integrated Accelerated Nuclear DNA Equipment (ANDE) instrument previously designed for analysis of buccal swab and other high DNA content samples (Investigative Genet. 4(1):1-15, 2013). The LDC BCS performs efficient DNA purification followed by microfluidic ultrafiltration of the purified DNA, maximizing the quantity of DNA available for subsequent amplification and electrophoretic separation and detection of amplified fragments. The system demonstrates accuracy, precision, resolution, signal strength, and peak height ratios appropriate for casework analysis. The LDC rapid DNA analysis system is effective for the generation of STR profiles from a wide range of sample types. The technology broadens the range of sample types that can be processed and minimizes the time between sample collection, sample processing and analysis, and generation of actionable intelligence. The fully integrated Expert System is capable of interpreting a wide range or sample types and input DNA quantities, allowing samples to be processed and interpreted without a technical operator.

Aerosol sampling system for collection of Capstone depleted uranium particles in a high-energy environment.

PubMed

Holmes, Thomas D; Guilmette, Raymond A; Cheng, Yung Sung; Parkhurst, Mary Ann; Hoover, Mark D

2009-03-01

The Capstone Depleted Uranium (DU) Aerosol Study was undertaken to obtain aerosol samples resulting from a large-caliber DU penetrator striking an Abrams or Bradley test vehicle. The sampling strategy was designed to (1) optimize the performance of the samplers and maintain their integrity in the extreme environment created during perforation of an armored vehicle by a DU penetrator, (2) collect aerosols as a function of time post perforation, and (3) obtain size-classified samples for analysis of chemical composition, particle morphology, and solubility in lung fluid. This paper describes the experimental setup and sampling methodologies used to achieve these objectives. Custom-designed arrays of sampling heads were secured to the inside of the target in locations approximating the breathing zones of the crew locations in the test vehicles. Each array was designed to support nine filter cassettes and nine cascade impactors mounted with quick-disconnect fittings. Shielding and sampler placement strategies were used to minimize sampler loss caused by the penetrator impact and the resulting fragments of eroded penetrator and perforated armor. A cyclone train was used to collect larger quantities of DU aerosol for measurement of chemical composition and solubility. A moving filter sample was used to obtain semicontinuous samples for DU concentration determination. Control for the air samplers was provided by five remotely located valve control and pressure monitoring units located inside and around the test vehicle. These units were connected to a computer interface chassis and controlled using a customized LabVIEW engineering computer control program. The aerosol sampling arrays and control systems for the Capstone study provided the needed aerosol samples for physicochemical analysis, and the resultant data were used for risk assessment of exposure to DU aerosol.

Aerosol Sampling System for Collection of Capstone Depleted Uranium Particles in a High-Energy Environment

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

Holmes, Thomas D.; Guilmette, Raymond A.; Cheng, Yung-Sung

2009-03-01

The Capstone Depleted Uranium Aerosol Study was undertaken to obtain aerosol samples resulting from a kinetic-energy cartridge with a large-caliber depleted uranium (DU) penetrator striking an Abrams or Bradley test vehicle. The sampling strategy was designed to (1) optimize the performance of the samplers and maintain their integrity in the extreme environment created during perforation of an armored vehicle by a DU penetrator, (2) collect aerosols as a function of time post-impact, and (3) obtain size-classified samples for analysis of chemical composition, particle morphology, and solubility in lung fluid. This paper describes the experimental setup and sampling methodologies used tomore » achieve these objectives. Custom-designed arrays of sampling heads were secured to the inside of the target in locations approximating the breathing zones of the vehicle commander, loader, gunner, and driver. Each array was designed to support nine filter cassettes and nine cascade impactors mounted with quick-disconnect fittings. Shielding and sampler placement strategies were used to minimize sampler loss caused by the penetrator impact and the resulting fragments of eroded penetrator and perforated armor. A cyclone train was used to collect larger quantities of DU aerosol for chemical composition and solubility. A moving filter sample was used to obtain semicontinuous samples for depleted uranium concentration determination. Control for the air samplers was provided by five remotely located valve control and pressure monitoring units located inside and around the test vehicle. These units were connected to a computer interface chassis and controlled using a customized LabVIEW engineering computer control program. The aerosol sampling arrays and control systems for the Capstone study provided the needed aerosol samples for physicochemical analysis, and the resultant data were used for risk assessment of exposure to DU aerosol.« less

Integrated biochemical, molecular genetic, and bioacoustical analysis of mesoscale variability of the euphausiid Nematoscelis difficilis in the California Current

NASA Astrophysics Data System (ADS)

Bucklin, Ann; Wiebe, Peter H.; Smolenack, Sara B.; Copley, Nancy J.; Clarke, M. Elizabeth

2002-03-01

Integrated assessment of the euphausiid Nematoscelis difficilis (Crustacea; Euphausiacea) and the zooplankton assemblage of the California Current was designed to investigate individual, population, and community responses to mesoscale variability in biological and physical characters of the ocean. Zooplankton samples and observational data were collected along a cross-shelf transect of the California Current in association with the California Cooperative Fisheries Investigations (CalCOFI) Survey during October 1996. The transect crossed three domains defined by temperature and salinity: nearshore, mid-Current, and offshore. Individual N. difficilis differed in physiological condition along the transect, with higher size-corrected concentrations of four central metabolic enzymes (citrate synthetase, hexokinase, lactate dehydrogenase (LDH), and phosphoglucose isomerase (PGI)) for euphausiids collected in nearshore waters than in mid-Current and offshore waters. There was little variation in the DNA sequences of the genes encoding PGI and LDH (all DNA changes were either silent or heterozygous base substitutions), suggesting that differences in enzyme concentration did not result from underlying molecular genetic variation. The population genetic makeup of N. difficilis varied from sample to sample based on haplotype frequencies of mitochondrial cytochrome oxidase I (mtCOI; P=0.029). There were significant differences between pooled nearshore and offshore samples, based on allele frequencies at two sites of common substitutions in the mtCOI sequence ( P=0.020 and 0.026). Silhouette and bioacoustical backscattering measurements of the zooplankton assemblage of the top 100 m showed marked diel vertical migration of the scattering layer, of which euphausiids were a small but significant fraction. The biochemical and molecular assays are used as indices of complex physiological (i.e., growth and condition) and genetic (i.e., mortality) processes; the bioacoustical observations provide insight into the ecosystem context for the single-species measurements. All data are intended for integration into predictive models of secondary production and biomass concentration in the ocean.

Evaluation of the method of collecting suspended sediment from large rivers by discharge-weighted pumping and separation by continuous- flow centrifugation

USGS Publications Warehouse

Moody, J.A.; Meade, R.H.

1994-01-01

The efficacy of the method is evaluated by comparing the particle size distributions of sediment collected by the discharge-weighted pumping method with the particle size distributions of sediment collected by depth integration and separated by gravitational settling. The pumping method was found to undersample the suspended sand sized particles (>63 ??m) but to collect a representative sample of the suspended silt and clay sized particles (<63??m). The success of the discharge-weighted pumping method depends on how homogeneously the silt and clay sized particles (<63 ??m) are distributed in the vertical direction in the river. The degree of homogeneity depends on the composition and degree of aggregation of the suspended sediment particles. -from Authors

Occupational Therapy Students' Perceptions of Spirituality in Training.

PubMed

Mthembu, Thuli Godfrey; Ahmed, Firdous; Nkuna, Thembi; Yaca, Khalipha

2015-12-01

Spirituality is recognized as an essential and integral component of a holistic approach in occupational therapy practice. However, little is known about occupational therapy students' perceptions regarding spirituality in learning context. This study used qualitative exploratory, descriptive design to explore the occupational therapy students' perceptions about spirituality in training. Using purposive sampling, four semi-structured interviews were conducted with two students, a lecturer and an occupational therapist. In addition, two focus groups were conducted with students in order to collect data. Data collected were audio-taped; transcribed and thematic analysis was used to identify themes. The analysis resulted in emergence of four themes: "Unique to every individual," "Spirituality in occupational therapy," "To be or not to be taught," and "The Real world." Participants perceived spirituality as an individually experienced. The study contributes to the body of knowledge base of occupational therapy education regarding spirituality. However, there is a need for guidelines to integrate spirituality in occupational therapy training.

Innovative flow controller for time integrated passive sampling using SUMMA canisters

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

Simon, P.; Farant, J.P.; Cole, H.

1996-12-31

To restrict the entry of gaseous contaminants inside evacuated vessels such as SUMMA canisters, mechanical flow controllers are used to collect integrated atmospheric samples. From the passive force generated by the pressure gradient, the motion of gas can be controlled to obtain a constant flow rate. Presently, devices based on the principle of critical orifices are used and they are all limited to an upper integrated sampling time. A novel flow controller which can be designed to achieve any desired sampling time when used on evacuated vessels was recently developed. It can extend the sampling time for hours, days, weeksmore » or even months for the benefits of environmental, engineering and toxicological professionals. The design of the controller is obtained from computer simulations done with an original set of equations derived from fluid mechanic and gas kinetic laws. To date, the experimental results have shown excellent agreement, with predictions obtained from the mathematical model. This new controller has already found numerous applications. Units able to deliver a constant sampling rate between vacuum and approximately -10 inches Hg during continuous long term duration have been used with SUMMA canisters of different volumes (500 ml, 1 litre and 61). Essentially, any combination of sampling time and sampler volume is possible. The innovative flow controller has contributed to an air quality assessment around a sanitary landfill (indoor/outdoor), and inside domestic wastewater and pulpmill sludge treatment facilities. It is presently being used as an alternative methodology for atmospheric sampling in the Russian orbital station Mir. This device affords true long term passive monitoring of selected gaseous air pollutants for environmental studies. 14 refs., 3 figs.« less

Complex mixtures of Pesticides in Midwest U.S. streams indicated by POCIS time-integrating samplers

USGS Publications Warehouse

Van Metre, Peter C.; Alvarez, David; Mahler, Barbara J.; Nowell, Lisa H.; Sandstrom, Mark W.; Moran, Patrick W.

2017-01-01

The Midwest United States is an intensely agricultural region where pesticides in streams pose risks to aquatic biota, but temporal variability in pesticide concentrations makes characterization of their exposure to organisms challenging. To compensate for the effects of temporal variability, we deployed polar organic chemical integrative samplers (POCIS) in 100 small streams across the Midwest for about 5 weeks during summer 2013 and analyzed the extracts for 227 pesticide compounds. Analysis of water samples collected weekly for pesticides during POCIS deployment allowed for comparison of POCIS results with periodic water-sampling results. The median number of pesticides detected in POCIS extracts was 62, and 141 compounds were detected at least once, indicating a high level of pesticide contamination of streams in the region. Sixty-five of the 141 compounds detected were pesticide degradates. Mean water concentrations estimated using published POCIS sampling rates strongly correlated with means of weekly water samples collected concurrently, however, the POCIS-estimated concentrations generally were lower than the measured water concentrations. Summed herbicide concentrations (units of ng/POCIS) were greater at agricultural sites than at urban sites but summed concentrations of insecticides and fungicides were greater at urban sites. Consistent with these differences, summed concentrations of herbicides correlate to percent cultivated crops in the watersheds and summed concentrations of insecticides and fungicides correlate to percent urban land use. With the exception of malathion concentrations at nine sites, POCIS-estimated water concentrations of pesticides were lower than aquatic-life benchmarks. The POCIS provide an alternative approach to traditional water sampling for characterizing chronic exposure to pesticides in streams across the Midwest region.

Complex mixtures of Pesticides in Midwest U.S. streams indicated by POCIS time-integrating samplers.

PubMed

Van Metre, Peter C; Alvarez, David A; Mahler, Barbara J; Nowell, Lisa; Sandstrom, Mark; Moran, Patrick

2017-01-01

The Midwest United States is an intensely agricultural region where pesticides in streams pose risks to aquatic biota, but temporal variability in pesticide concentrations makes characterization of their exposure to organisms challenging. To compensate for the effects of temporal variability, we deployed polar organic chemical integrative samplers (POCIS) in 100 small streams across the Midwest for about 5 weeks during summer 2013 and analyzed the extracts for 227 pesticide compounds. Analysis of water samples collected weekly for pesticides during POCIS deployment allowed for comparison of POCIS results with periodic water-sampling results. The median number of pesticides detected in POCIS extracts was 62, and 141 compounds were detected at least once, indicating a high level of pesticide contamination of streams in the region. Sixty-five of the 141 compounds detected were pesticide degradates. Mean water concentrations estimated using published POCIS sampling rates strongly correlated with means of weekly water samples collected concurrently, however, the POCIS-estimated concentrations generally were lower than the measured water concentrations. Summed herbicide concentrations (units of ng/POCIS) were greater at agricultural sites than at urban sites but summed concentrations of insecticides and fungicides were greater at urban sites. Consistent with these differences, summed concentrations of herbicides correlate to percent cultivated crops in the watersheds and summed concentrations of insecticides and fungicides correlate to percent urban land use. With the exception of malathion concentrations at nine sites, POCIS-estimated water concentrations of pesticides were lower than aquatic-life benchmarks. The POCIS provide an alternative approach to traditional water sampling for characterizing chronic exposure to pesticides in streams across the Midwest region. Published by Elsevier Ltd.

Large Scale Environmental Monitoring through Integration of Sensor and Mesh Networks.

PubMed

Jurdak, Raja; Nafaa, Abdelhamid; Barbirato, Alessio

2008-11-24

Monitoring outdoor environments through networks of wireless sensors has received interest for collecting physical and chemical samples at high spatial and temporal scales. A central challenge to environmental monitoring applications of sensor networks is the short communication range of the sensor nodes, which increases the complexity and cost of monitoring commodities that are located in geographically spread areas. To address this issue, we propose a new communication architecture that integrates sensor networks with medium range wireless mesh networks, and provides users with an advanced web portal for managing sensed information in an integrated manner. Our architecture adopts a holistic approach targeted at improving the user experience by optimizing the system performance for handling data that originates at the sensors, traverses the mesh network, and resides at the server for user consumption. This holistic approach enables users to set high level policies that can adapt the resolution of information collected at the sensors, set the preferred performance targets for their application, and run a wide range of queries and analysis on both real-time and historical data. All system components and processes will be described in this paper.

Acoustically enriching, large-depth aquatic sampler.

PubMed

Jonsson, Jonas; Ogden, Sam; Johansson, Linda; Hjort, Klas; Thornell, Greger

2012-05-07

In marine biology, it is useful to collect water samples when exploring the distribution and diversity of microbial communities in underwater environments. In order to provide, e.g., a miniaturized submersible explorer with the capability of collecting microorganisms, a compact sample enrichment system has been developed. The sampler is 30 mm long, 15 mm wide, and just a few millimetres thick. Integrated in a multilayer steel, polyimide and glass construction is a microfluidic channel with piezoelectric transducers, where microorganism and particle samples are collected and enriched, using acoustic radiation forces for gentle and labelless trapping. High-pressure, latchable valves, using paraffin as the actuation material, at each end of the microfluidic channel keep the collected sample pristine. A funnel structure raised above the surface of the device directs water into the microfluidic channel as the vehicle propels itself or when there is a flow across its hull. The valves proved leak proof to a pressure of 2.1 MPa for 19 hours and momentary pressures of 12.5 MPa, corresponding to an ocean depth of more than 1200 metres. By reactivating the latching mechanism, small leakages through the valves could be remedied, which could thus increase the leak-less operational time. Fluorescent particles, 1.9 μm in diameter, were successfully trapped in the microfluidic channel at flow rates up to 15 μl min(-1), corresponding to an 18.5 cm s(-1) external flow rate of the sampler. In addition, liquid-suspended GFP-marked yeast cells were successfully trapped.

Minerva: An Integrated Geospatial/Temporal Toolset for Real-time Science Decision Making and Data Collection

NASA Astrophysics Data System (ADS)

Lees, D. S.; Cohen, T.; Deans, M. C.; Lim, D. S. S.; Marquez, J.; Heldmann, J. L.; Hoffman, J.; Norheim, J.; Vadhavk, N.

2016-12-01

Minerva integrates three capabilities that are critical to the success of NASA analogs. It combines NASA's Exploration Ground Data Systems (xGDS) and Playbook software, and MIT's Surface Exploration Traverse Analysis and Navigation Tool (SEXTANT). Together, they help to plan, optimize, and monitor traverses; schedule and track activity; assist with science decision-making and document sample and data collection. Pre-mission, Minerva supports planning with a priori map data (e.g., UAV and satellite imagery) and activity scheduling. During missions, xGDS records and broadcasts live data to a distributed team who take geolocated notes and catalogue samples. Playbook provides live schedule updates and multi-media chat. Post-mission, xGDS supports data search and visualization for replanning and analysis. NASA's BASALT (Biologic Analog Science Associated with Lava Terrains) and FINESSE (Field Investigations to Enable Solar System Science and Exploration) projects use Minerva to conduct field science under simulated Mars mission conditions including 5 and 15 minute one-way communication delays. During the recent BASALT-FINESSE mission, two field scientists (EVA team) executed traverses across volcanic terrain to characterize and sample basalts. They wore backpacks with communications and imaging capabilities, and carried field portable spectrometers. The Science Team was 40 km away in a simulated mission control center. The Science Team monitored imaging (video and still), spectral, voice, location and physiological data from the EVA team via the network from the field, under communication delays. Minerva provided the Science Team with a unified context of operations at the field site, so they could make meaningful remote contributions to the collection of 10's of geotagged samples. Minerva's mission architecture will be presented with technical details and capabilities. Through the development, testing and application of Minerva, we are defining requirements for the design of future capabilities to support human and human-robotic missions to deep space and Mars.

PMF5.0 vs. CMB8.2: An inter-comparison study based on the new European SPECIEUROPE database

NASA Astrophysics Data System (ADS)

Bove, Maria Chiara; Massabò, Dario; Prati, Paolo

2018-03-01

Receptor Models are tools widely adopted in source apportionment studies. We describe here an experiment in which we integrated two different approaches, i.e. Positive Matrix Factorization (PMF) and Chemical Mass Balance (CMB) to apportion a set of PM10 (i.e. Particulate Matter with aerodynamic diameter lower than 10 μm) concentration values. The study was performed in the city of Genoa (Italy): a sampling campaign was carried out collecting daily PM10 samples for about two months in an urban background site. PM10 was collected on Quartz fiber filters by a low-volume sampler. A quite complete speciation of PM samples was obtained via Energy Dispersive-X Ray Fluorescence (ED-XRF, for elements), Ionic Chromatography (IC, for major ions and levoglucosan), thermo-optical Analysis (TOT, for organic and elemental carbon). The chemical analyses provided the input database for source apportionment by both PMF and CMB. Source profiles were directly calculated from the input data by PMF while in the CMB runs they were first calculated by averaging the profiles of similar sources collected in the European database SPECIEUROPE. Differences between the two receptor models emerged in particular with PM10 sources linked to very local processes. For this reason, PMF source profiles were adopted in refined CMB runs thus testing a new hybrid approach. Finally, PMF and the "tuned" CMB showed a better agreement even if some discrepancies could not completely been resolved. In this work, we compared the results coming from the last available PMF and CMB versions applied on a set of PM10 samples. Input profiles used in CMB analysis were obtained by averaging the profiles of the new European SPECIEUROPE database. The main differences between PMF and CMB results were linked to very local processes: we obtained the best solution by integrating the two different approaches with the implementation of some output PMF profiles to CMB runs.

Electron Microscopist | Center for Cancer Research

Cancer.gov

PROGRAM DESCRIPTION The Cancer Research Technology Program (CRTP) develops and implements emerging technology, cancer biology expertise and research capabilities to accomplish NCI research objectives. The CRTP is an outward-facing, multi-disciplinary hub purposed to enable the external cancer research community and provides dedicated support to NCI’s intramural Center for Cancer Research (CCR). The dedicated units provide electron microscopy, protein characterization, protein expression, optical microscopy and genetics. These research efforts are an integral part of CCR at the Frederick National Laboratory for Cancer Research (FNLCR). CRTP scientists also work collaboratively with intramural NCI investigators to provide research technologies and expertise. KEY ROLES/RESPONSIBILITIES - THIS POSITION IS CONTINGENT UPON FUNDING APPROVAL The Electron Microscopist will: Operate ultramicrotomes (Leica) and other instrumentation related to the preparation of embedded samples for EM (TEM and SEM) Operate TEM microscopes, (specifically Hitachi, FEI T20 and FEI T12) as well as SEM microscopes (Hitachi); task will include loading samples, screening, and performing data collection for a variety of samples: from cells to proteins Manage maintenance for the TEM and SEM microscopes Provide technical advice to investigators on sample preparation and data collection

HyperCard to SPSS: improving data integrity.

PubMed

Gostel, R

1993-01-01

This article describes a database design that captures responses in a HyperCard stack and moves the data to SPSS for the Macintosh without the need to rekey data. Pregnant women used an interactive computer application with a touch screen to answer questions and receive educational information about fetal alcohol syndrome. A database design was created to capture survey responses through interaction with a computer by a sample of prenatal women during formative evaluation trials. The author does not compare this method of data collection to other methods. This article simply describes the method of data collection as a useful research tool.

Capture and exploration of sample quality data to inform and improve the management of a screening collection.

PubMed

Charles, Isabel; Sinclair, Ian; Addison, Daniel H

2014-04-01

A new approach to the storage, processing, and interrogation of the quality data for screening samples has improved analytical throughput and confidence and enhanced the opportunities for learning from the accumulating records. The approach has entailed the design, development, and implementation of a database-oriented system, capturing information from the liquid chromatography-mass spectrometry capabilities used for assessing the integrity of samples in AstraZeneca's screening collection. A Web application has been developed to enable the visualization and interactive annotation of the analytical data, monitor the current sample queue, and report the throughput rate. Sample purity and identity are certified automatically on the chromatographic peaks of interest if predetermined thresholds are reached on key parameters. Using information extracted in parallel from the compound registration and container inventory databases, the chromatographic and spectroscopic profiles for each vessel are linked to the sample structures and storage histories. A search engine facilitates the direct comparison of results for multiple vessels of the same or similar compounds, for single vessels analyzed at different time points, or for vessels related by their origin or process flow. Access to this network of information has provided a deeper understanding of the multiple factors contributing to sample quality assurance.

Bias of Tedlar bags in the measurement of agricultural odorants.

PubMed

Trabue, Steven L; Anhalt, Jennifer C; Zahn, James A

2006-01-01

Odor regulations typically specify the use of dynamic dilution olfactometery (DDO) as a method to quantify odor emissions, and Tedlar bags are the preferred holding container for grab samples. This study was conducted to determine if Tedlar bags affect the integrity of sampled air from animal operations. Air samples were collected simultaneously in both Tedlar bags and Tenax thermal desorption tubes. Sample sources originated from either a hydrocarbon-free air tank, dynamic headspace chamber (DHC), or swine-production facility, and were analyzed by gas chromatography-mass spectrometry-olfactometry (GC-MS-O). Several background contaminants were identified from Tedlar bags, which included the odorous compounds N,N-dimethyl acetamide (DMAC), acetic acid, and phenol. Samples from the DHC demonstrated that recovery of malodor compounds was dependent on residence time in the Tedlar bag with longer residence time leading to lower recovery. After 24 h of storage, recovery of C3-C6 volatile fatty acids (VFA) averaged 64%, 4-methylphenol and 4-ethylphenol averaged 10%, and indole and 3-methylindole were below the detection limits of GC-MS-O. The odor activity value (OAV) of grab samples collected in Tedlar bags were 33 to 65% lower following 24 h of storage. These results indicate that significant odorant bias occurs when using Tedlar bags for the sampling of odors from animal production facilities.

Groundwater noble gas, age, and temperature signatures in an Alpine watershed: Valuable tools in conceptual model development

USGS Publications Warehouse

Manning, Andrew H.; Caine, Jonathan S.

2007-01-01

Bedrock groundwater in alpine watersheds is poorly understood, mainly because of a scarcity of wells in alpine settings. Groundwater noble gas, age, and temperature data were collected from springs and wells with depths of 3–342 m in Handcart Gulch, an alpine watershed in Colorado. Temperature profiles indicate active groundwater circulation to a maximum depth (aquifer thickness) of about 200 m, or about 150 m below the water table. Dissolved noble gas data show unusually high excess air concentrations (>0.02 cm3 STP/g, ΔNe > 170%) in the bedrock, consistent with unusually large seasonal water table fluctuations (up to 50 m) observed in the upper part of the watershed. Apparent 3H/3He ages are positively correlated with sample depth and excess air concentrations. Integrated samples were collected from artesian bedrock wells near the trunk stream and are assumed to approximate flow‐weighted samples reflecting bedrock aquifer mean residence times. Exponential mean ages for these integrated samples are remarkably consistent along the stream, four of five being from 8 to 11 years. The tracer data in combination with other hydrologic and geologic data support a relatively simple conceptual model of groundwater flow in the watershed in which (1) permeability is primarily a function of depth; (2) water table fluctuations increase with distance from the stream; and (3) recharge, aquifer thickness, and porosity are relatively uniform throughout the watershed in spite of the geological complexity of the Proterozoic crystalline rocks that underlie it.

[Assessment of Cyto- and Genotoxicity of Underground Waters from the Far Eastern Center on Radioactive Waste Treatment Site].

PubMed

Oudalova, A A; Pyatkova, S V; Geras'kin, S A; Kiselev, S M; Akhromeev, S V

2016-01-01

This study has been completed in the frames of activities on the environment assessment in the vicinity of the Far Eastern center (FEC) on radioactive waste treatment (a branch of Fokino, Sysoev Bay). Underground waters collected at the FEC technical site were surveyed both with instrumental techniques and bioassays. Concentrations of some chemicals (ranged to the third hazard category) in the samples collected are over the permitted limits. Activities of 137Cs and 90Sr in waters amount up to 3.8 and 16.2 Bq/l, correspondingly. The integral pollution index is over 1 in all the samples and could amount up to 165. The Allium-test application allows the detection of the sample points where underground waters have an enhanced mutagenic potential. Dependencies between biological effects and pollution levels are analyzed. The findings obtained could be used for the monitoring optimized and decision making on rehabilitation measures to decrease negative influence of the enterprise on the environment.

Applications of X-Ray Micro-Beam for Data Collection.

PubMed

Sanishvili, Ruslan; Fischetti, Robert F

2017-01-01

Micro-diffraction tools for macromolecular crystallography, first developed at the end of 1990s and now an integral part of many synchrotron beamlines, enable some of the experiments which were not feasible just a decade or so ago. These include data collection from very small samples, just a few micrometers in size; from larger, but severely inhomogeneous samples; and from samples which are optically invisible. Improved micro-diffraction tools led to improved signal-to-noise ratio, to mitigation of radiation damage in some cases, and to better-designed diffraction experiments. Small, micron-scale beams can be attained in different ways and knowing the details of the implementation is important in order to design the diffraction experiment properly. Similarly, precision, reproducibility and stability of the goniometry, and caveats of detection systems need to be taken into account. Lastly, to make micro-diffraction widely applicable, the sophistication, robustness, and user-friendliness of these tools are just as important as the technical capabilities.

Central Colorado Assessment Project (CCAP)-Geochemical data for rock, sediment, soil, and concentrate sample media

USGS Publications Warehouse

Granitto, Matthew; DeWitt, Ed H.; Klein, Terry L.

2010-01-01

This database was initiated, designed, and populated to collect and integrate geochemical data from central Colorado in order to facilitate geologic mapping, petrologic studies, mineral resource assessment, definition of geochemical baseline values and statistics, environmental impact assessment, and medical geology. The Microsoft Access database serves as a geochemical data warehouse in support of the Central Colorado Assessment Project (CCAP) and contains data tables describing historical and new quantitative and qualitative geochemical analyses determined by 70 analytical laboratory and field methods for 47,478 rock, sediment, soil, and heavy-mineral concentrate samples. Most samples were collected by U.S. Geological Survey (USGS) personnel and analyzed either in the analytical laboratories of the USGS or by contract with commercial analytical laboratories. These data represent analyses of samples collected as part of various USGS programs and projects. In addition, geochemical data from 7,470 sediment and soil samples collected and analyzed under the Atomic Energy Commission National Uranium Resource Evaluation (NURE) Hydrogeochemical and Stream Sediment Reconnaissance (HSSR) program (henceforth called NURE) have been included in this database. In addition to data from 2,377 samples collected and analyzed under CCAP, this dataset includes archived geochemical data originally entered into the in-house Rock Analysis Storage System (RASS) database (used by the USGS from the mid-1960s through the late 1980s) and the in-house PLUTO database (used by the USGS from the mid-1970s through the mid-1990s). All of these data are maintained in the Oracle-based National Geochemical Database (NGDB). Retrievals from the NGDB and from the NURE database were used to generate most of this dataset. In addition, USGS data that have been excluded previously from the NGDB because the data predate earliest USGS geochemical databases, or were once excluded for programmatic reasons, have been included in the CCAP Geochemical Database and are planned to be added to the NGDB.

Analysis of Mars analogue soil samples using solid-phase microextraction, organic solvent extraction and gas chromatography/mass spectrometry

NASA Astrophysics Data System (ADS)

Orzechowska, G. E.; Kidd, R. D.; Foing, B. H.; Kanik, I.; Stoker, C.; Ehrenfreund, P.

2011-07-01

Polycyclic aromatic hydrocarbons (PAHs) are robust and abundant molecules in extraterrestrial environments. They are found ubiquitously in the interstellar medium and have been identified in extracts of meteorites collected on Earth. PAHs are important target molecules for planetary exploration missions that investigate the organic inventory of planets, moons and small bodies. This study is part of an interdisciplinary preparation phase to search for organic molecules and life on Mars. We have investigated PAH compounds in desert soils to determine their composition, distribution and stability. Soil samples (Mars analogue soils) were collected at desert areas of Utah in the vicinity of the Mars Desert Research Station (MDRS), in the Arequipa region in Peru and from the Jutland region of Denmark. The aim of this study was to optimize the solid-phase microextraction (SPME) method for fast screening and determination of PAHs in soil samples. This method minimizes sample handling and preserves the chemical integrity of the sample. Complementary liquid extraction was used to obtain information on five- and six-ring PAH compounds. The measured concentrations of PAHs are, in general, very low, ranging from 1 to 60 ng g-1. The texture of soils is mostly sandy loam with few samples being 100 % silt. Collected soils are moderately basic with pH values of 8-9 except for the Salten Skov soil, which is slightly acidic. Although the diverse and variable microbial populations of the samples at the sample sites might have affected the levels and variety of PAHs detected, SPME appears to be a rapid, viable field sampling technique with implications for use on planetary missions.

Analysis of Mars Analogue Soil Samples Using Solid-Phase Microextraction, Organic Solvent Extraction and Gas Chromatography/Mass Spectrometry

NASA Technical Reports Server (NTRS)

Orzechowska, G. E.; Kidd, R. D.; Foing, B. H.; Kanik, I.; Stoker, C.; Ehrenfreund, P.

2011-01-01

Polycyclic aromatic hydrocarbons (PAHs) are robust and abundant molecules in extraterrestrial environments. They are found ubiquitously in the interstellar medium and have been identified in extracts of meteorites collected on Earth. PAHs are important target molecules for planetary exploration missions that investigate the organic inventory of planets, moons and small bodies. This study is part of an interdisciplinary preparation phase to search for organic molecules and life on Mars. We have investigated PAH compounds in desert soils to determine their composition, distribution and stability. Soil samples (Mars analogue soils) were collected at desert areas of Utah in the vicinity of the Mars Desert Research Station (MDRS), in the Arequipa region in Peru and from the Jutland region of Denmark. The aim of this study was to optimize the solid-phase microextraction (SPME) method for fast screening and determination of PAHs in soil samples. This method minimizes sample handling and preserves the chemical integrity of the sample. Complementary liquid extraction was used to obtain information on five- and six-ring PAH compounds. The measured concentrations of PAHs are, in general, very low, ranging from 1 to 60 ng g(sup -1). The texture of soils is mostly sandy loam with few samples being 100% silt. Collected soils are moderately basic with pH values of 8-9 except for the Salten Skov soil, which is slightly acidic. Although the diverse and variable microbial populations of the samples at the sample sites might have affected the levels and variety of PAHs detected, SPME appears to be a rapid, viable field sampling technique with implications for use on planetary missions.

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

Kovalev, Andrew N.

The authors describe a measurement of the top quark mass using events with two charged leptons collected by the CDF II Detector from pmore » $$\\bar{p}$$ collisions with √s = 1.96 TeV at the Fermilab Tevatron. The posterior probability distribution of the top quark pole mass is calculated using the differential cross-section for the t$$\\bar{t}$$ production and decay expressed with respect to observed leptons and jets momenta. The presence of background events in the collected sample is modeled using calculations of the differential cross-sections for major background processes. This measurement represents the first application of this method to events with two charged leptons. In a data sample with integrated luminosity of 340 pb -1, they observe 33 candidate events and measure M top = 165.2 ± 61. stat ± 3.4 syst GeV/c 2.« less

Integration of Magnetic and Geotechnical methods for Shallow Subsurface Soil Characterization at Sungai Batu, Kedah, Malaysia

NASA Astrophysics Data System (ADS)

Samuel, Y. M.; Saad, R.; Muztaza, N. M.; Saidin, M. M.; Muhammad, S. B.

2018-04-01

Magnetic and geotechnical methods were used for shallow subsurface soil characterization at Sungai Batu, Kedah, (Malaysia). Ground magnetic data were collected along a survey line of length 160 m long at 2 m constant station spacing, while soil drilling using hand auger was conducted at 21 m on the survey line using 0.2 m sampling interval drilled to a depth of 5 m. Result from the processed magnetic profile data shows distribution of magnetic residuals in the range of -4.55 to 1.61 nT, with magnetic low (-4.55 nT to -0.058 nT) and were identified at distances 4 m, 10 to 16 m, 20 to 26 m, 58 m, 82 m, 104 to 106 m, 118 m, and 124 to 140 m. The magnetic lows are attributes of sediments. The result from the soil drilling shows sticky samples with variable sizes, greyish to brownish / reddish in colour, and some of the samples show the presence of shiny and black spots. The characteristics of the samples suggest the soil as a by-product of completely weathered rock; weak with high water content and classified as Grade V soil. The study concludes; integration of geophysical and geotechnical methods aided in characterizing the subsurface soil at Sungai Batu. The result was correlated with previous studies and confirms the importance of integrated approach in minimising ambiguity in interpretation.

Comparison of Reflectance Measurements Acquired with a Contact Probe and an Integration Sphere: Implications for the Spectral Properties of Vegetation at a Leaf Level

PubMed Central

Potůčková, Markéta; Červená, Lucie; Kupková, Lucie; Lhotáková, Zuzana; Lukeš, Petr; Hanuš, Jan; Novotný, Jan; Albrechtová, Jana

2016-01-01

Laboratory spectroscopy in visible and infrared regions is an important tool for studies dealing with plant ecophysiology and early recognition of plant stress due to changing environmental conditions. Leaf optical properties are typically acquired with a spectroradiometer coupled with an integration sphere (IS) in a laboratory or with a contact probe (CP), which has the advantage of operating flexibility and the provision of repetitive in-situ reflectance measurements. Experiments comparing reflectance spectra measured with different devices and device settings are rarely reported in literature. Thus, in our study we focused on a comparison of spectra collected with two ISs on identical samples ranging from a Spectralon and coloured papers as reference standards to vegetation samples with broadleaved (Nicotiana Rustica L.) and coniferous (Picea abies L. Karst.) leaf types. First, statistical measures such as mean absolute difference, median of differences, standard deviation and paired-sample t-test were applied in order to evaluate differences between collected reflectance values. The possibility of linear transformation between spectra was also tested. Moreover, correlation between normalised differential indexes (NDI) derived for each device and all combinations of wavelengths between 450 nm and 1800 nm were assessed. Finally, relationships between laboratory measured leaf compounds (total chlorophyll, carotenoids and water content), NDI and selected spectral indices often used in remote sensing were studied. The results showed differences between spectra acquired with different devices. While differences were negligible in the case of the Spectralon and they were possible to be modelled with a linear transformation in the case of coloured papers, the spectra collected with the CP and the ISs differed significantly in the case of vegetation samples. Regarding the spectral indices calculated from the reflectance data collected with the three devices, their mean values were in the range of the corresponding standard deviations in the case of broadleaved leaf type. Larger differences in optical leaf properties of spruce needles collected with the CP and ISs are implicated from the different measurement procedure due to needle-like leaf where shoots with spatially oriented needles were measured with the CP and individual needles with the IS. The study shows that a direct comparison between the spectra collected with two devices is not advisable as spectrally dependent offsets may likely exist. We propose that the future studies shall focus on standardisation of measurement procedures so that open access spectral libraries could serve as a reliable input for modelling of optical properties on a leaf level. PMID:27801818

Comparison of Reflectance Measurements Acquired with a Contact Probe and an Integration Sphere: Implications for the Spectral Properties of Vegetation at a Leaf Level.

PubMed

Potůčková, Markéta; Červená, Lucie; Kupková, Lucie; Lhotáková, Zuzana; Lukeš, Petr; Hanuš, Jan; Novotný, Jan; Albrechtová, Jana

2016-10-28

Laboratory spectroscopy in visible and infrared regions is an important tool for studies dealing with plant ecophysiology and early recognition of plant stress due to changing environmental conditions. Leaf optical properties are typically acquired with a spectroradiometer coupled with an integration sphere (IS) in a laboratory or with a contact probe (CP), which has the advantage of operating flexibility and the provision of repetitive in-situ reflectance measurements. Experiments comparing reflectance spectra measured with different devices and device settings are rarely reported in literature. Thus, in our study we focused on a comparison of spectra collected with two ISs on identical samples ranging from a Spectralon and coloured papers as reference standards to vegetation samples with broadleaved ( Nicotiana Rustica L.) and coniferous ( Picea abies L. Karst.) leaf types. First, statistical measures such as mean absolute difference, median of differences, standard deviation and paired-sample t-test were applied in order to evaluate differences between collected reflectance values. The possibility of linear transformation between spectra was also tested. Moreover, correlation between normalised differential indexes (NDI) derived for each device and all combinations of wavelengths between 450 nm and 1800 nm were assessed. Finally, relationships between laboratory measured leaf compounds (total chlorophyll, carotenoids and water content), NDI and selected spectral indices often used in remote sensing were studied. The results showed differences between spectra acquired with different devices. While differences were negligible in the case of the Spectralon and they were possible to be modelled with a linear transformation in the case of coloured papers, the spectra collected with the CP and the ISs differed significantly in the case of vegetation samples. Regarding the spectral indices calculated from the reflectance data collected with the three devices, their mean values were in the range of the corresponding standard deviations in the case of broadleaved leaf type. Larger differences in optical leaf properties of spruce needles collected with the CP and ISs are implicated from the different measurement procedure due to needle-like leaf where shoots with spatially oriented needles were measured with the CP and individual needles with the IS. The study shows that a direct comparison between the spectra collected with two devices is not advisable as spectrally dependent offsets may likely exist. We propose that the future studies shall focus on standardisation of measurement procedures so that open access spectral libraries could serve as a reliable input for modelling of optical properties on a leaf level.

Filter forensics: microbiota recovery from residential HVAC filters.

PubMed

Maestre, Juan P; Jennings, Wiley; Wylie, Dennis; Horner, Sharon D; Siegel, Jeffrey; Kinney, Kerry A

2018-01-30

Establishing reliable methods for assessing the microbiome within the built environment is critical for understanding the impact of biological exposures on human health. High-throughput DNA sequencing of dust samples provides valuable insights into the microbiome present in human-occupied spaces. However, the effect that different sampling methods have on the microbial community recovered from dust samples is not well understood across sample types. Heating, ventilation, and air conditioning (HVAC) filters hold promise as long-term, spatially integrated, high volume samplers to characterize the airborne microbiome in homes and other climate-controlled spaces. In this study, the effect that dust recovery method (i.e., cut and elution, swabbing, or vacuuming) has on the microbial community structure, membership, and repeatability inferred by Illumina sequencing was evaluated. The results indicate that vacuum samples captured higher quantities of total, bacterial, and fungal DNA than swab or cut samples. Repeated swab and vacuum samples collected from the same filter were less variable than cut samples with respect to both quantitative DNA recovery and bacterial community structure. Vacuum samples captured substantially greater bacterial diversity than the other methods, whereas fungal diversity was similar across all three methods. Vacuum and swab samples of HVAC filter dust were repeatable and generally superior to cut samples. Nevertheless, the contribution of environmental and human sources to the bacterial and fungal communities recovered via each sampling method was generally consistent across the methods investigated. Dust recovery methodologies have been shown to affect the recovery, repeatability, structure, and membership of microbial communities recovered from dust samples in the built environment. The results of this study are directly applicable to indoor microbiota studies utilizing the filter forensics approach. More broadly, this study provides a better understanding of the microbial community variability attributable to sampling methodology and helps inform interpretation of data collected from other types of dust samples collected from indoor environments.

Development of Sorbents for Extraction and Stabilization of Nucleic Acids

DTIC Science & Technology

2016-09-13

ensure safe food and water supplies and to maintain the health and readiness of deployed troops. Identification of molecular signatures (genomic...biological, environmental, forensics, and food safety, drive the need for preservation of nucleic acid integrity during sample collection, transportation... antimicrobial activity as well as the potential for multiple and complex cationic interactions with nucleic acids (Fig. 10). Two different approaches were used

Stable isotope estimates of evaporation: inflow and water residence time for lakes across the United States as a tool for national lake water quality assessments

EPA Science Inventory

Stable isotope ratios of water (delta18O and delta2H) can be very useful in large-scale monitoring programs because water samples are easy to collect and isotope ratios integrate information about basic hydrologic processes such as evaporation as a percentage of inflow (E/I) and ...

A Structural Examination of Academic Integration, Perceived Stress, Academic Performance, and Goal Commitment from an Elaborated Model of Adult Student Persistence.

ERIC Educational Resources Information Center

Sandler, Martin E.

The effects of selected variables on the academic persistence of adult students were examined in a study of a random sample of 469 adult students aged 24 years or older enrolled in a four-year college. The survey questionnaire, the Adult Student Experiences Survey, collected data regarding 12 endogenous variables and 13 exogenous variables…

First measurement of T -odd moments in D 0 → K S 0 π + π - π 0 decays

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

Prasanth, K.; Libby, J.; Adachi, I.

2017-05-01

We report the first measurement of the T-odd moments in the decay D 0 → Kmore » $$0\\atop{S}$$π +π -π 0 from a data sample corresponding to an integrated luminosity of 966 fb -1 collected by the Belle experiment at the KEKB asymmetric-energy eþe- collider.« less

Integrative Lifecourse and Genetic Analysis of Military Working Dogs

DTIC Science & Technology

2015-12-01

done as the samples are collected in order to avoid experimental variability and batch effects . Detailed description and discussion of this task...associated loss of power to detect all associations but those of large effect sizes) and latent variables (e.g., population structure – addressed in...processes associated with tissue development and maintenance are thus grouped with external environmental effects . This in turn suggests how those

Biodiversity and hypervirulence of Listeria monocytogenes.

PubMed

Grad, Yonatan H; Fortune, Sarah M

2016-03-01

The integration of large, well-sampled collections of bacterial isolates with genomics and experimental methods provides opportunities for 'top-down' discovery of the genetic basis of phenotypes of interest. In a new report, the authors apply this approach to investigate the heterogeneity in manifestations of disease caused by Listeria monocytogenes and demonstrate that a previously uncharacterized cellobiose PTS system is involved in central nervous system infection.

A new comprehensive database of global volcanic gas analyses

NASA Astrophysics Data System (ADS)

Clor, L. E.; Fischer, T. P.; Lehnert, K. A.; McCormick, B.; Hauri, E. H.

2013-12-01

Volcanic volatiles are the driving force behind eruptions, powerful indicators of magma provenance, present localized hazards, and have implications for climate. Studies of volcanic emissions are necessary for understanding volatile cycling from the mantle to the atmosphere. Gas compositions vary with volcanic activity, making it important to track their chemical variability over time. As studies become increasingly interdisciplinary, it is critical to have a mechanism to integrate decades of gas studies across disciplines. Despite the value of this research to a variety of fields, there is currently no integrated network to house all volcanic and hydrothermal gas data, making spatial, temporal, and interdisciplinary comparison studies time-consuming. To remedy this, we are working to establish a comprehensive database of volcanic gas emissions and compositions worldwide, as part of the Deep Carbon Observatory's DECADE (Deep Carbon Degassing) initiative. Volcanic gas data have been divided into two broad categories: 1) chemical analyses from samples collected directly at the volcanic source, and 2) measurements of gas concentrations and fluxes, such as remotely by mini-DOAS or satellite, or in-plume such as by multiGAS. The gas flux database effort is realized by the Global Volcanism Program of the Smithsonian Institution (abstract by Brendan McCormick, this meeting). The direct-sampling data is the subject of this presentation. Data from direct techniques include samples of gases collected at the volcanic source from fumaroles and springs, tephras analyzed for gas contents, filter pack samples of gases collected in a plume, and any other data types that involve collection of a sample. Data are incorporated into the existing framework of the Petrological Database, PetDB. Association with PetDB is advantageous as it will allow volcanic gas data to be linked to chemical data from lava or tephra samples, forming more complete ties between the eruptive products and the source magma. Eventually our goal is to have a seamless gas database that allows the user to easily access all gas data ever collected at volcanoes. This database will be useful in a variety of science applications: 1) correlating volcanic gas composition to volcanic activity; 2) establishing a characteristic gas composition or total volatile budget for a volcano or region in studies of global chemical cycles; 3) better quantifying the flux and source of volcanic carbon to the atmosphere. The World Organization of Volcano Observatories is populating a volcano monitoring database, WOVOdat, which centers on data collected during times of volcanic unrest for monitoring and hazard purposes. The focus of our database is to gain insight into volcanic degassing specifically, during both eruptive and quiescent times. Coordination of the new database with WOVOdat will allow comparison studies of gas compositions with seismic and other monitoring data during times of unrest, as well as promote comprehensive and cross-disciplinary questions about volcanic degassing.

How iSamples (Internet of Samples in the Earth Sciences) Improves Sample and Data Stewardship in the Next Generation of Geoscientists

NASA Astrophysics Data System (ADS)

Hallett, B. W.; Dere, A. L. D.; Lehnert, K.; Carter, M.

2016-12-01

Vast numbers of physical samples are routinely collected by geoscientists to probe key scientific questions related to global climate change, biogeochemical cycles, magmatic processes, mantle dynamics, etc. Despite their value as irreplaceable records of nature the majority of these samples remain undiscoverable by the broader scientific community because they lack a digital presence or are not well-documented enough to facilitate their discovery and reuse for future scientific and educational use. The NSF EarthCube iSamples Research Coordination Network seeks to develop a unified approach across all Earth Science disciplines for the registration, description, identification, and citation of physical specimens in order to take advantage of the new opportunities that cyberinfrastructure offers. Even as consensus around best practices begins to emerge, such as the use of the International Geo Sample Number (IGSN), more work is needed to communicate these practices to investigators to encourage widespread adoption. Recognizing the importance of students and early career scientists in particular to transforming data and sample management practices, the iSamples Education and Training Working Group is developing training modules for sample collection, documentation, and management workflows. These training materials are made available to educators/research supervisors online at http://earthcube.org/group/isamples and can be modularized for supervisors to create a customized research workflow. This study details the design and development of several sample management tutorials, created by early career scientists and documented in collaboration with undergraduate research students in field and lab settings. Modules under development focus on rock outcrops, rock cores, soil cores, and coral samples, with an emphasis on sample management throughout the collection, analysis and archiving process. We invite others to share their sample management/registration workflows and to develop training modules. This educational approach, with evolving digital materials, can help prepare future scientists to perform research in a way that will contribute to EarthCube data integration and discovery.

49 CFR 40.43 - What steps must operators of collection sites take to protect the security and integrity of urine...

Code of Federal Regulations, 2010 CFR

2010-10-01

... to protect the security and integrity of urine collections? 40.43 Section 40.43 Transportation Office... PROGRAMS Collection Sites, Forms, Equipment and Supplies Used in DOT Urine Collections § 40.43 What steps must operators of collection sites take to protect the security and integrity of urine collections? (a...

49 CFR 40.43 - What steps must operators of collection sites take to protect the security and integrity of urine...

Code of Federal Regulations, 2012 CFR

2012-10-01

... to protect the security and integrity of urine collections? 40.43 Section 40.43 Transportation Office... PROGRAMS Collection Sites, Forms, Equipment and Supplies Used in DOT Urine Collections § 40.43 What steps must operators of collection sites take to protect the security and integrity of urine collections? (a...

49 CFR 40.43 - What steps must operators of collection sites take to protect the security and integrity of urine...

Code of Federal Regulations, 2011 CFR

2011-10-01

... to protect the security and integrity of urine collections? 40.43 Section 40.43 Transportation Office... PROGRAMS Collection Sites, Forms, Equipment and Supplies Used in DOT Urine Collections § 40.43 What steps must operators of collection sites take to protect the security and integrity of urine collections? (a...

49 CFR 40.43 - What steps must operators of collection sites take to protect the security and integrity of urine...

Code of Federal Regulations, 2014 CFR

2014-10-01

... to protect the security and integrity of urine collections? 40.43 Section 40.43 Transportation Office... PROGRAMS Collection Sites, Forms, Equipment and Supplies Used in DOT Urine Collections § 40.43 What steps must operators of collection sites take to protect the security and integrity of urine collections? (a...

49 CFR 40.43 - What steps must operators of collection sites take to protect the security and integrity of urine...

Code of Federal Regulations, 2013 CFR

2013-10-01

... to protect the security and integrity of urine collections? 40.43 Section 40.43 Transportation Office... PROGRAMS Collection Sites, Forms, Equipment and Supplies Used in DOT Urine Collections § 40.43 What steps must operators of collection sites take to protect the security and integrity of urine collections? (a...

A fluid collection system for dermal wounds in clinical investigations

PubMed Central

Klopfer, Michael; Li, G.-P.; Widgerow, Alan; Bachman, Mark

2016-01-01

In this work, we demonstrate the use of a thin, self adherent, and clinically durable patch device that can collect fluid from a wound site for analysis. This device is manufactured from laminated silicone layers using a novel all-silicone double-molding process. In vitro studies for flow and delivery were followed by a clinical demonstration for exudate collection efficiency from a clinically presented partial thickness burn. The demonstrated utility of this device lends itself for use as a research implement used to clinically sample wound exudate for analysis. This device can serve as a platform for future integration of wearable technology into wound monitoring and care. The demonstrated fabrication method can be used for devices requiring thin membrane construction. PMID:27051470

76 FR 17145 - Agency Information Collection Activities: Business Transformation-Automated Integrated Operating...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-28

... Collection Activities: Business Transformation--Automated Integrated Operating Environment (IOE), New... Transformation--Integrated Operating Environment (IOE); OMB Control No. 1615-NEW. SUMMARY: USCIS is developing an automated Integrated Operating Environment (IOE) to process benefit applications. The IOE will collect...

Sediment source fingerprinting to quantify fine sediment sources in forested catchments, Chile.

NASA Astrophysics Data System (ADS)

Schuller, P.; Walling, D. E.; Iroume, A.; Castillo, A.; Quilodran, C.

2012-04-01

A study to improve the understanding of the primary sediment sources and transfer pathways in catchments disturbed following forest plantation harvesting is being undertaken in South-Central Chile. The study focuses on two sets of paired experimental catchments (treatment and control), located about 400 km apart, with similar soil type but contrasting mean annual rainfall: Nacimiento (1,200 mm year-1) and Los Ulmos (2,500 mm year-1). Sediment source fingerprinting techniques are being used to document the primary fine sediment sources. In each catchment, three potential sediment sources were defined: clearcut slopes (Z1), forest roads (Z2) and the stream channel (Z3). In each catchment, multiple representative composite samples of the different potential source materials were collected before harvest operations from the upper 1 cm layer in Z1, Z2, and from the channel bank and bed for Z3. A time-integrating trap sampler installed in the discharge monitoring station constructed at the outlet of each catchment has been used to collect samples of the suspended sediment and these have been supplemented by sediment collected from the weir pools. Total suspended sediment load is been quantified in the monitoring stations using discharge records and integrated water sampling. Caesium-137 (137Cs), excess lead-210 (210Pbex) and other sediment properties are being used as fingerprints. After air-drying, oven-drying at 40°C and disaggregation, both the source material samples and the sediment samples collected in the discharge monitoring stations were sieved through a 63-μm sieve and the <63-μm fractions were used for subsequent analyses. For radionuclide assay, the samples were sealed in Petri dishes and after 4 weeks the mass activity density (activity concentration) of 137Cs and 210Pbex was determined by gamma analysis, using an ORTEC extended range Ge detector of 53% relative efficiency. The 137Cs and 210Pbex activity and organic carbon (Corg) concentration associated with potential source materials and the target sediment show that the two radionuclides used in combination with the Corg property provide effective source fingerprints. Additional work using a mixing model taking account of particle size effects is required to establish the relative contributions of the three sources to the fine sediment loads of the study catchments. This research is supported by the Chilean Government through FONDECYT Project 1090574 and by the IAEA through CRP D1.20.11 (Contract CHI-15531 and Technical Contract 15478) and the RLA 05/051 Project.

Application of an imputation method for geospatial inventory of forest structural attributes across multiple spatial scales in the Lake States, U.S.A

NASA Astrophysics Data System (ADS)

Deo, Ram K.

Credible spatial information characterizing the structure and site quality of forests is critical to sustainable forest management and planning, especially given the increasing demands and threats to forest products and services. Forest managers and planners are required to evaluate forest conditions over a broad range of scales, contingent on operational or reporting requirements. Traditionally, forest inventory estimates are generated via a design-based approach that involves generalizing sample plot measurements to characterize an unknown population across a larger area of interest. However, field plot measurements are costly and as a consequence spatial coverage is limited. Remote sensing technologies have shown remarkable success in augmenting limited sample plot data to generate stand- and landscape-level spatial predictions of forest inventory attributes. Further enhancement of forest inventory approaches that couple field measurements with cutting edge remotely sensed and geospatial datasets are essential to sustainable forest management. We evaluated a novel Random Forest based k Nearest Neighbors (RF-kNN) imputation approach to couple remote sensing and geospatial data with field inventory collected by different sampling methods to generate forest inventory information across large spatial extents. The forest inventory data collected by the FIA program of US Forest Service was integrated with optical remote sensing and other geospatial datasets to produce biomass distribution maps for a part of the Lake States and species-specific site index maps for the entire Lake State. Targeting small-area application of the state-of-art remote sensing, LiDAR (light detection and ranging) data was integrated with the field data collected by an inexpensive method, called variable plot sampling, in the Ford Forest of Michigan Tech to derive standing volume map in a cost-effective way. The outputs of the RF-kNN imputation were compared with independent validation datasets and extant map products based on different sampling and modeling strategies. The RF-kNN modeling approach was found to be very effective, especially for large-area estimation, and produced results statistically equivalent to the field observations or the estimates derived from secondary data sources. The models are useful to resource managers for operational and strategic purposes.

The Chernobyl Tissue Bank — A Repository for Biomaterial and Data Used in Integrative and Systems Biology Modeling the Human Response to Radiation

PubMed Central

Thomas, Geraldine; Unger, Kristian; Krznaric, Marko; Galpine, Angela; Bethel, Jackie; Tomlinson, Christopher; Woodbridge, Mark; Butcher, Sarah

2012-01-01

The only unequivocal radiological effect of the Chernobyl accident on human health is the increase in thyroid cancer in those exposed in childhood or early adolescence. In response to the scientific interest in studying the molecular biology of thyroid cancer post Chernobyl, the Chernobyl Tissue Bank (CTB: www.chernobyltissuebank.com) was established in 1998. Thus far it is has collected biological samples from 3,861 individuals, and provided 27 research projects with 11,254 samples. The CTB was designed from its outset as a resource to promote the integration of research and clinical data to facilitate a systems biology approach to radiation related thyroid cancer. The project has therefore developed as a multidisciplinary collaboration between clinicians, dosimetrists, molecular biologists and bioinformaticians and serves as a paradigm for tissue banking in the omics era. PMID:24704918

Survalytics: An Open-Source Cloud-Integrated Experience Sampling, Survey, and Analytics and Metadata Collection Module for Android Operating System Apps

PubMed Central

Mackey, Sean

2016-01-01

Background We describe here Survalytics, a software module designed to address two broad areas of need. The first area is in the domain of surveys and app analytics: developers of mobile apps in both academic and commercial environments require information about their users, as well as how the apps are being used, to understand who their users are and how to optimally approach app development. The second area of need is in the field of ecological momentary assessment, also referred to as experience sampling: researchers in a wide variety of fields, spanning from the social sciences to psychology to clinical medicine, would like to be able to capture daily or even more frequent data from research subjects while in their natural environment. Objective Survalytics is an open-source solution for the collection of survey responses as well as arbitrary analytic metadata from users of Android operating system apps. Methods Surveys may be administered in any combination of one-time questions and ongoing questions. The module may be deployed as a stand-alone app for experience sampling purposes or as an add-on to existing apps. The module takes advantage of free-tier NoSQL cloud database management offered by the Amazon Web Services DynamoDB platform to package a secure, flexible, extensible data collection module. DynamoDB is capable of Health Insurance Portability and Accountability Act compliant storage of personal health information. Results The provided example app may be used without modification for a basic experience sampling project, and we provide example questions for daily collection of blood glucose data from study subjects. Conclusions The module will help researchers in a wide variety of fields rapidly develop tailor-made Android apps for a variety of data collection purposes. PMID:27261155

Survalytics: An Open-Source Cloud-Integrated Experience Sampling, Survey, and Analytics and Metadata Collection Module for Android Operating System Apps.

PubMed

O'Reilly-Shah, Vikas; Mackey, Sean

2016-06-03

We describe here Survalytics, a software module designed to address two broad areas of need. The first area is in the domain of surveys and app analytics: developers of mobile apps in both academic and commercial environments require information about their users, as well as how the apps are being used, to understand who their users are and how to optimally approach app development. The second area of need is in the field of ecological momentary assessment, also referred to as experience sampling: researchers in a wide variety of fields, spanning from the social sciences to psychology to clinical medicine, would like to be able to capture daily or even more frequent data from research subjects while in their natural environment. Survalytics is an open-source solution for the collection of survey responses as well as arbitrary analytic metadata from users of Android operating system apps. Surveys may be administered in any combination of one-time questions and ongoing questions. The module may be deployed as a stand-alone app for experience sampling purposes or as an add-on to existing apps. The module takes advantage of free-tier NoSQL cloud database management offered by the Amazon Web Services DynamoDB platform to package a secure, flexible, extensible data collection module. DynamoDB is capable of Health Insurance Portability and Accountability Act compliant storage of personal health information. The provided example app may be used without modification for a basic experience sampling project, and we provide example questions for daily collection of blood glucose data from study subjects. The module will help researchers in a wide variety of fields rapidly develop tailor-made Android apps for a variety of data collection purposes.

The Community Integration Questionnaire - Revised: Australian normative data and measurement of electronic social networking.

PubMed

Callaway, Libby; Winkler, Dianne; Tippett, Alice; Herd, Natalie; Migliorini, Christine; Willer, Barry

2016-06-01

Consideration of the relationship between meaningful participation, health and wellbeing underpins occupational therapy intervention, and drives measurement of community integration following acquired brain injury (ABI). However, utility of community integration measures has been limited to date by lack of normative data against which to compare outcomes, and none examine the growing use of electronic social networking (ESN) for social participation. This research had four aims: (i) develop and pilot items assessing ESN to add to the Community Integration Questionnaire, producing the Community Integration Questionnaire-Revised (CIQ-R); (ii) examine factor structure of the CIQ-R; (iii) collect Australian CIQ-R normative data; and (iv) assess test-retest reliability of the revised measure. Australia. A convenience sample of adults without ABI (N = 124) was used to develop and pilot ESN items. A representative general population sample of adults without ABI aged 18-64 years (N = 1973) was recruited to gather normative CIQ-R data. Cross-sectional survey. Demographic items and the CIQ-R. The CIQ-R demonstrated acceptable psychometric properties, with minor modification to the original scoring based on the factor analyses provided. Large representative general population CIQ-R normative data have been established, detailing contribution of a range of independent demographic variables to community integration. The addition of electronic social networking items to the CIQ-R offers a contemporary method of assessing community integration following ABI. Normative CIQ-R data enhance the understanding of community integration in the general population, allowing occupational therapists and other clinicians to make more meaningful comparisons between groups. © 2016 Occupational Therapy Australia.

Study of double parton interactions in diphoton + dijet events in $$p\\bar{p}$$ collisions at $$\\sqrt{s} = 1.96$$ TeV

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

Abazov, Victor Mukhamedovich

We use a sample of diphoton+dijet events to measure the effective cross section of double parton interactions, which characterizes the area containing the interacting partons in proton-antiproton collisions, and find it to be σ eff=19.3±1.4(stat)±7.8(syst) mb. The sample was collected by the D0 detector at the Fermilab Tevatron collider inmore » $$p\\bar{p}$$ collisions at $$\\sqrt{s} = 1.96$$ TeV and corresponds to an integrated luminosity of 8.7 fb -1.« less

Study of double parton interactions in diphoton + dijet events in $$p\\bar{p}$$ collisions at $$\\sqrt{s} = 1.96$$ TeV

DOE PAGES

Abazov, Victor Mukhamedovich

2016-03-01

We use a sample of diphoton+dijet events to measure the effective cross section of double parton interactions, which characterizes the area containing the interacting partons in proton-antiproton collisions, and find it to be σ eff=19.3±1.4(stat)±7.8(syst) mb. The sample was collected by the D0 detector at the Fermilab Tevatron collider inmore » $$p\\bar{p}$$ collisions at $$\\sqrt{s} = 1.96$$ TeV and corresponds to an integrated luminosity of 8.7 fb -1.« less

Study of double parton interactions in diphoton + dijet events in p p ¯ collisions at s = 1.96 TeV

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

Abazov, V. M.; Abbott, B.; Acharya, B. S.

2016-03-01

We use a sample of diphoton + dijet events to measure the effective cross section of double parton interactions, which characterizes the area containing the interacting partons in proton-antiproton collisions, and find it to be σ eff = 19.3 ± 1.4 ( stat ) ± 7.8 ( syst ) mb . The sample was collected by the D0 detector at the Fermilab Tevatron collider in pmore » $$\\bar{p}$$ collisions at √ s = 1.96 TeV and corresponds to an integrated luminosity of 8.7 fb - 1 .« less

Teaching calculus using module based on cooperative learning strategy

NASA Astrophysics Data System (ADS)

Arbin, Norazman; Ghani, Sazelli Abdul; Hamzah, Firdaus Mohamad

2014-06-01

The purpose of the research is to evaluate the effectiveness of a module which utilizes the cooperative learning for teaching Calculus for limit, derivative and integral. The sample consists of 50 semester 1 students from the Science Programme (AT 16) Sultan Idris Education University. A set of questions of related topics (pre and post) has been used as an instrument to collect data. The data is analyzed using inferential statistics involving the paired sample t-test and the independent t-test. The result shows that students have positive inclination towards the modulein terms of understanding.

Cross-section-constrained top-quark mass measurement from dilepton events at the Tevatron.

PubMed

Aaltonen, T; Adelman, J; Akimoto, T; Albrow, M G; Alvarez González, B; Amerio, S; Amidei, D; Anastassov, A; Annovi, A; Antos, J; Aoki, M; Apollinari, G; Apresyan, A; Arisawa, T; Artikov, A; Ashmanskas, W; Attal, A; Aurisano, A; Azfar, F; Azzi-Bacchetta, P; Azzurri, P; Bacchetta, N; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Baroiant, S; Bartsch, V; Bauer, G; Beauchemin, P-H; Bedeschi, F; Bednar, P; Behari, S; Bellettini, G; Bellinger, J; Belloni, A; Benjamin, D; Beretvas, A; Beringer, J; Berry, T; Bhatti, A; Binkley, M; Bisello, D; Bizjak, I; Blair, R E; Blocker, C; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bolla, G; Bolshov, A; Bortoletto, D; Boudreau, J; Boveia, A; Brau, B; Bridgeman, A; Brigliadori, L; Bromberg, C; Brubaker, E; Budagov, J; Budd, H S; Budd, S; Burkett, K; Busetto, G; Bussey, P; Buzatu, A; Byrum, K L; Cabrera, S; Campanelli, M; Campbell, M; Canelli, F; Canepa, A; Carlsmith, D; Carosi, R; Carrillo, S; Carron, S; Casal, B; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chang, S H; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, K; Chokheli, D; Chou, J P; Choudalakis, G; Chuang, S H; Chung, K; Chung, W H; Chung, Y S; Ciobanu, C I; Ciocci, M A; Clark, A; Clark, D; Compostella, G; Convery, M E; Conway, J; Cooper, B; Copic, K; Cordelli, M; Cortiana, G; Crescioli, F; Cuenca Almenar, C; Cuevas, J; Culbertson, R; Cully, J C; Dagenhart, D; Datta, M; Davies, T; de Barbaro, P; DeCecco, S; Deisher, A; De Lentdecker, G; De Lorenzo, G; Dell'Orso, M; Demortier, L; Deng, J; Deninno, M; De Pedis, D; Derwent, P F; Di Giovanni, G P; Dionisi, C; Di Ruzza, B; Dittmann, J R; D'Onofrio, M; Donati, S; Dong, P; Donini, J; Dorigo, T; Dube, S; Efron, J; Erbacher, R; Errede, D; Errede, S; Eusebi, R; Fang, H C; Farrington, S; Fedorko, W T; Feild, R G; Feindt, M; Fernandez, J P; Ferrazza, C; Field, R; Flanagan, G; Forrest, R; Forrester, S; Franklin, M; Freeman, J C; Furic, I; Gallinaro, M; Galyardt, J; Garberson, F; Garcia, J E; Garfinkel, A F; Gerberich, H; Gerdes, D; Giagu, S; Giakoumopolou, V; Giannetti, P; Gibson, K; Gimmell, J L; Ginsburg, C M; Giokaris, N; Giordani, M; Giromini, P; Giunta, M; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Golossanov, A; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gresele, A; Grinstein, S; Grosso-Pilcher, C; Grundler, U; Guimaraes da Costa, J; Gunay-Unalan, Z; Haber, C; Hahn, K; Hahn, S R; Halkiadakis, E; Hamilton, A; Han, B-Y; Han, J Y; Handler, R; Happacher, F; Hara, K; Hare, D; Hare, M; Harper, S; Harr, R F; Harris, R M; Hartz, M; Hatakeyama, K; Hauser, J; Hays, C; Heck, M; Heijboer, A; Heinemann, B; Heinrich, J; Henderson, C; Herndon, M; Heuser, J; Hewamanage, S; Hidas, D; Hill, C S; Hirschbuehl, D; Hocker, A; Hou, S; Houlden, M; Hsu, S-C; Huffman, B T; Hughes, R E; Husemann, U; Huston, J; Incandela, J; Introzzi, G; Iori, M; Ivanov, A; Iyutin, B; James, E; Jayatilaka, B; Jeans, D; Jeon, E J; Jindariani, S; Johnson, W; Jones, M; Joo, K K; Jun, S Y; Jung, J E; Junk, T R; Kamon, T; Kar, D; Karchin, P E; Kato, Y; Kephart, R; Kerzel, U; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kimura, N; Kirsch, L; Klimenko, S; Klute, M; Knuteson, B; Ko, B R; Koay, S A; Kondo, K; Kong, D J; Konigsberg, J; Korytov, A; Kotwal, A V; Kraus, J; Kreps, M; Kroll, J; Krumnack, N; Kruse, M; Krutelyov, V; Kubo, T; Kuhlmann, S E; Kuhr, T; Kulkarni, N P; Kusakabe, Y; Kwang, S; Laasanen, A T; Lai, S; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; Lazzizzera, I; LeCompte, T; Lee, J; Lee, J; Lee, Y J; Lee, S W; Lefèvre, R; Leonardo, N; Leone, S; Levy, S; Lewis, J D; Lin, C; Lin, C S; Linacre, J; Lindgren, M; Lipeles, E; Lister, A; Litvintsev, D O; Liu, T; Lockyer, N S; Loginov, A; Loreti, M; Lovas, L; Lu, R-S; Lucchesi, D; Lueck, J; Luci, C; Lujan, P; Lukens, P; Lungu, G; Lyons, L; Lys, J; Lysak, R; Lytken, E; Mack, P; MacQueen, D; Madrak, R; Maeshima, K; Makhoul, K; Maki, T; Maksimovic, P; Malde, S; Malik, S; Manca, G; Manousakis, A; Margaroli, F; Marino, C; Marino, C P; Martin, A; Martin, M; Martin, V; Martínez, M; Martínez-Ballarín, R; Maruyama, T; Mastrandrea, P; Masubuchi, T; Mattson, M E; Mazzanti, P; McFarland, K S; McIntyre, P; McNulty, R; Mehta, A; Mehtala, P; Menzemer, S; Menzione, A; Merkel, P; Mesropian, C; Messina, A; Miao, T; Miladinovic, N; Miles, J; Miller, R; Mills, C; Milnik, M; Mitra, A; Mitselmakher, G; Miyake, H; Moed, S; Moggi, N; Moon, C S; Moore, R; Morello, M; Movilla Fernandez, P; Mülmenstädt, J; Mukherjee, A; Muller, Th; Mumford, R; Murat, P; Mussini, M; Nachtman, J; Nagai, Y; Nagano, A; Naganoma, J; Nakamura, K; Nakano, I; Napier, A; Necula, V; Neu, C; Neubauer, M S; Nielsen, J; Nodulman, L; Norman, M; Norniella, O; Nurse, E; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Oldeman, R; Orava, R; Osterberg, K; Pagan Griso, S; Pagliarone, C; Palencia, E; Papadimitriou, V; Papaikonomou, A; Paramonov, A A; Parks, B; Pashapour, S; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Pellett, D E; Penzo, A; Phillips, T J; Piacentino, G; Piedra, J; Pinera, L; Pitts, K; Plager, C; Pondrom, L; Portell, X; Poukhov, O; Pounder, N; Prakoshyn, F; Pronko, A; Proudfoot, J; Ptohos, F; Punzi, G; Pursley, J; Rademacker, J; Rahaman, A; Ramakrishnan, V; Ranjan, N; Redondo, I; Reisert, B; Rekovic, V; Renton, P; Rescigno, M; Richter, S; Rimondi, F; Ristori, L; Robson, A; Rodrigo, T; Rogers, E; Rolli, S; Roser, R; Rossi, M; Rossin, R; Roy, P; Ruiz, A; Russ, J; Rusu, V; Saarikko, H; Safonov, A; Sakumoto, W K; Salamanna, G; Saltó, O; Santi, L; Sarkar, S; Sartori, L; Sato, K; Savoy-Navarro, A; Scheidle, T; Schlabach, P; Schmidt, E E; Schmidt, M A; Schmidt, M P; Schmitt, M; Schwarz, T; Scodellaro, L; Scott, A L; Scribano, A; Scuri, F; Sedov, A; Seidel, S; Seiya, Y; Semenov, A; Sexton-Kennedy, L; Sfyria, A; Shalhout, S Z; Shapiro, M D; Shears, T; Shepard, P F; Sherman, D; Shimojima, M; Shochet, M; Shon, Y; Shreyber, I; Sidoti, A; Sinervo, P; Sisakyan, A; Slaughter, A J; Slaunwhite, J; Sliwa, K; Smith, J R; Snider, F D; Snihur, R; Soderberg, M; Soha, A; Somalwar, S; Sorin, V; Spalding, J; Spinella, F; Spreitzer, T; Squillacioti, P; Stanitzki, M; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Stuart, D; Suh, J S; Sukhanov, A; Sun, H; Suslov, I; Suzuki, T; Taffard, A; Takashima, R; Takeuchi, Y; Tanaka, R; Tecchio, M; Teng, P K; Terashi, K; Thom, J; Thompson, A S; Thompson, G A; Thomson, E; Tipton, P; Tiwari, V; Tkaczyk, S; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Tourneur, S; Trischuk, W; Tu, Y; Turini, N; Ukegawa, F; Uozumi, S; Vallecorsa, S; van Remortel, N; Varganov, A; Vataga, E; Vázquez, F; Velev, G; Vellidis, C; Veszpremi, V; Vidal, M; Vidal, R; Vila, I; Vilar, R; Vine, T; Vogel, M; Volobouev, I; Volpi, G; Würthwein, F; Wagner, P; Wagner, R G; Wagner, R L; Wagner-Kuhr, J; Wagner, W; Wakisaka, T; Wallny, R; Wang, S M; Warburton, A; Waters, D; Weinberger, M; Wester, W C; Whitehouse, B; Whiteson, D; Wicklund, A B; Wicklund, E; Williams, G; Williams, H H; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, C; Wright, T; Wu, X; Wynne, S M; Yagil, A; Yamamoto, K; Yamaoka, J; Yamashita, T; Yang, C; Yang, U K; Yang, Y C; Yao, W M; Yeh, G P; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanello, L; Zanetti, A; Zaw, I; Zhang, X; Zheng, Y; Zucchelli, S

2008-02-15

We report the first top-quark mass measurement that uses a cross-section constraint to improve the mass determination. This measurement is made with a dilepton tt event candidate sample collected with the Collider Detector II at Fermilab. From a data sample corresponding to an integrated luminosity of 1.2 fb(-1), we measure a top-quark mass of 170.7(-3.9)(+4.2)(stat)+/-2.6(syst)+/-2.4(theory) GeV/c(2). The measurement without the cross-section constraint is 169.7(-4.9)(+5.2)(stat)+/-3.1(syst) GeV/c(2).

A Nonparametric, Multiple Imputation-Based Method for the Retrospective Integration of Data Sets.

PubMed

Carrig, Madeline M; Manrique-Vallier, Daniel; Ranby, Krista W; Reiter, Jerome P; Hoyle, Rick H

2015-01-01

Complex research questions often cannot be addressed adequately with a single data set. One sensible alternative to the high cost and effort associated with the creation of large new data sets is to combine existing data sets containing variables related to the constructs of interest. The goal of the present research was to develop a flexible, broadly applicable approach to the integration of disparate data sets that is based on nonparametric multiple imputation and the collection of data from a convenient, de novo calibration sample. We demonstrate proof of concept for the approach by integrating three existing data sets containing items related to the extent of problematic alcohol use and associations with deviant peers. We discuss both necessary conditions for the approach to work well and potential strengths and weaknesses of the method compared to other data set integration approaches.

A Nonparametric, Multiple Imputation-Based Method for the Retrospective Integration of Data Sets

PubMed Central

Carrig, Madeline M.; Manrique-Vallier, Daniel; Ranby, Krista W.; Reiter, Jerome P.; Hoyle, Rick H.

2015-01-01

Complex research questions often cannot be addressed adequately with a single data set. One sensible alternative to the high cost and effort associated with the creation of large new data sets is to combine existing data sets containing variables related to the constructs of interest. The goal of the present research was to develop a flexible, broadly applicable approach to the integration of disparate data sets that is based on nonparametric multiple imputation and the collection of data from a convenient, de novo calibration sample. We demonstrate proof of concept for the approach by integrating three existing data sets containing items related to the extent of problematic alcohol use and associations with deviant peers. We discuss both necessary conditions for the approach to work well and potential strengths and weaknesses of the method compared to other data set integration approaches. PMID:26257437

Electrolyte-Sensing Transistor Decals Enabled by Ultrathin Microbial Nanocellulose

PubMed Central

Yuen, Jonathan D.; Walper, Scott A.; Melde, Brian J.; Daniele, Michael A.; Stenger, David A.

2017-01-01

We report an ultra-thin electronic decal that can simultaneously collect, transmit and interrogate a bio-fluid. The described technology effectively integrates a thin-film organic electrochemical transistor (sensing component) with an ultrathin microbial nanocellulose wicking membrane (sample handling component). As far as we are aware, OECTs have not been integrated in thin, permeable membrane substrates for epidermal electronics. The design of the biocompatible decal allows for the physical isolation of the electronics from the human body while enabling efficient bio-fluid delivery to the transistor via vertical wicking. High currents and ON-OFF ratios were achieved, with sensitivity as low as 1 mg·L−1. PMID:28102316

An integrated model of feedback-seeking behavior: disposition, context, and cognition.

PubMed

VandeWalle, D; Ganesan, S; Challagalla, G N; Brown, S P

2000-12-01

This study replicates, integrates, and extends prior research on the dispositional, contextual, and cognitive antecedents of feedback-seeking behavior. Regression analysis was used to analyze data collected from a sample of salespeople (N = 310) from 2 Fortune 500 companies. The study hypotheses were supported with the following results. First, the individual disposition of learning goal orientation and the contextual factors of leader consideration and leader initiation of structure influenced cognitions about the perceived cost and value of feedback seeking. Second, the strength of the relationship of learning goal orientation with the cost and value perceptions was moderated by the leadership style of the supervisor.

Electrolyte-Sensing Transistor Decals Enabled by Ultrathin Microbial Nanocellulose

NASA Astrophysics Data System (ADS)

Yuen, Jonathan D.; Walper, Scott A.; Melde, Brian J.; Daniele, Michael A.; Stenger, David A.

2017-01-01

We report an ultra-thin electronic decal that can simultaneously collect, transmit and interrogate a bio-fluid. The described technology effectively integrates a thin-film organic electrochemical transistor (sensing component) with an ultrathin microbial nanocellulose wicking membrane (sample handling component). As far as we are aware, OECTs have not been integrated in thin, permeable membrane substrates for epidermal electronics. The design of the biocompatible decal allows for the physical isolation of the electronics from the human body while enabling efficient bio-fluid delivery to the transistor via vertical wicking. High currents and ON-OFF ratios were achieved, with sensitivity as low as 1 mg·L-1.

The Upgrade Programme for the Structural Biology beamlines at the European Synchrotron Radiation Facility - High throughput sample evaluation and automation

NASA Astrophysics Data System (ADS)

Theveneau, P.; Baker, R.; Barrett, R.; Beteva, A.; Bowler, M. W.; Carpentier, P.; Caserotto, H.; de Sanctis, D.; Dobias, F.; Flot, D.; Guijarro, M.; Giraud, T.; Lentini, M.; Leonard, G. A.; Mattenet, M.; McCarthy, A. A.; McSweeney, S. M.; Morawe, C.; Nanao, M.; Nurizzo, D.; Ohlsson, S.; Pernot, P.; Popov, A. N.; Round, A.; Royant, A.; Schmid, W.; Snigirev, A.; Surr, J.; Mueller-Dieckmann, C.

2013-03-01

Automation and advances in technology are the key elements in addressing the steadily increasing complexity of Macromolecular Crystallography (MX) experiments. Much of this complexity is due to the inter-and intra-crystal heterogeneity in diffraction quality often observed for crystals of multi-component macromolecular assemblies or membrane proteins. Such heterogeneity makes high-throughput sample evaluation an important and necessary tool for increasing the chances of a successful structure determination. The introduction at the ESRF of automatic sample changers in 2005 dramatically increased the number of samples that were tested for diffraction quality. This "first generation" of automation, coupled with advances in software aimed at optimising data collection strategies in MX, resulted in a three-fold increase in the number of crystal structures elucidated per year using data collected at the ESRF. In addition, sample evaluation can be further complemented using small angle scattering experiments on the newly constructed bioSAXS facility on BM29 and the micro-spectroscopy facility (ID29S). The construction of a second generation of automated facilities on the MASSIF (Massively Automated Sample Screening Integrated Facility) beam lines will build on these advances and should provide a paradigm shift in how MX experiments are carried out which will benefit the entire Structural Biology community.

Integrated multiscale biomaterials experiment and modelling: a perspective

PubMed Central

Buehler, Markus J.; Genin, Guy M.

2016-01-01

Advances in multiscale models and computational power have enabled a broad toolset to predict how molecules, cells, tissues and organs behave and develop. A key theme in biological systems is the emergence of macroscale behaviour from collective behaviours across a range of length and timescales, and a key element of these models is therefore hierarchical simulation. However, this predictive capacity has far outstripped our ability to validate predictions experimentally, particularly when multiple hierarchical levels are involved. The state of the art represents careful integration of multiscale experiment and modelling, and yields not only validation, but also insights into deformation and relaxation mechanisms across scales. We present here a sampling of key results that highlight both challenges and opportunities for integrated multiscale experiment and modelling in biological systems. PMID:28981126

77 FR 52739 - Federal Acquisition Regulation; Information Collection; Integrity of Unit Prices

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-30

...; Information Collection; Integrity of Unit Prices AGENCY: Department of Defense (DOD), General Services... requirement concerning Integrity of Unit Prices. Public comments are particularly invited on: Whether this... Information Collection 9000- 0080, Integrity of Unit Prices by any of the following methods: Regulations.gov...

EarthChem and SESAR: Data Resources and Interoperability for EarthScope Cyberinfrastructure

NASA Astrophysics Data System (ADS)

Lehnert, K. A.; Walker, D.; Block, K.; Vinay, S.; Ash, J.

2008-12-01

Data management within the EarthScope Cyberinfrastructure needs to pursue two goals in order to advance and maximize the broad scientific application and impact of the large volumes of observational data acquired by EarthScope facilities: (a) to provide access to all data acquired by EarthScope facilities, and to promote their use by broad audiences, and (b) to facilitate discovery of, access to, and integration of multi-disciplinary data sets that complement EarthScope data in support of EarthScope science. EarthChem and SESAR, the System for Earth Sample Registration, are two projects within the Geoinformatics for Geochemistry program that offer resources for EarthScope CI. EarthChem operates a data portal that currently provides access to >13 million analytical values for >600,000 samples, more than half of which are from North America, including data from the USGS and all data from the NAVDAT database, a web-accessible repository for age, chemical and isotopic data from Mesozoic and younger igneous rocks in western North America. The new EarthChem GEOCHRON database will house data collected in association with GeoEarthScope, storing and serving geochronological data submitted by participating facilities. The EarthChem Deep Lithosphere Dataset is a compilation of petrological data for mantle xenoliths, initiated in collaboration with GeoFrame to complement geophysical endeavors within EarthScope science. The EarthChem Geochemical Resource Library provides a home for geochemical and petrological data products and data sets. Parts of the digital data in EarthScope CI refer to physical samples such as drill cores, igneous rocks, or water and gas samples, collected, for example, by SAFOD or by EarthScope science projects and acquired through lab-based analysis. Management of sample-based data requires the use of global unique identifiers for samples, so that distributed data for individual samples generated in different labs and published in different papers can be unambiguously linked and integrated. SESAR operates a registry for Earth samples that assigns and administers the International GeoSample Numbers (IGSN) as a global unique identifier for samples. Registration of EarthScope samples with SESAR and use of the IGSN will ensure their unique identification in publications and data systems, thus facilitating interoperability among sample-based data relevant to EarthScope CI and globally. It will also make these samples visible to global audiences via the SESAR Global Sample Catalog.

Vintage venoms: proteomic and pharmacological stability of snake venoms stored for up to eight decades.

PubMed

Jesupret, Clémence; Baumann, Kate; Jackson, Timothy N W; Ali, Syed Abid; Yang, Daryl C; Greisman, Laura; Kern, Larissa; Steuten, Jessica; Jouiaei, Mahdokht; Casewell, Nicholas R; Undheim, Eivind A B; Koludarov, Ivan; Debono, Jordan; Low, Dolyce H W; Rossi, Sarah; Panagides, Nadya; Winter, Kelly; Ignjatovic, Vera; Summerhayes, Robyn; Jones, Alun; Nouwens, Amanda; Dunstan, Nathan; Hodgson, Wayne C; Winkel, Kenneth D; Monagle, Paul; Fry, Bryan Grieg

2014-06-13

For over a century, venom samples from wild snakes have been collected and stored around the world. However, the quality of storage conditions for "vintage" venoms has rarely been assessed. The goal of this study was to determine whether such historical venom samples are still biochemically and pharmacologically viable for research purposes, or if new sample efforts are needed. In total, 52 samples spanning 5 genera and 13 species with regional variants of some species (e.g., 14 different populations of Notechis scutatus) were analysed by a combined proteomic and pharmacological approach to determine protein structural stability and bioactivity. When venoms were not exposed to air during storage, the proteomic results were virtually indistinguishable from that of fresh venom and bioactivity was equivalent or only slightly reduced. By contrast, a sample of Acanthophis antarcticus venom that was exposed to air (due to a loss of integrity of the rubber stopper) suffered significant degradation as evidenced by the proteomics profile. Interestingly, the neurotoxicity of this sample was nearly the same as fresh venom, indicating that degradation may have occurred in the free N- or C-terminus chains of the proteins, rather than at the tips of loops where the functional residues are located. These results suggest that these and other vintage venom collections may be of continuing value in toxin research. This is particularly important as many snake species worldwide are declining due to habitat destruction or modification. For some venoms (such as N. scutatus from Babel Island, Flinders Island, King Island and St. Francis Island) these were the first analyses ever conducted and these vintage samples may represent the only venom ever collected from these unique island forms of tiger snakes. Such vintage venoms may therefore represent the last remaining stocks of some local populations and thus are precious resources. These venoms also have significant historical value as the Oxyuranus venoms analysed include samples from the first coastal taipan (Oxyuranus scutellatus) collected for antivenom production (the snake that killed the collector Kevin Budden), as well as samples from the first Oxyuranus microlepidotus specimen collected after the species' rediscovery in 1976. These results demonstrate that with proper storage techniques, venom samples can retain structural and pharmacological stability. This article is part of a Special Issue entitled: Proteomics of non-model organisms. Copyright © 2014 Elsevier B.V. All rights reserved.

Miniature open channel scrubbers for gas collection.

PubMed

Toda, Kei; Koga, Tomoko; Tanaka, Toshinori; Ohira, Shin-Ichi; Berg, Jordan M; Dasgupta, Purnendu K

2010-10-15

An open channel scrubber is proposed as a miniature fieldable gas collector. The device is 100mm in length, 26 mm in width and 22 mm in thickness. The channel bottom is rendered hydrophilic and liquid flows as a thin layer on the bottom. Air sample flows atop the appropriately chosen flowing liquid film and analyte molecules are absorbed into the liquid. There is no membrane at the air-liquid interface: they contact directly each other. Analyte species collected over a 10 min interval are determined by fluorometric flow analysis or ion chromatography. A calculation algorithm was developed to estimate the collection efficiency a priori; experimental and simulated results agreed well. The characteristics of the open channel scrubber are discussed in this paper from both theoretical and experimental points of view. In addition to superior collection efficiencies at relatively high sample air flow rates, this geometry is particularly attractive that there is no change in collection performance due to membrane fouling. We demonstrate field use for analysis of ambient SO(2) near an active volcano. This is basic investigation of membraneless miniature scrubber and is expected to lead development of an excellent micro-gas analysis system integrated with a detector for continuous measurements. Copyright © 2010 Elsevier B.V. All rights reserved.

Accumulation of polycyclic aromatic hydrocarbons by Neocalanus copepods in Port Valdez, Alaska.

PubMed

Carls, Mark G; Short, Jeffrey W; Payne, James

2006-11-01

Sampling zooplankton is a useful strategy for observing trace hydrocarbon concentrations in water because samples represent an integrated average over a considerable effective sampling volume and are more representative of the sampled environment than discretely collected water samples. We demonstrate this method in Port Valdez, Alaska, an approximately 100 km(2) basin that receives about 0.5-2.4 kg of polynuclear aromatic hydrocarbons (PAH) per day. Total PAH (TPAH) concentrations (0.61-1.31 microg/g dry weight), composition, and spatial distributions in a lipid-rich copepod, Neocalanus were consistent with the discharge as the source of contamination. Although Neocalanus acquire PAH from water or suspended particulate matter, total PAH concentrations in these compartments were at or below method detection limits, demonstrating plankton can amplify trace concentrations to detectable levels useful for study.

Effective use of metadata in the integration and analysis of multi-dimensional optical data

NASA Astrophysics Data System (ADS)

Pastorello, G. Z.; Gamon, J. A.

2012-12-01

Data discovery and integration relies on adequate metadata. However, creating and maintaining metadata is time consuming and often poorly addressed or avoided altogether, leading to problems in later data analysis and exchange. This is particularly true for research fields in which metadata standards do not yet exist or are under development, or within smaller research groups without enough resources. Vegetation monitoring using in-situ and remote optical sensing is an example of such a domain. In this area, data are inherently multi-dimensional, with spatial, temporal and spectral dimensions usually being well characterized. Other equally important aspects, however, might be inadequately translated into metadata. Examples include equipment specifications and calibrations, field/lab notes and field/lab protocols (e.g., sampling regimen, spectral calibration, atmospheric correction, sensor view angle, illumination angle), data processing choices (e.g., methods for gap filling, filtering and aggregation of data), quality assurance, and documentation of data sources, ownership and licensing. Each of these aspects can be important as metadata for search and discovery, but they can also be used as key data fields in their own right. If each of these aspects is also understood as an "extra dimension," it is possible to take advantage of them to simplify the data acquisition, integration, analysis, visualization and exchange cycle. Simple examples include selecting data sets of interest early in the integration process (e.g., only data collected according to a specific field sampling protocol) or applying appropriate data processing operations to different parts of a data set (e.g., adaptive processing for data collected under different sky conditions). More interesting scenarios involve guided navigation and visualization of data sets based on these extra dimensions, as well as partitioning data sets to highlight relevant subsets to be made available for exchange. The DAX (Data Acquisition to eXchange) Web-based tool uses a flexible metadata representation model and takes advantage of multi-dimensional data structures to translate metadata types into data dimensions, effectively reshaping data sets according to available metadata. With that, metadata is tightly integrated into the acquisition-to-exchange cycle, allowing for more focused exploration of data sets while also increasing the value of, and incentives for, keeping good metadata. The tool is being developed and tested with optical data collected in different settings, including laboratory, field, airborne, and satellite platforms.

Collection, Evaluation, and Coagulum Dissolution of Semen from Goeldi's Monkey, Callimico goeldii.

PubMed

Arakaki, Paloma Rocha; Carvalho, Fernanda Maria de; Castro, Paulo Henrique Gomes de; Muniz, José Augusto Pereira Carneiro; Valle, Rodrigo Del Rio do

2017-01-01

Research on Neotropical primates' reproduction is necessary due to the lack of available information and the increasing threat to these species. Callimico goeldii is listed as Vulnerable on the IUCN Red List of Threatened Species. This study aimed to test rectal electrostimulation for semen collection and evaluate seminal characteristics. Therefore, semen from 6 captive Goeldi's monkeys was collected and, for the first time, seminal characteristics are described. Coagulum formation was noted in all ejaculates, and we obtained partial or complete liquefaction of the samples. Results were (means ± SD): volume = 26.9 ± 11.87 μL; pH = 7.61 ± 0.28; concentration = 143.18 ± 174.96 × 106 spermatozoa/mL; total sperm motility = 83.33 ± 5.16%; linear progressive motility = 46 ± 24.08%; plasma membrane integrity = 36.38 ± 16.11%; acrosome integrity using fast-green/bengal-rose staining = 63.41 ± 11.72%, and kit Spermac® = 69.36 ± 11.81%; abnormal sperm = 72.5 ± 17.7%, with 16.2 ± 7.7% major defects and 56.3 ± 10% minor defects; sperm with high mitochondrial activity class I = 16.45 ± 22.25%. Rectal electrostimulation was an efficient method for semen collection in this species. Investigations are required to improve semen collection and handling, including cryopreservation methods. © 2017 S. Karger AG, Basel.

Analysis of pesticide residues in strawberries and soils by GC-MS/MS, LC-MS/MS and two-dimensional GC-time-of-flight MS comparing organic and integrated pest management farming

USDA-ARS?s Scientific Manuscript database

The issue of pesticide residues in foods is growing in importance due to greater global food trade and increasing public concern. Therefore, appropriate control and monitoring of residues in food must be conducted. In this study, we analyzed 22 strawberry and soil samples after their collection over...

Validation of Procedures for Monitoring Crewmember Immune Function - Short Duration Biological Investigation

NASA Technical Reports Server (NTRS)

Sams, Clarence; Crucian, Brian; Stowe, Raymond; Pierson, Duane; Mehta, Satish; Morukov, Boris; Uchakin, Peter; Nehlsen-Cannarella, Sandra

2008-01-01

Validation of Procedures for Monitoring Crew Member Immune Function - Short Duration Biological Investigation (Integrated Immune-SDBI) will assess the clinical risks resulting from the adverse effects of space flight on the human immune system and will validate a flightcompatible immune monitoring strategy. Immune system changes will be monitored by collecting and analyzing blood, urine and saliva samples from crewmembers before, during and after space flight.

Global Characterization of Protein Altering Mutations in Prostate Cancer

DTIC Science & Technology

2011-08-01

prevalence of candidate cancer genes observed here in prostate cancer. (3) Perform integrative analyses of somatic mutation with gene expression and copy...analyses of somatic mutation with gene expression and copy number change data collected on the same samples. Body This is a “synergy” project between...However, to perform initial verification/validation studies, we have evaluated the mutation calls for several genes discovered initially by the

Measurement of the e+e-→KSKLπ0 cross section in the energy range √{s }=1.3 -2.0 GeV

NASA Astrophysics Data System (ADS)

Achasov, M. N.; Aulchenko, V. M.; Barnyakov, A. Yu.; Beloborodov, K. I.; Berdyugin, A. V.; Berkaev, D. E.; Bogdanchikov, A. G.; Botov, A. A.; Dimova, T. V.; Druzhinin, V. P.; Golubev, V. B.; Kardapoltsev, L. V.; Kasaev, A. S.; Kharlamov, A. G.; Kirpotin, A. N.; Koop, I. A.; Korneev, L. A.; Korol, A. A.; Kovrizhin, D. P.; Koshuba, S. V.; Kupich, A. S.; Melnikova, N. A.; Martin, K. A.; Obrazovsky, A. E.; Otboev, A. V.; Pakhtusova, E. V.; Pugachev, K. V.; Rogovsky, Yu. A.; Senchenko, A. I.; Serednyakov, S. I.; Silagadze, Z. K.; Shatunov, Yu. M.; Shtol, D. A.; Shwartz, D. B.; Surin, I. K.; Usov, Yu. V.; Vasiljev, A. V.

2018-02-01

The e+e-→KSKLπ0 cross section is measured in the center-of-mass energy range √{s }=1.3 - 2.0 GeV . The analysis is based on the data sample with an integrated luminosity of 33.5 pb-1 collected with the SND detector at the VEPP-2000 e+e- collider.

Tangential-flow ultrafiltration with integrated inhibition detection for recovery of surrogates and human pathogens from large-volume source water and finished drinking water.

PubMed

Gibson, Kristen E; Schwab, Kellogg J

2011-01-01

Tangential-flow ultrafiltration was optimized for the recovery of Escherichia coli, Enterococcus faecalis, Clostridium perfringens spores, bacteriophages MS2 and PRD1, murine norovirus, and poliovirus seeded into 100-liter surface water (SW) and drinking water (DW) samples. SW and DW collected from two drinking water treatment plants were then evaluated for human enteric viruses.

COmet Nucleus Dust and Organics Return (CONDOR): a New Frontiers 4 Mission Proposal

NASA Astrophysics Data System (ADS)

Choukroun, M.; Raymond, C.; Wadhwa, M.

2017-09-01

CONDOR would collect and return a ≥ 50 g sample from the surface of 67P/Churyumov-Gerasimenko for detailed analysis in terrestrial laboratories. It would carry a simple payload comprising a narrow-angle camera and mm-wave radiometer to select a sampling site, and perform a gravity science investigation to survey changes of 67P since Rosetta. The proposed sampling system uses the BiBlade tool to acquire a sample down to 15 cm depth in a Touch-and-Go event. The Stardust-based sample return capsule is augmented with cooling and purge systems to maintain sample integrity during landing and until delivery to JSC's Astromaterials Curation Facility. Analysis of rock-forming minerals, organics, water and noble gases would probe the origin of these materials, and their evolution from the primordial molecular cloud to the 67P environment.

Technical note: Mineralogical, chemical, morphological, and optical interrelationships of mineral dust re-suspensions

NASA Astrophysics Data System (ADS)

Engelbrecht, Johann P.; Moosmüller, Hans; Pincock, Samuel; Jayanty, R. K. M.; Lersch, Traci; Casuccio, Gary

2016-08-01

This paper promotes an understanding of the mineralogical, chemical, and physical interrelationships of re-suspended mineral dusts collected as grab samples from global dust sources. Surface soils were collected from arid regions, including the southwestern USA, Mali, Chad, Morocco, Canary Islands, Cabo Verde, Djibouti, Afghanistan, Iraq, Kuwait, Qatar, UAE, Serbia, China, Namibia, Botswana, Australia, and Chile. The < 38 µm sieved fraction of each sample was re-suspended in a chamber, from which the airborne mineral dust could be extracted, sampled, and analyzed. Instruments integrated into the entrainment facility included two PM10 and two PM2.5 filter samplers, a beta attenuation gauge for the continuous measurement of PM10 and PM2.5 particulate mass fractions, an aerodynamic particle size analyzer, and a three-wavelength (405, 532, 781 nm) photoacoustic instrument with integrating reciprocal nephelometer for monitoring absorption and scattering coefficients during the dust re-suspension process. Filter sampling media included Teflon® membrane and quartz fiber filters for chemical analysis and Nuclepore® filters for individual particle analysis by scanning electron microscopy (SEM). The < 38 µm sieved fractions were also analyzed by X-ray diffraction for their mineral content while the > 75, < 125 µm soil fractions were mineralogically assessed by optical microscopy. Presented here are results of the optical measurements, showing the interdependency of single-scattering albedos (SSA) at three different wavelengths and mineralogical content of the entrained dust samples. To explain the elevated concentrations of iron (Fe) and Fe / Al ratios in the soil re-suspensions, we propose that dust particles are to a large extent composed of nano-sized particles of micas, clays, metal oxides, and ions of potassium (K+), calcium (Ca2+), and sodium (Na+) evenly dispersed as a colloid or adsorbed in amorphous clay-like material. Also shown are differences in SSA of the kaolinite/hematite/goethite samples from Mali and those from colloidal soils elsewhere. Results from this study can be integrated into a database of mineral dust properties, for applications in climate modeling, remote sensing, visibility, health (medical geology), ocean fertilization, and impact on equipment.

Biobanking of fresh frozen tissue from clinical surgical specimens: transport logistics, sample selection, and histologic characterization.

PubMed

Botling, Johan; Micke, Patrick

2011-01-01

Access to high-quality fresh frozen tissue is critical for translational cancer research and molecular -diagnostics. Here we describe a workflow for the collection of frozen solid tissue samples derived from fresh human patient specimens after surgery. The routines have been in operation at Uppsala University Hospital since 2001. We have integrated cryosection and histopathologic examination of each biobank sample into the biobank manual. In this way, even small, macroscopically ill-defined lesions can be -procured without a diagnostic hazard due to the removal of uncharacterized tissue from a clinical -specimen. Also, knowledge of the histomorphology of the frozen tissue sample - tumor cell content, stromal components, and presence of necrosis - is pivotal before entering a biobank case into costly molecular profiling studies.

Baseline tests for arc melter vitrification of INEL buried wastes. Volume II: Baseline test data appendices

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

Oden, L.L.; O`Conner, W.K.; Turner, P.C.

1993-11-19

This report presents field results and raw data from the Buried Waste Integrated Demonstration (BWID) Arc Melter Vitrification Project Phase 1 baseline test series conducted by the Idaho National Engineering Laboratory (INEL) in cooperation with the U.S. Bureau of Mines (USBM). The baseline test series was conducted using the electric arc melter facility at the USBM Albany Research Center in Albany, Oregon. Five different surrogate waste feed mixtures were tested that simulated thermally-oxidized, buried, TRU-contaminated, mixed wastes and soils present at the INEL. The USBM Arc Furnace Integrated Waste Processing Test Facility includes a continuous feed system, the arc meltingmore » furnace, an offgas control system, and utilities. The melter is a sealed, 3-phase alternating current (ac) furnace approximately 2 m high and 1.3 m wide. The furnace has a capacity of 1 metric ton of steel and can process as much as 1,500 lb/h of soil-type waste materials. The surrogate feed materials included five mixtures designed to simulate incinerated TRU-contaminated buried waste materials mixed with INEL soil. Process samples, melter system operations data and offgas composition data were obtained during the baseline tests to evaluate the melter performance and meet test objectives. Samples and data gathered during this program included (a) automatically and manually logged melter systems operations data, (b) process samples of slag, metal and fume solids, and (c) offgas composition, temperature, velocity, flowrate, moisture content, particulate loading and metals content. This report consists of 2 volumes: Volume I summarizes the baseline test operations. It includes an executive summary, system and facility description, review of the surrogate waste mixtures, and a description of the baseline test activities, measurements, and sample collection. Volume II contains the raw test data and sample analyses from samples collected during the baseline tests.« less

Baseline tests for arc melter vitrification of INEL buried wastes. Volume 1: Facility description and summary data report

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

Oden, L.L.; O`Connor, W.K.; Turner, P.C.

1993-11-19

This report presents field results and raw data from the Buried Waste Integrated Demonstration (BWID) Arc Melter Vitrification Project Phase 1 baseline test series conducted by the Idaho National Engineering Laboratory (INEL) in cooperation with the U.S. Bureau of Mines (USBM). The baseline test series was conducted using the electric arc melter facility at the USBM Albany Research Center in Albany, Oregon. Five different surrogate waste feed mixtures were tested that simulated thermally-oxidized, buried, TRU-contaminated, mixed wastes and soils present at the INEL. The USBM Arc Furnace Integrated Waste Processing Test Facility includes a continuous feed system, the arc meltingmore » furnace, an offgas control system, and utilities. The melter is a sealed, 3-phase alternating current (ac) furnace approximately 2 m high and 1.3 m wide. The furnace has a capacity of 1 metric ton of steel and can process as much as 1,500 lb/h of soil-type waste materials. The surrogate feed materials included five mixtures designed to simulate incinerated TRU-contaminated buried waste materials mixed with INEL soil. Process samples, melter system operations data and offgas composition data were obtained during the baseline tests to evaluate the melter performance and meet test objectives. Samples and data gathered during this program included (a) automatically and manually logged melter systems operations data, (b) process samples of slag, metal and fume solids, and (c) offgas composition, temperature, velocity, flowrate, moisture content, particulate loading and metals content. This report consists of 2 volumes: Volume I summarizes the baseline test operations. It includes an executive summary, system and facility description, review of the surrogate waste mixtures, and a description of the baseline test activities, measurements, and sample collection. Volume II contains the raw test data and sample analyses from samples collected during the baseline tests.« less

Integrated cluster- and case-based surveillance for detecting stage III zoonotic pathogens: an example of Nipah virus surveillance in Bangladesh.

PubMed

Naser, A M; Hossain, M J; Sazzad, H M S; Homaira, N; Gurley, E S; Podder, G; Afroj, S; Banu, S; Rollin, P E; Daszak, P; Ahmed, B-N; Rahman, M; Luby, S P

2015-07-01

This paper explores the utility of cluster- and case-based surveillance established in government hospitals in Bangladesh to detect Nipah virus, a stage III zoonotic pathogen. Physicians listed meningo-encephalitis cases in the 10 surveillance hospitals and identified a cluster when ⩾2 cases who lived within 30 min walking distance of one another developed symptoms within 3 weeks of each other. Physicians collected blood samples from the clustered cases. As part of case-based surveillance, blood was collected from all listed meningo-encephalitis cases in three hospitals during the Nipah season (January-March). An investigation team visited clustered cases' communities to collect epidemiological information and blood from the living cases. We tested serum using Nipah-specific IgM ELISA. Up to September 2011, in 5887 listed cases, we identified 62 clusters comprising 176 encephalitis cases. We collected blood from 127 of these cases. In 10 clusters, we identified a total of 62 Nipah cases: 18 laboratory-confirmed and 34 probable. We identified person-to-person transmission of Nipah virus in four clusters. From case-based surveillance, we identified 23 (4%) Nipah cases. Faced with thousands of encephalitis cases, integrated cluster surveillance allows targeted deployment of investigative resources to detect outbreaks by stage III zoonotic pathogens in resource-limited settings.

Lessons from the Navajo: assistance with environmental data collection ensures cultural humility and data relevance.

PubMed

DeLemos, Jamie; Rock, Tommy; Brugge, Doug; Slagowski, Naomi; Manning, Thomas; Lewis, Johnnye

2007-01-01

The Navajo Nation suffers from a legacy of environmental pollution from historical uranium mining activities, resulting in adverse public health outcomes and continuous exposure. Partner with a Navajo graduate student and community members in a field campaign to characterize the spatial distribution and geochemistry of uranium for a multipathway uranium exposure assessment under development by the Dine Network for Environmental Health (DiNEH) project. Attend community meetings, acquire Navajo language skills, and integrate local knowledge into sampling approach of sediment, water, and vegetation. Navajo participation (1) helped to foster trust in research efforts during community interactions, (2) taught aspects of Navajo culture and language to maintain positive and respectful relations, and (3) conveyed information on Navajo culture that would impact sampling strategies. Community engagement helps to sustain equitable partnerships and aids in culturally appropriate, relevant data collection.

Lessons from the Navajo: Assistance with Environmental Data Collection Ensures Cultural Humility and Data Relevance

PubMed Central

deLemos, Jamie; Rock, Tommy; Brugge, Doug; Slagowski, Naomi; Manning, Thomas; Lewis, Johnnye

2008-01-01

Background The Navajo Nation suffers from a legacy of environmental pollution from historical uranium mining activities, resulting in adverse public health outcomes and continuous exposure. Objective Partner with a Navajo graduate student and community members in a field campaign to characterize the spatial distribution and geochemistry of uranium for a multipathway uranium exposure assessment under development by the Dine Network for Environmental Health (DiNEH) project. Methods Attend community meetings, acquire Navajo language skills, and integrate local knowledge into sampling approach of sediment, water, and vegetation. Results Navajo participation (1) helped to foster trust in research efforts during community interactions, (2) taught aspects of Navajo culture and language to maintain positive and respectful relations, and (3) conveyed information on Navajo culture that would impact sampling strategies. Conclusions Community engagement helps to sustain equitable partnerships and aids in culturally appropriate, relevant data collection. PMID:19655034

Organization of a tumor bank: the experience of the National Cancer Institute of Mexico.

PubMed

Ruíz-Godoy, L; Meneses-García, A; Suárez-Roa, L; Enriquez, V; Lechuga-Rojas, R; Reyes-Lira, E

2010-01-01

A tumor bank (TB) is an ordered collection of neoplastic samples, normal tissue, and/or fluids preserved under optimal conditions, as well as storing patients' clinical information. The objective of this article is to outline the planning and logistics necessary for the functioning of the Instituto Nacional de Cancerología (INCan) TB in Mexico City. For the planning and logistics of a TB, several technical, legal, medical, structural, and physical aspects were considered, which can be grouped under four headings: (1) design and structure, (2) equipping the area and informatics, (3) ethical-legal aspects, and (4) sample collection, preservation, and quality control. One crucial element of interinstitutional interest will be the transfer of these concepts to the different oncological centers, integrating in this manner a network that enables the exploration of the different pathologies from therapeutic, epidemiological, and molecular points of view. 2010 S. Karger AG, Basel.

Cleaning the IceMole: collection of englacial samples from Blood Falls, Antarctica

NASA Astrophysics Data System (ADS)

Mikucki, J.; Digel, I.; Chua, M.; Davis, J.; Ghosh, D.; Lyons, W. B.; Welch, K. A.; Purcell, A.; Francke, G.; Feldmann, M.; Espe, C.; Heinen, D.; Dachwald, B.; Kowalski, J.; Tulaczyk, S. M.

2016-12-01

The Minimally Invasive Direct Glacial Access project (MIDGE) used a maneuverable thermoelectric melting probe called the IceMole to collect the first englacial samples of brine from Blood Falls, Antarctica. In order to maintain the scientific integrity of samples collected and minimize impact to this specially protected ecosystem, microbial and chemical contamination of the IceMole needed to be minimized. Guidelines have been established for research in Antarctic subglacial systems by the scientific and regulatory community and have been detailed by the "Code of Conduct for the Exploration and Research of Subglacial Aquatic Environments" put forth by the Scientific Committee on Antarctic Research (SCAR) Action Group, and was submitted to the Antarctic Treaty System. This Code of Conduct (CoC) recognizes the ecological importance and pristine nature of subglacial habitats and recommends a path forward towards clean exploration. Similarly, the US and European space agencies (NASA and ESA) have detailed instrument preparation protocols for the exploration of icy worlds in our solar system for planetary protection. Given the synergistic aims of these two groups we have adopted protocols from both subglacial and space exploration approaches. Here we present our approach to cleaning the IceMole in the field and report on ability to reduce the bioload inherent on the melter. Specifically our protocol reduced the exterior bio-load by an order of magnitude, to levels common in most clean rooms, and 1-3 orders of magnitude below that of Taylor Glacier ice surrounding Blood Falls. Our results indicate that the collection of englacial samples for microbiological analysis is feasible with melting probes.

Surface-water quality at fixed sites in the Western Lake Michigan Drainages, Wisconsin and Michigan, and the effects of natural and human factors, 1993-95

USGS Publications Warehouse

Richards, K.D.; Sullivan, D.J.; Stewart, J.S.

1998-01-01

Streamwater samples were collected from April 1993 through July 1995 at 11 fixed sites in the Western Lake Michigan Drainages Study Unit of the U.S. Geological Survey's National Water-Quality Assessment Program. Water samples were collected monthly at all Fixed Sites, and an additional two to four samples were collected each year during periods of high flow. Streamflow was monitored continuously at the Fixed Sites for the duration of the study period. This report describes field techniques used to collect the water samples, and the analytical methods used for laboratory analyses, statistical analyses of the data, and an attempt to determine the effect of natural and anthropogenic factors on concentrations of nutrients and selected major ions and suspended solids. Locations of eight of the Fixed Sites were selected to represent areas with unique combinations of land use/land cover, surficial deposits, and bedrock geology and are referred to as 'indicator sites.' The remaining three sites were located near the mouths of major rivers and are referred to as 'integrator sites.' The integrator sites represent a large part of the total flow from the Study Unit to Green Bay and western Lake Michigan, and drain various combinations of land use, bedrock, and surficial deposits. These data indicate that land use and surficial deposits may be the primary factors affecting nitrate and total phosphorus concentrations in this Study Unit. Median concentrations of nitrate at the forested sites were less than the National Median Concentration (NMC), and those at urban fixed sites were similar to the NMC. Median nitrate concentrations at the Tomorrow River, North Branch Milwaukee River, and Duck Creek agricultural indicator sites were twice the NMC, but median concentrations at the remaining agricultural indicator sites were similar to the NMC. Nitrate concentrations at one agricultural indicator site exceeded the U. S. Environmental Protection Agency (USEPA) maximum contaminant level in three run-off samples in the growing seasons of 1994 and 1995. Median concentrations of total phosphorus at the forested indicator sites were below the NMC. Tomorrow River was the only agricultural indicator site where the median total-phosphorus concentration was less than the NMC; median concentrations at the remaining agricultural Fixed Sites were similar to the NMC and exceeded 0.1 mg/L, the USEPA suggested total-phosphorus concentration in flowing water. The USEPA recommends that total-phosphorus concentration not exceed this limit to discourage excessive aquatic plant growth in flowing waters. Median total-phosphorus concentration at the urban indicator site was less than the urban NMC. Median concentrations for both nitrate and total phosphorus at the mouth of the Fox River and the Milwaukee River integrator sites were similar to the NMC for the dominant land use, agriculture, within their basins, and were lower than that at the Menominee River integrator site with a dominant forest land use. During this study, potassium concentrations were generally highest in areas of clay-dominated surficial deposits, silica was generally highest in areas of sandy surficial deposits, iron generally highest in areas of igneous/metamorphic bedrock, and calcium generally highest in areas of carbonate bedrock. The highest median fluoride concentration occurred at an urban site that receives treated water.

Subsoil erosion dominates the supply of fine sediment to rivers draining into Princess Charlotte Bay, Australia.

PubMed

Olley, Jon; Brooks, Andrew; Spencer, John; Pietsch, Timothy; Borombovits, Daniel

2013-10-01

The Laura-Normanby River (catchment area: 24,350 km(2)), which drains into Princess Charlotte Bay, has been identified in previous studies as the third largest contributor of sediment to the Great Barrier Reef World Heritage Area. These catchment scale modelling studies also identified surface soil erosion as supplying >80% of the sediment. Here we use activity concentrations of the fallout radionuclides (137)Cs and (210)Pbex to test the hypothesis that surface soil erosion dominates the supply of fine (<10 μm) sediment in the river systems draining into Princess Charlotte Bay. Our results contradict these previous studies, and are consistent with channel and gully erosion being the dominant source of fine sediment in this catchment. The hypothesis that surface soil erosion dominates the supply of fine sediment to Princess Charlotte Bay is rejected. River sediment samples were collected using both time-integrated samplers and sediment drape deposits. We show that there is no detectable difference in (137)Cs and (210)Pbex activity concentrations between samples collected using these two methods. Two methods were also used to collect samples to characterise (137)Cs and (210)Pbex concentrations in sediment derived from surface soil erosion; sampling of surface-wash deposits and deployment of surface runoff traps that collected samples during rain events. While there was no difference in the (137)Cs activity concentrations for samples collected using these two methods, (210)Pbex activity concentrations were significantly higher in the samples collected using the runoff traps. The higher (210)Pbex concentrations are shown to be correlated with loss-on-ignition (r(2) = 0.79) and therefore are likely to be related to higher organic concentrations in the runoff trap samples. As a result of these differences we use a three end member mixing model (channel/gully, hillslope surface-wash and hillslope runoff traps) to determine the relative contribution from surface soil erosion. Probability distributions for (137)Cs and (210)Pbex concentrations were determined for each of the end members, with these distributions then used to estimate the surface soil contribution to each of the collected river sediment samples. The mean estimate of contribution of surface derived sediment for all river samples (n = 70) is 16 ± 2%. This study reinforces the importance of testing model predictions before they are used to target investment in remedial action and adds to the body of evidence that the primary source of sediment delivered to tropical river systems is derived from subsoil erosion. Copyright © 2013 Elsevier Ltd. All rights reserved.

Mars Science Laboratory Drill

NASA Technical Reports Server (NTRS)

Okon, Avi B.; Brown, Kyle M.; McGrath, Paul L.; Klein, Kerry J.; Cady, Ian W.; Lin, Justin Y.; Ramirez, Frank E.; Haberland, Matt

2012-01-01

This drill (see Figure 1) is the primary sample acquisition element of the Mars Science Laboratory (MSL) that collects powdered samples from various types of rock (from clays to massive basalts) at depths up to 50 mm below the surface. A rotary-percussive sample acquisition device was developed with an emphasis on toughness and robustness to handle the harsh environment on Mars. It is the first rover-based sample acquisition device to be flight-qualified (see Figure 2). This drill features an autonomous tool change-out on a mobile robot, and novel voice-coil-based percussion. The drill comprises seven subelements. Starting at the end of the drill, there is a bit assembly that cuts the rock and collects the sample. Supporting the bit is a subassembly comprising a chuck mechanism to engage and release the new and worn bits, respectively, and a spindle mechanism to rotate the bit. Just aft of that is a percussion mechanism, which generates hammer blows to break the rock and create the dynamic environment used to flow the powdered sample. These components are mounted to a translation mechanism, which provides linear motion and senses weight-on-bit with a force sensor. There is a passive-contact sensor/stabilizer mechanism that secures the drill fs position on the rock surface, and flex harness management hardware to provide the power and signals to the translating components. The drill housing serves as the primary structure of the turret, to which the additional tools and instruments are attached. The drill bit assembly (DBA) is a passive device that is rotated and hammered in order to cut rock (i.e. science targets) and collect the cuttings (powder) in a sample chamber until ready for transfer to the CHIMRA (Collection and Handling for Interior Martian Rock Analysis). The DBA consists of a 5/8-in. (.1.6- cm) commercial hammer drill bit whose shank has been turned down and machined with deep flutes designed for aggressive cutting removal. Surrounding the shank of the bit is a thick-walled maraging steel collection tube allowing the powdered sample to be augured up the hole into the sample chamber. For robustness, the wall thickness of the DBA was maximized while still ensuring effective sample collection. There are four recesses in the bit tube that are used to retain the fresh bits in their bit box. The rotating bit is supported by a back-to-back duplex bearing pair within a housing that is connected to the outer DBA housing by two titanium diaphragms. The only bearings on the drill in the sample flow are protected by a spring-energized seal, and an integrated shield that diverts the ingested powdered sample from the moving interface. The DBA diaphragms provide radial constraint of the rotating bit and form the sample chambers. Between the diaphragms there is a sample exit tube from which the sample is transferred to the CHIMRA. To ensure that the entire collected sample is retained, no matter the orientation of the drill with respect to gravity during sampling, the pass-through from the forward to the aft chamber resides opposite to the exit tube.

Standardisation of a novel sperm banking kit - NextGen(®) - to preserve sperm parameters during shipment.

PubMed

Agarwal, A; Sharma, R; Singh, A; Gupta, S; Sharma, R

2016-08-01

Many male patients diagnosed with cancer are within their reproductive years. These men are advised to freeze their spermatozoa prior to the start of cancer treatment. Very often, sperm banking facilities may not be readily available and patients may be required to travel to distant sperm bank centres. Our objective was to design and standardise a remote home shipping sperm kit that allows patients to collect a semen sample at home and ship it overnight to a sperm bank. A total of 21 semen samples and two transport media (refrigeration media and human tubal fluid) and five different combinations of ice packs were tested for maintaining desired shipping temperature. Ten semen samples were assessed for pre- and post-shipment changes in sperm motility, membrane integrity, total motile spermatozoa and recovery of motile spermatozoa. Even though motility, membrane integrity and total motile spermatozoa declined both in samples examined under simulated shipped conditions and in overnight-shipped samples, the observed motility and total motile spermatozoa were adequate for use with assisted reproductive techniques. Using refrigeration media, cooling sleeve and ice packs, adequate sperm motility can be maintained utilising NextGen(®) kit and these spermatozoa can be used for procreation utilising ART techniques such as intracytoplasmic sperm injection. © 2015 Blackwell Verlag GmbH.

Biological and chemical analysis of the toxic potency of pesticides in rainwater.

PubMed

Hamers, T; Smit, M G; Murk, A J; Koeman, J H

2001-11-01

A newly developed method for measuring the integrated esterase inhibiting potency of rainwater samples was applied in practice, and the results are compared to the toxic potency calculated from concentrations of 31 organophosphate (OP) and carbamate pesticides, out of a total of 66 chemically analyzed pesticides. In addition, the general toxic potency of the rainwater samples was evaluated in a microtiter luminescence assay with Vibrio fischeri bacteria. Rainwater samples were collected over four consecutive 14-day periods in both open and wet-only samplers. The esterase inhibiting potency of the open rainwater samples (expressed as ng dichlorvos-equivalents/l) corresponded well with the chemical analyses of the rainwater samples collected by both types of samplers (r = 0.83-0.86). By far, the highest esterase inhibiting potency was found in a sample collected in an area with intense horticultural activities in June, and was attributed to high concentrations of dichlorvos, mevinphos, pirimiphos-methyl and methiocarb. The esterase inhibiting potency of this sample was equivalent to a dichlorvos concentration of 1380 ng/l in the rainwater, which is almost 2000 times higher than the maximum permissible concentration (MPC) of dichlorvos set for surface water in Netherlands. Maximum individual concentrations of dichlorvos and pirimiphos-methyl even exceeded the EC50 for Daphnia, suggesting that pesticides in rainwater pose a risk for aquatic organisms. Not all responses of the luminescence-assay for general toxicity could be explained by the analyzed pesticide concentrations. The bio-assays enable a direct assessment the toxic potency of all individual compounds present in the complex mixture of rainwater pollutants, even if they are unknown or present at concentrations below the detection limit. Therefore, they are valuable tools for prescreening and hazard characterization purposes.

Reframing the challenges to integrated care: a complex-adaptive systems perspective.

PubMed

Tsasis, Peter; Evans, Jenna M; Owen, Susan

2012-01-01

Despite over two decades of international experience and research on health systems integration, integrated care has not developed widely. We hypothesized that part of the problem may lie in how we conceptualize the integration process and the complex systems within which integrated care is enacted. This study aims to contribute to discourse regarding the relevance and utility of a complex-adaptive systems (CAS) perspective on integrated care. In the Canadian province of Ontario, government mandated the development of fourteen Local Health Integration Networks in 2006. Against the backdrop of these efforts to integrate care, we collected focus group data from a diverse sample of healthcare professionals in the Greater Toronto Area using convenience and snowball sampling. A semi-structured interview guide was used to elicit participant views and experiences of health systems integration. We use a CAS framework to describe and analyze the data, and to assess the theoretical fit of a CAS perspective with the dominant themes in participant responses. Our findings indicate that integration is challenged by system complexity, weak ties and poor alignment among professionals and organizations, a lack of funding incentives to support collaborative work, and a bureaucratic environment based on a command and control approach to management. Using a CAS framework, we identified several characteristics of CAS in our data, including diverse, interdependent and semi-autonomous actors; embedded co-evolutionary systems; emergent behaviours and non-linearity; and self-organizing capacity. One possible explanation for the lack of systems change towards integration is that we have failed to treat the healthcare system as complex-adaptive. The data suggest that future integration initiatives must be anchored in a CAS perspective, and focus on building the system's capacity to self-organize. We conclude that integrating care requires policies and management practices that promote system awareness, relationship-building and information-sharing, and that recognize change as an evolving learning process rather than a series of programmatic steps.

Cryopreservation of ram semen with antioxidant supplemented soybean lecithin-based extenders and impacts on incubation resilience.

PubMed

Toker, M Berk; Alcay, Selim; Gokce, Elif; Ustuner, Burcu

2016-06-01

The scope of this study was investigation the affects of various antioxidants on 1% soybean lecithin-based semen extenders for ram semen cryopreservation. Ejaculates, collected via electrically stimulated ejaculation, that have a thick consistency, rapid wave motion (3-5 on a 0-5 scale) and >75% initial motility were pooled. The pooled samples were split into four equal aliquots as 5 mM Methionine, 5 mM Cysteamine, 1 mM Cysteine and a sample of antioxidant-free control group. Each sample group was diluted to a ratio of 1/5 (semen/extender, v/v) as final concentration and two step dilution method was used for cryopreservation. Extender groups were assessed for sperm motility, plasma membrane functional integrity using hypoosmotic swelling test (HOST), damaged acrosome using FITC-Pisum sativum agglutinin (PSA-FITC) and DNA integrity using terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL). Semen samples also incubated for 6 h in humidified air with 5% CO2 at 39 °C to evaluate post-thaw incubation resilience of semen characteristics. The results showed that freezing and thawing procedures had negative effects on motility (P < 0.05), plasma membrane integrity (P < 0.05) and acrosomal integrity (P < 0.05). After 6 h of incubation time, the Cysteine supplemented extender group yielded significantly higher results than other extender groups in terms of spermatological parameters. Furthermore MDA levels in the antioxidant groups were lower than control group (P < 0.05). Nevertheless, there were no significant differences among antioxidant groups. Copyright © 2016 Elsevier Inc. All rights reserved.

Development of an integrated semi-automated system for in vitro pharmacodynamic modelling.

PubMed

Wang, Liangsu; Wismer, Michael K; Racine, Fred; Conway, Donald; Giacobbe, Robert A; Berejnaia, Olga; Kath, Gary S

2008-11-01

The aim of this study was to develop an integrated system for in vitro pharmacodynamic modelling of antimicrobials with greater flexibility, easier control and better accuracy than existing in vitro models. Custom-made bottle caps, fittings, valve controllers and a modified bench-top shaking incubator were used. A temperature-controlled automated sample collector was built. Computer software was developed to manage experiments and to control the entire system including solenoid pinch valves, peristaltic pumps and the sample collector. The system was validated by pharmacokinetic simulations of linezolid 600 mg infusion. The antibacterial effect of linezolid against multiple Staphylococcus aureus strains was also studied in this system. An integrated semi-automated bench-top system was built and validated. The temperature-controlled automated sample collector allowed unattended collection and temporary storage of samples. The system software reduced the labour necessary for many tasks and also improved the timing accuracy for performing simultaneous actions in multiple parallel experiments. The system was able to simulate human pharmacokinetics of linezolid 600 mg intravenous infusion accurately. A pharmacodynamic study of linezolid against multiple S. aureus strains with a range of MICs showed that the required 24 h free drug AUC/MIC ratio was approximately 30 in order to keep the organism counts at the same level as their initial inoculum and was about > or = 68 in order to achieve > 2 log(10) cfu/mL reduction in the in vitro model. The integrated semi-automated bench-top system provided the ability to overcome many of the drawbacks of existing in vitro models. It can be used for various simple or complicated pharmacokinetic/pharmacodynamic studies efficiently and conveniently.

Progress Towards a Global Understanding of Plankton Dynamics: The Global Alliance of CPR Surveys (GACS)

NASA Astrophysics Data System (ADS)

Batten, S.; Richardson, A.; Melrose, C.; Muxagata, E.; Hosie, G.; Verheye, H.; Hall, J.; Edwards, M.; Koubbi, P.; Abu-Alhaija, R.; Chiba, S.; Wilson, W.; Nagappa, R.; Takahashi, K.

2016-02-01

The Continuous Plankton Recorder (CPR) was first used in 1931 to routinely sample plankton and its continued deployment now sustains the longest-running, and spatially most extensive marine biological sampling programme in the world. Towed behind, for the most part commercial, ships it collects plankton samples from the surface waters that are subsequently analysed to provide taxonomically-resolved abundance data on a broad range of planktonic organisms from the size of coccolithophores to euphausiids. Plankton appear to integrate changes in the physical environment and by underpinning most marine food-webs, pass on this variability to higher trophic levels which have societal value. CPRs are deployed increasingly around the globe in discrete regional surveys that until recently interacted in an informal way. In 2011 the Global Alliance of CPR Surveys (GACS) was launched to bring these surveys together to collaborate more productively and address issues such as: methodological standardization, data integration, capacity building, and data analysis. Early products include a combined global database and regularly-released global marine ecological status reports. There are, of course, limitations to the exploitation of CPR data as well as the current geographic coverage. A current focus of GACS is integration of the data with models to meaningfully extrapolate across time and space. In this way the output could be used to provide more robust synoptic representations of key plankton variables. Recent years have also seen the CPR used as a platform in itself with the inclusion of additional sensors and water samplers that can sample the microplankton. The archive of samples has already been used for some molecular investigations and curation of samples is maintained for future studies. Thus the CPR is a key element of any regional to global ocean observing system of biodiversity.

Quantitative measurement of airborne cockroach allergen in New York City apartments

PubMed Central

Esposito, W. A.; Chew, G. L.; Correa, J. C.; Chillrud, S. N.; Miller, R. L.; Kinney, P. L.

2013-01-01

We designed and tested a sampling and analysis system for quantitative measurement of airborne cockroach allergen with sufficient sensitivity for residential exposure assessment. Integrated 1-week airborne particle samples were collected at 10–15 LPM in 19 New York City apartments in which an asthmatic child who was allergic to cockroach allergen resided. Four simultaneous air samples were collected in each home: at heights of 0.3 and 1 m in the child's bedroom and in the kitchen. Extracts of air samples were analyzed by ELISA for the cockroach allergen Bla g2, modified by amplifying the colorimetric signal generated via use of AMPLI-Q detection system (DAKO Corporation, Carpinteria, CA, USA). Settled dust samples were quantified by conventional ELISA. Of the homes where cockroach allergen was detected in settled dust, Bla g2 also was detected in 87% and 93% of air samples in the bedroom and kitchen, respectively. Airborne Bla g2 levels were highly correlated within and between the bedroom and kitchen locations (P < 0.001). Expressed as picogram per cubic meter, the room average geometric mean for Bla g2 concentrations was 1.9 pg/m3 (95% CI 0.63, 4.57) and 3.8 pg/m3 (95% CI 1.35, 9.25) in bedrooms and kitchens, respectively. This method offers an attractive supplement to settled dust sampling for cockroach allergen exposure health studies. PMID:21658130

Recent developments and future trends in solid phase microextraction techniques towards green analytical chemistry.

PubMed

Spietelun, Agata; Marcinkowski, Łukasz; de la Guardia, Miguel; Namieśnik, Jacek

2013-12-20

Solid phase microextraction find increasing applications in the sample preparation step before chromatographic determination of analytes in samples with a complex composition. These techniques allow for integrating several operations, such as sample collection, extraction, analyte enrichment above the detection limit of a given measuring instrument and the isolation of analytes from sample matrix. In this work the information about novel methodological and instrumental solutions in relation to different variants of solid phase extraction techniques, solid-phase microextraction (SPME), stir bar sorptive extraction (SBSE) and magnetic solid phase extraction (MSPE) is presented, including practical applications of these techniques and a critical discussion about their advantages and disadvantages. The proposed solutions fulfill the requirements resulting from the concept of sustainable development, and specifically from the implementation of green chemistry principles in analytical laboratories. Therefore, particular attention was paid to the description of possible uses of novel, selective stationary phases in extraction techniques, inter alia, polymeric ionic liquids, carbon nanotubes, and silica- and carbon-based sorbents. The methodological solutions, together with properly matched sampling devices for collecting analytes from samples with varying matrix composition, enable us to reduce the number of errors during the sample preparation prior to chromatographic analysis as well as to limit the negative impact of this analytical step on the natural environment and the health of laboratory employees. Copyright © 2013 Elsevier B.V. All rights reserved.

Robotic sampling system for an unmanned Mars mission

NASA Technical Reports Server (NTRS)

Chun, Wendell

1989-01-01

A major robotics opportunity for NASA will be the Mars Rover/Sample Return Mission which could be launched as early as the 1990s. The exploratory portion of this mission will include two autonomous subsystems: the rover vehicle and a sample handling system. The sample handling system is the key to the process of collecting Martian soils. This system could include a core drill, a general-purpose manipulator, tools, containers, a return canister, certification hardware and a labeling system. Integrated into a functional package, the sample handling system is analogous to a complex robotic workcell. Discussed here are the different components of the system, their interfaces, forseeable problem areas and many options based on the scientific goals of the mission. The various interfaces in the sample handling process (component to component and handling system to rover) will be a major engineering effort. Two critical evaluation criteria that will be imposed on the system are flexibility and reliability. It needs to be flexible enough to adapt to different scenarios and environments and acquire the most desirable specimens for return to Earth. Scientists may decide to change the distribution and ratio of core samples to rock samples in the canister. The long distance and duration of this planetary mission places a reliability burden on the hardware. The communication time delay between Earth and Mars minimizes operator interaction (teleoperation, supervisory modes) with the sample handler. An intelligent system will be required to plan the actions, make sample choices, interpret sensor inputs, and query unknown surroundings. A combination of autonomous functions and supervised movements will be integrated into the sample handling system.

Baseline integrated behavioural and biological assessment among most at-risk populations in six high-prevalence states of India: design and implementation challenges.

PubMed

Saidel, Tobi; Adhikary, Rajatashuvra; Mainkar, Mandar; Dale, Jayesh; Loo, Virginia; Rahman, Motiur; Ramesh, Banadakoppa M; Paranjape, Ramesh S

2008-12-01

This paper presents key methodological approaches and challenges in implementing and analysing the first round of the integrated biobehavioural assessment of most-at-risk populations, conducted in conjunction with evaluation of Avahan, the India AIDS initiative. The survey collected data on HIV risk behaviours, sexually transmitted infections and HIV prevalence in 29 districts in six high-prevalence states of India. Groups included female sex workers and clients, men who have sex with men, injecting drug users and truck drivers. Strategies for overcoming some challenges of the large-scale surveys among vulnerable populations, including sampling hidden populations, involvement of the communities targeted by the survey, laboratory and quality control in remote, non-clinic field settings, and data analysis and data use are presented. Satisfying the need for protocols, guidelines and tools that allowed for sufficient standardization, while being tailored enough to fit diverse local situations on such a large scale, with so many implementing partners, emerged as a major management challenge. A major lesson from the first round is the vital importance of investing upfront time in tailoring the sampling methods, data collection instruments, and analysis plan to match measurement objectives. Despite the challenges, the integrated biobehavioural assessment was a huge achievement, and was largely successful in providing previously unavailable information about the HIV situation among populations that are critical to the curtailment of HIV spread in India. Lessons from the first round will be used to evolve the second round into an exercise with increased evaluative capability for Avahan.

Current dichotomy between traditional molecular biological and omic research in cancer biology and pharmacology.

PubMed

Reinhold, William C

2015-12-10

There is currently a split within the cancer research community between traditional molecular biological hypothesis-driven and the more recent "omic" forms or research. While the molecular biological approach employs the tried and true single alteration-single response formulations of experimentation, the omic employs broad-based assay or sample collection approaches that generate large volumes of data. How to integrate the benefits of these two approaches in an efficient and productive fashion remains an outstanding issue. Ideally, one would merge the understandability, exactness, simplicity, and testability of the molecular biological approach, with the larger amounts of data, simultaneous consideration of multiple alterations, consideration of genes both of known interest along with the novel, cross-sample comparisons among cell lines and patient samples, and consideration of directed questions while simultaneously gaining exposure to the novel provided by the omic approach. While at the current time integration of the two disciplines remains problematic, attempts to do so are ongoing, and will be necessary for the understanding of the large cell line screens including the Developmental Therapeutics Program's NCI-60, the Broad Institute's Cancer Cell Line Encyclopedia, and the Wellcome Trust Sanger Institute's Cancer Genome Project, as well as the the Cancer Genome Atlas clinical samples project. Going forward there is significant benefit to be had from the integration of the molecular biological and the omic forms or research, with the desired goal being improved translational understanding and application.

An integrated and accessible sample data library for Mars sample return science

NASA Astrophysics Data System (ADS)

Tuite, M. L., Jr.; Williford, K. H.

2015-12-01

Over the course of the next decade or more, many thousands of geological samples will be collected and analyzed in a variety of ways by researchers at the Jet Propulsion Laboratory (California Institute of Technology) in order to facilitate discovery and contextualize observations made of Mars rocks both in situ and here on Earth if samples are eventually returned. Integration of data from multiple analyses of samples including petrography, thin section and SEM imaging, isotope and organic geochemistry, XRF, XRD, and Raman spectrometry is a challenge and a potential obstacle to discoveries that require supporting lines of evidence. We report the development of a web-accessible repository, the Sample Data Library (SDL) for the sample-based data that are generated by the laboratories and instruments that comprise JPL's Center for Analysis of Returned Samples (CARS) in order to facilitate collaborative interpretation of potential biosignatures in Mars-analog geological samples. The SDL is constructed using low-cost, open-standards-based Amazon Web Services (AWS), including web-accessible storage, relational data base services, and a virtual web server. The data structure is sample-centered with a shared registry for assigning unique identifiers to all samples including International Geo-Sample Numbers. Both raw and derived data produced by instruments and post-processing workflows are automatically uploaded to online storage and linked via the unique identifiers. Through the web interface, users are able to find all the analyses associated with a single sample or search across features shared by multiple samples, sample localities, and analysis types. Planned features include more sophisticated search and analytical interfaces as well as data discoverability through NSF's EarthCube program.

Isotopic change in the tissues of Bothrops atrox in captivity collected from environments of the eastern Amazon

NASA Astrophysics Data System (ADS)

Martinez, M. G.; Chalkidis, H. D.; Amazonas, D. R.; da Silva, A. M.; De Oliveira, R., Jr.; Camargo, P. B.

2013-12-01

The Bothrops atrox is little studied because it is sympatric Amazonian animals, and very little is known about the ecology and natural history of this species. It has a generalist diet and the distribution of this species is very wide. The adult animals forage mostly on the ground, while the younger animals prefer to stay on the vegetation. They are easily find in the rainy months in areas near lakes and seasonally flooded and are difficult to find in the driest months, a period where there is less availability of preys in these environments. Due to its aggressiveness, is considered one of the most feared snakes in South America and in the eastern Amazon, being responsible for the largest number of snakebites in the region. Through stable isotope carbon-13 and nitrogen-15, is intended to characterize the variations of the feeding habits of these collected animals in different environments and also when they are kept in captivity, feeding the animal's bioterium. The serpents were collected in environments with different land uses, such as native forest, savannah, pasture and have been brought to the serpentarium Integrated College Tapajos (FIT), being retained in order to Samplings throughout the experiment with feeding mice's own bioterium. When these snakes came from different locations, samples were collected scales and blood (T0), before receiving the new supply (captive), and every time we fed the mice the vivarium, new tissue samples were collected, (T1, T2, T3) to exchange all the nature of food for the food captivity.Based on the results of δ13C and δ15N, the samples collected in the tissues of snakes of different environments (nature and captivity), it was observed that changes in food sources reflect changes in tissues (blood and scales), also reflecting the production of poison different periods of turnover of absorbed material in those tissues, contributing to the study of animal ecology and behavior in relation to habitat.

Airborne pesticide residues along the Mississippi River

USGS Publications Warehouse

Majewski, M.S.; Foreman, W.T.; Goolsbys, D.A.; Nakagaki, N.

1998-01-01

The occurrence, concentration, and geographical distribution of agricultural pesticides were determined in air over the Mississippi River from New Orleans, LA, to St. Paul, MN, during the first 10 days of June 1994. Air samples were collected from a research vessel by pulling air through polyurethane foam plugs at about 100 L/min for up to 24 h. Each sample was analyzed for 42 pesticides and 3 pesticide transformation products. Twenty- five compounds-15 herbicides, 7 insecticides, and 3 pesticide transformation products-were detected in one or more samples with concentrations ranging from 0.05 to 80 ng/m3. Alachlor, chlorpyrifos, diazinon, fonofos, malathion, methyl parathion, metolachlor, metribuzin, pendimethalin, and trifluralin were detected in 80% or more of the samples. The highest concentrations for chlorpyrifos (1.6 ng/m3), diazinon (0.36 ng/m3), and malathion (4.6 ng/m3) all occurred near major metropolitan areas. These samples represent a 'snapshot in time', a spatial and temporal integration of which pesticides were present in the air during each sampling period. The occurrence and atmospheric concentrations of the observed pesticides were most closely related to their use on cropland within 40 km of the river.The occurrence, concentration, and geographical distribution of agricultural pesticides were determined in air over the Mississippi River from New Orleans, LA, to St. Paul, MN, during the first 10 days of June 1994. Air samples were collected from a research vessel by pulling air through polyurethane foam plugs at about 100 L/min for up to 24 h. Each sample was analyzed for 42 pesticides and 3 pesticide transformation products. Twenty-five compounds-15 herbicides, 7 insecticides, and 3 pesticide transformation products-were detected in one or more samples with concentrations ranging from 0.05 to 80 ng/m3. Alachlor, chlorpyrifos, diazinon, fonofos, malathion, methyl parathion, metolachlor, metribuzin, pendimethalin, and trifluralin were detected in 80% or more of the samples. The highest concentrations for chlorpyrifos (1.6 ng/m3), diazinon (0.36 ng/m3), and malathion (4.6 ng/m3) all occurred near major metropolitan areas. These samples represent a 'snapshot in time', a spatial and temporal integration of which pesticides were present in the air during each sampling period. The occurrence and atmospheric concentrations of the observed pesticides were most closely related to their use on cropland within 40 km of the river.

Large Scale Environmental Monitoring through Integration of Sensor and Mesh Networks

PubMed Central

Jurdak, Raja; Nafaa, Abdelhamid; Barbirato, Alessio

2008-01-01

Monitoring outdoor environments through networks of wireless sensors has received interest for collecting physical and chemical samples at high spatial and temporal scales. A central challenge to environmental monitoring applications of sensor networks is the short communication range of the sensor nodes, which increases the complexity and cost of monitoring commodities that are located in geographically spread areas. To address this issue, we propose a new communication architecture that integrates sensor networks with medium range wireless mesh networks, and provides users with an advanced web portal for managing sensed information in an integrated manner. Our architecture adopts a holistic approach targeted at improving the user experience by optimizing the system performance for handling data that originates at the sensors, traverses the mesh network, and resides at the server for user consumption. This holistic approach enables users to set high level policies that can adapt the resolution of information collected at the sensors, set the preferred performance targets for their application, and run a wide range of queries and analysis on both real-time and historical data. All system components and processes will be described in this paper. PMID:27873941

Mineralogical, Chemical, and Optical Interrelationships of Airborne Mineral Dusts

NASA Astrophysics Data System (ADS)

Engelbrecht, J. P.; Moosmuller, H.; Pincock, S. L.; Jayanty, R. K. M.; Casuccio, G.

2014-12-01

The purpose of the project was to provide information on the mineralogical, chemical and physical interrelationships of re-suspended mineral dust samples collected as grab samples from global dust sources. Surface soil samples were collected from about 65 desert sites, including the southwestern USA (12), Mali (3), Chad (3), Morocco (1), Canary Islands (8), Cape Verde (1), Djibouti (1), Afghanistan (3), Iraq (6), Kuwait (5), Qatar (1), UAE (1), Serbia (3), China (5), Namibia (3), Botswana (4), Australia (3), and Chile (1). The < 38 μm sieved fraction of each sample was re-suspended in an entrainment chamber, from which the airborne mineral dust could be monitored, sampled and analyzed. Instruments integrated into the entrainment facility included two PM10 and two PM2.5 filter samplers, a beta attenuation gauge for the continuous measurement of PM10 and PM2.5 particulate mass fractions, an aerodynamic particle size (APS) analyzer, and a three wavelength (405, 532, 781nm) photoacoustic resonator with integrating reciprocal nephelometer for monitoring absorption and scattering coefficients during the dust re-suspension process. Filter sample media included Teflon® membrane and quartz fiber filters for chemical analysis (71 species), and Nuclepore® filters for individual particle analysis by Scanning Electron Microscopy (SEM). The < 38 μm sieved fractions were also analyzed by X-ray diffraction for their mineral content while the > 38 μm, < 125 μm soil fractions were mineralogically characterized by optical microscopy. We will be presenting results on the optical measurements, also showing the relationship between single scattering albedo (SSA) at three different wavelengths, and chemical as well as mineralogical content and interdependencies of the entrained dust samples. Examples showing the relationships between the single scattering albedos of airborne dusts, and iron (Fe) in hematite, goethite, and clay minerals (montmorillonite, illite, palygorskite), will be discussed. Differences between the clay minerals in samples from Mali and those from other localities are demonstrated. We intend establishing a data base for applications in climate modeling, remote sensing, visibility, health (medical geology), ocean fertilization, and damage to equipment.

Comparison of solar system measured data for various sample rates. [conducted using Marshall Space Flight Center Solar House

NASA Technical Reports Server (NTRS)

Chiou, J., Sr.

1977-01-01

The results of solar house data for sample rates of 50, 100, 250, 300, and 600 seconds were compared. The data considered for summer days were the heat incident on the collectors, the heat used by the air conditioner generator, and the heat used by the auxiliary heater. For winter days, the heat incident, the heat collected and the heat used by the heat exchanger were computed. These data were compared for different weather days such as clear days, partly cloudy days, cloudy days, and very cloudy days. Also, data for the integration of all these weather days were compared. The precentage differences for these data, using 50 second sample rate as a base, are also presented.

Nevada Applied Ecology Group procedures handbook for environmental transuranics

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

White, M.G.; Dunaway, P.B.

The activities of the Nevada Applied Ecology Group (NAEG) integrated research studies of environmental plutonium and other transuranics at the Nevada Test Site have required many standardized field and laboratory procedures. These include sampling techniques, collection and preparation, radiochemical and wet chemistry analysis, data bank storage and reporting, and statistical considerations for environmental samples of soil, vegetation, resuspended particles, animals, and others. This document, printed in two volumes, includes most of the Nevada Applied Ecology Group standard procedures, with explanations as to the specific applications involved in the environmental studies. Where there is more than one document concerning a procedure,more » it has been included to indicate special studies or applications perhaps more complex than the routine standard sampling procedures utilized.« less

Nevada Applied Ecology Group procedures handbook for environmental transuranics

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

White, M.G.; Dunaway, P.B.

The activities of the Nevada Applied Ecology Group (NAEG) integrated research studies of environmental plutonium and other transuranics at the Nevada Test Site have required many standardized field and laboratory procedures. These include sampling techniques, collection and preparation, radiochemical and wet chemistry analysis, data bank storage and reporting, and statistical considerations for environmental samples of soil, vegetation, resuspended particles, animals, and other biological material. This document, printed in two volumes, includes most of the Nevada Applied Ecology Group standard procedures, with explanations as to the specific applications involved in the environmental studies. Where there is more than one document concerningmore » a procedure, it has been included to indicate special studies or applications more complex than the routine standard sampling procedures utilized.« less

The Delaware Bay Estuary as a Classroom: A Research Experience for Future Elementary Grade-Level Teachers

NASA Astrophysics Data System (ADS)

Madsen, J.; Fifield, S.; Allen, D.; Shipman, H.; Ford, D.; Dagher, Z.; Brickhouse, N.

2004-05-01

With supplemental funding from the National Science Foundation (NSF), students from the University of Delaware's Science Semester course took part in a two-day research cruise in the Delaware Bay Estuary. The Science Semester, an NSF-funded project, is an integrated 15-credit sequence that encompasses the entire course work for the spring semester for approximately 60 sophomore-level elementary education majors. The semester includes the earth, life, and physical science content courses and the education science methods course integrated into one curriculum. In this curriculum, problem-based learning and other inquiry-based approaches are applied to foster integrated understandings of science and pedagogy that future elementary teachers need to effectively use inquiry-based approaches in their classrooms. The research cruise was conducted as part of one of the four major investigations during the course. The investigation focused on Delaware's state marine animal, Limulus polyphemus. It is one of the four remaining species of horseshoe crabs; the largest spawning population of Limulus is found in Delaware Bay. Within the problem- and inquiry-based learning approaches of the Science Semester course, the students became aware that very little data exists on the benthic habitat of Limulus polyphemus. In order to learn more about this habitat, a cohort of seven students from the course was recruited as part of the scientific party to take part in the research cruise to collect data on the floor of Delaware Bay. The data included: multibeam bathymetry/backscatter data, grab samples of bay bottom sediments, and CTD profiles. Prior to the cruise, all students in the course took part in laboratory exercises to learn about topographic maps and navigation charts using the Delaware Bay area as the region of study. While "at-sea", the cruise participants sent the ship's latitude and longitude positions as a function of time. The positions were used by the on-land students to investigate motion and data representation (e.g., distance vs. time, velocity vs. time plots). After the at-sea experience, and using the data collected, all of the students plotted the sampling locations on their navigation charts and examined and quantitatively described the bottom sediments collected with the grab samples. The CTD data were used to investigate solutions, salinity, and conductivity. The ability to participate in, and use the data collected from, the two-day cruise provided an excellent opportunity for these future elementary teachers to experience real-time scientific research. The students onboard the ship were able to observe, and more importantly, engage in the collection of data from an oceanographic research vessel. All of the students in the course through hands-on laboratory exercises were able to see the link between data collection and analysis and its subsequent interpretation within the scope of a real scientific problem, namely the study of the benthic habitat of an important marine animal.

Macro to microfluidics system for biological environmental monitoring.

PubMed

Delattre, Cyril; Allier, Cédric P; Fouillet, Yves; Jary, Dorothée; Bottausci, Frederic; Bouvier, Denis; Delapierre, Guillaume; Quinaud, Manuelle; Rival, Arnaud; Davoust, Laurent; Peponnet, Christine

2012-01-01

Biological environmental monitoring (BEM) is a growing field of research which challenges both microfluidics and system automation. The aim is to develop a transportable system with analysis throughput which satisfies the requirements: (i) fully autonomous, (ii) complete protocol integration from sample collection to final analysis, (iii) detection of diluted molecules or biological species in a large real life environmental sample volume, (iv) robustness and (v) flexibility and versatility. This paper discusses all these specifications in order to define an original fluidic architecture based on three connected modules, a sampling module, a sample preparation module and a detection module. The sample preparation module highly concentrates on the pathogens present in a few mL samples of complex and unknown solutions and purifies the pathogens' nucleic acids into a few μL of a controlled buffer. To do so, a two-step concentration protocol based on magnetic beads is automated in a reusable macro-to-micro fluidic system. The detection module is a PCR based miniaturized platform using digital microfluidics, where reactions are performed in 64 nL droplets handled by electrowetting on dielectric (EWOD) actuation. The design and manufacture of the two modules are reported as well as their respective performances. To demonstrate the integration of the complete protocol in the same system, first results of pathogen detection are shown. Copyright © 2012 Elsevier B.V. All rights reserved.

Effect of cooling rate on sperm quality of cryopreserved Andalusian donkey spermatozoa.

PubMed

Demyda-Peyrás, S; Bottrel, M; Acha, D; Ortiz, I; Hidalgo, M; Carrasco, J J; Gómez-Arrones, V; Gósalvez, J; Dorado, J

2018-06-01

The aim of this study was to evaluate the effect of different cooling rates on post-thaw quality of cryopreserved donkey spermatozoa. Eighteen ejaculates from six adult Andalusian donkeys (three ejaculates per donkey) were collected using an artificial vagina. Pooled semen samples (two ejaculates per pool) were divided into three aliquots, and frozen in Gent freezing extender using three different cryopreservation protocols (P): P1 (conventional slow freezing, as control): semen pre-cooled in an Equitainer for 2 h and frozen in liquid nitrogen (LN 2 ) vapour; P2 (controlled pre-freeze cooling rate): semen pre-cooled at a controlled rate for 73 min and frozen in LN 2 vapour; and P3 (rapid freezing) semen frozen immediately in LN 2 vapour. After thawing at 37 °C for 30 s, semen samples were assessed for motility, morphology, acrosome and plasma membrane integrity; spermatozoa were also tested for DNA integrity. Significant (P < 0.01) differences were found between the cryopreservation protocols for all sperm parameters evaluated, except for DNA integrity. Semen samples frozen using P2 showed significantly (P < 0.01) higher values for sperm motility, morphology, sperm membrane integrity, and acrosome integrity. On the contrary, P3 reduced sperm motility (P < 0.01) and increased the percentage of spermatozoa with damaged plasma membrane (P < 0.001). In our study, we demonstrated that the sperm of Andalusian donkey is particularly sensitive to the cooling rate used before freezing. Furthermore, Andalusian donkey semen can be successfully cryopreserved using controlled cooling rates combined with freezing in LN 2 vapour. Copyright © 2018 Elsevier B.V. All rights reserved.

Integrated species distribution models: combining presence-background data and site-occupancy data with imperfect detection

USGS Publications Warehouse

Koshkina, Vira; Wang, Yang; Gordon, Ascelin; Dorazio, Robert; White, Matthew; Stone, Lewi

2017-01-01

Two main sources of data for species distribution models (SDMs) are site-occupancy (SO) data from planned surveys, and presence-background (PB) data from opportunistic surveys and other sources. SO surveys give high quality data about presences and absences of the species in a particular area. However, due to their high cost, they often cover a smaller area relative to PB data, and are usually not representative of the geographic range of a species. In contrast, PB data is plentiful, covers a larger area, but is less reliable due to the lack of information on species absences, and is usually characterised by biased sampling. Here we present a new approach for species distribution modelling that integrates these two data types.We have used an inhomogeneous Poisson point process as the basis for constructing an integrated SDM that fits both PB and SO data simultaneously. It is the first implementation of an Integrated SO–PB Model which uses repeated survey occupancy data and also incorporates detection probability.The Integrated Model's performance was evaluated, using simulated data and compared to approaches using PB or SO data alone. It was found to be superior, improving the predictions of species spatial distributions, even when SO data is sparse and collected in a limited area. The Integrated Model was also found effective when environmental covariates were significantly correlated. Our method was demonstrated with real SO and PB data for the Yellow-bellied glider (Petaurus australis) in south-eastern Australia, with the predictive performance of the Integrated Model again found to be superior.PB models are known to produce biased estimates of species occupancy or abundance. The small sample size of SO datasets often results in poor out-of-sample predictions. Integrated models combine data from these two sources, providing superior predictions of species abundance compared to using either data source alone. Unlike conventional SDMs which have restrictive scale-dependence in their predictions, our Integrated Model is based on a point process model and has no such scale-dependency. It may be used for predictions of abundance at any spatial-scale while still maintaining the underlying relationship between abundance and area.

Planetary Sample Caching System Design Options

NASA Technical Reports Server (NTRS)

Collins, Curtis; Younse, Paulo; Backes, Paul

2009-01-01

Potential Mars Sample Return missions would aspire to collect small core and regolith samples using a rover with a sample acquisition tool and sample caching system. Samples would need to be stored in individual sealed tubes in a canister that could be transfered to a Mars ascent vehicle and returned to Earth. A sample handling, encapsulation and containerization system (SHEC) has been developed as part of an integrated system for acquiring and storing core samples for application to future potential MSR and other potential sample return missions. Requirements and design options for the SHEC system were studied and a recommended design concept developed. Two families of solutions were explored: 1)transfer of a raw sample from the tool to the SHEC subsystem and 2)transfer of a tube containing the sample to the SHEC subsystem. The recommended design utilizes sample tool bit change out as the mechanism for transferring tubes to and samples in tubes from the tool. The SHEC subsystem design, called the Bit Changeout Caching(BiCC) design, is intended for operations on a MER class rover.

Development of an optical fiber SERS microprobe for minimally invasive sensing applications

NASA Astrophysics Data System (ADS)

Mamun, Md Abdullah Al; Juodkazis, Saulius; Mahadevan-Jansen, Anita; Stoddart, Paul R.

2018-02-01

Numerous potential biomedical sensing applications of surface-enhanced Raman scattering (SERS) have been reported, but its practical use has been limited by the lack of a robust sensing platform. Optical fiber SERS probes show great promise, but are limited by the prominent silica Raman background, which requires the use of bulky optics for filtering the signal collection and excitation delivery paths. In the present study, a SERS microprobe has been designed and developed to eliminate the bottlenecks outlined above. For efficient excitation and delivery of the SERS signal, both hollow core photonic crystal fiber and double clad fiber have been investigated. While the hollow core fiber was still found to have excessive silica background, the double clad fiber allows efficient signal collection via the multi-mode inner cladding. A micro filtering mechanism has been designed, which can be integrated into the tip of the optical fiber SERS probe, providing filtering to suppress silica Raman background and thus avoiding the need for bulky optics. The design also assists in the efficient collection of SERS signal from the sample by rejecting Rayleigh scattered light from the sample. Optical fiber cleaving using ultra-short laser pulses was tested for improved control of the fiber tip geometry. With this miniaturized and integrated filtering mechanism, it is expected that the developed probe will promote the use of SERS for minimally invasive biomedical monitoring and sensing applications in future. The probe could potentially be placed inside a small gauge hypodermic needle and would be compatible with handheld portable spectrometers.

High-Flow-Rate Impinger for the Study of Concentration, Viability, Metabolic Activity, and Ice-Nucleation Activity of Airborne Bacteria.

PubMed

Šantl-Temkiv, Tina; Amato, Pierre; Gosewinkel, Ulrich; Thyrhaug, Runar; Charton, Anaïs; Chicot, Benjamin; Finster, Kai; Bratbak, Gunnar; Löndahl, Jakob

2017-10-03

The study of airborne bacteria relies on a sampling strategy that preserves their integrity and in situ physiological state, e.g. viability, cultivability, metabolic activity, and ice-nucleation activity. Because ambient air harbors low concentrations of bacteria, an effective bioaerosol sampler should have a high sampling efficiency and a high airflow. We characterize a high-flow-rate impinger with respect to particle collection and retention efficiencies in the range 0.5-3.0 μm, and we investigated its ability to preserve the physiological state of selected bacterial species and seawater bacterial community in comparison with four commercial bioaerosol samplers. The collection efficiency increased with particle size and the cutoff diameter was between 0.5 and 1 μm. During sampling periods of 120-300 min, the impinger retained the cultivability, metabolic activity, viability, and ice-nucleation activity of investigated bacteria. Field studies in semiurban, high-altitude, and polar environments included periods of low bacterial air concentrations, thus demonstrating the benefits of the impinger's high flow rate. In conclusion, the impinger described here has many advantages compared with other bioaerosol samplers currently on the market: a potential for long sampling time, a high flow rate, a high sampling and retention efficiency, low costs, and applicability for diverse downstream microbiological and molecular analyses.

A straightforward experimental method to evaluate the Lamb-Mössbauer factor of a 57Co/Rh source

NASA Astrophysics Data System (ADS)

Spina, G.; Lantieri, M.

2014-01-01

In analyzing Mössbauer spectra by means of the integral transmission function, a correct evaluation of the recoilless fs factor of the source at the position of the sample is needed. A novel method to evaluate fs for a 57Co source is proposed. The method uses the standard transmission experimental set up and it does not need further measurements but the ones that are mandatory in order to center the Mössbauer line and to calibrate the Mössbauer transducer. Firstly, the background counts are evaluated by collecting a standard Multi Channel Scaling (MCS) spectrum of a tick metal iron foil absorber and two Pulse Height Analysis (PHA) spectra with the same life-time and setting the maximum velocity of the transducer at the same value of the MCS spectrum. Secondly, fs is evaluated by fitting the collected MCS spectrum throughout the integral transmission approach. A test of the suitability of the technique is presented, too.

Comprehensive outsourcing biobanking facility to serve the international research community.

PubMed

Diaferia, Giuseppe R; Biunno, Ida; DeBlasio, Pasquale

2011-06-01

The validity of results from biomarker studies using archived specimens depends on the integrity of the specimens and the manner in which they are collected, processed, and stored. The management of a huge amount of biomaterial generated from research studies and clinical trials is becoming a very demanding task and many organizations are facing the choice between in-house storage and processing and outsourcing some activities. Storage and logistic functions are the prime targets for outsourcing, because to sustain these critical assets organizations must have the expertise, the dedicated qualified personnel, the proper quality control programs, and available resources to fulfill the mandatory requirements to maintain the integrity of the samples. External biobanks are dedicated and certified infrastructures (ISO, GMP, etc.) that apply efficient logistic and shipping activities, use validated standard operating procedures, install appropriate monitoring back-up systems, and, most of all, have room for expansion. Thus, the choice between in-house biobanking and outsourcing cannot be exclusively based on a financial decision; it must also consider (i) type of collection/project, (ii) logistic complexity (number and locations of collection sites), (iii) safety requirements, (iv) functional expertise, and (v) business priorities.

Impact of sampling techniques on measured stormwater quality data for small streams

USGS Publications Warehouse

Harmel, R.D.; Slade, R.M.; Haney, R.L.

2010-01-01

Science-based sampling methodologies are needed to enhance water quality characterization for setting appropriate water quality standards, developing Total Maximum Daily Loads, and managing nonpoint source pollution. Storm event sampling, which is vital for adequate assessment of water quality in small (wadeable) streams, is typically conducted by manual grab or integrated sampling or with an automated sampler. Although it is typically assumed that samples from a single point adequately represent mean cross-sectional concentrations, especially for dissolved constituents, this assumption of well-mixed conditions has received limited evaluation. Similarly, the impact of temporal (within-storm) concentration variability is rarely considered. Therefore, this study evaluated differences in stormwater quality measured in small streams with several common sampling techniques, which in essence evaluated within-channel and within-storm concentration variability. Constituent concentrations from manual grab samples and from integrated samples were compared for 31 events, then concentrations were also compared for seven events with automated sample collection. Comparison of sampling techniques indicated varying degrees of concentration variability within channel cross sections for both dissolved and particulate constituents, which is contrary to common assumptions of substantial variability in particulate concentrations and of minimal variability in dissolved concentrations. Results also indicated the potential for substantial within-storm (temporal) concentration variability for both dissolved and particulate constituents. Thus, failing to account for potential cross-sectional and temporal concentration variability in stormwater monitoring projects can introduce additional uncertainty in measured water quality data. Copyright ?? 2010 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

Integrative Lifecourse and Genetic Analysis of Military Working Dogs

DTIC Science & Technology

2013-10-01

Working Dogs 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-11-2-0225 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) C. Guillermo Couto, DVM, Diplomate...protocol for the collection of biological samples and Lackland veterinary approval was granted ; and final Lackland AFB oversight approval was granted and...those documents were submitted to DoD CDMRP grant administration. Currently, there is one final approval from ACURO pending (and expected

Integrative Lifecourse and Genetic Analysis of Military Working Dogs

DTIC Science & Technology

2013-10-01

Working Dogs 5b. GRANT NUMBER W81XWH-11-2-0226 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Dr. Kun Huang 5d. PROJECT NUMBER 5e. TASK...we submitted final revisions on our IACUC protocol for the collection of biological samples and Lackland veterinary approval was granted ; and...final Lackland AFB oversight approval was granted and those documents were submitted to DoD CDMRP grant administration. Currently, there is one final

A system architecture for online data interpretation and reduction in fluorescence microscopy

NASA Astrophysics Data System (ADS)

Röder, Thorsten; Geisbauer, Matthias; Chen, Yang; Knoll, Alois; Uhl, Rainer

2010-01-01

In this paper we present a high-throughput sample screening system that enables real-time data analysis and reduction for live cell analysis using fluorescence microscopy. We propose a novel system architecture capable of analyzing a large amount of samples during the experiment and thus greatly minimizing the post-analysis phase that is the common practice today. By utilizing data reduction algorithms, relevant information of the target cells is extracted from the online collected data stream, and then used to adjust the experiment parameters in real-time, allowing the system to dynamically react on changing sample properties and to control the microscope setup accordingly. The proposed system consists of an integrated DSP-FPGA hybrid solution to ensure the required real-time constraints, to execute efficiently the underlying computer vision algorithms and to close the perception-action loop. We demonstrate our approach by addressing the selective imaging of cells with a particular combination of markers. With this novel closed-loop system the amount of superfluous collected data is minimized, while at the same time the information entropy increases.

Versatile combustion-amalgamation technique for the photometric determination of mercury in fish and environmental samples

USGS Publications Warehouse

Willford, Wayne A.; Hesselberg, Robert J.; Bergman, Harold L.

1973-01-01

Total mercury in a variety of substances is determined rapidly and precisely by direct sample combustion, collection of released mercury by amalgamation, and photometric measurement of mercury volatilized from the heated amalgam. Up to 0.2 g fish tissue is heated in a stream of O2 (1.2 L/min) for 3.5 min in 1 tube of a 2-tube induction furnace. The released mercury vapor and combustion products are carried by the stream of O2 through a series of traps (6% NaOH scrubber, water condenser, and Mg(CIO4)2 drying tube) and the mercury is collected in a 10 mm diameter column of 24 gauge gold wire (8 g) cut into 3 mm lengths. The resulting amalgam is heated in the second tube of the induction furnace and the volatilized mercury is measured with a mercury vapor meter equipped with a recorder-integrator. Total analysis time is approximately 8 min/sample. The detection limit is less than 0.002 μg and the system is easily converted for use with other biological materials, water, and sediments.

Conservation science in a terrorist age: the impact of airport security screening on the viability and DNA integrity of frozen felid spermatozoa.

PubMed

Gloor, Kayleen T; Winget, Doug; Swanson, William F

2006-09-01

In response to growing terrorism concerns, the Transportation Security Administration now requires that all checked baggage at U.S. airports be scanned through a cabinet x-ray system, which may increase risk of radiation damage to transported biologic samples and other sensitive genetic material. The objective of this study was to investigate the effect of these new airport security regulations on the viability and DNA integrity of frozen felid spermatozoa. Semen was collected from two domestic cats (Felis silvestris catus) and one fishing cat (Prionailurus viverrinus), cryopreserved in plastic freezing straws, and transferred into liquid nitrogen dry shippers for security screening. Treatment groups included frozen samples from each male scanned once or three times using a Transportation Security Administration-operated cabinet x-ray system, in addition to non-scanned samples (i.e., negative control) and samples previously scanned three times and exposed to five additional high-intensity x-ray bursts (i.e., positive control). Dosimeters placed in empty dry shippers were used to quantify radiation exposure. Following treatment, straws were thawed and spermatozoa analyzed for post-thaw motility (percentage motile and rate of progressive movement), acrosome status, and DNA integrity using single-cell gel electrophoresis (i.e., the comet assay). Dosimeter measurements determined that each airport screening procedure produced approximately 16 mrem of radiation exposure. Our results indicated that all levels of radiation exposure adversely affected (P < 0.05) post-thaw sperm motility, but the percentage of acrosome-intact spermatozoa did not differ (P > 0.05) among treatment groups. Results also showed that the amount of double-stranded DNA damage was greater (P < 0.05) in sperm samples from both cat species scanned three times compared to samples scanned once or negative controls. Findings suggest that new airport security measures may cause radiation-induced damage to frozen spermatozoa and other valuable biologic samples transported on passenger aircraft and that alternative modes of sample transportation should be used whenever possible.

Analysis of Method TO-14 target analytes using a cryofocusing high-speed gas chromatograph interfaced to a high-speed time-of-flight mass spectrometer

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

Berkley, R.E.; Gardner, B.D.; Holland, J.F.

1997-12-31

A high-speed gas chromatograph coupled with a high-speed time-of-flight mass spectrometer was used to gain a six-fold increase in overall rate of analytical throughput for analysis of EPA Method TO-14 target compounds. Duration of chromatograms was 180 seconds. One hundred mass spectra per second, ranging from 35 to 270 mass units, were collected. Single ion chromatograms were searched at appropriate retention times for chromatographic peaks, which were integrated. Thirty-eight of the forty-one TO-14 target compounds were calibrated using standards at five concentrations from 2.5 to 40 ppb. Four grab samples of ambient air were collected at four different locations atmore » an automobile repair facility, and two grab samples were collected less than one minute apart at a site near a chemical plant, just before and just after passage of three large diesel trucks. All samples were analyzed on the same day they were collected. Most of the duplicate analyses were in close agreement. Ability of the high-speed TOF/GC/MS system to perform analyses of TO-14 target compounds rapidly and precisely was demonstrated. This paper has been reviewed according to US Environmental Protection Agency peer and administrative review policies and approved for presentation and publication. Mention of trade names or commercial products does not constitute endorsement or recommendation for use.« less

Working Up a Good Sweat – The Challenges of Standardising Sweat Collection for Metabolomics Analysis

PubMed Central

Hussain, Joy N; Mantri, Nitin; Cohen, Marc M

2017-01-01

Introduction Human sweat is a complex biofluid of interest to diverse scientific fields. Metabolomics analysis of sweat promises to improve screening, diagnosis and self-monitoring of numerous conditions through new applications and greater personalisation of medical interventions. Before these applications can be fully developed, existing methods for the collection, handling, processing and storage of human sweat need to be revised. This review presents a cross-disciplinary overview of the origins, composition, physical characteristics and functional roles of human sweat, and explores the factors involved in standardising sweat collection for metabolomics analysis. Methods A literature review of human sweat analysis over the past 10 years (2006–2016) was performed to identify studies with metabolomics or similarly applicable ‘omics’ analysis. These studies were reviewed with attention to sweat induction and sampling techniques, timing of sweat collection, sweat storage conditions, laboratory derivation, processing and analytical platforms. Results Comparative analysis of 20 studies revealed numerous factors that can significantly impact the validity, reliability and reproducibility of sweat analysis including: anatomical site of sweat sampling, skin integrity and preparation; temperature and humidity at the sweat collection sites; timing and nature of sweat collection; metabolic quenching; transport and storage; qualitative and quantitative measurements of the skin microbiota at sweat collection sites; and individual variables such as diet, emotional state, metabolic conditions, pharmaceutical, recreational drug and supplement use. Conclusion Further development of standard operating protocols for human sweat collection can open the way for sweat metabolomics to significantly add to our understanding of human physiology in health and disease. PMID:28798503

A Scanning Transmission Electron Microscopy Method for Determining Manganese Composition in Welding Fume as a Function of Primary Particle Size

PubMed Central

Richman, Julie D.; Livi, Kenneth J.T.; Geyh, Alison S.

2011-01-01

Increasing evidence suggests that the physicochemical properties of inhaled nanoparticles influence the resulting toxicokinetics and toxicodynamics. This report presents a method using scanning transmission electron microscopy (STEM) to measure the Mn content throughout the primary particle size distribution of welding fume particle samples collected on filters for application in exposure and health research. Dark field images were collected to assess the primary particle size distribution and energy-dispersive X-ray and electron energy loss spectroscopy were performed for measurement of Mn composition as a function of primary particle size. A manual method incorporating imaging software was used to measure the primary particle diameter and to select an integration region for compositional analysis within primary particles throughout the size range. To explore the variation in the developed metric, the method was applied to 10 gas metal arc welding (GMAW) fume particle samples of mild steel that were collected under a variety of conditions. The range of Mn composition by particle size was −0.10 to 0.19 %/nm, where a positive estimate indicates greater relative abundance of Mn increasing with primary particle size and a negative estimate conversely indicates decreasing Mn content with size. However, the estimate was only statistically significant (p<0.05) in half of the samples (n=5), which all had a positive estimate. In the remaining samples, no significant trend was measured. Our findings indicate that the method is reproducible and that differences in the abundance of Mn by primary particle size among welding fume samples can be detected. PMID:21625364

A Scanning Transmission Electron Microscopy Method for Determining Manganese Composition in Welding Fume as a Function of Primary Particle Size.

PubMed

Richman, Julie D; Livi, Kenneth J T; Geyh, Alison S

2011-06-01

Increasing evidence suggests that the physicochemical properties of inhaled nanoparticles influence the resulting toxicokinetics and toxicodynamics. This report presents a method using scanning transmission electron microscopy (STEM) to measure the Mn content throughout the primary particle size distribution of welding fume particle samples collected on filters for application in exposure and health research. Dark field images were collected to assess the primary particle size distribution and energy-dispersive X-ray and electron energy loss spectroscopy were performed for measurement of Mn composition as a function of primary particle size. A manual method incorporating imaging software was used to measure the primary particle diameter and to select an integration region for compositional analysis within primary particles throughout the size range. To explore the variation in the developed metric, the method was applied to 10 gas metal arc welding (GMAW) fume particle samples of mild steel that were collected under a variety of conditions. The range of Mn composition by particle size was -0.10 to 0.19 %/nm, where a positive estimate indicates greater relative abundance of Mn increasing with primary particle size and a negative estimate conversely indicates decreasing Mn content with size. However, the estimate was only statistically significant (p<0.05) in half of the samples (n=5), which all had a positive estimate. In the remaining samples, no significant trend was measured. Our findings indicate that the method is reproducible and that differences in the abundance of Mn by primary particle size among welding fume samples can be detected.

Molecular dynamics based enhanced sampling of collective variables with very large time steps.

PubMed

Chen, Pei-Yang; Tuckerman, Mark E

2018-01-14

Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.

Molecular dynamics based enhanced sampling of collective variables with very large time steps

NASA Astrophysics Data System (ADS)

Chen, Pei-Yang; Tuckerman, Mark E.

2018-01-01

Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.

The Index to Marine and Lacustrine Geological Samples (IMLGS): Linking Digital Data to Physical Samples for the Marine Community

NASA Astrophysics Data System (ADS)

Stroker, K. J.; Jencks, J. H.; Eakins, B.

2016-12-01

The Index to Marine and Lacustrine Geological Samples (IMLGS) is a community designed and maintained resource enabling researchers to locate and request seafloor and lakebed geologic samples curated by partner institutions. The Index was conceived in the dawn of the digital age by representatives from U.S. academic and government marine core repositories and the NOAA National Geophysical Data Center, now the National Centers for Environmental Information (NCEI), at a 1977 meeting convened by the National Science Foundation (NSF). The Index is based on core concepts of community oversight, common vocabularies, consistent metadata and a shared interface. The Curators Consortium, international in scope, meets biennially to share ideas and discuss best practices. NCEI serves the group by providing database access and maintenance, a list server, digitizing support and long-term archival of sample metadata, data and imagery. Over three decades, participating curators have performed the laborious task of creating and contributing metadata for over 205,000 sea floor and lake-bed cores, grabs, and dredges archived in their collections. Some partners use the Index for primary web access to their collections while others use it to increase exposure of more in-depth institutional systems. The IMLGS has a persistent URL/Digital Object Identifier (DOI), as well as DOIs assigned to partner collections for citation and to provide a persistent link to curator collections. The Index is currently a geospatially-enabled relational database, publicly accessible via Web Feature and Web Map Services, and text- and ArcGIS map-based web interfaces. To provide as much knowledge as possible about each sample, the Index includes curatorial contact information and links to related data, information and images : 1) at participating institutions, 2) in the NCEI archive, and 3) through a Linked Data interface maintained by the Rolling Deck to Repository R2R. Over 43,000 International GeoSample Numbers (IGSNs) linking to the System for Earth Sample Registration (SESAR) are included in anticipation of opportunities for interconnectivity with Integrated Earth Data Applications (IEDA) systems. The paper will discuss the database with a goal to increase the connections and links to related data at partner institutions.

Technical note: The development of a methodology for ruminal and colon tissue biopsying of young Holstein dairy calves.

PubMed

van Niekerk, J K; Middeldorp, M; Steele, M A

2018-05-09

The objectives of this study were to develop a methodology for biopsying the rumen and colon of young dairy calves and to collect suitable quality tissue samples for microscopic and gene expression analysis. Six Holstein dairy bull calves (45.0 ± 1.5 kg birth weight) were ruminally cannulated during the second week of life and weaned at the end of wk 6. Ruminal and colon tissue samples were collected at the end of wk 5, 6, 7, 8, and 12. Calves were not sedated but were restrained in a chute for sampling. The endoscope (100 cm length, 9.8 mm diameter) was introduced through the rumen cannula to harvest ruminal tissue. Endoscopic biopsies of the rumen with endoscopic biopsy forceps were unsuccessful 85% of the time because they were unable to shear the ruminal tissue. Thereafter, an Allis clamp was used to retrieve the blind sac through the rumen cannula to perform direct tissue biopsying with surgical scissors. To biopsy the colon, the lubricated distal tip of an endoscope was slowly inserted into the calf's anus. A total of 6 colon tissue samples (12.6 ± 0.74 mg) were collected per calf per time point from the distal colon 30 to 40 cm from the calf's anus using endoscopic biopsy forceps, which were inserted through the instrument channel. A new forcep was used between sites and calves. Between calves, the outside of the endoscope was washed with 4% chlorohexidine and rinsed with water and the instrument channel was washed with distilled water and 70% ethanol. Colon and ruminal samples were processed for histological measurements, and RNA was isolated and sequenced. High-quality RNA (RNA integrity number 8.8 ± 0.08) was collected from samples, and light and electron microscopy was performed on samples. In conclusion, endoscopic biopsying can be used for tissue harvest in the colon of young calves. However, it was found that collecting ruminal tissue by retracting the rumen from the cannula and taking samples with surgical scissors was more successful than an endoscopic biopsy. This method allows for tissue collection of the same animal throughout time, which can help the research community investigate the effect of weaning regimens, feed rations, and age on the structure and function of the gastrointestinal tract. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Workshop on New Views of the Moon: Integrated Remotely Sensed, Geophysical, and Sample Datasets

NASA Technical Reports Server (NTRS)

Jolliff, Brad L. (Editor); Ryder, Graham (Editor)

1998-01-01

It has been more than 25 years since Apollo 17 returned the last of the Apollo lunar samples. Since then, a vast amount of data has been obtained from the study of rocks and soils from the Apollo and Luna sample collections and, more recently, on a set of about a dozen lunar meteorites collected on Earth. Based on direct studies of the samples, many constraints have been established for the age, early differentiation, crust and mantle structure, and subsequent impact modification of the Moon. In addition, geophysical experiments at the surface, as well as remote sensing from orbit and Earth-based telescopic studies, have provided additional datasets about the Moon that constrain the nature of its surface and internal structure. Some might be tempted to say that we know all there is to know about the Moon and that it is time to move on from this simple satellite to more complex objects. However, the ongoing Lunar Prospector mission and the highly successful Clementine mission have provided important clues to the real geological complexity of the Moon, and have shown us that we still do not yet adequately understand the geologic history of Earth's companion. These missions, like Galileo during its lunar flyby, are providing global information viewed through new kinds of windows, and providing a fresh context for models of lunar origin, evolution, and resources, and perhaps even some grist for new questions and new hypotheses. The probable detection and characterization of water ice at the poles, the extreme concentration of Th and other radioactive elements in the Procellarum-Imbrium-Frigon's resurfaced areas of the nearside of the Moon, and the high-resolution gravity modeling enabled by these missions are examples of the kinds of exciting new results that must be integrated with the extant body of knowledge based on sample studies, in situ experiments, and remote-sensing missions to bring about the best possible understanding of the Moon and its history.

Knowledge exchange processes in organizations and policy arenas: a narrative systematic review of the literature.

PubMed

Contandriopoulos, Damien; Lemire, Marc; Denis, Jean-Louis; Tremblay, Emile

2010-12-01

This article presents the main results from a large-scale analytical systematic review on knowledge exchange interventions at the organizational and policymaking levels. The review integrated two broad traditions, one roughly focused on the use of social science research results and the other focused on policymaking and lobbying processes. Data collection was done using systematic snowball sampling. First, we used prospective snowballing to identify all documents citing any of a set of thirty-three seminal papers. This process identified 4,102 documents, 102 of which were retained for in-depth analysis. The bibliographies of these 102 documents were merged and used to identify retrospectively all articles cited five times or more and all books cited seven times or more. All together, 205 documents were analyzed. To develop an integrated model, the data were synthesized using an analytical approach. This article developed integrated conceptualizations of the forms of collective knowledge exchange systems, the nature of the knowledge exchanged, and the definition of collective-level use. This literature synthesis is organized around three dimensions of context: level of polarization (politics), cost-sharing equilibrium (economics), and institutionalized structures of communication (social structuring). The model developed here suggests that research is unlikely to provide context-independent evidence for the intrinsic efficacy of knowledge exchange strategies. To design a knowledge exchange intervention to maximize knowledge use, a detailed analysis of the context could use the kind of framework developed here. © 2010 Milbank Memorial Fund. Published by Wiley Periodicals Inc.

Knowledge Exchange Processes in Organizations and Policy Arenas: A Narrative Systematic Review of the Literature

PubMed Central

Contandriopoulos, Damien; Lemire, Marc; Denis, Jean-Louis; Tremblay, Émile

2010-01-01

Context: This article presents the main results from a large-scale analytical systematic review on knowledge exchange interventions at the organizational and policymaking levels. The review integrated two broad traditions, one roughly focused on the use of social science research results and the other focused on policymaking and lobbying processes. Methods: Data collection was done using systematic snowball sampling. First, we used prospective snowballing to identify all documents citing any of a set of thirty-three seminal papers. This process identified 4,102 documents, 102 of which were retained for in-depth analysis. The bibliographies of these 102 documents were merged and used to identify retrospectively all articles cited five times or more and all books cited seven times or more. All together, 205 documents were analyzed. To develop an integrated model, the data were synthesized using an analytical approach. Findings: This article developed integrated conceptualizations of the forms of collective knowledge exchange systems, the nature of the knowledge exchanged, and the definition of collective-level use. This literature synthesis is organized around three dimensions of context: level of polarization (politics), cost-sharing equilibrium (economics), and institutionalized structures of communication (social structuring). Conclusions: The model developed here suggests that research is unlikely to provide context-independent evidence for the intrinsic efficacy of knowledge exchange strategies. To design a knowledge exchange intervention to maximize knowledge use, a detailed analysis of the context could use the kind of framework developed here. PMID:21166865

Integrating field methodology and web-based data collection to assess the reliability of the Alcohol Use Disorders Identification Test (AUDIT).

PubMed

Celio, Mark A; Vetter-O'Hagen, Courtney S; Lisman, Stephen A; Johansen, Gerard E; Spear, Linda P

2011-12-01

Field methodologies offer a unique opportunity to collect ecologically valid data on alcohol use and its associated problems within natural drinking environments. However, limitations in follow-up data collection methods have left unanswered questions regarding the psychometric properties of field-based measures. The aim of the current study is to evaluate the reliability of self-report data collected in a naturally occurring environment - as indexed by the Alcohol Use Disorders Identification Test (AUDIT) - compared to self-report data obtained through an innovative web-based follow-up procedure. Individuals recruited outside of bars (N=170; mean age=21; range 18-32) provided a BAC sample and completed a self-administered survey packet that included the AUDIT. BAC feedback was provided anonymously through a dedicated web page. Upon sign in, follow-up participants (n=89; 52%) were again asked to complete the AUDIT before receiving their BAC feedback. Reliability analyses demonstrated that AUDIT scores - both continuous and dichotomized at the standard cut-point - were stable across field- and web-based administrations. These results suggest that self-report data obtained from acutely intoxicated individuals in naturally occurring environments are reliable when compared to web-based data obtained after a brief follow-up interval. Furthermore, the results demonstrate the feasibility, utility, and potential of integrating field methods and web-based data collection procedures. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Upsilon production cross section in pp collisions at √s=7  TeV

DOE PAGES

Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; ...

2011-06-15

The Υ(1S), Υ(2S), and Υ(3S) production cross sections in proton-proton collisions at √s=7 TeV are measured using a data sample collected with the CMS detector at the LHC, corresponding to an integrated luminosity of 3.1±0.3 pb⁻¹. Integrated over the rapidity range |y|<2, we find the product of the Υ(1S) production cross section and branching fraction to dimuons to be σ(pp→Υ(1S)X) · B(Υ(1S)→μ⁺μ⁻)=7.37±0.13 +0.61 -0.42±0.81 nb, where the first uncertainty is statistical, the second is systematic, and the third is associated with the estimation of the integrated luminosity of the data sample. This cross section is obtained assuming unpolarized Υ(1S) production.more » With the assumption of fully transverse or fully longitudinal production polarization, the measured cross section changes by about 20%. We also report the measurement of the Υ(1S), Υ(2S), and Υ(3S) differential cross sections as a function of transverse momentum and rapidity.« less

Chesapeake Bay Climate Study Partnership: Undergraduate Student Experiential Learning on Microclimates at the University of Hawai'i, Hilo

NASA Astrophysics Data System (ADS)

Ozbay, G.; Sriharan, S.; Fan, C.; Adolf, J.

2015-12-01

Undergraduate student experiential learning activities focused on microclimates of Hawai'i Island, Hawai'i. Six students from Virginia State University, three students from Delaware State University and faculty advisors were hosted by the University of Hawai'i at Hilo (UHH) Department of Marine Science. This partnership provided integrated, cohesive, and innovative education and research capabilities to minority students on climate change science. Activities included a summer course, instrumentation training, field and laboratory research training, sampling, data collection, logging, analysis, interpretation, report preparation, and research presentation. Most training activities used samples collected during students' field sampling in Hilo Bay. Water quality and phytoplankton data were collected along a 220 degree line transect from the mouth of the Wailuku River to the pelagic zone outside of Hilo Bay into the Pacific Ocean to a distance of 15.5 km. Water clarity, turbidity, chlorophyll, physical water quality parameters, and atmospheric CO2 levels were measured along the transect. Phytoplankton samples were collected for analysis by Scanning Electron Microscopy and Flow Cytometry. Data showed the extent of anthropogenic activity on water quality, with implications for food web dynamics. In addition, atmospheric CO2 concentration, island vegetation, and GPS points were recorded throughout the island of Hawai'i to investigate how variations in microclimate, elevation, and land development affect the amount of CO2 in the atmosphere, vegetation, and water quality. Water quality results at locations near rivers were completely different from other study sites, requiring students' critical thinking skills to find possible reasons for the difference. Our data show a correlation between population density and CO2 concentrations. Anthropogenic activities affecting CO2 and ocean conditions in Hawaiian microclimates can potentially have deleterious effects on the life that call these areas home.

Documenting of Geologic Field Activities in Real-Time in Four Dimensions: Apollo 17 as a Case Study for Terrestrial Analogues and Future Exploration

NASA Technical Reports Server (NTRS)

Feist, B.; Bleacher, J. E.; Petro, N. E.; Niles, P. B.

2018-01-01

During the Apollo exploration of the lunar surface, thousands of still images, 16 mm videos, TV footage, samples, and surface experiments were captured and collected. In addition, observations and descriptions of what was observed was radioed to Mission Control as part of standard communications and subsequently transcribed. The archive of this material represents perhaps the best recorded set of geologic field campaigns and will serve as the example of how to conduct field work on other planetary bodies for decades to come. However, that archive of material exists in disparate locations and formats with varying levels of completeness, making it not easily cross-referenceable. While video and audio exist for the missions, it is not time synchronized, and images taken during the missions are not time or location tagged. Sample data, while robust, is not easily available in a context of where the samples were collected, their descriptions by the astronauts are not connected to them, or the video footage of their collection (if available). A more than five year undertaking to reconstruct and reconcile the Apollo 17 mission archive, from launch through splashdown, has generated an integrated record of the entire mission, resulting in searchable, synchronized image, voice, and video data, with geologic context provided at the time each sample was collected. Through www.apollo17.org the documentation of the field investigation conducted by the Apollo 17 crew is presented in chronologic sequence, with additional context provided by high-resolution Lunar Reconnaissance Orbiter Camera (LROC) Narrow Angle Camera (NAC) images and a corresponding digital terrain model (DTM) of the Taurus-Littrow Valley.

A factorial design experiment as a pilot study for noninvasive genetic sampling.

PubMed

Renan, Sharon; Speyer, Edith; Shahar, Naama; Gueta, Tomer; Templeton, Alan R; Bar-David, Shirli

2012-11-01

Noninvasive genetic sampling has increasingly been used in ecological and conservation studies during the last decade. A major part of the noninvasive genetic literature is dedicated to the search for optimal protocols, by comparing different methods of collection, preservation and extraction of DNA from noninvasive materials. However, the lack of quantitative comparisons among these studies and the possibility that different methods are optimal for different systems make it difficult to decide which protocol to use. Moreover, most studies that have compared different methods focused on a single factor - collection, preservation or extraction - while there could be interactions between these factors. We designed a factorial experiment, as a pilot study, aimed at exploring the effect of several collection, preservation and extraction methods, and the interactions between them, on the quality and amplification success of DNA obtained from Asiatic wild ass (Equus hemionus) faeces in Israel. The amplification success rates of one mitochondrial DNA and four microsatellite markers differed substantially as a function of collection, preservation and extraction methods and their interactions. The most efficient combination for our system integrated the use of swabs as a collection method with preservation at -20 °C and with the Qiagen DNA Stool Kit with modifications as the DNA extraction method. The significant interaction found between the collection, preservation methods and the extraction methods reinforces the importance of conducting a factorial design experiment, rather than examining each factor separately, as a pilot study before initiating a full-scale noninvasive research project. © 2012 Blackwell Publishing Ltd.

76 FR 32367 - Agency Information Collection Activities, Proposed Collection; Comment Request; Integrated Public...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-06

...; Integrated Public Alert and Warning Systems (IPAWS) Inventory AGENCY: Federal Emergency Management Agency... proposed revision of the information collection concerning public alert and warning systems at the Federal... evaluation and assessment of existing public alert and warning resources and their integration with the...