An innovative approach to sampling complex industrial emissions for use in animal toxicity tests: application to iron casting operations.

PubMed

Palmer, W G; Scholz, R C; Moorman, W J

1983-03-01

Sampling of complex mixtures of airborne contaminants for chronic animal toxicity tests often involves numerous sampling devices, requires extensive sampling time, and yields forms of collected materials unsuitable for administration to animals. A method is described which used a high volume, wet venturi scrubber for collection of respirable fractions of emissions from iron foundry casting operations. The construction and operation of the sampler are presented along with collection efficiency data and its application to the preparation of large quantities of samples to be administered to animals by intratracheal instillation.

A high-throughput core sampling device for the evaluation of maize stalk composition

PubMed Central

2012-01-01

Background A major challenge in the identification and development of superior feedstocks for the production of second generation biofuels is the rapid assessment of biomass composition in a large number of samples. Currently, highly accurate and precise robotic analysis systems are available for the evaluation of biomass composition, on a large number of samples, with a variety of pretreatments. However, the lack of an inexpensive and high-throughput process for large scale sampling of biomass resources is still an important limiting factor. Our goal was to develop a simple mechanical maize stalk core sampling device that can be utilized to collect uniform samples of a dimension compatible with robotic processing and analysis, while allowing the collection of hundreds to thousands of samples per day. Results We have developed a core sampling device (CSD) to collect maize stalk samples compatible with robotic processing and analysis. The CSD facilitates the collection of thousands of uniform tissue cores consistent with high-throughput analysis required for breeding, genetics, and production studies. With a single CSD operated by one person with minimal training, more than 1,000 biomass samples were obtained in an eight-hour period. One of the main advantages of using cores is the high level of homogeneity of the samples obtained and the minimal opportunity for sample contamination. In addition, the samples obtained with the CSD can be placed directly into a bath of ice, dry ice, or liquid nitrogen maintaining the composition of the biomass sample for relatively long periods of time. Conclusions The CSD has been demonstrated to successfully produce homogeneous stalk core samples in a repeatable manner with a throughput substantially superior to the currently available sampling methods. Given the variety of maize developmental stages and the diversity of stalk diameter evaluated, it is expected that the CSD will have utility for other bioenergy crops as well. PMID:22548834

Bridging the gap between sample collection and laboratory analysis: using dried blood spots to identify human exposure to chemical agents

NASA Astrophysics Data System (ADS)

Hamelin, Elizabeth I.; Blake, Thomas A.; Perez, Jonas W.; Crow, Brian S.; Shaner, Rebecca L.; Coleman, Rebecca M.; Johnson, Rudolph C.

2016-05-01

Public health response to large scale chemical emergencies presents logistical challenges for sample collection, transport, and analysis. Diagnostic methods used to identify and determine exposure to chemical warfare agents, toxins, and poisons traditionally involve blood collection by phlebotomists, cold transport of biomedical samples, and costly sample preparation techniques. Use of dried blood spots, which consist of dried blood on an FDA-approved substrate, can increase analyte stability, decrease infection hazard for those handling samples, greatly reduce the cost of shipping/storing samples by removing the need for refrigeration and cold chain transportation, and be self-prepared by potentially exposed individuals using a simple finger prick and blood spot compatible paper. Our laboratory has developed clinical assays to detect human exposures to nerve agents through the analysis of specific protein adducts and metabolites, for which a simple extraction from a dried blood spot is sufficient for removing matrix interferents and attaining sensitivities on par with traditional sampling methods. The use of dried blood spots can bridge the gap between the laboratory and the field allowing for large scale sample collection with minimal impact on hospital resources while maintaining sensitivity, specificity, traceability, and quality requirements for both clinical and forensic applications.

Efficiently sampling conformations and pathways using the concurrent adaptive sampling (CAS) algorithm

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

Ahn, Surl-Hee; Grate, Jay W.; Darve, Eric F.

Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run microseconds or longer simulations using femtoseconds time steps. While there are several existing methods to overcome this timescale barrier and efficiently sample thermodynamic and/or kinetic properties, problems remain in regard to being able to sample un- known systems, deal with high-dimensional space of collective variables, and focus the computational effort on slow timescales. Hence, a new sampling method, called the “Concurrent Adaptive Sampling (CAS) algorithm,”more » has been developed to tackle these three issues and efficiently obtain conformations and pathways. The method is not constrained to use only one or two collective variables, unlike most reaction coordinate-dependent methods. Instead, it can use a large number of collective vari- ables and uses macrostates (a partition of the collective variable space) to enhance the sampling. The exploration is done by running a large number of short simula- tions, and a clustering technique is used to accelerate the sampling. In this paper, we introduce the new methodology and show results from two-dimensional models and bio-molecules, such as penta-alanine and triazine polymer« less

A comparison of shoreline seines with fyke nets for sampling littoral fish communities in floodplain lakes

USGS Publications Warehouse

Clark, S.J.; Jackson, J.R.; Lochmann, S.E.

2007-01-01

We compared shoreline seines with fyke nets in terms of their ability to sample fish species in the littoral zone of 22 floodplain lakes of the White River, Arkansas. Lakes ranged in size from less than 0.5 to 51.0 ha. Most contained large amounts of coarse woody debris within the littoral zone, thus making seining in shallow areas difficult. We sampled large lakes (>2 ha) using three fyke nets; small lakes (<2 ha) were sampled using two fyke nets. Fyke nets were set for 24 h. Large lakes were sampled with an average of 11 seine hauls/ lake and small lakes were sampled with an average of 3 seine hauls/lake, but exact shoreline seining effort varied among lakes depending on the amount of open shoreline. Fyke nets collected more fish and produced greater species richness and diversity measures than did seining. Species evenness was similar for the two gear types. Two species were unique to seine samples, whereas 13 species and 3 families were unique to fyke-net samples. Although fyke nets collected more fish and more species than did shoreline seines, neither gear collected all the species present in the littoral zone of floodplain lakes. These results confirm the need for a multiple-gear approach to fully characterize the littoral fish assemblages in floodplain lakes. ?? Copyright by the American Fisheries Society 2007.

The Apollo 17 samples: The Massifs and landslide

NASA Technical Reports Server (NTRS)

Ryder, Graham

1992-01-01

More than 50 kg of rock and regolith samples, a little less than half the total Apollo 17 sample mass, was collected from the highland stations at Taurus-Littrow. Twice as much material was collected from the North Massif as from the South Massif and its landslide (the apparent disproportionate collecting at the mare sites is mainly a reflection of the large size of a few individual basalt samples). Descriptions of the collection, documentation, and nature of the samples are given. A comprehensive catalog is currently being produced. Many of the samples have been intensely studied over the last 20 years and some of the rocks have become very familiar and depicted in popular works, particularly the dunite clast (72415), the troctolite sample (76535), and the station 6 boulder samples. Most of the boulder samples have been studied in Consortium mode, and many of the rake samples have received a basic petrological/geochemical characterization.

Instrument to collect fogwater for chemical analysis

NASA Astrophysics Data System (ADS)

Jacob, Daniel J.; Waldman, Jed M.; Haghi, Mehrdad; Hoffmann, Michael R.; Flagan, Richard C.

1985-06-01

An instrument is presented which collects large samples of ambient fogwater by impaction of droplets on a screen. The collection efficiency of the instrument is determined as a function of droplet size, and it is shown that fog droplets in the range 3-100-μm diameter are efficiently collected. No significant evaporation or condensation occurs at any stage of the collection process. Field testing indicates that samples collected are representative of the ambient fogwater. The instrument may easily be automated, and is suitable for use in routine air quality monitoring programs.

Crowdsourcing for Cognitive Science – The Utility of Smartphones

PubMed Central

Brown, Harriet R.; Zeidman, Peter; Smittenaar, Peter; Adams, Rick A.; McNab, Fiona; Rutledge, Robb B.; Dolan, Raymond J.

2014-01-01

By 2015, there will be an estimated two billion smartphone users worldwide. This technology presents exciting opportunities for cognitive science as a medium for rapid, large-scale experimentation and data collection. At present, cost and logistics limit most study populations to small samples, restricting the experimental questions that can be addressed. In this study we investigated whether the mass collection of experimental data using smartphone technology is valid, given the variability of data collection outside of a laboratory setting. We presented four classic experimental paradigms as short games, available as a free app and over the first month 20,800 users submitted data. We found that the large sample size vastly outweighed the noise inherent in collecting data outside a controlled laboratory setting, and show that for all four games canonical results were reproduced. For the first time, we provide experimental validation for the use of smartphones for data collection in cognitive science, which can lead to the collection of richer data sets and a significant cost reduction as well as provide an opportunity for efficient phenotypic screening of large populations. PMID:25025865

Crowdsourcing for cognitive science--the utility of smartphones.

PubMed

Brown, Harriet R; Zeidman, Peter; Smittenaar, Peter; Adams, Rick A; McNab, Fiona; Rutledge, Robb B; Dolan, Raymond J

2014-01-01

By 2015, there will be an estimated two billion smartphone users worldwide. This technology presents exciting opportunities for cognitive science as a medium for rapid, large-scale experimentation and data collection. At present, cost and logistics limit most study populations to small samples, restricting the experimental questions that can be addressed. In this study we investigated whether the mass collection of experimental data using smartphone technology is valid, given the variability of data collection outside of a laboratory setting. We presented four classic experimental paradigms as short games, available as a free app and over the first month 20,800 users submitted data. We found that the large sample size vastly outweighed the noise inherent in collecting data outside a controlled laboratory setting, and show that for all four games canonical results were reproduced. For the first time, we provide experimental validation for the use of smartphones for data collection in cognitive science, which can lead to the collection of richer data sets and a significant cost reduction as well as provide an opportunity for efficient phenotypic screening of large populations.

Comparative evaluation of saliva collection methods for proteome analysis.

PubMed

Golatowski, Claas; Salazar, Manuela Gesell; Dhople, Vishnu Mukund; Hammer, Elke; Kocher, Thomas; Jehmlich, Nico; Völker, Uwe

2013-04-18

Saliva collection devices are widely used for large-scale screening approaches. This study was designed to compare the suitability of three different whole-saliva collection approaches for subsequent proteome analyses. From 9 young healthy volunteers (4 women and 5 men) saliva samples were collected either unstimulated by passive drooling or stimulated using a paraffin gum or Salivette® (cotton swab). Saliva volume, protein concentration and salivary protein patterns were analyzed comparatively. Samples collected using paraffin gum showed the highest saliva volume (4.1±1.5 ml) followed by Salivette® collection (1.8±0.4 ml) and drooling (1.0±0.4 ml). Saliva protein concentrations (average 1145 μg/ml) showed no significant differences between the three sampling schemes. Each collection approach facilitated the identification of about 160 proteins (≥2 distinct peptides) per subject, but collection-method dependent variations in protein composition were observed. Passive drooling, paraffin gum and Salivette® each allows similar coverage of the whole saliva proteome, but the specific proteins observed depended on the collection approach. Thus, only one type of collection device should be used for quantitative proteome analysis in one experiment, especially when performing large-scale cross-sectional or multi-centric studies. Copyright © 2013 Elsevier B.V. All rights reserved.

Electrofishing Effort Required to Estimate Biotic Condition in Southern Idaho Rivers

EPA Science Inventory

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...

Comparison of water-quality samples collected by siphon samplers and automatic samplers in Wisconsin

USGS Publications Warehouse

Graczyk, David J.; Robertson, Dale M.; Rose, William J.; Steur, Jeffrey J.

2000-01-01

In small streams, flow and water-quality concentrations often change quickly in response to meteorological events. Hydrologists, field technicians, or locally hired stream ob- servers involved in water-data collection are often unable to reach streams quickly enough to observe or measure these rapid changes. Therefore, in hydrologic studies designed to describe changes in water quality, a combination of manual and automated sampling methods have commonly been used manual methods when flow is relatively stable and automated methods when flow is rapidly changing. Auto- mated sampling, which makes use of equipment programmed to collect samples in response to changes in stage and flow of a stream, has been shown to be an effective method of sampling to describe the rapid changes in water quality (Graczyk and others, 1993). Because of the high cost of automated sampling, however, especially for studies examining a large number of sites, alternative methods have been considered for collecting samples during rapidly changing stream conditions. One such method employs the siphon sampler (fig. 1). also referred to as the "single-stage sampler." Siphon samplers are inexpensive to build (about $25- $50 per sampler), operate, and maintain, so they are cost effective to use at a large number of sites. Their ability to collect samples representing the average quality of water passing though the entire cross section of a stream, however, has not been fully demonstrated for many types of stream sites.

Dynamics of airborne fungal populations in a large office building

NASA Technical Reports Server (NTRS)

Burge, H. A.; Pierson, D. L.; Groves, T. O.; Strawn, K. F.; Mishra, S. K.

2000-01-01

The increasing concern with bioaerosols in large office buildings prompted this prospective study of airborne fungal concentrations in a newly constructed building on the Gulf coast. We collected volumetric culture plate air samples on 14 occasions over the 18-month period immediately following building occupancy. On each sampling occasion, we collected duplicate samples from three sites on three floors of this six-story building, and an outdoor sample. Fungal concentrations indoors were consistently below those outdoors, and no sample clearly indicated fungal contamination in the building, although visible growth appeared in the ventilation system during the course of the study. We conclude that modern mechanically ventilated buildings prevent the intrusion of most of the outdoor fungal aerosol, and that even relatively extensive air sampling protocols may not sufficiently document the microbial status of buildings.

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

Puls, R.W.; Powell, R.M.

R.S. Kerr Environmental Research Laboratory (RSKERL) personnel have evaluated sampling procedures for the collection of representative, accurate, and reproducible ground water quality samples for metals for the past four years. Intensive sampling research at three different field sites has shown that the method by which samples are collected has a greater impact on sample quality, accuracy, and reproducibility than whether the samples are filtered or not. In particular, sample collection practices that induce artifically high levels of turbidity have been shown to have the greatest negative impacts on sample quality. Results indicated the ineffectiveness of bailer for collection of representativemore » metal samples. Inconsistent operator usage together with excessive purging generally resulted in excessive turbidity and large differences in filtered and unfiltered metal samples. The use of low flow rate purging and sampling consistently produced filtered and unfiltered samples that showed no significant differences in concentrations. Turbidity levels were generally less than 5 NTUs, even in fine-textured glacial till. The authors recommend the use of low flow rates, during both purging and sampling.« less

A COMPARISON OF SIX BENTHIC MACROINVERTEBRATE SAMPLING METHODS IN FOUR LARGE RIVERS

EPA Science Inventory

In 1999, a study was conducted to compare six macroinvertebrate sampling methods in four large (boatable) rivers that drain into the Ohio River. Two methods each were adapted from existing methods used by the USEPA, USGS and Ohio EPA. Drift nets were unable to collect a suffici...

Guidelines for the processing and quality assurance of benthic invertebrate samples collected as part of the National Water-Quality Assessment Program

USGS Publications Warehouse

Cuffney, T.F.; Gurtz, M.E.; Meador, M.R.

1993-01-01

Benthic invertebrate samples are collected as part of the U.S. Geological Survey's National Water-Quality Assessment Program. This is a perennial, multidisciplinary program that integrates biological, physical, and chemical indicators of water quality to evaluate status and trends and to develop an understanding of the factors controlling observed water quality. The Program examines water quality in 60 study units (coupled ground- and surface-water systems) that encompass most of the conterminous United States and parts of Alaska and Hawaii. Study-unit teams collect and process qualitative and semi-quantitative invertebrate samples according to standardized procedures. These samples are processed (elutriated and subsampled) in the field to produce as many as four sample components: large-rare, main-body, elutriate, and split. Each sample component is preserved in 10-percent formalin, and two components, large-rare and main-body, are sent to contract laboratories for further processing. The large-rare component is composed of large invertebrates that are removed from the sample matrix during field processing and placed in one or more containers. The main-body sample component consists of the remaining sample materials (sediment, detritus, and invertebrates) and is subsampled in the field to achieve a volume of 750 milliliters or less. The remaining two sample components, elutriate and split, are used for quality-assurance and quality-control purposes. Contract laboratories are used to identify and quantify invertebrates from the large-rare and main-body sample components according to the procedures and guidelines specified within this document. These guidelines allow the use of subsampling techniques to reduce the volume of sample material processed and to facilitate identifications. These processing procedures and techniques may be modified if the modifications provide equal or greater levels of accuracy and precision. The intent of sample processing is to determine the quantity of each taxon present in the semi-quantitative samples or to list the taxa present in qualitative samples. The processing guidelines provide standardized laboratory forms, sample labels, detailed sample processing flow charts, standardized format for electronic data, quality-assurance procedures and checks, sample tracking standards, and target levels for taxonomic determinations. The contract laboratory (1) is responsible for identifications and quantifications, (2) constructs reference collections, (3) provides data in hard copy and electronic forms, (4) follows specified quality-assurance and quality-control procedures, and (5) returns all processed and unprocessed portions of the samples. The U.S. Geological Survey's Quality Management Group maintains a Biological Quality-Assurance Unit, located at the National Water-Quality Laboratory, Arvada, Colorado, to oversee the use of contract laboratories and ensure the quality of data obtained from these laboratories according to the guidelines established in this document. This unit establishes contract specifications, reviews contractor performance (timeliness, accuracy, and consistency), enters data into the National Water Information System-II data base, maintains in-house reference collections, deposits voucher specimens in outside museums, and interacts with taxonomic experts within and outside the U.S. Geological Survey. This unit also modifies the existing sample processing and quality-assurance guidelines, establishes criteria and testing procedures for qualifying potential contract laboratories, identifies qualified taxonomic experts, and establishes voucher collections.

Comparison of Submental Blood Collection with the Retroorbital and Submandibular Methods in Mice (Mus musculus)

PubMed Central

Regan, Rainy D; Fenyk-Melody, Judy E; Tran, Sam M; Chen, Guang; Stocking, Kim L

2016-01-01

Nonterminal blood sample collection of sufficient volume and quality for research is complicated in mice due to their small size and anatomy. Large (>100 μL) nonterminal volumes of unhemolyzed or unclotted blood currently are typically collected from the retroorbital sinus or submandibular plexus. We developed a third method—submental blood collection—which is similar in execution to the submandibular method but with minor changes in animal restraint and collection location. Compared with other techniques, submental collection is easier to perform due to the direct visibility of the target vessels, which are located in a sparsely furred region. Compared with the submandibular method, the submental method did not differ regarding weight change and clotting score but significantly decreased hemolysis and increased the overall number of high-quality samples. The submental method was performed with smaller lancets for the majority of the bleeds, yet resulted in fewer repeat collection attempts, fewer insufficient samples, and less extraneous blood loss and was qualitatively less traumatic. Compared with the retroorbital technique, the submental method was similar regarding weight change but decreased hemolysis, clotting, and the number of overall high-quality samples; however the retroorbital method resulted in significantly fewer incidents of insufficient sample collection. Extraneous blood loss was roughly equivalent between the submental and retroorbital methods. We conclude that the submental method is an acceptable venipuncture technique for obtaining large, nonterminal volumes of blood from mice. PMID:27657712

Geochemical and isotopic water results, Barrow, Alaska, 2012-2013

DOE Data Explorer

Heikoop, Jeff; Wilson, Cathy; Newman, Brent

2012-07-18

Data include a large suite of analytes (geochemical and isotopic) for samples collected in Barrow, Alaska (2012-2013). Sample types are indicated, and include soil pore waters, drainage waters, snowmelt, precipitation, and permafrost samples.

Fog collecting biomimetic surfaces: Influence of microstructure and wettability.

PubMed

Azad, M A K; Ellerbrok, D; Barthlott, W; Koch, K

2015-01-19

We analyzed the fog collection efficiency of three different sets of samples: replica (with and without microstructures), copper wire (smooth and microgrooved) and polyolefin mesh (hydrophilic, superhydrophilic and hydrophobic). The collection efficiency of the samples was compared in each set separately to investigate the influence of microstructures and/or the wettability of the surfaces on fog collection. Based on the controlled experimental conditions chosen here large differences in the efficiency were found. We found that microstructured plant replica samples collected 2-3 times higher amounts of water than that of unstructured (smooth) samples. Copper wire samples showed similar results. Moreover, microgrooved wires had a faster dripping of water droplets than that of smooth wires. The superhydrophilic mesh tested here was proved more efficient than any other mesh samples with different wettability. The amount of collected fog by superhydrophilic mesh was about 5 times higher than that of hydrophilic (untreated) mesh and was about 2 times higher than that of hydrophobic mesh.

Using Technology to Better Characterize the Apollo Sample Suite: A Retroactive PET Analysis and Potential Model for Future Sample Return Missions

NASA Technical Reports Server (NTRS)

Zeigler, R. A.

2015-01-01

From 1969-1972 the Apollo missions collected 382 kg of lunar samples from six distinct locations on the Moon. Studies of the Apollo sample suite have shaped our understanding of the formation and early evolution of the Earth-Moon system, and have had important implications for studies of the other terrestrial planets (e.g., through the calibration of the crater counting record) and even the outer planets (e.g., the Nice model of the dynamical evolution of the Solar System). Despite nearly 50 years of detailed research on Apollo samples, scientists are still developing new theories about the origin and evolution of the Moon. Three areas of active research are: (1) the abundance of water (and other volatiles) in the lunar mantle, (2) the timing of the formation of the Moon and the duration of lunar magma ocean crystallization, (3) the formation of evolved lunar lithologies (e.g., granites) and implications for tertiary crustal processes on the Moon. In order to fully understand these (and many other) theories about the Moon, scientists need access to "new" lunar samples, particularly new plutonic samples. Over 100 lunar meteorites have been identified over the past 30 years, and the study of these samples has greatly aided in our understanding of the Moon. However, terrestrial alteration and the lack of geologic context limit what can be learned from the lunar meteorites. Although no "new" large plutonic samples (i.e., hand-samples) remain to be discovered in the Apollo sample collection, there are many large polymict breccias in the Apollo collection containing relatively large (approximately 1 cm or larger) previously identified plutonic clasts, as well as a large number of unclassified lithic clasts. In addition, new, previously unidentified plutonic clasts are potentially discoverable within these breccias. The question becomes how to non-destructively locate and identify new lithic clasts of interest while minimizing the contamination and physical degradation of the samples.

Guide to the US collection of antarctic meteorites 1976-1988 (everything you wanted to know about the meteorite collection). Antarctic Meteorite Newsletter, Volume 13, Number 1

NASA Technical Reports Server (NTRS)

Score, Roberta; Lindstrom, Marilyn M.

1990-01-01

The state of the collection of Antarctic Meteorites is summarized. This guide is intended to assist investigators plan their meteorite research and select and request samples. Useful information is presented for all classified meteorites from 1976 to 1988 collections, as of Sept. 1989. The meteorite collection has grown over 13 years to include 4264 samples of which 2754 have been classified. Most of the unclassified meteorites are ordinary chondrites because the collections have been culled for specimens of special petrologic type. The guide consists of two large classification tables. They are preceded by a list of sample locations and important notes to make the tables understandable.

Analysis of the research sample collections of Uppsala biobank.

PubMed

Engelmark, Malin T; Beskow, Anna H

2014-10-01

Uppsala Biobank is the joint and only biobank organization of the two principals, Uppsala University and Uppsala University Hospital. Biobanks are required to have updated registries on sample collection composition and management in order to fulfill legal regulations. We report here the results from the first comprehensive and overall analysis of the 131 research sample collections organized in the biobank. The results show that the median of the number of samples in the collections was 700 and that the number of samples varied from less than 500 to over one million. Blood samples, such as whole blood, serum, and plasma, were included in the vast majority, 84.0%, of the research sample collections. Also, as much as 95.5% of the newly collected samples within healthcare included blood samples, which further supports the concept that blood samples have fundamental importance for medical research. Tissue samples were also commonly used and occurred in 39.7% of the research sample collections, often combined with other types of samples. In total, 96.9% of the 131 sample collections included samples collected for healthcare, showing the importance of healthcare as a research infrastructure. Of the collections that had accessed existing samples from healthcare, as much as 96.3% included tissue samples from the Department of Pathology, which shows the importance of pathology samples as a resource for medical research. Analysis of different research areas shows that the most common of known public health diseases are covered. Collections that had generated the most publications, up to over 300, contained a large number of samples collected systematically and repeatedly over many years. More knowledge about existing biobank materials, together with public registries on sample collections, will support research collaborations, improve transparency, and bring us closer to the goals of biobanks, which is to save and prolong human lives and improve health and quality of life.

Extracting samples of high diversity from thematic collections of large gene banks using a genetic-distance based approach

PubMed Central

2010-01-01

Background Breeding programs are usually reluctant to evaluate and use germplasm accessions other than the elite materials belonging to their advanced populations. The concept of core collections has been proposed to facilitate the access of potential users to samples of small sizes, representative of the genetic variability contained within the gene pool of a specific crop. The eventual large size of a core collection perpetuates the problem it was originally proposed to solve. The present study suggests that, in addition to the classic core collection concept, thematic core collections should be also developed for a specific crop, composed of a limited number of accessions, with a manageable size. Results The thematic core collection obtained meets the minimum requirements for a core sample - maintenance of at least 80% of the allelic richness of the thematic collection, with, approximately, 15% of its size. The method was compared with other methodologies based on the M strategy, and also with a core collection generated by random sampling. Higher proportions of retained alleles (in a core collection of equal size) or similar proportions of retained alleles (in a core collection of smaller size) were detected in the two methods based on the M strategy compared to the proposed methodology. Core sub-collections constructed by different methods were compared regarding the increase or maintenance of phenotypic diversity. No change on phenotypic diversity was detected by measuring the trait "Weight of 100 Seeds", for the tested sampling methods. Effects on linkage disequilibrium between unlinked microsatellite loci, due to sampling, are discussed. Conclusions Building of a thematic core collection was here defined by prior selection of accessions which are diverse for the trait of interest, and then by pairwise genetic distances, estimated by DNA polymorphism analysis at molecular marker loci. The resulting thematic core collection potentially reflects the maximum allele richness with the smallest sample size from a larger thematic collection. As an example, we used the development of a thematic core collection for drought tolerance in rice. It is expected that such thematic collections increase the use of germplasm by breeding programs and facilitate the study of the traits under consideration. The definition of a core collection to study drought resistance is a valuable contribution towards the understanding of the genetic control and the physiological mechanisms involved in water use efficiency in plants. PMID:20576152

After site selection and before data analysis: sampling, sorting, and laboratory procedures used in stream benthic macroinvertebrate monitoring programs by USA state agencies

USGS Publications Warehouse

Carter, James L.; Resh, Vincent H.

2001-01-01

A survey of methods used by US state agencies for collecting and processing benthic macroinvertebrate samples from streams was conducted by questionnaire; 90 responses were received and used to describe trends in methods. The responses represented an estimated 13,000-15,000 samples collected and processed per year. Kicknet devices were used in 64.5% of the methods; other sampling devices included fixed-area samplers (Surber and Hess), artificial substrates (Hester-Dendy and rock baskets), grabs, and dipnets. Regional differences existed, e.g., the 1-m kicknet was used more often in the eastern US than in the western US. Mesh sizes varied among programs but 80.2% of the methods used a mesh size between 500 and 600 (mu or u)m. Mesh size variations within US Environmental Protection Agency regions were large, with size differences ranging from 100 to 700 (mu or u)m. Most samples collected were composites; the mean area sampled was 1.7 m2. Samples rarely were collected using a random method (4.7%); most samples (70.6%) were collected using "expert opinion", which may make data obtained operator-specific. Only 26.3% of the methods sorted all the organisms from a sample; the remainder subsampled in the laboratory. The most common method of subsampling was to remove 100 organisms (range = 100-550). The magnification used for sorting ranged from 1 (sorting by eye) to 30x, which results in inconsistent separation of macroinvertebrates from detritus. In addition to subsampling, 53% of the methods sorted large/rare organisms from a sample. The taxonomic level used for identifying organisms varied among taxa; Ephemeroptera, Plecoptera, and Trichoptera were generally identified to a finer taxonomic resolution (genus and species) than other taxa. Because there currently exists a large range of field and laboratory methods used by state programs, calibration among all programs to increase data comparability would be exceptionally challenging. However, because many techniques are shared among methods, limited testing could be designed to evaluate whether procedural differences affect the ability to determine levels of environmental impairment using benthic macroinvertebrate communities.

Integrating resource selection into spatial capture-recapture models for large carnivores

USGS Publications Warehouse

Proffitt, Kelly M.; Goldberg, Joshua; Hebblewite, Mark; Russell, Robin E.; Jimenez, Ben; Robinson, Hugh S.; Pilgrim, Kristine; Schwartz, Michael K.

2015-01-01

Wildlife managers need reliable methods to estimate large carnivore densities and population trends; yet large carnivores are elusive, difficult to detect, and occur at low densities making traditional approaches intractable. Recent advances in spatial capture-recapture (SCR) models have provided new approaches for monitoring trends in wildlife abundance and these methods are particularly applicable to large carnivores. We applied SCR models in a Bayesian framework to estimate mountain lion densities in the Bitterroot Mountains of west central Montana. We incorporate an existing resource selection function (RSF) as a density covariate to account for heterogeneity in habitat use across the study area and include data collected from harvested lions. We identify individuals through DNA samples collected by (1) biopsy darting mountain lions detected in systematic surveys of the study area, (2) opportunistically collecting hair and scat samples, and (3) sampling all harvested mountain lions. We included 80 DNA samples collected from 62 individuals in the analysis. Including information on predicted habitat use as a covariate on the distribution of activity centers reduced the median estimated density by 44%, the standard deviation by 7%, and the width of 95% credible intervals by 10% as compared to standard SCR models. Within the two management units of interest, we estimated a median mountain lion density of 4.5 mountain lions/100 km2 (95% CI = 2.9, 7.7) and 5.2 mountain lions/100 km2 (95% CI = 3.4, 9.1). Including harvested individuals (dead recovery) did not create a significant bias in the detection process by introducing individuals that could not be detected after removal. However, the dead recovery component of the model did have a substantial effect on results by increasing sample size. The ability to account for heterogeneity in habitat use provides a useful extension to SCR models, and will enhance the ability of wildlife managers to reliably and economically estimate density of wildlife populations, particularly large carnivores.

HIGH VOLUME INJECTION FOR GCMS ANALYSIS OF PARTICULATE ORGANIC SPECIES IN AMBIENT AIR

EPA Science Inventory

Detection of organic species in ambient particulate matter typically requires large air sample volumes, frequently achieved by grouping samples into monthly composites. Decreasing the volume of air sample required would allow shorter collection times and more convenient sample c...

A STANDARDIZED ASSESSMENT METHOD (SAM) FOR RIVERINE MACROINVERTEBRATES

EPA Science Inventory

A macroinvertebrate sampling method for large rivers based on desirable characteristics of existing nonwadeable methods was developed and tested. Six sites each were sampled on the Great Miami and Kentucky Rivers, reflecting a human disturbance gradient. Samples were collected ...

Mosquitoes (Diptera: Culicidae) Collected From Residential Yards and Dog Kennels in Florida Using Two Aspirators, a Sweep Net, or a CDC Trap.

PubMed

Holderman, C J; Gezan, S A; Stone, A E S; Connelly, C R; Kaufman, P E

2018-01-10

Mosquito surveillance typically uses Centers for Disease Control and Prevention (CDC) mosquito light traps baited with CO2. From January 2013 to March 2015, we sampled seven field sites using three active mosquito-trapping techniques (two different aspirators and a sweep net) and the stationary CO2-baited CDC mosquito light trap to determine mosquito capture efficacy for each technique. Sampling occurred in four suburban backyards and three dog kennel facilities near Gainesville, FL, USA; species collection and relative abundance were measured. A total of 32 species and 70,090 individual mosquitoes were collected, including a new record for Alachua County, Florida, Aedes hendersoni (Cockerell). The dominant (>5% of total capture) mosquito species collected during the study included Aedes atlanticus (Dyar and Knab), Aedes infirmatus (Dyar and Knab), Anopheles crucians Wiedemann, Culiseta melanura (Coquillett), Culex erraticus (Dyar and Knab), Culex nigripalpus Theobald, and Uranotaenia sapphirina (Osten Sacken). The CDC trap captured the most species (29), followed by large aspirator (28), small aspirator (26), and the sweep net (23). All dominant species were captured with each sampling technique. Excluding Wyeomyia mitchellii (Theobald), all subdominant species (1-5% of total capture) were collected with each sampling technique. Future sampling should consider the utility (e.g., large numbers are readily collected) and limitations (e.g., personnel requirements) of aspirator collections when designing field-based mosquito sampling projects, especially those in residential areas or those focused upon species captured. © The Author(s) 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

OGLE Collection of Star Clusters. New Objects in the Outskirts of the Large Magellanic Cloud

NASA Astrophysics Data System (ADS)

Sitek, M.; Szymański, M. K.; Skowron, D. M.; Udalski, A.; Kostrzewa-Rutkowska, Z.; Skowron, J.; Karczmarek, P.; Cieślar, M.; Wyrzykowski, Ł.; Kozłowski, S.; Pietrukowicz, P.; Soszyński, I.; Mróz, P.; Pawlak, M.; Poleski, R.; Ulaczyk, K.

2016-09-01

The Magellanic System (MS), consisting of the Large Magellanic Cloud (LMC), the Small Magellanic Cloud (SMC) and the Magellanic Bridge (MBR), contains diverse sample of star clusters. Their spatial distribution, ages and chemical abundances may provide important information about the history of formation of the whole System. We use deep photometric maps derived from the images collected during the fourth phase of the Optical Gravitational Lensing Experiment (OGLE-IV) to construct the most complete catalog of star clusters in the Large Magellanic Cloud using the homogeneous photometric data. In this paper we present the collection of star clusters found in the area of about 225 square degrees in the outer regions of the LMC. Our sample contains 679 visually identified star cluster candidates, 226 of which were not listed in any of the previously published catalogs. The new clusters are mainly young small open clusters or clusters similar to associations.

Evaluation of residual uranium contamination in the dirt floor of an abandoned metal rolling mill.

PubMed

Glassford, Eric; Spitz, Henry; Lobaugh, Megan; Spitler, Grant; Succop, Paul; Rice, Carol

2013-02-01

A single, large, bulk sample of uranium-contaminated material from the dirt floor of an abandoned metal rolling mill was separated into different types and sizes of aliquots to simulate samples that would be collected during site remediation. The facility rolled approximately 11,000 tons of hot-forged ingots of uranium metal approximately 60 y ago, and it has not been used since that time. Thirty small mass (≈ 0.7 g) and 15 large mass (≈ 70 g) samples were prepared from the heterogeneously contaminated bulk material to determine how measurements of the uranium contamination vary with sample size. Aliquots of bulk material were also resuspended in an exposure chamber to produce six samples of respirable particles that were obtained using a cascade impactor. Samples of removable surface contamination were collected by wiping 100 cm of the interior surfaces of the exposure chamber with 47-mm-diameter fiber filters. Uranium contamination in each of the samples was measured directly using high-resolution gamma ray spectrometry. As expected, results for isotopic uranium (i.e., U and U) measured with the large-mass and small-mass samples are significantly different (p < 0.001), and the coefficient of variation (COV) for the small-mass samples was greater than for the large-mass samples. The uranium isotopic concentrations measured in the air and on the wipe samples were not significantly different and were also not significantly different (p > 0.05) from results for the large- or small-mass samples. Large-mass samples are more reliable for characterizing heterogeneously distributed radiological contamination than small-mass samples since they exhibit the least variation compared to the mean. Thus, samples should be sufficiently large in mass to insure that the results are truly representative of the heterogeneously distributed uranium contamination present at the facility. Monitoring exposure of workers and the public as a result of uranium contamination resuspended during site remediation should be evaluated using samples of sufficient size and type to accommodate the heterogeneous distribution of uranium in the bulk material.

Sampling large geographic areas for rare species using environmental DNA: A study of bull trout Salvelinus confluentus occupancy in western Montana

Treesearch

Kevin McKelvey; Michael Young; W. L. Knotek; K. J. Carim; T. M. Wilcox; T. M. Padgett-Stewart; Michael Schwartz

2016-01-01

This study tested the efficacy of environmental DNA (eDNA) sampling to delineate the distribution of bull trout Salvelinus confluentus in headwater streams in western Montana, U.S.A. Surveys proved fast, reliable and sensitive: 124 samples were collected across five basins by a single crew in c. 8days. Results were largely consistent with past electrofishing,...

Molecular epidemiology biomarkers-Sample collection and processing considerations

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

Holland, Nina T.; Pfleger, Laura; Berger, Eileen

2005-08-07

Biomarker studies require processing and storage of numerous biological samples with the goals of obtaining a large amount of information and minimizing future research costs. An efficient study design includes provisions for processing of the original samples, such as cryopreservation, DNA isolation, and preparation of specimens for exposure assessment. Use of standard, two-dimensional and nanobarcodes and customized electronic databases assure efficient management of large sample collections and tracking results of data analyses. Standard operating procedures and quality control plans help to protect sample quality and to assure validity of the biomarker data. Specific state, federal and international regulations are inmore » place regarding research with human samples, governing areas including custody, safety of handling, and transport of human samples. Appropriate informed consent must be obtained from the study subjects prior to sample collection and confidentiality of results maintained. Finally, examples of three biorepositories of different scale (European Cancer Study, National Cancer Institute and School of Public Health Biorepository, University of California, Berkeley) are used to illustrate challenges faced by investigators and the ways to overcome them. New software and biorepository technologies are being developed by many companies that will help to bring biological banking to a new level required by molecular epidemiology of the 21st century.« less

Evaluation of Sampling Methods for Bacillus Spore ...

EPA Pesticide Factsheets

Journal Article Following a wide area release of biological materials, mapping the extent of contamination is essential for orderly response and decontamination operations. HVAC filters process large volumes of air and therefore collect highly representative particulate samples in buildings. HVAC filter extraction may have great utility in rapidly estimating the extent of building contamination following a large-scale incident. However, until now, no studies have been conducted comparing the two most appropriate sampling approaches for HVAC filter materials: direct extraction and vacuum-based sampling.

The effectiveness of large household water storage tanks for protecting the quality of drinking water.

PubMed

Graham, Jay P; VanDerslice, James

2007-06-01

Many communities along the US-Mexico border remain without infrastructure for water and sewage. Residents in these communities often collect and store their water in open 55-gallon drums. This study evaluated changes in drinking water quality resulting from an intervention that provided large closed water storage tanks (2,500-gallons) to individual homes lacking a piped water supply. After the intervention, many of the households did not change the source of their drinking water to the large storage tanks. Therefore, water quality results were first compared based on the source of the household's drinking water: store or vending machine, large tank, or collected from a public supply and transported by the household. Of the households that used the large storage tank as their drinking water supply, drinking water quality was generally of poorer quality. Fifty-four percent of samples collected prior to intervention had detectable levels of total coliforms, while 82% of samples were positive nine months after the intervention (p < 0.05). Exploratory analyses were also carried out to measure water quality at different points between collection by water delivery trucks and delivery to the household's large storage tank. Thirty percent of the samples taken immediately after water was delivered to the home had high total coliforms (> 10 CFU/100 ml). Mean free chlorine levels dropped from 0.43 mg/l, where the trucks filled their tanks, to 0.20 mg/l inside the household's tank immediately after delivery. Results of this study have implications for interventions that focus on safe water treatment and storage in the home, and for guidelines regarding the level of free chlorine required in water delivered by water delivery trucks.

Large sample area and size are needed for forest soil seed bank studies to ensure low discrepancy with standing vegetation.

PubMed

Shen, You-xin; Liu, Wei-li; Li, Yu-hui; Guan, Hui-lin

2014-01-01

A large number of small-sized samples invariably shows that woody species are absent from forest soil seed banks, leading to a large discrepancy with the seedling bank on the forest floor. We ask: 1) Does this conventional sampling strategy limit the detection of seeds of woody species? 2) Are large sample areas and sample sizes needed for higher recovery of seeds of woody species? We collected 100 samples that were 10 cm (length) × 10 cm (width) × 10 cm (depth), referred to as larger number of small-sized samples (LNSS) in a 1 ha forest plot, and placed them to germinate in a greenhouse, and collected 30 samples that were 1 m × 1 m × 10 cm, referred to as small number of large-sized samples (SNLS) and placed them (10 each) in a nearby secondary forest, shrub land and grass land. Only 15.7% of woody plant species of the forest stand were detected by the 100 LNSS, contrasting with 22.9%, 37.3% and 20.5% woody plant species being detected by SNLS in the secondary forest, shrub land and grassland, respectively. The increased number of species vs. sampled areas confirmed power-law relationships for forest stand, the LNSS and SNLS at all three recipient sites. Our results, although based on one forest, indicate that conventional LNSS did not yield a high percentage of detection for woody species, but SNLS strategy yielded a higher percentage of detection for woody species in the seed bank if samples were exposed to a better field germination environment. A 4 m2 minimum sample area derived from power equations is larger than the sampled area in most studies in the literature. Increased sample size also is needed to obtain an increased sample area if the number of samples is to remain relatively low.

Radon-222 content of natural gas samples from Upper and Middle Devonian sandstone and shale reservoirs in Pennsylvania—preliminary data

USGS Publications Warehouse

Rowan, E.L.; Kraemer, T.F.

2012-01-01

Samples of natural gas were collected as part of a study of formation water chemistry in oil and gas reservoirs in the Appalachian Basin. Nineteen samples (plus two duplicates) were collected from 11 wells producing gas from Upper Devonian sandstones and the Middle Devonian Marcellus Shale in Pennsylvania. The samples were collected from valves located between the wellhead and the gas-water separator. Analyses of the radon content of the gas indicated 222Rn (radon-222) activities ranging from 1 to 79 picocuries per liter (pCi/L) with an overall median of 37 pCi/L. The radon activities of the Upper Devonian sandstone samples overlap to a large degree with the activities of the Marcellus Shale samples.

PAH and PCB in the Baltic -- A budget approach including fluxes, occurrence and concentration variability in air, suspended and settling particulates in water, surface sediments and river water

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

Broman, D.; Axelman, J.; Bandh, C.

In order to study the fate and occurrence of two groups of hydrophobic compounds in the Baltic aquatic environment a large number of samples were collected from the southern Baltic proper to the northern Bothnian Bay for the analyses of polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs). The following sample matrices were collected; bottom surface sediments (0--1 cm, collected with gravity corer), settling particulate matter (collected with sediment traps), open water samples and over water samples (suspended particulates and dissolved fraction sampled by filtration) and air samples (aerosols and vapor phase sampled by filtration). All samples (except over watermore » and air) were collected at open sea in the Baltic. The analyses results have been used to make a model approach on the whole Baltic and to elucidate different aspects of the behavior of PAHs and PCBs in the Baltic, such as the occurrence of the compounds in water and sediment, the total content as well as the concentration variabilities over such a large geographical area, Further, the data on settling particulate matter as well as the air concentration data were used to estimate the total fluxes of PAHs and PCBs to the bottoms of the Baltic and t o the total water area of the Baltic, respectively. Further, data on the PAH and PCB content in river water from four major rivers provides rough estimates of the riverine input to the Baltic. The dynamics of PAHs and PCBs within the water mass have also been studied in terms of settling velocities and residence times in the water mass for these type of compounds in the open Baltic.« less

Comparison of Grab, Air, and Surface Results for Radiation Site Characterization

NASA Astrophysics Data System (ADS)

Glassford, Eric Keith

2011-12-01

The use of proper sampling methods and sample types for evaluating sites believed to be contaminated with radioactive materials is necessary to avoid misrepresenting conditions at the site. This study was designed to investigate if the site characterization, based upon uranium contamination measured in different types of samples, is dependent upon the mass of the sample collected. A bulk sample of potentially contaminated interior dirt was collected from an abandoned metal processing mill that rolled uranium between 1948 and 1956. The original mill dates from 1910 and has a dirt floor. The bulk sample was a mixture of dirt, black and yellow particles of metal dust, and small fragments of natural debris. Small mass (approximately 0.75 grams (g)) and large mass (approximately 70g) grab samples were prepared from the bulk sample material to simulate collection of a "grab" type sample. Air sampling was performed by re-suspending a portion of the bulk sample material using a vibration table to simulate airborne contamination that might be present during site remediation. Additionally, samples of removable contaminated surface dust were collected on 47 mm diameter filter paper by wiping the surfaces of the exposure chamber used to resuspend the bulk material. Certified reference materials, one containing a precisely known quantity of U 3O8 and one containing a known quantity of natural uranium, were utilized to calibrate the gamma spectrometry measurement system. Non-destructive gamma spectrometry measurements were used to determine the content of uranium-235 (235U) at 185 keV and 143 keV, thorium-234 (234Th) at 63 keV, and protactinium-234m (234mPa) at 1001 keV in each sample. Measurement of natural uranium in small, 1 g samples is usually accomplished by radiochemical analysis in order to measure alpha particles emitted by 238U, 235U, and 234U. However, uranium in larger bulk samples can also be measured non-destructively using gamma spectrometry to detect the low energy photons from 234Th and 234mPa, the short-lived decay products of 238U, and 235U. Two sided t-tests and coefficient of variation were used to compare sampling types. The large grab samples had the lowest calculated coefficient of variation results for activity and atom percentage. The wipe samples had the highest calculated coefficient of variation of mean specific activity (dis/sec/g) for all three energies. The air filter samples had the highest coefficient of variation calculation for mean atom percentage, for both uranium isotopes examined. The data indicated that the large mass sample was the most effective at characterizing the rolling mill radioactive site conditions, since this would indicate which samples had the smallest variations compared to the mean. Additionally, measurement results of natural uranium in the samples indicate that the distribution of radioactive contamination at the sampling location is most likely non-homogeneous and that the size of the sample collected and analyzed must be sufficiently large to insure that the analytical results are truly representative of the activity present.

Guano exposed: Impact of aerobic conditions on bat fecal microbiota.

PubMed

Fofanov, Viacheslav Y; Furstenau, Tara N; Sanchez, Daniel; Hepp, Crystal M; Cocking, Jill; Sobek, Colin; Pagel, Nicole; Walker, Faith; Chambers, Carol L

2018-06-01

Bats and their associated guano microbiota provide important terrestrial and subterranean ecosystem services and serve as a reservoir for a wide range of epizootic and zoonotic diseases. Unfortunately, large-scale studies of bats and their guano microbiotas are limited by the time and cost of sample collection, which requires specially trained individuals to work at night to capture bats when they are most active. Indirectly surveying bat gut microbiota through guano deposits could be a more cost-effective alternative, but it must first be established whether the postdefecation exposure to an aerobic environment has a large impact on the guano microbial community. A number of recent studies on mammalian feces have shown that the impact of aerobic exposure is highly species specific; therefore, it is difficult to predict how exposure will affect the bat guano microbiota without empirical data. In our study, we collected fresh guano samples from 24 individuals of 10 bat species that are common throughout the arid environments of the American southwest and subjected the samples to 0, 1, and 12 hr of exposure. The biodiversity decreased rapidly after the shift from an anaerobic to an aerobic environment-much faster than previously reported in mammalian species. However, the relative composition of the core guano microbiota remained stable and, using highly sensitive targeted PCR methods, we found that pathogens present in the original, non-exposed samples could still be recovered after 12 hr of exposure. These results suggest that with careful sample analysis protocols, a more efficient passive collection strategy is feasible; for example, guano could be collected on tarps placed near the roost entrance. Such passive collection methods would greatly reduce the cost of sample collection by allowing more sites or roosts to be surveyed with a fraction of trained personnel, time, and effort investments needed.

Antarctic Meteorite Newsletter, Volume 11, Number 2, August 1988

NASA Technical Reports Server (NTRS)

1988-01-01

Presented are classifications and descriptions of a large number of meteorites which include the last samples from the 1984 collection and the first samples from the 1987 collection. There is a particularly good selection of meteorites of special petrologic type in the 1987 collection. The achondrites include aubrites, ureilites, howardites, eucrites, and a diogenite. The howardites are particularly notable because of their size and previous scarcity in the Antarctic collection. Noteworthy among the 7 irons and 3 mesosiderities are 2 anamolous irons and 2 large mesosiderites. The carbonaceous chondrites include good suites of C2 and C4 meteorites, and 2 highly equilibrated carbonaceous chondrites tentatively identified as C5 and C6 meteorites. Also included are surveys of numerous meteorites for Al-26 and thermoluminescence. These studies provide information on the thermal and radiation histories of the meteorites and can be used as measures of their terrestrial ages.

Colloidal-facilitated transport of inorganic contaminants in ground water: part 1, sampling considerations

USGS Publications Warehouse

Puls, Robert W.; Eychaner, James H.; Powell, Robert M.

1996-01-01

Investigations at Pinal Creek, Arizona, evaluated routine sampling procedures for determination of aqueous inorganic geochemistry and assessment of contaminant transport by colloidal mobility. Sampling variables included pump type and flow rate, collection under air or nitrogen, and filter pore diameter. During well purging and sample collection, suspended particle size and number as well as dissolved oxygen, temperature, specific conductance, pH, and redox potential were monitored. Laboratory analyses of both unfiltered samples and the filtrates were performed by inductively coupled argon plasma, atomic absorption with graphite furnace, and ion chromatography. Scanning electron microscopy with Energy Dispersive X-ray was also used for analysis of filter particulates. Suspended particle counts consistently required approximately twice as long as the other field-monitored indicators to stabilize. High-flow-rate pumps entrained normally nonmobile particles. Difference in elemental concentrations using different filter-pore sizes were generally not large with only two wells having differences greater than 10 percent in most wells. Similar differences (>10%) were observed for some wells when samples were collected under nitrogen rather than in air. Fe2+/Fe3+ ratios for air-collected samples were smaller than for samples collected under a nitrogen atmosphere, reflecting sampling-induced oxidation.

Inferring microevolution from museum collections and resampling: lessons learned from Cepaea.

PubMed

Ożgo, Małgorzata; Liew, Thor-Seng; Webster, Nicole B; Schilthuizen, Menno

2017-01-01

Natural history collections are an important and largely untapped source of long-term data on evolutionary changes in wild populations. Here, we utilize three large geo-referenced sets of samples of the common European land-snail Cepaea nemoralis stored in the collection of Naturalis Biodiversity Center in Leiden, the Netherlands. Resampling of these populations allowed us to gain insight into changes occurring over 95, 69, and 50 years. Cepaea nemoralis is polymorphic for the colour and banding of the shell; the mode of inheritance of these patterns is known, and the polymorphism is under both thermal and predatory selection. At two sites the general direction of changes was towards lighter shells (yellow and less heavily banded), which is consistent with predictions based on on-going climatic change. At one site no directional changes were detected. At all sites there were significant shifts in morph frequencies between years, and our study contributes to the recognition that short-term changes in the states of populations often exceed long-term trends. Our interpretation was limited by the few time points available in the studied collections. We therefore stress the need for natural history collections to routinely collect large samples of common species, to allow much more reliable hind-casting of evolutionary responses to environmental change.

Optimization of scat detection methods for a social ungulate, the wild pig, and experimental evaluation of factors affecting detection of scat

USGS Publications Warehouse

Keiter, David A.; Cunningham, Fred L.; Rhodes, Olin E.; Irwin, Brian J.; Beasley, James

2016-01-01

Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocols with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig (Sus scrofa) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. Knowledge of relationships between environmental variables and scat detection may allow researchers to optimize sampling protocols to maximize utility of noninvasive sampling for wild pigs and other social ungulates.

Optimization of scat detection methods for a social ungulate, the wild pig, and experimental evaluation of factors affecting detection of scat

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

Keiter, David A.; Cunningham, Fred L.; Rhodes, Jr., Olin E.

Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocolsmore » with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig ( Sus scrofa) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. In conclusion, knowledge of relationships between environmental variables and scat detection may allow researchers to optimize sampling protocols to maximize utility of noninvasive sampling for wild pigs and other social ungulates.« less

Optimization of Scat Detection Methods for a Social Ungulate, the Wild Pig, and Experimental Evaluation of Factors Affecting Detection of Scat.

PubMed

Keiter, David A; Cunningham, Fred L; Rhodes, Olin E; Irwin, Brian J; Beasley, James C

2016-01-01

Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocols with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig (Sus scrofa) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. Knowledge of relationships between environmental variables and scat detection may allow researchers to optimize sampling protocols to maximize utility of noninvasive sampling for wild pigs and other social ungulates.

Optimization of scat detection methods for a social ungulate, the wild pig, and experimental evaluation of factors affecting detection of scat

DOE PAGES

Keiter, David A.; Cunningham, Fred L.; Rhodes, Jr., Olin E.; ...

2016-05-25

Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocolsmore » with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig ( Sus scrofa) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. In conclusion, knowledge of relationships between environmental variables and scat detection may allow researchers to optimize sampling protocols to maximize utility of noninvasive sampling for wild pigs and other social ungulates.« less

Fisheries research and monitoring activities of the Lake Erie Biological Station, 2013

USGS Publications Warehouse

Kraus, Richard T.; Rogers, Mark W.; Kocovsky, Patrick; Edwards, William; Bodamer Scarbro, Betsy L.; Keretz, Kevin R.; Berkman, Stephanie A.

2014-01-01

In 2013, the U.S. Geological Survey’s Lake Erie Biological Station successfully completed large vessel surveys in all three of Lake Erie’s basins. Lake Erie Biological Station’s primary vessel surveys included the Western Basin Forage Fish Assessment and East Harbor Forage Fish Assessment as well as contributing to the cooperative multi-agency Central Basin Hydroacoustics Assessment and the Eastern Basin Coldwater Community Assessment (see Forage Task Group and Coldwater Task Group reports, respectively). Further large vessel sampling included individual research data collection as well as assisting with University (e.g., University of Toledo) and agency (e.g., USFWS, USEPA) large vessel sampling needs. Our 2013 vessel operations began on April 4th and concluded on November 21 with a total of 77 large vessel sampling days (83 total days). During this time, crews of the R/V Muskie and R/V Bowfin deployed 174 trawls covering 147 km of lake-bottom, over 13 km of gillnet, collected hydroacoustic data that extended over 250 km of the central and eastern basins, and approximately 180 collective zooplankton, benthos, and water samples. 2013 was the first complete sampling year using the R/V Muskie. Technologies available on the new platform provided opportunities for LEBS to improve data sampling methods and results. An investment was made in mensuration gear for the trawls. This gear is attached to the trawl’s headrope, footrope, and wings; thus, allowing measurement of the area swept and conversion of catches to densities. Another improvement included real-time output of water parameter sonde profiles (e.g., temperature, dissolved oxygen). The ability to view profile data on a tablet allowed quick identification of thermoclines as well as the presence (or absence) of hypoxia. Minor modifications were made to survey designs relative to last year (see 2013 report), and thus, collection of long-term data from the R/V Muskie has commenced. One minor change was that we are now indexing yellow perch maturation data during our fall trawl surveys in response to a request from the Lake Erie Yellow Perch Task Group. Within the following sections, we describe results from our 2013 sampling efforts in Lake Erie.

Xenosurveillance reflects traditional sampling techniques for the identification of human pathogens: A comparative study in West Africa

PubMed Central

Fakoli, Lawrence S.; Bolay, Kpehe; Bolay, Fatorma K.; Diclaro, Joseph W.; Brackney, Doug E.; Stenglein, Mark D.; Ebel, Gregory D.

2018-01-01

Background Novel surveillance strategies are needed to detect the rapid and continuous emergence of infectious disease agents. Ideally, new sampling strategies should be simple to implement, technologically uncomplicated, and applicable to areas where emergence events are known to occur. To this end, xenosurveillance is a technique that makes use of blood collected by hematophagous arthropods to monitor and identify vertebrate pathogens. Mosquitoes are largely ubiquitous animals that often exist in sizable populations. As well, many domestic or peridomestic species of mosquitoes will preferentially take blood-meals from humans, making them a unique and largely untapped reservoir to collect human blood. Methodology/Principal findings We sought to take advantage of this phenomenon by systematically collecting blood-fed mosquitoes during a field trail in Northern Liberia to determine whether pathogen sequences from blood engorged mosquitoes accurately mirror those obtained directly from humans. Specifically, blood was collected from humans via finger-stick and by aspirating bloodfed mosquitoes from the inside of houses. Shotgun metagenomic sequencing of RNA and DNA derived from these specimens was performed to detect pathogen sequences. Samples obtained from xenosurveillance and from finger-stick blood collection produced a similar number and quality of reads aligning to two human viruses, GB virus C and hepatitis B virus. Conclusions/Significance This study represents the first systematic comparison between xenosurveillance and more traditional sampling methodologies, while also demonstrating the viability of xenosurveillance as a tool to sample human blood for circulating pathogens. PMID:29561834

Xenosurveillance reflects traditional sampling techniques for the identification of human pathogens: A comparative study in West Africa.

PubMed

Fauver, Joseph R; Weger-Lucarelli, James; Fakoli, Lawrence S; Bolay, Kpehe; Bolay, Fatorma K; Diclaro, Joseph W; Brackney, Doug E; Foy, Brian D; Stenglein, Mark D; Ebel, Gregory D

2018-03-01

Novel surveillance strategies are needed to detect the rapid and continuous emergence of infectious disease agents. Ideally, new sampling strategies should be simple to implement, technologically uncomplicated, and applicable to areas where emergence events are known to occur. To this end, xenosurveillance is a technique that makes use of blood collected by hematophagous arthropods to monitor and identify vertebrate pathogens. Mosquitoes are largely ubiquitous animals that often exist in sizable populations. As well, many domestic or peridomestic species of mosquitoes will preferentially take blood-meals from humans, making them a unique and largely untapped reservoir to collect human blood. We sought to take advantage of this phenomenon by systematically collecting blood-fed mosquitoes during a field trail in Northern Liberia to determine whether pathogen sequences from blood engorged mosquitoes accurately mirror those obtained directly from humans. Specifically, blood was collected from humans via finger-stick and by aspirating bloodfed mosquitoes from the inside of houses. Shotgun metagenomic sequencing of RNA and DNA derived from these specimens was performed to detect pathogen sequences. Samples obtained from xenosurveillance and from finger-stick blood collection produced a similar number and quality of reads aligning to two human viruses, GB virus C and hepatitis B virus. This study represents the first systematic comparison between xenosurveillance and more traditional sampling methodologies, while also demonstrating the viability of xenosurveillance as a tool to sample human blood for circulating pathogens.

Fluid sample collection and distribution system. [qualitative analysis of aqueous samples from several points

NASA Technical Reports Server (NTRS)

Brooks, R. L. (Inventor)

1979-01-01

A multipoint fluid sample collection and distribution system is provided wherein the sample inputs are made through one or more of a number of sampling valves to a progressive cavity pump which is not susceptible to damage by large unfiltered particles. The pump output is through a filter unit that can provide a filtered multipoint sample. An unfiltered multipoint sample is also provided. An effluent sample can be taken and applied to a second progressive cavity pump for pumping to a filter unit that can provide one or more filtered effluent samples. The second pump can also provide an unfiltered effluent sample. Means are provided to periodically back flush each filter unit without shutting off the whole system.

Chemistry of water collected from an unventilated drift, Yucca Mountain, Nevada

USGS Publications Warehouse

Marshall, B.D.; Oliver, T.A.; Peterman, Z.E.

2007-01-01

Water samples (referred to as puddle water samples) were collected from the surfaces of a conveyor belt and plastic sheeting in the unventilated portion of the Enhanced Characterization of the Repository Block (ECRB) Cross Drift in 2003 and 2005 at Yucca Mountain, Nevada. The chemistry of these puddle water samples is very different than that of pore water samples from borehole cores in the same region of the Cross Drift or than seepage water samples collected from the Exploratory Studies Facility tunnel in 2005. The origin of the puddle water is condensation on surfaces of introduced materials and its chemistry is dominated by components of the introduced materials. Large CO2 concentrations may be indicative of localized chemical conditions induced by biologic activity. ?? 2007 Materials Research Society.

A PRIOR EVALUATION OF TWO-STAGE CLUSTER SAMPLING FOR ACCURACY ASSESSMENT OF LARGE-AREA LAND-COVER MAPS

EPA Science Inventory

Two-stage cluster sampling reduces the cost of collecting accuracy assessment reference data by constraining sample elements to fall within a limited number of geographic domains (clusters). However, because classification error is typically positively spatially correlated, withi...

The brominated flame retardants, PBDEs and HBCD, in Canadian human milk samples collected from 1992 to 2005; concentrations and trends.

PubMed

Ryan, John Jake; Rawn, Dorothea F K

2014-09-01

Human milk samples were collected from individuals residing in various regions across Canada mostly in the years 1992 to 2005. These included five large cities in southern Canada as well as samples from Nunavik in northern Quebec. Comparative samples were also collected from residents of Austin, Texas, USA in 2002 and 2004. More than 300 milk samples were analysed for the brominated flame retardants (BFRs), PBDEs and HBCD, by extraction, purification and quantification using either isotope dilution gas chromatography-mass spectrometry (GC-MS) or liquid chromatography-MS. The Canadian total PBDE values in the years 2002-2005 show median levels of about 20μg/kg on a lipid basis; a value significantly higher than in the 1980s and 1990s. Milk samples from Inuit donors in the northern region of Nunavik were slightly lower in PBDE concentrations than those from populated regions in the south of Quebec. Milk samples from Ontario contained slightly lower amounts of PBDEs in two time periods than those from Texas. HBCD levels in most milk samples were usually less than 1ppb milk lipid and dominated by the α-isomer. This large data set of BFRs in Canadian human milk demonstrates an increase in the last few decades in human exposure to BFRs which now appears to have stabilized. Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

Impact of Use of Smaller Volume, Smaller Vacuum Blood Collection Tubes on Hemolysis in Emergency Department Blood Samples.

PubMed

Phelan, Michael P; Reineks, Edmunds Z; Berriochoa, Jacob P; Schold, Jesse D; Hustey, Fredric M; Chamberlin, Janelle; Kovach, Annmarie

2017-10-01

Hemolyzed blood samples commonly occur in hospital emergency departments (EDs). Our objective was to determine whether replacing standard large-volume/high-vacuum sample tubes with low-volume/low-vacuum tubes would significantly affect ED hemolysis. This was a prospective intervention of the use of small-volume/vacuum collection tubes. We evaluated all potassium samples in ED patients and associated hemolysis. We used χ2 tests to compare hemolysis incidence prior to and following utilization of small tubes for chemistry collection. There were 35,481 blood samples collected during the study period. Following implementation of small-volume tubes, overall hemolysis decreased from a baseline of 11.8% to 2.9% (P < .001) with corresponding reductions in hemolysis with comment (8.95% vs 1.99%; P < .001) gross hemolysis (2.84% vs 0.90%; P < .007). This work demonstrates that significant improvements in ED hemolysis can be achieved by utilization of small-volume/vacuum sample collection tubes. © American Society for Clinical Pathology, 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Iberian fish records in the vertebrate collection of the Museum of Zoology of the University of Navarra

PubMed Central

Rodeles, Amaia A.; Galicia, David; Miranda, Rafael

2016-01-01

The study of freshwater fish species biodiversity and community composition is essential for understanding river systems, the effects of human activities on rivers, and the changes these animals face. Conducting this type of research requires quantitative information on fish abundance, ideally with long-term series and fish body measurements. This Data Descriptor presents a collection of 12 datasets containing a total of 146,342 occurrence records of 41 freshwater fish species sampled in 233 localities of various Iberian river basins. The datasets also contain 148,749 measurement records (length and weight) for these fish. Data were collected in different sampling campaigns (from 1992 to 2015). Eleven datasets represent large projects conducted over several years, and another combines small sampling campaigns. The Iberian Peninsula contains high fish biodiversity, with numerous endemic species threatened by various menaces, such as water extraction and invasive species. These data may support the development of large biodiversity conservation studies. PMID:27727236

Iberian fish records in the vertebrate collection of the Museum of Zoology of the University of Navarra.

PubMed

Rodeles, Amaia A; Galicia, David; Miranda, Rafael

2016-10-11

The study of freshwater fish species biodiversity and community composition is essential for understanding river systems, the effects of human activities on rivers, and the changes these animals face. Conducting this type of research requires quantitative information on fish abundance, ideally with long-term series and fish body measurements. This Data Descriptor presents a collection of 12 datasets containing a total of 146,342 occurrence records of 41 freshwater fish species sampled in 233 localities of various Iberian river basins. The datasets also contain 148,749 measurement records (length and weight) for these fish. Data were collected in different sampling campaigns (from 1992 to 2015). Eleven datasets represent large projects conducted over several years, and another combines small sampling campaigns. The Iberian Peninsula contains high fish biodiversity, with numerous endemic species threatened by various menaces, such as water extraction and invasive species. These data may support the development of large biodiversity conservation studies.

Current collection from the space plasma through defects in high voltage solar array insulation. Ph.D. Thesis. Final Report

NASA Technical Reports Server (NTRS)

Stillwell, R. P.

1983-01-01

For spacecraft operation in the near Earth environment, solar cell arrays constitute the major source of reliable long term power. Optimization of mass and power efficiency results in a general requirement for high voltage solar arrays. The space plasma environment, though, can result in large currents being collected by exposed solar cells. The solution of a protective covering of transparent insulation is not a complete solution, inasmuch as defects in the insulation result in anomalously large currents being collected through the defects. Tests simulating the electron collection from small defects in an insulation have shown that there are two major collection modes. The first mode involves current enhancement by means of a surface phenomenon involving the surrounding insulator. In the second mode the current collection is enhanced by vaporization and ionization of the insulators materials, in addition to the surface enhancement of the first mode. A model for the electron collection is the surface enhanced collection mode was developed. The model relates the secondary electron emission yield to the electron collection. It correctly predicts the qualitative effects of hole size, sample temperature and roughening of sample surface. The theory was also shown to predict electron collection within a factor of two for the polymers teflon and polyimide.

THE QUANTIFICATION OF AQUEOUS TRACERS IN LABORATORY AQUIFER MODELS USING LIGHT TRANSMISSION VISUALIZATION METHOD

EPA Science Inventory

The quantification of solute concentrations in laboratory aquifer models has been largely limited to the use of sampling ports, from which samples are collected for external analysis. One of the drawbacks to this method is that the act of sampling may disturb plume dynamics and ...

Method and Apparatus for the Collection Storage and Real Time Analysis of Blood and Other Bodily Fluids

NASA Technical Reports Server (NTRS)

Whitson, Peggy A. (Inventor); Clift, Vaughan L. (Inventor)

1997-01-01

The present invention provides an apparatus for separating a relatively large volume of blood into cellular and acellular fractions without the need for centrifugation. The apparatus comprises a housing divided by a fibrous filter into a blood sample collection chamber having a volume of at least about 1 milliliter and a serum sample collection chamber. The fibrous filter has a pore size of less than about 3 microns, and is coated with a mixture of mannitol and plasma fraction protein (or an animal or vegetable equivalent thereof). The coating causes the cellular fraction to be trapped by the small pores, leaving the cellular fraction intact on the fibrous filter while the acellular fraction passes through the filter for collection in unaltered form from the serum sample collection chamber.

Differences in results of analyses of concurrent and split stream-water samples collected and analyzed by the US Geological Survey and the Illinois Environmental Protection Agency, 1985-91

USGS Publications Warehouse

Melching, C.S.; Coupe, R.H.

1995-01-01

During water years 1985-91, the U.S. Geological Survey (USGS) and the Illinois Environmental Protection Agency (IEPA) cooperated in the collection and analysis of concurrent and split stream-water samples from selected sites in Illinois. Concurrent samples were collected independently by field personnel from each agency at the same time and sent to the IEPA laboratory, whereas the split samples were collected by USGS field personnel and divided into aliquots that were sent to each agency's laboratory for analysis. The water-quality data from these programs were examined by means of the Wilcoxon signed ranks test to identify statistically significant differences between results of the USGS and IEPA analyses. The data sets for constituents and properties identified by the Wilcoxon test as having significant differences were further examined by use of the paired t-test, mean relative percentage difference, and scattergrams to determine if the differences were important. Of the 63 constituents and properties in the concurrent-sample analysis, differences in only 2 (pH and ammonia) were statistically significant and large enough to concern water-quality engineers and planners. Of the 27 constituents and properties in the split-sample analysis, differences in 9 (turbidity, dissolved potassium, ammonia, total phosphorus, dissolved aluminum, dissolved barium, dissolved iron, dissolved manganese, and dissolved nickel) were statistically significant and large enough to con- cern water-quality engineers and planners. The differences in concentration between pairs of the concurrent samples were compared to the precision of the laboratory or field method used. The differences in concentration between pairs of the concurrent samples were compared to the precision of the laboratory or field method used. The differences in concentration between paris of split samples were compared to the precision of the laboratory method used and the interlaboratory precision of measuring a given concentration or property. Consideration of method precision indicated that differences between concurrent samples were insignificant for all concentrations and properties except pH, and that differences between split samples were significant for all concentrations and properties. Consideration of interlaboratory precision indicated that the differences between the split samples were not unusually large. The results for the split samples illustrate the difficulty in obtaining comparable and accurate water-quality data.

A global database of ant species abundances

USGS Publications Warehouse

Gibb, Heloise; Dunn, Rob R.; Sanders, Nathan J.; Grossman, Blair F.; Photakis, Manoli; Abril, Silvia; Agosti, Donat; Andersen, Alan N.; Angulo, Elena; Armbrecht, Ingre; Arnan, Xavier; Baccaro, Fabricio B.; Bishop, Tom R.; Boulay, Raphael; Bruhl, Carsten; Castracani, Cristina; Cerda, Xim; Del Toro, Israel; Delsinne, Thibaut; Diaz, Mireia; Donoso, David A.; Ellison, Aaron M.; Enriquez, Martha L.; Fayle, Tom M.; Feener Jr., Donald H.; Fisher, Brian L.; Fisher, Robert N.; Fitpatrick, Matthew C.; Gomez, Cristanto; Gotelli, Nicholas J.; Gove, Aaron; Grasso, Donato A.; Groc, Sarah; Guenard, Benoit; Gunawardene, Nihara; Heterick, Brian; Hoffmann, Benjamin; Janda, Milan; Jenkins, Clinton; Kaspari, Michael; Klimes, Petr; Lach, Lori; Laeger, Thomas; Lattke, John; Leponce, Maurice; Lessard, Jean-Philippe; Longino, John; Lucky, Andrea; Luke, Sarah H.; Majer, Jonathan; McGlynn, Terrence P.; Menke, Sean; Mezger, Dirk; Mori, Alessandra; Moses, Jimmy; Munyai, Thinandavha Caswell; Pacheco, Renata; Paknia, Omid; Pearce-Duvet, Jessica; Pfeiffer, Martin; Philpott, Stacy M.; Resasco, Julian; Retana, Javier; Silva, Rogerio R.; Sorger, Magdalena D.; Souza, Jorge; Suarez, Andrew V.; Tista, Melanie; Vasconcelos, Heraldo L.; Vonshak, Merav; Weiser, Michael D.; Yates, Michelle; Parr, Catherine L.

2017-01-01

What forces structure ecological assemblages? A key limitation to general insights about assemblage structure is the availability of data that are collected at a small spatial grain (local assemblages) and a large spatial extent (global coverage). Here, we present published and unpublished data from 51,388 ant abundance and occurrence records of more than 2693 species and 7953 morphospecies from local assemblages collected at 4212 locations around the world. Ants were selected because they are diverse and abundant globally, comprise a large fraction of animal biomass in most terrestrial communities, and are key contributors to a range of ecosystem functions. Data were collected between 1949 and 2014, and include, for each geo-referenced sampling site, both the identity of the ants collected and details of sampling design, habitat type and degree of disturbance. The aim of compiling this dataset was to provide comprehensive species abundance data in order to test relationships between assemblage structure and environmental and biogeographic factors. Data were collected using a variety of standardised methods, such as pitfall and Winkler traps, and will be valuable for studies investigating large-scale forces structuring local assemblages. Understanding such relationships is particularly critical under current rates of global change. We encourage authors holding additional data on systematically collected ant assemblages, especially those in dry and cold, and remote areas, to contact us and contribute their data to this growing dataset.

Rare Earth Element and Trace Element Data Associated with Hydrothermal Spring Reservoir Rock, Idaho

DOE Data Explorer

Quillinan, Scott; Bagdonas, Davin

2017-06-22

These data represent rock samples collected in Idaho that correspond with naturally occurring hydrothermal samples that were collected and analyzed by INL (Idaho Falls, ID). Representative samples of type rocks were selected to best represent the various regions of Idaho in which naturally occurring hydrothermal waters occur. This includes the Snake River Plain (SRP), Basin and Range type structures east of the SRP, and large scale/deep seated orogenic uplift of the Sawtooth Mountains, ID. Analysis includes ICP-OES and ICP-MS methods for Major, Trace, and REE concentrations.

Astronaut John Young photographed collecting lunar samples

NASA Technical Reports Server (NTRS)

1972-01-01

Astronaut John W. Young, commander of the Apollo 16 lunar landing mission, is photographed collecting lunar samples near North Ray crater during the third Apollo 16 extravehicular activity (EVA-3) at the Descartes landing site. This picture was taken by Astronaut Charles M. Duke Jr., lunar module pilot. Young is using the lunar surface rake and a set of tongs. The Lunar Roving Vehicle is parked in the field of large boulders in the background.

THE QUANTIFICATION OF AQUEOUS TRACERS IN LABORATORY AQUIFER MODELS USING A LIGHT TRANSMISSION VISUALIZATION METHOD - 3

EPA Science Inventory

The quantification of solute concentrations in laboratory aquifer models has been largely limited to the use of sampling ports, from which samples are collected for external analysis. One of the drawbacks to this method is that the act of sampling may disturb plume dynamics and ...

THE QUANTIFICATION OF AQUEOUS TRACERS IN LABORATORY AQUIFER MODELS USING A LIGHT TRANSMISSION VISUALIZATION METHOD - 2

EPA Science Inventory

The quantification of solute concentrations in laboratory aquifer models has been largely limited to the use of sampling ports, from which samples are collected for external analysis. One of the drawbacks to this method is that the act of sampling may disturb plume dynamics and ...

THE QUANTIFICATION OF AQUEOUS TRACERS IN LABORATORY AQUIFER MODELS USING A LIGHT TRANSMISSION VISUALIZATION METHOD - 1

EPA Science Inventory

The quantification of solute concentrations in laboratory aquifer models has been largely limited to the use of sampling ports, from which samples are collected for external analysis. One of the drawbacks to this method is that the act of sampling may disturb plume dynamics and ...

DogMATIC--A Remote Biospecimen Collection Kit for Biobanking.

PubMed

Milley, Kristi M; Nimmo, Judith S; Bacci, Barbara; Ryan, Stewart D; Richardson, Samantha J; Danks, Janine A

2015-08-01

Canine tumors are valuable comparative oncology models. This research was designed to create a sustainable biobank of canine mammary tumors for breast cancer research. The aim was to provide a well-characterized sample cohort for specimen sharing, data mining, and long-term research aims. Canine mammary tumors are most frequently managed at a local veterinary clinic or hospital. We adopted a biobank framework based on a large number of participating veterinary hospitals and clinics acting as collection centers that were serviced by a centralized storage facility. Recruitment was targeted at rural veterinary clinics. A tailored, stable collection kit (DogMATIC) was designed that was used by veterinarians in remote or rural locations to collect both fresh and fixed tissue for submission to the biobank. To validate this methodology the kit design, collection rate, and sample quality were analyzed. The Australian Veterinary Cancer Biobank was established as a network of 47 veterinary clinics and three veterinary pathology laboratories spanning over 200,000 km(2). In the first 12 months, 30 canine mammary tumor cases were submitted via the DogMATIC kit. Pure intact RNA was isolated in over 80% of samples with an average yield of 14.49 μg. A large network biobank, utilizing off-site collection with the DogMATIC kit, was successfully coordinated. The creation of the Australian Veterinary Cancer Biobank has established a long-term, sustainable, comparative oncology research resource in Australia. There are broader implications for biobanking with this very different form of collection and banking.

25OHD analogues and vacuum blood collection tubes dramatically affect the accuracy of automated immunoassays

PubMed Central

Yu, Songlin; Cheng, Xinqi; Fang, Huiling; Zhang, Ruiping; Han, Jianhua; Qin, Xuzhen; Cheng, Qian; Su, Wei; Hou, Li’an; Xia, Liangyu; Qiu, Ling

2015-01-01

Variations in vitamin D quantification methods are large, and influences of vitamin D analogues and blood collection methods have not been systematically examined. We evaluated the effects of vitamin D analogues 25OHD2 and 3-epi 25OHD3 and blood collection methods on vitamin D measurement, using five immunoassay systems and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Serum samples (332) were selected from routine vitamin D assay requests, including samples with or without 25OHD2 or 3-epi 25OHD3, and analysed using various immunoassay systems. In samples with no 25OHD2 or 3-epi 25OHD3, all immunoassays correlated well with LC-MS/MS. However, the Siemens system produced a large positive mean bias of 12.5 ng/mL and a poor Kappa value when using tubes with clot activator and gel separator. When 25OHD2 or 3-epi 25OHD3 was present, correlations and clinical agreement decreased for all immunoassays. Serum 25OHD in VACUETTE tubes with gel and clot activator, as measured by the Siemens system, produced significantly higher values than did samples collected in VACUETTE tubes with no additives. Bias decreased and clinical agreement improved significantly when using tubes with no additives. In conclusion, most automated immunoassays showed acceptable correlation and agreement with LC-MS/MS; however, 25OHD analogues and blood collection tubes dramatically affected accuracy. PMID:26420221

25OHD analogues and vacuum blood collection tubes dramatically affect the accuracy of automated immunoassays.

PubMed

Yu, Songlin; Cheng, Xinqi; Fang, Huiling; Zhang, Ruiping; Han, Jianhua; Qin, Xuzhen; Cheng, Qian; Su, Wei; Hou, Li'an; Xia, Liangyu; Qiu, Ling

2015-09-30

Variations in vitamin D quantification methods are large, and influences of vitamin D analogues and blood collection methods have not been systematically examined. We evaluated the effects of vitamin D analogues 25OHD2 and 3-epi 25OHD3 and blood collection methods on vitamin D measurement, using five immunoassay systems and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Serum samples (332) were selected from routine vitamin D assay requests, including samples with or without 25OHD2 or 3-epi 25OHD3, and analysed using various immunoassay systems. In samples with no 25OHD2 or 3-epi 25OHD3, all immunoassays correlated well with LC-MS/MS. However, the Siemens system produced a large positive mean bias of 12.5 ng/mL and a poor Kappa value when using tubes with clot activator and gel separator. When 25OHD2 or 3-epi 25OHD3 was present, correlations and clinical agreement decreased for all immunoassays. Serum 25OHD in VACUETTE tubes with gel and clot activator, as measured by the Siemens system, produced significantly higher values than did samples collected in VACUETTE tubes with no additives. Bias decreased and clinical agreement improved significantly when using tubes with no additives. In conclusion, most automated immunoassays showed acceptable correlation and agreement with LC-MS/MS; however, 25OHD analogues and blood collection tubes dramatically affected accuracy.

Breathing life into fisheries stock assessments with citizen science

PubMed Central

Fairclough, D. V.; Brown, J. I.; Carlish, B. J.; Crisafulli, B. M.; Keay, I. S.

2014-01-01

Citizen science offers a potentially cost-effective way for researchers to obtain large data sets over large spatial scales. However, it is not used widely to support biological data collection for fisheries stock assessments. Overfishing of demersal fishes along 1,000 km of the west Australian coast led to restrictive management to recover stocks. This diminished opportunities for scientists to cost-effectively monitor stock recovery via fishery-dependent sampling, particularly of the recreational fishing sector. As fishery-independent methods would be too expensive and logistically-challenging to implement, a citizen science program, Send us your skeletons (SUYS), was developed. SUYS asks recreational fishers to voluntarily donate fish skeletons of important species from their catch to allow biological data extraction by scientists to produce age structures and conduct stock assessment analyses. During SUYS, recreational fisher involvement, sample sizes and spatial and temporal coverage of samples have dramatically increased, while the collection cost per skeleton has declined substantially. SUYS is ensuring sampling objectives for stock assessments are achieved via fishery-dependent collection and reliable and timely scientific advice can be provided to managers. The program is also encouraging public ownership through involvement in the monitoring process, which can lead to greater acceptance of management decisions. PMID:25431103

Breathing life into fisheries stock assessments with citizen science.

PubMed

Fairclough, D V; Brown, J I; Carlish, B J; Crisafulli, B M; Keay, I S

2014-11-28

Citizen science offers a potentially cost-effective way for researchers to obtain large data sets over large spatial scales. However, it is not used widely to support biological data collection for fisheries stock assessments. Overfishing of demersal fishes along 1,000 km of the west Australian coast led to restrictive management to recover stocks. This diminished opportunities for scientists to cost-effectively monitor stock recovery via fishery-dependent sampling, particularly of the recreational fishing sector. As fishery-independent methods would be too expensive and logistically-challenging to implement, a citizen science program, Send us your skeletons (SUYS), was developed. SUYS asks recreational fishers to voluntarily donate fish skeletons of important species from their catch to allow biological data extraction by scientists to produce age structures and conduct stock assessment analyses. During SUYS, recreational fisher involvement, sample sizes and spatial and temporal coverage of samples have dramatically increased, while the collection cost per skeleton has declined substantially. SUYS is ensuring sampling objectives for stock assessments are achieved via fishery-dependent collection and reliable and timely scientific advice can be provided to managers. The program is also encouraging public ownership through involvement in the monitoring process, which can lead to greater acceptance of management decisions.

The Dutch Pancreas Biobank Within the Parelsnoer Institute: A Nationwide Biobank of Pancreatic and Periampullary Diseases.

PubMed

Strijker, Marin; Gerritsen, Arja; van Hilst, Jony; Bijlsma, Maarten F; Bonsing, Bert A; Brosens, Lodewijk A; Bruno, Marco J; van Dam, Ronald M; Dijk, Frederike; van Eijck, Casper H; Farina Sarasqueta, Arantza; Fockens, Paul; Gerhards, Michael F; Groot Koerkamp, Bas; van der Harst, Erwin; de Hingh, Ignace H; van Hooft, Jeanin E; Huysentruyt, Clément J; Kazemier, Geert; Klaase, Joost M; van Laarhoven, Cornelis J; van Laarhoven, Hanneke W; Liem, Mike S; de Meijer, Vincent E; van Rijssen, L Bengt; van Santvoort, Hjalmar C; Suker, Mustafa; Verhagen, Judith H; Verheij, Joanne; Verspaget, Hein W; Wennink, Roos A; Wilmink, Johanna W; Molenaar, I Quintus; Boermeester, Marja A; Busch, Olivier R; Besselink, Marc G

2018-04-01

Large biobanks with uniform collection of biomaterials and associated clinical data are essential for translational research. The Netherlands has traditionally been well organized in multicenter clinical research on pancreatic diseases, including the nationwide multidisciplinary Dutch Pancreatic Cancer Group and Dutch Pancreatitis Study Group. To enable high-quality translational research on pancreatic and periampullary diseases, these groups established the Dutch Pancreas Biobank. The Dutch Pancreas Biobank is part of the Parelsnoer Institute and involves all 8 Dutch university medical centers and 5 nonacademic hospitals. Adult patients undergoing pancreatic surgery (all indications) are eligible for inclusion. Preoperative blood samples, tumor tissue from resected specimens, pancreatic cyst fluid, and follow-up blood samples are collected. Clinical parameters are collected in conjunction with the mandatory Dutch Pancreatic Cancer Audit. Between January 2015 and May 2017, 488 patients were included in the first 5 participating centers: 4 university medical centers and 1 nonacademic hospital. Over 2500 samples were collected: 1308 preoperative blood samples, 864 tissue samples, and 366 follow-up blood samples. Prospective collection of biomaterials and associated clinical data has started in the Dutch Pancreas Biobank. Subsequent translational research will aim to improve treatment decisions based on disease characteristics.

Lead in rice: analysis of baseline lead levels in market and field collected rice grains.

PubMed

Norton, Gareth J; Williams, Paul N; Adomako, Eureka E; Price, Adam H; Zhu, Yongguan; Zhao, Fang-Jie; McGrath, Steve; Deacon, Claire M; Villada, Antia; Sommella, Alessia; Lu, Ying; Ming, Lei; De Silva, P Mangala C S; Brammer, Hugh; Dasgupta, Tapash; Islam, M Rafiqul; Meharg, Andrew A

2014-07-01

In a large scale survey of rice grains from markets (13 countries) and fields (6 countries), a total of 1578 rice grain samples were analysed for lead. From the market collected samples, only 0.6% of the samples exceeded the Chinese and EU limit of 0.2 μg g(-1) lead in rice (when excluding samples collected from known contaminated/mine impacted regions). When evaluating the rice grain samples against the Food and Drug Administration's (FDA) provisional total tolerable intake (PTTI) values for children and pregnant women, it was found that only people consuming large quantities of rice were at risk of exceeding the PTTI from rice alone. Furthermore, 6 field experiments were conducted to evaluate the proportion of the variation in lead concentration in rice grains due to genetics. A total of 4 of the 6 field experiments had significant differences between genotypes, but when the genotypes common across all six field sites were assessed, only 4% of the variation was explained by genotype, with 9.5% and 11% of the variation explained by the environment and genotype by environment interaction respectively. Further work is needed to identify the sources of lead contamination in rice, with detailed information obtained on the locations and environments where the rice is sampled, so that specific risk assessments can be performed. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

Efficiency of Different Sampling Tools for Aquatic Macroinvertebrate Collections in Malaysian Streams

PubMed Central

Ghani, Wan Mohd Hafezul Wan Abdul; Rawi, Che Salmah Md; Hamid, Suhaila Abd; Al-Shami, Salman Abdo

2016-01-01

This study analyses the sampling performance of three benthic sampling tools commonly used to collect freshwater macroinvertebrates. Efficiency of qualitative D-frame and square aquatic nets were compared to a quantitative Surber sampler in tropical Malaysian streams. The abundance and diversity of macroinvertebrates collected using each tool evaluated along with their relative variations (RVs). Each tool was used to sample macroinvertebrates from three streams draining different areas: a vegetable farm, a tea plantation and a forest reserve. High macroinvertebrate diversities were recorded using the square net and Surber sampler at the forested stream site; however, very low species abundance was recorded by the Surber sampler. Relatively large variations in the Surber sampler collections (RVs of 36% and 28%) were observed for the vegetable farm and tea plantation streams, respectively. Of the three sampling methods, the square net was the most efficient, collecting a greater diversity of macroinvertebrate taxa and a greater number of specimens (i.e., abundance) overall, particularly from the vegetable farm and the tea plantation streams (RV<25%). Fewer square net sample passes (<8 samples) were sufficient to perform a biological assessment of water quality, but each sample required a slightly longer processing time (±20 min) compared with those gathered via the other samplers. In conclusion, all three apparatuses were suitable for macroinvertebrate collection in Malaysian streams and gathered assemblages that resulted in the determination of similar biological water quality classes using the Family Biotic Index (FBI) and the Biological Monitoring Working Party (BMWP). However, despite a slightly longer processing time, the square net was more efficient (lowest RV) at collecting samples and more suitable for the collection of macroinvertebrates from deep, fast flowing, wadeable streams with coarse substrates. PMID:27019685

Automated array assembly, phase 2

NASA Technical Reports Server (NTRS)

Carbajal, B. G.

1979-01-01

Tasks of scaling up the tandem junction cell (TJC) from 2 cm x 2 cm to 6.2 cm and the assembly of several modules using these large area TJC's are described. The scale-up of the TJC was based on using the existing process and doing the necessary design activities to increase the cell area to an acceptably large area. The design was carried out using available device models. The design was verified and sample large area TJCs were fabricated. Mechanical and process problems occurred causing a schedule slippage that resulted in contract expiration before enough large-area TJCs were fabricated to populate the sample tandem junction modules (TJM). A TJM design was carried out in which the module interconnects served to augment the current collecting buses on the cell. No sample TJMs were assembled due to a shortage of large-area TJCs.

LOGISTICS OF ECOLOGICAL SAMPLING ON LARGE RIVERS

EPA Science Inventory

The objectives of this document are to provide an overview of the logistical problems associated with the ecological sampling of boatable rivers and to suggest solutions to those problems. It is intended to be used as a resource for individuals preparing to collect biological dat...

Quality variations in black musli (curculigo orchioides gaertn.).

PubMed

Mathew, P P Joy Samuel; Savithri, K E; Skaria, Baby P; Kurien, Kochurani

2004-07-01

Black musli (Curculigo orchioides Gaertn.) one of the ayurvedic dasapushpa and a rejuvenating and aphrodisiac drug. Is on the verge of extinction and needs to be conserved and cultivated. Large variations are also observed in the quality of the crude drug available in the market. Study on the quality of C. orchioides in natural habitat, under cultivation and in trade in south India showed that there was considerable variation with biotypes and habitats. Drugs collected form the natural habitat was superior in quality to that produced by cultivation. Among the market samples collected from the various Zones of kerala, those from the High Ranges were superior in most of the quality parameters, which indicated its superiority for high quality drug formulation. Among the southern states, Tamil Nadu samples ranked next to High Range samples in this respect. There exists large variability in the market samples and there is felt-need for proper standardization of the crude drug for ensuring quality in the drug formulations.

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.

Workforce Readiness: A Study of University Students' Fluency with Information Technology

ERIC Educational Resources Information Center

Kaminski, Karen; Switzer, Jamie; Gloeckner, Gene

2009-01-01

This study with data collected from a large sample of freshmen in 2001 and a random stratified sample of seniors in 2005 examined students perceived FITness (fluency with Information Technology). In the fall of 2001 freshmen at a medium sized research-one institution completed a survey and in spring 2005 a random sample of graduating seniors…

BOREAS TE-2 NSA Soil Lab Data

NASA Technical Reports Server (NTRS)

Veldhuis, Hugo; Hall, Forrest G. (Editor); Knapp, David E. (Editor)

2000-01-01

This data set contains the major soil properties of soil samples collected in 1994 at the tower flux sites in the Northern Study Area (NSA). The soil samples were collected by Hugo Veldhuis and his staff from the University of Manitoba. The mineral soil samples were largely analyzed by Barry Goetz, under the supervision of Dr. Harold Rostad at the University of Saskatchewan. The organic soil samples were largely analyzed by Peter Haluschak, under the supervision of Hugo Veldhuis at the Centre for Land and Biological Resources Research in Winnipeg, Manitoba. During the course of field investigation and mapping, selected surface and subsurface soil samples were collected for laboratory analysis. These samples were used as benchmark references for specific soil attributes in general soil characterization. Detailed soil sampling, description, and laboratory analysis were performed on selected modal soils to provide examples of common soil physical and chemical characteristics in the study area. The soil properties that were determined include soil horizon; dry soil color; pH; bulk density; total, organic, and inorganic carbon; electric conductivity; cation exchange capacity; exchangeable sodium, potassium, calcium, magnesium, and hydrogen; water content at 0.01, 0.033, and 1.5 MPascals; nitrogen; phosphorus: particle size distribution; texture; pH of the mineral soil and of the organic soil; extractable acid; and sulfur. These data are stored in ASCII text files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

Non-Destructive Classification Approaches for Equilbrated Ordinary Chondrites

NASA Technical Reports Server (NTRS)

Righter, K.; Harrington, R.; Schroeder, C.; Morris, R. V.

2013-01-01

Classification of meteorites is most effectively carried out by petrographic and mineralogic studies of thin sections, but a rapid and accurate classification technique for the many samples collected in dense collection areas (hot and cold deserts) is of great interest. Oil immersion techniques have been used to classify a large proportion of the US Antarctic meteorite collections since the mid-1980s [1]. This approach has allowed rapid characterization of thousands of samples over time, but nonetheless utilizes a piece of the sample that has been ground to grains or a powder. In order to compare a few non-destructive techniques with the standard approaches, we have characterized a group of chondrites from the Larkman Nunatak region using magnetic susceptibility and Moessbauer spectroscopy.

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.

Human and bovine viruses in urban and rural streams: Hydrologic and season patterns of wastewater influence

USDA-ARS?s Scientific Manuscript database

Viruses are the cause of many waterborne diseases contracted from fecal-contaminated waters. Collection of samples that properly represent virus concentrations throughout relevant hydrologic periods has historically been difficult due to the large water volume collection and filtration required for ...

A novel portable filtration system for sampling and concentration of microorganisms: Demonstration on marine microalgae with subsequent quantification using IC-NASBA.

PubMed

Loukas, Christos-Moritz; Mowlem, Matthew C; Tsaloglou, Maria-Nefeli; Green, Nicolas G

2018-05-01

This paper presents a novel portable sample filtration/concentration system, designed for use on samples of microorganisms with very low cell concentrations and large volumes, such as water-borne parasites, pathogens associated with faecal matter, or toxic phytoplankton. The example application used for demonstration was the in-field collection and concentration of microalgae from seawater samples. This type of organism is responsible for Harmful Algal Blooms (HABs), an example of which is commonly referred to as "red tides", which are typically the result of rapid proliferation and high biomass accumulation of harmful microalgal species in the water column or at the sea surface. For instance, Karenia brevis red tides are the cause of aquatic organism mortality and persistent blooms may cause widespread die-offs of populations of other organisms including vertebrates. In order to respond to, and adequately manage HABs, monitoring of toxic microalgae is required and large-volume sample concentrators would be a useful tool for in situ monitoring of HABs. The filtering system presented in this work enables consistent sample collection and concentration from 1 L to 1 mL in five minutes, allowing for subsequent benchtop sample extraction and analysis using molecular methods such as NASBA and IC-NASBA. The microalga Tetraselmis suecica was successfully detected at concentrations ranging from 2 × 10 5  cells/L to 20 cells/L. Karenia brevis was also detected and quantified at concentrations between 10 cells/L and 10 6  cells/L. Further analysis showed that the filter system, which concentrates cells from very large volumes with consequently more reliable sampling, produced samples that were more consistent than the independent non-filtered samples (benchtop controls), with a logarithmic dependency on increasing cell numbers. This filtering system provides simple, rapid, and consistent sample collection and concentration for further analysis, and could be applied to a wide range of different samples and target organisms in situations lacking laboratories. Copyright © 2018. Published by Elsevier B.V.

Evaluation of the Biological Sampling Kit (BiSKit) for Large-Area Surface Sampling

PubMed Central

Buttner, Mark P.; Cruz, Patricia; Stetzenbach, Linda D.; Klima-Comba, Amy K.; Stevens, Vanessa L.; Emanuel, Peter A.

2004-01-01

Current surface sampling methods for microbial contaminants are designed to sample small areas and utilize culture analysis. The total number of microbes recovered is low because a small area is sampled, making detection of a potential pathogen more difficult. Furthermore, sampling of small areas requires a greater number of samples to be collected, which delays the reporting of results, taxes laboratory resources and staffing, and increases analysis costs. A new biological surface sampling method, the Biological Sampling Kit (BiSKit), designed to sample large areas and to be compatible with testing with a variety of technologies, including PCR and immunoassay, was evaluated and compared to other surface sampling strategies. In experimental room trials, wood laminate and metal surfaces were contaminated by aerosolization of Bacillus atrophaeus spores, a simulant for Bacillus anthracis, into the room, followed by settling of the spores onto the test surfaces. The surfaces were sampled with the BiSKit, a cotton-based swab, and a foam-based swab. Samples were analyzed by culturing, quantitative PCR, and immunological assays. The results showed that the large surface area (1 m2) sampled with the BiSKit resulted in concentrations of B. atrophaeus in samples that were up to 10-fold higher than the concentrations obtained with the other methods tested. A comparison of wet and dry sampling with the BiSKit indicated that dry sampling was more efficient (efficiency, 18.4%) than wet sampling (efficiency, 11.3%). The sensitivities of detection of B. atrophaeus on metal surfaces were 42 ± 5.8 CFU/m2 for wet sampling and 100.5 ± 10.2 CFU/m2 for dry sampling. These results demonstrate that the use of a sampling device capable of sampling larger areas results in higher sensitivity than that obtained with currently available methods and has the advantage of sampling larger areas, thus requiring collection of fewer samples per site. PMID:15574898

A global database of ant species abundances.

PubMed

Gibb, Heloise; Dunn, Rob R; Sanders, Nathan J; Grossman, Blair F; Photakis, Manoli; Abril, Silvia; Agosti, Donat; Andersen, Alan N; Angulo, Elena; Armbrecht, Inge; Arnan, Xavier; Baccaro, Fabricio B; Bishop, Tom R; Boulay, Raphaël; Brühl, Carsten; Castracani, Cristina; Cerda, Xim; Del Toro, Israel; Delsinne, Thibaut; Diaz, Mireia; Donoso, David A; Ellison, Aaron M; Enriquez, Martha L; Fayle, Tom M; Feener, Donald H; Fisher, Brian L; Fisher, Robert N; Fitzpatrick, Matthew C; Gómez, Crisanto; Gotelli, Nicholas J; Gove, Aaron; Grasso, Donato A; Groc, Sarah; Guenard, Benoit; Gunawardene, Nihara; Heterick, Brian; Hoffmann, Benjamin; Janda, Milan; Jenkins, Clinton; Kaspari, Michael; Klimes, Petr; Lach, Lori; Laeger, Thomas; Lattke, John; Leponce, Maurice; Lessard, Jean-Philippe; Longino, John; Lucky, Andrea; Luke, Sarah H; Majer, Jonathan; McGlynn, Terrence P; Menke, Sean; Mezger, Dirk; Mori, Alessandra; Moses, Jimmy; Munyai, Thinandavha Caswell; Pacheco, Renata; Paknia, Omid; Pearce-Duvet, Jessica; Pfeiffer, Martin; Philpott, Stacy M; Resasco, Julian; Retana, Javier; Silva, Rogerio R; Sorger, Magdalena D; Souza, Jorge; Suarez, Andrew; Tista, Melanie; Vasconcelos, Heraldo L; Vonshak, Merav; Weiser, Michael D; Yates, Michelle; Parr, Catherine L

2017-03-01

What forces structure ecological assemblages? A key limitation to general insights about assemblage structure is the availability of data that are collected at a small spatial grain (local assemblages) and a large spatial extent (global coverage). Here, we present published and unpublished data from 51 ,388 ant abundance and occurrence records of more than 2,693 species and 7,953 morphospecies from local assemblages collected at 4,212 locations around the world. Ants were selected because they are diverse and abundant globally, comprise a large fraction of animal biomass in most terrestrial communities, and are key contributors to a range of ecosystem functions. Data were collected between 1949 and 2014, and include, for each geo-referenced sampling site, both the identity of the ants collected and details of sampling design, habitat type, and degree of disturbance. The aim of compiling this data set was to provide comprehensive species abundance data in order to test relationships between assemblage structure and environmental and biogeographic factors. Data were collected using a variety of standardized methods, such as pitfall and Winkler traps, and will be valuable for studies investigating large-scale forces structuring local assemblages. Understanding such relationships is particularly critical under current rates of global change. We encourage authors holding additional data on systematically collected ant assemblages, especially those in dry and cold, and remote areas, to contact us and contribute their data to this growing data set. © 2016 by the Ecological Society of America.

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

Broxton, D.E.

A total of 338 water and 1877 sediment samples were collected over a 20,700-km/sup 2/ area from 2125 locations at a nominal density of one sample per 10 km/sup 2/. Water samples were collected from wells, streams, springs, and artificial ponds. Sediment samples were collected from streams, springs, natural ponds, and artificial ponds. Arbitrary anomaly thresholds of two standard deviations above the mean were chosen for both water and sediment sample populations. The U concentrations in waters collected in the Tularosa quadrangle range from below the detection limit of 0.2 parts per billion (ppB) to 57.8 ppB. Most clusters ofmore » water samples containing anomalously high uranium concentrations were collected from locations in uplifts underlain either by volcanic rocks of the mid-Tertiary Datil group or by sedimentary rocks of late Paleozoic and Mesozoic age. Other groups of anomalous waters are from wells that tap Cenozoic aquifers in the intermontane basins. In those areas where the water-sample location coverage is adequate, the known U occurrences are generally associated with high or anomalous U concentrations in water samples. With the exception of one sample with a U concentration of 67.7 ppM, sediments collected in this study have U concentrations that range between 0.2 and 15.2 ppM. Most sediments with U concentrations above the arbitrary anomaly threshold value are from locations which occur in or parallel outcrops of Precambrian crystalline rock exposed in the San Andres and Oscura Mountains. Other anomalous sediments occur as more discreet groups in areas underlain by mid-Tertiary volcanic rocks of the Datil group. Several anomalous samples from the Mogollon-Datil volcanic field were collected along ring fracture systems that surround large volcanic cauldrons.« less

A robust clustering algorithm for identifying problematic samples in genome-wide association studies.

PubMed

Bellenguez, Céline; Strange, Amy; Freeman, Colin; Donnelly, Peter; Spencer, Chris C A

2012-01-01

High-throughput genotyping arrays provide an efficient way to survey single nucleotide polymorphisms (SNPs) across the genome in large numbers of individuals. Downstream analysis of the data, for example in genome-wide association studies (GWAS), often involves statistical models of genotype frequencies across individuals. The complexities of the sample collection process and the potential for errors in the experimental assay can lead to biases and artefacts in an individual's inferred genotypes. Rather than attempting to model these complications, it has become a standard practice to remove individuals whose genome-wide data differ from the sample at large. Here we describe a simple, but robust, statistical algorithm to identify samples with atypical summaries of genome-wide variation. Its use as a semi-automated quality control tool is demonstrated using several summary statistics, selected to identify different potential problems, and it is applied to two different genotyping platforms and sample collections. The algorithm is written in R and is freely available at www.well.ox.ac.uk/chris-spencer chris.spencer@well.ox.ac.uk Supplementary data are available at Bioinformatics online.

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%.

Evaluation of a novel dried blood spot collection device (HemaSpot™) to test blood samples collected from dogs for antibodies to Leishmania infantum.

PubMed

Rosypal, Alexa C; Pick, Leanne D; Hernandez, Jaime O Esquivel; Lindsay, David S

2014-09-15

Collection of blood samples from veterinary and wildlife patients is often challenging because the samples have to be collected on farm or in the wild under various environmental conditions. This poses many technical problems associated with venipuncture materials, their safe use and disposal, transportation and processing of collected samples. Dried blood spot (DBS) sample collection techniques offer a simple and practical alternative to traditional blood collection methods to obtain blood samples from animals for parasite antibody evaluation. The DBS collection devices are compact, simple to use, and are particularly useful for large number of samples. Additionally, DBS samples take up less space and they are easier to transport than traditional venipuncture-collected blood samples. Visceral leishmaniasis (VL) is a potentially fatal parasitic disease of dogs and humans and it is frequently diagnosed by antibody tests. Immunochromatographic tests (ICT) for antibodies to Leishmania infantum are commercially available for dogs and they produce qualitative results in minutes. Measurement of canine antibodies to L. infantum with the ICT using traditional venipuncture has been validated previously, but the use of DBS samples has not been evaluated using this method. The purpose of the present study was to determine the ability of DBS samples to detect antibodies to L. infantum in dogs using a commercial ICT assay. One hundred plasma samples from dogs experimentally infected with the LIVT-1 strain of L. infantum were collected by venipuncture and frozen. Individual samples were thawed, and then 80 μl plasma (2 drops) was aliquotted onto the 8-spoked disk pad on individual DBS sample collection devices (HemaSpot™, Spot-On Sciences, Austin, TX), dried, and stored in the dark at room temperature. After one month and six months, respectively, 2 spokes of the 8 spokes of the disk pad of each DBS sample were removed and eluted in 200 μl PBS. The eluate was used to test for antibodies in the ICT and compared to ICT results using thawed plasma (same initial source). Sensitivity and specificity of the ICT using DBS were determined by using ICT results from traditional blood collection samples for comparison. After 1 month, DBS samples showed 100% sensitivity and specificity when compared to ICT results on thawed plasma samples collected by traditional venipuncture. After six months storage at room temperature, DBS samples demonstrated 79% sensitivity and 100% specificity compared to traditional blood collection. Results from this study indicate that dried blood spot collection may be a useful tool for screening dogs for antibodies to L. infantum with the ICT assay. Copyright © 2014 Elsevier B.V. All rights reserved.

A comparison of liver sampling techniques in dogs.

PubMed

Kemp, S D; Zimmerman, K L; Panciera, D L; Monroe, W E; Leib, M S; Lanz, O I

2015-01-01

The liver sampling technique in dogs that consistently provides samples adequate for accurate histopathologic interpretation is not known. To compare histopathologic results of liver samples obtained by punch, cup, and 14 gauge needle to large wedge samples collected at necropsy. Seventy dogs undergoing necropsy. Prospective study. Liver specimens were obtained from the left lateral liver lobe with an 8 mm punch, a 5 mm cup, and a 14 gauge needle. After sample acquisition, two larger tissue samples were collected near the center of the left lateral lobe to be used as a histologic standard for comparison. Histopathologic features and numbers of portal triads in each sample were recorded. The mean number of portal triads obtained by each sampling method were 2.9 in needle samples, 3.4 in cup samples, 12 in punch samples, and 30.7 in the necropsy samples. The diagnoses in 66% of needle samples, 60% of cup samples, and 69% of punch samples were in agreement with the necropsy samples, and these proportions were not significantly different from each other. The corresponding kappa coefficients were 0.59 for needle biopsies, 0.52 for cup biopsies, and 0.62 for punch biopsies. The histopathologic interpretation of a liver sample in the dog is unlikely to vary if the liver biopsy specimen contains at least 3-12 portal triads. However, in comparison large necropsy samples, the accuracy of all tested methods was relatively low. Copyright © 2014 by the American College of Veterinary Internal Medicine.

Errors in patient specimen collection: application of statistical process control.

PubMed

Dzik, Walter Sunny; Beckman, Neil; Selleng, Kathleen; Heddle, Nancy; Szczepiorkowski, Zbigniew; Wendel, Silvano; Murphy, Michael

2008-10-01

Errors in the collection and labeling of blood samples for pretransfusion testing increase the risk of transfusion-associated patient morbidity and mortality. Statistical process control (SPC) is a recognized method to monitor the performance of a critical process. An easy-to-use SPC method was tested to determine its feasibility as a tool for monitoring quality in transfusion medicine. SPC control charts were adapted to a spreadsheet presentation. Data tabulating the frequency of mislabeled and miscollected blood samples from 10 hospitals in five countries from 2004 to 2006 were used to demonstrate the method. Control charts were produced to monitor process stability. The participating hospitals found the SPC spreadsheet very suitable to monitor the performance of the sample labeling and collection and applied SPC charts to suit their specific needs. One hospital monitored subcategories of sample error in detail. A large hospital monitored the number of wrong-blood-in-tube (WBIT) events. Four smaller-sized facilities, each following the same policy for sample collection, combined their data on WBIT samples into a single control chart. One hospital used the control chart to monitor the effect of an educational intervention. A simple SPC method is described that can monitor the process of sample collection and labeling in any hospital. SPC could be applied to other critical steps in the transfusion processes as a tool for biovigilance and could be used to develop regional or national performance standards for pretransfusion sample collection. A link is provided to download the spreadsheet for free.

A compilation of K-Ar-ages for southern California

USGS Publications Warehouse

Miller, Fred K.; Morton, Douglas M.; Morton, Janet L.; Miller, David M.

2014-01-01

The purpose of this report is to make available a large body of conventional K-Ar ages for granitic, volcanic, and metamorphic rocks collected in southern California. Although one interpretive map is included, the report consists primarily of a systematic listing, without discussion or interpretation, of published and unpublished ages that may be of value in future regional and other geologic studies. From 1973 to 1979, 468 rock samples from southern California were collected for conventional K-Ar dating under a regional geologic mapping project of Southern California (predecessor of the Southern California Areal Mapping Project). Most samples were collected and dated between 1974 and 1977. For 61 samples (13 percent of those collected), either they were discarded for varying reasons, or the original collection data were lost. For the remaining samples, 518 conventional K-Ar ages are reported here; coexisting mineral pairs were dated from many samples. Of these K-Ar ages, 225 are previously unpublished, and identified as such in table 1. All K-Ar ages are by conventional K-Ar analysis; no 40Ar/39Ar dating was done. Subsequent to the rock samples collected in the 1970s and reported here, 33 samples were collected and 38 conventional K-Ar ages determined under projects directed at (1) characterization of the Mesozoic and Cenozoic igneous rocks in and on both sides of the Transverse Ranges and (2) clarifying the Mesozoic and Cenozoic tectonics of the eastern Mojave Desert. Although previously published (Beckerman et al., 1982), another eight samples and 11 conventional K-Ar ages are included here, because they augment those completed under the previous two projects.

EVALUATION OF DISPOSABLE DIAPERS FOR QUANTATIVE MEASUREMENTS OF PESTICIDE METABOLITES AND CREATININE IN URINE SAMPLES

EPA Science Inventory

This project consisted of a laboratory study to evaluate an extraction and analysis method for quantifying biomarkers of pesticide exposure and creatinine in urine samples collected with commercially-available disposable diapers. For large exposure studies, such as the National ...

Evaluation of hygiene practices in catering premises at large-scale events in the UK: identifying risks for the Olympics 2012.

PubMed

Willis, C; Elviss, N; Aird, H; Fenelon, D; McLauchlin, J

2012-08-01

To investigate hygiene practices of caterers at large events in order to: support the production of guidance on catering at such events; to compare hygiene standards at weekends with other times in the week; and to learn lessons in preparation for the London Olympics in 2012. UK-wide study of caterers at large events, including questionnaires on hygiene procedures and microbiological examination of food, water and environmental samples. In total, 1364 samples of food, water, surface swabs and cloths were collected at 139 events, by local authority sampling officers, and transported to laboratories for microbiological analysis. Eight percent of food samples were of an unsatisfactory quality, and a further 2% contained potentially hazardous levels of Bacillus spp. A significantly higher proportion of unsatisfactory food samples were taken from vendors without adequate food safety procedures in place. Fifty-two percent of water samples, 38% of swabs and 71% of cloths were also unsatisfactory. The majority of samples (57%) were collected on Saturdays, Sundays or bank holidays. Environmental swab results were significantly poorer at weekends compared with other days of the week. This study reinforces the fact that food hygiene is a continuing cause for concern in mobile vendors, and indicates a need for an ongoing programme of training and monitoring of caterers in preparation for the London Olympics. Copyright © 2012 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

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.

Concentrations of prioritized pharmaceuticals in effluents from 50 large wastewater treatment plants in the US and implications for risk estimation

EPA Science Inventory

We measured the concentrations of 56 active pharmaceutical ingredients (APIs) and seven metabolites, including 50 prioritized APIs, in 24-hour composite effluent samples collected from 50 very large municipal wastewater treatment plants across the US. Hydrochlorothiazide was foun...

Generation Scotland: Donor DNA Databank; A control DNA resource.

PubMed

Kerr, Shona M; Liewald, David C M; Campbell, Archie; Taylor, Kerrie; Wild, Sarah H; Newby, David; Turner, Marc; Porteous, David J

2010-11-23

Many medical disorders of public health importance are complex diseases caused by multiple genetic, environmental and lifestyle factors. Recent technological advances have made it possible to analyse the genetic variants that predispose to complex diseases. Reliable detection of these variants requires genome-wide association studies in sufficiently large numbers of cases and controls. This approach is often hampered by difficulties in collecting appropriate control samples. The Generation Scotland: Donor DNA Databank (GS:3D) aims to help solve this problem by providing a resource of control DNA and plasma samples accessible for research. GS:3D participants were recruited from volunteer blood donors attending Scottish National Blood Transfusion Service (SNBTS) clinics across Scotland. All participants gave full written consent for GS:3D to take spare blood from their normal donation. Participants also supplied demographic data by completing a short questionnaire. Over five thousand complete sets of samples, data and consent forms were collected. DNA and plasma were extracted and stored. The data and samples were unlinked from their original SNBTS identifier number. The plasma, DNA and demographic data are available for research. New data obtained from analysis of the resource will be fed back to GS:3D and will be made available to other researchers as appropriate. Recruitment of blood donors is an efficient and cost-effective way of collecting thousands of control samples. Because the collection is large, subsets of controls can be selected, based on age range, gender, and ethnic or geographic origin. The GS:3D resource should reduce time and expense for investigators who would otherwise have had to recruit their own controls.

Slaughterhouses Fungal Burden Assessment: A Contribution for the Pursuit of a Better Assessment Strategy

PubMed Central

Viegas, Carla; Faria, Tiago; dos Santos, Mateus; Carolino, Elisabete; Sabino, Raquel; Quintal Gomes, Anita; Viegas, Susana

2016-01-01

In slaughterhouses, the biological risk is present not only from the direct or indirect contact with animal matter, but also from the exposure to bioaerosols. Fungal contamination was already reported from the floors and walls of slaughterhouses. This study intends to assess fungal contamination by cultural and molecular methods in poultry, swine/bovine and large animal slaughterhouses. Air samples were collected through an impaction method, while surface samples were collected by the swabbing method and subjected to further macro- and micro-scopic observations. In addition, we collected air samples using the impinger method in order to perform real-time quantitative PCR (qPCR) amplification of genes from specific fungal species, namely A. flavus, A. fumigatus and A. ochraceus complexes. Poultry and swine/bovine slaughterhouses presented each two sampling sites that surpass the guideline of 150 CFU/m3. Scopulariopsis candida was the most frequently isolated (59.5%) in poultry slaughterhouse air; Cladosporium sp. (45.7%) in the swine/bovine slaughterhouse; and Penicillium sp. (80.8%) in the large animal slaughterhouse. Molecular tools successfully amplified DNA from the A. fumigatus complex in six sampling sites where the presence of this fungal species was not identified by conventional methods. This study besides suggesting the indicators that are representative of harmful fungal contamination, also indicates a strategy as a protocol to ensure a proper characterization of fungal occupational exposure. PMID:27005642

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...

INFORMATION MANAGEMENT AND RELATED QUALITY ASSURANCE FOR A LARGE SCALE, MULTI-SITE RESEARCH PROJECT

EPA Science Inventory

During the summer of 2000, as part of a U.S. Environmental Protection Agency study designed to improve microbial water quality monitoring protocols at public beaches, over 11,000 water samples were collected at five selected beaches across the country. At each beach, samples wer...

Toxinotyping and antimicrobial susceptibility of enterotoxigenic Clostridium perfringens isolates from mutton, beef and chicken meat.

PubMed

Khan, Madiha; Nazir, Jawad; Anjum, Aftab Ahmad; Ahmad, Mansur-Ud-Din; Nawaz, Muhammad; Shabbir, Muhammad Zubair

2015-08-01

A total of 300 meat samples comprising mutton, beef, and chicken meat (n = 100) collected from either local butcher shops or large meat outlets situated at various areas of Lahore City located in Punjab province of Pakistan were tested for the isolation of Clostridium perfringens. Prevalence of the organism was highest in the chicken (6 %) followed by mutton (5 %) and beef (1 %). Contamination level was high (10/150) in the samples collected from local butcher shops in comparison to the samples collected from large meat outlets (2/150). All of the raw meat samples were negative for the presence of alpha, beta and epsilon toxins of C. perfringens as detected through ELISA. Out of a total number of 12 isolates only half were capable of producing enterotoxins when cultured in trypticase glucose yeast (TGY) broth. Toxinotyping of the isolates showed that 3 were of type A while one each of the remaining three belonged to type B, C, and D. Antibiotic susceptibility testing of the toxin producing isolates revealed that C. perfringens were susceptible to chloramphenicol, ciprofloxacin, metronidazole, and ceftriaxone. All of the other drugs were relatively less effective with a least activity of amoxicillin against the isolates.

Anopheles sinensis mosquito insecticide resistance: comparison of three mosquito sample collection and preparation methods and mosquito age in resistance measurements.

PubMed

Xu, Tielong; Zhong, Daibin; Tang, Linhua; Chang, Xuelian; Fu, Fengyang; Yan, Guiyun; Zheng, Bin

2014-01-28

Insecticide resistance monitoring in malaria mosquitoes is essential for guiding the rational use of insecticides in vector control programs. Resistance bioassay is the first step for insecticide monitoring and it lays an important foundation for molecular examination of resistance mechanisms. In the literature, various mosquito sample collection and preparation methods have been used, but how mosquito sample collection and preparation methods affect insecticide susceptibility bioassay results is largely unknown. The objectives of this study were to determine whether mosquito sample collection and preparation methods affected bioassay results, which may cause incorrect classification of mosquito resistance status. The study was conducted in Anopheles sinensis mosquitoes in two study sites in central China. Three mosquito sample collection and preparation methods were compared for insecticide susceptibility, kdr frequencies and metabolic enzyme activities: 1) adult mosquitoes collected from the field; 2) F1 adults from field collected, blood-fed mosquitoes; and 3) adult mosquitoes reared from field collected larvae. Mosquito sample collection and preparation methods significantly affected mortality rates in the standard WHO tube resistance bioassay. Mortality rate of field-collected female adults was 10-15% higher than in mosquitoes reared from field-collected larvae and F1 adults from field collected blood-fed females. This pattern was consistent in mosquitoes from the two study sites. High kdr mutation frequency (85-95%) with L1014F allele as the predominant mutation was found in our study populations. Field-collected female adults consistently exhibited the highest monooxygenase and GST activities. The higher mortality rate observed in the field-collected female mosquitoes may have been caused by a mixture of mosquitoes of different ages, as older mosquitoes were more susceptible to deltamethrin than younger mosquitoes. Female adults reared from field-collected larvae in resistance bioassays are recommended to minimize the effect of confounding factors such as mosquito age and blood feeding status so that more reliable and reproducible mortality may be obtained.

Buccal Swabbing as a Noninvasive Method To Determine Bacterial, Archaeal, and Eukaryotic Microbial Community Structures in the Rumen

PubMed Central

Kirk, Michelle R.; Jonker, Arjan; McCulloch, Alan

2015-01-01

Analysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (R = 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (R = 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants. PMID:26276109

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

Evaluation of Buccal Cell Samples for Studies of Oral Microbiota.

PubMed

Yu, Guoqin; Phillips, Steve; Gail, Mitchell H; Goedert, James J; Humphrys, Michael; Ravel, Jacques; Ren, Yanfang; Caporaso, Neil E

2017-02-01

The human microbiota is postulated to affect cancer risk, but collecting microbiota specimens with prospective follow-up for diseases will take time. Buccal cell samples have been obtained from mouthwash for the study of human genomic DNA in many cohort studies. Here, we evaluate the feasibility of using buccal cell samples to examine associations of human microbiota and disease risk. We obtained buccal cells from mouthwash in 41 healthy participants using a protocol that is widely employed to obtain buccal cells for the study of human DNA. We compared oral microbiota from buccal cells with that from eight other oral sample types collected by following the protocols of the Human Microbiome Project. Microbiota profiles were determined by sequencing 16S rRNA gene V3-V4 region. Compared with each of the eight other oral samples, the buccal cell samples had significantly more observed species (P < 0.002) and higher alpha diversity (Shannon index, P < 0.02). The microbial communities were more similar (smaller beta diversity) among buccal cells samples than in the other samples (P < 0.001 for 12 of 16 weighted and unweighted UniFrac distance comparisons). Buccal cell microbial profiles closely resembled saliva but were distinct from dental plaque and tongue dorsum. Stored buccal cell samples in prospective cohort studies are a promising resource to study associations of oral microbiota with disease. The feasibility of using existing buccal cell collections in large prospective cohorts allows investigations of the role of oral microbiota in chronic disease etiology in large population studies possible today. Cancer Epidemiol Biomarkers Prev; 26(2); 249-53. ©2016 AACR. ©2016 American Association for Cancer Research.

Plasma cortisol and faecal cortisol metabolites concentrations in stereotypic and non-stereotypic horses: do stereotypic horses cope better with poor environmental conditions?

PubMed Central

2013-01-01

Background Stereotypic behaviours, i.e. repetitive behaviours induced by frustration, repeated attempts to cope and/or brain dysfunction, are intriguing as they occur in a variety of domestic and captive species without any clear adaptive function. Among the different hypotheses, the coping hypothesis predicts that stereotypic behaviours provide a way for animals in unfavourable environmental conditions to adjust. As such, they are expected to have a lower physiological stress level (glucocorticoids) than non-stereotypic animals. Attempts to link stereotypic behaviours with glucocorticoids however have yielded contradictory results. Here we investigated correlates of oral and motor stereotypic behaviours and glucocorticoid levels in two large samples of domestic horses (NStudy1 = 55, NStudy2 = 58), kept in sub-optimal conditions (e.g. confinement, social isolation), and already known to experience poor welfare states. Each horse was observed in its box using focal sampling (study 1) and instantaneous scan sampling (study 2). Plasma samples (collected in study 1) but also non-invasive faecal samples (collected in both studies) were retrieved in order to assess cortisol levels. Results Results showed that 1) plasma cortisol and faecal cortisol metabolites concentrations did not differ between horses displaying stereotypic behaviours and non-stereotypic horses and 2) both oral and motor stereotypic behaviour levels did not predict plasma cortisol or faecal cortisol metabolites concentrations. Conclusions Cortisol measures, collected in two large samples of horses using both plasma sampling as well as faecal sampling (the latter method minimizing bias due to a non-invasive sampling procedure), therefore do not indicate that stereotypic horses cope better, at least in terms of adrenocortical activity. PMID:23289406

Improvements in medical quality and patient safety through implementation of a case bundle management strategy in a large outpatient blood collection center.

PubMed

Zhao, Shuzhen; He, Lujia; Feng, Chenchen; He, Xiaoli

2018-06-01

Laboratory errors in blood collection center (BCC) are most common in the preanalytical phase. It is, therefore, of vital importance for administrators to take measures to improve healthcare quality and patient safety.In 2015, a case bundle management strategy was applied in a large outpatient BCC to improve its medical quality and patient safety.Unqualified blood sampling, complications, patient waiting time, largest number of patients waiting during peak hours, patient complaints, and patient satisfaction were compared over the period from 2014 to 2016.The strategy reduced unqualified blood sampling, complications, patient waiting time, largest number of patients waiting during peak hours, and patient complaints, while improving patient satisfaction.This strategy was effective in improving BCC healthcare quality and patient safety.

Semi-automatic surface sediment sampling system - A prototype to be implemented in bivalve fishing surveys

NASA Astrophysics Data System (ADS)

Rufino, Marta M.; Baptista, Paulo; Pereira, Fábio; Gaspar, Miguel B.

2018-01-01

In the current work we propose a new method to sample surface sediment during bivalve fishing surveys. Fishing institutes all around the word carry out regular surveys with the aim of monitoring the stocks of commercial species. These surveys comprise often more than one hundred of sampling stations and cover large geographical areas. Although superficial sediment grain sizes are among the main drivers of benthic communities and provide crucial information for studies on coastal dynamics, overall there is a strong lack of this type of data, possibly, because traditional surface sediment sampling methods use grabs, that require considerable time and effort to be carried out on regular basis or on large areas. In face of these aspects, we developed an easy and un-expensive method to sample superficial sediments, during bivalve fisheries monitoring surveys, without increasing survey time or human resources. The method was successfully evaluated and validated during a typical bivalve survey carried out on the Northwest coast of Portugal, confirming that it had any interference with the survey objectives. Furthermore, the method was validated by collecting samples using a traditional Van Veen grabs (traditional method), which showed a similar grain size composition to the ones collected by the new method, on the same localities. We recommend that the procedure is implemented on regular bivalve fishing surveys, together with an image analysis system to analyse the collected samples. The new method will provide substantial quantity of data on surface sediment in coastal areas, using a non-expensive and efficient manner, with a high potential application in different fields of research.

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

A new sampler for stratified lagoon chemical and microbiological assessments.

PubMed

McLaughlin, M R; Brooks, J P; Adeli, A

2014-07-01

A sampler was needed for a spatial and temporal study of microbial and chemical stratification in a large swine manure lagoon that was known to contain zoonotic bacteria. Conventional samplers were limited to collections of surface water samples near the bank or required a manned boat. A new sampler was developed to allow simultaneous collection of multiple samples at different depths, up to 2.3 m, without a manned boat. The sampler was tethered for stability, used remote control (RC) for sample collection, and accommodated rapid replacement of sterile tubing modules and sample containers. The sampler comprised a PVC pontoon with acrylic deck and watertight enclosures, for a 12 VDC gearmotor, to operate the collection module, and vacuum system, to draw samples into reusable autoclavable tubing and 250-mL bottles. Although designed primarily for water samples, the sampler was easily modified to collect sludge. The sampler held a stable position during deployment, created minimal disturbance in the water column, and was readily cleaned and sanitized for transport. The sampler was field tested initially in a shallow fresh water lake and subsequently in a swine manure treatment lagoon. Analyses of water samples from the lagoon tests showed that chemical and bacterial levels, pH, and EC did not differ between 0.04, 0.47, and 1.0 m depths, but some chemical and bacterial levels differed between winter and spring collections. These results demonstrated the utility of the sampler and suggested that future manure lagoon studies employ fewer or different depths and more sampling dates.

Massive Sorghum Collection Genotyped with SSR Markers to Enhance Use of Global Genetic Resources

PubMed Central

Bouchet, Sophie; Chantereau, Jacques; Deu, Monique; Gardes, Laetitia; Noyer, Jean-Louis; Rami, Jean-François; Rivallan, Ronan; Li, Yu; Lu, Ping; Wang, Tianyu; Folkertsma, Rolf T.; Arnaud, Elizabeth; Upadhyaya, Hari D.; Glaszmann, Jean-Christophe; Hash, C. Thomas

2013-01-01

Large ex situ collections require approaches for sampling manageable amounts of germplasm for in-depth characterization and use. We present here a large diversity survey in sorghum with 3367 accessions and 41 reference nuclear SSR markers. Of 19 alleles on average per locus, the largest numbers of alleles were concentrated in central and eastern Africa. Cultivated sorghum appeared structured according to geographic regions and race within region. A total of 13 groups of variable size were distinguished. The peripheral groups in western Africa, southern Africa and eastern Asia were the most homogeneous and clearly differentiated. Except for Kafir, there was little correspondence between races and marker-based groups. Bicolor, Caudatum, Durra and Guinea types were each dispersed in three groups or more. Races should therefore better be referred to as morphotypes. Wild and weedy accessions were very diverse and scattered among cultivated samples, reinforcing the idea that large gene-flow exists between the different compartments. Our study provides an entry to global sorghum germplasm collections. Our reference marker kit can serve to aggregate additional studies and enhance international collaboration. We propose a core reference set in order to facilitate integrated phenotyping experiments towards refined functional understanding of sorghum diversity. PMID:23565161

Placers of cosmic dust in the blue ice lakes of Greenland

NASA Technical Reports Server (NTRS)

Maurette, M.; Hammer, C.; Reeh, N.; Brownlee, D. E.; Thomsen, H. H.

1986-01-01

A concentration process occurring in the melt zone of the Greenland ice cap has produced the richest known deposit of cosmic dust on the surface of the earth. Extraterrestrial particles collected from this region are well preserved and are collectable in large quantities. The collected particles are generally identical to cosmic spheres found on the ocean floor, but a pure glass type was discovered that has not been seen in deep-sea samples. Iron-rich spheres are conspicuously rare in the collected material.

Bloodmeal Host Congregation and Landscape Structure Impact the Estimation of Female Mosquito (Diptera: Culicidae) Abundance Using Dry Ice-Baited Traps

PubMed Central

THIEMANN, TARA; NELMS, BRITTANY; REISEN, WILLIAM K.

2011-01-01

Vegetation patterns and the presence of large numbers of nesting herons and egrets significantly altered the number of host-seeking Culex tarsalis Coquillett (Diptera: Culicidae) collected at dry ice-baited traps. The numbers of females collected per trap night at traps along the ecotone of Eucalyptus stands with and without a heron colony were always greater or equal to numbers collected at traps within or under canopy. No Cx. tarsalis were collected within or under Eucaplytus canopy during the peak heron nesting season, even though these birds frequently were infected with West Nile virus and large number of engorged females could be collected at resting boxes. These data indicate a diversion of host-seeking females from traps to nesting birds reducing sampling efficiency. PMID:21661310

Bias in fallout data from nuclear surface shot SMALL BOY: an evaluation of sample perturbation by sieve sizing. Technical report

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

Pascual, J.N.

1967-06-26

Evaluation of sample bias introduced by the mechanical sieving of Small Boy fallout samples for 10 minutes revealed the following: Up to 20% of the mass and 30% of the gamma-ray activity can be lost from the large-particle (greater than 1400 microns) fraction. The pan fraction (less than 44 microns) can gain in weight by as much as 79%, and in activity by as much as 44%. The gamma-ray spectra of the fractions were not noticeably altered by the process. Examination of unbiased pan fractions (before mechanical sieving) indicated bimodality of the mass-size distribution in a sample collected 9,200 feetmore » from ground zero, but not in a sample collected at 13,300 feet.« less

Field and laboratory data describing physical and chemical characteristics of metal-contaminated flood-plain deposits downstream from Lead, west-central South Dakota

USGS Publications Warehouse

Marron, D.C.

1988-01-01

Samples from metal-contaminated flood-plain sediments at 9 sites downstream from Lead, in west-central South Dakota, were collected during the summers of 1985-87 to characterize aspects of the sedimentology, chemistry, and geometry of a deposit that resulted from the discharge of a large volume of mining wastes into a river system. Field and laboratory data include stratigraphic descriptions, chemical contents and grain-size distributions of samples, and surveyed flood-plain positions of samples. This report describes sampling-site locations, and methods of sample collection and preservation, and subsequent laboratory analysis. Field and laboratory data are presented in 4 figures and 11 tables in the ' Supplemental Data ' section at the back of the report. (USGS)

Improved technique that allows the performance of large-scale SNP genotyping on DNA immobilized by FTA technology.

PubMed

He, Hongbin; Argiro, Laurent; Dessein, Helia; Chevillard, Christophe

2007-01-01

FTA technology is a novel method designed to simplify the collection, shipment, archiving and purification of nucleic acids from a wide variety of biological sources. The number of punches that can normally be obtained from a single specimen card are often however, insufficient for the testing of the large numbers of loci required to identify genetic factors that control human susceptibility or resistance to multifactorial diseases. In this study, we propose an improved technique to perform large-scale SNP genotyping. We applied a whole genome amplification method to amplify DNA from buccal cell samples stabilized using FTA technology. The results show that using the improved technique it is possible to perform up to 15,000 genotypes from one buccal cell sample. Furthermore, the procedure is simple. We consider this improved technique to be a promising methods for performing large-scale SNP genotyping because the FTA technology simplifies the collection, shipment, archiving and purification of DNA, while whole genome amplification of FTA card bound DNA produces sufficient material for the determination of thousands of SNP genotypes.

Photonic-crystal fiber as a multifunctional optical sensor and sample collector.

PubMed

Konorov, Stanislav; Zheltikov, Aleksei; Scalora, Michael

2005-05-02

Two protocols of optical sensing realized with the same photonic-crystal fiber are compared. In the first protocol, diode-laser radiation is delivered to a sample through the central core of a dual-cladding photonic-crystal fiber with a diameter of a few micrometers, while the large-diameter fiber cladding serves to collect the fluorescent response from the sample and to guide it to a detector in the backward direction. In the second scheme, liquid sample is collected by a microcapillary array in the fiber cladding and is interrogated by laser radiation guided in the fiber modes. For sample fluids with refractive indices exceeding the refractive index of the fiber material, fluid channels in photonic-crystal fibers can guide laser light by total internal reflection, providing an 80% overlap of interrogating radiation with sample fluid.

Characterization of endocrine-disruption and clinical manifestations in large-mouth bass from Florida lakes

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

Gross, D.A.; Gross, T.S.; Johnson, B.

1995-12-31

Previous efforts from this laboratory have documented altered endocrine function and sexual differentiation for alligators and turtles from Lake Apopka in Central Florida. This lake has been exposed to a variety of contaminants which are potentially endocrine-disrupting. Therefore, a survey of large mouth bass populations was conducted on several lakes in North Central Florida to examine reproductive and clinical health. Large-mouth bass were collected from lakes Apopka, Griffin, Jessup and Woodruff. Approximately 24 fish (12 males and 12 females) were collected from each lake during the spawning (March--April) and non-reproductive (July--August) seasons. Plasma samples were collected for analysis of estrogen,more » testosterone and 11-keto-testosterone concentrations. Gonadal and liver tissues were collected for histological analysis. General blood chemistry analyses and parasite surveys were also conducted to estimate general health. Additionally, fillet samples were collected and analyzed for pesticide levels. Fish from Lake Apopka had unusual concentrations of estrogen and 11-keto-testosterone in plasma when compared to bass from Lakes Woodruff, Jessup and Griffin. Parasites loads were significantly higher for bass from lake Apopka than from the other lakes. Male bass on Apopka had depressed concentrations of 11-keto-testosterone, skewing the E/T ratios upward while female bass had higher concentrations of estrogens than females from the other lakes, again resulting in skewed E/T ratios. These skewed E/T ratios are similar to those observed for alligators on the same lake and raise the possibility that they are caused by contaminants. However, contaminant levels in fillets did not differ significantly between lakes. These studies indicate potentially altered reproductive and immunological function for large-mouth bass living in a contaminated lake.« less

Measurement of the intrinsic variability within protein crystals: implications for sample-evaluation and data-collection strategies.

PubMed

Bowler, Michael G; Bowler, Matthew W

2014-01-01

The advent of micro-focused X-ray beams has led to the development of a number of advanced methods of sample evaluation and data collection. In particular, multiple-position data-collection and helical oscillation strategies are now becoming commonplace in order to alleviate the problems associated with radiation damage. However, intra-crystal and inter-crystal variation means that it is not always obvious on which crystals or on which region or regions of a crystal these protocols should be performed. For the automation of this process for large-scale screening, and to provide an indication of the best strategy for data collection, a metric of crystal variability could be useful. Here, measures of the intrinsic variability within protein crystals are presented and their implications for optimal data-collection strategies are discussed.

Alcohol Policies and Free to be Foolish: An Analysis of College Students.

ERIC Educational Resources Information Center

Reis, Janet; Chamberlain, Elizabeth Ann

1994-01-01

Results of a convenience sample of predominately white undergraduate students from a large public university in the Midwest. Students were surveyed with regard to their views about alcohol consumption. The sample was divided between 239 libertarians and 192 supporters of collective responsibility as defined by their positions on alcohol…

Career Transitions: The Experiences of Unemployed Women Managers

ERIC Educational Resources Information Center

Sheridan, Terry A.

2008-01-01

A sample of 45 women managers was surveyed in a qualitative study to explore their experiences of being unemployed. The sample was purposeful, and the data were collected on a website-based survey. The experience of unemployment for female managers was far different from what was previously presumed from research largely drawn from male …

Nursing Home Staff Turnover: Impact on Nursing Home Compare Quality Measures

ERIC Educational Resources Information Center

Castle, Nicholas G.; Engberg, John; Men, Aiju

2007-01-01

Purpose: We used data from a large sample of nursing homes to examine the association between staff turnover and quality. Design and Methods: The staff turnover measures came from primary data collected from 2,840 nursing homes in 2004 (representing a 71% response rate). Data collection included measures for nurse aides, licensed practical nurses,…

It's not just how high; it's how clean: Sampling the spring 2001 flood in the Upper Mississippi River Basin

USGS Publications Warehouse

Patterson, Glenn; Kolpin, Dana W.; Kalkhoff, Stephen J.; Lee, Kathy E.; Schnoebelen, Douglas J.; Barnes, Kimberlee K.; Coupe, Richard H.

2001-01-01

Floods can cause water-quality problems because of the large amounts of contaminants (sediment, nutrients, pesticides, and bacteria) that can be transported by floodwaters. during the flood on the Upper Mississippi River in 2001, water-quality and water-quality data were collected during near-record streamflow. This is the first time that samples for determining organic wastewater contaminants (pharmaceuticals, hormones, and industrial/household use compounds) and pesticide degradates have been collected during a flood of this magnitude.

Numerical simulations of regolith sampling processes

NASA Astrophysics Data System (ADS)

Schäfer, Christoph M.; Scherrer, Samuel; Buchwald, Robert; Maindl, Thomas I.; Speith, Roland; Kley, Wilhelm

2017-07-01

We present recent improvements in the simulation of regolith sampling processes in microgravity using the numerical particle method smooth particle hydrodynamics (SPH). We use an elastic-plastic soil constitutive model for large deformation and failure flows for dynamical behaviour of regolith. In the context of projected small body (asteroid or small moons) sample return missions, we investigate the efficiency and feasibility of a particular material sampling method: Brushes sweep material from the asteroid's surface into a collecting tray. We analyze the influence of different material parameters of regolith such as cohesion and angle of internal friction on the sampling rate. Furthermore, we study the sampling process in two environments by varying the surface gravity (Earth's and Phobos') and we apply different rotation rates for the brushes. We find good agreement of our sampling simulations on Earth with experiments and provide estimations for the influence of the material properties on the collecting rate.

Exposure to microbial components and allergens in population studies: a comparison of two house dust collection methods applied by participants and fieldworkers.

PubMed

Schram-Bijkerk, D; Doekes, G; Boeve, M; Douwes, J; Riedler, J; Ublagger, E; von Mutius, E; Benz, M; Pershagen, G; Wickman, M; Alfvén, T; Braun-Fahrländer, C; Waser, M; Brunekreef, B

2006-12-01

Dust collection by study participants instead of fieldworkers would be a practical and cost-effective alternative in large-scale population studies estimating exposure to indoor allergens and microbial agents. We aimed to compare dust weights and biological agent levels in house dust samples taken by study participants with nylon socks, with those in samples taken by fieldworkers using the sampling nozzle of the Allergology Laboratory Copenhagen (ALK). In homes of 216 children, parents and fieldworkers collected house dust within the same year. Dust samples were analyzed for levels of allergens, endotoxin, (1-->3)-beta-D-glucans and fungal extracellular polysaccharides (EPS). Socks appeared to yield less dust from mattresses at relatively low dust amounts and more dust at high dust amounts than ALK samples. Correlations between the methods ranged from 0.47-0.64 for microbial agents and 0.64-0.87 for mite and pet allergens. Cat allergen levels were two-fold lower and endotoxin levels three-fold higher in socks than in ALK samples. Levels of allergens and microbial agents in sock samples taken by study participants are moderately to highly correlated to levels in ALK samples taken by fieldworkers. Absolute levels may differ, probably because of differences in the method rather than in the person who performed the sampling. Practical Implications Dust collection by participants is a reliable and practical option for allergen and microbial agent exposure assessment. Absolute levels of biological agents are not (always) comparable between studies using different dust collection methods, even when expressed per gram dust, because of potential differences in particle-size constitution of the collected dust.

U.S. Geological Survey Catskill/Delaware Water-Quality Network: Water-Quality Report Water Year 2006

USGS Publications Warehouse

McHale, Michael R.; Siemion, Jason

2010-01-01

The U.S. Geological Survey operates a 60-station streamgaging network in the New York City Catskill/Delaware Water Supply System. Water-quality samples were collected at 13 of the stations in the Catskill/Delaware streamgaging network to provide resource managers with water-quality and water-quantity data from the water-supply system that supplies about 85 percent of the water needed by the more than 9 million residents of New York City. This report summarizes water-quality data collected at those 13 stations plus one additional station operated as a part of the U.S. Environmental Protection Agency's Regional Long-Term Monitoring Network for the 2006 water year (October 1, 2005 to September 30, 2006). An average of 62 water-quality samples were collected at each station during the 2006 water year, including grab samples collected every other week and storm samples collected with automated samplers. On average, 8 storms were sampled at each station during the 2006 water year. The 2006 calendar year was the second warmest on record and the summer of 2006 was the wettest on record for the northeastern United States. A large storm on June 26-28, 2006, caused extensive flooding in the western part of the network where record peak flows were measured at several watersheds.

A panel of microsatellites to individually identify leopards and its application to leopard monitoring in human dominated landscapes.

PubMed

Mondol, Samrat; Navya, R; Athreya, Vidya; Sunagar, Kartik; Selvaraj, Velu Mani; Ramakrishnan, Uma

2009-12-04

Leopards are the most widely distributed of the large cats, ranging from Africa to the Russian Far East. Because of habitat fragmentation, high human population densities and the inherent adaptability of this species, they now occupy landscapes close to human settlements. As a result, they are the most common species involved in human wildlife conflict in India, necessitating their monitoring. However, their elusive nature makes such monitoring difficult. Recent advances in DNA methods along with non-invasive sampling techniques can be used to monitor populations and individuals across large landscapes including human dominated ones. In this paper, we describe a DNA-based method for leopard individual identification where we used fecal DNA samples to obtain genetic material. Further, we apply our methods to non-invasive samples collected in a human-dominated landscape to estimate the minimum number of leopards in this human-leopard conflict area in Western India. In this study, 25 of the 29 tested cross-specific microsatellite markers showed positive amplification in 37 wild-caught leopards. These loci revealed varied levels of polymorphism (four-12 alleles) and heterozygosity (0.05-0.79). Combining data on amplification success (including non-invasive samples) and locus specific polymorphisms, we showed that eight loci provide a sibling probability of identity of 0.0005, suggesting that this panel can be used to discriminate individuals in the wild. When this microsatellite panel was applied to fecal samples collected from a human-dominated landscape, we identified 7 individuals, with a sibling probability of identity of 0.001. Amplification success of field collected scats was up to 72%, and genotype error ranged from 0-7.4%. Our results demonstrated that the selected panel of eight microsatellite loci can conclusively identify leopards from various kinds of biological samples. Our methods can be used to monitor leopards over small and large landscapes to assess population trends, as well as could be tested for population assignment in forensic applications.

A panel of microsatellites to individually identify leopards and its application to leopard monitoring in human dominated landscapes

PubMed Central

2009-01-01

Background Leopards are the most widely distributed of the large cats, ranging from Africa to the Russian Far East. Because of habitat fragmentation, high human population densities and the inherent adaptability of this species, they now occupy landscapes close to human settlements. As a result, they are the most common species involved in human wildlife conflict in India, necessitating their monitoring. However, their elusive nature makes such monitoring difficult. Recent advances in DNA methods along with non-invasive sampling techniques can be used to monitor populations and individuals across large landscapes including human dominated ones. In this paper, we describe a DNA-based method for leopard individual identification where we used fecal DNA samples to obtain genetic material. Further, we apply our methods to non-invasive samples collected in a human-dominated landscape to estimate the minimum number of leopards in this human-leopard conflict area in Western India. Results In this study, 25 of the 29 tested cross-specific microsatellite markers showed positive amplification in 37 wild-caught leopards. These loci revealed varied levels of polymorphism (four-12 alleles) and heterozygosity (0.05-0.79). Combining data on amplification success (including non-invasive samples) and locus specific polymorphisms, we showed that eight loci provide a sibling probability of identity of 0.0005, suggesting that this panel can be used to discriminate individuals in the wild. When this microsatellite panel was applied to fecal samples collected from a human-dominated landscape, we identified 7 individuals, with a sibling probability of identity of 0.001. Amplification success of field collected scats was up to 72%, and genotype error ranged from 0-7.4%. Conclusion Our results demonstrated that the selected panel of eight microsatellite loci can conclusively identify leopards from various kinds of biological samples. Our methods can be used to monitor leopards over small and large landscapes to assess population trends, as well as could be tested for population assignment in forensic applications. PMID:19961605

SyPRID sampler: A large-volume, high-resolution, autonomous, deep-ocean precision plankton sampling system

NASA Astrophysics Data System (ADS)

Billings, Andrew; Kaiser, Carl; Young, Craig M.; Hiebert, Laurel S.; Cole, Eli; Wagner, Jamie K. S.; Van Dover, Cindy Lee

2017-03-01

The current standard for large-volume (thousands of cubic meters) zooplankton sampling in the deep sea is the MOCNESS, a system of multiple opening-closing nets, typically lowered to within 50 m of the seabed and towed obliquely to the surface to obtain low-spatial-resolution samples that integrate across 10 s of meters of water depth. The SyPRID (Sentry Precision Robotic Impeller Driven) sampler is an innovative, deep-rated (6000 m) plankton sampler that partners with the Sentry Autonomous Underwater Vehicle (AUV) to obtain paired, large-volume plankton samples at specified depths and survey lines to within 1.5 m of the seabed and with simultaneous collection of sensor data. SyPRID uses a perforated Ultra-High-Molecular-Weight (UHMW) plastic tube to support a fine mesh net within an outer carbon composite tube (tube-within-a-tube design), with an axial flow pump located aft of the capture filter. The pump facilitates flow through the system and reduces or possibly eliminates the bow wave at the mouth opening. The cod end, a hollow truncated cone, is also made of UHMW plastic and includes a collection volume designed to provide an area where zooplankton can collect, out of the high flow region. SyPRID attaches as a saddle-pack to the Sentry vehicle. Sentry itself is configured with a flight control system that enables autonomous survey paths to low altitudes. In its verification deployment at the Blake Ridge Seep (2160 m) on the US Atlantic Margin, SyPRID was operated for 6 h at an altitude of 5 m. It recovered plankton samples, including delicate living larvae, from the near-bottom stratum that is seldom sampled by a typical MOCNESS tow. The prototype SyPRID and its next generations will enable studies of plankton or other particulate distributions associated with localized physico-chemical strata in the water column or above patchy habitats on the seafloor.

Quantitative assessment of anthrax vaccine immunogenicity using the dried blood spot matrix.

PubMed

Schiffer, Jarad M; Maniatis, Panagiotis; Garza, Ilana; Steward-Clark, Evelene; Korman, Lawrence T; Pittman, Phillip R; Mei, Joanne V; Quinn, Conrad P

2013-03-01

The collection, processing and transportation to a testing laboratory of large numbers of clinical samples during an emergency response situation present significant cost and logistical issues. Blood and serum are common clinical samples for diagnosis of disease. Serum preparation requires significant on-site equipment and facilities for immediate processing and cold storage, and significant costs for cold-chain transport to testing facilities. The dried blood spot (DBS) matrix offers an alternative to serum for rapid and efficient sample collection with fewer on-site equipment requirements and considerably lower storage and transport costs. We have developed and validated assay methods for using DBS in the quantitative anti-protective antigen IgG enzyme-linked immunosorbent assay (ELISA), one of the primary assays for assessing immunogenicity of anthrax vaccine and for confirmatory diagnosis of Bacillus anthracis infection in humans. We have also developed and validated high-throughput data analysis software to facilitate data handling for large clinical trials and emergency response. Published by Elsevier Ltd.

Monitoring suspended sediment and associated trace element and nutrient fluxes in large river basins in the USA

USGS Publications Warehouse

Horowitz, A.J.

2004-01-01

In 1996, the US Geological Survey converted its occurrence and distribution-based National Stream Quality Accounting Network (NASQAN) to a national, flux-based water-quality monitoring programme. The main objective of the revised programme is to characterize large USA river basins by measuring the fluxes of selected constituents at critical nodes in various basins. Each NASQAN site was instrumented to determine daily discharge, but water and suspended sediment samples are collected no more than 12-15 times per year. Due to the limited sampling programme, annual suspended sediment fluxes were determined from site-specific sediment rating (transport) curves. As no significant relationship could be found between either discharge or suspended sediment concentration (SSC) and suspended sediment chemistry, trace element and nutrient fluxes are estimated using site-specific mean or median chemical levels determined from a number of samples collected over a period of years, and under a variety of flow conditions.

Rainfall, Streamflow, and Water-Quality Data During Stormwater Monitoring, Halawa Stream Drainage Basin, Oahu, Hawaii, July 1, 2000 to June 30, 2001

USGS Publications Warehouse

Presley, Todd K.

2001-01-01

The State of Hawaii Department of Transportation Stormwater Monitoring Program was implemented on January 1, 2001. The program includes the collection of rainfall, streamflow, and water-quality data at selected sites in the Halawa Stream drainage basin. Rainfall and streamflow data were collected from July 1, 2000 to June 30, 2001. Few storms during the year met criteria for antecedent dry conditions or provided enough runoff to sample. The storm of June 5, 2001 was sufficiently large to cause runoff. On June 5, 2001, grab samples were collected at five sites along North Halawa and Halawa Streams. The five samples were later analyzed for nutrients, trace metals, oil and grease, total petroleum hydrocarbons, fecal coliform, biological and chemical oxygen demands, total suspended solids, and total dissolved solids.

Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples

PubMed Central

Snyder-Mackler, Noah; Majoros, William H.; Yuan, Michael L.; Shaver, Amanda O.; Gordon, Jacob B.; Kopp, Gisela H.; Schlebusch, Stephen A.; Wall, Jeffrey D.; Alberts, Susan C.; Mukherjee, Sayan; Zhou, Xiang; Tung, Jenny

2016-01-01

Research on the genetics of natural populations was revolutionized in the 1990s by methods for genotyping noninvasively collected samples. However, these methods have remained largely unchanged for the past 20 years and lag far behind the genomics era. To close this gap, here we report an optimized laboratory protocol for genome-wide capture of endogenous DNA from noninvasively collected samples, coupled with a novel computational approach to reconstruct pedigree links from the resulting low-coverage data. We validated both methods using fecal samples from 62 wild baboons, including 48 from an independently constructed extended pedigree. We enriched fecal-derived DNA samples up to 40-fold for endogenous baboon DNA and reconstructed near-perfect pedigree relationships even with extremely low-coverage sequencing. We anticipate that these methods will be broadly applicable to the many research systems for which only noninvasive samples are available. The lab protocol and software (“WHODAD”) are freely available at www.tung-lab.org/protocols-and-software.html and www.xzlab.org/software.html, respectively. PMID:27098910

Morphological diversity of Trichuris spp. eggs observed during an anthelminthic drug trial in Yunnan, China, and relative performance of parasitologic diagnostic tools.

PubMed

Steinmann, Peter; Rinaldi, Laura; Cringoli, Giuseppe; Du, Zun-Wei; Marti, Hanspeter; Jiang, Jin-Yong; Zhou, Hui; Zhou, Xiao-Nong; Utzinger, Jürg

2015-01-01

The presence of large Trichuris spp. eggs in human faecal samples is occasionally reported. Such eggs have been described as variant Trichuris trichiura or Trichuris vulpis eggs. Within the frame of a randomised controlled trial, faecal samples collected from 115 Bulang individuals from Yunnan, People's Republic of China were subjected to the Kato-Katz technique (fresh stool samples) and the FLOTAC and ether-concentration techniques (sodium acetate-acetic acid-formalin (SAF)-fixed stool samples). Large Trichuris spp. eggs were noted in faecal samples with a prevalence of 6.1% before and 21.7% after anthelminthic drug administration. The observed prevalence of standard-sized T. trichiura eggs was reduced from 93.0% to 87.0% after treatment. Considerably more cases of large Trichuris spp. eggs and slightly more cases with normal-sized T. trichiura eggs were identified by FLOTAC compared to the ether-concentration technique. No large Trichuris spp. eggs were observed on the Kato-Katz thick smears. Copyright © 2014 Elsevier B.V. All rights reserved.

Large-Scale Interaction Effects Reveal Missing Heritability in Schizophrenia, Bipolar Disorder and Posttraumatic Stress Disorder

DTIC Science & Technology

2017-04-11

polymorphisms (SNPs) reached genome-wide significance. In contrast, when SNPs were selected in groups ( containing up to thousands each) and the collective...the underlying genetic factors has been challen- ging because of high polygenicity, necessitating large sample sizes in meta-analyses.4 Possible ways...partners simultaneously considered beyond SNP pairs by using the regularized inference of high -dimensional interactions within large SNP groups. Over

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

Ji, Yanfeng; Hui, Fei; Shi, Yuanyuan

The conductive atomic force microscope (CAFM) has become an essential tool for the nanoscale electronic characterization of many materials and devices. When studying photoactive samples, the laser used by the CAFM to detect the deflection of the cantilever can generate photocurrents that perturb the current signals collected, leading to unreliable characterization. In metal-coated semiconductor samples, this problem is further aggravated, and large currents above the nanometer range can be observed even without the application of any bias. Here we present the first characterization of the photocurrents introduced by the laser of the CAFM, and we quantify the amount of lightmore » arriving to the surface of the sample. The mechanisms for current collection when placing the CAFM tip on metal-coated photoactive samples are also analyzed in-depth. Finally, we successfully avoided the laser-induced perturbations using a two pass technique: the first scan collects the topography (laser ON) and the second collects the current (laser OFF). We also demonstrate that CAFMs without a laser (using a tuning fork for detecting the deflection of the tip) do not have this problem.« less

Vapor-phase concentrations of PAHs and their derivatives determined in a large city: correlations with their atmospheric aerosol concentrations.

PubMed

Barrado, Ana Isabel; García, Susana; Sevillano, Marisa Luisa; Rodríguez, Jose Antonio; Barrado, Enrique

2013-11-01

Thirteen PAHs, five nitro-PAHs and two hydroxy-PAHs were determined in 55 vapor-phase samples collected in a suburban area of a large city (Madrid, Spain), from January 2008 to February 2009. The data obtained revealed correlations between the concentrations of these compounds and a series of meteorological factors (e.g., temperature, atmospheric pressure) and physical-chemical factors (e.g., nitrogen and sulfur oxides). As a consequence, seasonal trends were observed in the atmospheric pollutants. A "mean sample" for the 14-month period would contain a total PAH concentration of 13835±1625 pg m(-3) and 122±17 pg m(-3) of nitro-PAHs. When the data were stratified by season, it emerged that a representative sample of the coldest months would contain 18900±2140 pg m(-3) of PAHs and 150±97 pg m(-3) of nitro-PAHs, while in an average sample collected in the warmest months, these values drop to 9293±1178 pg m(-3) for the PAHs and to 97±13 pg m(-3) for the nitro-PAHs. Total vapor phase concentrations of PAHs were one order of magnitude higher than concentrations detected in atmospheric aerosol samples collected on the same dates. Total nitro-PAH concentrations were comparable to their aerosol concentrations whereas vapor phase OH-PAHs were below their limits of the detection, indicating these were trapped in airborne particles. Copyright © 2013 Elsevier Ltd. All rights reserved.

Search for large extra dimensions in final states containing one photon or jet and large missing transverse energy produced in pp collisions at square root[s]=1.96 TeV.

PubMed

Aaltonen, T; Adelman, J; Akimoto, T; Albrow, M G; Alvarez González, B; Amerio, S; Amidei, D; Anastassov, A; Annovi, A; Antos, J; Apollinari, G; Apresyan, A; Arisawa, T; Artikov, A; Ashmanskas, W; Attal, A; Aurisano, A; Azfar, F; Azzurri, P; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Bartsch, V; Bauer, G; Beauchemin, P-H; Bedeschi, F; Bednar, P; Beecher, D; Behari, S; Bellettini, G; Bellinger, J; Benjamin, D; Beretvas, A; Beringer, J; Bhatti, A; Binkley, M; Bisello, D; Bizjak, I; Blair, R E; Blocker, C; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bolla, G; 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; Calancha, C; 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; Cavaliere, V; 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; Copic, K; Cordelli, M; Cortiana, G; Cox, D J; Crescioli, F; Cuenca Almenar, C; Cuevas, J; Culbertson, R; Cully, J C; Dagenhart, D; Datta, M; Davies, T; de Barbaro, P; De Cecco, S; Deisher, A; De Lorenzo, G; Dell'orso, M; Deluca, C; Demortier, L; Deng, J; Deninno, M; 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; Elagin, A; 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; Franklin, M; Freeman, J C; Furic, I; Gallinaro, M; Galyardt, J; Garberson, F; Garcia, J E; Garfinkel, A F; Genser, K; Gerberich, H; Gerdes, D; Gessler, A; Giagu, S; Giakoumopoulou, V; Giannetti, P; Gibson, K; Gimmell, J L; Ginsburg, C M; Giokaris, N; Giordani, M; Giromini, P; Giunta, M; Giurgiu, G; 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; 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; James, E; Jayatilaka, B; Jeon, E J; Jha, M K; 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; Keung, J; 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; Knuteson, B; Ko, B R; Koay, S A; Kondo, K; Kong, D J; Konigsberg, J; Korytov, A; Kotwal, A V; Kreps, M; Kroll, J; Krop, D; Krumnack, N; Kruse, M; Krutelyov, V; Kubo, T; Kuhr, T; Kulkarni, N P; Kurata, M; Kusakabe, Y; Kwang, S; Laasanen, A T; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; Lazzizzera, I; Lecompte, T; Lee, E; Lee, H S; Lee, S W; Leone, S; Lewis, J D; Lin, C S; Linacre, J; Lindgren, M; Lipeles, E; Lister, A; Litvintsev, D O; Liu, C; 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-Katsikakis, A; Margaroli, F; Marino, C; Marino, C P; Martin, A; 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; Menzione, A; Merkel, P; Mesropian, C; Miao, T; Miladinovic, N; Miller, R; Mills, C; Milnik, M; Mitra, A; Mitselmakher, G; Miyake, H; Moggi, N; Moon, C S; Moore, R; Morello, M J; Morlok, J; 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; Oakes, L; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; 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; Pianori, E; Pinera, L; Pitts, K; Plager, C; Pondrom, L; Poukhov, O; Pounder, N; Prakoshyn, F; Pronko, A; Proudfoot, J; Ptohos, F; Pueschel, E; 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; Rodriguez, 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; Saltó, O; Santi, L; Sarkar, S; Sartori, L; Sato, K; Savard, P; Savoy-Navarro, A; Scheidle, T; Schlabach, P; Schmidt, A; 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; Sfyrla, A; Shalhout, S Z; Shears, T; Shepard, P F; Sherman, D; Shimojima, M; Shiraishi, S; 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; Soha, A; Somalwar, S; Sorin, V; Spalding, J; 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; 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; Totaro, P; Tourneur, S; Tu, Y; Turini, N; Ukegawa, F; 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; Xie, S; Yagil, A; Yamamoto, K; Yamaoka, J; 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

2008-10-31

We present the results of searches for large extra dimensions in samples of events with large missing transverse energy E_{T} and either a photon or a jet produced in pp[over ] collisions at sqrt[s]=1.96 TeV collected with the Collider Detector at Fermilab II. For gamma+E_{T} and jet+E_{T} candidate samples corresponding to 2.0 and 1.1 fb;{-1} of integrated luminosity, respectively, we observe good agreement with standard model expectations and obtain a combined lower limit on the fundamental parameter of the large extra dimensions model M_{D} as a function of the number of extra dimensions in the model.

Review of sampling, sample and data collection procedures in nursing research--An example of research on ethical climate as perceived by nurses.

PubMed

Suhonen, Riitta; Stolt, Minna; Katajisto, Jouko; Leino-Kilpi, Helena

2015-12-01

To report a review of quality regarding sampling, sample and data collection procedures of empirical nursing research of ethical climate studies where nurses were informants. Surveys are needed to obtain generalisable information about topics sensitive to nursing. Methodological quality of the studies is of key concern, especially the description of sampling and data collection procedures. Methodological literature review. Using the electronic MEDLINE database, empirical nursing research articles focusing on ethical climate were accessed in 2013 (earliest-22 November 2013). Using the search terms 'ethical' AND ('climate*' OR 'environment*') AND ('nurse*' OR 'nursing'), 376 citations were retrieved. Based on a four-phase retrieval process, 26 studies were included in the detailed analysis. Sampling method was reported in 58% of the studies, and it was random in a minority of the studies (26%). The identification of target sample and its size (92%) was reported, whereas justification for sample size was less often given. In over two-thirds (69%) of the studies with identifiable response rate, it was below 75%. A variety of data collection procedures were used with large amount of missing data about the details of who distributed, recruited and collected the questionnaires. Methods to increase response rates were seldom described. Discussion about nonresponse, representativeness of the sample and generalisability of the results was missing in many studies. This review highlights the methodological challenges and developments that need to be considered in ensuring the use of valid information in developing health care through research findings. © 2015 Nordic College of Caring Science.

Buccal swabbing as a noninvasive method to determine bacterial, archaeal, and eukaryotic microbial community structures in the rumen.

PubMed

Kittelmann, Sandra; Kirk, Michelle R; Jonker, Arjan; McCulloch, Alan; Janssen, Peter H

2015-11-01

Analysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (R = 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (R = 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Association between Early Marriage and Intimate Partner Violence in India: A Focus on Youth from Bihar and Rajasthan

ERIC Educational Resources Information Center

Speizer, Ilene S.; Pearson, Erin

2011-01-01

The relationship between intimate partner violence (IPV) and early marriage is explored using the 2005-2006 India National Family Health Survey (NFHS-3). The NFHS-3 collected data from a representative sample of women and men in India with a large enough sample size to have a representative sample at the state level. The focus is on youth from…

Secondary analysis of national survey datasets.

PubMed

Boo, Sunjoo; Froelicher, Erika Sivarajan

2013-06-01

This paper describes the methodological issues associated with secondary analysis of large national survey datasets. Issues about survey sampling, data collection, and non-response and missing data in terms of methodological validity and reliability are discussed. Although reanalyzing large national survey datasets is an expedient and cost-efficient way of producing nursing knowledge, successful investigations require a methodological consideration of the intrinsic limitations of secondary survey analysis. Nursing researchers using existing national survey datasets should understand potential sources of error associated with survey sampling, data collection, and non-response and missing data. Although it is impossible to eliminate all potential errors, researchers using existing national survey datasets must be aware of the possible influence of errors on the results of the analyses. © 2012 The Authors. Japan Journal of Nursing Science © 2012 Japan Academy of Nursing Science.

Sampling design and procedures for fixed surface-water sites in the Georgia-Florida coastal plain study unit, 1993

USGS Publications Warehouse

Hatzell, H.H.; Oaksford, E.T.; Asbury, C.E.

1995-01-01

The implementation of design guidelines for the National Water-Quality Assessment (NAWQA) Program has resulted in the development of new sampling procedures and the modification of existing procedures commonly used in the Water Resources Division of the U.S. Geological Survey. The Georgia-Florida Coastal Plain (GAFL) study unit began the intensive data collection phase of the program in October 1992. This report documents the implementation of the NAWQA guidelines by describing the sampling design and procedures for collecting surface-water samples in the GAFL study unit in 1993. This documentation is provided for agencies that use water-quality data and for future study units that will be entering the intensive phase of data collection. The sampling design is intended to account for large- and small-scale spatial variations, and temporal variations in water quality for the study area. Nine fixed sites were selected in drainage basins of different sizes and different land-use characteristics located in different land-resource provinces. Each of the nine fixed sites was sampled regularly for a combination of six constituent groups composed of physical and chemical constituents: field measurements, major ions and metals, nutrients, organic carbon, pesticides, and suspended sediments. Some sites were also sampled during high-flow conditions and storm events. Discussion of the sampling procedure is divided into three phases: sample collection, sample splitting, and sample processing. A cone splitter was used to split water samples for the analysis of the sampling constituent groups except organic carbon from approximately nine liters of stream water collected at four fixed sites that were sampled intensively. An example of the sample splitting schemes designed to provide the sample volumes required for each sample constituent group is described in detail. Information about onsite sample processing has been organized into a flowchart that describes a pathway for each of the constituent groups.

Understanding Microplastic Distribution: A Global Citizen Monitoring Effort

NASA Astrophysics Data System (ADS)

Barrows, A.

2016-02-01

Understanding distribution and abundance of microplastics in the world's oceans will continue to help inform global law-making. Through recruiting and training over 500 volunteers our study has collected over 1000 samples from remote and populated areas world-wide. Samples include water collected at the sea surface and throughout the water column. Surface to depth sampling has provided insight into vertical plastic distribution. The development of unique field and laboratory methodology has enabled plastics to be quantified down to 50 µm. In 2015, the study expanded to include global freshwater systems. By understanding plastic patterns, distribution and concentration in large and small watersheds we will better understand how freshwater systems are contributing to marine microplastic pollution.

A metagenomic framework for the study of airborne microbial communities.

PubMed

Yooseph, Shibu; Andrews-Pfannkoch, Cynthia; Tenney, Aaron; McQuaid, Jeff; Williamson, Shannon; Thiagarajan, Mathangi; Brami, Daniel; Zeigler-Allen, Lisa; Hoffman, Jeff; Goll, Johannes B; Fadrosh, Douglas; Glass, John; Adams, Mark D; Friedman, Robert; Venter, J Craig

2013-01-01

Understanding the microbial content of the air has important scientific, health, and economic implications. While studies have primarily characterized the taxonomic content of air samples by sequencing the 16S or 18S ribosomal RNA gene, direct analysis of the genomic content of airborne microorganisms has not been possible due to the extremely low density of biological material in airborne environments. We developed sampling and amplification methods to enable adequate DNA recovery to allow metagenomic profiling of air samples collected from indoor and outdoor environments. Air samples were collected from a large urban building, a medical center, a house, and a pier. Analyses of metagenomic data generated from these samples reveal airborne communities with a high degree of diversity and different genera abundance profiles. The identities of many of the taxonomic groups and protein families also allows for the identification of the likely sources of the sampled airborne bacteria.

A Metagenomic Framework for the Study of Airborne Microbial Communities

PubMed Central

Tenney, Aaron; McQuaid, Jeff; Williamson, Shannon; Thiagarajan, Mathangi; Brami, Daniel; Zeigler-Allen, Lisa; Hoffman, Jeff; Goll, Johannes B.; Fadrosh, Douglas; Glass, John; Adams, Mark D.; Friedman, Robert; Venter, J. Craig

2013-01-01

Understanding the microbial content of the air has important scientific, health, and economic implications. While studies have primarily characterized the taxonomic content of air samples by sequencing the 16S or 18S ribosomal RNA gene, direct analysis of the genomic content of airborne microorganisms has not been possible due to the extremely low density of biological material in airborne environments. We developed sampling and amplification methods to enable adequate DNA recovery to allow metagenomic profiling of air samples collected from indoor and outdoor environments. Air samples were collected from a large urban building, a medical center, a house, and a pier. Analyses of metagenomic data generated from these samples reveal airborne communities with a high degree of diversity and different genera abundance profiles. The identities of many of the taxonomic groups and protein families also allows for the identification of the likely sources of the sampled airborne bacteria. PMID:24349140

Blood meal analysis of tabanid fly after it biting the rare Sumatran rhinoceros.

PubMed

Rovie-Ryan, Jeffrine Japning; Zainuddin, Zainal Zahari; Marni, Wahap; Ahmad, Abdul Hamid; Ambu, Laurentius N; Payne, Junaidi

2013-02-01

To demonstrate a noninvasive large mammalian genetic sampling method using blood meal obtained from a tabanid fly. Blood meal was recovered from the abdomen of an engorged tabanid fly (Haematopota sp.) which was captured immediately after biting a Sumatran rhino in captivity. The blood was applied on to a Whatman FTA(®) blood card. Subsequent laboratory work was conducted to extract, amplify and sequence the DNA from the sample. Validation was done by sampling the hair follicles and blood samples from the rhinoceros and subjecting it to the same laboratory process. BLAST search and constructed phylogenetic trees confirmed the blood meal samples were indeed from the rhino. This method could be used in the field application to noninvasively collect genetic samples. Collection of tabanids and other haematophagous arthropods (e.g. mosquitoes and ticks) and other blood-sucking parasites (e.g. leeches and worms) could also provide information on vector-borne diseases.

Large-scale monitoring of effects of clothianidin-dressed oilseed rape seeds on pollinating insects in northern Germany: residues of clothianidin in pollen, nectar and honey.

PubMed

Rolke, Daniel; Persigehl, Markus; Peters, Britta; Sterk, Guido; Blenau, Wolfgang

2016-11-01

This study was part of a large-scale monitoring project to assess the possible effects of Elado ® (10 g clothianidin & 2 g β-cyfluthrin/kg seed)-dressed oilseed rape seeds on different pollinators in Northern Germany. Firstly, residues of clothianidin and its active metabolites thiazolylnitroguanidine and thiazolylmethylurea were measured in nectar and pollen from Elado ® -dressed (test site, T) and undressed (reference site, R) oilseed rape collected by honey bees confined within tunnel tents. Clothianidin and its metabolites could not be detected or quantified in samples from R fields. Clothianidin concentrations in samples from T fields were 1.3 ± 0.9 μg/kg and 1.7 ± 0.9 μg/kg in nectar and pollen, respectively. Secondly, pollen and nectar for residue analyses were sampled from free flying honey bees, bumble bees and mason bees, placed at six study locations each in the R and T sites at the start of oilseed rape flowering. Honey samples were analysed from all honey bee colonies at the end of oilseed rape flowering. Neither clothianidin nor its metabolites were detectable or quantifiable in R site samples. Clothianidin concentrations in samples from the T site were below the limit of quantification (LOQ, 1.0 µg/kg) in most pollen and nectar samples collected by bees and 1.4 ± 0.5 µg/kg in honey taken from honey bee colonies. In summary, the study provides reliable semi-field and field data of clothianidin residues in nectar and pollen collected by different bee species in oilseed rape fields under common agricultural conditions.

Environmental geochemistry of abandoned mercury mines in West-Central Nevada, USA

USGS Publications Warehouse

Gray, J.E.; Crock, J.G.; Fey, D.L.

2002-01-01

The Humboldt River is a closed basin and is the longest river in Nevada. Numerous abandoned Hg mines are located within the basin, and because Hg is a toxic heavy metal, the potential transport of Hg from these mines into surrounding ecosystems, including the Humboldt River, is of environmental concern Samples of ore, sediment, water, calcines (roasted ore), and leachates of the calcines were analyzed for Hg and other heavy metals to evaluate geochemical dispersion from the mines. Cinnabar-bearing ore samples collected from the mines contain highly elevated Hg concentrations, up to 6.9 %, whereas calcines collected from the mines contain up to 2000 mg Hg/kg. Stream-sediment samples collected within 1 km of the mines contain as much as 170 mg Hg/kg, but those collected distal from the mines (> 5 km) contain 8 km from the Humboldt River, and Hg is transported and diluted through a large volume of pediment before it reaches the Humboldt River. ?? 2002 Elsevier Science Ltd. All rights reserved.

Evaluation of rayon swab surface sample collection method for Bacillus spores from nonporous surfaces.

PubMed

Brown, G S; Betty, R G; Brockmann, J E; Lucero, D A; Souza, C A; Walsh, K S; Boucher, R M; Tezak, M S; Wilson, M C; Rudolph, T; Lindquist, H D A; Martinez, K F

2007-10-01

To evaluate US Centers for Disease Control and Prevention recommended swab surface sample collection method for recovery efficiency and limit of detection for powdered Bacillus spores from nonporous surfaces. Stainless steel and painted wallboard surface coupons were seeded with dry aerosolized Bacillus atrophaeus spores and surface concentrations determined. The observed mean rayon swab recovery efficiency from stainless steel was 0.41 with a standard deviation (SD) of +/-0.17 and for painted wallboard was 0.41 with an SD of +/-0.23. Evaluation of a sonication extraction method for the rayon swabs produced a mean extraction efficiency of 0.76 with an SD of +/-0.12. Swab recovery quantitative limits of detection were estimated at 25 colony forming units (CFU) per sample area for both stainless steel and painted wallboard. The swab sample collection method may be appropriate for small area sampling (10 -25 cm2) with a high agent concentration, but has limited value for large surface areas with a low agent concentration. The results of this study provide information necessary for the interpretation of swab environmental sample collection data, that is, positive swab samples are indicative of high surface concentrations and may imply a potential for exposure, whereas negative swab samples do not assure that organisms are absent from the surfaces sampled and may not assure the absence of the potential for exposure. It is critical from a public health perspective that the information obtained is accurate and reproducible. The consequence of an inappropriate public health response founded on information gathered using an ineffective or unreliable sample collection method has the potential for undesired social and economic impact.

Successful application of FTA Classic Card technology and use of bacteriophage phi29 DNA polymerase for large-scale field sampling and cloning of complete maize streak virus genomes.

PubMed

Owor, Betty E; Shepherd, Dionne N; Taylor, Nigel J; Edema, Richard; Monjane, Adérito L; Thomson, Jennifer A; Martin, Darren P; Varsani, Arvind

2007-03-01

Leaf samples from 155 maize streak virus (MSV)-infected maize plants were collected from 155 farmers' fields in 23 districts in Uganda in May/June 2005 by leaf-pressing infected samples onto FTA Classic Cards. Viral DNA was successfully extracted from cards stored at room temperature for 9 months. The diversity of 127 MSV isolates was analysed by PCR-generated RFLPs. Six representative isolates having different RFLP patterns and causing either severe, moderate or mild disease symptoms, were chosen for amplification from FTA cards by bacteriophage phi29 DNA polymerase using the TempliPhi system. Full-length genomes were inserted into a cloning vector using a unique restriction enzyme site, and sequenced. The 1.3-kb PCR product amplified directly from FTA-eluted DNA and used for RFLP analysis was also cloned and sequenced. Comparison of cloned whole genome sequences with those of the original PCR products indicated that the correct virus genome had been cloned and that no errors were introduced by the phi29 polymerase. This is the first successful large-scale application of FTA card technology to the field, and illustrates the ease with which large numbers of infected samples can be collected and stored for downstream molecular applications such as diversity analysis and cloning of potentially new virus genomes.

Measurements of Organic Composition of Aerosol and Rainwater Samples Using Offline Aerosol Mass Spectrometry

NASA Astrophysics Data System (ADS)

OBrien, R. E.; Ridley, K. J.; Canagaratna, M. R.; Croteau, P.; Budisulistiorini, S. H.; Cui, T.; Green, H. S.; Surratt, J. D.; Jayne, J. T.; Kroll, J. H.

2016-12-01

A thorough understanding of the sources, evolution, and budgets of atmospheric organic aerosol requires widespread measurements of the amount and chemical composition of atmospheric organic carbon in the condensed phase (within particles and water droplets). Collecting such datasets requires substantial spatial and temporal (long term) coverage, which can be challenging when relying on online measurements by state-of-the-art research-grade instrumentation (such as those used in atmospheric chemistry field studies). Instead, samples are routinely collected using relatively low-cost techniques, such as aerosol filters, for offline analysis of their chemical composition. However, measurements made by online and offline instruments can be fundamentally different, leading to disparities between data from field studies and those from more routine monitoring. To better connect these two approaches, and take advantage of the benefits of each, we have developed a method to introduce collected samples into online aerosol instruments using nebulization. Because nebulizers typically require tens to hundreds of milliliters of solution, limiting this technique to large samples, we developed a new, ultrasonic micro-nebulizer that requires only small volumes (tens of microliters) of sample for chemical analysis. The nebulized (resuspended) sample is then sent into a high-resolution Aerosol Mass Spectrometer (AMS), a widely-used instrument that provides key information on the chemical composition of aerosol particulate matter (elemental ratios, carbon oxidation state, etc.), measurements that are not typically made for collected atmospheric samples. Here, we compare AMS data collected using standard on-line techniques with our offline analysis, demonstrating the utility of this new technique to aerosol filter samples. We then apply this approach to organic aerosol filter samples collected in remote regions, as well as rainwater samples from across the US. This data provides information on the sample composition and changes in key chemical characteristics across locations and seasons.

Reproducibility of urinary biomarkers in multiple 24-h urine samples.

PubMed

Sun, Qi; Bertrand, Kimberly A; Franke, Adrian A; Rosner, Bernard; Curhan, Gary C; Willett, Walter C

2017-01-01

Limited knowledge regarding the reproducibility of biomarkers in 24-h urine samples has hindered the collection and use of the samples in epidemiologic studies. We aimed to evaluate the reproducibility of various markers in repeat 24-h urine samples. We calculated intraclass correlation coefficients (ICCs) of biomarkers measured in 24-h urine samples that were collected in 3168 participants in the NHS (Nurses' Health Study), NHSII (Nurses' Health Study II), and Health Professionals Follow-Up Study. In 742 women with 4 samples each collected over the course of 1 y, ICCs for sodium were 0.32 in the NHS and 0.34 in the NHSII. In 2439 men and women with 2 samples each collected over 1 wk to ≥1 mo, the ICCs ranged from 0.33 to 0.68 for sodium at various intervals between collections. The urinary excretion of potassium, calcium, magnesium, phosphate, sulfate, and other urinary markers showed generally higher reproducibility (ICCs >0.4). In 47 women with two 24-h urine samples, ICCs ranged from 0.15 (catechin) to 0.75 (enterolactone) for polyphenol metabolites. For phthalates, ICCs were generally ≤0.26 except for monobenzyl phthalate (ICC: 0.55), whereas the ICC was 0.39 for bisphenol A (BPA). We further estimated that, for the large majority of the biomarkers, the mean of three 24-h urine samples could provide a correlation of ≥0.8 with true long-term urinary excretion. These data suggest that the urinary excretion of various biomarkers, such as minerals, electrolytes, most polyphenols, and BPA, is reasonably reproducible in 24-h urine samples that are collected within a few days or ≤1 y. Our findings show that three 24-h samples are sufficient for the measurement of long-term exposure status in epidemiologic studies. © 2017 American Society for Nutrition.

Reproducibility of urinary biomarkers in multiple 24-h urine samples123

PubMed Central

Sun, Qi; Bertrand, Kimberly A; Franke, Adrian A; Rosner, Bernard; Curhan, Gary C; Willett, Walter C

2017-01-01

Background: Limited knowledge regarding the reproducibility of biomarkers in 24-h urine samples has hindered the collection and use of the samples in epidemiologic studies. Objective: We aimed to evaluate the reproducibility of various markers in repeat 24-h urine samples. Design: We calculated intraclass correlation coefficients (ICCs) of biomarkers measured in 24-h urine samples that were collected in 3168 participants in the NHS (Nurses’ Health Study), NHSII (Nurses’ Health Study II), and Health Professionals Follow-Up Study. Results: In 742 women with 4 samples each collected over the course of 1 y, ICCs for sodium were 0.32 in the NHS and 0.34 in the NHSII. In 2439 men and women with 2 samples each collected over 1 wk to ≥1 mo, the ICCs ranged from 0.33 to 0.68 for sodium at various intervals between collections. The urinary excretion of potassium, calcium, magnesium, phosphate, sulfate, and other urinary markers showed generally higher reproducibility (ICCs >0.4). In 47 women with two 24-h urine samples, ICCs ranged from 0.15 (catechin) to 0.75 (enterolactone) for polyphenol metabolites. For phthalates, ICCs were generally ≤0.26 except for monobenzyl phthalate (ICC: 0.55), whereas the ICC was 0.39 for bisphenol A (BPA). We further estimated that, for the large majority of the biomarkers, the mean of three 24-h urine samples could provide a correlation of ≥0.8 with true long-term urinary excretion. Conclusions: These data suggest that the urinary excretion of various biomarkers, such as minerals, electrolytes, most polyphenols, and BPA, is reasonably reproducible in 24-h urine samples that are collected within a few days or ≤1 y. Our findings show that three 24-h samples are sufficient for the measurement of long-term exposure status in epidemiologic studies. PMID:28049663

Measurements of airborne methylene diphenyl diisocyanate (MDI) concentration in the U.S. workplace.

PubMed

Booth, Karroll; Cummings, Barbara; Karoly, William J; Mullins, Sharon; Robert, William P; Spence, Mark; Lichtenberg, Fran W; Banta, J

2009-04-01

This article summarizes a large body of industry air sampling data (8134 samples) in which airborne MDI concentrations were measured in a wide variety of manufacturing processes that use either polymeric MDI (PMDI) or monomeric (pure) MDI. Data were collected during the period 1984 through 1999. A total of 606 surveys were conducted for 251 companies at 317 facilities. The database includes 3583 personal (breathing zone) samples and 4551 area samples. Data demonstrate that workplace airborne MDI concentrations are extremely low in a majority of the manufacturing operations. Most (74.6%) of the airborne MDI concentrations measured in the personal samples were nondetectable, i.e., below the limits of quantification (LOQs). A variety of validated industrial hygiene sampling/analytical methods were used for data collection; most are modifications of OSHA Method 47. The LOQs for these methods ranged from 0.1-0.5 microg/sample. The very low vapor pressures of both monomeric MDI and PMDI largely explain the low airborne concentrations found in most operations. However, processes or applications in which the chemical is sprayed or heated may result in higher airborne concentrations and higher exposure potentials if appropriate control measures are not implemented. Data presented in this article will be a useful reference for employers in helping them to manage their health and safety program as it relates to respiratory protection during MDI/PMDI applications.

Seed germination from lowland tapir (Tapirus terrestris) fecal samples collected during the dry season in the Northern Brazilian Amazon.

PubMed

Barcelos, Adriana Renata; Bobrowiec, Paulo Estefano D; Sanaiotti, Tânia Margarete; Gribel, Rogério

2013-03-01

This study evaluated the potential of lowland tapirs as seed dispersers in the northern Brazilian Amazon. The study analyzed the viability of seeds after passage through the gut. Fecal samples were collected from 6 different vegetation physiognomies in Viruá National Park during the dry season. The samples were then kept in a greenhouse for 16 months to allow the seeds to germinate. The seedling species were identified and classified according to the type of fruit, plant habit, seed size and type of ingestion. Of the 111 fecal samples, 94 (84.7%) had viable seeds of 75 species. Melastomataceae was the most frequent family with viable seeds in the fecal samples (69.1% of samples, N= 18 species). The data suggest that the importance of the lowland tapirs as dispersers is not restricted to the species consumed actively by frugivory but also extends to species accidentally consumed during browsing. The occurrence of both large and small viable seeds in the fecal samples as well as a number of large drupes, which probably cannot be transported via endozoochory by any other animal species, provide evidence of the ecological importance of lowland tapirs to the dynamics of the forest-campinarana vegetation mosaic in the region. © 2012 Wiley Publishing Asia Pty Ltd, ISZS and IOZ/CAS.

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.

Fixation filter, device for the rapid in situ preservation of particulate samples

NASA Astrophysics Data System (ADS)

Taylor, C. D.; Edgcomb, V. P.; Doherty, K. W.; Engstrom, I.; Shanahan, T.; Pachiadaki, M. G.; Molyneaux, S. J.; Honjo, S.

2015-02-01

Niskin bottle rosettes have for years been the workhorse technology for collection of water samples used in biological and chemical oceanography. Studies of marine microbiology and biogeochemical cycling that aim to analyze labile organic molecules including messenger RNA, must take into account factors associated with sampling methodology that obscure an accurate picture of in situ activities/processes. With Niskin sampling, the large and often variable times between sample collection and preservation on deck of a ship, and the sometimes significant physico-chemical changes (e.g., changes in pressure, light, temperature, redox state, etc.) that water samples and organisms are exposed to, are likely to introduce artifacts. These concerns are likely more significant when working with phototrophs, deep-sea microbes, and/or organisms inhabiting low-oxygen or anoxic environments. We report here the development of a new technology for the in situ collection and chemical preservation of particulate microbial samples for a variety of downstream analyses depending on preservative choice by the user. The Fixation Filter Unit, version 3 (FF3) permits filtration of water sample through 47 mm diameter filters of the user's choice and upon completion of filtration, chemically preserves the retained sample within 10's of seconds. The stand-alone devices can be adapted to hydrocasting or mooring-based platforms.

Geologic setting of the apollo 14 samples

USGS Publications Warehouse

Swann, G.A.; Trask, N.J.; Hait, M.H.; Sutton, R.L.

1971-01-01

The apollo 14 lunar module landed in a region of the lunar highlands that is part of a widespread blanket of ejecta surrounding the Mare Imbrium basin. Samples were collected from the regolith developed on a nearly level plain, a ridge 100 meters high, and a blacky ejecta deposit around a young crater. Large boulders in the vicinity of the landing site are coherent fragmental rocks as are some of the returned samples.

Multielement geochemical dataset of surficial materials for the northern Great Basin

USGS Publications Warehouse

Coombs, Mary Jane; Kotlyar, Boris B.; Ludington, Steve; Folger, Helen W.; Mossotti, Victor G.

2002-01-01

This report presents geochemical data generated during mineral and environmental assessments for the Bureau of Land Management in northern Nevada, northeastern California, southeastern Oregon, and southwestern Idaho, along with metadata and map representations of selected elements. The dataset presented here is a compilation of chemical analyses of over 10,200 stream-sediment and soil samples originally collected during the National Uranium Resource Evaluation's (NURE) Hydrogeochemical and Stream Sediment Reconnaissance (HSSR) program of the Department of Energy and its predecessors and reanalyzed to support a series of mineral-resource assessments by the U.S. Geological Survey (USGS). The dataset also includes the analyses of additional samples collected by the USGS in 1992. The sample sites are in southeastern Oregon, southwestern Idaho, northeastern California, and, primarily, in northern Nevada. These samples were collected from 1977 to 1983, before the development of most of the present-day large-scale mining infrastructure in northern Nevada. As such, these data may serve as an important baseline for current and future geoenvironmental studies. Largely because of the very diverse analytical methods used by the NURE HSSR program, the original NURE analyses in this area yielded little useful geochemical information. The Humboldt, Malheur-Jordan-Andrews, and Winnemucca-Surprise studies were designed to provide useful geochemical data via improved analytical methods (lower detection levels and higher precision) and, in the Malheur-Jordan-Andrews and Winnemucca Surprise areas, to collect additional stream-sediment samples to increase sampling coverage. The data are provided in *.xls (Microsoft Excel) and *.csv (comma-separated-value) format. We also present graphically 35 elements, interpolated ("gridded") in a geographic information system (GIS) and overlain by major geologic trends, so that users may view the variation in elemental concentrations over the landscape and reach their own conclusions regarding correlation among geochemistry, geologic features, and known mineral deposits. Quality-control issues are discussed for the grids and data.

Stability of Proteins in Dried Blood Spot Biobanks*

PubMed Central

Björkesten, Johan; Enroth, Stefan; Shen, Qiujin; Wik, Lotta; Hougaard, David M.; Cohen, Arieh S.; Sörensen, Lene; Giedraitis, Vilmantas; Ingelsson, Martin; Larsson, Anders; Kamali-Moghaddam, Masood; Landegren, Ulf

2017-01-01

An important motivation for the construction of biobanks is to discover biomarkers that identify diseases at early, potentially curable stages. This will require biobanks from large numbers of individuals, preferably sampled repeatedly, where the samples are collected and stored under conditions that preserve potential biomarkers. Dried blood samples are attractive for biobanking because of the ease and low cost of collection and storage. Here we have investigated their suitability for protein measurements. Ninety-two proteins with relevance for oncology were analyzed using multiplex proximity extension assays (PEA) in dried blood spots collected on paper and stored for up to 30 years at either +4 °C or −24 °C. Our main findings were that (1) the act of drying only slightly influenced detection of blood proteins (average correlation of 0.970), and in a reproducible manner (correlation of 0.999), (2) detection of some proteins was not significantly affected by storage over the full range of three decades (34 and 76% of the analyzed proteins at +4 °C and −24 °C, respectively), whereas levels of others decreased slowly during storage with half-lives in the range of 10 to 50 years, and (3) detectability of proteins was less affected in dried samples stored at −24 °C compared with at +4 °C, as the median protein abundance had decreased to 80 and 93% of starting levels after 10 years of storage at +4 °C or −24 °C, respectively. The results of our study are encouraging as they suggest an inexpensive means to collect large numbers of blood samples, even by the donors themselves, and to transport, and store biobanked samples as spots of whole blood dried on paper. Combined with emerging means to measure hundreds or thousands of protein, such biobanks could prove of great medical value by greatly enhancing discovery as well as routine analysis of blood biomarkers. PMID:28501802

Geochemical survey of the Chattahoochee Roadless Area, Towns, Union, and White counties, Georgia

USGS Publications Warehouse

Koeppen, Robert P.; Nelson, Arthur E.

1989-01-01

Th U.S. Geological Survey made a reconnaissance geochemical survey of the Chattahoochee Roadless Area (fig. 1) to search for unexposed mineral deposits which might be recognized by a geochemical signature in the abundance or distribution patterns of trace elements. As part of a regional geochemical reconnaissance, M/ Hurst (University of Georgia) collected 51 fine-grained stream-sediment samples and 45 planned-concentrate samples  of alluvial gravels in the Chattahoochee study area (see figure 1). A.E. Nelson, in conjunction with detailed geologic mapping (Nelso, 1983), collected 10 rock-chip samples for geochemical analysis in addition to a large number of hand specimens for thin-section study. In order to evaluate isolated anomalies indicated by the earlier sampling, R.P. Koeppen, D.M. Sutphin, and P.D. Schruben collected several additional panned-concentrate, stream-sediment, and rock samples from the area in 1986. Both the geologic study by Nelson (1983) and this geochemical survey provide the basis for our mineral-resource assessment of the Chattahoochee Roadless Area (Nelson and others, 1983). 

Faster the better: a reliable technique to sample anopluran lice in large hosts.

PubMed

Leonardi, María Soledad

2014-06-01

Among Anoplura, the family Echinophthiriidae includes those species that infest mainly the pinnipeds. Working with large hosts implies methodological considerations as the time spent in the sampling, and the way in that the animal is restrained. Previous works on echinophthiriids combined a diverse array of analyses including field counts of lice and in vitro observations. To collect lice, the authors used forceps, and each louse was collected individually. This implied a long manipulation time, i.e., ≈60 min and the need to physically and/or chemically immobilize the animal. The present work described and discussed for the first a sample technique that minimized the manipulation time and also avoiding the use of anesthesia. This methodology implied combing the host's pelage with a fine-tooth plastic comb, as used in the treatment of human pediculosis, and keeping the comb with the lice retained in a Ziploc® bag with ethanol. This technique was used successfully in studies of population dynamic, habitat selection, and transmission pattern, being a reliable methodology. Lice are collected entirely and are in a good condition to prepare them for mounting for studying under light or scanning electron microscopy. Moreover, the use of the plastic comb protects from damaging taxonomically important structures as spines being also recommended to reach taxonomic or morphological goals.

Reconnaissance techniques for determining soil-gas radon concentrations: an example from Prince Georges County, Maryland

USGS Publications Warehouse

Reimer, G.M.

1990-01-01

Radon reconnaissance requires some special considerations because a large area must be covered in a short period of time and analyses must be made soon after collection because of Rn decay. A simple approach to collection and field analysis consists of a small-diameter probe pounded into the ground to a depth of at least 0.75 m. Analysis is by an alpha-scintillometer. Soil-gas samples collected along a traverse in Prince Georges County, Maryland, demonstrates the utility of the technique. The reconnaissance sampling revealed Rn soil-gas concentrations of up to 2500 pCi/L (picocuries per liter) indicating that the potential exists for indoor accumulations in excess of 4 pCi/L. -from Author

Tracking pan-continental trends in environmental contamination using sentinel raptors-what types of samples should we use?

PubMed

Espín, S; García-Fernández, A J; Herzke, D; Shore, R F; van Hattum, B; Martínez-López, E; Coeurdassier, M; Eulaers, I; Fritsch, C; Gómez-Ramírez, P; Jaspers, V L B; Krone, O; Duke, G; Helander, B; Mateo, R; Movalli, P; Sonne, C; van den Brink, N W

2016-05-01

Biomonitoring using birds of prey as sentinel species has been mooted as a way to evaluate the success of European Union directives that are designed to protect people and the environment across Europe from industrial contaminants and pesticides. No such pan-European evaluation currently exists. Coordination of such large scale monitoring would require harmonisation across multiple countries of the types of samples collected and analysed-matrices vary in the ease with which they can be collected and the information they provide. We report the first ever pan-European assessment of which raptor samples are collected across Europe and review their suitability for biomonitoring. Currently, some 182 monitoring programmes across 33 European countries collect a variety of raptor samples, and we discuss the relative merits of each for monitoring current priority and emerging compounds. Of the matrices collected, blood and liver are used most extensively for quantifying trends in recent and longer-term contaminant exposure, respectively. These matrices are potentially the most effective for pan-European biomonitoring but are not so widely and frequently collected as others. We found that failed eggs and feathers are the most widely collected samples. Because of this ubiquity, they may provide the best opportunities for widescale biomonitoring, although neither is suitable for all compounds. We advocate piloting pan-European monitoring of selected priority compounds using these matrices and developing read-across approaches to accommodate any effects that trophic pathway and species differences in accumulation may have on our ability to track environmental trends in contaminants.

Large Volume In-Situ Filtration During Sofex: an Overview of Preliminary Results

NASA Astrophysics Data System (ADS)

Lam, P. J.; Wood, T. J.; Bishop, J. K.

2002-12-01

We deployed the Multiple Unit Large Volume in-situ Filtration System (MULVFS) during the Southern Ocean Iron Experiment (SOFeX) in Jan/Feb 2002 from the R/V Revelle. The MULVFS collected samples over 4 hours of pumping at depths between the surface and 1000m from 3 flow channels: size-fractionated particles (>51μm, 1-51μm, and nominally <1μm) using a 51μm polyester mesh and a pair of microquartz fiber filters (1μm) in sequence from up to 12,000L of seawater; Th samples through absorber cartridges from up to 3500L; and >0.4μm and >0.7μm particles from up to 25L. Samples were shared with several groups in SOFeX. Profiles from the North Patch (55S 172W; hereafter "55S") were collected on Julian Day 12 before the first Fe infusion, and "in the patch" on JD 19 and 40. Five profiles were collected in the South Patch (66S, 172W; hereafter "66S"): two "out of the patch" profiles on JD 24 and 34, and three "in the patch" profiles on JD 28, 31, and 35. We observed the following in the (>51μm) size fraction: 55S was initially characterized by a predominance of small particles in the mixed layer, with very little captured on the >51μm filters. Four weeks after the first Fe addition, the >51μm samples from 35m were heavily loaded. There was a clear increase in large sized organic matter in the mixed layer, but there was no visible evidence of enhanced deep particle export at this point in the experiment. Samples collected over a shorter (12 day) period at 66S showed a concurrent natural bloom outside of the patch, obscuring detection of biomass differences inside the patch. We have calculated POC in our samples using gravimetric techniques in the >51μm fraction (polyester filter) and measured directly in the 1-51 μm and "<1μm" fractions (quartz fiber filters). We will also present preliminary results of bulk chemical analyses for CaCO3, Si, and acid leacheable bioactive trace metals, with an emphasis on iron.

Continuity of Functional-Somatic Symptoms from Late Childhood to Young Adulthood in a Community Sample

ERIC Educational Resources Information Center

Steinhausen, Hans-Christoph; Metzke, Christa Winkler

2007-01-01

Background: The goal of this study was to assess the course of functional-somatic symptoms from late childhood to young adulthood and the associations of these symptoms with young adult psychopathology. Methods: Data were collected in a large community sample at three different points in time (1994, 1997, and 2001). Functional-somatic symptoms…

High School and Beyond Transcripts Survey (1982). Data File User's Manual. Contractor Report.

ERIC Educational Resources Information Center

Jones, Calvin; And Others

This data file user's manual documents the procedures used to collect and process high school transcripts for a large sample of the younger cohort (1980 sophomores) in the High School and Beyond survey. The manual provides the user with the technical assistance needed to use the computer file and also discusses the following: (1) sample design for…

Quantitative Research on the Outcomes of China's Inland Tibetan Classes and Schools Policy: A Survey of Graduates

ERIC Educational Resources Information Center

Xiaorong, Wu

2015-01-01

Under the Inland Tibetan Classes and Schools Policy, China has trained a large number of personnel to facilitate the social, economic, and cultural development of Tibet. This study used a multistage, random sample survey to collect data on the comprehensive qualities of two sample groups of personnel in Tibet: graduates and nongraduates of inland…

Parent-Reported Feeding and Feeding Problems in a Sample of Dutch Toddlers

ERIC Educational Resources Information Center

de Moor, Jan; Didden, Robert; Korzilius, Hubert

2007-01-01

Little is known about the feeding behaviors and problems with feeding in toddlers. In the present questionnaire study, data were collected on the feeding behaviors and feeding problems in a relatively large (n = 422) sample of Dutch healthy toddlers (i.e. 18-36 months old) who lived at home with their parents. Results show that three meals a day…

Search for neutrinoless double-electron capture of 156Dy

NASA Astrophysics Data System (ADS)

Finch, S. W.; Tornow, W.

2015-12-01

Background: Multiple large collaborations are currently searching for neutrinoless double-β decay, with the ultimate goal of differentiating the Majorana-Dirac nature of the neutrino. Purpose: Investigate the feasibility of resonant neutrinoless double-electron capture, an experimental alternative to neutrinoless double-β decay. Method: Two clover germanium detectors were operated underground in coincidence to search for the de-excitation γ rays of 156Gd following the neutrinoless double-electron capture of 156Dy. 231.95 d of data were collected at the Kimballton underground research facility with a 231.57 mg enriched 156Dy sample. Results: No counts were seen above background and half-life limits are set at O (1016-1018) yr for the various decay modes of 156Dy. Conclusion: Low background spectra were efficiently collected in the search for neutrinoless double-electron capture of 156Dy, although the low natural abundance and associated lack of large quantities of enriched samples hinders the experimental reach.

Bringing together raptor collections in Europe for contaminant research and monitoring in relation to chemicals regulations.

PubMed

Movalli, Paola; Dekker, René; Koschorreck, Jan; Treu, Gabriele

2017-11-01

Raptors are good sentinels of environmental contamination and there is good capability for raptor biomonitoring in Europe. Raptor biomonitoring can benefit from natural history museums (NHMs), environmental specimen banks (ESBs) and other collections (e.g. specialist raptor specimen collections). Europe's NHMs, ESBs and other collections hold large numbers of raptor specimens and samples, covering long periods of time. These collections are potentially a valuable resource for contaminant studies over time and space. There are strong needs to monitor contaminants in the environment to support EU and national chemical management. However, data on raptor specimens in NHMs, ESBs and other collections are dispersed, few are digitised, and they are thus not easy to access. Specimen coverage is patchy in terms of species, space and time. Contaminant research with raptors would be facilitated by creating a framework to link relevant collections, digitising all collections, developing a searchable meta-database covering all existing collections, making them more visible and accessible for contaminant research. This would also help identify gaps in coverage and stimulate specimen collection to fill gaps in support of prioritised contaminant monitoring. Collections can further support raptor biomonitoring by making samples available for analysis on request.

Isotope analysis of crystalline impact melt rocks from Apollo 16 stations 11 and 13, North Ray Crater

NASA Technical Reports Server (NTRS)

Reimold, W. U.; Nyquist, L. E.; Bansal, B. M.; Shih, C.-Y.; Weismann, H.; Wooden, J. L.; Mackinnon, I. D. R.

1985-01-01

The North Ray Crater Target Rock Consortium was formed to study a large number of rake samples collected at Apollo 16 stations 11 and 13 with comparative chemical, mineralogical, and chronological techniques in order to provide a larger data base for the discussion of lunar highland evolution in the vicinity of the Apollo 16 landing region. The present investigation is concerned with Rb-Sr and Sm-Nd isotopic analyses of a number of whole-rock samples of feldspathic microporhyritic (FM) impact melt, a sample type especially abundant among the North Ray crater (station 11) sample collection. Aspects of sample mineralogy and analytical procedures are discussed, taking into account FM impact melt rocks 6715 and 63538, intergranular impact melt rock 67775, subophitic impact melt rock 67747, subophitic impact melt rock 67559, and studies based on the utilization of electron microscopy and mass spectroscopy.

Simulated ground-water flow and water quality of the Mississippi River alluvium near Burlington, Iowa, 1999

USGS Publications Warehouse

Boyd, Robert A.

2001-01-01

Water samples collected from the alluvium indicated ground water can be classified as a calcium-magnesium-bicarbonate type. Reducing conditions likely occur in some localized areas of the alluvium, as suggested by relatively large concentrations of dissolved iron (4,390 micrograms per liter) and manganese (2, 430 micrograms per liter) in some ground-water samples. Nitrite plus nitrate was detected at concentrations greater than or equal to 8 milligrams per liter in three samples collected from observation wells completed in close proximity to cropland; the nitrite plus nitrate concentration in one groundwater sample exceeded the U.S. Environmental Protection Agency Maximum Contaminant Level for nitrate in drinking water (10 milligrams per liter as N). Triazine herbicides (atrazine, cyanazine, propazine, simazine, and selected degradation products) and chloroacetanilide herbicides (acetochlor, alachlor, and metolachlor) were detected in some water samples. A greater number of herbicide compounds were detected in surface-water samples than in ground-water samples. Herbicide concentrations typically were at least an order of magnitude greater in surfacewater samples than in ground-water samples. The Maximum Contaminant Level for alachlor (2 micrograms per liter) was exceeded in a sample from Dry Branch Creek at Tama Road and for atrazine (3 micrograms per liter) was exceeded in samples collected from Dry Branch Creek at Tama Road and the county drainage ditch at Tama Road.

Efficiently sampling conformations and pathways using the concurrent adaptive sampling (CAS) algorithm

NASA Astrophysics Data System (ADS)

Ahn, Surl-Hee; Grate, Jay W.; Darve, Eric F.

2017-08-01

Molecular dynamics simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules, but they are limited by the time scale barrier. That is, we may not obtain properties' efficiently because we need to run microseconds or longer simulations using femtosecond time steps. To overcome this time scale barrier, we can use the weighted ensemble (WE) method, a powerful enhanced sampling method that efficiently samples thermodynamic and kinetic properties. However, the WE method requires an appropriate partitioning of phase space into discrete macrostates, which can be problematic when we have a high-dimensional collective space or when little is known a priori about the molecular system. Hence, we developed a new WE-based method, called the "Concurrent Adaptive Sampling (CAS) algorithm," to tackle these issues. The CAS algorithm is not constrained to use only one or two collective variables, unlike most reaction coordinate-dependent methods. Instead, it can use a large number of collective variables and adaptive macrostates to enhance the sampling in the high-dimensional space. This is especially useful for systems in which we do not know what the right reaction coordinates are, in which case we can use many collective variables to sample conformations and pathways. In addition, a clustering technique based on the committor function is used to accelerate sampling the slowest process in the molecular system. In this paper, we introduce the new method and show results from two-dimensional models and bio-molecules, specifically penta-alanine and a triazine trimer.

The macromorphoscopic databank.

PubMed

Hefner, Joseph T

2018-04-20

The development of identification standards in forensic anthropology requires large and appropriate reference samples comprising individuals with modern birth years. Recent advances in macromorphoscopic trait data collection and analysis have created a need for reference data for classification models and biological distance analyses. The Macromorphoscopic Databank (N ∼ 7,397) serves that function, making publicly available trait scores for a large sample (n = 2,363) of modern American populations and world-wide groups of various geographic origins (n = 1,790). In addition, the MaMD stores reference data for a large sample (n = 3,244) of pre-, proto- and historic Amerindian data, useful for biodistance studies and finer-levels of analysis during NAGPRA-related investigations and repatriations. In developing this database, particular attention was given to the level of classification needed during the estimation of ancestry in a forensic context. To fill the knowledge gap that currently exists in the analysis of these data, the following overview outlines many of the issues and their potential solutions. Developing valuable tools that are useful to other practitioners is the purpose of growing a databank. As the Macromorphoscopic Databank develops through data collection efforts and contributions from the field, its utility as a research and teaching tool will also mature, in turn creating a vital resource for forensic anthropologists for future generations. © 2018 Wiley Periodicals, Inc.

EXONSAMPLER: a computer program for genome-wide and candidate gene exon sampling for targeted next-generation sequencing.

PubMed

Cosart, Ted; Beja-Pereira, Albano; Luikart, Gordon

2014-11-01

The computer program EXONSAMPLER automates the sampling of thousands of exon sequences from publicly available reference genome sequences and gene annotation databases. It was designed to provide exon sequences for the efficient, next-generation gene sequencing method called exon capture. The exon sequences can be sampled by a list of gene name abbreviations (e.g. IFNG, TLR1), or by sampling exons from genes spaced evenly across chromosomes. It provides a list of genomic coordinates (a bed file), as well as a set of sequences in fasta format. User-adjustable parameters for collecting exon sequences include a minimum and maximum acceptable exon length, maximum number of exonic base pairs (bp) to sample per gene, and maximum total bp for the entire collection. It allows for partial sampling of very large exons. It can preferentially sample upstream (5 prime) exons, downstream (3 prime) exons, both external exons, or all internal exons. It is written in the Python programming language using its free libraries. We describe the use of EXONSAMPLER to collect exon sequences from the domestic cow (Bos taurus) genome for the design of an exon-capture microarray to sequence exons from related species, including the zebu cow and wild bison. We collected ~10% of the exome (~3 million bp), including 155 candidate genes, and ~16,000 exons evenly spaced genomewide. We prioritized the collection of 5 prime exons to facilitate discovery and genotyping of SNPs near upstream gene regulatory DNA sequences, which control gene expression and are often under natural selection. © 2014 John Wiley & Sons Ltd.

[Water and suspended matter sampling in fresh water networks].

PubMed

Galas, Chiara; Stellato, Luisa; Barbizzi, Sabrina; Belli, Maria; Sansone, Umberto

2005-01-01

Metals and radionuclides in water systems can be easily adsorbed on suspended matter and, finally, they could eventually accumulate in the aquatic environment. The assessment of the health of a water body needs also sampling of the suspended matter fraction. In this paper sampling systems to characterise contaminants associated with the suspended matter fraction are described, with a particular attention to the collection and preservation of samples. Sampling must be representative, to obtain reliable conclusions. In this context it is stressed the importance of the evaluation of the sampling uncertainty, which contributes to a large extent to the total uncertainty.

Immunophenotype Discovery, Hierarchical Organization, and Template-Based Classification of Flow Cytometry Samples

DOE PAGES

Azad, Ariful; Rajwa, Bartek; Pothen, Alex

2016-08-31

We describe algorithms for discovering immunophenotypes from large collections of flow cytometry samples and using them to organize the samples into a hierarchy based on phenotypic similarity. The hierarchical organization is helpful for effective and robust cytometry data mining, including the creation of collections of cell populations’ characteristic of different classes of samples, robust classification, and anomaly detection. We summarize a set of samples belonging to a biological class or category with a statistically derived template for the class. Whereas individual samples are represented in terms of their cell populations (clusters), a template consists of generic meta-populations (a group ofmore » homogeneous cell populations obtained from the samples in a class) that describe key phenotypes shared among all those samples. We organize an FC data collection in a hierarchical data structure that supports the identification of immunophenotypes relevant to clinical diagnosis. A robust template-based classification scheme is also developed, but our primary focus is in the discovery of phenotypic signatures and inter-sample relationships in an FC data collection. This collective analysis approach is more efficient and robust since templates describe phenotypic signatures common to cell populations in several samples while ignoring noise and small sample-specific variations. We have applied the template-based scheme to analyze several datasets, including one representing a healthy immune system and one of acute myeloid leukemia (AML) samples. The last task is challenging due to the phenotypic heterogeneity of the several subtypes of AML. However, we identified thirteen immunophenotypes corresponding to subtypes of AML and were able to distinguish acute promyelocytic leukemia (APL) samples with the markers provided. Clinically, this is helpful since APL has a different treatment regimen from other subtypes of AML. Core algorithms used in our data analysis are available in the flowMatch package at www.bioconductor.org. It has been downloaded nearly 6,000 times since 2014.« less

Immunophenotype Discovery, Hierarchical Organization, and Template-Based Classification of Flow Cytometry Samples

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

Azad, Ariful; Rajwa, Bartek; Pothen, Alex

We describe algorithms for discovering immunophenotypes from large collections of flow cytometry samples and using them to organize the samples into a hierarchy based on phenotypic similarity. The hierarchical organization is helpful for effective and robust cytometry data mining, including the creation of collections of cell populations’ characteristic of different classes of samples, robust classification, and anomaly detection. We summarize a set of samples belonging to a biological class or category with a statistically derived template for the class. Whereas individual samples are represented in terms of their cell populations (clusters), a template consists of generic meta-populations (a group ofmore » homogeneous cell populations obtained from the samples in a class) that describe key phenotypes shared among all those samples. We organize an FC data collection in a hierarchical data structure that supports the identification of immunophenotypes relevant to clinical diagnosis. A robust template-based classification scheme is also developed, but our primary focus is in the discovery of phenotypic signatures and inter-sample relationships in an FC data collection. This collective analysis approach is more efficient and robust since templates describe phenotypic signatures common to cell populations in several samples while ignoring noise and small sample-specific variations. We have applied the template-based scheme to analyze several datasets, including one representing a healthy immune system and one of acute myeloid leukemia (AML) samples. The last task is challenging due to the phenotypic heterogeneity of the several subtypes of AML. However, we identified thirteen immunophenotypes corresponding to subtypes of AML and were able to distinguish acute promyelocytic leukemia (APL) samples with the markers provided. Clinically, this is helpful since APL has a different treatment regimen from other subtypes of AML. Core algorithms used in our data analysis are available in the flowMatch package at www.bioconductor.org. It has been downloaded nearly 6,000 times since 2014.« less

Photographs of the Sea Floor of Western Massachusetts Bay, Offshore of Boston, Massachusett, July 1999

USGS Publications Warehouse

Gutierrez, Benjamin T.; Butman, Bradford; Blackwood, Dann S.

2001-01-01

This CD-ROM contains photographs and sediment sample analyses of the sea floor obtained at 142 sites in western Massachusetts Bay (Figure 1) during a research cruise (USGS cruise ISBL99024) aboard the Fishing Vessel (FV) Isabel S. (Figure 2) conducted July 18-21, 1999. These photographs and samples provide critical ground truth information for the interpretation of shaded relief and backscatter intensity maps created using data collected with a multibeam echo sounder system (Butman and others, in press, a, b, c; Valentine and others, in press, a, b, c). Collection of these photographs and samples was undertaken in support of a large project whose overall objective is to map and describe the sea floor of Massachusetts Bay.

Geochemical survey of the Blood Mountain Roadless Area, Union and Lumpkin counties, Georgia

USGS Publications Warehouse

Koeppen, Robert P.; Nelson, Arthur E.

1989-01-01

The U.S. Geological Survey (USGS) made a reconnaissance geochemical survey of the Blood Mountain Roadless Area to search for unexposed mineral deposits which might be recognized by a geochemical signature in the abundance of distribution patterns of trace elements. Forty five fine-grained stream-sediment samples and 45 panned-concentrate samples were collected in the Blood Mountain study area (fig. 1). A.E. Nelson, in conjunction with detailed geologic mapping, collected 13 rock-chip samples for geochemical analysis, in addition to a large number of hand specimins for thin-section study. Nelson's geologic study (1983), combined with this geochemical survey, provide the basis for our mineral-resource assessment of the Blood Mountain Roadless Area (Koeppen and others, 1983).

Carbon-13 Isotopic Abundance and Concentration of Atmospheric Methane for Background Air in the Southern and Northern Hemispheres from 1978 to 1989 (NDP-049)

DOE Data Explorer

Stevens, C. M. [Chemical Technology Division, Argonne National Laboratory, Argonne, Illinois (USA)

2012-01-01

This data package presents atmospheric CH4 concentration and 13C isotopic abundance data derived from air samples collected over the period 1978-1989 at globally distributed clean-air sites. The data set comprises 201 records, 166 from the Northern Hemisphere and 35 from the Southern Hemisphere. The air samples were collected mostly in rural or marine locations remote from large sources of CH4 and are considered representative of tropospheric background conditions. The air samples were processed by isolation of CH4 from air and conversion to CO2 for isotopic analysis by isotope ratio mass spectrometry. These data represent one of the earliest records of 13C isotopic yy!measurements for atmospheric methane and have been used to refine estimates of CH4 emissions, calculate annual growth rates of emissions from changing sources, and provide evidence for changes in the rate of atmospheric removal of CH4. The data records consist of sample collection date; number of samples combined for analysis; sampling location; analysis date; CH4 concentration; 13C isotopic abundance; and flag codes to indicate outliers, repeated analyses, and other information.

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

Hurley, D.F.; Whitehouse, J.M.

A dedicated low-flow groundwater sample collection system was designed for implementation in a post-closure ACL monitoring program at the Yaworski Lagoon NPL site in Canterbury, Connecticut. The system includes dedicated bladder pumps with intake ports located in the screened interval of the monitoring wells. This sampling technique was implemented in the spring of 1993. The system was designed to simultaneously obtain samples directly from the screened interval of nested wells in three distinct water bearing zones. Sample collection is begun upon stabilization of field parameters. Other than line volume, no prior purging of the well is required. It was foundmore » that dedicated low-flow sampling from the screened interval provides a method of representative sample collection without the bias of suspended solids introduced by traditional techniques of pumping and bailing. Analytical data indicate that measured chemical constituents are representative of groundwater migrating through the screened interval. Upon implementation of the low-flow monitoring system, analytical results exhibited a decrease in concentrations of some organic compounds and metals. The system has also proven to be a cost effective alternative to pumping and bailing which generate large volumes of purge water requiring containment and disposal.« less

Protection of obstetric dimensions in a small-bodied human sample.

PubMed

Kurki, Helen K

2007-08-01

In human females, the bony pelvis must find a balance between being small (narrow) for efficient bipedal locomotion, and being large to accommodate a relatively large newborn. It has been shown that within a given population, taller/larger-bodied women have larger pelvic canals. This study investigates whether in a population where small body size is the norm, pelvic geometry (size and shape), on average, shows accommodation to protect the obstetric canal. Osteometric data were collected from the pelves, femora, and clavicles (body size indicators) of adult skeletons representing a range of adult body size. Samples include Holocene Later Stone Age (LSA) foragers from southern Africa (n = 28 females, 31 males), Portuguese from the Coimbra-identified skeletal collection (CISC) (n = 40 females, 40 males) and European-Americans from the Hamann-Todd osteological collection (H-T) (n = 40 females, 40 males). Patterns of sexual dimorphism are similar in the samples. Univariate and multivariate analyses of raw and Mosimann shape-variables indicate that compared to the CISC and H-T females, the LSA females have relatively large midplane and outlet canal planes (particularly posterior and A-P lengths). The LSA males also follow this pattern, although with absolutely smaller pelves in multivariate space. The CISC females, who have equally small stature, but larger body mass, do not show the same type of pelvic canal size and shape accommodation. The results suggest that adaptive allometric modeling in at least some small-bodied populations protects the obstetric canal. These findings support the use of population-specific attributes in the clinical evaluation of obstetric risk. (c) 2007 Wiley-Liss, Inc.

Validation of standard operating procedures in a multicenter retrospective study to identify -omics biomarkers for chronic low back pain.

PubMed

Dagostino, Concetta; De Gregori, Manuela; Gieger, Christian; Manz, Judith; Gudelj, Ivan; Lauc, Gordan; Divizia, Laura; Wang, Wei; Sim, Moira; Pemberton, Iain K; MacDougall, Jane; Williams, Frances; Van Zundert, Jan; Primorac, Dragan; Aulchenko, Yurii; Kapural, Leonardo; Allegri, Massimo

2017-01-01

Chronic low back pain (CLBP) is one of the most common medical conditions, ranking as the greatest contributor to global disability and accounting for huge societal costs based on the Global Burden of Disease 2010 study. Large genetic and -omics studies provide a promising avenue for the screening, development and validation of biomarkers useful for personalized diagnosis and treatment (precision medicine). Multicentre studies are needed for such an effort, and a standardized and homogeneous approach is vital for recruitment of large numbers of participants among different centres (clinical and laboratories) to obtain robust and reproducible results. To date, no validated standard operating procedures (SOPs) for genetic/-omics studies in chronic pain have been developed. In this study, we validated an SOP model that will be used in the multicentre (5 centres) retrospective "PainOmics" study, funded by the European Community in the 7th Framework Programme, which aims to develop new biomarkers for CLBP through three different -omics approaches: genomics, glycomics and activomics. The SOPs describe the specific procedures for (1) blood collection, (2) sample processing and storage, (3) shipping details and (4) cross-check testing and validation before assays that all the centres involved in the study have to follow. Multivariate analysis revealed the absolute specificity and homogeneity of the samples collected by the five centres for all genetics, glycomics and activomics analyses. The SOPs used in our multicenter study have been validated. Hence, they could represent an innovative tool for the correct management and collection of reliable samples in other large-omics-based multicenter studies.

Preparation of water samples for carbon-14 dating

USGS Publications Warehouse

Feltz, H.R.; Hanshaw, Bruce B.

1963-01-01

For most natural water, a large sample is required to provide the 3 grams of carbon needed for a carbon-14 determination. A field procedure for isolating total dissolved-carbonate species is described. Carbon dioxide gas is evolved by adding sulfuric acid to the water sample; the gas is then collected in a sodium hydroxide trap by recycling in a closed system. The trap is then transported to the dating laboratory where the carbon-14 is counted.

Sparse imaging for fast electron microscopy

NASA Astrophysics Data System (ADS)

Anderson, Hyrum S.; Ilic-Helms, Jovana; Rohrer, Brandon; Wheeler, Jason; Larson, Kurt

2013-02-01

Scanning electron microscopes (SEMs) are used in neuroscience and materials science to image centimeters of sample area at nanometer scales. Since imaging rates are in large part SNR-limited, large collections can lead to weeks of around-the-clock imaging time. To increase data collection speed, we propose and demonstrate on an operational SEM a fast method to sparsely sample and reconstruct smooth images. To accurately localize the electron probe position at fast scan rates, we model the dynamics of the scan coils, and use the model to rapidly and accurately visit a randomly selected subset of pixel locations. Images are reconstructed from the undersampled data by compressed sensing inversion using image smoothness as a prior. We report image fidelity as a function of acquisition speed by comparing traditional raster to sparse imaging modes. Our approach is equally applicable to other domains of nanometer microscopy in which the time to position a probe is a limiting factor (e.g., atomic force microscopy), or in which excessive electron doses might otherwise alter the sample being observed (e.g., scanning transmission electron microscopy).

The Canadian Geo-location Endeavour Using Isotopes and Trace Elements in Hair

NASA Astrophysics Data System (ADS)

Chartrand, Michelle M. G.; St-Jean, Gilles; Dalpe, Claude; Wojtyk, James

2010-05-01

The Canadian human hair provenance project has two main objectives: 1) to build a Canadian database of isotopes and trace elements from tap water and hair samples, and 2) to assess the extent of temporal effects on these samples. To address objective 1, a cross-Canada sampling campaign has been started to collect hair and tap water samples. In the past two years, our group has collected samples from the eastern part of Canada (Newfoundland, Nova Scotia, New Brunswick, Prince Edward Island, Quebec and Ontario). Water samples are divided into three groups - groundwater, surface water and bottled water. The GIS maps show the isotopic distribution of the tap water sources varies with latitude. Hair is analyzed for carbon (C), nitrogen (N) and hydrogen (H) isotopes. The C and N results show that in general, Canadians eat a typical diet showing a small isotopic variation. However, some cases will be presented which may explain why some people have C and N values outlying the collected sample average. In terms of H isotopes in human hair, GIS maps illustrate the distribution of this isotope in the eastern provinces of Canada. In some cases, a large variation in H was observed for the same locality with no significant difference in human activities and/or consumption. However, based on hair collected from across Canada from previous years, H isotopes in hair show a correlation to water collected from the same locality. To address objective 2, hair and tap water samples were collected at 4 month intervals (to represent different seasons in Canada) from several volunteers residing in two cities located in the province of Ontario (i.e. Sudbury and Ottawa) and one city from the province of Quebec (i.e. Montreal). For all isotopes measured, there was little variation observed over the course of the year in any individual from those small to medium-size cities. On-going sampling efforts will address if any variation may occur on a yearly basis.

Collection of Oral Fluids Using Cotton Ropes as a Sampling Method to Detect Foot-and-Mouth Disease Virus Infection in Pigs.

PubMed

Vosloo, W; Morris, J; Davis, A; Giles, M; Wang, J; Nguyen, H T T; Kim, P V; Quach, N V; Le, P T T; Nguyen, P H N; Dang, H; Tran, H X; Vu, P P; Hung, V V; Le, Q T; Tran, T M; Mai, T M T; Le, Q T V; Singanallur, N B

2015-10-01

In high-density farming practices, it is important to constantly monitor for infectious diseases, especially diseases that have the potential to spread rapidly between holdings. Pigs are known to amplify foot-and-mouth disease (FMD) by excreting large amounts of virus, and it is therefore important to detect the virus quickly and accurately to minimize the spread of disease. Ropes were used to collect oral fluid samples from pigs, and each sample was compared to saliva samples collected from individual animals by detecting FMD virus RNA using real-time PCR. Two different experiments are described where groups of pigs were infected with different serotypes of FMD virus, either with or without vaccination, and unvaccinated pigs were kept in aerosol contact. The sensitivity of the rope sampling varied between 0.67 and 0.92, and the statistical agreement between this method and individual sampling ranged from substantial to moderate for the two different serotypes. The ease of collecting oral fluids using ropes together with the high sensitivity of subsequent FMD detection through PCR indicates that this could be a useful method to monitor pig populations for FMD virus infection. With further validation of the sensitivity of detection of FMD virus RNA, this can be a cost-effective, non-invasive diagnostic tool. © 2013 Blackwell Verlag GmbH.

Determination of arsenic in ambient water at sub-part-per-trillion levels by hydride generation Pd coated platform collection and GFAAS detection.

PubMed

Liang, L; Lazoff, S; Chan, C; Horvat, M; Woods, J S

1998-11-01

A method for trace determination of total arsenic in ambient waters is described. Arsenic is separated on-line from a large volume water sample by hydride generation and purging, pre-collected on a Pd coated pyrolytic platform cuvette using a simple and inexpensive system, and finally detected by GFAAS. Instrument parameters, hydride generation, transportation, and collection were optimized. The analytical behavior for major species including As(3+), As(5+), monomethyl As (MMA), and dimethyl As (DMA) were investigated individually. Problems arising from use of the system were discussed and eliminated. The necessity of sample digestion and an efficient digestion method were studied. Sample digestion for water with low organic content such as tap water and clean ground water and some clean surface water can be omitted. The method detection limit (MDL) is 0.3 ng l(-1) for a 25 ml water sample. Recoveries close to 100% with R.S.D.<5% can be easily achieved. Typical aqueous samples including tap, ground, lake, river, rain, sewage effluent, and saline water from different origins in the US, China, and Canada were collected and analyzed using ultra clean sampling and analysis techniques. The background levels of As in most water analyzed were established for the first time, and found to be far above the EPA's health effect criteria, 18 ng l(-1).

The Indigo V Indian Ocean Expedition: a prototype for citizen microbial oceanography

NASA Astrophysics Data System (ADS)

Lauro, Federico; Senstius, Jacob; Cullen, Jay; Lauro, Rachelle; Neches, Russell; Grzymski, Joseph

2014-05-01

Microbial Oceanography has long been an extremely expensive discipline, requiring ship time for sample collection and thereby economically constraining the number of samples collected. This is especially true for under-sampled water bodies such as the Indian Ocean. Specialised scientific equipment only adds to the costs. Moreover, long term monitoring of microbial communities and large scale modelling of global biogeochemical cycles requires the collection of high-density data both temporally and spatially in a cost-effective way. Thousands of private ocean-going vessels are cruising around the world's oceans every day. We believe that a combination of new technologies, appropriate laboratory protocols and strategic operational partnerships will allow researchers to broaden the scope of participation in basic oceanographic research. This will be achieved by equipping sailing vessels with small, satcom-equipped sampling devices, user-friendly collection techniques and a 'pre-addressed-stamped-envelope' to send in the samples for analysis. We aim to prove that 'bigger' is not necessarily 'better' and the key to greater understanding of the world's oceans is to forge the way to easier and cheaper sample acquisition. The ultimate goal of the Indigo V Expedition is to create a working blue-print for 'citizen microbial oceanography'. We will present the preliminary outcomes of the first Indigo V expedition, from Capetown to Singapore, highlighting the challenges and opportunities of such endeavours.

Waste Workers’ Exposure to Airborne Fungal and Bacterial Species in the Truck Cab and During Waste Collection

PubMed Central

Madsen, Anne Mette; Alwan, Taif; Ørberg, Anders; Uhrbrand, Katrine; Jørgensen, Marie Birk

2016-01-01

A large number of people work with garbage collection, and exposure to microorganisms is considered an occupational health problem. However, knowledge on microbial exposure at species level is limited. The aim of the study was to achieve knowledge on waste collectors’ exposure to airborne inhalable fungal and bacterial species during waste collection with focus on the transport of airborne microorganisms into the truck cab. Airborne microorganisms were collected with samplers mounted in the truck cab, on the workers’ clothes, and outdoors. Fungal and bacterial species were quantified and identified. The study showed that the workers were exposed to between 112 and 4.8×104 bacteria m−3 air and 326 and 4.6×104 fungi m−3 air. The personal exposures to bacteria and fungi were significantly higher than the concentrations measured in the truck cabs and in the outdoor references. On average, the fungal and bacterial concentrations in truck cabs were 111 and 7.7 times higher than outdoor reference measurements. In total, 23 fungal and 38 bacterial species were found and identified. Most fungal species belonged to the genus Penicillium and in total 11 Penicillium species were found. Identical fungal species were often found both in a personal sample and in the same person’s truck cab, but concentrations were on average 27 times higher in personal samples. Concentrations of fungal and bacterial species found only in the personal samples were lower than concentrations of species also found in truck cabs. Skin-related bacteria constituted a large fraction of bacterial isolates found in personal and truck cab samples. In total, six Staphylococcus species were found. In outdoor samples, no skin-related bacteria were found. On average, concentrations of bacterial species found both in the truck cab and personal samples were 77 times higher in personal samples than in truck cab samples. In conclusion, high concentrations of fungi were found in truck cabs, but the highest concentrations were found in personal samples; fungal and bacterial species found in high concentrations in personal samples were also found in truck cabs, but in lower concentrations indicating that both fungi and bacteria are transported by the workers into the truck cab, and are subsequently aerosolized in the truck cab. PMID:27098185

Projection x-ray topography system at 1-BM x-ray optics test beamline at the advanced photon source

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

Stoupin, Stanislav, E-mail: sstoupin@aps.anl.gov; Liu, Zunping; Trakhtenberg, Emil

2016-07-27

Projection X-ray topography of single crystals is a classic technique for the evaluation of intrinsic crystal quality of large crystals. In this technique a crystal sample and an area detector (e.g., X-ray film) collecting intensity of a chosen crystallographic reflection are translated simultaneously across an X-ray beam collimated in the diffraction scattering plane (e.g., [1, 2]). A bending magnet beamline of a third-generation synchrotron source delivering x-ray beam with a large horizontal divergence, and therefore, a large horizontal beam size at a crystal sample position offers an opportunity to obtain X-ray topographs of large crystalline samples (e.g., 6-inch wafers) inmore » just a few exposures. Here we report projection X-ray topography system implemented recently at 1-BM beamline of the Advanced Photon Source. A selected X-ray topograph of a 6-inch wafer of 4H-SiC illustrates capabilities and limitations of the technique.« less

Whale sharks target dense prey patches of sergestid shrimp off Tanzania

PubMed Central

Rohner, Christoph A.; Armstrong, Amelia J.; Pierce, Simon J.; Prebble, Clare E. M.; Cagua, E. Fernando; Cochran, Jesse E. M.; Berumen, Michael L.; Richardson, Anthony J.

2015-01-01

Large planktivores require high-density prey patches to make feeding energetically viable. This is a major challenge for species living in tropical and subtropical seas, such as whale sharks Rhincodon typus. Here, we characterize zooplankton biomass, size structure and taxonomic composition from whale shark feeding events and background samples at Mafia Island, Tanzania. The majority of whale sharks were feeding (73%, 380 of 524 observations), with the most common behaviour being active surface feeding (87%). We used 20 samples collected from immediately adjacent to feeding sharks and an additional 202 background samples for comparison to show that plankton biomass was ∼10 times higher in patches where whale sharks were feeding (25 vs. 2.6 mg m−3). Taxonomic analyses of samples showed that the large sergestid Lucifer hanseni (∼10 mm) dominated while sharks were feeding, accounting for ∼50% of identified items, while copepods (<2 mm) dominated background samples. The size structure was skewed towards larger animals representative of L.hanseni in feeding samples. Thus, whale sharks at Mafia Island target patches of dense, large, zooplankton dominated by sergestids. Large planktivores, such as whale sharks, which generally inhabit warm oligotrophic waters, aggregate in areas where they can feed on dense prey to obtain sufficient energy. PMID:25814777

Lichen elemental content bioindicators for air quality in upper Midwest, USA: A model for large-scale monitoring

Treesearch

Susan Will-Wolf; Sarah Jovan; Michael C. Amacher

2017-01-01

Our development of lichen elemental bioindicators for a United States of America (USA) national monitoring program is a useful model for other large-scale programs. Concentrations of 20 elements were measured, validated, and analyzed for 203 samples of five common lichen species. Collections were made by trained non-specialists near 75 permanent plots and an expert...

The State of Sleep among College Students at a Large Public University

ERIC Educational Resources Information Center

Orzech, Kathryn M.; Salafsky, David B.; Hamilton, Lee Ann

2011-01-01

Objective: Data about college student sleep were collected and used to develop an education campaign to improve sleep. Participants: On-campus residents at a large state university were surveyed on 4 occasions, October 2005 to April 2007. Sample size was 675 to 1,823 students. Fall 2005 mean age = 18.5 years, SD = 1.03 (range 18-30) years. Initial…

Reinforced dynamics for enhanced sampling in large atomic and molecular systems

NASA Astrophysics Data System (ADS)

Zhang, Linfeng; Wang, Han; E, Weinan

2018-03-01

A new approach for efficiently exploring the configuration space and computing the free energy of large atomic and molecular systems is proposed, motivated by an analogy with reinforcement learning. There are two major components in this new approach. Like metadynamics, it allows for an efficient exploration of the configuration space by adding an adaptively computed biasing potential to the original dynamics. Like deep reinforcement learning, this biasing potential is trained on the fly using deep neural networks, with data collected judiciously from the exploration and an uncertainty indicator from the neural network model playing the role of the reward function. Parameterization using neural networks makes it feasible to handle cases with a large set of collective variables. This has the potential advantage that selecting precisely the right set of collective variables has now become less critical for capturing the structural transformations of the system. The method is illustrated by studying the full-atom explicit solvent models of alanine dipeptide and tripeptide, as well as the system of a polyalanine-10 molecule with 20 collective variables.

Summary of surface-water-quality data collected for the Northern Rockies Intermontane Basins National Water-Quality Assessment Program in the Clark Fork-Pend Oreille and Spokane River basins, Montana, Idaho, and Washington, water years 1999-2001

USGS Publications Warehouse

Beckwith, Michael A.

2003-01-01

Water-quality samples were collected at 10 sites in the Clark Fork-Pend Oreille and Spokane River Basins in water years 1999 – 2001 as part of the Northern Rockies Intermontane Basins (NROK) National Water-Quality Assessment (NAWQA) Program. Sampling sites were located in varied environments ranging from small streams and rivers in forested, mountainous headwater areas to large rivers draining diverse landscapes. Two sampling sites were located immediately downstream from the large lakes; five sites were located downstream from large-scale historical mining and oreprocessing areas, which are now the two largest “Superfund” (environmental remediation) sites in the Nation. Samples were collected during a wide range of streamflow conditions, more frequently during increasing and high streamflow and less frequently during receding and base-flow conditions. Sample analyses emphasized major ions, nutrients, and selected trace elements. Streamflow during the study ranged from more than 130 percent of the long-term average in 1999 at some sites to 40 percent of the long-term average in 2001. River and stream water in the study area exhibited small values for specific conductance, hardness, alkalinity, and dissolved solids. Dissolved oxygen concentrations in almost all samples were near saturation. Median total nitrogen and total phosphorus concentrations in samples from most sites were smaller than median concentrations reported for many national programs and other NAWQA Program study areas. The only exceptions were two sites downstream from large wastewater-treatment facilities, where median concentrations of total nitrogen exceeded the national median. Maximum concentrations of total phosphorus in samples from six sites exceeded the 0.1 milligram per liter threshold recommended for limiting nuisance aquatic growth. Concentrations of arsenic, cadmium, copper, lead, mercury, and zinc were largest in samples from sites downstream from historical mining and ore-processing areas in the upper Clark Fork in Montana and the South Fork Coeur d’Alene River in Idaho. Concentrations of dissolved lead in all 32 samples from the South Fork Coeur d’Alene River exceeded the Idaho chronic criterion for the protection of aquatic life at the median hardness level measured during the study. Concentrations of dissolved zinc in all samples collected at this site exceeded both the chronic and acute criteria at all hardness levels measured. When all data from all NROK sites were combined, median concentrations of dissolved arsenic, dissolved and total recoverable copper, total recoverable lead, and total recoverable zinc in the NROK study area appeared to be similar to or slightly smaller than median concentrations at sites in other NAWQA Program study areas in the Western United States affected by historical mining activities. Although the NROK median total recoverable lead concentration was the smallest among the three Western study areas compared, concentrations in several NROK samples were an order of magnitude larger than the maximum concentrations measured in the Upper Colorado River and Great Salt Lake Basins. Dissolved cadmium, dissolved lead, and total recoverable zinc concentrations at NROK sites were more variable than in the other study areas; concentrations ranged over almost three orders of magnitude between minimum and maximum values; the range of dissolved zinc concentrations in the NROK study area exceeded three orders of magnitude.

A Taxometric Investigation of the Latent Structure of Worry: Dimensionality and Associations with Depression, Anxiety, and Stress

ERIC Educational Resources Information Center

Olatunji, Bunmi O.; Broman-Fulks, Joshua J.; Bergman, Shawn M.; Green, Bradley A.; Zlomke, Kimberly R.

2010-01-01

Worry has been described as a core feature of several disorders, particularly generalized anxiety disorder (GAD). The present study examined the latent structure of worry by applying 3 taxometric procedures (MAXEIG, MAMBAC, and L-Mode) to data collected from 2 large samples. Worry in the first sample (Study 1) of community participants (n = 1,355)…

Technologies for imaging neural activity in large volumes

PubMed Central

Ji, Na; Freeman, Jeremy; Smith, Spencer L.

2017-01-01

Neural circuitry has evolved to form distributed networks that act dynamically across large volumes. Collecting data from individual planes, conventional microscopy cannot sample circuitry across large volumes at the temporal resolution relevant to neural circuit function and behaviors. Here, we review emerging technologies for rapid volume imaging of neural circuitry. We focus on two critical challenges: the inertia of optical systems, which limits image speed, and aberrations, which restrict the image volume. Optical sampling time must be long enough to ensure high-fidelity measurements, but optimized sampling strategies and point spread function engineering can facilitate rapid volume imaging of neural activity within this constraint. We also discuss new computational strategies for the processing and analysis of volume imaging data of increasing size and complexity. Together, optical and computational advances are providing a broader view of neural circuit dynamics, and help elucidate how brain regions work in concert to support behavior. PMID:27571194

Organizational Commitment and Nurses' Characteristics as Predictors of Job Involvement.

PubMed

Alammar, Kamila; Alamrani, Mashael; Alqahtani, Sara; Ahmad, Muayyad

2016-01-01

To predict nurses' job involvement on the basis of their organizational commitment and personal characteristics at a large tertiary hospital in Saudi Arabia. Data were collected in 2015 from a convenience sample of 558 nurses working at a large tertiary hospital in Riyadh, Saudi Arabia. A cross-sectional correlational design was used in this study. Data were collected using a structured questionnaire. All commitment scales had significant relationships. Multiple linear regression analysis revealed that the model predicted a sizeable proportion of variance in nurses' job involvement (p < 0.001). High organizational commitment enhances job involvement, which may lead to more organizational stability and effectiveness.

Comparative AMS radiocarbon dating of pretreated versus non-pretreated tropical wood samples

NASA Astrophysics Data System (ADS)

Patrut, Adrian; von Reden, Karl F.; Lowy, Daniel A.; Mayne, Diana H.; Elder, Kathryn E.; Roberts, Mark L.; McNichol, Ann P.

2010-04-01

Several wood samples collected from Dorslandboom, a large iconic African baobab ( Adansonia digitata L.) from Namibia, were investigated by AMS radiocarbon dating subsequent to pretreatment and, alternatively, without pretreatment. The comparative statistical evaluation of results showed that there were no significant differences between fraction modern values and radiocarbon dates of the samples analyzed after pretreatment and without pretreatment, respectively. The radiocarbon date of the oldest sample was 993 ± 20 BP. Dating results also revealed that Dorslandboom is a multi-generation tree, with several stems showing different ages.

A metabolomics guided exploration of marine natural product chemical space.

PubMed

Floros, Dimitrios J; Jensen, Paul R; Dorrestein, Pieter C; Koyama, Nobuhiro

2016-09-01

Natural products from culture collections have enormous impact in advancing discovery programs for metabolites of biotechnological importance. These discovery efforts rely on the metabolomic characterization of strain collections. Many emerging approaches compare metabolomic profiles of such collections, but few enable the analysis and prioritization of thousands of samples from diverse organisms while delivering chemistry specific read outs. In this work we utilize untargeted LC-MS/MS based metabolomics together with molecular networking to. This approach annotated 76 molecular families (a spectral match rate of 28 %), including clinically and biotechnologically important molecules such as valinomycin, actinomycin D, and desferrioxamine E. Targeting a molecular family produced primarily by one microorganism led to the isolation and structure elucidation of two new molecules designated maridric acids A and B. Molecular networking guided exploration of large culture collections allows for rapid dereplication of know molecules and can highlight producers of uniques metabolites. These methods, together with large culture collections and growing databases, allow for data driven strain prioritization with a focus on novel chemistries.

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

Using LUCAS topsoil database to estimate soil organic carbon content in local spectral libraries

NASA Astrophysics Data System (ADS)

Castaldi, Fabio; van Wesemael, Bas; Chabrillat, Sabine; Chartin, Caroline

2017-04-01

The quantification of the soil organic carbon (SOC) content over large areas is mandatory to obtain accurate soil characterization and classification, which can improve site specific management at local or regional scale exploiting the strong relationship between SOC and crop growth. The estimation of the SOC is not only important for agricultural purposes: in recent years, the increasing attention towards global warming highlighted the crucial role of the soil in the global carbon cycle. In this context, soil spectroscopy is a well consolidated and widespread method to estimate soil variables exploiting the interaction between chromophores and electromagnetic radiation. The importance of spectroscopy in soil science is reflected by the increasing number of large soil spectral libraries collected in the world. These large libraries contain soil samples derived from a consistent number of pedological regions and thus from different parent material and soil types; this heterogeneity entails, in turn, a large variability in terms of mineralogical and organic composition. In the light of the huge variability of the spectral responses to SOC content and composition, a rigorous classification process is necessary to subset large spectral libraries and to avoid the calibration of global models failing to predict local variation in SOC content. In this regard, this study proposes a method to subset the European LUCAS topsoil database into soil classes using a clustering analysis based on a large number of soil properties. The LUCAS database was chosen to apply a standardized multivariate calibration approach valid for large areas without the need for extensive field and laboratory work for calibration of local models. Seven soil classes were detected by the clustering analyses and the samples belonging to each class were used to calibrate specific partial least square regression (PLSR) models to estimate SOC content of three local libraries collected in Belgium (Loam belt and Wallonia) and Luxembourg. The three local libraries only consist of spectral data (199 samples) acquired using the same protocol as the one used for the LUCAS database. SOC was estimated with a good accuracy both within each local library (RMSE: 1.2 ÷ 5.4 g kg-1; RPD: 1.41 ÷ 2.06) and for the samples of the three libraries together (RMSE: 3.9 g kg-1; RPD: 2.47). The proposed approach could allow to estimate SOC everywhere in Europe only collecting spectra, without the need for chemical laboratory analyses, exploiting the potentiality of the LUCAS database and specific PLSR models.

Characterization of aerosolized bacteria and fungi from desert dust events in Mali, West Africa

USGS Publications Warehouse

Kellogg, C.A.; Griffin, Dale W.; Garrison, V.H.; Peak, K.K.; Royall, N.; Smith, R.R.; Shinn, E.A.

2004-01-01

Millions of metric tons of African desert dust blow across the Atlantic Ocean each year, blanketing the Caribbean and southeastern United States. Previous work in the Caribbean has shown that atmospheric samples collected during dust events contain living microbes, including plant and opportunistic human pathogens. To better understand the potential downwind public health and ecosystem effects of the dust microbes, it is important to characterize the source population. We describe 19 genera of bacteria and 3 genera of fungi isolated from air samples collected in Mali, a known source region for dust storms, and over which large dust storms travel.

Blood meal analysis of tabanid fly after it biting the rare Sumatran rhinoceros

PubMed Central

Rovie-Ryan, Jeffrine Japning; Zainuddin, Zainal Zahari; Marni, Wahap; Ahmad, Abdul Hamid; Ambu, Laurentius N.; Payne, Junaidi

2013-01-01

Objective To demonstrate a noninvasive large mammalian genetic sampling method using blood meal obtained from a tabanid fly. Methods Blood meal was recovered from the abdomen of an engorged tabanid fly (Haematopota sp.) which was captured immediately after biting a Sumatran rhino in captivity. The blood was applied on to a Whatman FTA® blood card. Subsequent laboratory work was conducted to extract, amplify and sequence the DNA from the sample. Validation was done by sampling the hair follicles and blood samples from the rhinoceros and subjecting it to the same laboratory process. Results BLAST search and constructed phylogenetic trees confirmed the blood meal samples were indeed from the rhino. Conclusions This method could be used in the field application to noninvasively collect genetic samples. Collection of tabanids and other haematophagous arthropods (e.g. mosquitoes and ticks) and other blood-sucking parasites (e.g. leeches and worms) could also provide information on vector-borne diseases. PMID:23593586

Preconcentrator with high volume chiller for high vapor pressure particle detection

DOEpatents

Linker, Kevin L

2013-10-22

Apparatus and method for collecting particles of both high and low vapor pressure target materials entrained in a large volume sample gas stream. Large volume active cooling provides a cold air supply which is mixed with the sample gas stream to reduce the vapor pressure of the particles. In embodiments, a chiller cools air from ambient conditions to 0-15.degree. C. with the volumetric flow rate of the cold air supply being at least equal to the volumetric flow rate of the sample gas stream. In further embodiments an adsorption media is heated in at least two stages, a first of which is below a threshold temperature at which decomposition products of the high vapor pressure particle are generated.

Area estimation using multiyear designs and partial crop identification

NASA Technical Reports Server (NTRS)

Sielken, R. L., Jr.

1984-01-01

Statistical procedures were developed for large area assessments using both satellite and conventional data. Crop acreages, other ground cover indices, and measures of change were the principal characteristics of interest. These characteristics are capable of being estimated from samples collected possibly from several sources at varying times, with different levels of identification. Multiyear analysis techniques were extended to include partially identified samples; the best current year sampling design corresponding to a given sampling history was determined; weights reflecting the precision or confidence in each observation were identified and utilized, and the variation in estimates incorporating partially identified samples were quantified.

Risk factors associated with high potential for serious crashes.

DOT National Transportation Integrated Search

2015-09-01

Crashes are random events and low traffic volumes therefore dont always make crash hot-spot : identification possible. This project has used extensive data collection and analysis for a large sample : of Oregons low volume roads to develop a ri...

Bedload Rating and Flow Competence Curves Vary With Watershed and Bed Material Parameters

NASA Astrophysics Data System (ADS)

Bunte, K.; Abt, S. R.

2003-12-01

Bedload transport rating curves and flow competence curves (largest bedload size for specified flow) are usually not known for streams unless a large number of bedload samples has been collected and analyzed. However, this information is necessary for assessing instream flow needs and stream responses to watershed effects. This study therefore analyzed whether bedload transport rating and flow competence curves were related to stream parameters. Bedload transport rating curves and flow competence curves were obtained from extensive bedload sampling in six gravel- and cobble-bed mountain streams. Samples were collected using bedload traps and a large net sampler, both of which provide steep and relatively well-defined bedload rating and flow competence curves due to a long sampling duration, a large sampler opening and a large sampler capacity. The sampled streams have snowmelt regimes, steep (1-9%) gradients, and watersheds that are mainly forested and relatively undisturbed with basin area sizes of 8 to 105 km2. The channels are slightly incised and can contain flows of more than 1.5 times bankfull with little overbank flow. Exponents of bedload rating and flow competence curves obtained from these measurements were found to systematically increase with basin area size and decrease with the degree of channel armoring. By contrast, coefficients of bedload rating and flow competence curves decreased with basin size and increased with armoring. All of these relationships were well-defined (0.86 < r2 < 0.99). Data sets from other studies in coarse-bedded streams fit the indicated trend if the sampling device used allows measuring bedload transport rates over a wide range and if bedload supply is somewhat low. The existence of a general positive trend between bedload rating curve exponents and basin area, and a negative trend between coefficients and basin area, is confirmed by a large data set of bedload rating curves obtained from Helley-Smith samples. However, in this case, the trends only become visible as basin area sizes span a wide range (1 - 10,000 km2). The well-defined relationships obtained from the bedload trap and the large net sampler suggest that exponents and coefficients of bedload transport rating curves (and flow competence curves) are predictable from an easily obtainable parameter such as basin size. However, the relationships of bedload rating curve exponents and coefficients with basin size and armoring appear to be influenced by the sampling device used and the watershed sediment production.

Meta-Storms: efficient search for similar microbial communities based on a novel indexing scheme and similarity score for metagenomic data.

PubMed

Su, Xiaoquan; Xu, Jian; Ning, Kang

2012-10-01

It has long been intriguing scientists to effectively compare different microbial communities (also referred as 'metagenomic samples' here) in a large scale: given a set of unknown samples, find similar metagenomic samples from a large repository and examine how similar these samples are. With the current metagenomic samples accumulated, it is possible to build a database of metagenomic samples of interests. Any metagenomic samples could then be searched against this database to find the most similar metagenomic sample(s). However, on one hand, current databases with a large number of metagenomic samples mostly serve as data repositories that offer few functionalities for analysis; and on the other hand, methods to measure the similarity of metagenomic data work well only for small set of samples by pairwise comparison. It is not yet clear, how to efficiently search for metagenomic samples against a large metagenomic database. In this study, we have proposed a novel method, Meta-Storms, that could systematically and efficiently organize and search metagenomic data. It includes the following components: (i) creating a database of metagenomic samples based on their taxonomical annotations, (ii) efficient indexing of samples in the database based on a hierarchical taxonomy indexing strategy, (iii) searching for a metagenomic sample against the database by a fast scoring function based on quantitative phylogeny and (iv) managing database by index export, index import, data insertion, data deletion and database merging. We have collected more than 1300 metagenomic data from the public domain and in-house facilities, and tested the Meta-Storms method on these datasets. Our experimental results show that Meta-Storms is capable of database creation and effective searching for a large number of metagenomic samples, and it could achieve similar accuracies compared with the current popular significance testing-based methods. Meta-Storms method would serve as a suitable database management and search system to quickly identify similar metagenomic samples from a large pool of samples. ningkang@qibebt.ac.cn Supplementary data are available at Bioinformatics online.

Fully automatic characterization and data collection from crystals of biological macromolecules

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

Svensson, Olof; Malbet-Monaco, Stéphanie; Popov, Alexander

A fully automatic system has been developed that performs X-ray centring and characterization of, and data collection from, large numbers of cryocooled crystals without human intervention. Considerable effort is dedicated to evaluating macromolecular crystals at synchrotron sources, even for well established and robust systems. Much of this work is repetitive, and the time spent could be better invested in the interpretation of the results. In order to decrease the need for manual intervention in the most repetitive steps of structural biology projects, initial screening and data collection, a fully automatic system has been developed to mount, locate, centre to themore » optimal diffraction volume, characterize and, if possible, collect data from multiple cryocooled crystals. Using the capabilities of pixel-array detectors, the system is as fast as a human operator, taking an average of 6 min per sample depending on the sample size and the level of characterization required. Using a fast X-ray-based routine, samples are located and centred systematically at the position of highest diffraction signal and important parameters for sample characterization, such as flux, beam size and crystal volume, are automatically taken into account, ensuring the calculation of optimal data-collection strategies. The system is now in operation at the new ESRF beamline MASSIF-1 and has been used by both industrial and academic users for many different sample types, including crystals of less than 20 µm in the smallest dimension. To date, over 8000 samples have been evaluated on MASSIF-1 without any human intervention.« less

Ultra-broadband ptychography with self-consistent coherence estimation from a high harmonic source

NASA Astrophysics Data System (ADS)

Odstrčil, M.; Baksh, P.; Kim, H.; Boden, S. A.; Brocklesby, W. S.; Frey, J. G.

2015-09-01

With the aim of improving imaging using table-top extreme ultraviolet sources, we demonstrate coherent diffraction imaging (CDI) with relative bandwidth of 20%. The coherence properties of the illumination probe are identified using the same imaging setup. The presented methods allows for the use of fewer monochromating optics, obtaining higher flux at the sample and thus reach higher resolution or shorter exposure time. This is important in the case of ptychography when a large number of diffraction patterns need to be collected. Our microscopy setup was tested on a reconstruction of an extended sample to show the quality of the reconstruction. We show that high harmonic generation based EUV tabletop microscope can provide reconstruction of samples with a large field of view and high resolution without additional prior knowledge about the sample or illumination.

Uranium hydrogeochemical and stream sediment reconnaissance of the Cortez NTMS Quadrangle, Colorado/Utah, including concentrations of forty-three additional elements

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

Warren, R.G.

1979-05-01

During the summers of 1976, 1977, and 1978, 598 water and 1657 sediment samples were collected from 1775 locations within the 19,600-km/sup 2/ area of the Cortez Quadrangle, Colorado and Utah. Water samples were collected from streams, springs, and wells; sediment samples were collected from stream channels (wet and dry) and from springs. Each water sample was analyzed for 13 elements, and each sediment sample was analyzed for 43 elements. Uranium concentrations in water samples range from below the detection limit of 0.02 to 241.47 ppB and have a median of 0.87 ppB and a mean of 3.80 ppB. Backgroundmore » uranium concentrations are 2 to 5 ppB in several nonmountainous regions but are much lower in mountainous areas, particularly in the northeastern portion of the quadrangle. Water samples containing high uranium concentrations (>20 ppB) generally are associated with high conductivities, high concentrations of other metallic elements, and geologic units, such as the Mancos shale, that are unfavorable for uranium mineralization. However, four ground-water samples exhibit high uranium concentrations without concomitant high conductivities or high concentrations of other metallic elements. Two of these samples were collected from sites in the Slick Rock U--V district, and two were collected in the Morrison formation in the southern portion of the quadrangle where large uranium deposits are not known. Water samples collected from the northwestern corner of the quadrangle uniformly exhibit background uranium values but generally contain high nickel concentrations. In this area, U--Cu (White Canyon-type) deposits are hosted primarily by the Shinarump member of the Chinle formation. Uranium concentrations in sediment samples range from 0.51 to 76.41 ppM and have a median of 2.76 ppM and a mean of 3.08 ppM. Background uranium and metallic element concentrations decrease to the southwest from the highest values in the northeastern portion of the quadrangle.« less

Sampling populations of humans across the world: ELSI issues.

PubMed

Knoppers, Bartha Maria; Zawati, Ma'n H; Kirby, Emily S

2012-01-01

There are an increasing number of population studies collecting data and samples to illuminate gene-environment contributions to disease risk and health. The rising affordability of innovative technologies capable of generating large amounts of data helps achieve statistical power and has paved the way for new international research collaborations. Most data and sample collections can be grouped into longitudinal, disease-specific, or residual tissue biobanks, with accompanying ethical, legal, and social issues (ELSI). Issues pertaining to consent, confidentiality, and oversight cannot be examined using a one-size-fits-all approach-the particularities of each biobank must be taken into account. It remains to be seen whether current governance approaches will be adequate to handle the impact of next-generation sequencing technologies on communication with participants in population biobanking studies.

Sampling and detection of airborne influenza virus towards point-of-care applications.

PubMed

Ladhani, Laila; Pardon, Gaspard; Meeuws, Hanne; van Wesenbeeck, Liesbeth; Schmidt, Kristiane; Stuyver, Lieven; van der Wijngaart, Wouter

2017-01-01

Airborne transmission of the influenza virus contributes significantly to the spread of this infectious pathogen, particularly over large distances when carried by aerosol droplets with long survival times. Efficient sampling of virus-loaded aerosol in combination with a low limit of detection of the collected virus could enable rapid and early detection of airborne influenza virus at the point-of-care setting. Here, we demonstrate a successful sampling and detection of airborne influenza virus using a system specifically developed for such applications. Our system consists of a custom-made electrostatic precipitation (ESP)-based bioaerosol sampler that is coupled with downstream quantitative polymerase chain reaction (qPCR) analysis. Aerosolized viruses are sampled directly into a miniaturized collector with liquid volume of 150 μL, which constitutes a simple and direct interface with subsequent biological assays. This approach reduces sample dilution by at least one order of magnitude when compared to other liquid-based aerosol bio-samplers. Performance of our ESP-based sampler was evaluated using influenza virus-loaded sub-micron aerosols generated from both cultured and clinical samples. Despite the miniaturized collection volume, we demonstrate a collection efficiency of at least 10% and sensitive detection of a minimum of 3721 RNA copies. Furthermore, we show that an improved extraction protocol can allow viral recovery of down to 303 RNA copies and a maximum sampler collection efficiency of 47%. A device with such a performance would reduce sampling times dramatically, from a few hours with current sampling methods down to a couple of minutes with our ESP-based bioaerosol sampler.

Quality of groundwater at and near an aquifer storage and recovery site, Bexar, Atascosa, and Wilson Counties, Texas, June 2004-August 2008

USGS Publications Warehouse

Otero, Cassi L.; Petri, Brian L.

2010-01-01

The U.S. Geological Survey, in cooperation with the San Antonio Water System, did a study during 2004-08 to characterize the quality of native groundwater from the Edwards aquifer and pre- and post-injection water from the Carrizo aquifer at and near an aquifer storage and recovery (ASR) site in Bexar, Atascosa, and Wilson Counties, Texas. Groundwater samples were collected and analyzed for selected physical properties and constituents to characterize the quality of native groundwater from the Edwards aquifer and pre- and post-injection water from the Carrizo aquifer at and near the ASR site. Geochemical and isotope data indicated no substantial changes in major-ion, trace-element, and isotope chemistry occurred as the water from the Edwards aquifer was transferred through a 38-mile pipeline to the aquifer storage and recovery site. The samples collected from the four ASR recovery wells were similar in major-ion and stable isotope chemistry compared to the samples collected from the Edwards aquifer source wells and the ASR injection well. The similarity could indicate that as Edwards aquifer water was injected, it displaced native Carrizo aquifer water, or, alternatively, if mixing of Edwards and Carrizo aquifer waters was occurring, the major-ion and stable isotope signatures for the Carrizo aquifer water might have been obscured by the signatures of the injected Edwards aquifer water. Differences in the dissolved iron and dissolved manganese concentrations indicate that either minor amounts of mixing occurred between the waters from the two aquifers, or as Edwards aquifer water displaced Carrizo aquifer water it dissolved the iron and manganese directly from the Carrizo Sand. Concentrations of radium-226 in the samples collected at the ASR recovery wells were smaller than the concentrations in samples collected from the Edwards aquifer source wells and from the ASR injection well. The smaller radium-226 concentrations in the samples collected from the ASR recovery wells likely indicate some degree of mixing of the two waters occurred rather than continued decay of radium-226 in the injected water. Geochemical and isotope data measured in samples collected in May 2005 from two Carrizo aquifer monitoring wells and in July 2008 from the three ASR production-only wells in the northern section of the ASR site indicate that injected Edwards aquifer water had not migrated to these five sites. Geochemical and isotope data measured in samples collected from Carrizo aquifer wells in 2004, 2005, and 2008 were graphically analyzed to determine if changes in chemistry could be detected. Major-ion, trace element, and isotope chemistry varied spatially in the samples collected from the Carrizo aquifer. With the exception of a few samples, major-ion concentrations measured in samples collected in Carrizo aquifer wells in 2004, 2005, and 2008 were similar. A slightly larger sulfate con-centration and a slightly smaller bicarbonate concentration were measured in samples collected in 2005 and 2008 from well NC1 compared to samples collected at well NC1 in 2004. Larger sodium concentrations and smaller calcium, magnesium, bicarbonate, and sulfate concentrations were measured in samples collected in 2008 from well WC1 than in samples collected at this well in 2004 and 2005. Larger calcium and magnesium concentrations and a smaller sodium concentration were measured in the samples collected in 2008 at well EC2 compared to samples collected at this well in 2004 and 2005. While in some cases the computed percent differences (compared to concentrations from June 2004) in dissolved iron and dissolved manganese concentrations in 11 wells sampled in the Carrizo aquifer in 2005 and 2008 were quite large, no trends that might have been caused by migration of injected Edwards aquifer water were observed. Because of the natural variation in geochemical data in the Carrizo aquifer and the small data set collected for this study, differences in major-ion and

Some connections between importance sampling and enhanced sampling methods in molecular dynamics.

PubMed

Lie, H C; Quer, J

2017-11-21

In molecular dynamics, enhanced sampling methods enable the collection of better statistics of rare events from a reference or target distribution. We show that a large class of these methods is based on the idea of importance sampling from mathematical statistics. We illustrate this connection by comparing the Hartmann-Schütte method for rare event simulation (J. Stat. Mech. Theor. Exp. 2012, P11004) and the Valsson-Parrinello method of variationally enhanced sampling [Phys. Rev. Lett. 113, 090601 (2014)]. We use this connection in order to discuss how recent results from the Monte Carlo methods literature can guide the development of enhanced sampling methods.

Some connections between importance sampling and enhanced sampling methods in molecular dynamics

NASA Astrophysics Data System (ADS)

Lie, H. C.; Quer, J.

2017-11-01

In molecular dynamics, enhanced sampling methods enable the collection of better statistics of rare events from a reference or target distribution. We show that a large class of these methods is based on the idea of importance sampling from mathematical statistics. We illustrate this connection by comparing the Hartmann-Schütte method for rare event simulation (J. Stat. Mech. Theor. Exp. 2012, P11004) and the Valsson-Parrinello method of variationally enhanced sampling [Phys. Rev. Lett. 113, 090601 (2014)]. We use this connection in order to discuss how recent results from the Monte Carlo methods literature can guide the development of enhanced sampling methods.

Concentrations of selected constituents in surface-water and streambed-sediment samples collected from streams in and near an area of oil and natural-gas development, south-central Texas, 2011-13

USGS Publications Warehouse

Opsahl, Stephen P.; Crow, Cassi L.

2014-01-01

During collection of streambed-sediment samples, additional samples from a subset of three sites (the SAR Elmendorf, SAR 72, and SAR McFaddin sites) were processed by using a 63-µm sieve on one aliquot and a 2-mm sieve on a second aliquot for PAH and n-alkane analyses. The purpose of analyzing PAHs and n-alkanes on a sample containing sand, silt, and clay versus a sample containing only silt and clay was to provide data that could be used to determine if these organic constituents had a greater affinity for silt- and clay-sized particles relative to sand-sized particles. The greater concentrations of PAHs in the <63-μm size-fraction samples at all three of these sites are consistent with a greater percentage of binding sites associated with fine-grained (<63 μm) sediment versus coarse-grained (<2 mm) sediment. The larger difference in total PAHs between the <2-mm and <63-μm size-fraction samples at the SAR Elmendorf site might be related to the large percentage of sand in the <2-mm size-fraction sample which was absent in the <63-μm size-fraction sample. In contrast, the <2-mm size-fraction sample collected from the SAR McFaddin site contained very little sand and was similar in particle-size composition to the <63-μm size-fraction sample.

Seeded amplification of chronic wasting disease prions in nasal brushings and recto-anal mucosal associated lymphoid tissues from elk by real time quaking-induced conversion

USGS Publications Warehouse

Haley, Nicholas J.; Siepker, Chris; Hoon-Hanks , Laura L.; Mitchell, Gordon; Walter, W. David; Manca, Matteo; Monello, Ryan J.; Powers, Jenny G.; Wild, Margaret A.; Hoover, Edward A.; Caughey, Byron; Richt, Jürgen a.; Fenwick, B.W.

2016-01-01

Chronic wasting disease (CWD), a transmissible spongiform encephalopathy of cervids, was first documented nearly 50 years ago in Colorado and Wyoming and has since been detected across North America and the Republic of Korea. The expansion of this disease makes the development of sensitive diagnostic assays and antemortem sampling techniques crucial for the mitigation of its spread; this is especially true in cases of relocation/reintroduction or prevalence studies of large or protected herds, where depopulation may be contraindicated. This study evaluated the sensitivity of the real-time quaking-induced conversion (RT-QuIC) assay of recto-anal mucosa-associated lymphoid tissue (RAMALT) biopsy specimens and nasal brushings collected antemortem. These findings were compared to results of immunohistochemistry (IHC) analysis of ante- and postmortem samples. RAMALT samples were collected from populations of farmed and free-ranging Rocky Mountain elk (Cervus elaphus nelsoni; n = 323), and nasal brush samples were collected from a subpopulation of these animals (n = 205). We hypothesized that the sensitivity of RT-QuIC would be comparable to that of IHC analysis of RAMALT and would correspond to that of IHC analysis of postmortem tissues. We found RAMALT sensitivity (77.3%) to be highly correlative between RT-QuIC and IHC analysis. Sensitivity was lower when testing nasal brushings (34%), though both RAMALT and nasal brush test sensitivities were dependent on both the PRNP genotype and disease progression determined by the obex score. These data suggest that RT-QuIC, like IHC analysis, is a relatively sensitive assay for detection of CWD prions in RAMALT biopsy specimens and, with further investigation, has potential for large-scale and rapid automated testing of antemortem samples for CWD.

Increased prevalence of antibiotic-resistant E. coli in gulls sampled in southcentral Alaska is associated with urban environments

USGS Publications Warehouse

Atterby, Clara; Ramey, Andrew M.; Gustafsson Hall, Gabriel; Jarhult, Josef; Borjesson, Stefan; Bonnedahl, Jonas

2016-01-01

BackgroundAntibiotic-resistant bacteria pose challenges to healthcare delivery systems globally; however, limited information is available regarding the prevalence and spread of such bacteria in the environment. The aim of this study was to compare the prevalence of antibiotic-resistant bacteria in large-bodied gulls (Larus spp.) at urban and remote locations in Southcentral Alaska to gain inference into the association between antibiotic resistance in wildlife and anthropogenically influenced habitats.MethodsEscherichia coli was cultured (n=115 isolates) from fecal samples of gulls (n=160) collected from a remote location, Middleton Island, and a more urban setting on the Kenai Peninsula.ResultsScreening of E. coli from fecal samples collected from glaucous-winged gulls (Larus glaucescens) at Middleton Island revealed 8% of isolates were resistant to one or more antibiotics and 2% of the isolates were resistant to three or more antibiotics. In contrast, 55% of E. coli isolates derived from fecal samples collected from large-bodied gulls (i.e. glaucous, herring [Larus argentatus], and potentially hybrid gulls) on the Kenai Peninsula were resistant to one or more antibiotics and 22% were resistant to three or more antibiotics. In addition, total of 16% of the gull samples from locations on the Kenai Peninsula harbored extended-spectrum cephalosporin-resistant E. coli isolates (extended-spectrum beta-lactamases [ESBL] and plasmid-encoded AmpC [pAmpC]), in contrast to Middleton Island where no ESBL- or pAmpC-producing isolates were detected.ConclusionOur findings indicate that increased prevalence of antibiotic resistance is associated with urban environments in Southcentral Alaska and presumably influenced by anthropogenic impacts. Further investigation is warranted to assess how migratory birds may maintain and spread antimicrobial-resistant bacteria of relevance to human and animal health.

Survey research with a random digit dial national mobile phone sample in Ghana: Methods and sample quality.

PubMed

L'Engle, Kelly; Sefa, Eunice; Adimazoya, Edward Akolgo; Yartey, Emmanuel; Lenzi, Rachel; Tarpo, Cindy; Heward-Mills, Nii Lante; Lew, Katherine; Ampeh, Yvonne

2018-01-01

Generating a nationally representative sample in low and middle income countries typically requires resource-intensive household level sampling with door-to-door data collection. High mobile phone penetration rates in developing countries provide new opportunities for alternative sampling and data collection methods, but there is limited information about response rates and sample biases in coverage and nonresponse using these methods. We utilized data from an interactive voice response, random-digit dial, national mobile phone survey in Ghana to calculate standardized response rates and assess representativeness of the obtained sample. The survey methodology was piloted in two rounds of data collection. The final survey included 18 demographic, media exposure, and health behavior questions. Call outcomes and response rates were calculated according to the American Association of Public Opinion Research guidelines. Sample characteristics, productivity, and costs per interview were calculated. Representativeness was assessed by comparing data to the Ghana Demographic and Health Survey and the National Population and Housing Census. The survey was fielded during a 27-day period in February-March 2017. There were 9,469 completed interviews and 3,547 partial interviews. Response, cooperation, refusal, and contact rates were 31%, 81%, 7%, and 39% respectively. Twenty-three calls were dialed to produce an eligible contact: nonresponse was substantial due to the automated calling system and dialing of many unassigned or non-working numbers. Younger, urban, better educated, and male respondents were overrepresented in the sample. The innovative mobile phone data collection methodology yielded a large sample in a relatively short period. Response rates were comparable to other surveys, although substantial coverage bias resulted from fewer women, rural, and older residents completing the mobile phone survey in comparison to household surveys. Random digit dialing of mobile phones offers promise for future data collection in Ghana and may be suitable for other developing countries.

Survey research with a random digit dial national mobile phone sample in Ghana: Methods and sample quality

PubMed Central

Sefa, Eunice; Adimazoya, Edward Akolgo; Yartey, Emmanuel; Lenzi, Rachel; Tarpo, Cindy; Heward-Mills, Nii Lante; Lew, Katherine; Ampeh, Yvonne

2018-01-01

Introduction Generating a nationally representative sample in low and middle income countries typically requires resource-intensive household level sampling with door-to-door data collection. High mobile phone penetration rates in developing countries provide new opportunities for alternative sampling and data collection methods, but there is limited information about response rates and sample biases in coverage and nonresponse using these methods. We utilized data from an interactive voice response, random-digit dial, national mobile phone survey in Ghana to calculate standardized response rates and assess representativeness of the obtained sample. Materials and methods The survey methodology was piloted in two rounds of data collection. The final survey included 18 demographic, media exposure, and health behavior questions. Call outcomes and response rates were calculated according to the American Association of Public Opinion Research guidelines. Sample characteristics, productivity, and costs per interview were calculated. Representativeness was assessed by comparing data to the Ghana Demographic and Health Survey and the National Population and Housing Census. Results The survey was fielded during a 27-day period in February-March 2017. There were 9,469 completed interviews and 3,547 partial interviews. Response, cooperation, refusal, and contact rates were 31%, 81%, 7%, and 39% respectively. Twenty-three calls were dialed to produce an eligible contact: nonresponse was substantial due to the automated calling system and dialing of many unassigned or non-working numbers. Younger, urban, better educated, and male respondents were overrepresented in the sample. Conclusions The innovative mobile phone data collection methodology yielded a large sample in a relatively short period. Response rates were comparable to other surveys, although substantial coverage bias resulted from fewer women, rural, and older residents completing the mobile phone survey in comparison to household surveys. Random digit dialing of mobile phones offers promise for future data collection in Ghana and may be suitable for other developing countries. PMID:29351349

Identifying Etiological Agents Causing Diarrhea in Low Income Ecuadorian Communities

PubMed Central

Vasco, Gabriela; Trueba, Gabriel; Atherton, Richard; Calvopiña, Manuel; Cevallos, William; Andrade, Thamara; Eguiguren, Martha; Eisenberg, Joseph N. S.

2014-01-01

Continued success in decreasing diarrheal disease burden requires targeted interventions. To develop such interventions, it is crucial to understand which pathogens cause diarrhea. Using a case-control design we tested stool samples, collected in both rural and urban Ecuador, for 15 pathogenic microorganisms. Pathogens were present in 51% of case and 27% of control samples from the urban community, and 62% of case and 18% of control samples collected from the rural community. Rotavirus and Shigellae were associated with diarrhea in the urban community; co-infections were more pathogenic than single infection; Campylobacter and Entamoeba histolytica were found in large numbers in cases and controls; and non-typhi Salmonella and enteropathogenic Escherichia coli were not found in any samples. Consistent with the Global Enteric Multicenter Study, focused in south Asia and sub-Saharan Africa, we found that in Ecuador a small group of pathogens accounted for a significant amount of the diarrheal disease burden. PMID:25048373

Chemical concentrations in water and suspended sediment, Green River to Lower Duwamish Waterway near Seattle, Washington, 2016–17

USGS Publications Warehouse

Conn, Kathleen E.; Black, Robert W.; Peterson, Norman T.; Senter, Craig A.; Chapman, Elena A.

2018-01-05

From August 2016 to March 2017, the U.S. Geological Survey (USGS) collected representative samples of filtered and unfiltered water and suspended sediment (including the colloidal fraction) at USGS streamgage 12113390 (Duwamish River at Golf Course, at Tukwila, Washington) during 13 periods of differing flow conditions. Samples were analyzed by Washington-State-accredited laboratories for a large suite of compounds, including metals, dioxins/furans, semivolatile compounds including polycyclic aromatic hydrocarbons, butyltins, the 209 polychlorinated biphenyl (PCB) congeners, and total and dissolved organic carbon. Concurrent with the chemistry sampling, water-quality field parameters were measured, and representative water samples were collected and analyzed for river suspended-sediment concentration and particle-size distribution. The results provide new data that can be used to estimate sediment and chemical loads transported by the Green River to the Lower Duwamish Waterway.

A passive ozone sampler based on a reaction with nitrite.

PubMed

Koutrakis, P; Wolfson, J M; Bunyaviroch, A; Froehlich, S

1994-02-01

Standard ozone monitoring techniques utilize large, heavy, and expensive instruments that are not easily adapted for personal or microenvironmental monitoring. For large-scale monitoring projects that examine spatial variations of a pollutant and human exposure assessments, passive sampling devices can provide the methodology to meet monitoring and statistical goals. Recently, we developed a coated filter for ozone collection that we used in a commercially available passive sampling device. Successful preliminary results merited further validation tests, which are presented in this report. The passive ozone sampler used in field and laboratory experiments consists of a badge clip supporting a barrel-shaped body that contains two coated glass fiber filters. The principle component of the coating is nitrite ion, which in the presence of ozone is oxidized to nitrate ion on the filter medium (NO2- + O3 produces NO3- + O2). After sample collection, the filters were extracted with ultrapure water and analyzed for nitrate ion by ion chromatography. The results from laboratory and field validation tests indicated excellent agreement between the passive method and standard ozone monitoring techniques. We determined that relative humidity (ranging from 10% to 80%) and temperature (ranging from 0 degrees C to 40 degrees C) at typical ambient ozone levels (40 to 100 parts per billion) do not influence sampler performance. Face velocity and sampler orientation with respect to wind direction were found to affect the sampler's collection rate of ozone. Using a protective cup, which acts as both a wind screen and a rain cover, we were able to obtain a constant collection rate over a wide range of wind speeds.

REGIONAL METHODS INITIATIVE RESEARCH PROJECTS AT HEASD

EPA Science Inventory

EPA Regional Laboratories are currently using high volume samplers with a combination of filter and sorbent vapor trap to collect large volume samples (250 liter/min for 24 hours) of semi-volatile organic compounds (SVOCs) and non-volatile organic compounds (NVOCs). These are su...

ISOLATION AND IDENTIFICATION OF NONTUBERCULOUS MYCOBACTERIA FROM FOODS AS POSSIBLE EXPOSURE SOURCES

EPA Science Inventory

A variety of foods collected from local supermarkets and produce stands were examined as possible sources of nontuberculous mycobacterial exposure. Food samples were combined with sterile ultrapure water and manually shaken. To remove large particles, the suspensions were filtere...

In Vitro Absorption of Atmospheric Carbon Monoxide and Hydrogen Cyanide in Undisturbed Pooled Blood

DOT National Transportation Integrated Search

2012-09-01

Biological samples from victims of aircraft accidents are analyzed for carboxyhemoglobin (COHb) and cyanide ion : (CN) in blood. Such victims quite often suffer large open wounds near the autopsy blood collection sites. Many : aircraft crashes resu...

A comparison of diets of blueback herring (Alosa aestivalis) and threadfin shad (Dorosoma petenense) in a large southeastern U.S. Reservoir

USGS Publications Warehouse

Winkelman, D.L.; Van Den Avyle, M.J.

2002-01-01

The objective of this study was to determine dietary overlap between blueback herring and threadfin shad in J. Strom Thrumond Reservoir, South Carolina/Georgia. We also evaluated prey selectivity for each speices and diet differences between two size categories of blueback herring. Diet and zooplankton samples were collected every other month from April 1992 to February 1994. We examined stomachs containing prey from 170 large blueback herring (>140mm), 96 small blueback herring (<140mm), and 109 threadfin shad, and we also examined 45 zooplankton samples. Large blueback herring diets differed significantly from threadfin shad diets on 11 of 12 sampling dates, and small blueback herring diets differed from threadfin shad diets on all sampling dates. In general, blueback herring consumed proportionally more copepods and fewer Bosmina sp. and rotifers than threadfin shad. Large and small blueback herring diets were significantly different on five of eight sampling dates, primarily due to the tendency of small blueback herring to eat proportionally more Bosmina sp. than large blueback herring. Both blueback herring and threadfin shad fed selectively during some periods of the year. Diet differences between the species may contribute to their coexistence; however, both blueback herring and threadfin shad showed a strong preference for Bosmina sp., increasing the chance that they may negatively influence one another.

A High-Performance Vacuum Cleaner for Bed Bug Sampling: A Useful Tool for Medical Entomology.

PubMed

Bérenger, Jean-Michel; Almeras, Lionel; Leulmi, Hamza; Parola, Philippe

2015-05-01

Arthropods can be captured by two modes: a passive mode using traps or an active mode mainly based on the use of mouth or powered aspirators. These apparatuses are useful tools for collecting large numbers of crawling, flying, resting, or jumping arthropod specimens, particularly small specimens, such as mosquitoes or sandflies, for laboratory experiments or breeding. Different aspirator models are used to collect various arthropod specimens. However, to our knowledge, no specific system is currently available for the reliable sampling of live bed bugs in the field. Thus, we described a new system based on a classic autonomous house aspirator that requires few modifications for the collecting bed bugs. The low weight and size of this apparatus is advantageous, and it provides for rapid and secure bed bug sampling for medical entomology purposes. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Groundwater quality data from the National Water-Quality Assessment Project, May 2012 through December 2013

USGS Publications Warehouse

Arnold, Terri L.; Desimone, Leslie A.; Bexfield, Laura M.; Lindsey, Bruce D.; Barlow, Jeannie R.; Kulongoski, Justin T.; Musgrove, MaryLynn; Kingsbury, James A.; Belitz, Kenneth

2016-06-20

Groundwater-quality data were collected from 748 wells as part of the National Water-Quality Assessment Project of the U.S. Geological Survey National Water-Quality Program from May 2012 through December 2013. The data were collected from four types of well networks: principal aquifer study networks, which assess the quality of groundwater used for public water supply; land-use study networks, which assess land-use effects on shallow groundwater quality; major aquifer study networks, which assess the quality of groundwater used for domestic supply; and enhanced trends networks, which evaluate the time scales during which groundwater quality changes. Groundwater samples were analyzed for a large number of water-quality indicators and constituents, including major ions, nutrients, trace elements, volatile organic compounds, pesticides, and radionuclides. These groundwater quality data are tabulated in this report. Quality-control samples also were collected; data from blank and replicate quality-control samples are included in this report.

Optical properties (bidirectional reflectance distribution function) of shot fabric.

PubMed

Lu, R; Koenderink, J J; Kappers, A M

2000-11-01

To study the optical properties of materials, one needs a complete set of the angular distribution functions of surface scattering from the materials. Here we present a convenient method for collecting a large set of bidirectional reflectance distribution function (BRDF) samples in the hemispherical scattering space. Material samples are wrapped around a right-circular cylinder and irradiated by a parallel light source, and the scattered radiance is collected by a digital camera. We tilted the cylinder around its center to collect the BRDF samples outside the plane of incidence. This method can be used with materials that have isotropic and anisotropic scattering properties. We demonstrate this method in a detailed investigation of shot fabrics. The warps and the fillings of shot fabrics are dyed different colors so that the fabric appears to change color at different viewing angles. These color-changing characteristics are found to be related to the physical and geometrical structure of shot fabric. Our study reveals that the color-changing property of shot fabrics is due mainly to an occlusion effect.

The impact of study design and diagnostic approach in a large multi-centre ADHD study: Part 2: Dimensional measures of psychopathology and intelligence.

PubMed

Müller, Ueli C; Asherson, Philip; Banaschewski, Tobias; Buitelaar, Jan K; Ebstein, Richard P; Eisenberg, Jaques; Gill, Michael; Manor, Iris; Miranda, Ana; Oades, Robert D; Roeyers, Herbert; Rothenberger, Aribert; Sergeant, Joseph A; Sonuga-Barke, Edmund Js; Thompson, Margaret; Faraone, Stephen V; Steinhausen, Hans-Christoph

2011-04-07

The International Multi-centre ADHD Genetics (IMAGE) project with 11 participating centres from 7 European countries and Israel has collected a large behavioural and genetic database for present and future research. Behavioural data were collected from 1068 probands with ADHD and 1446 unselected siblings. The aim was to describe and analyse questionnaire data and IQ measures from all probands and siblings. In particular, to investigate the influence of age, gender, family status (proband vs. sibling), informant, and centres on sample homogeneity in psychopathological measures. Conners' Questionnaires, Strengths and Difficulties Questionnaires, and Wechsler Intelligence Scores were used to describe the phenotype of the sample. Data were analysed by use of robust statistical multi-way procedures. Besides main effects of age, gender, informant, and centre, there were considerable interaction effects on questionnaire data. The larger differences between probands and siblings at home than at school may reflect contrast effects in the parents. Furthermore, there were marked gender by status effects on the ADHD symptom ratings with girls scoring one standard deviation higher than boys in the proband sample but lower than boys in the siblings sample. The multi-centre design is another important source of heterogeneity, particularly in the interaction with the family status. To a large extent the centres differed from each other with regard to differences between proband and sibling scores. When ADHD probands are diagnosed by use of fixed symptom counts, the severity of the disorder in the proband sample may markedly differ between boys and girls and across age, particularly in samples with a large age range. A multi-centre design carries the risk of considerable phenotypic differences between centres and, consequently, of additional heterogeneity of the sample even if standardized diagnostic procedures are used. These possible sources of variance should be counteracted in genetic analyses either by using age and gender adjusted diagnostic procedures and regional normative data or by adjusting for design artefacts by use of covariate statistics, by eliminating outliers, or by other methods suitable for reducing heterogeneity.

Alzheimer's disease cerebrospinal fluid biomarkers are not influenced by gravity drip or aspiration extraction methodology.

PubMed

Rembach, Alan; Evered, Lisbeth A; Li, Qiao-Xin; Nash, Tabitha; Vidaurre, Lesley; Fowler, Christopher J; Pertile, Kelly K; Rumble, Rebecca L; Trounson, Brett O; Maher, Sarah; Mooney, Francis; Farrow, Maree; Taddei, Kevin; Rainey-Smith, Stephanie; Laws, Simon M; Macaulay, S Lance; Wilson, William; Darby, David G; Martins, Ralph N; Ames, David; Collins, Steven; Silbert, Brendan; Masters, Colin L; Doecke, James D

2015-11-19

Cerebrospinal fluid (CSF) biomarkers, although of established utility in the diagnostic evaluation of Alzheimer's disease (AD), are known to be sensitive to variation based on pre-analytical sample processing. We assessed whether gravity droplet collection versus syringe aspiration was another factor influencing CSF biomarker analyte concentrations and reproducibility. Standardized lumbar puncture using small calibre atraumatic spinal needles and CSF collection using gravity fed collection followed by syringe aspirated extraction was performed in a sample of elderly individuals participating in a large long-term observational research trial. Analyte assay concentrations were compared. For the 44 total paired samples of gravity collection and aspiration, reproducibility was high for biomarker CSF analyte assay concentrations (concordance correlation [95%CI]: beta-amyloid1-42 (Aβ42) 0.83 [0.71 - 0.90]), t-tau 0.99 [0.98 - 0.99], and phosphorylated tau (p-tau) 0.82 [95 % CI 0.71 - 0.89]) and Bonferroni corrected paired sample t-tests showed no significant differences (group means (SD): Aβ42 366.5 (86.8) vs 354.3 (82.6), p = 0.10; t-tau 83.9 (46.6) vs 84.7 (47.4) p = 0.49; p-tau 43.5 (22.8) vs 40.0 (17.7), p = 0.05). The mean duration of collection was 10.9 minutes for gravity collection and <1 minute for aspiration. Our results demonstrate that aspiration of CSF is comparable to gravity droplet collection for AD biomarker analyses but could considerably accelerate throughput and improve the procedural tolerability for assessment of CSF biomarkers.

A comparison of two cloudwater/fogwater collectors: The rotating arm collector and the caltech active strand cloudwater collector

NASA Astrophysics Data System (ADS)

Collett, Jeffrey L.; Daube, Bruce C.; Munger, J. William; Hoffmann, Michael R.

A side-by-side comparison of the Rotating Arm Collector (RAC) and the Caltech Active Strand Cloudwater Collector (CASCC) was conducted at an elevated coastal site near the eastern end of the Santa Barbara Channel in southern California. The CASCC was observed to collect cloudwater at rates of up to 8.5 ml min -1. The ratio of cloudwater collection rates was found to be close to the theoretical prediction of 4.2:1 (CASCC:RAC) over a wide range of liquid water contents (LWC). At low LWC, however, this ratio climbed rapidly, possibly reflecting a predominance of small droplets under these conditions, coupled with a greater collection efficiency of small droplets by the CASCC. Cloudwater samples collected by the RAC had significantly higher concentrations of Na +, Ca 2+, Mg 2+ and Cl - than those collected by the CASCC. These higher concentrations may be due to differences in the chemical composition of large vs small droplets. No significant differences were observed in concentrations of NO 3-, SO 42- or NH 4+ in samples collected by the two instruments.

Filter Paper Blood Spot Enzyme Linked Immunoassay for Insulin and Application in the Evaluation of Determinants of Child Insulin Resistance

PubMed Central

Martin, Richard M.; Patel, Rita; Zinovik, Alexander; Kramer, Michael S.; Oken, Emily; Vilchuck, Konstantin; Bogdanovich, Natalia; Sergeichick, Natalia; Gunnarsson, Robert; Grufman, Lisa; Foo, Ying; Gusina, Nina

2012-01-01

Background In large-scale epidemiology, bloodspot sampling by fingerstick onto filter paper has many advantages, including ease and low costs of collection, processing and transport. We describe the development of an enzyme-linked immunoassay (ELISA) for quantifying insulin from dried blood spots and demonstrate its application in a large trial. Methods We adapted an existing commercial kit (Mercodia Human Insulin ELISA, 10-1113-01) to quantify insulin from two 3-mm diameter discs (≈6 µL of blood) punched from whole blood standards and from trial samples. Paediatricians collected dried blood spots in a follow-up of 13,879 fasted children aged 11.5 years (interquartile range 11.3–11.8 years) from 31 trial sites across Belarus. We quantified bloodspot insulin levels and examined their distribution by demography and anthropometry. Results Mean intra-assay (n = 157) coefficients of variation were 15% and 6% for ‘low’ (6.7 mU/L) and ‘high’ (23.1 mU/L) values, respectively; the respective inter-assay values (n = 33) were 23% and 11%. The intraclass correlation coefficient between 50 paired whole bloodspot versus serum samples, collected simultaneously, was 0.90 (95% confidence interval 0.85 to 0.95). Bloodspot insulin was stable for at least 31 months at −80°C, for one week at +30°C and following four freeze-thaw cycles. Paediatricians collected a median of 8 blood spots from 13,487 (97%) children. The geometric mean insulin (log standard deviation) concentrations amongst 12,812 children were 3.0 mU/L (1.1) in boys and 4.0 mU/L (1.0) in girls and were positively associated with pubertal stage, measures of central and peripheral adiposity, height and fasting glucose. Conclusions Our simple and convenient bloodspot assay is suitable for the measurement of insulin in very small volumes of blood collected on filter paper cards and can be applied to large-scale epidemiology studies of the early-life determinants of circulating insulin. PMID:23056434

Evaluating effectiveness of down-sampling for stratified designs and unbalanced prevalence in Random Forest models of tree species distributions in Nevada

Treesearch

Elizabeth A. Freeman; Gretchen G. Moisen; Tracy S. Frescino

2012-01-01

Random Forests is frequently used to model species distributions over large geographic areas. Complications arise when data used to train the models have been collected in stratified designs that involve different sampling intensity per stratum. The modeling process is further complicated if some of the target species are relatively rare on the landscape leading to an...

Phenotypic Association Analyses With Copy Number Variation in Recurrent Depressive Disorder.

PubMed

Rucker, James J H; Tansey, Katherine E; Rivera, Margarita; Pinto, Dalila; Cohen-Woods, Sarah; Uher, Rudolf; Aitchison, Katherine J; Craddock, Nick; Owen, Michael J; Jones, Lisa; Jones, Ian; Korszun, Ania; Barnes, Michael R; Preisig, Martin; Mors, Ole; Maier, Wolfgang; Rice, John; Rietschel, Marcella; Holsboer, Florian; Farmer, Anne E; Craig, Ian W; Scherer, Stephen W; McGuffin, Peter; Breen, Gerome

2016-02-15

Defining the molecular genomic basis of the likelihood of developing depressive disorder is a considerable challenge. We previously associated rare, exonic deletion copy number variants (CNV) with recurrent depressive disorder (RDD). Sex chromosome abnormalities also have been observed to co-occur with RDD. In this reanalysis of our RDD dataset (N = 3106 cases; 459 screened control samples and 2699 population control samples), we further investigated the role of larger CNVs and chromosomal abnormalities in RDD and performed association analyses with clinical data derived from this dataset. We found an enrichment of Turner's syndrome among cases of depression compared with the frequency observed in a large population sample (N = 34,910) of live-born infants collected in Denmark (two-sided p = .023, odds ratio = 7.76 [95% confidence interval = 1.79-33.6]), a case of diploid/triploid mosaicism, and several cases of uniparental isodisomy. In contrast to our previous analysis, large deletion CNVs were no more frequent in cases than control samples, although deletion CNVs in cases contained more genes than control samples (two-sided p = .0002). After statistical correction for multiple comparisons, our data do not support a substantial role for CNVs in RDD, although (as has been observed in similar samples) occasional cases may harbor large variants with etiological significance. Genetic pleiotropy and sample heterogeneity suggest that very large sample sizes are required to study conclusively the role of genetic variation in mood disorders. Copyright © 2016 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Challenges for conducting blood collection and biochemical analysis in a large multicenter school-based study with adolescents: lessons from ERICA in Brazil.

PubMed

Cureau, Felipe Vogt; Bloch, Katia Vergetti; Henz, Aline; Schaan, Camila W; Klein, Carlos Henrique; Oliveira, Cecília Lacroix de; Giannini, Denise Tavares; Leon, Elisa Brosina de; Abreu, Gabriela de Azevedo; Telo, Gabriela Heiden; Dias, Glauber Monteiro; Carvalho, Kênia Mara Baiocchi de; Barufaldi, Laura Augusta; Kuschnir, Maria Cristina Caetano; Szklo, Moyses; Montenegro, Renan; Silva, Thiago Luiz Nogueira da; Ekelund, Ulf; Schaan, Beatriz D

2017-05-18

The Study of Cardiovascular Risk in Adolescents (ERICA) is a pioneering study that aimed to assess the prevalence of cardiovascular risk factors, including metabolic syndrome components in Brazilian adolescents. This study aims to describe the methodological aspects related to blood collection as well as to report pertaining results of the preparation, transport, storage, and exams in ERICA. Exams in ERICA were performed in a single laboratory and blood samples were collected in schools in a standardized manner. Logistics involved air transportation of samples to the reference laboratory with controlled temperature since sample collection. The serum was stored in local biorepositories in four centers to be used in future analyses. During the study, 284,247 exams were performed and rate of participation in exams was 56.2%, thus involving 40,732 adolescents. From the total, 92.6% of the samples reached the reference laboratory maintaining the temperature between 0-10°C. No clinical significant changes in results due to temperature changes were identified. External quality control recorded satisfactory results in 98.7% of the evaluations. Four biorepositories with samples of 7,785 adolescents were created. Thus, we can consider that the logistics adopted in ERICA was fairly successful and description of this as well as the difficulties experienced in Brazil can inform and facilitate the planning of future studies, especially in developing countries.

Enhanced-locality fiber-optic two-photon-fluorescence live-brain interrogation

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

Fedotov, I. V.; Doronina-Amitonova, L. V.; Russian Quantum Center, ul. Novaya 100, Skolkovo, Moscow Region 1430125

2014-02-24

Two-photon excitation is shown to substantially enhance the locality of fiber-based optical interrogation of strongly scattering biotissues. In our experiments, a high-numerical-aperture, large-core-are fiber probe is used to deliver the 200-fs output of a 100-MHz mode-locked ytterbium fiber laser to samples of live mouse brain, induce two-photon fluorescence of nitrogen–vacancy centers in diamond markers in brain sample. Fiber probes with a high numerical aperture and a large core area are shown to enable locality enhancement in fiber-laser–fiber-probe two-photon brain excitation and interrogation without sacrificing the efficiency of fluorescence response collection.

Comparative Study of Seven Commercial Kits for Human DNA Extraction from Urine Samples Suitable for DNA Biomarker-Based Public Health Studies

PubMed Central

El Bali, Latifa; Diman, Aurélie; Bernard, Alfred; Roosens, Nancy H. C.; De Keersmaecker, Sigrid C. J.

2014-01-01

Human genomic DNA extracted from urine could be an interesting tool for large-scale public health studies involving characterization of genetic variations or DNA biomarkers as a result of the simple and noninvasive collection method. These studies, involving many samples, require a rapid, easy, and standardized extraction protocol. Moreover, for practicability, there is a necessity to collect urine at a moment different from the first void and to store it appropriately until analysis. The present study compared seven commercial kits to select the most appropriate urinary human DNA extraction procedure for epidemiological studies. DNA yield has been determined using different quantification methods: two classical, i.e., NanoDrop and PicoGreen, and two species-specific real-time quantitative (q)PCR assays, as DNA extracted from urine contains, besides human, microbial DNA also, which largely contributes to the total DNA yield. In addition, the kits giving a good yield were also tested for the presence of PCR inhibitors. Further comparisons were performed regarding the sampling time and the storage conditions. Finally, as a proof-of-concept, an important gene related to smoking has been genotyped using the developed tools. We could select one well-performing kit for the human DNA extraction from urine suitable for molecular diagnostic real-time qPCR-based assays targeting genetic variations, applicable to large-scale studies. In addition, successful genotyping was possible using DNA extracted from urine stored at −20°C for several months, and an acceptable yield could also be obtained from urine collected at different moments during the day, which is particularly important for public health studies. PMID:25365790

Implementation of Dynamic Extensible Adaptive Locally Exchangeable Measures (IDEALEM) v 0.1

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

Sim, Alex; Lee, Dongeun; Wu, K. John

2016-03-04

Handling large streaming data is essential for various applications such as network traffic analysis, social networks, energy cost trends, and environment modeling. However, it is in general intractable to store, compute, search, and retrieve large streaming data. This software addresses a fundamental issue, which is to reduce the size of large streaming data and still obtain accurate statistical analysis. As an example, when a high-speed network such as 100 Gbps network is monitored, the collected measurement data rapidly grows so that polynomial time algorithms (e.g., Gaussian processes) become intractable. One possible solution to reduce the storage of vast amounts ofmore » measured data is to store a random sample, such as one out of 1000 network packets. However, such static sampling methods (linear sampling) have drawbacks: (1) it is not scalable for high-rate streaming data, and (2) there is no guarantee of reflecting the underlying distribution. In this software, we implemented a dynamic sampling algorithm, based on the recent technology from the relational dynamic bayesian online locally exchangeable measures, that reduces the storage of data records in a large scale, and still provides accurate analysis of large streaming data. The software can be used for both online and offline data records.« less

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.

Timoides agassizii Bigelow, 1904, little-known hydromedusa (Cnidaria), appears briefly in large numbers off Oman, March 2011, with additional notes about species of the genus Timoides.

PubMed

Purushothaman, Jasmine; Kharusi, Lubna Al; Mills, Claudia E; Ghielani, Hamed; Marzouki, Mohammad Al

2013-12-11

A bloom of the hydromedusan jellyfish, Timoides agassizii, occurred in February 2011 off the coast of Sohar, Al Batinah, Sultanate of Oman, in the Gulf of Oman. This species was first observed in 1902 in great numbers off Haddummati Atoll in the Maldive Islands in the Indian Ocean and has rarely been seen since. The species appeared briefly in large numbers off Oman in 2011 and subsequent observation of our 2009 samples of zooplankton from Sohar revealed that it was also present in low numbers (two collected) in one sample in 2009; these are the first records in the Indian Ocean north of the Maldives. Medusae collected off Oman were almost identical to those recorded previously from the Maldive Islands, Papua New Guinea, the Marshall Islands, Guam, the South China Sea, and Okinawa. T. agassizii is a species that likely lives for several months. It was present in our plankton samples together with large numbers of the oceanic siphonophore Physalia physalis only during a single month's samples, suggesting that the temporary bloom off Oman was likely due to the arrival of mature, open ocean medusae into nearshore waters. We see no evidence that T. agassizii has established a new population along Oman, since if so, it would likely have been present in more than one sample period. We are unable to deduce further details of the life cycle of this species from blooms of many mature individuals nearshore, about a century apart. Examination of a single damaged T. agassizii medusa from Guam, calls into question the existence of its congener, T. latistyla, known only from a single specimen.

World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonisation Project: I. Surgical phenotype data collection in endometriosis research

PubMed Central

Becker, Christian M.; Laufer, Marc R.; Stratton, Pamela; Hummelshoj, Lone; Missmer, Stacey A.; Zondervan, Krina T.; Adamson, G. David; Adamson, G.D.; Allaire, C.; Anchan, R.; Becker, C.M.; Bedaiwy, M.A.; Buck Louis, G.M.; Calhaz-Jorge, C.; Chwalisz, K.; D'Hooghe, T.M.; Fassbender, A.; Faustmann, T.; Fazleabas, A.T.; Flores, I.; Forman, A.; Fraser, I.; Giudice, L.C.; Gotte, M.; Gregersen, P.; Guo, S.-W.; Harada, T.; Hartwell, D.; Horne, A.W.; Hull, M.L.; Hummelshoj, L.; Ibrahim, M.G.; Kiesel, L.; Laufer, M.R.; Machens, K.; Mechsner, S.; Missmer, S.A.; Montgomery, G.W.; Nap, A.; Nyegaard, M.; Osteen, K.G.; Petta, C.A.; Rahmioglu, N.; Renner, S.P.; Riedlinger, J.; Roehrich, S.; Rogers, P.A.; Rombauts, L.; Salumets, A.; Saridogan, E.; Seckin, T.; Stratton, P.; Sharpe-Timms, K.L.; Tworoger, S.; Vigano, P.; Vincent, K.; Vitonis, A.F.; Wienhues-Thelen, U.-H.; Yeung, P.P.; Yong, P.; Zondervan, K.T.

2014-01-01

Objective To standardize the recording of surgical phenotypic information on endometriosis and related sample collections obtained at laparoscopy, allowing large-scale collaborative research into the condition. Design An international collaboration involving 34 clinical/academic centers and three industry collaborators from 16 countries. Setting Two workshops were conducted in 2013, bringing together 54 clinical, academic, and industry leaders in endometriosis research and management worldwide. Patient(s) None. Intervention(s) A postsurgical scoring sheet containing general and gynecological patient and procedural information, extent of disease, the location and type of endometriotic lesion, and any other findings was developed during several rounds of review. Comments and any systematic surgical data collection tools used in the reviewers' centers were incorporated. Main Outcome Measure(s) The development of a standard recommended (SSF) and minimum required (MSF) form to collect data on the surgical phenotype of endometriosis. Result(s) SSF and MSF include detailed descriptions of lesions, modes of procedures and sample collection, comorbidities, and potential residual disease at the end of surgery, along with previously published instruments such as the revised American Society for Reproductive Medicine and Endometriosis Fertility Index classification tools for comparison and validation. Conclusion(s) This is the first multicenter, international collaboration between academic centers and industry addressing standardization of phenotypic data collection for a specific disease. The Endometriosis Phenome and Biobanking Harmonisation Project SSF and MSF are essential tools to increase our understanding of the pathogenesis of endometriosis by allowing large-scale collaborative research into the condition. PMID:25150390

Mesh-size effects on drift sample composition as determined with a triple net sampler

USGS Publications Warehouse

Slack, K.V.; Tilley, L.J.; Kennelly, S.S.

1991-01-01

Nested nets of three different mesh apertures were used to study mesh-size effects on drift collected in a small mountain stream. The innermost, middle, and outermost nets had, respectively, 425 ??m, 209 ??m and 106 ??m openings, a design that reduced clogging while partitioning collections into three size groups. The open area of mesh in each net, from largest to smallest mesh opening, was 3.7, 5.7 and 8.0 times the area of the net mouth. Volumes of filtered water were determined with a flowmeter. The results are expressed as (1) drift retained by each net, (2) drift that would have been collected by a single net of given mesh size, and (3) the percentage of total drift (the sum of the catches from all three nets) that passed through the 425 ??m and 209 ??m nets. During a two day period in August 1986, Chironomidae larvae were dominant numerically in all 209 ??m and 106 ??m samples and midday 425 ??m samples. Large drifters (Ephemerellidae) occurred only in 425 ??m or 209 ??m nets, but the general pattern was an increase in abundance and number of taxa with decreasing mesh size. Relatively more individuals occurred in the larger mesh nets at night than during the day. The two larger mesh sizes retained 70% of the total sediment/detritus in the drift collections, and this decreased the rate of clogging of the 106 ??m net. If an objective of a sampling program is to compare drift density or drift rate between areas or sampling dates, the same mesh size should be used for all sample collection and processing. The mesh aperture used for drift collection should retain all species and life stages of significance in a study. The nested net design enables an investigator to test the adequacy of drift samples. ?? 1991 Kluwer Academic Publishers.

A novel enhanced diffusion sampler for collecting gaseous pollutants without air agitation.

PubMed

Pan, Xuelian; Zhuo, Shaojie; Zhong, Qirui; Chen, Yuanchen; Du, Wei; Cheng, Hefa; Wang, Xilong; Zeng, Eddy Y; Xing, Baoshan; Tao, Shu

2018-03-06

A novel enhanced diffusion sampler for collecting gaseous phase polycyclic aromatic hydrocarbons (PAHs) without air agitation is proposed. The diffusion of target compounds into a sampling chamber is facilitated by continuously purging through a closed-loop flow to create a large concentration difference between the ambient air and the air in the sampling chamber. A glass-fiber filter-based prototype was developed. It was demonstrated that the device could collect gaseous PAHs at a much higher rate (1.6 ± 1.4 L/min) than regular passive samplers, while the ambient air is not agitated. The prototype was also tested in both the laboratory and field for characterizing the concentration gradients over a short distance from the soil surface. The sampler has potential to be applied in other similar situations to characterize the concentration profiles of other chemicals.

Large-Scale Variability of Inpatient Tacrolimus Therapeutic Drug Monitoring at an Academic Transplant Center: a Retrospective Study.

PubMed

Strohbehn, Garth W; Pan, Warren W; Petrilli, Christopher M; Heidemann, Lauren; Larson, Sophia; Aaronson, Keith D; Johnson, Matt; Ellies, Tammy; Heung, Michael

2018-04-30

Inpatient tacrolimus therapeutic drug monitoring (TDM) lacks standardized guidelines. In this study, the authors analyzed variability in the pre-analytical phase of the inpatient tacrolimus TDM process at their institution. Patients receiving tacrolimus (twice-daily formulation) and tacrolimus laboratory analysis were included in the study. Times of tacrolimus administration and laboratory study collection were extracted and time distribution plots for each step in the inpatient TDM process were generated. Trough levels were drawn appropriately in 25.9% of the cases. Timing between doses was consistent, with 91.9% of the following dose administrations occurring 12 +/- 2 hours after the previous dose. Only 38.1% of the drug administrations occurred within one hour of laboratory study collection. Tacrolimus-related patient safety events were reported at a rate of 1.9 events per month while incorrect timing of TDM sample collection occurred approximately 200 times per month. Root cause analysis identified a TDM process marked by a lack of communication and coordination of drug administration and TDM sample collection. Extrapolating findings nationwide, we estimate $22 million in laboratory costs wasted annually. Based on this large single-center study, the authors concluded that the inpatient TDM process is prone to timing errors, thus is financially wasteful, and at its worst harmful to patients due to clinical decisions being made on the basis of unreliable data. Further work is needed on systems solutions to better align the laboratory study collection and drug administration processes.

DEVELOPMENT OF MACROINVERTEBRATE INDICATORS FOR NONWADEABLE TRIBUTARIES TO THE OHIO AND MISSISSIPPI RIVERS

EPA Science Inventory

In 2004-02005, macroinvertebrates were sampled from selected large rivers of the upper Midwest to develop appropriate assessment indicators. Macroinvertebrates, habitat and water chemistry data were collected from 132 randomly selected sites across 6 rivers with varying land cove...

COMPARISON OF LARGE RIVER SAMPLING METHOD USING DIATOM METRICS

EPA Science Inventory

We compared the results of four methods used to assess the algal communities at 60 sites distributed among four rivers. Based on Principle Component Analysis of physical habitat data collected concomitantly with the algal data, sites were separated into those with a mean thalweg...

COMPARISON OF LARGE RIVER SAMPLING METHODS ON ALGAL METRICS

EPA Science Inventory

We compared the results of four methods used to assess the algal communities at 60 sites distributed among four rivers. Based on Principle Component Analysis of physical habitat data collected concomitantly with the algal data, sites were separated into those with a mean thalweg...

Large-Scale Biomonitoring of Remote and Threatened Ecosystems via High-Throughput Sequencing

PubMed Central

Gibson, Joel F.; Shokralla, Shadi; Curry, Colin; Baird, Donald J.; Monk, Wendy A.; King, Ian; Hajibabaei, Mehrdad

2015-01-01

Biodiversity metrics are critical for assessment and monitoring of ecosystems threatened by anthropogenic stressors. Existing sorting and identification methods are too expensive and labour-intensive to be scaled up to meet management needs. Alternately, a high-throughput DNA sequencing approach could be used to determine biodiversity metrics from bulk environmental samples collected as part of a large-scale biomonitoring program. Here we show that both morphological and DNA sequence-based analyses are suitable for recovery of individual taxonomic richness, estimation of proportional abundance, and calculation of biodiversity metrics using a set of 24 benthic samples collected in the Peace-Athabasca Delta region of Canada. The high-throughput sequencing approach was able to recover all metrics with a higher degree of taxonomic resolution than morphological analysis. The reduced cost and increased capacity of DNA sequence-based approaches will finally allow environmental monitoring programs to operate at the geographical and temporal scale required by industrial and regulatory end-users. PMID:26488407

Genetic analysis of floating Enteromorpha prolifera in the Yellow Sea with AFLP marker

NASA Astrophysics Data System (ADS)

Liu, Cui; Zhang, Jing; Sun, Xiaoyu; Li, Jian; Zhang, Xi; Liu, Tao

2011-09-01

Extremely large accumulation of green algae Enteromorpha prolifera floated along China' coastal region of the Yellow Sea ever since the summer of 2008. Amplified Fragment Length Polymorphism (AFLP) analysis was applied to assess the genetic diversity and relationships among E. prolifera samples collected from 9 affected areas of the Yellow Sea. Two hundred reproducible fragments were generated with 8 AFLP primer combinations, of which 194 (97%) were polymorphic. The average Nei's genetic diversity, the coefficiency of genetic differentiation (Gst), and the average gene flow estimated from Gst in the 9 populations were 0.4018, 0.6404 and 0.2807 respectively. Cluster analysis based on the unweighed pair group method with arithmetic averages (UPGMA) showed that the genetic relationships within one population or among different populations were all related to their collecting locations and sampling time. Large genetic differentiation was detected among the populations. The E. prolifera originated from different areas and were undergoing a course of mixing.

AirLab: a cloud-based platform to manage and share antibody-based single-cell research.

PubMed

Catena, Raúl; Özcan, Alaz; Jacobs, Andrea; Chevrier, Stephane; Bodenmiller, Bernd

2016-06-29

Single-cell analysis technologies are essential tools in research and clinical diagnostics. These methods include flow cytometry, mass cytometry, and other microfluidics-based technologies. Most laboratories that employ these methods maintain large repositories of antibodies. These ever-growing collections of antibodies, their multiple conjugates, and the large amounts of data generated in assays using specific antibodies and conditions makes a dedicated software solution necessary. We have developed AirLab, a cloud-based tool with web and mobile interfaces, for the organization of these data. AirLab streamlines the processes of antibody purchase, organization, and storage, antibody panel creation, results logging, and antibody validation data sharing and distribution. Furthermore, AirLab enables inventory of other laboratory stocks, such as primers or clinical samples, through user-controlled customization. Thus, AirLab is a mobile-powered and flexible tool that harnesses the capabilities of mobile tools and cloud-based technology to facilitate inventory and sharing of antibody and sample collections and associated validation data.

Evaluation of the US Army Institute of Public Health Destination Monitoring Program, a food safety surveillance program.

PubMed

Rapp-Santos, Kamala; Havas, Karyn; Vest, Kelly

2015-01-01

The Destination Monitoring Program, operated by the US Army Public Health Command (APHC), is one component that supports the APHC Veterinary Service's mission to ensure safety and quality of food procured for the Department of Defense (DoD). This program relies on retail product testing to ensure compliance of production facilities and distributors that supply food to the DoD. This program was assessed to determine the validity and timeliness by specifically evaluating whether sample size of items collected was adequate, if food samples collected were representative of risk, and whether the program returns results in a timely manner. Data was collected from the US Army Veterinary Services Lotus Notes database, including all food samples collected and submitted from APHC Region-North for the purposes of destination monitoring from January 1, 2013 to December 31, 2013. For most food items, only one sample was submitted for testing. The ability to correctly identify a contaminated food lot may be limited by reliance on test results from only one sample, as the level of confidence in a negative test result is low. The food groups most frequently sampled by APHC correlated with the commodities that were implicated in foodborne illness in the United States. Food items to be submitted were equally distributed among districts and branches, but sections within large branches submitted relatively few food samples compared to sections within smaller branches and districts. Finally, laboratory results were not available for about half the food items prior to their respective expiration dates.

Disposable Polydimethylsiloxane (PDMS)-Coated Fused Silica Optical Fibers for Sampling Pheromones of Moths.

PubMed

Lievers, Rik; Groot, Astrid T

2016-01-01

In the past decades, the sex pheromone composition in female moths has been analyzed by different methods, ranging from volatile collections to gland extractions, which all have some disadvantage: volatile collections can generally only be conducted on (small) groups of females to detect the minor pheromone compounds, whereas gland extractions are destructive. Direct-contact SPME overcomes some of these disadvantages, but is expensive, the SPME fiber coating can be damaged due to repeated usage, and samples need to be analyzed relatively quickly after sampling. In this study, we assessed the suitability of cheap and disposable fused silica optical fibers coated with 100 μm polydimethylsiloxane (PDMS) by sampling the pheromone of two noctuid moths, Heliothis virescens and Heliothis subflexa. By rubbing the disposable PDMS fibers over the pheromone glands of females that had called for at least 15 minutes and subsequently extracting the PDMS fibers in hexane, we collected all known pheromone compounds, and we found a strong positive correlation for most pheromone compounds between the disposable PDMS fiber rubs and the corresponding gland extracts of the same females. When comparing this method to volatile collections and the corresponding gland extracts, we generally found comparable percentages between the three techniques, with some differences that likely stem from the chemical properties of the individual pheromone compounds. Hexane extraction of cheap, disposable, PDMS coated fused silica optical fibers allows for sampling large quantities of individual females in a short time, eliminates the need for immediate sample analysis, and enables to use the same sample for multiple chemical analyses.

Disposable Polydimethylsiloxane (PDMS)-Coated Fused Silica Optical Fibers for Sampling Pheromones of Moths

PubMed Central

Lievers, Rik; Groot, Astrid T.

2016-01-01

In the past decades, the sex pheromone composition in female moths has been analyzed by different methods, ranging from volatile collections to gland extractions, which all have some disadvantage: volatile collections can generally only be conducted on (small) groups of females to detect the minor pheromone compounds, whereas gland extractions are destructive. Direct-contact SPME overcomes some of these disadvantages, but is expensive, the SPME fiber coating can be damaged due to repeated usage, and samples need to be analyzed relatively quickly after sampling. In this study, we assessed the suitability of cheap and disposable fused silica optical fibers coated with 100 μm polydimethylsiloxane (PDMS) by sampling the pheromone of two noctuid moths, Heliothis virescens and Heliothis subflexa. By rubbing the disposable PDMS fibers over the pheromone glands of females that had called for at least 15 minutes and subsequently extracting the PDMS fibers in hexane, we collected all known pheromone compounds, and we found a strong positive correlation for most pheromone compounds between the disposable PDMS fiber rubs and the corresponding gland extracts of the same females. When comparing this method to volatile collections and the corresponding gland extracts, we generally found comparable percentages between the three techniques, with some differences that likely stem from the chemical properties of the individual pheromone compounds. Hexane extraction of cheap, disposable, PDMS coated fused silica optical fibers allows for sampling large quantities of individual females in a short time, eliminates the need for immediate sample analysis, and enables to use the same sample for multiple chemical analyses. PMID:27533064

An intelligent tool for activity data collection.

PubMed

Sarkar, A M Jehad

2011-01-01

Activity recognition systems using simple and ubiquitous sensors require a large variety of real-world sensor data for not only evaluating their performance but also training the systems for better functioning. However, a tremendous amount of effort is required to setup an environment for collecting such data. For example, expertise and resources are needed to design and install the sensors, controllers, network components, and middleware just to perform basic data collections. It is therefore desirable to have a data collection method that is inexpensive, flexible, user-friendly, and capable of providing large and diverse activity datasets. In this paper, we propose an intelligent activity data collection tool which has the ability to provide such datasets inexpensively without physically deploying the testbeds. It can be used as an inexpensive and alternative technique to collect human activity data. The tool provides a set of web interfaces to create a web-based activity data collection environment. It also provides a web-based experience sampling tool to take the user's activity input. The tool generates an activity log using its activity knowledge and the user-given inputs. The activity knowledge is mined from the web. We have performed two experiments to validate the tool's performance in producing reliable datasets.

Triangle area water supply monitoring project, October 1988 through September 2001, North Carolina -- description of the water-quality network, sampling and analysis methods, and quality-assurance practices

USGS Publications Warehouse

Oblinger, Carolyn J.

2004-01-01

The Triangle Area Water Supply Monitoring Project was initiated in October 1988 to provide long-term water-quality data for six area water-supply reservoirs and their tributaries. In addition, the project provides data that can be used to determine the effectiveness of large-scale changes in water-resource management practices, document differences in water quality among water-supply types (large multiuse reservoir, small reservoir, run-of-river), and tributary-loading and in-lake data for water-quality modeling of Falls and Jordan Lakes. By September 2001, the project had progressed in four phases and included as many as 34 sites (in 1991). Most sites were sampled and analyzed by the U.S. Geological Survey. Some sites were already a part of the North Carolina Division of Water Quality statewide ambient water-quality monitoring network and were sampled by the Division of Water Quality. The network has provided data on streamflow, physical properties, and concentrations of nutrients, major ions, metals, trace elements, chlorophyll, total organic carbon, suspended sediment, and selected synthetic organic compounds. Project quality-assurance activities include written procedures for sample collection, record management and archive, collection of field quality-control samples (blank samples and replicate samples), and monitoring the quality of field supplies. In addition to project quality-assurance activities, the quality of laboratory analyses was assessed through laboratory quality-assurance practices and an independent laboratory quality-control assessment provided by the U.S. Geological Survey Branch of Quality Systems through the Blind Inorganic Sample Project and the Organic Blind Sample Project.

Level of endogenous formaldehyde in maple syrup as determined by spectrofluorimetry.

PubMed

Lagacé, Luc; Guay, Stéphane; Martin, Nathalie

2003-01-01

The level of endogenous formaldehyde in maple syrup was established from a large number (n = 300) of authentic maple syrup samples collected during 2000 and 2001 in the province of Quebec, Canada. The average level of formaldehyde from these authentic samples was measured at 0.18 mg/kg in 2000 and 0.28 mg/kg in 2001, which is lower than previously published. These average values can be attributed to the improved spectrofluorimetric method used for the determination. However, the formaldehyde values obtained demonstrate a relatively large distribution with maximums observed at 1.04 and 1.54 mg/kg. These values are still under the maximum tolerance level of 2.0 mg/kg paraformaldehyde pesticide residue. Extensive heat treatment of maple syrup samples greatly enhanced the formaldehyde concentration of the samples, suggesting that extensive heat degradation of the sap constituents during evaporation could be responsible for the highest formaldehyde values in maple syrup.

Ultra-rapid auxin metabolite profiling for high-throughput mutant screening in Arabidopsis.

PubMed

Pencík, Aleš; Casanova-Sáez, Rubén; Pilarová, Veronika; Žukauskaite, Asta; Pinto, Rui; Micol, José Luis; Ljung, Karin; Novák, Ondrej

2018-04-27

Auxin (indole-3-acetic acid, IAA) plays fundamental roles as a signalling molecule during numerous plant growth and development processes. The formation of local auxin gradients and auxin maxima/minima, which is very important for these processes, is regulated by auxin metabolism (biosynthesis, degradation, and conjugation) as well as transport. When studying auxin metabolism pathways it is crucial to combine data obtained from genetic investigations with the identification and quantification of individual metabolites. Thus, to facilitate efforts to elucidate auxin metabolism and its roles in plants, we have developed a high-throughput method for simultaneously quantifying IAA and its key metabolites in minute samples (<10 mg FW) of Arabidopsis thaliana tissues by in-tip micro solid-phase extraction and fast LC-tandem MS. As a proof of concept, we applied the method to a collection of Arabidopsis mutant lines and identified lines with altered IAA metabolite profiles using multivariate data analysis. Finally, we explored the correlation between IAA metabolite profiles and IAA-related phenotypes. The developed rapid analysis of large numbers of samples (>100 samples d-1) is a valuable tool to screen for novel regulators of auxin metabolism and homeostasis among large collections of genotypes.

Diversity of epothilone producers among Sorangium strains in producer-positive soil habitats.

PubMed

Li, Shu-Guang; Zhao, Lin; Han, Kui; Li, Peng-Fei; Li, Zhi-Feng; Hu, Wei; Liu, Hong; Wu, Zhi-Hong; Li, Yue-Zhong

2014-03-01

Large-scale surveys show that the anti-tumour compounds known as epothilones are produced by only a small proportion of Sorangium strains, thereby greatly hampering the research and development of these valuable compounds. In this study, to investigate the niche diversity of epothilone-producing Sorangium strains, we re-surveyed four soil samples where epothilone producers were previously found. Compared with the < 2.5% positive strains collected from different places, epothilone producers comprised 25.0-75.0% of the Sorangium isolates in these four positive soil samples. These sympatric epothilone producers differed not only in their 16S rRNA gene sequences and morphologies but also in their production of epothilones and biosynthesis genes. A further exploration of 14 soil samples collected from a larger area around a positive site showed a similar high positive ratio of epothilone producers among the Sorangium isolates. The present results suggest that, in an area containing epothilone producers, the long-term genetic variations and refinements resulting from selective pressure form a large reservoir of epothilone-producing Sorangium strains with diverse genetic compositions. © 2013 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

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.

Salmon redd identification using environmental DNA (eDNA)

USGS Publications Warehouse

Pilliod, David S.; Laramie, Matthew B.

2016-06-10

IntroductionThe purpose of this project was to develop a technique to use environmental DNA (eDNA) to distinguish between redds made by Chinook salmon (Oncorhynchus tshawytscha) and redds made by Coho salmon (O. kisutch) and to distinguish utilized redds from test/abandoned redds or scours that have the appearance of redds. The project had two phases:Phase 1. Develop, test, and optimize a molecular assay for detecting and identifying Coho salmon DNA and differentiating it from Chinook salmon DNA.Phase 2. Demonstrate the efficacy of the technique.Collect and preserve water samples from the interstitial spaces of 10 known redds (as identified by expert observers) of each species and 10 gravel patches that do not include a redd of either species.Collect control samples from the water column adjacent to each redd to establish background eDNA levels.Analyze the samples using the developed molecular assays for Coho salmon (phase I) and Chinook salmon (Laramie and others, 2015).Evaluate whether samples collected from Chinook and Coho redds have significantly higher levels of eDNA of the respective species than background levels (that is, from gravel, water column).Evaluate whether samples collected from the interstitial spaces of gravel patches that are not redds are similar to background eDNA levels.The Sandy River is a large tributary of the Columbia River. The Sandy River meets the Columbia River approximately 23 km upstream of Portland, Oregon. The Sandy River Basin provides overlapping spawning habitat for both Chinook and Coho salmon.Samples provided by Portland Water Bureau for analysis were collected from the Bull Run River, Sixes Creek, Still Creek, Arrah Wanna Side Channel, and Side Channel 18.

Collection and Analysis of Firn Air from the South Pole, 2001

NASA Astrophysics Data System (ADS)

Butler, J. H.; Montzka, S. A.; Battle, M.; Clarke, A. D.; Mondeel, D. J.; Lind, J. A.; Hall, B. D.; Elkins, J. W.

2001-12-01

In January 2001, we collected an archive of 20th century air from the firn (snowpack) at the South Pole. Samples were collected into separate pairs of 3L glass flasks for measurements of O2/N2 (Bowdoin/Princeton) and carbon cycle gases (CMDL); individual 3L stainless steel and glass flasks for measurements of halocarbons, N2O, SF6, and COS; large (33L) stainless steel canisters for maintaining an archive of air for future analyses; and a few canisters each for measurement of 14CH4 (NIWA/CSIRO) and very low-level analyses of SF6 (SIO). Although it was hoped to obtain air dating back to the turn of the century, the analyses suggest that the earliest date was 1925 for CO2 and the mid- to late teens for heavier gases such as methyl bromide or methyl chloride. This talk will compare the analyses of halocarbons in these recently collected samples to those of air in flasks sampled at the South Pole in 1995. We also will present some results for compounds not measured in the 1995 South Pole samples owing to a paucity of air. Measurements made of the same gases in the firn air at both ends of this six-year interval, along with real-time atmospheric measurements of the same gases, are useful in evaluating assumptions about diffusion in the firn and may allow for the direct calculation of diffusion coefficients at low temperatures. This, in turn, would improve age estimates for firn air samples. New measurements will add to our existing histories established for the 20th century from analyses of firn air samples collected in both Greenland and Antarctica.

A DNA Barcoding Approach to Characterize Pollen Collected by Honeybees

PubMed Central

Bruni, Ilaria; Scaccabarozzi, Daniela; Sandionigi, Anna; Barbuto, Michela; Casiraghi, Maurizio; Labra, Massimo

2014-01-01

In the present study, we investigated DNA barcoding effectiveness to characterize honeybee pollen pellets, a food supplement largely used for human nutrition due to its therapeutic properties. We collected pollen pellets using modified beehives placed in three zones within an alpine protected area (Grigna Settentrionale Regional Park, Italy). A DNA barcoding reference database, including rbcL and trnH-psbA sequences from 693 plant species (104 sequenced in this study) was assembled. The database was used to identify pollen collected from the hives. Fifty-two plant species were identified at the molecular level. Results suggested rbcL alone could not distinguish among congeneric plants; however, psbA-trnH identified most of the pollen samples at the species level. Substantial variability in pollen composition was observed between the highest elevation locality (Alpe Moconodeno), characterized by arid grasslands and a rocky substrate, and the other two sites (Cornisella and Ortanella) at lower altitudes. Pollen from Ortanella and Cornisella showed the presence of typical deciduous forest species; however in samples collected at Ortanella, pollen of the invasive Lonicera japonica, and the ornamental Pelargonium x hortorum were observed. Our results indicated pollen composition was largely influenced by floristic local biodiversity, plant phenology, and the presence of alien flowering species. Therefore, pollen molecular characterization based on DNA barcoding might serve useful to beekeepers in obtaining honeybee products with specific nutritional or therapeutic characteristics desired by food market demands. PMID:25296114

Comparison of microbial populations in the small intestine, large intestine and feces of healthy horses using terminal restriction fragment length polymorphism

PubMed Central

2013-01-01

Background The composition of the microbiota of the equine intestinal tract is complex. Determining whether the microbial composition of fecal samples is representative of proximal compartments of the digestive tract could greatly simplify future studies. The objectives of this study were to compare the microbial populations of the duodenum, ileum, cecum, colon and rectum (feces) within and between healthy horses, and to determine whether rectal (fecal) samples are representative of proximal segments of the gastrointestinal tract. Intestinal samples were collected from ten euthanized horses. 16S rRNA gene PCR-based TRFLP was used to investigate microbiota richness in various segments of the gastrointestinal tract, and dice similarity indices were calculated to compare the samples. Results Within horses large variations of microbial populations along the gastrointestinal tract were seen. The microbiota in rectal samples was only partially representative of other intestinal compartments. The highest similarity was obtained when feces were compared to the cecum. Large compartmental variations were also seen when microbial populations were compared between six horses with similar dietary and housing management. Conclusion Rectal samples were not entirely representative of intestinal compartments in the small or large intestine. This should be taken into account when designing studies using fecal sampling to assess other intestinal compartments. Similarity between horses with similar dietary and husbandry management was also limited, suggesting that parts of the intestinal microbiota were unique to each animal in this study. PMID:23497580

Where Will All Your Samples Go?

NASA Astrophysics Data System (ADS)

Lehnert, K.

2017-12-01

Even in the digital age, physical samples remain an essential component of Earth and space science research. Geoscientists collect samples, sometimes locally, often in remote locations during expensive field expeditions, or at sample repositories and museums. They take these samples to their labs to describe and analyze them. When the analyses are completed and the results are published, the samples get stored away in sheds, basements, or desk drawers, where they remain unknown and inaccessible to the broad science community. In some cases, they will get re-analyzed or shared with other researchers, who know of their existence through personal connections. The sad end comes when the researcher retires: There are many stories of samples and entire collections being discarded to free up space for new samples or other purposes, even though these samples may be unique and irreplaceable. Institutions do not feel obligated and do not have the resources to store samples in perpetuity. Only samples collected in large sampling campaigns such as the Ocean Discovery Program or cores taken on ships find a home in repositories that curate and preserve them for reuse in future science endeavors. In the era of open, transparent, and reproducible science, preservation and persistent access to samples must be considered a mandate. Policies need to be developed that guide investigators, institutions, and funding agencies to plan and implement solutions for reliably and persistently curating and providing access to samples. Registration of samples in online catalogs and use of persistent identifiers such as the International Geo Sample Number are first steps to ensure discovery and access of samples. But digital discovery and access loses its value if the physical objects are not preserved and accessible. It is unreasonable to expect that every sample ever collected can be archived. Selection of those samples that are worth preserving requires guidelines and policies. We also need to define standards that institutions must comply with to function as a trustworthy sample repository similar to trustworthy digital repositories. The iSamples Research Coordination Network of the EarthCube program aims to address some of these questions in workshops planned for 2018. This panel session offers an opportunity to ignite the discussion.

1979 Reserve Force Studies Surveys: Survey Design, Sample Design and Administrative Procedures,

DTIC Science & Technology

1981-08-01

three factors: the need for a statistically significant number of usable questionnaires from different groups within the random sampls and from...Because of the multipurpose nature of these surveys and the large number of questions needed to fully address some of the topics covered, we...varies. Collection of data at the unit level is needed to accurately estimate actual reserve compensation and benefits and their possible role in both

Speciation Mapping of Environmental Samples Using XANES Imaging

EPA Science Inventory

Fast X-ray detectors with large solid angles and high dynamic ranges open the door to XANES imaging, in which millions of spectra are collected to image the speciation of metals at micrometre resolution, over areas up to several square centimetres. This paper explores how such mu...

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...

Algal Assemblages for Large River Monitoring: Comparison Among Biovolume, Absolute and Relative Abundance Metrics

EPA Science Inventory

Periphyton and phytoplankton samples were collected and analyzed from 393 locations in three mid-continent (US) great rivers: the Upper Mississippi, Missouri and Ohio rivers. From the 410 taxa identified, 303 taxa were common enough for multivariate analyses. Algae assemblages we...

An analysis of human pathogens found in horse/mule manure along the John Muir Trail in Kings Canyon and Sequoia and Yosemite National Parks.

PubMed

Derlet, Robert Wayne; Carlson, James Reynolds

2002-01-01

To determine the prevalence of microorganisms that are potentially pathogenic for humans in horse/mule manure along the John Muir Trail (JMT). Random samples of horse/mule manure were collected along sections of the JMT in Yosemite, Kings Canyon, and Sequoia national parks (NP), as well as in portions of the Pacific Crest Trail (PCT) and selected JMT/PCT access trails. Convenience samples of wild animal scat found within I mile of trails were also collected. The fresh specimens were individually preserved both in 0.9% saline and polyvinyl alcohol (PVA)-containing tubes and stored at 4 degrees C until time of analysis. Bacteriological analysis was performed using standard microbiology laboratory procedures. PVA samples were stained with trichrome and were then examined by a parasitologist. Collection: A total of 186 trail miles were sampled, including 113 on the JMT (Yosemite 37, Kings 53, and Sequoia 23). The PCT samplings included 24 miles, and NP and wilderness area access trails added an additional 49 miles. A total of 102 samples were collected, which included 81 samples from pack animals and 21 identified as having come from wild animals. Pack Animal Bacteria: All plated specimens grew large numbers of commensal gut flora. Potential pathogenic bacteria were found in only 12 samples and included Hafnia alvei (4), Serratia odorifera (1), Citrobacter freundii (1), Escherichia vulneris (1), Clostridium clostridioforme (1), Yersinia enterocolitica (1), Sherwinella putraformus (1), and Enterobacter spp (4). No Escherichia coli O157, Salmonella, or Aeromonas were found. Microscopic examination for protozoal organisms revealed occasional commensal ciliates and I Giardia. Wild Animal Pathogens: One specimen grew Y enterocolitica, and another grew Enterobacter amnigenus. We found a low prevalence of human pathogens in pack animal manure on the JMT.

Preparation of highly multiplexed small RNA sequencing libraries.

PubMed

Persson, Helena; Søkilde, Rolf; Pirona, Anna Chiara; Rovira, Carlos

2017-08-01

MicroRNAs (miRNAs) are ~22-nucleotide-long small non-coding RNAs that regulate the expression of protein-coding genes by base pairing to partially complementary target sites, preferentially located in the 3´ untranslated region (UTR) of target mRNAs. The expression and function of miRNAs have been extensively studied in human disease, as well as the possibility of using these molecules as biomarkers for prognostication and treatment guidance. To identify and validate miRNAs as biomarkers, their expression must be screened in large collections of patient samples. Here, we develop a scalable protocol for the rapid and economical preparation of a large number of small RNA sequencing libraries using dual indexing for multiplexing. Combined with the use of off-the-shelf reagents, more samples can be sequenced simultaneously on large-scale sequencing platforms at a considerably lower cost per sample. Sample preparation is simplified by pooling libraries prior to gel purification, which allows for the selection of a narrow size range while minimizing sample variation. A comparison with publicly available data from benchmarking of miRNA analysis platforms showed that this method captures absolute and differential expression as effectively as commercially available alternatives.

Calculation of the Local Free Energy Landscape in the Restricted Region by the Modified Tomographic Method.

PubMed

Chen, Changjun

2016-03-31

The free energy landscape is the most important information in the study of the reaction mechanisms of the molecules. However, it is difficult to calculate. In a large collective variable space, a molecule must take a long time to obtain the sufficient sampling during the simulation. To save the calculation quantity, decreasing the sampling region and constructing the local free energy landscape is required in practice. However, the restricted region in the collective variable space may have an irregular shape. Simply restricting one or more collective variables of the molecule cannot satisfy the requirement. In this paper, we propose a modified tomographic method to perform the simulation. First, it divides the restricted region by some hyperplanes and connects the centers of hyperplanes together by a curve. Second, it forces the molecule to sample on the curve and the hyperplanes in the simulation and calculates the free energy data on them. Finally, all the free energy data are combined together to form the local free energy landscape. Without consideration of the area outside the restricted region, this free energy calculation can be more efficient. By this method, one can further optimize the path quickly in the collective variable space.

Plume particle collection and sizing from static firing of solid rocket motors

NASA Technical Reports Server (NTRS)

Sambamurthi, Jay K.

1995-01-01

A unique dart system has been designed and built at the NASA Marshall Space Flight Center to collect aluminum oxide plume particles from the plumes of large scale solid rocket motors, such as the space shuttle RSRM. The capability of this system to collect clean samples from both the vertically fired MNASA (18.3% scaled version of the RSRM) motors and the horizontally fired RSRM motor has been demonstrated. The particle mass averaged diameters, d43, measured from the samples for the different motors, ranged from 8 to 11 mu m and were independent of the dart collection surface and the motor burn time. The measured results agreed well with those calculated using the industry standard Hermsen's correlation within the standard deviation of the correlation . For each of the samples analyzed from both MNASA and RSRM motors, the distribution of the cumulative mass fraction of the plume oxide particles as a function of the particle diameter was best described by a monomodal log-normal distribution with a standard deviation of 0.13 - 0.15. This distribution agreed well with the theoretical prediction by Salita using the OD3P code for the RSRM motor at the nozzle exit plane.

The use of Stable Isotopes to Assess Climatic Controls on Groundwater Recharge in the Southern Sacramento Mountains, New Mexico

NASA Astrophysics Data System (ADS)

Newton, B. T.; Timmons, S. S.; Rawling, G. C.; Kludt, T.; Eastoe, C. J.

2008-12-01

We used the stable isotopes of hydrogen and oxygen to relate the temporal variability of groundwater recharge to climatic conditions in the southern Sacramento Mountains as a part of a larger regional hydrogeologic study. The southern Sacramento Mountains are the primary recharge source not only to local aquifers, but also to the Lower Pecos River Basin, the Roswell Artesian aquifer and aquifers in the Salt Basin. Aquifers in the study area mainly consist of fractured limestone. In years prior to 2006, groundwater levels within the study area showed a steady decline. We observed a significant increase in regional groundwater levels and spring discharge during and shortly after the unusually wet 2006 monsoon season. We developed a local meteoric water line (LMWL) in δ18O vs. δD space based on precipitation samples collected from several different elevations over a period of two years. The stable isotopic compositions of streams during base flow conditions define an evaporation line with a slope of 5.5 that intersects the LMWL in the region that represents winter precipitation. Spring and well samples collected in 2003 and spring samples collected in 2008 exhibit isotopic compositions that plot near the evaporation line, indicating that groundwater recharge is largely snow melt that has subsequently undergone evaporation in local streams. After the unusually wet 2006 monsoon season, the isotopic compositions of springs sampled in fall of 2006 and wells sampled in spring of 2007 deviated from the evaporation line, plotting closer to the LMWL. This observed isotopic trend is thought to represent a large input of 2006 monsoon precipitation to the groundwater system via relatively short fracture-dominated flow paths. Stable isotope results indicate that while snow melt is probably the main source of groundwater recharge in the southern Sacramento Mountains, as exhibited by the 2003 and 2008 samples, above average summer precipitation events, such as in 2006, can also contribute to significant groundwater recharge.

Source apportionment of methane using a triple isotope approach - Method development and application in the Baltic Sea

NASA Astrophysics Data System (ADS)

Steinbach, Julia; Holmstrand, Henry; Semiletov, Igor; Shakhova, Natalia; Shcherbakova, Kseniia; Kosmach, Denis; Sapart, Célia J.; Gustafsson, Örjan

2015-04-01

We present a method for measurements of the stable and radiocarbon isotope systems of methane in seawater and sediments. The triple isotope characterization of methane is useful in distinguishing different sources and for improving our understanding of biogeochemical processes affecting methane in the water column. D14C-CH4 is an especially powerful addition to stable isotope analyses in distinguishing between thermogenic and biogenic origins of the methane. Such measurements require large sample sizes, due to low natural abundance of the radiocarbon in CH4. Our system for sample collection, methane extraction and purification builds on the approach by Kessler and Reeburgh (Limn. & Ocean. Meth., 2005). An in-field system extracts methane from 30 -120 l water or 1-2 l sediment (depending on the in-situ methane concentration) by purging the samples with Helium to transfer the dissolved methane to the headspace and circulating it through cryogenically cooled absorbent traps where methane is collected. The in-field preparation eliminates the risks of storage and transport of large seawater quantities and subsequent leakage of sample gas as well as ongoing microbial processes and chemical reactions that may alter the sample composition. In the subsequent shore-based treatment, a laboratory system is used to purify and combust the collected CH4 to AMS-amenable CO2. Subsamples from the methane traps are analyzed for stable isotopes and compared to stable isotope measurements directly measured from small water samples taken in parallel, to correct for any potential fractionation occurring during this process. The system has been successfully tested and used on several shorter shipboard expeditions in the Baltic Sea and on a long summer expedition across the Arctic Ocean. Here we present the details of the method and testing, as well as first triple isotope field data from two cruises to the Landsort Deep area in the Central Baltic Sea.

A self-learning algorithm for biased molecular dynamics

PubMed Central

Tribello, Gareth A.; Ceriotti, Michele; Parrinello, Michele

2010-01-01

A new self-learning algorithm for accelerated dynamics, reconnaissance metadynamics, is proposed that is able to work with a very large number of collective coordinates. Acceleration of the dynamics is achieved by constructing a bias potential in terms of a patchwork of one-dimensional, locally valid collective coordinates. These collective coordinates are obtained from trajectory analyses so that they adapt to any new features encountered during the simulation. We show how this methodology can be used to enhance sampling in real chemical systems citing examples both from the physics of clusters and from the biological sciences. PMID:20876135

The ESO Diffuse Interstellar Band Large Exploration Survey (EDIBLES)

NASA Astrophysics Data System (ADS)

Cami, J.; Cox, N. L.; Farhang, A.; Smoker, J.; Elyajouri, M.; Lallement, R.; Bacalla, X.; Bhatt, N. H.; Bron, E.; Cordiner, M. A.; de Koter, A..; Ehrenfreund, P.; Evans, C.; Foing, B. H.; Javadi, A.; Joblin, C.; Kaper, L.; Khosroshahi, H. G.; Laverick, M.; Le Petit, F..; Linnartz, H.; Marshall, C. C.; Monreal-Ibero, A.; Mulas, G.; Roueff, E.; Royer, P.; Salama, F.; Sarre, P. J.; Smith, K. T.; Spaans, M.; van Loon, J. T..; Wade, G.

2018-03-01

The ESO Diffuse Interstellar Band Large Exploration Survey (EDIBLES) is a Large Programme that is collecting high-signal-to-noise (S/N) spectra with UVES of a large sample of O and B-type stars covering a large spectral range. The goal of the programme is to extract a unique sample of high-quality interstellar spectra from these data, representing different physical and chemical environments, and to characterise these environments in great detail. An important component of interstellar spectra is the diffuse interstellar bands (DIBs), a set of hundreds of unidentified interstellar absorption lines. With the detailed line-of-sight information and the high-quality spectra, EDIBLES will derive strong constraints on the potential DIB carrier molecules. EDIBLES will thus guide the laboratory experiments necessary to identify these interstellar “mystery molecules”, and turn DIBs into powerful diagnostics of their environments in our Milky Way Galaxy and beyond. We present some preliminary results showing the unique capabilities of the EDIBLES programme.

Windshield splatter analysis with the Galaxy metagenomic pipeline

PubMed Central

Kosakovsky Pond, Sergei; Wadhawan, Samir; Chiaromonte, Francesca; Ananda, Guruprasad; Chung, Wen-Yu; Taylor, James; Nekrutenko, Anton

2009-01-01

How many species inhabit our immediate surroundings? A straightforward collection technique suitable for answering this question is known to anyone who has ever driven a car at highway speeds. The windshield of a moving vehicle is subjected to numerous insect strikes and can be used as a collection device for representative sampling. Unfortunately the analysis of biological material collected in that manner, as with most metagenomic studies, proves to be rather demanding due to the large number of required tools and considerable computational infrastructure. In this study, we use organic matter collected by a moving vehicle to design and test a comprehensive pipeline for phylogenetic profiling of metagenomic samples that includes all steps from processing and quality control of data generated by next-generation sequencing technologies to statistical analyses and data visualization. To the best of our knowledge, this is also the first publication that features a live online supplement providing access to exact analyses and workflows used in the article. PMID:19819906

Evaluation of water-quality characteristics and sampling design for streams in North Dakota, 1970–2008

USGS Publications Warehouse

Galloway, Joel M.; Vecchia, Aldo V.; Vining, Kevin C.; Densmore, Brenda K.; Lundgren, Robert F.

2012-01-01

In response to the need to examine the large amount of historic water-quality data comprehensively across North Dakota and evaluate the efficiency of the State-wide sampling programs, a study was done by the U.S. Geological Survey in cooperation with the North Dakota State Water Commission and the North Dakota Department of Health to describe the water-quality data collected for the various programs and determine an efficient State-wide sampling design for monitoring future water-quality conditions. Although data collected for the North Dakota State Water Commission High-Low Sampling Program, the North Dakota Department of Health Ambient Water-Quality Network, and other projects and programs provide valuable information on the quality of water in streams in North Dakota, the objectives vary among the programs, some of the programs overlap spatially and temporally, and the various sampling designs may not be the most efficient or relevant to the objectives of the individual programs as they have changed through time. One objective of a State-wide sampling program was to evaluate ways to describe the spatial variability of water-quality conditions across the State in the most efficient manner. Weighted least-squares regression analysis was used to relate the average absolute difference between paired downstream and upstream concentrations, expressed as a percent of the average downstream concentration, to the average absolute difference in daily flow between the downstream and upstream pairs, expressed as a percent of the average downstream flow. The analysis showed that a reasonable spatial network would consist of including the most downstream sites in large basins first, followed by the next upstream site(s) that roughly bisect the downstream flows at the first sites, followed by the next upstream site(s) that roughly bisect flows for the second sites. Sampling sites to be included in a potential State-wide network were prioritized into 3 design levels: level 1 (highest priority), level 2 (second priority), and level 3 (third priority). Given the spatial distribution and priority designation (levels 1–3) of sites in the potential spatial network, the next consideration was to determine the appropriate temporal sampling frequency to use for monitoring future water-quality conditions. The time-series model used to detect concentration trends for this report also was used to evaluate sampling designs to monitor future water-quality trends. Sampling designs were evaluated with regard to their sensitivity to detect seasonal trends that occurred during three 4-month seasons—March through June, July through October, and November through February. For the 34 level-1 sites, samples would be collected for major ions, trace metals, nutrients, bacteria, and sediment eight times per year, with samples in January, April (2 samples),May, June, July, August, and October. For the 21 level-2 sites, samples would be collected for major ions, trace metals, and nutrients six times per year (January, April, May, June, August, and October), and for the 26 level-3 sites, samples would be collected for these constituents four times per year (April, June, August, and October).

Evaluation of a New Technique for iFOBT Utilising a New Sample Collection Device with Increased Buffer Stability.

PubMed

Bruns-Toepler, Markus; Hardt, Philip

2017-07-01

The aims of the present study were: (i) Evaluate specificity and sensitivity of Hb Smart enzyme-linked immunosorbent assay (ELISA) (ScheBo Biotech) compared to colonoscopy results and (ii) assess stability of a new sample collection device containing a newly formulated buffer to extract haemoglobin using buffer and stool samples spiked with defined concentrations of haemoglobin. Stool samples were quantified with the ELISA method. The stability of haemoglobin in the extraction buffer and in native stool samples, respectively, was determined daily by ELISA during storage for 5 days at 4°C and at room temperature after addition of haemoglobin. Haemoglobin ELISA had a sensitivity of 78.4% for detection of CRC with a specificity of 98%. Haemoglobin extracted in corresponding extraction buffer demonstrated stability throughout storage for 5 days at 4°C and at room temperature. Hb Smart represents a very promising tool for large-scale screening of CRC with regard to sample handling, stability and analysis of haemoglobin in faeces. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

Deriving photometric redshifts using fuzzy archetypes and self-organizing maps - I. Methodology

NASA Astrophysics Data System (ADS)

Speagle, Joshua S.; Eisenstein, Daniel J.

2017-07-01

We propose a method to substantially increase the flexibility and power of template fitting-based photometric redshifts by transforming a large number of galaxy spectral templates into a corresponding collection of 'fuzzy archetypes' using a suitable set of perturbative priors designed to account for empirical variation in dust attenuation and emission-line strengths. To bypass widely separated degeneracies in parameter space (e.g. the redshift-reddening degeneracy), we train self-organizing maps (SOMs) on large 'model catalogues' generated from Monte Carlo sampling of our fuzzy archetypes to cluster the predicted observables in a topologically smooth fashion. Subsequent sampling over the SOM then allows full reconstruction of the relevant probability distribution functions (PDFs). This combined approach enables the multimodal exploration of known variation among galaxy spectral energy distributions with minimal modelling assumptions. We demonstrate the power of this approach to recover full redshift PDFs using discrete Markov chain Monte Carlo sampling methods combined with SOMs constructed from Large Synoptic Survey Telescope ugrizY and Euclid YJH mock photometry.

A large-scale investigation of microplastic contamination: Abundance and characteristics of microplastics in European beach sediment.

PubMed

Lots, Froukje A E; Behrens, Paul; Vijver, Martina G; Horton, Alice A; Bosker, Thijs

2017-10-15

Here we present the large-scale distribution of microplastic contamination in beach sediment across Europe. Sediment samples were collected from 23 locations across 13 countries by citizen scientists, and analysed using a standard operating procedure. We found significant variability in the concentrations of microplastics, ranging from 72±24 to 1512±187 microplastics per kg of dry sediment, with high variability within sampling locations. Three hotspots of microplastic accumulation (>700 microplastics per kg of dry sediment) were found. There was limited variability in the physico-chemical characteristics of the plastics across sampling locations. The majority of the microplastics were fibrous, <1mm in size, and blue/black in colour. In addition, using Raman spectrometry we identified particles as polyester, polyethylene, and polypropylene. Our research is the first large spatial-scale analysis of microplastics on European beaches giving insights into the nature and extent of the microplastic challenge. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Importance of Meteorite Collections to Sample Return Missions: Past, Present, and Future Considerations

NASA Technical Reports Server (NTRS)

Welzenbach, L. C.; McCoy, T. J.; Glavin, D. P.; Dworkin, J. P.; Abell, P. A.

2012-01-01

While much of the scientific community s current attention is drawn to sample return missions, it is the existing meteorite and cosmic dust collections that both provide the paradigms to be tested by these missions and the context for interpreting the results. Recent sample returns from the Stardust and Hayabusa missions provided us with new materials and insights about our Solar System history and processes. As an example, Stardust sampled CAIs among the population of cometary grains, requiring extensive and unexpected radial mixing in the early solar nebula. This finding would not have been possible, however, without extensive studies of meteoritic CAIs that established their high-temperature, inner Solar System formation. Samples returned by Stardust also revealed the first evidence of a cometary amino acid, a discovery that would not have been possible with current in situ flight instrument technology. The Hayabusa mission provided the final evidence linking ordinary chondrites and S asteroids, a hypothesis that developed from centuries of collection and laboratory and ground-based telescopic studies. In addition to these scientific findings, studies of existing meteorite collections have defined and refined the analytical techniques essential to studying returned samples. As an example, the fortuitous fall of the Allende CV3 and Murchison CM2 chondrites within months before the return of Apollo samples allowed testing of new state-of-the-art analytical facilities. The results of those studies not only prepared us to better study lunar materials, but unanticipated discoveries changed many of our concepts about the earliest history and processes of the solar nebula. This synergy between existing collections and future space exploration is certainly not limited to sample return missions. Laboratory studies confirmed the existence of meteorites from Mars and raised the provocative possibility of preservation of ancient microbial life. The laboratory studies in turn led to a new wave of Mars exploration that ultimately could lead to sample return focused on evidence for past or present life. This partnership between collections and missions will be increasingly important in the coming decades as we discover new questions to be addressed and identify targets for for both robotic and human exploration . Nowhere is this more true than in the ultimate search for the abiotic and biotic processes that produced life. Existing collections also provide the essential materials for developing and testing new analytical schemes to detect the rare markers of life and distinguish them from abiotic processes. Large collections of meteorites and the new types being identified within these collections, which come to us at a fraction of the cost of a sample return mission, will continue to shape the objectives of future missions and provide new ways of interpreting returned samples.

Bacterial microbiota compositions of naturally fermented milk are shaped by both geographic origin and sample type.

PubMed

Zhong, Z; Hou, Q; Kwok, L; Yu, Z; Zheng, Y; Sun, Z; Menghe, B; Zhang, H

2016-10-01

Naturally fermented dairy products contain a rich microbial biodiversity. This study aimed to provide an overview on the bacterial microbiota biodiversity of 85 samples, previously collected across a wide region of China, Mongolia, and Russia. Data from these 85 samples, including 55 yogurts, 18 naturally fermented yak milks, 6 koumisses, and 6 cheeses, were retrieved and collectively analyzed. The most prevalent phyla shared across samples were Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria, which together accounted for 99% of bacterial sequences. The predominant genera were Lactobacillus, Lactococcus, Streptococcus, Acetobacter, Acinetobacter, Leuconostoc, and Macrococcus, which together corresponded to 96.63% of bacterial sequences. Further multivariate statistical analyses revealed significant differences in the microbiota structure across sample geographic origin and type. First, on the principal coordinate score plot, samples representing the 3 main sample collection regions (Russia, Xinjiang, and Tibet) were mostly located respectively in the upper left, lower right, and lower left quadrants, although slight overlapping occurred. In contrast, samples from the minor sampling areas (Inner Mongolia, Mongolia, Gansu, and Sichuan) were predominantly distributed in the lower left quadrant. These results suggest a possible association between sample geographical origin and microbiota composition. Second, bacterial microbiota structure was stratified by sample type. In particular, the microbiota of cheese was largely distinct from the other sample types due to its high abundances of Lactococcus and Streptococcus. The fermented yak milk microbiota was most like that of the yogurts. Koumiss samples had the lowest microbial diversity and richness. In conclusion, both geographic origin and sample type shape the microbial diversity of naturally fermented milk. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

The characterisation of diesel exhaust particles - composition, size distribution and partitioning.

PubMed

Alam, Mohammed S; Zeraati-Rezaei, Soheil; Stark, Christopher P; Liang, Zhirong; Xu, Hongming; Harrison, Roy M

2016-07-18

A number of major research questions remain concerning the sources and properties of road traffic generated particulate matter. A full understanding of the composition of primary vehicle exhaust aerosol and its contribution to secondary organic aerosol (SOA) formation still remains elusive, and many uncertainties exist relating to the semi-volatile component of the particles. Semi-Volatile Organic Compounds (SVOCs) are compounds which partition directly between the gas and aerosol phases under ambient conditions. The SVOCs in engine exhaust are typically hydrocarbons in the C15-C35 range, and are largely uncharacterised because they are unresolved by traditional gas chromatography, forming a large hump in the chromatogram referred to as Unresolved Complex Mixture (UCM). In this study, thermal desorption coupled to comprehensive Two Dimensional Gas-Chromatography Time-of-Flight Mass-Spectrometry (TD-GC × GC-ToF-MS) was exploited to characterise and quantify the composition of SVOCs from the exhaust emission. Samples were collected from the exhaust of a diesel engine, sampling before and after a diesel oxidation catalyst (DOC), while testing at steady state conditions. Engine exhaust was diluted with air and collected using both filter and impaction (nano-MOUDI), to resolve total mass and size resolved mass respectively. Adsorption tubes were utilised to collect SVOCs in the gas phase and they were then analysed using thermal desorption, while particle size distribution was evaluated by sampling with a DMS500. The SVOCs were observed to contain predominantly n-alkanes, branched alkanes, alkyl-cycloalkanes, alkyl-benzenes, PAHs and various cyclic aromatics. Particle phase compounds identified were similar to those observed in engine lubricants, while vapour phase constituents were similar to those measured in fuels. Preliminary results are presented illustrating differences in the particle size distribution and SVOCs composition when collecting samples with and without a DOC. The results indicate that the DOC tested is of very limited efficiency, under the studied engine operating conditions, for removal of SVOCs, especially at the upper end of the molecular weight range.

A Large Ordinary Chondrite Shower in the Dominion Range

NASA Technical Reports Server (NTRS)

Satterwhite, C. E.; Righter, K.; Harrington, R.; McBride, K. M.; Funk, R.

2017-01-01

The US Antarctic Meteorite Program has visited the Dominion Range in the Transantarctic Mountains during several different seasons, including the 1985, 2003, 2008, 2010, and 2014 seasons. Total recovered meteorites from this region is over 2000. The 2008 and 2010 seasons have been fully classified and, respectively) revealing the presence of a large meteorite shower that comprises approximately 60% of all samples recovered in those two seasons. The oil immersion classification suggests that this shower is LL chondrite material, whereas published magnetic susceptibility (MS; log chi) measurements yield L chondrite values. However, usually random sampling of a large collection like this would uncover EOC material for which we have prepared thin sections. In this case, no LL chondrite materials have been found in thin section, suggesting that the shower might instead be an L chondrite. L and LL chondrites are notoriously difficult to distinguish using oil immersion techniques. To better characterize this large group of samples, we have decided to examine some of the large members of this group, using EMPA analysis of the olivines to verify the classifications. With a compositional link between this subset of samples, and the MS measurements, we can more confidently classify the samples making up this pairing group. Subsequently, more accurate and meaningful comparisons may be drawn between this pairing group and some other Antarctic pairing groups such as from the Queen Alexandra Range (QUE), and Lewis Cliffs Ice Tongue (LEW). electron microprobe analysis

Detection and Characterization of Circulating Tumour Cells from Frozen Peripheral Blood Mononuclear Cells

PubMed Central

Lu, David; Graf, Ryon P.; Harvey, Melissa; Madan, Ravi A.; Heery, Christopher; Marte, Jennifer; Beasley, Sharon; Tsang, Kwong Y.; Krupa, Rachel; Louw, Jessica; Wahl, Justin; Bales, Natalee; Landers, Mark; Marrinucci, Dena; Schlom, Jeffrey; Gulley, James L.; Dittamore, Ryan

2015-01-01

Retrospective analysis of patient tumour samples is a cornerstone of clinical research. CTC biomarker characterization offers a non-invasive method to analyse patient samples. However, current CTC technologies require prospective blood collection, thereby reducing the ability to utilize archived clinical cohorts with long-term outcome data. We sought to investigate CTC recovery from frozen, archived patient PBMC pellets. Matched samples from both mCRPC patients and mock samples, which were prepared by spiking healthy donor blood with cultured prostate cancer cell line cells, were processed “fresh” via Epic CTC Platform or from “frozen” PBMC pellets. Samples were analysed for CTC enumeration and biomarker characterization via immunofluorescent (IF) biomarkers, fluorescence in-situ hybridization (FISH) and CTC morphology. In the frozen patient PMBC samples, the median CTC recovery was 18%, compared to the freshly processed blood. However, abundance and localization of cytokeratin (CK) and androgen receptor (AR) protein, as measured by IF, were largely concordant between the fresh and frozen CTCs. Furthermore, a FISH analysis of PTEN loss showed high concordance in fresh vs. frozen. The observed data indicate that CTC biomarker characterization from frozen archival samples is feasible and representative of prospectively collected samples. PMID:28936240

Entomofauna of Ziban Oasis, Biskra, Algeria

PubMed Central

Deghiche-Diab, Nassima; Porcelli, Francisco; Belhamra, Mohamed

2015-01-01

An inventory was carried out at five stations in the oasis of Ziban, an oasis that is characterized by its high-quality dates, in order to study the relationships between the oasis ecosystem and its insect fauna. Specimens were sampled using pitfall traps containing ethylene glycol as a preservative. In total, 115 arthropod species were collected during 5 months of survey. These species belonged to 61 families, 17 orders, and 4 classes (12 orders from Insecta, 3 from Arachnida, 1 from Chilopoda, and 1 from Malocostraca). The most represented insect orders were Coleoptera (44.42%), Hymenoptera (20.86%), and Lepidoptera (7.87%). Represented in the collections were phytophagous, omnivorous, and predator/parasite species. Given the large number of species collected, and the largely unknown relationships existing between the various ecological groups, this study is a first step in the description of the oasis entomofauna. PMID:25855607

Fecal-indicator bacteria in the Allegheny, Monongahela, and Ohio Rivers and selected tributaries, Allegheny County, Pennsylvania, 2001-2005

USGS Publications Warehouse

Buckwalter, Theodore F.; Zimmerman, Tammy M.; Fulton, John W.

2006-01-01

Concentrations of fecal-indicator bacteria were determined in 1,027 water-quality samples collected from July 2001 through August 2005 during dry- (72-hour dry antecedent period) and wet-weather (48-hour dry antecedent period and at least 0.3 inch of rain in a 24-hour period) conditions in the Allegheny, Monongahela, and Ohio Rivers (locally referred to as the Three Rivers) and selected tributaries in Allegheny County. Samples were collected at five sampling sites on the Three Rivers and at eight sites on four tributaries to the Three Rivers having combined sewer overflows. Water samples were analyzed for three fecal-indicator organisms fecal coliform, Escherichia coli (E. coli), and enterococci bacteria. Left-bank and right-bank surface-water samples were collected in addition to a cross-section composite sample at each site. Concentrations of fecal coliform, E. coli, and enterococci were detected in 98.6, 98.5, and 87.7 percent of all samples, respectively. The maximum fecal-indicator bacteria concentrations were collected from Sawmill Run, a tributary to the Ohio River; Sawmill Run at Duquesne Heights had concentrations of fecal coliform, E. coli, and enterococci of 410,000, 510,000, and 180,000 col/100 mL, respectively, following a large storm. The samples collected in the Three Rivers and selected tributaries frequently exceeded established recreational standards and criteria for bacteria. Concentrations of fecal coliform exceeded the Pennsylvania water-quality standard (200 col/100 mL) in approximately 63 percent of the samples. Sample concentrations of E. coli and enterococci exceeded the U.S. Environmental Protection Agency (USEPA) water-quality criteria (235 and 61 col/100 mL, respectively) in about 53 and 47 percent, respectively, of the samples. Fecal-indicator bacteria were most strongly correlated with streamflow, specific conductance, and turbidity. These correlations most frequently were observed in samples collected from tributary sites. Fecal-indicator bacteria concentrations and turbidity were correlated to the location of sample collection in the cross section. Most differences were between bank and composite samples; differences between right-bank and left-bank samples were rarely observed. The Allegheny River sites had more significant correlations than the Monongahela or Ohio River sites. Comparisons were made between fecal-indicator bacteria in composite samples collected during dry-weather, wet-weather day-one, wet-weather day-two (tributary sites only), and wet-weather day-three (Three Rivers sites only) events in the Three Rivers and selected tributary sites. The lowest median bacteria concentrations generally were observed in the dry-weather composite samples. All median bacteria concentrations in dry-weather composite samples in the five Three Rivers sites were below water-quality standards and criteria; bacteria concentrations in the upstream tributary sites rarely met all standards or criteria. Only Turtle Creek, Thompson Run, and Chartiers Creek had at least one median bacteria concentration below water-quality standards or criteria. Median bacteria concentrations in the composite samples generally were higher the day after a wet-weather event compared to dry-weather composite samples and other wet-weather composite samples collected. In the five Three Rivers sites, median bacteria concentrations 3 days after a wet-weather event in composite samples tended to fall below the water-quality standards and criteria; in the eight tributary sites, median bacteria concentrations in the dry-weather and wet-weather composite samples generally were above the water-quality standards or criteria. Composite samples collected at the upstream sites on the Three Rivers and selected tributaries generally had lower median bacteria concentrations than composite samples collected at the downstream sites during dry- and wet-weather events. Higher concentrations downstream may be because o

Assessment of possible sources of microbiological contamination and water-quality characteristics of the Jacks Fork, Ozark National Scenic Riverways, Missouri; phase II

USGS Publications Warehouse

Davis, Jerri V.; Richards, Joseph M.

2002-01-01

In 1998, an 8-mile reach of the Jacks Fork was included on Missouri?s list of impaired waters as required by Section 303(d) of the Federal Clean Water Act. The identified pollutant on the Jacks Fork was fecal coliform bacteria. Potential sources of fecal contamination to the Jacks Fork include a wastewater treatment plant; campground pit-toilet or septic-system effluent; a large commercial, cross-country horseback trail riding facility; canoeists, boaters, and tubers; and cows.The U.S. Geological Survey, in cooperation with the National Park Service, conducted a study to better understand the extent and sources of microbiological contamination within the Jacks Fork from Alley Spring to the mouth, which includes the 8-mile 303(d) reach. Identification of the sources would provide the National Park Service and the State of Missouri with the information needed to craft a solution of abatement, regulation, prevention, and mitigation with the end result being the removal of the Jacks Fork from the 303(d) list. Fifteen sites were sampled from November 1999 through December 2000. An additional site was sampled one time. Samples were collected mostly during base-flow conditions during a variety of nonrecreational and recreational season river uses. Samples were analyzed for selected fecal indicator bacteria, physical properties, nutrients, and wastewater organic compounds. During the sampling period, the whole-body-contact recreation standard for fecal coliform (200 colonies per 100 milliliters of sample) was exceeded at three sites on August 10, 2000, and also at one site on May 11, June 7, and October 3, 2000. Fecal coliform densities and instantaneous loads generally increased from background concentrations at the Eminence site, peaked about 2 river miles downstream, and then decreased until the most downstream site sampled. Generally, the largest densities and loads at sites downstream from Eminence not related to wet-weather flow were observed during a trail ride held August 6 to12, 2000. A 24-hour sample collection effort was conducted the weekend of July 15 and 16, 2000, to investigate the effect that large numbers of swimmers, canoeists, and tubers had on fecal coliform densities in the Jacks Fork. Five or six samples were collected at six sites between Saturday morning and the following Sunday afternoon. No fecal coliform density at any of the sites sampled exceeded the whole-body-contact recreation standard. Because bacteria survive longer in stream-bed sediments than in water, a source of bacteria in the water column could be from resuspension of accumulated bacteria from streambed sediments. Water and streambed-sediment samples were collected at three sites on August 3, 2000, 1 week before a trail ride and again at three sites on 2 Assessment of Possible Sources of Microbiological Contamination of the Jacks Fork, Missouri?Phase II August 8, 2000, during a trail ride. Results indicate that fecal coliform bacteria densities increased substantially in the streambed sediment and the water column during the trail ride.Sixty-five Escherichia coli isolates obtained from water samples collected at 9 sites and 23 Escherichia coli isolates obtained from stream-bed-sediment samples collected at 5 sites were submitted for ribotyping analysis. Samples were collected in 2000 during a variety of nonrecreational and recreational season river uses, including trail rides, canoeing, tubing, and swimming. Of the 65 isolates from water samples, 40 percent were identified as originating from sewage, 29 percent from horse, 11 percent from cow, and 20 percent from an unknown source. Of the 23 isolates from streambed-sediment samples, 39 percent were identified as originating from sewage, 35 percent from horse, 13 percent from cow, and 13 percent from unknown sources.Analysis of physical property (dissolved oxygen, pH, specific conductance, and temperature) and nutrient (dissolved nitrite plus nitrate and total phosphorus) data

University of TX Bureau of Economic Geology's Core Research Centers: The Time is Right for Registering Physical Samples and Assigning IGSN's - Workflows, Stumbling Blocks, and Successes.

NASA Astrophysics Data System (ADS)

Averett, A.; DeJarnett, B. B.

2016-12-01

The University Of Texas Bureau Of Economic Geology (BEG) serves as the geological survey for Texas and operates three geological sample repositories that house well over 2 million boxes of geological samples (cores and cuttings) and an abundant amount of geoscience data (geophysical logs, thin sections, geochemical analyses, etc.). Material is accessible and searchable online, and it is publically available to the geological community for research and education. Patrons access information about our collection by using our online core and log database (SQL format). BEG is currently undertaking a large project to: 1) improve the internal accuracy of metadata associated with the collection; 2) enhance the capabilities of the database for both BEG curators and researchers as well as our external patrons; and 3) ensure easy and efficient navigation for patrons through our online portal. As BEG undertakes this project, BEG is in the early stages of planning to export the metadata for its collection into SESAR (System for Earth Sample Registration) and have IGSN's (International GeoSample Numbers) assigned to its samples. Education regarding the value of IGSN's and an external registry (SESAR) has been crucial to receiving management support for the project because the concept and potential benefits of registering samples in a registry outside of the institution were not well-known prior to this project. Potential benefits such as increases in discoverability, repository recognition in publications, and interoperability were presented. The project was well-received by management, and BEG fully supports the effort to register our physical samples with SESAR. Since BEG is only in the initial phase of this project, any stumbling blocks, workflow issues, successes/failures, etc. can only be predicted at this point, but by mid-December, BEG expects to have several concrete issues to present in the session. Currently, our most pressing issue involves establishing the most efficient workflow for exporting of large amounts of metadata in a format that SESAR can easily ingest, and how this can be best accomplished with very few BEG staff assigned to the project.

Apparatus and process for microbial detection and enumeration

NASA Technical Reports Server (NTRS)

Wilkins, J. R.; Grana, D. (Inventor)

1982-01-01

An apparatus and process for detecting and enumerating specific microorganisms from large volume samples containing small numbers of the microorganisms is presented. The large volume samples are filtered through a membrane filter to concentrate the microorganisms. The filter is positioned between two absorbent pads and previously moistened with a growth medium for the microorganisms. A pair of electrodes are disposed against the filter and the pad electrode filter assembly is retained within a petri dish by retainer ring. The cover is positioned on base of petri dish and sealed at the edges by a parafilm seal prior to being electrically connected via connectors to a strip chart recorder for detecting and enumerating the microorganisms collected on filter.

Rapid Classification of Ordinary Chondrites Using Raman Spectroscopy

NASA Technical Reports Server (NTRS)

Fries, M.; Welzenbach, L.

2014-01-01

Classification of ordinary chondrites is typically done through measurements of the composition of olivine and pyroxenes. Historically, this measurement has usually been performed via electron microprobe, oil immersion or other methods which can be costly through lost sample material during thin section preparation. Raman microscopy can perform the same measurements but considerably faster and with much less sample preparation allowing for faster classification. Raman spectroscopy can facilitate more rapid classification of large amounts of chondrites such as those retrieved from North Africa and potentially Antarctica, are present in large collections, or are submitted to a curation facility by the public. With development, this approach may provide a completely automated classification method of all chondrite types.

Phytoforensics—Using trees to find contamination

USGS Publications Warehouse

Wilson, Jordan L.

2017-09-28

The water we drink, air we breathe, and soil we come into contact with have the potential to adversely affect our health because of contaminants in the environment. Environmental samples can characterize the extent of potential contamination, but traditional methods for collecting water, air, and soil samples below the ground (for example, well drilling or direct-push soil sampling) are expensive and time consuming. Trees are closely connected to the subsurface and sampling tree trunks can indicate subsurface pollutants, a process called phytoforensics. Scientists at the Missouri Water Science Center were among the first to use phytoforensics to screen sites for contamination before using traditional sampling methods, to guide additional sampling, and to show the large cost savings associated with tree sampling compared to traditional methods. 

Turbidity Threshold sampling in watershed research

Treesearch

Rand Eads; Jack Lewis

2003-01-01

Abstract - When monitoring suspended sediment for watershed research, reliable and accurate results may be a higher priority than in other settings. Timing and frequency of data collection are the most important factors influencing the accuracy of suspended sediment load estimates, and, in most watersheds, suspended sediment transport is dominated by a few, large...

Task Characteristics, Managerial Socialization, and Media Selection.

ERIC Educational Resources Information Center

Donabedian, Bairj; McKinnon, Sharon M.; Bruns, William J., Jr.

1998-01-01

Questions why managers choose one communication medium in preference to another. Proposes a role for social factors in media selection. Finds, employing a large field-collected sample, strong support for Information Richness Theory, a rational-choice model connecting managers' media choice to task characteristics like variety and analyzability.…

Employee Characteristics as Predictors of Turnover among Female Clerical Employees in Two Organizations

ERIC Educational Resources Information Center

Mowday, Richard T.; And Others

1978-01-01

Female clerical employees (N=314) in two regional offices of a large insurance company were administered Jackson's Personality Research Form. Turnover data were collected up to eight months following administration of the questionnaire. Relationships were found between employee characteristics and turnover in both samples. (Author)

76 FR 1621 - Proposed Collection; Comment Request; NIH Toolbox for Assessment of Neurological and Behavioral...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-11

..., emotional, motor and sensory) for use in large longitudinal or epidemiological studies where functioning is... of establishing comparative norms. Existing recruitment databases will be randomly sampled and... * Adult study participants, single assessment..... 3,150 1 3 9,450 Adult study participants, two...

78 FR 70015 - Proposed Information Collection; Comment Request; Large Pelagic Fishing Survey

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-22

...) target sample size from 10,780 to 15,900 interviews for Northeast and Southeast combined. Add up to five questions to the LPTS questionnaire. Add a non-response follow-up survey to the LPTS in the Southeast region... from 1,500 to 1,000 interviews. [[Page 70016

Flip This Classroom: A Comparative Study

ERIC Educational Resources Information Center

Unruh, Tiffany; Peters, Michelle L.; Willis, Jana

2016-01-01

The purpose of this research was to compare the beliefs and attitudes of teachers using the flipped versus the traditional class model. Survey and interview data were collected from a matched sample of in-service teachers representing both models from a large suburban southeastern Texas school district. The Attitude Towards Technology Scale, the…

Role of Teacher Characteristics and School Resources in Early Mathematics Learning

ERIC Educational Resources Information Center

Jung, Eunjoo; Brown, Elizabeth T.; Karp, Karen S.

2014-01-01

The authors investigated the degree to which school-level teacher characteristics and resources are related to the mathematics learning of kindergarten children using a sample drawn from a large US database. Kindergarten-level teacher characteristics were operationalised as collective teacher efficacy, teacher experience and teacher preparation;…

Intercomparison of fog water samplers

NASA Astrophysics Data System (ADS)

Schell, Dieter; Georgii, Hans-Walter; Maser, Rolf; Jaeschke, Wolfgang; Arends, Beate G.; Kos, Gerard P. A.; Winkler, Peter; Schneider, Thomas; Berner, Axel; Kruisz, Christian

1992-11-01

During the Po Valley Fog Experiment 1989, two fogwater collectors were operated simultaneously at the ground and the results were compared to each other. The chemical analyses of the samples as well as the collection efficiencies showed remarkable differences between both collectors. Some differences in the solute concentrations in the samples of both collectors could be expected due to small differences in the 50-percent cut-off diameters. The large differences in the collection efficiencies however cannot be explained by these small variations of d sub 50, because normally only a small fraction of the water mass is concentrated in the size range of 5-7-micron droplets. It is shown that it is not sufficient to characterize a fogwater collector only by its cut-off diameter. The results of several wind tunnel calibration tests show that the collection efficiencies of the fogwater collectors are a function of windspeed and shape of the droplet spectra.

Assessment of levels of bacterial contamination of large wild game meat in Europe.

PubMed

Membré, Jeanne-Marie; Laroche, Michel; Magras, Catherine

2011-08-01

The variations in prevalence and levels of pathogens and fecal contamination indicators in large wild game meat were studied to assess their potential impact on consumers. This analysis was based on hazard analysis, data generation and statistical analysis. A total of 2919 meat samples from three species (red deer, roe deer, wild boar) were collected at French game meat traders' facilities using two sampling protocols. Information was gathered on the types of meat cuts (forequarter or haunch; first sampling protocol) or type of retail-ready meat (stewing meat or roasting meat; second protocol), and also on the meat storage conditions (frozen or chilled), country of origin (eight countries) and shooting season (autumn, winter, spring). The samples were analyzed in both protocols for detection and enumeration of Escherichia coli, coagulase+staphylococci and Clostridium perfringens. In addition, detection and enumeration of thermotolerant coliforms and Listeria monocytogenes were performed for samples collected in the first and second protocols, respectively. The levels of bacterial contamination of the raw meat were determined by performing statistical analysis involving probabilistic techniques and Bayesian inference. C. perfringens was found in the highest numbers for the three indicators of microbial quality, hygiene and good handling, and L. monocytogenes in the lowest. Differences in contamination levels between game species and between meats distributed as chilled or frozen products were not significant. These results might be included in quantitative exposure assessments. Copyright © 2011 Elsevier Ltd. All rights reserved.

African Baobabs with False Inner Cavities: The Radiocarbon Investigation of the Lebombo Eco Trail Baobab

PubMed Central

Patrut, Adrian; Woodborne, Stephan; von Reden, Karl F.; Hall, Grant; Hofmeyr, Michele; Lowy, Daniel A.; Patrut, Roxana T.

2015-01-01

The article reports the radiocarbon investigation results of the Lebombo Eco Trail tree, a representative African baobab from Mozambique. Several wood samples collected from the large inner cavity and from the outer part of the tree were investigated by AMS radiocarbon dating. According to dating results, the age values of all samples increase from the sampling point with the distance into the wood. For samples collected from the cavity walls, the increase of age values with the distance into the wood (up to a point of maximum age) represents a major anomaly. The only realistic explanation for this anomaly is that such inner cavities are, in fact, natural empty spaces between several fused stems disposed in a ring-shaped structure. We named them false cavities. Several important differences between normal cavities and false cavities are presented. Eventually, we dated other African baobabs with false inner cavities. We found that this new architecture enables baobabs to reach large sizes and old ages. The radiocarbon date of the oldest sample was 1425 ± 24 BP, which corresponds to a calibrated age of 1355 ± 15 yr. The dating results also show that the Lebombo baobab consists of five fused stems, with ages between 900 and 1400 years; these five stems build the complete ring. The ring and the false cavity closed 800–900 years ago. The results also indicate that the stems stopped growing toward the false cavity over the past 500 years. PMID:25621989

Geochemical Data for Samples Collected in 2007 Near the Concealed Pebble Porphyry Cu-Au-Mo Deposit, Southwest Alaska

USGS Publications Warehouse

Fey, David L.; Granitto, Matthew; Giles, Stuart A.; Smith, Steven M.; Eppinger, Robert G.; Kelley, Karen D.

2008-01-01

In the summer of 2007, the U.S. Geological Survey (USGS) began an exploration geochemical research study over the Pebble porphyry copper-gold-molydenum (Cu-Au-Mo) deposit in southwest Alaska. The Pebble deposit is extremely large and is almost entirely concealed by tundra, glacial deposits, and post-Cretaceous volcanic and volcaniclastic rocks. The deposit is presently being explored by Northern Dynasty Minerals, Ltd., and Anglo-American LLC. The USGS undertakes unbiased, broad-scale mineral resource assessments of government lands to provide Congress and citizens with information on national mineral endowment. Research on known deposits is also done to refine and better constrain methods and deposit models for the mineral resource assessments. The Pebble deposit was chosen for this study because it is concealed by surficial cover rocks, it is relatively undisturbed (except for exploration company drill holes), it is a large mineral system, and it is fairly well constrained at depth by the drill hole geology and geochemistry. The goals of the USGS study are (1) to determine whether the concealed deposit can be detected with surface samples, (2) to better understand the processes of metal migration from the deposit to the surface, and (3) to test and develop methods for assessing mineral resources in similar concealed terrains. This report presents analytical results for geochemical samples collected in 2007 from the Pebble deposit and surrounding environs. The analytical data are presented digitally both as an integrated Microsoft 2003 Access? database and as Microsoft 2003 Excel? files. The Pebble deposit is located in southwestern Alaska on state lands about 30 km (18 mi) northwest of the village of Illiamna and 320 km (200 mi) southwest of Anchorage (fig. 1). Elevations in the Pebble area range from 287 m (940 ft) at Frying Pan Lake just south of the deposit to 1146 m (3760 ft) on Kaskanak Mountain about 5 km (5 mi) to the west. The deposit is in an area of relatively subdued topographic relief with an elevation of around 300 m (1000 ft). This portion of Alaska is part of the subarctic regime mountains division, Yukon intermontane plateaus-tayga-meadow province ecoregion, as defined by Bailey (U.S. Forest Service, 2007). Between June 28th and July 12th, 2007, scientists from the USGS collected soil, water, stream sediment, vegetation, heavy-mineral concentrate, till, and rock samples from the deposit area. This report contains analytical results for soil, water, stream sediment, and vegetation samples. Analyses for the heavy-mineral concentrate, till, and rock samples are still in progress. The sampling was undertaken during relatively dry and stable weather conditions. Only minor scattered rain showers occurred during the sampling period, so surface conditions were largely unaffected by weather. The predominant sample media collected were soils and surface waters. Soil and water (mostly from ponds and springs, some from small creeks) samples were collected along a single 7.8 km-long (4.8 mi) east-west traverse across the Pebble East and Pebble West zones and from more distal background areas around Koktuli and Kaskanak Mountains. Sample sites are shown on figure 2 and plate 1, and locality coordinates are provided in the accompanying Access and Excel files named FieldSite. Water samples were analyzed by USGS laboratories with one subset analyzed by Activation Laboratories (Actlabs), as indicated below. Soils and stream sediments were analyzed for their total content by SGS Minerals Services under a contract with the USGS. Soil samples were also leached by selected partial-extraction leaching procedures and then analyzed by several commercial laboratories, as described below. Vegetation samples were analyzed as indicated below.

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.

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.

Sporadic sampling, not climatic forcing, drives observed early hominin diversity.

PubMed

Maxwell, Simon J; Hopley, Philip J; Upchurch, Paul; Soligo, Christophe

2018-05-08

The role of climate change in the origin and diversification of early hominins is hotly debated. Most accounts of early hominin evolution link observed fluctuations in species diversity to directional shifts in climate or periods of intense climatic instability. None of these hypotheses, however, have tested whether observed diversity patterns are distorted by variation in the quality of the hominin fossil record. Here, we present a detailed examination of early hominin diversity dynamics, including both taxic and phylogenetically corrected diversity estimates. Unlike past studies, we compare these estimates to sampling metrics for rock availability (hominin-, primate-, and mammal-bearing formations) and collection effort, to assess the geological and anthropogenic controls on the sampling of the early hominin fossil record. Taxic diversity, primate-bearing formations, and collection effort show strong positive correlations, demonstrating that observed patterns of early hominin taxic diversity can be explained by temporal heterogeneity in fossil sampling rather than genuine evolutionary processes. Peak taxic diversity at 1.9 million years ago (Ma) is a sampling artifact, reflecting merely maximal rock availability and collection effort. In contrast, phylogenetic diversity estimates imply peak diversity at 2.4 Ma and show little relation to sampling metrics. We find that apparent relationships between early hominin diversity and indicators of climatic instability are, in fact, driven largely by variation in suitable rock exposure and collection effort. Our results suggest that significant improvements in the quality of the fossil record are required before the role of climate in hominin evolution can be reliably determined. Copyright © 2018 the Author(s). Published by PNAS.

Mercury contamination in bank swallows and double-crested cormorants from the Carson River, Nevada

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

Kim, R.; Brewer, R.; Peterson, S.C.

1995-12-31

An ecological risk assessment was performed in conjunction with a remedial investigation at the Carson River Mercury Site (CRMS) in northwestern Nevada. Large quantities of mercury used in the processing of gold and silver during mining operations in the mid to late 1800s are distributed throughout the Carson River ecosystem. Previous investigations indicated elevated levels of mercury in soil, sediment, water, and the aquatic food chain. Bird exposure to mercury was determined by measuring total mercury and monomethyl mercury in blood and feather samples from 15 unfledged double-crested cormorants (Phalacrocorax auritus), and in blood, feather, and liver samples from 18more » juvenile bank swallows (Riparia riparia) at both the CRMS and uncontaminated background locations. Monomethyl mercury accounted for 90 to 98% of the total mercury in the samples. Total mercury concentrations in bird tissues collected at the CRMS were significantly higher than at background locations. Average total mercury concentrations (wet weight) for the swallow blood, liver, and feather samples collected at the CRMS were 2.63, 3.96, and 2.01 mg/kg, respectively; compared with 0.74, 1,03, and 1.84 mg/kg, respectively at the background area. Average total mercury concentrations for cormorant samples collected at the CRMS were 17.07 mg/kg for blood, and 105.1 1 mg/kg for feathers. Cormorant samples collected at the background location had average total mercury concentrations of 0.49 mg/kg for blood and 8.99 mg/kg for feathers. Results are compared with published residue-effects levels to evaluate avian risks.« less

Deep-Sea Hydrothermal-Vent Sampler

NASA Technical Reports Server (NTRS)

Behar, Alberto E.; Venkateswaran, Kasthur; Matthews, Jaret B.

2008-01-01

An apparatus is being developed for sampling water for signs of microbial life in an ocean hydrothermal vent at a depth of as much as 6.5 km. Heretofore, evidence of microbial life in deep-sea hydrothermal vents has been elusive and difficult to validate. Because of the extreme conditions in these environments (high pressures and temperatures often in excess of 300 C), deep-sea hydrothermal- vent samplers must be robust. Because of the presumed low density of biomass of these environments, samplers must be capable of collecting water samples of significant volume. It is also essential to prevent contamination of samples by microbes entrained from surrounding waters. Prior to the development of the present apparatus, no sampling device was capable of satisfying these requirements. The apparatus (see figure) includes an intake equipped with a temperature probe, plus several other temperature probes located away from the intake. The readings from the temperature probes are utilized in conjunction with readings from flowmeters to determine the position of the intake relative to the hydrothermal plume and, thereby, to position the intake to sample directly from the plume. Because it is necessary to collect large samples of water in order to obtain sufficient microbial biomass but it is not practical to retain all the water from the samples, four filter arrays are used to concentrate the microbial biomass (which is assumed to consist of particles larger than 0.2 m) into smaller volumes. The apparatus can collect multiple samples per dive and is designed to process a total volume of 10 L of vent fluid, of which most passes through the filters, leaving a total possibly-microbe-containing sample volume of 200 mL remaining in filters. A rigid titanium nose at the intake is used for cooling the sample water before it enters a flexible inlet hose connected to a pump. As the water passes through the titanium nose, it must be cooled to a temperature that is above a mineral-precipitation temperature of 100 C but below the upper working temperature (230 C) of switching valves and tubes in the apparatus. The sample water then passes into a manifold tube, from whence the switching valves can direct the water through either a bypass tube or any one of the filter arrays, without contamination from a previous sample. Each filter array consists of series of filters having pore sizes decreasing in the direction of flow: 90-, 60-, 15-, and 7-micron prefilters and a large-surface-area 0.2-micron collection filter. All the filter taps are located between the intake and the bypass tube so that each time the bypass tube is used, the entire manifold tube is flushed as well.

Water-quality, streamflow, and ancillary data for nutrients in streams and rivers across the nation, 1992-2001

USGS Publications Warehouse

Mueller, David K.; Spahr, Norman E.

2005-01-01

Introduction: This report is the companion data report for: Nutrients in Streams and Rivers Across the Nation - 1992-2001 (D.K. Mueller and N.E. Spahr, U.S. Geological Survey written commun., 2005). The data contained in this report were collected as part of the National Water-Quality Assessment (NAWQA) Program. Investigations were conducted in 51 large river basins and aquifer systems, which are referred to as 'study units.' Implementation of study-unit investigations were phased so that high-intensity sampling occurred in about one-third of the study units at a time. Investigations in the first 20 study units began in 1991, and stream sampling began in 1992; however, most samples were collected during water years 1993-95. (Water year is defined as the period from October through September and is identified by the year in which it ends.) A second group of 16 study-unit investigations began in 1994, with most of the sampling completed during water years 1996-98. A third group, consisting of 15 study units, began in 1997 with most of the data collected during water years 1999-2001. At some sites, additional sampling continued after the high-intensity time period. Gilliom and others (1995) provide additional information about study-unit sampling design. Additional information about the NAWQA program is available at http://water.usgs.gov/nawqa/index.html.

A rapid method for the sampling of atmospheric water vapour for isotopic analysis.

PubMed

Peters, Leon I; Yakir, Dan

2010-01-01

Analysis of the stable isotopic composition of atmospheric moisture is widely applied in the environmental sciences. Traditional methods for obtaining isotopic compositional data from ambient moisture have required complicated sampling procedures, expensive and sophisticated distillation lines, hazardous consumables, and lengthy treatments prior to analysis. Newer laser-based techniques are expensive and usually not suitable for large-scale field campaigns, especially in cases where access to mains power is not feasible or high spatial coverage is required. Here we outline the construction and usage of a novel vapour-sampling system based on a battery-operated Stirling cycle cooler, which is simple to operate, does not require any consumables, or post-collection distillation, and is light-weight and highly portable. We demonstrate the ability of this system to reproduce delta(18)O isotopic compositions of ambient water vapour, with samples taken simultaneously by a traditional cryogenic collection technique. Samples were collected over 1 h directly into autosampler vials and were analysed by mass spectrometry after pyrolysis of 1 microL aliquots to CO. This yielded an average error of < +/-0.5 per thousand, approximately equal to the signal-to-noise ratio of traditional approaches. This new system provides a rapid and reliable alternative to conventional cryogenic techniques, particularly in cases requiring high sample throughput or where access to distillation lines, slurry maintenance or mains power is not feasible. Copyright 2009 John Wiley & Sons, Ltd.

Return of a giant: DNA from archival museum samples helps to identify a unique cutthroat trout lineage formerly thought to be extinct.

PubMed

Peacock, Mary M; Hekkala, Evon R; Kirchoff, Veronica S; Heki, Lisa G

2017-11-01

Currently one small, native population of the culturally and ecologically important Lahontan cutthroat trout ( Oncorhynchus clarkii henshawi , LCT, Federally listed) remains in the Truckee River watershed of northwestern Nevada and northeastern California. The majority of populations in this watershed were extirpated in the 1940s due to invasive species, overharvest, anthropogenic water consumption and changing precipitation regimes. In 1977, a population of cutthroat trout discovered in the Pilot Peak Mountains in the Bonneville basin of Utah, was putatively identified as the extirpated LCT lacustrine lineage native to Pyramid Lake in the Truckee River basin based on morphological and meristic characters. Our phylogenetic and Bayesian genotype clustering analyses of museum specimens collected from the large lakes (1872-1913) and contemporary samples collected from populations throughout the extant range provide evidence in support of a genetically distinct Truckee River basin origin for this population. Analysis of museum samples alone identified three distinct genotype clusters and historical connectivity among water bodies within the Truckee River basin. Baseline data from museum collections indicate that the extant Pilot Peak strain represents a remnant of the extirpated lacustrine lineage. Given the limitations on high-quality data when working with a sparse number of preserved museum samples, we acknowledge that, in the end, this may be a more complicated story. However, the paucity of remnant populations in the Truckee River watershed, in combination with data on the distribution of morphological, meristic and genetic data for Lahontan cutthroat trout, suggests that recovery strategies, particularly in the large lacustrine habitats should consider this lineage as an important part of the genetic legacy of this species.

Providing Undergraduate Research Opportunities Through the World Rivers Observatory Collaborative Network

NASA Astrophysics Data System (ADS)

Gillies, S. L.; Marsh, S. J.; Janmaat, A.; Peucker-Ehrenbrink, B.; Voss, B.; Holmes, R. M.

2013-12-01

Successful research collaboration exists between the University of the Fraser Valley (UFV), a primarily undergraduate-serving university located on the Fraser River in British Columbia, and the World Rivers Observatory that is coordinated through the Woods Hole Oceanographic Institution (WHOI) and the Woods Hole Research Center (WHRC). The World Rivers Observatory coordinates time-series sampling of 15 large rivers, with particular focus on the large Arctic rivers, the Ganges-Brahmaputra, Congo, Fraser, Yangtze (Changjiang), Amazon, and Mackenzie River systems. The success of this international observatory critically depends on the participation of local collaborators, such as UFV, that are necessary in order to collect temporally resolved data from these rivers. Several faculty members and undergraduate students from the Biology and Geography Departments of UFV received on-site training from the lead-PIs of the Global Rivers Observatory. To share information and ensure good quality control of sampling methods, WHOI and WHRC hosted two international workshops at Woods Hole for collaborators. For the past four years, faculty and students from UFV have been collecting a variety of bi-monthly water samples from the Fraser River for the World Rivers Observatory. UFV undergraduate students who become involved learn proper sampling techniques and are given the opportunity to design and conduct their own research. Students have collected, analyzed and presented data from this project at regional, national, and international scientific meetings. UFV undergraduate students have also been hosted by WHOI and WHRC as guest students to work on independent research projects. While at WHOI and WHRC, students are able to conduct research using state-of-the-art specialized research facilities not available at UFV.

Long term atmospheric aerosol characterization in the Amazon Basin

NASA Astrophysics Data System (ADS)

Artaxo, Paulo; Gerab, Fábio; Yamasoe, Marcia A.

This chapter presents a characterization of atmospheric aerosols collected in different places in the Amazon Basin. Both the biogenic aerosol emission from the forest and the particulate material which is emitted to the atmosphere due to the large scale man-made burns during the dry season were studied. The samples were collected during a three year period at three different locations in the Amazon (Cuiabá, Alta Floresta and Serra do Navio), using stacked filter units. Aerosol samples were also collected directly over fires of cerrado vegetation and tropical primary forest burns The samples were analyzed using several techniques for a number of elements. Gravimetric analyses were used to determine the total atmospheric aerosol concentration. Multivariate statistical analysis was used in order to identify and characterize the sources of the atmospheric aerosol present in the sampled regions. Cerrado burning emissions were enriched compared to forest ones, specially for Cl, K and Zn. High atmospheric aerosol concentrations were observed in large amazonian areas due to emissions from man-made burns in the period from June to September. The emissions from burns dominate the fine fraction of the atmospheric aerosol with characteristic high contents of black carbon, S and K. Aerosols emitted in biomass burning process are correlated to the increase in the aerosol optical thickness of the atmosphere during the Amazonian dry season. The Serra do Navio aerosol is characterized by biogenic emissions with strong marine influence. The presence of trace elements characteristic of soil particulate associated with this marine contribution indicates the existence of aerosol transport from Africa to South America. Similar composition characteristics were observed in the biogenic emission aerosols from Serra do Navio and Alta Floresta.

Return of a giant: DNA from archival museum samples helps to identify a unique cutthroat trout lineage formerly thought to be extinct

PubMed Central

Hekkala, Evon R.; Kirchoff, Veronica S.; Heki, Lisa G.

2017-01-01

Currently one small, native population of the culturally and ecologically important Lahontan cutthroat trout (Oncorhynchus clarkii henshawi, LCT, Federally listed) remains in the Truckee River watershed of northwestern Nevada and northeastern California. The majority of populations in this watershed were extirpated in the 1940s due to invasive species, overharvest, anthropogenic water consumption and changing precipitation regimes. In 1977, a population of cutthroat trout discovered in the Pilot Peak Mountains in the Bonneville basin of Utah, was putatively identified as the extirpated LCT lacustrine lineage native to Pyramid Lake in the Truckee River basin based on morphological and meristic characters. Our phylogenetic and Bayesian genotype clustering analyses of museum specimens collected from the large lakes (1872–1913) and contemporary samples collected from populations throughout the extant range provide evidence in support of a genetically distinct Truckee River basin origin for this population. Analysis of museum samples alone identified three distinct genotype clusters and historical connectivity among water bodies within the Truckee River basin. Baseline data from museum collections indicate that the extant Pilot Peak strain represents a remnant of the extirpated lacustrine lineage. Given the limitations on high-quality data when working with a sparse number of preserved museum samples, we acknowledge that, in the end, this may be a more complicated story. However, the paucity of remnant populations in the Truckee River watershed, in combination with data on the distribution of morphological, meristic and genetic data for Lahontan cutthroat trout, suggests that recovery strategies, particularly in the large lacustrine habitats should consider this lineage as an important part of the genetic legacy of this species. PMID:29291110

Efficiency of wipe sampling on hard surfaces for pesticides and PCB residues in dust.

PubMed

Cettier, Joane; Bayle, Marie-Laure; Béranger, Rémi; Billoir, Elise; Nuckols, John R; Combourieu, Bruno; Fervers, Béatrice

2015-02-01

Pesticides and polychlorinated biphenyls (PCBs) are commonly found in house dust and have been described as a valuable matrix to assess indoor pesticide and PCB contamination. The aim of this study was to assess the efficiency and precision of cellulose wipe for collecting 48 pesticides, eight PCBs, and one synergist at environmental concentrations. First, the efficiency and repeatability of wipe collection were determined for pesticide and PCB residues that were directly spiked onto three types of household floors (tile, laminate, and hardwood). Second, synthetic dust was used to assess the capacity of the wipe to collect dust. Third, we assessed the efficiency and repeatability of wipe collection of pesticides and PCB residues that was spiked onto synthetic dust and then applied to tile. In the first experiment, the overall collection efficiency was highest on tile (38%) and laminate (40%) compared to hardwood (34%), p<0.001. The second experiment confirmed that cellulose wipes can efficiently collect dust (82% collection efficiency). The third experiment showed that the overall collection efficiency was higher in the presence of dust (72% vs. 38% without dust, p<0.001). Furthermore, the mean repeatability also improved when compounds were spiked onto dust (<30% for the majority of compounds). To our knowledge, this is the first study to assess the efficiency of wipes as a sampling method using a large number of compounds at environmental concentrations and synthetic dust. Cellulose wipes appear to be efficient to sample the pesticides and PCBs that adsorb onto dust on smooth and hard surfaces. Copyright © 2014 Elsevier B.V. All rights reserved.

Validation of Rapid Radiochemical Method for Californium ...

EPA Pesticide Factsheets

Technical Brief In the event of a radiological/nuclear contamination event, the response community would need tools and methodologies to rapidly assess the nature and the extent of contamination. To characterize a radiologically contaminated outdoor area and to inform risk assessment, large numbers of environmental samples would be collected and analyzed over a short period of time. To address the challenge of quickly providing analytical results to the field, the U.S. EPA developed a robust analytical method. This method allows response officials to characterize contaminated areas and to assess the effectiveness of remediation efforts, both rapidly and accurately, in the intermediate and late phases of environmental cleanup. Improvement in sample processing and analysis leads to increased laboratory capacity to handle the analysis of a large number of samples following the intentional or unintentional release of a radiological/nuclear contaminant.

Quantification of Protozoa and Viruses from Small Water Volumes

PubMed Central

Bonilla, J. Alfredo; Bonilla, Tonya D.; Abdelzaher, Amir M.; Scott, Troy M.; Lukasik, Jerzy; Solo-Gabriele, Helena M.; Palmer, Carol J.

2015-01-01

Large sample volumes are traditionally required for the analysis of waterborne pathogens. The need for large volumes greatly limits the number of samples that can be processed. The goals of this study were to compare extraction and detection procedures for quantifying protozoan parasites and viruses from small volumes of marine water. The intent was to evaluate a logistically simpler method of sample collection and processing that would facilitate direct pathogen measures as part of routine monitoring programs. Samples were collected simultaneously using a bilayer device with protozoa capture by size (top filter) and viruses capture by charge (bottom filter). Protozoan detection technologies utilized for recovery of Cryptosporidium spp. and Giardia spp. were qPCR and the more traditional immunomagnetic separation—IFA-microscopy, while virus (poliovirus) detection was based upon qPCR versus plaque assay. Filters were eluted using reagents consistent with the downstream detection technologies. Results showed higher mean recoveries using traditional detection methods over qPCR for Cryptosporidium (91% vs. 45%) and poliovirus (67% vs. 55%) whereas for Giardia the qPCR-based methods were characterized by higher mean recoveries (41% vs. 28%). Overall mean recoveries are considered high for all detection technologies. Results suggest that simultaneous filtration may be suitable for isolating different classes of pathogens from small marine water volumes. More research is needed to evaluate the suitability of this method for detecting pathogens at low ambient concentration levels. PMID:26114244

Quantification of Protozoa and Viruses from Small Water Volumes.

PubMed

Bonilla, J Alfredo; Bonilla, Tonya D; Abdelzaher, Amir M; Scott, Troy M; Lukasik, Jerzy; Solo-Gabriele, Helena M; Palmer, Carol J

2015-06-24

Large sample volumes are traditionally required for the analysis of waterborne pathogens. The need for large volumes greatly limits the number of samples that can be processed. The aims of this study were to compare extraction and detection procedures for quantifying protozoan parasites and viruses from small volumes of marine water. The intent was to evaluate a logistically simpler method of sample collection and processing that would facilitate direct pathogen measures as part of routine monitoring programs. Samples were collected simultaneously using a bilayer device with protozoa capture by size (top filter) and viruses capture by charge (bottom filter). Protozoan detection technologies utilized for recovery of Cryptosporidium spp. and Giardia spp. were qPCR and the more traditional immunomagnetic separation-IFA-microscopy, while virus (poliovirus) detection was based upon qPCR versus plaque assay. Filters were eluted using reagents consistent with the downstream detection technologies. Results showed higher mean recoveries using traditional detection methods over qPCR for Cryptosporidium (91% vs. 45%) and poliovirus (67% vs. 55%) whereas for Giardia the qPCR-based methods were characterized by higher mean recoveries (41% vs. 28%). Overall mean recoveries are considered high for all detection technologies. Results suggest that simultaneous filtration may be suitable for isolating different classes of pathogens from small marine water volumes. More research is needed to evaluate the suitability of this method for detecting pathogens at low ambient concentration levels.

Distribution of Asellus aquaticus and microinvertebrates in a non-chlorinated drinking water supply system--effects of pipe material and sedimentation.

PubMed

Christensen, Sarah C B; Nissen, Erling; Arvin, Erik; Albrechtsen, Hans-Jørgen

2011-05-01

Danish drinking water supplies based on ground water without chlorination were investigated for the presence of the water louse, Asellus aquaticus, microinvertebrates (<2 mm) and annelida. In total, 52 water samples were collected from fire hydrants at 31 locations, and two elevated tanks (6000 and 36,000 m(3)) as well as one clean water tank at a waterworks (700 m(3)) were inspected. Several types of invertebrates from the phyla: arthropoda, annelida (worms), plathyhelminthes (flatworms) and mollusca (snails) were found. Invertebrates were found at 94% of the sampling sites in the piped system with A. aquaticus present at 55% of the sampling sites. Populations of A. aquaticus were present in the two investigated elevated tanks but not in the clean water tank at a waterworks. Both adult and juvenile A. aquaticus (length of 2-10 mm) were found in tanks as well as in pipes. A. aquaticus was found only in samples collected from two of seven investigated distribution zones (zone 1 and 2), each supplied directly by one of the two investigated elevated tanks containing A. aquaticus. Microinvertebrates were distributed throughout all zones. The distribution pattern of A. aquaticus had not changed considerably over 20 years when compared to data from samples collected in 1988-89. Centrifugal pumps have separated the distribution zones during the whole period and may have functioned as physical barriers in the distribution systems, preventing large invertebrates such as A. aquaticus to pass alive. Another factor characterising zone 1 and 2 was the presence of cast iron pipes. The frequency of A. aquaticus was significantly higher in cast iron pipes than in plastic pipes. A. aquaticus caught from plastic pipes were mainly single living specimens or dead specimens, which may have been transported passively trough by the water flow, while cast iron pipes provided an environment suitable for relatively large populations of A. aquaticus. Sediment volume for each sample was measured and our study described for the first time a clear connection between sediment volume and living A. aquaticus since living A. aquaticus were nearly only found in samples with sediment contents higher than 100 ml/m(3) sample. Presence of A. aquaticus was not correlated to turbidity of the water. Measurements by ATP, heterotrophic plate counting and Colilert(®) showed that the microbial quality of the water was high at all locations with or without animals. Four other large Danish drinking water supplies were additionally sampled (nine pipe samples and one elevated tank), and invertebrates were found in all systems, three of four containing A. aquaticus, indicating a nationwide occurrence. Copyright © 2011 Elsevier Ltd. All rights reserved.

Comparison of two sampling and culture systems for detection of Salmonella enterica in the environment of a large animal hospital.

PubMed

Ruple-Czerniak, A; Bolte, D S; Burgess, B A; Morley, P S

2014-07-01

Nosocomial salmonellosis is an important problem in veterinary hospitals that treat horses and other large animals. Detection and mitigation of outbreaks and prevention of healthcare-associated infections often require detection of Salmonella enterica in the hospital environment. To compare 2 previously published methods for detecting environmental contamination with S. enterica in a large animal veterinary teaching hospital. Hospital-based comparison of environmental sampling techniques. A total of 100 pairs of environmental samples were collected from stalls used to house large animal cases (horses, cows or New World camelids) that were confirmed to be shedding S. enterica by faecal culture. Stalls were cleaned and disinfected prior to sampling, and the same areas within each stall were sampled for the paired samples. One method of detection used sterile, premoistened sponges that were cultured using thioglycolate enrichment before plating on XLT-4 agar. The other method used electrostatic wipes that were cultured using buffered peptone water, tetrathionate and Rappaport-Vassiliadis R10 broths before plating on XLT-4 agar. Salmonella enterica was recovered from 14% of samples processed using the electrostatic wipe sampling and culture procedure, whereas S. enterica was recovered from only 4% of samples processed using the sponge sampling and culture procedure. There was test agreement for 85 pairs of culture-negative samples and 3 pairs of culture-positive samples. However, the remaining 12 pairs of samples with discordant results created significant disagreement between the 2 detection methods (P<0.01). Persistence of Salmonella in the environment of veterinary hospitals can occur even with rigorous cleaning and disinfection. Use of sensitive methods for detection of environmental contamination is critical when detecting and mitigating this problem in veterinary hospitals. These results suggest that the electrostatic wipe sampling and culture method was more sensitive than the sponge sampling and culture method. © 2013 EVJ Ltd.

Exploration of genetic and phenotypic diversity within Saccharomyces uvarum for driving strain improvement in winemaking.

PubMed

Verspohl, Alexandra; Solieri, Lisa; Giudici, Paolo

2017-03-01

The selection and genetic improvement of wine yeast is an ongoing process, since yeast strains should match new technologies in winemaking to satisfy evolving consumer preferences. A large genetic background is the necessary starting point for any genetic improvement programme. For this reason, we collected and characterized a large number of strains belonging to Saccharomyces uvarum. In particular, 70 strains were isolated from cold-stored must samples: they were identified and compared to S. uvarum strains originating from different collections, regarding fermentation profile, spore viability and stress response. The results demonstrate a large biodiversity among the new isolates, with particular emphasis to fermentation performances, genotypes and high spore viability, making the isolates suitable for further genetic improvement programmes. Furthermore, few of them are competitive with Saccharomyces cerevisiae and per se, suitable for wine fermentation, due to their resistance to stress, short lag phase and fermentation by-products.

Apparatus for measuring surface particulate contamination

DOEpatents

Woodmansee, Donald E.

2002-01-01

An apparatus for measuring surface particulate contamination includes a tool for collecting a contamination sample from a target surface, a mask having an opening of known area formed therein for defining the target surface, and a flexible connector connecting the tool to the mask. The tool includes a body portion having a large diameter section defining a surface and a small diameter section extending from the large diameter section. A particulate collector is removably mounted on the surface of the large diameter section for collecting the contaminants. The tool further includes a spindle extending from the small diameter section and a spool slidingly mounted on the spindle. A spring is disposed between the small diameter section and the spool for biasing the spool away from the small diameter section. An indicator is provided on the spindle so as to be revealed when the spool is pressed downward to compress the spring.

Free-living spirochetes from Cape Cod microbial mats detected by electron microscopy

NASA Technical Reports Server (NTRS)

Teal, T. H.; Chapman, M.; Guillemette, T.; Margulis, L.

1996-01-01

Spirochetes from microbial mats and anaerobic mud samples collected in salt marshes were studied by light microscopy, whole mount and thin section transmission electron microscopy. Enriched in cellobiose-rifampin medium, selective for Spirochaeta bajacaliforniensis, seven distinguishable spirochete morphotypes were observed. Their diameters ranged from 0.17 micron to > 0.45 micron. Six of these morphotypes came from southwest Cape Cod, Massachusetts: five from Microcoleus-dominated mat samples collected at Sippewissett salt marsh and one from anoxic mud collected at School Street salt marsh (on the east side of Eel Pond). The seventh morphotype was enriched from anoxic mud sampled from the north central Cape Cod, at the Sandy Neck salt marsh. Five of these morphotypes are similar or identical to previously described spirochetes (Leptospira, Spirochaeta halophila, Spirochaeta bajacaliforniensis, Spirosymplokos deltaeiberi and Treponema), whereas the other two have unique features that suggest they have not been previously described. One of the morphotypes resembles Spirosymplokos deltaeiberi (the largest free-living spirochete described), in its large variable diameter (0.4-3.0 microns), cytoplasmic granules, and spherical (round) bodies with composite structure. This resemblance permits its tentative identification as a Sippewissett strain of Spirosymplokos deltaeiberi. Microbial mats samples collected in sterile Petri dishes and stored dry for more than four years yielded many organisms upon rewetting, including small unidentified spirochetes in at least 4 out of 100 enrichments.

Study and interpretation of chemical composition of rainwater in selected urban and rural locations in India using multivariate analysis

NASA Astrophysics Data System (ADS)

Chakraborty, Bidisha; Gupta, Abhik

2018-04-01

Rainwater is an important untapped resource for all water managers and can be collected and used personally for all uses and simultaneously diverted to ground for recharge of depleting aquifers. Rain water is the most purest form of water until it is contaminated by the atmospheric pollution. Evaluation of rainwater quality analysis is also essential for non-potable applications and to match quality to specific uses. Rainwater quality analysis is, therefore, carried out to understand the problems of rainwater contamination with various pollutants. Rainwater samples were collected from the pre-monsoon season of March 2010 to post-monsoon of October 2013, from seven sampling sites namely Irongmara, Badarpur, Bongaigaon, Dolaigaon, BGR Township, Kolkata and Kharagpur, which characterised typical suburban, urban and industrialised locations respectively. A total of 943 samples were collected during this period from the sampling sites, taking utmost care in sampling and storage were analysed for heavy metals determination. Results for pH, EC, Pb, Cd, Ni, Zn, Cr and Co were reported in this study. The samples were collected using PVC bottles. The highest concentration of elements was observed at the beginning of the rainfall season when large amounts of dust accumulated in the atmosphere scavenged by rain. The values of pH in rainwater samples were relatively within the World Health Organization (WHO) standard for drinking water. Multivariate statistical analysis especially varimax rotation was applied to bring to focus the hidden yet important variables which influence the rainwater quality. It is also observed that rainwater contamination may not be restricted to industrial areas alone but vehicular emission may also contribute significantly in certain areas.

IDATEN and G-SITENNO: GUI-assisted software for coherent X-ray diffraction imaging experiments and data analyses at SACLA.

PubMed

Sekiguchi, Yuki; Yamamoto, Masaki; Oroguchi, Tomotaka; Takayama, Yuki; Suzuki, Shigeyuki; Nakasako, Masayoshi

2014-11-01

Using our custom-made diffraction apparatus KOTOBUKI-1 and two multiport CCD detectors, cryogenic coherent X-ray diffraction imaging experiments have been undertaken at the SPring-8 Angstrom Compact free electron LAser (SACLA) facility. To efficiently perform experiments and data processing, two software suites with user-friendly graphical user interfaces have been developed. The first is a program suite named IDATEN, which was developed to easily conduct four procedures during experiments: aligning KOTOBUKI-1, loading a flash-cooled sample into the cryogenic goniometer stage inside the vacuum chamber of KOTOBUKI-1, adjusting the sample position with respect to the X-ray beam using a pair of telescopes, and collecting diffraction data by raster scanning the sample with X-ray pulses. Named G-SITENNO, the other suite is an automated version of the original SITENNO suite, which was designed for processing diffraction data. These user-friendly software suites are now indispensable for collecting a large number of diffraction patterns and for processing the diffraction patterns immediately after collecting data within a limited beam time.

Testing of high-volume sampler inlets for the sampling of atmospheric radionuclides.

PubMed

Irshad, Hammad; Su, Wei-Chung; Cheng, Yung S; Medici, Fausto

2006-09-01

Sampling of air for radioactive particles is one of the most important techniques used to determine the nuclear debris from a nuclear weapon test in the Earth's atmosphere or those particles vented from underground or underwater tests. Massive-flow air samplers are used to sample air for any indication of radionuclides that are a signature of nuclear tests. The International Monitoring System of the Comprehensive Nuclear Test Ban Treaty Organization includes seismic, hydroacoustic, infrasound, and gaseous xenon isotopes sampling technologies, in addition to radionuclide sampling, to monitor for any violation of the treaty. Lovelace Respiratory Research Institute has developed a large wind tunnel to test the outdoor radionuclide samplers for the International Monitoring System. The inlets for these samplers are tested for their collection efficiencies for different particle sizes at various wind speeds. This paper describes the results from the testing of two radionuclide sampling units used in the International Monitoring System. The possible areas of depositional wall losses are identified and the losses in these areas are determined. Sampling inlet type 1 was tested at 2.2 m s wind speed for 5, 10, and 20-microm aerodynamic diameter particles. The global collection efficiency was about 87.6% for 10-microm particles for sampling inlet type 1. Sampling inlet type 2 was tested for three wind speeds at 0.56, 2.2, and 6.6 m s for 5, 10, and 20-microm aerodynamic diameter particles in two different configurations (sampling head lowered and raised). The global collection efficiencies for these configurations for 10-microm particles at 2.2 m s wind speed were 77.4% and 82.5%, respectively. The sampling flow rate was 600 m h for both sampling inlets.

Mercury accumulation in snow on the Idaho National Engineering and Environmental Laboratory and surrounding region, southeast Idaho, USA

USGS Publications Warehouse

Susong, D.D.; Abbott, M.L.; Krabbenhoft, D.P.

2003-01-01

Snow was sampled and analyzed for total mercury (THg) on the Idaho National Engineering and Environmental Laboratory (INEEL) and surrounding region prior to the start-up of a large (9-11 g/h) gaseous mercury emission source. The objective was to determine the effects of the source on local and regional atmospheric deposition of mercury. Snow samples collected from 48 points on a polar grid near the source had THg concentrations that ranged from 4.71 to 27.26 ng/L; snow collected from regional background sites had THg concentrations that ranged from 0.89 to 16.61 ng/L. Grid samples had higher concentrations than the regional background sites, which was unexpected because the source was not operating yet. Emission of Hg from soils is a possible source of Hg in snow on the INEEL. Evidence from Hg profiles in snow and from unfiltered/filtered split samples supports this hypothesis. Ongoing work on the INEEL is investigating Hg fluxes from soils and snow.

Temperature data from Norwegian and Russian waters of the northern Barents Sea collected by free-living ringed seals

NASA Astrophysics Data System (ADS)

Lydersen, Christian; Anders Nøst, Ole; Kovacs, Kit M.; Fedak, Mike A.

2004-05-01

Free-living ringed seals ( N=11) equipped with satellite-relayed data loggers (SRDLs) with incorporated oceanographic-quality temperature sensors were used to collect data from a large sector of the northern Barents Sea during the autumn and early winter. A total of 2346 temperature profiles were collected over a 4-month period from Norwegian and Russian arctic waters in areas that were at times 90-100% ice-covered. Temperature distributions at different depths from northeastern parts of Svalbard, Norway show warm North Atlantic water (NAW) flowing along the continental slope and gradually cooling at all depths as it flows eastwards. The data suggest that most of the cooling takes place west of 30°E. Vertical temperature profiles from the area between Svalbard and Franz Josef Land, Russia show how the surface water cools during freeze-up and demonstrate a warm water flow, which is probably NAW, coming in from the north through a deep trench west of Franz Josef Land. Global oceanographic and climate models require improved oceanographic databases from crucial areas where important hydrological phenomena occur. Such areas in arctic waters are often inaccessible during winter and logistically difficult to reach even in summer. The present study demonstrates how large amounts of oceanographic information can be collected and retrieved in a cost-efficient manner using ice-associated marine mammals as carrier of oceanographic sampling equipment. In addition to the oceanographic value of the data collected by marine mammals in this manner, a vast amount of information regarding the habitat of these animals is concomitantly sampled.

More than just records: analysing natural history collections for biodiversity planning.

PubMed

Ward, Darren F

2012-01-01

Natural History Collections (NHCs) play a central role as sources of data for biodiversity and conservation. Yet, few NHCs have examined whether the data they contain is adequately representative of local biodiversity. I examined over 15,000 databased records of Hymenoptera from 1435 locations across New Zealand collected over the past 90 years. These records are assessed in terms of their geographical, temporal, and environmental coverage across New Zealand. Results showed that the spatial coverage of records was significantly biased, with the top four areas contributing over 51% of all records. Temporal biases were also evident, with a large proportion (40%) of records collected within a short time period. The lack of repeat visits to specific locations indicated that the current set of NHC records would be of limited use for long-term ecological research. Consequently, analyses and interpretation of historical data, for example, shifts in community composition, would be limited. However, in general, NHC records provided good coverage of the diversity of New Zealand habitats and climatic environments, although fewer NHC records were represented at cooler temperatures (<5°C) and the highest rainfalls (>5000 mm/yr). Analyses of NHCs can be greatly enhanced by using simple techniques that examine collection records in terms of environmental and geographical space. NHCs that initiate a systematic sampling strategy will provide higher quality data for biodiversity research than ad hoc or point samples, as is currently the norm. Although NHCs provide a rich source of information they could be far better utilised in a range of large-scale ecological and conservation studies.

More Than Just Records: Analysing Natural History Collections for Biodiversity Planning

PubMed Central

Ward, Darren F.

2012-01-01

Natural History Collections (NHCs) play a central role as sources of data for biodiversity and conservation. Yet, few NHCs have examined whether the data they contain is adequately representative of local biodiversity. I examined over 15,000 databased records of Hymenoptera from 1435 locations across New Zealand collected over the past 90 years. These records are assessed in terms of their geographical, temporal, and environmental coverage across New Zealand. Results showed that the spatial coverage of records was significantly biased, with the top four areas contributing over 51% of all records. Temporal biases were also evident, with a large proportion (40%) of records collected within a short time period. The lack of repeat visits to specific locations indicated that the current set of NHC records would be of limited use for long-term ecological research. Consequently, analyses and interpretation of historical data, for example, shifts in community composition, would be limited. However, in general, NHC records provided good coverage of the diversity of New Zealand habitats and climatic environments, although fewer NHC records were represented at cooler temperatures (<5°C) and the highest rainfalls (>5000 mm/yr). Analyses of NHCs can be greatly enhanced by using simple techniques that examine collection records in terms of environmental and geographical space. NHCs that initiate a systematic sampling strategy will provide higher quality data for biodiversity research than ad hoc or point samples, as is currently the norm. Although NHCs provide a rich source of information they could be far better utilised in a range of large-scale ecological and conservation studies. PMID:23185605

Impacts of a large boreal wildfire on ground level atmospheric concentrations of PAHs, VOCs and ozone

NASA Astrophysics Data System (ADS)

Wentworth, Gregory R.; Aklilu, Yayne-abeba; Landis, Matthew S.; Hsu, Yu-Mei

2018-04-01

During May 2016 a very large boreal wildfire burned throughout the Athabasca Oil Sands Region (AOSR) in central Canada, and in close proximity to an extensive air quality monitoring network. This study examines speciated 24-h integrated polycyclic aromatic hydrocarbon (PAH) and volatile organic compound (VOC) measurements collected every sixth day at four and seven sites, respectively, from May to August 2016. The sum of PAHs (ΣPAH) was on average 17 times higher in fire-influenced samples (852 ng m-3, n = 8), relative to non-fire influenced samples (50 ng m-3, n = 64). Diagnostic PAH ratios in fire-influenced samples were indicative of a biomass burning source, whereas ratios in June to August samples showed additional influence from petrogenic and fossil fuel combustion. The average increase in the sum of VOCs (ΣVOC) was minor by comparison: 63 ppbv for fire-influenced samples (n = 16) versus 46 ppbv for non-fire samples (n = 90). The samples collected on August 16th and 22nd had large ΣVOC concentrations at all sites (average of 123 ppbv) that were unrelated to wildfire emissions, and composed primarily of acetaldehyde and methanol suggesting a photochemically aged air mass. Normalized excess enhancement ratios (ERs) were calculated for 20 VOCs and 23 PAHs for three fire influenced samples, and the former were generally consistent with previous observations. To our knowledge, this is the first study to report ER measurements for a number of VOCs and PAHs in fresh North American boreal wildfire plumes. During May the aged wildfire plume intercepted the cities of Edmonton (∼380 km south) or Lethbridge (∼790 km south) on four separate occasions. No enhancement in ground-level ozone (O3) was observed in these aged plumes despite an assumed increase in O3 precursors. In the AOSR, the only daily-averaged VOCs which approached or exceeded the hourly Alberta Ambient Air Quality Objectives (AAAQOs) were benzene (during the fire) and acetaldehyde (on August 16th and 22nd). Implications for local and regional air quality as well as suggestions for supplemental air monitoring during future boreal fires, are also discussed.

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.

Nurses' ethical conflicts in performance of utilization reviews.

PubMed

Bell, Sue Ellen

2003-09-01

This article describes the ethical conflicts that a sample of US nurse utilization reviewers faced in their work, and also each nurse's self-reported ethical orientation that was used to resolve the dilemmas. Data were collected from a sample of 97 registered nurses who were working at least 20 hours per week as utilization reviewers. Respondents were recruited from three managed care organizations that conduct utilization reviews in a large midwestern city. A cross-sectional survey design was used to collect demographic data and to ask closed-response, short-answer and open-ended questions. Ethical conflicts reported by nurses were similar across utilization review settings and many were justice orientated. Self-reported ethical orientations were similar across organizations, with beneficence dominating. Implications of these findings are discussed.

-A curated transcriptomic dataset collection relevant to embryonic development associated with in vitro fertilization in healthy individuals and patients with polycystic ovary syndrome.

PubMed

Mackeh, Rafah; Boughorbel, Sabri; Chaussabel, Damien; Kino, Tomoshige

2017-01-01

The collection of large-scale datasets available in public repositories is rapidly growing and providing opportunities to identify and fill gaps in different fields of biomedical research. However, users of these datasets should be able to selectively browse datasets related to their field of interest. Here we made available a collection of transcriptome datasets related to human follicular cells from normal individuals or patients with polycystic ovary syndrome, in the process of their development, during in vitro fertilization. After RNA-seq dataset exclusion and careful selection based on study description and sample information, 12 datasets, encompassing a total of 85 unique transcriptome profiles, were identified in NCBI Gene Expression Omnibus and uploaded to the Gene Expression Browser (GXB), a web application specifically designed for interactive query and visualization of integrated large-scale data. Once annotated in GXB, multiple sample grouping has been made in order to create rank lists to allow easy data interpretation and comparison. The GXB tool also allows the users to browse a single gene across multiple projects to evaluate its expression profiles in multiple biological systems/conditions in a web-based customized graphical views. The curated dataset is accessible at the following link: http://ivf.gxbsidra.org/dm3/landing.gsp.

­A curated transcriptomic dataset collection relevant to embryonic development associated with in vitro fertilization in healthy individuals and patients with polycystic ovary syndrome

PubMed Central

Mackeh, Rafah; Boughorbel, Sabri; Chaussabel, Damien; Kino, Tomoshige

2017-01-01

The collection of large-scale datasets available in public repositories is rapidly growing and providing opportunities to identify and fill gaps in different fields of biomedical research. However, users of these datasets should be able to selectively browse datasets related to their field of interest. Here we made available a collection of transcriptome datasets related to human follicular cells from normal individuals or patients with polycystic ovary syndrome, in the process of their development, during in vitro fertilization. After RNA-seq dataset exclusion and careful selection based on study description and sample information, 12 datasets, encompassing a total of 85 unique transcriptome profiles, were identified in NCBI Gene Expression Omnibus and uploaded to the Gene Expression Browser (GXB), a web application specifically designed for interactive query and visualization of integrated large-scale data. Once annotated in GXB, multiple sample grouping has been made in order to create rank lists to allow easy data interpretation and comparison. The GXB tool also allows the users to browse a single gene across multiple projects to evaluate its expression profiles in multiple biological systems/conditions in a web-based customized graphical views. The curated dataset is accessible at the following link: http://ivf.gxbsidra.org/dm3/landing.gsp. PMID:28413616

Analysis of Dust Samples Collected from an In-Service Interim Storage System at the Maine Yankee Nuclear Site.

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

Bryan, Charles R.; Enos, David

In July, 2016, the Electric Power Research Institute and industry partners performed a field test at the Maine Yankee Nuclear Site, located near Wiscasset, Maine. The primary goal of the field test was to evaluate the use of robots in surveying the surface of an in-service interim storage canister within an overpack; however, as part of the demonstration, dust and soluble salt samples were collected from horizontal surfaces within the interim storage system. The storage system is a vertical system made by NAC International, consisting of a steel-lined concrete overpack containing a 304 stainless steel (SS) welded storage canister. Themore » canister did not contain spent fuel but rather greater-than-class-C waste, which did not generate significant heat, limiting airflow through the storage system. The surfaces that were sampled for deposits included the top of the shield plug, the side of the canister, and a shelf at the bottom of the overpack, just below the level of the pillar on which the canister sits. The samples were sent to Sandia National Laboratories for analysis. This report summarizes the results of those analyses. Because the primary goal of the field test was to evaluate the use of robots in surveying the surface of the canister within the overpack, collection of dust samples was carried out in a qualitative fashion, using paper filters and sponges as the sampling media. The sampling focused mostly on determining the composition of soluble salts present in the dust. It was anticipated that a wet substrate would more effectively extract soluble salts from the surface that was sampled, so both the sponges and the filter paper were wetted prior to being applied to the surface of the metal. Sampling was accomplished by simply pressing the damp substrate against the metal surface for two minutes, and then removing it. It is unlikely that the sampling method quantitatively collected dust or salts from the metal surface; however, both substrates did extract a significant amount of material. The paper filters collected both particles, trapped within the cellulose fibers of the filter, and salts, while the sponges collected only the soluble salts, with very few particles. Upon delivery to Sandia, both collection media were analyzed using the same methods. The soluble salts were leached from the substrates and analyzed via ion chromatography, and insoluble minerals were analyzed by scanning electron microscopy and energy dispersive X-ray spectroscopy. The insoluble minerals were found to consist largely of terrestrially-derived mineral fragments, dominantly quartz and biotite. Large (mm-sized) aggregates of calcium carbonate, calcium silicate, and calcium aluminum silicate were also present. The aggregates had one flat, smooth surface and one well crystallized surface, and were interpreted to be efflorescence on the inside of the overpack and in the vent, formed by seepage of cement pore fluids through joints in the steel liner of the overpack. Such efflorescence was commonly observed during the boroscope inspection of the storage system at the site. The material may have flaked off and fallen to the point where the dust was collected, or may have brushed off onto the sponges when the robot was retrieved through the inlet vent. Chemical analysis showed that the soluble salts on the shield plug were Ca- and Na-rich, with lesser K and minor Mg; the anionic component was dominated by SO 4 and Cl, with minor amounts of NO 3 . The cation composition of the soluble salts from the overpack shelf and the canister surface was similar to the filter samples, but the anions differed significantly, being dominantly NO 3 with lesser Cl and only trace SO 4 . The salts appear to represent a mixture of sea-salts (probably partially converted to nitrates and sulfates by particle-gas conversion reactions) and continental salt aerosols. Ammonium, a common component in continental aerosols, was not observed and may have been lost by degassing from the canister surface or after collection during sample storage and transportation. The demonstration at Maine Yankee has shown that the robot and sampling method used for the test can successfully be used to collect soluble salts from metal surfaces within an interim storage system overpack. The results were consistent from sample to sample, suggesting that a representative sample of the soluble salts was being collected. However, it is unlikely that the salt samples collected here represent quantitative sampling of the salts on the surfaces evaluated; for that reason, chloride densities per unit area are not presented here. It should also be noted that the relevance to storage systems at the site that contain SNF may be limited, because a heat- generating canister will result in greater airflow through the overpack, affecting dust deposition rates and possibly salt compositions.« less

A priori evaluation of two-stage cluster sampling for accuracy assessment of large-area land-cover maps

USGS Publications Warehouse

Wickham, J.D.; Stehman, S.V.; Smith, J.H.; Wade, T.G.; Yang, L.

2004-01-01

Two-stage cluster sampling reduces the cost of collecting accuracy assessment reference data by constraining sample elements to fall within a limited number of geographic domains (clusters). However, because classification error is typically positively spatially correlated, within-cluster correlation may reduce the precision of the accuracy estimates. The detailed population information to quantify a priori the effect of within-cluster correlation on precision is typically unavailable. Consequently, a convenient, practical approach to evaluate the likely performance of a two-stage cluster sample is needed. We describe such an a priori evaluation protocol focusing on the spatial distribution of the sample by land-cover class across different cluster sizes and costs of different sampling options, including options not imposing clustering. This protocol also assesses the two-stage design's adequacy for estimating the precision of accuracy estimates for rare land-cover classes. We illustrate the approach using two large-area, regional accuracy assessments from the National Land-Cover Data (NLCD), and describe how the a priorievaluation was used as a decision-making tool when implementing the NLCD design.

The UK Biobank sample handling and storage validation studies.

PubMed

Peakman, Tim C; Elliott, Paul

2008-04-01

and aims UK Biobank is a large prospective study in the United Kingdom to investigate the role of genetic factors, environmental exposures and lifestyle in the causes of major diseases of late and middle age. It involves the collection of blood and urine from 500 000 individuals aged between 40 and 69 years. How the samples are collected, processed and stored will have a major impact on the future scientific usefulness of the UK Biobank resource. A series of validation studies was recommended to test the robustness of the draft sample handling and storage protocol. Samples of blood and urine were collected from 40 healthy volunteers and either processed immediately according to the protocol or maintained at specified temperatures (4 degrees C for all tubes with the exception of vacutainers containing acid citrate dextrose that were maintained at 18 degrees C) for 12, 24 or 36 h prior to processing. A further sample was maintained for 24 h at 4 degrees C, processed and the aliquots frozen at -80 degrees C for 20 days and then thawed under controlled conditions. The stability of the samples was compared for the different times in a wide variety of assays. The samples maintained at 4 degrees C were stable for at least 24 h after collection for a wide range of assays. Small but significant changes were observed in metabonomic studies in samples maintained at 4 degrees C for 36 h. There was no degradation of the samples for a range of biochemical assays after short-term freezing and thawing under controlled conditions. Whole blood maintained at 18 degrees C for 24 h in vacutainers containing acid citrate dextrose is suitable for viral immortalization techniques. The validation studies reported in this supplement provide justification for the sample handling and storage procedures adopted in the UK Biobank project.

AUTOMATED DEAD-END ULTRAFILTRATION FOR ENHANCED SURVEILLANCE OF LEGIONELLA 2 PNEUMOPHILA AND LEGIONELLA SPP. IN COOLING TOWER WATERS

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

Brigmon, R.; Leskinen, S.; Kearns, E.

2011-10-10

Detection of Legionella pneumophila in cooling towers and domestic hot water systems involves concentration by centrifugation or membrane filtration prior to inoculation onto growth media or analysis using techniques such as PCR or immunoassays. The Portable Multi-use Automated Concentration System (PMACS) was designed for concentrating microorganisms from large volumes of water in the field and was assessed for enhancing surveillance of L. pneumophila at the Savannah River Site, SC. PMACS samples (100 L; n = 28) were collected from six towers between August 2010 and April 2011 with grab samples (500 ml; n = 56) being collected before and aftermore » each PMACS sample. All samples were analyzed for the presence of L. pneumophila by direct fluorescence immunoassay (DFA) using FITC-labeled monoclonal antibodies targeting serogroups 1, 2, 4 and 6. QPCR was utilized for detection of Legionella spp. in the same samples. Counts of L. pneumophila from DFA and of Legionella spp. from qPCR were normalized to cells/L tower water. Concentrations were similar between grab and PMACS samples collected throughout the study by DFA analysis (P = 0.4461; repeated measures ANOVA). The same trend was observed with qPCR. However, PMACS concentration proved advantageous over membrane filtration by providing larger volume, more representative samples of the cooling tower environment, which led to reduced variability among sampling events and increasing the probability of detection of low level targets. These data highlight the utility of the PMACS for enhanced surveillance of L. pneumophila by providing improved sampling of the cooling tower environment.« less

Determining the physical and chemical processes behind four caldera-forming eruptions in rapid succession in the San Juan caldera cluster, Colorado, USA

NASA Astrophysics Data System (ADS)

Curry, A. C.; Caricchi, L.; Lipman, P. W.

2017-12-01

A primary goal of volcanology is to understand the frequency and magnitude of large, explosive volcanic eruptions to mitigate their impact on society. Recent studies show that the average magma flux and the time between magma injections into a given magmatic-volcanic system fundamentally control the frequency and magnitude of volcanic eruptions, yet these parameters are unknown for many volcanic regions on Earth. We focus on major and trace element chemistry of individual phases and whole-rock samples, initial zircon ID-TIMS analyses, and zircon SIMS oxygen isotope analyses of four caldera-forming ignimbrites from the San Juan caldera cluster in the Southern Rocky Mountain volcanic field, Colorado, to determine the physical and chemical processes leading to large eruptions. We collected outflow samples along stratigraphy of the three caldera-forming ignimbrites of the San Luis caldera complex: the Rat Creek Tuff ( 150 km3), Cebolla Creek Tuff ( 250 km3), and Nelson Mountain Tuff (>500 km3); and we collected samples of both outflow and intracaldera facies of the Snowshoe Mountain Tuff (>500 km3), which formed the Creede caldera. Single-crystal sanidine 40Ar/39Ar ages show that these large eruptions occurred in rapid succession between 26.91 ± 0.02 Ma (Rat Creek Tuff) and 26.87 ± 0.02 Ma (Snowshoe Mountain Tuff), providing an opportunity to investigate the temporal evolution of magmatic systems feeding large, explosive volcanic eruptions. Major and trace element analyses show that the first and last eruption of the San Luis caldera complex (Rat Creek Tuff and Nelson Mountain Tuff) are rhyolitic to dacitic ignimbrites, whereas the Cebolla Creek Tuff and Snowshoe Mountain Tuff are crystal-rich, dacitic ignimbrites. Trace elements show enrichment in light rare-earth elements (LREEs) over heavy rare-earth elements (HREEs), and whereas the trace element patterns are similar for each caldera cycle, trace element values for each ignimbrite show variability in HREE concentrations. This variability indicates that these large eruptions sampled a magmatic system with some degree of internal heterogeneity. These results have implications for the chemical and physical processes, such as magmatic flux and injection periodicity, leading to the formation of large magmatic systems prior to large, explosive eruptions.

Intensity of Territorial Marking Predicts Wolf Reproduction: Implications for Wolf Monitoring

PubMed Central

García, Emilio J.

2014-01-01

Background The implementation of intensive and complex approaches to monitor large carnivores is resource demanding, restricted to endangered species, small populations, or small distribution ranges. Wolf monitoring over large spatial scales is difficult, but the management of such contentious species requires regular estimations of abundance to guide decision-makers. The integration of wolf marking behaviour with simple sign counts may offer a cost-effective alternative to monitor the status of wolf populations over large spatial scales. Methodology/Principal Findings We used a multi-sampling approach, based on the collection of visual and scent wolf marks (faeces and ground scratching) and the assessment of wolf reproduction using howling and observation points, to test whether the intensity of marking behaviour around the pup-rearing period (summer-autumn) could reflect wolf reproduction. Between 1994 and 2007 we collected 1,964 wolf marks in a total of 1,877 km surveyed and we searched for the pups' presence (1,497 howling and 307 observations points) in 42 sampling sites with a regular presence of wolves (120 sampling sites/year). The number of wolf marks was ca. 3 times higher in sites with a confirmed presence of pups (20.3 vs. 7.2 marks). We found a significant relationship between the number of wolf marks (mean and maximum relative abundance index) and the probability of wolf reproduction. Conclusions/Significance This research establishes a real-time relationship between the intensity of wolf marking behaviour and wolf reproduction. We suggest a conservative cutting point of 0.60 for the probability of wolf reproduction to monitor wolves on a regional scale combined with the use of the mean relative abundance index of wolf marks in a given area. We show how the integration of wolf behaviour with simple sampling procedures permit rapid, real-time, and cost-effective assessments of the breeding status of wolf packs with substantial implications to monitor wolves at large spatial scales. PMID:24663068

Nickel and vanadium in air particulates at Dhahran (Saudi Arabia) during and after the Kuwait oil fires

NASA Astrophysics Data System (ADS)

Sadiq, M.; Mian, A. A.

Air particulates, both the total suspended (TSP) and inhalable (PM 10, smaller than 10 microns in size), were collected during and after the Kuwait oil fires (from March 1991 to July 1992) using Hi-Vol samplers. These samples were wet-digested at 120°C in an aqua regia and perchloric acids mixture for 3 h. Air particulate samples collected in 1982 at the same location were prepared similarly. Concentrations of nickel and vanadium were determined in the aliquot samples using an inductively coupled argon plasma analyser (ICAP). The monthly mean concentrations of nickel and vanadium, on volume basis, increased rapidly from March to June and decreased sharply during July-August in 1991. The minimum mean concentrations of these elements were found in the particulate samples collected in December 1991 which gradually increased through May 1992. Like 1991, nickel and vanadium concentrations in the air particulates spiked in June and decreased again in July 1992. This distribution pattern of nickel and vanadium concentrations was similar to that of the predominant wind from the north (Kuwait). In general, concentrations of these elements were higher in the air particulates collected during April-July 1991 as compared with those collected in 1992 during the same period. The TSPs contained higher concentrations of nickel and vanadium than those found in the PM 10 samples. However, this trend was reversed when concentrations of nickel and vanadium, on were expressed on particulate weight basis. The monthly mean concentrations of nickel and vanadium, on weight basis, decreased gradually through 1991 and increased slightly from March to July 1992. Concentrations of these elements were significantly higher in the air particulate samples collected in 1991 than those samples collected during 1982 at the same location. The data of this study suggest a contribution of the Kuwait oil fires in elevating nickel and vanadium concentrations in the air particulates at Dhahran during April-July 1991. Concentrations of these elements were largely below their proposed limits in the ambient air (for nickel-50 μg m -3, air; for vanadium—1 μg m -3 air). It is, therefore, anticipated that concentrations of nickel and vanadium in the air particulate samples were not a health concern during Kuwait oil fires at Dhahran, Saudi Arabia.

Killer smog of London, 50 years on: particle properties and oxidative capacity.

PubMed

Whittaker, Andy; BéruBé, Kelly; Jones, Tim; Maynard, Robert; Richards, Roy

2004-12-01

Total suspended particulate (TSP) samples collected on glass fibre filters in London before (1955) and after (1958-1974) the Clean Air Act was examined for physicochemical characteristics and oxidative capacity. High-resolution microscopy identified most of the material as soot with smelter spheres, fly ash (FA), sodium chloride and calcium sulphate particles. Image analysis (IA) was used to show that most of the soot aggregates were less than 1 microm in size and contained chains of individual particles of 10-50 nm. Speed mapping of large agglomerates of the historic particles confirmed that the samples were enriched with soot probably derived from a sulphur-rich coal called nutty slack which was used extensively at this time. Inductively coupled plasma-mass spectrometry (ICP-MS) was used to examine elemental composition. Meaningful quantitation of certain elements (Mg, Al and Zn) proved impossible because they were in high quantities in the glass fibre filters. However, high quantities of Fe>Pb>Cu>Mn>V>As were detected which may explain in part the bioreactivity of the samples. Using a simple in vitro test of oxidative capacity (plasmid assay), one historic particulate sample (1958) showed three times the activity of a modern-day diesel exhaust particle (DEP) sample but ten times less activity than a modern-day urban ambient particle collection. Such studies are continuing to link particle physicochemical properties and bioreactivity with a wider range of the samples collected between 1955 and 74 and how such historic samples compare with present-day London ambient particles.

An Intelligent Tool for Activity Data Collection

PubMed Central

Jehad Sarkar, A. M.

2011-01-01

Activity recognition systems using simple and ubiquitous sensors require a large variety of real-world sensor data for not only evaluating their performance but also training the systems for better functioning. However, a tremendous amount of effort is required to setup an environment for collecting such data. For example, expertise and resources are needed to design and install the sensors, controllers, network components, and middleware just to perform basic data collections. It is therefore desirable to have a data collection method that is inexpensive, flexible, user-friendly, and capable of providing large and diverse activity datasets. In this paper, we propose an intelligent activity data collection tool which has the ability to provide such datasets inexpensively without physically deploying the testbeds. It can be used as an inexpensive and alternative technique to collect human activity data. The tool provides a set of web interfaces to create a web-based activity data collection environment. It also provides a web-based experience sampling tool to take the user’s activity input. The tool generates an activity log using its activity knowledge and the user-given inputs. The activity knowledge is mined from the web. We have performed two experiments to validate the tool’s performance in producing reliable datasets. PMID:22163832

Comparison of Two Methods for Estimating the Sampling-Related Uncertainty of Satellite Rainfall Averages Based on a Large Radar Data Set

NASA Technical Reports Server (NTRS)

Lau, William K. M. (Technical Monitor); Bell, Thomas L.; Steiner, Matthias; Zhang, Yu; Wood, Eric F.

2002-01-01

The uncertainty of rainfall estimated from averages of discrete samples collected by a satellite is assessed using a multi-year radar data set covering a large portion of the United States. The sampling-related uncertainty of rainfall estimates is evaluated for all combinations of 100 km, 200 km, and 500 km space domains, 1 day, 5 day, and 30 day rainfall accumulations, and regular sampling time intervals of 1 h, 3 h, 6 h, 8 h, and 12 h. These extensive analyses are combined to characterize the sampling uncertainty as a function of space and time domain, sampling frequency, and rainfall characteristics by means of a simple scaling law. Moreover, it is shown that both parametric and non-parametric statistical techniques of estimating the sampling uncertainty produce comparable results. Sampling uncertainty estimates, however, do depend on the choice of technique for obtaining them. They can also vary considerably from case to case, reflecting the great variability of natural rainfall, and should therefore be expressed in probabilistic terms. Rainfall calibration errors are shown to affect comparison of results obtained by studies based on data from different climate regions and/or observation platforms.

Detection of environmental DNA of Bigheaded Carps in samples collected from selected locations in the St. Croix River and in the Mississippi River

USGS Publications Warehouse

Amberg, Jon J.; McCalla, S. Grace; Miller, Loren; Sorensen, Peter; Gaikowski, Mark P.

2013-01-01

The use of molecular methods, such as the detection of environmental deoxyribonucleic acid (eDNA), have become an increasingly popular tool in surveillance programs that monitor for the presence of invasive species in aquatic systems. One early application of these methods in aquatic systems was surveillance for DNA of Asian carps (specifically bighead carp Hypophthalmichthys nobilis and silver carp H. molitrix) in water samples taken from the Chicago Area Waterway System. The ability to identify DNA of a species in an environmental sample presents a potentially powerful tool because these sensitive analyses can presumably detect the presence of DNA in water even when the species is not abundant or are difficult to catch or monitor with traditional gear. Prior to research presented in this report, an initial eDNA surveillance effort was completed in selected locations in the Upper Mississippi and St. Croix Rivers in 2011 after the capture of a bighead carp in the St. Croix River near Prescott, WI. Data presented in this report were developed to duplicate the 2011 monitoring results from the Upper Mississippi and St. Croix Rivers and to provide critical insight into the technique to inform future work in these locations. We specifically sought to understand the potential confounding effects of other pathways of eDNA movement (e.g., fish-eating birds, watercraft) on the variation in background DNA by collecting water samples from (1) sites within the St. Croix River and the upper Mississippi River where the DNA of silver carp was previously detected, (2) sites considered to be free of Asian carp, and (3) a site known to have a large population of Asian carp. We also sought to establish a baseline Asian carp eDNA signature to which future eDNA sampling efforts could be compared. All samples taken as part of this effort were processed using conventional polymerase chain reaction (PCR) according to procedures outlined in the U.S. Army Corps of Engineers Quality Assurance Project Plan with minor deviations designed to enhance the rigor of our data. Presence of DNA in PCR-positive samples was confirmed by Sanger sequencing (forward and reverse) and sequences were considered positive only if sequences (forward and reverse) of ≥150 base pairs had a match of ≥95% to those of published sequences for bighead carp or silver carp. The DNA of bighead carp and silver carp was not detected in environmental samples collected above and below St. Croix Falls Dam on the St. Croix River, above and below the Coon Rapids Dam and below Lock and Dam 1 on the Upper Mississippi River, and from two negative control lakes, Square Lake and Lake Riley. The DNA of silver carp was detected in environmental samples collected below Lock and Dam 19 at Keokuk, Iowa, a reach of the river with high silver carp abundance. The portion (68%) of environmental samples taken below Lock and Dam 19 that were determined to contain the DNA of silver carp was similar to that reported in the scientific literature for other abundant species. The DNA of bighead carp, however, was not detected in environmental samples collected below Lock and Dam 19, a reach of the river known to have bighead carp. Previous reported detections of the DNA of silver carp in samples collected in 2011 were not replicated in this study. Additional analyses are planned for the DNA extracted from the samples collected in 2012. Those analyses may provide additional information regarding the lack of amplification of bighead carp DNA and the lengths of the sequences of silver carp DNA present in samples taken below Lock and Dam 19. These additional analyses may help inform the use of eDNA monitoring in large, complex systems like the Mississippi River.

Coordinated Microanalyses of Seven Particles of Probable Interstellar Origin from the Stardust Mission

NASA Technical Reports Server (NTRS)

Westphal, Andrew J.; Stroud, Rhonda M.; Bechtel, Hans A.; Brenker, Frank E.; Butterworth, Anna L.; Flynn, George J.; Frank, David R.; Gainsforth, Zack; Hillier, Jon K.; Postberg, Frank;

West Nile Virus Activity in a Winter Roost of American Crows (Corvus brachyrhynchos): Is Bird-To-Bird Transmission Important in Persistence and Amplification?

PubMed

Hinton, M G; Reisen, W K; Wheeler, S S; Townsend, A K

2015-07-01

Since its emergence in North America, West Nile virus (WNV) has had a large impact on equines, humans, and wild bird communities, yet gaps remain in our understanding of how the virus persists at temperate latitudes when winter temperatures preclude virus replication and host-seeking activity by mosquito vectors. Bird-to-bird transmission at large communal American Crow roosts could provide one mechanism for WNV persistence. Herein, we describe seasonal patterns of crow and Culex mosquito abundance, WNV infection rates, and the prevalence of WNV-positive fecal samples at a winter crow roost to test the hypothesis that bird-to-bird transmission allows WNV to persist at winter crow roosts. Samples were collected from large winter crow roosts in the Sacramento Valley of California from January 2013 until August 2014, encompassing two overwintering roost periods. West Nile virus RNA was detected in local crow carcasses in both summer [13/18 (72% WNV positive)] and winter [18/44 (41% WNV positive)] 2013-2014. Winter infections were unlikely to have arisen by recent bites from infected mosquitoes because Culex host-seeking activity was very low in winter and all Culex mosquitoes collected during winter months tested negative for WNV. Opportunities existed for fecal-oral transfer at the overwintering roost: most carcasses that tested positive for WNV had detectable viral RNA in both kidney and cloacal swabs, suggesting that infected crows were shedding virus in their feces, and >50% of crows at the roost were stained with feces by mid-winter. Moreover, 2.3% of fecal samples collected in late summer, when mosquitoes were active, tested positive for WNV RNA. Nevertheless, none of the 1,119 feces collected from three roosts over two winters contained detectable WNV RNA. This study provided evidence of WNV infection in overwintering American crows without mosquito vector activity, but did not elucidate a mechanism of WNV transmission during winter. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Attempted semen collection using the massage technique in blue-fronted Amazon parrots (Amazona aestiva aestiva).

PubMed

Della Volpe, Angelique; Volker, Schmidt; Krautwald-Junghanns, Maria-Elisabeth

2011-03-01

The purpose of this study was to establish a technique for collecting semen from blue-fronted Amazon parrots (Amazona aestiva aestiva) and to evaluate the samples that were collected. The massage method is the most common technique used to collect semen in birds and has been proven successful in several psittacine species; however, collection attempts in larger parrots have been unsatisfactory. Six blue-fronted Amazon parrot males, 3 paired with hens and 3 unpaired, were used in this study. The semen collection technique was revised to allow collection from individual birds by a single person. Semen collection was attempted from the 6 parrots on 52-56 occasions, which totaled 330 single attempts. Nineteen ejaculates were collected, and each bird produced at least 1 ejaculate that contained spermatozoa. Large ranges of sample volume (1-15.4 microL), sperm quality (motility = 2%-60%; live:dead ratio = 2:198 to 185:15), sperm concentration (0.79-3.3 x 10(6) sperm/mL), and contamination rate (0%-100%) were observed. Measured parameters did not appear to be significantly impacted by birds being paired or kept singly. Because of the relatively short acclimation period, the birds appeared to be sexually inactive for the majority of the study. Further research using sexually active birds will be necessary to determine standard spermatological parameters and verify the success of the methodology used here.

Rapid Identification of a Cooling Tower-Associated Legionnaires' Disease Outbreak Supported by Polymerase Chain Reaction Testing of Environmental Samples, New York City, 2014-2015.

PubMed

Benowitz, Isaac; Fitzhenry, Robert; Boyd, Christopher; Dickinson, Michelle; Levy, Michael; Lin, Ying; Nazarian, Elizabeth; Ostrowsky, Belinda; Passaretti, Teresa; Rakeman, Jennifer; Saylors, Amy; Shamoonian, Elena; Smith, Terry-Ann; Balter, Sharon

2018-04-01

We investigated an outbreak of eight Legionnaires' disease cases among persons living in an urban residential community of 60,000 people. Possible environmental sources included two active cooling towers (air-conditioning units for large buildings) <1 km from patient residences, a market misting system, a community-wide water system used for heating and cooling, and potable water. To support a timely public health response, we used real-time polymerase chain reaction (PCR) to identify Legionella DNA in environmental samples within hours of specimen collection. We detected L. pneumophila serogroup 1 DNA only at a power plant cooling tower, supporting the decision to order remediation before culture results were available. An isolate from a power plant cooling tower sample was indistinguishable from a patient isolate by pulsed-field gel electrophoresis, suggesting the cooling tower was the outbreak source. PCR results were available <1 day after sample collection, and culture results were available as early as 5 days after plating. PCR is a valuable tool for identifying Legionella DNA in environmental samples in outbreak settings.

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.

New directions in childhood obesity research: how a comprehensive biorepository will allow better prediction of outcomes

PubMed Central

2010-01-01

Background Childhood obesity is associated with the early development of diseases such as type 2 diabetes and cardiovascular disease. Unfortunately, to date, traditional methods of research have failed to identify effective prevention and treatment strategies, and large numbers of children and adolescents continue to be at high risk of developing weight-related disease. Aim To establish a unique 'biorepository' of data and biological samples from overweight and obese children, in order to investigate the complex 'gene × environment' interactions that govern disease risk. Methods The 'Childhood Overweight BioRepository of Australia' collects baseline environmental, clinical and anthropometric data, alongside storage of blood samples for genetic, metabolic and hormonal profiles. Opportunities for longitudinal data collection have also been incorporated into the study design. National and international harmonisation of data and sample collection will achieve required statistical power. Results Ethical approval in the parent site has been obtained and early data indicate a high response rate among eligible participants (71%) with a high level of compliance for comprehensive data collection (range 56% to 97% for individual study components). Multi-site ethical approval is now underway. Conclusions In time, it is anticipated that this comprehensive approach to data collection will allow early identification of individuals most susceptible to disease, as well as facilitating refinement of prevention and treatment programs. PMID:20969745

BRC4Env, a network of Biological Resource Centres for research in environmental and agricultural sciences.

PubMed

Mougin, Christian; Artige, Emmanuelle; Marchand, Frédéric; Mondy, Samuel; Ratié, Céline; Sellier, Nadine; Castagnone-Sereno, Philippe; D'Acier, Armelle Cœur; Esmenjaud, Daniel; Faivre-Primot, Céline; Granjon, Laurent; Hamelet, Valérie; Lange, Frederic; Pagès, Sylvie; Rimet, Frédéric; Ris, Nicolas; Sallé, Guillaume

2018-04-19

The Biological Resource Centre for the Environment BRC4Env is a network of Biological Resource Centres (BRCs) and collections whose leading objectives are to improve the visibility of genetic and biological resources maintained by its BRCs and collections and to facilitate their use by a large research community, from agriculture research to life sciences and environmental sciences. Its added value relies on sharing skills, harmonizing practices, triggering projects in comparative biology, and ultimately proposing a single-entry portal to facilitate access to documented samples, taking into account the partnership policies of research institutions as well as the legal frame which varies with the biological nature of resources. BRC4Env currently includes three BRCs: the Centre for Soil Genetic Resources of the platform GenoSol, in partnership with the European Conservatory of Soil Samples; the Egg Parasitoids Collection (EP-Coll); and the collection of ichthyological samples, Colisa. BRC4Env is also associated to several biological collections: microbial consortia (entomopathogenic bacteria, freshwater microalgae…), terrestrial arthropods, nematodes (plant parasitic, entomopathogenic, animal parasitic...), and small mammals. The BRCs and collections of BRC4Env are involved in partnership with academic scientists, as well as private companies, in the fields of medicinal mining, biocontrol, sustainable agriculture, and additional sectors. Moreover, the staff of the BRCs is involved in many training courses for students from French licence degree to Ph.D, engineers, as well as ongoing training.

The Central Asiatic (Tibet, Xinjiang, Pamir) petrological collections of Sven Hedin (1865 1952) — Swedish explorer and adventurer

NASA Astrophysics Data System (ADS)

Weinberg, Roberto F.; Green, Owen R.

2002-02-01

During a 42 year period (1893-1935), the Swedish explorer Sven Hedin led and co-ordinated four expeditions to remote and inhospitable parts of Central Asia (Tibet, Xinjiang, Pamir). Along with collaborators he collected a diverse collection of just under 3100 petrological specimens. Petrographic examples of high pressure metamorphic blueschists, mantle peridotites and serpentinites, granitoids, K-rich alkaline lavas, mylonites, and a range of clastic and fossil rich carbonate sedimentary rocks are present. This collection is a major asset for scientists studying the history of continental collision between India and Asia, and the uplift of the Tibetan plateau. A spreadsheet listing all the samples collected during Hedin's first three expeditions into Tibet (commencing 1893, 1899, 1906) includes a brief description and location of each specimen, with additional information on the availability of thin sections. Samples are cross-referenced with the geographical position of Hedin's campsites indicated on maps published with his extensive reports. Most samples, and a number of thin sections, are available for loan from the Swedish Museum of Natural History, Stockholm. We also describe a smaller collection of specimens and thin sections from Hedin's fourth (1927-35, Sino-Swedish) expedition, currently housed at the Institute of Earth Sciences, Uppsala University. Hedin's career as an explorer, highlighting the geological significance of his work and the reasons that it has remained largely ignored by the majority of Himalayan and Central Asian researchers for so many years, is outlined.

Micro-technology for planetary exploration and education

NASA Technical Reports Server (NTRS)

Miller, David P.; Varsi, Giulio

1991-01-01

The use of combined miniaturization technology and distributed information systems in planetary exploration is discussed. Missions in which teams of microrovers collect samples from planetary surfaces are addressed, emphasizing the ability of rovers to provide coverage of large areas, reliability through redundancy, and participation of a large group of investigators. The latter could involve people from a variety of institutions, increasing the opportunity for wide education and the increased interest of society in general in space exploration. A three-phase program to develop the present approach is suggested.

Effects of Specimen Collection Methodologies and Storage Conditions on the Short-Term Stability of Oral Microbiome Taxonomy.

PubMed

Luo, Ting; Srinivasan, Usha; Ramadugu, Kirtana; Shedden, Kerby A; Neiswanger, Katherine; Trumble, Erika; Li, Jiean J; McNeil, Daniel W; Crout, Richard J; Weyant, Robert J; Marazita, Mary L; Foxman, Betsy

2016-09-15

Community profiling of the oral microbiome requires the recovery of quality sequences in order to accurately describe microbial community structure and composition. Our objective was to assess the effects of specimen collection method, storage medium, and storage conditions on the relative abundance of taxa in saliva and plaque identified using 16S rRNA genes. We also assessed short-term changes in taxon composition and relative abundance and compared the salivary and dental plaque communities in children and adults. Over a 2-week period, four successive saliva and dental plaque specimens were collected from four adults with no dental decay (108 samples), and two successive specimens were collected from six children with four or more erupted teeth (48 samples). There were minimal differences in community composition at the phylum and operational taxonomic unit levels between dental plaque collection using a scaler and collection using a CytoSoft brush. Plaque samples stored in OMNIgene medium showed higher within-sample Shannon diversity, were compositionally different, and were more similar to each other than plaque stored in liquid dental transport medium. Saliva samples stored in OMNIgene recovered similar communities for at least a week following storage at room temperature. However, the microbial communities recovered from plaque and saliva stored in OMNIgene were significantly different in composition from their counterparts stored in liquid dental transport medium. Dental plaque communities collected from the same tooth type over four successive visits from the same adult did not significantly differ in structure or composition. Large-scale epidemiologic studies require collection over time and space, often with multiple teams collecting, storing, and processing data. Therefore, it is essential to understand how sensitive study results are to modest changes in collection and storage protocols that may occur with variation in personnel, resources available at a study site, and shipping requirements. The research presented in this paper measures the effects of multiple storage parameters and collection methodologies on the measured ecology of the oral microbiome from healthy adults and children. These results will potentially enable investigators to conduct oral microbiome studies at maximal efficiency by guiding informed administrative decisions pertaining to the necessary field or clinical work. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Effects of Specimen Collection Methodologies and Storage Conditions on the Short-Term Stability of Oral Microbiome Taxonomy

PubMed Central

Luo, Ting; Srinivasan, Usha; Ramadugu, Kirtana; Shedden, Kerby A.; Neiswanger, Katherine; Trumble, Erika; Li, Jiean J.; McNeil, Daniel W.; Crout, Richard J.; Weyant, Robert J.; Marazita, Mary L.

2016-01-01

ABSTRACT Community profiling of the oral microbiome requires the recovery of quality sequences in order to accurately describe microbial community structure and composition. Our objective was to assess the effects of specimen collection method, storage medium, and storage conditions on the relative abundance of taxa in saliva and plaque identified using 16S rRNA genes. We also assessed short-term changes in taxon composition and relative abundance and compared the salivary and dental plaque communities in children and adults. Over a 2-week period, four successive saliva and dental plaque specimens were collected from four adults with no dental decay (108 samples), and two successive specimens were collected from six children with four or more erupted teeth (48 samples). There were minimal differences in community composition at the phylum and operational taxonomic unit levels between dental plaque collection using a scaler and collection using a CytoSoft brush. Plaque samples stored in OMNIgene medium showed higher within-sample Shannon diversity, were compositionally different, and were more similar to each other than plaque stored in liquid dental transport medium. Saliva samples stored in OMNIgene recovered similar communities for at least a week following storage at room temperature. However, the microbial communities recovered from plaque and saliva stored in OMNIgene were significantly different in composition from their counterparts stored in liquid dental transport medium. Dental plaque communities collected from the same tooth type over four successive visits from the same adult did not significantly differ in structure or composition. IMPORTANCE Large-scale epidemiologic studies require collection over time and space, often with multiple teams collecting, storing, and processing data. Therefore, it is essential to understand how sensitive study results are to modest changes in collection and storage protocols that may occur with variation in personnel, resources available at a study site, and shipping requirements. The research presented in this paper measures the effects of multiple storage parameters and collection methodologies on the measured ecology of the oral microbiome from healthy adults and children. These results will potentially enable investigators to conduct oral microbiome studies at maximal efficiency by guiding informed administrative decisions pertaining to the necessary field or clinical work. PMID:27371581

Perilla frutescens var. frutescens in northern Laos.

PubMed

Ito, Michiho; Honda, Gisho; Sydara, Kongmany

2008-04-01

Twenty-eight samples of mericarps of Perilla frutescens var. frutescens were collected through fieldwork performed in Phongsali and Xieng Khouang provinces in northern Laos. No perilla samples were collected from Savannakhet province in the south although more than 20 sites were investigated. Perilla plants are mostly grown mixed with dry-paddy rice by slash-and-burn cultivation in Laos. The most popular local name for perilla mericarps in the area was "Ma Nga Chan". Weight of 1,000 grains and hardness of the mericarps were measured, and all mericarps were found to be large (weight of 1,000 grains around 2 g) and soft (limit load weight under 300 g), which were preferred for culinary use in Laos. The composition of the essential oils obtained from the herbaceous plants raised from the mericarps was divided into five types, perillaketone, elemicine plus myristicine, shisofuran, piperitenon, and myristicine, and GC-MS analysis of these Laotian perilla samples showed that they were similar to those of corresponding types of known Japanese perilla strains. One of the shisofuran-type perilla contained large amounts of putative alpha-naginatene, which is likely to be an intermediate of the biosynthesis of naginataketone. The farmers' indifference to the oil type of the leaf seems to leave Laotian perilla as a good genetic resource for studies of the biosynthesis of oil compounds.

AMS Radiocarbon Dating of Large Za Baobabs (Adansonia za) of Madagascar

PubMed Central

Patrut, Adrian; Patrut, Roxana T.; Danthu, Pascal; Leong Pock-Tsy, Jean-Michel; Rakosy, Laszlo; Lowy, Daniel A.; von Reden, Karl F.

2016-01-01

The article reports the radiocarbon investigation of Anzapalivoro, the largest za baobab (Adansonia za) specimen of Madagascar and of another za, namely the Big cistern baobab. Several wood samples collected from the large inner cavity and from the outer part/exterior of the tree were investigated by AMS (accelerator mass spectrometry) radiocarbon dating. For samples collected from the cavity walls, the age values increase with the distance into the wood up to a point of maximum age, after which the values decrease toward the outer part. This anomaly of age sequences indicates that the inner cavity of Anzapalivoro is a false cavity, practically an empty space between several fused stems disposed in a ring-shaped structure. The radiocarbon date of the oldest sample was 780 ± 30 bp, which corresponds to a calibrated age of around 735 yr. Dating results indicate that Anzapalivoro has a closed ring-shaped structure, which consists of 5 fused stems that close a false cavity. The oldest part of the biggest za baobab has a calculated age of 900 years. We also disclose results of the investigation of a second za baobab, the Big cistern baobab, which was hollowed out for water storage. This specimen, which consists of 4 fused stems, was found to be around 260 years old. PMID:26760300

AMS Radiocarbon Dating of Large Za Baobabs (Adansonia za) of Madagascar.

PubMed

Patrut, Adrian; Patrut, Roxana T; Danthu, Pascal; Leong Pock-Tsy, Jean-Michel; Rakosy, Laszlo; Lowy, Daniel A; von Reden, Karl F

2016-01-01

The article reports the radiocarbon investigation of Anzapalivoro, the largest za baobab (Adansonia za) specimen of Madagascar and of another za, namely the Big cistern baobab. Several wood samples collected from the large inner cavity and from the outer part/exterior of the tree were investigated by AMS (accelerator mass spectrometry) radiocarbon dating. For samples collected from the cavity walls, the age values increase with the distance into the wood up to a point of maximum age, after which the values decrease toward the outer part. This anomaly of age sequences indicates that the inner cavity of Anzapalivoro is a false cavity, practically an empty space between several fused stems disposed in a ring-shaped structure. The radiocarbon date of the oldest sample was 780 ± 30 bp, which corresponds to a calibrated age of around 735 yr. Dating results indicate that Anzapalivoro has a closed ring-shaped structure, which consists of 5 fused stems that close a false cavity. The oldest part of the biggest za baobab has a calculated age of 900 years. We also disclose results of the investigation of a second za baobab, the Big cistern baobab, which was hollowed out for water storage. This specimen, which consists of 4 fused stems, was found to be around 260 years old.

Deep-sea sampling on CMarZ cruises in the Atlantic Ocean - an Introduction

NASA Astrophysics Data System (ADS)

Wiebe, Peter H.; Bucklin, Ann; Madin, Laurence; Angel, Martin V.; Sutton, Tracey; Pagés, Francesc; Hopcroft, Russell R.; Lindsay, Dhugal

2010-12-01

The deep-sea zooplankton assemblage is hypothesized to have high species diversity, with low abundances of each species. However, even rare species may have huge population sizes and play a critical role in the dynamics of deep-sea environments. The Census of Marine Zooplankton (CMarZ) study sought to accurately assess zooplankton diversity in the mesopelagic and bathypelagic zones of the subtropical/tropical of the northwest and eastern sections of the Atlantic Ocean using integrated morphological and molecular analysis of large-volume samples to depths of 5,000 m. The field surveys in April 2006 and November 2007 included scientists and students associated with the CMarZ. The cruise field work entailed at-sea analysis of samples and identification of specimens by expert taxonomists, with at-sea DNA sequencing to determine a barcode (i.e., a short DNA sequence for species recognition) for selected species. Environmental data and zooplankton samples were collected with 1-m 2 and 10-m 2 opening/closing MOCNESS (0-1000 m and 1000-5000 m, respectively), and with either a 0.25-m 2 MOCNESS or a 0.5-m 2 Multi-net above 1000 m. More than 500 species were identified and more than 1000 specimens placed in a queue for barcoding on each cruise; several hundred species were barcoded at sea. For several taxonomic groups, a significant fraction of the region's known species were collected and identified. For example, in the northwest Atlantic 93 of 140 known ostracod species for the Atlantic Ocean were collected, 6 undescribed species were found, and the first DNA barcode for a planktonic ostracod was obtained. The deployment of trawls with fine-mesh nets to sample large volumes at great depths for small zooplankton confirmed that there is considerable species diversity at depth, with more species yet to be discovered.

Benthic macroinvertebrate assemblages and their relations with environmental variables in the Sacramento and San Joaquin River drainages, California, 1993-1997

USGS Publications Warehouse

Brown, Larry R.; May, Jason T.

2000-01-01

Data were collected in the San Joaquin and Sacramento river drainages to evaluate associations between macroinvertebrate assemblages and environmental variables as part of the National Water-Quality Assessment Program of the U.S. Geological Survey. Samples were collected at 53 sites from 1993 to 1995 in the San Joaquin River drainage and in 1996 and 1997 in the Sacramento River drainage. Macroinvertebrates were collected from riffles or from large woody debris (snags) when riffles were absent. Macroinvertebrate taxa were aggregated to the family (or higher) level of taxonomic organization, resulting in 81 taxa for analyses. Only the 50 most common taxa were used for two-way indicator species analysis (TWINSPAN) and canonical correspondence analysis. TWINSPAN analysis defined four groups of riffle samples and four groups of snag samples based on macroinvertebrate assemblages. Analysis of variance identified differences in environmental and biotic characteristics of the groups. These results combined with the results of canonical correspondence analysis indicated that patterns in riffle sample assemblage structure were highly correlated with a gradient in physical and chemical conditions associated with elevation. The results also suggested that flow regulation associated with large storage reservoirs has negative effects on the total number of taxa and density of macroinvertebrates below foothill dams. Analysis of the snag samples showed that, although elevation remained a significant variable, mean dominant substrate size, gradient, specific conductance, water temperature, percentage of the basin in agricultural land use, and percentage of the basin in combined agricultural and urban land uses were more important factors in explaining assemblage structure. Macroinvertebrate assemblages on snags may be useful in family level bioassessments of environmental conditions in valley floor habitats. In the Sierra Nevada and its foothills, the strong influence of elevation made it difficult to attribute differences in macroinvertebrate assemblage structure among sites to specific environmental conditions. Additional work is needed in the foothills and Sierra Nevada to better define macroinvertebrate assemblages and their relations to environmental variables.

Total airborne mold particle sampling: evaluation of sample collection, preparation and counting procedures, and collection devices.

PubMed

Godish, Diana; Godish, Thad

2008-02-01

This study was conducted to evaluate (i) procedures used to collect, prepare, and count total airborne mold spore/particle concentrations, and (ii) the relative field performance of three commercially available total airborne mold spore/particle sampling devices. Differences between factory and laboratory airflow calibration values of axial fan-driven sampling instruments (used in the study) indicated a need for laboratory calibration using a mass flow meter to ensure that sample results were accurately calculated. An aniline blue-amended Calberla's solution adjusted to a pH of 4.2-4.4 provided good sample mounting/counting results using Dow Corning high vacuum grease, Dow Corning 280A adhesive, and Dow Corning 316 silicone release spray for samples collected using mini-Burkard and Allergenco samplers. Count variability among analysts was most pronounced in 5% counts of relatively low mold particle deposition density samples and trended downward with increased count percentage and particle deposition density. No significant differences were observed among means of 5, 10, and 20% counts and among analysts; a significant interaction effect was observed between analysts' counts and particle deposition densities. Significantly higher mini-Burkard and Air-O-Cell total mold spore/particle counts for 600x vs. 400x (1.9 and 2.3 x higher, respectively), 1000x vs. 600x (1.9 and 2.2 x higher, respectively) and 1000x vs. 400x (3.6 and 4.6 x higher, respectively) comparisons indicated that 1000x magnification counts best quantified total airborne mold spore/particles using light microscopy, and that lower magnification counts may result in unacceptable underreporting of airborne mold spore/particle concentrations. Modest but significantly higher (1.2x) total mold spore concentrations were observed with Allergenco vs. mini-Burkard samples collected in co-located, concurrently operated sampler studies; moderate but significantly higher mini-Burkard count values (1.4x) were observed in similar studies with Air-O-Cell samplers. These count differences were relatively small compared with the large differences observed among three count magnifications.

Charm dimuon production in neutrino-nucleon interactions in the NOMAD experiment

NASA Astrophysics Data System (ADS)

Petti, Roberto; Samoylov, Oleg

2012-09-01

We present our new measurement of charm dimuon production in neutrino-iron interactions based upon the full statistics collected by the NOMAD experiment. After background subtraction we observe 15,340 charm dimuon events, providing the largest sample currently available. The analysis exploits the large inclusive charged current sample (about 9 million events after all analysis cuts) to constrain the total systematic uncertainty to about 2%. The extraction of strange sea and charm production parameters is also discussed.

Charm dimuon production in neutrino-nucleon interactions in the NOMAD experiment

NASA Astrophysics Data System (ADS)

Petti, R.; Samoylov, O. B.

2011-12-01

We present our new measurement of charm dimuon production in neutrino-iron interactions based upon the full statistics collected by the NOMAD experiment. After background subtraction we observe 15,340 charm dimuon events, providing the largest sample currently available. The analysis exploits the large inclusive charged current sample (about 9 million events after all analysis cuts) to constrain the total systematic uncertainty to ˜2%. The extraction of strange sea and charm production parameters is also discussed.

Trace gas emissions from a mid-latitude prescribed chaparral fire

NASA Technical Reports Server (NTRS)

Cofer, Wesley R., III; Levine, Joel S.; Sebacher, Daniel I.; Riggan, Philip J.; Winstead, Edward L.; Shaw, Edwin F., Jr.; Brass, James A.; Ambrosia, Vincent G.

1988-01-01

Smoke-plume gas samples were collected at altitudes from 35-670 m above the ground over the San Dimas Experimental Forest during a 400-acre prescribed chaparral fire. Mean emission ratios relative to CO2 for CO, H2, CH4, and total nonmethane hydrocarbons were lower than previous values obtained for large biomass-burning field experiments. Comparison of samples from vigorously flaming and mixed stages of combustion revealed little differences in CO2 normalized emission ratios for these gases (except for N2O).

gbpA as a Novel qPCR Target for the Species-Specific Detection of Vibrio cholerae O1, O139, Non-O1/Non-O139 in Environmental, Stool, and Historical Continuous Plankton Recorder Samples

PubMed Central

Vezzulli, Luigi; Stauder, Monica; Grande, Chiara; Pezzati, Elisabetta; Verheye, Hans M.; Owens, Nicholas J. P.; Pruzzo, Carla

2015-01-01

The Vibrio cholerae N-acetyl glucosamine-binding protein A (GbpA) is a chitin-binding protein involved in V. cholerae attachment to environmental chitin surfaces and human intestinal cells. We previously investigated the distribution and genetic variations of gbpA in a large collection of V. cholerae strains and found that the gene is consistently present and highly conserved in this species. Primers and probe were designed from the gbpA sequence of V. cholerae and a new Taq-based qPCR protocol was developed for diagnostic detection and quantification of the bacterium in environmental and stool samples. In addition, the positions of primers targeting the gbpA gene region were selected to obtain a short amplified fragment of 206 bp and the protocol was optimized for the analysis of formalin-fixed samples, such as historical Continuous Plankton Recorder (CPR) samples. Overall, the method is sensitive (50 gene copies), highly specific for V. cholerae and failed to amplify strains of the closely-related species Vibrio mimicus. The sensitivity of the assay applied to environmental and stool samples spiked with V. cholerae ATCC 39315 was comparable to that of pure cultures and was of 102 genomic units/l for drinking and seawater samples, 101 genomic units/g for sediment and 102 genomic units/g for bivalve and stool samples. The method also performs well when tested on artificially formalin-fixed and degraded genomic samples and was able to amplify V. cholerae DNA in historical CPR samples, the earliest of which date back to August 1966. The detection of V. cholerae in CPR samples collected in cholera endemic areas such as the Benguela Current Large Marine Ecosystem (BCLME) is of particular significance and represents a proof of concept for the possible use of the CPR technology and the developed qPCR assay in cholera studies. PMID:25915771

gbpA as a Novel qPCR Target for the Species-Specific Detection of Vibrio cholerae O1, O139, Non-O1/Non-O139 in Environmental, Stool, and Historical Continuous Plankton Recorder Samples.

PubMed

Vezzulli, Luigi; Stauder, Monica; Grande, Chiara; Pezzati, Elisabetta; Verheye, Hans M; Owens, Nicholas J P; Pruzzo, Carla

2015-01-01

The Vibrio cholerae N-acetyl glucosamine-binding protein A (GbpA) is a chitin-binding protein involved in V. cholerae attachment to environmental chitin surfaces and human intestinal cells. We previously investigated the distribution and genetic variations of gbpA in a large collection of V. cholerae strains and found that the gene is consistently present and highly conserved in this species. Primers and probe were designed from the gbpA sequence of V. cholerae and a new Taq-based qPCR protocol was developed for diagnostic detection and quantification of the bacterium in environmental and stool samples. In addition, the positions of primers targeting the gbpA gene region were selected to obtain a short amplified fragment of 206 bp and the protocol was optimized for the analysis of formalin-fixed samples, such as historical Continuous Plankton Recorder (CPR) samples. Overall, the method is sensitive (50 gene copies), highly specific for V. cholerae and failed to amplify strains of the closely-related species Vibrio mimicus. The sensitivity of the assay applied to environmental and stool samples spiked with V. cholerae ATCC 39315 was comparable to that of pure cultures and was of 102 genomic units/l for drinking and seawater samples, 101 genomic units/g for sediment and 102 genomic units/g for bivalve and stool samples. The method also performs well when tested on artificially formalin-fixed and degraded genomic samples and was able to amplify V. cholerae DNA in historical CPR samples, the earliest of which date back to August 1966. The detection of V. cholerae in CPR samples collected in cholera endemic areas such as the Benguela Current Large Marine Ecosystem (BCLME) is of particular significance and represents a proof of concept for the possible use of the CPR technology and the developed qPCR assay in cholera studies.

Microcomputer Referents in Elementary Mathematics: A Sample Approach.

ERIC Educational Resources Information Center

Connell, Michael L.

The mathematical experiences of elementary students often focus on memorizing facts and rules as opposed to making sense of the subject and developing problem solving skills. Students spend large amounts of time processing, memorizing and sorting collections of data which are tasks well performed by computer technology. To correct this situation,…

THE EFFECT OF VARYING ELECTROFISHING DESIGN ON BIOASSESSMENT RESULTS OF FOUR LARGE RIVERS IN THE OHIO RIVER BASIN

EPA Science Inventory

In 1999, the effect of electrofishing design (single bank or paired banks) and sampling distance on bioassessment results was studied in four boatable rivers in the Ohio River basin. The relationship between the number of species collected and the total distance electrofished wa...

Longitudinal Surveys of Australian Youth (LSAY): 1995 Cohort: User Guide. Technical Report 49

ERIC Educational Resources Information Center

National Centre for Vocational Education Research (NCVER), 2009

2009-01-01

The Longitudinal Surveys of Australian Youth (LSAY) is a research program that tracks young people as they move from school into further study, work and other destinations. It uses large, nationally representative samples of young people to collect information about education and training, work, and social development. It includes surveys…

Wildfires and tourist behaviors in Florida

Treesearch

Brijesh Thapa; Ignatius Cahyanto; Stephen M. Holland; James D. Absher

2013-01-01

The impacts of wildfires on tourism have largely been examined with emphasis on economic losses and recovery strategies. Given the limited research from a demand perspective, this study examined tourist risk perceptions and reactionary behaviors toward wildfires in Florida. Data (N ¼ 771) was collected among a U.S. sample of non-resident overnight leisure travelers...

The effect of extraction, storage, and analysis techniques on the measurement of airborne endotoxin from a large dairy

USDA-ARS?s Scientific Manuscript database

The objective of this study was to fill in additional knowledge gaps with respect to the extraction, storage, and analysis of airborne endotoxin, with a specific focus on samples from a dairy production facility. We utilized polycarbonate filters to collect total airborne endotoxins, sonication as ...

Longitudinal Study on Fluency among Novice Learners of Japanese

ERIC Educational Resources Information Center

Hirotani, Maki; Matsumoto, Kazumi; Fukada, Atsusi

2012-01-01

The present study examined various aspects of the development of learners' fluency in Japanese using a large set of speech samples collected over a long period, using an online speaking practice/assessment system called "Speak Everywhere." The purpose of the present study was to examine: (1) how the fluency related measures changed over…

Degradation of triclosan and triclocarban and formation of transformation products in activated sludge using benchtop bioreactors

USDA-ARS?s Scientific Manuscript database

Benchtop bioreactors were run aerobically with activated sludge samples collected from a large municipal wastewater treatment plant (WWTP) to understand how increased hydraulic retention time (HRT) and varying treatment temperatures (21°C and 30°C) impact concentrations of the endocrine disrupting a...

Automated Proposition Density Analysis for Discourse in Aphasia

ERIC Educational Resources Information Center

Fromm, Davida; Greenhouse, Joel; Hou, Kaiyue; Russell, G. Austin; Cai, Xizhen; Forbes, Margaret; Holland, Audrey; MacWhinney, Brian

2016-01-01

Purpose: This study evaluates how proposition density can differentiate between persons with aphasia (PWA) and individuals in a control group, as well as among subtypes of aphasia, on the basis of procedural discourse and personal narratives collected from large samples of participants. Method: Participants were 195 PWA and 168 individuals in a…

Initial Development and Validation of the BullyHARM: The Bullying, Harassment, and Aggression Receipt Measure

ERIC Educational Resources Information Center

Hall, William J.

2016-01-01

This article describes the development and preliminary validation of the Bullying, Harassment, and Aggression Receipt Measure (BullyHARM). The development of the BullyHARM involved a number of steps and methods, including a literature review, expert review, cognitive testing, readability testing, data collection from a large sample, reliability…

4-H Participation and Science Interest in Youth

ERIC Educational Resources Information Center

Heck, Katherine; Carlos, Ramona M.; Barnett, Cynthia; Smith, Martin H.

2012-01-01

The study reported here investigated the impacts of participation in 4-H on young people's interest and participation in science. Survey data were collected from relatively large and ethnically diverse samples of elementary and high school-aged students in California. Results indicated that although elementary-grade 4-H members are not more…

Conduct, Biological Factors and Adult Delinquency in a Longitudinal Perspective.

ERIC Educational Resources Information Center

Magnusson, David

In the course of a longitudinal research program conducted in Sweden, data were being collected on biological and psychological aspects of individual functioning and on environmental factors for a fairly large representative sample (approximately 1,000) of Swedish males and females between 10 and 27 years of age. Based on data from the…

Protocol to Reconstruct Historical Contaminant Loading to Large Lakes: The Lake Michigan Sediment Record of Mercury

EPA Science Inventory

Samples of opportunity from Pb-210 dated sediment cores collected from Lake Michigan between 1994 and 1996 were analyzed for mercury. The storage of both anthropogenic and total (post-1850) mercury in the lake was calculated to be 186 and 228 metric tons, respectively. By setti...

The Structure of Diagnostic and Statistical Manual of Mental Disorders (4th Edition, Text Revision) Personality Disorder Symptoms in a Large National Sample

PubMed Central

Trull, Timothy J.; Vergés, Alvaro; Wood, Phillip K.; Jahng, Seungmin; Sher, Kenneth J.

2013-01-01

We examined the latent structure underlying the criteria for DSM–IV–TR (American Psychiatric Association, 2000, Diagnostic and statistical manual of mental disorders (4th ed., text revision). Washington, DC: Author.) personality disorders in a large nationally representative sample of U.S. adults. Personality disorder symptom data were collected using a structured diagnostic interview from approximately 35,000 adults assessed over two waves of data collection in the National Epidemiologic Survey on Alcohol and Related Conditions. Our analyses suggested that a seven-factor solution provided the best fit for the data, and these factors were marked primarily by one or at most two personality disorder criteria sets. A series of regression analyses that used external validators tapping Axis I psychopathology, treatment for mental health problems, functioning scores, interpersonal conflict, and suicidal ideation and behavior provided support for the seven-factor solution. We discuss these findings in the context of previous studies that have examined the structure underlying the personality disorder criteria as well as the current proposals for DSM-5 personality disorders. PMID:22506626

Variations in the source, metal content and bioreactivity of technogenic aerosols: a case study from Port Talbot, Wales, UK.

PubMed

Moreno, Teresa; Merolla, Luciano; Gibbons, Wes; Greenwell, Leona; Jones, Tim; Richards, Roy

2004-10-15

Atmospheric aerosol samples were collected during different prevailing wind directions from a site located close to a busy motorway, a major steelworks, and the town of Port Talbot (Wales, UK). A high-volume collector was used (1100 l/min), enabling relatively large amounts of particulate matter (PM(10-2.5) and PM(2.5)) samples to be obtained on a polyurethane foam [PUF, H(2)N-C(O)O-CH(2)CH(3)] substrate over periods of 2-7 days. Four samples were chosen to exemplify different particle mixtures: SE- and NE-derived samples for particles moving along and across the motorway, a NW-derived sample from the town, and a mixed SW/SE-derived sample containing a mixture of particles from both steelworks and motorway. The latter sample showed the highest average collection rate (0.9 mg/h, 13 microg/m(3)) and included a prominent pollution episode when rainy winds were blowing from the direction of the steelworks. Both NW and SE samples were collected under dry conditions and show the same collection rate (0.7 mg/h, 10 microg/m(3)), whereas the NE sample was collected during wetter weather and shows the lowest rate (0.3 mg/h, 5 microg/m(3)). Scanning electron microscopy (SEM) and energy-dispersive X-ray microanalysis system (EDX) analyses show all samples are dominated by elemental and organic carbon compounds (EOCC) and nitrates, with lesser amounts of sulphates, felsic silicates, chlorides and metals. ICP-MS analyses show the SW/SE sample to be richest in metals, especially Fe, Zn, Ni, and Mn, these being attributed to an origin from the steelworks. The SE sample, blown along the motorway corridor, shows enhanced levels of Pb, V, Ti, As, and Ce, these metals being interpreted as defining a traffic-related chemical fingerprint. The NW sample shows a very low metal content. DNA plasmid assay data on the samples show TM(50) values varying from 66 to 175 microg/ml for the adjusted whole sample and 89 to 203 microg/ml for the soluble fraction. The SW/SE-mixed metalliferous sample is the most bioreactive (both whole and soluble) and the soluble fraction of the metal-depleted NW sample is the least bioreactive. The metal content of the aerosol samples, especially soluble metals such as Zn, is suggested to be the primary component responsible for oxidative damage of the DNA, and therefore most implicated in any health effects arising from the inhalation of these particulate cocktails.

Assessing the sustainable construction of large construction companies in Malaysia

NASA Astrophysics Data System (ADS)

Adewale, Bamgbade Jibril; Mohammed, Kamaruddeen Ahmed; Nasrun, Mohd Nawi Mohd

2016-08-01

Considering the increasing concerns for the consideration of sustainability issues in construction project delivery within the construction industry, this paper assesses the extent of sustainable construction among Malaysian large contractors, in order to ascertain the level of the industry's impacts on both the environment and the society. Sustainable construction explains the construction industry's responsibility to efficiently utilise the finite resources while also reducing construction impacts on both humans and the environment throughout the phases of construction. This study used proportionate stratified random sampling to conduct a field study with a sample of 172 contractors out of the 708 administered questionnaires. Data were collected from large contractors in the eleven states of peninsular Malaysia. Using the five-level rating scale (which include: 1= Very Low; 2= Low; 3= Moderate; 4= High; 5= Very High) to describe the level of sustainable construction of Malaysian contractors based on previous studies, statistical analysis reveals that environmental, social and economic sustainability of Malaysian large contractors are high.

Individual and collective modes of surface magnetoplasmon in thiolate-protected silver nanoparticles studied by MCD spectroscopy

NASA Astrophysics Data System (ADS)

Yao, Hiroshi; Shiratsu, Taisuke

2016-05-01

Large magneto-optical (MO) responses at the energy of localized surface plasmon resonance (LSPR), namely, surface magnetoplasmons, are demonstrated for the first time in thiolate-protected silver nanoparticles with magnetic circular dichroism (MCD) spectroscopy. The samples examined are decanethiol (DT)-, azobenzenethiol (ABT)-, and ABT/DT mixed-monolayer-protected Ag nanoparticles. ABT-protected Ag nanoparticles are somewhat aggregated and thus exhibit a broad, collective mode of plasmonic absorption, whereas other samples with highly-dispersed nanoparticles show an individual mode of LSPR absorption. In all Ag nanoparticles, a derivative-like MCD signal is observed under an applied magnetic field of 1.6 T, which can be explained in terms of two circular modes of magnetoplasmon caused by the increase (or decrease) in the Lorentz force imparted on the free electrons that oscillate in the left (or right) circular orbits in the nanosphere. For the Ag nanoparticles exhibiting an individual LSPR mode, in particular, simultaneous deconvolution analysis of UV-vis absorption and MCD spectra reveal that (i) the amplitude of the magnetoplasmonic component with lower frequency (ω-), resulting from the reduction in the confinement strength of collective electrons by the Lorentz force, is stronger than that with a higher frequency (ω+) (ii) the accurate shift or cyclotron frequency between two magnetoplasmonic modes (ωc = ω+ - ω-) is size-dependent, and presents a very large value with implications for the apparent enhancement of the local magnetic-field in the Ag nanoparticles. These results strongly suggest that the Ag-thiolate layer or Ag-S bonding on the nanoparticle surface plays a significant role in the MO enhancement.Large magneto-optical (MO) responses at the energy of localized surface plasmon resonance (LSPR), namely, surface magnetoplasmons, are demonstrated for the first time in thiolate-protected silver nanoparticles with magnetic circular dichroism (MCD) spectroscopy. The samples examined are decanethiol (DT)-, azobenzenethiol (ABT)-, and ABT/DT mixed-monolayer-protected Ag nanoparticles. ABT-protected Ag nanoparticles are somewhat aggregated and thus exhibit a broad, collective mode of plasmonic absorption, whereas other samples with highly-dispersed nanoparticles show an individual mode of LSPR absorption. In all Ag nanoparticles, a derivative-like MCD signal is observed under an applied magnetic field of 1.6 T, which can be explained in terms of two circular modes of magnetoplasmon caused by the increase (or decrease) in the Lorentz force imparted on the free electrons that oscillate in the left (or right) circular orbits in the nanosphere. For the Ag nanoparticles exhibiting an individual LSPR mode, in particular, simultaneous deconvolution analysis of UV-vis absorption and MCD spectra reveal that (i) the amplitude of the magnetoplasmonic component with lower frequency (ω-), resulting from the reduction in the confinement strength of collective electrons by the Lorentz force, is stronger than that with a higher frequency (ω+) (ii) the accurate shift or cyclotron frequency between two magnetoplasmonic modes (ωc = ω+ - ω-) is size-dependent, and presents a very large value with implications for the apparent enhancement of the local magnetic-field in the Ag nanoparticles. These results strongly suggest that the Ag-thiolate layer or Ag-S bonding on the nanoparticle surface plays a significant role in the MO enhancement. Electronic supplementary information (ESI) available: EDX spectroscopic analysis of various Ag nanoparticle samples; MCD signals normalized to absorbance for the Ag(DT)L and Ag(DT)S samples; deconvolution of UV-vis absorption and MCD spectra using three Lorentzian components; IR spectral changes upon photoisomerization; thermal cis-to-trans relaxation of azobenzene in the Ag(ABT) sample; UV-vis absorption spectra of Ag nanoparticle samples in the presence/absence of a magnetic field of 1.6 T. See DOI: 10.1039/c6nr00631k

Psychiatric Brain Banking: Three Perspectives on Current Trends and Future Directions

PubMed Central

Deep-Soboslay, Amy; Benes, Francine M.; Haroutunian, Vahram; Ellis, Justin K.; Kleinman, Joel E.; Hyde, Thomas M.

2011-01-01

Introduction The study of postmortem human brain tissue is central to the advancement of the neurobiological studies of psychiatric illness, particularly for the study of brain-specific isoforms and molecules. Methods The state-of-the-art methods and recommendations for maintaining a successful brain bank for psychiatric disorders are discussed, using the convergence of viewpoints from three brain collections, the National Institute of Mental Health Brain Collection (NIMH), the Harvard Brain Tissue Resource Center (HBTRC), and the Mt. Sinai School of Medicine Brain Bank (MSSM-BB), with diverse research interests and divergent approaches to tissue acquisition. Results While the NIMH obtains donations from medical examiners for its collection, and places particular emphasis on clinical diagnosis, toxicology, and building lifespan control cohorts, the HBTRC is uniquely designed as a repository whose sole purpose is to collect large-volume, high quality brain tissue from community-based donors based on relationships across an expansive nationwide network, and places emphasis on the accessibility of its bank in disseminating tissue and related data to research groups worldwide. The MSSM-BB collection has shown that, with dedication, prospective recruitment is a successful approach to tissue donation, and places particular emphasis on rigorous clinical diagnosis through antemortem contact with donors. The MSSM-BB places great importance on stereological tissue sampling methods for neuroanatomical studies, and frozen tissue sampling approaches that enable multiple assessments (RNA, DNA, protein, enzyme activity, binding, etc.) of the same tissue block. Promising scientific approaches for elucidating the molecular and cellular pathways in brain that may contribute to schizophrenia and/or bipolar disorder, such as cell culture techniques and microarray-based gene expression and genotyping studies are briefly discussed. Conclusions Despite unique perspectives from three established brain collections, there is a consensus that (1) diverse strategies for tissue acquisition, (2) rigor in tissue and diagnostic characterization, (3) the importance of sample accessibility, and (4) continual application of innovative scientific approaches to the study of brain tissue are all integral to the success and future of psychiatric brain banking. The future of neuropsychiatric research depends upon in the availability of high quality brain specimens from large numbers of subjects, including non-psychiatric controls. PMID:20673875

Filter Paper Blood Spot Enzyme Linked Immunoassay for Adiponectin and Application in the Evaluation of Determinants of Child Insulin Sensitivity

PubMed Central

Martin, Richard M.; Patel, Rita; Oken, Emily; Thompson, Jennifer; Zinovik, Alexander; Kramer, Michael S.; Vilchuck, Konstantin; Bogdanovich, Natalia; Sergeichick, Natalia; Foo, Ying; Gusina, Nina

2013-01-01

Background Adiponectin is an adipocyte-derived hormone that acts as a marker of insulin sensitivity. Bloodspot sampling by fingerstick onto filter paper may increase the feasibility of large-scale studies of the determinants of insulin sensitivity. We first describe the validation of an enzyme-linked immunoassay (ELISA) for quantifying adiponectin from dried blood spots and then demonstrate its application in a large trial (PROBIT). Methods We quantified adiponectin from 3-mm diameter discs (≈3 µL of blood) punched from dried blood spots obtained from: i) whole blood standards (validation); and ii) PROBIT trial samples (application) in which paediatricians collected blood spots from 13,879 children aged 11.5 years from 31 sites across Belarus. We examined the distribution of bloodspot adiponectin by demographic and anthropometric factors, fasting insulin and glucose. Results In the validation study, mean intra-assay coefficients of variation (n = 162) were 15%, 13% and 10% for ‘low’ (6.78 µg/ml), ‘medium’ (18.18 µg/ml) and 'high’ (33.13 µg/ml) internal quality control (IQC) samples, respectively; the respective inter-assay values (n = 40) were 23%, 21% and 14%. The correlation coefficient between 50 paired whole bloodspot versus plasma samples, collected simultaneously, was 0.87 (95% CI: 0.78 to 0.93). Recovery of known quantities of adiponectin (between 4.5 to 36 µg/ml) was 100.3–133%. Bloodspot adiponectin was stable for at least 30 months at −80°C. In PROBIT, we successfully quantified fasting adiponectin from dried blood spots in 13,329 of 13,879 (96%) children. Mean adiponectin (standard deviation) concentrations were 17.34 µg/ml (7.54) in boys and 18.41 µg/ml (7.92) in girls and were inversely associated with body mass index, fat mass, triceps and subscapular skin-fold thickness, waist circumference, height and fasting glucose. Conclusions Bloodspot ELISA is suitable for measuring adiponectin in very small volumes of blood collected on filter paper and can be applied to large-scale studies. PMID:23936498

Internet cognitive testing of large samples needed in genetic research.

PubMed

Haworth, Claire M A; Harlaar, Nicole; Kovas, Yulia; Davis, Oliver S P; Oliver, Bonamy R; Hayiou-Thomas, Marianna E; Frances, Jane; Busfield, Patricia; McMillan, Andrew; Dale, Philip S; Plomin, Robert

2007-08-01

Quantitative and molecular genetic research requires large samples to provide adequate statistical power, but it is expensive to test large samples in person, especially when the participants are widely distributed geographically. Increasing access to inexpensive and fast Internet connections makes it possible to test large samples efficiently and economically online. Reliability and validity of Internet testing for cognitive ability have not been previously reported; these issues are especially pertinent for testing children. We developed Internet versions of reading, language, mathematics and general cognitive ability tests and investigated their reliability and validity for 10- and 12-year-old children. We tested online more than 2500 pairs of 10-year-old twins and compared their scores to similar internet-based measures administered online to a subsample of the children when they were 12 years old (> 759 pairs). Within 3 months of the online testing at 12 years, we administered standard paper and pencil versions of the reading and mathematics tests in person to 30 children (15 pairs of twins). Scores on Internet-based measures at 10 and 12 years correlated .63 on average across the two years, suggesting substantial stability and high reliability. Correlations of about .80 between Internet measures and in-person testing suggest excellent validity. In addition, the comparison of the internet-based measures to ratings from teachers based on criteria from the UK National Curriculum suggests good concurrent validity for these tests. We conclude that Internet testing can be reliable and valid for collecting cognitive test data on large samples even for children as young as 10 years.

Screening and Quantification of Aliphatic Primary Alkyl Corrosion Inhibitor Amines in Water Samples by Paper Spray Mass Spectrometry.

PubMed

Jjunju, Fred P M; Maher, Simon; Damon, Deidre E; Barrett, Richard M; Syed, S U; Heeren, Ron M A; Taylor, Stephen; Badu-Tawiah, Abraham K

2016-01-19

Direct analysis and identification of long chain aliphatic primary diamine Duomeen O (n-oleyl-1,3-diaminopropane), corrosion inhibitor in raw water samples taken from a large medium pressure water tube boiler plant water samples at low LODs (<0.1 pg) has been demonstrated for the first time, without any sample preparation using paper spray mass spectrometry (PS-MS). The presence of Duomeen O in water samples was confirmed via tandem mass spectrometry using collision-induced dissociation and supported by exact mass measurement and reactive paper spray experiments using an LTQ Orbitrap Exactive instrument. Data shown herein indicate that paper spray ambient ionization can be readily used as a rapid and robust method for in situ direct analysis of polymanine corrosion inhibitors in an industrial water boiler plant and other related samples in the water treatment industry. This approach was applied for the analysis of three complex water samples including feedwater, condensate water, and boiler water, all collected from large medium pressure (MP) water tube boiler plants, known to be dosed with varying amounts of polyamine and amine corrosion inhibitor components. Polyamine chemistry is widely used for example in large high pressure (HP) boilers operating in municipal waste and recycling facilities to prevent corrosion of metals. The samples used in this study are from such a facility in Coventry waste treatment facility, U.K., which has 3 × 40 tonne/hour boilers operating at 17.5 bar.

Salmonella surveillance in a collection of rattlesnakes (Crotalus spp.).

PubMed

Grupka, Lisa M; Ramsay, Edward C; Bemis, David A

2006-09-01

Over the past 15 yr, Salmonella enterica ssp. arizonae (IIIa) 56:z4,z23:- has repeatedly been isolated from individual Crotalus willardi rattlesnakes with progressively debilitating osteomyelitis at the Knoxville Zoological Gardens. In April 2004, the serotype was linked with a fatal case of septicemia in another Crotalus species in this collection. Although the association of IIIa 56:z4,z23:- with disease in this colony of C. willardi is well established, prior disease or isolation of this serotype outside of the C. willardi colony had not been documented previously, and the serotype's distribution throughout the remainder of the Crotalus collection had yet to be determined. Forty-one fecal samples were obtained from each individual (n = 36) or exhibit group (n = 5) of crotalid snakes, representing nine species, housed at the zoo. Salmonella spp. were isolated from every sample, with 21 different serotypes. The 21 serotypes were distributed among S. enterica ssp. I (24%), IIIa (9%), and IIIb (67%). Although not recovered in the primary study, S. arizonae 56:z4,z23:- was recovered from additional samples taken from two C. willardi willardi. Although the overall recovery rate of this serotype from feces has been low, it seems that its distribution among the Crotalus collection at Knoxville Zoological Gardens remains largely restricted to the C. willardi species.

Vertical oviposition activity of mosquitoes in the Atlantic Forest of Brazil with emphasis on the sylvan vector, Haemagogus leucocelaenus (Diptera: Culicidae).

PubMed

Alencar, Jeronimo; de Mello, Cecilia Ferreira; Gil-Santana, Hélcio R; Guimarães, Anthony Érico; de Almeida, Sergio Antonio Silva; Gleiser, Raquel M

2016-06-01

This study aimed to assess the vertical patterns of oviposition and temporal changes in the distribution of mosquito species in an area of the Atlantic Forest in Rio de Janeiro State, Brazil, and in particular, the behavior and oviposition of potential yellow fever virus vectors. Mosquito samples were collected from the Ecological Reserve Guapiaçu (REGUA, Brazil), which includes a somewhat disturbed forest, with a large diversity of plants and animals. In all, 5,458 specimens (ten species from seven genera) were collected. Haemagogus leucocelaenus was the most frequently captured species, representing 73% of the specimens collected. Species richness and diversity were the highest in the samples collected from the ground-level ovitraps and decreased with height. Species composition also differed significantly among heights. The largest species differences were detected between ovitraps set at the ground level and those set at 7 m and 9 m; Hg. leucocelaenus, Limatus durhamii, and Limatus paraensis contributed most to these differences. Sampling month and climatic variables had significant effects on species richness and diversity. Species diversity and richness decreased with height, suggesting that the conditions for mosquito breeding are more favorable closer to the ground. Species composition also showed vertical differences. © 2016 The Society for Vector Ecology.

Holding effects on coliform enumeration in drinking water samples.

PubMed Central

McDaniels, A E; Bordner, R H; Gartside, P S; Haines, J R; Brenner, K P; Rankin, C C

1985-01-01

Standard procedures for analyzing drinking water stress the need to adhere to the time and temperature conditions recommended for holding samples collected for microbiological testing. The National Drinking Water Laboratory Certification Program requires compliance with these holding limits, but some investigators have reported difficulties in meeting them. Research was conducted by standard analytical methods to determine if changes occurred when samples were held at 5 and 22 degrees C and analyzed at 0, 24, 30, and 48 h. Samples were analyzed for coliforms by the membrane filter and fermentation-tube procedures and for heterotrophs by the pour plate method. A total of 17 treated water samples were collected from a large municipal distribution system from August to December 1981, and 12 samples were collected from January to May 1983. The samples were dosed with coliforms previously isolated from the water system, Enterobacter cloacae in 1981 and Citrobacter freundii in 1983. The coliform counts declined linearly over time, and the rates of decline were significant at both 5 and 22 degrees C. Within 24 h at 22 degrees C, levels of E. cloacae and C. freundii decreased by 47 and 26%, respectively, and at 5 degrees C, E. cloacae numbers declined by 23%. Results from these representative laboratory-grown coliforms reinforced those previously obtained with naturally occurring coliforms under the same experimental conditions. Significantly, some samples with initially unacceptable counts (greater than 4/100 ml) met the safe drinking water limits after storage at 24 h at 5 and 22 degrees C and would have been classified as satisfactory.(ABSTRACT TRUNCATED AT 250 WORDS) Images PMID:4083877

Concentrations and Loads of Organic Compounds and Trace Elements in Tributaries to Newark and Raritan Bays, New Jersey

USGS Publications Warehouse

Wilson, Timothy P.; Bonin, Jennifer L.

2007-01-01

A study was undertaken to determine the concentrations and loads of sediment and chemicals delivered to Newark and Raritan Bays by five major tributaries: the Raritan, Passaic, Rahway, Elizabeth, and Hackensack Rivers. This study was initiated by the State of New Jersey as Study I-C of the New Jersey Toxics Reduction Workplan for the New York-New Jersey Harbor, working under the NY-NJ Harbor Estuary Program (HEP) Contaminant Assessment and Reduction Program (CARP). The CARP is a comprehensive effort to evaluate the levels and sources of toxic contaminants to the tributaries and estuarine areas of the NY-NJ Harbor, including Newark and Raritan Bays. The Raritan and Passaic Rivers are large rivers (mean daily discharges of 1,189 and 1,132 cubic feet per second (ft3/s), respectively), that drain large, mixed rural/urban basins. The Elizabeth and Rahway Rivers are small rivers (mean daily discharges of 25.9 and 49.1 ft3/s, respectively) that drain small, highly urbanized and industrialized basins. The Hackensack River drains a small, mixed rural/urban basin, and its flow is highly controlled by an upstream reservoir (mean daily discharge of 90.4 ft3/s). These rivers flow into urbanized estuaries and ultimately, to the Atlantic Ocean. Each of these tributaries were sampled during two to four storm events, and twice each during low-flow discharge conditions. Samples were collected using automated equipment installed at stations adjacent to U.S. Geological Survey streamflow-gaging stations near the heads-of-tide of these rivers. Large-volume (greater than 50 liters of water and a target of 1 gram of sediment), flow-weighted composite samples were collected for chemical analysis using filtration to collect suspended particulates and exchange resin (XAD-2) to sequester dissolved contaminants. Composite whole-water samples were collected for dissolved polycyclic aromatic hydrocarbons (PAH) and for trace element analysis. Additional discrete grab samples were collected throughout each event for trace-element analysis, and multiple samples were collected for suspended sediment (SS), particulate carbon (POC), and dissolved organic carbon (DOC) analysis. The suspended sediment and exchange resin were analyzed for 114 polychlorinated biphenyls (PCBs, by US EPA method 1668A, modified), seven 2,3,7,8-substituted chlorinated dibenzo-p-dioxins (CDD) and 10 dibenzo-p-difurans (CDF) (by US EPA method 1613), 24 PAHs (by low-resolution isotope dilution/mass-spectral methods), 27 organo-chlorine pesticides (OCPs) (by high resolution isotope dilution/mass-spectral methods), and the trace elements mercury (Hg), methyl-mercury (MeHg), lead (Pb), and cadmium (Cd). Isotope dilution methods using gas chromatography and high-and low-resolution mass spectral (GC/MS) detection were used to accurately identify and quantify organic compounds in the sediment and water phases. Trace elements were measured using inductively coupled plasma-mass spectrometry and cold-vapor atomic fluorescence spectrometry methods. The loads of sediment, carbon, and chemicals were calculated for each storm and low-flow event sampled. Because only a few storm events were sampled, yearly loads of sediment were calculated from rating curves developed using historical SS and POC data. The average annual loads of sediment and carbon were calculated for the period 1975-2000, along with the loads for the selected water years being modeled as part of the New York New Jersey Harbor Estuary Program CARP. Comparison of loads calculated using the rating curve method to loads measured during the sampled storm events indicated that the rating curve method likely underpredicts annual loads. Average annual loads of suspended sediment in the tributaries were estimated to be 395,000 kilograms per year (kg/yr) in the Hackensack River, 417,000 kg/yr in the Elizabeth River, 882,000 kg/yr in the Rahway River, 22,700,000 kg/yr in the Passaic River, and 93,100,000 kg/yr in the Raritan River. Averag

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

Using oral fluids samples for indirect influenza A virus surveillance in farmed UK pigs.

PubMed

Gerber, Priscilla F; Dawson, Lorna; Strugnell, Ben; Burgess, Robert; Brown, Helen; Opriessnig, Tanja

2017-02-01

Influenza A virus (IAV) is economically important in pig production and has broad public health implications. In Europe, active IAV surveillance includes demonstration of antigen in nasal swabs and/or demonstration of antibodies in serum (SER) samples; however, collecting appropriate numbers of individual pig samples can be costly and labour-intensive. The objective of this study was to compare the probability of detecting IAV antibody positive populations using SER versus oral fluid (OF) samples. Paired pen samples, one OF and 5-14 SER samples, were collected cross-sectional or longitudinally. A commercial nucleoprotein (NP)-based blocking ELISA was used to test 244 OF and 1004 SER samples from 123 pens each containing 20-540 pigs located in 27 UK herds. Overall, the IAV antibody detection rate was higher in SER samples compared to OFs under the study conditions. Pig age had a significant effect on the probability of detecting positive pens. For 3-9-week-old pigs the probability of detecting IAV antibody positive samples in a pen with 95% confidence intervals was 40% (23-60) for OF and 61% (0.37-0.80) for SER ( P  =   0.04), for 10-14-week-old pigs it was 19% (8-40) for OF and 93% (0.71-0.99) for SER ( P  <   0.01), and for 18-20-week-old pigs it was 67% (41-85) for OF and 81% (0.63-0.91) for SER ( P  =   0.05). Collecting more than one OF sample in pens with more than 25 less than 18-week-old pigs should be further investigated in the future to elucidate the suitability of OF for IAV surveillance in herds with large pen sizes.

Analysis of cannabis in oral fluid specimens by GC-MS with automatic SPE.

PubMed

Choi, Hyeyoung; Baeck, Seungkyung; Kim, Eunmi; Lee, Sooyeun; Jang, Moonhee; Lee, Juseon; Choi, Hwakyung; Chung, Heesun

2009-12-01

Methamphetamine (MA) is the most commonly abused drug in Korea, followed by cannabis. Traditionally, MA analysis is carried out on both urine and hair samples and cannabis analysis in urine samples only. Despite the fact that oral fluid has become increasingly popular as an alternative specimen in the field of driving under the influence of drugs (DUID) and work place drug testing, its application has not been expanded to drug analysis in Korea. Oral fluid is easy to collect and handle and can provide an indication of recent drug abuse. In this study, we present an analytical method using GC-MS to determine tetrahydrocannabinol (THC) and its main metabolite 11-nor-delta9-tetrahydrocannabinol-9-carboxylic acid (THC-COOH) in oral fluid. The validated method was applied to oral fluid samples collected from drug abuse suspects and the results were compared with those in urine. The stability of THC and THC-COOH in oral fluid stored in different containers was also investigated. Oral fluid specimens from 12 drug abuse suspects, submitted by the police, were collected by direct expectoration. The samples were screened with microplate ELISA. For confirmation they were extracted using automated SPE with mixed-mode cation exchange cartridge, derivatized and analyzed by GC-MS using selective ion monitoring (SIM). The concentrations ofTHC and THC-COOH in oral fluid showed a large variation and the results from oral fluid and urine samples from cannabis abusers did not show any correlation. Thus, detailed information about time interval between drug use and sample collection is needed to interpret the oral fluid results properly. In addition, further investigation about the detection time window ofTHC and THC-COOH in oral fluid is required to substitute oral fluid for urine in drug testing.

Comparative Proteomic Analysis of Whole-Gut Lavage Fluid and Pancreatic Juice Reveals a Less Invasive Method of Sampling Pancreatic Secretions

PubMed Central

Rocker, Jana M; Tan, Marcus C; Thompson, Lee W; Contreras, Carlo M; DiPalma, Jack A; Pannell, Lewis K

2016-01-01

OBJECTIVES: There are currently no reliable, non-invasive screening tests for pancreatic ductal adenocarcinoma. The fluid secreted from the pancreatic ductal system (“pancreatic juice”) has been well-studied as a potential source of cancer biomarkers. However, it is invasive to collect. We recently observed that the proteomic profile of intestinal effluent from the bowel in response to administration of an oral bowel preparation solution (also known as whole-gut lavage fluid, WGLF) contains large amounts of pancreas-derived proteins. We therefore hypothesized that the proteomic profile is similar to that of pancreatic juice. In this study, we compared the proteomic profiles of 77 patients undergoing routine colonoscopy with the profiles of 19 samples of pure pancreatic juice collected during surgery. METHODS: WGLF was collected from patients undergoing routine colonoscopy, and pancreatic juice was collected from patients undergoing pancreatic surgery. Protein was isolated from both samples using an optimized method and analyzed by LC-MS/MS. Identified proteins were compared between samples and groups to determine similarity of the two fluids. We then compared our results with literature reports of pancreatic juice-based studies to determine similarity. RESULTS: We found 104 proteins in our pancreatic juice samples, of which 90% were also found in our WGLF samples. The majority (67%) of the total proteins found in the WGLF were common to pancreatic juice, with intestine-specific proteins making up a smaller proportion. CONCLUSIONS: WGLF and pancreatic juice appear to have similar proteomic profiles. This supports the notion that WGLF is a non-invasive, surrogate bio-fluid for pancreatic juice. Further studies are required to further elucidate its role in the diagnosis of pancreatic cancer. PMID:27228405

Next generation sensing platforms for extended deployments in large-scale, multidisciplinary, adaptive sampling and observational networks

NASA Astrophysics Data System (ADS)

Cross, J. N.; Meinig, C.; Mordy, C. W.; Lawrence-Slavas, N.; Cokelet, E. D.; Jenkins, R.; Tabisola, H. M.; Stabeno, P. J.

2016-12-01

New autonomous sensors have dramatically increased the resolution and accuracy of oceanographic data collection, enabling rapid sampling over extremely fine scales. Innovative new autonomous platofrms like floats, gliders, drones, and crawling moorings leverage the full potential of these new sensors by extending spatiotemporal reach across varied environments. During 2015 and 2016, The Innovative Technology for Arctic Exploration Program at the Pacific Marine Environmental Laboratory tested several new types of fully autonomous platforms with increased speed, durability, and power and payload capacity designed to deliver cutting-edge ecosystem assessment sensors to remote or inaccessible environments. The Expendable Ice-Tracking (EXIT) gloat developed by the NOAA Pacific Marine Environmental Laboratory (PMEL) is moored near bottom during the ice-free season and released on an autonomous timer beneath the ice during the following winter. The float collects a rapid profile during ascent, and continues to collect critical, poorly-accessible under-ice data until melt, when data is transmitted via satellite. The autonomous Oculus sub-surface glider developed by the University of Washington and PMEL has a large power and payload capacity and an enhanced buoyancy engine. This 'coastal truck' is designed for the rapid water column ascent required by optical imaging systems. The Saildrone is a solar and wind powered ocean unmanned surface vessel (USV) developed by Saildrone, Inc. in partnership with PMEL. This large-payload (200 lbs), fast (1-7 kts), durable (46 kts winds) platform was equipped with 15 sensors designed for ecosystem assessment during 2016, including passive and active acoustic systems specially redesigned for autonomous vehicle deployments. The senors deployed on these platforms achieved rigorous accuracy and precision standards. These innovative platforms provide new sampling capabilities and cost efficiencies in high-resolution sensor deployment, including reconnaissance for annual fisheries and marine mammal surveys; better linkages between sustained observing platforms; and adaptive deployments that can easily target anomalies as they arise.

Detection of Poliovirus Circulation by Environmental Surveillance in the Absence of Clinical Cases in Israel and the Palestinian Authority

PubMed Central

Manor, Y.; Handsher, R.; Halmut, T.; Neuman, M.; Bobrov, A.; Rudich, H.; Vonsover, A.; Shulman, L.; Kew, O.; Mendelson, E.

1999-01-01

The global eradication of poliomyelitis, believed to be achievable around the year 2000, relies on strategies which include high routine immunization coverage and mass vaccination campaigns, along with continuous monitoring of wild-type virus circulation by using the laboratory-based acute flaccid paralysis (AFP) surveillance. Israel and the Palestinian Authority are located in a geographical region in which poliovirus is still endemic but have been free of poliomyelitis since 1988 as a result of intensive immunization programs and mass vaccination campaigns. To monitor the wild-type virus circulation, environmental surveillance of sewage samples collected monthly from 25 to 30 sites across the country was implemented in 1989 and AFP surveillance began in 1994. The sewage samples were processed in the laboratory with a double-selective tissue culture system, which enabled economical processing of large number of samples. Between 1989 and 1997, 2,294 samples were processed, and wild-type poliovirus was isolated from 17 of them in four clusters, termed “silent outbreaks,” in September 1990 (type 3), between May and September 1991 (type 1), between October 1994 and June 1995 (type 1), and in December 1996 (type 1). Fifteen of the 17 positive samples were collected in the Gaza Strip, 1 was collected in the West Bank, and 1 was collected in the Israeli city of Ashdod, located close to the Gaza Strip. The AFP surveillance system failed to detect the circulating wild-type viruses. These findings further emphasize the important role that environmental surveillance can play in monitoring the eradication of polioviruses. PMID:10325305

Determining the prevalence of cytomegalovirus infection in a cohort of preterm infants.

PubMed

Pitlick, Mitchell M; Orr, Kristin; Momany, Allison M; McDonald, Erin L; Murray, Jeffrey C; Ryckman, Kelli K

2015-01-01

Preterm birth is a global public health problem that is a significant cause of infant morbidity and mortality. Congenital cytomegalovirus (CMV) infection has been proposed as a risk factor for preterm birth, but the rate of CMV in infants born preterm is unclear. CMV is the leading infectious cause of sensorineural hearing loss, which will affect 15% - 20% of congenitally infected infants later in their childhood. 90% of infected infants are asymptomatic at birth and are not recognized as at risk for CMV-associated deficits. To determine the prevalence of CMV infection in a large cohort of preterm infants. DNA was extracted from cord blood, peripheral blood, saliva, and buccal swab samples collected from preterm infants. A total of 1200 unique DNA samples were tested for CMV using a nested PCR protocol. The proportions of preterm infants with CMV was compared by sample collection type, race, gender, and gestational age. A total of 37 infants tested positive for CMV (3.08%). After excluding twins, siblings, and infants older than two weeks at the time of sample collection, two out of 589 infants were CMV positive (0.3%), which was lower than the proportion of CMV observed in the general population. All positive samples came from buccal swabs. Our work suggests that while CMV infection may not be greater in preterm infants than in the general population, given the neurologic consequences of CMV in preterm infants, screening of this population may still be warranted. If so, our results suggest buccal swabs, collected at pregnancy or at birth, may be an ideal method for such a program.

The effect of mode and context on survey results: Analysis of data from the Health Survey for England 2006 and the Boost Survey for London

PubMed Central

2010-01-01

Background Health-related data at local level could be provided by supplementing national health surveys with local boosts. Self-completion surveys are less costly than interviews, enabling larger samples to be achieved for a given cost. However, even when the same questions are asked with the same wording, responses to survey questions may vary by mode of data collection. These measurement differences need to be investigated further. Methods The Health Survey for England in London ('Core') and a London Boost survey ('Boost') used identical sampling strategies but different modes of data collection. Some data were collected by face-to-face interview in the Core and by self-completion in the Boost; other data were collected by self-completion questionnaire in both, but the context differed. Results were compared by mode of data collection using two approaches. The first examined differences in results that remained after adjusting the samples for differences in response. The second compared results after using propensity score matching to reduce any differences in sample composition. Results There were no significant differences between the two samples for prevalence of some variables including long-term illness, limiting long-term illness, current rates of smoking, whether participants drank alcohol, and how often they usually drank. However, there were a number of differences, some quite large, between some key measures including: general health, GHQ12 score, portions of fruit and vegetables consumed, levels of physical activity, and, to a lesser extent, smoking consumption, the number of alcohol units reported consumed on the heaviest day of drinking in the last week and perceived social support (among women only). Conclusion Survey mode and context can both affect the responses given. The effect is largest for complex question modules but was also seen for identical self-completion questions. Some data collected by interview and self-completion can be safely combined. PMID:20868528

Chemical Characterization and Source Apportionment of Size Fractionated Atmospheric Aerosols, and, Evaluating Student Attitudes and Learning in Large Lecture General Chemistry Classes

NASA Astrophysics Data System (ADS)

Allen, Gregory Harold

Chemical speciation and source apportionment of size fractionated atmospheric aerosols were investigated using laser desorption time-of-flight mass spectrometry (LD TOF-MS) and source apportionment was carried out using carbon-14 accelerator mass spectrometry (14C AMS). Sample collection was carried out using the Davis Rotating-drum Unit for Monitoring impact analyzer in Davis, Colfax, and Yosemite, CA. Ambient atmospheric aerosols collected during the winter of 2010/11 and 2011/12 showed a significant difference in the types of compounds found in the small and large sized particles. The difference was due to the increase number of oxidized carbon species that were found in the small particles size ranges, but not in the large particles size ranges. Overall, the ambient atmospheric aerosols collected during the winter in Davis, CA had and average fraction modern of F14C = 0.753 +/- 0.006, indicating that the majority of the size fractionated particles originated from biogenic sources. Samples collected during the King Fire in Colfax, CA were used to determine the contribution of biomass burning (wildfire) aerosols. Factor analysis was used to reduce the ions found in the LD TOF-MS analysis of the King Fire samples. The final factor analysis generated a total of four factors that explained an overall 83% of the variance in the data set. Two of the factors correlated heavily with increased smoke events during the sample period. The increased smoke events produced a large number of highly oxidized organic aerosols (OOA2) and aromatic compounds that are indicative of biomass burning organic aerosols (WBOA). The signal intensities of the factors generated in the King Fire data were investigated in samples collected in Yosemite and Davis, CA to look at the impact of biomass burning on ambient atmospheric aerosols. In both comparison sample collections the OOA2 and WBOA factors both increased during biomass burning events located near the sampling sites. The correlation between the OOA2 and WBOA factors and smoke levels indicates that these factors can be used to identify the influence of biomass burning on ambient aerosols. The effectiveness of using the ChemWiki instead of a traditional textbook was investigated during the spring quarter of 2014. Student performance was measured using common midterms, a final, and a pre/post content exams. We also employed surveys, the Colorado Learning Attitudes about Science Survey (CLASS) for Chemistry, and a weekly time-on-task survey to quantify students' attitudes and study habits. The effectiveness of the ChemWiki compared to a traditional textbook was examined using multiple linear regression analysis with a standard non-inferiority testing framework. Results show that the performance of students in the section who were assigned readings from the ChemWiki was non-inferior to the performance of students in the section who were assigned readings from the traditional textbook, indicating that the ChemWiki does not substantially differ from the standard textbook in terms of student learning outcomes. The results from the surveys also suggest that the two classes were similar in their beliefs about chemistry and overall average time spent studying. These results indicate that the ChemWiki is a viable cost-saving alternative to traditional textbooks. The impact of using active learning techniques in a large lecture general chemistry class was investigated by assessing student performance and attitudes during the fall 2014 and winter 2015 quarters. One instructor applied active learning strategies while the remaining instructors employed more traditional lecture styles. Student performance, learning, learning environments, and attitudes were measured using a standardized pre/post exams, common final exams, classroom observations, and the CLASS chemistry instrument in large lecture general chemistry courses. Classroom observation data showed that the active learning class was the most student centered and of the other classes two instructors were transitional in their teaching style and the remaining two primarily employed traditional lecture techniques. The active learning class had the highest student performance but the difference was only statistically significant when compared to the two traditional lecture classes. Overall, our data showed a trend that student performance increased as the instructional style became more student centered. Student attitudes didn't seem to correlate with any specific instructional style and the students in the active learning class had similar attitudes to the other general students. The active learning class was successful in increasing the average time students spent studying outside of the class, a statistically significant difference of about 1.5 to 3.0 hrs/week.

Surface-water quality in rivers and drainage basins discharging to the southern part of Hood Canal, Mason and Kitsap Counties, Washington, 2004

USGS Publications Warehouse

Frans, L.M.; Paulson, A.J.; Huffman, R.L.; Osbourne, S.N.

2006-01-01

Concentrations of nutrients, major ions, organic carbon, suspended sediment, and the nitrogen isotope ratio of nitrate (delta15N) were collected at surface-water sites in rivers and drainage basins discharging to the southern part of Hood Canal, Mason and Kitsap Counties, Washington. Base-flow samples were collected from sites on the Union, Tahuya, and Skokomish Rivers from June to August 2004. Concentrations of nutrients at all sites were low. Ammonia and orthophosphate were less than the detection limit for most samples, and nitrate plus nitrite concentrations ranged from less than the detection limit of 0.06 to 0.49 milligram per liter (mg/L). Nitrate plus nitrite concentrations were near the detection limit of 0.06 mg/L in the North Fork, South Fork, and mainstem of the Skokomish River. The concentration of nitrate plus nitrite in the Tahuya River system above Lake Tahuya was 0.17 mg/L, but decreased to 0.1 mg/L or less downstream of Lake Tahuya. Overall, the Union River contained the highest nitrate plus nitrite concentrations of the three large river systems, ranging from 0.12 to 0.28 mg/L. delta15N generally was within the range that encompasses most sources, providing little information on nitrate sources. Most nitrogen was in the dissolved inorganic form. Dissolved inorganic nitrogen in Lake Tahuya was converted into particulate and dissolved organic nitrogen. Dissolved organic carbon concentrations generally were less than 1 mg/L in the Tahuya and Skokomish Rivers and averaged 1.3 mg/L in the Union River. Dissolved organic carbon concentrations of 2.6 to 2.7 mg/L at sites just downstream of Lake Tahuya were highest for the three large river systems, and decreased to concentrations less than 1 mg/L, which was similar to concentrations in the Skokomish River. Total nitrogen concentrations near 0.5 mg/L were measured at two sites: Unnamed Creek at Purdy-Cutoff Road (site S2b) and downstream of Lake Devereaux (site SP5). Concentrations of nitrate plus nitrite were highest at site S2b (0.49 mg/L), and dissolved organic carbon concentrations (3.3 mg/L) were highest at the outlet of Lake Devereaux. However, the overall impact of these sites on the nutrient loading to Hood Canal probably is negligible because of the low streamflow and small loads. Springtime samples were collected from the Union River, Tahuya River, Mission Creek, and three smaller drainage basins in March 2004. Samples were collected during spring rain events to determine if increased runoff contributes larger amounts of sediment and nutrients from the land into the surface water. There was little difference in nutrient concentrations between samples collected in the spring and base-flow samples collected in the summer. This is likely due to the fact that the springtime samples were collected during a rain event and not necessarily during a peak in the hydrograph.

Characterizing the environmental impact of metals in construction and demolition waste.

PubMed

Yu, Danfeng; Duan, Huabo; Song, Qingbin; Li, Xiaoyue; Zhang, Hao; Zhang, Hui; Liu, Yicheng; Shen, Weijun; Wang, Jinben

2018-05-01

Large quantities of construction and demolition (C&D) waste are generated in China every year, but their potential environmental impacts on the surrounding areas are rarely assessed. This study focuses on metals contained in C&D waste, characterizing the metal concentrations and their related environmental risks. C&D waste samples were collected in Shenzhen City, China, from building demolition sites, renovation areas undergoing refurbishment, landfill sites, and recycling companies (all located in Shenzhen city) that produce recycled aggregate, in order to identify pollution levels of the metals As, Cd, Cr, Cu, Pb, Ni, and Zn. The results showed that (1) the metal concentrations in most demolition and renovation waste samples were below the soil environmental quality standard for agricultural purposes (SQ-Agr.) in China; (2) Cd, Cu, and Zn led to relatively higher environmental risks than other metals, especially for Zn (DM5 tile sample, 360 mg/kg; R4 tile sample, 281 mg/kg); (3) non-inert C&D waste such as wall insulation and foamed plastic had high concentrations of As and Cd, so that these materials required special attention for sound waste management; and (4) C&D waste collected from landfill sites had higher concentrations of Cd and Cu than did waste collected from demolition and refurbishment sites.

Regional surnames and genetic structure in Great Britain.

PubMed

Kandt, Jens; Cheshire, James A; Longley, Paul A

2016-10-01

Following the increasing availability of DNA-sequenced data, the genetic structure of populations can now be inferred and studied in unprecedented detail. Across social science, this innovation is shaping new bio-social research agendas, attracting substantial investment in the collection of genetic, biological and social data for large population samples. Yet genetic samples are special because the precise populations that they represent are uncertain and ill-defined. Unlike most social surveys, a genetic sample's representativeness of the population cannot be established by conventional procedures of statistical inference, and the implications for population-wide generalisations about bio-social phenomena are little understood. In this paper, we seek to address these problems by linking surname data to a censored and geographically uneven sample of DNA scans, collected for the People of the British Isles study. Based on a combination of global and local spatial correspondence measures, we identify eight regions in Great Britain that are most likely to represent the geography of genetic structure of Great Britain's long-settled population. We discuss the implications of this regionalisation for bio-social investigations. We conclude that, as the often highly selective collection of DNA and biomarkers becomes a more common practice, geography is crucial to understanding variation in genetic information within diverse populations.

Measuring Charge Collection Efficiency in Diamond Vertex Detectors

NASA Astrophysics Data System (ADS)

Josey, Brian; Seidel, Sally; Hoeferkamp, Martin

2011-10-01

As currently used at the Large Hadron Collider, vertex detectors are composed primarily of silicon sensors that image particle tracks by detecting the creation of electron-hole pairs caused by the excitation of the silicon atoms. We are investigating replacing these silicon detectors with detectors made out of diamond. Diamond is advantageous due to its radiation hardness. We are measuring the charge collection efficiency of diamond as a function of fluence. We are building a characterization station. Diamond samples will be placed into the characterization station and exposed to a strontium-90 beta source, before and after I irradiate them with 800 MeV protons at LANL. The radiation from the Sr-90 source will create electron-hole pairs. These will be read out by applying an electric field across the sample. The system is triggered by a scintillator-photomultiplier tube assembly. The goal of this measurement is to record collected charge as a function of bias voltage. The diamond charge collection data will be compared to silicon and predictions about detector operation at the LHC will be made.

Evaluation of an offline method for the analysis of atmospheric reactive gaseous mercury and particulate mercury

USGS Publications Warehouse

Rutter, A.P.; Hanford, K.L.; Zwers, J.T.; Perillo-Nicholas, A. L.; Schauer, J.J.; Olson, M.L.

2008-01-01

Reactive gaseous mercury (RGM) and particulate mercury (PHg) were collected in Milwaukee, WI, between April 2004 and May 2005, and in Riverside, CA, between July 25 and August 7, 2005 using sorbent and filter substrates. The substrates were analyzed for mercury by thermal desorption analysis (TDA) using a purpose-built instrument. Results from this offline-TDA method were compared with measurements using a real-time atmospheric mercury analyzer. RGM measurements made with the offline-TDA agreed well with a commercial real-time method. However, the offline TDA reported PHg concentrations 2.7 times higher than the real-time method, indicating evaporative losses might be occurring from the real-time instrument during sample collection. TDA combined with reactive mercury collection on filter and absorbent substrates was cheap, relatively easy to use, did not introduce biases due to a semicontinuous sample collection strategy, and had a dynamic range appropriate for use in rural and urban locations. The results of this study demonstrate that offline-TDA is a feasible method for collecting reactive mercury concentrations in a large network of filter-based samplers. Copyright 2008 Air & Waste Management Association.

Accuracy assessment in the Large Area Crop Inventory Experiment

NASA Technical Reports Server (NTRS)

Houston, A. G.; Pitts, D. E.; Feiveson, A. H.; Badhwar, G.; Ferguson, M.; Hsu, E.; Potter, J.; Chhikara, R.; Rader, M.; Ahlers, C.

1979-01-01

The Accuracy Assessment System (AAS) of the Large Area Crop Inventory Experiment (LACIE) was responsible for determining the accuracy and reliability of LACIE estimates of wheat production, area, and yield, made at regular intervals throughout the crop season, and for investigating the various LACIE error sources, quantifying these errors, and relating them to their causes. Some results of using the AAS during the three years of LACIE are reviewed. As the program culminated, AAS was able not only to meet the goal of obtaining accurate statistical estimates of sampling and classification accuracy, but also the goal of evaluating component labeling errors. Furthermore, the ground-truth data processing matured from collecting data for one crop (small grains) to collecting, quality-checking, and archiving data for all crops in a LACIE small segment.

Evaluation of Streck BCT and PAXgene Stabilised Blood Collection Tubes for Cell-Free Circulating DNA Studies in Plasma.

PubMed

Warton, Kristina; Yuwono, Nicole L; Cowley, Mark J; McCabe, Mark J; So, Alwin; Ford, Caroline E

2017-10-01

Blood samples for studies of circulating DNA in disease are often collected in clinical settings where prompt processing of samples is not possible. In order to avoid problems associated with leukocyte lysis after prolonged blood storage, stabilised blood tubes have been developed containing preservatives that prevent cell lysis. We evaluated Streck BCT tubes and PAXgene ccfDNA tubes, as well as standard EDTA blood collection tubes, in terms of DNA yield and fragment size. Blood was collected in EDTA, Streck BCT or PAXgene ccfDNA tubes and stored for 1 h at 4 °C, or 4 days at room temperature. DNA was extracted using the QIAamp Circulating Nucleic Acids kit, and visualised on an agarose gel or quantitated by qPCR. Ratios of a 247-base and a 115-base amplicon of the Alu repetitive element were used to infer size distribution. While plasma DNA in EDTA tube blood samples increased by ~10- to 20-fold after 4 days of storage at room temperature, both Streck BCT tubes and PAXgene ccfDNA tubes maintained stable plasma DNA concentrations. A slight decrease in DNA yield following 1 h of blood storage at 4 °C was observed in Streck BCT and PAXgene ccfDNA tubes relative to EDTA tubes. This decrease was reversed by increasing the proteinase digest step of the DNA extraction protocol to 60 min, as recommended by Streck tube product literature. Visualisation of the extracted DNA on an agarose gel showed that after 4 days of room temperature storage, samples collected in EDTA tubes contained abundant high-molecular weight DNA, which was partially fragmented in a ladder pattern. A slight increase in high-molecular weight DNA in samples stored for 4 days at room temperature in Streck BCT tubes was also observed, but this was not reflected in a change in large and small Alu fragment ratios as measured by qPCR. Tubes containing preservative to prevent cell lysis can extend the scope for blood collection in clinical settings; however, slight differences between samples collected in different tube types underscore the requirement for standardised protocols, as well as attention to sample handling.

Self-adaptive enhanced sampling in the energy and trajectory spaces: accelerated thermodynamics and kinetic calculations.

PubMed

Gao, Yi Qin

2008-04-07

Here, we introduce a simple self-adaptive computational method to enhance the sampling in energy, configuration, and trajectory spaces. The method makes use of two strategies. It first uses a non-Boltzmann distribution method to enhance the sampling in the phase space, in particular, in the configuration space. The application of this method leads to a broad energy distribution in a large energy range and a quickly converged sampling of molecular configurations. In the second stage of simulations, the configuration space of the system is divided into a number of small regions according to preselected collective coordinates. An enhanced sampling of reactive transition paths is then performed in a self-adaptive fashion to accelerate kinetics calculations.

Fog chemistry in the Texas-Louisiana Gulf Coast corridor

NASA Astrophysics Data System (ADS)

Raja, Suresh; Raghunathan, Ravikrishna; Yu, Xiao-Ying; Lee, Taehyoung; Chen, Jing; Kommalapati, Raghava R.; Murugesan, Karthik; Shen, Xinhua; Qingzhong, Yuan; Valsaraj, Kalliat T.; Collett, Jeffrey L.

Fog samples were collected in two population centers of the US Gulf Coast (Houston, Texas and Baton Rouge, Louisiana) using Caltech active strand cloud collectors. A total of 32 fogwater samples were collected in Baton Rouge (November 2004-February 2005) and Houston (February 2006). These samples were analyzed for pH, total and dissolved organic carbon, major inorganic ions, and a variety of organic compounds including organic acids, aromatics, carbonyls, and linear alkanes. Fogs in both environments were of moderate density, with typical fog liquid water contents <100 mg m -3. Fog samples collected in Houston reflect a clear influence of marine and anthropogenic inputs, while Baton Rouge samples also reflect agricultural inputs. The volume-weighted mean fog pH was somewhat more acidic (˜4.3) in Houston than in Baton Rouge (˜5.0). A wide pH range was observed in fog at both locations. Houston fog had higher concentrations of Cl -, NO 3-, Na +, Mg 2+, and Ca 2+. Sulfate to nitrate ratios were high in fogs at both locations, typical of many clouds in the eastern US. Total organic carbon concentrations were much higher in Houston fogs than in Baton Rouge fogs. Efforts to speciate dissolved organic carbon (DOC) reveal large contributions from organic acids and carbonyls, with smaller contributions from other organic compound families including aromatics, alkanes, amides, and alcohols. Approximately 40% of the fog DOC was unspeciated in samples from both study locations.

Potential sources of bacteriological pollution for two bays with marinas in Trinidad.

PubMed

Bullock, Christine Ann; Moonesar, Indar

2005-05-01

Welcome Bay and Chaguaramas Bay in the northwest peninsula of Trinidad contain large marinas and smaller sections of bathing beaches. Bacteriological surveys were conducted at both bays to assess water quality and to determine potential sources of pollution. These surveys were conducted during the wet season of 1996 and the dry season of 1997. Eleven sample stations were established at Welcome Bay and 12 at Chaguaramas Bay. Freshwater samples were collected from rivers and drains within the survey area. Marine water samples were collected from marinas, bathing beaches and inshore and outer areas at both bays. Five water samples were collected from each sampling station during the wet season of 1996 and six during the dry season of 1997. The membrane filter technique was used to determine faecal coliform and Escherichia coli levels in all samples. There was a seasonal effect on water quality, with significantly higher faecal coliform levels in the wet season, when water quality was not in compliance with international standards. This represents a potential health risk in bathing areas. Water quality was better at the outer area of both bays. Water quality at the inner bay areas was most likely adversely affected by land-based sources of pollution identified in this study. These sources include three drains and two rivers, which discharged into the bays. Yachts were apparently not a source of sewage pollution: there was no significant relationship between yacht number and faecal coliform levels.

Perfluoroalkyl substances and extractable organic fluorine in surface sediments and cores from Lake Ontario.

PubMed

Yeung, Leo W Y; De Silva, Amila O; Loi, Eva I H; Marvin, Chris H; Taniyasu, Sachi; Yamashita, Nobuyoshi; Mabury, Scott A; Muir, Derek C G; Lam, Paul K S

2013-09-01

Fourteen perfluoroalkyl substances (PFASs) including short-chain perfluorocarboxylates (PFCAs, C4-C6) and perfluoroalkane sulfonates (PFSAs, C4 and C6) were measured in surface sediment samples from 26 stations collected in 2008 and sediment core samples from three stations (Niagara, Mississauga, and Rochester basins) collected in 2006 in Lake Ontario. Perfluorooctanesulfonate (PFOS), perfluorooctanoate (PFOA), perfluorononanoate (PFNA), perfluorodecanoate (PFDA), and perfluoroundecanoate (PFUnDA) were detected in all 26 surface sediment samples, whereas perfluorohexane sulfonate (PFHxS), perfluorooctane sulfonamide (FOSA), perfluorododecanoate (PFDoDA) and perfluorobutanoate (PFBA) were detected in over 70% of the surface sediment samples. PFOS was detected in all of the sediment core samples (range: 0.492-30.1ngg(-1) d.w.) over the period 1952-2005. The C8 to C11 PFCAs, FOSA, and PFBA increased in early 1970s. An overall increasing trend in sediment PFAS concentrations/fluxes from older to more recently deposited sediments was evident in the three sediment cores. The known PFCAs and PFSAs accounted for 2-44% of the anionic fraction of the extractable organic fluorine in surface sediment, suggesting that a large proportion of fluorine in this fraction remained unknown. Sediment core samples collected from Niagara basin showed an increase in unidentified organic fluorine in recent years (1995-2006). These results suggest that the use and manufacture of fluorinated organic compounds other than known PFCAs and PFSAs has diversified and increased. © 2013.

Field Tests of Real-time In-situ Dissolved CO2 Monitoring for CO2 Leakage Detection in Groundwater

NASA Astrophysics Data System (ADS)

Yang, C.; Zou, Y.; Delgado, J.; Guzman, N.; Pinedo, J.

2016-12-01

Groundwater monitoring for detecting CO2 leakage relies on groundwater sampling from water wells drilled into aquifers. Usually groundwater samples are required be collected periodically in field and analyzed in the laboratory. Obviously groundwater sampling is labor and cost-intensive for long-term monitoring of large areas. Potential damage and contamination of water samples during the sampling process can degrade accuracy, and intermittent monitoring may miss changes in the geochemical parameters of groundwater, and therefore signs of CO2 leakage. Real-time in-situ monitoring of geochemical parameters with chemical sensors may play an important role for CO2 leakage detection in groundwater at a geological carbon sequestration site. This study presents field demonstration of a real-time in situ monitoring system capable of covering large areas for detection of low levels of dissolved CO2 in groundwater and reliably differentiating natural variations of dissolved CO2 concentration from small changes resulting from leakage. The sand-alone system includes fully distributed fiber optic sensors for carbon dioxide detection with a unique sensor technology developed by Intelligent Optical Systems. The systems were deployed to the two research sites: the Brackenridge Field Laboratory where the aquifer is shallow at depths of 10-20 ft below surface and the Devine site where the aquifer is much deeper at depths of 140 to 150 ft. Groundwater samples were periodically collected from the water wells which were installed with the chemical sensors and further compared to the measurements of the chemical sensors. Our study shows that geochemical monitoring of dissolved CO2 with fiber optic sensors could provide reliable CO2 leakage signal detection in groundwater as long as CO2 leakage signals are stronger than background noises at the monitoring locations.

Compound Passport Service: supporting corporate collection owners in open innovation.

PubMed

Andrews, David M; Degorce, Sébastien L; Drake, David J; Gustafsson, Magnus; Higgins, Kevin M; Winter, Jon J

2015-10-01

A growing number of early discovery collaborative agreements are being put in place between large pharma companies and partners in which the rights for assets can reside with a partner, exclusively or jointly. Our corporate screening collection, like many others, was built on the premise that compounds generated in-house and not the subject of paper or patent disclosure were proprietary to the company. Collaborative screening arrangements and medicinal chemistry now make the origin, ownership rights and usage of compounds difficult to determine and manage. The Compound Passport Service is a dynamic database, managed and accessed through a set of reusable services that borrows from social media concepts to allow sample owners to take control of their samples in a much more active way. Copyright © 2015 Elsevier Ltd. All rights reserved.

A new bathyal sipunculan from Southern California, with ecological notes

NASA Astrophysics Data System (ADS)

Thompson, Bruce E.

1980-11-01

Golfingia (Nephasoma) nicolasi n. sp. is described. It is a long, slender species with a filiform introvert that is 6 to 7 times the length of the trunk. The species was often the numerically dominant taxon in samples collected from the San Nicolas Basin, California, and was also callected from several other basins off southern California. Analyses of several collections from the San Nicolas Basin show that the population was spatially patchy; temporal variation was also indicated but only one year was sampled adequately. Average population densities were highest at the base of the slopes descending into the basin from the highly productive Santa Rosa-Cortes Ridge and Tanner Bank. G. nicolasi appears to feed on the large amounts of organic detritus that accumulate from this source.

An indoor positioning technology in the BLE mobile payment system

NASA Astrophysics Data System (ADS)

Han, Tiantian; Ding, Lei

2017-05-01

Mobile payment system for large supermarkets, the core function is through the BLE low-power Bluetooth technology to achieve the amount of payment in the mobile payment system, can through an indoor positioning technology to achieve value-added services. The technology by collecting Bluetooth RSSI, the fingerprint database of sampling points corresponding is established. To get Bluetooth module RSSI by the AP. Then, to use k-Nearest Neighbor match the value of the fingerprint database. Thereby, to help businesses find customers through the mall location, combined settlement amount of the customer's purchase of goods, to analyze customer's behavior. When the system collect signal strength, the distribution of the sampling points of RSSI is analyzed and the value is filtered. The system, used in the laboratory is designed to demonstrate the feasibility.

Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering

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

Hong, Liang; Jain, Nitin; Cheng, Xiaolin

Protein function often depends on global, collective internal motions. However, the simultaneous quantitative experimental determination of the forms, amplitudes, and time scales of these motions has remained elusive. We demonstrate that a complete description of these large-scale dynamic modes can be obtained using coherent neutron-scattering experiments on perdeuterated samples. With this approach, a microscopic relationship between the structure, dynamics, and function in a protein, cytochrome P450cam, is established. The approach developed here should be of general applicability to protein systems.

Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering

DOE PAGES

Hong, Liang; Jain, Nitin; Cheng, Xiaolin; ...

2016-10-14

Protein function often depends on global, collective internal motions. However, the simultaneous quantitative experimental determination of the forms, amplitudes, and time scales of these motions has remained elusive. We demonstrate that a complete description of these large-scale dynamic modes can be obtained using coherent neutron-scattering experiments on perdeuterated samples. With this approach, a microscopic relationship between the structure, dynamics, and function in a protein, cytochrome P450cam, is established. The approach developed here should be of general applicability to protein systems.

Twenty five years of planetary science: Discoveries and new questions

NASA Astrophysics Data System (ADS)

Hauck, Steven A.; Baratoux, David; Stanley, Sabine

2016-10-01

This year marks the 25th anniversary of the first issue of JGR-Planets. We are marking this occasion with a collection of review papers focused on enduring and fundamental themes in planetary science that have framed the past quarter century and will strongly influence research and exploration in the next quarter century. With topics covering bodies small and large, processes on and in solid planets and giant planets, in atmospheres, and around other stars, this collection samples the broad scope of planetary science and of JGR-Planets.

Geochemical and radiological characterization of soils from former radium processing sites

USGS Publications Warehouse

Landa, E.R.

1984-01-01

Soil samples were collected from former radium processing sites in Denver, CO, and East Orange, NJ. Particle-size separations and radiochemical analyses of selected samples showed that while the greatest contents of both 226Ra and U were generally found in the finest (< 45 ??m) fraction, the pattern was not always of progressive increase in radionuclide content with decreasing particle size. Leaching tests on these samples showed a large portion of the 225Ra and U to be soluble in dilute hydrochloric acid. Radon-emanation coefficients measured for bulk samples of contaminated soil were about 20%. Recovery of residual uranium and vanadium, as an adjunct to any remedial action program, appears unlikely due to economic considerations.

Effects of Engineered Wettability on the Efficiency of Dew Collection.

PubMed

Gerasopoulos, Konstantinos; Luedeman, William L; Ölçeroglu, Emre; McCarthy, Matthew; Benkoski, Jason J

2018-01-31

Surface wettability plays an important role in dew collection. Nucleation is faster on hydrophilic surfaces, while droplets slide more readily on hydrophobic surfaces. Plants and animals in coastal desert environments appear to overcome this trade-off through biphilic surfaces with patterned wettability. In this study, we investigate the effects of millimeter-scale wettability patterns, mimicking those of the Stenocara beetle, on the rate of water collection from humid air. The rate of water collection per unit area is measured as a function of subcooling (ΔT = 1, 7, and 27 °C) and angle of inclination (from 10° to 90°). It is then compared for superbiphilic, hydrophilic, hydrophobic, and surperhydrophobic surfaces. For large subcooling, neither wettability nor tilt angle has a significant effect because the rate of condensation is so great. For 1 °C subcooling and large angles, hydrophilic surfaces perform best because condensation is the rate-limiting step. For low angles of inclination, superhydrophobic samples are best because droplet sliding is the rate-limiting step. Superbiphilic surfaces, in contrast to their superior fog collecting capabilities, generally collected dew at the slowest rate due to their inherent contact angle hysteresis. Theoretical considerations suggest that this finding may apply more generally to surfaces with patterned wettability.

Validation sampling can reduce bias in health care database studies: an illustration using influenza vaccination effectiveness.

PubMed

Nelson, Jennifer Clark; Marsh, Tracey; Lumley, Thomas; Larson, Eric B; Jackson, Lisa A; Jackson, Michael L

2013-08-01

Estimates of treatment effectiveness in epidemiologic studies using large observational health care databases may be biased owing to inaccurate or incomplete information on important confounders. Study methods that collect and incorporate more comprehensive confounder data on a validation cohort may reduce confounding bias. We applied two such methods, namely imputation and reweighting, to Group Health administrative data (full sample) supplemented by more detailed confounder data from the Adult Changes in Thought study (validation sample). We used influenza vaccination effectiveness (with an unexposed comparator group) as an example and evaluated each method's ability to reduce bias using the control time period before influenza circulation. Both methods reduced, but did not completely eliminate, the bias compared with traditional effectiveness estimates that do not use the validation sample confounders. Although these results support the use of validation sampling methods to improve the accuracy of comparative effectiveness findings from health care database studies, they also illustrate that the success of such methods depends on many factors, including the ability to measure important confounders in a representative and large enough validation sample, the comparability of the full sample and validation sample, and the accuracy with which the data can be imputed or reweighted using the additional validation sample information. Copyright © 2013 Elsevier Inc. All rights reserved.

Validation sampling can reduce bias in healthcare database studies: an illustration using influenza vaccination effectiveness

PubMed Central

Nelson, Jennifer C.; Marsh, Tracey; Lumley, Thomas; Larson, Eric B.; Jackson, Lisa A.; Jackson, Michael

2014-01-01

Objective Estimates of treatment effectiveness in epidemiologic studies using large observational health care databases may be biased due to inaccurate or incomplete information on important confounders. Study methods that collect and incorporate more comprehensive confounder data on a validation cohort may reduce confounding bias. Study Design and Setting We applied two such methods, imputation and reweighting, to Group Health administrative data (full sample) supplemented by more detailed confounder data from the Adult Changes in Thought study (validation sample). We used influenza vaccination effectiveness (with an unexposed comparator group) as an example and evaluated each method’s ability to reduce bias using the control time period prior to influenza circulation. Results Both methods reduced, but did not completely eliminate, the bias compared with traditional effectiveness estimates that do not utilize the validation sample confounders. Conclusion Although these results support the use of validation sampling methods to improve the accuracy of comparative effectiveness findings from healthcare database studies, they also illustrate that the success of such methods depends on many factors, including the ability to measure important confounders in a representative and large enough validation sample, the comparability of the full sample and validation sample, and the accuracy with which data can be imputed or reweighted using the additional validation sample information. PMID:23849144

USGS environmental characterization of flood sediments left in the New Orleans area after Hurricanes Katrina and Rita, 2005--Progress Report

USGS Publications Warehouse

Plumlee, Geoffrey S.; Meeker, Gregory P.; Lovelace, John K.; Rosenbauer, Robert J.; Lamothe, Paul J.; Furlong, Edward T.; Demas, Charles R.

2006-01-01

Introduction: The flooding in the greater New Orleans area that resulted from Hurricanes Katrina and Rita in September, 2005, left behind accumulations of sediments up to many centimeters thick on streets, lawns, parking lots, and other flat surfaces. These flood sediment deposits have been the focus of extensive study by the US Environmental Protection Agency (EPA) and Louisiana Department of Environmental Quality (LDEQ) due to concerns that the sediments may contain elevated levels of heavy metals, organic contaminants, and microbes. The U.S. Geological Survey (USGS) is characterizing a limited number of flood sediment samples that were collected on September 15-16 and October 6-7, 2005, from the greater New Orleans area by personnel from the USGS Louisiana Water Science Center in Baton Rouge. Small samples (< 3 pints each) of wet to dry flood sediment were collected from 11 localities around downtown New Orleans on September 15, 2005, and two large samples (40 pints each) of wet flood sediment were collected from the Chalmette area on September 16. Twelve additional samples (8-10 pints each) were collected from New Orleans, Slidell, Rigolets, and Violet on October 6 and 7. The USGS characterization studies of these flood sediments are designed to produce data and interpretations regarding how the sediments and any contained contaminants may respond to environmental processes. This information will be of use to cleanup managers and DoI/USGS scientists assessing environmental impacts of the hurricanes and subsequent cleanup activities.

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.

Collecting cometary soil samples? Development of the ROSETTA sample acquisition system

NASA Technical Reports Server (NTRS)

Coste, P. A.; Fenzi, M.; Eiden, Michael

1993-01-01

In the reference scenario of the ROSETTA CNRS mission, the Sample Acquisition System is mounted on the Comet Lander. Its tasks are to acquire three kinds of cometary samples and to transfer them to the Earth Return Capsule. Operations are to be performed in vacuum and microgravity, on a probably rough and dusty surface, in a largely unknown material, at temperatures in the order of 100 K. The concept and operation of the Sample Acquisition System are presented. The design of the prototype corer and surface sampling tool, and of the equipment for testing them at cryogenic temperatures in ambient conditions and in vacuum in various materials representing cometary soil, are described. Results of recent preliminary tests performed in low temperature thermal vacuum in a cometary analog ice-dust mixture are provided.

A Future Moon Mission: Curatorial Statistics on Regolith Fragments Applicable to Sample Collection by Raking

NASA Technical Reports Server (NTRS)

Allton, J. H.; Bevill, T. J.

2003-01-01

The strategy of raking rock fragments from the lunar regolith as a means of acquiring representative samples has wide support due to science return, spacecraft simplicity (reliability) and economy [3, 4, 5]. While there exists widespread agreement that raking or sieving the bulk regolith is good strategy, there is lively discussion about the minimum sample size. Advocates of consor-tium studies desire fragments large enough to support petrologic and isotopic studies. Fragments from 5 to 10 mm are thought adequate [4, 5]. Yet, Jolliff et al. [6] demonstrated use of 2-4 mm fragments as repre-sentative of larger rocks. Here we make use of cura-torial records and sample catalogs to give a different perspective on minimum sample size for a robotic sample collector.

The Population Reference Sample, POPRES: A Resource for Population, Disease, and Pharmacological Genetics Research

PubMed Central

Nelson, Matthew R.; Bryc, Katarzyna; King, Karen S.; Indap, Amit; Boyko, Adam R.; Novembre, John; Briley, Linda P.; Maruyama, Yuka; Waterworth, Dawn M.; Waeber, Gérard; Vollenweider, Peter; Oksenberg, Jorge R.; Hauser, Stephen L.; Stirnadel, Heide A.; Kooner, Jaspal S.; Chambers, John C.; Jones, Brendan; Mooser, Vincent; Bustamante, Carlos D.; Roses, Allen D.; Burns, Daniel K.; Ehm, Margaret G.; Lai, Eric H.

2008-01-01

Technological and scientific advances, stemming in large part from the Human Genome and HapMap projects, have made large-scale, genome-wide investigations feasible and cost effective. These advances have the potential to dramatically impact drug discovery and development by identifying genetic factors that contribute to variation in disease risk as well as drug pharmacokinetics, treatment efficacy, and adverse drug reactions. In spite of the technological advancements, successful application in biomedical research would be limited without access to suitable sample collections. To facilitate exploratory genetics research, we have assembled a DNA resource from a large number of subjects participating in multiple studies throughout the world. This growing resource was initially genotyped with a commercially available genome-wide 500,000 single-nucleotide polymorphism panel. This project includes nearly 6,000 subjects of African-American, East Asian, South Asian, Mexican, and European origin. Seven informative axes of variation identified via principal-component analysis (PCA) of these data confirm the overall integrity of the data and highlight important features of the genetic structure of diverse populations. The potential value of such extensively genotyped collections is illustrated by selection of genetically matched population controls in a genome-wide analysis of abacavir-associated hypersensitivity reaction. We find that matching based on country of origin, identity-by-state distance, and multidimensional PCA do similarly well to control the type I error rate. The genotype and demographic data from this reference sample are freely available through the NCBI database of Genotypes and Phenotypes (dbGaP). PMID:18760391

GenoCore: A simple and fast algorithm for core subset selection from large genotype datasets.

PubMed

Jeong, Seongmun; Kim, Jae-Yoon; Jeong, Soon-Chun; Kang, Sung-Taeg; Moon, Jung-Kyung; Kim, Namshin

2017-01-01

Selecting core subsets from plant genotype datasets is important for enhancing cost-effectiveness and to shorten the time required for analyses of genome-wide association studies (GWAS), and genomics-assisted breeding of crop species, etc. Recently, a large number of genetic markers (>100,000 single nucleotide polymorphisms) have been identified from high-density single nucleotide polymorphism (SNP) arrays and next-generation sequencing (NGS) data. However, there is no software available for picking out the efficient and consistent core subset from such a huge dataset. It is necessary to develop software that can extract genetically important samples in a population with coherence. We here present a new program, GenoCore, which can find quickly and efficiently the core subset representing the entire population. We introduce simple measures of coverage and diversity scores, which reflect genotype errors and genetic variations, and can help to select a sample rapidly and accurately for crop genotype dataset. Comparison of our method to other core collection software using example datasets are performed to validate the performance according to genetic distance, diversity, coverage, required system resources, and the number of selected samples. GenoCore selects the smallest, most consistent, and most representative core collection from all samples, using less memory with more efficient scores, and shows greater genetic coverage compared to the other software tested. GenoCore was written in R language, and can be accessed online with an example dataset and test results at https://github.com/lovemun/Genocore.

Concept Study For A Near-term Mars Surface Sample Return Mission

NASA Astrophysics Data System (ADS)

Smith, M. F.; Thatcher, J.; Sallaberger, C.; Reedman, T.; Pillinger, C. T.; Sims, M. R.

The return of samples from the surface of Mars is a challenging problem. Present mission planning is for complex missions to return large, focused samples sometime in the next decade. There is, however, much scientific merit in returning a small sample of Martian regolith before the end of this decade at a fraction of the cost of the more ambitious missions. This paper sets out the key elements of this concept that builds on the work of the Beagle 2 project and space robotics work in Canada. The paper will expand the science case for returning a regolith sample that is only in the range of 50-250g but would nevertheless include plenty of interesting mate- rial as the regolith comprises soil grains from a wide variety of locations i.e. nearby rocks, sedimentary formations and materials moved by fluids, winds and impacts. It is possible that a fine core sample could also be extracted and returned. The mission concept is to send a lander sized at around 130kg on the 2007 or 2009 opportunity, immediately collect the sample from the surface, launch it to Mars orbit, collect it by the lander parent craft and make an immediate Earth return. Return to Earth orbit is envisaged rather than direct Earth re-entry. The lander concept is essen- tially a twice-size Beagle 2 carrying the sample collection and return capsule loading equipment plus the ascent vehicle. The return capsule is envisaged as no more than 1kg. An overall description of the mission along with methods for sample acquisition, or- bital rendezvous and capsule return will be outlined and the overall systems budgets presented. To demonstrate the near term feasibility of the mission, the use of existing Canadian and European technologies will be highlighted.

The survival of large organic molecules during hypervelocity impacts with water ice: implications for sampling the icy surfaces of moons

NASA Astrophysics Data System (ADS)

Hurst, A.; Bowden, S. A.; Parnell, J.; Burchell, M. J.; Ball, A. J.

2007-12-01

There are a number of measurements relevant to planetary geology that can only be adequately performed by physically contacting a sample. This necessitates landing on the surface of a moon or planetary body or returning samples to earth. The need to physically contact a sample is particularly important in the case of measurements that could detect medium to low concentrations of large organic molecules present in surface materials. Large organic molecules, although a trace component of many meteoritic materials and rocks on the surface of earth, carry crucial information concerning the processing of meteoritic material in the surface and subsurface environments, and can be crucial indicators for the presence of life. Unfortunately landing on the surface of a small planetary body or moon is complicated, particularly if surface topography is only poorly characterised and the atmosphere thin thus requiring a propulsion system for a soft landing. One alternative to a surface landing may be to use an impactor launched from an orbiting spacecraft to launch material from the planets surface and shallow sub-surface into orbit. Ejected material could then be collected by a follow-up spacecraft and analyzed. The mission scenario considered in the Europa-Ice Clipper mission proposal included both sample return and the analysis of captured particles. Employing such a sampling procedure to analyse large organic molecules is only viable if large organic molecules present in ices survive hypervelocity impacts (HVIs). To investigate the survival of large organic molecules in HVIs with icy bodies a two stage light air gas gun was used to fire steel projectiles (1-1.5 mm diameter) at samples of water ice containing large organic molecules (amino acids, anthracene and beta-carotene a biological pigment) at velocities > 4.8 km/s.UV-VIS spectroscopy of ejected material detected beta-carotene indicating large organic molecules can survive hypervelocity impacts. These preliminary results are yet to be scaled up to a point where they can be accurately interpreted in the context of a likely mission scenario. However, they strongly indicate that in a low mass payload mission scenario where a lander has been considered unfeasible, such a sampling strategy merits further consideration.

Suspected seminal vesiculitis in an Asian elephant (Elephas maximus).

PubMed

Kilburn, Jennifer J; Velguth, Karen E; Backues, Kay A

2011-09-01

A 32-year-old male Asian elephant (Elephas maximus) underwent routine transrectal stimulation for semen collection as part of an artificial insemination program. The procedure consisted of a preinsemination semen collection followed by two consecutive days of semen collections for artificial insemination. The second day's sample contained large numbers of inflammatory cells, intracellular bacteria, and phagocytized sperm. Semen was submitted for culture and sensitivity. Culture revealed Acinetobacter lwoffii, Staphylococcus intermedius, Kocuria roseus, and an unidentified gram-positive organism. Empirical antibiotic therapy with trimethoprim sulfa was initiated and then changed to enrofloxacin based on sensitivity panel results for a total of 28 days of treatment. Diagnostic semen collections were performed during treatment and 2 wk posttreatment to determine the success of therapy. Posttreatment collections revealed resolution of the inflammation. The origin of the infection was suspected to be the seminal vesicles.

Assessing the efficacy of single-pass backpack electrofishing to characterize fish community structure

USGS Publications Warehouse

Meador, M.R.; McIntyre, J.P.; Pollock, K.H.

2003-01-01

Two-pass backpack electrofishing data collected as part of the U.S. Geological Survey's National Water-Quality Assessment Program were analyzed to assess the efficacy of single-pass backpack electrofishing. A two-capture removal model was used to estimate, within 10 river basins across the United States, proportional fish species richness from one-pass electrofishing and probabilities of detection for individual fish species. Mean estimated species richness from first-pass sampling (ps1) ranged from 80.7% to 100% of estimated total species richness for each river basin, based on at least seven samples per basin. However, ps1 values for individual sites ranged from 40% to 100% of estimated total species richness. Additional species unique to the second pass were collected in 50.3% of the samples. Of these, cyprinids and centrarchids were collected most frequently. Proportional fish species richness estimated for the first pass increased significantly with decreasing stream width for 1 of the 10 river basins. When used to calculate probabilities of detection of individual fish species, the removal model failed 48% of the time because the number of individuals of a species was greater in the second pass than in the first pass. Single-pass backpack electrofishing data alone may make it difficult to determine whether characterized fish community structure data are real or spurious. The two-pass removal model can be used to assess the effectiveness of sampling species richness with a single electrofishing pass. However, the two-pass removal model may have limited utility to determine probabilities of detection of individual species and, thus, limit the ability to assess the effectiveness of single-pass sampling to characterize species relative abundances. Multiple-pass (at least three passes) backpack electrofishing at a large number of sites may not be cost-effective as part of a standardized sampling protocol for large-geographic-scale studies. However, multiple-pass electrofishing at some sites may be necessary to better evaluate the adequacy of single-pass electrofishing and to help make meaningful interpretations of fish community structure.

Tiny videos: a large data set for nonparametric video retrieval and frame classification.

PubMed

Karpenko, Alexandre; Aarabi, Parham

2011-03-01

In this paper, we present a large database of over 50,000 user-labeled videos collected from YouTube. We develop a compact representation called "tiny videos" that achieves high video compression rates while retaining the overall visual appearance of the video as it varies over time. We show that frame sampling using affinity propagation-an exemplar-based clustering algorithm-achieves the best trade-off between compression and video recall. We use this large collection of user-labeled videos in conjunction with simple data mining techniques to perform related video retrieval, as well as classification of images and video frames. The classification results achieved by tiny videos are compared with the tiny images framework [24] for a variety of recognition tasks. The tiny images data set consists of 80 million images collected from the Internet. These are the largest labeled research data sets of videos and images available to date. We show that tiny videos are better suited for classifying scenery and sports activities, while tiny images perform better at recognizing objects. Furthermore, we demonstrate that combining the tiny images and tiny videos data sets improves classification precision in a wider range of categories.

Modern Foraminifera from a depth transect offshore Brunei Darussalam: diversity, sedimentation rate and preservation pathways.

NASA Astrophysics Data System (ADS)

Briguglio, Antonino; Goeting, Sulia; Kusli, Rosnani; Roslim, Amajida; Polgar, Gianluca; Kocsis, Laszlo

2016-04-01

For this study, 11 samples have been collected by scuba diving from 5 to 35 meters water depth off shore Brunei Darussalam. The locations sampled are known as: Pelong Rock (5 samples, shallow reef with soft and stony corals and larger foraminifera, 5 to 8 meters water depth), Abana Rock (1 sample, shallow reef with mainly soft corals and larger foraminifera, 13 to 18 meters water depth), Oil Rig wreck (1 sample, very sandy bottom with larger foraminifera, 18 meters water depth), Dolphin wreck (1 sample, muddy sand with many small rotaliids, 24 meters water depth), US wreck, (1 sample, sand with small clay fraction, 28 meters water depth), Australian wreck (1 sample, mainly medium to coarse sand with larger foraminifera, 34 meters water depth) and Blue water wreck (1 sample, mainly coarse sand, coral rubble and larger foraminifera, 35 meters water depth). Those samples closer to the river inputs are normally richer in clay, while the most distant samples are purely sandy. Some additional samples have been collected next to reef environments which, even if very shallow, are mainly sandy with almost no clay fraction. The deepest sample, which is 30 km offshore, contains some planktonic foraminifera and is characterized by a large range of preservations concerning foraminifera, thus testifying the presence or relict sediments at the sea bottom. The presence of relict sediments was already pointed out by older oil-related field studies offshore Brunei Darussalam, and now it is possible to draw the depth limit of these deposits. The diversity of the benthic foraminiferal fauna is relatively high but not as higher as neighboring regions as some studies have highlighted. The species collected and identified are more than 50: in reef environment the most abundant are Calcarina defrancii, Neorotalia calcar and the amphisteginidae; deeper in the muddy sediments the most abundant is Pararotalia schroeteriana and in the deepest sandy sample the most abundant are Calcarina hispida, followed by Operculina ammonoides.

Risks, Assets, and Negative Health Behaviors among Arkansas' Hispanic Adolescents

ERIC Educational Resources Information Center

Fitzpatrick, Kevin M.; Choudary, Wendie; Kearney, Anne; Piko, Bettina F.

2013-01-01

This study examined the relationship between risk, assets, and negative health behaviors among a large sample of Hispanic adolescents. Data were collected from over 1,000 Hispanic youth in grades 6, 8, 10, and 12 attending school in a moderate size school district in Northwest Arkansas. Logistic regression models examined the variation in the odds…

Factors Associated with School Meal Participation and the Relationship between Different Participation Measures. Final Report

ERIC Educational Resources Information Center

Moore, Quinn; Hulsey, Lara; Ponza, Michael

2009-01-01

This report investigates three important aspects of National School Lunch Program (NSLP) and School Breakfast Program (SBP) participation using recently collected data on a large, nationally representative sample of students certified for free and reduced-price meals during the 2005-2006 school year. First, we examine the factors that influence…

The Requirement for Vocational Skills in the Engineering Industry in the Areas of Modena and Vienna. Synthesis Report.

ERIC Educational Resources Information Center

Gatti, Mario; Mereu, Maria Grazia; Tagliaferro, Claudio; Markowitsch, Jorg; Neuberger, Robert

Requirements for vocational skills in the engineering industry in Modena, Italy, and Vienna, Austria, were studied. In Modena, employees of a representative sample of 90 small, medium, and large firms in the mechanical processing, agricultural machinery, and sports car manufacturing sectors were interviewed. In Vienna, data were collected through…

From Hospital to Nursing Facility: Factors Influencing Decisions

ERIC Educational Resources Information Center

Mason, Susan E.; Auerbach, Charles; LaPorte, Heidi Heft

2009-01-01

This study addresses the factors influencing decisions to send medicine-surgical (med-surg) patients home or to nursing facilities (NFs). The sample (n = 7,852) was taken from a large, urban, teaching, med-surg unit where discharges were documented and data collected over a two-and-a-half-year period. Using logistical regression, the factors found…

Mothers' and Fathers' Personality and Parenting: The Mediating Role of Sense of Competence

ERIC Educational Resources Information Center

De Haan, Amaranta D.; Prinzie, Peter; Dekoviv, Maja

2009-01-01

This prospective longitudinal study addressed 3 key questions regarding the processes of parenting in a large community sample of mothers (n = 589) and fathers (n = 518). First, the collective impact of parental Big Five personality dimensions on overreactive and warm parenting, assessed 6 years later by adolescents, was examined. Second,…

The Main Sources of Intersubject Variability in Neuronal Activation for Reading Aloud

ERIC Educational Resources Information Center

Kherif, Ferath; Josse, Goulven; Seghier, Mohamed L.; Price, Cathy J.

2009-01-01

The aim of this study was to find the most prominent source of intersubject variability in neuronal activation for reading familiar words aloud. To this end, we collected functional imaging data from a large sample of subjects (n = 76) with different demographic characteristics such as handedness, sex, and age, while reading. The…

Longitudinal Outcomes for Youth Receiving Runaway/Homeless Shelter Services

ERIC Educational Resources Information Center

Pollio, David E.; Thompson, Sanna J.; Tobias, Lisa; Reid, Donna; Spitznagel, Edward

2006-01-01

This research examined outcomes and use of specific types of services 6 weeks, 3 and 6 months post-discharge for a large sample of runaway/homeless youth using crisis shelter services. Data were collected for 371 runaway/homeless youth using emergency shelter and crisis services at eleven agencies across a four-state midwestern region. Outcomes…

SOURCE APPORTIONMENT OF INDOOR, OUTDOOR, AND PERSONAL PM2.5 IN SEATTLE, WASHINGTON, USING POSITIVE MATRIX FACTORIZATION

EPA Science Inventory

As part of a large exposure assessment and health effects panel study, 33 trace elements and light-absorbing carbon were measured on 24-hr particulate matter with an aero-dynamic diameter <2.5 um (PM2.5) fixed-site filter samples collected between September 26, 2000, and May 25, ...

Examining the Relationship between Classroom Climate and Student Achievement of Middle School Students

ERIC Educational Resources Information Center

Barksdale, Christopher J.

2017-01-01

The purpose of this sequential mixed method study was to examine the relationship between classroom climate and student achievement of middle school students. This study included a review of data collected from the Learning Environment Inventory from a purposeful sample of middle school students from a large suburban school district. A purposeful…

The Effect of a Teacher's Sex on Career Development.

ERIC Educational Resources Information Center

Reich, Carol

A survey was conducted of a sample of 1,163 male and female teachers, consultants, and administrators of a large, urban school system. Data was collected about their formal qualifications, job performance, the extent to which they had been encouraged to apply for promotion, the number of applications they had made, and the positions they had held.…

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...

Measuring Perceptions of the Learning Environment and Approaches to Learning: Validation of the Learn Questionnaire

ERIC Educational Resources Information Center

Herrmann, Kim Jesper; Bager-Elsborg, Anna; Parpala, Anna

2017-01-01

While focus on quality in Danish higher education has been growing in recent years, limited attention has been devoted to developing and thoroughly validating instruments that allow collecting data about university students' perceptions of the teaching-learning environment. Based on data from a large sample of Danish university students, a Danish…

An assessment of re-randomization methods in bark beetle (Scolytidae) trapping bioassays

Treesearch

Christopher J. Fettig; Christopher P. Dabney; Stepehen R. McKelvey; Robert R. Borys

2006-01-01

Numerous studies have explored the role of semiochemicals in the behavior of bark beetles (Scolytidae). Multiple funnel traps are often used to elucidate these behavioral responses. Sufficient sample sizes are obtained by using large numbers of traps to which treatments are randomly assigned once, or by frequent collection of trap catches and subsequent re-...

Investigating the Relationship between School Level and a School Growth Mindset

ERIC Educational Resources Information Center

Hanson, Janet; Ruff, William; Bangert, Arthur

2016-01-01

This study explored the relationship between school level and the psychosocial construct of a growth mindset school culture. Data was collected on the What's My School Mindset (WMSM) Survey from a stratified random sample of PK-12 faculty and administrators (n = 347) in 30 schools across a large northwestern state. The overarching research…

A new sampling strategy for cosmogenic surface exposure dating of moraines: Amalgamated Boulder Chips (ABCs)

NASA Astrophysics Data System (ADS)

Akif Sarıkaya, M.; Çiner, Attila; Yıldırım, Cengiz

2017-04-01

Cosmogenic surface exposure dating has been applied to date numerous moraines worldwide. The geochronological data obtained from these studies have improved our knowledge on the timing of glaciation and allow us to reconstruct the paleoclimate. Due to the geomorphic complications after deposition, such as degradation, exhumation, bedrock erosion, snow cover and toppling of boulders, several (n>5) large boulder (>1-2 m) samples should be dated to obtain a reliable age distribution. Generally, the ages on a well-preserved moraine surface show unimodal normal distribution. Frequently, erosion, exhumation and boulder toppling are blamed for the younger outliers. On the other hand, although infrequent, older outliers will indicate inherited nuclide concentration from pre-exposure to cosmic radiation. To obtain the true age of a moraine deposit, one needs to collect several samples that not only greatly increases the budget of the project but also is time consuming. To overcome this problem, we developed a new sampling strategy for dating moraine surfaces by cosmogenic nuclides. We collected rock chips (each 20-50 grams) from large boulder (>1 m) tops located on the crest of moraines. Fourteen to 32 boulders were chosen for sampling every 20 m. All rock chips were amalgamated to make one sample. To test the suitability of the method, we also sampled 3 large boulders (>1 m), as it is done classically, from the same surface. The age results from the two Late Pleistocene moraines and one rock glacier surface show no difference in terms of boulder exposure ages. Three 36Cl ages from one single lateral moraine in Çimi Valley of Geyikdaǧ, central Taurus, Turkey, are 11.9±0.9 ka, 14.0±1.1 ka and 11.9±0.9 ka (all ages have no erosion corrections) and yield a mean age of 12.6±0.9 ka, while the amalgamated boulder chips' (ABCs) age is 12.0±0.9 ka. Another well developed terminal moraine (so called Zor Moraine) in the Güneycik Valley of Geyikdaǧ, yielded ages as 4.9±0.4 ka, 7.7±0.6 ka and 3.7±0.3 ka, while the ABCs' age is 6.4±0.6 ka. The rock glacier boulder samples yielded ages of 12.2±0.9 ka, 14.0±1.0 ka and 9.2±0.8 ka, while the rock glacier ABCs' age is 10.7±0.9 ka. These results clearly indicate that the age obtained from ABCs is reliable and can safely replace classical methodology that requires collection of several samples from a moraine surface. The use of ABCs sampling strategy will considerably decrease the time and budget allocated to date a landform. This work was supported by TUBITAK 112Y139 project.

Population of collective modes in light scattering by many atoms

NASA Astrophysics Data System (ADS)

Guerin, William; Kaiser, Robin

2017-05-01

The interaction of light with an atomic sample containing a large number of particles gives rise to many collective (or cooperative) effects, such as multiple scattering, superradiance, and subradiance, even if the atomic density is low and the incident optical intensity weak (linear optics regime). Tracing over the degrees of freedom of the light field, the system can be well described by an effective atomic Hamiltonian, which contains the light-mediated dipole-dipole interaction between atoms. This long-range interaction is at the origin of the various collective effects, or of collective excitation modes of the system. Even though an analysis of the eigenvalues and eigenfunctions of these collective modes does allow distinguishing superradiant modes, for instance, from other collective modes, this is not sufficient to understand the dynamics of a driven system, as not all collective modes are significantly populated. Here, we study how the excitation parameters, i.e., the driving field, determines the population of the collective modes. We investigate in particular the role of the laser detuning from the atomic transition, and demonstrate a simple relation between the detuning and the steady-state population of the modes. This relation allows understanding several properties of cooperative scattering, such as why superradiance and subradiance become independent of the detuning at large enough detuning without vanishing, and why superradiance, but not subradiance, is suppressed near resonance. We also show that the spatial properties of the collective modes allow distinguishing diffusive modes, responsible for radiation trapping, from subradiant modes.

New estimates of nitrous oxide emissions from biomass burning

NASA Technical Reports Server (NTRS)

Cofer, W. R., III; Levine, J. S.; Winstead, E. L.; Stocks, B. J.

1991-01-01

The recent discovery of an artifact producing increased levels of N2O in combustion gas samples collected and stored in grab bottles before chemical analysis has resulted in the downgrading of fossil-fuel combustion and the questioning of biomass burning as important sources of N2O. As almost all reported analyses of N2O produced from biomass burning have involved essentially the same collection and analysis protocols as used in the fossil-fuel studies, this source of N2O must also be reexamined. Here, measurements of N2O made over a large prescribed fire using a near real-time in situ measurement technique are reported and compared with measurements of N2O from simultaneously collected grab-bottle samples. The results from 27 small laboratory biomass test fires are also used to help clarify the validity of earlier assessments. It is concluded that biomass burning contributes about seven percent of atmospheric N2O, as opposed to earlier estimates of several times this value.

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.

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.

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.

First molecular detection of Dirofilaria immitis (Spirurida: Onchocercidae) infection in dogs from Northern Algeria.

PubMed

Tahir, Djamel; Damene, Hanane; Davoust, Bernard; Parola, Philippe

2017-04-01

Dirofilaria immitis and Dirofilaria repens are mosquito-borne filarioid nematodes that affect dogs and other domestic and wild carnivores, causing heartworm disease and subcutaneous dirofilariosis, respectively. In Algeria, the data about the epidemiology of these infections is largely unknown. The present study was designed to establish the occurrence of D. immitis and D. repens in dogs in Algeria using molecular tools. In 2014 and 2015, a total of 209 dogs over one year of age of different breed and sex, living in Northern Algeria, were examined and blood samples were collected from each dog. The presence of D. immitis and D. repens in these samples was detected by real-time PCR followed by standard PCR and sequencing. Overall, the blood of 209 dogs from two departments was collected and only 3 (1.4%) of the blood samples were found positive for D. immitis DNA. Sequencing of the corresponding amplicon displayed a 99.8% identity to D. immitis, confirming the presence of this mosquito-borne nematode in Algeria. Furthermore, all tested samples were negative for D. repens. Copyright © 2017 Elsevier Ltd. All rights reserved.

Assessment of organic contaminants in emissions from refuse-derived fuel combustion

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

Chrostowski, J.; Wait, D.; Kwong, E.

1985-09-01

Organic contaminants in emissions from refuse-derived fuel combustion were investigated in a 20-inch-diameter atmospheric fluidized-bed combustor. Combinations of coal/EcoFuel/MSW/toluene were burned inthe combustor with temperatures ranging from 1250 to 1550 degrees F. A Source Assessment Sampling System (SASS) was used to sample the stack gas; Level 1 methodology was used to analyze the organic-contaminant levels. Combustion efficiencies of 93 to 98 percent were achieved in the test burns. Combustion of the EcoFuel generated fewer organic emissions than combustion of coal at similar combustion temperatures. The fine particulate collected by the SASS train filter contained higher concentrations of extractable organics thanmore » the reactor fly ash and the SASS cyclone samples. Combustion of a toluene/EcoFuel mix generated a large number of benzene derivatives not seen in the combustion of pure EcoFuel. Polycyclic aromatic hydrocarbons were the dominant organic compounds contained in the XAD-2 resin extract from coal combustion. A number of different priority pollutants were identified in the samples collected.« less

Proceedings Abstracts: American Water Resources Association's Symposium on the National Water-Quality Assessment (NAWQA) Program--November 7-9, 1994, Chicago, Illinois

USGS Publications Warehouse

Sorenson, Stephen K.

1994-01-01

Approximately 418,000 pounds of triazine herbicides are applied annually to control weeds in crops grown in the Albemarle-Pamilico Sound drainage basin, located in North Carolina and Virginia. An enzyme-linked immunosorbent assay was used to detect concentrations of total triazine herbicides in streams draining into Albemarle-Pamlico Sound. Water samples were collected in May and June during the application of triazine herbicides and in early September during low streamflows at approximately 40 sites on streams in the Coastal Plain and Piedmont Physiographic Provinces. Triazine concentrations exceeded 0.2 ?g/L (micrograms per liter) in 67 percent of the water samples collected In June, and 13 percent of the water samples exceeded 0.2 ?g/L in September during low streamflows. The enzyme-linked immunosorbent assay for total triazine herbicides provides a low-cost and rapid analytical method for screening water samples prior to sending them to a laboratory and for semiquantitatively assessing seasonal concentrations of triazine herbicides in streams throughout a large region.

Ichthyoplankton abundance and variance in a large river system concerns for long-term monitoring

USGS Publications Warehouse

Holland-Bartels, Leslie E.; Dewey, Michael R.; Zigler, Steven J.

1995-01-01

System-wide spatial patterns of ichthyoplankton abundance and variability were assessed in the upper Mississippi and lower Illinois rivers to address the experimental design and statistical confidence in density estimates. Ichthyoplankton was sampled from June to August 1989 in primary milieus (vegetated and non-vegated backwaters and impounded areas, main channels and main channel borders) in three navigation pools (8, 13 and 26) of the upper Mississippi River and in a downstream reach of the Illinois River. Ichthyoplankton densities varied among stations of similar aquatic landscapes (milieus) more than among subsamples within a station. An analysis of sampling effort indicated that the collection of single samples at many stations in a given milieu type is statistically and economically preferable to the collection of multiple subsamples at fewer stations. Cluster analyses also revealed that stations only generally grouped by their preassigned milieu types. Pilot studies such as this can define station groupings and sources of variation beyond an a priori habitat classification. Thus the minimum intensity of sampling required to achieve a desired statistical confidence can be identified before implementing monitoring efforts.

Comparison of the Organic Composition of Cometary Samples with Residues Formed from the UV Irradiation of Astrophysical Ice Analogs

NASA Technical Reports Server (NTRS)

Milam, S. N.; Nuevo, M.; Sandford, S. A.; Cody, G. D.; Kilcoyne, A. L. D.; Stroud, R. M.; DeGregorio, B. T.

2010-01-01

The NASA Stardust mission successfully collected material from Comet 81P/Wild 2 [1], including authentic cometary grains [2]. X-ray absorption near-edge structure (XANES) spectroscopy analysis of these samples indicates the presence of oxygen-rich and nitrogen-rich organic materials, which contain a broad variety of functional groups (carbonyls, C=C bonds, aliphatic chains, amines, arnides, etc.) [3]. One component of these organics appears to contain very little aromatic carbon and bears some similarity to the organic residues produced by the irradiation of ices of interstellar/cometary composition, Stardust samples were also recently shown to contain glycine, the smallest biological amino acid [4]. Organic residues produced froth the UV irradiation of astrophysical ice analogs are already known to contain a large suite of organic molecules including amino acids [5-7], amphiphilic compounds (fatty acids) [8], and other complex species. This work presents a comparison between XANES spectra measured from organic residues formed in the laboratory with similar data of cometary samples collected by the Stardust mission

Variability of 137Cs inventory at a reference site in west-central Iran.

PubMed

Bazshoushtari, Nasim; Ayoubi, Shamsollah; Abdi, Mohammad Reza; Mohammadi, Mohammad

2016-12-01

137 Cs technique has been widely used for the evaluation rates and patterns of soil erosion and deposition. This technique requires an accurate estimate of the values of 137 Cs inventory at the reference site. This study was conducted to evaluate the variability of the inventory of 137 Cs regarding to the sampling program including sample size, distance and sampling method at a reference site located in vicinity of Fereydan district in Isfahan province, west-central Iran. Two 3 × 8 grids were established comprising large grid (35 m length and 8 m width), and small grid (24 m length and 6 m width). At each grid intersection two soil samples were collected from 0 to 15 cm and 15-30 cm depths, totally 96 soil samples from 48 sampling points. Coefficients of variation for 137 Cs inventory in the soil samples was relatively low (CV = 15%), and the sampling distance and methods used did not significantly affect the 137 Cs inventories across the studied reference site. To obtain a satisfactory estimate of the mean 137 Cs activity in the reference sites, particularly those located in the semiarid regions, it is recommended to collect at least four samples along in a grid pattern 3 m apart. Copyright © 2016 Elsevier Ltd. All rights reserved.

Pesticides in Water and Suspended Sediment of the Alamo and New Rivers, Imperial Valley/Salton Sea Basin, California, 2006-2007

USGS Publications Warehouse

Orlando, James L.; Smalling, Kelly L.; Kuivila, Kathryn

2008-01-01

Water and suspended-sediment samples were collected at eight sites on the Alamo and New Rivers in the Imperial Valley/Salton Sea Basin of California and analyzed for both current-use and organochlorine pesticides by the U.S. Geological Survey. Samples were collected in the fall of 2006 and spring of 2007, corresponding to the seasons of greatest pesticide use in the basin. Large-volume water samples (up to 650 liters) were collected at each site and processed using a flow-through centrifuge to isolate suspended sediments. One-liter water samples were collected from the effluent of the centrifuge for the analysis of dissolved pesticides. Additional samples were collected for analysis of dissolved organic carbon and for suspended-sediment concentrations. Water samples were analyzed for a suite of 61 current-use and organochlorine pesticides using gas chromatography/mass spectrometry. A total of 25 pesticides were detected in the water samples, with seven pesticides detected in more than half of the samples. Dissolved concentrations of pesticides observed in this study ranged from below their respective method detection limits to 8,940 nanograms per liter (EPTC). The most frequently detected compounds in the water samples were chlorpyrifos, DCPA, EPTC, and trifluralin, which were observed in more than 75 percent of the samples. The maximum concentrations of most pesticides were detected in samples from the Alamo River. Maximum dissolved concentrations of carbofuran, chlorpyrifos, diazinon, and malathion exceeded aquatic life benchmarks established by the U.S. Environmental Protection Agency for these pesticides. Suspended sediments were analyzed for 87 current-use and organochlorine pesticides using microwave-assisted extraction, gel permeation chromatography for sulfur removal, and either carbon/alumina stacked solid-phase extraction cartridges or deactivated Florisil for removal of matrix interferences. Twenty current-use pesticides were detected in the suspended-sediment samples, including pyrethroid insecticides and fungicides. Fourteen legacy organochlorine pesticides also were detected in the suspended-sediment samples. Greater numbers of current-use and organochlorine pesticides were observed in the Alamo River samples in comparison with the New River samples. Maximum concentrations of current-use pesticides in suspended-sediment samples ranged from below their method detection limits to 174 micrograms per kilogram (pendimethalin). Most organochlorine pesticides were detected at or below their method detection limits, with the exception of p,p'-DDE, which had a maximum concentration of 54.2 micrograms per kilogram. The most frequently detected current-use pesticides in the suspended-sediment samples were chlorpyrifos, permethrin, tetraconazole, and trifluralin, which were observed in more than 83 percent of the samples. The organochlorine degradates p,p'-DDD and p,p'-DDE were detected in all suspended-sediment samples.

Collective behavior of large-scale neural networks with GPU acceleration.

PubMed

Qu, Jingyi; Wang, Rubin

2017-12-01

In this paper, the collective behaviors of a small-world neuronal network motivated by the anatomy of a mammalian cortex based on both Izhikevich model and Rulkov model are studied. The Izhikevich model can not only reproduce the rich behaviors of biological neurons but also has only two equations and one nonlinear term. Rulkov model is in the form of difference equations that generate a sequence of membrane potential samples in discrete moments of time to improve computational efficiency. These two models are suitable for the construction of large scale neural networks. By varying some key parameters, such as the connection probability and the number of nearest neighbor of each node, the coupled neurons will exhibit types of temporal and spatial characteristics. It is demonstrated that the implementation of GPU can achieve more and more acceleration than CPU with the increasing of neuron number and iterations. These two small-world network models and GPU acceleration give us a new opportunity to reproduce the real biological network containing a large number of neurons.

Maximizing fluorescence collection efficiency in multiphoton microscopy

PubMed Central

Zinter, Joseph P.; Levene, Michael J.

2011-01-01

Understanding fluorescence propagation through a multiphoton microscope is of critical importance in designing high performance systems capable of deep tissue imaging. Optical models of a scattering tissue sample and the Olympus 20X 0.95NA microscope objective were used to simulate fluorescence propagation as a function of imaging depth for physiologically relevant scattering parameters. The spatio-angular distribution of fluorescence at the objective back aperture derived from these simulations was used to design a simple, maximally efficient post-objective fluorescence collection system. Monte Carlo simulations corroborated by data from experimental tissue phantoms demonstrate collection efficiency improvements of 50% – 90% over conventional, non-optimized fluorescence collection geometries at large imaging depths. Imaging performance was verified by imaging layer V neurons in mouse cortex to a depth of 850 μm. PMID:21934897

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