Apparatus and method for handheld sampling

DOEpatents

Staab, Torsten A.

2005-09-20

The present invention includes an apparatus, and corresponding method, for taking a sample. The apparatus is built around a frame designed to be held in at least one hand. A sample media is used to secure the sample. A sample media adapter for securing the sample media is operated by a trigger mechanism connectively attached within the frame to the sample media adapter.

Soil sampling kit and a method of sampling therewith

DOEpatents

Thompson, C.V.

1991-02-05

A soil sampling device and a sample containment device for containing a soil sample is disclosed. In addition, a method for taking a soil sample using the soil sampling device and soil sample containment device to minimize the loss of any volatile organic compounds contained in the soil sample prior to analysis is disclosed. The soil sampling device comprises two close fitting, longitudinal tubular members of suitable length, the inner tube having the outward end closed. With the inner closed tube withdrawn a selected distance, the outer tube can be inserted into the ground or other similar soft material to withdraw a sample of material for examination. The inner closed end tube controls the volume of the sample taken and also serves to eject the sample. The soil sample containment device has a sealing member which is adapted to attach to an analytical apparatus which analyzes the volatile organic compounds contained in the sample. The soil sampling device in combination with the soil sample containment device allows an operator to obtain a soil sample containing volatile organic compounds and minimizing the loss of the volatile organic compounds prior to analysis of the soil sample for the volatile organic compounds. 11 figures.

7 CFR 29.110 - Method of sampling.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Method of sampling. 29.110 Section 29.110 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... INSPECTION Regulations Inspectors, Samplers, and Weighers § 29.110 Method of sampling. In sampling tobacco...

7 CFR 29.110 - Method of sampling.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 2 2011-01-01 2011-01-01 false Method of sampling. 29.110 Section 29.110 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... INSPECTION Regulations Inspectors, Samplers, and Weighers § 29.110 Method of sampling. In sampling tobacco...

Uniform Sampling Table Method and its Applications II--Evaluating the Uniform Sampling by Experiment.

PubMed

Chen, Yibin; Chen, Jiaxi; Chen, Xuan; Wang, Min; Wang, Wei

2015-01-01

A new method of uniform sampling is evaluated in this paper. The items and indexes were adopted to evaluate the rationality of the uniform sampling. The evaluation items included convenience of operation, uniformity of sampling site distribution, and accuracy and precision of measured results. The evaluation indexes included operational complexity, occupation rate of sampling site in a row and column, relative accuracy of pill weight, and relative deviation of pill weight. They were obtained from three kinds of drugs with different shape and size by four kinds of sampling methods. Gray correlation analysis was adopted to make the comprehensive evaluation by comparing it with the standard method. The experimental results showed that the convenience of uniform sampling method was 1 (100%), odds ratio of occupation rate in a row and column was infinity, relative accuracy was 99.50-99.89%, reproducibility RSD was 0.45-0.89%, and weighted incidence degree exceeded the standard method. Hence, the uniform sampling method was easy to operate, and the selected samples were distributed uniformly. The experimental results demonstrated that the uniform sampling method has good accuracy and reproducibility, which can be put into use in drugs analysis.

A LITERATURE REVIEW OF WIPE SAMPLING METHODS ...

EPA Pesticide Factsheets

Wipe sampling is an important technique for the estimation of contaminant deposition in buildings, homes, or outdoor surfaces as a source of possible human exposure. Numerousmethods of wipe sampling exist, and each method has its own specification for the type of wipe, wetting solvent, and determinative step to be used, depending upon the contaminant of concern. The objective of this report is to concisely summarize the findings of a literature review that was conducted to identify the state-of-the-art wipe sampling techniques for a target list of compounds. This report describes the methods used to perform the literature review; a brief review of wipe sampling techniques in general; an analysis of physical and chemical properties of each target analyte; an analysis of wipe sampling techniques for the target analyte list; and asummary of the wipe sampling techniques for the target analyte list, including existing data gaps. In general, no overwhelming consensus can be drawn from the current literature on how to collect a wipe sample for the chemical warfare agents, organophosphate pesticides, and other toxic industrial chemicals of interest to this study. Different methods, media, and wetting solvents have been recommended and used by various groups and different studies. For many of the compounds of interest, no specific wipe sampling methodology has been established for their collection. Before a wipe sampling method (or methods) can be established for the co

19 CFR 151.83 - Method of sampling.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 19 Customs Duties 2 2010-04-01 2010-04-01 false Method of sampling. 151.83 Section 151.83 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Cotton § 151.83 Method of sampling. For...

Sampling bee communities using pan traps: alternative methods increase sample size

USDA-ARS?s Scientific Manuscript database

Monitoring of the status of bee populations and inventories of bee faunas require systematic sampling. Efficiency and ease of implementation has encouraged the use of pan traps to sample bees. Efforts to find an optimal standardized sampling method for pan traps have focused on pan trap color. Th...

Sample normalization methods in quantitative metabolomics.

PubMed

Wu, Yiman; Li, Liang

2016-01-22

To reveal metabolomic changes caused by a biological event in quantitative metabolomics, it is critical to use an analytical tool that can perform accurate and precise quantification to examine the true concentration differences of individual metabolites found in different samples. A number of steps are involved in metabolomic analysis including pre-analytical work (e.g., sample collection and storage), analytical work (e.g., sample analysis) and data analysis (e.g., feature extraction and quantification). Each one of them can influence the quantitative results significantly and thus should be performed with great care. Among them, the total sample amount or concentration of metabolites can be significantly different from one sample to another. Thus, it is critical to reduce or eliminate the effect of total sample amount variation on quantification of individual metabolites. In this review, we describe the importance of sample normalization in the analytical workflow with a focus on mass spectrometry (MS)-based platforms, discuss a number of methods recently reported in the literature and comment on their applicability in real world metabolomics applications. Sample normalization has been sometimes ignored in metabolomics, partially due to the lack of a convenient means of performing sample normalization. We show that several methods are now available and sample normalization should be performed in quantitative metabolomics where the analyzed samples have significant variations in total sample amounts. Copyright © 2015 Elsevier B.V. All rights reserved.

7 CFR 58.812 - Methods of sample analysis.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 3 2010-01-01 2010-01-01 false Methods of sample analysis. 58.812 Section 58.812... Procedures § 58.812 Methods of sample analysis. Samples shall be tested according to the applicable methods of laboratory analysis contained in either DA Instruction 918-RL, as issued by the USDA, Agricultural...

7 CFR 58.245 - Method of sample analysis.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 3 2010-01-01 2010-01-01 false Method of sample analysis. 58.245 Section 58.245... Procedures § 58.245 Method of sample analysis. Samples shall be tested according to the applicable methods of laboratory analysis contained in either DA Instruction 918-RL as issued by the USDA, Agricultural Marketing...

[Respondent-Driven Sampling: a new sampling method to study visible and hidden populations].

PubMed

Mantecón, Alejandro; Juan, Montse; Calafat, Amador; Becoña, Elisardo; Román, Encarna

2008-01-01

The paper introduces a variant of chain-referral sampling: respondent-driven sampling (RDS). This sampling method shows that methods based on network analysis can be combined with the statistical validity of standard probability sampling methods. In this sense, RDS appears to be a mathematical improvement of snowball sampling oriented to the study of hidden populations. However, we try to prove its validity with populations that are not within a sampling frame but can nonetheless be contacted without difficulty. The basics of RDS are explained through our research on young people (aged 14 to 25) who go clubbing, consume alcohol and other drugs, and have sex. Fieldwork was carried out between May and July 2007 in three Spanish regions: Baleares, Galicia and Comunidad Valenciana. The presentation of the study shows the utility of this type of sampling when the population is accessible but there is a difficulty deriving from the lack of a sampling frame. However, the sample obtained is not a random representative one in statistical terms of the target population. It must be acknowledged that the final sample is representative of a 'pseudo-population' that approximates to the target population but is not identical to it.

Extending the solvent-free MALDI sample preparation method.

PubMed

Hanton, Scott D; Parees, David M

2005-01-01

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is an important technique to characterize many different materials, including synthetic polymers. MALDI mass spectral data can be used to determine the polymer average molecular weights, repeat units, and end groups. One of the key issues in traditional MALDI sample preparation is making good solutions of the analyte and the matrix. Solvent-free sample preparation methods have been developed to address these issues. Previous results of solvent-free or dry prepared samples show some advantages over traditional wet sample preparation methods. Although the results of the published solvent-free sample preparation methods produced excellent mass spectra, we found the method to be very time-consuming, with significant tool cleaning, which presents a significant possibility of cross contamination. To address these issues, we developed an extension of the solvent-free method that replaces the mortar and pestle grinding with ball milling the sample in a glass vial with two small steel balls. This new method generates mass spectra with equal quality of the previous methods, but has significant advantages in productivity, eliminates cross contamination, and is applicable to liquid and soft or waxy analytes.

Fluidics platform and method for sample preparation

DOEpatents

Benner, Henry W.; Dzenitis, John M.

2016-06-21

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

Sampling Methods in Cardiovascular Nursing Research: An Overview.

PubMed

Kandola, Damanpreet; Banner, Davina; O'Keefe-McCarthy, Sheila; Jassal, Debbie

2014-01-01

Cardiovascular nursing research covers a wide array of topics from health services to psychosocial patient experiences. The selection of specific participant samples is an important part of the research design and process. The sampling strategy employed is of utmost importance to ensure that a representative sample of participants is chosen. There are two main categories of sampling methods: probability and non-probability. Probability sampling is the random selection of elements from the population, where each element of the population has an equal and independent chance of being included in the sample. There are five main types of probability sampling including simple random sampling, systematic sampling, stratified sampling, cluster sampling, and multi-stage sampling. Non-probability sampling methods are those in which elements are chosen through non-random methods for inclusion into the research study and include convenience sampling, purposive sampling, and snowball sampling. Each approach offers distinct advantages and disadvantages and must be considered critically. In this research column, we provide an introduction to these key sampling techniques and draw on examples from the cardiovascular research. Understanding the differences in sampling techniques may aid nurses in effective appraisal of research literature and provide a reference pointfor nurses who engage in cardiovascular research.

New prior sampling methods for nested sampling - Development and testing

NASA Astrophysics Data System (ADS)

Stokes, Barrie; Tuyl, Frank; Hudson, Irene

2017-06-01

Nested Sampling is a powerful algorithm for fitting models to data in the Bayesian setting, introduced by Skilling [1]. The nested sampling algorithm proceeds by carrying out a series of compressive steps, involving successively nested iso-likelihood boundaries, starting with the full prior distribution of the problem parameters. The "central problem" of nested sampling is to draw at each step a sample from the prior distribution whose likelihood is greater than the current likelihood threshold, i.e., a sample falling inside the current likelihood-restricted region. For both flat and informative priors this ultimately requires uniform sampling restricted to the likelihood-restricted region. We present two new methods of carrying out this sampling step, and illustrate their use with the lighthouse problem [2], a bivariate likelihood used by Gregory [3] and a trivariate Gaussian mixture likelihood. All the algorithm development and testing reported here has been done with Mathematica® [4].

Configurations and calibration methods for passive sampling techniques.

PubMed

Ouyang, Gangfeng; Pawliszyn, Janusz

2007-10-19

Passive sampling technology has developed very quickly in the past 15 years, and is widely used for the monitoring of pollutants in different environments. The design and quantification of passive sampling devices require an appropriate calibration method. Current calibration methods that exist for passive sampling, including equilibrium extraction, linear uptake, and kinetic calibration, are presented in this review. A number of state-of-the-art passive sampling devices that can be used for aqueous and air monitoring are introduced according to their calibration methods.

Evaluation of common methods for sampling invertebrate pollinator assemblages: net sampling out-perform pan traps.

PubMed

Popic, Tony J; Davila, Yvonne C; Wardle, Glenda M

2013-01-01

Methods for sampling ecological assemblages strive to be efficient, repeatable, and representative. Unknowingly, common methods may be limited in terms of revealing species function and so of less value for comparative studies. The global decline in pollination services has stimulated surveys of flower-visiting invertebrates, using pan traps and net sampling. We explore the relative merits of these two methods in terms of species discovery, quantifying abundance, function, and composition, and responses of species to changing floral resources. Using a spatially-nested design we sampled across a 5000 km(2) area of arid grasslands, including 432 hours of net sampling and 1296 pan trap-days, between June 2010 and July 2011. Net sampling yielded 22% more species and 30% higher abundance than pan traps, and better reflected the spatio-temporal variation of floral resources. Species composition differed significantly between methods; from 436 total species, 25% were sampled by both methods, 50% only by nets, and the remaining 25% only by pans. Apart from being less comprehensive, if pan traps do not sample flower-visitors, the link to pollination is questionable. By contrast, net sampling functionally linked species to pollination through behavioural observations of flower-visitation interaction frequency. Netted specimens are also necessary for evidence of pollen transport. Benefits of net-based sampling outweighed minor differences in overall sampling effort. As pan traps and net sampling methods are not equivalent for sampling invertebrate-flower interactions, we recommend net sampling of invertebrate pollinator assemblages, especially if datasets are intended to document declines in pollination and guide measures to retain this important ecosystem service.

Evaluation of Common Methods for Sampling Invertebrate Pollinator Assemblages: Net Sampling Out-Perform Pan Traps

PubMed Central

Popic, Tony J.; Davila, Yvonne C.; Wardle, Glenda M.

2013-01-01

Methods for sampling ecological assemblages strive to be efficient, repeatable, and representative. Unknowingly, common methods may be limited in terms of revealing species function and so of less value for comparative studies. The global decline in pollination services has stimulated surveys of flower-visiting invertebrates, using pan traps and net sampling. We explore the relative merits of these two methods in terms of species discovery, quantifying abundance, function, and composition, and responses of species to changing floral resources. Using a spatially-nested design we sampled across a 5000 km2 area of arid grasslands, including 432 hours of net sampling and 1296 pan trap-days, between June 2010 and July 2011. Net sampling yielded 22% more species and 30% higher abundance than pan traps, and better reflected the spatio-temporal variation of floral resources. Species composition differed significantly between methods; from 436 total species, 25% were sampled by both methods, 50% only by nets, and the remaining 25% only by pans. Apart from being less comprehensive, if pan traps do not sample flower-visitors, the link to pollination is questionable. By contrast, net sampling functionally linked species to pollination through behavioural observations of flower-visitation interaction frequency. Netted specimens are also necessary for evidence of pollen transport. Benefits of net-based sampling outweighed minor differences in overall sampling effort. As pan traps and net sampling methods are not equivalent for sampling invertebrate-flower interactions, we recommend net sampling of invertebrate pollinator assemblages, especially if datasets are intended to document declines in pollination and guide measures to retain this important ecosystem service. PMID:23799127

Systems and methods for sample analysis

DOEpatents

Cooks, Robert Graham; Li, Guangtao; Li, Xin; Ouyang, Zheng

2015-01-13

The invention generally relates to systems and methods for sample analysis. In certain embodiments, the invention provides a system for analyzing a sample that includes a probe including a material connected to a high voltage source, a device for generating a heated gas, and a mass analyzer.

40 CFR Appendix I to Part 261 - Representative Sampling Methods

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 25 2010-07-01 2010-07-01 false Representative Sampling Methods I...—Representative Sampling Methods The methods and equipment used for sampling waste materials will vary with the form and consistency of the waste materials to be sampled. Samples collected using the sampling...

40 CFR Appendix I to Part 261 - Representative Sampling Methods

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 26 2011-07-01 2011-07-01 false Representative Sampling Methods I...—Representative Sampling Methods The methods and equipment used for sampling waste materials will vary with the form and consistency of the waste materials to be sampled. Samples collected using the sampling...

Mixed Methods Sampling: A Typology with Examples

ERIC Educational Resources Information Center

Teddlie, Charles; Yu, Fen

2007-01-01

This article presents a discussion of mixed methods (MM) sampling techniques. MM sampling involves combining well-established qualitative and quantitative techniques in creative ways to answer research questions posed by MM research designs. Several issues germane to MM sampling are presented including the differences between probability and…

Log sampling methods and software for stand and landscape analyses.

Treesearch

Lisa J. Bate; Torolf R. Torgersen; Michael J. Wisdom; Edward O. Garton; Shawn C. Clabough

2008-01-01

We describe methods for efficient, accurate sampling of logs at landscape and stand scales to estimate density, total length, cover, volume, and weight. Our methods focus on optimizing the sampling effort by choosing an appropriate sampling method and transect length for specific forest conditions and objectives. Sampling methods include the line-intersect method and...

New methods for sampling sparse populations

Treesearch

Anna Ringvall

2007-01-01

To improve surveys of sparse objects, methods that use auxiliary information have been suggested. Guided transect sampling uses prior information, e.g., from aerial photographs, for the layout of survey strips. Instead of being laid out straight, the strips will wind between potentially more interesting areas. 3P sampling (probability proportional to prediction) uses...

SOIL AND SEDIMENT SAMPLING METHODS

EPA Science Inventory

The EPA Office of Solid Waste and Emergency Response's (OSWER) Office of Superfund Remediation and Technology Innovation (OSRTI) needs innovative methods and techniques to solve new and difficult sampling and analytical problems found at the numerous Superfund sites throughout th...

Modified electrokinetic sample injection method in chromatography and electrophoresis analysis

DOEpatents

Davidson, J. Courtney; Balch, Joseph W.

2001-01-01

A sample injection method for horizontal configured multiple chromatography or electrophoresis units, each containing a number of separation/analysis channels, that enables efficient introduction of analyte samples. This method for loading when taken in conjunction with horizontal microchannels allows much reduced sample volumes and a means of sample stacking to greatly reduce the concentration of the sample. This reduction in the amount of sample can lead to great cost savings in sample preparation, particularly in massively parallel applications such as DNA sequencing. The essence of this method is in preparation of the input of the separation channel, the physical sample introduction, and subsequent removal of excess material. By this method, sample volumes of 100 nanoliter to 2 microliters have been used successfully, compared to the typical 5 microliters of sample required by the prior separation/analysis method.

Rapid method for sampling metals for materials identification

NASA Technical Reports Server (NTRS)

Higgins, L. E.

1971-01-01

Nondamaging process similar to electrochemical machining is useful in obtaining metal samples from places inaccessible to conventional sampling methods or where methods would be hazardous or contaminating to specimens. Process applies to industries where metals or metal alloys play a vital role.

Comparability of river suspended-sediment sampling and laboratory analysis methods

USGS Publications Warehouse

Groten, Joel T.; Johnson, Gregory D.

2018-03-06

Accurate measurements of suspended sediment, a leading water-quality impairment in many Minnesota rivers, are important for managing and protecting water resources; however, water-quality standards for suspended sediment in Minnesota are based on grab field sampling and total suspended solids (TSS) laboratory analysis methods that have underrepresented concentrations of suspended sediment in rivers compared to U.S. Geological Survey equal-width-increment or equal-discharge-increment (EWDI) field sampling and suspended sediment concentration (SSC) laboratory analysis methods. Because of this underrepresentation, the U.S. Geological Survey, in collaboration with the Minnesota Pollution Control Agency, collected concurrent grab and EWDI samples at eight sites to compare results obtained using different combinations of field sampling and laboratory analysis methods.Study results determined that grab field sampling and TSS laboratory analysis results were biased substantially low compared to EWDI sampling and SSC laboratory analysis results, respectively. Differences in both field sampling and laboratory analysis methods caused grab and TSS methods to be biased substantially low. The difference in laboratory analysis methods was slightly greater than field sampling methods.Sand-sized particles had a strong effect on the comparability of the field sampling and laboratory analysis methods. These results indicated that grab field sampling and TSS laboratory analysis methods fail to capture most of the sand being transported by the stream. The results indicate there is less of a difference among samples collected with grab field sampling and analyzed for TSS and concentration of fines in SSC. Even though differences are present, the presence of strong correlations between SSC and TSS concentrations provides the opportunity to develop site specific relations to address transport processes not captured by grab field sampling and TSS laboratory analysis methods.

Sampling of temporal networks: Methods and biases

NASA Astrophysics Data System (ADS)

Rocha, Luis E. C.; Masuda, Naoki; Holme, Petter

2017-11-01

Temporal networks have been increasingly used to model a diversity of systems that evolve in time; for example, human contact structures over which dynamic processes such as epidemics take place. A fundamental aspect of real-life networks is that they are sampled within temporal and spatial frames. Furthermore, one might wish to subsample networks to reduce their size for better visualization or to perform computationally intensive simulations. The sampling method may affect the network structure and thus caution is necessary to generalize results based on samples. In this paper, we study four sampling strategies applied to a variety of real-life temporal networks. We quantify the biases generated by each sampling strategy on a number of relevant statistics such as link activity, temporal paths and epidemic spread. We find that some biases are common in a variety of networks and statistics, but one strategy, uniform sampling of nodes, shows improved performance in most scenarios. Given the particularities of temporal network data and the variety of network structures, we recommend that the choice of sampling methods be problem oriented to minimize the potential biases for the specific research questions on hand. Our results help researchers to better design network data collection protocols and to understand the limitations of sampled temporal network data.

A Method for Choosing the Best Samples for Mars Sample Return

PubMed Central

Gordon, Peter R.

2018-01-01

Abstract Success of a future Mars Sample Return mission will depend on the correct choice of samples. Pyrolysis-FTIR can be employed as a triage instrument for Mars Sample Return. The technique can thermally dissociate minerals and organic matter for detection. Identification of certain mineral types can determine the habitability of the depositional environment, past or present, while detection of organic matter may suggest past or present habitation. In Mars' history, the Theiikian era represents an attractive target for life search missions and the acquisition of samples. The acidic and increasingly dry Theiikian may have been habitable and followed a lengthy neutral and wet period in Mars' history during which life could have originated and proliferated to achieve relatively abundant levels of biomass with a wide distribution. Moreover, the sulfate minerals produced in the Theiikian are also known to be good preservers of organic matter. We have used pyrolysis-FTIR and samples from a Mars analog ferrous acid stream with a thriving ecosystem to test the triage concept. Pyrolysis-FTIR identified those samples with the greatest probability of habitability and habitation. A three-tier scoring system was developed based on the detection of (i) organic signals, (ii) carbon dioxide and water, and (iii) sulfur dioxide. The presence of each component was given a score of A, B, or C depending on whether the substance had been detected, tentatively detected, or not detected, respectively. Single-step (for greatest possible sensitivity) or multistep (for more diagnostic data) pyrolysis-FTIR methods informed the assignments. The system allowed the highest-priority samples to be categorized as AAA (or A*AA if the organic signal was complex), while the lowest-priority samples could be categorized as CCC. Our methods provide a mechanism with which to rank samples and identify those that should take the highest priority for return to Earth during a Mars Sample Return mission

A Method for Choosing the Best Samples for Mars Sample Return.

PubMed

Gordon, Peter R; Sephton, Mark A

2018-05-01

Success of a future Mars Sample Return mission will depend on the correct choice of samples. Pyrolysis-FTIR can be employed as a triage instrument for Mars Sample Return. The technique can thermally dissociate minerals and organic matter for detection. Identification of certain mineral types can determine the habitability of the depositional environment, past or present, while detection of organic matter may suggest past or present habitation. In Mars' history, the Theiikian era represents an attractive target for life search missions and the acquisition of samples. The acidic and increasingly dry Theiikian may have been habitable and followed a lengthy neutral and wet period in Mars' history during which life could have originated and proliferated to achieve relatively abundant levels of biomass with a wide distribution. Moreover, the sulfate minerals produced in the Theiikian are also known to be good preservers of organic matter. We have used pyrolysis-FTIR and samples from a Mars analog ferrous acid stream with a thriving ecosystem to test the triage concept. Pyrolysis-FTIR identified those samples with the greatest probability of habitability and habitation. A three-tier scoring system was developed based on the detection of (i) organic signals, (ii) carbon dioxide and water, and (iii) sulfur dioxide. The presence of each component was given a score of A, B, or C depending on whether the substance had been detected, tentatively detected, or not detected, respectively. Single-step (for greatest possible sensitivity) or multistep (for more diagnostic data) pyrolysis-FTIR methods informed the assignments. The system allowed the highest-priority samples to be categorized as AAA (or A*AA if the organic signal was complex), while the lowest-priority samples could be categorized as CCC. Our methods provide a mechanism with which to rank samples and identify those that should take the highest priority for return to Earth during a Mars Sample Return mission. Key Words

Appearance-based representative samples refining method for palmprint recognition

NASA Astrophysics Data System (ADS)

Wen, Jiajun; Chen, Yan

2012-07-01

The sparse representation can deal with the lack of sample problem due to utilizing of all the training samples. However, the discrimination ability will degrade when more training samples are used for representation. We propose a novel appearance-based palmprint recognition method. We aim to find a compromise between the discrimination ability and the lack of sample problem so as to obtain a proper representation scheme. Under the assumption that the test sample can be well represented by a linear combination of a certain number of training samples, we first select the representative training samples according to the contributions of the samples. Then we further refine the training samples by an iteration procedure, excluding the training sample with the least contribution to the test sample for each time. Experiments on PolyU multispectral palmprint database and two-dimensional and three-dimensional palmprint database show that the proposed method outperforms the conventional appearance-based palmprint recognition methods. Moreover, we also explore and find out the principle of the usage for the key parameters in the proposed algorithm, which facilitates to obtain high-recognition accuracy.

A cryopreservation method for Pasteurella multocida from wetland samples

USGS Publications Warehouse

Moore, Melody K.; Shadduck, D.J.; Goldberg, Diana R.; Samuel, M.D.

1998-01-01

A cryopreservation method and improved isolation techniques for detection of Pasteurella multocida from wetland samples were developed. Wetland water samples were collected in the field, diluted in dimethyl sulfoxide (DMSO, final concentration 10%), and frozen at -180 C in a liquid nitrogen vapor shipper. Frozen samples were transported to the laboratory where they were subsequently thawed and processed in Pasteurella multocida selective broth (PMSB) to isolate P. multocida. This method allowed for consistent isolation of 2 to 18 organisms/ml from water seeded with known concentrations of P. multocida. The method compared favorably with the standard mouse inoculation method and allowed for preservation of the samples until they could be processed in the laboratory.

Prevalence of Mixed-Methods Sampling Designs in Social Science Research

ERIC Educational Resources Information Center

Collins, Kathleen M. T.

2006-01-01

The purpose of this mixed-methods study was to document the prevalence of sampling designs utilised in mixed-methods research and to examine the interpretive consistency between interpretations made in mixed-methods studies and the sampling design used. Classification of studies was based on a two-dimensional mixed-methods sampling model. This…

Rapid method to determine 226Ra in steel samples

DOE PAGES

Maxwell, Sherrod L.; Culligan, Brian; Hutchison, Jay B.; ...

2017-09-22

The rapid measurement of 226Ra in steel samples is very important in the event of a radiological emergency. 226Ra (T 1/2 = 1600 y) is a natural radionuclide present in the environment and a highly toxic alpha-emitter. Due to its long life and tendency to concentrate in bones, 226Ra ingestion or inhalation can lead to significant committed dose to individuals. A new method for the determination of 226Ra in steel samples has been developed at the Savannah River Environmental Laboratory. The new method employs a rugged acid digestion method that includes hydrofluoric acid, followed by a single precipitation step tomore » rapidly preconcentrate the radium and remove most of the dissolved steel sample matrix. Radium is then separated using a combination of cation exchange and extraction chromatography, and 226Ra is measured by alpha spectrometry. This approach has a sample preparation time of ~ 8 h for steel samples, has a very high tracer yield (> 88%), and removes interferences effectively. A 133Ba yield tracer is used so that samples can be counted immediately following the separation method, avoiding lengthy ingrowth times that are required in other methods.« less

Rapid method to determine 226Ra in steel samples

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

Maxwell, Sherrod L.; Culligan, Brian; Hutchison, Jay B.

The rapid measurement of 226Ra in steel samples is very important in the event of a radiological emergency. 226Ra (T 1/2 = 1600 y) is a natural radionuclide present in the environment and a highly toxic alpha-emitter. Due to its long life and tendency to concentrate in bones, 226Ra ingestion or inhalation can lead to significant committed dose to individuals. A new method for the determination of 226Ra in steel samples has been developed at the Savannah River Environmental Laboratory. The new method employs a rugged acid digestion method that includes hydrofluoric acid, followed by a single precipitation step tomore » rapidly preconcentrate the radium and remove most of the dissolved steel sample matrix. Radium is then separated using a combination of cation exchange and extraction chromatography, and 226Ra is measured by alpha spectrometry. This approach has a sample preparation time of ~ 8 h for steel samples, has a very high tracer yield (> 88%), and removes interferences effectively. A 133Ba yield tracer is used so that samples can be counted immediately following the separation method, avoiding lengthy ingrowth times that are required in other methods.« less

Interval sampling methods and measurement error: a computer simulation.

PubMed

Wirth, Oliver; Slaven, James; Taylor, Matthew A

2014-01-01

A simulation study was conducted to provide a more thorough account of measurement error associated with interval sampling methods. A computer program simulated the application of momentary time sampling, partial-interval recording, and whole-interval recording methods on target events randomly distributed across an observation period. The simulation yielded measures of error for multiple combinations of observation period, interval duration, event duration, and cumulative event duration. The simulations were conducted up to 100 times to yield measures of error variability. Although the present simulation confirmed some previously reported characteristics of interval sampling methods, it also revealed many new findings that pertain to each method's inherent strengths and weaknesses. The analysis and resulting error tables can help guide the selection of the most appropriate sampling method for observation-based behavioral assessments. © Society for the Experimental Analysis of Behavior.

Capillary microextraction: A new method for sampling methamphetamine vapour.

PubMed

Nair, M V; Miskelly, G M

2016-11-01

Clandestine laboratories pose a serious health risk to first responders, investigators, decontamination companies, and the public who may be inadvertently exposed to methamphetamine and other chemicals used in its manufacture. Therefore there is an urgent need for reliable methods to detect and measure methamphetamine at such sites. The most common method for determining methamphetamine contamination at former clandestine laboratory sites is selected surface wipe sampling, followed by analysis with gas chromatography-mass spectrometry (GC-MS). We are investigating the use of sampling for methamphetamine vapour to complement such wipe sampling. In this study, we report the use of capillary microextraction (CME) devices for sampling airborne methamphetamine, and compare their sampling efficiency with a previously reported dynamic SPME method. The CME devices consisted of PDMS-coated glass filter strips inside a glass tube. The devices were used to dynamically sample methamphetamine vapour in the range of 0.42-4.2μgm -3 , generated by a custom-built vapour dosing system, for 1-15min, and methamphetamine was analysed using a GC-MS fitted with a ChromatoProbe thermal desorption unit. The devices showed good reproducibility (RSD<15%), and a curvilinear pre-equilibrium relationship between sampling times and peak area, which can be utilised for calibration. Under identical sampling conditions, the CME devices were approximately 30 times more sensitive than the dynamic SPME method. The CME devices could be stored for up to 3days after sampling prior to analysis. Consecutive sampling of methamphetamine and its isotopic substitute, d-9 methamphetamine showed no competitive displacement. This suggests that CME devices, pre-loaded with an internal standard, could be a feasible method for sampling airborne methamphetamine at former clandestine laboratories. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Methods for sample size determination in cluster randomized trials

PubMed Central

Rutterford, Clare; Copas, Andrew; Eldridge, Sandra

2015-01-01

Background: The use of cluster randomized trials (CRTs) is increasing, along with the variety in their design and analysis. The simplest approach for their sample size calculation is to calculate the sample size assuming individual randomization and inflate this by a design effect to account for randomization by cluster. The assumptions of a simple design effect may not always be met; alternative or more complicated approaches are required. Methods: We summarise a wide range of sample size methods available for cluster randomized trials. For those familiar with sample size calculations for individually randomized trials but with less experience in the clustered case, this manuscript provides formulae for a wide range of scenarios with associated explanation and recommendations. For those with more experience, comprehensive summaries are provided that allow quick identification of methods for a given design, outcome and analysis method. Results: We present first those methods applicable to the simplest two-arm, parallel group, completely randomized design followed by methods that incorporate deviations from this design such as: variability in cluster sizes; attrition; non-compliance; or the inclusion of baseline covariates or repeated measures. The paper concludes with methods for alternative designs. Conclusions: There is a large amount of methodology available for sample size calculations in CRTs. This paper gives the most comprehensive description of published methodology for sample size calculation and provides an important resource for those designing these trials. PMID:26174515

40 CFR Appendix I to Part 261 - Representative Sampling Methods

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 27 2013-07-01 2013-07-01 false Representative Sampling Methods I Appendix I to Part 261 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) SOLID WASTES...—Representative Sampling Methods The methods and equipment used for sampling waste materials will vary with the...

Neutron activation analysis of certified samples by the absolute method

NASA Astrophysics Data System (ADS)

Kadem, F.; Belouadah, N.; Idiri, Z.

2015-07-01

The nuclear reactions analysis technique is mainly based on the relative method or the use of activation cross sections. In order to validate nuclear data for the calculated cross section evaluated from systematic studies, we used the neutron activation analysis technique (NAA) to determine the various constituent concentrations of certified samples for animal blood, milk and hay. In this analysis, the absolute method is used. The neutron activation technique involves irradiating the sample and subsequently performing a measurement of the activity of the sample. The fundamental equation of the activation connects several physical parameters including the cross section that is essential for the quantitative determination of the different elements composing the sample without resorting to the use of standard sample. Called the absolute method, it allows a measurement as accurate as the relative method. The results obtained by the absolute method showed that the values are as precise as the relative method requiring the use of standard sample for each element to be quantified.

[Recent advances in sample preparation methods of plant hormones].

PubMed

Wu, Qian; Wang, Lus; Wu, Dapeng; Duan, Chunfeng; Guan, Yafeng

2014-04-01

Plant hormones are a group of naturally occurring trace substances which play a crucial role in controlling the plant development, growth and environment response. With the development of the chromatography and mass spectroscopy technique, chromatographic analytical method has become a widely used way for plant hormone analysis. Among the steps of chromatographic analysis, sample preparation is undoubtedly the most vital one. Thus, a highly selective and efficient sample preparation method is critical for accurate identification and quantification of phytohormones. For the three major kinds of plant hormones including acidic plant hormones & basic plant hormones, brassinosteroids and plant polypeptides, the sample preparation methods are reviewed in sequence especially the recently developed methods. The review includes novel methods, devices, extractive materials and derivative reagents for sample preparation of phytohormones analysis. Especially, some related works of our group are included. At last, the future developments in this field are also prospected.

Sample Size Calculations for Population Size Estimation Studies Using Multiplier Methods With Respondent-Driven Sampling Surveys.

PubMed

Fearon, Elizabeth; Chabata, Sungai T; Thompson, Jennifer A; Cowan, Frances M; Hargreaves, James R

2017-09-14

While guidance exists for obtaining population size estimates using multiplier methods with respondent-driven sampling surveys, we lack specific guidance for making sample size decisions. To guide the design of multiplier method population size estimation studies using respondent-driven sampling surveys to reduce the random error around the estimate obtained. The population size estimate is obtained by dividing the number of individuals receiving a service or the number of unique objects distributed (M) by the proportion of individuals in a representative survey who report receipt of the service or object (P). We have developed an approach to sample size calculation, interpreting methods to estimate the variance around estimates obtained using multiplier methods in conjunction with research into design effects and respondent-driven sampling. We describe an application to estimate the number of female sex workers in Harare, Zimbabwe. There is high variance in estimates. Random error around the size estimate reflects uncertainty from M and P, particularly when the estimate of P in the respondent-driven sampling survey is low. As expected, sample size requirements are higher when the design effect of the survey is assumed to be greater. We suggest a method for investigating the effects of sample size on the precision of a population size estimate obtained using multipler methods and respondent-driven sampling. Uncertainty in the size estimate is high, particularly when P is small, so balancing against other potential sources of bias, we advise researchers to consider longer service attendance reference periods and to distribute more unique objects, which is likely to result in a higher estimate of P in the respondent-driven sampling survey. ©Elizabeth Fearon, Sungai T Chabata, Jennifer A Thompson, Frances M Cowan, James R Hargreaves. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 14.09.2017.

Standard methods for sampling North American freshwater fishes

USGS Publications Warehouse

Bonar, Scott A.; Hubert, Wayne A.; Willis, David W.

2009-01-01

This important reference book provides standard sampling methods recommended by the American Fisheries Society for assessing and monitoring freshwater fish populations in North America. Methods apply to ponds, reservoirs, natural lakes, and streams and rivers containing cold and warmwater fishes. Range-wide and eco-regional averages for indices of abundance, population structure, and condition for individual species are supplied to facilitate comparisons of standard data among populations. Provides information on converting nonstandard to standard data, statistical and database procedures for analyzing and storing standard data, and methods to prevent transfer of invasive species while sampling.

Field evaluation of personal sampling methods for multiple bioaerosols.

PubMed

Wang, Chi-Hsun; Chen, Bean T; Han, Bor-Cheng; Liu, Andrew Chi-Yeu; Hung, Po-Chen; Chen, Chih-Yong; Chao, Hsing Jasmine

2015-01-01

Ambient bioaerosols are ubiquitous in the daily environment and can affect health in various ways. However, few studies have been conducted to comprehensively evaluate personal bioaerosol exposure in occupational and indoor environments because of the complex composition of bioaerosols and the lack of standardized sampling/analysis methods. We conducted a study to determine the most efficient collection/analysis method for the personal exposure assessment of multiple bioaerosols. The sampling efficiencies of three filters and four samplers were compared. According to our results, polycarbonate (PC) filters had the highest relative efficiency, particularly for bacteria. Side-by-side sampling was conducted to evaluate the three filter samplers (with PC filters) and the NIOSH Personal Bioaerosol Cyclone Sampler. According to the results, the Button Aerosol Sampler and the IOM Inhalable Dust Sampler had the highest relative efficiencies for fungi and bacteria, followed by the NIOSH sampler. Personal sampling was performed in a pig farm to assess occupational bioaerosol exposure and to evaluate the sampling/analysis methods. The Button and IOM samplers yielded a similar performance for personal bioaerosol sampling at the pig farm. However, the Button sampler is more likely to be clogged at high airborne dust concentrations because of its higher flow rate (4 L/min). Therefore, the IOM sampler is a more appropriate choice for performing personal sampling in environments with high dust levels. In summary, the Button and IOM samplers with PC filters are efficient sampling/analysis methods for the personal exposure assessment of multiple bioaerosols.

[Sampling methods for PM2.5 from stationary sources: a review].

PubMed

Jiang, Jing-Kun; Deng, Jian-Guo; Li, Zhen; Li, Xing-Hua; Duan, Lei; Hao, Ji-Ming

2014-05-01

The new China national ambient air quality standard has been published in 2012 and will be implemented in 2016. To meet the requirements in this new standard, monitoring and controlling PM2,,5 emission from stationary sources are very important. However, so far there is no national standard method on sampling PM2.5 from stationary sources. Different sampling methods for PM2.5 from stationary sources and relevant international standards were reviewed in this study. It includes the methods for PM2.5 sampling in flue gas and the methods for PM2.5 sampling after dilution. Both advantages and disadvantages of these sampling methods were discussed. For environmental management, the method for PM2.5 sampling in flue gas such as impactor and virtual impactor was suggested as a standard to determine filterable PM2.5. To evaluate environmental and health effects of PM2.5 from stationary sources, standard dilution method for sampling of total PM2.5 should be established.

Evaluating Composite Sampling Methods of Bacillus Spores at Low Concentrations

PubMed Central

Hess, Becky M.; Amidan, Brett G.; Anderson, Kevin K.; Hutchison, Janine R.

2016-01-01

Restoring all facility operations after the 2001 Amerithrax attacks took years to complete, highlighting the need to reduce remediation time. Some of the most time intensive tasks were environmental sampling and sample analyses. Composite sampling allows disparate samples to be combined, with only a single analysis needed, making it a promising method to reduce response times. We developed a statistical experimental design to test three different composite sampling methods: 1) single medium single pass composite (SM-SPC): a single cellulose sponge samples multiple coupons with a single pass across each coupon; 2) single medium multi-pass composite: a single cellulose sponge samples multiple coupons with multiple passes across each coupon (SM-MPC); and 3) multi-medium post-sample composite (MM-MPC): a single cellulose sponge samples a single surface, and then multiple sponges are combined during sample extraction. Five spore concentrations of Bacillus atrophaeus Nakamura spores were tested; concentrations ranged from 5 to 100 CFU/coupon (0.00775 to 0.155 CFU/cm2). Study variables included four clean surface materials (stainless steel, vinyl tile, ceramic tile, and painted dry wallboard) and three grime coated/dirty materials (stainless steel, vinyl tile, and ceramic tile). Analysis of variance for the clean study showed two significant factors: composite method (p< 0.0001) and coupon material (p = 0.0006). Recovery efficiency (RE) was higher overall using the MM-MPC method compared to the SM-SPC and SM-MPC methods. RE with the MM-MPC method for concentrations tested (10 to 100 CFU/coupon) was similar for ceramic tile, dry wall, and stainless steel for clean materials. RE was lowest for vinyl tile with both composite methods. Statistical tests for the dirty study showed RE was significantly higher for vinyl and stainless steel materials, but lower for ceramic tile. These results suggest post-sample compositing can be used to reduce sample analysis time when

Evaluating Composite Sampling Methods of Bacillus Spores at Low Concentrations.

PubMed

Hess, Becky M; Amidan, Brett G; Anderson, Kevin K; Hutchison, Janine R

2016-01-01

Restoring all facility operations after the 2001 Amerithrax attacks took years to complete, highlighting the need to reduce remediation time. Some of the most time intensive tasks were environmental sampling and sample analyses. Composite sampling allows disparate samples to be combined, with only a single analysis needed, making it a promising method to reduce response times. We developed a statistical experimental design to test three different composite sampling methods: 1) single medium single pass composite (SM-SPC): a single cellulose sponge samples multiple coupons with a single pass across each coupon; 2) single medium multi-pass composite: a single cellulose sponge samples multiple coupons with multiple passes across each coupon (SM-MPC); and 3) multi-medium post-sample composite (MM-MPC): a single cellulose sponge samples a single surface, and then multiple sponges are combined during sample extraction. Five spore concentrations of Bacillus atrophaeus Nakamura spores were tested; concentrations ranged from 5 to 100 CFU/coupon (0.00775 to 0.155 CFU/cm2). Study variables included four clean surface materials (stainless steel, vinyl tile, ceramic tile, and painted dry wallboard) and three grime coated/dirty materials (stainless steel, vinyl tile, and ceramic tile). Analysis of variance for the clean study showed two significant factors: composite method (p< 0.0001) and coupon material (p = 0.0006). Recovery efficiency (RE) was higher overall using the MM-MPC method compared to the SM-SPC and SM-MPC methods. RE with the MM-MPC method for concentrations tested (10 to 100 CFU/coupon) was similar for ceramic tile, dry wall, and stainless steel for clean materials. RE was lowest for vinyl tile with both composite methods. Statistical tests for the dirty study showed RE was significantly higher for vinyl and stainless steel materials, but lower for ceramic tile. These results suggest post-sample compositing can be used to reduce sample analysis time when

GROUND WATER PURGING AND SAMPLING METHODS: HISTORY VS. HYSTERIA

EPA Science Inventory

It has been over 10 years since the low-flow ground water purging and sampling method was initially reported in the literature. The method grew from the recognition that well purging was necessary to collect representative samples, bailers could not achieve well purging, and high...

Approximation of the exponential integral (well function) using sampling methods

NASA Astrophysics Data System (ADS)

Baalousha, Husam Musa

2015-04-01

Exponential integral (also known as well function) is often used in hydrogeology to solve Theis and Hantush equations. Many methods have been developed to approximate the exponential integral. Most of these methods are based on numerical approximations and are valid for a certain range of the argument value. This paper presents a new approach to approximate the exponential integral. The new approach is based on sampling methods. Three different sampling methods; Latin Hypercube Sampling (LHS), Orthogonal Array (OA), and Orthogonal Array-based Latin Hypercube (OA-LH) have been used to approximate the function. Different argument values, covering a wide range, have been used. The results of sampling methods were compared with results obtained by Mathematica software, which was used as a benchmark. All three sampling methods converge to the result obtained by Mathematica, at different rates. It was found that the orthogonal array (OA) method has the fastest convergence rate compared with LHS and OA-LH. The root mean square error RMSE of OA was in the order of 1E-08. This method can be used with any argument value, and can be used to solve other integrals in hydrogeology such as the leaky aquifer integral.

Out-of-Sample Extensions for Non-Parametric Kernel Methods.

PubMed

Pan, Binbin; Chen, Wen-Sheng; Chen, Bo; Xu, Chen; Lai, Jianhuang

2017-02-01

Choosing suitable kernels plays an important role in the performance of kernel methods. Recently, a number of studies were devoted to developing nonparametric kernels. Without assuming any parametric form of the target kernel, nonparametric kernel learning offers a flexible scheme to utilize the information of the data, which may potentially characterize the data similarity better. The kernel methods using nonparametric kernels are referred to as nonparametric kernel methods. However, many nonparametric kernel methods are restricted to transductive learning, where the prediction function is defined only over the data points given beforehand. They have no straightforward extension for the out-of-sample data points, and thus cannot be applied to inductive learning. In this paper, we show how to make the nonparametric kernel methods applicable to inductive learning. The key problem of out-of-sample extension is how to extend the nonparametric kernel matrix to the corresponding kernel function. A regression approach in the hyper reproducing kernel Hilbert space is proposed to solve this problem. Empirical results indicate that the out-of-sample performance is comparable to the in-sample performance in most cases. Experiments on face recognition demonstrate the superiority of our nonparametric kernel method over the state-of-the-art parametric kernel methods.

Integrated Hamiltonian sampling: a simple and versatile method for free energy simulations and conformational sampling.

PubMed

Mori, Toshifumi; Hamers, Robert J; Pedersen, Joel A; Cui, Qiang

2014-07-17

Motivated by specific applications and the recent work of Gao and co-workers on integrated tempering sampling (ITS), we have developed a novel sampling approach referred to as integrated Hamiltonian sampling (IHS). IHS is straightforward to implement and complementary to existing methods for free energy simulation and enhanced configurational sampling. The method carries out sampling using an effective Hamiltonian constructed by integrating the Boltzmann distributions of a series of Hamiltonians. By judiciously selecting the weights of the different Hamiltonians, one achieves rapid transitions among the energy landscapes that underlie different Hamiltonians and therefore an efficient sampling of important regions of the conformational space. Along this line, IHS shares similar motivations as the enveloping distribution sampling (EDS) approach of van Gunsteren and co-workers, although the ways that distributions of different Hamiltonians are integrated are rather different in IHS and EDS. Specifically, we report efficient ways for determining the weights using a combination of histogram flattening and weighted histogram analysis approaches, which make it straightforward to include many end-state and intermediate Hamiltonians in IHS so as to enhance its flexibility. Using several relatively simple condensed phase examples, we illustrate the implementation and application of IHS as well as potential developments for the near future. The relation of IHS to several related sampling methods such as Hamiltonian replica exchange molecular dynamics and λ-dynamics is also briefly discussed.

Comparison of preprocessing methods and storage times for touch DNA samples

PubMed Central

Dong, Hui; Wang, Jing; Zhang, Tao; Ge, Jian-ye; Dong, Ying-qiang; Sun, Qi-fan; Liu, Chao; Li, Cai-xia

2017-01-01

Aim To select appropriate preprocessing methods for different substrates by comparing the effects of four different preprocessing methods on touch DNA samples and to determine the effect of various storage times on the results of touch DNA sample analysis. Method Hand touch DNA samples were used to investigate the detection and inspection results of DNA on different substrates. Four preprocessing methods, including the direct cutting method, stubbing procedure, double swab technique, and vacuum cleaner method, were used in this study. DNA was extracted from mock samples with four different preprocessing methods. The best preprocess protocol determined from the study was further used to compare performance after various storage times. DNA extracted from all samples was quantified and amplified using standard procedures. Results The amounts of DNA and the number of alleles detected on the porous substrates were greater than those on the non-porous substrates. The performances of the four preprocessing methods varied with different substrates. The direct cutting method displayed advantages for porous substrates, and the vacuum cleaner method was advantageous for non-porous substrates. No significant degradation trend was observed as the storage times increased. Conclusion Different substrates require the use of different preprocessing method in order to obtain the highest DNA amount and allele number from touch DNA samples. This study provides a theoretical basis for explorations of touch DNA samples and may be used as a reference when dealing with touch DNA samples in case work. PMID:28252870

Evaluation of sampling methods for Bacillus spore-contaminated HVAC filters

PubMed Central

Calfee, M. Worth; Rose, Laura J.; Tufts, Jenia; Morse, Stephen; Clayton, Matt; Touati, Abderrahmane; Griffin-Gatchalian, Nicole; Slone, Christina; McSweeney, Neal

2016-01-01

The objective of this study was to compare an extraction-based sampling method to two vacuum-based sampling methods (vacuum sock and 37 mm cassette filter) with regards to their ability to recover Bacillus atrophaeus spores (surrogate for Bacillus anthracis) from pleated heating, ventilation, and air conditioning (HVAC) filters that are typically found in commercial and residential buildings. Electrostatic and mechanical HVAC filters were tested, both without and after loading with dust to 50% of their total holding capacity. The results were analyzed by one-way ANOVA across material types, presence or absence of dust, and sampling device. The extraction method gave higher relative recoveries than the two vacuum methods evaluated (p ≤ 0.001). On average, recoveries obtained by the vacuum methods were about 30% of those achieved by the extraction method. Relative recoveries between the two vacuum methods were not significantly different (p > 0.05). Although extraction methods yielded higher recoveries than vacuum methods, either HVAC filter sampling approach may provide a rapid and inexpensive mechanism for understanding the extent of contamination following a wide-area biological release incident. PMID:24184312

Systems and methods for self-synchronized digital sampling

NASA Technical Reports Server (NTRS)

Samson, Jr., John R. (Inventor)

2008-01-01

Systems and methods for self-synchronized data sampling are provided. In one embodiment, a system for capturing synchronous data samples is provided. The system includes an analog to digital converter adapted to capture signals from one or more sensors and convert the signals into a stream of digital data samples at a sampling frequency determined by a sampling control signal; and a synchronizer coupled to the analog to digital converter and adapted to receive a rotational frequency signal from a rotating machine, wherein the synchronizer is further adapted to generate the sampling control signal, and wherein the sampling control signal is based on the rotational frequency signal.

Evaluating Composite Sampling Methods of Bacillus spores at Low Concentrations

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

Hess, Becky M.; Amidan, Brett G.; Anderson, Kevin K.

Restoring facility operations after the 2001 Amerithrax attacks took over three months to complete, highlighting the need to reduce remediation time. The most time intensive tasks were environmental sampling and sample analyses. Composite sampling allows disparate samples to be combined, with only a single analysis needed, making it a promising method to reduce response times. We developed a statistical experimental design to test three different composite sampling methods: 1) single medium single pass composite: a single cellulose sponge samples multiple coupons; 2) single medium multi-pass composite: a single cellulose sponge is used to sample multiple coupons; and 3) multi-medium post-samplemore » composite: a single cellulose sponge samples a single surface, and then multiple sponges are combined during sample extraction. Five spore concentrations of Bacillus atrophaeus Nakamura spores were tested; concentrations ranged from 5 to 100 CFU/coupon (0.00775 to 0.155CFU/cm2, respectively). Study variables included four clean surface materials (stainless steel, vinyl tile, ceramic tile, and painted wallboard) and three grime coated/dirty materials (stainless steel, vinyl tile, and ceramic tile). Analysis of variance for the clean study showed two significant factors: composite method (p-value < 0.0001) and coupon material (p-value = 0.0008). Recovery efficiency (RE) was higher overall using the post-sample composite (PSC) method compared to single medium composite from both clean and grime coated materials. RE with the PSC method for concentrations tested (10 to 100 CFU/coupon) was similar for ceramic tile, painted wall board, and stainless steel for clean materials. RE was lowest for vinyl tile with both composite methods. Statistical tests for the dirty study showed RE was significantly higher for vinyl and stainless steel materials, but significantly lower for ceramic tile. These results suggest post-sample compositing can be used to reduce sample analysis time

Method and apparatus for sampling atmospheric mercury

DOEpatents

Trujillo, Patricio E.; Campbell, Evan E.; Eutsler, Bernard C.

1976-01-20

A method of simultaneously sampling particulate mercury, organic mercurial vapors, and metallic mercury vapor in the working and occupational environment and determining the amount of mercury derived from each such source in the sampled air. A known volume of air is passed through a sampling tube containing a filter for particulate mercury collection, a first adsorber for the selective adsorption of organic mercurial vapors, and a second adsorber for the adsorption of metallic mercury vapor. Carbon black molecular sieves are particularly useful as the selective adsorber for organic mercurial vapors. The amount of mercury adsorbed or collected in each section of the sampling tube is readily quantitatively determined by flameless atomic absorption spectrophotometry.

A Sequential Optimization Sampling Method for Metamodels with Radial Basis Functions

PubMed Central

Pan, Guang; Ye, Pengcheng; Yang, Zhidong

2014-01-01

Metamodels have been widely used in engineering design to facilitate analysis and optimization of complex systems that involve computationally expensive simulation programs. The accuracy of metamodels is strongly affected by the sampling methods. In this paper, a new sequential optimization sampling method is proposed. Based on the new sampling method, metamodels can be constructed repeatedly through the addition of sampling points, namely, extrema points of metamodels and minimum points of density function. Afterwards, the more accurate metamodels would be constructed by the procedure above. The validity and effectiveness of proposed sampling method are examined by studying typical numerical examples. PMID:25133206

Characterizing lentic freshwater fish assemblages using multiple sampling methods

USGS Publications Warehouse

Fischer, Jesse R.; Quist, Michael C.

2014-01-01

Characterizing fish assemblages in lentic ecosystems is difficult, and multiple sampling methods are almost always necessary to gain reliable estimates of indices such as species richness. However, most research focused on lentic fish sampling methodology has targeted recreationally important species, and little to no information is available regarding the influence of multiple methods and timing (i.e., temporal variation) on characterizing entire fish assemblages. Therefore, six lakes and impoundments (48–1,557 ha surface area) were sampled seasonally with seven gear types to evaluate the combined influence of sampling methods and timing on the number of species and individuals sampled. Probabilities of detection for species indicated strong selectivities and seasonal trends that provide guidance on optimal seasons to use gears when targeting multiple species. The evaluation of species richness and number of individuals sampled using multiple gear combinations demonstrated that appreciable benefits over relatively few gears (e.g., to four) used in optimal seasons were not present. Specifically, over 90 % of the species encountered with all gear types and season combinations (N = 19) from six lakes and reservoirs were sampled with nighttime boat electrofishing in the fall and benthic trawling, modified-fyke, and mini-fyke netting during the summer. Our results indicated that the characterization of lentic fish assemblages was highly influenced by the selection of sampling gears and seasons, but did not appear to be influenced by waterbody type (i.e., natural lake, impoundment). The standardization of data collected with multiple methods and seasons to account for bias is imperative to monitoring of lentic ecosystems and will provide researchers with increased reliability in their interpretations and decisions made using information on lentic fish assemblages.

Evaluation of sampling methods for Bacillus spore-contaminated HVAC filters.

PubMed

Calfee, M Worth; Rose, Laura J; Tufts, Jenia; Morse, Stephen; Clayton, Matt; Touati, Abderrahmane; Griffin-Gatchalian, Nicole; Slone, Christina; McSweeney, Neal

2014-01-01

The objective of this study was to compare an extraction-based sampling method to two vacuum-based sampling methods (vacuum sock and 37mm cassette filter) with regards to their ability to recover Bacillus atrophaeus spores (surrogate for Bacillus anthracis) from pleated heating, ventilation, and air conditioning (HVAC) filters that are typically found in commercial and residential buildings. Electrostatic and mechanical HVAC filters were tested, both without and after loading with dust to 50% of their total holding capacity. The results were analyzed by one-way ANOVA across material types, presence or absence of dust, and sampling device. The extraction method gave higher relative recoveries than the two vacuum methods evaluated (p≤0.001). On average, recoveries obtained by the vacuum methods were about 30% of those achieved by the extraction method. Relative recoveries between the two vacuum methods were not significantly different (p>0.05). Although extraction methods yielded higher recoveries than vacuum methods, either HVAC filter sampling approach may provide a rapid and inexpensive mechanism for understanding the extent of contamination following a wide-area biological release incident. Published by Elsevier B.V.

RAPID SEPARATION METHOD FOR EMERGENCY WATER AND URINE SAMPLES

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

Maxwell, S.; Culligan, B.

2008-08-27

The Savannah River Site Environmental Bioassay Lab participated in the 2008 NRIP Emergency Response program administered by the National Institute for Standards and Technology (NIST) in May, 2008. A new rapid column separation method was used for analysis of actinides and {sup 90}Sr the NRIP 2008 emergency water and urine samples. Significant method improvements were applied to reduce analytical times. As a result, much faster analysis times were achieved, less than 3 hours for determination of {sup 90}Sr and 3-4 hours for actinides. This represents a 25%-33% improvement in analysis times from NRIP 2007 and a {approx}100% improvement compared tomore » NRIP 2006 report times. Column flow rates were increased by a factor of two, with no significant adverse impact on the method performance. Larger sample aliquots, shorter count times, faster cerium fluoride microprecipitation and streamlined calcium phosphate precipitation were also employed. Based on initial feedback from NIST, the SRS Environmental Bioassay Lab had the most rapid analysis times for actinides and {sup 90}Sr analyses for NRIP 2008 emergency urine samples. High levels of potential matrix interferences may be present in emergency samples and rugged methods are essential. Extremely high levels of {sup 210}Po were found to have an adverse effect on the uranium results for the NRIP-08 urine samples, while uranium results for NRIP-08 water samples were not affected. This problem, which was not observed for NRIP-06 or NRIP-07 urine samples, was resolved by using an enhanced {sup 210}Po removal step, which will be described.« less

Evaluation of seven aquatic sampling methods for amphibians and other aquatic fauna

USGS Publications Warehouse

Gunzburger, M.S.

2007-01-01

To design effective and efficient research and monitoring programs researchers must have a thorough understanding of the capabilities and limitations of their sampling methods. Few direct comparative studies exist for aquatic sampling methods for amphibians. The objective of this study was to simultaneously employ seven aquatic sampling methods in 10 wetlands to compare amphibian species richness and number of individuals detected with each method. Four sampling methods allowed counts of individuals (metal dipnet, D-frame dipnet, box trap, crayfish trap), whereas the other three methods allowed detection of species (visual encounter, aural, and froglogger). Amphibian species richness was greatest with froglogger, box trap, and aural samples. For anuran species, the sampling methods by which each life stage was detected was related to relative length of larval and breeding periods and tadpole size. Detection probability of amphibians varied across sampling methods. Box trap sampling resulted in the most precise amphibian count, but the precision of all four count-based methods was low (coefficient of variation > 145 for all methods). The efficacy of the four count sampling methods at sampling fish and aquatic invertebrates was also analyzed because these predatory taxa are known to be important predictors of amphibian habitat distribution. Species richness and counts were similar for fish with the four methods, whereas invertebrate species richness and counts were greatest in box traps. An effective wetland amphibian monitoring program in the southeastern United States should include multiple sampling methods to obtain the most accurate assessment of species community composition at each site. The combined use of frogloggers, crayfish traps, and dipnets may be the most efficient and effective amphibian monitoring protocol. ?? 2007 Brill Academic Publishers.

Sampling trace organic compounds in water: a comparison of a continuous active sampler to continuous passive and discrete sampling methods

USGS Publications Warehouse

Coes, Alissa L.; Paretti, Nicholas V.; Foreman, William T.; Iverson, Jana L.; Alvarez, David A.

2014-01-01

A continuous active sampling method was compared to continuous passive and discrete sampling methods for the sampling of trace organic compounds (TOCs) in water. Results from each method are compared and contrasted in order to provide information for future investigators to use while selecting appropriate sampling methods for their research. The continuous low-level aquatic monitoring (CLAM) sampler (C.I.Agent® Storm-Water Solutions) is a submersible, low flow-rate sampler, that continuously draws water through solid-phase extraction media. CLAM samplers were deployed at two wastewater-dominated stream field sites in conjunction with the deployment of polar organic chemical integrative samplers (POCIS) and the collection of discrete (grab) water samples. All samples were analyzed for a suite of 69 TOCs. The CLAM and POCIS samples represent time-integrated samples that accumulate the TOCs present in the water over the deployment period (19–23 h for CLAM and 29 days for POCIS); the discrete samples represent only the TOCs present in the water at the time and place of sampling. Non-metric multi-dimensional scaling and cluster analysis were used to examine patterns in both TOC detections and relative concentrations between the three sampling methods. A greater number of TOCs were detected in the CLAM samples than in corresponding discrete and POCIS samples, but TOC concentrations in the CLAM samples were significantly lower than in the discrete and (or) POCIS samples. Thirteen TOCs of varying polarity were detected by all of the three methods. TOC detections and concentrations obtained by the three sampling methods, however, are dependent on multiple factors. This study found that stream discharge, constituent loading, and compound type all affected TOC concentrations detected by each method. In addition, TOC detections and concentrations were affected by the reporting limits, bias, recovery, and performance of each method.

Sampling trace organic compounds in water: a comparison of a continuous active sampler to continuous passive and discrete sampling methods.

PubMed

Coes, Alissa L; Paretti, Nicholas V; Foreman, William T; Iverson, Jana L; Alvarez, David A

2014-03-01

A continuous active sampling method was compared to continuous passive and discrete sampling methods for the sampling of trace organic compounds (TOCs) in water. Results from each method are compared and contrasted in order to provide information for future investigators to use while selecting appropriate sampling methods for their research. The continuous low-level aquatic monitoring (CLAM) sampler (C.I.Agent® Storm-Water Solutions) is a submersible, low flow-rate sampler, that continuously draws water through solid-phase extraction media. CLAM samplers were deployed at two wastewater-dominated stream field sites in conjunction with the deployment of polar organic chemical integrative samplers (POCIS) and the collection of discrete (grab) water samples. All samples were analyzed for a suite of 69 TOCs. The CLAM and POCIS samples represent time-integrated samples that accumulate the TOCs present in the water over the deployment period (19-23 h for CLAM and 29 days for POCIS); the discrete samples represent only the TOCs present in the water at the time and place of sampling. Non-metric multi-dimensional scaling and cluster analysis were used to examine patterns in both TOC detections and relative concentrations between the three sampling methods. A greater number of TOCs were detected in the CLAM samples than in corresponding discrete and POCIS samples, but TOC concentrations in the CLAM samples were significantly lower than in the discrete and (or) POCIS samples. Thirteen TOCs of varying polarity were detected by all of the three methods. TOC detections and concentrations obtained by the three sampling methods, however, are dependent on multiple factors. This study found that stream discharge, constituent loading, and compound type all affected TOC concentrations detected by each method. In addition, TOC detections and concentrations were affected by the reporting limits, bias, recovery, and performance of each method. Published by Elsevier B.V.

Convenient mounting method for electrical measurements of thin samples

NASA Technical Reports Server (NTRS)

Matus, L. G.; Summers, R. L.

1986-01-01

A method for mounting thin samples for electrical measurements is described. The technique is based on a vacuum chuck concept in which the vacuum chuck simultaneously holds the sample and established electrical contact. The mounting plate is composed of a glass-ceramic insulating material and the surfaces of the plate and vacuum chuck are polished. The operation of the vacuum chuck is examined. The contacts on the sample and mounting plate, which are sputter-deposited through metal masks, are analyzed. The mounting method was utilized for van der Pauw measurements.

Dynamic Method for Identifying Collected Sample Mass

NASA Technical Reports Server (NTRS)

Carson, John

2008-01-01

G-Sample is designed for sample collection missions to identify the presence and quantity of sample material gathered by spacecraft equipped with end effectors. The software method uses a maximum-likelihood estimator to identify the collected sample's mass based on onboard force-sensor measurements, thruster firings, and a dynamics model of the spacecraft. This makes sample mass identification a computation rather than a process requiring additional hardware. Simulation examples of G-Sample are provided for spacecraft model configurations with a sample collection device mounted on the end of an extended boom. In the absence of thrust knowledge errors, the results indicate that G-Sample can identify the amount of collected sample mass to within 10 grams (with 95-percent confidence) by using a force sensor with a noise and quantization floor of 50 micrometers. These results hold even in the presence of realistic parametric uncertainty in actual spacecraft inertia, center-of-mass offset, and first flexibility modes. Thrust profile knowledge is shown to be a dominant sensitivity for G-Sample, entering in a nearly one-to-one relationship with the final mass estimation error. This means thrust profiles should be well characterized with onboard accelerometers prior to sample collection. An overall sample-mass estimation error budget has been developed to approximate the effect of model uncertainty, sensor noise, data rate, and thrust profile error on the expected estimate of collected sample mass.

SOIL AND SEDIMENT SAMPLING METHODS | Science ...

EPA Pesticide Factsheets

The EPA Office of Solid Waste and Emergency Response's (OSWER) Office of Superfund Remediation and Technology Innovation (OSRTI) needs innovative methods and techniques to solve new and difficult sampling and analytical problems found at the numerous Superfund sites throughout the United States. Inadequate site characterization and a lack of knowledge of surface and subsurface contaminant distributions hinders EPA's ability to make the best decisions on remediation options and to conduct the most effective cleanup efforts. To assist OSWER, NERL conducts research to improve their capability to more accurately, precisely, and efficiently characterize Superfund, RCRA, LUST, oil spills, and brownfield sites and to improve their risk-based decision making capabilities, research is being conducted on improving soil and sediment sampling techniques and improving the sampling and handling of volatile organic compound (VOC) contaminated soils, among the many research programs and tasks being performed at ESD-LV.Under this task, improved sampling approaches and devices will be developed for characterizing the concentration of VOCs in soils. Current approaches and devices used today can lose up to 99% of the VOCs present in the sample due inherent weaknesses in the device and improper/inadequate collection techniques. This error generally causes decision makers to markedly underestimate the soil VOC concentrations and, therefore, to greatly underestimate the ecological

Methods for collection and analysis of water samples

USGS Publications Warehouse

Rainwater, Frank Hays; Thatcher, Leland Lincoln

1960-01-01

This manual contains methods used by the U.S. Geological Survey to collect, preserve, and analyze water samples. Throughout, the emphasis is on obtaining analytical results that accurately describe the chemical composition of the water in situ. Among the topics discussed are selection of sampling sites, frequency of sampling, field equipment, preservatives and fixatives, analytical techniques of water analysis, and instruments. Seventy-seven laboratory and field procedures are given for determining fifty-three water properties.

Nonclinical dose formulation analysis method validation and sample analysis.

PubMed

Whitmire, Monica Lee; Bryan, Peter; Henry, Teresa R; Holbrook, John; Lehmann, Paul; Mollitor, Thomas; Ohorodnik, Susan; Reed, David; Wietgrefe, Holly D

2010-12-01

Nonclinical dose formulation analysis methods are used to confirm test article concentration and homogeneity in formulations and determine formulation stability in support of regulated nonclinical studies. There is currently no regulatory guidance for nonclinical dose formulation analysis method validation or sample analysis. Regulatory guidance for the validation of analytical procedures has been developed for drug product/formulation testing; however, verification of the formulation concentrations falls under the framework of GLP regulations (not GMP). The only current related regulatory guidance is the bioanalytical guidance for method validation. The fundamental parameters for bioanalysis and formulation analysis validations that overlap include: recovery, accuracy, precision, specificity, selectivity, carryover, sensitivity, and stability. Divergence in bioanalytical and drug product validations typically center around the acceptance criteria used. As the dose formulation samples are not true "unknowns", the concept of quality control samples that cover the entire range of the standard curve serving as the indication for the confidence in the data generated from the "unknown" study samples may not always be necessary. Also, the standard bioanalytical acceptance criteria may not be directly applicable, especially when the determined concentration does not match the target concentration. This paper attempts to reconcile the different practices being performed in the community and to provide recommendations of best practices and proposed acceptance criteria for nonclinical dose formulation method validation and sample analysis.

Validated Test Method 5030C: Purge-and-Trap for Aqueous Samples

EPA Pesticide Factsheets

This method describes a purge-and-trap procedure for the analysis of volatile organic compoundsin aqueous samples & water miscible liquid samples. It also describes the analysis of high concentration soil and waste sample extracts prepared in Method 5035.

Examination of Hydrate Formation Methods: Trying to Create Representative Samples

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

Kneafsey, T.J.; Rees, E.V.L.; Nakagawa, S.

2011-04-01

Forming representative gas hydrate-bearing laboratory samples is important so that the properties of these materials may be measured, while controlling the composition and other variables. Natural samples are rare, and have often experienced pressure and temperature changes that may affect the property to be measured [Waite et al., 2008]. Forming methane hydrate samples in the laboratory has been done a number of ways, each having advantages and disadvantages. The ice-to-hydrate method [Stern et al., 1996], contacts melting ice with methane at the appropriate pressure to form hydrate. The hydrate can then be crushed and mixed with mineral grains under controlledmore » conditions, and then compacted to create laboratory samples of methane hydrate in a mineral medium. The hydrate in these samples will be part of the load-bearing frame of the medium. In the excess gas method [Handa and Stupin, 1992], water is distributed throughout a mineral medium (e.g. packed moist sand, drained sand, moistened silica gel, other porous media) and the mixture is brought to hydrate-stable conditions (chilled and pressurized with gas), allowing hydrate to form. This method typically produces grain-cementing hydrate from pendular water in sand [Waite et al., 2004]. In the dissolved gas method [Tohidi et al., 2002], water with sufficient dissolved guest molecules is brought to hydrate-stable conditions where hydrate forms. In the laboratory, this is can be done by pre-dissolving the gas of interest in water and then introducing it to the sample under the appropriate conditions. With this method, it is easier to form hydrate from more soluble gases such as carbon dioxide. It is thought that this method more closely simulates the way most natural gas hydrate has formed. Laboratory implementation, however, is difficult, and sample formation is prohibitively time consuming [Minagawa et al., 2005; Spangenberg and Kulenkampff, 2005]. In another version of this technique, a specified quantity

Turbidity threshold sampling: Methods and instrumentation

Treesearch

Rand Eads; Jack Lewis

2001-01-01

Traditional methods for determining the frequency of suspended sediment sample collection often rely on measurements, such as water discharge, that are not well correlated to sediment concentration. Stream power is generally not a good predictor of sediment concentration for rivers that transport the bulk of their load as fines, due to the highly variable routing of...

Towards robust and repeatable sampling methods in eDNA based studies.

PubMed

Dickie, Ian A; Boyer, Stephane; Buckley, Hannah; Duncan, Richard P; Gardner, Paul; Hogg, Ian D; Holdaway, Robert J; Lear, Gavin; Makiola, Andreas; Morales, Sergio E; Powell, Jeff R; Weaver, Louise

2018-05-26

DNA based techniques are increasingly used for measuring the biodiversity (species presence, identity, abundance and community composition) of terrestrial and aquatic ecosystems. While there are numerous reviews of molecular methods and bioinformatic steps, there has been little consideration of the methods used to collect samples upon which these later steps are based. This represents a critical knowledge gap, as methodologically sound field sampling is the foundation for subsequent analyses. We reviewed field sampling methods used for metabarcoding studies of both terrestrial and freshwater ecosystem biodiversity over a nearly three-year period (n = 75). We found that 95% (n = 71) of these studies used subjective sampling methods, inappropriate field methods, and/or failed to provide critical methodological information. It would be possible for researchers to replicate only 5% of the metabarcoding studies in our sample, a poorer level of reproducibility than for ecological studies in general. Our findings suggest greater attention to field sampling methods and reporting is necessary in eDNA-based studies of biodiversity to ensure robust outcomes and future reproducibility. Methods must be fully and accurately reported, and protocols developed that minimise subjectivity. Standardisation of sampling protocols would be one way to help to improve reproducibility, and have additional benefits in allowing compilation and comparison of data from across studies. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

COMPARISON OF MACROINVERTEBRATE SAMPLING METHODS FOR NONWADEABLE STREAMS

EPA Science Inventory

The bioassessment of nonwadeable streams in the United States is increasing, but methods for these systems are not as well developed as for wadeable streams. In this study, we compared six benthic macroinvertebrate field sampling methods for nonwadeable streams based on those us...

Comparison of Collection Methods for Fecal Samples in Microbiome Studies

PubMed Central

Vogtmann, Emily; Chen, Jun; Amir, Amnon; Shi, Jianxin; Abnet, Christian C.; Nelson, Heidi; Knight, Rob; Chia, Nicholas; Sinha, Rashmi

2017-01-01

Prospective cohort studies are needed to assess the relationship between the fecal microbiome and human health and disease. To evaluate fecal collection methods, we determined technical reproducibility, stability at ambient temperature, and accuracy of 5 fecal collection methods (no additive, 95% ethanol, RNAlater Stabilization Solution, fecal occult blood test cards, and fecal immunochemical test tubes). Fifty-two healthy volunteers provided fecal samples at the Mayo Clinic in Rochester, Minnesota, in 2014. One set from each sample collection method was frozen immediately, and a second set was incubated at room temperature for 96 hours and then frozen. Intraclass correlation coefficients (ICCs) were calculated for the relative abundance of 3 phyla, 2 alpha diversity metrics, and 4 beta diversity metrics. Technical reproducibility was high, with ICCs for duplicate fecal samples between 0.64 and 1.00. Stability for most methods was generally high, although the ICCs were below 0.60 for 95% ethanol in metrics that were more sensitive to relative abundance. When compared with fecal samples that were frozen immediately, the ICCs were below 0.60 for the metrics that were sensitive to relative abundance; however, the remaining 2 alpha diversity and 3 beta diversity metrics were all relatively accurate, with ICCs above 0.60. In conclusion, all fecal sample collection methods appear relatively reproducible, stable, and accurate. Future studies could use these collection methods for microbiome analyses. PMID:27986704

Measuring larval nematode contamination on cattle pastures: Comparing two herbage sampling methods.

PubMed

Verschave, S H; Levecke, B; Duchateau, L; Vercruysse, J; Charlier, J

2015-06-15

Assessing levels of pasture larval contamination is frequently used to study the population dynamics of the free-living stages of parasitic nematodes of livestock. Direct quantification of infective larvae (L3) on herbage is the most applied method to measure pasture larval contamination. However, herbage collection remains labour intensive and there is a lack of studies addressing the variation induced by the sampling method and the required sample size. The aim of this study was (1) to compare two different sampling methods in terms of pasture larval count results and time required to sample, (2) to assess the amount of variation in larval counts at the level of sample plot, pasture and season, respectively and (3) to calculate the required sample size to assess pasture larval contamination with a predefined precision using random plots across pasture. Eight young stock pastures of different commercial dairy herds were sampled in three consecutive seasons during the grazing season (spring, summer and autumn). On each pasture, herbage samples were collected through both a double-crossed W-transect with samples taken every 10 steps (method 1) and four random located plots of 0.16 m(2) with collection of all herbage within the plot (method 2). The average (± standard deviation (SD)) pasture larval contamination using sampling methods 1 and 2 was 325 (± 479) and 305 (± 444)L3/kg dry herbage (DH), respectively. Large discrepancies in pasture larval counts of the same pasture and season were often seen between methods, but no significant difference (P = 0.38) in larval counts between methods was found. Less time was required to collect samples with method 2. This difference in collection time between methods was most pronounced for pastures with a surface area larger than 1 ha. The variation in pasture larval counts from samples generated by random plot sampling was mainly due to the repeated measurements on the same pasture in the same season (residual variance

14 CFR 25.1445 - Equipment standards for the oxygen distributing system.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 14 Aeronautics and Space 1 2014-01-01 2014-01-01 false Equipment standards for the oxygen... Miscellaneous Equipment § 25.1445 Equipment standards for the oxygen distributing system. (a) When oxygen is... crew on duty. (b) Portable walk-around oxygen units of the continuous flow, diluter-demand, and...

14 CFR 25.1445 - Equipment standards for the oxygen distributing system.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 14 Aeronautics and Space 1 2011-01-01 2011-01-01 false Equipment standards for the oxygen... Miscellaneous Equipment § 25.1445 Equipment standards for the oxygen distributing system. (a) When oxygen is... crew on duty. (b) Portable walk-around oxygen units of the continuous flow, diluter-demand, and...

14 CFR 25.1445 - Equipment standards for the oxygen distributing system.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 14 Aeronautics and Space 1 2012-01-01 2012-01-01 false Equipment standards for the oxygen... Miscellaneous Equipment § 25.1445 Equipment standards for the oxygen distributing system. (a) When oxygen is... crew on duty. (b) Portable walk-around oxygen units of the continuous flow, diluter-demand, and...

14 CFR 25.1445 - Equipment standards for the oxygen distributing system.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false Equipment standards for the oxygen... Miscellaneous Equipment § 25.1445 Equipment standards for the oxygen distributing system. (a) When oxygen is... crew on duty. (b) Portable walk-around oxygen units of the continuous flow, diluter-demand, and...

14 CFR 25.1445 - Equipment standards for the oxygen distributing system.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 14 Aeronautics and Space 1 2013-01-01 2013-01-01 false Equipment standards for the oxygen... Miscellaneous Equipment § 25.1445 Equipment standards for the oxygen distributing system. (a) When oxygen is... crew on duty. (b) Portable walk-around oxygen units of the continuous flow, diluter-demand, and...

Clustering Methods with Qualitative Data: A Mixed Methods Approach for Prevention Research with Small Samples

PubMed Central

Henry, David; Dymnicki, Allison B.; Mohatt, Nathaniel; Allen, James; Kelly, James G.

2016-01-01

Qualitative methods potentially add depth to prevention research, but can produce large amounts of complex data even with small samples. Studies conducted with culturally distinct samples often produce voluminous qualitative data, but may lack sufficient sample sizes for sophisticated quantitative analysis. Currently lacking in mixed methods research are methods allowing for more fully integrating qualitative and quantitative analysis techniques. Cluster analysis can be applied to coded qualitative data to clarify the findings of prevention studies by aiding efforts to reveal such things as the motives of participants for their actions and the reasons behind counterintuitive findings. By clustering groups of participants with similar profiles of codes in a quantitative analysis, cluster analysis can serve as a key component in mixed methods research. This article reports two studies. In the first study, we conduct simulations to test the accuracy of cluster assignment using three different clustering methods with binary data as produced when coding qualitative interviews. Results indicated that hierarchical clustering, K-Means clustering, and latent class analysis produced similar levels of accuracy with binary data, and that the accuracy of these methods did not decrease with samples as small as 50. Whereas the first study explores the feasibility of using common clustering methods with binary data, the second study provides a “real-world” example using data from a qualitative study of community leadership connected with a drug abuse prevention project. We discuss the implications of this approach for conducting prevention research, especially with small samples and culturally distinct communities. PMID:25946969

Clustering Methods with Qualitative Data: a Mixed-Methods Approach for Prevention Research with Small Samples.

PubMed

Henry, David; Dymnicki, Allison B; Mohatt, Nathaniel; Allen, James; Kelly, James G

2015-10-01

Qualitative methods potentially add depth to prevention research but can produce large amounts of complex data even with small samples. Studies conducted with culturally distinct samples often produce voluminous qualitative data but may lack sufficient sample sizes for sophisticated quantitative analysis. Currently lacking in mixed-methods research are methods allowing for more fully integrating qualitative and quantitative analysis techniques. Cluster analysis can be applied to coded qualitative data to clarify the findings of prevention studies by aiding efforts to reveal such things as the motives of participants for their actions and the reasons behind counterintuitive findings. By clustering groups of participants with similar profiles of codes in a quantitative analysis, cluster analysis can serve as a key component in mixed-methods research. This article reports two studies. In the first study, we conduct simulations to test the accuracy of cluster assignment using three different clustering methods with binary data as produced when coding qualitative interviews. Results indicated that hierarchical clustering, K-means clustering, and latent class analysis produced similar levels of accuracy with binary data and that the accuracy of these methods did not decrease with samples as small as 50. Whereas the first study explores the feasibility of using common clustering methods with binary data, the second study provides a "real-world" example using data from a qualitative study of community leadership connected with a drug abuse prevention project. We discuss the implications of this approach for conducting prevention research, especially with small samples and culturally distinct communities.

A comprehensive comparison of perpendicular distance sampling methods for sampling downed coarse woody debris

Treesearch

Jeffrey H. Gove; Mark J. Ducey; Harry T. Valentine; Michael S. Williams

2013-01-01

Many new methods for sampling down coarse woody debris have been proposed in the last dozen or so years. One of the most promising in terms of field application, perpendicular distance sampling (PDS), has several variants that have been progressively introduced in the literature. In this study, we provide an overview of the different PDS variants and comprehensive...

A comparison of fitness-case sampling methods for genetic programming

NASA Astrophysics Data System (ADS)

Martínez, Yuliana; Naredo, Enrique; Trujillo, Leonardo; Legrand, Pierrick; López, Uriel

2017-11-01

Genetic programming (GP) is an evolutionary computation paradigm for automatic program induction. GP has produced impressive results but it still needs to overcome some practical limitations, particularly its high computational cost, overfitting and excessive code growth. Recently, many researchers have proposed fitness-case sampling methods to overcome some of these problems, with mixed results in several limited tests. This paper presents an extensive comparative study of four fitness-case sampling methods, namely: Interleaved Sampling, Random Interleaved Sampling, Lexicase Selection and Keep-Worst Interleaved Sampling. The algorithms are compared on 11 symbolic regression problems and 11 supervised classification problems, using 10 synthetic benchmarks and 12 real-world data-sets. They are evaluated based on test performance, overfitting and average program size, comparing them with a standard GP search. Comparisons are carried out using non-parametric multigroup tests and post hoc pairwise statistical tests. The experimental results suggest that fitness-case sampling methods are particularly useful for difficult real-world symbolic regression problems, improving performance, reducing overfitting and limiting code growth. On the other hand, it seems that fitness-case sampling cannot improve upon GP performance when considering supervised binary classification.

Photoacoustic sample vessel and method of elevated pressure operation

DOEpatents

Autrey, Tom; Yonker, Clement R.

2004-05-04

An improved photoacoustic vessel and method of photoacoustic analysis. The photoacoustic sample vessel comprises an acoustic detector, an acoustic couplant, and an acoustic coupler having a chamber for holding the acoustic couplant and a sample. The acoustic couplant is selected from the group consisting of liquid, solid, and combinations thereof. Passing electromagnetic energy through the sample generates an acoustic signal within the sample, whereby the acoustic signal propagates through the sample to and through the acoustic couplant to the acoustic detector.

Shear Strength of Remoulding Clay Samples Using Different Methods of Moulding

NASA Astrophysics Data System (ADS)

Norhaliza, W.; Ismail, B.; Azhar, A. T. S.; Nurul, N. J.

2016-07-01

Shear strength for clay soil was required to determine the soil stability. Clay was known as a soil with complex natural formations and very difficult to obtain undisturbed samples at the site. The aim of this paper was to determine the unconfined shear strength of remoulded clay on different methods in moulding samples which were proctor compaction, hand operated soil compacter and miniature mould methods. All the samples were remoulded with the same optimum moisture content (OMC) and density that were 18% and 1880 kg/m3 respectively. The unconfined shear strength results of remoulding clay soils for proctor compaction method was 289.56kPa with the strain 4.8%, hand operated method was 261.66kPa with the strain 4.4% and miniature mould method was 247.52kPa with the strain 3.9%. Based on the proctor compaction method, the reduction percentage of unconfined shear strength of remoulded clay soil of hand operated method was 9.66%, and for miniature mould method was 14.52%. Thus, because there was no significant difference of reduction percentage of unconfined shear strength between three different methods, so it can be concluded that remoulding clay by hand operated method and miniature mould method were accepted and suggested to perform remoulding clay samples by other future researcher. However for comparison, the hand operated method was more suitable to form remoulded clay sample in term of easiness, saving time and less energy for unconfined shear strength determination purposes.

A new method to sample stuttering in preschool children.

PubMed

O'Brian, Sue; Jones, Mark; Pilowsky, Rachel; Onslow, Mark; Packman, Ann; Menzies, Ross

2010-06-01

This study reports a new method for sampling the speech of preschool stuttering children outside the clinic environment. Twenty parents engaged their stuttering children in an everyday play activity in the home with a telephone handset nearby. A remotely located researcher telephoned the parent and recorded the play session with a phone-recording jack attached to a digital audio recorder at the remote location. The parent placed an audio recorder near the child for comparison purposes. Children as young as 2 years complied with the remote method of speech sampling. The quality of the remote recordings was superior to that of the in-home recordings. There was no difference in means or reliability of stutter-count measures made from the remote recordings compared with those made in-home. Advantages of the new method include: (1) cost efficiency of real-time measurement of percent syllables stuttered in naturalistic situations, (2) reduction of bias associated with parent-selected timing of home recordings, (3) standardization of speech sampling procedures, (4) improved parent compliance with sampling procedures, (5) clinician or researcher on-line control of the acoustic and linguistic quality of recordings, and (6) elimination of the need to lend equipment to parents for speech sampling.

Efficiency of snake sampling methods in the Brazilian semiarid region.

PubMed

Mesquita, Paula C M D; Passos, Daniel C; Cechin, Sonia Z

2013-09-01

The choice of sampling methods is a crucial step in every field survey in herpetology. In countries where time and financial support are limited, the choice of the methods is critical. The methods used to sample snakes often lack objective criteria, and the traditional methods have apparently been more important when making the choice. Consequently researches using not-standardized methods are frequently found in the literature. We have compared four commonly used methods for sampling snake assemblages in a semiarid area in Brazil. We compared the efficacy of each method based on the cost-benefit regarding the number of individuals and species captured, time, and financial investment. We found that pitfall traps were the less effective method in all aspects that were evaluated and it was not complementary to the other methods in terms of abundance of species and assemblage structure. We conclude that methods can only be considered complementary if they are standardized to the objectives of the study. The use of pitfall traps in short-term surveys of the snake fauna in areas with shrubby vegetation and stony soil is not recommended.

Investigating Test Equating Methods in Small Samples through Various Factors

ERIC Educational Resources Information Center

Asiret, Semih; Sünbül, Seçil Ömür

2016-01-01

In this study, equating methods for random group design using small samples through factors such as sample size, difference in difficulty between forms, and guessing parameter was aimed for comparison. Moreover, which method gives better results under which conditions was also investigated. In this study, 5,000 dichotomous simulated data…

40 CFR 80.8 - Sampling methods for gasoline and diesel fuel.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 17 2012-07-01 2012-07-01 false Sampling methods for gasoline and... gasoline and diesel fuel. The sampling methods specified in this section shall be used to collect samples of gasoline and diesel fuel for purposes of determining compliance with the requirements of this part...

40 CFR 80.8 - Sampling methods for gasoline and diesel fuel.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 16 2011-07-01 2011-07-01 false Sampling methods for gasoline and... gasoline and diesel fuel. The sampling methods specified in this section shall be used to collect samples of gasoline and diesel fuel for purposes of determining compliance with the requirements of this part...

40 CFR 80.8 - Sampling methods for gasoline and diesel fuel.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 17 2013-07-01 2013-07-01 false Sampling methods for gasoline and... gasoline and diesel fuel. The sampling methods specified in this section shall be used to collect samples of gasoline and diesel fuel for purposes of determining compliance with the requirements of this part...

Comparability among four invertebrate sampling methods, Fountain Creek Basin, Colorado, 2010-2012

USGS Publications Warehouse

Zuellig, Robert E.; Bruce, James F.; Stogner, Sr., Robert W.; Brown, Krystal D.

2014-01-01

The U.S. Geological Survey, in cooperation with Colorado Springs City Engineering and Colorado Springs Utilities, designed a study to determine if sampling method and sample timing resulted in comparable samples and assessments of biological condition. To accomplish this task, annual invertebrate samples were collected concurrently using four sampling methods at 15 U.S. Geological Survey streamflow gages in the Fountain Creek basin from 2010 to 2012. Collectively, the four methods are used by local (U.S. Geological Survey cooperative monitoring program) and State monitoring programs (Colorado Department of Public Health and Environment) in the Fountain Creek basin to produce two distinct sample types for each program that target single-and multiple-habitats. This study found distinguishable differences between single-and multi-habitat sample types using both community similarities and multi-metric index values, while methods from each program within sample type were comparable. This indicates that the Colorado Department of Public Health and Environment methods were compatible with the cooperative monitoring program methods within multi-and single-habitat sample types. Comparisons between September and October samples found distinguishable differences based on community similarities for both sample types, whereas only differences were found for single-habitat samples when multi-metric index values were considered. At one site, differences between September and October index values from single-habitat samples resulted in opposing assessments of biological condition. Direct application of the results to inform the revision of the existing Fountain Creek basin U.S. Geological Survey cooperative monitoring program are discussed.

Methods of sampling airborne fungi in working environments of waste treatment facilities.

PubMed

Černá, Kristýna; Wittlingerová, Zdeňka; Zimová, Magdaléna; Janovský, Zdeněk

2016-01-01

The objective of the present study was to evaluate and compare the efficiency of a filter based sampling method and a high volume sampling method for sampling airborne culturable fungi present in waste sorting facilities. Membrane filters method was compared with surface air system method. The selected sampling methods were modified and tested in 2 plastic waste sorting facilities. The total number of colony-forming units (CFU)/m3 of airborne fungi was dependent on the type of sampling device, on the time of sampling, which was carried out every hour from the beginning of the work shift, and on the type of cultivation medium (p < 0.001). Detected concentrations of airborne fungi ranged 2×102-1.7×106 CFU/m3 when using the membrane filters (MF) method, and 3×102-6.4×104 CFU/m3 when using the surface air system (SAS) method. Both methods showed comparable sensitivity to the fluctuations of the concentrations of airborne fungi during the work shifts. The SAS method is adequate for a fast indicative determination of concentration of airborne fungi. The MF method is suitable for thorough assessment of working environment contamination by airborne fungi. Therefore we recommend the MF method for the implementation of a uniform standard methodology of airborne fungi sampling in working environments of waste treatment facilities. This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.

Surveying immigrants without sampling frames - evaluating the success of alternative field methods.

PubMed

Reichel, David; Morales, Laura

2017-01-01

This paper evaluates the sampling methods of an international survey, the Immigrant Citizens Survey, which aimed at surveying immigrants from outside the European Union (EU) in 15 cities in seven EU countries. In five countries, no sample frame was available for the target population. Consequently, alternative ways to obtain a representative sample had to be found. In three countries 'location sampling' was employed, while in two countries traditional methods were used with adaptations to reach the target population. The paper assesses the main methodological challenges of carrying out a survey among a group of immigrants for whom no sampling frame exists. The samples of the survey in these five countries are compared to results of official statistics in order to assess the accuracy of the samples obtained through the different sampling methods. It can be shown that alternative sampling methods can provide meaningful results in terms of core demographic characteristics although some estimates differ to some extent from the census results.

Flow cytometric detection method for DNA samples

DOEpatents

Nasarabadi, Shanavaz [Livermore, CA; Langlois, Richard G [Livermore, CA; Venkateswaran, Kodumudi S [Round Rock, TX

2011-07-05

Disclosed herein are two methods for rapid multiplex analysis to determine the presence and identity of target DNA sequences within a DNA sample. Both methods use reporting DNA sequences, e.g., modified conventional Taqman.RTM. probes, to combine multiplex PCR amplification with microsphere-based hybridization using flow cytometry means of detection. Real-time PCR detection can also be incorporated. The first method uses a cyanine dye, such as, Cy3.TM., as the reporter linked to the 5' end of a reporting DNA sequence. The second method positions a reporter dye, e.g., FAM.TM. on the 3' end of the reporting DNA sequence and a quencher dye, e.g., TAMRA.TM., on the 5' end.

Flow cytometric detection method for DNA samples

DOEpatents

Nasarabadi, Shanavaz [Livermore, CA; Langlois, Richard G [Livermore, CA; Venkateswaran, Kodumudi S [Livermore, CA

2006-08-01

Disclosed herein are two methods for rapid multiplex analysis to determine the presence and identity of target DNA sequences within a DNA sample. Both methods use reporting DNA sequences, e.g., modified conventional Taqman.RTM. probes, to combine multiplex PCR amplification with microsphere-based hybridization using flow cytometry means of detection. Real-time PCR detection can also be incorporated. The first method uses a cyanine dye, such as, Cy3.TM., as the reporter linked to the 5' end of a reporting DNA sequence. The second method positions a reporter dye, e.g., FAM, on the 3' end of the reporting DNA sequence and a quencher dye, e.g., TAMRA, on the 5' end.

Development of an automated data processing method for sample to sample comparison of seized methamphetamines.

PubMed

Choe, Sanggil; Lee, Jaesin; Choi, Hyeyoung; Park, Yujin; Lee, Heesang; Pyo, Jaesung; Jo, Jiyeong; Park, Yonghoon; Choi, Hwakyung; Kim, Suncheun

2012-11-30

The information about the sources of supply, trafficking routes, distribution patterns and conspiracy links can be obtained from methamphetamine profiling. The precursor and synthetic method for the clandestine manufacture can be estimated from the analysis of minor impurities contained in methamphetamine. Also, the similarity between samples can be evaluated using the peaks that appear in chromatograms. In South Korea, methamphetamine was the most popular drug but the total seized amount of methamphetamine whole through the country was very small. Therefore, it would be more important to find the links between samples than the other uses of methamphetamine profiling. Many Asian countries including Japan and South Korea have been using the method developed by National Research Institute of Police Science of Japan. The method used gas chromatography-flame ionization detector (GC-FID), DB-5 column and four internal standards. It was developed to increase the amount of impurities and minimize the amount of methamphetamine. After GC-FID analysis, the raw data have to be processed. The data processing steps are very complex and require a lot of time and effort. In this study, Microsoft Visual Basic Application (VBA) modules were developed to handle these data processing steps. This module collected the results from the data into an Excel file and then corrected the retention time shift and response deviation generated from the sample preparation and instruments analysis. The developed modules were tested for their performance using 10 samples from 5 different cases. The processed results were analyzed with Pearson correlation coefficient for similarity assessment and the correlation coefficient of the two samples from the same case was more than 0.99. When the modules were applied to 131 seized methamphetamine samples, four samples from two different cases were found to have the common origin and the chromatograms of the four samples were appeared visually identical

Monitoring benthic aIgal communides: A comparison of targeted and coefficient sampling methods

USGS Publications Warehouse

Edwards, Matthew S.; Tinker, M. Tim

2009-01-01

Choosing an appropriate sample unit is a fundamental decision in the design of ecological studies. While numerous methods have been developed to estimate organism abundance, they differ in cost, accuracy and precision.Using both field data and computer simulation modeling, we evaluated the costs and benefits associated with two methods commonly used to sample benthic organisms in temperate kelp forests. One of these methods, the Targeted Sampling method, relies on different sample units, each "targeted" for a specific species or group of species while the other method relies on coefficients that represent ranges of bottom cover obtained from visual esti-mates within standardized sample units. Both the field data and the computer simulations suggest that both methods yield remarkably similar estimates of organism abundance and among-site variability, although the Coefficient method slightly underestimates variability among sample units when abundances are low. In contrast, the two methods differ considerably in the effort needed to sample these communities; the Targeted Sampling requires more time and twice the personnel to complete. We conclude that the Coefficent Sampling method may be better for environmental monitoring programs where changes in mean abundance are of central concern and resources are limiting, but that the Targeted sampling methods may be better for ecological studies where quantitative relationships among species and small-scale variability in abundance are of central concern.

A flexible importance sampling method for integrating subgrid processes

DOE PAGES

Raut, E. K.; Larson, V. E.

2016-01-29

Numerical models of weather and climate need to compute grid-box-averaged rates of physical processes such as microphysics. These averages are computed by integrating subgrid variability over a grid box. For this reason, an important aspect of atmospheric modeling is spatial integration over subgrid scales. The needed integrals can be estimated by Monte Carlo integration. Monte Carlo integration is simple and general but requires many evaluations of the physical process rate. To reduce the number of function evaluations, this paper describes a new, flexible method of importance sampling. It divides the domain of integration into eight categories, such as the portion that containsmore » both precipitation and cloud, or the portion that contains precipitation but no cloud. It then allows the modeler to prescribe the density of sample points within each of the eight categories. The new method is incorporated into the Subgrid Importance Latin Hypercube Sampler (SILHS). Here, the resulting method is tested on drizzling cumulus and stratocumulus cases. In the cumulus case, the sampling error can be considerably reduced by drawing more sample points from the region of rain evaporation.« less

Efficient free energy calculations by combining two complementary tempering sampling methods

NASA Astrophysics Data System (ADS)

Xie, Liangxu; Shen, Lin; Chen, Zhe-Ning; Yang, Mingjun

2017-01-01

Although energy barriers can be efficiently crossed in the reaction coordinate (RC) guided sampling, this type of method suffers from identification of the correct RCs or requirements of high dimensionality of the defined RCs for a given system. If only the approximate RCs with significant barriers are used in the simulations, hidden energy barriers with small to medium height would exist in other degrees of freedom (DOFs) relevant to the target process and consequently cause the problem of insufficient sampling. To address the sampling in this so-called hidden barrier situation, here we propose an effective approach to combine temperature accelerated molecular dynamics (TAMD), an efficient RC-guided sampling method, with the integrated tempering sampling (ITS), a generalized ensemble sampling method. In this combined ITS-TAMD method, the sampling along the major RCs with high energy barriers is guided by TAMD and the sampling of the rest of the DOFs with lower but not negligible barriers is enhanced by ITS. The performance of ITS-TAMD to three systems in the processes with hidden barriers has been examined. In comparison to the standalone TAMD or ITS approach, the present hybrid method shows three main improvements. (1) Sampling efficiency can be improved at least five times even if in the presence of hidden energy barriers. (2) The canonical distribution can be more accurately recovered, from which the thermodynamic properties along other collective variables can be computed correctly. (3) The robustness of the selection of major RCs suggests that the dimensionality of necessary RCs can be reduced. Our work shows more potential applications of the ITS-TAMD method as the efficient and powerful tool for the investigation of a broad range of interesting cases.

Efficient free energy calculations by combining two complementary tempering sampling methods.

PubMed

Xie, Liangxu; Shen, Lin; Chen, Zhe-Ning; Yang, Mingjun

2017-01-14

Although energy barriers can be efficiently crossed in the reaction coordinate (RC) guided sampling, this type of method suffers from identification of the correct RCs or requirements of high dimensionality of the defined RCs for a given system. If only the approximate RCs with significant barriers are used in the simulations, hidden energy barriers with small to medium height would exist in other degrees of freedom (DOFs) relevant to the target process and consequently cause the problem of insufficient sampling. To address the sampling in this so-called hidden barrier situation, here we propose an effective approach to combine temperature accelerated molecular dynamics (TAMD), an efficient RC-guided sampling method, with the integrated tempering sampling (ITS), a generalized ensemble sampling method. In this combined ITS-TAMD method, the sampling along the major RCs with high energy barriers is guided by TAMD and the sampling of the rest of the DOFs with lower but not negligible barriers is enhanced by ITS. The performance of ITS-TAMD to three systems in the processes with hidden barriers has been examined. In comparison to the standalone TAMD or ITS approach, the present hybrid method shows three main improvements. (1) Sampling efficiency can be improved at least five times even if in the presence of hidden energy barriers. (2) The canonical distribution can be more accurately recovered, from which the thermodynamic properties along other collective variables can be computed correctly. (3) The robustness of the selection of major RCs suggests that the dimensionality of necessary RCs can be reduced. Our work shows more potential applications of the ITS-TAMD method as the efficient and powerful tool for the investigation of a broad range of interesting cases.

SnagPRO: snag and tree sampling and analysis methods for wildlife

Treesearch

Lisa J. Bate; Michael J. Wisdom; Edward O. Garton; Shawn C. Clabough

2008-01-01

We describe sampling methods and provide software to accurately and efficiently estimate snag and tree densities at desired scales to meet a variety of research and management objectives. The methods optimize sampling effort by choosing a plot size appropriate for the specified forest conditions and sampling goals. Plot selection and data analyses are supported by...

Soil separator and sampler and method of sampling

DOEpatents

O'Brien, Barry H [Idaho Falls, ID; Ritter, Paul D [Idaho Falls, ID

2010-02-16

A soil sampler includes a fluidized bed for receiving a soil sample. The fluidized bed may be in communication with a vacuum for drawing air through the fluidized bed and suspending particulate matter of the soil sample in the air. In a method of sampling, the air may be drawn across a filter, separating the particulate matter. Optionally, a baffle or a cyclone may be included within the fluidized bed for disentrainment, or dedusting, so only the finest particulate matter, including asbestos, will be trapped on the filter. The filter may be removable, and may be tested to determine the content of asbestos and other hazardous particulate matter in the soil sample.

Molecular cancer classification using a meta-sample-based regularized robust coding method.

PubMed

Wang, Shu-Lin; Sun, Liuchao; Fang, Jianwen

2014-01-01

Previous studies have demonstrated that machine learning based molecular cancer classification using gene expression profiling (GEP) data is promising for the clinic diagnosis and treatment of cancer. Novel classification methods with high efficiency and prediction accuracy are still needed to deal with high dimensionality and small sample size of typical GEP data. Recently the sparse representation (SR) method has been successfully applied to the cancer classification. Nevertheless, its efficiency needs to be improved when analyzing large-scale GEP data. In this paper we present the meta-sample-based regularized robust coding classification (MRRCC), a novel effective cancer classification technique that combines the idea of meta-sample-based cluster method with regularized robust coding (RRC) method. It assumes that the coding residual and the coding coefficient are respectively independent and identically distributed. Similar to meta-sample-based SR classification (MSRC), MRRCC extracts a set of meta-samples from the training samples, and then encodes a testing sample as the sparse linear combination of these meta-samples. The representation fidelity is measured by the l2-norm or l1-norm of the coding residual. Extensive experiments on publicly available GEP datasets demonstrate that the proposed method is more efficient while its prediction accuracy is equivalent to existing MSRC-based methods and better than other state-of-the-art dimension reduction based methods.

Detecting spatial structures in throughfall data: The effect of extent, sample size, sampling design, and variogram estimation method

NASA Astrophysics Data System (ADS)

Voss, Sebastian; Zimmermann, Beate; Zimmermann, Alexander

2016-09-01

In the last decades, an increasing number of studies analyzed spatial patterns in throughfall by means of variograms. The estimation of the variogram from sample data requires an appropriate sampling scheme: most importantly, a large sample and a layout of sampling locations that often has to serve both variogram estimation and geostatistical prediction. While some recommendations on these aspects exist, they focus on Gaussian data and high ratios of the variogram range to the extent of the study area. However, many hydrological data, and throughfall data in particular, do not follow a Gaussian distribution. In this study, we examined the effect of extent, sample size, sampling design, and calculation method on variogram estimation of throughfall data. For our investigation, we first generated non-Gaussian random fields based on throughfall data with large outliers. Subsequently, we sampled the fields with three extents (plots with edge lengths of 25 m, 50 m, and 100 m), four common sampling designs (two grid-based layouts, transect and random sampling) and five sample sizes (50, 100, 150, 200, 400). We then estimated the variogram parameters by method-of-moments (non-robust and robust estimators) and residual maximum likelihood. Our key findings are threefold. First, the choice of the extent has a substantial influence on the estimation of the variogram. A comparatively small ratio of the extent to the correlation length is beneficial for variogram estimation. Second, a combination of a minimum sample size of 150, a design that ensures the sampling of small distances and variogram estimation by residual maximum likelihood offers a good compromise between accuracy and efficiency. Third, studies relying on method-of-moments based variogram estimation may have to employ at least 200 sampling points for reliable variogram estimates. These suggested sample sizes exceed the number recommended by studies dealing with Gaussian data by up to 100 %. Given that most previous

NEW COLUMN SEPARATION METHOD FOR EMERGENCY URINE SAMPLES

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

Maxwell, S; Brian Culligan, B

2007-08-28

The Savannah River Site Environmental Bioassay Lab participated in the 2007 NRIP Emergency Response program administered by the National Institute for Standards and Technology (NIST) in May, 2007. A new rapid column separation method was applied directly to the NRIP 2007 emergency urine samples, with only minimal sample preparation to reduce preparation time. Calcium phosphate precipitation, previously used to pre-concentrate actinides and Sr-90 in NRIP 2006 urine and water samples, was not used for the NRIP 2007 urine samples. Instead, the raw urine was acidified and passed directly through the stacked resin columns (TEVA+TRU+SR Resins) to separate the actinides andmore » strontium from the NRIP urine samples more quickly. This improvement reduced sample preparation time for the NRIP 2007 emergency urine analyses significantly. This approach works well for small volume urine samples expected during an emergency response event. Based on initial feedback from NIST, the SRS Environmental Bioassay Lab had the most rapid analysis times for actinides and strontium-90 analyses for NRIP 2007 urine samples.« less

Passive Samplers for Investigations of Air Quality: Method Description, Implementation, and Comparison to Alternative Sampling Methods

EPA Science Inventory

This Paper covers the basics of passive sampler design, compares passive samplers to conventional methods of air sampling, and discusses considerations when implementing a passive sampling program. The Paper also discusses field sampling and sample analysis considerations to ensu...

Detection of protozoa in water samples by formalin/ether concentration method.

PubMed

Lora-Suarez, Fabiana; Rivera, Raul; Triviño-Valencia, Jessica; Gomez-Marin, Jorge E

2016-09-01

Methods to detect protozoa in water samples are expensive and laborious. We evaluated the formalin/ether concentration method to detect Giardia sp., Cryptosporidium sp. and Toxoplasma in water. In order to test the properties of the method, we spiked water samples with different amounts of each protozoa (0, 10 and 50 cysts or oocysts) in a volume of 10 L of water. Immunofluorescence assay was used for detection of Giardia and Cryptosporidium. Toxoplasma oocysts were identified by morphology. The mean percent of recovery in 10 repetitions of the entire method, in 10 samples spiked with ten parasites and read by three different observers, were for Cryptosporidium 71.3 ± 12, for Giardia 63 ± 10 and for Toxoplasma 91.6 ± 9 and the relative standard deviation of the method was of 17.5, 17.2 and 9.8, respectively. Intraobserver variation as measured by intraclass correlation coefficient, was fair for Toxoplasma, moderate for Cryptosporidium and almost perfect for Giardia. The method was then applied in 77 samples of raw and drinkable water in three different plant of water treatment. Cryptosporidium was found in 28 of 77 samples (36%) and Giardia in 31 of 77 samples (40%). Theses results identified significant differences in treatment process to reduce the presence of Giardia and Cryptosporidium. In conclusion, the formalin ether method to concentrate protozoa in water is a new alternative for low resources countries, where is urgently need to monitor and follow the presence of theses protozoa in drinkable water. Copyright © 2016 Elsevier Ltd. All rights reserved.

Oral sampling methods are associated with differences in immune marker concentrations.

PubMed

Fakhry, Carole; Qeadan, Fares; Gilman, Robert H; Yori, Pablo; Kosek, Margaret; Patterson, Nicole; Eisele, David W; Gourin, Christine G; Chitguppi, Chandala; Marks, Morgan; Gravitt, Patti

2018-06-01

To determine whether the concentration and distribution of immune markers in paired oral samples were similar. Clinical research. Cross-sectional study. Paired saliva and oral secretions (OS) samples were collected. The concentration of immune markers was estimated using Luminex multiplex assay (Thermo Fisher Scientific, Waltham, MA). For each sample, the concentration of respective immune markers was normalized to total protein present and log-transformed. Median concentrations of immune markers were compared between both types of samples. Intermarker correlation in each sampling method and across sampling methods was evaluated. There were 90 study participants. Concentrations of immune markers in saliva samples were significantly different from concentrations in OS samples. Oral secretions samples showed higher concentrations of immunoregulatory markers, whereas the saliva samples contained proinflammatory markers in higher concentration. The immune marker profile in saliva samples is distinct from the immune marker profile in paired OS samples. 2b. Laryngoscope, 128:E214-E221, 2018. © 2017 The American Laryngological, Rhinological and Otological Society, Inc.

Comparison of sampling methods for radiocarbon dating of carbonyls in air samples via accelerator mass spectrometry

NASA Astrophysics Data System (ADS)

Schindler, Matthias; Kretschmer, Wolfgang; Scharf, Andreas; Tschekalinskij, Alexander

2016-05-01

Three new methods to sample and prepare various carbonyl compounds for radiocarbon measurements were developed and tested. Two of these procedures utilized the Strecker synthetic method to form amino acids from carbonyl compounds with either sodium cyanide or trimethylsilyl cyanide. The third procedure used semicarbazide to form crystalline carbazones with the carbonyl compounds. The resulting amino acids and semicarbazones were then separated and purified using thin layer chromatography. The separated compounds were then combusted to CO2 and reduced to graphite to determine 14C content by accelerator mass spectrometry (AMS). All of these methods were also compared with the standard carbonyl compound sampling method wherein a compound is derivatized with 2,4-dinitrophenylhydrazine and then separated by high-performance liquid chromatography (HPLC).

Experimental Investigations on Subsequent Yield Surface of Pure Copper by Single-Sample and Multi-Sample Methods under Various Pre-Deformation.

PubMed

Liu, Gui-Long; Huang, Shi-Hong; Shi, Che-Si; Zeng, Bin; Zhang, Ke-Shi; Zhong, Xian-Ci

2018-02-10

Using copper thin-walled tubular specimens, the subsequent yield surfaces under pre-tension, pre-torsion and pre-combined tension-torsion are measured, where the single-sample and multi-sample methods are applied respectively to determine the yield stresses at specified offset strain. The rule and characteristics of the evolution of the subsequent yield surface are investigated. Under the conditions of different pre-strains, the influence of test point number, test sequence and specified offset strain on the measurement of subsequent yield surface and the concave phenomenon for measured yield surface are studied. Moreover, the feasibility and validity of the two methods are compared. The main conclusions are drawn as follows: (1) For the single or multi-sample method, the measured subsequent yield surfaces are remarkably different from cylindrical yield surfaces proposed by the classical plasticity theory; (2) there are apparent differences between the test results from the two kinds of methods: the multi-sample method is not influenced by the number of test points, test order and the cumulative effect of residual plastic strain resulting from the other test point, while those are very influential in the single-sample method; and (3) the measured subsequent yield surface may appear concave, which can be transformed to convex for single-sample method by changing the test sequence. However, for the multiple-sample method, the concave phenomenon will disappear when a larger offset strain is specified.

Method and sample spinning apparatus for measuring the NMR spectrum of an orientationally disordered sample

DOEpatents

Pines, Alexander; Samoson, Ago

1990-01-01

An improved NMR apparatus and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise orientationally disordered samples. The apparatus spins the sample about an axis. The angle of the axis is mechanically varied such that the time average of two or more Legendre polynomials are zero.

New Methods of Sample Preparation for Atom Probe Specimens

NASA Technical Reports Server (NTRS)

Kuhlman, Kimberly, R.; Kowalczyk, Robert S.; Ward, Jennifer R.; Wishard, James L.; Martens, Richard L.; Kelly, Thomas F.

2003-01-01

Magnetite is a common conductive mineral found on Earth and Mars. Disk-shaped precipitates approximately 40 nm in diameter have been shown to have manganese and aluminum concentrations. Atom-probe field-ion microscopy (APFIM) is the only technique that can potentially quantify the composition of these precipitates. APFIM will be used to characterize geological and planetary materials, analyze samples of interest for geomicrobiology; and, for the metrology of nanoscale instrumentation. Prior to APFIM sample preparation was conducted by electropolishing, the method of sharp shards (MSS), or Bosch process (deep reactive ion etching) with focused ion beam (FIB) milling as a final step. However, new methods are required for difficult samples. Many materials are not easily fabricated using electropolishing, MSS, or the Bosch process, FIB milling is slow and expensive, and wet chemistry and the reactive ion etching are typically limited to Si and other semiconductors. APFIM sample preparation using the dicing saw is commonly used to section semiconductor wafers into individual devices following manufacture. The dicing saw is a time-effective method for preparing high aspect ratio posts of poorly conducting materials. Femtosecond laser micromachining is also suitable for preparation of posts. FIB time required is reduced by about a factor of 10 and multi-tip specimens can easily be fabricated using the dicing saw.

Volatile organic compounds: sampling methods and their worldwide profile in ambient air.

PubMed

Kumar, Anuj; Víden, Ivan

2007-08-01

The atmosphere is a particularly difficult analytical system because of the very low levels of substances to be analysed, sharp variations in pollutant levels with time and location, differences in wind, temperature and humidity. This makes the selection of an efficient sampling technique for air analysis a key step to reliable results. Generally, methods for volatile organic compounds sampling include collection of the whole air or preconcentration of samples on adsorbents. All the methods vary from each other according to the sampling technique, type of sorbent, method of extraction and identification technique. In this review paper we discuss various important aspects for sampling of volatile organic compounds by the widely used and advanced sampling methods. Characteristics of various adsorbents used for VOCs sampling are also described. Furthermore, this paper makes an effort to comprehensively review the concentration levels of volatile organic compounds along with the methodology used for analysis, in major cities of the world.

Detecting spatial structures in throughfall data: the effect of extent, sample size, sampling design, and variogram estimation method

NASA Astrophysics Data System (ADS)

Voss, Sebastian; Zimmermann, Beate; Zimmermann, Alexander

2016-04-01

In the last three decades, an increasing number of studies analyzed spatial patterns in throughfall to investigate the consequences of rainfall redistribution for biogeochemical and hydrological processes in forests. In the majority of cases, variograms were used to characterize the spatial properties of the throughfall data. The estimation of the variogram from sample data requires an appropriate sampling scheme: most importantly, a large sample and an appropriate layout of sampling locations that often has to serve both variogram estimation and geostatistical prediction. While some recommendations on these aspects exist, they focus on Gaussian data and high ratios of the variogram range to the extent of the study area. However, many hydrological data, and throughfall data in particular, do not follow a Gaussian distribution. In this study, we examined the effect of extent, sample size, sampling design, and calculation methods on variogram estimation of throughfall data. For our investigation, we first generated non-Gaussian random fields based on throughfall data with heavy outliers. Subsequently, we sampled the fields with three extents (plots with edge lengths of 25 m, 50 m, and 100 m), four common sampling designs (two grid-based layouts, transect and random sampling), and five sample sizes (50, 100, 150, 200, 400). We then estimated the variogram parameters by method-of-moments and residual maximum likelihood. Our key findings are threefold. First, the choice of the extent has a substantial influence on the estimation of the variogram. A comparatively small ratio of the extent to the correlation length is beneficial for variogram estimation. Second, a combination of a minimum sample size of 150, a design that ensures the sampling of small distances and variogram estimation by residual maximum likelihood offers a good compromise between accuracy and efficiency. Third, studies relying on method-of-moments based variogram estimation may have to employ at least

Compendium of selected methods for sampling and analysis at geothermal facilities

NASA Astrophysics Data System (ADS)

Kindle, C. H.; Pool, K. H.; Ludwick, J. D.; Robertson, D. E.

1984-06-01

An independent study of the field has resulted in a compilation of the best methods for sampling, preservation and analysis of potential pollutants from geothermally fueled electric power plants. These methods are selected as the most usable over the range of application commonly experienced in the various geothermal plant sample locations. In addition to plant and well piping, techniques for sampling cooling towers, ambient gases, solids, surface and subsurface waters are described. Emphasis is placed on the use of sampling proves to extract samples from heterogeneous flows. Certain sampling points, constituents and phases of plant operation are more amenable to quality assurance improvement in the emission measurements than others and are so identified.

A Mixed Methods Investigation of Mixed Methods Sampling Designs in Social and Health Science Research

ERIC Educational Resources Information Center

Collins, Kathleen M. T.; Onwuegbuzie, Anthony J.; Jiao, Qun G.

2007-01-01

A sequential design utilizing identical samples was used to classify mixed methods studies via a two-dimensional model, wherein sampling designs were grouped according to the time orientation of each study's components and the relationship of the qualitative and quantitative samples. A quantitative analysis of 121 studies representing nine fields…

Transformation-cost time-series method for analyzing irregularly sampled data

NASA Astrophysics Data System (ADS)

Ozken, Ibrahim; Eroglu, Deniz; Stemler, Thomas; Marwan, Norbert; Bagci, G. Baris; Kurths, Jürgen

2015-06-01

Irregular sampling of data sets is one of the challenges often encountered in time-series analysis, since traditional methods cannot be applied and the frequently used interpolation approach can corrupt the data and bias the subsequence analysis. Here we present the TrAnsformation-Cost Time-Series (TACTS) method, which allows us to analyze irregularly sampled data sets without degenerating the quality of the data set. Instead of using interpolation we consider time-series segments and determine how close they are to each other by determining the cost needed to transform one segment into the following one. Using a limited set of operations—with associated costs—to transform the time series segments, we determine a new time series, that is our transformation-cost time series. This cost time series is regularly sampled and can be analyzed using standard methods. While our main interest is the analysis of paleoclimate data, we develop our method using numerical examples like the logistic map and the Rössler oscillator. The numerical data allows us to test the stability of our method against noise and for different irregular samplings. In addition we provide guidance on how to choose the associated costs based on the time series at hand. The usefulness of the TACTS method is demonstrated using speleothem data from the Secret Cave in Borneo that is a good proxy for paleoclimatic variability in the monsoon activity around the maritime continent.

Transformation-cost time-series method for analyzing irregularly sampled data.

PubMed

Ozken, Ibrahim; Eroglu, Deniz; Stemler, Thomas; Marwan, Norbert; Bagci, G Baris; Kurths, Jürgen

2015-06-01

Irregular sampling of data sets is one of the challenges often encountered in time-series analysis, since traditional methods cannot be applied and the frequently used interpolation approach can corrupt the data and bias the subsequence analysis. Here we present the TrAnsformation-Cost Time-Series (TACTS) method, which allows us to analyze irregularly sampled data sets without degenerating the quality of the data set. Instead of using interpolation we consider time-series segments and determine how close they are to each other by determining the cost needed to transform one segment into the following one. Using a limited set of operations-with associated costs-to transform the time series segments, we determine a new time series, that is our transformation-cost time series. This cost time series is regularly sampled and can be analyzed using standard methods. While our main interest is the analysis of paleoclimate data, we develop our method using numerical examples like the logistic map and the Rössler oscillator. The numerical data allows us to test the stability of our method against noise and for different irregular samplings. In addition we provide guidance on how to choose the associated costs based on the time series at hand. The usefulness of the TACTS method is demonstrated using speleothem data from the Secret Cave in Borneo that is a good proxy for paleoclimatic variability in the monsoon activity around the maritime continent.

Self-contained cryogenic gas sampling apparatus and method

DOEpatents

McManus, G.J.; Motes, B.G.; Bird, S.K.; Kotter, D.K.

1996-03-26

Apparatus for obtaining a whole gas sample, is composed of: a sample vessel having an inlet for receiving a gas sample; a controllable valve mounted for controllably opening and closing the inlet; a valve control coupled to the valve for opening and closing the valve at selected times; a portable power source connected for supplying operating power to the valve control; and a cryogenic coolant in thermal communication with the vessel for cooling the interior of the vessel to cryogenic temperatures. A method is described for obtaining an air sample using the apparatus described above, by: placing the apparatus at a location at which the sample is to be obtained; operating the valve control to open the valve at a selected time and close the valve at a selected subsequent time; and between the selected times maintaining the vessel at a cryogenic temperature by heat exchange with the coolant. 3 figs.

Self-contained cryogenic gas sampling apparatus and method

DOEpatents

McManus, Gary J.; Motes, Billy G.; Bird, Susan K.; Kotter, Dale K.

1996-01-01

Apparatus for obtaining a whole gas sample, composed of: a sample vessel having an inlet for receiving a gas sample; a controllable valve mounted for controllably opening and closing the inlet; a valve control coupled to the valve for opening and closing the valve at selected times; a portable power source connected for supplying operating power to the valve control; and a cryogenic coolant in thermal communication with the vessel for cooling the interior of the vessel to cryogenic temperatures. A method of obtaining an air sample using the apparatus described above, by: placing the apparatus at a location at which the sample is to be obtained; operating the valve control to open the valve at a selected time and close the valve at a selected subsequent time; and between the selected times maintaining the vessel at a cryogenic temperature by heat exchange with the coolant.

Different methods for volatile sampling in mammals

PubMed Central

Möller, Manfred; Marcillo, Andrea; Einspanier, Almuth; Weiß, Brigitte M.

2017-01-01

Previous studies showed that olfactory cues are important for mammalian communication. However, many specific compounds that convey information between conspecifics are still unknown. To understand mechanisms and functions of olfactory cues, olfactory signals such as volatile compounds emitted from individuals need to be assessed. Sampling of animals with and without scent glands was typically conducted using cotton swabs rubbed over the skin or fur and analysed by gas chromatography-mass spectrometry (GC-MS). However, this method has various drawbacks, including a high level of contaminations. Thus, we adapted two methods of volatile sampling from other research fields and compared them to sampling with cotton swabs. To do so we assessed the body odor of common marmosets (Callithrix jacchus) using cotton swabs, thermal desorption (TD) tubes and, alternatively, a mobile GC-MS device containing a thermal desorption trap. Overall, TD tubes comprised most compounds (N = 113), with half of those compounds being volatile (N = 52). The mobile GC-MS captured the fewest compounds (N = 35), of which all were volatile. Cotton swabs contained an intermediate number of compounds (N = 55), but very few volatiles (N = 10). Almost all compounds found with the mobile GC-MS were also captured with TD tubes (94%). Hence, we recommend TD tubes for state of the art sampling of body odor of mammals or other vertebrates, particularly for field studies, as they can be easily transported, stored and analysed with high performance instruments in the lab. Nevertheless, cotton swabs capture compounds which still may contribute to the body odor, e.g. after bacterial fermentation, while profiles from mobile GC-MS include only the most abundant volatiles of the body odor. PMID:28841690

Comparison of methods for sampling plant bugs on cotton in South Texas (2010)

USDA-ARS?s Scientific Manuscript database

A total of 26 cotton fields were sampled by experienced and inexperienced samplers at 3 growth stages using 5 methods to compare the most efficient and accurate method for sampling plant bugs in cotton. Each of the 5 methods had its own distinct advantages and disadvantages as a sampling method (too...

A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments.

PubMed

Olesen, Scott W; Vora, Suhani; Techtmann, Stephen M; Fortney, Julian L; Bastidas-Oyanedel, Juan R; Rodríguez, Jorge; Hazen, Terry C; Alm, Eric J

2016-01-01

Many microbial ecology experiments use sequencing data to measure a community's response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samples and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method's validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of "bottle effects".

A random spatial sampling method in a rural developing nation

Treesearch

Michelle C. Kondo; Kent D.W. Bream; Frances K. Barg; Charles C. Branas

2014-01-01

Nonrandom sampling of populations in developing nations has limitations and can inaccurately estimate health phenomena, especially among hard-to-reach populations such as rural residents. However, random sampling of rural populations in developing nations can be challenged by incomplete enumeration of the base population. We describe a stratified random sampling method...

Sampling methods for terrestrial amphibians and reptiles.

Treesearch

Paul Stephen Corn; R. Bruce Bury

1990-01-01

Methods described for sampling amphibians and reptiles in Douglas-fir forests in the Pacific Northwest include pitfall trapping, time-constrained collecting, and surveys of coarse woody debris. The herpetofauna of this region differ in breeding and nonbreeding habitats and vagility, so that no single technique is sufficient for a community study. A combination of...

Universal nucleic acids sample preparation method for cells, spores and their mixture

DOEpatents

Bavykin, Sergei [Darien, IL

2011-01-18

The present invention relates to a method for extracting nucleic acids from biological samples. More specifically the invention relates to a universal method for extracting nucleic acids from unidentified biological samples. An advantage of the presently invented method is its ability to effectively and efficiently extract nucleic acids from a variety of different cell types including but not limited to prokaryotic or eukaryotic cells and/or recalcitrant organisms (i.e. spores). Unlike prior art methods which are focused on extracting nucleic acids from vegetative cell or spores, the present invention effectively extracts nucleic acids from spores, multiple cell types or mixtures thereof using a single method. Important that the invented method has demonstrated an ability to extract nucleic acids from spores and vegetative bacterial cells with similar levels effectiveness. The invented method employs a multi-step protocol which erodes the cell structure of the biological sample, isolates, labels, fragments nucleic acids and purifies labeled samples from the excess of dye.

Profiling Cholinesterase Adduction: A High-Throughput Prioritization Method for Organophosphate Exposure Samples

PubMed Central

Carter, Melissa D.; Crow, Brian S.; Pantazides, Brooke G.; Watson, Caroline M.; deCastro, B. Rey; Thomas, Jerry D.; Blake, Thomas A.; Johnson, Rudolph C.

2017-01-01

A high-throughput prioritization method was developed for use with a validated confirmatory method detecting organophosphorus nerve agent exposure by immunomagnetic separation-HPLC-MS/MS. A ballistic gradient was incorporated into this analytical method in order to profile unadducted butyrylcholinesterase (BChE) in clinical samples. With Zhang, et al. 1999’s Z′-factor of 0.88 ± 0.01 (SD) of control analytes and Z-factor of 0.25 ± 0.06 (SD) of serum samples, the assay is rated an “excellent assay” for the synthetic peptide controls used and a “double assay” when used to prioritize clinical samples. Hits, defined as samples containing BChE Ser-198 adducts or no BChE present, were analyzed in a confirmatory method for identification and quantitation of the BChE adduct, if present. The ability to prioritize samples by highest exposure for confirmatory analysis is of particular importance in an exposure to cholinesterase inhibitors such as organophosphorus nerve agents where a large number of clinical samples may be collected. In an initial blind screen, 67 out of 70 samples were accurately identified giving an assay accuracy of 96% and yielded no false negatives. The method is the first to provide a high-throughput prioritization assay for profiling adduction of Ser-198 BChE in clinical samples. PMID:23954929

Simplified sample preparation method for triclosan and methyltriclosan determination in biota and foodstuff samples.

PubMed

Canosa, P; Rodríguez, I; Rubí, E; Ramil, M; Cela, R

2008-04-25

An improved method for the determination of triclosan (TCS) and methyltriclosan (MTCS) in fish and foodstuff samples is presented. Analytes were simultaneously extracted and purified using the matrix solid-phase dispersion (MSPD) technique, and then selectively determined by gas chromatography with tandem mass spectrometry (GC-MS/MS). Several combinations of dispersants, clean-up co-sorbents and extraction solvents were tested in order to obtain lipid-free extracts and quantitative recoveries for TCS and MTCS. Under optimised conditions, 0.5 g samples were dispersed using 1.5 g of neutral silica in a mortar with a pestle, and transferred to a polypropylene cartridge containing 3 g of silica impregnated with 10% of sulphuric acid (SiO2-H2SO4, 10%, w/w). Analytes were recovered with 10 mL of dichloromethane whereas lipids were oxidized in the layer of acidic silica. The extract was concentrated to dryness and re-constituted with 1 mL of ethyl acetate. Then, a fraction of 0.5 mL was mixed with 50 microL of N-methyl-N-(tert-butyldimethylsilyl)trifluoroacetamide (MTBSTFA) and injected in the GC-MS/MS system. The developed method provided absolute recoveries between 77 and 120% for different samples spiked at the low ng g(-1) level, quantification limits in the range of 1-2 ng g(-1) and a considerable simplicity in comparison with previously developed sample preparation approaches. Experiments carried out placing sliced food samples in direct contact with TCS-treated kitchenware surfaces showed the capability of the biocide to migrate into foodstuffs.

Fluidics platform and method for sample preparation and analysis

DOEpatents

Benner, W. Henry; Dzenitis, John M.; Bennet, William J.; Baker, Brian R.

2014-08-19

Herein provided are fluidics platform and method for sample preparation and analysis. The fluidics platform is capable of analyzing DNA from blood samples using amplification assays such as polymerase-chain-reaction assays and loop-mediated-isothermal-amplification assays. The fluidics platform can also be used for other types of assays and analyzes. In some embodiments, a sample in a sealed tube can be inserted directly. The following isolation, detection, and analyzes can be performed without a user's intervention. The disclosed platform may also comprises a sample preparation system with a magnetic actuator, a heater, and an air-drying mechanism, and fluid manipulation processes for extraction, washing, elution, assay assembly, assay detection, and cleaning after reactions and between samples.

Method and apparatus for imaging a sample on a device

DOEpatents

Trulson, Mark; Stern, David; Fiekowsky, Peter; Rava, Richard; Walton, Ian; Fodor, Stephen P. A.

2001-01-01

A method and apparatus for imaging a sample are provided. An electromagnetic radiation source generates excitation radiation which is sized by excitation optics to a line. The line is directed at a sample resting on a support and excites a plurality of regions on the sample. Collection optics collect response radiation reflected from the sample I and image the reflected radiation. A detector senses the reflected radiation and is positioned to permit discrimination between radiation reflected from a certain focal plane in the sample and certain other planes within the sample.

Comparison of individual and pooled sampling methods for detecting bacterial pathogens of fish

USGS Publications Warehouse

Mumford, Sonia; Patterson, Chris; Evered, J.; Brunson, Ray; Levine, J.; Winton, J.

2005-01-01

Examination of finfish populations for viral and bacterial pathogens is an important component of fish disease control programs worldwide. Two methods are commonly used for collecting tissue samples for bacteriological culture, the currently accepted standards for detection of bacterial fish pathogens. The method specified in the Office International des Epizooties Manual of Diagnostic Tests for Aquatic Animals permits combining renal and splenic tissues from as many as 5 fish into pooled samples. The American Fisheries Society (AFS) Blue Book/US Fish and Wildlife Service (USFWS) Inspection Manual specifies the use of a bacteriological loop for collecting samples from the kidney of individual fish. An alternative would be to more fully utilize the pooled samples taken for virology. If implemented, this approach would provide substantial savings in labor and materials. To compare the relative performance of the AFS/USFWS method and this alternative approach, cultures of Yersinia ruckeri were used to establish low-level infections in groups of rainbow trout (Oncorhynchus mykiss) that were sampled by both methods. Yersinia ruckeri was cultured from 22 of 37 groups by at least 1 method. The loop method yielded 18 positive groups, with 1 group positive in the loop samples but negative in the pooled samples. The pooled samples produced 21 positive groups, with 4 groups positive in the pooled samples but negative in the loop samples. There was statistically significant agreement (Spearman coefficient 0.80, P < 0.001) in the relative ability of the 2 sampling methods to permit detection of low-level bacterial infections of rainbow trout.

Sampling methods for amphibians in streams in the Pacific Northwest.

Treesearch

R. Bruce Bury; Paul Stephen Corn

1991-01-01

Methods describing how to sample aquatic and semiaquatic amphibians in small streams and headwater habitats in the Pacific Northwest are presented. We developed a technique that samples 10-meter stretches of selected streams, which was adequate to detect presence or absence of amphibian species and provided sample sizes statistically sufficient to compare abundance of...

A quantitative evaluation of two methods for preserving hair samples

USGS Publications Warehouse

Roon, David A.; Waits, L.P.; Kendall, K.C.

2003-01-01

Hair samples are an increasingly important DNA source for wildlife studies, yet optimal storage methods and DNA degradation rates have not been rigorously evaluated. We tested amplification success rates over a one-year storage period for DNA extracted from brown bear (Ursus arctos) hair samples preserved using silica desiccation and -20C freezing. For three nuclear DNA microsatellites, success rates decreased significantly after a six-month time point, regardless of storage method. For a 1000 bp mitochondrial fragment, a similar decrease occurred after a two-week time point. Minimizing delays between collection and DNA extraction will maximize success rates for hair-based noninvasive genetic sampling projects.

Comparison of DNA preservation methods for environmental bacterial community samples

USGS Publications Warehouse

Gray, Michael A.; Pratte, Zoe A.; Kellogg, Christina A.

2013-01-01

Field collections of environmental samples, for example corals, for molecular microbial analyses present distinct challenges. The lack of laboratory facilities in remote locations is common, and preservation of microbial community DNA for later study is critical. A particular challenge is keeping samples frozen in transit. Five nucleic acid preservation methods that do not require cold storage were compared for effectiveness over time and ease of use. Mixed microbial communities of known composition were created and preserved by DNAgard™, RNAlater®, DMSO–EDTA–salt (DESS), FTA® cards, and FTA Elute® cards. Automated ribosomal intergenic spacer analysis and clone libraries were used to detect specific changes in the faux communities over weeks and months of storage. A previously known bias in FTA® cards that results in lower recovery of pure cultures of Gram-positive bacteria was also detected in mixed community samples. There appears to be a uniform bias across all five preservation methods against microorganisms with high G + C DNA. Overall, the liquid-based preservatives (DNAgard™, RNAlater®, and DESS) outperformed the card-based methods. No single liquid method clearly outperformed the others, leaving method choice to be based on experimental design, field facilities, shipping constraints, and allowable cost.

Sampling Methods and the Accredited Population in Athletic Training Education Research

ERIC Educational Resources Information Center

Carr, W. David; Volberding, Jennifer

2009-01-01

Context: We describe methods of sampling the widely-studied, yet poorly defined, population of accredited athletic training education programs (ATEPs). Objective: There are two purposes to this study; first to describe the incidence and types of sampling methods used in athletic training education research, and second to clearly define the…

Estimating uncertainty in respondent-driven sampling using a tree bootstrap method.

PubMed

Baraff, Aaron J; McCormick, Tyler H; Raftery, Adrian E

2016-12-20

Respondent-driven sampling (RDS) is a network-based form of chain-referral sampling used to estimate attributes of populations that are difficult to access using standard survey tools. Although it has grown quickly in popularity since its introduction, the statistical properties of RDS estimates remain elusive. In particular, the sampling variability of these estimates has been shown to be much higher than previously acknowledged, and even methods designed to account for RDS result in misleadingly narrow confidence intervals. In this paper, we introduce a tree bootstrap method for estimating uncertainty in RDS estimates based on resampling recruitment trees. We use simulations from known social networks to show that the tree bootstrap method not only outperforms existing methods but also captures the high variability of RDS, even in extreme cases with high design effects. We also apply the method to data from injecting drug users in Ukraine. Unlike other methods, the tree bootstrap depends only on the structure of the sampled recruitment trees, not on the attributes being measured on the respondents, so correlations between attributes can be estimated as well as variability. Our results suggest that it is possible to accurately assess the high level of uncertainty inherent in RDS.

A Typology of Mixed Methods Sampling Designs in Social Science Research

ERIC Educational Resources Information Center

Onwuegbuzie, Anthony J.; Collins, Kathleen M. T.

2007-01-01

This paper provides a framework for developing sampling designs in mixed methods research. First, we present sampling schemes that have been associated with quantitative and qualitative research. Second, we discuss sample size considerations and provide sample size recommendations for each of the major research designs for quantitative and…

System and method for measuring fluorescence of a sample

DOEpatents

Riot, Vincent J

2015-03-24

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

Photoacoustic spectroscopy sample array vessels and photoacoustic spectroscopy methods for using the same

DOEpatents

Amonette, James E.; Autrey, S. Thomas; Foster-Mills, Nancy S.

2006-02-14

Methods and apparatus for simultaneous or sequential, rapid analysis of multiple samples by photoacoustic spectroscopy are disclosed. Particularly, a photoacoustic spectroscopy sample array vessel including a vessel body having multiple sample cells connected thereto is disclosed. At least one acoustic detector is acoustically positioned near the sample cells. Methods for analyzing the multiple samples in the sample array vessels using photoacoustic spectroscopy are provided.

Sparse feature learning for instrument identification: Effects of sampling and pooling methods.

PubMed

Han, Yoonchang; Lee, Subin; Nam, Juhan; Lee, Kyogu

2016-05-01

Feature learning for music applications has recently received considerable attention from many researchers. This paper reports on the sparse feature learning algorithm for musical instrument identification, and in particular, focuses on the effects of the frame sampling techniques for dictionary learning and the pooling methods for feature aggregation. To this end, two frame sampling techniques are examined that are fixed and proportional random sampling. Furthermore, the effect of using onset frame was analyzed for both of proposed sampling methods. Regarding summarization of the feature activation, a standard deviation pooling method is used and compared with the commonly used max- and average-pooling techniques. Using more than 47 000 recordings of 24 instruments from various performers, playing styles, and dynamics, a number of tuning parameters are experimented including the analysis frame size, the dictionary size, and the type of frequency scaling as well as the different sampling and pooling methods. The results show that the combination of proportional sampling and standard deviation pooling achieve the best overall performance of 95.62% while the optimal parameter set varies among the instrument classes.

Active Search on Carcasses versus Pitfall Traps: a Comparison of Sampling Methods.

PubMed

Zanetti, N I; Camina, R; Visciarelli, E C; Centeno, N D

2016-04-01

The study of insect succession in cadavers and the classification of arthropods have mostly been done by placing a carcass in a cage, protected from vertebrate scavengers, which is then visited periodically. An alternative is to use specific traps. Few studies on carrion ecology and forensic entomology involving the carcasses of large vertebrates have employed pitfall traps. The aims of this study were to compare both sampling methods (active search on a carcass and pitfall trapping) for each coleopteran family, and to establish whether there is a discrepancy (underestimation and/or overestimation) in the presence of each family by either method. A great discrepancy was found for almost all families with some of them being more abundant in samples obtained through active search on carcasses and others in samples from traps, whereas two families did not show any bias towards a given sampling method. The fact that families may be underestimated or overestimated by the type of sampling technique highlights the importance of combining both methods, active search on carcasses and pitfall traps, in order to obtain more complete information on decomposition, carrion habitat and cadaveric families or species. Furthermore, a hypothesis advanced on the reasons for the underestimation by either sampling method showing biases towards certain families. Information about the sampling techniques indicating which would be more appropriate to detect or find a particular family is provided.

Perilymph sampling from the cochlear apex: a reliable method to obtain higher purity perilymph samples from scala tympani.

PubMed

Salt, Alec N; Hale, Shane A; Plonkte, Stefan K R

2006-05-15

Measurements of drug levels in the fluids of the inner ear are required to establish kinetic parameters and to determine the influence of specific local delivery protocols. For most substances, this requires cochlear fluids samples to be obtained for analysis. When auditory function is of primary interest, the drug level in the perilymph of scala tympani (ST) is most relevant, since drug in this scala has ready access to the auditory sensory cells. In many prior studies, ST perilymph samples have been obtained from the basal turn, either by aspiration through the round window membrane (RWM) or through an opening in the bony wall. A number of studies have demonstrated that such samples are likely to be contaminated with cerebrospinal fluid (CSF). CSF enters the basal turn of ST through the cochlear aqueduct when the bony capsule is perforated or when fluid is aspirated. The degree of sample contamination has, however, not been widely appreciated. Recent studies have shown that perilymph samples taken through the round window membrane are highly contaminated with CSF, with samples greater than 2microL in volume containing more CSF than perilymph. In spite of this knowledge, many groups continue to sample from the base of the cochlea, as it is a well-established method. We have developed an alternative, technically simple method to increase the proportion of ST perilymph in a fluid sample. The sample is taken from the apex of the cochlea, a site that is distant from the cochlear aqueduct. A previous problem with sampling through a perforation in the bone was that the native perilymph rapidly leaked out driven by CSF pressure and was lost to the middle ear space. We therefore developed a procedure to collect all the fluid that emerged from the perforated apex after perforation. We evaluated the method using a marker ion trimethylphenylammonium (TMPA). TMPA was applied to the perilymph of guinea pigs either by RW irrigation or by microinjection into the apical turn. The

Perilymph Sampling from the Cochlear Apex: A Reliable Method to Obtain Higher Purity Perilymph Samples from Scala Tympani

PubMed Central

Salt, Alec N.; Hale, Shane A.; Plontke, Stefan K. R.

2006-01-01

Measurements of drug levels in the fluids of the inner ear are required to establish kinetic parameters and to determine the influence of specific local delivery protocols. For most substances, this requires cochlear fluids samples to be obtained for analysis. When auditory function is of primary interest, the drug level in the perilymph of scala tympani (ST) is most relevant, since drug in this scala has ready access to the auditory sensory cells. In many prior studies, ST perilymph samples have been obtained from the basal turn, either by aspiration through the round window membrane (RWM) or through an opening in the bony wall. A number of studies have demonstrated that such samples are likely to be contaminated with cerebrospinal fluid (CSF). CSF enters the basal turn of ST through the cochlear aqueduct when the bony capsule is perforated or when fluid is aspirated. The degree of sample contamination has, however, not been widely appreciated. Recent studies have shown that perilymph samples taken through the round window membrane are highly contaminated with CSF, with samples greater than 2 μL in volume containing more CSF than perilymph. In spite of this knowledge, many groups continue to sample from the base of the cochlea, as it is a well-established method. We have developed an alternative, technically simple method to increase the proportion of ST perilymph in a fluid sample. The sample is taken from the apex of the cochlea, a site that is distant from the cochlear aqueduct. A previous problem with sampling through a perforation in the bone was that the native perilymph rapidly leaked out driven by CSF pressure and was lost to the middle ear space. We therefore developed a procedure to collect all the fluid that emerged from the perforated apex after perforation. We evaluated the method using a marker ion trimethylphenylammonium (TMPA). TMPA was applied to the perilymph of guinea pigs either by RW irrigation or by microinjection into the apical turn. The

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

A multi-threshold sampling method for TOF-PET signal processing

NASA Astrophysics Data System (ADS)

Kim, H.; Kao, C. M.; Xie, Q.; Chen, C. T.; Zhou, L.; Tang, F.; Frisch, H.; Moses, W. W.; Choong, W. S.

2009-04-01

As an approach to realizing all-digital data acquisition for positron emission tomography (PET), we have previously proposed and studied a multi-threshold sampling method to generate samples of a PET event waveform with respect to a few user-defined amplitudes. In this sampling scheme, one can extract both the energy and timing information for an event. In this paper, we report our prototype implementation of this sampling method and the performance results obtained with this prototype. The prototype consists of two multi-threshold discriminator boards and a time-to-digital converter (TDC) board. Each of the multi-threshold discriminator boards takes one input and provides up to eight threshold levels, which can be defined by users, for sampling the input signal. The TDC board employs the CERN HPTDC chip that determines the digitized times of the leading and falling edges of the discriminator output pulses. We connect our prototype electronics to the outputs of two Hamamatsu R9800 photomultiplier tubes (PMTs) that are individually coupled to a 6.25×6.25×25 mm3 LSO crystal. By analyzing waveform samples generated by using four thresholds, we obtain a coincidence timing resolution of about 340 ps and an ˜18% energy resolution at 511 keV. We are also able to estimate the decay-time constant from the resulting samples and obtain a mean value of 44 ns with an ˜9 ns FWHM. In comparison, using digitized waveforms obtained at a 20 GSps sampling rate for the same LSO/PMT modules we obtain ˜300 ps coincidence timing resolution, ˜14% energy resolution at 511 keV, and ˜5 ns FWHM for the estimated decay-time constant. Details of the results on the timing and energy resolutions by using the multi-threshold method indicate that it is a promising approach for implementing digital PET data acquisition.

A Mixed Methods Sampling Methodology for a Multisite Case Study

ERIC Educational Resources Information Center

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

2012-01-01

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

7 CFR 51.308 - Methods of sampling and calculation of percentages.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Grades of Apples Methods of Sampling and Calculation of Percentages § 51.308 Methods of sampling and... weigh ten pounds or less, or in any container where the minimum diameter of the smallest apple does not vary more than 1/2 inch from the minimum diameter of the largest apple, percentages shall be calculated...

7 CFR 51.308 - Methods of sampling and calculation of percentages.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Grades of Apples Methods of Sampling and Calculation of Percentages § 51.308 Methods of sampling and... weigh ten pounds or less, or in any container where the minimum diameter of the smallest apple does not vary more than 1/2 inch from the minimum diameter of the largest apple, percentages shall be calculated...

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

EPA Science Inventory

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

[Standard sample preparation method for quick determination of trace elements in plastic].

PubMed

Yao, Wen-Qing; Zong, Rui-Long; Zhu, Yong-Fa

2011-08-01

Reference sample was prepared by masterbatch method, containing heavy metals with known concentration of electronic information products (plastic), the repeatability and precision were determined, and reference sample preparation procedures were established. X-Ray fluorescence spectroscopy (XRF) analysis method was used to determine the repeatability and uncertainty in the analysis of the sample of heavy metals and bromine element. The working curve and the metrical methods for the reference sample were carried out. The results showed that the use of the method in the 200-2000 mg x kg(-1) concentration range for Hg, Pb, Cr and Br elements, and in the 20-200 mg x kg(-1) range for Cd elements, exhibited a very good linear relationship, and the repeatability of analysis methods for six times is good. In testing the circuit board ICB288G and ICB288 from the Mitsubishi Heavy Industry Company, results agreed with the recommended values.

Flagging versus dragging as sampling methods for nymphal Ixodes scapularis (Acari: Ixodidae)

USGS Publications Warehouse

Rulison, Eric L.; Kuczaj, Isis; Pang, Genevieve; Hickling, Graham J.; Tsao, Jean I.; Ginsberg, Howard S.

2013-01-01

The nymphal stage of the blacklegged tick, Ixodes scapularis (Acari: Ixodidae), is responsible for most transmission of Borrelia burgdorferi, the etiologic agent of Lyme disease, to humans in North America. From 2010 to fall of 2012, we compared two commonly used techniques, flagging and dragging, as sampling methods for nymphal I. scapularis at three sites, each with multiple sampling arrays (grids), in the eastern and central United States. Flagging and dragging collected comparable numbers of nymphs, with no consistent differences between methods. Dragging collected more nymphs than flagging in some samples, but these differences were not consistent among sites or sampling years. The ratio of nymphs collected by flagging vs dragging was not significantly related to shrub density, so habitat type did not have a strong effect on the relative efficacy of these methods. Therefore, although dragging collected more ticks in a few cases, the numbers collected by each method were so variable that neither technique had a clear advantage for sampling nymphal I. scapularis.

Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett's Acceptance Ratio and Enveloping Distribution Sampling Methods.

PubMed

König, Gerhard; Miller, Benjamin T; Boresch, Stefan; Wu, Xiongwu; Brooks, Bernard R

2012-10-09

One of the key requirements for the accurate calculation of free energy differences is proper sampling of conformational space. Especially in biological applications, molecular dynamics simulations are often confronted with rugged energy surfaces and high energy barriers, leading to insufficient sampling and, in turn, poor convergence of the free energy results. In this work, we address this problem by employing enhanced sampling methods. We explore the possibility of using self-guided Langevin dynamics (SGLD) to speed up the exploration process in free energy simulations. To obtain improved free energy differences from such simulations, it is necessary to account for the effects of the bias due to the guiding forces. We demonstrate how this can be accomplished for the Bennett's acceptance ratio (BAR) and the enveloping distribution sampling (EDS) methods. While BAR is considered among the most efficient methods available for free energy calculations, the EDS method developed by Christ and van Gunsteren is a promising development that reduces the computational costs of free energy calculations by simulating a single reference state. To evaluate the accuracy of both approaches in connection with enhanced sampling, EDS was implemented in CHARMM. For testing, we employ benchmark systems with analytical reference results and the mutation of alanine to serine. We find that SGLD with reweighting can provide accurate results for BAR and EDS where conventional molecular dynamics simulations fail. In addition, we compare the performance of EDS with other free energy methods. We briefly discuss the implications of our results and provide practical guidelines for conducting free energy simulations with SGLD.

Photoacoustic spectroscopy sample array vessel and photoacoustic spectroscopy method for using the same

DOEpatents

Amonette, James E.; Autrey, S. Thomas; Foster-Mills, Nancy S.; Green, David

2005-03-29

Methods and apparatus for analysis of multiple samples by photoacoustic spectroscopy are disclosed. Particularly, a photoacoustic spectroscopy sample array vessel including a vessel body having multiple sample cells connected thereto is disclosed. At least one acoustic detector is acoustically coupled with the vessel body. Methods for analyzing the multiple samples in the sample array vessels using photoacoustic spectroscopy are provided.

Some refinements on the comparison of areal sampling methods via simulation

Treesearch

Jeffrey Gove

2017-01-01

The design of forest inventories and development of new sampling methods useful in such inventories normally have a two-fold target of design unbiasedness and minimum variance in mind. Many considerations such as costs go into the choices of sampling method for operational and other levels of inventory. However, the variance in terms of meeting a specified level of...

The Precision Efficacy Analysis for Regression Sample Size Method.

ERIC Educational Resources Information Center

Brooks, Gordon P.; Barcikowski, Robert S.

The general purpose of this study was to examine the efficiency of the Precision Efficacy Analysis for Regression (PEAR) method for choosing appropriate sample sizes in regression studies used for precision. The PEAR method, which is based on the algebraic manipulation of an accepted cross-validity formula, essentially uses an effect size to…

Comparison of four sampling methods for the detection of Salmonella in broiler litter.

PubMed

Buhr, R J; Richardson, L J; Cason, J A; Cox, N A; Fairchild, B D

2007-01-01

Experiments were conducted to compare litter sampling methods for the detection of Salmonella. In experiment 1, chicks were challenged orally with a suspension of naladixic acid-resistant Salmonella and wing banded, and additional nonchallenged chicks were placed into each of 2 challenge pens. Nonchallenged chicks were placed into each nonchallenge pen located adjacent to the challenge pens. At 7, 8, 10, and 11 wk of age the litter was sampled using 4 methods: fecal droppings, litter grab, drag swab, and sock. For the challenge pens, Salmonella-positive samples were detected in 3 of 16 fecal samples, 6 of 16 litter grab samples, 7 of 16 drag swabs samples, and 7 of 16 sock samples. Samples from the nonchallenge pens were Salmonella positive in 2 of 16 litter grab samples, 9 of 16 drag swab samples, and 9 of 16 sock samples. In experiment 2, chicks were challenged with Salmonella, and the litter in the challenge and adjacent nonchallenge pens were sampled at 4, 6, and 8 wk of age with broilers remaining in all pens. For the challenge pens, Salmonella was detected in 10 of 36 fecal samples, 20 of 36 litter grab samples, 14 of 36 drag swab samples, and 26 of 36 sock samples. Samples from the adjacent nonchallenge pens were positive for Salmonella in 6 of 36 fecal droppings samples, 4 of 36 litter grab samples, 7 of 36 drag swab samples, and 19 of 36 sock samples. Sock samples had the highest rates of Salmonella detection. In experiment 3, the litter from a Salmonella-challenged flock was sampled at 7, 8, and 9 wk by socks and drag swabs. In addition, comparisons with drag swabs that were stepped on during sampling were made. Both socks (24 of 36, 67%) and drag swabs that were stepped on (25 of 36, 69%) showed significantly more Salmonella-positive samples than the traditional drag swab method (16 of 36, 44%). Drag swabs that were stepped on had comparable Salmonella detection level to that for socks. Litter sampling methods that incorporate stepping on the sample

Determination of Oebalus pugnax (Hemiptera: Pentatomidae) spatial pattern in rice and development of visual sampling methods and population sampling plans.

PubMed

Espino, L; Way, M O; Wilson, L T

2008-02-01

Commercial rice, Oryza sativa L., fields in southeastern Texas were sampled during 2003 and 2004, and visual samples were compared with sweep net samples. Fields were sampled at different stages of panicle development, times of day, and by different operators. Significant differences were found between perimeter and within field sweep net samples, indicating that samples taken 9 m from the field margin overestimate within field Oebalus pugnax (F.) (Hemiptera: Pentatomidae) populations. Time of day did not significantly affect the number of O. pugnax caught with the sweep net; however, there was a trend to capture more insects during morning than afternoon. For all sampling methods evaluated during this study, O. pugnax was found to have an aggregated spatial pattern at most densities. When comparing sweep net with visual sampling methods, one sweep of the "long stick" and two sweeps of the "sweep stick" correlated well with the sweep net (r2 = 0.639 and r2 = 0.815, respectively). This relationship was not affected by time of day of sampling, stage of panicle development, type of planting or operator. Relative cost-reliability, which incorporates probability of adoption, indicates the visual methods are more cost-reliable than the sweep net for sampling O.

Method and apparatus for sampling low-yield wells

DOEpatents

Last, George V.; Lanigan, David C.

2003-04-15

An apparatus and method for collecting a sample from a low-yield well or perched aquifer includes a pump and a controller responsive to water level sensors for filling a sample reservoir. The controller activates the pump to fill the reservoir when the water level in the well reaches a high level as indicated by the sensor. The controller deactivates the pump when the water level reaches a lower level as indicated by the sensors. The pump continuously activates and deactivates the pump until the sample reservoir is filled with a desired volume, as indicated by a reservoir sensor. At the beginning of each activation cycle, the controller optionally can select to purge an initial quantity of water prior to filling the sample reservoir. The reservoir can be substantially devoid of air and the pump is a low volumetric flow rate pump. Both the pump and the reservoir can be located either inside or outside the well.

On the Exploitation of Sensitivity Derivatives for Improving Sampling Methods

NASA Technical Reports Server (NTRS)

Cao, Yanzhao; Hussaini, M. Yousuff; Zang, Thomas A.

2003-01-01

Many application codes, such as finite-element structural analyses and computational fluid dynamics codes, are capable of producing many sensitivity derivatives at a small fraction of the cost of the underlying analysis. This paper describes a simple variance reduction method that exploits such inexpensive sensitivity derivatives to increase the accuracy of sampling methods. Three examples, including a finite-element structural analysis of an aircraft wing, are provided that illustrate an order of magnitude improvement in accuracy for both Monte Carlo and stratified sampling schemes.

The study of combining Latin Hypercube Sampling method and LU decomposition method (LULHS method) for constructing spatial random field

NASA Astrophysics Data System (ADS)

WANG, P. T.

2015-12-01

Groundwater modeling requires to assign hydrogeological properties to every numerical grid. Due to the lack of detailed information and the inherent spatial heterogeneity, geological properties can be treated as random variables. Hydrogeological property is assumed to be a multivariate distribution with spatial correlations. By sampling random numbers from a given statistical distribution and assigning a value to each grid, a random field for modeling can be completed. Therefore, statistics sampling plays an important role in the efficiency of modeling procedure. Latin Hypercube Sampling (LHS) is a stratified random sampling procedure that provides an efficient way to sample variables from their multivariate distributions. This study combines the the stratified random procedure from LHS and the simulation by using LU decomposition to form LULHS. Both conditional and unconditional simulations of LULHS were develpoed. The simulation efficiency and spatial correlation of LULHS are compared to the other three different simulation methods. The results show that for the conditional simulation and unconditional simulation, LULHS method is more efficient in terms of computational effort. Less realizations are required to achieve the required statistical accuracy and spatial correlation.

Method for using polarization gating to measure a scattering sample

DOEpatents

Baba, Justin S.

2015-08-04

Described herein are systems, devices, and methods facilitating optical characterization of scattering samples. A polarized optical beam can be directed to pass through a sample to be tested. The optical beam exiting the sample can then be analyzed to determine its degree of polarization, from which other properties of the sample can be determined. In some cases, an apparatus can include a source of an optical beam, an input polarizer, a sample, an output polarizer, and a photodetector. In some cases, a signal from a photodetector can be processed through attenuation, variable offset, and variable gain.

Method and apparatus for imaging a sample on a device

DOEpatents

Trulson, Mark; Stern, David; Fiekowsky, Peter; Rava, Richard; Walton, Ian; Fodor, Stephen P. A.

1996-01-01

The present invention provides methods and systems for detecting a labeled marker on a sample located on a support. The imaging system comprises a body for immobilizing the support, an excitation radiation source and excitation optics to generate and direct the excitation radiation at the sample. In response, labeled material on the sample emits radiation which has a wavelength that is different from the excitation wavelength, which radiation is collected by collection optics and imaged onto a detector which generates an image of the sample.

Standard methods for sampling freshwater fishes: Opportunities for international collaboration

USGS Publications Warehouse

Bonar, Scott A.; Mercado-Silva, Norman; Hubert, Wayne A.; Beard, Douglas; Dave, Göran; Kubečka, Jan; Graeb, Brian D. S.; Lester, Nigel P.; Porath, Mark T.; Winfield, Ian J.

2017-01-01

With publication of Standard Methods for Sampling North American Freshwater Fishes in 2009, the American Fisheries Society (AFS) recommended standard procedures for North America. To explore interest in standardizing at intercontinental scales, a symposium attended by international specialists in freshwater fish sampling was convened at the 145th Annual AFS Meeting in Portland, Oregon, in August 2015. Participants represented all continents except Australia and Antarctica and were employed by state and federal agencies, universities, nongovernmental organizations, and consulting businesses. Currently, standardization is practiced mostly in North America and Europe. Participants described how standardization has been important for management of long-term data sets, promoting fundamental scientific understanding, and assessing efficacy of large spatial scale management strategies. Academics indicated that standardization has been useful in fisheries education because time previously used to teach how sampling methods are developed is now more devoted to diagnosis and treatment of problem fish communities. Researchers reported that standardization allowed increased sample size for method validation and calibration. Group consensus was to retain continental standards where they currently exist but to further explore international and intercontinental standardization, specifically identifying where synergies and bridges exist, and identify means to collaborate with scientists where standardization is limited but interest and need occur.

Sampling methods for the study of pneumococcal carriage: a systematic review.

PubMed

Gladstone, R A; Jefferies, J M; Faust, S N; Clarke, S C

2012-11-06

Streptococcus pneumoniae is an important pathogen worldwide. Accurate sampling of S. pneumoniae carriage is central to surveillance studies before and following conjugate vaccination programmes to combat pneumococcal disease. Any bias introduced during sampling will affect downstream recovery and typing. Many variables exist for the method of collection and initial processing, which can make inter-laboratory or international comparisons of data complex. In February 2003, a World Health Organisation working group published a standard method for the detection of pneumococcal carriage for vaccine trials to reduce or eliminate variability. We sought to describe the variables associated with the sampling of S. pneumoniae from collection to storage in the context of the methods recommended by the WHO and those used in pneumococcal carriage studies since its publication. A search of published literature in the online PubMed database was performed on the 1st June 2012, to identify published studies that collected pneumococcal carriage isolates, conducted after the publication of the WHO standard method. After undertaking a systematic analysis of the literature, we show that a number of differences in pneumococcal sampling protocol continue to exist between studies since the WHO publication. The majority of studies sample from the nasopharynx, but the choice of swab and swab transport media is more variable between studies. At present there is insufficient experimental data that supports the optimal sensitivity of any standard method. This may have contributed to incomplete adoption of the primary stages of the WHO detection protocol, alongside pragmatic or logistical issues associated with study design. Consequently studies may not provide a true estimate of pneumococcal carriage. Optimal sampling of carriage could lead to improvements in downstream analysis and the evaluation of pneumococcal vaccine impact and extrapolation to pneumococcal disease control therefore

A novel analysis method for paired-sample microbial ecology experiments

DOE PAGES

Olesen, Scott W.; Vora, Suhani; Techtmann, Stephen M.; ...

2016-05-06

Many microbial ecology experiments use sequencing data to measure a community s response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samplesmore » and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method s validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Furthermore, our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of bottle effects .« less

Comparison of DNA preservation methods for environmental bacterial community samples.

PubMed

Gray, Michael A; Pratte, Zoe A; Kellogg, Christina A

2013-02-01

Field collections of environmental samples, for example corals, for molecular microbial analyses present distinct challenges. The lack of laboratory facilities in remote locations is common, and preservation of microbial community DNA for later study is critical. A particular challenge is keeping samples frozen in transit. Five nucleic acid preservation methods that do not require cold storage were compared for effectiveness over time and ease of use. Mixed microbial communities of known composition were created and preserved by DNAgard(™), RNAlater(®), DMSO-EDTA-salt (DESS), FTA(®) cards, and FTA Elute(®) cards. Automated ribosomal intergenic spacer analysis and clone libraries were used to detect specific changes in the faux communities over weeks and months of storage. A previously known bias in FTA(®) cards that results in lower recovery of pure cultures of Gram-positive bacteria was also detected in mixed community samples. There appears to be a uniform bias across all five preservation methods against microorganisms with high G + C DNA. Overall, the liquid-based preservatives (DNAgard(™), RNAlater(®), and DESS) outperformed the card-based methods. No single liquid method clearly outperformed the others, leaving method choice to be based on experimental design, field facilities, shipping constraints, and allowable cost. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

A novel analysis method for paired-sample microbial ecology experiments

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

Olesen, Scott W.; Vora, Suhani; Techtmann, Stephen M.

Many microbial ecology experiments use sequencing data to measure a community s response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samplesmore » and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method s validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Furthermore, our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of bottle effects .« less

Probability Sampling Method for a Hidden Population Using Respondent-Driven Sampling: Simulation for Cancer Survivors.

PubMed

Jung, Minsoo

2015-01-01

When there is no sampling frame within a certain group or the group is concerned that making its population public would bring social stigma, we say the population is hidden. It is difficult to approach this kind of population survey-methodologically because the response rate is low and its members are not quite honest with their responses when probability sampling is used. The only alternative known to address the problems caused by previous methods such as snowball sampling is respondent-driven sampling (RDS), which was developed by Heckathorn and his colleagues. RDS is based on a Markov chain, and uses the social network information of the respondent. This characteristic allows for probability sampling when we survey a hidden population. We verified through computer simulation whether RDS can be used on a hidden population of cancer survivors. According to the simulation results of this thesis, the chain-referral sampling of RDS tends to minimize as the sample gets bigger, and it becomes stabilized as the wave progresses. Therefore, it shows that the final sample information can be completely independent from the initial seeds if a certain level of sample size is secured even if the initial seeds were selected through convenient sampling. Thus, RDS can be considered as an alternative which can improve upon both key informant sampling and ethnographic surveys, and it needs to be utilized for various cases domestically as well.

Determination of phenolic priority pollutants utilizing permeation sampling method

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

Zhang, Guozheng.

1990-01-01

A passive permeation sampling method for the determination of phenolic priority pollutants in water was developed. Phenols in an aqueous solution permeate a polymeric membrane and are collected on a solid adsorbent in a sampling device. Both solvent and thermal desorption techniques were employed to recovery phenolic pollutants collected. In the solvent desorption, phenolic compounds collected on the XAD-7 resin, and then desorbed by acetonitrile. In the thermal desorption, phenolic compounds collected on Tenax-TA were recovered thermally, Separation and quantification is achieved by a SPB-5 capillary column gas chromatography using a flame ionization detector. There are linear relationships between themore » amount of phenolic compounds collected and the products of the exposure times and concentrations over the range from 5 ppb to 20 ppm with precisions no worse than 13%. The permeation rates of the phenolic pollutants depend upon the exposure temperature, solution pH and membrane area. Samples collected can be stored for up to two weeks without loss. This method provides a simple, convenient and inexpensive way for monitoring the time-weighted-average concentration without the use of a pumping system. An automated sampler which combines the permeation and the thermal desorption techniques together was also developed for water sample obtained from grab sampling. The on-line setup provides a high degree of automation. Detection limits at 10 ppb can be achieved using this sampler.« less

Rock sampling. [method for controlling particle size distribution

NASA Technical Reports Server (NTRS)

Blum, P. (Inventor)

1971-01-01

A method for sampling rock and other brittle materials and for controlling resultant particle sizes is described. The method involves cutting grooves in the rock surface to provide a grouping of parallel ridges and subsequently machining the ridges to provide a powder specimen. The machining step may comprise milling, drilling, lathe cutting or the like; but a planing step is advantageous. Control of the particle size distribution is effected primarily by changing the height and width of these ridges. This control exceeds that obtainable by conventional grinding.

Method for producing a thin sample band in a microchannel device

DOEpatents

Griffiths, Stewart K [Livermore, CA; Nilson, Robert H [Cardiff, CA

2004-08-03

The present invention improves the performance of microchannel systems for chemical and biological synthesis and analysis by providing a method and apparatus for producing a thin band of a species sample. Thin sample bands improve the resolution of microchannel separation processes, as well as many other processes requiring precise control of sample size and volume. The new method comprises a series of steps in which a species sample is manipulated by controlled transport through a junction formed at the intersection of four or more channels. A sample is first inserted into the end of one of these channels in the vicinity of the junction. Next, this sample is thinned by transport across the junction one or more times. During these thinning steps, flow enters the junction through one of the channels and exists through those remaining, providing a divergent flow field that progressively stretches and thins the band with each traverse of the junction. The thickness of the resulting sample band may be smaller than the channel width. Moreover, the thickness of the band may be varied and controlled by altering the method alone, without modification to the channel or junction geometries. The invention is applicable to both electroosmotic and electrophoretic transport, to combined electrokinetic transport, and to some special cases in which bulk fluid transport is driven by pressure gradients. It is further applicable to channels that are open, filled with a gel or filled with a porous or granular material.

Simulated Tempering Distributed Replica Sampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methods for Conformational Sampling.

PubMed

Rauscher, Sarah; Neale, Chris; Pomès, Régis

2009-10-13

Generalized-ensemble algorithms in temperature space have become popular tools to enhance conformational sampling in biomolecular simulations. A random walk in temperature leads to a corresponding random walk in potential energy, which can be used to cross over energetic barriers and overcome the problem of quasi-nonergodicity. In this paper, we introduce two novel methods: simulated tempering distributed replica sampling (STDR) and virtual replica exchange (VREX). These methods are designed to address the practical issues inherent in the replica exchange (RE), simulated tempering (ST), and serial replica exchange (SREM) algorithms. RE requires a large, dedicated, and homogeneous cluster of CPUs to function efficiently when applied to complex systems. ST and SREM both have the drawback of requiring extensive initial simulations, possibly adaptive, for the calculation of weight factors or potential energy distribution functions. STDR and VREX alleviate the need for lengthy initial simulations, and for synchronization and extensive communication between replicas. Both methods are therefore suitable for distributed or heterogeneous computing platforms. We perform an objective comparison of all five algorithms in terms of both implementation issues and sampling efficiency. We use disordered peptides in explicit water as test systems, for a total simulation time of over 42 μs. Efficiency is defined in terms of both structural convergence and temperature diffusion, and we show that these definitions of efficiency are in fact correlated. Importantly, we find that ST-based methods exhibit faster temperature diffusion and correspondingly faster convergence of structural properties compared to RE-based methods. Within the RE-based methods, VREX is superior to both SREM and RE. On the basis of our observations, we conclude that ST is ideal for simple systems, while STDR is well-suited for complex systems.

A self-sampling method to obtain large volumes of undiluted cervicovaginal secretions.

PubMed

Boskey, Elizabeth R; Moench, Thomas R; Hees, Paul S; Cone, Richard A

2003-02-01

Studies of vaginal physiology and pathophysiology sometime require larger volumes of undiluted cervicovaginal secretions than can be obtained by current methods. A convenient method for self-sampling these secretions outside a clinical setting can facilitate such studies of reproductive health. The goal was to develop a vaginal self-sampling method for collecting large volumes of undiluted cervicovaginal secretions. A menstrual collection device (the Instead cup) was inserted briefly into the vagina to collect secretions that were then retrieved from the cup by centrifugation in a 50-ml conical tube. All 16 women asked to perform this procedure found it feasible and acceptable. Among 27 samples, an average of 0.5 g of secretions (range, 0.1-1.5 g) was collected. This is a rapid and convenient self-sampling method for obtaining relatively large volumes of undiluted cervicovaginal secretions. It should prove suitable for a wide range of assays, including those involving sexually transmitted diseases, microbicides, vaginal physiology, immunology, and pathophysiology.

PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology

USGS Publications Warehouse

Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; DeSantis, Todd Z.; Zawada, David G.; Andersen, Gary L.

2012-01-01

Interest in coral microbial ecology has been increasing steadily over the last decade, yet standardized methods of sample collection still have not been defined. Two methods were compared for their ability to sample coral-associated microbial communities: tissue punches and foam swabs, the latter being less invasive and preferred by reef managers. Four colonies of star coral, Montastraea annularis, were sampled in the Dry Tortugas National Park (two healthy and two with white plague disease). The PhyloChip™ G3 microarray was used to assess microbial community structure of amplified 16S rRNA gene sequences. Samples clustered based on methodology rather than coral colony. Punch samples from healthy and diseased corals were distinct. All swab samples clustered closely together with the seawater control and did not group according to the health state of the corals. Although more microbial taxa were detected by the swab method, there is a much larger overlap between the water control and swab samples than punch samples, suggesting some of the additional diversity is due to contamination from water absorbed by the swab. While swabs are useful for noninvasive studies of the coral surface mucus layer, these results show that they are not optimal for studies of coral disease.

PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology.

PubMed

Kellogg, Christina A; Piceno, Yvette M; Tom, Lauren M; DeSantis, Todd Z; Zawada, David G; Andersen, Gary L

2012-01-01

Interest in coral microbial ecology has been increasing steadily over the last decade, yet standardized methods of sample collection still have not been defined. Two methods were compared for their ability to sample coral-associated microbial communities: tissue punches and foam swabs, the latter being less invasive and preferred by reef managers. Four colonies of star coral, Montastraea annularis, were sampled in the Dry Tortugas National Park (two healthy and two with white plague disease). The PhyloChip™ G3 microarray was used to assess microbial community structure of amplified 16S rRNA gene sequences. Samples clustered based on methodology rather than coral colony. Punch samples from healthy and diseased corals were distinct. All swab samples clustered closely together with the seawater control and did not group according to the health state of the corals. Although more microbial taxa were detected by the swab method, there is a much larger overlap between the water control and swab samples than punch samples, suggesting some of the additional diversity is due to contamination from water absorbed by the swab. While swabs are useful for noninvasive studies of the coral surface mucus layer, these results show that they are not optimal for studies of coral disease. Published by Elsevier B.V.

Flaw Growth in Complex Structure. Volume 1. Technical Discussion

DTIC Science & Technology

1977-12-01

I, " RESIDUAL STRENGTH LOAD REQUIREMENT PXX LT PXX DM Pxx ESV PXX PWV PXX G([E "XX IfI FOR SAID PERIOD I I I STRUCTURE COMPLEES IN SERVICE DFPOT OX...INSPECTABILITY T THROUGH PERIOD XTX FE In-Flight Evident Return to Base PFE 2GE Ground Evident 1 Flight P GE 2WV Walkaround 50 Flights PWV SV Special

Method and apparatus for processing a test sample to concentrate an analyte in the sample from a solvent in the sample

DOEpatents

Turner, Terry D.; Beller, Laurence S.; Clark, Michael L.; Klingler, Kerry M.

1997-01-01

A method of processing a test sample to concentrate an analyte in the sample from a solvent in the sample includes: a) boiling the test sample containing the analyte and solvent in a boiling chamber to a temperature greater than or equal to the solvent boiling temperature and less than the analyte boiling temperature to form a rising sample vapor mixture; b) passing the sample vapor mixture from the boiling chamber to an elongated primary separation tube, the separation tube having internal sidewalls and a longitudinal axis, the longitudinal axis being angled between vertical and horizontal and thus having an upper region and a lower region; c) collecting the physically transported liquid analyte on the internal sidewalls of the separation tube; and d) flowing the collected analyte along the angled internal sidewalls of the separation tube to and pass the separation tube lower region. The invention also includes passing a turbulence inducing wave through a vapor mixture to separate physically transported liquid second material from vaporized first material. Apparatus are also disclosed for effecting separations. Further disclosed is a fluidically powered liquid test sample withdrawal apparatus for withdrawing a liquid test sample from a test sample container and for cleaning the test sample container.

Method and apparatus for processing a test sample to concentrate an analyte in the sample from a solvent in the sample

DOEpatents

Turner, T.D.; Beller, L.S.; Clark, M.L.; Klingler, K.M.

1997-10-14

A method of processing a test sample to concentrate an analyte in the sample from a solvent in the sample includes: (a) boiling the test sample containing the analyte and solvent in a boiling chamber to a temperature greater than or equal to the solvent boiling temperature and less than the analyte boiling temperature to form a rising sample vapor mixture; (b) passing the sample vapor mixture from the boiling chamber to an elongated primary separation tube, the separation tube having internal sidewalls and a longitudinal axis, the longitudinal axis being angled between vertical and horizontal and thus having an upper region and a lower region; (c) collecting the physically transported liquid analyte on the internal sidewalls of the separation tube; and (d) flowing the collected analyte along the angled internal sidewalls of the separation tube to and pass the separation tube lower region. The invention also includes passing a turbulence inducing wave through a vapor mixture to separate physically transported liquid second material from vaporized first material. Apparatus is also disclosed for effecting separations. Further disclosed is a fluidically powered liquid test sample withdrawal apparatus for withdrawing a liquid test sample from a test sample container and for cleaning the test sample container. 8 figs.

Recording 2-D Nutation NQR Spectra by Random Sampling Method

PubMed Central

Sinyavsky, Nikolaj; Jadzyn, Maciej; Ostafin, Michal; Nogaj, Boleslaw

2010-01-01

The method of random sampling was introduced for the first time in the nutation nuclear quadrupole resonance (NQR) spectroscopy where the nutation spectra show characteristic singularities in the form of shoulders. The analytic formulae for complex two-dimensional (2-D) nutation NQR spectra (I = 3/2) were obtained and the condition for resolving the spectral singularities for small values of an asymmetry parameter η was determined. Our results show that the method of random sampling of a nutation interferogram allows significant reduction of time required to perform a 2-D nutation experiment and does not worsen the spectral resolution. PMID:20949121

Quantifying Uncertainties from Presence Data Sampling Methods for Species Distribution Modeling: Focused on Vegetation.

NASA Astrophysics Data System (ADS)

Sung, S.; Kim, H. G.; Lee, D. K.; Park, J. H.; Mo, Y.; Kil, S.; Park, C.

2016-12-01

The impact of climate change has been observed throughout the globe. The ecosystem experiences rapid changes such as vegetation shift, species extinction. In these context, Species Distribution Model (SDM) is one of the popular method to project impact of climate change on the ecosystem. SDM basically based on the niche of certain species with means to run SDM present point data is essential to find biological niche of species. To run SDM for plants, there are certain considerations on the characteristics of vegetation. Normally, to make vegetation data in large area, remote sensing techniques are used. In other words, the exact point of presence data has high uncertainties as we select presence data set from polygons and raster dataset. Thus, sampling methods for modeling vegetation presence data should be carefully selected. In this study, we used three different sampling methods for selection of presence data of vegetation: Random sampling, Stratified sampling and Site index based sampling. We used one of the R package BIOMOD2 to access uncertainty from modeling. At the same time, we included BioCLIM variables and other environmental variables as input data. As a result of this study, despite of differences among the 10 SDMs, the sampling methods showed differences in ROC values, random sampling methods showed the lowest ROC value while site index based sampling methods showed the highest ROC value. As a result of this study the uncertainties from presence data sampling methods and SDM can be quantified.

A distance limited method for sampling downed coarse woody debris

Treesearch

Jeffrey H. Gove; Mark J. Ducey; Harry T. Valentine; Michael S. Williams

2012-01-01

A new sampling method for down coarse woody debris is proposed based on limiting the perpendicular distance from individual pieces to a randomly chosen sample point. Two approaches are presented that allow different protocols to be used to determine field measurements; estimators for each protocol are also developed. Both protocols are compared via simulation against...

Adaptive cluster sampling: An efficient method for assessing inconspicuous species

Treesearch

Andrea M. Silletti; Joan Walker

2003-01-01

Restorationistis typically evaluate the success of a project by estimating the population sizes of species that have been planted or seeded. Because total census is raely feasible, they must rely on sampling methods for population estimates. However, traditional random sampling designs may be inefficient for species that, for one reason or another, are challenging to...

A novel heterogeneous training sample selection method on space-time adaptive processing

NASA Astrophysics Data System (ADS)

Wang, Qiang; Zhang, Yongshun; Guo, Yiduo

2018-04-01

The performance of ground target detection about space-time adaptive processing (STAP) decreases when non-homogeneity of clutter power is caused because of training samples contaminated by target-like signals. In order to solve this problem, a novel nonhomogeneous training sample selection method based on sample similarity is proposed, which converts the training sample selection into a convex optimization problem. Firstly, the existing deficiencies on the sample selection using generalized inner product (GIP) are analyzed. Secondly, the similarities of different training samples are obtained by calculating mean-hausdorff distance so as to reject the contaminated training samples. Thirdly, cell under test (CUT) and the residual training samples are projected into the orthogonal subspace of the target in the CUT, and mean-hausdorff distances between the projected CUT and training samples are calculated. Fourthly, the distances are sorted in order of value and the training samples which have the bigger value are selective preference to realize the reduced-dimension. Finally, simulation results with Mountain-Top data verify the effectiveness of the proposed method.

Sampling and data handling methods for inhalable particulate sampling. Final report nov 78-dec 80

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

Smith, W.B.; Cushing, K.M.; Johnson, J.W.

1982-05-01

The report reviews the objectives of a research program on sampling and measuring particles in the inhalable particulate (IP) size range in emissions from stationary sources, and describes methods and equipment required. A computer technique was developed to analyze data on particle-size distributions of samples taken with cascade impactors from industrial process streams. Research in sampling systems for IP matter included concepts for maintaining isokinetic sampling conditions, necessary for representative sampling of the larger particles, while flowrates in the particle-sizing device were constant. Laboratory studies were conducted to develop suitable IP sampling systems with overall cut diameters of 15 micrometersmore » and conforming to a specified collection efficiency curve. Collection efficiencies were similarly measured for a horizontal elutriator. Design parameters were calculated for horizontal elutriators to be used with impactors, the EPA SASS train, and the EPA FAS train. Two cyclone systems were designed and evaluated. Tests on an Andersen Size Selective Inlet, a 15-micrometer precollector for high-volume samplers, showed its performance to be with the proposed limits for IP samplers. A stack sampling system was designed in which the aerosol is diluted in flow patterns and with mixing times simulating those in stack plumes.« less

Comparing two sampling methods to engage hard-to-reach communities in research priority setting.

PubMed

Valerio, Melissa A; Rodriguez, Natalia; Winkler, Paula; Lopez, Jaime; Dennison, Meagen; Liang, Yuanyuan; Turner, Barbara J

2016-10-28

Effective community-partnered and patient-centered outcomes research needs to address community priorities. However, optimal sampling methods to engage stakeholders from hard-to-reach, vulnerable communities to generate research priorities have not been identified. In two similar rural, largely Hispanic communities, a community advisory board guided recruitment of stakeholders affected by chronic pain using a different method in each community: 1) snowball sampling, a chain- referral method or 2) purposive sampling to recruit diverse stakeholders. In both communities, three groups of stakeholders attended a series of three facilitated meetings to orient, brainstorm, and prioritize ideas (9 meetings/community). Using mixed methods analysis, we compared stakeholder recruitment and retention as well as priorities from both communities' stakeholders on mean ratings of their ideas based on importance and feasibility for implementation in their community. Of 65 eligible stakeholders in one community recruited by snowball sampling, 55 (85 %) consented, 52 (95 %) attended the first meeting, and 36 (65 %) attended all 3 meetings. In the second community, the purposive sampling method was supplemented by convenience sampling to increase recruitment. Of 69 stakeholders recruited by this combined strategy, 62 (90 %) consented, 36 (58 %) attended the first meeting, and 26 (42 %) attended all 3 meetings. Snowball sampling recruited more Hispanics and disabled persons (all P < 0.05). Despite differing recruitment strategies, stakeholders from the two communities identified largely similar ideas for research, focusing on non-pharmacologic interventions for management of chronic pain. Ratings on importance and feasibility for community implementation differed only on the importance of massage services (P = 0.045) which was higher for the purposive/convenience sampling group and for city improvements/transportation services (P = 0.004) which was higher for the

Mapping species distributions with MAXENT using a geographically biased sample of presence data: a performance assessment of methods for correcting sampling bias.

PubMed

Fourcade, Yoan; Engler, Jan O; Rödder, Dennis; Secondi, Jean

2014-01-01

MAXENT is now a common species distribution modeling (SDM) tool used by conservation practitioners for predicting the distribution of a species from a set of records and environmental predictors. However, datasets of species occurrence used to train the model are often biased in the geographical space because of unequal sampling effort across the study area. This bias may be a source of strong inaccuracy in the resulting model and could lead to incorrect predictions. Although a number of sampling bias correction methods have been proposed, there is no consensual guideline to account for it. We compared here the performance of five methods of bias correction on three datasets of species occurrence: one "virtual" derived from a land cover map, and two actual datasets for a turtle (Chrysemys picta) and a salamander (Plethodon cylindraceus). We subjected these datasets to four types of sampling biases corresponding to potential types of empirical biases. We applied five correction methods to the biased samples and compared the outputs of distribution models to unbiased datasets to assess the overall correction performance of each method. The results revealed that the ability of methods to correct the initial sampling bias varied greatly depending on bias type, bias intensity and species. However, the simple systematic sampling of records consistently ranked among the best performing across the range of conditions tested, whereas other methods performed more poorly in most cases. The strong effect of initial conditions on correction performance highlights the need for further research to develop a step-by-step guideline to account for sampling bias. However, this method seems to be the most efficient in correcting sampling bias and should be advised in most cases.

Effectiveness of sampling methods employed for Acanthamoeba keratitis diagnosis by culture.

PubMed

Muiño, Laura; Rodrigo, Donoso; Villegas, Rodrigo; Romero, Pablo; Peredo, Daniel E; Vargas, Rafael A; Liempi, Daniela; Osuna, Antonio; Jercic, María Isabel

2018-06-18

This retrospective, observational study was designed to evaluate the effectiveness of the sampling methods commonly used for the collection of corneal scrapes for the diagnosis of Acanthamoeba keratitis (AK) by culture, in terms of their ability to provide a positive result. A total of 553 samples from 380 patients with suspected AK received at the Parasitology Section of the Public Health Institute of Chile, between January 2005 and December 2015, were evaluated. A logistic regression model was used to determine the correlation between the culture outcome (positive or negative) and the method for sample collection. The year of sample collection was also included in the analysis as a confounding variable. Three hundred and sixty-five samples (27%) from 122 patients (32.1%) were positive by culture. The distribution of sample types was as follows: 142 corneal scrapes collected using a modified bezel needle (a novel method developed by a team of Chilean corneologists), 176 corneal scrapes obtained using a scalpel, 50 corneal biopsies, 30 corneal swabs, and 155 non-biological materials including contact lens and its paraphernalia. Biopsy provided the highest likelihood ratio for a positive result by culture (1.89), followed by non-biological materials (1.10) and corneal scrapes obtained using a modified needle (1.00). The lowest likelihood ratio was estimated for corneal scrapes obtained using a scalpel (0.88) and cotton swabs (0.78). Apart from biopsy, optimum corneal samples for the improved diagnosis of AK can be obtained using a modified bezel needle instead of a scalpel, while cotton swabs are not recommended.

Sampling for Patient Exit Interviews: Assessment of Methods Using Mathematical Derivation and Computer Simulations.

PubMed

Geldsetzer, Pascal; Fink, Günther; Vaikath, Maria; Bärnighausen, Till

2018-02-01

(1) To evaluate the operational efficiency of various sampling methods for patient exit interviews; (2) to discuss under what circumstances each method yields an unbiased sample; and (3) to propose a new, operationally efficient, and unbiased sampling method. Literature review, mathematical derivation, and Monte Carlo simulations. Our simulations show that in patient exit interviews it is most operationally efficient if the interviewer, after completing an interview, selects the next patient exiting the clinical consultation. We demonstrate mathematically that this method yields a biased sample: patients who spend a longer time with the clinician are overrepresented. This bias can be removed by selecting the next patient who enters, rather than exits, the consultation room. We show that this sampling method is operationally more efficient than alternative methods (systematic and simple random sampling) in most primary health care settings. Under the assumption that the order in which patients enter the consultation room is unrelated to the length of time spent with the clinician and the interviewer, selecting the next patient entering the consultation room tends to be the operationally most efficient unbiased sampling method for patient exit interviews. © 2016 The Authors. Health Services Research published by Wiley Periodicals, Inc. on behalf of Health Research and Educational Trust.

Sampling Methods for Detection and Monitoring of the Asian Citrus Psyllid (Hemiptera: Psyllidae).

PubMed

Monzo, C; Arevalo, H A; Jones, M M; Vanaclocha, P; Croxton, S D; Qureshi, J A; Stansly, P A

2015-06-01

The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama is a key pest of citrus due to its role as vector of citrus greening disease or "huanglongbing." ACP monitoring is considered an indispensable tool for management of vector and disease. In the present study, datasets collected between 2009 and 2013 from 245 citrus blocks were used to evaluate precision, sensitivity for detection, and efficiency of five sampling methods. The number of samples needed to reach a 0.25 standard error-mean ratio was estimated using Taylor's power law and used to compare precision among sampling methods. Comparison of detection sensitivity and time expenditure (cost) between stem-tap and other sampling methodologies conducted consecutively at the same location were also assessed. Stem-tap sampling was the most efficient sampling method when ACP densities were moderate to high and served as the basis for comparison with all other methods. Protocols that grouped trees near randomly selected locations across the block were more efficient than sampling trees at random across the block. Sweep net sampling was similar to stem-taps in number of captures per sampled unit, but less precise at any ACP density. Yellow sticky traps were 14 times more sensitive than stem-taps but much more time consuming and thus less efficient except at very low population densities. Visual sampling was efficient for detecting and monitoring ACP at low densities. Suction sampling was time consuming and taxing but the most sensitive of all methods for detection of sparse populations. This information can be used to optimize ACP monitoring efforts. © 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.

Methods for collection and analysis of aquatic biological and microbiological samples

USGS Publications Warehouse

Britton, L.J.; Greeson, P.E.

1989-01-01

The series of chapters on techniques describes methods used by the U.S. Geological Survey for planning and conducting water-resources investigations. The material is arranged under major subject headings called books and is further subdivided into sections and chapters. Book 5 is on laboratory analysis. Section A is on water. The unit of publication, the chapter, is limited to a narrow field of subject matter. "Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" is the fourth chapter to be published under Section A of Book 5. The chapter number includes the letter of the section.This chapter was prepared by several aquatic biologists and microbiologists of the U.S. Geological Survey to provide accurate and precise methods for the collection and analysis of aquatic biological and microbiological samples.Use of brand, firm, and trade names in this chapter is for identification purposes only and does not constitute endorsement by the U.S. Geological Survey.This chapter supersedes "Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" edited by P.E. Greeson, T.A. Ehlke, G.A. Irwin, B.W. Lium, and K.V. Slack (U.S. Geological Survey Techniques of Water-Resources Investigations, Book 5, Chapter A4, 1977) and also supersedes "A Supplement to-Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" by P.E. Greeson (U.S. Geological Survey Techniques of Water-Resources Investigations, Book 5, Chapter A4), Open-File Report 79-1279, 1979.

A nonparametric method to generate synthetic populations to adjust for complex sampling design features.

PubMed

Dong, Qi; Elliott, Michael R; Raghunathan, Trivellore E

2014-06-01

Outside of the survey sampling literature, samples are often assumed to be generated by a simple random sampling process that produces independent and identically distributed (IID) samples. Many statistical methods are developed largely in this IID world. Application of these methods to data from complex sample surveys without making allowance for the survey design features can lead to erroneous inferences. Hence, much time and effort have been devoted to develop the statistical methods to analyze complex survey data and account for the sample design. This issue is particularly important when generating synthetic populations using finite population Bayesian inference, as is often done in missing data or disclosure risk settings, or when combining data from multiple surveys. By extending previous work in finite population Bayesian bootstrap literature, we propose a method to generate synthetic populations from a posterior predictive distribution in a fashion inverts the complex sampling design features and generates simple random samples from a superpopulation point of view, making adjustment on the complex data so that they can be analyzed as simple random samples. We consider a simulation study with a stratified, clustered unequal-probability of selection sample design, and use the proposed nonparametric method to generate synthetic populations for the 2006 National Health Interview Survey (NHIS), and the Medical Expenditure Panel Survey (MEPS), which are stratified, clustered unequal-probability of selection sample designs.

A nonparametric method to generate synthetic populations to adjust for complex sampling design features

PubMed Central

Dong, Qi; Elliott, Michael R.; Raghunathan, Trivellore E.

2017-01-01

Outside of the survey sampling literature, samples are often assumed to be generated by a simple random sampling process that produces independent and identically distributed (IID) samples. Many statistical methods are developed largely in this IID world. Application of these methods to data from complex sample surveys without making allowance for the survey design features can lead to erroneous inferences. Hence, much time and effort have been devoted to develop the statistical methods to analyze complex survey data and account for the sample design. This issue is particularly important when generating synthetic populations using finite population Bayesian inference, as is often done in missing data or disclosure risk settings, or when combining data from multiple surveys. By extending previous work in finite population Bayesian bootstrap literature, we propose a method to generate synthetic populations from a posterior predictive distribution in a fashion inverts the complex sampling design features and generates simple random samples from a superpopulation point of view, making adjustment on the complex data so that they can be analyzed as simple random samples. We consider a simulation study with a stratified, clustered unequal-probability of selection sample design, and use the proposed nonparametric method to generate synthetic populations for the 2006 National Health Interview Survey (NHIS), and the Medical Expenditure Panel Survey (MEPS), which are stratified, clustered unequal-probability of selection sample designs. PMID:29200608

Optical Methods for Identifying Hard Clay Core Samples During Petrophysical Studies

NASA Astrophysics Data System (ADS)

Morev, A. V.; Solovyeva, A. V.; Morev, V. A.

2018-01-01

X-ray phase analysis of the general mineralogical composition of core samples from one of the West Siberian fields was performed. Electronic absorption spectra of the clay core samples with an added indicator were studied. The speed and availability of applying the two methods in petrophysical laboratories during sample preparation for standard and special studies were estimated.

Determining an Appropriate Sampling Method. School Accountability Series. Monograph 3.

ERIC Educational Resources Information Center

McCallon, Earl; McClaran, Rutledge

This is one of a series of eight short monographs intended to aid practicing educators in planning and conducting accountability programs in schools. This booklet discusses how to determine a sampling method that is appropriate to the objectives of a particular research or evaluation effort. Short sections focus in turn on why and when to sample,…

Geostatistical Sampling Methods for Efficient Uncertainty Analysis in Flow and Transport Problems

NASA Astrophysics Data System (ADS)

Liodakis, Stylianos; Kyriakidis, Phaedon; Gaganis, Petros

2015-04-01

In hydrogeological applications involving flow and transport of in heterogeneous porous media the spatial distribution of hydraulic conductivity is often parameterized in terms of a lognormal random field based on a histogram and variogram model inferred from data and/or synthesized from relevant knowledge. Realizations of simulated conductivity fields are then generated using geostatistical simulation involving simple random (SR) sampling and are subsequently used as inputs to physically-based simulators of flow and transport in a Monte Carlo framework for evaluating the uncertainty in the spatial distribution of solute concentration due to the uncertainty in the spatial distribution of hydraulic con- ductivity [1]. Realistic uncertainty analysis, however, calls for a large number of simulated concentration fields; hence, can become expensive in terms of both time and computer re- sources. A more efficient alternative to SR sampling is Latin hypercube (LH) sampling, a special case of stratified random sampling, which yields a more representative distribution of simulated attribute values with fewer realizations [2]. Here, term representative implies realizations spanning efficiently the range of possible conductivity values corresponding to the lognormal random field. In this work we investigate the efficiency of alternative methods to classical LH sampling within the context of simulation of flow and transport in a heterogeneous porous medium. More precisely, we consider the stratified likelihood (SL) sampling method of [3], in which attribute realizations are generated using the polar simulation method by exploring the geometrical properties of the multivariate Gaussian distribution function. In addition, we propose a more efficient version of the above method, here termed minimum energy (ME) sampling, whereby a set of N representative conductivity realizations at M locations is constructed by: (i) generating a representative set of N points distributed on the

Fluid sampling apparatus and method

DOEpatents

Yeamans, David R.

1998-01-01

Incorporation of a bellows in a sampling syringe eliminates ingress of contaminants, permits replication of amounts and compression of multiple sample injections, and enables remote sampling for off-site analysis.

Rapid method for the determination of 226Ra in hydraulic fracturing wastewater samples

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

Maxwell, Sherrod L.; Culligan, Brian K.; Warren, Richard A.

A new method that rapidly preconcentrates and measures 226Ra from hydraulic fracturing wastewater samples was developed in the Savannah River Environmental Laboratory. The method improves the quality of 226Ra measurements using gamma spectrometry by providing up to 100x preconcentration of 226Ra from this difficult sample matrix, which contains very high levels of calcium, barium, strontium, magnesium and sodium. The high chemical yield, typically 80-90%, facilitates a low detection limit, important for lower level samples, and indicates method ruggedness. Ba-133 tracer is used to determine chemical yield and correct for geometry-related counting issues. The 226Ra sample preparation takes < 2 hours.

Rapid method for the determination of 226Ra in hydraulic fracturing wastewater samples

DOE PAGES

Maxwell, Sherrod L.; Culligan, Brian K.; Warren, Richard A.; ...

2016-03-24

A new method that rapidly preconcentrates and measures 226Ra from hydraulic fracturing wastewater samples was developed in the Savannah River Environmental Laboratory. The method improves the quality of 226Ra measurements using gamma spectrometry by providing up to 100x preconcentration of 226Ra from this difficult sample matrix, which contains very high levels of calcium, barium, strontium, magnesium and sodium. The high chemical yield, typically 80-90%, facilitates a low detection limit, important for lower level samples, and indicates method ruggedness. Ba-133 tracer is used to determine chemical yield and correct for geometry-related counting issues. The 226Ra sample preparation takes < 2 hours.

40 CFR 80.8 - Sampling methods for gasoline, diesel fuel, fuel additives, and renewable fuels.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 17 2014-07-01 2014-07-01 false Sampling methods for gasoline, diesel... Provisions § 80.8 Sampling methods for gasoline, diesel fuel, fuel additives, and renewable fuels. The sampling methods specified in this section shall be used to collect samples of gasoline, diesel fuel...

Systems and methods for separating particles and/or substances from a sample fluid

DOEpatents

Mariella, Jr., Raymond P.; Dougherty, George M.; Dzenitis, John M.; Miles, Robin R.; Clague, David S.

2016-11-01

Systems and methods for separating particles and/or toxins from a sample fluid. A method according to one embodiment comprises simultaneously passing a sample fluid and a buffer fluid through a chamber such that a fluidic interface is formed between the sample fluid and the buffer fluid as the fluids pass through the chamber, the sample fluid having particles of interest therein; applying a force to the fluids for urging the particles of interest to pass through the interface into the buffer fluid; and substantially separating the buffer fluid from the sample fluid.

A fast learning method for large scale and multi-class samples of SVM

NASA Astrophysics Data System (ADS)

Fan, Yu; Guo, Huiming

2017-06-01

A multi-class classification SVM(Support Vector Machine) fast learning method based on binary tree is presented to solve its low learning efficiency when SVM processing large scale multi-class samples. This paper adopts bottom-up method to set up binary tree hierarchy structure, according to achieved hierarchy structure, sub-classifier learns from corresponding samples of each node. During the learning, several class clusters are generated after the first clustering of the training samples. Firstly, central points are extracted from those class clusters which just have one type of samples. For those which have two types of samples, cluster numbers of their positive and negative samples are set respectively according to their mixture degree, secondary clustering undertaken afterwards, after which, central points are extracted from achieved sub-class clusters. By learning from the reduced samples formed by the integration of extracted central points above, sub-classifiers are obtained. Simulation experiment shows that, this fast learning method, which is based on multi-level clustering, can guarantee higher classification accuracy, greatly reduce sample numbers and effectively improve learning efficiency.

Fluid sampling apparatus and method

DOEpatents

Yeamans, D.R.

1998-02-03

Incorporation of a bellows in a sampling syringe eliminates ingress of contaminants, permits replication of amounts and compression of multiple sample injections, and enables remote sampling for off-site analysis. 3 figs.

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

PubMed Central

White, James Robert; Nagarajan, Niranjan; Pop, Mihai

2009-01-01

Numerous studies are currently underway to characterize the microbial communities inhabiting our world. These studies aim to dramatically expand our understanding of the microbial biosphere and, more importantly, hope to reveal the secrets of the complex symbiotic relationship between us and our commensal bacterial microflora. An important prerequisite for such discoveries are computational tools that are able to rapidly and accurately compare large datasets generated from complex bacterial communities to identify features that distinguish them. We present a statistical method for comparing clinical metagenomic samples from two treatment populations on the basis of count data (e.g. as obtained through sequencing) to detect differentially abundant features. Our method, Metastats, employs the false discovery rate to improve specificity in high-complexity environments, and separately handles sparsely-sampled features using Fisher's exact test. Under a variety of simulations, we show that Metastats performs well compared to previously used methods, and significantly outperforms other methods for features with sparse counts. We demonstrate the utility of our method on several datasets including a 16S rRNA survey of obese and lean human gut microbiomes, COG functional profiles of infant and mature gut microbiomes, and bacterial and viral metabolic subsystem data inferred from random sequencing of 85 metagenomes. The application of our method to the obesity dataset reveals differences between obese and lean subjects not reported in the original study. For the COG and subsystem datasets, we provide the first statistically rigorous assessment of the differences between these populations. The methods described in this paper are the first to address clinical metagenomic datasets comprising samples from multiple subjects. Our methods are robust across datasets of varied complexity and sampling level. While designed for metagenomic applications, our software can also be applied

Effect of the absolute statistic on gene-sampling gene-set analysis methods.

PubMed

Nam, Dougu

2017-06-01

Gene-set enrichment analysis and its modified versions have commonly been used for identifying altered functions or pathways in disease from microarray data. In particular, the simple gene-sampling gene-set analysis methods have been heavily used for datasets with only a few sample replicates. The biggest problem with this approach is the highly inflated false-positive rate. In this paper, the effect of absolute gene statistic on gene-sampling gene-set analysis methods is systematically investigated. Thus far, the absolute gene statistic has merely been regarded as a supplementary method for capturing the bidirectional changes in each gene set. Here, it is shown that incorporating the absolute gene statistic in gene-sampling gene-set analysis substantially reduces the false-positive rate and improves the overall discriminatory ability. Its effect was investigated by power, false-positive rate, and receiver operating curve for a number of simulated and real datasets. The performances of gene-set analysis methods in one-tailed (genome-wide association study) and two-tailed (gene expression data) tests were also compared and discussed.

Detection and monitoring of invasive exotic plants: a comparison of four sampling methods

Treesearch

Cynthia D. Huebner

2007-01-01

The ability to detect and monitor exotic invasive plants is likely to vary depending on the sampling method employed. Methods with strong qualitative thoroughness for species detection often lack the intensity necessary to monitor vegetation change. Four sampling methods (systematic plot, stratified-random plot, modified Whittaker, and timed meander) in hemlock and red...

Suitability of the line intersect method for sampling hardwood logging residues

Treesearch

A. Jeff Martin

1976-01-01

The line intersect method of sampling logging residues was tested in Appalachian hardwoods and was found to provide unbiased estimates of the volume of residue in cubic feet per acre. Thirty-two chains of sample line were established on each of sixteen 1-acre plots on cutover areas in a variety of conditions. Estimates from these samples were then compared to actual...

Mapping Species Distributions with MAXENT Using a Geographically Biased Sample of Presence Data: A Performance Assessment of Methods for Correcting Sampling Bias

PubMed Central

Fourcade, Yoan; Engler, Jan O.; Rödder, Dennis; Secondi, Jean

2014-01-01

MAXENT is now a common species distribution modeling (SDM) tool used by conservation practitioners for predicting the distribution of a species from a set of records and environmental predictors. However, datasets of species occurrence used to train the model are often biased in the geographical space because of unequal sampling effort across the study area. This bias may be a source of strong inaccuracy in the resulting model and could lead to incorrect predictions. Although a number of sampling bias correction methods have been proposed, there is no consensual guideline to account for it. We compared here the performance of five methods of bias correction on three datasets of species occurrence: one “virtual” derived from a land cover map, and two actual datasets for a turtle (Chrysemys picta) and a salamander (Plethodon cylindraceus). We subjected these datasets to four types of sampling biases corresponding to potential types of empirical biases. We applied five correction methods to the biased samples and compared the outputs of distribution models to unbiased datasets to assess the overall correction performance of each method. The results revealed that the ability of methods to correct the initial sampling bias varied greatly depending on bias type, bias intensity and species. However, the simple systematic sampling of records consistently ranked among the best performing across the range of conditions tested, whereas other methods performed more poorly in most cases. The strong effect of initial conditions on correction performance highlights the need for further research to develop a step-by-step guideline to account for sampling bias. However, this method seems to be the most efficient in correcting sampling bias and should be advised in most cases. PMID:24818607

Methods for collection and analysis of aquatic biological and microbiological samples

USGS Publications Warehouse

Greeson, Phillip E.; Ehlke, T.A.; Irwin, G.A.; Lium, B.W.; Slack, K.V.

1977-01-01

Chapter A4 contains methods used by the U.S. Geological Survey to collect, preserve, and analyze waters to determine their biological and microbiological properties. Part 1 discusses biological sampling and sampling statistics. The statistical procedures are accompanied by examples. Part 2 consists of detailed descriptions of more than 45 individual methods, including those for bacteria, phytoplankton, zooplankton, seston, periphyton, macrophytes, benthic invertebrates, fish and other vertebrates, cellular contents, productivity, and bioassays. Each method is summarized, and the application, interferences, apparatus, reagents, collection, analysis, calculations, reporting of results, precision and references are given. Part 3 consists of a glossary. Part 4 is a list of taxonomic references.

Fast identification of microplastics in complex environmental samples by a thermal degradation method.

PubMed

Dümichen, Erik; Eisentraut, Paul; Bannick, Claus Gerhard; Barthel, Anne-Kathrin; Senz, Rainer; Braun, Ulrike

2017-05-01

In order to determine the relevance of microplastic particles in various environmental media, comprehensive investigations are needed. However, no analytical method exists for fast identification and quantification. At present, optical spectroscopy methods like IR and RAMAN imaging are used. Due to their time consuming procedures and uncertain extrapolation, reliable monitoring is difficult. For analyzing polymers Py-GC-MS is a standard method. However, due to a limited sample amount of about 0.5 mg it is not suited for analysis of complex sample mixtures like environmental samples. Therefore, we developed a new thermoanalytical method as a first step for identifying microplastics in environmental samples. A sample amount of about 20 mg, which assures the homogeneity of the sample, is subjected to complete thermal decomposition. The specific degradation products of the respective polymer are adsorbed on a solid-phase adsorber and subsequently analyzed by thermal desorption gas chromatography mass spectrometry. For certain identification, the specific degradation products for the respective polymer were selected first. Afterwards real environmental samples from the aquatic (three different rivers) and the terrestrial (bio gas plant) systems were screened for microplastics. Mainly polypropylene (PP), polyethylene (PE) and polystyrene (PS) were identified for the samples from the bio gas plant and PE and PS from the rivers. However, this was only the first step and quantification measurements will follow. Copyright © 2017 Elsevier Ltd. All rights reserved.

Small Body GN and C Research Report: G-SAMPLE - An In-Flight Dynamical Method for Identifying Sample Mass [External Release Version

NASA Technical Reports Server (NTRS)

Carson, John M., III; Bayard, David S.

2006-01-01

G-SAMPLE is an in-flight dynamical method for use by sample collection missions to identify the presence and quantity of collected sample material. The G-SAMPLE method implements a maximum-likelihood estimator to identify the collected sample mass, based on onboard force sensor measurements, thruster firings, and a dynamics model of the spacecraft. With G-SAMPLE, sample mass identification becomes a computation rather than an extra hardware requirement; the added cost of cameras or other sensors for sample mass detection is avoided. Realistic simulation examples are provided for a spacecraft configuration with a sample collection device mounted on the end of an extended boom. In one representative example, a 1000 gram sample mass is estimated to within 110 grams (95% confidence) under realistic assumptions of thruster profile error, spacecraft parameter uncertainty, and sensor noise. For convenience to future mission design, an overall sample-mass estimation error budget is developed to approximate the effect of model uncertainty, sensor noise, data rate, and thrust profile error on the expected estimate of collected sample mass.

Sampling methods, dispersion patterns, and fixed precision sequential sampling plans for western flower thrips (Thysanoptera: Thripidae) and cotton fleahoppers (Hemiptera: Miridae) in cotton.

PubMed

Parajulee, M N; Shrestha, R B; Leser, J F

2006-04-01

A 2-yr field study was conducted to examine the effectiveness of two sampling methods (visual and plant washing techniques) for western flower thrips, Frankliniella occidentalis (Pergande), and five sampling methods (visual, beat bucket, drop cloth, sweep net, and vacuum) for cotton fleahopper, Pseudatomoscelis seriatus (Reuter), in Texas cotton, Gossypium hirsutum (L.), and to develop sequential sampling plans for each pest. The plant washing technique gave similar results to the visual method in detecting adult thrips, but the washing technique detected significantly higher number of thrips larvae compared with the visual sampling. Visual sampling detected the highest number of fleahoppers followed by beat bucket, drop cloth, vacuum, and sweep net sampling, with no significant difference in catch efficiency between vacuum and sweep net methods. However, based on fixed precision cost reliability, the sweep net sampling was the most cost-effective method followed by vacuum, beat bucket, drop cloth, and visual sampling. Taylor's Power Law analysis revealed that the field dispersion patterns of both thrips and fleahoppers were aggregated throughout the crop growing season. For thrips management decision based on visual sampling (0.25 precision), 15 plants were estimated to be the minimum sample size when the estimated population density was one thrips per plant, whereas the minimum sample size was nine plants when thrips density approached 10 thrips per plant. The minimum visual sample size for cotton fleahoppers was 16 plants when the density was one fleahopper per plant, but the sample size decreased rapidly with an increase in fleahopper density, requiring only four plants to be sampled when the density was 10 fleahoppers per plant. Sequential sampling plans were developed and validated with independent data for both thrips and cotton fleahoppers.

Optimization of fecal cytology in the dog: comparison of three sampling methods.

PubMed

Frezoulis, Petros S; Angelidou, Elisavet; Diakou, Anastasia; Rallis, Timoleon S; Mylonakis, Mathios E

2017-09-01

Dry-mount fecal cytology (FC) is a component of the diagnostic evaluation of gastrointestinal diseases. There is limited information on the possible effect of the sampling method on the cytologic findings of healthy dogs or dogs admitted with diarrhea. We aimed to: (1) establish sampling method-specific expected values of selected cytologic parameters (isolated or clustered epithelial cells, neutrophils, lymphocytes, macrophages, spore-forming rods) in clinically healthy dogs; (2) investigate if the detection of cytologic abnormalities differs among methods in dogs admitted with diarrhea; and (3) investigate if there is any association between FC abnormalities and the anatomic origin (small- or large-bowel diarrhea) or the chronicity of diarrhea. Sampling with digital examination (DE), rectal scraping (RS), and rectal lavage (RL) was prospectively assessed in 37 healthy and 34 diarrheic dogs. The median numbers of isolated ( p = 0.000) or clustered ( p = 0.002) epithelial cells, and of lymphocytes ( p = 0.000), differed among the 3 methods in healthy dogs. In the diarrheic dogs, the RL method was the least sensitive in detecting neutrophils, and isolated or clustered epithelial cells. Cytologic abnormalities were not associated with the origin or the chronicity of diarrhea. Sampling methods differed in their sensitivity to detect abnormalities in FC; DE or RS may be of higher sensitivity compared to RL. Anatomic origin or chronicity of diarrhea do not seem to affect the detection of cytologic abnormalities.

Molecular Method for Detection of Total Coliforms in Drinking Water Samples

PubMed Central

Boudreau, Dominique K.; Bisson, Marc-Antoine; Dion-Dupont, Vanessa; Bouchard, Sébastien; Nkuranga, Martine; Bergeron, Michel G.; Rodriguez, Manuel J.

2014-01-01

This work demonstrates the ability of a bacterial concentration and recovery procedure combined with three different PCR assays targeting the lacZ, wecG, and 16S rRNA genes, respectively, to detect the presence of total coliforms in 100-ml samples of potable water (presence/absence test). PCR assays were first compared to the culture-based Colilert and MI agar methods to determine their ability to detect 147 coliform strains representing 76 species of Enterobacteriaceae encountered in fecal and environmental settings. Results showed that 86 (58.5%) and 109 (74.1%) strains yielded a positive signal with Colilert and MI agar methods, respectively, whereas the lacZ, wecG, and 16S rRNA PCR assays detected 133 (90.5%), 111 (75.5%), and 146 (99.3%) of the 147 total coliform strains tested. These assays were then assessed by testing 122 well water samples collected in the Québec City region of Canada. Results showed that 97 (79.5%) of the samples tested by culture-based methods and 95 (77.9%), 82 (67.2%), and 98 (80.3%) of samples tested using PCR-based methods contained total coliforms, respectively. Consequently, despite the high genetic variability of the total coliform group, this study demonstrated that it is possible to use molecular assays to detect total coliforms in potable water: the 16S rRNA molecular assay was shown to be as efficient as recommended culture-based methods. This assay might be used in combination with an Escherichia coli molecular assay to assess drinking water quality. PMID:24771030

An adaptive sampling method for variable-fidelity surrogate models using improved hierarchical kriging

NASA Astrophysics Data System (ADS)

Hu, Jiexiang; Zhou, Qi; Jiang, Ping; Shao, Xinyu; Xie, Tingli

2018-01-01

Variable-fidelity (VF) modelling methods have been widely used in complex engineering system design to mitigate the computational burden. Building a VF model generally includes two parts: design of experiments and metamodel construction. In this article, an adaptive sampling method based on improved hierarchical kriging (ASM-IHK) is proposed to refine the improved VF model. First, an improved hierarchical kriging model is developed as the metamodel, in which the low-fidelity model is varied through a polynomial response surface function to capture the characteristics of a high-fidelity model. Secondly, to reduce local approximation errors, an active learning strategy based on a sequential sampling method is introduced to make full use of the already required information on the current sampling points and to guide the sampling process of the high-fidelity model. Finally, two numerical examples and the modelling of the aerodynamic coefficient for an aircraft are provided to demonstrate the approximation capability of the proposed approach, as well as three other metamodelling methods and two sequential sampling methods. The results show that ASM-IHK provides a more accurate metamodel at the same simulation cost, which is very important in metamodel-based engineering design problems.

A novel sampling method for multiple multiscale targets from scattering amplitudes at a fixed frequency

NASA Astrophysics Data System (ADS)

Liu, Xiaodong

2017-08-01

A sampling method by using scattering amplitude is proposed for shape and location reconstruction in inverse acoustic scattering problems. Only matrix multiplication is involved in the computation, thus the novel sampling method is very easy and simple to implement. With the help of the factorization of the far field operator, we establish an inf-criterion for characterization of underlying scatterers. This result is then used to give a lower bound of the proposed indicator functional for sampling points inside the scatterers. While for the sampling points outside the scatterers, we show that the indicator functional decays like the bessel functions as the sampling point goes away from the boundary of the scatterers. We also show that the proposed indicator functional continuously depends on the scattering amplitude, this further implies that the novel sampling method is extremely stable with respect to errors in the data. Different to the classical sampling method such as the linear sampling method or the factorization method, from the numerical point of view, the novel indicator takes its maximum near the boundary of the underlying target and decays like the bessel functions as the sampling points go away from the boundary. The numerical simulations also show that the proposed sampling method can deal with multiple multiscale case, even the different components are close to each other.

Method for Operating a Sensor to Differentiate Between Analytes in a Sample

DOEpatents

Kunt, Tekin; Cavicchi, Richard E; Semancik, Stephen; McAvoy, Thomas J

1998-07-28

Disclosed is a method for operating a sensor to differentiate between first and second analytes in a sample. The method comprises the steps of determining a input profile for the sensor which will enhance the difference in the output profiles of the sensor as between the first analyte and the second analyte; determining a first analyte output profile as observed when the input profile is applied to the sensor; determining a second analyte output profile as observed when the temperature profile is applied to the sensor; introducing the sensor to the sample while applying the temperature profile to the sensor, thereby obtaining a sample output profile; and evaluating the sample output profile as against the first and second analyte output profiles to thereby determine which of the analytes is present in the sample.

A novel method to handle the effect of uneven sampling effort in biodiversity databases.

PubMed

Pardo, Iker; Pata, María P; Gómez, Daniel; García, María B

2013-01-01

How reliable are results on spatial distribution of biodiversity based on databases? Many studies have evidenced the uncertainty related to this kind of analysis due to sampling effort bias and the need for its quantification. Despite that a number of methods are available for that, little is known about their statistical limitations and discrimination capability, which could seriously constrain their use. We assess for the first time the discrimination capacity of two widely used methods and a proposed new one (FIDEGAM), all based on species accumulation curves, under different scenarios of sampling exhaustiveness using Receiver Operating Characteristic (ROC) analyses. Additionally, we examine to what extent the output of each method represents the sampling completeness in a simulated scenario where the true species richness is known. Finally, we apply FIDEGAM to a real situation and explore the spatial patterns of plant diversity in a National Park. FIDEGAM showed an excellent discrimination capability to distinguish between well and poorly sampled areas regardless of sampling exhaustiveness, whereas the other methods failed. Accordingly, FIDEGAM values were strongly correlated with the true percentage of species detected in a simulated scenario, whereas sampling completeness estimated with other methods showed no relationship due to null discrimination capability. Quantifying sampling effort is necessary to account for the uncertainty in biodiversity analyses, however, not all proposed methods are equally reliable. Our comparative analysis demonstrated that FIDEGAM was the most accurate discriminator method in all scenarios of sampling exhaustiveness, and therefore, it can be efficiently applied to most databases in order to enhance the reliability of biodiversity analyses.

A Novel Method to Handle the Effect of Uneven Sampling Effort in Biodiversity Databases

PubMed Central

Pardo, Iker; Pata, María P.; Gómez, Daniel; García, María B.

2013-01-01

How reliable are results on spatial distribution of biodiversity based on databases? Many studies have evidenced the uncertainty related to this kind of analysis due to sampling effort bias and the need for its quantification. Despite that a number of methods are available for that, little is known about their statistical limitations and discrimination capability, which could seriously constrain their use. We assess for the first time the discrimination capacity of two widely used methods and a proposed new one (FIDEGAM), all based on species accumulation curves, under different scenarios of sampling exhaustiveness using Receiver Operating Characteristic (ROC) analyses. Additionally, we examine to what extent the output of each method represents the sampling completeness in a simulated scenario where the true species richness is known. Finally, we apply FIDEGAM to a real situation and explore the spatial patterns of plant diversity in a National Park. FIDEGAM showed an excellent discrimination capability to distinguish between well and poorly sampled areas regardless of sampling exhaustiveness, whereas the other methods failed. Accordingly, FIDEGAM values were strongly correlated with the true percentage of species detected in a simulated scenario, whereas sampling completeness estimated with other methods showed no relationship due to null discrimination capability. Quantifying sampling effort is necessary to account for the uncertainty in biodiversity analyses, however, not all proposed methods are equally reliable. Our comparative analysis demonstrated that FIDEGAM was the most accurate discriminator method in all scenarios of sampling exhaustiveness, and therefore, it can be efficiently applied to most databases in order to enhance the reliability of biodiversity analyses. PMID:23326357

Comparison of three sampling and analytical methods for the determination of airborne hexavalent chromium.

PubMed

Boiano, J M; Wallace, M E; Sieber, W K; Groff, J H; Wang, J; Ashley, K

2000-08-01

A field study was conducted with the goal of comparing the performance of three recently developed or modified sampling and analytical methods for the determination of airborne hexavalent chromium (Cr(VI)). The study was carried out in a hard chrome electroplating facility and in a jet engine manufacturing facility where airborne Cr(VI) was expected to be present. The analytical methods evaluated included two laboratory-based procedures (OSHA Method ID-215 and NIOSH Method 7605) and a field-portable method (NIOSH Method 7703). These three methods employ an identical sampling methodology: collection of Cr(VI)-containing aerosol on a polyvinyl chloride (PVC) filter housed in a sampling cassette, which is connected to a personal sampling pump calibrated at an appropriate flow rate. The basis of the analytical methods for all three methods involves extraction of the PVC filter in alkaline buffer solution, chemical isolation of the Cr(VI) ion, complexation of the Cr(VI) ion with 1,5-diphenylcarbazide, and spectrometric measurement of the violet chromium diphenylcarbazone complex at 540 nm. However, there are notable specific differences within the sample preparation procedures used in three methods. To assess the comparability of the three measurement protocols, a total of 20 side-by-side air samples were collected, equally divided between a chromic acid electroplating operation and a spray paint operation where water soluble forms of Cr(VI) were used. A range of Cr(VI) concentrations from 0.6 to 960 microg m(-3), with Cr(VI) mass loadings ranging from 0.4 to 32 microg, was measured at the two operations. The equivalence of the means of the log-transformed Cr(VI) concentrations obtained from the different analytical methods was compared. Based on analysis of variance (ANOVA) results, no statistically significant differences were observed between mean values measured using each of the three methods. Small but statistically significant differences were observed between

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

Application of a Permethrin Immunosorbent Assay Method to Residential Soil and Dust Samples

EPA Science Inventory

A low-cost, high throughput bioanalytical screening method was developed for monitoring cis/trans-permethrin in dust and soil samples. The method consisted of a simple sample preparation procedure [sonication with dichloromethane followed by a solvent exchange into methanol:wate...

Well purge and sample apparatus and method

DOEpatents

Schalla, Ronald; Smith, Ronald M.; Hall, Stephen H.; Smart, John E.; Gustafson, Gregg S.

1995-01-01

The present invention specifically permits purging and/or sampling of a well but only removing, at most, about 25% of the fluid volume compared to conventional methods and, at a minimum, removing none of the fluid volume from the well. The invention is an isolation assembly with a packer, pump and exhaust, that is inserted into the well. The isolation assembly is designed so that only a volume of fluid between the outside diameter of the isolation assembly and the inside diameter of the well over a fluid column height from the bottom of the well to the top of the active portion (lower annulus) is removed. The packer is positioned above the active portion thereby sealing the well and preventing any mixing or contamination of inlet fluid with fluid above the packer. Ports in the wall of the isolation assembly permit purging and sampling of the lower annulus along the height of the active portion.

Well purge and sample apparatus and method

DOEpatents

Schalla, R.; Smith, R.M.; Hall, S.H.; Smart, J.E.; Gustafson, G.S.

1995-10-24

The present invention specifically permits purging and/or sampling of a well but only removing, at most, about 25% of the fluid volume compared to conventional methods and, at a minimum, removing none of the fluid volume from the well. The invention is an isolation assembly with a packer, pump and exhaust, that is inserted into the well. The isolation assembly is designed so that only a volume of fluid between the outside diameter of the isolation assembly and the inside diameter of the well over a fluid column height from the bottom of the well to the top of the active portion (lower annulus) is removed. The packer is positioned above the active portion thereby sealing the well and preventing any mixing or contamination of inlet fluid with fluid above the packer. Ports in the wall of the isolation assembly permit purging and sampling of the lower annulus along the height of the active portion. 8 figs.

40 CFR 80.8 - Sampling methods for gasoline and diesel fuel.

Code of Federal Regulations, 2010 CFR

2010-07-01

... applicable procedures specified in American Society for Testing and Materials (ASTM) method D 4057-95(2000... applicable procedures specified in ASTM method D 4177-95(2000), entitled “Standard Practice for Automatic... applicable procedures in ASTM method D 5842-95(2000), entitled “Standard Practice for Sampling and Handling...

Rapid method to determine 89Sr/ 90Sr in large concrete samples

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

Maxwell, Sherrod L.; Culligan, Brian; Hutchison, Jay B.

Here, a new rapid method has been developed that provides high quality low-level measurements of 89,90Sr in concrete samples with an MDA (Minimum Detectable Activity) of <1 mBq g -1. The new method is fast, meets new decommissioning regulatory limits and is robust even if refractory particles are present. The method utilizes a rapid fusion to ensure total dissolution of samples and rapid preconcentration and separation of 89,90Sr from 5-10 g concrete samples. When, the 89Sr/ 90Sr ratio is high, Sr can be isolated from up to 5g concrete samples, total 89/90Sr measured, and then 90Sr determined via 90Y separatedmore » after a period of ingrowth. Another approach allows the immediate determination of 90Sr in 10 g concrete aliquots without waiting for 90Y ingrowth, in instances where the shorter lived 89Sr is unlikely to be encountered.« less

Rapid method to determine 89Sr/ 90Sr in large concrete samples

DOE PAGES

Maxwell, Sherrod L.; Culligan, Brian; Hutchison, Jay B.; ...

2016-03-24

Here, a new rapid method has been developed that provides high quality low-level measurements of 89,90Sr in concrete samples with an MDA (Minimum Detectable Activity) of <1 mBq g -1. The new method is fast, meets new decommissioning regulatory limits and is robust even if refractory particles are present. The method utilizes a rapid fusion to ensure total dissolution of samples and rapid preconcentration and separation of 89,90Sr from 5-10 g concrete samples. When, the 89Sr/ 90Sr ratio is high, Sr can be isolated from up to 5g concrete samples, total 89/90Sr measured, and then 90Sr determined via 90Y separatedmore » after a period of ingrowth. Another approach allows the immediate determination of 90Sr in 10 g concrete aliquots without waiting for 90Y ingrowth, in instances where the shorter lived 89Sr is unlikely to be encountered.« less

[4D-MRI using the synchronized sampling method (SSM)].

PubMed

Shimada, Yasuhiro; Fujimoto, Ichirou; Takemoto, Hironori; Takano, Sayoko; Masaki, Shinobu; Honda, Kiyoshi; Takeo, Kazuhiro

2002-12-01

A synchronized sampling method (SSM) was developed for the study of voluntary movements by combining the electrocardiographic (ECG) gating method with an external triggering device, and four-dimensional magnetic resonance imaging (4D-MRI) at a rate of 30 frames per second was accomplished by volumetric imaging with the SSM. This method was first applied to the motion imaging of articulatory organs during repetitions of a Japanese five-vowel sequence, and the dynamic change in vocal tract area function was demonstrated with sufficient temporal resolution. This paper describes the methodology, applicability, and limitations of 4D-MRI with the SSM.

Impact of culture media and sampling methods on Staphylococcus aureus aerosols.

PubMed

Chang, C-W; Wang, L-J

2015-10-01

Staphylococcus aureus has been detected indoors and is associated with human infection. Reliable quantification of S. aureus using a sampling technique followed by culture assay helps in assessing the risks of human exposure. The efficiency of five culture media and eight sampling methods in recovering S. aureus aerosols were evaluated. Methods to extract cells from filters were also studied. Tryptic soy agar (TSA) presented greater bacterial recovery than mannitol salt agar (MSA), CHROMagar staph aureus, Chapman stone medium, and Baird-Park agarose (P < 0.05). Moreover, 93 ± 2%-95 ± 2% and 42 ± 1%-49 ± 2% of S. aureus were, respectively, recovered by a 15-min heating of gelatin filters and 2-min vortex of polycarbonate (PC) filters. Evaluation of two filtration (IOM with gelatin filter and cassette with PC filter), two impaction (Andersen 1-STG loaded with TSA and MSA) and four impingement methods [AGI-30 and BioSampler filled with Tween mixture (TM) and phosphate-buffered saline (PBS)] revealed the BioSampler/TM performed best over 30 and 60 min of sampling (P < 0.05), while low recovery efficiencies were associated with the IOM/gelatin, cassette/PC, and AGI-30/PBS combinations (P < 0.05). In addition to BioSampler/TM, collecting S. aureus onto TSA from the Andersen 1-STG is also recommended, as it is the second best method at the 60-min sampling (P < 0.05). © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Duplex sampling apparatus and method

DOEpatents

Brown, Paul E.; Lloyd, Robert

1992-01-01

An improved apparatus is provided for sampling a gaseous mixture and for measuring mixture components. The apparatus includes two sampling containers connected in series serving as a duplex sampling apparatus. The apparatus is adapted to independently determine the amounts of condensable and noncondensable gases in admixture from a single sample. More specifically, a first container includes a first port capable of selectively connecting to and disconnecting from a sample source and a second port capable of selectively connecting to and disconnecting from a second container. A second container also includes a first port capable of selectively connecting to and disconnecting from the second port of the first container and a second port capable of either selectively connecting to and disconnecting from a differential pressure source. By cooling a mixture sample in the first container, the condensable vapors form a liquid, leaving noncondensable gases either as free gases or dissolved in the liquid. The condensed liquid is heated to drive out dissolved noncondensable gases, and all the noncondensable gases are transferred to the second container. Then the first and second containers are separated from one another in order to separately determine the amount of noncondensable gases and the amount of condensable gases in the sample.

Methods, compounds and systems for detecting a microorganism in a sample

DOEpatents

Colston, Jr, Bill W.; Fitch, J. Patrick; Gardner, Shea N.; Williams, Peter L.; Wagner, Mark C.

2016-09-06

Methods to identify a set of probe polynucleotides suitable for detecting a set of targets and in particular methods for identification of primers suitable for detection of target microorganisms related polynucleotides, set of polynucleotides and compositions, and related methods and systems for detection and/or identification of microorganisms in a sample.

Note: A simple image processing based fiducial auto-alignment method for sample registration.

PubMed

Robertson, Wesley D; Porto, Lucas R; Ip, Candice J X; Nantel, Megan K T; Tellkamp, Friedjof; Lu, Yinfei; Miller, R J Dwayne

2015-08-01

A simple method for the location and auto-alignment of sample fiducials for sample registration using widely available MATLAB/LabVIEW software is demonstrated. The method is robust, easily implemented, and applicable to a wide variety of experiment types for improved reproducibility and increased setup speed. The software uses image processing to locate and measure the diameter and center point of circular fiducials for distance self-calibration and iterative alignment and can be used with most imaging systems. The method is demonstrated to be fast and reliable in locating and aligning sample fiducials, provided here by a nanofabricated array, with accuracy within the optical resolution of the imaging system. The software was further demonstrated to register, load, and sample the dynamically wetted array.

Final Report for X-ray Diffraction Sample Preparation Method Development

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

Ely, T. M.; Meznarich, H. K.; Valero, T.

WRPS-1500790, “X-ray Diffraction Saltcake Sample Preparation Method Development Plan/Procedure,” was originally prepared with the intent of improving the specimen preparation methodology used to generate saltcake specimens suitable for XRD-based solid phase characterization. At the time that this test plan document was originally developed, packed powder in cavity supports with collodion binder was the established XRD specimen preparation method. An alternate specimen preparation method less vulnerable, if not completely invulnerable to preferred orientation effects, was desired as a replacement for the method.

Evaluation of an alternate method for sampling benthic macroinvertebrates in low-gradient streams sampled as part of the National Rivers and Streams Assessment.

PubMed

Flotemersch, Joseph E; North, Sheila; Blocksom, Karen A

2014-02-01

Benthic macroinvertebrates are sampled in streams and rivers as one of the assessment elements of the US Environmental Protection Agency's National Rivers and Streams Assessment. In a 2006 report, the recommendation was made that different yet comparable methods be evaluated for different types of streams (e.g., low gradient vs. high gradient). Consequently, a research element was added to the 2008-2009 National Rivers and Streams Assessment to conduct a side-by-side comparison of the standard macroinvertebrate sampling method with an alternate method specifically designed for low-gradient wadeable streams and rivers that focused more on stream edge habitat. Samples were collected using each method at 525 sites in five of nine aggregate ecoregions located in the conterminous USA. Methods were compared using the benthic macroinvertebrate multimetric index developed for the 2006 Wadeable Streams Assessment. Statistical analysis did not reveal any trends that would suggest the overall assessment of low-gradient streams on a regional or national scale would change if the alternate method was used rather than the standard sampling method, regardless of the gradient cutoff used to define low-gradient streams. Based on these results, the National Rivers and Streams Survey should continue to use the standard field method for sampling all streams.

Methods of human body odor sampling: the effect of freezing.

PubMed

Lenochova, Pavlina; Roberts, S Craig; Havlicek, Jan

2009-02-01

Body odor sampling is an essential tool in human chemical ecology research. However, methodologies of individual studies vary widely in terms of sampling material, length of sampling, and sample processing. Although these differences might have a critical impact on results obtained, almost no studies test validity of current methods. Here, we focused on the effect of freezing samples between collection and use in experiments involving body odor perception. In 2 experiments, we tested whether axillary odors were perceived differently by raters when presented fresh or having been frozen and whether several freeze-thaw cycles affected sample quality. In the first experiment, samples were frozen for 2 weeks, 1 month, or 4 months. We found no differences in ratings of pleasantness, attractiveness, or masculinity between fresh and frozen samples. Similarly, almost no differences between repeatedly thawed and fresh samples were found. We found some variations in intensity; however, this was unrelated to length of storage. The second experiment tested differences between fresh samples and those frozen for 6 months. Again no differences in subjective ratings were observed. These results suggest that freezing has no significant effect on perceived odor hedonicity and that samples can be reliably used after storage for relatively long periods.

Molecular method for detection of total coliforms in drinking water samples.

PubMed

Maheux, Andrée F; Boudreau, Dominique K; Bisson, Marc-Antoine; Dion-Dupont, Vanessa; Bouchard, Sébastien; Nkuranga, Martine; Bergeron, Michel G; Rodriguez, Manuel J

2014-07-01

This work demonstrates the ability of a bacterial concentration and recovery procedure combined with three different PCR assays targeting the lacZ, wecG, and 16S rRNA genes, respectively, to detect the presence of total coliforms in 100-ml samples of potable water (presence/absence test). PCR assays were first compared to the culture-based Colilert and MI agar methods to determine their ability to detect 147 coliform strains representing 76 species of Enterobacteriaceae encountered in fecal and environmental settings. Results showed that 86 (58.5%) and 109 (74.1%) strains yielded a positive signal with Colilert and MI agar methods, respectively, whereas the lacZ, wecG, and 16S rRNA PCR assays detected 133 (90.5%), 111 (75.5%), and 146 (99.3%) of the 147 total coliform strains tested. These assays were then assessed by testing 122 well water samples collected in the Québec City region of Canada. Results showed that 97 (79.5%) of the samples tested by culture-based methods and 95 (77.9%), 82 (67.2%), and 98 (80.3%) of samples tested using PCR-based methods contained total coliforms, respectively. Consequently, despite the high genetic variability of the total coliform group, this study demonstrated that it is possible to use molecular assays to detect total coliforms in potable water: the 16S rRNA molecular assay was shown to be as efficient as recommended culture-based methods. This assay might be used in combination with an Escherichia coli molecular assay to assess drinking water quality. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Persistent Organic Pollutant Determination in Killer Whale Scat Samples: Optimization of a Gas Chromatography/Mass Spectrometry Method and Application to Field Samples.

PubMed

Lundin, Jessica I; Dills, Russell L; Ylitalo, Gina M; Hanson, M Bradley; Emmons, Candice K; Schorr, Gregory S; Ahmad, Jacqui; Hempelmann, Jennifer A; Parsons, Kim M; Wasser, Samuel K

2016-01-01

Biologic sample collection in wild cetacean populations is challenging. Most information on toxicant levels is obtained from blubber biopsy samples; however, sample collection is invasive and strictly regulated under permit, thus limiting sample numbers. Methods are needed to monitor toxicant levels that increase temporal and repeat sampling of individuals for population health and recovery models. The objective of this study was to optimize measuring trace levels (parts per billion) of persistent organic pollutants (POPs), namely polychlorinated-biphenyls (PCBs), polybrominated-diphenyl-ethers (PBDEs), dichlorodiphenyltrichloroethanes (DDTs), and hexachlorocyclobenzene, in killer whale scat (fecal) samples. Archival scat samples, initially collected, lyophilized, and extracted with 70 % ethanol for hormone analyses, were used to analyze POP concentrations. The residual pellet was extracted and analyzed using gas chromatography coupled with mass spectrometry. Method detection limits ranged from 11 to 125 ng/g dry weight. The described method is suitable for p,p'-DDE, PCBs-138, 153, 180, and 187, and PBDEs-47 and 100; other POPs were below the limit of detection. We applied this method to 126 scat samples collected from Southern Resident killer whales. Scat samples from 22 adult whales also had known POP concentrations in blubber and demonstrated significant correlations (p < 0.01) between matrices across target analytes. Overall, the scat toxicant measures matched previously reported patterns from blubber samples of decreased levels in reproductive-age females and a decreased p,p'-DDE/∑PCB ratio in J-pod. Measuring toxicants in scat samples provides an unprecedented opportunity to noninvasively evaluate contaminant levels in wild cetacean populations; these data have the prospect to provide meaningful information for vital management decisions.

The effect of sampling techniques used in the multiconfigurational Ehrenfest method

NASA Astrophysics Data System (ADS)

Symonds, C.; Kattirtzi, J. A.; Shalashilin, D. V.

2018-05-01

In this paper, we compare and contrast basis set sampling techniques recently developed for use in the ab initio multiple cloning method, a direct dynamics extension to the multiconfigurational Ehrenfest approach, used recently for the quantum simulation of ultrafast photochemistry. We demonstrate that simultaneous use of basis set cloning and basis function trains can produce results which are converged to the exact quantum result. To demonstrate this, we employ these sampling methods in simulations of quantum dynamics in the spin boson model with a broad range of parameters and compare the results to accurate benchmarks.

The effect of sampling techniques used in the multiconfigurational Ehrenfest method.

PubMed

Symonds, C; Kattirtzi, J A; Shalashilin, D V

2018-05-14

In this paper, we compare and contrast basis set sampling techniques recently developed for use in the ab initio multiple cloning method, a direct dynamics extension to the multiconfigurational Ehrenfest approach, used recently for the quantum simulation of ultrafast photochemistry. We demonstrate that simultaneous use of basis set cloning and basis function trains can produce results which are converged to the exact quantum result. To demonstrate this, we employ these sampling methods in simulations of quantum dynamics in the spin boson model with a broad range of parameters and compare the results to accurate benchmarks.

Validated method for quantification of genetically modified organisms in samples of maize flour.

PubMed

Kunert, Renate; Gach, Johannes S; Vorauer-Uhl, Karola; Engel, Edwin; Katinger, Hermann

2006-02-08

Sensitive and accurate testing for trace amounts of biotechnology-derived DNA from plant material is the prerequisite for detection of 1% or 0.5% genetically modified ingredients in food products or raw materials thereof. Compared to ELISA detection of expressed proteins, real-time PCR (RT-PCR) amplification has easier sample preparation and detection limits are lower. Of the different methods of DNA preparation CTAB method with high flexibility in starting material and generation of sufficient DNA with relevant quality was chosen. Previous RT-PCR data generated with the SYBR green detection method showed that the method is highly sensitive to sample matrices and genomic DNA content influencing the interpretation of results. Therefore, this paper describes a real-time DNA quantification based on the TaqMan probe method, indicating high accuracy and sensitivity with detection limits of lower than 18 copies per sample applicable and comparable to highly purified plasmid standards as well as complex matrices of genomic DNA samples. The results were evaluated with ValiData for homology of variance, linearity, accuracy of the standard curve, and standard deviation.

An improved SRC method based on virtual samples for face recognition

NASA Astrophysics Data System (ADS)

Fu, Lijun; Chen, Deyun; Lin, Kezheng; Li, Ao

2018-07-01

The sparse representation classifier (SRC) performs classification by evaluating which class leads to the minimum representation error. However, in real world, the number of available training samples is limited due to noise interference, training samples cannot accurately represent the test sample linearly. Therefore, in this paper, we first produce virtual samples by exploiting original training samples at the aim of increasing the number of training samples. Then, we take the intra-class difference as data representation of partial noise, and utilize the intra-class differences and training samples simultaneously to represent the test sample in a linear way according to the theory of SRC algorithm. Using weighted score level fusion, the respective representation scores of the virtual samples and the original training samples are fused together to obtain the final classification results. The experimental results on multiple face databases show that our proposed method has a very satisfactory classification performance.

Comparison of indoor air sampling and dust collection methods for fungal exposure assessment using quantitative PCR

EPA Science Inventory

Evaluating fungal contamination indoors is complicated because of the many different sampling methods utilized. In this study, fungal contamination was evaluated using five sampling methods and four matrices for results. The five sampling methods were a 48 hour indoor air sample ...

Probe Heating Method for the Analysis of Solid Samples Using a Portable Mass Spectrometer

PubMed Central

Kumano, Shun; Sugiyama, Masuyuki; Yamada, Masuyoshi; Nishimura, Kazushige; Hasegawa, Hideki; Morokuma, Hidetoshi; Inoue, Hiroyuki; Hashimoto, Yuichiro

2015-01-01

We previously reported on the development of a portable mass spectrometer for the onsite screening of illicit drugs, but our previous sampling system could only be used for liquid samples. In this study, we report on an attempt to develop a probe heating method that also permits solid samples to be analyzed using a portable mass spectrometer. An aluminum rod is used as the sampling probe. The powdered sample is affixed to the sampling probe or a droplet of sample solution is placed on the tip of the probe and dried. The probe is then placed on a heater to vaporize the sample. The vapor is then introduced into the portable mass spectrometer and analyzed. With the heater temperature set to 130°C, the developed system detected 1 ng of methamphetamine, 1 ng of amphetamine, 3 ng of 3,4-methylenedioxymethamphetamine, 1 ng of 3,4-methylenedioxyamphetamine, and 0.3 ng of cocaine. Even from mixtures consisting of clove powder and methamphetamine powder, methamphetamine ions were detected by tandem mass spectrometry. The developed probe heating method provides a simple method for the analysis of solid samples. A portable mass spectrometer incorporating this method would thus be useful for the onsite screening of illicit drugs. PMID:26819909

A novel sample preparation method using rapid nonheated saponification method for the determination of cholesterol in emulsified foods.

PubMed

Jeong, In-Seek; Kwak, Byung-Man; Ahn, Jang-Hyuk; Leem, Donggil; Yoon, Taehyung; Yoon, Changyong; Jeong, Jayoung; Park, Jung-Min; Kim, Jin-Man

2012-10-01

In this study, nonheated saponification was employed as a novel, rapid, and easy sample preparation method for the determination of cholesterol in emulsified foods. Cholesterol content was analyzed using gas chromatography with a flame ionization detector (GC-FID). The cholesterol extraction method was optimized for maximum recovery from baby food and infant formula. Under these conditions, the optimum extraction solvent was 10 mL ethyl ether per 1 to 2 g sample, and the saponification solution was 0.2 mL KOH in methanol. The cholesterol content in the products was determined to be within the certified range of certified reference materials (CRMs), NIST SRM 1544 and SRM 1849. The results of the recovery test performed using spiked materials were in the range of 98.24% to 99.45% with an relative standard devitation (RSD) between 0.83% and 1.61%. This method could be used to reduce sample pretreatment time and is expected to provide an accurate determination of cholesterol in emulsified food matrices such as infant formula and baby food. A novel, rapid, and easy sample preparation method using nonheated saponification was developed for cholesterol detection in emulsified foods. Recovery tests of CRMs were satisfactory, and the recoveries of spiked materials were accurate and precise. This method was effective and decreased the time required for analysis by 5-fold compared to the official method. © 2012 Institute of Food Technologists®

METHOD FOR MICRORNA ISOLATION FROM CLINICAL SERUM SAMPLES

PubMed Central

Li, Yu; Kowdley, Kris V.

2012-01-01

MicroRNAs are a group of intracellular non-coding RNA molecules that have been implicated in a variety of human diseases. Due to their high stability in blood, microRNAs released into circulation could be potentially utilized as non-invasive biomarkers for diagnosis or prognosis. Current microRNA isolation protocols are specifically designed for solid tissues and are impractical for biomarker development utilizing small-volume serum samples on a large scale. Thus, a protocol for microRNA isolation from serum is needed to accommodate these conditions in biomarker development. To establish such a protocol, we developed a simplified approach to normalize sample input by using single synthetic spike-in microRNA. We evaluated three commonly used commercial microRNA isolation kits for the best performance by comparing RNA quality and yield. The manufacturer’s protocol was further modified to improve the microRNA yield from 200 μL of human serum. MicroRNAs isolated from a large set of clinical serum samples were tested on the miRCURY LNA real-time PCR panel and confirmed to be suitable for high-throughput microRNA profiling. In conclusion, we have established a proven method for microRNA isolation from clinical serum samples suitable for microRNA biomarker development. PMID:22982505

Method to make accurate concentration and isotopic measurements for small gas samples

NASA Astrophysics Data System (ADS)

Palmer, M. R.; Wahl, E.; Cunningham, K. L.

2013-12-01

Carbon isotopic ratio measurements of CO2 and CH4 provide valuable insight into carbon cycle processes. However, many of these studies, like soil gas, soil flux, and water head space experiments, provide very small gas sample volumes, too small for direct measurement by current constant-flow Cavity Ring-Down (CRDS) isotopic analyzers. Previously, we addressed this issue by developing a sample introduction module which enabled the isotopic ratio measurement of 40ml samples or smaller. However, the system, called the Small Sample Isotope Module (SSIM), does dilute the sample during the delivery with inert carrier gas which causes a ~5% reduction in concentration. The isotopic ratio measurements are not affected by this small dilution, but researchers are naturally interested accurate concentration measurements. We present the accuracy and precision of a new method of using this delivery module which we call 'double injection.' Two portions of the 40ml of the sample (20ml each) are introduced to the analyzer, the first injection of which flushes out the diluting gas and the second injection is measured. The accuracy of this new method is demonstrated by comparing the concentration and isotopic ratio measurements for a gas sampled directly and that same gas measured through the SSIM. The data show that the CO2 concentration measurements were the same within instrument precision. The isotopic ratio precision (1σ) of repeated measurements was 0.16 permil for CO2 and 1.15 permil for CH4 at ambient concentrations. This new method provides a significant enhancement in the information provided by small samples.

Observational studies of patients in the emergency department: a comparison of 4 sampling methods.

PubMed

Valley, Morgan A; Heard, Kennon J; Ginde, Adit A; Lezotte, Dennis C; Lowenstein, Steven R

2012-08-01

We evaluate the ability of 4 sampling methods to generate representative samples of the emergency department (ED) population. We analyzed the electronic records of 21,662 consecutive patient visits at an urban, academic ED. From this population, we simulated different models of study recruitment in the ED by using 2 sample sizes (n=200 and n=400) and 4 sampling methods: true random, random 4-hour time blocks by exact sample size, random 4-hour time blocks by a predetermined number of blocks, and convenience or "business hours." For each method and sample size, we obtained 1,000 samples from the population. Using χ(2) tests, we measured the number of statistically significant differences between the sample and the population for 8 variables (age, sex, race/ethnicity, language, triage acuity, arrival mode, disposition, and payer source). Then, for each variable, method, and sample size, we compared the proportion of the 1,000 samples that differed from the overall ED population to the expected proportion (5%). Only the true random samples represented the population with respect to sex, race/ethnicity, triage acuity, mode of arrival, language, and payer source in at least 95% of the samples. Patient samples obtained using random 4-hour time blocks and business hours sampling systematically differed from the overall ED patient population for several important demographic and clinical variables. However, the magnitude of these differences was not large. Common sampling strategies selected for ED-based studies may affect parameter estimates for several representative population variables. However, the potential for bias for these variables appears small. Copyright © 2012. Published by Mosby, Inc.

Molecular analyses of two bacterial sampling methods in ligature-induced periodontitis in rats.

PubMed

Fontana, Carla Raquel; Grecco, Clovis; Bagnato, Vanderlei Salvador; de Freitas, Laura Marise; Boussios, Constantinos I; Soukos, Nikolaos S

2018-02-01

The prevalence profile of periodontal pathogens in dental plaque can vary as a function of the detection method; however, the sampling technique may also play a role in determining dental plaque microbial profiles. We sought to determine the bacterial composition comparing two sampling methods, one well stablished and a new one proposed here. In this study, a ligature-induced periodontitis model was used in 30 rats. Twenty-seven days later, ligatures were removed and microbiological samples were obtained directly from the ligatures as well as from the periodontal pockets using absorbent paper points. Microbial analysis was performed using DNA probes to a panel of 40 periodontal species in the checkerboard assay. The bacterial composition patterns were similar for both sampling methods. However, detection levels for all species were markedly higher for ligatures compared with paper points. Ligature samples provided more bacterial counts than paper points, suggesting that the technique for induction of periodontitis could also be applied for sampling in rats. Our findings may be helpful in designing studies of induced periodontal disease-associated microbiota.

Eigenvector method for umbrella sampling enables error analysis

PubMed Central

Thiede, Erik H.; Van Koten, Brian; Weare, Jonathan; Dinner, Aaron R.

2016-01-01

Umbrella sampling efficiently yields equilibrium averages that depend on exploring rare states of a model by biasing simulations to windows of coordinate values and then combining the resulting data with physical weighting. Here, we introduce a mathematical framework that casts the step of combining the data as an eigenproblem. The advantage to this approach is that it facilitates error analysis. We discuss how the error scales with the number of windows. Then, we derive a central limit theorem for averages that are obtained from umbrella sampling. The central limit theorem suggests an estimator of the error contributions from individual windows, and we develop a simple and computationally inexpensive procedure for implementing it. We demonstrate this estimator for simulations of the alanine dipeptide and show that it emphasizes low free energy pathways between stable states in comparison to existing approaches for assessing error contributions. Our work suggests the possibility of using the estimator and, more generally, the eigenvector method for umbrella sampling to guide adaptation of the simulation parameters to accelerate convergence. PMID:27586912

Cytotoxicity of Light-Cured Dental Materials according to Different Sample Preparation Methods

PubMed Central

Lee, Myung-Jin; Kim, Mi-Joo; Kwon, Jae-Sung; Lee, Sang-Bae; Kim, Kwang-Mahn

2017-01-01

Dental light-cured resins can undergo different degrees of polymerization when applied in vivo. When polymerization is incomplete, toxic monomers may be released into the oral cavity. The present study assessed the cytotoxicity of different materials, using sample preparation methods that mirror clinical conditions. Composite and bonding resins were used and divided into four groups according to sample preparation method: uncured; directly cured samples, which were cured after being placed on solidified agar; post-cured samples were polymerized before being placed on agar; and “removed unreacted layer” samples had their oxygen-inhibition layer removed after polymerization. Cytotoxicity was evaluated using an agar diffusion test, MTT assay, and confocal microscopy. Uncured samples were the most cytotoxic, while removed unreacted layer samples were the least cytotoxic (p < 0.05). In the MTT assay, cell viability increased significantly in every group as the concentration of the extracts decreased (p < 0.05). Extracts from post-cured and removed unreacted layer samples of bonding resin were less toxic than post-cured and removed unreacted layer samples of composite resin. Removal of the oxygen-inhibition layer resulted in the lowest cytotoxicity. Clinicians should remove unreacted monomers on the resin surface immediately after restoring teeth with light-curing resin to improve the restoration biocompatibility. PMID:28772647

Validation of a standardized extraction method for formalin-fixed paraffin-embedded tissue samples.

PubMed

Lagheden, Camilla; Eklund, Carina; Kleppe, Sara Nordqvist; Unger, Elizabeth R; Dillner, Joakim; Sundström, Karin

2016-07-01

Formalin-fixed paraffin-embedded (FFPE) samples can be DNA-extracted and used for human papillomavirus (HPV) genotyping. The xylene-based gold standard for extracting FFPE samples is laborious, suboptimal and involves health hazards for the personnel involved. To compare extraction with the standard xylene method to a xylene-free method used in an HPV LabNet Global Reference Laboratory at the Centers for Disease Control (CDC); based on a commercial method with an extra heating step. Fifty FFPE samples were randomly selected from a national audit of all cervical cancer cases diagnosed in Sweden during 10 years. For each case-block, a blank-block was sectioned, as a control for contamination. For xylene extraction, the standard WHO Laboratory Manual protocol was used. For the CDC method, the manufacturers' protocol was followed except for an extra heating step, 120°C for 20min. Samples were extracted and tested in parallel with β-globin real-time PCR, HPV16 real-time PCR and HPV typing using modified general primers (MGP)-PCR and Luminex assays. For a valid result the blank-block had to be betaglobin-negative in all tests and the case-block positive for beta-globin. Overall, detection was improved with the heating method and the amount of HPV-positive samples increased from 70% to 86% (p=0.039). For all samples where HPV type concordance could be evaluated, there was 100% type concordance. A xylene-free and robust extraction method for HPV-DNA typing in FFPE material is currently in great demand. Our proposed standardized protocol appears to be generally useful. Copyright © 2016. Published by Elsevier B.V.

Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution

PubMed Central

Ingala, Melissa R.; Simmons, Nancy B.; Wultsch, Claudia; Krampis, Konstantinos; Speer, Kelly A.; Perkins, Susan L.

2018-01-01

The gut microbiome is a community of host-associated symbiotic microbes that fulfills multiple key roles in host metabolism, immune function, and tissue development. Given the ability of the microbiome to impact host fitness, there is increasing interest in studying the microbiome of wild animals to better understand these communities in the context of host ecology and evolution. Human microbiome research protocols are well established, but wildlife microbiome research is still a developing field. Currently, there is no standardized set of best practices guiding the collection of microbiome samples from wildlife. Gut microflora are typically sampled either by fecal collection, rectal swabbing, or by destructively sampling the intestinal contents of the host animal. Studies rarely include more than one sampling technique and no comparison of these methods currently exists for a wild mammal. Although some studies have hypothesized that the fecal microbiome is a nested subset of the intestinal microbiome, this hypothesis has not been formally tested. To address these issues, we examined guano (feces) and distal intestinal mucosa from 19 species of free-ranging bats from Lamanai, Belize, using 16S rRNA amplicon sequencing to compare microbial communities across sample types. We found that the diversity and composition of intestine and guano samples differed substantially. In addition, we conclude that signatures of host evolution are retained by studying gut microbiomes based on mucosal tissue samples, but not fecal samples. Conversely, fecal samples retained more signal of host diet than intestinal samples. These results suggest that fecal and intestinal sampling methods are not interchangeable, and that these two microbiotas record different information about the host from which they are isolated. PMID:29765359

Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution.

PubMed

Ingala, Melissa R; Simmons, Nancy B; Wultsch, Claudia; Krampis, Konstantinos; Speer, Kelly A; Perkins, Susan L

2018-01-01

The gut microbiome is a community of host-associated symbiotic microbes that fulfills multiple key roles in host metabolism, immune function, and tissue development. Given the ability of the microbiome to impact host fitness, there is increasing interest in studying the microbiome of wild animals to better understand these communities in the context of host ecology and evolution. Human microbiome research protocols are well established, but wildlife microbiome research is still a developing field. Currently, there is no standardized set of best practices guiding the collection of microbiome samples from wildlife. Gut microflora are typically sampled either by fecal collection, rectal swabbing, or by destructively sampling the intestinal contents of the host animal. Studies rarely include more than one sampling technique and no comparison of these methods currently exists for a wild mammal. Although some studies have hypothesized that the fecal microbiome is a nested subset of the intestinal microbiome, this hypothesis has not been formally tested. To address these issues, we examined guano (feces) and distal intestinal mucosa from 19 species of free-ranging bats from Lamanai, Belize, using 16S rRNA amplicon sequencing to compare microbial communities across sample types. We found that the diversity and composition of intestine and guano samples differed substantially. In addition, we conclude that signatures of host evolution are retained by studying gut microbiomes based on mucosal tissue samples, but not fecal samples. Conversely, fecal samples retained more signal of host diet than intestinal samples. These results suggest that fecal and intestinal sampling methods are not interchangeable, and that these two microbiotas record different information about the host from which they are isolated.

The experience sampling method: Investigating students' affective experience

NASA Astrophysics Data System (ADS)

Nissen, Jayson M.; Stetzer, MacKenzie R.; Shemwell, Jonathan T.

2013-01-01

Improving non-cognitive outcomes such as attitudes, efficacy, and persistence in physics courses is an important goal of physics education. This investigation implemented an in-the-moment surveying technique called the Experience Sampling Method (ESM) [1] to measure students' affective experience in physics. Measurements included: self-efficacy, cognitive efficiency, activation, intrinsic motivation, and affect. Data are presented that show contrasts in students' experiences (e.g., in physics vs. non-physics courses).

Sample Size Methods for Estimating HIV Incidence from Cross-Sectional Surveys

PubMed Central

Brookmeyer, Ron

2015-01-01

Summary Understanding HIV incidence, the rate at which new infections occur in populations, is critical for tracking and surveillance of the epidemic. In this paper we derive methods for determining sample sizes for cross-sectional surveys to estimate incidence with sufficient precision. We further show how to specify sample sizes for two successive cross-sectional surveys to detect changes in incidence with adequate power. In these surveys biomarkers such as CD4 cell count, viral load, and recently developed serological assays are used to determine which individuals are in an early disease stage of infection. The total number of individuals in this stage, divided by the number of people who are uninfected, is used to approximate the incidence rate. Our methods account for uncertainty in the durations of time spent in the biomarker defined early disease stage. We find that failure to account for this uncertainty when designing surveys can lead to imprecise estimates of incidence and underpowered studies. We evaluated our sample size methods in simulations and found that they performed well in a variety of underlying epidemics. Code for implementing our methods in R is available with this paper at the Biometrics website on Wiley Online Library. PMID:26302040

Ensemble-Biased Metadynamics: A Molecular Simulation Method to Sample Experimental Distributions

PubMed Central

Marinelli, Fabrizio; Faraldo-Gómez, José D.

2015-01-01

We introduce an enhanced-sampling method for molecular dynamics (MD) simulations referred to as ensemble-biased metadynamics (EBMetaD). The method biases a conventional MD simulation to sample a molecular ensemble that is consistent with one or more probability distributions known a priori, e.g., experimental intramolecular distance distributions obtained by double electron-electron resonance or other spectroscopic techniques. To this end, EBMetaD adds an adaptive biasing potential throughout the simulation that discourages sampling of configurations inconsistent with the target probability distributions. The bias introduced is the minimum necessary to fulfill the target distributions, i.e., EBMetaD satisfies the maximum-entropy principle. Unlike other methods, EBMetaD does not require multiple simulation replicas or the introduction of Lagrange multipliers, and is therefore computationally efficient and straightforward in practice. We demonstrate the performance and accuracy of the method for a model system as well as for spin-labeled T4 lysozyme in explicit water, and show how EBMetaD reproduces three double electron-electron resonance distance distributions concurrently within a few tens of nanoseconds of simulation time. EBMetaD is integrated in the open-source PLUMED plug-in (www.plumed-code.org), and can be therefore readily used with multiple MD engines. PMID:26083917

Sample size methods for estimating HIV incidence from cross-sectional surveys.

PubMed

Konikoff, Jacob; Brookmeyer, Ron

2015-12-01

Understanding HIV incidence, the rate at which new infections occur in populations, is critical for tracking and surveillance of the epidemic. In this article, we derive methods for determining sample sizes for cross-sectional surveys to estimate incidence with sufficient precision. We further show how to specify sample sizes for two successive cross-sectional surveys to detect changes in incidence with adequate power. In these surveys biomarkers such as CD4 cell count, viral load, and recently developed serological assays are used to determine which individuals are in an early disease stage of infection. The total number of individuals in this stage, divided by the number of people who are uninfected, is used to approximate the incidence rate. Our methods account for uncertainty in the durations of time spent in the biomarker defined early disease stage. We find that failure to account for this uncertainty when designing surveys can lead to imprecise estimates of incidence and underpowered studies. We evaluated our sample size methods in simulations and found that they performed well in a variety of underlying epidemics. Code for implementing our methods in R is available with this article at the Biometrics website on Wiley Online Library. © 2015, The International Biometric Society.

Testing common stream sampling methods for broad-scale, long-term monitoring

Treesearch

Eric K. Archer; Brett B. Roper; Richard C. Henderson; Nick Bouwes; S. Chad Mellison; Jeffrey L. Kershner

2004-01-01

We evaluated sampling variability of stream habitat sampling methods used by the USDA Forest Service and the USDI Bureau of Land Management monitoring program for the upper Columbia River Basin. Three separate studies were conducted to describe the variability of individual measurement techniques, variability between crews, and temporal variation throughout the summer...

Sampling naturally contaminated broiler carcasses for Salmonella by three different methods

USDA-ARS?s Scientific Manuscript database

Postchill neck skin (NS) maceration and whole carcass rinsing (WCR) are frequently used methods to detect salmonellae from commercially processed broilers. These are practical, nondestructive methods, but they are insensitive and may result in frequent false negatives (20 to 40%). NS samples only ...

Rapid-viability PCR method for detection of live, virulent Bacillus anthracis in environmental samples.

PubMed

Létant, Sonia E; Murphy, Gloria A; Alfaro, Teneile M; Avila, Julie R; Kane, Staci R; Raber, Ellen; Bunt, Thomas M; Shah, Sanjiv R

2011-09-01

In the event of a biothreat agent release, hundreds of samples would need to be rapidly processed to characterize the extent of contamination and determine the efficacy of remediation activities. Current biological agent identification and viability determination methods are both labor- and time-intensive such that turnaround time for confirmed results is typically several days. In order to alleviate this issue, automated, high-throughput sample processing methods were developed in which real-time PCR analysis is conducted on samples before and after incubation. The method, referred to as rapid-viability (RV)-PCR, uses the change in cycle threshold after incubation to detect the presence of live organisms. In this article, we report a novel RV-PCR method for detection of live, virulent Bacillus anthracis, in which the incubation time was reduced from 14 h to 9 h, bringing the total turnaround time for results below 15 h. The method incorporates a magnetic bead-based DNA extraction and purification step prior to PCR analysis, as well as specific real-time PCR assays for the B. anthracis chromosome and pXO1 and pXO2 plasmids. A single laboratory verification of the optimized method applied to the detection of virulent B. anthracis in environmental samples was conducted and showed a detection level of 10 to 99 CFU/sample with both manual and automated RV-PCR methods in the presence of various challenges. Experiments exploring the relationship between the incubation time and the limit of detection suggest that the method could be further shortened by an additional 2 to 3 h for relatively clean samples.

Comparison of three methods of sampling trout blood for measurements of hematocrit

USGS Publications Warehouse

Steucke, Erwin W.; Schoettger, Richard A.

1967-01-01

Trout blood is frequently collected for hematocrit measurements by excising the caudal fin (Snieszko, 1960), but this technique is impractical if valuable fish are to be sampled or if repeated observations are desired. Schiffman (1959) and Snieszko (1960) collected blood from the dorsal aorta and the heart, but these methods are relatively slow and require the preparation of needles and syringes. The use of pointed capillary tubes for cardiac punctures increases the speed of sampling, but body fluids may dilute the blood (Perkins, 1957; Larsen and Snieszko, 1961; and Normandau, 1962). There is need for methods of sampling which are rapid and which neither influence hematological determinations nor harm the fish.

Nonuniform sampling and non-Fourier signal processing methods in multidimensional NMR.

PubMed

Mobli, Mehdi; Hoch, Jeffrey C

2014-11-01

Beginning with the introduction of Fourier Transform NMR by Ernst and Anderson in 1966, time domain measurement of the impulse response (the free induction decay, FID) consisted of sampling the signal at a series of discrete intervals. For compatibility with the discrete Fourier transform (DFT), the intervals are kept uniform, and the Nyquist theorem dictates the largest value of the interval sufficient to avoid aliasing. With the proposal by Jeener of parametric sampling along an indirect time dimension, extension to multidimensional experiments employed the same sampling techniques used in one dimension, similarly subject to the Nyquist condition and suitable for processing via the discrete Fourier transform. The challenges of obtaining high-resolution spectral estimates from short data records using the DFT were already well understood, however. Despite techniques such as linear prediction extrapolation, the achievable resolution in the indirect dimensions is limited by practical constraints on measuring time. The advent of non-Fourier methods of spectrum analysis capable of processing nonuniformly sampled data has led to an explosion in the development of novel sampling strategies that avoid the limits on resolution and measurement time imposed by uniform sampling. The first part of this review discusses the many approaches to data sampling in multidimensional NMR, the second part highlights commonly used methods for signal processing of such data, and the review concludes with a discussion of other approaches to speeding up data acquisition in NMR. Copyright © 2014 Elsevier B.V. All rights reserved.

Nonuniform sampling and non-Fourier signal processing methods in multidimensional NMR

PubMed Central

Mobli, Mehdi; Hoch, Jeffrey C.

2017-01-01

Beginning with the introduction of Fourier Transform NMR by Ernst and Anderson in 1966, time domain measurement of the impulse response (the free induction decay, FID) consisted of sampling the signal at a series of discrete intervals. For compatibility with the discrete Fourier transform (DFT), the intervals are kept uniform, and the Nyquist theorem dictates the largest value of the interval sufficient to avoid aliasing. With the proposal by Jeener of parametric sampling along an indirect time dimension, extension to multidimensional experiments employed the same sampling techniques used in one dimension, similarly subject to the Nyquist condition and suitable for processing via the discrete Fourier transform. The challenges of obtaining high-resolution spectral estimates from short data records using the DFT were already well understood, however. Despite techniques such as linear prediction extrapolation, the achievable resolution in the indirect dimensions is limited by practical constraints on measuring time. The advent of non-Fourier methods of spectrum analysis capable of processing nonuniformly sampled data has led to an explosion in the development of novel sampling strategies that avoid the limits on resolution and measurement time imposed by uniform sampling. The first part of this review discusses the many approaches to data sampling in multidimensional NMR, the second part highlights commonly used methods for signal processing of such data, and the review concludes with a discussion of other approaches to speeding up data acquisition in NMR. PMID:25456315

A General Linear Method for Equating with Small Samples

ERIC Educational Resources Information Center

Albano, Anthony D.

2015-01-01

Research on equating with small samples has shown that methods with stronger assumptions and fewer statistical estimates can lead to decreased error in the estimated equating function. This article introduces a new approach to linear observed-score equating, one which provides flexible control over how form difficulty is assumed versus estimated…

Sampling methods for recovery of human enteric viruses from environmental surfaces.

PubMed

Turnage, Nicole L; Gibson, Kristen E

2017-10-01

Acute gastroenteritis causes the second highest infectious disease burden worldwide. Human enteric viruses have been identified as leading causative agents of acute gastroenteritis as well as foodborne illnesses in the U.S. and are generally transmitted by fecal-oral contamination. There is growing evidence of transmission occurring via contaminated fomite including food contact surfaces. Additionally, human enteric viruses have been shown to remain infectious on fomites over prolonged periods of time. To better understand viral persistence, there is a need for more studies to investigate this phenomenon. Therefore, optimization of surface sampling methods is essential to aid in understanding environmental contamination to ensure proper preventative measures are being applied. In general, surface sampling studies are limited and highly variable among recovery efficiencies and research parameters used (e.g., virus type/density, surface type, elution buffers, tools). This review aims to discuss the various factors impacting surface sampling of viruses from fomites and to explore how researchers could move towards a more sensitive and standard sampling method. Copyright © 2017 Elsevier B.V. All rights reserved.

Comparing respondent-driven sampling and targeted sampling methods of recruiting injection drug users in San Francisco.

PubMed

Kral, Alex H; Malekinejad, Mohsen; Vaudrey, Jason; Martinez, Alexis N; Lorvick, Jennifer; McFarland, Willi; Raymond, H Fisher

2010-09-01

The objective of this article is to compare demographic characteristics, risk behaviors, and service utilization among injection drug users (IDUs) recruited from two separate studies in San Francisco in 2005, one which used targeted sampling (TS) and the other which used respondent-driven sampling (RDS). IDUs were recruited using TS (n = 651) and RDS (n = 534) and participated in quantitative interviews that included demographic characteristics, risk behaviors, and service utilization. Prevalence estimates and 95% confidence intervals (CIs) were calculated to assess whether there were differences in these variables by sampling method. There was overlap in 95% CIs for all demographic variables except African American race (TS: 45%, 53%; RDS: 29%, 44%). Maps showed that the proportion of IDUs distributed across zip codes were similar for the TS and RDS sample, with the exception of a single zip code that was more represented in the TS sample. This zip code includes an isolated, predominantly African American neighborhood where only the TS study had a field site. Risk behavior estimates were similar for both TS and RDS samples, although self-reported hepatitis C infection was lower in the RDS sample. In terms of service utilization, more IDUs in the RDS sample reported no recent use of drug treatment and syringe exchange program services. Our study suggests that perhaps a hybrid sampling plan is best suited for recruiting IDUs in San Francisco, whereby the more intensive ethnographic and secondary analysis components of TS would aid in the planning of seed placement and field locations for RDS.

Optical method for the characterization of laterally-patterned samples in integrated circuits

DOEpatents

Maris, Humphrey J.

2001-01-01

Disclosed is a method for characterizing a sample having a structure disposed on or within the sample, comprising the steps of applying a first pulse of light to a surface of the sample for creating a propagating strain pulse in the sample, applying a second pulse of light to the surface so that the second pulse of light interacts with the propagating strain pulse in the sample, sensing from a reflection of the second pulse a change in optical response of the sample, and relating a time of occurrence of the change in optical response to at least one dimension of the structure.

Optical method for the characterization of laterally-patterned samples in integrated circuits

DOEpatents

Maris, Humphrey J.

2010-08-24

Disclosed is a method for characterizing a sample having a structure disposed on or within the sample, comprising the steps of applying a first pulse of light to a surface of the sample for creating a propagating strain pulse in the sample, applying a second pulse of light to the surface so that the second pulse of light interacts with the propagating strain pulse in the sample, sensing from a reflection of the second pulse a change in optical response of the sample, and relating a time of occurrence of the change in optical response to at least one dimension of the structure.

Optical method for the characterization of laterally patterned samples in integrated circuits

DOEpatents

Maris, Humphrey J [Barrington, RI

2009-03-17

Disclosed is a method for characterizing a sample having a structure disposed on or within the sample, comprising the steps of applying a first pulse of light to a surface of the sample for creating a propagating strain pulse in the sample, applying a second pulse of light to the surface so that the second pulse of light interacts with the propagating strain pulse in the sample, sensing from a reflection of the second pulse a change in optical response of the sample, and relating a time of occurrence of the change in optical response to at least one dimension of the structure.

Real-Time PCR Method for Detection of Salmonella spp. in Environmental Samples.

PubMed

Kasturi, Kuppuswamy N; Drgon, Tomas

2017-07-15

The methods currently used for detecting Salmonella in environmental samples require 2 days to produce results and have limited sensitivity. Here, we describe the development and validation of a real-time PCR Salmonella screening method that produces results in 18 to 24 h. Primers and probes specific to the gene invA , group D, and Salmonella enterica serovar Enteritidis organisms were designed and evaluated for inclusivity and exclusivity using a panel of 329 Salmonella isolates representing 126 serovars and 22 non- Salmonella organisms. The invA - and group D-specific sets identified all the isolates accurately. The PCR method had 100% inclusivity and detected 1 to 2 copies of Salmonella DNA per reaction. Primers specific for Salmonella -differentiating fragment 1 (Sdf-1) in conjunction with the group D set had 100% inclusivity for 32 S Enteritidis isolates and 100% exclusivity for the 297 non-Enteritidis Salmonella isolates. Single-laboratory validation performed on 1,741 environmental samples demonstrated that the PCR method detected 55% more positives than the V itek i mmuno d iagnostic a ssay s ystem (VIDAS) method. The PCR results correlated well with the culture results, and the method did not report any false-negative results. The receiver operating characteristic (ROC) analysis documented excellent agreement between the results from the culture and PCR methods (area under the curve, 0.90; 95% confidence interval of 0.76 to 1.0) confirming the validity of the PCR method. IMPORTANCE This validated PCR method detects 55% more positives for Salmonella in half the time required for the reference method, VIDAS. The validated PCR method will help to strengthen public health efforts through rapid screening of Salmonella spp. in environmental samples.

Real-Time PCR Method for Detection of Salmonella spp. in Environmental Samples

PubMed Central

Drgon, Tomas

2017-01-01

ABSTRACT The methods currently used for detecting Salmonella in environmental samples require 2 days to produce results and have limited sensitivity. Here, we describe the development and validation of a real-time PCR Salmonella screening method that produces results in 18 to 24 h. Primers and probes specific to the gene invA, group D, and Salmonella enterica serovar Enteritidis organisms were designed and evaluated for inclusivity and exclusivity using a panel of 329 Salmonella isolates representing 126 serovars and 22 non-Salmonella organisms. The invA- and group D-specific sets identified all the isolates accurately. The PCR method had 100% inclusivity and detected 1 to 2 copies of Salmonella DNA per reaction. Primers specific for Salmonella-differentiating fragment 1 (Sdf-1) in conjunction with the group D set had 100% inclusivity for 32 S. Enteritidis isolates and 100% exclusivity for the 297 non-Enteritidis Salmonella isolates. Single-laboratory validation performed on 1,741 environmental samples demonstrated that the PCR method detected 55% more positives than the Vitek immunodiagnostic assay system (VIDAS) method. The PCR results correlated well with the culture results, and the method did not report any false-negative results. The receiver operating characteristic (ROC) analysis documented excellent agreement between the results from the culture and PCR methods (area under the curve, 0.90; 95% confidence interval of 0.76 to 1.0) confirming the validity of the PCR method. IMPORTANCE This validated PCR method detects 55% more positives for Salmonella in half the time required for the reference method, VIDAS. The validated PCR method will help to strengthen public health efforts through rapid screening of Salmonella spp. in environmental samples. PMID:28500041

[Comparison study on sampling methods of Oncomelania hupensis snail survey in marshland schistosomiasis epidemic areas in China].

PubMed

An, Zhao; Wen-Xin, Zhang; Zhong, Yao; Yu-Kuan, Ma; Qing, Liu; Hou-Lang, Duan; Yi-di, Shang

2016-06-29

To optimize and simplify the survey method of Oncomelania hupensis snail in marshland endemic region of schistosomiasis and increase the precision, efficiency and economy of the snail survey. A quadrate experimental field was selected as the subject of 50 m×50 m size in Chayegang marshland near Henghu farm in the Poyang Lake region and a whole-covered method was adopted to survey the snails. The simple random sampling, systematic sampling and stratified random sampling methods were applied to calculate the minimum sample size, relative sampling error and absolute sampling error. The minimum sample sizes of the simple random sampling, systematic sampling and stratified random sampling methods were 300, 300 and 225, respectively. The relative sampling errors of three methods were all less than 15%. The absolute sampling errors were 0.221 7, 0.302 4 and 0.047 8, respectively. The spatial stratified sampling with altitude as the stratum variable is an efficient approach of lower cost and higher precision for the snail survey.

Relative efficiency of anuran sampling methods in a restinga habitat (Jurubatiba, Rio de Janeiro, Brazil).

PubMed

Rocha, C F D; Van Sluys, M; Hatano, F H; Boquimpani-Freitas, L; Marra, R V; Marques, R V

2004-11-01

Studies on anurans in restinga habitats are few and, as a result, there is little information on which methods are more efficient for sampling them in this environment. Ten methods are usually used for sampling anuran communities in tropical and sub-tropical areas. In this study we evaluate which methods are more appropriate for this purpose in the restinga environment of Parque Nacional da Restinga de Jurubatiba. We analyzed six methods among those usually used for anuran samplings. For each method, we recorded the total amount of time spent (in min.), the number of researchers involved, and the number of species captured. We calculated a capture efficiency index (time necessary for a researcher to capture an individual frog) in order to make comparable the data obtained. Of the methods analyzed, the species inventory (9.7 min/searcher /ind.- MSI; richness = 6; abundance = 23) and the breeding site survey (9.5 MSI; richness = 4; abundance = 22) were the most efficient. The visual encounter inventory (45.0 MSI) and patch sampling (65.0 MSI) methods were of comparatively lower efficiency restinga, whereas the plot sampling and the pit-fall traps with drift-fence methods resulted in no frog capture. We conclude that there is a considerable difference in efficiency of methods used in the restinga environment and that the complete species inventory method is highly efficient for sampling frogs in the restinga studied and may be so in other restinga environments. Methods that are usually efficient in forested areas seem to be of little value in open restinga habitats.

Sampling pig farms at the abattoir in a cross-sectional study - Evaluation of a sampling method.

PubMed

Birkegård, Anna Camilla; Halasa, Tariq; Toft, Nils

2017-09-15

A cross-sectional study design is relatively inexpensive, fast and easy to conduct when compared to other study designs. Careful planning is essential to obtaining a representative sample of the population, and the recommended approach is to use simple random sampling from an exhaustive list of units in the target population. This approach is rarely feasible in practice, and other sampling procedures must often be adopted. For example, when slaughter pigs are the target population, sampling the pigs on the slaughter line may be an alternative to on-site sampling at a list of farms. However, it is difficult to sample a large number of farms from an exact predefined list, due to the logistics and workflow of an abattoir. Therefore, it is necessary to have a systematic sampling procedure and to evaluate the obtained sample with respect to the study objective. We propose a method for 1) planning, 2) conducting, and 3) evaluating the representativeness and reproducibility of a cross-sectional study when simple random sampling is not possible. We used an example of a cross-sectional study with the aim of quantifying the association of antimicrobial resistance and antimicrobial consumption in Danish slaughter pigs. It was not possible to visit farms within the designated timeframe. Therefore, it was decided to use convenience sampling at the abattoir. Our approach was carried out in three steps: 1) planning: using data from meat inspection to plan at which abattoirs and how many farms to sample; 2) conducting: sampling was carried out at five abattoirs; 3) evaluation: representativeness was evaluated by comparing sampled and non-sampled farms, and the reproducibility of the study was assessed through simulated sampling based on meat inspection data from the period where the actual data collection was carried out. In the cross-sectional study samples were taken from 681 Danish pig farms, during five weeks from February to March 2015. The evaluation showed that the sampling

Quantitative method of determining beryllium or a compound thereof in a sample

DOEpatents

McCleskey, T. Mark; Ehler, Deborah S.; John, Kevin D.; Burrell, Anthony K.; Collis, Gavin E.; Minogue, Edel M.; Warner, Benjamin P.

2006-10-31

A method of determining beryllium or a beryllium compound thereof in a sample, includes providing a sample suspected of comprising beryllium or a compound thereof, extracting beryllium or a compound thereof from the sample by dissolving in a solution, adding a fluorescent indicator to the solution to thereby bind any beryllium or a compound thereof to the fluorescent indicator, and determining the presence or amount of any beryllium or a compound thereof in the sample by measuring fluorescence.

Quantitative method of determining beryllium or a compound thereof in a sample

DOEpatents

McCleskey, T. Mark; Ehler, Deborah S.; John, Kevin D.; Burrell, Anthony K.; Collis, Gavin E.; Minogue, Edel M.; Warner, Benjamin P.

2010-08-24

A method of determining beryllium or a beryllium compound thereof in a sample, includes providing a sample suspected of comprising beryllium or a compound thereof, extracting beryllium or a compound thereof from the sample by dissolving in a solution, adding a fluorescent indicator to the solution to thereby bind any beryllium or a compound thereof to the fluorescent indicator, and determining the presence or amount of any beryllium or a compound thereof in the sample by measuring fluorescence.

Electrodeposition as an alternate method for preparation of environmental samples for iodide by AMS

DOE PAGES

Adamic, M. L.; Lister, T. E.; Dufek, E. J.; ...

2015-03-25

This paper presents an evaluation of an alternate method for preparing environmental samples for 129I analysis by accelerator mass spectrometry (AMS) at Idaho National Laboratory. The optimal sample preparation method is characterized by ease of preparation, capability of processing very small quantities of iodide, and ease of loading into a cathode. Electrodeposition of iodide on a silver wire was evaluated using these criteria. This study indicates that the electrochemically-formed silver iodide deposits produce ion currents similar to those from precipitated silver iodide for the same sample mass. Furthermore, precipitated silver iodide samples are usually mixed with niobium or silver powdermore » prior to loading in a cathode. Using electrodeposition, the silver is already mixed with the sample and can simply be picked up with tweezers, placed in the sample die, and pressed into a cathode. The major advantage of this method is that the silver wire/electrodeposited silver iodide is much easier to load into a cathode.« less

Fast acquisition of multidimensional NMR spectra of solids and mesophases using alternative sampling methods.

PubMed

Lesot, Philippe; Kazimierczuk, Krzysztof; Trébosc, Julien; Amoureux, Jean-Paul; Lafon, Olivier

2015-11-01

Unique information about the atom-level structure and dynamics of solids and mesophases can be obtained by the use of multidimensional nuclear magnetic resonance (NMR) experiments. Nevertheless, the acquisition of these experiments often requires long acquisition times. We review here alternative sampling methods, which have been proposed to circumvent this issue in the case of solids and mesophases. Compared to the spectra of solutions, those of solids and mesophases present some specificities because they usually display lower signal-to-noise ratios, non-Lorentzian line shapes, lower spectral resolutions and wider spectral widths. We highlight herein the advantages and limitations of these alternative sampling methods. A first route to accelerate the acquisition time of multidimensional NMR spectra consists in the use of sparse sampling schemes, such as truncated, radial or random sampling ones. These sparsely sampled datasets are generally processed by reconstruction methods differing from the Discrete Fourier Transform (DFT). A host of non-DFT methods have been applied for solids and mesophases, including the G-matrix Fourier transform, the linear least-square procedures, the covariance transform, the maximum entropy and the compressed sensing. A second class of alternative sampling consists in departing from the Jeener paradigm for multidimensional NMR experiments. These non-Jeener methods include Hadamard spectroscopy as well as spatial or orientational encoding of the evolution frequencies. The increasing number of high field NMR magnets and the development of techniques to enhance NMR sensitivity will contribute to widen the use of these alternative sampling methods for the study of solids and mesophases in the coming years. Copyright © 2015 John Wiley & Sons, Ltd.

THE INFLUENCE OF PHYSICAL FACTORS ON COMPARATIVE PERFORMANCE OF SAMPLING METHODS IN LARGE RIVERS

EPA Science Inventory

In 1999, we compared five existing benthic macroinvertebrate sampling methods used in boatable rivers. Each sampling protocol was performed at each of 60 sites distributed among four rivers in the Ohio River drainage basin. Initial comparison of methods using key macroinvertebr...

Laser based water equilibration method for d18O determination of water samples

NASA Astrophysics Data System (ADS)

Mandic, Magda; Smajgl, Danijela; Stoebener, Nils

2017-04-01

Determination of d18O with water equilibration method using mass spectrometers equipped with equilibration unit or Gas Bench is known already for many years. Now, with development of laser spectrometers this extends methods and possibilities to apply different technologies in laboratory but also in the field. The Thermo Scientific™ Delta Ray™ Isotope Ratio Infrared Spectrometer (IRIS) analyzer with the Universal Reference Interface (URI) Connect and Teledyne Cetac ASX-7100 offers high precision and throughput of samples. It employs optical spectroscopy for continuous measurement of isotope ratio values and concentration of carbon dioxide in ambient air, and also for analysis of discrete samples from vials, syringes, bags, or other user-provided sample containers. Test measurements and conformation of precision and accuracy of method determination d18O in water samples were done in Thermo Fisher application laboratory with three lab standards, namely ANST, Ocean II and HBW. All laboratory standards were previously calibrated with international reference material VSMOW2 and SLAP2 to assure accuracy of the isotopic values of the water. With method that we present in this work achieved repeatability and accuracy are 0.16‰ and 0.71‰, respectively, which fulfill requirements of regulatory method for wine and must after equilibration with CO2.

Method of analyzing multiple sample simultaneously by detecting absorption and systems for use in such a method

DOEpatents

Yeung, Edward S.; Gong, Xiaoyi

2004-09-07

The present invention provides a method of analyzing multiple samples simultaneously by absorption detection. The method comprises: (i) providing a planar array of multiple containers, each of which contains a sample comprising at least one absorbing species, (ii) irradiating the planar array of multiple containers with a light source and (iii) detecting absorption of light with a detetion means that is in line with the light source at a distance of at leaat about 10 times a cross-sectional distance of a container in the planar array of multiple containers. The absorption of light by a sample indicates the presence of an absorbing species in it. The method can further comprise: (iv) measuring the amount of absorption of light detected in (iii) indicating the amount of the absorbing species in the sample. Also provided by the present invention is a system for use in the abov metho.The system comprises; (i) a light source comrnpising or consisting essentially of at leaat one wavelength of light, the absorption of which is to be detected, (ii) a planar array of multiple containers, and (iii) a detection means that is in line with the light source and is positioned in line with and parallel to the planar array of multiple contiainers at a distance of at least about 10 times a cross-sectional distance of a container.

Materials and Methods for Streamlined Laboratory Analysis of Environmental Samples, FY 2016 Report

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

Addleman, Raymond S.; Naes, Benjamin E.; McNamara, Bruce K.

The International Atomic Energy Agency (IAEA) relies upon laboratory analysis of environmental samples (typically referred to as “swipes”) collected during on-site inspections of safeguarded facilities to support the detection and deterrence of undeclared activities. Unfortunately, chemical processing and assay of the samples is slow and expensive. A rapid, effective, and simple extraction process and analysis method is needed to provide certified results with improved timeliness at reduced costs (principally in the form of reduced labor), while maintaining or improving sensitivity and efficacy. To address these safeguard needs the Pacific Northwest National Laboratory (PNNL) explored and demonstrated improved methods for environmentalmore » sample (ES) analysis. Improvements for both bulk and particle analysis were explored. To facilitate continuity and adoption, the new sampling materials and processing methods will be compatible with existing IAEA protocols for ES analysis. PNNL collaborated with Oak Ridge National Laboratory (ORNL), which performed independent validation of the new bulk analysis methods and compared performance to traditional IAEA’s Network of Analytical Laboratories (NWAL) protocol. ORNL efforts are reported separately. This report describes PNNL’s FY 2016 progress, which was focused on analytical application supporting environmental monitoring of uranium enrichment plants and nuclear fuel processing. In the future the technology could be applied to other safeguard applications and analytes related to fuel manufacturing, reprocessing, etc. PNNL’s FY 2016 efforts were broken into two tasks and a summary of progress, accomplishments and highlights are provided below. Principal progress and accomplishments on Task 1, Optimize Materials and Methods for ICP-MS Environmental Sample Analysis, are listed below. • Completed initial procedure for rapid uranium extraction from ES swipes based upon carbonate-peroxide chemistry (delivered to

Comparison of the acetyl bromide spectrophotometric method with other analytical lignin methods for determining lignin concentration in forage samples.

PubMed

Fukushima, Romualdo S; Hatfield, Ronald D

2004-06-16

Present analytical methods to quantify lignin in herbaceous plants are not totally satisfactory. A spectrophotometric method, acetyl bromide soluble lignin (ABSL), has been employed to determine lignin concentration in a range of plant materials. In this work, lignin extracted with acidic dioxane was used to develop standard curves and to calculate the derived linear regression equation (slope equals absorptivity value or extinction coefficient) for determining the lignin concentration of respective cell wall samples. This procedure yielded lignin values that were different from those obtained with Klason lignin, acid detergent acid insoluble lignin, or permanganate lignin procedures. Correlations with in vitro dry matter or cell wall digestibility of samples were highest with data from the spectrophotometric technique. The ABSL method employing as standard lignin extracted with acidic dioxane has the potential to be employed as an analytical method to determine lignin concentration in a range of forage materials. It may be useful in developing a quick and easy method to predict in vitro digestibility on the basis of the total lignin content of a sample.

GROUND WATER MONITORING AND SAMPLING: MULTI-LEVEL VERSUS TRADITIONAL METHODS WHATS WHAT?

EPA Science Inventory

After years of research and many publications, the question still remains: What is the best method to collect representative ground water samples from monitoring wells? Numerous systems and devices are currently available for obtaining both multi-level samples as well as traditi...

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...

Analysis of methods commonly used in biomedicine for treatment versus control comparison of very small samples.

PubMed

Ristić-Djurović, Jasna L; Ćirković, Saša; Mladenović, Pavle; Romčević, Nebojša; Trbovich, Alexander M

2018-04-01

A rough estimate indicated that use of samples of size not larger than ten is not uncommon in biomedical research and that many of such studies are limited to strong effects due to sample sizes smaller than six. For data collected from biomedical experiments it is also often unknown if mathematical requirements incorporated in the sample comparison methods are satisfied. Computer simulated experiments were used to examine performance of methods for qualitative sample comparison and its dependence on the effectiveness of exposure, effect intensity, distribution of studied parameter values in the population, and sample size. The Type I and Type II errors, their average, as well as the maximal errors were considered. The sample size 9 and the t-test method with p = 5% ensured error smaller than 5% even for weak effects. For sample sizes 6-8 the same method enabled detection of weak effects with errors smaller than 20%. If the sample sizes were 3-5, weak effects could not be detected with an acceptable error; however, the smallest maximal error in the most general case that includes weak effects is granted by the standard error of the mean method. The increase of sample size from 5 to 9 led to seven times more accurate detection of weak effects. Strong effects were detected regardless of the sample size and method used. The minimal recommended sample size for biomedical experiments is 9. Use of smaller sizes and the method of their comparison should be justified by the objective of the experiment. Copyright © 2018 Elsevier B.V. All rights reserved.

A two-step electrodialysis method for DNA purification from polluted metallic environmental samples.

PubMed

Rodríguez-Mejía, José Luis; Martínez-Anaya, Claudia; Folch-Mallol, Jorge Luis; Dantán-González, Edgar

2008-08-01

Extracting DNA from samples of polluted environments using standard methods often results in low yields of poor-quality material unsuited to subsequent manipulation and analysis by molecular biological techniques. Here, we report a novel two-step electrodialysis-based method for the extraction of DNA from environmental samples. This technique permits the rapid and efficient isolation of high-quality DNA based on its acidic nature, and without the requirement for phenol-chloroform-isoamyl alcohol cleanup and ethanol precipitation steps. Subsequent PCR, endonuclease restriction, and cloning reactions were successfully performed utilizing DNA obtained by electrodialysis, whereas some or all of these techniques failed using DNA extracted with two alternative methods. We also show that his technique is applicable to purify DNA from a range of polluted and nonpolluted samples.

Rapid fusion method for the determination of Pu, Np, and Am in large soil samples

DOE PAGES

Maxwell, Sherrod L.; Culligan, Brian; Hutchison, Jay B.; ...

2015-02-14

A new rapid sodium hydroxide fusion method for the preparation of 10-20 g soil samples has been developed by the Savannah River National Laboratory (SRNL). The method enables lower detection limits for plutonium, neptunium, and americium in environmental soil samples. The method also significantly reduces sample processing time and acid fume generation compared to traditional soil digestion techniques using hydrofluoric acid. Ten gram soil aliquots can be ashed and fused using the new method in 1-2 hours, completely dissolving samples, including refractory particles. Pu, Np and Am are separated using stacked 2mL cartridges of TEVA and DGA Resin and measuredmore » using alpha spectrometry. The method can be adapted for measurement by inductively-coupled plasma mass spectrometry (ICP-MS). Two 10 g soil aliquots of fused soil may be combined prior to chromatographic separations to further improve detection limits. Total sample preparation time, including chromatographic separations and alpha spectrometry source preparation, is less than 8 hours.« less

Synchronization sampling method based on delta-sigma analog-digital converter for underwater towed array system.

PubMed

Jiang, Jia-Jia; Duan, Fa-Jie; Li, Yan-Chao; Hua, Xiang-Ning

2014-03-01

Synchronization sampling is very important in underwater towed array system where every acquisition node (AN) samples analog signals by its own analog-digital converter (ADC). In this paper, a simple and effective synchronization sampling method is proposed to ensure synchronized operation among different ANs of the underwater towed array system. We first present a master-slave synchronization sampling model, and then design a high accuracy phase-locked loop to synchronize all delta-sigma ADCs to a reference clock. However, when the master-slave synchronization sampling model is used, both the time-delay (TD) of messages traveling along the wired transmission medium and the jitter of the clocks will bring out synchronization sampling error (SSE). Therefore, a simple method is proposed to estimate and compensate the TD of the messages transmission, and then another effective method is presented to overcome the SSE caused by the jitter of the clocks. An experimental system with three ANs is set up, and the related experimental results verify the validity of the synchronization sampling method proposed in this paper.

Synchronization sampling method based on delta-sigma analog-digital converter for underwater towed array system

NASA Astrophysics Data System (ADS)

Jiang, Jia-Jia; Duan, Fa-Jie; Li, Yan-Chao; Hua, Xiang-Ning

2014-03-01

Synchronization sampling is very important in underwater towed array system where every acquisition node (AN) samples analog signals by its own analog-digital converter (ADC). In this paper, a simple and effective synchronization sampling method is proposed to ensure synchronized operation among different ANs of the underwater towed array system. We first present a master-slave synchronization sampling model, and then design a high accuracy phase-locked loop to synchronize all delta-sigma ADCs to a reference clock. However, when the master-slave synchronization sampling model is used, both the time-delay (TD) of messages traveling along the wired transmission medium and the jitter of the clocks will bring out synchronization sampling error (SSE). Therefore, a simple method is proposed to estimate and compensate the TD of the messages transmission, and then another effective method is presented to overcome the SSE caused by the jitter of the clocks. An experimental system with three ANs is set up, and the related experimental results verify the validity of the synchronization sampling method proposed in this paper.

Rapid fusion method for the determination of refractory thorium and uranium isotopes in soil samples

DOE PAGES

Maxwell, Sherrod L.; Hutchison, Jay B.; McAlister, Daniel R.

2015-02-14

Recently, approximately 80% of participating laboratories failed to accurately determine uranium isotopes in soil samples in the U.S Department of Energy Mixed Analyte Performance Evaluation Program (MAPEP) Session 30, due to incomplete dissolution of refractory particles in the samples. Failing laboratories employed acid dissolution methods, including hydrofluoric acid, to recover uranium from the soil matrix. The failures illustrate the importance of rugged soil dissolution methods for the accurate measurement of analytes in the sample matrix. A new rapid fusion method has been developed by the Savannah River National Laboratory (SRNL) to prepare 1-2 g soil sample aliquots very quickly, withmore » total dissolution of refractory particles. Soil samples are fused with sodium hydroxide at 600 ºC in zirconium crucibles to enable complete dissolution of the sample. Uranium and thorium are separated on stacked TEVA and TRU extraction chromatographic resin cartridges, prior to isotopic measurements by alpha spectrometry on cerium fluoride microprecipitation sources. Plutonium can also be separated and measured using this method. Batches of 12 samples can be prepared for measurement in <5 hours.« less

A Novel Method for Sampling Alpha-Helical Protein Backbones

DOE R&D Accomplishments Database

Fain, Boris; Levitt, Michael

2001-01-01

We present a novel technique of sampling the configurations of helical proteins. Assuming knowledge of native secondary structure, we employ assembly rules gathered from a database of existing structures to enumerate the geometrically possible 3-D arrangements of the constituent helices. We produce a library of possible folds for 25 helical protein cores. In each case the method finds significant numbers of conformations close to the native structure. In addition we assign coordinates to all atoms for 4 of the 25 proteins. In the context of database driven exhaustive enumeration our method performs extremely well, yielding significant percentages of structures (0.02%--82%) within 6A of the native structure. The method's speed and efficiency make it a valuable contribution towards the goal of predicting protein structure.

Improved Butanol-Methanol (BUME) Method by Replacing Acetic Acid for Lipid Extraction of Biological Samples.

PubMed

Cruz, Mutya; Wang, Miao; Frisch-Daiello, Jessica; Han, Xianlin

2016-07-01

Extraction of lipids from biological samples is a critical step in lipidomics, especially for shotgun lipidomics where lipid extracts are directly infused into a mass spectrometer. The butanol-methanol (BUME) extraction method was originally developed to extract lipids from plasma samples with 1 % acetic acid. Considering some lipids are sensitive to acidic environments, we modified this protocol by replacing acetic acid with lithium chloride solution and extended the modified extraction to tissue samples. Although no significant reduction of plasmalogen levels in the acidic BUME extracts of rat heart samples was found, the modified method was established to extract various tissue samples, including rat liver, heart, and plasma. Essentially identical profiles of the majority of lipid classes were obtained from the extracts of the modified BUME and traditional Bligh-Dyer methods. However, it was found that neither the original, nor the modified BUME method was suitable for 4-hydroxyalkenal species measurement in biological samples.

Improved Butanol-Methanol (BUME) Method by Replacing Acetic Acid for Lipid Extraction of Biological Samples

PubMed Central

Cruz, Mutya; Wang, Miao; Frisch-Daiello, Jessica; Han, Xianlin

2016-01-01

Extraction of lipids from biological samples is a critical step in lipidomics, especially for shotgun lipidomics where lipid extracts are directly infused into a mass spectrometer. The butanol-methanol (BUME) extraction method was originally developed to extract lipids from plasma samples with 1% acetic acid. Considering some lipids are sensitive to acidic environments, we modified this protocol by replacing acetic acid with lithium chloride solution and extended the modified extraction to tissue samples. Although no significant reduction of plasmalogen levels in the acidic BUME extracts of rat heart samples was found, the modified method was established to extract various tissue samples, including rat liver, heart, and plasma. Essentially identical profiles of the majority of lipid classes were obtained from the extracts of the modified BUME and traditional Bligh-Dyer methods. However, it was found that neither the original, nor the modified BUME method was suitable for 4-hydroxyalkenal species measurement in biological samples. PMID:27245345

Decontamination methods for samples preserved in cetylpyridinium chloride and cultured on thin-layer agar.

PubMed

Ardizzoni, E; Mulders, W; Sanchez-Padilla, E; Varaine, F; de Jong, B C; Rigouts, L

2014-08-01

Long transportation times of samples to culture laboratories can lead to higher contamination rates and significant loss of viability, resulting in lower culture positivity rates. Thin-layer agar (TLA) is a sensitive culture method for the isolation of Mycobacterium tuberculosis that has been optimised with N-acetyl-L-cysteine-sodium hydroxide (NALC-NaOH) decontaminated samples. The combination of the TLA culture method and other decontamination procedures has not been extensively validated. Among 390 smear-positive samples, we compared the culture positivity of samples decontaminated using the Petroff method vs. NALC-NaOH neutralised with phosphate buffer (PBS), applied to samples preserved with cetylpyridinium chloride (CPC) or CPC-free, and then of CPC-preserved samples decontaminated with NALC-NaOH neutralised using Difco neutralising buffer. The sediments were inoculated on TLA, and then on MGIT 960 or Löwenstein-Jensen (LJ) as gold standards. Decontamination with NALC-NaOH yielded higher culture positivity in TLA than in the Petroff method, which was further enhanced by neutralising CPC with the Difco buffer. Surprisingly, culture positivity on LJ also increased after using Difco buffer, suggesting that CPC may not be completely neutralised in egg-based medium. After transportation in CPC, decontamination using NALC-NaOH followed by neutralisation using Difco buffer resulted in the best recovery rates for samples inoculated on TLA and on LJ.

[Wound microbial sampling methods in surgical practice, imprint techniques].

PubMed

Chovanec, Z; Veverková, L; Votava, M; Svoboda, J; Peštál, A; Doležel, J; Jedlička, V; Veselý, M; Wechsler, J; Čapov, I

2012-12-01

The wound is a damage of tissue. The process of healing is influenced by many systemic and local factors. The most crucial and the most discussed local factor of wound healing is infection. Surgical site infection in the wound is caused by micro-organisms. This information is known for many years, however the conditions leading to an infection occurrence have not been sufficiently described yet. Correct sampling technique, correct storage, transportation, evaluation, and valid interpretation of these data are very important in clinical practice. There are many methods for microbiological sampling, but the best one has not been yet identified and validated. We aim to discuss the problem with the focus on the imprint technique.

A Predictive Model for Toxicity Effects Assessment of Biotransformed Hepatic Drugs Using Iterative Sampling Method.

PubMed

Tharwat, Alaa; Moemen, Yasmine S; Hassanien, Aboul Ella

2016-12-09

Measuring toxicity is one of the main steps in drug development. Hence, there is a high demand for computational models to predict the toxicity effects of the potential drugs. In this study, we used a dataset, which consists of four toxicity effects:mutagenic, tumorigenic, irritant and reproductive effects. The proposed model consists of three phases. In the first phase, rough set-based methods are used to select the most discriminative features for reducing the classification time and improving the classification performance. Due to the imbalanced class distribution, in the second phase, different sampling methods such as Random Under-Sampling, Random Over-Sampling and Synthetic Minority Oversampling Technique are used to solve the problem of imbalanced datasets. ITerative Sampling (ITS) method is proposed to avoid the limitations of those methods. ITS method has two steps. The first step (sampling step) iteratively modifies the prior distribution of the minority and majority classes. In the second step, a data cleaning method is used to remove the overlapping that is produced from the first step. In the third phase, Bagging classifier is used to classify an unknown drug into toxic or non-toxic. The experimental results proved that the proposed model performed well in classifying the unknown samples according to all toxic effects in the imbalanced datasets.

A non-uniformly under-sampled blade tip-timing signal reconstruction method for blade vibration monitoring.

PubMed

Hu, Zheng; Lin, Jun; Chen, Zhong-Sheng; Yang, Yong-Min; Li, Xue-Jun

2015-01-22

High-speed blades are often prone to fatigue due to severe blade vibrations. In particular, synchronous vibrations can cause irreversible damages to the blade. Blade tip-timing methods (BTT) have become a promising way to monitor blade vibrations. However, synchronous vibrations are unsuitably monitored by uniform BTT sampling. Therefore, non-equally mounted probes have been used, which will result in the non-uniformity of the sampling signal. Since under-sampling is an intrinsic drawback of BTT methods, how to analyze non-uniformly under-sampled BTT signals is a big challenge. In this paper, a novel reconstruction method for non-uniformly under-sampled BTT data is presented. The method is based on the periodically non-uniform sampling theorem. Firstly, a mathematical model of a non-uniform BTT sampling process is built. It can be treated as the sum of certain uniform sample streams. For each stream, an interpolating function is required to prevent aliasing in the reconstructed signal. Secondly, simultaneous equations of all interpolating functions in each sub-band are built and corresponding solutions are ultimately derived to remove unwanted replicas of the original signal caused by the sampling, which may overlay the original signal. In the end, numerical simulations and experiments are carried out to validate the feasibility of the proposed method. The results demonstrate the accuracy of the reconstructed signal depends on the sampling frequency, the blade vibration frequency, the blade vibration bandwidth, the probe static offset and the number of samples. In practice, both types of blade vibration signals can be particularly reconstructed by non-uniform BTT data acquired from only two probes.

A Non-Uniformly Under-Sampled Blade Tip-Timing Signal Reconstruction Method for Blade Vibration Monitoring

PubMed Central

Hu, Zheng; Lin, Jun; Chen, Zhong-Sheng; Yang, Yong-Min; Li, Xue-Jun

2015-01-01

High-speed blades are often prone to fatigue due to severe blade vibrations. In particular, synchronous vibrations can cause irreversible damages to the blade. Blade tip-timing methods (BTT) have become a promising way to monitor blade vibrations. However, synchronous vibrations are unsuitably monitored by uniform BTT sampling. Therefore, non-equally mounted probes have been used, which will result in the non-uniformity of the sampling signal. Since under-sampling is an intrinsic drawback of BTT methods, how to analyze non-uniformly under-sampled BTT signals is a big challenge. In this paper, a novel reconstruction method for non-uniformly under-sampled BTT data is presented. The method is based on the periodically non-uniform sampling theorem. Firstly, a mathematical model of a non-uniform BTT sampling process is built. It can be treated as the sum of certain uniform sample streams. For each stream, an interpolating function is required to prevent aliasing in the reconstructed signal. Secondly, simultaneous equations of all interpolating functions in each sub-band are built and corresponding solutions are ultimately derived to remove unwanted replicas of the original signal caused by the sampling, which may overlay the original signal. In the end, numerical simulations and experiments are carried out to validate the feasibility of the proposed method. The results demonstrate the accuracy of the reconstructed signal depends on the sampling frequency, the blade vibration frequency, the blade vibration bandwidth, the probe static offset and the number of samples. In practice, both types of blade vibration signals can be particularly reconstructed by non-uniform BTT data acquired from only two probes. PMID:25621612

A Two-Stage Method to Determine Optimal Product Sampling considering Dynamic Potential Market

PubMed Central

Hu, Zhineng; Lu, Wei; Han, Bing

2015-01-01

This paper develops an optimization model for the diffusion effects of free samples under dynamic changes in potential market based on the characteristics of independent product and presents a two-stage method to figure out the sampling level. The impact analysis of the key factors on the sampling level shows that the increase of the external coefficient or internal coefficient has a negative influence on the sampling level. And the changing rate of the potential market has no significant influence on the sampling level whereas the repeat purchase has a positive one. Using logistic analysis and regression analysis, the global sensitivity analysis gives a whole analysis of the interaction of all parameters, which provides a two-stage method to estimate the impact of the relevant parameters in the case of inaccuracy of the parameters and to be able to construct a 95% confidence interval for the predicted sampling level. Finally, the paper provides the operational steps to improve the accuracy of the parameter estimation and an innovational way to estimate the sampling level. PMID:25821847

A sample preparation method for recovering suppressed analyte ions in MALDI TOF MS.

PubMed

Lou, Xianwen; de Waal, Bas F M; Milroy, Lech-Gustav; van Dongen, Joost L J

2015-05-01

In matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS), analyte signals can be substantially suppressed by other compounds in the sample. In this technical note, we describe a modified thin-layer sample preparation method that significantly reduces the analyte suppression effect (ASE). In our method, analytes are deposited on top of the surface of matrix preloaded on the MALDI plate. To prevent embedding of analyte into the matrix crystals, the sample solution were prepared without matrix and efforts were taken not to re-dissolve the preloaded matrix. The results with model mixtures of peptides, synthetic polymers and lipids show that detection of analyte ions, which were completely suppressed using the conventional dried-droplet method, could be effectively recovered by using our method. Our findings suggest that the incorporation of analytes in the matrix crystals has an important contributory effect on ASE. By reducing ASE, our method should be useful for the direct MALDI MS analysis of multicomponent mixtures. Copyright © 2015 John Wiley & Sons, Ltd.

Field methods for sampling and storing nectar from flowers with low nectar volumes.

PubMed

Morrant, D S; Schumann, R; Petit, S

2009-02-01

Although several methods of sampling and storing floral nectar are available, little information exists on sampling and storing nectar from flowers with low nectar volumes. Methods for sampling and storing nectar from the flowers of species with low floral nectar volumes (<1 microL) were investigated using the flowers of Eucalyptus species. Sampling with microcapillary tubes, blotting up with filter paper, washing and rinsing were compared to determine masses of sugars recovered and differences in sugar ratios. Storage methods included room temperature, refrigeration and freezing treatments; the addition of antimicrobial agents benzyl alcohol or methanol to some of these treatments was also evaluated. Nectar samples were analysed using high-performance liquid chromatography and the masses of sucrose, glucose and fructose in each sample were determined. Masses of sugars varied significantly among sampling treatments, but the highest yielding methods, rinsing and washing, were not significantly different. A washing time of 1 min was as effective as one of 20 min. Storage trials showed that the sugar concentration measurements of nectar solutions changed rapidly, with the best results achieved for refrigeration with no additive (sucrose and fructose were stable for at least 2 weeks). Sugar ratios, however, remained relatively stable in most treatments and did not change significantly across 4 weeks for the methanol plus refrigerator and freezing treatments, and 2 weeks for the refrigeration treatment with no additive. Washing is recommended for nectar collection from flowers with low nectar volumes in the field (with the understanding that one wash underestimates the amounts of sugars present in a flower), as is immediate analysis of sugar mass. In view of the great variation in results depending on nectar collection and storage methods, caution should be exercised in their choice, and their accuracy should be evaluated. The use of pulsed amperometric detection, more

Chromium speciation in environmental samples using a solid phase spectrophotometric method

NASA Astrophysics Data System (ADS)

Amin, Alaa S.; Kassem, Mohammed A.

2012-10-01

A solid phase extraction technique is proposed for preconcentration and speciation of chromium in natural waters using spectrophotometric analysis. The procedure is based on sorption of chromium(III) as 4-(2-benzothiazolylazo)2,2'-biphenyldiol complex on dextran-type anion-exchange gel (Sephadex DEAE A-25). After reduction of Cr(VI) by 0.5 ml of 96% concentrated H2SO4 and ethanol, the system was applied to the total chromium. The concentration of Cr(VI) was calculated as the difference between the total Cr and the Cr(III) content. The influences of some analytical parameters such as: pH of the aqueous solution, amounts of 4-(2-benzothiazolylazo)2,2'-biphenyldiol (BTABD), and sample volumes were investigated. The absorbance of the gel, at 628 and 750 nm, packed in a 1.0 mm cell, is measured directly. The molar absorptivities were found to be 2.11 × 107 and 3.90 × 107 L mol-1 cm-1 for 500 and 1000 ml, respectively. Calibration is linear over the range 0.05-1.45 μg L-1 with RSD of <1.85% (n = 8.0). Using 35 mg exchanger, the detection and quantification limits were 13 and 44 ng L-1 for 500 ml sample, whereas for 1000 ml sample were 8.0 and 27 ng L-1, respectively. Increasing the sample volume can enhance the sensitivity. No considerable interferences have been observed from other investigated anions and cations on the chromium speciation. The proposed method was applied to the speciation of chromium in natural waters and total chromium preconcentration in microwave digested tobacco, coffee, tea, and soil samples. The results were simultaneously compared with those obtained using an ET AAS method, whereby the validity of the method has been tested.

Chromium speciation in environmental samples using a solid phase spectrophotometric method.

PubMed

Amin, Alaa S; Kassem, Mohammed A

2012-10-01

A solid phase extraction technique is proposed for preconcentration and speciation of chromium in natural waters using spectrophotometric analysis. The procedure is based on sorption of chromium(III) as 4-(2-benzothiazolylazo)2,2'-biphenyldiol complex on dextran-type anion-exchange gel (Sephadex DEAE A-25). After reduction of Cr(VI) by 0.5 ml of 96% concentrated H(2)SO(4) and ethanol, the system was applied to the total chromium. The concentration of Cr(VI) was calculated as the difference between the total Cr and the Cr(III) content. The influences of some analytical parameters such as: pH of the aqueous solution, amounts of 4-(2-benzothiazolylazo)2,2'-biphenyldiol (BTABD), and sample volumes were investigated. The absorbance of the gel, at 628 and 750 nm, packed in a 1.0 mm cell, is measured directly. The molar absorptivities were found to be 2.11×10(7) and 3.90×10(7) L mol(-1)cm(-1) for 500 and 1000 ml, respectively. Calibration is linear over the range 0.05-1.45 μg L(-1) with RSD of <1.85% (n=8.0). Using 35 mg exchanger, the detection and quantification limits were 13 and 44 ng L(-1) for 500 ml sample, whereas for 1000 ml sample were 8.0 and 27 ng L(-1), respectively. Increasing the sample volume can enhance the sensitivity. No considerable interferences have been observed from other investigated anions and cations on the chromium speciation. The proposed method was applied to the speciation of chromium in natural waters and total chromium preconcentration in microwave digested tobacco, coffee, tea, and soil samples. The results were simultaneously compared with those obtained using an ET AAS method, whereby the validity of the method has been tested. Copyright © 2012 Elsevier B.V. All rights reserved.

Method validation for control determination of mercury in fresh fish and shrimp samples by solid sampling thermal decomposition/amalgamation atomic absorption spectrometry.

PubMed

Torres, Daiane Placido; Martins-Teixeira, Maristela Braga; Cadore, Solange; Queiroz, Helena Müller

2015-01-01

A method for the determination of total mercury in fresh fish and shrimp samples by solid sampling thermal decomposition/amalgamation atomic absorption spectrometry (TDA AAS) has been validated following international foodstuff protocols in order to fulfill the Brazilian National Residue Control Plan. The experimental parameters have been previously studied and optimized according to specific legislation on validation and inorganic contaminants in foodstuff. Linearity, sensitivity, specificity, detection and quantification limits, precision (repeatability and within-laboratory reproducibility), robustness as well as accuracy of the method have been evaluated. Linearity of response was satisfactory for the two range concentrations available on the TDA AAS equipment, between approximately 25.0 and 200.0 μg kg(-1) (square regression) and 250.0 and 2000.0 μg kg(-1) (linear regression) of mercury. The residues for both ranges were homoscedastic and independent, with normal distribution. Correlation coefficients obtained for these ranges were higher than 0.995. Limits of quantification (LOQ) and of detection of the method (LDM), based on signal standard deviation (SD) for a low-in-mercury sample, were 3.0 and 1.0 μg kg(-1), respectively. Repeatability of the method was better than 4%. Within-laboratory reproducibility achieved a relative SD better than 6%. Robustness of the current method was evaluated and pointed sample mass as a significant factor. Accuracy (assessed as the analyte recovery) was calculated on basis of the repeatability, and ranged from 89% to 99%. The obtained results showed the suitability of the present method for direct mercury measurement in fresh fish and shrimp samples and the importance of monitoring the analysis conditions for food control purposes. Additionally, the competence of this method was recognized by accreditation under the standard ISO/IEC 17025.

An economic passive sampling method to detect particulate pollutants using magnetic measurements.

PubMed

Cao, Liwan; Appel, Erwin; Hu, Shouyun; Ma, Mingming

2015-10-01

Identifying particulate matter (PM) emitted from industrial processes into the atmosphere is an important issue in environmental research. This paper presents a passive sampling method using simple artificial samplers that maintains the advantage of bio-monitoring, but overcomes some of its disadvantages. The samplers were tested in a heavily polluted area (Linfen, China) and compared to results from leaf samples. Spatial variations of magnetic susceptibility from artificial passive samplers and leaf samples show very similar patterns. Scanning electron microscopy suggests that the collected PM are mostly in the range of 2-25 μm; frequent occurrence of spherical shape indicates industrial combustion dominates PM emission. Magnetic properties around power plants show different features than other plants. This sampling method provides a suitable and economic tool for semi-quantifying temporal and spatial distribution of air quality; they can be installed in a regular grid and calibrate the weight of PM. Copyright © 2015 Elsevier Ltd. All rights reserved.

Sediment sampling and processing methods in Hungary, and possible improvements

NASA Astrophysics Data System (ADS)

Tamas, Eniko Anna; Koch, Daniel; Varga, Gyorgy

2016-04-01

The importance of the monitoring of sediment processes is unquestionable: sediment balance of regulated rivers suffered substantial alterations in the past century, affecting navigation, energy production, fish habitats and floodplain ecosystems alike; infiltration times to our drinking water wells have shortened, exposing them to an eventual pollution event and making them vulnerable; and sediment-attached contaminants accumulate in floodplains and reservoirs, threatening our healthy environment. The changes in flood characteristics and rating curves of our rivers are regularly being researched and described, involving state-of-the-art measurement methods, modeling tools and traditional statistics. Sediment processes however, are much less known. Unlike the investigation of flow processes, sediment-related research is scarce, which is partly due to the outdated methodology and poor database background in the specific field. Sediment-related data, information and analyses form an important and integral part of Civil engineering in relation to rivers all over the world. In relation to the second largest river of Europe, the Danube, it is widely known in expert community and for long discussed at different expert forums that the sediment balance of the river Danube has changed drastically over the past century. Sediment monitoring on the river Danube started as early as the end of the 19th century, with scattered measurements carried out. Regular sediment sampling was developed in the first half of the 20th century all along the river, with different station density and monitoring frequencies in different countries. After the first few decades of regular sampling, the concept of (mainly industrial) development changed along the river and data needs changed as well, furthermore the complicated and inexact methods of sampling bed load on the alluvial reach of the river were not developed further. Frequency of suspended sediment sampling is very low along the river

Harmonisation of microbial sampling and testing methods for distillate fuels

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

Hill, G.C.; Hill, E.C.

1995-05-01

Increased incidence of microbial infection in distillate fuels has led to a demand for organisations such as the Institute of Petroleum to propose standards for microbiological quality, based on numbers of viable microbial colony forming units. Variations in quality requirements, and in the spoilage significance of contaminating microbes plus a tendency for temporal and spatial changes in the distribution of microbes, makes such standards difficult to implement. The problem is compounded by a diversity in the procedures employed for sampling and testing for microbial contamination and in the interpretation of the data obtained. The following paper reviews these problems andmore » describes the efforts of The Institute of Petroleum Microbiology Fuels Group to address these issues and in particular to bring about harmonisation of sampling and testing methods. The benefits and drawbacks of available test methods, both laboratory based and on-site, are discussed.« less

A New Method for Estimating Bacterial Abundances in Natural Samples using Sublimation

NASA Technical Reports Server (NTRS)

Glavin, Daniel P.; Cleaves, H. James; Schubert, Michael; Aubrey, Andrew; Bada, Jeffrey L.

2004-01-01

We have developed a new method based on the sublimation of adenine from Escherichia coli to estimate bacterial cell counts in natural samples. To demonstrate this technique, several types of natural samples including beach sand, seawater, deep-sea sediment, and two soil samples from the Atacama Desert were heated to a temperature of 500 C for several seconds under reduced pressure. The sublimate was collected on a cold finger and the amount of adenine released from the samples then determined by high performance liquid chromatography (HPLC) with UV absorbance detection. Based on the total amount of adenine recovered from DNA and RNA in these samples, we estimated bacterial cell counts ranging from approx. l0(exp 5) to l0(exp 9) E. coli cell equivalents per gram. For most of these samples, the sublimation based cell counts were in agreement with total bacterial counts obtained by traditional DAPI staining. The simplicity and robustness of the sublimation technique compared to the DAPI staining method makes this approach particularly attractive for use by spacecraft instrumentation. NASA is currently planning to send a lander to Mars in 2009 in order to assess whether or not organic compounds, especially those that might be associated with life, are present in Martian surface samples. Based on our analyses of the Atacama Desert soil samples, several million bacterial cells per gam of Martian soil should be detectable using this sublimation technique.

Woodstove Emission Sampling Methods Comparability Analysis and In-situ Evaluation of New Technology Woodstoves.

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

Simons, Carl A.

1988-06-01

One major objective of this study was to compare several woodstove particulate emission sampling methods under laboratory and in-situ conditions. The laboratory work compared the EPA Method 5H, EPA Method 5G, and OMNI Automated Woodstove Emission Sampler (AWES)/Data LOG'r particulate emission sampling systems. A second major objective of the study was to evaluate the performance of two integral catalytic, two low emission non-catalytic, and two conventional technology woodstoves under in-situ conditions with AWES/Data LOG'r system. The AWES/Data LOG'r and EPA Method 5G sampling systems were also compared in an in-situ test on one of the integral catalytic woodstove models. 7more » figs., 12 tabs.« less

METHOD DEVELOPMENT FOR THE DETERMINATION OF FORMALDEHYDE IN SAMPLES OF ENVIRONMENTAL ORIGIN

EPA Science Inventory

An analytical method was developed for the determination of formaldehyde in samples of environmental origin. After a review of the current literature, five candidate methods involving chemical derivatization were chosen for evaluation. The five derivatization reagents studied wer...

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.

Comparison of methods for determination of total oil sands-derived naphthenic acids in water samples.

PubMed

Hughes, Sarah A; Huang, Rongfu; Mahaffey, Ashley; Chelme-Ayala, Pamela; Klamerth, Nikolaus; Meshref, Mohamed N A; Ibrahim, Mohamed D; Brown, Christine; Peru, Kerry M; Headley, John V; Gamal El-Din, Mohamed

2017-11-01

There are several established methods for the determination of naphthenic acids (NAs) in waters associated with oil sands mining operations. Due to their highly complex nature, measured concentration and composition of NAs vary depending on the method used. This study compared different common sample preparation techniques, analytical instrument methods, and analytical standards to measure NAs in groundwater and process water samples collected from an active oil sands operation. In general, the high- and ultrahigh-resolution methods, namely high performance liquid chromatography time-of-flight mass spectrometry (UPLC-TOF-MS) and Orbitrap mass spectrometry (Orbitrap-MS), were within an order of magnitude of the Fourier transform infrared spectroscopy (FTIR) methods. The gas chromatography mass spectrometry (GC-MS) methods consistently had the highest NA concentrations and greatest standard error. Total NAs concentration was not statistically different between sample preparation of solid phase extraction and liquid-liquid extraction. Calibration standards influenced quantitation results. This work provided a comprehensive understanding of the inherent differences in the various techniques available to measure NAs and hence the potential differences in measured amounts of NAs in samples. Results from this study will contribute to the analytical method standardization for NA analysis in oil sands related water samples. Copyright © 2017 Elsevier Ltd. All rights reserved.

Simple Sodium Dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS-based Proteomic Applications

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

Zhou, Jianying; Dann, Geoffrey P.; Shi, Tujin

2012-03-10

Sodium dodecyl sulfate (SDS) is one of the most popular laboratory reagents used for highly efficient biological sample extraction; however, SDS presents a significant challenge to LC-MS-based proteomic analyses due to its severe interference with reversed-phase LC separations and electrospray ionization interfaces. This study reports a simple SDS-assisted proteomic sample preparation method facilitated by a novel peptide-level SDS removal protocol. After SDS-assisted protein extraction and digestion, SDS was effectively (>99.9%) removed from peptides through ion substitution-mediated DS- precipitation with potassium chloride (KCl) followed by {approx}10 min centrifugation. Excellent peptide recovery (>95%) was observed for less than 20 {mu}g of peptides.more » Further experiments demonstrated the compatibility of this protocol with LC-MS/MS analyses. The resulting proteome coverage from this SDS-assisted protocol was comparable to or better than those obtained from other standard proteomic preparation methods in both mammalian tissues and bacterial samples. These results suggest that this SDS-assisted protocol is a practical, simple, and broadly applicable proteomic sample processing method, which can be particularly useful when dealing with samples difficult to solubilize by other methods.« less

Well fluid isolation and sample apparatus and method

DOEpatents

Schalla, Ronald; Smith, Ronald M.; Hall, Stephen H.; Smart, John E.

1995-01-01

The present invention specifically permits purging and/or sampling of a well but only removing, at most, about 25% of the fluid volume compared to conventional methods and, at a minimum, removing none of the fluid volume from the well. The invention is an isolation assembly that is inserted into the well. The isolation assembly is designed so that only a volume of fluid between the outside diameter of the isolation assembly and the inside diameter of the well over a fluid column height from the bottom of the well to the top of the active portion (lower annulus) is removed. A seal may be positioned above the active portion thereby sealing the well and preventing any mixing or contamination of inlet fluid with fluid above the packer. Purged well fluid is stored in a riser above the packer. Ports in the wall of the isolation assembly permit purging and sampling of the lower annulus along the height of the active portion.

System and Method for Isolation of Samples

NASA Technical Reports Server (NTRS)

Zhang, Ye (Inventor); Wu, Honglu (Inventor)

2014-01-01

Systems and methods for isolating samples are provided. The system comprises a first membrane and a second membrane disposed within an enclosure. First and second reservoirs can also be disposed within the enclosure and adapted to contain one or more reagents therein. A first valve can be disposed within the enclosure and in fluid communication with the first reservoir, the second reservoir, or both. The first valve can also be in fluid communication with the first or second membranes or both. The first valve can be adapted to selectively regulate the flow of the reagents from the first reservoir, through at least one of the first and second membranes, and into the second reservoir.

Estimation of the sensitivity of various environmental sampling methods for detection of Salmonella in duck flocks.

PubMed

Arnold, Mark E; Mueller-Doblies, Doris; Gosling, Rebecca J; Martelli, Francesca; Davies, Robert H

2015-01-01

Reports of Salmonella in ducks in the UK currently rely upon voluntary submissions from the industry, and as there is no harmonized statutory monitoring and control programme, it is difficult to compare data from different years in order to evaluate any trends in Salmonella prevalence in relation to sampling methodology. Therefore, the aim of this project was to assess the sensitivity of a selection of environmental sampling methods, including the sampling of faeces, dust and water troughs or bowls for the detection of Salmonella in duck flocks, and a range of sampling methods were applied to 67 duck flocks. Bayesian methods in the absence of a gold standard were used to provide estimates of the sensitivity of each of the sampling methods relative to the within-flock prevalence. There was a large influence of the within-flock prevalence on the sensitivity of all sample types, with sensitivity reducing as the within-flock prevalence reduced. Boot swabs (individual and pool of four), swabs of faecally contaminated areas and whole house hand-held fabric swabs showed the overall highest sensitivity for low-prevalence flocks and are recommended for use to detect Salmonella in duck flocks. The sample type with the highest proportion positive was a pool of four hair nets used as boot swabs, but this was not the most sensitive sample for low-prevalence flocks. All the environmental sampling types (faeces swabs, litter pinches, drag swabs, water trough samples and dust) had higher sensitivity than individual faeces sampling. None of the methods consistently identified all the positive flocks, and at least 10 samples would be required for even the most sensitive method (pool of four boot swabs) to detect a 5% prevalence. The sampling of dust had a low sensitivity and is not recommended for ducks.

Comparison of indoor air sampling and dust collection methods for fungal exposure assessment using quantitative PCR.

PubMed

Cox, Jennie; Indugula, Reshmi; Vesper, Stephen; Zhu, Zheng; Jandarov, Roman; Reponen, Tiina

2017-10-18

Evaluating fungal contamination indoors is complicated because of the many different sampling methods utilized. In this study, fungal contamination was evaluated using five sampling methods and four matrices for results. The five sampling methods were a 48 hour indoor air sample collected with a Button™ inhalable aerosol sampler and four types of dust samples: a vacuumed floor dust sample, newly settled dust collected for four weeks onto two types of electrostatic dust cloths (EDCs) in trays, and a wipe sample of dust from above floor surfaces. The samples were obtained in the bedrooms of asthmatic children (n = 14). Quantitative polymerase chain reaction (qPCR) was used to analyze the dust and air samples for the 36 fungal species that make up the Environmental Relative Moldiness Index (ERMI). The results from the samples were compared by four matrices: total concentration of fungal cells, concentration of fungal species associated with indoor environments, concentration of fungal species associated with outdoor environments, and ERMI values (or ERMI-like values for air samples). The ERMI values for the dust samples and the ERMI-like values for the 48 hour air samples were not significantly different. The total cell concentrations of the 36 species obtained with the four dust collection methods correlated significantly (r = 0.64-0.79, p < 0.05), with the exception of the vacuumed floor dust and newly settled dust. In addition, fungal cell concentrations of indoor associated species correlated well between all four dust sampling methods (r = 0.68-0.86, p < 0.01). No correlation was found between the fungal concentrations in the air and dust samples primarily because of differences in concentrations of Cladosporium cladosporioides Type 1 and Epicoccum nigrum. A representative type of dust sample and a 48 hour air sample might both provide useful information about fungal exposures.

RAPID METHOD FOR DETERMINATION OF RADIOSTRONTIUM IN EMERGENCY MILK SAMPLES

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

Maxwell, S.; Culligan, B.

2008-07-17

A new rapid separation method for radiostrontium in emergency milk samples was developed at the Savannah River Site (SRS) Environmental Bioassay Laboratory (Aiken, SC, USA) that will allow rapid separation and measurement of Sr-90 within 8 hours. The new method uses calcium phosphate precipitation, nitric acid dissolution of the precipitate to coagulate residual fat/proteins and a rapid strontium separation using Sr Resin (Eichrom Technologies, Darien, IL, USA) with vacuum-assisted flow rates. The method is much faster than previous method that use calcination or cation exchange pretreatment, has excellent chemical recovery, and effectively removes beta interferences. When a 100 ml samplemore » aliquot is used, the method has a detection limit of 0.5 Bq/L, well below generic emergency action levels.« less

Component-based subspace linear discriminant analysis method for face recognition with one training sample

NASA Astrophysics Data System (ADS)

Huang, Jian; Yuen, Pong C.; Chen, Wen-Sheng; Lai, J. H.

2005-05-01

Many face recognition algorithms/systems have been developed in the last decade and excellent performances have also been reported when there is a sufficient number of representative training samples. In many real-life applications such as passport identification, only one well-controlled frontal sample image is available for training. Under this situation, the performance of existing algorithms will degrade dramatically or may not even be implemented. We propose a component-based linear discriminant analysis (LDA) method to solve the one training sample problem. The basic idea of the proposed method is to construct local facial feature component bunches by moving each local feature region in four directions. In this way, we not only generate more samples with lower dimension than the original image, but also consider the face detection localization error while training. After that, we propose a subspace LDA method, which is tailor-made for a small number of training samples, for the local feature projection to maximize the discrimination power. Theoretical analysis and experiment results show that our proposed subspace LDA is efficient and overcomes the limitations in existing LDA methods. Finally, we combine the contributions of each local component bunch with a weighted combination scheme to draw the recognition decision. A FERET database is used for evaluating the proposed method and results are encouraging.

A fast method for detecting Cryptosporidium parvum oocysts in real world samples

NASA Astrophysics Data System (ADS)

Stewart, Shona; McClelland, Lindy; Maier, John

2005-04-01

Contamination of drinking water with pathogenic microorganisms such as Cryptosporidium has become an increasing concern in recent years. Cryptosporidium oocysts are particularly problematic, as infections caused by this organism can be life threatening in immunocompromised patients. Current methods for monitoring and analyzing water are often laborious and require experts to conduct. In addition, many of the techniques require very specific reagents to be employed. These factors add considerable cost and time to the analytical process. Raman spectroscopy provides specific molecular information on samples, and offers advantages of speed, sensitivity and low cost over current methods of water monitoring. Raman spectroscopy is an optical method that has demonstrated the capability to identify and differentiate microorganisms at the species and strain levels. In addition, this technique has exhibited sensitivities down to the single organism detection limit. We have employed Raman spectroscopy and Raman Chemical Imaging, in conjunction with chemometric techniques, to detect small numbers of oocysts in the presence of interferents derived from real-world water samples. Our investigations have also indicated that Raman Chemical Imaging may provide chemical and physiological information about an oocyst sample which complements information provided by the traditional methods. This work provides evidence that Raman imaging is a useful technique for consideration in the water quality industry.

Generalized Likelihood Uncertainty Estimation (GLUE) Using Multi-Optimization Algorithm as Sampling Method

NASA Astrophysics Data System (ADS)

Wang, Z.

2015-12-01

For decades, distributed and lumped hydrological models have furthered our understanding of hydrological system. The development of hydrological simulation in large scale and high precision elaborated the spatial descriptions and hydrological behaviors. Meanwhile, the new trend is also followed by the increment of model complexity and number of parameters, which brings new challenges of uncertainty quantification. Generalized Likelihood Uncertainty Estimation (GLUE) has been widely used in uncertainty analysis for hydrological models referring to Monte Carlo method coupled with Bayesian estimation. However, the stochastic sampling method of prior parameters adopted by GLUE appears inefficient, especially in high dimensional parameter space. The heuristic optimization algorithms utilizing iterative evolution show better convergence speed and optimality-searching performance. In light of the features of heuristic optimization algorithms, this study adopted genetic algorithm, differential evolution, shuffled complex evolving algorithm to search the parameter space and obtain the parameter sets of large likelihoods. Based on the multi-algorithm sampling, hydrological model uncertainty analysis is conducted by the typical GLUE framework. To demonstrate the superiority of the new method, two hydrological models of different complexity are examined. The results shows the adaptive method tends to be efficient in sampling and effective in uncertainty analysis, providing an alternative path for uncertainty quantilization.

Method and apparatus for the preparation of liquid samples for determination of boron

DOEpatents

Siemer, D.D.

A method and apparatus are described for the preparation of a liquid sample for the quantitative determination of boron by flame photometry. The sample is combined in a vessel with sulfuric acid, and an excess of methanol is added thereto. The methanol reacts with any boron present in the sample to form trimethyl borate which is volatilized by the heat of reaction between the excess methanol and sulfuric acid. The volatilized trimethyl borate is withdrawn from the vessel by either a partial vacuum or a positive pressure and is rapidly transferred to a standard flame photometer. The method is free of interference from typical boron concomitants.

Method and apparatus for the preparation of liquid samples for determination of boron

DOEpatents

Siemer, Darryl D.

1986-01-01

A method and apparatus for the preparation of a liquid sample for the quantitative determination of boron by flame photometry. The sample is combined in a vessel with sulfuric acid, and an excess of methanol is added thereto. The methanol reacts with any boron present in the sample to form trimethyl borate which is volatilized by the heat of reaction between the excess methanol and sulfuric acid. The volatilized trimethyl borate is withdrawn from the vessel by either a partial vacuum or a positive pressure and is rapidly transferred to a standard flame photometer. The method is free of interference from typical boron concomitants.

Method and apparatus for the preparation of liquid samples for determination of boron

DOEpatents

Siemer, Darryl D.

1986-03-04

A method and apparatus for the preparation of a liquid sample for the quantitative determination of boron by flame photometry. The sample is combined in a vessel with sulfuric acid, and an excess of methanol is added thereto. The methanol reacts with any boron present in the sample to form trimethyl borate which is volatilized by the heat of reaction between the excess methanol and sulfuric acid. The volatilized trimethyl borate is withdrawn from the vessel by either a partial vacuum or a positive pressure and is rapidly transferred to a standard flame photometer. The method is free of interference from typical boron concomitants.

Methods for point-of-care detection of nucleic acid in a sample

DOEpatents

Bearinger, Jane P.; Dugan, Lawrence C.

2015-12-29

Provided herein are methods and apparatus for detecting a target nucleic acid in a sample and related methods and apparatus for diagnosing a condition in an individual. The condition is associated with presence of nucleic acid produced by certain pathogens in the individual.

Novel joint selection methods can reduce sample size for rheumatoid arthritis clinical trials with ultrasound endpoints.

PubMed

Allen, John C; Thumboo, Julian; Lye, Weng Kit; Conaghan, Philip G; Chew, Li-Ching; Tan, York Kiat

2018-03-01

To determine whether novel methods of selecting joints through (i) ultrasonography (individualized-ultrasound [IUS] method), or (ii) ultrasonography and clinical examination (individualized-composite-ultrasound [ICUS] method) translate into smaller rheumatoid arthritis (RA) clinical trial sample sizes when compared to existing methods utilizing predetermined joint sites for ultrasonography. Cohen's effect size (ES) was estimated (ES^) and a 95% CI (ES^L, ES^U) calculated on a mean change in 3-month total inflammatory score for each method. Corresponding 95% CIs [nL(ES^U), nU(ES^L)] were obtained on a post hoc sample size reflecting the uncertainty in ES^. Sample size calculations were based on a one-sample t-test as the patient numbers needed to provide 80% power at α = 0.05 to reject a null hypothesis H 0 : ES = 0 versus alternative hypotheses H 1 : ES = ES^, ES = ES^L and ES = ES^U. We aimed to provide point and interval estimates on projected sample sizes for future studies reflecting the uncertainty in our study ES^S. Twenty-four treated RA patients were followed up for 3 months. Utilizing the 12-joint approach and existing methods, the post hoc sample size (95% CI) was 22 (10-245). Corresponding sample sizes using ICUS and IUS were 11 (7-40) and 11 (6-38), respectively. Utilizing a seven-joint approach, the corresponding sample sizes using ICUS and IUS methods were nine (6-24) and 11 (6-35), respectively. Our pilot study suggests that sample size for RA clinical trials with ultrasound endpoints may be reduced using the novel methods, providing justification for larger studies to confirm these observations. © 2017 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd.

Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods.

PubMed

Abella, Jayvee R; Moll, Mark; Kavraki, Lydia E

2018-01-01

The ability to efficiently sample structurally diverse protein conformations allows one to gain a high-level view of a protein's energy landscape. Algorithms from robot motion planning have been used for conformational sampling, and several of these algorithms promote diversity by keeping track of "coverage" in conformational space based on the local sampling density. However, large proteins present special challenges. In particular, larger systems require running many concurrent instances of these algorithms, but these algorithms can quickly become memory intensive because they typically keep previously sampled conformations in memory to maintain coverage estimates. In addition, robotics-inspired algorithms depend on defining useful perturbation strategies for exploring the conformational space, which is a difficult task for large proteins because such systems are typically more constrained and exhibit complex motions. In this article, we introduce two methodologies for maintaining and enhancing diversity in robotics-inspired conformational sampling. The first method addresses algorithms based on coverage estimates and leverages the use of a low-dimensional projection to define a global coverage grid that maintains coverage across concurrent runs of sampling. The second method is an automatic definition of a perturbation strategy through readily available flexibility information derived from B-factors, secondary structure, and rigidity analysis. Our results show a significant increase in the diversity of the conformations sampled for proteins consisting of up to 500 residues when applied to a specific robotics-inspired algorithm for conformational sampling. The methodologies presented in this article may be vital components for the scalability of robotics-inspired approaches.

Shear wave speed estimation by adaptive random sample consensus method.

PubMed

Lin, Haoming; Wang, Tianfu; Chen, Siping

2014-01-01

This paper describes a new method for shear wave velocity estimation that is capable of extruding outliers automatically without preset threshold. The proposed method is an adaptive random sample consensus (ARANDSAC) and the metric used here is finding the certain percentage of inliers according to the closest distance criterion. To evaluate the method, the simulation and phantom experiment results were compared using linear regression with all points (LRWAP) and radon sum transform (RS) method. The assessment reveals that the relative biases of mean estimation are 20.00%, 4.67% and 5.33% for LRWAP, ARANDSAC and RS respectively for simulation, 23.53%, 4.08% and 1.08% for phantom experiment. The results suggested that the proposed ARANDSAC algorithm is accurate in shear wave speed estimation.

Effect of DNA extraction and sample preservation method on rumen bacterial population.

PubMed

Fliegerova, Katerina; Tapio, Ilma; Bonin, Aurelie; Mrazek, Jakub; Callegari, Maria Luisa; Bani, Paolo; Bayat, Alireza; Vilkki, Johanna; Kopečný, Jan; Shingfield, Kevin J; Boyer, Frederic; Coissac, Eric; Taberlet, Pierre; Wallace, R John

2014-10-01

The comparison of the bacterial profile of intracellular (iDNA) and extracellular DNA (eDNA) isolated from cow rumen content stored under different conditions was conducted. The influence of rumen fluid treatment (cheesecloth squeezed, centrifuged, filtered), storage temperature (RT, -80 °C) and cryoprotectants (PBS-glycerol, ethanol) on quality and quantity parameters of extracted DNA was evaluated by bacterial DGGE analysis, real-time PCR quantification and metabarcoding approach using high-throughput sequencing. Samples clustered according to the type of extracted DNA due to considerable differences between iDNA and eDNA bacterial profiles, while storage temperature and cryoprotectants additives had little effect on sample clustering. The numbers of Firmicutes and Bacteroidetes were lower (P < 0.01) in eDNA samples. The qPCR indicated significantly higher amount of Firmicutes in iDNA sample frozen with glycerol (P < 0.01). Deep sequencing analysis of iDNA samples revealed the prevalence of Bacteroidetes and similarity of samples frozen with and without cryoprotectants, which differed from sample stored with ethanol at room temperature. Centrifugation and consequent filtration of rumen fluid subjected to the eDNA isolation procedure considerably changed the ratio of molecular operational taxonomic units (MOTUs) of Bacteroidetes and Firmicutes. Intracellular DNA extraction using bead-beating method from cheesecloth sieved rumen content mixed with PBS-glycerol and stored at -80 °C was found as the optimal method to study ruminal bacterial profile. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

PubMed

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

2018-04-01

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

Rapid-Viability PCR Method for Detection of Live, Virulent Bacillus anthracis in Environmental Samples ▿

PubMed Central

Létant, Sonia E.; Murphy, Gloria A.; Alfaro, Teneile M.; Avila, Julie R.; Kane, Staci R.; Raber, Ellen; Bunt, Thomas M.; Shah, Sanjiv R.

2011-01-01

In the event of a biothreat agent release, hundreds of samples would need to be rapidly processed to characterize the extent of contamination and determine the efficacy of remediation activities. Current biological agent identification and viability determination methods are both labor- and time-intensive such that turnaround time for confirmed results is typically several days. In order to alleviate this issue, automated, high-throughput sample processing methods were developed in which real-time PCR analysis is conducted on samples before and after incubation. The method, referred to as rapid-viability (RV)-PCR, uses the change in cycle threshold after incubation to detect the presence of live organisms. In this article, we report a novel RV-PCR method for detection of live, virulent Bacillus anthracis, in which the incubation time was reduced from 14 h to 9 h, bringing the total turnaround time for results below 15 h. The method incorporates a magnetic bead-based DNA extraction and purification step prior to PCR analysis, as well as specific real-time PCR assays for the B. anthracis chromosome and pXO1 and pXO2 plasmids. A single laboratory verification of the optimized method applied to the detection of virulent B. anthracis in environmental samples was conducted and showed a detection level of 10 to 99 CFU/sample with both manual and automated RV-PCR methods in the presence of various challenges. Experiments exploring the relationship between the incubation time and the limit of detection suggest that the method could be further shortened by an additional 2 to 3 h for relatively clean samples. PMID:21764960

Experience-Sampling Research Methods and Their Potential for Education Research

ERIC Educational Resources Information Center

Zirkel, Sabrina; Garcia, Julie A.; Murphy, Mary C.

2015-01-01

Experience-sampling methods (ESM) enable us to learn about individuals' lives in context by measuring participants' feelings, thoughts, actions, context, and/or activities as they go about their daily lives. By capturing experience, affect, and action "in the moment" and with repeated measures, ESM approaches allow researchers…

A unified method to process biosolids samples for the recovery of bacterial, viral, and helminths pathogens.

PubMed

Alum, Absar; Rock, Channah; Abbaszadegan, Morteza

2014-01-01

For land application, biosolids are classified as Class A or Class B based on the levels of bacterial, viral, and helminths pathogens in residual biosolids. The current EPA methods for the detection of these groups of pathogens in biosolids include discrete steps. Therefore, a separate sample is processed independently to quantify the number of each group of the pathogens in biosolids. The aim of the study was to develop a unified method for simultaneous processing of a single biosolids sample to recover bacterial, viral, and helminths pathogens. At the first stage for developing a simultaneous method, nine eluents were compared for their efficiency to recover viruses from a 100 gm spiked biosolids sample. In the second stage, the three top performing eluents were thoroughly evaluated for the recovery of bacteria, viruses, and helminthes. For all three groups of pathogens, the glycine-based eluent provided higher recovery than the beef extract-based eluent. Additional experiments were performed to optimize performance of glycine-based eluent under various procedural factors such as, solids to eluent ratio, stir time, and centrifugation conditions. Last, the new method was directly compared with the EPA methods for the recovery of the three groups of pathogens spiked in duplicate samples of biosolids collected from different sources. For viruses, the new method yielded up to 10% higher recoveries than the EPA method. For bacteria and helminths, recoveries were 74% and 83% by the new method compared to 34% and 68% by the EPA method, respectively. The unified sample processing method significantly reduces the time required for processing biosolids samples for different groups of pathogens; it is less impacted by the intrinsic variability of samples, while providing higher yields (P = 0.05) and greater consistency than the current EPA methods.

An atomic-absorption method for the determination of gold in large samples of geologic materials

USGS Publications Warehouse

VanSickle, Gordon H.; Lakin, Hubert William

1968-01-01

A laboratory method for the determination of gold in large (100-gram) samples has been developed for use in the study of the gold content of placer deposits and of trace amounts of gold in other geologic materials. In this method the sample is digested with bromine and ethyl ether, the gold is extracted into methyl isobutyl ketone, and the determination is made by atomicabsorption spectrophotometry. The lower limit of detection is 0.005 part per million in the sample. The few data obtained so far by this method agree favorably with those obtained by assay and by other atomic-absorption methods. About 25 determinations can be made per man-day.

Lipidomic analysis of biological samples: Comparison of liquid chromatography, supercritical fluid chromatography and direct infusion mass spectrometry methods.

PubMed

Lísa, Miroslav; Cífková, Eva; Khalikova, Maria; Ovčačíková, Magdaléna; Holčapek, Michal

2017-11-24

Lipidomic analysis of biological samples in a clinical research represents challenging task for analytical methods given by the large number of samples and their extreme complexity. In this work, we compare direct infusion (DI) and chromatography - mass spectrometry (MS) lipidomic approaches represented by three analytical methods in terms of comprehensiveness, sample throughput, and validation results for the lipidomic analysis of biological samples represented by tumor tissue, surrounding normal tissue, plasma, and erythrocytes of kidney cancer patients. Methods are compared in one laboratory using the identical analytical protocol to ensure comparable conditions. Ultrahigh-performance liquid chromatography/MS (UHPLC/MS) method in hydrophilic interaction liquid chromatography mode and DI-MS method are used for this comparison as the most widely used methods for the lipidomic analysis together with ultrahigh-performance supercritical fluid chromatography/MS (UHPSFC/MS) method showing promising results in metabolomics analyses. The nontargeted analysis of pooled samples is performed using all tested methods and 610 lipid species within 23 lipid classes are identified. DI method provides the most comprehensive results due to identification of some polar lipid classes, which are not identified by UHPLC and UHPSFC methods. On the other hand, UHPSFC method provides an excellent sensitivity for less polar lipid classes and the highest sample throughput within 10min method time. The sample consumption of DI method is 125 times higher than for other methods, while only 40μL of organic solvent is used for one sample analysis compared to 3.5mL and 4.9mL in case of UHPLC and UHPSFC methods, respectively. Methods are validated for the quantitative lipidomic analysis of plasma samples with one internal standard for each lipid class. Results show applicability of all tested methods for the lipidomic analysis of biological samples depending on the analysis requirements