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

PubMed

Elliott, Paul; Peakman, Tim C

2008-04-01

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

Nucleic acid amplification of HIV-1 integrase sequence subtypes CRF01_AE and B for development of HIV anti-integrase drug resistance genotyping assay

NASA Astrophysics Data System (ADS)

Adlar, F. R.; Bela, B.

2017-08-01

To anticipate the potential use of anti-integrase drugs in Indonesia for treatment of HIV-1 infection, the development of a drug resistance genotyping assay for anti-integrase is crucial in identifying the genetic drug resistance profile of Indonesian HIV-1 strains. This experiment aimed to amplify a target region in the integrase gene of Indonesian HIV-1 subtypes CRF01_AE and B that contain genetic mutations known to confer resistance to anti-integrase drug. Eleven archived plasma samples from individuals living with HIV-1 were obtained from the Virology and Cancer Pathobiology Research Center for Health Service (VCPRC FKUI-RSCM) laboratory. One of the plasma samples contained HIV-1 subtype B, and the remaining plasma samples contained subtype CRF01_AE. The target regions for all samples were amplified through RT-PCR, with an annealing temperature of 55 °C, using the primer pair AE_POL 4086F and AE_POL 5232R that were designed by VCPRC FKUI-RSCM. The results of this experiment show that 18.2% (2/11) of the samples were successfully amplified using the one-step RT-PCR. While the primer pair was effective in amplifying the target region in the integrase gene sequence for subtype B (100%; 1/1), it had a low efficacy (10%, 1/10) for subtype CRF01_AE. In conclusion, the primer pair can be used to amplify the target region in Indonesian HIV-1 strain subtypes CRF01_AE and B. However, optimization of the PCR condition and an increased number of samples would help to determine an accurate representation of the efficacy of the primer pair.

PCB Analysis Plan for Tank Archive Samples

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

NGUYEN, D.M.

2001-03-22

This analysis plan specifies laboratory analysis, quality assurance/quality control (QA/QC), and data reporting requirements for analyzing polychlorinated biphenyls (PCB) concentrations in archive samples. Tank waste archive samples that are planned for PCB analysis are identified in Nguyen 2001. The tanks and samples are summarized in Table 1-1. The analytical data will be used to establish a PCB baseline inventory in Hanford tanks.

Space plasma physics research

NASA Technical Reports Server (NTRS)

Comfort, Richard H.; Horwitz, James L.

1993-01-01

During the course of this grant, work was performed on a variety of topics and there were a number of significant accomplishments. A summary of these accomplishments is included. The topics studied include empirical model data base, data reduction for archiving, semikinetic modeling of low energy plasma in the inner terrestrial magnetosphere and ionosphere, O(+) outflows, equatorial plasma trough, and plasma wave ray-tracing studies. A list of publications and presentations which have resulted from this research is also included.

Plasma processing conditions substantially influence circulating microRNA biomarker levels.

PubMed

Cheng, Heather H; Yi, Hye Son; Kim, Yeonju; Kroh, Evan M; Chien, Jason W; Eaton, Keith D; Goodman, Marc T; Tait, Jonathan F; Tewari, Muneesh; Pritchard, Colin C

2013-01-01

Circulating, cell-free microRNAs (miRNAs) are promising candidate biomarkers, but optimal conditions for processing blood specimens for miRNA measurement remain to be established. Our previous work showed that the majority of plasma miRNAs are likely blood cell-derived. In the course of profiling lung cancer cases versus healthy controls, we observed a broad increase in circulating miRNA levels in cases compared to controls and that higher miRNA expression correlated with higher platelet and particle counts. We therefore hypothesized that the quantity of residual platelets and microparticles remaining after plasma processing might impact miRNA measurements. To systematically investigate this, we subjected matched plasma from healthy individuals to stepwise processing with differential centrifugation and 0.22 µm filtration and performed miRNA profiling. We found a major effect on circulating miRNAs, with the majority (72%) of detectable miRNAs substantially affected by processing alone. Specifically, 10% of miRNAs showed 4-30x variation, 46% showed 30-1,000x variation, and 15% showed >1,000x variation in expression solely from processing. This was predominantly due to platelet contamination, which persisted despite using standard laboratory protocols. Importantly, we show that platelet contamination in archived samples could largely be eliminated by additional centrifugation, even in frozen samples stored for six years. To minimize confounding effects in microRNA biomarker studies, additional steps to limit platelet contamination for circulating miRNA biomarker studies are necessary. We provide specific practical recommendations to help minimize confounding variation attributable to plasma processing and platelet contamination.

Evaluation of the Aptima HIV-1 Quant Dx Assay Using Plasma and Dried Blood Spots

PubMed Central

Sahoo, Malaya K.; Varghese, Vici; White, Elizabeth; Winslow, Meg; Katzenstein, David A.; Shafer, Robert W.

2016-01-01

HIV-1 RNA quantitation in plasma, or virus load testing, is the primary method by which the response to antiretroviral therapy is monitored. Here we describe evaluation of the Aptima HIV-1 Quant Dx assay (Aptima) performed on the automated Panther system. The clinical performance of Aptima was compared to that of the Cobas AmpliPrep/Cobas TaqMan HIV-1 Test v2.0 (CAP/CTM) using 162 EDTA plasma samples collected from patients undergoing HIV-1 monitoring. Overall agreement was 84.0% (136/162), with a kappa statistic of 0.723 (standard error, 0.047; 95% confidence interval [CI], 0.630 to 0.815), indicating substantial agreement. Using the 86 clinical samples quantifiable by both methods, Passing-Bablok regression revealed a regression line of Y = (1.069 × X) − 0.346 (95% CI of the slope [1.003 to 1.139] and intercept [−0.666 to −0.074]), and Bland-Altman analysis demonstrated a mean difference (Aptima-CAP/CTM) of −0.075 log10 copies/ml (95% limits of agreement of −0.624 to 0.475), consistent with negative bias. Comparison of Aptima results for paired dried blood spot (DBS) and plasma specimens archived from participants in the Peninsula AIDS Research Cohort Study (PARC) demonstrated an overall agreement of 94.7% (90/95) when 1,000 copies/ml was used as the threshold. In conclusion, the Aptima HIV-1 Quant Dx assay provides a suitable alternative for HIV-1 monitoring in plasma and DBS. PMID:27535684

Evaluation of the Aptima HIV-1 Quant Dx Assay Using Plasma and Dried Blood Spots.

PubMed

Sahoo, Malaya K; Varghese, Vici; White, Elizabeth; Winslow, Meg; Katzenstein, David A; Shafer, Robert W; Pinsky, Benjamin A

2016-10-01

HIV-1 RNA quantitation in plasma, or virus load testing, is the primary method by which the response to antiretroviral therapy is monitored. Here we describe evaluation of the Aptima HIV-1 Quant Dx assay (Aptima) performed on the automated Panther system. The clinical performance of Aptima was compared to that of the Cobas AmpliPrep/Cobas TaqMan HIV-1 Test v2.0 (CAP/CTM) using 162 EDTA plasma samples collected from patients undergoing HIV-1 monitoring. Overall agreement was 84.0% (136/162), with a kappa statistic of 0.723 (standard error, 0.047; 95% confidence interval [CI], 0.630 to 0.815), indicating substantial agreement. Using the 86 clinical samples quantifiable by both methods, Passing-Bablok regression revealed a regression line of Y = (1.069 × X) - 0.346 (95% CI of the slope [1.003 to 1.139] and intercept [-0.666 to -0.074]), and Bland-Altman analysis demonstrated a mean difference (Aptima-CAP/CTM) of -0.075 log10 copies/ml (95% limits of agreement of -0.624 to 0.475), consistent with negative bias. Comparison of Aptima results for paired dried blood spot (DBS) and plasma specimens archived from participants in the Peninsula AIDS Research Cohort Study (PARC) demonstrated an overall agreement of 94.7% (90/95) when 1,000 copies/ml was used as the threshold. In conclusion, the Aptima HIV-1 Quant Dx assay provides a suitable alternative for HIV-1 monitoring in plasma and DBS. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Comparative study on decontamination treatment of paper-based materials in corona discharge and HF cold plasma

NASA Astrophysics Data System (ADS)

Ioanid, E. G.; Dunca, S.; Rusu, D.; Tǎnase, C.

2012-04-01

Documents decontamination using dry methods, less invasive than the wet ones implying toxic nocuous substances for cellulose-based materials, has been the object of numerous studies. In recent years mixed researchers teams have been studying the possibility of one-step document decontamination performed by a dry treatment, the risks of repeated wet manipulation thus being reduced. Among physical methods appropriate to this end, high-frequency cold plasma and corona effect can be mentioned. Our studies were carried out on samples taken from ancient books with no cultural heritage value. The decontamination efficiency and the impact on paper of the two types of treatments were determined by: microbiological analysis, scanning electron microscopy, FTIR, chromatic alterations and gloss determination. The above-mentioned procedures eliminate the use of chemical conservation substances, nocuous for the paper support. At the same time the health risk for conservators, restorers, archivists or archive's users is removed.

Dose-Response Analysis of RNA-Seq Profiles in Archival ...

EPA Pesticide Factsheets

Use of archival resources has been limited to date by inconsistent methods for genomic profiling of degraded RNA from formalin-fixed paraffin-embedded (FFPE) samples. RNA-sequencing offers a promising way to address this problem. Here we evaluated transcriptomic dose responses using RNA-sequencing in paired FFPE and frozen (FROZ) samples from two archival studies in mice, one 20 years old. Experimental treatments included 3 different doses of di(2-ethylhexyl)phthalate or dichloroacetic acid for the recently archived and older studies, respectively. Total RNA was ribo-depleted and sequenced using the Illumina HiSeq platform. In the recently archived study, FFPE samples had 35% lower total counts compared to FROZ samples but high concordance in fold-change values of differentially expressed genes (DEGs) (r2 = 0.99), highly enriched pathways (90% overlap with FROZ), and benchmark dose estimates for preselected target genes (2% difference vs FROZ). In contrast, older FFPE samples had markedly lower total counts (3% of FROZ) and poor concordance in global DEGs and pathways. However, counts from FFPE and FROZ samples still positively correlated (r2 = 0.84 across all transcripts) and showed comparable dose responses for more highly expressed target genes. These findings highlight potential applications and issues in using RNA-sequencing data from FFPE samples. Recently archived FFPE samples were highly similar to FROZ samples in sequencing q

Freezer anthropology: new uses for old blood.

PubMed Central

Merriwether, D A

1999-01-01

Archived blood fractions (plasma, settled red cells, white cells) have proved to be a rich and valuable source of DNA for human genetic studies. Large numbers of such samples were collected between 1960 and the present for protein and blood group studies, many of which are languishing in freezers or have already been discarded. More are discarded each year because the usefulness of these samples is not widely understood. Data from DNA derived from 10-35-year-old blood samples have been used to address the peopling of the New World and of the Pacific. Mitochondrial DNA haplotypes from studies using this source DNA support a single wave of migration into the New World (or a single source population for the New World), and that Mongolia was the likely source of the founding population. Data from Melanesia have shown that Polynesians are recent immigrants into the Pacific and did not arise from Melanesia. PMID:10091252

Interactive Plasma Physics Education Using Data from Fusion Experiments

NASA Astrophysics Data System (ADS)

Calderon, Brisa; Davis, Bill; Zwicker, Andrew

2010-11-01

The Internet Plasma Physics Education Experience (IPPEX) website was created in 1996 to give users access to data from plasma and fusion experiments. Interactive material on electricity, magnetism, matter, and energy was presented to generate interest and prepare users to understand data from a fusion experiment. Initially, users were allowed to analyze real-time and archival data from the Tokamak Fusion Test Reactor (TFTR) experiment. IPPEX won numerous awards for its novel approach of allowing users to participate in ongoing research. However, the latest revisions of IPPEX were in 2001 and the interactive material is no longer functional on modern browsers. Also, access to real-time data was lost when TFTR was shut down. The interactive material on IPPEX is being rewritten in ActionScript3.0, and real-time and archival data from the National Spherical Tokamak Experiment (NSTX) will be made available to users. New tools like EFIT animations, fast cameras, and plots of important plasma parameters will be included along with an existing Java-based ``virtual tokamak.'' Screenshots from the upgraded website and future directions will be presented.

Analysis of data from the plasma composition experiment on the International Sun-Earth Explorer (ISEE 1)

NASA Technical Reports Server (NTRS)

Lennartsson, O. W.

1994-01-01

The Lockheed plasma composition experiment on the ISEE 1 spacecraft has provided one of the largest and most varied sets of data on earth's energetic plasma environment, covering both the solar wind, well beyond the bow shock, and the near equatorial magnetosphere to a distance of almost 23 earth radii. This report is an overview of the last four years of data analysis and archiving. The archiving for NSSDC includes most data obtained during the initial 28-months of instrument operation, from early November 1977 through the end of February 1980. The data products are a combination of spectra (mass and energy angle) and velocity moments. A copy of the data user's guide and examples of the data products are attached as appendix A. The data analysis covers three major areas: solar wind ions upstream and downstream of the day side bowshock, especially He(++) ions; terrestrial ions flowing upward from the auroral regions, especially H(+), O(+), and He(+) ions; and ions of both solar and terrestrial origins in the tail plasma sheet and lobe regions. Copies of publications are attached.

PERFLUORINATED COMPOUNDS IN ARCHIVED HOUSE-DUST SAMPLES

EPA Science Inventory

Archived house-dust samples were analyzed for 13 perfluorinated compounds (PFCs). Results show that PFCs are found in house-dust samples, and the data are log-normally distributed. PFOS/PFOA were present in 94.6% and 96.4% of the samples respectively. Concentrations ranged fro...

Coupling meteorology, metal concentrations, and Pb isotopes for source attribution in archived precipitation samples.

PubMed

Graney, Joseph R; Landis, Matthew S

2013-03-15

A technique that couples lead (Pb) isotopes and multi-element concentrations with meteorological analysis was used to assess source contributions to precipitation samples at the Bondville, Illinois USA National Trends Network (NTN) site. Precipitation samples collected over a 16month period (July 1994-October 1995) at Bondville were parsed into six unique meteorological flow regimes using a minimum variance clustering technique on back trajectory endpoints. Pb isotope ratios and multi-element concentrations were measured using high resolution inductively coupled plasma-sector field mass spectrometry (ICP-SFMS) on the archived precipitation samples. Bondville is located in central Illinois, ~250km downwind from smelters in southeast Missouri. The Mississippi Valley Type ore deposits in Missouri provided a unique multi-element and Pb isotope fingerprint for smelter emissions which could be contrasted to industrial emissions from the Chicago and Indianapolis urban areas (~125km north and east, of Bondville respectively) and regional emissions from electric utility facilities. Differences in Pb isotopes and element concentrations in precipitation corresponded to flow regime. Industrial sources from urban areas, and thorogenic Pb from coal use, could be differentiated from smelter emissions from Missouri by coupling Pb isotopes with variations in element ratios and relative mass factors. Using a three endmember mixing model based on Pb isotope ratio differences, industrial processes in urban airsheds contributed 56±19%, smelters in southeast Missouri 26±13%, and coal combustion 18±7%, of the Pb in precipitation collected in Bondville in the mid-1990s. Copyright © 2012 Elsevier B.V. All rights reserved.

An Optimized DNA Analysis Workflow for the Sampling, Extraction, and Concentration of DNA obtained from Archived Latent Fingerprints.

PubMed

Solomon, April D; Hytinen, Madison E; McClain, Aryn M; Miller, Marilyn T; Dawson Cruz, Tracey

2018-01-01

DNA profiles have been obtained from fingerprints, but there is limited knowledge regarding DNA analysis from archived latent fingerprints-touch DNA "sandwiched" between adhesive and paper. Thus, this study sought to comparatively analyze a variety of collection and analytical methods in an effort to seek an optimized workflow for this specific sample type. Untreated and treated archived latent fingerprints were utilized to compare different biological sampling techniques, swab diluents, DNA extraction systems, DNA concentration practices, and post-amplification purification methods. Archived latent fingerprints disassembled and sampled via direct cutting, followed by DNA extracted using the QIAamp® DNA Investigator Kit, and concentration with Centri-Sep™ columns increased the odds of obtaining an STR profile. Using the recommended DNA workflow, 9 of the 10 samples provided STR profiles, which included 7-100% of the expected STR alleles and two full profiles. Thus, with carefully selected procedures, archived latent fingerprints can be a viable DNA source for criminal investigations including cold/postconviction cases. © 2017 American Academy of Forensic Sciences.

Restoration and PDS Archive of Apollo Lunar Rock Sample Data

NASA Technical Reports Server (NTRS)

Garcia, P. A.; Todd, N. S.; Lofgren, G. E.; Stefanov, W. L.; Runco, S. K.; LaBasse, D.; Gaddis, L. R.

2011-01-01

In 2008, scientists at the Johnson Space Center (JSC) Lunar Sample Laboratory and Image Science & Analysis Laboratory (under the auspices of the Astromaterials Research and Exploration Science Directorate or ARES) began work on a 4-year project to digitize the original film negatives of Apollo Lunar Rock Sample photographs. These rock samples together with lunar regolith and core samples were collected as part of the lander missions for Apollos 11, 12, 14, 15, 16 and 17. The original film negatives are stored at JSC under cryogenic conditions. This effort is data restoration in the truest sense. The images represent the only record available to scientists which allows them to view the rock samples when making a sample request. As the negatives are being scanned, they are also being formatted and documented for permanent archive in the NASA Planetary Data System (PDS) archive. The ARES group is working collaboratively with the Imaging Node of the PDS on the archiving.

Kinetic modeling of storage effects on biomarkers related to B vitamin status and one-carbon metabolism.

PubMed

Hustad, Steinar; Eussen, Simone; Midttun, Øivind; Ulvik, Arve; van de Kant, Puck M; Mørkrid, Lars; Gislefoss, Randi; Ueland, Per M

2012-02-01

Biomarkers and metabolites related to B vitamin function and one-carbon metabolism have been studied as predictors of chronic diseases in studies based on samples stored in biobanks. For most biomarkers, stability data are lacking or fragmentary. Degradation and accumulation kinetics of 32 biomarkers were determined at 23 °C in serum and plasma (EDTA, heparin, and citrate) collected from 16 individuals and stored for up to 8 days. In frozen serum (-25 °C), stability was studied cross-sectionally in 650 archival samples stored for up to 29 years. Concentration vs time curves were fitted to monoexponential, biexponential, linear, and nonlinear models. For many biomarkers, stability was highest in EDTA plasma. Storage effects were similar at room temperature and at -25 °C; notable exceptions were methionine, which could be recovered as methionine sulfoxide, and cystathionine, which decreased in frozen samples. Cobalamin, betaine, dimethylglycine, sarcosine, total homocysteine, total cysteine, tryptophan, asymetric and symmetric dimethyl argenine, creatinine, and methylmalonic acid were essentially stable under all conditions. Most B vitamins (folate and vitamins B2 and B6) were unstable; choline increased markedly, and some amino acids also increased, particularly in serum. The kynurenines showed variable stability. For many biomarkers, degradation (folate and flavin mononucleotide) or accumulation (pyridoxal, riboflavin, choline, amino acids) kinetics at room temperature were non-first order. Data on stability and deterioration kinetics for individual biomarkers are required to optimize procedures for handling serum and plasma, and for addressing preanalytical bias in epidemiological and clinical studies.

A Systematic Study of Kelvin-Helmholtz Instability in Galaxy Clusters

NASA Astrophysics Data System (ADS)

Su, Yuanyuan

2017-09-01

Kelvin-Helmholtz instabilities (KHI) were observed at cold fronts in a handful of clusters. KHI are predicted at all cold fronts in hydro simulation of intracluster medium (ICM). Their presence and absence provides a unique probe of transport processes in the hot plasma, which are essential to the dissipation and redistribution of the energy in the ICM. We propose the first systematic study of the prevalence of KHI in galaxy clusters by analyzing the archived Chandra observations of a sample of 50 nearby galaxy clusters. We will associate the occurrence and properties of KHI rolls with various cluster parameters such as their gas temperature and density, and put constraints on effective transport coefficients in the ICM

Archiving Microgravity Flight Data and Samples

NASA Technical Reports Server (NTRS)

1996-01-01

To obtain help in evaluating its current strategy for archiving data and samples obtained in microgravity research, NASA's Microgravity Science and Applications Division (MSAD) asked the Space Studies Board's Committee on Microgravity Research for guidance on the following questions: What data should be archived and where should it be kept? In what form should the data be maintained (electronic files, photographs, hard copy, samples)? What should the general format of the database be? To what extent should it be universally accessible and through what mechanisms? Should there be a period of time for which principal investigators have proprietary access? If so, how long should proprietary data be stored? What provisions should be made for data obtained from ground-based experiments? What should the deadline be for investigators placing their data in the archive? How long should data be saved? How long should data be easily accessible? As a prelude to making recommendations for optimum selection and storage of microgravity data and samples, the committee in this report briefly describes NASA's past archiving practices and outlines MSAD's current archiving strategy. Although the committee found that only a limited number of experiments have thus far been archived, it concluded that the general archiving strategy, characterized by MSAD as minimalist, appears viable. A central focus of attention is the Experiment Data Management Plan (EDMP), MSAD's recently instituted data management and archiving framework for flight experiments. Many of the report's recommendations are aimed at enhancing the effectiveness of the EDMP approach, which the committee regards as an appropriate data management method for MSAD. Other recommendations provide guidance on broader issues related to the questions listed above. This report does not address statutory or regulatory records retention requirements.

Publications - GMC 407 | Alaska Division of Geological & Geophysical

Science.gov Websites

locations, and archive inventory for 32 near-shore marine sediment Vibracore samples, West Dock Causeway , Drilling procedures, sample descriptions, boring logs, borehole locations, and archive inventory for 32

PDS Archive Release of Apollo 11, Apollo 12, and Apollo 17 Lunar Rock Sample Images

NASA Technical Reports Server (NTRS)

Garcia, P. A.; Stefanov, W. L.; Lofgren, G. E.; Todd, N. S.; Gaddis, L. R.

2013-01-01

Scientists at the Johnson Space Center (JSC) Lunar Sample Laboratory, Information Resources Directorate, and Image Science & Analysis Laboratory have been working to digitize (scan) the original film negatives of Apollo Lunar Rock Sample photographs [1, 2]. The rock samples, and associated regolith and lunar core samples, were obtained during the Apollo 11, 12, 14, 15, 16 and 17 missions. The images allow scientists to view the individual rock samples in their original or subdivided state prior to requesting physical samples for their research. In cases where access to the actual physical samples is not practical, the images provide an alternate mechanism for study of the subject samples. As the negatives are being scanned, they have been formatted and documented for permanent archive in the NASA Planetary Data System (PDS). The Astromaterials Research and Exploration Science Directorate (which includes the Lunar Sample Laboratory and Image Science & Analysis Laboratory) at JSC is working collaboratively with the Imaging Node of the PDS on the archiving of these valuable data. The PDS Imaging Node is now pleased to announce the release of the image archives for Apollo missions 11, 12, and 17.

Plasma levels of selenium-containing proteins in Inuit adults from Nunavik.

PubMed

Achouba, Adel; Dumas, Pierre; Ouellet, Nathalie; Lemire, Mélanie; Ayotte, Pierre

2016-11-01

Selenium (Se) is highly abundant in marine foods traditionally consumed by Inuit of Nunavik (Northern Quebec, Canada) and accordingly, their Se intake is among the highest in the world. However, little is known regarding the biological implications of this high Se status in this Arctic indigenous population. We used a method combining affinity chromatography and inductively coupled plasma-mass spectrometry with quantification by post-column isotope dilution to determine total Se levels and concentrations of Se-containing proteins in archived plasma samples of Inuit adults who participated to the 2004 Nunavik Inuit Health Survey (N = 852). Amounts of mercury (Hg) associated with Se-containing proteins were also quantified. Results show that glutathione peroxidase 3 (GPx3), selenoprotein P (SelP) and selenoalbumin (SeAlb) represented respectively 25%, 52% and 23% of total plasma Se concentrations. In addition, small amounts of Hg co-eluted with each Se-containing protein and up to 50% of plasma Hg was associated to SelP. Total plasma Se concentrations (median = 139 μg L− 1; interquartile range (IQR) = 22.7 μg L− 1) were markedly lower and less variable than whole blood Se concentration (median = 261 μg L− 1, IQR = 166 μg L− 1). A non linear relation was observed between whole blood Se and plasma Se levels, with plasma Se concentrations leveling off at approximately 200 μg L− 1, whereas 16% and 3% of individuals exhibited whole blood concentrations higher than 500 μg L− 1 and 1000 μg L− 1, respectively. In contrast, a linear relationship was previously reported in communities consuming Brazil nuts which are rich Se, mainly present as selenomethionine. This suggests that a different selenocompound, possibly selenoneine, is present in the Arctic marine food chain and accumulates in the blood cellular fraction of Inuit.

Evaluating Quality of Aged Archival Formalin-Fixed Paraffin-Embedded Samples for RNA-Sequencing

EPA Science Inventory

Archival formalin-fixed paraffin-embedded (FFPE) samples offer a vast, untapped source of genomic data for biomarker discovery. However, the quality of FFPE samples is often highly variable, and conventional methods to assess RNA quality for RNA-sequencing (RNA-seq) are not infor...

The effects of age-in-block on RNA-seq analysis of archival formalin-fixed paraffin-embedded (FFPE) samples

EPA Science Inventory

Archival samples represent a vast resource for identification of chemical and pharmaceutical targets. Previous use of formalin-fixed paraffin-embedded (FFPE) samples has been limited due to changes in RNA introduced by fixation and embedding procedures. Recent advances in RNA-seq...

Hepatitis C virus genotyping of organ donor samples to aid in transplantation of HCV-positive organs.

PubMed

Gentile, Caren; Van Deerlin, Vivianna M; Goldberg, David S; Reese, Peter P; Hasz, Richard D; Abt, Peter; Blumberg, Emily; Farooqi, Midhat S

2018-02-01

Given the availability of new highly efficacious anti-HCV therapies, some clinicians have advocated for wider use of kidneys from hepatitis C virus-positive (HCV+) donors, including transplanting them into HCV-negative recipients. As treatment regimens for HCV are commonly guided by genotype, pretransplant HCV genotyping of tissue donors would be beneficial. To our knowledge, donor HCV genotyping has never been reported. We retrieved archived frozen plasma samples for 17 previous organ donors through a local organ procurement organization. We performed HCV genotyping using the eSensor HCVg Direct Test (GenMark Diagnostics) and also by Sanger sequencing, for confirmation (Retrogen). In addition, viral loads were measured using the COBAS AmpliPrep/TaqMan system (Roche Diagnostics). We found that most of the samples (n = 14) were HCV Genotype 1a with the remainder being Genotype 2b (n = 1) or Genotype 3 (n = 2). All genotyping results were concordant with Sanger sequencing. The average HCV viral load in the sample group was ~ 1.6 million IU/mL (range: ~16 000 IU/mL to 7 million IU/mL). We demonstrate that viral RNA from organ donor plasma can be successfully genotyped for HCV. This ability suggests that transplantation of HCV+ kidneys into HCV-negative recipients, followed by genotype-guided antiviral therapy, could be feasible. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Increasing Access to Archival Records in Library Online Public Access Catalogs.

ERIC Educational Resources Information Center

Gilmore, Matthew B.

1988-01-01

Looks at the use of online public access catalogs, the utility of subject and call-number searching, and possible archival applications. The Wallace Archives at the Claremont Colleges is used as an example of the availability of bibliographic descriptions of multiformat archival materials through the library catalog. Sample records and searches…

A biological survey on the Ottoman Archive papers and determination of the D10 value

NASA Astrophysics Data System (ADS)

Kantoğlu, Ömer; Ergun, Ece; Ozmen, Dilan; Halkman, Hilal B. D.

2018-03-01

The Ottoman Archives have one of the richest archive collections in the world. However, not all the archived documents are well preserved and some undergo biodeterioration. Therefore, a rapid and promising treatment method is necessary to preserve the collection for following generations as heritage. Radiation presents as an alternative for the treatment of archival materials for this purpose. In this study, we conducted a survey to determine the contamination species and the D10 values of the samples obtained from the shelves of the Ottoman Archives. The samples also included several insect pests collected at using a pheromone trap placed in the archive storage room. With the exception of few localized problems, no active pest presence was observed. The D10 values of mold contamination and reference mold (A. niger) were found to be 1.0 and 0.68 kGy, respectively. Based on these results, it can be concluded that an absorbed dose of 6 kGy is required to remove the contamination from the materials stored in the Ottoman Archives.

Attitudes of the Japanese public and doctors towards use of archived information and samples without informed consent: preliminary findings based on focus group interviews.

PubMed

Asai, Atsushi; Ohnishi, Motoki; Nishigaki, Etsuyo; Sekimoto, Miho; Fukuhara, Shunichi; Fukui, Tsuguya

2002-01-09

The purpose of this study is to explore laypersons' attitudes toward the use of archived (existing) materials such as medical records and biological samples and to compare them with the attitudes of physicians who are involved in medical research. Three focus group interviews were conducted, in which seven Japanese male members of the general public, seven female members of the general public and seven physicians participated. It was revealed that the lay public expressed diverse attitudes towards the use of archived information and samples without informed consent. Protecting a subject's privacy, maintaining confidentiality, and communicating the outcomes of studies to research subjects were regarded as essential preconditions if researchers were to have access to archived information and samples used for research without the specific informed consent of the subjects who provided the material. Although participating physicians thought that some kind of prior permission from subjects was desirable, they pointed out the difficulties involved in obtaining individual informed consent in each case. The present preliminary study indicates that the lay public and medical professionals may have different attitudes towards the use of archived information and samples without specific informed consent. This hypothesis, however, is derived from our focus groups interviews, and requires validation through research using a larger sample.

Stability of mercury concentration measurements in archived soil and peat samples

USGS Publications Warehouse

Navrátil, Tomáš; Burns, Douglas; Nováková, Tereza; Kaňa, Jiří; Rohovec, Jan; Roll, Michal; Ettler, Vojtěch

2018-01-01

Archived soil samples can provide important information on the history of environmental contamination and by comparison with recently collected samples, temporal trends can be inferred. Little previous work has addressed whether mercury (Hg) concentrations in soil samples are stable with long-term storage under standard laboratory conditions. In this study, we have re-analyzed using cold vapor atomic adsorption spectroscopy a set of archived soil samples that ranged from relatively pristine mountainous sites to a polluted site near a non-ferrous metal smelter with a wide range of Hg concentrations (6 - 6485 µg kg-1). Samples included organic and mineral soils and peats with a carbon content that ranged from 0.2 to 47.7%. Soil samples were stored in polyethylene bags or bottles and held in laboratory rooms where temperature was not kept to a constant value. Mercury concentrations in four subsets of samples were originally measured in 2000, 2005, 2006 and 2007, and re-analyzed in 2017, i.e. after 17, 12, 11 and 10 years of storage. Statistical analyses of either separated or lumped data yielded no significant differences between the original and current Hg concentrations. Based on these analyses, we show that archived soil and peat samples can be used to evaluate historical soil mercury contamination.

NHEXAS PHASE I REGION 5 STUDY--STANDARD OPERATING PROCEDURE--NHEXAS FILTER HANDLING, WEIGHING AND ARCHIVING PROCEDURES FOR AEROSOL SAMPLES (RTI/ACS-AP-209-011)

EPA Science Inventory

This protocol describes the procedures for weighing, handling, and archiving aerosol filters and for managing the associated analytical and quality assurance data. Filter samples were weighed for aerosol mass at RTI laboratory, with only the automated field sampling data transfer...

Subject Access Points in the MARC Record and Archival Finding Aid: Enough or Too Many?

ERIC Educational Resources Information Center

Cox, Elizabeth; Czechowski, Leslie

2007-01-01

In this research project, the authors set out to discover the current practice in both the archival and cataloging worlds for usage of access points in descriptive records and to learn how archival descriptive practices fit into long-established library cataloging procedures and practices. A sample of archival finding aids and MARC records at 123…

St. Petersburg Coastal and Marine Science Center's Core Archive Portal

USGS Publications Warehouse

Reich, Chris; Streubert, Matt; Dwyer, Brendan; Godbout, Meg; Muslic, Adis; Umberger, Dan

2012-01-01

This Web site contains information on rock cores archived at the U.S. Geological Survey (USGS) St. Petersburg Coastal and Marine Science Center (SPCMSC). Archived cores consist of 3- to 4-inch-diameter coral cores, 1- to 2-inch-diameter rock cores, and a few unlabeled loose coral and rock samples. This document - and specifically the archive Web site portal - is intended to be a 'living' document that will be updated continually as additional cores are collected and archived. This document may also contain future references and links to a catalog of sediment cores. Sediment cores will include vibracores, pushcores, and other loose sediment samples collected for research purposes. This document will: (1) serve as a database for locating core material currently archived at the USGS SPCMSC facility; (2) provide a protocol for entry of new core material into the archive system; and, (3) set the procedures necessary for checking out core material for scientific purposes. Core material may be loaned to other governmental agencies, academia, or non-governmental organizations at the discretion of the USGS SPCMSC curator.

Evaluation of Targeted Sequencing for Transcriptional Analysis of Archival Formalin-Fixed Paraffin-Embedded (FFPE) Samples

EPA Science Inventory

Next-generation sequencing provides unprecedented access to genomic information in archival FFPE tissue samples. However, costs and technical challenges related to RNA isolation and enrichment limit use of whole-genome RNA-sequencing for large-scale studies of FFPE specimens. Rec...

Effects of anticoagulant, processing delay, and assay method (branched DNA versus reverse transcriptase PCR) on measurement of human immunodeficiency virus type 1 RNA levels in plasma.

PubMed

Kirstein, L M; Mellors, J W; Rinaldo, C R; Margolick, J B; Giorgi, J V; Phair, J P; Dietz, E; Gupta, P; Sherlock, C H; Hogg, R; Montaner, J S; Muñoz, A

1999-08-01

We conducted two studies to determine the potential influence of delays in blood processing, type of anticoagulant, and assay method on human immunodeficiency virus type 1 (HIV-1) RNA levels in plasma. The first was an experimental study in which heparin- and EDTA-anticoagulated blood samples were collected from 101 HIV-positive individuals and processed to plasma after delays of 2, 6, and 18 h. HIV-1 RNA levels in each sample were then measured by both branched-DNA (bDNA) and reverse transcriptase PCR (RT-PCR) assays. Compared to samples processed within 2 h, the loss (decay) of HIV-1 RNA in heparinized blood was significant (P < 0.05) but small after 6 h (bDNA assay, -0.12 log(10) copies/ml; RT-PCR, -0.05 log(10) copies/ml) and after 18 h (bDNA assay, -0.27 log(10) copies/ml; RT-PCR, -0.15 log(10) copies/ml). Decay in EDTA-anticoagulated blood was not significant after 6 h (bDNA assay, -0.002 log(10) copies/ml; RT-PCR, -0.02 log(10) copies/ml), but it was after 18 h (bDNA assay, -0.09 log(10) copies/ml; RT-PCR, -0.09 log(10) copies/ml). Only 4% of samples processed after 6 h lost more than 50% (>/=0.3 log(10) copies/ml) of the HIV-1 RNA, regardless of the anticoagulant or the assay that was used. The second study compared HIV-1 RNA levels in samples from the Multicenter AIDS Cohort Study (MACS; samples were collected in heparin-containing tubes in 1985, had a 6-h average processing delay, and were assayed by bDNA assay) and the British Columbia Drug Treatment Program (BCDTP) (collected in EDTA- or acid citrate dextrose-containing tubes in 1996 and 1997, had a 2-h maximum processing delay, and were assayed by RT-PCR). HIV-1 RNA levels in samples from the two cohorts were not significantly different after adjusting for CD4(+)-cell count and converting bDNA assay values to those corresponding to the RT-PCR results. In summary, the decay of HIV-1 RNA measured in heparinized blood after 6 h was small (-0.05 to -0.12 log(10) copies/ml), and the minor impact of this decay on HIV-1 RNA concentrations in archived plasma samples of the MACS was confirmed by the similarity of CD4(+)-cell counts and assay-adjusted HIV-1 RNA concentrations in the MACS and BCDTP.

The preservation of microbial DNA in archived soils of various genetic types.

PubMed

Ivanova, Ekaterina A; Korvigo, Ilia O; Aparin, Boris F; Chirak, Evgenii L; Pershina, Elizaveta V; Romaschenko, Nikolay S; Provorov, Nikolai A; Andronov, Evgeny E

2017-01-01

This study is a comparative analysis of samples of archived (stored for over 70-90 years) and modern soils of two different genetic types-chernozem and sod-podzolic soils. We revealed a reduction in biodiversity of archived soils relative to their modern state. Particularly, long-term storage in the museum exerted a greater impact on the microbiomes of sod-podzolic soils, while chernozem samples better preserved the native community. Thus, the persistence of microbial DNA in soil is largely determined by the physico-chemical characteristics that differ across soil types. Chernozems create better conditions for the long-term DNA preservation than sod-podzolic soils. This results in supposedly higher levels of biodiversity conservation in the microbiomes of chernozem with preservation of major microbial taxa dominant in the modern (control) soil samples, which makes archived chernozems a promising object for paleosoil studies.

The preservation of microbial DNA in archived soils of various genetic types

PubMed Central

Korvigo, Ilia O.; Aparin, Boris F.; Chirak, Evgenii L.; Pershina, Elizaveta V.; Romaschenko, Nikolay S.; Provorov, Nikolai A.; Andronov, Evgeny E.

2017-01-01

This study is a comparative analysis of samples of archived (stored for over 70–90 years) and modern soils of two different genetic types–chernozem and sod-podzolic soils. We revealed a reduction in biodiversity of archived soils relative to their modern state. Particularly, long-term storage in the museum exerted a greater impact on the microbiomes of sod-podzolic soils, while chernozem samples better preserved the native community. Thus, the persistence of microbial DNA in soil is largely determined by the physico-chemical characteristics that differ across soil types. Chernozems create better conditions for the long-term DNA preservation than sod-podzolic soils. This results in supposedly higher levels of biodiversity conservation in the microbiomes of chernozem with preservation of major microbial taxa dominant in the modern (control) soil samples, which makes archived chernozems a promising object for paleosoil studies. PMID:28339464

Dose-Response Analysis of RNA-Seq Profiles in Archival Formalin-Fixed Paraffin-Embedded (FFPE) Samples.

EPA Science Inventory

Use of archival resources has been limited to date by inconsistent methods for genomic profiling of degraded RNA from formalin-fixed paraffin-embedded (FFPE) samples. RNA-sequencing offers a promising way to address this problem. Here we evaluated transcriptomic dose responses us...

Mining the archives: a cross-platform analysis of gene expression profiles in archival formalin-fixed paraffin-embedded (FFPE) tissue.

EPA Science Inventory

Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a potentially invaluable resource for genomic research into the molecular basis of disease. However, use of FFPE samples in gene expression studies has been limited by technical challenges resulting from degradation...

A Method to Evaluate Genome-Wide Methylation in Archival Formalin-Fixed, Paraffin-Embedded Ovarian Epithelial Cells

PubMed Central

Li, Qiling; Li, Min; Ma, Li; Li, Wenzhi; Wu, Xuehong; Richards, Jendai; Fu, Guoxing; Xu, Wei; Bythwood, Tameka; Li, Xu; Wang, Jianxin; Song, Qing

2014-01-01

Background The use of DNA from archival formalin and paraffin embedded (FFPE) tissue for genetic and epigenetic analyses may be problematic, since the DNA is often degraded and only limited amounts may be available. Thus, it is currently not known whether genome-wide methylation can be reliably assessed in DNA from archival FFPE tissue. Methodology/Principal Findings Ovarian tissues, which were obtained and formalin-fixed and paraffin-embedded in either 1999 or 2011, were sectioned and stained with hematoxylin-eosin (H&E).Epithelial cells were captured by laser micro dissection, and their DNA subjected to whole genomic bisulfite conversion, whole genomic polymerase chain reaction (PCR) amplification, and purification. Sequencing and software analyses were performed to identify the extent of genomic methylation. We observed that 31.7% of sequence reads from the DNA in the 1999 archival FFPE tissue, and 70.6% of the reads from the 2011 sample, could be matched with the genome. Methylation rates of CpG on the Watson and Crick strands were 32.2% and 45.5%, respectively, in the 1999 sample, and 65.1% and 42.7% in the 2011 sample. Conclusions/Significance We have developed an efficient method that allows DNA methylation to be assessed in archival FFPE tissue samples. PMID:25133528

Analytical validation of BRAF mutation testing from circulating free DNA using the amplification refractory mutation testing system.

PubMed

Aung, Kyaw L; Donald, Emma; Ellison, Gillian; Bujac, Sarah; Fletcher, Lynn; Cantarini, Mireille; Brady, Ged; Orr, Maria; Clack, Glen; Ranson, Malcolm; Dive, Caroline; Hughes, Andrew

2014-05-01

BRAF mutation testing from circulating free DNA (cfDNA) using the amplification refractory mutation testing system (ARMS) holds potential as a surrogate for tumor mutation testing. Robust assay validation is needed to establish the optimal clinical matrix for measurement and cfDNA-specific mutation calling criteria. Plasma- and serum-derived cfDNA samples from 221 advanced melanoma patients were analyzed for BRAF c.1799T>A (p.V600E) mutation using ARMS in two stages in a blinded fashion. cfDNA-specific mutation calling criteria were defined in stage 1 and validated in stage 2. cfDNA concentrations in serum and plasma, and the sensitivities and specificities of BRAF mutation detection in these two clinical matrices were compared. Sensitivity of BRAF c.1799T>A (p.V600E) mutation detection in cfDNA was increased by using mutation calling criteria optimized for cfDNA (these criteria were adjusted from those used for archival tumor biopsies) without compromising specificity. Sensitivity of BRAF mutation detection in serum was 44% (95% CI, 35% to 53%) and in plasma 52% (95% CI, 43% to 61%). Specificity was 96% (95% CI, 90% to 99%) in both matrices. Serum contains significantly higher total cfDNA than plasma, whereas the proportion of tumor-derived mutant DNA was significantly higher in plasma. Using mutation calling criteria optimized for cfDNA improves sensitivity of BRAF c.1799T>A (p.V600E) mutation detection. The proportion of tumor-derived cfDNA in plasma was significantly higher than in serum. Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Archival policies and collections database for the Woods Hole Science Center's marine sediment samples

USGS Publications Warehouse

Buczkowski, Brian J.; Kelsey, Sarah A.

2007-01-01

The Woods Hole Science Center of the U.S. Geological Survey (USGS) has been an active member of the Woods Hole research community, Woods Hole, Massachusetts, for over 40 years. In that time there have been many projects that involved the collection of sediment samples conducted by USGS scientists and technicians for the research and study of seabed environments and processes. These samples were collected at sea or near shore and then brought back to the Woods Hole Science Center (WHSC) for analysis. While at the center, samples are stored in ambient temperature, refrigerated and freezing conditions ranging from +2º Celsius to -18º Celsius, depending on the best mode of preparation for the study being conducted or the duration of storage planned for the samples. Recently, storage methods and available storage space have become a major concern at the WHSC. The core and sediment archive program described herein has been initiated to set standards for the management, methods, and duration of sample storage. A need has arisen to maintain organizational consistency and define storage protocol. This handbook serves as a reference and guide to all parties interested in using and accessing the WHSC's sample archive and also defines all the steps necessary to construct and maintain an organized collection of geological samples. It answers many questions as to the way in which the archive functions.

Atmospheric Fluoroform (CHF3, HFC-23) at Cape Grim, Tasmania (1978-1995)

DOE Data Explorer

Oram, D. E. [University of East Anglia, Norwich, United Kingdom; Sturges, W. T. [University of East Anglia, Norwich, United Kingdom; Penkett, S. A. [University of East Anglia, Norwich, United Kingdom; McCulloch, A. [ICI Chemicals and Polymers, Ltd., Cheshire, United Kingdom; Fraser, P. J. [CRC for Southern Hemisphere Meteorology, Victoria, Australia

2000-10-01

The sampling and analytical methods are described more fully in Oram et al. (1998). In summary, air samples were taken from the archive of Cape Grim, Tasmania (41oS, 145oE) air samples collected from 1978 through 1995. Comparisons of CFC-11, CFC-12, CFC-113, CH3CCl3, and CH4 data between archive samples and corresponding in-situ samples for the same dates confirm that the archive samples are both representative and stable over time. Samples were analyzed by gas chromatography-mass spectrometry (GC-MS), using a KCl-passivated alumina PLOT column. Fluoroform was monitored on mass 69 (CF3+). The analytical precision (one standard deviation of the mean) for two or three replicate analyses was typically ± 1% of the mean measured value. The overall uncertainty of the observed data is ± 10%, taking into account uncertainties in the preparation of the primary standards, the purity of the fluoroform used to make the primary standards, as well as the analytical precision.

NHEXAS PHASE I ARIZONA STUDY--STANDARD OPERATING PROCEDURE FOR ARCHIVE PROCEDURE FOR STUDY SAMPLES (UA-G-4.0)

EPA Science Inventory

The purpose of this SOP is to outline the archive/custody guidelines used by the NHEXAS Arizona research project. This procedure was followed to maintain and locate samples, extracts, tracings and hard copy results after laboratory analysis during the Arizona NHEXAS project and ...

One-step preparation of nanostructured martite catalyst and graphite electrode by glow discharge plasma for heterogeneous electro-Fenton like process.

PubMed

Khataee, Alireza; Sajjadi, Saeed; Hasanzadeh, Aliyeh; Vahid, Behrouz; Joo, Sang Woo

2017-09-01

Natural Martite ore particles and graphite were modified by alternating current (AC) glow discharge plasma to form nanostructured catalyst and cathode electrode for using in the heterogeneous-electro Fenton-like (Het-EF-like) process. The performance of the plasma-treated martite (PTM) and graphite electrode (PTGE) was studied for the treatment of paraquat herbicide in a batch system. 85.78% degradation efficiency for 20 mg L -1 paraquat was achieved in the modified process under desired operational conditions (i.e. current intensity of 300 mA, catalyst amount of 1 g L -1 , pH = 6, and background electrolyte (Na 2 SO 4 ) concentration of 0.05 mol L -1 ) which was higher than the 41.03% for the unmodified one after 150 min of treatment. The ecofriendly modification of the martite particles and the graphite electrode, no chemical needed, low leached iron and milder operational pH were the main privileges of plasma utilization. Moreover, the degradation efficiency through the process was not declined after five repeated cycles at the optimized conditions, which proved the stability of the nanostructured PTM and PTGE in the long-term usage. The archived results exhibit this method is the first example of high efficient, cost-effective, and environment-friendly method for generation of nanostructured samples. Copyright © 2017 Elsevier Ltd. All rights reserved.

Development and Validation of an Ultradeep Next-Generation Sequencing Assay for Testing of Plasma Cell-Free DNA from Patients with Advanced Cancer.

PubMed

Janku, Filip; Zhang, Shile; Waters, Jill; Liu, Li; Huang, Helen J; Subbiah, Vivek; Hong, David S; Karp, Daniel D; Fu, Siqing; Cai, Xuyu; Ramzanali, Nishma M; Madwani, Kiran; Cabrilo, Goran; Andrews, Debra L; Zhao, Yue; Javle, Milind; Kopetz, E Scott; Luthra, Rajyalakshmi; Kim, Hyunsung J; Gnerre, Sante; Satya, Ravi Vijaya; Chuang, Han-Yu; Kruglyak, Kristina M; Toung, Jonathan; Zhao, Chen; Shen, Richard; Heymach, John V; Meric-Bernstam, Funda; Mills, Gordon B; Fan, Jian-Bing; Salathia, Neeraj S

2017-09-15

Purpose: Tumor-derived cell-free DNA (cfDNA) in plasma can be used for molecular testing and provide an attractive alternative to tumor tissue. Commonly used PCR-based technologies can test for limited number of alterations at the time. Therefore, novel ultrasensitive technologies capable of testing for a broad spectrum of molecular alterations are needed to further personalized cancer therapy. Experimental Design: We developed a highly sensitive ultradeep next-generation sequencing (NGS) assay using reagents from TruSeqNano library preparation and NexteraRapid Capture target enrichment kits to generate plasma cfDNA sequencing libraries for mutational analysis in 61 cancer-related genes using common bioinformatics tools. The results were retrospectively compared with molecular testing of archival primary or metastatic tumor tissue obtained at different points of clinical care. Results: In a study of 55 patients with advanced cancer, the ultradeep NGS assay detected 82% (complete detection) to 87% (complete and partial detection) of the aberrations identified in discordantly collected corresponding archival tumor tissue. Patients with a low variant allele frequency (VAF) of mutant cfDNA survived longer than those with a high VAF did ( P = 0.018). In patients undergoing systemic therapy, radiological response was positively associated with changes in cfDNA VAF ( P = 0.02), and compared with unchanged/increased mutant cfDNA VAF, decreased cfDNA VAF was associated with longer time to treatment failure (TTF; P = 0.03). Conclusions: Ultradeep NGS assay has good sensitivity compared with conventional clinical mutation testing of archival specimens. A high VAF in mutant cfDNA corresponded with shorter survival. Changes in VAF of mutated cfDNA were associated with TTF. Clin Cancer Res; 23(18); 5648-56. ©2017 AACR . ©2017 American Association for Cancer Research.

Seabird tissue archival and monitoring project: Protocol for collecting and banking seabird eggs

USGS Publications Warehouse

Weston-York, Geoff; Porter, Barbara J.; Pugh, Rebecca S.; Roseneau, David G.; Simac, Kristin S.; Becker, Paul R.; Thorsteinson, Lyman K.; Wise, Stephen A.

2001-01-01

Archiving biological and environmental samples for retrospective analysis is a major component of systematic environmental monitoring. The long-term storage of carefully selected, representative samples in an environmental specimen bank is an important complement to the real-time monitoring of the environment. These archived samples permit:The use of subsequently developed innovative analytical technology that was not available at the time the samples were archived, for clear state-of-art identification an~ quantification of analytes of interest,The identification and quantification of analytes that are of subsequent interest but that were not of interest at the time the samples were archived, andThe comparison of present and past analytical techniques and values, providing continued credibility of past analytical values, and allowing flexibility in environmental monitoring programs.Seabirds, including albatrosses, pelicans, cormorants, terns, kittiwakes, murres, guillemots, and puffins spend most of their lives at sea and have special adaptations for feeding in the marine environment, including the ability to excrete the excess salt obtained from ingesting seawater. Many species nest in dense groups (colonies) on steep, precipitous sea-cliffs and headlands.Seabirds are long-lived and slow to mature. They occupy high positions in the marine food web and are considered sensitive indicators for the marine environment (prey includes krill, small fish, and squid). Breeding success, timing of nesting, diets, and survival rates may provide early indications of changing environmental conditions (e.g., see Hatch et aI., 1993). Chemical analysis of seabird tissues, including egg contents, can be particularly useful in determining whether contaminants (and potential biological effects) associated with human industrial activities, such as offshore petroleum and mineral exploration and development, are accumulating in marine environments. The collection and archival of seabird tissues over a period of several years will be a resource for future analyses, providing samples that can be used to determine historical baseline contaminant levels.

Establishing a Southern Swedish Malignant Melanoma OMICS and biobank clinical capability

PubMed Central

2013-01-01

Background The objectives and goals of the Southern Swedish Malignant Melanoma (SSMM) are to develop, build and utilize cutting edge biobanks and OMICS platforms to better understand disease pathology and drug mechanisms. The SSMM research team is a truly cross-functional group with members from oncology, surgery, bioinformatics, proteomics, and genomics initiatives. Within the research team there are members who daily diagnose patients with suspect melanomas, do follow-ups on malignant melanoma patients and remove primary or metastatic lesions by surgery. This inter-disciplinary clinical patient care ensures a competence build as well as a best practice procedure where the patient benefits. Methods Clinical materials from patients before, during and after treatments with clinical end points are being collected. Tissue samples as well as bio-fluid samples such as blood fractions, plasma, serum and whole blood will be archived in 384-high density sample tube formats. Standardized approaches for patient selections, patient sampling, sample-processing and analysis platforms with dedicated protein assays and genomics platforms that will hold value for the research community are used. The patient biobank archives are fully automated with novel ultralow temperature biobank storage units and used as clinical resources. Results An IT-infrastructure using a laboratory information management system (LIMS) has been established, that is the key interface for the research teams in order to share and explore data generated within the project. The cross-site data repository in Lund forms the basis for sample processing, together with biological samples in southern Sweden, including blood fractions and tumor tissues. Clinical registries are associated with the biobank materials, including pathology reports on disease diagnosis on the malignant melanoma (MM) patients. Conclusions We provide data on the developments of protein profiling and targeted protein assays on isolated melanoma tumors, as well as reference blood standards that is used by the team members in the respective laboratories. These pilot data show biobank access and feasibility of performing quantitative proteomics in MM biobank repositories collected in southern Sweden. The scientific outcomes further strengthen the build of healthcare benefit in the complex challenges of malignant melanoma pathophysiology that is addressed by the novel personalized medicines entering the market. PMID:23445834

Establishing a Southern Swedish Malignant Melanoma OMICS and biobank clinical capability.

PubMed

Welinder, Charlotte; Jönsson, Göran; Ingvar, Christian; Lundgren, Lotta; Olsson, Håkan; Breslin, Thomas; Végvári, Akos; Laurell, Thomas; Rezeli, Melinda; Jansson, Bo; Baldetorp, Bo; Marko-Varga, György

2013-02-27

The objectives and goals of the Southern Swedish Malignant Melanoma (SSMM) are to develop, build and utilize cutting edge biobanks and OMICS platforms to better understand disease pathology and drug mechanisms. The SSMM research team is a truly cross-functional group with members from oncology, surgery, bioinformatics, proteomics, and genomics initiatives. Within the research team there are members who daily diagnose patients with suspect melanomas, do follow-ups on malignant melanoma patients and remove primary or metastatic lesions by surgery. This inter-disciplinary clinical patient care ensures a competence build as well as a best practice procedure where the patient benefits. Clinical materials from patients before, during and after treatments with clinical end points are being collected. Tissue samples as well as bio-fluid samples such as blood fractions, plasma, serum and whole blood will be archived in 384-high density sample tube formats. Standardized approaches for patient selections, patient sampling, sample-processing and analysis platforms with dedicated protein assays and genomics platforms that will hold value for the research community are used. The patient biobank archives are fully automated with novel ultralow temperature biobank storage units and used as clinical resources. An IT-infrastructure using a laboratory information management system (LIMS) has been established, that is the key interface for the research teams in order to share and explore data generated within the project. The cross-site data repository in Lund forms the basis for sample processing, together with biological samples in southern Sweden, including blood fractions and tumor tissues. Clinical registries are associated with the biobank materials, including pathology reports on disease diagnosis on the malignant melanoma (MM) patients. We provide data on the developments of protein profiling and targeted protein assays on isolated melanoma tumors, as well as reference blood standards that is used by the team members in the respective laboratories. These pilot data show biobank access and feasibility of performing quantitative proteomics in MM biobank repositories collected in southern Sweden. The scientific outcomes further strengthen the build of healthcare benefit in the complex challenges of malignant melanoma pathophysiology that is addressed by the novel personalized medicines entering the market.

Getting something for nothing: Regeneration of peptide signals from apparently exhausted MALDI samples by “waterboarding"

USDA-ARS?s Scientific Manuscript database

An often cited advantage of MALDI-MS is the ability to archive and reuse sample plates after the initial analysis is complete. However, experience demonstrates that the peptide ion signals decay rapidly as the number of laser shots becomes large. Thus, the signal level obtainable from an archived sa...

U.S.-MEXICO BORDER PROGRAM ARIZONA BORDER STUDY--STANDARD OPERATING PROCEDURE FOR ARCHIVE PROCEDURE FOR STUDY SAMPLES (UA-G-4.0)

EPA Science Inventory

The purpose of this SOP is to outline the archive/custody guidelines used by the Arizona Border Study. This procedure was followed to maintain and locate samples, extracts, tracings and hard copy results after laboratory analysis during the Arizona NHEXAS project and the Border ...

Potential concerns with analytical methods used for the detection of Batrachochytrium salamandrivorans from archived DNA of amphibian swab samples, Oregon, USA

Treesearch

Deborah D. Iwanowicz; William B. Schill; Deanna H. Olson; Michael J. Adams; Christine Densmore; R. Scott Cornman; Cynthia Adams; Jr. Figiel; Chauncey W. Anderson; Andrew R. Blaustein; Tara Chestnut

2017-01-01

We report on the results of surveillance for the salamander chytrid fungus, Batrachochytrium salamandrivorans (Bsal). Two samples from archived DNA used in a previous chytrid study in Oregon were Bsal-positive, alerting us to the first potential finding of this pathogen in North America, infecting American...

The Stool DNA Test is More Accurate than the Plasma Septin 9 Test in Detecting Colorectal Neoplasia

PubMed Central

Ahlquist, David A.; Taylor, William R.; Mahoney, Douglas W.; Zou, Hongzhi; Domanico, Michael; Thibodeau, Stephen N.; Boardman, Lisa A.; Berger, Barry M.; Lidgard, Graham P.

2014-01-01

Background & Aims Several noninvasive tests have been developed for colorectal cancer (CRC) screening. We compared the sensitivities of a multi-marker test for stool DNA (sDNA) and a plasma test for methylated Septin 9 (SEPT9) in identifying patients with large adenomas or CRC. Methods We analyzed paired stool and plasma samples from 30 patients with CRC and 22 with large adenomas from Mayo Clinic archives. Stool (n=46) and plasma (n=49) samples from age- and sex-matched patients with normal colonoscopy results were used as controls. The sDNA test is an assay for methylated BMP3, NDRG4, vimentin, and TFPI2; mutant KRAS; the β-actin gene, and quantity of hemoglobin (by the porphyrin method). It was performed blindly at Exact Sciences (Madison WI); the test for SEPT9 was performed at ARUP Laboratories (Salt Lake City UT). Results were considered positive based on the manufacturer's specificity cutoff values of 90% and 89%, respectively. Results The sDNA test detected adenomas (median 2 cm, range 1–5 cm) with 82% sensitivity (95% confidence interval [CI], 60%–95%); SEPT9 had 14% sensitivity (95% CI, 3%–35%; P=.0001). The sDNA test identified patients with CRC with 87% sensitivity (95% CI, 69%–96%); SEPT9 had 60% sensitivity (95% CI, 41%–77%; P=.046). The sDNA test identified patients with stage I–III CRC with 91% sensitivity (95% CI, 71%–99%); SEPT9 had 50% sensitivity (95% CI, 28%–72%; P=.013); for stage IV CRC, sensitivity values were 75% (95% CI, 35%–97%) and 88% (95% CI, 47%–100%), respectively (P=.56). False-positive rates were 7% for the sDNA test and 27% for SEPT9. Conclusions Based on analyses of paired samples, the sDNA test detects non-metastatic CRC and large adenomas with significantly greater levels of sensitivity than the SEPT9 test. These findings might be used to modify approaches for CRC prevention and early detection. PMID:22019796

Sampling and Chemical Analysis of Potable Water for ISS Expeditions 12 and 13

NASA Technical Reports Server (NTRS)

Straub, John E. II; Plumlee, Deborah K.; Schultz, John R.

2007-01-01

The crews of Expeditions 12 and 13 aboard the International Space Station (ISS) continued to rely on potable water from two different sources, regenerated humidity condensate and Russian ground-supplied water. The Space Shuttle launched twice during the 12- months spanning both expeditions and docked with the ISS for delivery of hardware and supplies. However, no Shuttle potable water was transferred to the station during either of these missions. The chemical quality of the ISS onboard potable water supplies was verified by performing ground analyses of archival water samples at the Johnson Space Center (JSC) Water and Food Analytical Laboratory (WAFAL). Since no Shuttle flights launched during Expedition 12 and there was restricted return volume on the Russian Soyuz vehicle, only one chemical archive potable water sample was collected with U.S. hardware and returned during Expedition 12. This sample was collected in March 2006 and returned on Soyuz 11. The number and sensitivity of the chemical analyses performed on this sample were limited due to low sample volume. Shuttle flights STS-121 (ULF1.1) and STS-115 (12A) docked with the ISS in July and September of 2006, respectively. These flights returned to Earth with eight chemical archive potable water samples that were collected with U.S. hardware during Expedition 13. The average collected volume increased for these samples, allowing full chemical characterization to be performed. This paper presents a discussion of the results from chemical analyses performed on Expeditions 12 and 13 archive potable water samples. In addition to the results from the U.S. samples analyzed, results from pre-flight samples of Russian potable water delivered to the ISS on Progress vehicles and in-flight samples collected with Russian hardware during Expeditions 12 and 13 and analyzed at JSC are also discussed.

Discovering time-trends of the German populations exposure to contaminants by analysis of human samples of the German Environmental Specimen Bank (ESB).

PubMed

Göen, Thomas; Lermen, Dominik; Hildebrand, Jörg; Bartel-Steinbach, Martina; Weber, Till; Kolossa-Gehring, Marike

2018-06-12

The German Environmental Specimen Bank (ESB) is a monitoring instrument of the German Federal Ministry for the Environment, Nature Conservationand Nuclear Safety. The permanent biobank facility is run since 1981 containing environmental and human samples from Germany. All samples are collected according to standard operating procedures (SOP). An annually standardized collection of human samples at four different regional sites of the country has been established since 1997. Routine sampling is done once a year, recruiting healthy non occupationally exposed students aged 20-29 years, in an equal gender distribution. The number of participants recruited is approximately 120 students per site and year. Directly after the annual sampling process, the human samples are analyzed for selected environmental chemicals. The time-trends of lead in blood, mercury and pentachlorophenol in 24 h-urine and polychlorinated biphenyls in plasma demonstrated a decrease of exposure during the last two decades by about 40 - 90 percent. In parallel retrospective studies using cryo-archived samples revealed increasing time trends of emerging chemicals used as substitutes for regulated toxicants. The data demonstrates the great relevance of the ESB for the health related environmental monitoring and shows the importance of human biomonitoring as a tool in information based policy making. Copyright © 2018 Elsevier B.V. All rights reserved.

Progress in Development of the ITER Plasma Control System Simulation Platform

NASA Astrophysics Data System (ADS)

Walker, Michael; Humphreys, David; Sammuli, Brian; Ambrosino, Giuseppe; de Tommasi, Gianmaria; Mattei, Massimiliano; Raupp, Gerhard; Treutterer, Wolfgang; Winter, Axel

2017-10-01

We report on progress made and expected uses of the Plasma Control System Simulation Platform (PCSSP), the primary test environment for development of the ITER Plasma Control System (PCS). PCSSP will be used for verification and validation of the ITER PCS Final Design for First Plasma, to be completed in 2020. We discuss the objectives of PCSSP, its overall structure, selected features, application to existing devices, and expected evolution over the lifetime of the ITER PCS. We describe an archiving solution for simulation results, methods for incorporating physics models of the plasma and physical plant (tokamak, actuator, and diagnostic systems) into PCSSP, and defining characteristics of models suitable for a plasma control development environment such as PCSSP. Applications of PCSSP simulation models including resistive plasma equilibrium evolution are demonstrated. PCSSP development supported by ITER Organization under ITER/CTS/6000000037. Resistive evolution code developed under General Atomics' Internal funding. The views and opinions expressed herein do not necessarily reflect those of the ITER Organization.

Antibody against infectious salmon anaemia virus among feral Atlantic salmon (Salmo salar)

USGS Publications Warehouse

Cipriano, R.C.

2009-01-01

Archived sera from Atlantic salmon (Salmo salar) that returned to the Penobscot River (Maine), Merrimack River (Massachusetts), and Connecticut River (in Massachusetts) from 1995 to 2002 were analysed for antibodies against infectious salmon anaemia virus (ISAV) using an enzyme-linked immunosorbent assay (ELISA). Up to 60 samples were archived per river system per year. In a given year, the number of fish sampled by ELISA for ISAV antibodies in the Penobscot River ranged from 2.9 to 11.2, and the range of salmon sampled in the Merrimack River and the Connecticut River was 31.3-100 and 20.0-67.5, respectively. Archived sera were not available for the 1995 and 2002 year classes from the Connecticut River. In all, 1141 samples were processed; 14 serum samples tested positive for antibodies to ISAV. In the Penobscot River, serum from one fish tested positive in each of the 1995 and 1999 year-class returns, and sera from two fish tested positive in the 1998 returns. In the Merrimack River, sera from four fish tested positive in each of the 1996 and 1997 returns, and sera from two fish were positive in the 2002 return. None of the archived sera from Atlantic salmon that returned to the Connecticut River tested positive. ?? 2009 United States Government, Department of the Interior.

Analytical test results for archived core composite samples from tanks 241-TY-101 and 241-TY-103

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

Beck, M.A.

1993-07-16

This report describes the analytical tests performed on archived core composite samples form a 1.085 sampling of the 241-TY-101 (101-TY) and 241-TY-103 (103-TY) single shell waste tanks. Both tanks are suspected of containing quantities of ferrocyanide compounds, as a result of process activities in the late 1950`s. Although limited quantities of the composite samples remained, attempts were made to obtain as much analytical information as possible, especially regarding the chemical and thermal properties of the material.

Osteopontin and splice variant expression level in human malignant glioma: radiobiologic effects and prognosis after radiotherapy.

PubMed

Güttler, Antje; Giebler, Maria; Cuno, Peter; Wichmann, Henri; Keßler, Jacqueline; Ostheimer, Christian; Söling, Ariane; Strauss, Christian; Illert, Jörg; Kappler, Matthias; Vordermark, Dirk; Bache, Matthias

2013-09-01

We investigated the role of the hypoxia-associated secreted glycoprotein osteopontin (OPN) in the response of malignant glioma to radiotherapy by characterizing OPN and its splice variants in vitro and in patient material. The effect of siRNA knockdown of OPN splice variants on cellular and radiobiologic behavior was analyzed in U251MG cells using OpnS siRNA (inhibition of all OPN splice variants) and OpnAC siRNA (knockdown only of OPNa and OPNc). OPN and splice variant mRNA levels were quantified in archival material of 41 glioblastoma tumor samples. Plasma OPN was prospectively measured in 33 malignant glioma patients. Inhibition of OPNa and OPNc (OpnAC) reduced clonogenic survival in U251MG cells but did not affect proliferation, migration or apoptosis. Knockdown of all OPN splice variants (OpnS) resulted in an even stronger inhibition of clonogenic survival, while cell proliferation and migration were reduced and rate of apoptosis was increased. Additional irradiation had additive effects with both siRNAs. Plasma OPN increased continuously in malignant glioma patients and was associated with poor survival. OPNb is partially able to compensate the effects of OPNa and OPNc knockdown in U251MG cells. High OPN plasma levels at the end of radiotherapy are associated with poor survival. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Chorionic Villus Sampling (CVS)

MedlinePlus

... Careers Archives Health Topics Pregnancy Before or between pregnancies Nutrition, weight & fitness Prenatal care Is it safe? Labor & ... Report Cards Careers Archives Pregnancy Before or between pregnancies Nutrition, weight & fitness Prenatal care Is it safe? Labor & ...

Sample Curation in Support of the OSIRIS-REx Asteroid Sample Return Mission

NASA Technical Reports Server (NTRS)

Righter, Kevin; Nakamura-Messenger, Keiko

2017-01-01

The OSIRIS-REx asteroid sample return mission launched to asteroid Bennu Sept. 8, 2016. The spacecraft will arrive at Bennu in late 2019, orbit and map the asteroid, and perform a touch and go (TAG) sampling maneuver in July 2020. After sample is stowed and confirmed the spacecraft will return to Earth, and the sample return capsule (SRC) will land in Utah in September 2023. Samples will be recovered from Utah [2] and then transported and stored in a new sample cleanroom at NASA Johnson Space Center in Houston [3]. The materials curated for the mission are described here. a) Materials Archive and Witness Plate Collection: The SRC and TAGSAM were built between March 2014 and Summer of 2015, and instruments (OTES,OVIRS, OLA, OCAMS, REXIS) were integrated from Summer 2015 until May 2016. A total of 395 items were received for the materials archive at NASA-JSC, with archiving finishing 30 days after launch (with the final archived items being related to launch operations)[4]. The materials fall into several general categories including metals (stainless steel, aluminum, titanium alloys, brass and BeCu alloy), epoxies, paints, polymers, lubricants, non-volatile-residue samples (NVR), sapphire, and various miscellaneous materials. All through the ATLO process (from March 2015 until late August 2016) contamination knowledge witness plates (Si wafer and Al foil) were deployed in the various cleanrooms in Denver and KSC to provide an additional record of particle counts and volatiles that is archived for current and future scientific studies. These plates were deployed in roughly monthly increments with each unit containing 4 Si wafers and 4 Al foils. We archived 128 individual witness plates (64 Si wafers and 64 Al foils); one of each witness plate (Si and Al) was analyzed immediately by the science team after archiving, while the remaining 3 of each are archived indefinitely. Information about each material archived is stored in an extensive database at NASA-JSC, and key summary information for each will be presented in an online catalog. b) Bulk Asteroid sample: The Touch and Go Sampling Mechanism (TAGSAM) head will contain up to 1.5 kg of asteroid material. Upon return to Earth, the TAGSAM head with the sample canister will be subjected to a nitrogen purge and then opened in a nitrogen cabinet in Houston. Once the TAGSAM head is removed from the canister, it will be dis-assembled slowly and carefully under nitrogen until the sample can be removed for processing in a dedicated nitrogen glovebox. Bennu surface samples are expected to be sub-cm sized, based on thermal infrared and radar polarization ratio measurements [1]. The upper limit on material collected by the TAGSAM head is 2 cm. Therefore, we will be prepared to handle, subdivide, and characterize materials of a wide grain size (from 10 ?m to 2 cm), and for both organic (UV fluorescence) and inorganic (SEM, FTIR, optical) properties. Representative portions of the bulk sample will be prepared for JAXA (0.5 %; see also [5]) and Canadian Space Agency (4%), with the remaining divided between the science team (<25%) and archived for future studies (NASA) (>75%). c) Contact Pad samples: The base of the TAGSAM head contains 24 contact pads that are designed to trap the upper surface layer of material and thus offer an opportunity to study asteroid samples that have resided at the very top surface of the regolith. Asteroid material is trapped on the pads in spring steel Velcro hooks, and material will have to be removed from these pads by curation specialists in the lab. d) Hardware: Some canister and SRC hardware items will contain information that will be important to understanding the collected samples, including the canister gas filter, temperature strips, flight witness plates, and the TAGSAM and canister parts that might have adhering dust grains. Some challenges remaining for both bulk sample and contact pad samples include: i) working with intermediate size range (200 to 500 micron) samples - a size range NASA has not previously worked in such detail; ii) techniques for removal of contact pad material from the spring steel hooks, iii) static electrical effects of dust sized particles during sample handling and curation is likely to be significant, and iv) the TAGSAM head and associated canister hardware will undoubtedly be coated with fine adhering dust grains from Bennu. In the case of collection of a large bulk sample mass, the adhering dust grains may be of lower priority. If a small sample mass is returned, the adhering dust may attain a higher priority, so recovery of adhering dust grains is an additional challenge to consider. In the year leading up to sample return we plan a variety of sample handling rehearsals that will enables the curation team to be prepared for many new aspects posed by this sample suite.

Effects of Anticoagulant, Processing Delay, and Assay Method (Branched DNA versus Reverse Transcriptase PCR) on Measurement of Human Immunodeficiency Virus Type 1 RNA Levels in Plasma

PubMed Central

Kirstein, Lynn M.; Mellors, John W.; Rinaldo, Charles R.; Margolick, Joseph B.; Giorgi, Janis V.; Phair, John P.; Dietz, Edith; Gupta, Phalguni; Sherlock, Christopher H.; Hogg, Robert; Montaner, J. S. G.; Muñoz, Alvaro

1999-01-01

We conducted two studies to determine the potential influence of delays in blood processing, type of anticoagulant, and assay method on human immunodeficiency virus type 1 (HIV-1) RNA levels in plasma. The first was an experimental study in which heparin- and EDTA-anticoagulated blood samples were collected from 101 HIV-positive individuals and processed to plasma after delays of 2, 6, and 18 h. HIV-1 RNA levels in each sample were then measured by both branched-DNA (bDNA) and reverse transcriptase PCR (RT-PCR) assays. Compared to samples processed within 2 h, the loss (decay) of HIV-1 RNA in heparinized blood was significant (P < 0.05) but small after 6 h (bDNA assay, −0.12 log10 copies/ml; RT-PCR, −0.05 log10 copies/ml) and after 18 h (bDNA assay, −0.27 log10 copies/ml; RT-PCR, −0.15 log10 copies/ml). Decay in EDTA-anticoagulated blood was not significant after 6 h (bDNA assay, −0.002 log10 copies/ml; RT-PCR, −0.02 log10 copies/ml), but it was after 18 h (bDNA assay, −0.09 log10 copies/ml; RT-PCR, −0.09 log10 copies/ml). Only 4% of samples processed after 6 h lost more than 50% (≥0.3 log10 copies/ml) of the HIV-1 RNA, regardless of the anticoagulant or the assay that was used. The second study compared HIV-1 RNA levels in samples from the Multicenter AIDS Cohort Study (MACS; samples were collected in heparin-containing tubes in 1985, had a 6-h average processing delay, and were assayed by bDNA assay) and the British Columbia Drug Treatment Program (BCDTP) (collected in EDTA- or acid citrate dextrose-containing tubes in 1996 and 1997, had a 2-h maximum processing delay, and were assayed by RT-PCR). HIV-1 RNA levels in samples from the two cohorts were not significantly different after adjusting for CD4+-cell count and converting bDNA assay values to those corresponding to the RT-PCR results. In summary, the decay of HIV-1 RNA measured in heparinized blood after 6 h was small (−0.05 to −0.12 log10 copies/ml), and the minor impact of this decay on HIV-1 RNA concentrations in archived plasma samples of the MACS was confirmed by the similarity of CD4+-cell counts and assay-adjusted HIV-1 RNA concentrations in the MACS and BCDTP. PMID:10405379

Computing and data processing

NASA Technical Reports Server (NTRS)

Smarr, Larry; Press, William; Arnett, David W.; Cameron, Alastair G. W.; Crutcher, Richard M.; Helfand, David J.; Horowitz, Paul; Kleinmann, Susan G.; Linsky, Jeffrey L.; Madore, Barry F.

1991-01-01

The applications of computers and data processing to astronomy are discussed. Among the topics covered are the emerging national information infrastructure, workstations and supercomputers, supertelescopes, digital astronomy, astrophysics in a numerical laboratory, community software, archiving of ground-based observations, dynamical simulations of complex systems, plasma astrophysics, and the remote control of fourth dimension supercomputers.

Evaluation of a new optic-enabled portable X-ray fluorescence spectrometry instrument for measuring toxic metals/metalloids in consumer goods and cultural products

NASA Astrophysics Data System (ADS)

Guimarães, Diana; Praamsma, Meredith L.; Parsons, Patrick J.

2016-08-01

X-ray fluorescence spectrometry (XRF) is a rapid, non-destructive multi-elemental analytical technique used for determining elemental contents ranging from percent down to the μg/g level. Although detection limits are much higher for XRF compared to other laboratory-based methods, such as inductively coupled plasma mass spectrometry (ICP-MS), ICP-optical emission spectrometry (OES) and atomic absorption spectrometry (AAS), its portability and ease of use make it a valuable tool, especially for field-based studies. A growing necessity to monitor human exposure to toxic metals and metalloids in consumer goods, cultural products, foods and other sample types while performing the analysis in situ has led to several important developments in portable XRF technology. In this study, a new portable XRF analyzer based on the use of doubly curved crystal optics (HD Mobile®) was evaluated for detecting toxic elements in foods, medicines, cosmetics and spices used in many Asian communities. Two models of the HD Mobile® (a pre-production and a final production unit) were investigated. Performance parameters including accuracy, precision and detection limits were characterized in a laboratory setting using certified reference materials (CRMs) and standard solutions. Bias estimates for key elements of public health significance such as As, Cd, Hg and Pb ranged from - 10% to 11% for the pre-production, and - 14% to 16% for the final production model. Five archived public health samples including herbal medicine products, ethnic spices and cosmetic products were analyzed using both XRF instruments. There was good agreement between the pre-production and final production models for the four key elements, such that the data were judged to be fit-for-purpose for the majority of samples analyzed. Detection of the four key elements of interest using the HD Mobile® was confirmed using archived samples for which ICP-OES data were available based on digested sample materials. The HD Mobile® XRF units were shown to be suitable for rapid screening of samples likely to be encountered in field based studies.

Detection of Gastric Cancer with Novel Methylated DNA Markers: Discovery, Tissue Validation, and Pilot Testing in Plasma.

PubMed

Anderson, Bradley W; Suh, Yun-Suhk; Choi, Boram; Lee, Hyuk-Joon; Yab, Tracy C; Taylor, William; Dukek, Brian A; Berger, Calise K; Cao, Xiaoming; Foote, Patrick H; Devens, Mary E; Boardman, Lisa A; Kisiel, John B; Mahoney, Douglas W; Slettedahl, Seth W; Allawi, Hatim T; Lidgard, Graham P; Smyrk, Thomas C; Yang, Han-Kwang; Ahlquist, David A

2018-05-29

Gastric adenocarcinoma (GAC) is the third most common cause of cancer mortality worldwide. Accurate and affordable non-invasive detection methods have potential value for screening and surveillance. Herein, we identify novel methylated DNA markers (MDMs) for GAC, validate their discrimination for GAC in tissues from geographically separate cohorts, explore marker acquisition through the oncogenic cascade, and describe distributions of candidate MDMs in plasma from GAC cases and normal controls. Following discovery by unbiased whole methylome sequencing, candidate MDMs were validated by blinded methylation-specific PCR in archival case-control tissues from U.S. and South Korean patients. Top MDMs were then assayed by an analytically sensitive method (quantitative real-time allele-specific target and signal amplification) in a blinded pilot study on archival plasma from GAC cases and normal controls. Whole methylome discovery yielded novel and highly discriminant candidate MDMs. In tissue, a panel of candidate MDMs detected GAC in 92-100% of U.S. and S. Korean cohorts at 100% specificity. Levels of most MDMs increased progressively from normal mucosa through metaplasia, adenoma, and GAC with variation in points of greatest marker acquisition. In plasma, a 3 marker panel ( ELMO1 , ZNF569 , C13orf18) detected 86% (95% CI 71-95%) of GACs at 95% specificity. Novel MDMs appear to accurately discriminate GAC from normal controls in both tissue and plasma. The point of aberrant methylation during oncogenesis varies by MDM, which may have relevance to marker selection in clinical applications. Further exploration of these MDMs for GAC screening and surveillance is warranted. Copyright ©2018, American Association for Cancer Research.

Operation of the Planetary Plasma Interactions Node of the Planetary Data System

NASA Technical Reports Server (NTRS)

Walker, Raymond J.

1997-01-01

Five years ago NASA selected the Planetary Plasma Interactions (PPI) Node at UCLA to help the scientific community locate, access and preserve particles and fields data from planetary missions. We propose to continue to serve for 5 more years. During the first five years we have served the scientific community by providing them with high quality data products. We worked with missions and individual scientists to secure the highest quality data possible and to thoroughly document it. We validated the data, placed it on long lasting media and made sure it was properly archived for future use. So far we have prepared and archived over 10(exp 11) bytes of data from 26 instruments on 4 spacecraft. We have produced 106 CD-ROMs with peer reviewed data. In so doing, we have developed an efficient system to prepare and archive the data and thereby have been able to steadily increase the rate at which the data are produced. Although we produced a substantial archive during the initial five years, we have an even larger amount of work in progress. This includes preparing CD-ROM data sets with all of the Voyager, Pioneer and Ulysses data at Jupiter and Saturn. We will have the Jupiter data ready for the Galileo encounter in December, 1995. We are also completing the Pioneer Venus data restoration. The Galileo Venus archive and radio science data from Magellan will be prepared early in the next period. We are assisting the Small Bodies Node of PDS in the preparation of comet data and will be archiving the asteroid data from Galileo. We will be moving in several new directions as well. We will archive the PPI Node's first Earth based data with data from the International Jupiter Watch and Hubble data taken in support of Ulysses particles and field observations. We will work with the Cassini mission in archive planning efforts. For the inner planets we will begin an archive of Mars data starting with Phobos data and will support the US and Russian Mars missions in the late 1990's. We will restore the Mercury data from Mariner 10 and prepare the lunar data from Clementine in time for the lunar data analysis program in 1995. We will work with the Discovery mission teams to plan their archive and have already started with one, NEAR. Finally we will begin archiving our first heliospheric data from Voyager, Galileo, and Mars observers. We will continue to serve the science community by providing access to the data products. During the past 19 months we have filled nearly 6000 requests for on-line and CD-ROM data. The data delivered directly by the PPI Node has been - 5 x 10(exp 11) bytes. In addition to providing the data, we have provided users with software tools to manage and read the data which are computer, operating system and format independent. We have developed scalable systems so that the same software we use to manage and access the data for the entire PPI Node can be used by individual investigators to manage the data on a single CD-ROM, thereby greatly reducing the software development effort for both the PPI Node and users. We deliver this software with the disks. Recent technical advances have made it possible for us to serve a broader community than before. In the next five year period we plan to extend our outreach to the general public and in particular to increase our support for education. Since planetary plasma data are varied and require expertise in many areas the PPI Node will continue to be distributed. In addition to the primary node at UCLA, the PPI Node has three subnodes with an Outer Planets Subnode at the University of Iowa, an Inner Planets Subnode at UCLA, and a Radio Science Subnode at Stanford University. During the first two years of the renewal period there will be a Radio Astronomy Data Node at GSFC. These organizations will provide scientific expertise on the data, participate in node data selection activities and help with data restoration and mission activities.

Dynamics Explorer 1: Energetic Ion Composition Spectrometer (EICS)

NASA Technical Reports Server (NTRS)

Shelley, E. G.; Peterson, W. K.; Collin, H. L.

1994-01-01

The Energetic Ion Composition Spectrometer (EICS) experiment was selected as part of the Dynamics Explorer (DE) Program. One of the primary goals of the DE program was to investigate in detail the plasma physics processes responsible for energizing thermal (approximately 1 eV) ionospheric ions and transporting them to the earth's plasma sheet and distant polar cap. The results of the EICS data analysis (including support of other investigators) and of the archiving efforts supported by this contract are summarized in this document. Also reported are some aspects of our operational support activities.

Impact of the School Outreach Tour Program of Citizens Archive of Pakistan on Students' Perceptions and Attitudes

ERIC Educational Resources Information Center

Alam, Qutbi

2017-01-01

This paper examines the impact of School Outreach Tour (SOT-A) program,one of the projects of the Citizens Archive of Pakistan (CAP), a non-profit organisation on the perceptions and attitudes of Grade-8 Students of partners' schools. The sample in this study consists of (n = 139) students of Grade-8, selected by convenience sampling from five…

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

PubMed Central

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

2015-01-01

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

The NASA Ames Life Sciences Data Archive: Biobanking for the Final Frontier

NASA Technical Reports Server (NTRS)

Rask, Jon; Chakravarty, Kaushik; French, Alison J.; Choi, Sungshin; Stewart, Helen J.

2017-01-01

The NASA Ames Institutional Scientific Collection involves the Ames Life Sciences Data Archive (ALSDA) and a biospecimen repository, which are responsible for archiving information and non-human biospecimens collected from spaceflight and matching ground control experiments. The ALSDA also manages a biospecimen sharing program, performs curation and long-term storage operations, and facilitates distribution of biospecimens for research purposes via a public website (https:lsda.jsc.nasa.gov). As part of our best practices, a tissue viability testing plan has been developed for the repository, which will assess the quality of samples subjected to long-term storage. We expect that the test results will confirm usability of the samples, enable broader science community interest, and verify operational efficiency of the archives. This work will also support NASA open science initiatives and guides development of NASA directives and policy for curation of biological collections.

VizieR Online Data Catalog: Ccompact group galaxies UV and IR SFR (Lenkic+, 2016)

NASA Astrophysics Data System (ADS)

Lenkic, L.; Tzanavaris, P.; Gallagher, S. C.; Desjardins, T. D.; Walker, L. M.; Johnson, K. E.; Fedotov, K.; Charlton, J.; Hornschemeier, A. E.; Durrell, P. R.; Gronwall, C.

2017-07-01

The sample of CGs studied here is the same sample studied by Walker et al. (2012AJ....143...69W) of 49 CGs: 33 Hickson Compact Groups and 16 Redshift Survey Compact Groups (RSCGs). The RSCG catalogue of 89 CGs was constructed by Barton et al. (1996AJ....112..871B). The data used in this study originated from 'fill-in' observations with UVOT's three UV filters (uvw2, uvm2, uvw1) as well as the bluest optical filter (u). All UV data (PI: Tzanavaris) were downloaded from the Swift archive. The Spitzer Infrared Array Camera images for our sample of CGs are archival data presented by Walker et al. (2012AJ....143...69W) Spitzer MIPS (24um) data were obtained from the Spitzer Heritage Archive. (4 data files).

[Quality of DNA from archival pathological samples of gallbladder cancer].

PubMed

Roa, Iván; de Toro, Gonzalo; Sánchez, Tamara; Slater, Jeannie; Ziegler, Anne Marie; Game, Anakaren; Arellano, Leonardo; Schalper, Kurt; de Aretxabala, Xabier

2013-12-01

The quality of the archival samples stored at pathology services could be a limiting factor for molecular biology studies. To determine the quality of DNA extracted from gallbladder cancer samples at different institutions. One hundred ninety four samples coming from five medical centers in Chile, were analyzed. DNA extraction was quantified determining genomic DNA concentration. The integrity of DNA was determined by polymerase chain reaction amplification of different length fragments of a constitutive gene (β-globin products of 110, 268 and 501 base pairs). The mean DNA concentration obtained in 194 gallbladder cancer samples was 48 ± 43.1 ng/µl. In 22% of samples, no amplification was achieved despite obtaining a mean DNA concentration of 58.3 ng/ul. In 81, 67 and 22% of samples, a DNA amplification of at least 110, 268 or 501 base pairs was obtained, respectively. No differences in DNA concentration according to the source of the samples were demonstrated. However, there were marked differences in DNA integrity among participating centers. Samples from public hospitals were of lower quality than those from private clinics. Despite some limitations, in 80% of cases, the integrity of DNA in archival samples from pathology services in our country would allow the use of molecular biology techniques.

Optimal extraction of quasar Lyman limit absorption systems from the IUE archive

NASA Technical Reports Server (NTRS)

Tytler, David

1992-01-01

The IUE archive contains a wealth of information on Lyman limit absorption systems (LLS) in quasar spectra. QSO spectra from the IUE data base were optimally extracted, coadded, and analyzed to yield a homogeneous samples of LLS at low red shifts. This sample comprise 36 LLS, twice the number previously analyzed low z samples. These systems are ideal for the determination of the origin, redshift evolution, ionization, velocity dispersions and the metal abundances of absorption systems. Two of them are also excellent targets for the primordial Deuterium to Hydrogen ratio.

Restoration and Archiving of Data from the Plasma Composition Experiment on the International Sun-Earth Explorer One (ISEE 1)

NASA Technical Reports Server (NTRS)

Lennartsson, O. W.

1997-01-01

The objective of this project has been to complete the archiving of energetic (10 eV/epsilon - 18 keV/epsilon) ion composition data from the Lockheed Plasma Composition Experiment on the International Sun-Earth Explorer One (ISEE 1) satellite, using a particular data format that had previously been approved by NASA and the NSSDC. That same format, a combination of ion velocity moments and differential flux spectra, had been used in 1991 to archive, at the NSSDC, the first 28 months (the "Prime" period of ISEE investigations) of data from the Lockheed instrument under NASA Contract NAS5-33047. With the completion of this project, the almost 4 1/2-year time span of these unique data is now covered by a very compact set, approximately 1 gigabyte in total, of electronic files with physical quantities, all in ASCII. The files are organized by data type and time of data acquisition, in Universal Time, and named according to year and day of year. Each calendar day has five separate files (five types of data), the lengths of which vary from day to day, depending on the instrument mode of operation. The data format and file structure are described in detail in appendices 1 and 2. The physical medium consists of high-density (6250 cpi) 9-track magnetic tapes, complemented by a set of hardcopy line plots of certain plasma parameters. In this case there are five tapes, to be added to the six previous ones from 1991, and 25 booklets of plots, one per month, to be added to the previous 28. The tapes, including an extra standard-density (1600 cpi) tape with electronic versions of the Data User's Guide and self-guiding VAX/VMS command files, and the hardcopy plots are being boxed for shipment to the NSSDC.

Measurements of CO2 Mole Fractionand δ13C in Archived Air Samples from Cape Meares, Oregon (USA) 1977 - 1998

NASA Astrophysics Data System (ADS)

Clark, O.; Rice, A. L.

2017-12-01

Carbon dioxide (CO2) is the most abundant, anthropogenically forced greenhouse gas (GHG) in the global atmosphere. Emissions of CO2 account for approximately 75% of the world's total GHG emissions. Atmospheric concentrations of CO2 are higher now than they've been at any other time in the past 800,000 years. Currently, the global mean concentration exceeds 400 ppm. Today, global networks regularly monitor CO2 concentrations and isotopic composition (δ13C and δ18O). However, past data is sparse. Over 200 ambient air samples from Cape Meares, Oregon (45.5°N, 124.0°W), a coastal site in Western United States, were obtained by researchers at Oregon Institute of Science and Technology (OGI, now Oregon Health & Science University), between the years of 1977 and 1998 as part of a global monitoring program of six different sites in the polar, middle, and tropical latitudes of the Northern and Southern Hemispheres. Air liquefaction was used to compress approximately 1000L of air (STP) to 30bar, into 33L electropolished (SUMMA) stainless steel canisters. Select archived air samples from the original network are maintained at Portland State University (PSU) Department of Physics. These archived samples are a valuable look at changing atmospheric concentrations of CO2 and δ13C, which can contribute to a better understanding of changes in sources during this time. CO2 concentrations and δ13C of CO2 were measured at PSU, with a Picarro Cavity Ringdown Spectrometer, model G1101-i analytical system. This study presents the analytical methods used, calibration techniques, precision, and reproducibility. Measurements of select samples from the archive show rising CO2 concentrations and falling δ13C over the 1977 to 1998 period, compatible with previous observations and rising anthropogenic sources of CO2. The resulting data set was statistically analyzed in MATLAB. Results of preliminary seasonal and secular trends from the archive samples are presented.

Research on heating, instabilities, turbulence and RF emission from electric field dominated plasmas

NASA Astrophysics Data System (ADS)

Roth, J. R.; Alexeff, Igor

1989-07-01

This contract has supported four research programs: (1) a program of research on plasma turbulence; (2) a program of research on plasma heating by collisional magnetic pumping; (3) a research program on the Orbitron submillimeter maser; and (4) the initial phase of a program on plasma cloaking of military targets for protection against radar and directed microwave energy weapons. Progress in these areas is documented in the text of this final report and in the twenty archival publications included in the appendices to this report. In addition to the above four research areas, work was continued on plasma diagnostic development, and the development of new state-of-the-art data analysis and reduction methods, including software development for online reduction of Langmuir probe, capacitive probe, and other diagnostic information. Also being developed is the capability to analyze electrostatic potential fluctuations by the methods of nonlinear dynamics. An important part of the research program was the training of graduate and undergraduate research assistants in state-of-the-art methods in the fields of high temperature plasma physics, plasma diagnostics, communications, and related areas.

The Cancer Digital Slide Archive - TCGA

Cancer.gov

Dr. David Gutman and Dr. Lee Cooper developed The Cancer Digital Slide Archive (CDSA), a web platform for accessing pathology slide images of TCGA samples. Find out how they did it and how to use the CDSA website in this Case Study.

Indirect Solar Wind Measurements Using Archival Cometary Tail Observations

NASA Astrophysics Data System (ADS)

Zolotova, Nadezhda; Sizonenko, Yuriy; Vokhmyanin, Mikhail; Veselovsky, Igor

2018-05-01

This paper addresses the problem of the solar wind behaviour during the Maunder minimum. Records on plasma tails of comets can shed light on the physical parameters of the solar wind in the past. We analyse descriptions and drawings of comets between the eleventh and eighteenth century. To distinguish between dust and plasma tails, we address their colour, shape, and orientation. Based on the calculations made by F.A. Bredikhin, we found that cometary tails deviate from the antisolar direction on average by more than 10°, which is typical for dust tails. We also examined the catalogues of Hevelius and Lubieniecki. The first indication of a plasma tail was revealed only for the great comet C/1769 P1.

Three Proposed Compendia for Genesis Solar Wind Samples: Science Results, Collector Materials Characterization and Cleaning Techniques

NASA Technical Reports Server (NTRS)

Allton, J. H.; Calaway, M. J.; Nyquist, L. E.; Jurewicz, A. J. G.; Burnett, D. S.

2018-01-01

Final Paper and not the abstract is attached. Introduction: Planetary material and cosmochemistry research using Genesis solar wind samples (including the development and implementation of cleaning and analytical techniques) has matured sufficiently that compilations on several topics, if made publically accessible, would be beneficial for researchers and reviewers. We propose here three compendia based on content, organization and source of documents (e.g. published peer-reviewed, published, internal memos, archives). For planning purposes, suggestions are solicited from potential users of Genesis solar wind samples for the type of science content and/or organizational style that would be most useful to them. These compendia are proposed as living documents, periodically updated. Similar to the existing compendia described below, the curation compendia are like library or archival finding aids, they are guides to published or archival documents and should not be cited as primary sources.

Identification of mycotoxins by UHPLC–QTOF MS in airborne fungi and fungi isolated from industrial paper and antique documents from the Archive of Bogotá

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

Castillo, Nancy I.; Ibáñez, María; Beltrán, Eduardo

Mold deterioration of historical documents in archives and libraries is a frequent and complex phenomenon that may have important economic and cultural consequences. In addition, exposure to toxic fungal metabolites might produce health problems. In this work, samples of broths of fungal species isolated from the documentary material and from indoor environmental samples of the Archive of Bogotá have been analyzed to investigate the presence of mycotoxins. High resolution mass spectrometry made possible to search for a large number of mycotoxins, even without reference standards available at the laboratory. For this purpose, a screening strategy based on ultra-high pressure liquidmore » chromatography coupled to quadrupole-time of flight mass spectrometry (UHPLC–QTOF MS) under MS{sup E} mode was applied. A customized home-made database containing elemental composition for around 600 mycotoxins was compiled. The presence of the (de)protonated molecule measured at its accurate mass was evaluated in the samples. When a peak was detected, collision induced dissociation fragments and characteristic isotopic ions were also evaluated and used for tentative identification, based on structure compatibility and comparison with literature data (if existing). Up to 44 mycotoxins were tentatively identified by UHPLC–QTOF MS. 34 of these tentative compounds were confirmed by subsequent analysis using a targeted LC–MS/MS method, supporting the strong potential of QTOF MS for identification/elucidation purposes. The presence of mycotoxins in these samples might help to reinforce safety measures for researchers and staff who work on reception, restoration and conservation of archival material, not only at the Archive of Bogotá but worldwide. - Highlights: • Mold deterioration of historical documents is a frequent and complex phenomenon. • Samples of broths of fungal species isolated from Archive of Bogotá analyzed. • UHPLC–QTOF MS (MS{sup E}) applied for mycotoxins screening, without reference standards. • Customized home-made database for around 600 mycotoxins compiled. • 44 mycotoxins tentatively identified, 34 of which confirmed by LC–MS/MS.« less

Kinetics, Longevity, and Cross-Reactivity of Antineuraminidase Antibody after Natural Infection with Influenza A Viruses.

PubMed

Changsom, Don; Jiang, Li; Lerdsamran, Hatairat; Iamsirithaworn, Sopon; Kitphati, Rungrueng; Pooruk, Phisanu; Auewarakul, Prasert; Puthavathana, Pilaipan

2017-12-01

The kinetics, longevity, and breadth of antibodies to influenza virus neuraminidase (NA) in archival, sequential serum/plasma samples from influenza A virus (IAV) H5N1 infection survivors and from patients infected with the 2009 pandemic IAV (H1N1) virus were determined using an enzyme-linked lectin-based assay. The reverse-genetics-derived H4N1 viruses harboring a hemagglutinin (HA) segment from A/duck/Shan Tou/461/2000 (H4N9) and an NA segment derived from either IAV H5N1 clade 1, IAV H5N1 clade 2.3.4, the 2009 pandemic IAV (H1N1) (H1N1pdm), or A/Puerto Rico/8/1934 (H1N1) virus were used as the test antigens. These serum/plasma samples were also investigated by microneutralization (MN) and/or hemagglutination inhibition (HI) assays. Neuraminidase-inhibiting (NI) antibodies against N1 NA of both homologous and heterologous viruses were observed in H5N1 survivors and H1N1pdm patients. H5N1 survivors who were never exposed to H1N1pdm virus developed NI antibodies to H1N1pdm NA. Seroconversion of NI antibodies was observed in 65% of the H1N1pdm patients at day 7 after disease onset, but an increase in titer was not observed in serum samples obtained late in infection. On the other hand, an increase in seroconversion rate with the HI assay was observed in the follow-up series of sera obtained on days 7, 14, 28, and 90 after infection. The study also showed that NI antibodies are broadly reactive, while MN and HI antibodies are more strain specific. Copyright © 2017 American Society for Microbiology.

Minireview: Hair Cortisol: A Novel Biomarker of Hypothalamic-Pituitary-Adrenocortical Activity

PubMed Central

Novak, Melinda A.

2012-01-01

Activity of the hypothalamic-pituitary-adrenocortical (HPA) axis is commonly assessed by measuring glucocorticoids such as cortisol (CORT). For many years, CORT was obtained primarily from blood plasma or urine, whereas later approaches added saliva and feces for noninvasive monitoring of HPA functioning. Despite the value of all these sample matrices for answering many research questions, they remain limited in the temporal range of assessment. Plasma and saliva are point samples that vary as a function of circadian rhythmicity and are susceptible to confounding by environmental disturbances. Even urine and feces generally assess HPA activity over a period of only 24 h or less. We and others have recently developed and validated methods for measuring the concentration of CORT in the body hair of animals (e.g. rhesus monkeys) and scalp hair of humans. CORT is constantly deposited in the growing hair shaft, as a consequence of which such deposition can serve as a biomarker of integrated HPA activity over weeks and months instead of minutes or hours. Since the advent of this methodological advance, hair CORT has already been used as an index of chronic HPA activity and stress in human clinical and nonclinical populations, in a variety of laboratory-housed and wild-living animal species, and in archival specimens that are many decades or even centuries old. Moreover, because human hair is known to grow at an average rate of about 1 cm/month, several studies suggest that CORT levels in hair segments that differ in proximity to the scalp can, under certain conditions, be used as a retrospective calendar of HPA activity during specific time periods preceding sample collection. PMID:22778226

Post-mortem testing; germline BRCA1/2 variant detection using archival FFPE non-tumor tissue. A new paradigm in genetic counseling.

PubMed

Petersen, Annabeth Høgh; Aagaard, Mads Malik; Nielsen, Henriette Roed; Steffensen, Karina Dahl; Waldstrøm, Marianne; Bojesen, Anders

2016-08-01

Accurate estimation of cancer risk in HBOC families often requires BRCA1/2 testing, but this may be impossible in deceased family members. Previous, testing archival formalin-fixed, paraffin-embedded (FFPE) tissue for germline BRCA1/2 variants was unsuccessful, except for the Jewish founder mutations. A high-throughput method to systematically test for variants in all coding regions of BRCA1/2 in archival FFPE samples of non-tumor tissue is described, using HaloPlex target enrichment and next-generation sequencing. In a validation study, correct identification of variants or wild-type was possible in 25 out of 30 (83%) FFPE samples (age range 1-14 years), with a known variant status in BRCA1/2. No false positive was found. Unsuccessful identification was due to highly degraded DNA or presence of large intragenic deletions. In clinical use, a total of 201 FFPE samples (aged 0-43 years) were processed. Thirty-six samples were rejected because of highly degraded DNA or failed library preparation. Fifteen samples were investigated to search for a known variant. In the remaining 150 samples (aged 0-38 years), three variants known to affect function and one variant likely to affect function in BRCA1, six variants known to affect function and one variant likely to affect function in BRCA2, as well as four variants of unknown significance (VUS) in BRCA1 and three VUS in BRCA2 were discovered. It is now possible to test for germline BRCA1/2 variants in deceased persons, using archival FFPE samples from non-tumor tissue. Accurate genetic counseling is achievable in families where variant testing would otherwise be impossible.

Post-mortem testing; germline BRCA1/2 variant detection using archival FFPE non-tumor tissue. A new paradigm in genetic counseling

PubMed Central

Petersen, Annabeth Høgh; Aagaard, Mads Malik; Nielsen, Henriette Roed; Steffensen, Karina Dahl; Waldstrøm, Marianne; Bojesen, Anders

2016-01-01

Accurate estimation of cancer risk in HBOC families often requires BRCA1/2 testing, but this may be impossible in deceased family members. Previous, testing archival formalin-fixed, paraffin-embedded (FFPE) tissue for germline BRCA1/2 variants was unsuccessful, except for the Jewish founder mutations. A high-throughput method to systematically test for variants in all coding regions of BRCA1/2 in archival FFPE samples of non-tumor tissue is described, using HaloPlex target enrichment and next-generation sequencing. In a validation study, correct identification of variants or wild-type was possible in 25 out of 30 (83%) FFPE samples (age range 1–14 years), with a known variant status in BRCA1/2. No false positive was found. Unsuccessful identification was due to highly degraded DNA or presence of large intragenic deletions. In clinical use, a total of 201 FFPE samples (aged 0–43 years) were processed. Thirty-six samples were rejected because of highly degraded DNA or failed library preparation. Fifteen samples were investigated to search for a known variant. In the remaining 150 samples (aged 0–38 years), three variants known to affect function and one variant likely to affect function in BRCA1, six variants known to affect function and one variant likely to affect function in BRCA2, as well as four variants of unknown significance (VUS) in BRCA1 and three VUS in BRCA2 were discovered. It is now possible to test for germline BRCA1/2 variants in deceased persons, using archival FFPE samples from non-tumor tissue. Accurate genetic counseling is achievable in families where variant testing would otherwise be impossible. PMID:26733283

The Hubble Spectroscopic Legacy Archive

NASA Astrophysics Data System (ADS)

Peeples, M.; Tumlinson, J.; Fox, A.; Aloisi, A.; Fleming, S.; Jedrzejewski, R.; Oliveira, C.; Ayres, T.; Danforth, C.; Keeney, B.; Jenkins, E.

2017-04-01

With no future space ultraviolet instruments currently planned, the data from the UV spectrographs aboard the Hubble Space Telescope have a legacy value beyond their initial science goals. The goal of the Hubble Spectroscopic Legacy Archive(HSLA) is to provide to the community new science-grade combined spectra for all publicly available data obtained by the Cosmic Origins Spectrograph (COS)and the Space Telescope Imaging Spectrograph (STIS). These data are packaged into "smart archives" according to target type and scientific themes to facilitate the construction of archival samples for common science uses. A new "quick look" capability makes the data easy for users to quickly access, assess the quality of,and download for archival science. The first generation of these products for the far-ultraviolet (FUV) modes of COS was made available online via the Mikulski Archive for Space Telescopes (MAST) in early 2016 and updated in early 2017; future releases will include COS/NUV and STIS/UV data.

Identification of mycotoxins by UHPLC-QTOF MS in airborne fungi and fungi isolated from industrial paper and antique documents from the Archive of Bogotá.

PubMed

Castillo, Nancy I; Ibáñez, María; Beltrán, Eduardo; Rivera-Monroy, Jhon; Ochoa, Juan Camilo; Páez-Castillo, Mónica; Posada-Buitrago, Martha L; Sulyok, Michael; Hernández, Félix

2016-01-01

Mold deterioration of historical documents in archives and libraries is a frequent and complex phenomenon that may have important economic and cultural consequences. In addition, exposure to toxic fungal metabolites might produce health problems. In this work, samples of broths of fungal species isolated from the documentary material and from indoor environmental samples of the Archive of Bogotá have been analyzed to investigate the presence of mycotoxins. High resolution mass spectrometry made possible to search for a large number of mycotoxins, even without reference standards available at the laboratory. For this purpose, a screening strategy based on ultra-high pressure liquid chromatography coupled to quadrupole-time of flight mass spectrometry (UHPLC-QTOF MS) under MS(E) mode was applied. A customized home-made database containing elemental composition for around 600 mycotoxins was compiled. The presence of the (de)protonated molecule measured at its accurate mass was evaluated in the samples. When a peak was detected, collision induced dissociation fragments and characteristic isotopic ions were also evaluated and used for tentative identification, based on structure compatibility and comparison with literature data (if existing). Up to 44 mycotoxins were tentatively identified by UHPLC-QTOF MS. 34 of these tentative compounds were confirmed by subsequent analysis using a targeted LC-MS/MS method, supporting the strong potential of QTOF MS for identification/elucidation purposes. The presence of mycotoxins in these samples might help to reinforce safety measures for researchers and staff who work on reception, restoration and conservation of archival material, not only at the Archive of Bogotá but worldwide. Copyright © 2015 Elsevier Inc. All rights reserved.

The Hubble Spectroscopic Legacy Archive

NASA Astrophysics Data System (ADS)

Peeples, Molly S.; Tumlinson, Jason; Fox, Andrew; Aloisi, Alessandra; Ayres, Thomas R.; Danforth, Charles; Fleming, Scott W.; Jenkins, Edward B.; Jedrzejewski, Robert I.; Keeney, Brian A.; Oliveira, Cristina M.

2016-01-01

With no future space ultraviolet instruments currently planned, the data from the UV spectrographs aboard the Hubble Space Telescope have a legacy value beyond their initial science goals. The Hubble Spectroscopic Legacy Archive will provide to the community new science-grade combined spectra for all publicly available data obtained by the Cosmic Origins Spectrograph (COS) and the Space Telescope Imaging Spectrograph (STIS). These data will be packaged into "smart archives" according to target type and scientific themes to facilitate the construction of archival samples for common science uses. A new "quick look" capability will make the data easy for users to quickly access, assess the quality of, and download for archival science starting in Cycle 24, with the first generation of these products for the FUV modes of COS available online via MAST in early 2016.

STABLE ISOPTOPE RATIOS IN ARCHIVED STRIPED BASS SCALES SUGGEST CHANGES IN TROPHIC STRUCTURE

EPA Science Inventory

Stable carbon isotope ratios were measured in archived striped bass, Morone saxatilis (Walbaum), scales to identify changes in the feeding behaviour of this species over time. Striped bass tissue and scale samples were collected from Rhode Island coastal waters during 1996 and ar...

U/Th dating by SHRIMP RG ion-microprobe mass spectrometry using single ion-exchange beads

NASA Astrophysics Data System (ADS)

Bischoff, James L.; Wooden, Joe; Murphy, Fred; Williams, Ross W.

2005-04-01

We present a new analytical method for U-series isotopes using the SHRIMP RG (Sensitive High mass Resolution Ion MicroProbe) mass spectrometer that utilizes the preconcentration of the U-series isotopes from a sample onto a single ion-exchange bead. Ion-microprobe mass spectrometry is capable of producing Th ionization efficiencies in excess of 2%. Analytical precision is typically better than alpha spectroscopy, but not as good as thermal ionization mass spectroscopy (TIMS) and inductively coupled plasma multicollector mass spectrometry (ICP-MS). Like TIMS and ICP-MS the method allows analysis of small samples sizes, but also adds the advantage of rapidity of analysis. A major advantage of ion-microprobe analysis is that U and Th isotopes are analyzed in the same bead, simplifying the process of chemical separation. Analytical time on the instrument is ˜60 min per sample, and a single instrument-loading can accommodate 15-20 samples to be analyzed in a 24-h day. An additional advantage is that the method allows multiple reanalyses of the same bead and that samples can be archived for reanalysis at a later time. Because the ion beam excavates a pit only a few μm deep, the mount can later be repolished and reanalyzed numerous times. The method described of preconcentrating a low concentration sample onto a small conductive substrate to allow ion-microprobe mass spectrometry is potentially applicable to many other systems.

U/Th dating by SHRIMP RG ion-microprobe mass spectrometry using single ion-exchange beads

USGS Publications Warehouse

Bischoff, J.L.; Wooden, J.; Murphy, F.; Williams, Ross W.

2005-01-01

We present a new analytical method for U-series isotopes using the SHRIMP RG (Sensitive High mass Resolution Ion MicroProbe) mass spectrometer that utilizes the preconcentration of the U-series isotopes from a sample onto a single ion-exchange bead. Ion-microprobe mass spectrometry is capable of producing Th ionization efficiencies in excess of 2%. Analytical precision is typically better than alpha spectroscopy, but not as good as thermal ionization mass spectroscopy (TIMS) and inductively coupled plasma multicollector mass spectrometry (ICP-MS). Like TIMS and ICP-MS the method allows analysis of small samples sizes, but also adds the advantage of rapidity of analysis. A major advantage of ion-microprobe analysis is that U and Th isotopes are analyzed in the same bead, simplifying the process of chemical separation. Analytical time on the instrument is ???60 min per sample, and a single instrument-loading can accommodate 15-20 samples to be analyzed in a 24-h day. An additional advantage is that the method allows multiple reanalyses of the same bead and that samples can be archived for reanalysis at a later time. Because the ion beam excavates a pit only a few ??m deep, the mount can later be repolished and reanalyzed numerous times. The method described of preconcentrating a low concentration sample onto a small conductive substrate to allow ion-microprobe mass spectrometry is potentially applicable to many other systems. Copyright ?? 2005 Elsevier Ltd.

Chemical Analysis Results for Potable Water from ISS Expeditions 21 Through 25

NASA Technical Reports Server (NTRS)

Straub, John E., II; Plumlee, Debrah K.; Schultz, John R.; McCoy, J. Torin

2011-01-01

The Johnson Space Center Water and Food Analytical Laboratory (WAFAL) performed detailed ground-based analyses of archival water samples for verification of the chemical quality of the International Space Station (ISS) potable water supplies for Expeditions 21 through 25. Over a 14-month period the Space Shuttle visited the ISS on four occasions to complete construction and deliver supplies. The onboard supplies of potable water available for consumption by the Expeditions 21 to 25 crews consisted of Russian ground-supplied potable water, Russian potable water regenerated from humidity condensate, and US potable water recovered from urine distillate and condensate. Chemical archival water samples that were collected with U.S. hardware during Expeditions 21 to 25 were returned on Shuttle flights STS-129 (ULF3), STS-130 (20A), STS-131 (19A), and STS-132 (ULF4), as well as on Soyuz flights 19-23. This paper reports the analytical results for these returned potable water archival samples and their compliance with ISS water quality standards.

Systematic Evaluation of the Use of Human Plasma and Serum for Mass-Spectrometry-Based Shotgun Proteomics.

PubMed

Lan, Jiayi; Núñez Galindo, Antonio; Doecke, James; Fowler, Christopher; Martins, Ralph N; Rainey-Smith, Stephanie R; Cominetti, Ornella; Dayon, Loïc

2018-04-06

Over the last two decades, EDTA-plasma has been used as the preferred sample matrix for human blood proteomic profiling. Serum has also been employed widely. Only a few studies have assessed the difference and relevance of the proteome profiles obtained from plasma samples, such as EDTA-plasma or lithium-heparin-plasma, and serum. A more complete evaluation of the use of EDTA-plasma, heparin-plasma, and serum would greatly expand the comprehensiveness of shotgun proteomics of blood samples. In this study, we evaluated the use of heparin-plasma with respect to EDTA-plasma and serum to profile blood proteomes using a scalable automated proteomic pipeline (ASAP 2 ). The use of plasma and serum for mass-spectrometry-based shotgun proteomics was first tested with commercial pooled samples. The proteome coverage consistency and the quantitative performance were compared. Furthermore, protein measurements in EDTA-plasma and heparin-plasma samples were comparatively studied using matched sample pairs from 20 individuals from the Australian Imaging, Biomarkers and Lifestyle (AIBL) Study. We identified 442 proteins in common between EDTA-plasma and heparin-plasma samples. Overall agreement of the relative protein quantification between the sample pairs demonstrated that shotgun proteomics using workflows such as the ASAP 2 is suitable in analyzing heparin-plasma and that such sample type may be considered in large-scale clinical research studies. Moreover, the partial proteome coverage overlaps (e.g., ∼70%) showed that measures from heparin-plasma could be complementary to those obtained from EDTA-plasma.

The GIK-Archive of sediment core radiographs with documentation

NASA Astrophysics Data System (ADS)

Grobe, Hannes; Winn, Kyaw; Werner, Friedrich; Driemel, Amelie; Schumacher, Stefanie; Sieger, Rainer

2017-12-01

The GIK-Archive of radiographs is a collection of X-ray negative and photographic images of sediment cores based on exposures taken since the early 1960s. During four decades of marine geological work at the University of Kiel, Germany, several thousand hours of sampling, careful preparation and X-raying were spent on producing a unique archive of sediment radiographs from several parts of the World Ocean. The archive consists of more than 18 500 exposures on chemical film that were digitized, geo-referenced, supplemented with metadata and archived in the data library PANGAEA®. With this publication, the images have become available open-access for use by the scientific community at https://doi.org/10.1594/PANGAEA.854841.

The SHADOZ Data Base: History, Archive Web Guide, and Sample Climatologies

NASA Technical Reports Server (NTRS)

White, J. C.; Thompson, A. M.; Einaudi, Franco (Technical Monitor)

2000-01-01

SHADOZ (Southern Hemisphere Additional Ozonesonde) is a project to augment and archive ozonesonde data from ten tropical and subtropical ozone stations. Started in 1998 by NASA's Goddard Space Flight Center and other US and international co-investigators, SHADOZ is an important tool for tropospheric ozone research in the equatorial region. The rationale for SHADOZ is to: (1) validate and improve remote sensing techniques (e.g., the Total Ozone Mapping Spectrometer (TOMS) satellite) for estimating tropical ozone, (2) contribute to climatology and trend analyses of tropical ozone and (3) provide research topics to scientists and educate students, especially in participating countries. SHADOZ is envisioned as a data service to the global scientific community by providing a central public archive location via the internet: http://code9l6.gsfc.nasa.gov/Data_services/shadoz. While the SHADOZ website maintains a standard data format for the archive, it also informs the data users on the differing stations' preparation techniques and data treatment. The presentation navigates through the SHADOZ website to access each station's sounding data and summarize each station's characteristics. Since the start of the project in 1998, the SHADOZ archive has accumulated over 600 ozonesonde profiles and received over 30,000 outside data requests. Data also includes launches from various SHADOZ supported field campaigns, such as, the Indian Ocean Experiment (INDOEX), Sounding of Ozone and Water in the Equatorial Region (SOWER) and Aerosols99 Atlantic Cruise. Using data from the archive, sample climatologies and profiles from selected stations and campaigns will be shown.

Histopathological findings in immunohistological staining of the granulomatous tissue reaction associated with tuberculosis.

PubMed

Karimi, Shirin; Shamaei, Masoud; Pourabdollah, Mihan; Sadr, Makan; Karbasi, Mehrdad; Kiani, Arda; Bahadori, Moslem

2014-01-01

Purpose. The histological diagnosis of Mycobacterium tuberculosis (MTB) remains a diagnostic challenge despite different methods. Immunohistochemistry (IHC) not only could confirm granulomatous tissue involvement but also can demonstrate MTB antigen immunolocalization. This study tries to clarify the details of immunohistochemical staining for MTB with pAbBCG. Materials/Methods. Twenty-three confirmed TB granulomatous tissue samples were studied by Ziehl-Neelsen and immunohistochemistry (IHC) staining with pAbBCG. Samples were selected from the archive of the Department of Pathology, National Research Institute of Tuberculosis and Lung Disease, Tehran, Iran. Results. IHC staining was positive in all samples, whereas Ziehl-Neelsen was positive in 9 cases out of 23 (39.1%). Tissue types used were pleural tissue, lymph nodes, and lung tissue. IHC showed positive coarse granular cytoplasmic and round, fragmented bacillary staining. In this study, epithelioid cells clearly showed more positive staining at the periphery of the granuloma rather than the center of granuloma. There is also positive staining in endothelial cells, fibroblasts, plasma cells, lymphocytes, and macrophages outside the granuloma. Conclusion. Considering the criteria of positive immunohistochemical staining of TB granulomatous reactions, this stain not only highlights the presence of mycobacterial antigens for tissue diagnosis, but also could morphologically localize its distribution in different cells.

Histopathological Findings in Immunohistological Staining of the Granulomatous Tissue Reaction Associated with Tuberculosis

PubMed Central

Karimi, Shirin; Pourabdollah, Mihan; Sadr, Makan; Karbasi, Mehrdad; Bahadori, Moslem

2014-01-01

Purpose. The histological diagnosis of Mycobacterium tuberculosis (MTB) remains a diagnostic challenge despite different methods. Immunohistochemistry (IHC) not only could confirm granulomatous tissue involvement but also can demonstrate MTB antigen immunolocalization. This study tries to clarify the details of immunohistochemical staining for MTB with pAbBCG. Materials/Methods. Twenty-three confirmed TB granulomatous tissue samples were studied by Ziehl-Neelsen and immunohistochemistry (IHC) staining with pAbBCG. Samples were selected from the archive of the Department of Pathology, National Research Institute of Tuberculosis and Lung Disease, Tehran, Iran. Results. IHC staining was positive in all samples, whereas Ziehl-Neelsen was positive in 9 cases out of 23 (39.1%). Tissue types used were pleural tissue, lymph nodes, and lung tissue. IHC showed positive coarse granular cytoplasmic and round, fragmented bacillary staining. In this study, epithelioid cells clearly showed more positive staining at the periphery of the granuloma rather than the center of granuloma. There is also positive staining in endothelial cells, fibroblasts, plasma cells, lymphocytes, and macrophages outside the granuloma. Conclusion. Considering the criteria of positive immunohistochemical staining of TB granulomatous reactions, this stain not only highlights the presence of mycobacterial antigens for tissue diagnosis, but also could morphologically localize its distribution in different cells. PMID:24511393

Extracting DNA from 'jaws': high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material.

PubMed

Nielsen, E E; Morgan, J A T; Maher, S L; Edson, J; Gauthier, M; Pepperell, J; Holmes, B J; Bennett, M B; Ovenden, J R

2017-05-01

Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high-yield sources of DNA for genomic-scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield. © 2016 John Wiley & Sons Ltd.

Migration Stories: Upgrading a PDS Archive to PDS4

NASA Astrophysics Data System (ADS)

Kazden, D. P.; Walker, R. J.; Mafi, J. N.; King, T. A.; Joy, S. P.; Moon, I. S.

2015-12-01

Increasing bandwidth, storage capacity and computational capabilities have greatly increased our ability to access data and use them. A significant challenge, however, is to make data archived under older standards useful in the new data environments. NASA's Planetary Data System (PDS) recently released version 4 of its information model (PDS4). PDS4 is an improvement and has advantages over previous versions. PDS4 adopts the XML standard for metadata and expresses structural requirements with XML Schema and content constraints by using Schematron. This allows for thorough validation by using off the shelf tools. This is a substantial improvement over previous PDS versions. PDS4 was designed to improve discoverability of products (resources) in a PDS archive. These additions allow for more uniform metadata harvesting from the collection level to the product level. New tools and services are being deployed that depend on the data adhering to the PDS4 model. However, the PDS has been an operational archive since 1989 and has large holdings that are compliant with previous versions of the PDS information model. The challenge is the make the older data accessible and useable with the new PDS4 based tools. To provide uniform utility and access to the entire archive the older data must be migrated to the PDS4 model. At the Planetary Plasma Interactions (PPI) Node of the PDS we've been actively planning and preparing to migrate our legacy archive to the new PDS4 standards for several years. With the release of the PDS4 standards we have begun the migration of our archive. In this presentation we will discuss the preparation of the data for the migration and how we are approaching this task. The presentation will consist of a series of stories to describe our experiences and the best practices we have learned.

Comparison of biochemical values in serum and plasma, fresh and frozen plasma, and hemolyzed samples from orange-winged Amazon parrots (Amazona amazonica).

PubMed

Hawkins, Michelle G; Kass, Philip H; Zinkl, Joseph G; Tell, Lisa A

2006-06-01

To the authors' knowledge, on the basis of sample type, storage condition, or hemolysis, differences in serum and plasma biochemical values have not been evaluated in orange-winged Amazon parrots (Amazona amazonica). The purpose of this study was to compare values for biochemical analytes in serum vs plasma, fresh vs frozen plasma, and nonhemolyzed vs hemolyzed samples in orange-winged Amazon parrots. We also compared differences in serum and plasma yield from whole-blood aliquots. Fifteen biochemical analytes were evaluated in paired serum and plasma, fresh and frozen plasma, nonhemolyzed and hemolyzed serum and plasma samples from orange-winged Amazon parrots (n = 10) using a wet reagent analyzer. Hemolysis was assessed qualitatively (visually) and quantitatively (hemoglobin [Hgb] measured spectrophotometrically). Serum and plasma yields from 500-microl whole-blood aliquots were determined from centrifuged samples. Analyte values significantly differed among sample groups, but were still within published reference intervals, with the exception of increases in potassium concentration in markedly hemolyzed serum and plasma samples. Clinically important changes in hemolyzed serum and plasma samples included increases in potassium, phosphorus, and albumin concentrations and lactate dehydrogenase activity. The degree of hemolysis assigned qualitatively did not correlate with quantitative Hgb concentration. A significantly greater yield of plasma (288 +/- 13 microL) than serum (241 +/- 44 microL) was obtained. Significant differences may occur in different sample types, however, only changes in potassium, phosphorus, albumin, and lactate dehydrogenase values in hemolyzed samples were considered clinically relevant. Lack of agreement between qualitative and quantitative Hgb concentration indicates the unreliability of visual estimation. Based on higher sample yield, and lack of clinically relevant differences from serum, plasma is a better sample choice for clinical chemistry analysis in birds.

VizieR Online Data Catalog: Galaxies and QSOs FIR size and surface brightness (Lutz+, 2016)

NASA Astrophysics Data System (ADS)

Lutz, D.; Berta, S.; Contursi, A.; Forster Schreiber, N. M.; Genzel, R.; Gracia-Carpio, J.; Herrera-Camus, R.; Netzer, H.; Sturm, E.; Tacconi, L. J.; Tadaki, K.; Veilleux, S.

2016-08-01

We use 70, 100, and 160um images from scan maps obtained with PACS on board Herschel, collecting archival data from various projects. In order to cover a wide range of galaxy properties, we first obtain an IR-selected local sample ranging from normal galaxies up to (ultra)luminous infrared galaxies. For that purpose, we searched the Herschel archive for all cz>=2000km/s objects from the IRAS Revised Bright Galaxy Sample (RBGS, Sanders et al., 2003, Cat. J/AJ/126/1607). (1 data file).

The DMSP Space Weather Sensors Data Archive Listing (1982-2013) and File Formats Descriptions

DTIC Science & Technology

2014-08-01

environment sensors including the auroral particle spectrometer (SSJ), the fluxgate magnetometer (SSM), the topside thermal plasma monitor (SSIES... Fluxgate Magnetometer (SSM) for the Defense Meteorological Satellite Program (DMSP) Block 5D-2, Flight 7, Instrument Papers, AFGL-TR-84-0225; ADA155229...Flux) SSM The fluxgate magnetometer . (Special Sensor, Magnetometer ) SSULI The ultraviolet limb imager SSUSI The ultraviolet spectrographic imager

Archival analyses of eyewitness identification test outcomes: what can they tell us about eyewitness memory?

PubMed

Horry, Ruth; Halford, Paul; Brewer, Neil; Milne, Rebecca; Bull, Ray

2014-02-01

Several archival studies of eyewitness identification have been conducted, but the results have been inconsistent and contradictory. We identify some avoidable pitfalls that have been present in previous analyses and present new data that address these pitfalls. We explored associations among various estimator variables and lineup outcomes for 833 "real life" lineups, including 588 lineups in which corroborating evidence of the suspect's guilt existed. Suspect identifications were associated with exposure duration, viewing distance, and the age of the witness. Nonidentifications were associated with the number of perpetrators. We also consider some of the inherent, unavoidable limitations with archival studies and consider what such studies can really tell researchers. We conclude that differences in sampling prohibit sensible comparisons between the results of laboratory and archival studies, and that the informational value of archival studies is actually rather limited.

MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive.

PubMed

Bernstein, Matthew N; Doan, AnHai; Dewey, Colin N

2017-09-15

The NCBI's Sequence Read Archive (SRA) promises great biological insight if one could analyze the data in the aggregate; however, the data remain largely underutilized, in part, due to the poor structure of the metadata associated with each sample. The rules governing submissions to the SRA do not dictate a standardized set of terms that should be used to describe the biological samples from which the sequencing data are derived. As a result, the metadata include many synonyms, spelling variants and references to outside sources of information. Furthermore, manual annotation of the data remains intractable due to the large number of samples in the archive. For these reasons, it has been difficult to perform large-scale analyses that study the relationships between biomolecular processes and phenotype across diverse diseases, tissues and cell types present in the SRA. We present MetaSRA, a database of normalized SRA human sample-specific metadata following a schema inspired by the metadata organization of the ENCODE project. This schema involves mapping samples to terms in biomedical ontologies, labeling each sample with a sample-type category, and extracting real-valued properties. We automated these tasks via a novel computational pipeline. The MetaSRA is available at metasra.biostat.wisc.edu via both a searchable web interface and bulk downloads. Software implementing our computational pipeline is available at http://github.com/deweylab/metasra-pipeline. cdewey@biostat.wisc.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Not the time or the place: the missing spatio-temporal link in publicly available genetic data.

PubMed

Pope, Lisa C; Liggins, Libby; Keyse, Jude; Carvalho, Silvia B; Riginos, Cynthia

2015-08-01

Genetic data are being generated at unprecedented rates. Policies of many journals, institutions and funding bodies aim to ensure that these data are publicly archived so that published results are reproducible. Additionally, publicly archived data can be 'repurposed' to address new questions in the future. In 2011, along with other leading journals in ecology and evolution, Molecular Ecology implemented mandatory public data archiving (the Joint Data Archiving Policy). To evaluate the effect of this policy, we assessed the genetic, spatial and temporal data archived for 419 data sets from 289 articles in Molecular Ecology from 2009 to 2013. We then determined whether archived data could be used to reproduce analyses as presented in the manuscript. We found that the journal's mandatory archiving policy has had a substantial positive impact, increasing genetic data archiving from 49 (pre-2011) to 98% (2011-present). However, 31% of publicly archived genetic data sets could not be recreated based on information supplied in either the manuscript or public archives, with incomplete data or inconsistent codes linking genetic data and metadata as the primary reasons. While the majority of articles did provide some geographic information, 40% did not provide this information as geographic coordinates. Furthermore, a large proportion of articles did not contain any information regarding date of sampling (40%). Although the inclusion of spatio-temporal data does require an increase in effort, we argue that the enduring value of publicly accessible genetic data to the molecular ecology field is greatly compromised when such metadata are not archived alongside genetic data. © 2015 John Wiley & Sons Ltd.

A fast ultrasound-assisted extraction procedure for trace elements determination in hair samples by ICP-MS for forensic analysis.

PubMed

Batista, Bruno Lemos; Rodrigues, Jairo Lisboa; Souza, Vanessa Cristina de Oliveira; Barbosa, Fernando

2009-11-20

An ultrasound-assisted extraction method is proposed for the determination of trace elements in hair samples by inductively coupled plasma-mass spectrometry (ICP-MS) for forensic investigation. Prior to analysis, 25mg of hair samples were accurately weighed into (15 mL) conical tubes. Then, 2 mL of 20% HNO(3) is added to the samples, sonicated at 2 min (50W, 100% amplitude), and then further diluted to 10 mL with Milli-Q water. Resulted diluted slurries are centrifuged and the analytes are directly determined in the supernatant. Calibrations against aqueous solutions were carried out with rhodium as internal standard. The method was successfully applied for the extraction of Al, As, Ba, Be, Cd, Co, Cr, Cu, Mn, Pb, Tl, U, V and Zn with a method detection limit (3s, n=20) of 0.1, 0.4, 0.2, 0.09, 0.08, 0.04, 0.1, 2.9, 1.0, 0.9, 0.04, 0.05, 0.1 and 4.2 ng/g, respectively. Method accuracy is traceable to Certified Reference Materials (CRMs) 85 and 86 human hair from the International Atomic Energy Agency (IAEA). Additional validation data are provided based on the analysis of hair samples from the trace elements intercomparison program operated by the Institut National de Sante' Publique du Quebec, Canada. The proposed method is very simple and can be applied for forensic purposes with the elimination of sample digestion step prior to analysis. Then, a considerable improvement in the sample throughput is archived with the use of the proposed method.

The use of frozen plasma samples in thromboelastometry.

PubMed

Schoergenhofer, Christian; Buchtele, Nina; Schwameis, Michael; Bartko, Johann; Jilma, Bernd; Jilma-Stohlawetz, Petra

2017-11-01

Thromboelastometry is increasingly used in the clinical and scientific setting. The use of frozen plasma samples may be useful in overcoming certain limitations such as local and timely availability. Whole blood (WB) samples of 20 healthy volunteers were obtained, and plasma was generated. NATEM (n = 20), EXTEM (n = 20) and INTEM (n = 8) analyses were performed in WB, fresh plasma and frozen and thawed plasma. Dabigatran (500, 1000 ng/ml), rivaroxaban (100, 200 ng/ml) or alteplase (333 ng/ml) were added ex vivo to WB, and thromboelastometry was performed in WB and in frozen and thawed plasma samples. Clot formation time, mean clot firmness and the area under the curve were significantly altered in plasma compared to WB. In INTEM and EXTEM analysis, clotting time (CT) was comparable between WB (100%) and fresh (INTEM 114% and EXTEM 93%, ratio of the means) and frozen plasma samples (85 and 99%), whereas in NATEM analysis, the CT increased in fresh (193%) and frozen plasma samples (130%). Dabigatran dose-dependently increased the CT approximately 5- and 9-fold in WB and even more pronounced 10- and 26-fold in plasma. Accordingly, rivaroxaban dose-dependently increased the CT 2- and 2.7-fold in WB, and 3.5- and 4-fold in plasma samples. Hyperfibrinolysis was achieved by addition of alteplase in all WB samples and was reproducible in plasma samples. In conclusion, thromboelastometry, especially INTEM and EXTEM analyses, is possible using frozen and stored plasma samples with comparable results to the corresponding whole blood samples.

Trends of brominated diphenyl ethers in fresh and archived Great Lakes fish (1979-2005)

USGS Publications Warehouse

Batterman, Stuart; Chernyak, Sergei; Gwynn, Erica; Cantonwine, David; Jia, Chunrong; Begnoche, Linda J.; Hickey, James P.

2007-01-01

While few environmental measurements of brominated diphenyl ethers (BDEs) were completed prior to the mid-1990s, analysis of appropriately archived samples might enable the determination of contaminant trends back to the introduction of these chemicals. In this paper, we first investigate the stability of BDEs in archived frozen and extracted fish samples, and then characterize trends of these chemicals in rainbow smelt (Osmerus mordax) and lake trout (Salvelinus namaycush) in each of the Great Lakes between 1979 and 2005. We focus on the four most common congeners (BDE-47, 100, 99 and 153) and use a change-point analysis to detect shifts in trends. Analyses of archived fish samples yielded precise BDE concentration measurements with only small losses (0.8% per year in frozen fish tissues, 2.2% per year in refrigerated extracts). Trends in fish from all Great Lakes showed large increases in BDE concentrations that started in the early to mid-1980s with fairly consistent doubling times (generally 2–4 years except in Lake Erie smelt where levels increased very slowly), though concentrations and trends show differences by congener, fish species and lake. The most recent data show that accumulation rates are slowing, and concentrations of penta- and hexa-congeners in trout from Lakes Ontario and Michigan and smelt from Lake Ontario started to decrease in the mid-1990s. Trends in smelt and trout are evolving somewhat differently, and trout concentrations in the five lakes are now ranked as Michigan > Superior = Ontario > Huron = Erie, and smelt concentrations as Michigan > Ontario > Huron > Superior > Erie. The analysis of properly archived samples permits the reconstruction of historical trends, congener distributions, biomagnification and other information that can aid the understanding and management of these contaminants.

Epstein-Barr virus latent membrane protein-1 (LMP-1) 30-bp deletion and Xho I-loss is associated with type III nasopharyngeal carcinoma in Malaysia

PubMed Central

See, Hui Shien; Yap, Yoke Yeow; Yip, Wai Kien; Seow, Heng Fong

2008-01-01

Background Nasopharyngeal carcinoma (NPC) is a human epithelial tumour with high prevalence amongst Chinese in Southern China and South East Asia and is associated with the Epstein-Barr virus (EBV). The viral genome harbours an oncogene, namely, the latent membrane protein 1 (LMP1) gene and known variants such as the 30-bp deletion and loss of XhoI restriction site have been found. Less is known about the relationship between these variants and the population characteristics and histological type. Methods In this study, the EBV LMP1 gene variants from 42 NPC and 10 non-malignant archived formalin fixed, paraffin-embedded tissues, as well as plasma from another 35 patients with nasopharyngeal carcinoma were determined by using Polymerase Chain Reaction (PCR). Statistical analysis was performed by using SPSS programme. Results LMP1 30-bp deletion was detected in 19/34 (55.9%) of NPC tissues, 7/29 (24.1%) of plasma but absent in non-malignant tissues (8/8). Coexistence of variants with and without 30bp deletion was found only in 5/29 (17.2%) plasma samples but not in NPC tissues. The loss of XhoI restriction site in LMP1 gene was found in 34/39 (87.2%) of the NPC tissues and 11/30 (36.7%) of plasma samples. None of the non-malignant nasopharyngeal tissues (8/8) harbour XhoI-loss variants. LMP1 30-bp deletion was detected in 16/18 Chinese versus 3/15 Malays and 13/16 type III (undifferentiated carcinoma) versus 1/6 type I (keratinizing squamous cell carcinoma). XhoI-loss was found in 19/19 Chinese versus 14/19 Malays and 18/18 type III (undifferentiated) versus 2/5 type I (keratinizing squamous cell carcinoma). Statistical analysis showed that these variants were associated with ethnic race (30-bp deletion, p < 0.05; XhoI-loss, p = 0.046) and histological type of NPC (30-bp deletion, p = 0.011; XhoI-loss, p = 0.006). Nineteen out of 32 NPC tissues (19/32; 59.4%) and 6/24 (25%) of plasma samples showed the coexistence of both the 30-bp deletion and the loss of XhoI restriction site. A significant relationship was found with the Chinese race but not histological type. Conclusion The incidence rate of 56% for LMP1 30-bp deletion was lower compared to previously reported rates of 75–100% in NPC tissues. Coexistence of variants with and without 30-bp deletion was found only in 5/29 plasma samples. The incidence rate of XhoI restriction site loss in NPC was comparable to other studies from endemic regions such as Southern China. For the first time, the presence of LMP1 30-bp deletion or XhoI-loss was associated with the Chinese race and type III NPC. Both these variants were not found in non-malignant tissues. The influence of these variants on disease progression and outcome in Chinese and type III NPC requires further investigation. PMID:18275617

University Counseling Center Clients' Expressed Preferences for Counselors: A Four Year Archival Exploration

ERIC Educational Resources Information Center

Speight, Suzette L.; Vera, Elizabeth M.

2005-01-01

This archival study explored patterns of client preferences from a randomized sample of 881 clients at a Midwestern university counseling center. Information from client intake forms was collected for a four year time frame. Results showed that 61% of the clients did not express preferences for particular types of counselors when asked on intake…

Selected Guidelines for the Management of Records and Archives: A RAMP Reader.

ERIC Educational Resources Information Center

Walne, Peter, Comp.

The guidelines contained in this book are taken from studies published by UNESCO's Records and Archives Management Program (RAMP) between 1981 and 1987. Each set of guidelines is accompanied by an introduction to provide chronological or methodological context. The guidelines are titled as follows: (1) "The Use of Sampling Techniques in the…

Trace metal depositional patterns from an open pit mining activity as revealed by archived avian gizzard contents.

PubMed

Bendell, L I

2011-02-15

Archived samples of blue grouse (Dendragapus obscurus) gizzard contents, inclusive of grit, collected yearly between 1959 and 1970 were analyzed for cadmium, lead, zinc, and copper content. Approximately halfway through the 12-year sampling period, an open-pit copper mine began activities, then ceased operations 2 years later. Thus the archived samples provided a unique opportunity to determine if avian gizzard contents, inclusive of grit, could reveal patterns in the anthropogenic deposition of trace metals associated with mining activities. Gizzard concentrations of cadmium and copper strongly coincided with the onset of opening and the closing of the pit mining activity. Gizzard zinc and lead demonstrated significant among year variation; however, maximum concentrations did not correlate to mining activity. The archived gizzard contents did provide a useful tool for documenting trends in metal depositional patterns related to an anthropogenic activity. Further, blue grouse ingesting grit particles during the time of active mining activity would have been exposed to toxicologically significant levels of cadmium. Gizzard lead concentrations were also of toxicological significance but not related to mining activity. This type of "pulse" toxic metal exposure as a consequence of open-pit mining activity would not necessarily have been revealed through a "snap-shot" of soil, plant or avian tissue trace metal analysis post-mining activity. Copyright © 2010 Elsevier B.V. All rights reserved.

DATA QUALITY OBJECTIVES FOR SELECTING WASTE SAMPLES FOR THE BENCH STEAM REFORMER TEST

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

BANNING DL

2010-08-03

This document describes the data quality objectives to select archived samples located at the 222-S Laboratory for Fluid Bed Steam Reformer testing. The type, quantity and quality of the data required to select the samples for Fluid Bed Steam Reformer testing are discussed. In order to maximize the efficiency and minimize the time to treat Hanford tank waste in the Waste Treatment and Immobilization Plant, additional treatment processes may be required. One of the potential treatment processes is the fluid bed steam reformer (FBSR). A determination of the adequacy of the FBSR process to treat Hanford tank waste is required.more » The initial step in determining the adequacy of the FBSR process is to select archived waste samples from the 222-S Laboratory that will be used to test the FBSR process. Analyses of the selected samples will be required to confirm the samples meet the testing criteria.« less

The AMBRE project: Parameterisation of FGK-type stars from the ESO:HARPS archived spectra

NASA Astrophysics Data System (ADS)

De Pascale, M.; Worley, C. C.; de Laverny, P.; Recio-Blanco, A.; Hill, V.; Bijaoui, A.

2014-10-01

Context. The AMBRE project is a collaboration between the European Southern Observatory (ESO) and the Observatoire de la Côte d'Azur (OCA). It has been established to determine the stellar atmospheric parameters of the archived spectra of four ESO spectrographs. Aims: The analysis of the ESO:HARPS archived spectra for the determination of their atmospheric parameters (effective temperature, surface gravity, global metallicities, and abundance of α-elements over iron) is presented. The sample being analysed (AMBRE:HARPS) covers the period from 2003 to 2010 and is comprised of 126 688 scientific spectra corresponding to ~17 218 different stars. Methods: For the analysis of the AMBRE:HARPS spectral sample, the automated pipeline developed for the analysis of the AMBRE:FEROS archived spectra has been adapted to the characteristics of the HARPS spectra. Within the pipeline, the stellar parameters are determined by the MATISSE algorithm, which has been developed at OCA for the analysis of large samples of stellar spectra in the framework of galactic archaeology. In the present application, MATISSE uses the AMBRE grid of synthetic spectra, which covers FGKM-type stars for a range of gravities and metallicities. Results: We first determined the radial velocity and its associated error for the ~15% of the AMBRE:HARPS spectra, for which this velocity had not been derived by the ESO:HARPS reduction pipeline. The stellar atmospheric parameters and the associated chemical index [α/Fe] with their associated errors have then been estimated for all the spectra of the AMBRE:HARPS archived sample. Based on key quality criteria, we accepted and delivered the parameterisation of 93 116 (74% of the total sample) spectra to ESO. These spectra correspond to ~10 706 stars; each are observed between one and several hundred times. This automatic parameterisation of the AMBRE:HARPS spectra shows that the large majority of these stars are cool main-sequence dwarfs with metallicities greater than -0.5 dex (as expected, given that HARPS has been extensively used for planet searches around GK-stars).

Plasma heating for containerless and microgravity materials processing

NASA Technical Reports Server (NTRS)

Leung, Emily W. (Inventor); Man, Kin F. (Inventor)

1994-01-01

A method for plasma heating of levitated samples to be used in containerless microgravity processing is disclosed. A sample is levitated by electrostatic, electromagnetic, aerodynamic, or acoustic systems, as is appropriate for the physical properties of the particular sample. The sample is heated by a plasma torch at atmospheric pressure. A ground plate is provided to help direct the plasma towards the sample. In addition, Helmholtz coils are provided to produce a magnetic field that can be used to spiral the plasma around the sample. The plasma heating system is oriented such that it does not interfere with the levitation system.

The importance of long‐term experiments in agriculture: their management to ensure continued crop production and soil fertility; the Rothamsted experience

PubMed Central

Johnston, A. E.

2018-01-01

Summary Long‐term field experiments that test a range of treatments and are intended to assess the sustainability of crop production, and thus food security, must be managed actively to identify any treatment that is failing to maintain or increase yields. Once identified, carefully considered changes can be made to the treatment or management, and if they are successful yields will change. If suitable changes cannot be made to an experiment to ensure its continued relevance to sustainable crop production, then it should be stopped. Long‐term experiments have many other uses. They provide a field resource and samples for research on plant and soil processes and properties, especially those properties where change occurs slowly and affects soil fertility. Archived samples of all inputs and outputs are an invaluable source of material for future research, and data from current and archived samples can be used to develop models to describe soil and plant processes. Such changes and uses in the Rothamsted experiments are described, and demonstrate that with the appropriate crop, soil and management, acceptable yields can be maintained for many years, with either organic manure or inorganic fertilizers. Highlights Long‐term experiments demonstrate sustainability and increases in crop yield when managed to optimize soil fertility.Shifting individual response curves into coincidence increases understanding of the factors involved.Changes in inorganic and organic pollutants in archived crop and soil samples are related to inputs over time.Models describing soil processes are developed from current and archived soil data. PMID:29527119

The Rosetta Science Archive: Status and Plans for Enhancing the Archive Content

NASA Astrophysics Data System (ADS)

Heather, David; Barthelemy, Maud; Besse, Sebastien; Fraga, Diego; Grotheer, Emmanuel; O'Rourke, Laurence; Taylor, Matthew; Vallat, Claire

2017-04-01

On 30 September 2016, Rosetta completed its incredible mission by landing on the surface of Comet 67P/Churyumov-Gerasimenko. Although this marked an end to the spacecraft's active operations, intensive work is still ongoing with instrument teams preparing their final science data deliveries for ingestion into ESA's Planetary Science Archive (PSA). In addition, ESA is establishing contracts with some instrument teams to enhance their data and documentation in an effort to provide the best long-term archive possible for the Rosetta mission. Currently, the majority of teams have delivered all of their data from the nominal mission (end of 2015), and are working on their remaining increments from the 1-year mission extension. The aim is to complete the nominal archiving with data from the complete mission by the end of this year, when a full mission archive review will be held. This review will assess the complete data holdings from Rosetta and ensure that the archive is ready for the long-term. With the resources from the operational mission coming to an end, ESA has established a number of 'enhanced archiving' contracts to ensure that the best possible data are delivered to the archive before instrument teams disband. Updates are focused on key aspects of an instrument's calibration or the production of higher level data / information, and are therefore specific to each instrument's needs. These contracts are currently being kicked off, and will run for various lengths depending upon the activities to be undertaken. The full 'archive enhancement' process will run until September 2019, when the post operations activities for Rosetta will end. Within these contracts, most instrument teams will work on providing a Science User Guide for their data, as well as updating calibrations. Several teams will also be delivering higher level and derived products. For example, the VIRTIS team will be updating both their spectral and geometrical calibrations, and will aim to deliver mapping products to the final archive. Similarly, the OSIRIS team will be improving their calibrations and delivering data additionally in FITS format. The Rosetta Plasma Consortium (RPC) instruments will complete cross-calibrations and a number of activities individual to each instrument. The MIDAS team will also be working on cross-calibrations and will produce a dust particle catalog from the comet coma. GIADA will be producing dust environment maps, with products in 3D plus time. A contract also exists to produce and deliver data set(s) containing sup-porting ground-based observations from amateur astronomers. In addition to these contracts, the Rosetta ESA archiving team will produce calibrated data sets for the NAVCAM instrument, and will work to include the latest shape models from the comet into the final Rosetta archive. Work is also underway to provide a centralized solution to the problem of geometry on the comet. This presentation will outline the current status of the Rosetta archive, as well as highlighting some of the 'enhanced archiving' activities planned with the various instrument teams on Rosetta.

Malignant Tumors and Forensics – Dilemmas and Proposals

PubMed Central

Budimlija, Zoran; Lu, Connie; Axler-DiPerte, Grace; Seifarth, Jessica; Popiolek, Dorota; Fogt, Franz; Prinz, Mechthild

2009-01-01

Aim To evaluate the effect of genetic instability and degradation in archived histology samples from cancerous tumors and to investigate the validity of short tandem repeat (STR) typing of these samples and its potential effect on human identification. Methods Two hundred and twenty eight slides of archival pathology tissues from 13 different types of malignant tumors were compared with healthy tissues from the same individuals. DNA analysis was performed using standard techniques for forensic STR analysis, PowerPlex®16 and Identifiler® on 2 distinct sample sets. Genetic instability was assessed by comparing reference tissues with cancerous tissues derived from the same individual. Loss of heterozygosity, a ≥50% reduction in heterozygosity ratio between healthy and diseased samples, and microsatellite instability, the presence of an additional allele not present in reference tissue, were assessed. The quality of profiles obtained with respect to completeness among the archived samples and degradation using the 2 platforms were also compared. Results Profiles obtained using the Identifiler® system were generally more complete, but showed 3-fold higher levels of instability (86%) than those obtained using PowerPlex® 16 (27%). Instances of genetic instability were distributed throughout all loci in both multiplex STR systems. Conclusion After having compared 2 widely used forensic chemistries, we suggest individual validation of each kit for use with samples likely to exhibit instability combined with fixation induced degradation or artifact. A “one size fits all” approach for interpretation of these samples among commercially available multiplexes is not recommended. PMID:19480018

Laboratory and Field Evaluation of a New Rapid Test for Detecting Wuchereria bancrofti Antigen in Human Blood

PubMed Central

Weil, Gary J.; Curtis, Kurt C.; Fakoli, Lawrence; Fischer, Kerstin; Gankpala, Lincoln; Lammie, Patrick J.; Majewski, Andrew C.; Pelletreau, Sonia; Won, Kimberly Y.; Bolay, Fatorma K.; Fischer, Peter U.

2013-01-01

Global Program to Eliminate Lymphatic Filariasis (GPELF) guidelines call for using filarial antigen testing to identify endemic areas that require mass drug administration (MDA) and for post-MDA surveillance. We compared a new filarial antigen test (the Alere Filariasis Test Strip) with the reference BinaxNOW Filariasis card test that has been used by the GPELF for more than 10 years. Laboratory testing of 227 archived serum or plasma samples showed that the two tests had similar high rates of sensitivity and specificity and > 99% agreement. However, the test strip detected 26.5% more people with filarial antigenemia (124/503 versus 98/503) and had better test result stability than the card test in a field study conducted in a filariasis-endemic area in Liberia. Based on its increased sensitivity and other practical advantages, we believe that the test strip represents a major step forward that will be welcomed by the GPELF and the filariasis research community. PMID:23690552

Method of high-precision microsampled blood and plasma mass densitometry

NASA Technical Reports Server (NTRS)

Hinghofer-Szalkay, H.

1986-01-01

The reliability of the mechanical oscillator technique for blood and plasma density measurements on samples of volumes less than 0.1 ml is examined, and a precision of 0.001 g/l is found if plasma-isodensic heparin solution and siliconized densitometers are employed. Sources of measurement errors in the density determinations include storage of plasma samples, inhomogeneity of blood samples, and density reading before adequate temperature equilibration. In tests of plasma sample storage, the best reproducibility was obtained with samples kept at 4 C. Linear correlations were found between plasma density and plasma protein concentration, blood density and blood hemoglobin concentration, and erythrocyte density and MCHC.

Microbiological contamination with moulds in work environment in libraries and archive storage facilities.

PubMed

Zielinska-Jankiewicz, Katarzyna; Kozajda, Anna; Piotrowska, Malgorzata; Szadkowska-Stanczyk, Irena

2008-01-01

Microbiological contamination with fungi, including moulds, can pose a significant health hazard to those working in archives or museums. The species involved include Aspergillus, Penicillium, Geotrichum, Alternaria, Cladosporium, Mucor, Rhizopus, Trichoderma, Fusarium which are associated mostly with allergic response of different types. The aim of the study was to analyse, both in quantitative and qualitative terms, workplace air samples collected in a library and archive storage facilities. Occupational exposure and the related health hazard from microbiological contamination with moulds were assessed in three archive storage buildings and one library. Air samples (total 60) were collected via impact method before work and at hourly intervals during work performance. Surface samples from the artifacts were collected by pressing a counting (RODAC) plate filled with malt extract agar against the surface of the artifacts. The air sample and surface sample analyses yielded 36 different mould species, classified into 19 genera, of which Cladosporium and Penicillium were the most prevalent. Twelve species were regarded as potentially pathogenic for humans: 8 had allergic and 11 toxic properties, the latter including Aspergillus fumigatus. Quantitative analysis revealed air microbiological contamination with moulds at the level ranging from 1.8 x 10(2)-2.3 x 10(3) cfu/m(3). In surface samples from library and archive artifacts, 11 fungal species were distinguished; the number of species per artifact varying from 1-6 and colony count ranging from 4 x 10(1) to 8-10(1) cfu/100 cm(2). Higher contamination levels were found only for Cladosporium cladosporioides (1.48 x 10(3) cfu/100 cm(2)) and Paecillomyces varioti (1.2 x 10(2) cfu/100 cm(2)). At the workposts examined, although no clearly visible signs of mould contamination could be found, the study revealed abundant micromycetes, with the predominant species of Cladosporium and Penicillium. The detected species included also potentially pathogenic microorganisms which can cause allergic and toxic effects, such as Aspergillus fumigatus, that could be hazardous to workers' health. For some species, the concentration levels exceeded the values considered the proposed hygienic standards for total microscopical fungi in occupational settings. The findings of the study point to unsatisfactory hygienic conditions at the worksites examined, resulting in microbiological contamination with moulds, as well as the necessity for prompt remedial activities on the part of the employers.

An Archive of Spectra from the Mayall Fourier Transform Spectrometer at Kitt Peak

NASA Astrophysics Data System (ADS)

Pilachowski, C. A.; Hinkle, K. H.; Young, M. D.; Dennis, H. B.; Gopu, A.; Henschel, R.; Hayashi, S.

2017-02-01

We describe the SpArc science gateway for spectral data obtained using the Fourier Transform Spectrometer (FTS) in operation at the Mayall 4-m telescope at the Kitt Peak National Observatory during the period from 1975 through 1995. SpArc is hosted by Indiana University Bloomington and is available for public access. The archive includes nearly 10,000 individual spectra of more than 800 different astronomical sources including stars, nebulae, galaxies, and solar system objects. We briefly describe the FTS instrument itself and summarize the conversion of the original interferograms into spectral data and the process for recovering the data into FITS files. The architecture of the archive is discussed and the process for retrieving data from the archive is introduced. Sample use cases showing typical FTS spectra are presented.

STP K Basin Sludge Sample Archive at the Pacific Northwest National Laboratory FY2014

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

Fiskum, Sandra K.; Smoot, Margaret R.; Schmidt, Andrew J.

2014-06-01

The Pacific Northwest National Laboratory (PNNL) currently houses 88 samples (~10.5 kg) of K Basin sludge (81 wet and seven dry samples) on behalf of the Sludge Treatment Project (STP), which is managed for the U.S. Department of Energy (DOE) by the CH2M Hill Plateau Remediation Company (CHPRC). Selected samples are intended to serve, in part, as sentinels to enhance understanding of sludge properties after long-term storage, and thus enhance understanding of sludge behavior following transfer to sludge transfer and storage containers (STSCs) and storage at the Hanford 200 Area central plateau. In addition, remaining samples serve in contingency formore » future testing requirements. At PNNL, the samples are tracked and maintained under a prescriptive and disciplined monthly sample-monitoring program implemented by PNNL staff. This report updates the status of the K Basin archive sludge sample inventory to April 2014. The previous inventory status report, PNNL 22245 (Fiskum et al. 2013, limited distribution report), was issued in February of 2013. This update incorporates changes in the inventory related to repackaging of 17 samples under test instructions 52578 TI052, K Basin Sludge Sample Repackaging for Continued Long Term Storage, and 52578 TI053, K Basin Sludge Sample Repackaging Post-2014 Shear Strength Measurements. Note that shear strength measurement results acquired in 2014 are provided separately. Specifically, this report provides the following: • a description of the K Basin sludge sample archive program and the sample inventory • a summary and images of the samples that were repackaged in April 2014 • up-to-date images and plots of the settled density and water loss from all applicable samples in the inventory • updated sample pedigree charts, which provide a roadmap of the genesis and processing history of each sample in the inventory • occurrence and deficiency reports associated with sample storage and repackaging« less

Global tropospheric experiment at the Hong Kong Atmosphere Chemistry Measurement Station

NASA Technical Reports Server (NTRS)

Carroll, Mary Ann; Wang, Tao

1995-01-01

The major activities of the Global Tropospheric Experiment at the Hong Kong Atmospheric Chemistry Measurement Station are presented for the period 1 January - 31 December 1995. Activities included data analysis, reduction, and archiving of atmospheric measurements and sampling. Sampling included O3, CO, SO2, NO, TSP, RSP, and ozone column density. A data archive was created for the surface meteorological data. Exploratory data analysis was performed, including examination of time series, frequency distributions, diurnal variations and correlation. The major results have been or will be published in scientific journals as well as presented at conferences/workshops. Abstracts are attached.

Multifunction display system, volume 1

NASA Technical Reports Server (NTRS)

1973-01-01

The design and construction of a multifunction display man/machine interface for use with a 4 pi IBM-360 System are described. The system is capable of displaying superimposed volatile alphanumeric and graphical data on a 512 x 512 element plasma panel, and holographically stored multicolor archival information. The volatile data may be entered from a keyboard or by means of an I/O interface to the 360 system. A 2-page memory local to the display is provided for storing the entered data. The archival data is stored as a phase hologram on a vinyl tape strip. This data is accessible by means of a rapid transport system which responds to inputs provided by the I/O channel on the keyboard. As many as 500 frames may be stored on a tape strip for access in under 6 seconds.

IL8 and IL16 levels indicate serum and plasma quality.

PubMed

Kofanova, Olga; Henry, Estelle; Quesada, Rocio Aguilar; Bulla, Alexandre; Linares, Hector Navarro; Lescuyer, Pierre; Shea, Kathi; Stone, Mars; Tybring, Gunnel; Bellora, Camille; Betsou, Fay

2018-02-09

Longer pre-centrifugation times alter the quality of serum and plasma samples. Markers for such delays in sample processing and hence for the sample quality, have been identified. Twenty cytokines in serum, EDTA plasma and citrate plasma samples were screened for changes in concentration induced by extended blood pre-centrifugation delays at room temperature. The two cytokines that showed the largest changes were further validated for their "diagnostic performance" in identifying serum or plasma samples with extended pre-centrifugation times. In this study, using R&D Systems ELISA kits, EDTA plasma samples and serum samples with a pre-centrifugation delay longer than 24 h had an IL16 concentration higher than 313 pg/mL, and an IL8 concentration higher than 125 pg/mL, respectively. EDTA plasma samples with a pre-centrifugation delay longer than 48 h had an IL16 concentration higher than 897 pg/mL, citrate plasma samples had an IL8 concentration higher than 21.5 pg/mL and serum samples had an IL8 concentration higher than 528 pg/mL. These robust and accurate tools, based on simple and commercially available ELISA assays can greatly facilitate qualification of serum and plasma legacy collections with undocumented pre-analytics.

A microfluidic device for dry sample preservation in remote settings.

PubMed

Begolo, Stefano; Shen, Feng; Ismagilov, Rustem F

2013-11-21

This paper describes a microfluidic device for dry preservation of biological specimens at room temperature that incorporates chemical stabilization matrices. Long-term stabilization of samples is crucial for remote medical analysis, biosurveillance, and archiving, but the current paradigm for transporting remotely obtained samples relies on the costly "cold chain" to preserve analytes within biospecimens. We propose an alternative approach that involves the use of microfluidics to preserve samples in the dry state with stabilization matrices, developed by others, that are based on self-preservation chemistries found in nature. We describe a SlipChip-based device that allows minimally trained users to preserve samples with the three simple steps of placing a sample at an inlet, closing a lid, and slipping one layer of the device. The device fills automatically, and a pre-loaded desiccant dries the samples. Later, specimens can be rehydrated and recovered for analysis in a laboratory. This device is portable, compact, and self-contained, so it can be transported and operated by untrained users even in limited-resource settings. Features such as dead-end and sequential filling, combined with a "pumping lid" mechanism, enable precise quantification of the original sample's volume while avoiding overfilling. In addition, we demonstrated that the device can be integrated with a plasma filtration module, and we validated device operations and capabilities by testing the stability of purified RNA solutions. These features and the modularity of this platform (which facilitates integration and simplifies operation) would be applicable to other microfluidic devices beyond this application. We envision that as the field of stabilization matrices develops, microfluidic devices will be useful for cost-effectively facilitating remote analysis and biosurveillance while also opening new opportunities for diagnostics, drug development, and other medical fields.

The Effect of Selenium Supplementation on Glucose Homeostasis and the Expression of Genes Related to Glucose Metabolism.

PubMed

Jablonska, Ewa; Reszka, Edyta; Gromadzinska, Jolanta; Wieczorek, Edyta; Krol, Magdalena B; Raimondi, Sara; Socha, Katarzyna; Borawska, Maria H; Wasowicz, Wojciech

2016-12-13

The aim of the study was to evaluate the effect of selenium supplementation on the expression of genes associated with glucose metabolism in humans, in order to explain the unclear relationship between selenium and the risk of diabetes. For gene expression analysis we used archival samples of cDNA from 76 non-diabetic subjects supplemented with selenium in the previous study. The supplementation period was six weeks and the daily dose of selenium was 200 µg (as selenium yeast). Blood for mRNA isolation was collected at four time points: before supplementation, after two and four weeks of supplementation, and after four weeks of washout. The analysis included 15 genes encoding selected proteins involved in insulin signaling and glucose metabolism. In addition, HbA1c and fasting plasma glucose were measured at three and four time points, respectively. Selenium supplementation was associated with a significantly decreased level of HbA1c but not fasting plasma glucose (FPG) and significant down-regulation of seven genes: INSR , ADIPOR1 , LDHA , PDHA , PDHB , MYC , and HIF1AN . These results suggest that selenium may affect glycemic control at different levels of regulation, linked to insulin signaling, glycolysis, and pyruvate metabolism. Further research is needed to investigate mechanisms of such transcriptional regulation and its potential implication in direct metabolic effects.

On a path towards long-term sampling following the Deepwater Horizon: Initial insights

NASA Astrophysics Data System (ADS)

Reddy, C. M.

2012-12-01

During the past two decades in the United States, few areas contaminated from an oil spill have been revisited on the time scales from months to years. The lack of sampling is a missed opportunity to shine light on long-term processes, evaluate recovery, identify compounds most likely to persist, and apply new chemical and biological techniques. To address this issue, my laboratory has begun a land-based effort to collect oiled samples from the Gulf of Mexico beaches from the Deepwater Horizon disaster. Each sample is archived, analyzed, and available for others via an online repository. Detailed analysis of many of these samples has already been fruitful on determining the fate of the spilled oil, which will be discussed. This meeting is an ideal time to discuss strategies for long-term sampling and archiving. With support from the Gulf Research Initiative for the next nine years, the opportunities to use these samples will be frequent.

Determination of low-level mercury in coralline aragonite by calcination-isotope dilution-inductively coupled plasma-mass spectrometry and its application to Diploria specimens from Castle Harbour, Bermuda

NASA Astrophysics Data System (ADS)

Lamborg, Carl H.; Swarr, Gretchen; Hughen, Konrad; Jones, Ross J.; Birdwhistell, Scot; Furby, Kathryn; Murty, Sujata A.; Prouty, Nancy; Tseng, Chun-Mao

2013-05-01

We have developed a technique that combines a high temperature quartz furnace with inductively coupled plasma-mass spectrometry for the determination of Hg stored in the annual CaCO3 bands found in coral skeletons. Substantial matrix effects, presumably due to the discontinuous introduction of CO2 to the gas stream, were corrected for by simultaneously supplying a stream of argon containing highly enriched elemental 202Hgo and observing peaks in the 200Hg/202Hg signal as the sample was decomposed. Primary signal calibration for Hg was achieved using gas injections from a saturated vapor standard. The absolute instrument detection limit was low (about 0.2 fmol), with a practical limit of detection (3σ of blanks) of 2 fmol. Reproducibility of samples was (RSD) 15-27%. We applied this method to the determination of Hg concentrations in two colonies of Diploria labyrinthiformis collected from Castle Harbour, Bermuda, at a site about to be buried under the municipal waste landfill. The temporal reconstructions of Castle Harbour seawater Hg concentrations implied by the coral record show a decline throughout the period of record (1949-2008). The coral archived no apparent signal associated with waste disposal practices in the Harbour (bulk waste land-filling or, since 1994, disposal of waste incinerator ash), and mercury concentrations in the coral did not correlate to growth rate as assessed by linear extension. There was, however, a large and nearly exponential decrease in apparent Hg concentration in the Harbour which circumstantially implicates the dredging and/or landfilling operations associated with the construction of the airport on St. David's Island.

The Transport of Solar Ions Through the Earth's Magnetosphere

NASA Technical Reports Server (NTRS)

Lennartsson, O. W.

1999-01-01

This report covers the initial phase of an investigation that was originally selected by NASA Headquarters for funding by a grant but was later transferred to NASA GSFC for continued funding under a new and separate contract. The principal objective of the investigation, led by Dr. O.W. Lennartsson, is to extract information about the solar origin plasma in Earth's magnetosphere, specifically about the entry and transport of this plasma, using energetic (10 eV/e to 18 keV/e) ion composition data from the Lockheed Plasma Composition Experiment on the NASA/ESA International Sun-Earth Explorer One (ISEE 1) satellite. These data were acquired many years ago, from November 1977 through March of 1982, but, because of subsequent failures of similar experiments on several other spacecraft, they are still the only substantial ion composition data available from Earth's magnetotail, beyond 10 R(sub E), in the critically important sub-kev to keV energy range. All of the Lockheed data now exist in a compacted scientific format, suitable for large-scale statistical investigations, which has been archived both at Lockheed Martin in Palo Alto and at the National Space Science Data Center (NSSDC) in Greenbelt. The completion of the archiving, by processing the remaining half of the data, was made possible by separate funding through a temporary NASA program for data restoration and was given priority over the data analysis by a no-cost extension of the subject grant. By chance, the period of performance coincided with an international study of source and loss processes of magnetospheric plasma, sponsored by the International Space Science Institute (ISSI) in Bern, Switzerland, for which Dr. Lennartsson was invited to serve as one of 12 co-chairs. This study meshed well with the continued analysis of the NASA/Lockheed ISEE ion composition data and provided a natural forum for a broader discussion of the results from this unique experiment. What follows is arranged, for the most part, in the context of the ISSI project.

Chemical Analysis Results for Potable Water from ISS Expeditions 21 to 25

NASA Technical Reports Server (NTRS)

Straub, John E., II; Plumlee, Debrah K.; Schultz, John R.; McCoy, J. Torin

2010-01-01

The Johnson Space Center Water and Food Analytical Laboratory (WAFAL) performed detailed ground-based analyses of archival water samples for verification of the chemical quality of the International Space Station (ISS) potable water supplies for Expeditions 21 to 25. Over a 14-month period, the Space Shuttle visited the ISS on five occasions to complete construction and deliver supplies. The onboard supplies of potable water available for consumption by the Expeditions 21 to 25 crews consisted of Russian ground-supplied potable water, Russian potable water regenerated from humidity condensate, and US potable water recovered from urine distillate and condensate. Chemical archival water samples that were collected with U.S. hardware during Expeditions 21 to 25 were returned on Shuttle flights STS-129 (ULF3), STS-130 (20A), STS-131 (19A), STS-132 (ULF4) and STS-133 (ULF5), as well as on Soyuz flights 19-22. This paper reports the analytical results for the returned archival water samples and evaluates their compliance with ISS water quality standards. The WAFAL also received and analyzed aliquots of some Russian potable water samples collected in-flight and pre-flight samples of Rodnik potable water delivered to the Station on the Russian Progress vehicle during Expeditions 21 to 25. These additional analytical results are also reported and discussed in this paper.

Digital Archive Issues from the Perspective of an Earth Science Data Producer

NASA Technical Reports Server (NTRS)

Barkstrom, Bruce R.

2004-01-01

Contents include the following: Introduction. A Producer Perspective on Earth Science Data. Data Producers as Members of a Scientific Community. Some Unique Characteristics of Scientific Data. Spatial and Temporal Sampling for Earth (or Space) Science Data. The Influence of the Data Production System Architecture. The Spatial and Temporal Structures Underlying Earth Science Data. Earth Science Data File (or Relation) Schemas. Data Producer Configuration Management Complexities. The Topology of Earth Science Data Inventories. Some Thoughts on the User Perspective. Science Data User Communities. Spatial and Temporal Structure Needs of Different Users. User Spatial Objects. Data Search Services. Inventory Search. Parameter (Keyword) Search. Metadata Searches. Documentation Search. Secondary Index Search. Print Technology and Hypertext. Inter-Data Collection Configuration Management Issues. An Archive View. Producer Data Ingest and Production. User Data Searching and Distribution. Subsetting and Supersetting. Semantic Requirements for Data Interchange. Tentative Conclusions. An Object Oriented View of Archive Information Evolution. Scientific Data Archival Issues. A Perspective on the Future of Digital Archives for Scientific Data. References Index for this paper.

A comparison of serum and plasma cytokine values using a multiplexed assay in cats.

PubMed

Gruen, Margaret E; Messenger, Kristen M; Thomson, Andrea E; Griffith, Emily H; Paradise, Hayley; Vaden, Shelly; Lascelles, B D X

2016-12-01

Degenerative joint disease (DJD) is highly prevalent in cats, and pain contributes to morbidity. In humans, alterations of cytokine concentrations have been associated with joint deterioration and pain. Similar changes have not been investigated in cats. Cytokine concentrations can be measured using multiplex technology with small samples of serum or plasma, however, serum and plasma are not interchangeable for most bioassays. Correlations for cytokine concentrations between serum and plasma have not been evaluated in cats. To evaluate the levels of detection and agreement between serum and plasma samples in cats. Paired serum and plasma samples obtained from 38 cats. Blood was collected into anti-coagulant free and EDTA Vacutainer ® tubes, serum or plasma extracted, and samples frozen at -80°C until testing. Duplicate samples were tested using a 19-plex feline cytokine/chemokine magnetic bead panel. Agreement between serum and plasma for many analytes was high, however correlation coefficients ranged from -0.01 to 0.97. Results from >50% of samples were below the lower limit of quantification for both serum and plasma for nine analytes, and for an additional three analytes for plasma only. While serum and plasma agreement was generally good, detection was improved using serum samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Evaluation of sample preservation methods for space mission

NASA Technical Reports Server (NTRS)

Schubert, W.; Rohatgi, N.; Kazarians, G.

2002-01-01

For interplanetary spacecraft that will travel to destinations where future life detection experiments may be conducted or samples are to be returned to earth, we should archive and preserve relevant samples from the spacecraft and cleanrooms for evaluation at a future date.

Real-time detection of BRAF V600E mutation from archival hairy cell leukemia FFPE tissue by nanopore sequencing.

PubMed

Vacca, Davide; Cancila, Valeria; Gulino, Alessandro; Lo Bosco, Giosuè; Belmonte, Beatrice; Di Napoli, Arianna; Florena, Ada Maria; Tripodo, Claudio; Arancio, Walter

2018-02-01

The MinION is a miniaturized high-throughput next generation sequencing platform of novel conception. The use of nucleic acids derived from formalin-fixed paraffin-embedded samples is highly desirable, but their adoption for molecular assays is hurdled by the high degree of fragmentation and by the chemical-induced mutations stemming from the fixation protocols. In order to investigate the suitability of MinION sequencing on formalin-fixed paraffin-embedded samples, the presence and frequency of BRAF c.1799T > A mutation was investigated in two archival tissue specimens of Hairy cell leukemia and Hairy cell leukemia Variant. Despite the poor quality of the starting DNA, BRAF mutation was successfully detected in the Hairy cell leukemia sample with around 50% of the reads obtained within 2 h of the sequencing start. Notably, the mutational burden of the Hairy cell leukemia sample as derived from nanopore sequencing proved to be comparable to a sensitive method for the detection of point mutations, namely the Digital PCR, using a validated assay. Nanopore sequencing can be adopted for targeted sequencing of genetic lesions on critical DNA samples such as those extracted from archival routine formalin-fixed paraffin-embedded samples. This result let speculating about the possibility that the nanopore sequencing could be trustably adopted for the real-time targeted sequencing of genetic lesions. Our report opens the window for the adoption of nanopore sequencing in molecular pathology for research and diagnostics.

The ESA Planetary Science Archive User Group (PSA-UG)

NASA Astrophysics Data System (ADS)

Pio Rossi, Angelo; Cecconi, Baptiste; Fraenz, Markus; Hagermann, Axel; Heather, David; Rosenblatt, Pascal; Svedhem, Hakan; Widemann, Thomas

2014-05-01

ESA has established a Planetary Science Archive User Group (PSA-UG), with the task of offering independent advice to ESA's Planetary Science Archive (e.g. Heather et al., 2013). The PSA-UG is an official and independent body that continuously evaluates services and tools provided by the PSA to the community of planetary data scientific users. The group has been tasked with the following top level objectives: a) Advise ESA on future development of the PSA. b) Act as a focus for the interests of the scientific community. c) Act as an advocate for the PSA. d) Monitor the PSA activities. Based on this, the PSA-UG will report through the official ESA channels. Disciplines and subjects represented by PSA-UG members include: Remote Sensing of both Atmosphere and Solid Surfaces, Magnetospheres, Plasmas, Radio Science and Auxilliary data. The composition of the group covers ESA missions populating the PSA both now and in the near future. The first members of the PSA-UG were selected in 2013 and will serve for 3 years, until 2016. The PSA-UG will address the community through workshops, conferences and the internet. Written recommendations will be made to the PSA coordinator, and an annual report on PSA and the PSA-UG activities will be sent to the Solar System Exploration Working Group (SSEWG). Any member of the community and planetary data user can get in touch with individual members of the PSA-UG or with the group as a whole via the contacts provided on the official PSA-UG web-page: http://archives.esac.esa.int/psa/psa-ug. The PSA is accessible via: http://archives.esac.esa.int/psa References: Heather, D., Barthelemy, M., Manaud, N., Martinez, S., Szumlas, M., Vazquez, J. L., Osuna, P. and the PSA Development Team (2013) ESA's Planetary Science Archive: Status, Activities and Plans. EuroPlanet Sci. Congr. #EPSC2013-626

Cluster Ion Spectrometry (CIS) Data Archiving in the CAA

NASA Astrophysics Data System (ADS)

Dandouras, I. S.; Barthe, A.; Penou, E.; Brunato, S.; Reme, H.; Kistler, L. M.; Blagau, A.; Facsko, G.; Kronberg, E.; Laakso, H. E.

2009-12-01

The Cluster Active Archive (CAA) aims at preserving the four Cluster spacecraft data, so that they are usable in the long-term by the scientific community as well as by the instrument team PIs and Co-Is. This implies that the data are filed together with the descriptive and documentary elements making it possible to select and interpret them. The CIS (Cluster Ion Spectrometry) experiment is a comprehensive ionic plasma spectrometry package onboard the four Cluster spacecraft, capable of obtaining full three-dimensional ion distributions (about 0 to 40 keV/e) with a time resolution of one spacecraft spin (4 sec) and with mass-per-charge composition determination. The CIS package consists of two different instruments, a Hot Ion Analyser (HIA) and a time-of-flight ion Composition Distribution Function (CODIF) analyser. For the archival of the CIS data a multi-level approach has been adopted. The CAA archival includes processed raw data (Level 1 data), moments of the ion distribution functions (Level 2 data), and calibrated high-resolution data in a variety of physical units (Level 3 data). The latter are 3-D ion distribution functions and 2-D pitch-angle distributions. In addition, a software package has been developed to allow the CAA user to interactively calculate partial or total moments of the ion distributions. Instrument cross-calibration has been an important activity in preparing the data for archival. The CIS data archive includes also experiment documentation, graphical products for browsing through the data, and data caveats. In addition, data quality indexes are under preparation, to help the user. Given the complexity of an ion spectrometer, and the variety of its operational modes, each one being optimised for a different magnetospheric region or measurement objective, consultation of the data caveats by the end user will always be a necessary step in the data analysis.

Plasma ESR1 Mutations and the Treatment of Estrogen Receptor-Positive Advanced Breast Cancer.

PubMed

Fribbens, Charlotte; O'Leary, Ben; Kilburn, Lucy; Hrebien, Sarah; Garcia-Murillas, Isaac; Beaney, Matthew; Cristofanilli, Massimo; Andre, Fabrice; Loi, Sherene; Loibl, Sibylle; Jiang, John; Bartlett, Cynthia Huang; Koehler, Maria; Dowsett, Mitch; Bliss, Judith M; Johnston, Stephen R D; Turner, Nicholas C

2016-09-01

ESR1 mutations are selected by prior aromatase inhibitor (AI) therapy in advanced breast cancer. We assessed the impact of ESR1 mutations on sensitivity to standard therapies in two phase III randomized trials that represent the development of the current standard therapy for estrogen receptor-positive advanced breast cancer. In a prospective-retrospective analysis, we assessed ESR1 mutations in available archived baseline plasma from the SoFEA (Study of Faslodex Versus Exemestane With or Without Arimidex) trial, which compared exemestane with fulvestrant-containing regimens in patients with prior sensitivity to nonsteroidal AI and in baseline plasma from the PALOMA3 (Palbociclib Combined With Fulvestrant in Hormone Receptor-Positive HER2-Negative Metastatic Breast Cancer After Endocrine Failure) trial, which compared fulvestrant plus placebo with fulvestrant plus palbociclib in patients with progression after receiving prior endocrine therapy. ESR1 mutations were analyzed by multiplex digital polymerase chain reaction. In SoFEA, ESR1 mutations were found in 39.1% of patients (63 of 161), of whom 49.1% (27 of 55) were polyclonal, with rates of mutation detection unaffected by delays in processing of archival plasma. Patients with ESR1 mutations had improved progression-free survival (PFS) after taking fulvestrant (n = 45) compared with exemestane (n = 18; hazard ratio [HR], 0.52; 95% CI, 0.30 to 0.92; P = .02), whereas patients with wild-type ESR1 had similar PFS after receiving either treatment (HR, 1.07; 95% CI, 0.68 to 1.67; P = .77). In PALOMA3, ESR1 mutations were found in the plasma of 25.3% of patients (91 of 360), of whom 28.6% (26 of 91) were polyclonal, with mutations associated with acquired resistance to prior AI. Fulvestrant plus palbociclib improved PFS compared with fulvestrant plus placebo in both ESR1 mutant (HR, 0.43; 95% CI, 0.25 to 0.74; P = .002) and ESR1 wild-type patients (HR, 0.49; 95% CI, 0.35 to 0.70; P < .001). ESR1 mutation analysis in plasma after progression after prior AI therapy may help direct choice of further endocrine-based therapy. Additional confirmatory studies are required. © 2016 by American Society of Clinical Oncology.

Long-term data archiving

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

Moore, David Steven

2009-01-01

Long term data archiving has much value for chemists, not only to retain access to research and product development records, but also to enable new developments and new discoveries. There are some recent regulatory requirements (e.g., FDA 21 CFR Part 11), but good science and good business both benefit regardless. A particular example of the benefits of and need for long term data archiving is the management of data from spectroscopic laboratory instruments. The sheer amount of spectroscopic data is increasing at a scary rate, and the pressures to archive come from the expense to create the data (or recreatemore » it if it is lost) as well as its high information content. The goal of long-term data archiving is to save and organize instrument data files as well as any needed meta data (such as sample ID, LIMS information, operator, date, time, instrument conditions, sample type, excitation details, environmental parameters, etc.). This editorial explores the issues involved in long-term data archiving using the example of Raman spectral databases. There are at present several such databases, including common data format libraries and proprietary libraries. However, such databases and libraries should ultimately satisfy stringent criteria for long term data archiving, including readability for long times into the future, robustness to changes in computer hardware and operating systems, and use of public domain data formats. The latter criterion implies the data format should be platform independent and the tools to create the data format should be easily and publicly obtainable or developable. Several examples of attempts at spectral libraries exist, such as the ASTM ANDI format, and the JCAMP-DX format. On the other hand, proprietary library spectra can be exchanged and manipulated using proprietary tools. As the above examples have deficiencies according to the three long term data archiving criteria, Extensible Markup Language (XML; a product of the World Wide Web Consortium, an independent standards body) as a new data interchange tool is being investigated and implemented. In order to facilitate data archiving, Raman data needs calibration as well as some other kinds of data treatment. Figure 1 illustrates schematically the present situation for Raman data calibration in the world-wide Raman spectroscopy community, and presents some of the terminology used.« less

High Quality Genomic Copy Number Data from Archival Formalin-Fixed Paraffin-Embedded Leiomyosarcoma: Optimisation of Universal Linkage System Labelling

PubMed Central

Salawu, Abdulazeez; Ul-Hassan, Aliya; Hammond, David; Fernando, Malee; Reed, Malcolm; Sisley, Karen

2012-01-01

Most soft tissue sarcomas are characterized by genetic instability and frequent genomic copy number aberrations that are not subtype-specific. Oligonucleotide microarray-based Comparative Genomic Hybridisation (array CGH) is an important technique used to map genome-wide copy number aberrations, but the traditional requirement for high-quality DNA typically obtained from fresh tissue has limited its use in sarcomas. Although large archives of Formalin-fixed Paraffin-embedded (FFPE) tumour samples are available for research, the degradative effects of formalin on DNA from these tissues has made labelling and analysis by array CGH technically challenging. The Universal Linkage System (ULS) may be used for a one-step chemical labelling of such degraded DNA. We have optimised the ULS labelling protocol to perform aCGH on archived FFPE leiomyosarcoma tissues using the 180k Agilent platform. Preservation age of samples ranged from a few months to seventeen years and the DNA showed a wide range of degradation (when visualised on agarose gels). Consistently high DNA labelling efficiency and low microarray probe-to-probe variation (as measured by the derivative log ratio spread) was seen. Comparison of paired fresh and FFPE samples from identical tumours showed good correlation of CNAs detected. Furthermore, the ability to macro-dissect FFPE samples permitted the detection of CNAs that were masked in fresh tissue. Aberrations were visually confirmed using Fluorescence in situ Hybridisation. These results suggest that archival FFPE tissue, with its relative abundance and attendant clinical data may be used for effective mapping for genomic copy number aberrations in such rare tumours as leiomyosarcoma and potentially unravel clues to tumour origins, progression and ultimately, targeted treatment. PMID:23209738

Discovery and Identification of Dimethylsilanediol as a Contaminant in ISS Potable Water

NASA Technical Reports Server (NTRS)

Rutz, Jeffrey A.; Schultz, John R.; Kuo, C. Mike; Cole, Hraold E.; Manuel, Sam; Curtis, Matthew; Jones, Patrick R.; Sparkman, O. David; McCoy, J. Torin

2010-01-01

In September of 2010, analysis of ISS potable water samples was undertaken to determine the contaminant responsible for a rise in total organic carbon (TOC). As analysis of the routine target list of organic compounds did not reveal the contaminant, efforts to look for unknown compounds was initiated, resulting in an unknown peak being discovered in the gas chromatography/mass spectrometry (GC/MS) analysis for glycols. A mass spectrum of the contaminant was then generated by concentrating one of the samples by evaporation and analyzing by GC/MS in full-scan mode. Although a computer match of the compound s identity could not be obtained with the instrument s database, a search with a more up to date mass spectral library yielded a good match with dimethylsilanediol (DMSD). Inductively Coupled Plasma/Mass Spectrometry (ICP/MS) analyses showed abnormally high silicon levels in the samples, confirming that the unknown contained silicon. DMSD was then synthesized to confirm the identification and provide a standard to develop a calibration curve. Further confirmation was provided by external Direct Analysis in Real Time (DART) GC/MS analysis. A preliminary GC/MS method was then developed and archived samples from various locations on ISS were analyzed to determine the extent of the contamination and provide data for troubleshooting. This paper describes these events in more detail as well as problems encountered in routine GC/MS analyses and the subsequent development of high performance liquid chromatography and LC/MS/MS methods for quantitation of DMSD.

Archiving of Wideband Plasma Wave Data

NASA Technical Reports Server (NTRS)

Kurth, William S.

1997-01-01

Beginning with the third year of funding, we began a more ambitious archiving production effort, minimizing work on new software and concentrating on building representative archives of the missions mentioned above, recognizing that only a small percentage of the data from any one mission can be archived with reasonable effort. We concentrated on data from Dynamics Explorer and ISEE 1, archiving orbits or significant fractions of orbits which attempt to capture the essence of the mission and provide data which will hopefully be sufficient for ongoing and new research as well as to provide a reference to upcoming and current ISTP missions which will not fly in the same regions of space as the older missions and which will not have continuous wideband data. We archived approximately 181 Gigabytes of data, accounting for some 1582 hours of data. Included in these data are all of the AMPTE chemical releases, all of the Spacelab 2/PDP data obtained during the free-flight portion of its mission, as well as significant portions of the S3, DE-1, Imp-6, Hawkeye, Injun 5, and ISEE 1 and 2 data sets. Table 1 summarizes these data. All of the data archived are summarized in gif-formatted images of frequency-time spectrograms which are directly accessible via the internet. Each of the gif files are identified by year, day, and time as described in the Web page. This provides a user with a specific date/time in mind a way of determining very quickly if there is data for the interval in question and, by clicking on the file name, browsing the data. Alternately, a user can browse the data for interesting features and events simply by viewing each of the gif files. When a user finds data of interest, he/she can notify us by email of the time period involved. Based on the user's needs, we can provide data on a convenient medium or by ftp, or we can mount the appropriate data and provide access to our analysis tools via the network. We can even produce products such as plots or spectrograms in hardcopy form based on the specific request of the user.

The ESA Planetary Science Archive User Group (PSA-UG)

NASA Astrophysics Data System (ADS)

Rossi, A. P.; Cecconi, B.; Fraenz, M.; Hagermann, A.; Heather, D.; Rosenblatt, P.; Svedhem, H.; Widemann, T.

2014-04-01

ESA has established a Planetary Science Archive User Group (PSA-UG), with the task of offering independent advice to ESA's Planetary Science Archive (e.g. Heather et al., 2013). The PSA-UG is an official and independent body that continuously evaluates services and tools provided by the PSA to the community of planetary data scientific users. The group has been tasked with the following top level objectives: a) Advise ESA on future development of the PSA. b) Act as a focus for the interests of the scientific community. c) Act as an advocate for the PSA. d) Monitor the PSA activities. Based on this, the PSA-UG will report through the official ESA channels. Disciplines and subjects represented by PSA-UG members include: Remote Sensing of both Atmosphere and Solid Surfaces, Magnetospheres, Plasmas, Radio Science and Auxilliary data. The composition of the group covers ESA missions populating the PSA both now and in the near future. The first members of the PSA-UG were selected in 2013 and will serve for 3 years, until 2016. The PSA-UG will address the community through workshops, conferences and the internet. Written recommendations will be made to the PSA coordinator, and an annual report on PSA and the PSA-UG activities will be sent to the Solar System Exploration Working Group (SSEWG). Any member of the community and planetary data user can get in touch with individual members of the PSA-UG or with the group as a whole via the contacts provided on the official PSA-UG web-page: http://archives.esac.esa.int/psa/psa-ug The PSA is accessible via: http://archives.esac.esa.int/psa

Detection of hepatitis B virus infection markers in dried plasma spots among patients in Congo-Brazzaville.

PubMed

Alidjinou, Enagnon Kazali; Moukassa, Donatien; Sané, Famara; Twagirimana Nyenyeli, Séraphin; Akoko, Estina Chandrelle; Mountou, Michèle Valy; Bocket, Laurence; Ibara, Jean-Rosaire; Hober, Didier

2014-03-01

The detection of hepatitis B virus (HBV) infection markers by using dried plasma spots from 32 patients living in Congo has been assessed. Considering frozen plasma samples as gold standard, the sensitivity and specificity of HBV serologic markers detection in dried plasma eluted from filter paper were 100%. The sensitivity and the specificity of HBV DNA detection reached 96% and 100%, respectively, with plasma samples dried on filter paper compared to standard samples. Dried plasma samples can represent an alternative to conventional sampling for HBV detection and management of the infection in developing countries. Copyright © 2014 Elsevier Inc. All rights reserved.

Special issue on enabling open and interoperable access to Planetary Science and Heliophysics databases and tools

NASA Astrophysics Data System (ADS)

2018-01-01

The large amount of data generated by modern space missions calls for a change of organization of data distribution and access procedures. Although long term archives exist for telescopic and space-borne observations, high-level functions need to be developed on top of these repositories to make Planetary Science and Heliophysics data more accessible and to favor interoperability. Results of simulations and reference laboratory data also need to be integrated to support and interpret the observations. Interoperable software and interfaces have recently been developed in many scientific domains. The Virtual Observatory (VO) interoperable standards developed for Astronomy by the International Virtual Observatory Alliance (IVOA) can be adapted to Planetary Sciences, as demonstrated by the VESPA (Virtual European Solar and Planetary Access) team within the Europlanet-H2020-RI project. Other communities have developed their own standards: GIS (Geographic Information System) for Earth and planetary surfaces tools, SPASE (Space Physics Archive Search and Extract) for space plasma, PDS4 (NASA Planetary Data System, version 4) and IPDA (International Planetary Data Alliance) for planetary mission archives, etc, and an effort to make them interoperable altogether is starting, including automated workflows to process related data from different sources.

Physiological stress and post-release mortality of white marlin (Kajikia albida) caught in the United States recreational fishery

PubMed Central

Schlenker, Lela S.; Latour, Robert J.; Brill, Richard W.; Graves, John E.

2016-01-01

White marlin, a highly migratory pelagic marine fish, support important commercial and recreational fisheries throughout their range in the tropical and subtropical Atlantic Ocean. More than 10 000 individuals can be caught annually in the United States recreational fishery, of which the vast majority are captured on circle hooks and released alive. The probability of post-release mortality of white marlin released from circle hooks has been documented to be <0.02, but the associated physiological stress resulting from capture and handling techniques has not been characterized despite its importance for understanding the health of released fish. We examined the physiological response of 68 white marlin caught on circle hooks in the recreational fishery and followed the fate of 22 of these fish with pop-up satellite archival tags programmed to release after 30 days. Measures of plasma sodium, chloride, glucose and lactate concentrations taken from fish that were briefly and consistently (mean = 120 s, standard deviation = 40 s) removed from the water increased with angling time, but post-release mortality was inversely related to angling time. The probability of post-release mortality was predicted by elevated plasma potassium concentrations and was more than 10 times greater than has been previously reported for white marlin caught on circle hooks that were not removed from the water. This disparity in estimates of post-release mortality suggests that removal of fish from the water for physiological sampling greatly heightens stress, disrupts homeostasis and thus increases the probability of post-release mortality. Our results demonstrate that elevated concentrations of plasma potassium predict mortality in white marlin and that the probability of post-release mortality is highly dependent on post-capture handling procedures. PMID:27293745

Physiological stress and post-release mortality of white marlin (Kajikia albida) caught in the United States recreational fishery.

PubMed

Schlenker, Lela S; Latour, Robert J; Brill, Richard W; Graves, John E

2016-01-01

White marlin, a highly migratory pelagic marine fish, support important commercial and recreational fisheries throughout their range in the tropical and subtropical Atlantic Ocean. More than 10 000 individuals can be caught annually in the United States recreational fishery, of which the vast majority are captured on circle hooks and released alive. The probability of post-release mortality of white marlin released from circle hooks has been documented to be <0.02, but the associated physiological stress resulting from capture and handling techniques has not been characterized despite its importance for understanding the health of released fish. We examined the physiological response of 68 white marlin caught on circle hooks in the recreational fishery and followed the fate of 22 of these fish with pop-up satellite archival tags programmed to release after 30 days. Measures of plasma sodium, chloride, glucose and lactate concentrations taken from fish that were briefly and consistently (mean = 120 s, standard deviation = 40 s) removed from the water increased with angling time, but post-release mortality was inversely related to angling time. The probability of post-release mortality was predicted by elevated plasma potassium concentrations and was more than 10 times greater than has been previously reported for white marlin caught on circle hooks that were not removed from the water. This disparity in estimates of post-release mortality suggests that removal of fish from the water for physiological sampling greatly heightens stress, disrupts homeostasis and thus increases the probability of post-release mortality. Our results demonstrate that elevated concentrations of plasma potassium predict mortality in white marlin and that the probability of post-release mortality is highly dependent on post-capture handling procedures.

Coupling Meteorology, Metal Concentrations, and Pb Isotopes for Source Attribution in Archived Precipitation Samples

EPA Science Inventory

A technique that couples lead (Pb) isotopes and multi-element concentrations with meteorological analysis was used to assess source contributions to precipitation samples at the Bondville, Illinois USA National Trends Network (NTN) site. Precipitation samples collected over a 16 ...

[Development Of 25-Year Imp 8 Bow Shock Crossing "List, Ingestion Of This List To Cdaweb, & Enhancement"

NASA Technical Reports Server (NTRS)

Merka, J.; Szabo, A.; Narock, T. W.; King, J. H.; Paularena, K. I.; Richardson, J. D.

2003-01-01

The MIT portion of this project was to use the plasma data from IMP 8 to identify bow shock crossings for construction of a bow shock data base. In collaboration with Goddard, we determined which shock parameters would be included in the catalog and developed a set of flags for characterizing the data. IMP 8 data from 1973-2001 were surveyed for bow shock crossings; the crossings apparent in the plasma data were compared to a list of crossing chosen in the magnetometer data by Goddard. Differences were reconciled to produce a single list. The data were then provided to the NSSDC for archiving. All the work ascribed to MIT in the proposal was completed.

Cracks and nanodroplets produced on tungsten surface samples by dense plasma jets

NASA Astrophysics Data System (ADS)

Ticoş, C. M.; Galaţanu, M.; Galaţanu, A.; Luculescu, C.; Scurtu, A.; Udrea, N.; Ticoş, D.; Dumitru, M.

2018-03-01

Small samples of 12.5 mm in diameter made from pure tungsten were exposed to a dense plasma jet produced by a coaxial plasma gun operated at 2 kJ. The surface of the samples was analyzed using a scanning electron microscope (SEM) before and after applying consecutive plasma shots. Cracks and craters were produced in the surface due to surface tensions during plasma heating. Nanodroplets and micron size droplets could be observed on the samples surface. An energy-dispersive spectroscopy (EDS) analysis revealed that the composition of these droplets coincided with that of the gun electrode material. Four types of samples were prepared by spark plasma sintering from powders with the average particle size ranging from 70 nanometers up to 80 μm. The plasma power load to the sample surface was estimated to be ≈4.7 MJ m-2 s-1/2 per shot. The electron temperature and density in the plasma jet had peak values 17 eV and 1.6 × 1022 m-3, respectively.

Sterilization of Turmeric by Atmospheric Pressure Dielectric Barrier Discharge Plasma

NASA Astrophysics Data System (ADS)

Setareh, Salarieh; Davoud, Dorranian

2013-11-01

In this study atmospheric pressure dielectric barrier discharge (DBD) plasma has been employed for sterilizing dry turmeric powders. A 6 kV, 6 kHz frequency generator was used to generate plasma with Ar, Ar/O2, He, and He/O2 gases between the 5 mm gap of two quartz covered electrodes. The complete sterilization time of samples due to plasma treatment was measured. The most important contaminant of turmeric is bacillus subtilis. The results show that the shortest sterilization time of 15 min is achieved by exposing the samples to Ar/O2 plasma. Survival curves of samples are exponential functions of time and the addition of oxygen to plasma leads to a significant increase of the absolute value of time constant of the curves. Magnitudes of protein and DNA in treated samples were increased to a similar value for all samples. Taste, color, and solubility of samples were not changed after the plasma treatment.

Cores to the rescue: how old cores enable new science

NASA Astrophysics Data System (ADS)

Ito, E.; Noren, A. J.; Brady, K.

2016-12-01

The value of archiving scientific specimens and collections for the purpose of enabling further research using new analytical techniques, resolving conflicting results, or repurposing them for entirely new research, is often discussed in abstract terms. We all agree that samples with adequate metadata ought to be archived systematically for easy access, for a long time and stored under optimal conditions. And yet, as storage space fills, there is a temptation to cull the collection, or when a researcher retires, to discard the collection unless the researcher manages to make his or her own arrangement for the collection to be accessioned elsewhere. Nobody has done anything with these samples in over 20 years! Who would want them? It turns out that plenty of us do want them, if we know how to find them and if they have sufficient metadata to assess past work and suitability for new analyses. The LacCore collection holds over 33 km of core from >6700 sites in diverse geographic locations worldwide with samples collected as early as 1950s. From these materials, there are many examples to illustrate the scientific value of archiving geologic samples. One example that benefitted Ito personally were cores from Lakes Mirabad and Zeribar, Iran, acquired in 1963 by Herb Wright and his associates. Several doctoral and postdoctoral students generated and published paleoecological reconstructions based on cladocerans, diatoms, pollen or plant macrofossils, mostly between 1963 and 1967. The cores were resampled in 1990s by a student being jointly advised by Wright and Ito for oxygen isotope analysis of endogenic calcite. The results were profitably compared with pollen and the results published in 2001 and 2006. From 1979 until very recently, visiting Iran for fieldwork was not pallowed for US scientists. Other examples will be given to further illustrate the power of archived samples to advance science.

Transient fields produced by a cylindrical electron beam flowing through a plasma

NASA Astrophysics Data System (ADS)

Firpo, Marie-Christine

2012-10-01

Fast ignition schemes (FIS) for inertial confinement fusion should involve in their final stage the interaction of an ignition beam composed of MeV electrons laser generated at the critical density surface with a dense plasma target. In this study, the out-of-equilibrium situation in which an initially sharp-edged cylindrical electron beam, that could e.g. model electrons flowing within a wire [1], is injected into a plasma is considered. A detailed computation of the subsequently produced magnetic field is presented [2]. The control parameter of the problem is shown to be the ratio of the beam radius to the electron skin depth. Two alternative ways to address analytically the problem are considered: one uses the usual Laplace transform approach, the other one involves Riemann's method in which causality conditions manifest through some integrals of triple products of Bessel functions.[4pt] [1] J.S. Green et al., Surface heating of wire plasmas using laser-irradiated cone geometries, Nature Physics 3, 853--856 (2007).[0pt] [2] M.-C. Firpo, http://hal.archives-ouvertes.fr/hal-00695629, to be published (2012).

Reduction of Photo Bleaching and Long Term Archiving of Chemically Cleared GFP-Expressing Mouse Brains

PubMed Central

Becker, Klaus; Hahn, Christian Markus; Saghafi, Saiedeh; Jährling, Nina; Wanis, Martina; Dodt, Hans-Ulrich

2014-01-01

Tissue clearing allows microscopy of large specimens as whole mouse brains or embryos. However, lipophilic tissue clearing agents as dibenzyl ether limit storage time of GFP-expressing samples to several days and do not prevent them from photobleaching during microscopy. To preserve GFP fluorescence, we developed a transparent solid resin formulation, which maintains the specimens' transparency and provides a constant signal to noise ratio even after hours of continuous laser irradiation. If required, high-power illumination or long exposure times can be applied with virtually no loss in signal quality and samples can be archived for years. PMID:25463047

An Archival Search For Young Globular Clusters in Galaxies

NASA Astrophysics Data System (ADS)

Whitmore, Brad

1995-07-01

One of the most intriguing results from HST has been the discovery of ultraluminous star clusters in interacting and merging galaxies. These clusters have the luminosities, colors, and sizes that would be expected of young globular clusters produced by the interaction. We propose to use the data in the HST Archive to determine how prevalent this phenomena is, and to determine whether similar clusters are produced in other environments. Three samples will be extracted and studied in a systematic and consistent manner: 1} interacting and merging galaxies, 2} starburst galaxies, 3} a control sample of ``normal'' galaxies. A preliminary search of the archives shows that there are at least 20 galaxies in each of these samples, and the number will grow by about 50 observations become available. The data will be used to determine the luminosity function, color histogram , spatial distribution, and structural properties of the clusters using the same techniques employed in our study of NGC 7252 {``Atoms -for-Peace'' galaxy} and NGC 4038/4039 {``The Antennae''}. Our ultimate goals are: 1} to understand how globular clusters form, and 2} to use the clusters as evolutionary tracers to unravel the histories of interacting galaxies.

Development of a Climatology of Vertically Complete Wind Profiles from Doppler Radar Wind Profiler Systems

NASA Technical Reports Server (NTRS)

Barbre, Robert E., Jr.

2015-01-01

This paper describes in detail the QC and splicing methodology for KSC's 50- and 915-MHz DRWP measurements that generates an extensive archive of vertically complete profiles from 0.20-18.45 km. The concurrent POR from each archive extends from April 2000 to December 2009. MSFC NE applies separate but similar QC processes to each of the 50- and 915-MHz DRWP archives. DRWP literature and data examination provide the basis for developing and applying the automated and manual QC processes on both archives. Depending on the month, the QC'ed 50- and 915-MHz DRWP archives retain 52-65% and 16-30% of the possible data, respectively. The 50- and 915-MHz DRWP QC archives retain 84-91% and 85-95%, respectively, of all the available data provided that data exist in the non- QC'ed archives. Next, MSFC NE applies an algorithm to splice concurrent measurements from both DRWP sources. Last, MSFC NE generates a composite profile from the (up to) five available spliced profiles to effectively characterize boundary layer winds and to utilize all possible 915-MHz DRWP measurements at each timestamp. During a given month, roughly 23,000-32,000 complete profiles exist from 0.25-18.45 km from the composite profiles' archive, and approximately 5,000- 27,000 complete profiles exist from an archive utilizing an individual 915-MHz DRWP. One can extract a variety of profile combinations (pairs, triplets, etc.) from this sample for a given application. The sample of vertically complete DRWP wind measurements not only gives launch vehicle customers greater confidence in loads and trajectory assessments versus using balloon output, but also provides flexibility to simulate different DOL situations across applicable altitudes. In addition to increasing sample size and providing more flexibility for DOL simulations in the vehicle design phase, the spliced DRWP database provides any upcoming launch vehicle program with the capability to utilize DRWP profiles on DOL to compute vehicle steering commands, provided the program applies the procedures that this report describes to new DRWP data on DOL. Decker et al. (2015) details how SLS is proposing to use DRWP data and splicing techniques on DOL. Although automation could enhance the current DOL 50-MHz DRWP QC process and could streamline any future DOL 915-MHz DRWP QC and splicing process, the DOL community would still require manual intervention to ensure that the vehicle only uses valid profiles. If a program desires to use high spatial resolution profiles, then the algorithm could randomly add high-frequency components to the DRWP profiles. The spliced DRWP database provides lots of flexibility in how one performs DOL simulations, and the algorithms that this report provides will assist the aerospace and atmospheric communities that are interested in utilizing the DRWP.

The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples.

PubMed

Deck, John; Gaither, Michelle R; Ewing, Rodney; Bird, Christopher E; Davies, Neil; Meyer, Christopher; Riginos, Cynthia; Toonen, Robert J; Crandall, Eric D

2017-08-01

The Genomic Observatories Metadatabase (GeOMe, http://www.geome-db.org/) is an open access repository for geographic and ecological metadata associated with biosamples and genetic data. Whereas public databases have served as vital repositories for nucleotide sequences, they do not accession all the metadata required for ecological or evolutionary analyses. GeOMe fills this need, providing a user-friendly, web-based interface for both data contributors and data recipients. The interface allows data contributors to create a customized yet standard-compliant spreadsheet that captures the temporal and geospatial context of each biosample. These metadata are then validated and permanently linked to archived genetic data stored in the National Center for Biotechnology Information's (NCBI's) Sequence Read Archive (SRA) via unique persistent identifiers. By linking ecologically and evolutionarily relevant metadata with publicly archived sequence data in a structured manner, GeOMe sets a gold standard for data management in biodiversity science.

The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples

PubMed Central

Deck, John; Gaither, Michelle R.; Ewing, Rodney; Bird, Christopher E.; Davies, Neil; Meyer, Christopher; Riginos, Cynthia; Toonen, Robert J.; Crandall, Eric D.

2017-01-01

The Genomic Observatories Metadatabase (GeOMe, http://www.geome-db.org/) is an open access repository for geographic and ecological metadata associated with biosamples and genetic data. Whereas public databases have served as vital repositories for nucleotide sequences, they do not accession all the metadata required for ecological or evolutionary analyses. GeOMe fills this need, providing a user-friendly, web-based interface for both data contributors and data recipients. The interface allows data contributors to create a customized yet standard-compliant spreadsheet that captures the temporal and geospatial context of each biosample. These metadata are then validated and permanently linked to archived genetic data stored in the National Center for Biotechnology Information’s (NCBI’s) Sequence Read Archive (SRA) via unique persistent identifiers. By linking ecologically and evolutionarily relevant metadata with publicly archived sequence data in a structured manner, GeOMe sets a gold standard for data management in biodiversity science. PMID:28771471

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

PubMed

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

2014-04-01

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

Plasma surface cleaning in a microwave plasma source

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

Tsai, C.C.; Nelson, W.D.; Haselton, H.H.

1994-03-01

A microwave electron cyclotron resonance (ECR) plasma source has been operated to produce reactive plasmas of oxygen and its mixture with argon. Aluminum samples (0.95 cm by 1.9 cm) were coated with thin films (<20 {mu}m in thickness) of Shell Vitrea oil and cleaned by using such reactive plasmas. The plasma cleaning was done in discharge conditions of microwave power up to 1300 W, radio frequency power up to 200 W, biased potential up to 400 V, gas pressures up to 5 mtorr, and operating time up to 35 min. The surface texture of the postcleaned samples has been examinedmore » visually. Mass loss of the samples after plasma cleaning was measured to estimate cleaning rates. Measured clean rates of low-pressure (0.5-mtorr) argon/oxygen plasmas were as high as 2.7 {mu}m/min. X-ray photoelectron spectroscopy (XPS) was used to determine cleanliness of the sample surfaces after plasma cleaning. The XPS study on polished samples confirmed the effectiveness of plasma cleaning in achieving atomic level of surface cleanliness. In this technical memorandum plasma properties, cleaning phenomena, and significant results are reported and discussed.« less

Stability of Atmospheric-Pressure Plasma Induced Changes on Polycarbonate Surfaces

NASA Technical Reports Server (NTRS)

Sharma, Rajesh; Holcomb, Edward; Trigwell, Steve

2006-01-01

Polycarbonate films are subjected to plasma treatment in a number of applications such as improving adhesion between polycarbonate and silicon alloy in protective and optical coatings. The changes in surface chemistry due to plasma treatment have tendency to revert back. Thus stability of the plasma induced changes on polymer surfaces over desired time period is very important. The objective of this study was to examine the effect of ageing on atmospheric pressure helium-plasma treated polycarbonate (PC) sample as a function of treatment time. The ageing effects were studied over a period of 10 days. The samples were plasma treated for 0.5, 2, 5 and 10 minutes. Contact angle measurements were made to study surface energy changes. Modification of surface chemical structure was examined using, X-ray Photoelectron Spectroscopy (XPS). Contact angle measurements on untreated and plasma treated surfaces were made immediately, 24, 48, 72 and 96 hrs after treatment. Contact angle decreased from 93 deg for untreated sample to 30 deg for sample plasma treated for 10 minutes. After 10 days the contact angles for the 10 minute plasma treated sample increased to 67 deg, but it never reverted back to that of untreated surface. Similarly the O/C ratio increased from 0.136 for untreated sample to 0.321 for 10 minute plasma treated sample indication increase in surface energy.

Dose-Response Analysis of RNA-Seq Profiles in Archival Formalin-fixed paraffin-embedded (FFPE) Samples

EPA Science Inventory

Formalin-fixed paraffin-embedded (FFPE) samples provide a vast untapped resource for chemical safety and translational science. To date, genomic profiling of FFPE samples has been limited by poor RNA quality and inconsistent results with limited utility in dose-response assessmen...

It's Time to Develop a New "Draft Test Protocol" for a Mars Sample Return Mission (or Two....)

NASA Astrophysics Data System (ADS)

Rummel, J. D.

2018-04-01

A Mars Sample Return (MSR) will involve analysis of those samples in containment, including their safe receiving, handling, testing, and archiving. With an MSR planned for the end of the next decade, it is time to update the existing MSR protocol.

A methodological study of genome-wide DNA methylation analyses using matched archival formalin-fixed paraffin embedded and fresh frozen breast tumors.

PubMed

Espinal, Allyson C; Wang, Dan; Yan, Li; Liu, Song; Tang, Li; Hu, Qiang; Morrison, Carl D; Ambrosone, Christine B; Higgins, Michael J; Sucheston-Campbell, Lara E

2017-02-28

DNA from archival formalin-fixed and paraffin embedded (FFPE) tissue is an invaluable resource for genome-wide methylation studies although concerns about poor quality may limit its use. In this study, we compared DNA methylation profiles of breast tumors using DNA from fresh-frozen (FF) tissues and three types of matched FFPE samples. For 9/10 patients, correlation and unsupervised clustering analysis revealed that the FF and FFPE samples were consistently correlated with each other and clustered into distinct subgroups. Greater than 84% of the top 100 loci previously shown to differentiate ER+ and ER- tumors in FF tissues were also FFPE DML. Weighted Correlation Gene Network Analyses (WCGNA) grouped the DML loci into 16 modules in FF tissue, with ~85% of the module membership preserved across tissue types. Restored FFPE and matched FF samples were profiled using the Illumina Infinium HumanMethylation450K platform. Methylation levels (β-values) across all loci and the top 100 loci previously shown to differentiate tumors by estrogen receptor status (ER+ or ER-) in a larger FF study, were compared between matched FF and FFPE samples using Pearson's correlation, hierarchical clustering and WCGNA. Positive predictive values and sensitivity levels for detecting differentially methylated loci (DML) in FF samples were calculated in an independent FFPE cohort. FFPE breast tumors samples show lower overall detection of DMLs versus FF, however FFPE and FF DMLs compare favorably. These results support the emerging consensus that the 450K platform can be employed to investigate epigenetics in large sets of archival FFPE tissues.

The new space and earth science information systems at NASA's archive

NASA Technical Reports Server (NTRS)

Green, James L.

1990-01-01

The on-line interactive systems of the National Space Science Data Center (NSSDC) are examined. The worldwide computer network connections that allow access to NSSDC users are outlined. The services offered by the NSSDC new technology on-line systems are presented, including the IUE request system, ozone TOMS data, and data sets on astrophysics, atmospheric science, land sciences, and space plasma physics. Plans for future increases in the NSSDC data holdings are considered.

The new space and Earth science information systems at NASA's archive

NASA Technical Reports Server (NTRS)

Green, James L.

1990-01-01

The on-line interactive systems of the National Space Science Data Center (NSSDC) are examined. The worldwide computer network connections that allow access to NSSDC users are outlined. The services offered by the NSSDC new technology on-line systems are presented, including the IUE request system, Total Ozone Mapping Spectrometer (TOMS) data, and data sets on astrophysics, atmospheric science, land sciences, and space plasma physics. Plans for future increases in the NSSDC data holdings are considered.

Creation of fluorocarbon barriers on surfaces of starch-based products through cold plasma treatment

NASA Astrophysics Data System (ADS)

Han, Yousoo

Two kinds of starch foam trays (starch and aspen-starch foam trays) were produced using a lab model baking machine. Surfaces of the trays were treated with CF4 and SF6 plasma to create fluorine-rich layers on the surfaces, which might show strong water resistance. The plasma parameters, such like RF power, gas pressure and reaction time, were varied to evaluate the effects of each parameter on fluorination of surfaces. The atomic concentrations of fluorine, oxygen and carbon on samples' surfaces were earned from ESCA (electron spectroscopy for chemical analysis) and contact angles of sample surfaces were measured for hydrophobicity. For water resistance of plasma treated surfaces, liquid water uptake and water vapor uptake test were performed. Also, equilibrium moisture contents of unmodified and plasma treated samples were measured to evaluate biodegradability of plasma treated samples. Fluorine-rich barriers were created on sample surfaces treated with CF 4 and SF6 plasma. The fluorine atomic concentrations of treated sample surfaces were ranged from 34.4% to 64.4% (CF4 treatment) and 43.6% to 57.9% (SF6 treatment). It was found at both plasma gases that plasma parameters affected total fluorine concentration and carbon-peak shapes in ESCA surveys, which imply different distributions of mono- or multi-fluoro carbon's contents. In various reaction times, it was found that total fluorine contents were decreased after a critical point as the reaction time was prolonged, which may imply that a dominant mechanism has been changed from deposition or functionalization to etching. Oxygen atomic concentration was decreased at sample surfaces treated by both plasmas. In the case of SF6 plasma, it was proved that the removal of oxygen surely occurred because there was no addition of sulfur species. Plasma treated sample surfaces had high contact angles with distilled water up to 150° and the high values of angles have been kept constant up to for 15 minutes. Fluorine-rich barriers created by plasma showed lower water liquid and vapor permeability than untreated surfaces did. Plasma treated samples had similar moisture contents with untreated samples at all relative humidity tested. AFM and SEM images were taken for sample surfaces' morphology and topography.

The WHISPER Relaxation Sounder and the CLUSTER Active Archive

NASA Astrophysics Data System (ADS)

Trotignon, J. G.; Décréau, P. M. E.; Rauch, J. L.; Vallières, X.; Rochel, A.; Kougblénou, S.; Lointier, G.; Facskó, G.; Canu, P.; Darrouzet, F.; Masson, A.

The Waves of HIgh frequency and Sounder for Probing of Electron density by Relaxation (WHISPER) instrument is part of the Wave Experiment Consortium (WEC) of the CLUSTER mission. With the help of the long double sphere antennae of the Electric Field and Wave (EFW) instrument and the Digital Wave Processor (DWP), it delivers active (sounding) and natural (transmitter off) electric field spectra, respectively from 4 to 82 kHz, and from 2 to 80 kHz. These frequency ranges have been chosen to include the electron plasma frequency, which is closely related to the total electron density, in most of the regions encountered by the CLUSTER spacecraft. Presented here is an overview of the WHISPER data products available in the CLUSTER Active Archive (CAA). The instrument and its performance are first recalled. The way the WHISPER products are obtained is then described, with particular attention being paid to the density determination. Both sounding and natural measurements are commonly used in this process, which depends on the ambient plasma regime. This is illustrated using drawings similar to the Bryant plots commonly used in the CLUSTER master science plan. These give a clear overview of typical density values and the parts of the orbits where they are obtained. More information on the applied software or on the quality/reliability of the density determination can also be highlighted.

{Interball-1 Plasma, Magnetic Field, and Energetic Particle Observations}

NASA Technical Reports Server (NTRS)

Sibeck, David G.

1998-01-01

Funding from NASA was received in two installments. The first installment supported research using Russian/Czech/Slovak/French Interball-1 plasma, magnetic field, and energetic particles observations in the vicinity of the magnetopause. The second installment provided salary support to review unsolicited proposals to NASA for data recovery and archiving, and also to survey ISTP data provision efforts. Two papers were published under the auspices of the grant. Sibeck et al. reported Interball-1 observations of a wave on the magnetopause with an amplitude in excess of 5 R(sub E), the largest ever reported to date. They attributed the wave to a hot flow anomaly striking the magnetopause and suggested that the hot flow anomaly itself formed during the interaction of an IMF discontinuity with the bow shock. Nemecek et al. used Interball-1's VDP Faraday cup to identify large transient increases in the magnetosheath density. They noted large variations in simultaneous Wind observations of the IMF cone angle, but were unable to establish any relationship between the cone angle variations at Wind and the density variations at Interball-1. Funds from the second installment were used to review over 20 proposals from various researchers in the scientific community who sought NASA support to restore or archive past observations. It also supported a survey of ISTP data provisions which was used as input to a Senior Review of ongoing NASA ISTP programs.

DATA QUALITY OBJECTIVES FOR SELECTING WASTE SAMPLES FOR BENCH-SCALE REFORMER TREATABILITY STUDIES

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

BANNING DL

2011-02-11

This document describes the data quality objectives to select archived samples located at the 222-S Laboratory for Bench-Scale Reforming testing. The type, quantity, and quality of the data required to select the samples for Fluid Bed Steam Reformer testing are discussed. In order to maximize the efficiency and minimize the time to treat Hanford tank waste in the Waste Treatment and Immobilization Plant, additional treatment processes may be required. One of the potential treatment processes is the fluidized bed steam reformer. A determination of the adequacy of the fluidized bed steam reformer process to treat Hanford tank waste is required.more » The initial step in determining the adequacy of the fluidized bed steam reformer process is to select archived waste samples from the 222-S Laboratory that will be used in a bench scale tests. Analyses of the selected samples will be required to confirm the samples meet the shipping requirements and for comparison to the bench scale reformer (BSR) test sample selection requirements.« less

Research methods of plasma stream interaction with heat-resistant materials

NASA Astrophysics Data System (ADS)

Tyuftyaev, A. S.; Gadzhiev, M. Kh; Sargsyan, M. A.; Chinnov, V. F.; Demirov, N. A.; Kavyrshin, D. I.; Ageev, A. G.; Khromov, M. A.

2016-11-01

An experimental automated system was designed and constructed for studying the parameters and characteristics of non-stationary interacting system high-enthalpy-plasma stream-investigated sample: enthalpy of plasma in the incident stream; speed and temperature of plasma stream; temperature of electrons and heavy particles, ionic composition and their spatial distribution; heat flux incident on the sample (kW/cm2); surface temperature of the sample; ablation of the sample material, and others. Measurements of achievable plasma heat flux levels are carried out by calorimetry of plasma streams incident on the surface of multisection copper calorimeter. Determination of acceleration characteristics for profiled plasma torch nozzle, as well as the gas flow rate is produced by measuring the total pressure using the Pitot tube. Video visualization of interacting system is carried out using synchronized high-speed cameras. Micropyrometry of the selected zone on the sample surface is carried out by high-speed, three-wavelength pyrometer. To measure the rate of mass loss of the sample, in addition to the weighing method of evaluation the methods of laser knife and two-position stereoscopy are used. Plasma and sample emission characteristics are performed with two separate spectrometers.

Studying The Spectral Shape And The X-ray/uv Variability Of Active Galactic Nuclei With Data From Swift And Xmm Archives

NASA Astrophysics Data System (ADS)

Turriziani, Sara

2011-01-01

Many efforts have been made in understanding the underlying origin of variability in Active Galactic Nuclei (AGN), but at present they could give still no conclusive answers. Since a deeper knowledge of variability will enable to understand better the accretion process onto supermassive black holes, I built the first ensemble struction function analysis of the X-ray variability of samples of quasars with data from Swift and XMM-Newton archives in order to study the average properties of their variability. Moreover, it is known that UV and X-ray luminosities of quasars are correlated and recent studies quantified this relation across 5 orders of magnitude. In this context, I presents results on the X-ray/UV ratio from simultaneous observations in UV and X-ray bands of a sample of quasars with data from XMM-Newton archive. Lastly, I will present a complete sample of Swift/SDSS faint blazars and other non-thermal dominated AGNs. I used this sample to calculate the general statistical properties of faint blazars and radio galaxies and in particular their Radio LogN-LogS with fluxes down to 10 mJy, in order to gain knowledge on the contribution to Cosmic Microwave Background (CMB) and gamma-ray background radiation from the faint tail of the radio population. I acknowledge financial support through Grant ASI I/088/06/0.

Serum samples can be substituted by plasma samples for the diagnosis of paratuberculosis.

PubMed

Goodridge, Amador; Correa, Ricardo; Castro, Paul; Escobar, Cecilia; de Waard, Jacobus H

2013-10-01

Employing plasma samples rather than serum samples for serological paratuberculosis diagnosis is practical, especially when bovine TB is assessed in the same cattle herd with the gamma interferon bovine avian (IFN-γ BA) test. We demonstrate that antibody titers in serum and plasma samples, utilizing the PARACHECK(®) ELISA kit, are highly comparable (Cohen's kappa test, k=0.955). We conclude that serum can be replaced with plasma in this commercially available antibody detection assay resulting in working hour savings for sampling and blood sample work-up and cost reductions for materials and sample storage. Copyright © 2013 Elsevier B.V. All rights reserved.

Influence of storage conditions on in vitro stability of atrial natriuretic peptide and of anesthesia on plasma atrial natriuretic peptide concentration in cats.

PubMed

Heishima, Yasuhiro; Hori, Yasutomo; Chikazawa, Seishiro; Kanai, Kazutaka; Hoshi, Fumio; Itoh, Naoyuki

2016-08-01

OBJECTIVE To investigate the in vitro stability of atrial natriuretic peptide (ANP) in plasma samples under various storage conditions and the influence of anesthesia on plasma ANP concentration in cats. ANIMALS 1 cat with congestive heart failure and 5 healthy adult mixed-breed cats. PROCEDURES A plasma sample from the cat with heart failure was serially diluted, and dilutional parallelism of ANP concentration was evaluated. Plasma samples containing aprotinin or serum samples from the 5 healthy cats were kept at room temperature (27°C) for ≤ 12 hours. Plasma samples from the same healthy cats were stored at -70°, -20°, or 4°C for ≤ 14 days. Plasma samples were obtained from the healthy cats before and during isoflurane anesthesia. Plasma ANP concentrations were measured at a commercial laboratory by use of a human ANP chemiluminescence assay. RESULTS Intra- and interassay coefficients of variation were 1.5% and 2.5%, respectively, and dilutional parallelism was established. Although ANP concentration decreased by 82.4 ± 13.6% (mean ± SD) after sample storage for 12 hours at room temperature, this decrease was prevented by aprotinin. Plasma ANP concentrations were stable for 7 days at -20°C and for 14 days at -70°C. However, concentrations decreased markedly to 57.6 ± 6.9% at -20°C and to 18.0 ± 3.0% at 4°C after 14 days. Plasma ANP concentration decreased significantly in cats during anesthesia and was correlated with blood pressure. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested that aprotinin should be added routinely in preparation of plasma samples from cats for measurement of ANP concentration, and those samples, if stored, should be frozen immediately at ≤ -20°C. General anesthesia or systemic blood pressure may affect plasma ANP concentration in cats.

Laying the groundwork for NEON's continental-scale ecological research

NASA Astrophysics Data System (ADS)

Dethloff, G.; Denslow, M.

2013-12-01

The National Ecological Observatory Network (NEON) is designed to examine a suite of ecological issues. Field-collected data from 96 terrestrial and aquatic sites across the U.S. will be combined with remotely sensed data and existing continental-scale data sets. Field collections will include a range of physical and biological types, including soil, sediment, surface water, groundwater, precipitation, plants, animals, insects, and microbes as well as biological sub-samples such as leaf material, blood and tissue samples, and DNA extracts. Initial data analyses and identifications of approximately 175,000 samples per year will occur at numerous external laboratories when all sites are fully staffed in 2017. Additionally, NEON will archive biotic and abiotic specimens at collections facilities where they will be curated and available for additional analyses by the scientific community. The number of archived specimens is currently estimated to exceed 130,000 per year by 2017. We will detail how NEON is addressing the complexities and challenges around this set of analyses and specimens and how the resulting high-quality data can impact ecological understanding. The raw data returned from external laboratories that is quality checked and served by NEON will be the foundation for many NEON data products. For example, sequence-quality nucleic acids extracted from surface waters, benthic biofilms, and soil samples will be building blocks for data products on microbial diversity. The raw sequence data will also be available for uses such as evolutionary investigations, and the extracts will be archived so others can acquire them for additional research. Currently, NEON is establishing contracts for the analysis and archiving of field-collected samples through 2017. During this period, NEON will gather information on the progress and success of this large-scale effort in order to determine the most effective course to pursue with external facilities. Two areas that NEON already knows to evaluate are the need for geographic expertise in taxonomic identifications and the capacity necessary to handle the volume of samples. NEON is also addressing challenges associated with external entities and the logistics of sample movement, data formatting, data ingestion, and reporting. For example, NEON is considering tools, such as web APIs, which could allow efficient transfer of data from external facilities. Having a standard format in place for that data will be critical to transfer success and quality assessment. NEON is also working on the implementation of quality control measures for diverse analytical and taxonomic processes across laboratories, and is developing an external audit process. Additionally, given NEON's open access approach, the Network is focused on selecting a sample identification protocol that aids in tracking samples with more involved analytical needs and also allows maximum utility for the scientific community. Given the complex nature and breadth of the project, NEON will be developing novel sample management systems as well as metadata schemas. These efforts insure integrity and quality from field to external facility to archive for each sample taken, providing high-quality data now and confidence in future research stemming from raw data generated by NEON and its collection specimens.

Europlanet/IDIS: Combining Diverse Planetary Observations and Models

NASA Astrophysics Data System (ADS)

Schmidt, Walter; Capria, Maria Teresa; Chanteur, Gerard

2013-04-01

Planetary research involves a diversity of research fields from astrophysics and plasma physics to atmospheric physics, climatology, spectroscopy and surface imaging. Data from all these disciplines are collected from various space-borne platforms or telescopes, supported by modelling teams and laboratory work. In order to interpret one set of data often supporting data from different disciplines and other missions are needed while the scientist does not always have the detailed expertise to access and utilize these observations. The Integrated and Distributed Information System (IDIS) [1], developed in the framework of the Europlanet-RI project, implements a Virtual Observatory approach ([2] and [3]), where different data sets, stored in archives around the world and in different formats, are accessed, re-formatted and combined to meet the user's requirements without the need of familiarizing oneself with the different technical details. While observational astrophysical data from different observatories could already earlier be accessed via Virtual Observatories, this concept is now extended to diverse planetary data and related model data sets, spectral data bases etc. A dedicated XML-based Europlanet Data Model (EPN-DM) [4] was developed based on data models from the planetary science community and the Virtual Observatory approach. A dedicated editor simplifies the registration of new resources. As the EPN-DM is a super-set of existing data models existing archives as well as new spectroscopic or chemical data bases for the interpretation of atmospheric or surface observations, or even modeling facilities at research institutes in Europe or Russia can be easily integrated and accessed via a Table Access Protocol (EPN-TAP) [5] adapted from the corresponding protocol of the International Virtual Observatory Alliance [6] (IVOA-TAP). EPN-TAP allows to search catalogues, retrieve data and make them available through standard IVOA tools if the access to the archive is compatible with IVOA standards. For some major data archives with different standards adaptation tools are available to make the access transparent to the user. EuroPlaNet-IDIS has contributed to the definition of PDAP, the Planetary Data Access Protocol of the International Planetary Data Alliance (IPDA) [7] to access the major planetary data archives of NASA in the USA [8], ESA in Europe [9] and JAXA in Japan [10]. Acknowledgement: Europlanet-RI was funded by the European Commission under the 7th Framework Program, grant 228319 "Capacities Specific Programme" - Research Infrastructures Action. Reference: [1] Details to IDIS and the Europlanet-RI via Web-site: http://www.idis.europlanet-ri.eu/ [2] Demonstrator implementation for Plasma-VO AMDA: http://cdpp-amda.cesr.fr/DDHTML/index.html [3] Demonstrator implementation for the IDIS-VO: http://www.idis-dyn.europlanet-ri.eu/vodev.shtml [4] Europlanet Data Model EPN-DM: http://www.europlanet-idis.fi/documents/public_documents/EPN-DM-v2.0.pdf [5] Europlanet Table Access Protocol EPN-TAP: http://www.europlanet-idis.fi/documents/public_documents/EPN-TAPV_0.26.pdf [6] International Virtual Observatory Alliance IVOA: http://www.ivoa.net [7] International Planetary Data Alliance IPDA: http://planetarydata.org/ [8] NASA's Planetary Data System: http://pds.jpl.nasa.gov/ [9] ESA's Planetary Science Archive PSA: http://www.sciops.esa.int/index.php?project=PSA [10] JAXAs Data Archive and Transmission System DARTS: http://darts.isas.jaxa.jp/

CDPP Tools in the IMPEx infrastructure

NASA Astrophysics Data System (ADS)

Gangloff, Michel; Génot, Vincent; Bourrel, Nataliya; Hess, Sébastien; Khodachenko, Maxim; Modolo, Ronan; Kallio, Esa; Alexeev, Igor; Al-Ubaidi, Tarek; Cecconi, Baptiste; André, Nicolas; Budnik, Elena; Bouchemit, Myriam; Dufourg, Nicolas; Beigbeder, Laurent

2014-05-01

The CDPP (Centre de Données de la Physique des Plasmas, http://cdpp.eu/), the French data center for plasma physics, is engaged for more than a decade in the archiving and dissemination of plasma data products from space missions and ground observatories. Besides these activities, the CDPP developed services like AMDA (http://amda.cdpp.eu/) which enables in depth analysis of large amount of data through dedicated functionalities such as: visualization, conditional search, cataloguing, and 3DView (http://3dview.cdpp.eu/) which provides immersive visualisations in planetary environments and is further developed to include simulation and observational data. Both tools implement the IMPEx protocol (http://impexfp7.oeaw.ac.at/) to give access to outputs of simulation runs and models in planetary sciences from several providers like LATMOS, FMI , SINP; prototypes have also been built to access some UCLA and CCMC simulations. These tools and their interaction will be presented together with the IMPEx simulation data model (http://impex.latmos.ipsl.fr/tools/DataModel.htm) used for the interface to model databases.

Repurposing Archival Samples for Investigating Toxicological Modes of Action

EPA Science Inventory

Little is known about formalin fixation induced genomic artifacts, limiting the use of formalin-fixed paraffin-embedded (FFPE) samples in toxicological and clinical studies. Previously, we identified a consistent shift in transcriptional profiles between paired frozen and FFPE sa...

Interplanetary space science data base and access/display tool on the NSSDC heliospheric CD-ROM

NASA Technical Reports Server (NTRS)

Papitashvili, N. E.; King, J. H.

1995-01-01

The National Space Science Data Center (NSSDC) has accumulated a rich archive of heliospheric, magnetospheric, and ionospheric data, as well as data from most other NASA-involved science disciplines. To facilitate access to and use of these data, NSSDC has begun to put selected data onto CD-ROM's. This paper describes one such CD-ROM, and the access and display software developed at NSSDC to support its use. The data on the CD-ROM consist primarily of hourly solar wind magnetic field and plasma data from many near-Earth spacecraft (OMNI) and deep space spacecraft (Voyagers, Pioneers, Helios, Pioneer Venus Orbiter). In addition, 5-minute resolution IMP-8 and ISEE-3 magnetic field and plasma data are also included. Data are stored in both ASCII and CDF formats.

Ammonia concentrations in canine whole blood, EDTA-anticoagulated whole blood, and plasma measured by use of a point-of-care ammonia meter.

PubMed

Odunayo, Adesola; Tobias, Karen M; Okafor, Chika C; Flatland, Bente

2017-11-01

OBJECTIVE To investigate the use of canine whole blood (WB) for measurement of ammonia concentration by use of a point-of-care ammonia meter and to compare results of measuring ammonia concentrations in WB, EDTA-anticoagulated WB, and plasma. ANIMALS 40 client-owned dogs. PROCEDURES A blood sample (2 mL) was obtained from each dog. One drop of WB was immediately applied to a test strip for evaluation with an ammonia meter. The remainder of the blood sample was placed in an EDTA-containing tube, and 1 drop of EDTA-anticoagulated WB was applied to a test strip. The remaining EDTA-anticoagulated WB sample was centrifuged, and the plasma was harvested and placed on ice. One drop of plasma was applied to a test strip; the remainder of the plasma sample was transported on ice and used for ammonia measurement with a reference laboratory instrument. All samples were tested within 1 hour after sample collection. Results were evaluated to detect significant differences in ammonia concentration. RESULTS Ammonia concentrations did not differ significantly between WB and EDTA-anticoagulated WB and between plasma samples measured with the meter and reference laboratory instrument. However, median ammonia concentration was significantly higher in plasma than in WB or EDTA-anti-coagulated WB. CONCLUSIONS AND CLINICAL RELEVANCE Anticoagulant-free WB was a valid sample for measurement by use of the ammonia meter. Plasma samples had higher ammonia concentrations than did WB samples. Results for each sample type should be interpreted by use of specimen- and method-specific reference intervals.

The importance of sample collection when using single cytokine levels and systemic cytokine profiles as biomarkers--a comparative study of serum versus plasma samples.

PubMed

Tvedt, Tor Henrik Anderson; Rye, Kristin Paulsen; Reikvam, Håkon; Brenner, Annette K; Bruserud, Øystein

2015-03-01

Cytokines, soluble adhesion molecules and metalloproteinases can be detected in human serum or plasma samples. Such systemic levels are widely used as biomarkers in epidemiological and clinical studies. We prepared serum samples and three types of plasma samples (EDTA, heparin, citric acid) from 20 healthy individuals. The levels of 31 cytokines, four soluble adhesion molecules and eight matrix metalloproteinases were analyzed by Luminex technology. Most mediators showed detectable levels in both plasma and serum. Several mediators that can be released by platelets showed increased serum levels, especially CCL5 and CD40L, but for the other mediators the serum levels did not correlate with peripheral blood platelet counts and for these last mediators serum and plasma levels often showed strong correlations. The use of bivalirudin for anticoagulation significantly increased and citric acid combined with platelet inhibitors (ticagrelor, acetylsalicylic acid plus prostaglandin E2) did not alter plasma levels of platelet-store mediators compared with citric acid alone. The impact of sample preparation differed between mediators; for many mediators strong correlations were seen between serum and plasma levels even when absolute levels differed. Soluble adhesion molecule levels showed only minor differences between samples. Unsupervised hierarchical clustering suggested that the effect of sampling/preparation was strongest for serum and heparin plasma samples. Careful standardization of sample preparation is usually necessary when analyzing systemic mediator levels, and differences caused by sample preparation should be considered as a possible explanation if studies show conflicting results. Copyright © 2015 Elsevier B.V. All rights reserved.

Chroni - an Android Application for Geochronologists to Access Archived Sample Analyses from the NSF-Funded Geochron.Org Data Repository.

NASA Astrophysics Data System (ADS)

Nettles, J. J.; Bowring, J. F.

2014-12-01

NSF requires data management plans as part of funding proposals and geochronologists, among other scientists, are archiving their data and results to the public cloud archives managed by the NSF-funded Integrated Earth Data Applications, or IEDA. GeoChron is a database for geochronology housed within IEDA. The software application U-Pb_Redux developed at the Cyber Infrastructure Research and Development Lab for the Earth Sciences (CIRDLES.org) at the College of Charleston provides seamless connectivity to GeoChron for uranium-lead (U-Pb) geochronologists to automatically upload and retrieve their data and results. U-Pb_Redux also manages publication-quality documents including report tables and graphs. CHRONI is a lightweight mobile application for Android devices that provides easy access to these archived data and results. With CHRONI, U-Pb geochronologists can view archived data and analyses downloaded from the Geochron database, or any other location, in a customizable format. CHRONI uses the same extensible markup language (XML) schema and documents used by U-Pb_Redux and GeoChron. Report Settings are special XML files that can be customized in U-Pb_Redux, stored in the cloud, and then accessed and used in CHRONI to create the same customized data display on the mobile device. In addition to providing geologists effortless and mobile access to archived data and analyses, CHRONI allows users to manage their GeoChron credentials, quickly download private and public files via a specified IEDA International Geo Sample Number (IGSN) or URL, and view specialized graphics associated with particular IGSNs. Future versions of CHRONI will be developed to support iOS compatible devices. CHRONI is an open source project under the Apache 2 license and is hosted at https://github.com/CIRDLES/CHRONI. We encourage community participation in its continued development.

Investigation of the effects of plasma treatments on biodeteriorated ancient paper

NASA Astrophysics Data System (ADS)

Laguardia, L.; Vassallo, E.; Cappitelli, F.; Mesto, E.; Cremona, A.; Sorlini, C.; Bonizzoni, G.

2005-11-01

Deterioration of paper-based materials is mainly due to the degradation of cellulose caused by a lot of factors such as chemical attack due to acidic hydrolysis, oxidative agent, light, air pollution and biological attack and also due to the presence of microorganisms like bacteria and fungi. It is therefore desirable to focus the research activities on restoration and conservation techniques to develop appropriate treatments. The aim of this paper is the removal or reduction of the microbial contamination and paper consolidation by means of plasma treatment. For plasma processes, different gas mixtures are utilised, and the different gas mixtures are compared as a function of pressure, power, and treatment time. To demonstrate the efficiency of the sterilisation treatment, two fungi: Aspergillus niger and Penicillium funiculosum, commonly found in libraries and archives were spread on naturally aged paper (19th century). Microorganisms were let to grow by using the organic compounds found in the historical records as a sole source of carbon and energy. The microbial abatement was measured before and after the plasma treatment by using the standard plate count method. Surface chemical and morphological characterisation of paper before and after plasma treatment has been carried out by X-ray photoelectron spectroscopy (XPS) and ATR infrared spectroscopy (ATR FTIR). The tensile strength of the plasma-treated papers was also determined. CNR Patent, n° Mi2004A000068, 21/01/2004.

Foliar and soil chemistry at red spruce sites in the Monongahela National Forest

Treesearch

Stephanie J. Connolly

2010-01-01

In 2005, soil and foliar chemistry were sampled from 10 sites in the Monongahela National Forest which support red spruce. Soils were sampled from hand-dug pits, by horizon, from the O-horizon to bedrock or 152 cm, and each pit was described fully. Replicate, archived samples also were collected.

ISS Potable Water Sampling and Chemical Analysis Results for 2016

NASA Technical Reports Server (NTRS)

Straub, John E., II; Plumlee, Debrah K.; Wallace William T.; Alverson, James T.; Benoit, Mickie J.; Gillispie, Robert L.; Hunter, David; Kuo, Mike; Rutz, Jeffrey A.; Hudson, Edgar K.;

ISS Potable Water Sampling and Chemical Analysis Results for 2016

NASA Technical Reports Server (NTRS)

Straub, John E., II; Plumlee, Debrah K.; Wallace, William T.; Alverson, James T.; Benoit, Mickie J.; Gillispie, Robert L.; Hunter, David; Kuo, Mike; Rutz, Jeffrey A.; Hudson, Edgar K.;

Use of vitamin B12 in joint lavage for determination of dilution factors of canine synovial fluid.

PubMed

de Bruin, Tanya; de Rooster, Hilde; van Bree, Henri; Cox, Eric

2005-11-01

To test a modified saline (0.9% NaCl) solution joint washing (lavage) technique that includes the use of vitamin B12 as an internal marker for the evaluation of synovial fluid dilution in lavage samples from canine joints. 9 plasma samples obtained from blood samples of 9 healthy dogs and 9 synovial fluid samples aspirated from stifle joints of 9 cadaveric dogs. Photometric absorbances of 25% vitamin B12 solution, canine synovial fluid, and canine plasma were measured in a spectrophotometer to establish an optimal wavelength for analysis. Canine synovial fluid and plasma samples were mixed with the 25% vitamin B12 solution to obtain 1%, 3%, 5%, 10%, 20%, and 50% solutions of synovial fluid or plasma. Diluted synovial fluid and plasma samples were used to simulate joint lavage samples and to examine the possible interference of these substances (synovial fluid or plasma) with the absorbance of the 25% vitamin B12 solution in photometric analysis. The optimal wavelength was found to be at 550 nm. Canine synovial fluid and plasma samples did not interfere with the absorbance measurements of the 25% vitamin B12 solution up to a 50% dilution of plasma or synovial fluid. The modified saline solution joint lavage method with the use of a 25% vitamin B12 solution as an internal standard provides an accurate and reliable technique for the evaluation of synovial fluid dilution in lavage samples from canine joints.

The Index to Marine and Lacustrine Geological Samples: Improving Sample Accessibility and Enabling Current and Future Research

NASA Astrophysics Data System (ADS)

Moore, C.

2011-12-01

The Index to Marine and Lacustrine Geological Samples is a community designed and maintained resource enabling researchers to locate and request sea floor and lakebed geologic samples archived by partner institutions. Conceived in the dawn of the digital age by representatives from U.S. academic and government marine core repositories and the NOAA National Geophysical Data Center (NGDC) at a 1977 meeting convened by the National Science Foundation (NSF), the Index is based on core concepts of community oversight, common vocabularies, consistent metadata and a shared interface. Form and content of underlying vocabularies and metadata continue to evolve according to the needs of the community, as do supporting technologies and access methodologies. The Curators Consortium, now international in scope, meets at partner institutions biennially to share ideas and discuss best practices. NGDC serves the group by providing database access and maintenance, a list server, digitizing support and long-term archival of sample metadata, data and imagery. Over three decades, participating curators have performed the herculean task of creating and contributing metadata for over 195,000 sea floor and lakebed cores, grabs, and dredges archived in their collections. Some partners use the Index for primary web access to their collections while others use it to increase exposure of more in-depth institutional systems. The Index is currently a geospatially-enabled relational database, publicly accessible via Web Feature and Web Map Services, and text- and ArcGIS map-based web interfaces. To provide as much knowledge as possible about each sample, the Index includes curatorial contact information and links to related data, information and images; 1) at participating institutions, 2) in the NGDC archive, and 3) at sites such as the Rolling Deck to Repository (R2R) and the System for Earth Sample Registration (SESAR). Over 34,000 International GeoSample Numbers (IGSNs) linking to SESAR are included in anticipation of opportunities for interconnectivity with Integrated Earth Data Applications (IEDA) systems. To promote interoperability and broaden exposure via the semantic web, NGDC is publishing lithologic classification schemes and terminology used in the Index as Simple Knowledge Organization System (SKOS) vocabularies, coordinating with R2R and the Consortium for Ocean Leadership for consistency. Availability in SKOS form will also facilitate use of the vocabularies in International Standards Organization (ISO) 19115-2 compliant metadata records. NGDC provides stewardship for the Index on behalf of U.S. repositories as the NSF designated "appropriate National Data Center" for data and metadata pertaining to sea floor samples as specified in the 2011 Division of Ocean Sciences Sample and Data Policy, and on behalf of international partners via a collocated World Data Center. NGDC operates on the Open Archival Information System (OAIS) reference model. Active Partners: Antarctic Marine Geology Research Facility, Florida State University; British Ocean Sediment Core Research Facility; Geological Survey of Canada; Integrated Ocean Drilling Program; Lamont-Doherty Earth Observatory; National Lacustrine Core Repository, University of Minnesota; Oregon State University; Scripps Institution of Oceanography; University of Rhode Island; U.S. Geological Survey; Woods Hole Oceanographic Institution.

In vitro flow-through assay for rapid detection of endotoxin in human sera: A proof-of-concept.

PubMed

Kalita, Prasanta; Chaturvedula, Lakshmi M; Sritharan, Venkataraman; Gupta, Shalini

2017-05-01

An increase in endotoxin concentration in the bloodstream can trigger activation of innate immune response leading to septic shock. There is currently no method available for rapid endotoxin detection at a patient's bedside. We demonstrate a simple, portable and cost-effective strategy to measure endotoxin levels in human serum within 5min using a flow-through assay. A drop of serum containing LPS was spotted on an endotoxin-affinity membrane placed over high-wicking absorbent pads. Subsequent addition of polymyxin B sulfate drug-conjugated gold nanoparticles allowed concentration-dependent visualization of spots by the naked eye in the clinically-relevant range of 10pg/mL to 10ng/mL. The results were quantified using a concentration-calibrated color chart and the assay performance was tested with archival plasma samples of 18 known septicemia patients. The results showed a reasonably good correlation with the patients' hematological data. This proof-of-concept study puts forth an interesting alternative for early septicemia diagnosis in future. Copyright © 2017 Elsevier Inc. All rights reserved.

Thallium as a tracer for preindustrial volcanic eruptions in an ice core record from Illimani, Bolivia.

PubMed

Kellerhals, Thomas; Tobler, Leonhard; Brütsch, Sabina; Sigl, Michael; Wacker, Lukas; Gäggeler, Heinz W; Schwikowski, Margit

2010-02-01

Trace element records from glacier and ice sheet archives provide insights into biogeochemical cycles, atmospheric circulation changes, and anthropogenic pollution history. We present the first continuous high-resolution thallium (Tl) record, derived from an accurately dated ice core from tropical South America, and discuss Tl as a tracer for volcanic eruptions. We identify four prominent Tl peaks and propose that they represent signals from the massive explosive eruptions of the "unknown 1258" A.D. volcano, of Kuwae ( approximately 1450 A.D.), Tambora (1815 A.D.), and Krakatoa (1883 A.D.). The highly resolved record was obtained with an improved setup for the continuous analysis of trace elements in ice with inductively coupled plasma sector field mass spectrometry (ICP-SFMS). The new setup allowed for a stronger initial acidification of the meltwater and shorter tubing length, thereby reducing the risk of memory effects and losses of analytes to the capillary walls. With a comparison of the continuous method to the established conventional decontamination and analysis procedure for discrete samples, we demonstrate the accuracy of the continuous method for Tl analyses.

Reproducibility of Clathromorphum compactum coralline algal Mg/Ca ratios and comparison to high-resolution sea surface temperature data

NASA Astrophysics Data System (ADS)

Hetzinger, S.; Halfar, J.; Kronz, A.; Simon, K.; Adey, W. H.; Steneck, R. S.

2018-01-01

The potential of crustose coralline algae as high-resolution archives of past ocean variability in mid- to high-latitudes has only recently been recognized. Few comparisons of coralline algal proxies, such as temperature-dependent algal magnesium to calcium (Mg/Ca) ratios, with in situ-measured surface ocean data exist, even rarer are well replicated records from individual sites. We present Mg/Ca records from nine coralline algal specimens (Clathromorphum compactum) from a single site in the Gulf of Maine, North Atlantic. Sections from algal mounds were analyzed using Laser Ablation-Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) yielding individual Mg/Ca records of up to 30 years in length. We first test intra- and intersample signal replication and show that algal Mg/Ca ratios are reproducible along several transects within individual sample specimens and between different samples from the same study site. In addition, LA-ICP-MS-derived Mg/Ca ratios are compared to electron microprobe (EMP) analyzed data on the longest-lived specimens and were found to be statistically commensurable. Second, we evaluate whether relationships between algal-based SST reconstructions and in situ temperature data can be improved by averaging Mg/Ca records from multiple algal specimens (intersample averages). We found that intersample averages yield stronger relationships to sea surface temperature (SST) data than Mg/Ca records derived from individual samples alone. Thus, Mg/Ca-based paleotemperature reconstructions from coralline algae can benefit from using multiple samples per site, and can expand temperature proxy precision from seasonal to monthly.

VizieR Online Data Catalog: M67 variable stars from Kepler/K2-Campaign-5 (Gonzalez, 2016)

NASA Astrophysics Data System (ADS)

Gonzalez, G.

2017-06-01

M 67 was observed continuously between 2015 April 27 and July 10 during the Kepler/K2-Campaign-5 (hereafter, 'Campaign-5 field'). It includes 28 850 long-cadence, 204 short-cadence, and several other special targets. Several data products for the Campaign-5 field were released to the public on the NASA Barbara A. Mikulski Archive for Space Telescopes (MAST) website on 2015 October 30 (https://archive.stsci.edu/k2/). We downloaded tar files containing all the long-cadence light-curve (CLC) files of the Campaign-5 targets from the MAST archive. In addition, we downloaded the comprehensive K2 input catalogue (EPIC) for the Campaign-5 field. We supplemented the NASA K2 data with ground-based data, of which Nardiello et al. (2016, Cat. J/MNRAS/455/2337) is our primary source. Nardiello et al. (2016, Cat. J/MNRAS/455/2337) list the positions and white-light magnitudes for 6905 objects in the M 67 field, but they only list BVRI magnitudes, proper motions and membership probabilities for a subset of this large sample. Cross-referencing (using coordinates) the Campaign-5 input catalogue with the Nardiello et al. (2016, Cat. J/MNRAS/455/2337) catalogue resulted in 3201 matches. Of these, 639 have light curves available in the MAST Campaign-5 archive. This will be the working sample. (1 data file).

Bacteria-killing ability of fresh blood plasma compared to frozen blood plasma

DOE PAGES

Jacobs, Anne C.; Fair, Jeanne Marie

2015-10-09

In recent years, the bacteria-killing assay (BKA) has become a popular technique among ecoimmunologists. New variations of that assay allow researchers to use smaller volumes of blood, an important consideration for those working on small-bodied animals. However, this version of the assay requires access to a lab with a nanodrop spectrophotometer, something that may not be available in the field. One possible solution is to freeze plasma for transport; however, this assumes that frozen plasma samples will give comparable results to fresh ones. Here, we tested this assumption using plasma samples from three species of birds: chickens (Gallus gallus), ash-throatedmore » flycatchers (Myiarchus cinerascens), and western bluebirds (Sialia mexicana). Chicken plasma samples lost most or all of their bacterial killing ability after freezing. This did not happen in flycatchers and bluebirds; however, frozen plasma did not produce results comparable to those obtained using fresh plasma. Finally, we caution researchers using the BKA to use fresh samples whenever possible, and to validate the use of frozen samples on a species-by-species basis.« less

Spatial-temporal diagnostics of the system of a plasma stream interacting with a surface of heat resistant material

NASA Astrophysics Data System (ADS)

Chinnov, V. F.; Sargsyan, M. A.; Gadzhiev, M. Kh; Khromov, M. A.; Kavyrshin, D. I.; Chistolinov, A. V.

2018-01-01

In an automated measuring complex using optical and spectral methods the spatial and temporal changes in the parameters and composition of nitrogen plasma jet were investigated. The plasma jet was flowing out of the nozzle of the plasma torch with 10-12 kK temperature and acting on the sample of MPG-6 graphite. Due to the heating of the sample to the temperatures of 2.5-3 kK the influence of the sublimating material of the sample on the plasma composition and temperature in the near-surface region of the sample was investigated. An original method based on the analysis of movement of optical inhomogeneities in the plasma flow was used to estimate the plasma jet velocity in the region where it interacts with the sample. The combined analysis of the results of two-positioning video recordings opens up the possibility of determining spatial-temporal distributions of the plasma jet velocities, in medium and high pressure environments, in the ranges from few to thousands of m/s and 3-15 kK temperatures.

Bacteria-killing ability of fresh blood plasma compared to frozen blood plasma.

PubMed

Jacobs, Anne C; Fair, Jeanne M

2016-01-01

In recent years, the bacteria-killing assay (BKA) has become a popular technique among ecoimmunologists. New variations of that assay allow researchers to use smaller volumes of blood, an important consideration for those working on small-bodied animals. However, this version of the assay requires access to a lab with a nanodrop spectrophotometer, something that may not be available in the field. One possible solution is to freeze plasma for transport; however, this assumes that frozen plasma samples will give comparable results to fresh ones. We tested this assumption using plasma samples from three species of birds: chickens (Gallus gallus), ash-throated flycatchers (Myiarchus cinerascens), and western bluebirds (Sialia mexicana). Chicken plasma samples lost most or all of their bacterial killing ability after freezing. This did not happen in flycatchers and bluebirds; however, frozen plasma did not produce results comparable to those obtained using fresh plasma. We caution researchers using the BKA to use fresh samples whenever possible, and to validate the use of frozen samples on a species-by-species basis. Copyright © 2015 Elsevier Inc. All rights reserved.

Bacteria-killing ability of fresh blood plasma compared to frozen blood plasma

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

Jacobs, Anne C.; Fair, Jeanne Marie

In recent years, the bacteria-killing assay (BKA) has become a popular technique among ecoimmunologists. New variations of that assay allow researchers to use smaller volumes of blood, an important consideration for those working on small-bodied animals. However, this version of the assay requires access to a lab with a nanodrop spectrophotometer, something that may not be available in the field. One possible solution is to freeze plasma for transport; however, this assumes that frozen plasma samples will give comparable results to fresh ones. Here, we tested this assumption using plasma samples from three species of birds: chickens (Gallus gallus), ash-throatedmore » flycatchers (Myiarchus cinerascens), and western bluebirds (Sialia mexicana). Chicken plasma samples lost most or all of their bacterial killing ability after freezing. This did not happen in flycatchers and bluebirds; however, frozen plasma did not produce results comparable to those obtained using fresh plasma. Finally, we caution researchers using the BKA to use fresh samples whenever possible, and to validate the use of frozen samples on a species-by-species basis.« less

Evaluating Trends in Historical PM2.5 Element Concentrations by Reanalyzing a 15-Year Sample Archive

NASA Astrophysics Data System (ADS)

Hyslop, N. P.; White, W. H.; Trzepla, K.

2014-12-01

The IMPROVE (Interagency Monitoring of PROtected Visual Environments) network monitors aerosol concentrations at 170 remote sites throughout the United States. Twenty-four-hour filter samples of particulate matter are collected every third day and analyzed for chemical composition. About 30 of the sites have operated continuously since 1988, and the sustained data record (http://views.cira.colostate.edu/web/) offers a unique window on regional aerosol trends. All elemental analyses have been performed by Crocker Nuclear Laboratory at the University of California in Davis, and sample filters collected since 1995 are archived on campus. The suite of reported elements has remained constant, but the analytical methods employed for their determination have evolved. For example, the elements Na - Mn were determined by PIXE until November 2001, then by XRF analysis in a He-flushed atmosphere through 2004, and by XRF analysis in vacuum since January 2005. In addition to these fundamental changes, incompletely-documented operational factors such as detector performance and calibration details have introduced variations in the measurements. Because the past analytical methods were non-destructive, the archived filters can be re-analyzed with the current analytical systems and protocols. The 15-year sample archives from Great Smoky Mountains (GRSM), Mount Rainier (MORA), and Point Reyes National Parks (PORE) were selected for reanalysis. The agreement between the new analyses and original determinations varies with element and analytical era. The graph below compares the trend estimates for all the elements measured by IMPROVE based on the original and repeat analyses; the elements identified in color are measured above the detection limit more than 90% of the time. The trend estimates are sensitive to the treatment of non-detect data. The original and reanalysis trends are indistinguishable (have overlapping confidence intervals) for most of the well-detected elements.

Reanalysis of a 15-year Archive of IMPROVE Samples

NASA Astrophysics Data System (ADS)

Hyslop, N. P.; White, W. H.; Trzepla, K.

2013-12-01

The IMPROVE (Interagency Monitoring of PROtected Visual Environments) network monitors aerosol concentrations at 170 remote sites throughout the United States. Twenty-four-hour filter samples of particulate matter are collected every third day and analyzed for chemical composition. About 30 of the sites have operated continuously since 1988, and the sustained data record (http://views.cira.colostate.edu/web/) offers a unique window on regional aerosol trends. All elemental analyses have been performed by Crocker Nuclear Laboratory at the University of California in Davis, and sample filters collected since 1995 are archived on campus. The suite of reported elements has remained constant, but the analytical methods employed for their determination have evolved. For example, the elements Na - Mn were determined by PIXE until November 2001, then by XRF analysis in a He-flushed atmosphere through 2004, and by XRF analysis in vacuum since January 2005. In addition to these fundamental changes, incompletely-documented operational factors such as detector performance and calibration details have introduced variations in the measurements. Because the past analytical methods were non-destructive, the archived filters can be re-analyzed with the current analytical systems and protocols. The 15-year sample archives from Great Smoky Mountains, Mount Rainier, and Point Reyes National Parks were selected for reanalysis. The agreement between the new analyses and original determinations varies with element and analytical era (Figure 1). Temporal trends for some elements are affected by these changes in measurement technique while others are not (Figure 2). Figure 1. Repeatability of analyses for sulfur and vanadium at Great Smoky Mountains National Park. Each point shows the ratio of mass loadings determined by the original analysis and recent reanalysis. Major method distinctions are indicated at the top. Figure 2. Trends, based on Thiel-Sen regression, in lead concentrations based on the original and reanalysis data.

Integration of In-Flight and Post-Flight Water Monitoring Resources in Addressing the U.S. Water Processor Assembly Total Organic Carbon (TOC) Anomaly

NASA Technical Reports Server (NTRS)

Straub, John E., II; McCly, J. Torin

2011-01-01

Beginning in June of 2010, the total organic carbon (TOC) concentration in the U.S. Water Processor Assembly (WPA) product water started to increase. A surprisingly consistent upward TOC trend was observed through weekly ISS total organic carbon analyzer (TOCA) monitoring. As TOC is a general organic compound indicator, return of water archive samples was needed to make better-informed crew health decisions on the specific compounds of concern and to aid in WPA troubleshooting. TOCA-measured TOC was more than halfway to the health-based screening limit of 3,000 g/L before archive samples were returned. Archive samples were returned on 22 Soyuz in September 2010 and on ULF5 in November of 2010. The samples were subjected to extensive analysis. Although TOC was confirmed to be elevated, somewhat surprisingly, none of the typical target compounds were detected at high levels. After some solid detective work, it was confirmed that the TOC was associated with a compound known as dimethylsilanediol (DMSD). DMSD is believed to be a breakdown product of siloxanes which are thought to be ubiquitous in the ISS atmosphere. A toxicological limit was set for DMSD and a forward plan was developed for conducting operations in the context of understanding the composition of the TOC measured in flight. This required careful consideration of existing ISS flight rules, coordination with ISS stakeholders, and development of a novel approach for the blending of inflight TOCA data with archive results to protect crew health. Among other challenges, team members had to determine how to utilize TOCA readings when making decisions about crew consumption of WPA water. This involved balancing very real concerns associated with the assumption that TOC would continue to be comprised of only DMSD. Demonstrated teamwork, multidisciplinary awareness, and innovative problem-solving were required to respond effectively to this anomaly.

The NASA Ames Research Center Institutional Scientific Collection: History, Best Practices and Scientific Opportunities

NASA Technical Reports Server (NTRS)

Rask, Jon C.; Chakravarty, Kaushik; French, Alison; Choi, Sungshin; Stewart, Helen

2017-01-01

The NASA Ames Life Sciences Institutional Scientific Collection (ISC), which is composed of the Ames Life Sciences Data Archive (ALSDA) and the Biospecimen Storage Facility (BSF), is managed by the Space Biosciences Division and has been operational since 1993. The ALSDA is responsible for archiving information and animal biospecimens collected from life science spaceflight experiments and matching ground control experiments. Both fixed and frozen spaceflight and ground tissues are stored in the BSF within the ISC. The ALSDA also manages a Biospecimen Sharing Program, performs curation and long-term storage operations, and makes biospecimens available to the scientific community for research purposes via the Life Science Data Archive public website (https:lsda.jsc.nasa.gov). As part of our best practices, a viability testing plan has been developed for the ISC, which will assess the quality of archived samples. We expect that results from the viability testing will catalyze sample use, enable broader science community interest, and improve operational efficiency of the ISC. The current viability test plan focuses on generating disposition recommendations and is based on using ribonucleic acid (RNA) integrity number (RIN) scores as a criteria for measurement of biospecimen viablity for downstream functional analysis. The plan includes (1) sorting and identification of candidate samples, (2) conducting a statiscally-based power analysis to generate representaive cohorts from the population of stored biospecimens, (3) completion of RIN analysis on select samples, and (4) development of disposition recommendations based on the RIN scores. Results of this work will also support NASA open science initiatives and guides development of the NASA Scientific Collections Directive (a policy on best practices for curation of biological collections). Our RIN-based methodology for characterizing the quality of tissues stored in the ISC since the 1980s also creates unique scientific opportunities for temporal assessment across historical missions. Support from the NASA Space Biology Program and the NASA Human Research Program is gratefully acknowledged.

Rapid Multiplex PCR Assay To Identify Respiratory Viral Pathogens: Moving Forward Diagnosing The Common Cold

PubMed Central

Gordon, Sarah M; Elegino-Steffens, Diane U; Agee, Willie; Barnhill, Jason; Hsue, Gunther

2013-01-01

Upper respiratory tract infections (URIs) can be a serious burden to the healthcare system. The majority of URIs are viral in etiology, but definitive diagnosis can prove difficult due to frequently overlapping clinical presentations of viral and bacterial infections, and the variable sensitivity, and lengthy turn-around time of viral culture. We tested new automated nested multiplex PCR technology, the FilmArray® system, in the TAMC department of clinical investigations, to determine the feasibility of replacing the standard viral culture with a rapid turn-around system. We conducted a feasibility study using a single-blinded comparison study, comparing PCR results with archived viral culture results from a convenience sample of cryopreserved archived nasopharyngeal swabs from acutely ill ED patients who presented with complaints of URI symptoms. A total of 61 archived samples were processed. Viral culture had previously identified 31 positive specimens from these samples. The automated nested multiplex PCR detected 38 positive samples. In total, PCR was 94.5% concordant with the previously positive viral culture results. However, PCR was only 63.4% concordant with the negative viral culture results, owing to PCR detection of 11 additional viral pathogens not recovered on viral culture. The average time to process a sample was 75 minutes. We determined that an automated nested multiplex PCR is a feasible alternative to viral culture in an acute clinical setting. We were able to detect at least 94.5% as many viral pathogens as viral culture is able to identify, with a faster turn-around time. PMID:24052914

Ameliorating effects of Mango (Mangifera indica L.) fruit on plasma ethanol level in a mouse model assessed with 1H-NMR based metabolic profiling

PubMed Central

Kim, So-Hyun; K. Cho, Somi; Min, Tae-Sun; Kim, Yujin; Yang, Seung-Ok; Kim, Hee-Su; Hyun, Sun-Hee; Kim, Hana; Kim, Young-Suk; Choi, Hyung-Kyoon

2011-01-01

The ameliorating effects of Mango (Mangifera indica L.) flesh and peel samples on plasma ethanol level were investigated using a mouse model. Mango fruit samples remarkably decreased mouse plasma ethanol levels and increased the activities of alcohol dehydrogenase and acetaldehyde dehydrogenase. The 1H-NMR-based metabolomic technique was employed to investigate the differences in metabolic profiles of mango fruits, and mouse plasma samples fed with mango fruit samples. The partial least squares-discriminate analysis of 1H-NMR spectral data of mouse plasma demonstrated that there were clear separations among plasma samples from mice fed with buffer, mango flesh and peel. A loading plot demonstrated that metabolites from mango fruit, such as fructose and aspartate, might stimulate alcohol degradation enzymes. This study suggests that mango flesh and peel could be used as resources for functional foods intended to decrease plasma ethanol level after ethanol uptake. PMID:21562641

A methodological study of genome-wide DNA methylation analyses using matched archival formalin-fixed paraffin embedded and fresh frozen breast tumors

PubMed Central

Yan, Li; Liu, Song; Tang, Li; Hu, Qiang; Morrison, Carl D.; Ambrosone, Christine B.; Higgins, Michael J.; Sucheston-Campbell, Lara E.

2017-01-01

Background DNA from archival formalin-fixed and paraffin embedded (FFPE) tissue is an invaluable resource for genome-wide methylation studies although concerns about poor quality may limit its use. In this study, we compared DNA methylation profiles of breast tumors using DNA from fresh-frozen (FF) tissues and three types of matched FFPE samples. Results For 9/10 patients, correlation and unsupervised clustering analysis revealed that the FF and FFPE samples were consistently correlated with each other and clustered into distinct subgroups. Greater than 84% of the top 100 loci previously shown to differentiate ER+ and ER– tumors in FF tissues were also FFPE DML. Weighted Correlation Gene Network Analyses (WCGNA) grouped the DML loci into 16 modules in FF tissue, with ~85% of the module membership preserved across tissue types. Materials and Methods Restored FFPE and matched FF samples were profiled using the Illumina Infinium HumanMethylation450K platform. Methylation levels (β-values) across all loci and the top 100 loci previously shown to differentiate tumors by estrogen receptor status (ER+ or ER−) in a larger FF study, were compared between matched FF and FFPE samples using Pearson's correlation, hierarchical clustering and WCGNA. Positive predictive values and sensitivity levels for detecting differentially methylated loci (DML) in FF samples were calculated in an independent FFPE cohort. Conclusions FFPE breast tumors samples show lower overall detection of DMLs versus FF, however FFPE and FF DMLs compare favorably. These results support the emerging consensus that the 450K platform can be employed to investigate epigenetics in large sets of archival FFPE tissues. PMID:28118602

Chemistry Testing on Plasma Versus Serum Samples in Dialysis Patients: Clinical and Quality Improvement Implications.

PubMed

Carey, Roger Neill; Jani, Chinu; Johnson, Curtis; Pearce, Jim; Hui-Ng, Patricia; Lacson, Eduardo

2016-09-07

Plasma samples collected in tubes containing separator gels have replaced serum samples for most chemistry tests in many hospital and commercial laboratories. Use of plasma samples for blood tests in the dialysis population eliminates delays in sample processing while waiting for clotting to complete, laboratory technical issues associated with fibrin formation, repeat sample collection, and patient care issues caused by delay of results because of incompletely clotted specimens. Additionally, a larger volume of plasma is produced than serum for the same amount of blood collected. Plasma samples are also acceptable for most chemical tests involved in the care of patients with ESRD. This information becomes very important when United States regulatory requirements for ESRD inadvertently limit the type of sample that can be used for government reporting, quality assessment, and value-based payment initiatives. In this narrative, we summarize the renal community experience and how the subsequent resolution of the acceptability of phosphorus levels measured from serum and plasma samples may have significant implications in the country's continued development of a value-based Medicare ESRD Quality Incentive Program. Copyright © 2016 by the American Society of Nephrology.

Synthesis and Characterization of Novel Compound Clusters

DTIC Science & Technology

1997-08-26

also be intrinsically stable, they cannot be formed by this plasma chemistry presumably because the metals are less reactive. Plasma chemistry reactions...samples without the presence of hydrogen. Vaporization of these composite samples produces the metal carbide clusters in many cases where plasma chemistry does...antimony or bismuth cannot be produced by the hydrocarbon plasma chemistry method, but they are produced readily from composite sample (metal film on

Interrogating trees for isotopic archives of atmospheric sulphur deposition and comparison to speleothem records.

PubMed

Wynn, P M; Loader, N J; Fairchild, I J

2014-04-01

Palaeorecords which depict changes in sulphur dynamics form an invaluable resource for recording atmospheric pollution. Tree rings constitute an archive that are ubiquitously available and can be absolutely dated, providing the potential to explore local- to regional-scale trends in sulphur availability. Rapid isotopic analysis by a novel "on-line" method using elemental analyser isotope ratio mass spectrometry (EA-IRMS) is developed, achieving sample precision of <0.4‰ using sample sizes of 40 mg wood powder. Tree cores from NE Italy show trends in pollution, evidenced through increasing concentrations of sulphur towards the youngest growth, and inverse trends in sulphur isotopes differentiating modern growth with light sulphur isotopes (+0.7‰) from pre-industrial growth (+7.5‰) influenced by bedrock composition. Comparison with speleothem records from the same location demonstrate replication, albeit offset in isotopic value due to groundwater storage. Using EA-IRMS, tree ring archives form a valuable resource for understanding local- to regional-scale sulphur pollution dynamics. Copyright © 2013 Elsevier Ltd. All rights reserved.

Nitrate deposition and preservation in the snowpack along a traverse from coast to the ice sheet summit (Dome A) in East Antarctica

NASA Astrophysics Data System (ADS)

Shi, Guitao; Hastings, Meredith G.; Yu, Jinhai; Ma, Tianming; Hu, Zhengyi; An, Chunlei; Li, Chuanjin; Ma, Hongmei; Jiang, Su; Li, Yuansheng

2018-04-01

Antarctic ice core nitrate (NO3-) can provide a unique record of the atmospheric reactive nitrogen cycle. However, the factors influencing the deposition and preservation of NO3- at the ice sheet surface must first be understood. Therefore, an intensive program of snow and atmospheric sampling was made on a traverse from the coast to the ice sheet summit, Dome A, East Antarctica. Snow samples in this observation include 120 surface snow samples (top ˜ 3 cm), 20 snow pits with depths of 150 to 300 cm, and 6 crystal ice samples (the topmost needle-like layer on Dome A plateau). The main purpose of this investigation is to characterize the distribution pattern and preservation of NO3- concentrations in the snow in different environments. Results show that an increasing trend of NO3- concentrations with distance inland is present in surface snow, and NO3- is extremely enriched in the topmost crystal ice (with a maximum of 16.1 µeq L-1). NO3- concentration profiles for snow pits vary between coastal and inland sites. On the coast, the deposited NO3- was largely preserved, and the archived NO3- fluxes are dominated by snow accumulation. The relationship between the archived NO3- and snow accumulation rate can be depicted well by a linear model, suggesting a homogeneity of atmospheric NO3- levels. It is estimated that dry deposition contributes 27-44 % of the archived NO3- fluxes, and the dry deposition velocity and scavenging ratio for NO3- were relatively constant near the coast. Compared to the coast, the inland snow shows a relatively weak correlation between archived NO3- and snow accumulation, and the archived NO3- fluxes were more dependent on concentration. The relationship between NO3- and coexisting ions (nssSO42-, Na+ and Cl-) was also investigated, and the results show a correlation between nssSO42- (fine aerosol particles) and NO3- in surface snow, while the correlation between NO3- and Na+ (mainly associated with coarse aerosol particles) is not significant. In inland snow, there were no significant relationships found between NO3- and the coexisting ions, suggesting a dominant role of NO3- recycling in determining the concentrations.

Investigating the potential role of persistent organic pollutants in Hawaiian green sea turtle fibropapillomatosis

USGS Publications Warehouse

Keller, Jennifer M.; Balazs, George H.; Nilsen, Frances; Rice, Marc; Work, Thierry M.; Jensen, Brenda A.

2014-01-01

It has been hypothesized for decades that environmental pollutants may contribute to green sea turtle fibropapillomatosis (FP), possibly through immunosuppression leading to greater susceptibility to the herpesvirus, the putative causative agent of this tumor-forming disease. To address this question, we measured concentrations of 164 persistent organic pollutants (POPs) and halogenated phenols in 53 Hawaiian green turtle (Chelonia mydas) plasma samples archived by the Biological and Environmental Monitoring and Archival of Sea Turtle Tissues (BEMAST) project at the National Institute of Standards and Technology Marine Environmental Specimen Bank. Four groups of turtles were examined: free-ranging turtles from Kiholo Bay (0% FP, Hawaii), Kailua Bay (low FP, 8%, Oahu), and Kapoho Bay (moderate FP, 38%, Hawaii) and severely tumored stranded turtles that required euthanasia (high FP, 100%, Main Hawaiian Islands). Four classes of POPs and seven halogenated phenols were detected in at least one of the turtles, and concentrations were low (often <200 pg/g wet mass). The presence of halogenated phenols in sea turtles is a novel discovery; their concentrations were higher than most man-made POPs, suggesting that the source of most of these compounds was likely natural (produced by the algal turtle diet) rather than metabolites of man-made POPs. None of the compounds measured increased in concentration with increasing prevalence of FP across the four groups of turtles, suggesting that these 164 compounds are not likely primary triggers for the onset of FP. However, the stranded, severely tumored, emaciated turtle group (n = 14) had the highest concentrations of POPs, which might suggest that mobilization of contaminants with lipids into the blood during late-stage weight loss could contribute to the progression of the disease. Taken together, these data suggest that POPs are not a major cofactor in causing the onset of FP.

Investigating the potential role of persistent organic pollutants in Hawaiian green sea turtle fibropapillomatosis.

PubMed

Keller, Jennifer M; Balazs, George H; Nilsen, Frances; Rice, Marc; Work, Thierry M; Jensen, Brenda A

2014-07-15

It has been hypothesized for decades that environmental pollutants may contribute to green sea turtle fibropapillomatosis (FP), possibly through immunosuppression leading to greater susceptibility to the herpesvirus, the putative causative agent of this tumor-forming disease. To address this question, we measured concentrations of 164 persistent organic pollutants (POPs) and halogenated phenols in 53 Hawaiian green turtle (Chelonia mydas) plasma samples archived by the Biological and Environmental Monitoring and Archival of Sea Turtle Tissues (BEMAST) project at the National Institute of Standards and Technology Marine Environmental Specimen Bank. Four groups of turtles were examined: free-ranging turtles from Kiholo Bay (0% FP, Hawaii), Kailua Bay (low FP, 8%, Oahu), and Kapoho Bay (moderate FP, 38%, Hawaii) and severely tumored stranded turtles that required euthanasia (high FP, 100%, Main Hawaiian Islands). Four classes of POPs and seven halogenated phenols were detected in at least one of the turtles, and concentrations were low (often <200 pg/g wet mass). The presence of halogenated phenols in sea turtles is a novel discovery; their concentrations were higher than most man-made POPs, suggesting that the source of most of these compounds was likely natural (produced by the algal turtle diet) rather than metabolites of man-made POPs. None of the compounds measured increased in concentration with increasing prevalence of FP across the four groups of turtles, suggesting that these 164 compounds are not likely primary triggers for the onset of FP. However, the stranded, severely tumored, emaciated turtle group (n=14) had the highest concentrations of POPs, which might suggest that mobilization of contaminants with lipids into the blood during late-stage weight loss could contribute to the progression of the disease. Taken together, these data suggest that POPs are not a major cofactor in causing the onset of FP.

Toward Automatic Georeferencing of Archival Aerial Photogrammetric Surveys

NASA Astrophysics Data System (ADS)

Giordano, S.; Le Bris, A.; Mallet, C.

2018-05-01

Images from archival aerial photogrammetric surveys are a unique and relatively unexplored means to chronicle 3D land-cover changes over the past 100 years. They provide a relatively dense temporal sampling of the territories with very high spatial resolution. Such time series image analysis is a mandatory baseline for a large variety of long-term environmental monitoring studies. The current bottleneck for accurate comparison between epochs is their fine georeferencing step. No fully automatic method has been proposed yet and existing studies are rather limited in terms of area and number of dates. State-of-the art shows that the major challenge is the identification of ground references: cartographic coordinates and their position in the archival images. This task is manually performed, and extremely time-consuming. This paper proposes to use a photogrammetric approach, and states that the 3D information that can be computed is the key to full automation. Its original idea lies in a 2-step approach: (i) the computation of a coarse absolute image orientation; (ii) the use of the coarse Digital Surface Model (DSM) information for automatic absolute image orientation. It only relies on a recent orthoimage+DSM, used as master reference for all epochs. The coarse orthoimage, compared with such a reference, allows the identification of dense ground references and the coarse DSM provides their position in the archival images. Results on two areas and 5 dates show that this method is compatible with long and dense archival aerial image series. Satisfactory planimetric and altimetric accuracies are reported, with variations depending on the ground sampling distance of the images and the location of the Ground Control Points.

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2014-01-01

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

X-ray Observations of the Bright Old Nova V603 Aquilae

NASA Technical Reports Server (NTRS)

Mukai, K.; Orio, M.

2004-01-01

We report on our Chandra and RXTE observations of the bright old nova, V603 Aql, performed in 2001 April, supplemented by our analysis of archival X-ray data on this object. We find that the RXTE data are contaminated by the Galactic Ridge X-ray emission. After accounting for this effect, we find a high level of aperiodic variability in the RXTE data, at a level consistent with the uncontaminated Chandra data. The Chandra HETG spectrum clearly originates in a multi-temperature plasma. We constrain the possible emission measure distribution of the plasma through a combination of global and local fits. The X-ray luminosity and the spectral shape of V603 Aql resemble those of SS Cyg in transition between quiescence and outburst. The fact that the X-ray flux variability is only weakly energy dependent can be interpreted by supposing that the variability is due to changes in the maximum temperature of the plasma. The plasma density is likely to be high, and the emission region is likely to be compact. Finally, the apparent overabundance of Ne is consistent with V603 Aql being a young system.

The Prevalence of PCR-Confirmed Pertussis Cases in Palestine From Archived Nasopharyngeal Samples.

PubMed

Dumaidi, Kamal; Al-Jawabreh, Amer

2018-05-01

Pertussis caused by Bordetella pertussis is a vaccine-preventable disease causing whooping cough in humans of all ages. This study reports infection rate of pertussis in Palestine between the years 2004-2008 from archived nasopharyngeal samples collected from clinically- suspected cases. A convenience archived DNA samples collected from 267 clinically-suspected pertussis cases were investigated for B. pertussis. Laboratory diagnosis was done by examining all DNA samples using polymerase chain reaction (PCR). Approximately 49% (130/267) were confirmed by PCR. A pertussis peak was shown to occur in 2008 with 77% (100/130) of PCR-confirmed cases isolated in that year. PCR-confirmed cases existed in all Palestinian districts with highest rate in Ramallah, Bethlehem, Jenin and Al-Khalil. Half of the PCR-confirmed cases (68/130) were less than 2 months old. The positivity rate among who had three doses of vaccine (at 2, 4 and 6 months) was 38%, and became 50% with the fourth dose at 12 months. The prevalence of pertussis was found to be significantly high among infants less than 2 months old. Active pertussis surveillance using rapid PCR assays is essential, as it is helpful in prompt diagnosis and treatment of patients with pertussis. © 2018 The Author(s). This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

A validated method for the quantification of fosfomycin on dried plasma spots by HPLC-MS/MS: application to a pilot pharmacokinetic study in humans.

PubMed

Parker, Suzanne L; Lipman, Jeffrey; Dimopoulos, George; Roberts, Jason A; Wallis, Steven C

2015-11-10

Quantification of fosfomycin in the plasma samples of patients is the basis of clinical pharmacokinetic studies from which evidence based dosing regimens can be devised to maximise antibiotic effectiveness against a pathogen. We have developed and validated a LC-MS/MS method to quantify fosfomycin using dried plasma spot sampling. Following HILIC chromatography, fosfomycin and ethylphosphonic acid, used as internal standard, were measured using negative-ion multiple reaction monitoring. The method was linear over the calibration range of 5-2000mg/L of fosfomycin. Intra-day assay results for dried plasma spot quality control samples at 15.6, 79.9 and 1581mg/L of fosfomycin had precision of ±4.2, 8.2, and 2.0%, respectively, and accuracy of +3.9, -0.1, and -1.2%, respectively. Recovery of fosfomycin from dried plasma spots was calculated as 83.6% and the dried plasma spot samples were found to be stable stored at room temperature for three months and when stored for four hours at 50°C. A Bland-Altman plot comparing DPS to plasma sampling found a negative bias of 16.6%, with all but one sample within the mean limits of agreement (-2.6 to 30.6%). Dried plasma spot sampling provides a useful tool for pharmacokinetic research of fosfomycin. Copyright © 2015 Elsevier B.V. All rights reserved.

Comparison of serum, EDTA plasma and P100 plasma for luminex-based biomarker multiplex assays in patients with chronic obstructive pulmonary disease in the SPIROMICS study.

PubMed

O'Neal, Wanda K; Anderson, Wayne; Basta, Patricia V; Carretta, Elizabeth E; Doerschuk, Claire M; Barr, R Graham; Bleecker, Eugene R; Christenson, Stephanie A; Curtis, Jeffrey L; Han, Meilan K; Hansel, Nadia N; Kanner, Richard E; Kleerup, Eric C; Martinez, Fernando J; Miller, Bruce E; Peters, Stephen P; Rennard, Stephen I; Scholand, Mary Beth; Tal-Singer, Ruth; Woodruff, Prescott G; Couper, David J; Davis, Sonia M

2014-01-08

As a part of the longitudinal Chronic Obstructive Pulmonary Disease (COPD) study, Subpopulations and Intermediate Outcome Measures in COPD study (SPIROMICS), blood samples are being collected from 3200 subjects with the goal of identifying blood biomarkers for sub-phenotyping patients and predicting disease progression. To determine the most reliable sample type for measuring specific blood analytes in the cohort, a pilot study was performed from a subset of 24 subjects comparing serum, Ethylenediaminetetraacetic acid (EDTA) plasma, and EDTA plasma with proteinase inhibitors (P100). 105 analytes, chosen for potential relevance to COPD, arranged in 12 multiplex and one simplex platform (Myriad-RBM) were evaluated in duplicate from the three sample types from 24 subjects. The reliability coefficient and the coefficient of variation (CV) were calculated. The performance of each analyte and mean analyte levels were evaluated across sample types. 20% of analytes were not consistently detectable in any sample type. Higher reliability and/or smaller CV were determined for 12 analytes in EDTA plasma compared to serum, and for 11 analytes in serum compared to EDTA plasma. While reliability measures were similar for EDTA plasma and P100 plasma for a majority of analytes, CV was modestly increased in P100 plasma for eight analytes. Each analyte within a multiplex produced independent measurement characteristics, complicating selection of sample type for individual multiplexes. There were notable detectability and measurability differences between serum and plasma. Multiplexing may not be ideal if large reliability differences exist across analytes measured within the multiplex, especially if values differ based on sample type. For some analytes, the large CV should be considered during experimental design, and the use of duplicate and/or triplicate samples may be necessary. These results should prove useful for studies evaluating selection of samples for evaluation of potential blood biomarkers.

Comparison of serum, EDTA plasma and P100 plasma for luminex-based biomarker multiplex assays in patients with chronic obstructive pulmonary disease in the SPIROMICS study

PubMed Central

2014-01-01

Background As a part of the longitudinal Chronic Obstructive Pulmonary Disease (COPD) study, Subpopulations and Intermediate Outcome Measures in COPD study (SPIROMICS), blood samples are being collected from 3200 subjects with the goal of identifying blood biomarkers for sub-phenotyping patients and predicting disease progression. To determine the most reliable sample type for measuring specific blood analytes in the cohort, a pilot study was performed from a subset of 24 subjects comparing serum, Ethylenediaminetetraacetic acid (EDTA) plasma, and EDTA plasma with proteinase inhibitors (P100™). Methods 105 analytes, chosen for potential relevance to COPD, arranged in 12 multiplex and one simplex platform (Myriad-RBM) were evaluated in duplicate from the three sample types from 24 subjects. The reliability coefficient and the coefficient of variation (CV) were calculated. The performance of each analyte and mean analyte levels were evaluated across sample types. Results 20% of analytes were not consistently detectable in any sample type. Higher reliability and/or smaller CV were determined for 12 analytes in EDTA plasma compared to serum, and for 11 analytes in serum compared to EDTA plasma. While reliability measures were similar for EDTA plasma and P100 plasma for a majority of analytes, CV was modestly increased in P100 plasma for eight analytes. Each analyte within a multiplex produced independent measurement characteristics, complicating selection of sample type for individual multiplexes. Conclusions There were notable detectability and measurability differences between serum and plasma. Multiplexing may not be ideal if large reliability differences exist across analytes measured within the multiplex, especially if values differ based on sample type. For some analytes, the large CV should be considered during experimental design, and the use of duplicate and/or triplicate samples may be necessary. These results should prove useful for studies evaluating selection of samples for evaluation of potential blood biomarkers. PMID:24397870

Effects of Data Sampling on Graphical Depictions of Learning

ERIC Educational Resources Information Center

Carey, Mary-Katherine; Bourret, Jason C.

2014-01-01

Continuous and discontinuous data-collection methods were compared in the context of discrete-trial programming. Archival data sets were analyzed using trial sampling (1st 5 trials, 1st 3 trials, and 1st trial only) and session sampling (every other session, every 3rd session, and every 5th session). Results showed that trial sampling…

Mixed-mode ion exchange-based integrated proteomics technology for fast and deep plasma proteome profiling.

PubMed

Xue, Lu; Lin, Lin; Zhou, Wenbin; Chen, Wendong; Tang, Jun; Sun, Xiujie; Huang, Peiwu; Tian, Ruijun

2018-06-09

Plasma proteome profiling by LC-MS based proteomics has drawn great attention recently for biomarker discovery from blood liquid biopsy. Due to standard multi-step sample preparation could potentially cause plasma protein degradation and analysis variation, integrated proteomics sample preparation technologies became promising solution towards this end. Here, we developed a fully integrated proteomics sample preparation technology for both fast and deep plasma proteome profiling under its native pH. All the sample preparation steps, including protein digestion and two-dimensional fractionation by both mixed-mode ion exchange and high-pH reversed phase mechanism were integrated into one spintip device for the first time. The mixed-mode ion exchange beads design achieved the sample loading at neutral pH and protein digestion within 30 min. Potential sample loss and protein degradation by pH changing could be voided. 1 μL of plasma sample with depletion of high abundant proteins was processed by the developed technology with 12 equally distributed fractions and analyzed with 12 h of LC-MS gradient time, resulting in the identification of 862 proteins. The combination of the Mixed-mode-SISPROT and data-independent MS method achieved fast plasma proteome profiling in 2 h with high identification overlap and quantification precision for a proof-of-concept study of plasma samples from 5 healthy donors. We expect that the Mixed-mode-SISPROT become a generally applicable sample preparation technology for clinical oriented plasma proteome profiling. Copyright © 2018 Elsevier B.V. All rights reserved.

Thermometry of the system “heat-resistant sample - incident plasma stream”

NASA Astrophysics Data System (ADS)

Sargsyan, M. A.; Chinnov, V. F.; Kavyrshin, D. I.; Gadzhiev, M. Kh; Khromov, M. A.; Chistolinov, A. V.; Senchenko, V. N.

2017-11-01

To study the interacting system “heat-resistant sample - an incident plasma stream” a setup of synchronized measurement equipment was developed and tested that recorded the main parameters of such interaction. Heat resistance tests were carried out on the samples of MPG-6 grade isotropic graphite, and samples of pyrolytic graphite that were subjected to a long (60 … 100 s) exposure to nitrogen, argon and air plasma streams at atmospheric pressure. As plasma generators a series of plasma torches with a vortex stabilization of the stream and an expanding anode channels was used. The temperature and composition of the plasma in the jet and near the sample were determined using two AvaSpec2048 and AvaSpec3648 scanning optical spectrometers and the MS5402i spectrograph with the Andor matrix at its outlet. The surface temperature of the sample was determined in real time using three independent ways: two pyrometric systems - a high-speed micro-pyrometer FMP1001 and a two-position visualization of the heated sample by high-speed Motion Pro X3 and VS-FAST cameras, and the spectral analysis of the wide-range thermal radiation of the samples. The main method for determining the rate of material loss during the action of a plasma jet on it was to analyze a two-position synchronous visualization of the “jet-sample” system. When a crater was formed on the surface of the sample under the “dagger” effect of a plasma jet, a video recording system of the crater zone was used, backlit using the “laser knife” method.

The Karlsruhe Metabolomics and Nutrition (KarMeN) Study: Protocol and Methods of a Cross-Sectional Study to Characterize the Metabolome of Healthy Men and Women

PubMed Central

Kriebel, Anita; Dörr, Claudia; Bandt, Susanne; Rist, Manuela; Roth, Alexander; Hummel, Eva; Kulling, Sabine; Hoffmann, Ingrid; Watzl, Bernhard

2016-01-01

Background The human metabolome is influenced by various intrinsic and extrinsic factors. A precondition to identify such biomarkers is the comprehensive understanding of the composition and variability of the metabolome of healthy humans. Sample handling aspects have an important impact on the composition of the metabolome; therefore, it is crucial for any metabolomics study to standardize protocols on sample collection, preanalytical sample handling, storage, and analytics to keep the nonbiological variability as low as possible. Objective The main objective of the KarMeN study is to analyze the human metabolome in blood and urine by targeted and untargeted metabolite profiling (gas chromatography-mass spectrometry [GC-MS], GC×GC-MS, liquid chromatography-mass spectrometry [LC-MS/MS], and1H nuclear magnetic resonance [NMR] spectroscopy) and to determine the impact of sex, age, body composition, diet, and physical activity on metabolite profiles of healthy women and men. Here, we report the outline of the study protocol with special regard to all aspects that should be considered in studies applying metabolomics. Methods Healthy men and women, aged 18 years or older, were recruited. In addition to a number of anthropometric (height, weight, body mass index, waist circumference, body composition), clinical (blood pressure, electrocardiogram, blood and urine clinical chemistry) and functional parameters (lung function, arterial stiffness), resting metabolic rate, physical activity, fitness, and dietary intake were assessed, and 24-hour urine, fasting spot urine, and plasma samples were collected. Standard operating procedures were established for all steps of the study design. Using different analytical techniques (LC-MS, GC×GC-MS,1H NMR spectroscopy), metabolite profiles of urine and plasma were determined. Data will be analyzed using univariate and multivariate as well as predictive modeling methods. Results The project was funded in 2011 and enrollment was carried out between March 2012 and July 2013. A total of 301 volunteers were eligible to participate in the study. Metabolite profiling of plasma and urine samples has been completed and data analysis is currently underway. Conclusions We established the KarMeN study applying a broad set of clinical and physiological examinations with a high degree of standardization. Our experimental approach of combining scheduled timing of examinations and sampling with the multiplatform approach (GC×GC-MS, GC-MS, LC-MS/MS, and1H NMR spectroscopy) will enable us to differentiate between current and long-term effects of diet and physical activity on metabolite profiles, while enabling us at the same time to consider confounders such as age and sex in the KarMeN study. Trial Registration German Clinical Trials Register DRKS00004890; https://drks-neu.uniklinik-freiburg.de/drks_web/navigate.do? navigationId=trial.HTML&TRIAL_ID=DRKS00004890 (Archived by WebCite at http://www.webcitation.org/6iyM8dMtx) PMID:27421387

UK National Data Centre archive of seismic recordings of (presumed) underground nuclear tests 1964-1996

NASA Astrophysics Data System (ADS)

Young, John; Peacock, Sheila

2016-04-01

The year 1996 has particular significance for forensic seismologists. This was the year when the Comprehensive Test Ban Treaty (CTBT) was signed in September at the United Nations, setting an international norm against nuclear testing. Blacknest, as a long time seismic centre for research into detecting and identifying underground explosions using seismology, provided significant technical advice during the CTBT negotiations. Since 1962 seismic recordings of both presumed nuclear explosions and earthquakes from the four seismometer arrays Eskdalemuir, Scotland (EKA), Yellowknife, Canada (YKA), Gauribidanur, India (GBA), and Warramunga, Australia (WRA) have been copied, digitised, and saved. There was a possibility this archive would be lost. It was decided to process the records and catalogue them for distribution to other groups and institutions. This work continues at Blacknest but the archive is no longer under threat. In addition much of the archive of analogue tape recordings has been re-digitised with modern equipment, allowing sampling rates of 100 rather than 20 Hz.

VizieR Online Data Catalog: Astrometric monitoring of ultracool dwarf binaries (Dupuy+, 2017)

NASA Astrophysics Data System (ADS)

Dupuy, T. J.; Liu, M. C.

2017-09-01

In Table 1 we list all 33 binaries in our Keck+CFHT astrometric monitoring sample, along with three other binaries that have published orbit and parallax measurements. We began obtaining resolved Keck AO astrometry in 2007-2008, and we combined our new astrometry with available data in the literature or public archives (e.g., HST and Gemini) to refine our orbital period estimates and thereby our prioritization for Keck observations. We present here new Keck/NIRC2 AO imaging and non-redundant aperture-masking observations, in addition to a re-analysis of our own previously published data and publicly available archival data for our sample binaries. Table 2 gives our measured astrometry and flux ratios for all Keck AO data used in our orbital analysis spanning 2003 Apr 15 to 2016 May 13. In total there are 339 distinct measurements (unique bandpass and epoch for a given target), where 302 of these are direct imaging and 37 are non-redundant aperture masking. Eight of the imaging measurements are from six unpublished archival data sets. See section 3.1.1 for further details. In addition to our Keck AO monitoring, we also obtained data for three T dwarf binaries over a three-year HST program using the Advanced Camera for Surveys (ACS) Wide Field Camera (WFC) in the F814W bandpass. See section 3.1.2 for further details. Many of our sample binaries have HST imaging data in the public archive. We have re-analyzed the available archival data coming from the WFPC2 Planetary Camera (WFPC2-PC1), ACS High Resolution Channel (ACS-HRC), and NICMOS Camera 1 (NICMOS-NIC1). See section 3.1.3 for further details. We present here an updated analysis of our data from the Hawaii Infrared Parallax Program that uses the CFHT facility infrared camera WIRCam. Our observing strategy and custom astrometry pipeline are described in detail in Dupuy & Liu (2012, J/ApJS/201/19). See section 3.2 for further explanations. (10 data files).

Analyzing Saturn's Magnetospheric Data After Cassini - Improving and Future-Proofing Cassini / MAPS Tools and Data

NASA Astrophysics Data System (ADS)

Brown, L. E.; Faden, J.; Vandegriff, J. D.; Kurth, W. S.; Mitchell, D. G.

2017-12-01

We present a plan to provide enhanced longevity to analysis software and science data used throughout the Cassini mission for viewing Magnetosphere and Plasma Science (MAPS) data. While a final archive is being prepared for Cassini, the tools that read from this archive will eventually become moribund as real world hardware and software systems evolve. We will add an access layer over existing and planned Cassini data products that will allow multiple tools to access many public MAPS datasets. The access layer is called the Heliophysics Application Programmer's Interface (HAPI), and this is a mechanism being adopted at many data centers across Heliophysics and planetary science for the serving of time series data. Two existing tools are also being enhanced to read from HAPI servers, namely Autoplot from the University of Iowa and MIDL (Mission Independent Data Layer) from The Johns Hopkins Applied Physics Lab. Thus both tools will be able to access data from RPWS, MAG, CAPS, and MIMI. In addition to being able to access data from each other's institutions, these tools will be able to read from all the new datasets expected to come online using the HAPI standard in the near future. The PDS also plans to use HAPI for all the holdings at the Planetary and Plasma Interactions (PPI) node. A basic presentation of the new HAPI data server mechanism is presented, as is an early demonstration of the modified tools.

Comparison of cross-sectional HIV incidence assay results from dried blood spots and plasma.

PubMed

Schlusser, Katherine E; Pilcher, Christopher; Kallas, Esper G; Santos, Breno R; Deeks, Steven G; Facente, Shelley; Keating, Sheila M; Busch, Michael P; Murphy, Gary; Welte, Alex; Quinn, Thomas; Eshleman, Susan H; Laeyendecker, Oliver

2017-01-01

Assays have been developed for cross-sectional HIV incidence estimation using plasma samples. Large scale surveillance programs are planned using dried blood spot (DBS) specimens for incidence assessment. However, limited information exists on the performance of HIV cross-sectional incidence assays using DBS. The assays evaluated were: Maxim HIV-1 Limiting Antigen Avidity EIA (LAg-Avidity), Sedia HIV-1 BED-Capture EIA (BED-CEIA), and CDC modified BioRad HIV-1/2 Plus O Avidity-based Assay (CDC-BioRad Avidity) using pre-determined cutoff values. 100 matched HIV-1 positive plasma and DBS samples, with known duration of infection, from the Consortium for the Evaluation and Performance of HIV Incidence Assays repository were tested. All assays were run in duplicate. To examine the degree of variability within and between results for each sample type, both categorical and continuous results were analyzed. Associations were assessed with Bland Altman, R2 values and Cohen's kappa coefficient (ĸ). Intra-assay variability using the same sample type was similar for all assays (R2 0.96 to 1.00). The R2 values comparing DBS and plasma results for LAg-Avidity, BED-CEIA, and CDC-BioRad Avidity were 0.96, 0.94, and 0.84, respectively. The concordance and ĸ values between DBS and plasma for all three assays were >87% and >0.64, respectively. The Bland-Altman analysis showed significant differences between plasma and DBS samples. For all three assays, a higher number of samples were classified as recent infections using DBS samples. DBS and plasma sample results were highly correlated. However, when compared to plasma, each assay performed somewhat differently in DBS at the lower and higher ends of the dynamic range. DBS samples were more likely to be classified as recently infected by all three assays, which may lead to overestimation of incidence in surveys using performance criteria derived for plasma samples.

Parvovirus B19V DNA contamination in Chinese plasma and plasma derivatives

PubMed Central

2012-01-01

Background To ensure the safety of plasma derivatives, screening for human parvovirus B19V genomic DNA in donated plasma using a pooling strategy is performed in some countries. We investigated the prevalence of B19V DNA and anti-B19V antibodies in Chinese plasma pools, plasma derivatives and plasma donations to evaluate the risk posed by B19V. Methods Using a Q-PCR assay developed in-house, we tested for B19V genomic DNA in 142 plasma pools collected between January 2009 and June 2011 from two Chinese blood products manufacturers. Plasma derivatives collected between 1993–1995 (10 batches of albumin, 155 batches of intravenous immunoglobulin, IVIG) and 2009–2011 (50 batches of albumin, 54 batches of IVIG, 35 batches of factor VIII, 7 batches of fibrinogen, and 17 batches of prothrombin complex concentrate, PCC) were also tested for B19V contamination. In addition, B19V genome prevalence in minipools(including 90 individual donations) of 49680 individual plasma samples collected between August 2011 and March 2012 by a single Chinese manufacturer was investigated. IgM/IgG was also investigated in plasma pools/derivatives and in minipools with B19V-DNA titers above 1x104 and 1x106 geq/mL using B19 ELISA IgM/IgG assay(Virion-Serion, Würzburg, Germany), respectively. Results B19V-DNA was detected in 54.2% of plasma pools from two Chinese blood product manufacturers; among recently produced blood products, B19V was detected in 21/54 IVIG samples, 19/35 factor VIII samples, 6/7 fibrinogen samples, and 12/17 PCC samples, but not in albumin samples. The levels of B19V-DNA in these samples varied from 102-107 geq/mL. In samples with >104 geq/mL genome DNA, B19V-specific IgG was also found in all corresponding plasma pools and IVIG, whereas none was detected in the majority of other plasma derivatives. Screening of plasma donations indicated that most minipools were contaminated with B19V-DNA (102-108 geq/mL) and one donation had 1.09 × 1010 geq/mL B19V genomic DNA along with a non-classical IgG/IgM profile. Conclusions Despite the implementation of some inactivation/removal methods designed to prevent viral contamination, B19V DNA was detectable in Chinese plasma pools and plasma derivatives. Thus, the introduction of B19V screening and discard donation with high viramic concentration for Chinese plasma donors would be desirable. PMID:22978673

Random and independent sampling of endogenous tryptic peptides from normal human EDTA plasma by liquid chromatography micro electrospray ionization and tandem mass spectrometry.

PubMed

Dufresne, Jaimie; Florentinus-Mefailoski, Angelique; Ajambo, Juliet; Ferwa, Ammara; Bowden, Peter; Marshall, John

2017-01-01

Normal human EDTA plasma samples were collected on ice, processed ice cold, and stored in a freezer at - 80 °C prior to experiments. Plasma test samples from the - 80 °C freezer were thawed on ice or intentionally warmed to room temperature. Protein content was measured by CBBR binding and the release of alcohol soluble amines by the Cd ninhydrin assay. Plasma peptides released over time were collected over C18 for random and independent sampling by liquid chromatography micro electrospray ionization and tandem mass spectrometry (LC-ESI-MS/MS) and correlated with X!TANDEM. Fully tryptic peptides by X!TANDEM returned a similar set of proteins, but was more computationally efficient, than "no enzyme" correlations. Plasma samples maintained on ice, or ice with a cocktail of protease inhibitors, showed lower background amounts of plasma peptides compared to samples incubated at room temperature. Regression analysis indicated that warming plasma to room temperature, versus ice cold, resulted in a ~ twofold increase in the frequency of peptide identification over hours-days of incubation at room temperature. The type I error rate of the protein identification from the X!TANDEM algorithm combined was estimated to be low compared to a null model of computer generated random MS/MS spectra. The peptides of human plasma were identified and quantified with low error rates by random and independent sampling that revealed 1000s of peptides from hundreds of human plasma proteins from endogenous tryptic peptides.

A liquid chromatography/tandem mass spectrometry assay for the analysis of atomoxetine in human plasma and in vitro cellular samples

PubMed Central

Appel, David I.; Brinda, Bryan; Markowitz, John S.; Newcorn, Jeffrey H.; Zhu, Hao-Jie

2012-01-01

A simple, rapid and sensitive method for quantification of atomoxetine by liquid chromatography- tandem mass spectrometry (LC-MS/MS) was developed. This assay represents the first LC-MS/MS quantification method for atomoxetine utilizing electrospray ionization. Deuterated atomoxetine (d3-atomoxetine) was adopted as the internal standard. Direct protein precipitation was utilized for sample preparation. This method was validated for both human plasma and in vitro cellular samples. The lower limit of quantification was 3 ng/ml and 10 nM for human plasma and cellular samples, respectively. The calibration curves were linear within the ranges of 3 ng/ml to 900 ng/ml and 10 nM to 10 μM for human plasma and cellular samples, respectively (r2 > 0.999). The intra- and inter-day assay accuracy and precision were evaluated using quality control samples at 3 different concentrations in both human plasma and cellular lysate. Sample run stability, assay selectivity, matrix effect, and recovery were also successfully demonstrated. The present assay is superior to previously published LC-MS and LC-MS/MS methods in terms of sensitivity or the simplicity of sample preparation. This assay is applicable to the analysis of atomoxetine in both human plasma and in vitro cellular samples. PMID:22275222

Evaluation of optimized bronchoalveolar lavage sampling designs for characterization of pulmonary drug distribution.

PubMed

Clewe, Oskar; Karlsson, Mats O; Simonsson, Ulrika S H

2015-12-01

Bronchoalveolar lavage (BAL) is a pulmonary sampling technique for characterization of drug concentrations in epithelial lining fluid and alveolar cells. Two hypothetical drugs with different pulmonary distribution rates (fast and slow) were considered. An optimized BAL sampling design was generated assuming no previous information regarding the pulmonary distribution (rate and extent) and with a maximum of two samples per subject. Simulations were performed to evaluate the impact of the number of samples per subject (1 or 2) and the sample size on the relative bias and relative root mean square error of the parameter estimates (rate and extent of pulmonary distribution). The optimized BAL sampling design depends on a characterized plasma concentration time profile, a population plasma pharmacokinetic model, the limit of quantification (LOQ) of the BAL method and involves only two BAL sample time points, one early and one late. The early sample should be taken as early as possible, where concentrations in the BAL fluid ≥ LOQ. The second sample should be taken at a time point in the declining part of the plasma curve, where the plasma concentration is equivalent to the plasma concentration in the early sample. Using a previously described general pulmonary distribution model linked to a plasma population pharmacokinetic model, simulated data using the final BAL sampling design enabled characterization of both the rate and extent of pulmonary distribution. The optimized BAL sampling design enables characterization of both the rate and extent of the pulmonary distribution for both fast and slowly equilibrating drugs.

Measurement of Clozapine, Norclozapine, and Amisulpride in Plasma and in Oral Fluid Obtained Using 2 Different Sampling Systems.

PubMed

Fisher, Danielle S; Beyer, Chad; van Schalkwyk, Gerrit; Seedat, Soraya; Flanagan, Robert J

2017-04-01

There is a poor correlation between total concentrations of proton-accepting compounds (most basic drugs) in unstimulated oral fluid and in plasma. The aim of this study was to compare clozapine, norclozapine, and amisulpride concentrations in plasma and in oral fluid collected using commercially available collection devices [Thermo Fisher Scientific Oral-Eze and Greiner Bio-One (GBO)]. Oral-Eze and GBO samples and plasma were collected in that order from patients prescribed clozapine. Analyte concentrations were measured by liquid chromatography-tandem mass spectrometry. There were 112 participants [96 men, aged (median, range) 47 (21-65) years and 16 women, aged 44 (21-65) years]: 74 participants provided 2 sets of samples and 7 provided 3 sets (overall 2 GBO samples not collected). Twenty-three patients were co-prescribed amisulpride, of whom 17 provided 2 sets of samples and 1 provided 3 sets. The median (range) oral fluid within the GBO samples was 52 (13%-86%). Nonadherence to clozapine was identified in all 3 samples in one instance. After correction for oral fluid content, analyte concentrations in the GBO and Oral-Eze samples were poorly correlated with plasma clozapine and norclozapine (R = 0.57-0.63) and plasma amisulpride (R = 0.65-0.72). Analyte concentrations in the 2 sets of oral fluid samples were likewise poorly correlated (R = 0.68-0.84). Mean (SD) plasma clozapine and norclozapine were 0.60 (0.46) and 0.25 (0.21) mg/L, respectively. Mean clozapine and norclozapine concentrations in the 2 sets of oral fluid samples were similar to those in plasma (0.9-1.8 times higher), that is, approximately 2- to 3-fold higher than those in unstimulated oral fluid. The mean (±SD) amisulpride concentrations (microgram per liter) in plasma (446 ± 297) and in the Oral-Eze samples (501 ± 461) were comparable and much higher than those in the GBO samples (233 ± 318). Oral fluid collected using either the GBO system or the Oral-Eze system cannot be used for quantitative clozapine and/or amisulpride therapeutic drug monitoring.

Experimental breakdown of selected anodized aluminum samples in dilute plasmas

NASA Technical Reports Server (NTRS)

Grier, Norman T.; Domitz, Stanley

1992-01-01

Anodized aluminum samples representative of Space Station Freedom structural material were tested for electrical breakdown under space plasma conditions. In space, this potential arises across the insulating anodized coating when the spacecraft structure is driven to a negative bias relative to the external plasma potential due to plasma-surface interaction phenomena. For anodized materials used in the tests, it was found that breakdown voltage varied from 100 to 2000 volts depending on the sample. The current in the arcs depended on the sample, the capacitor, and the voltage. The level of the arc currents varied from 60 to 1000 amperes. The plasma number density varied from 3 x 10 exp 6 to 10 exp 3 ions per cc. The time between arcs increased as the number density was lowered. Corona testing of anodized samples revealed that samples with higher corona inception voltage had higher arcing inception voltages. From this it is concluded that corona testing may provide a method of screening the samples.

Salivary levels of phosphorus and urea as indices of their plasma levels in nephropathic patients.

PubMed

Bilancio, Giancarlo; Cavallo, Pierpaolo; Lombardi, Cinzia; Guarino, Ermanno; Cozza, Vincenzo; Giordano, Francesco; Palladino, Giuseppe; Cirillo, Massimo

2018-03-30

Phosphorus and urea are measurable in saliva. Measurements of saliva phosphorus (S-Pho) and saliva urea (S-Urea) could be useful because of low invasivity. Data are limited to saliva tests methodology and to correlations between plasma and saliva compositions. S-Pho and S-Urea were investigated focusing on blind duplicates, differences between collection sites, differences between collection times, freezing-thawing effects, and plasma-saliva correlations. Tests were performed using fresh saliva collected by synthetic swap early morning after overnight fast (standard). Methodology was investigated in fifteen healthy volunteers. Plasma-saliva correlations were investigated in thirty nephropathic outpatients. S-Pho and S-Urea in all measurements ranged above detection limits (0.3 mmol/L). In healthy volunteers, S-Pho and S-Urea were similar in duplicates (results for S-Pho and S-Urea: % difference between samples ≤ 4.85%; R between samples ≥ .976, P < .001), in samples from different mouth sites (≤4.24%; R ≥ .887, P < .001), and in samples of different days (≤5.61%; R ≥ .606, P < .01) but, compared to standard, were substantially lower in after-breakfast samples (-28.0% and -21.3%; R ≥ .786, P < .001) and slightly lower in frozen-thawed samples (-12.4% and -5.92%; R ≥ .742, P < .001). In nephropathic patients, S-Pho was higher than but correlated with plasma phosphorus (saliva/plasma ratio 4.80; R = .686, P < .001), whereas S-Urea and plasma urea were similar and correlated with each other (saliva/plasma ratio 0.96; R = .944, P < .001). Post-dialysis changes in S-Pho and S-Urea paralleled post-dialysis changes in plasma phosphorus and urea. S-Pho and S-Urea reflect plasma phosphorus and plasma urea. Early morning fasting fresh samples are advisable because collection time and freezing-thawing affect saliva tests. © 2018 Wiley Periodicals, Inc.

Plasma surface cleaning using microwave plasmas

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

Tsai, C.C.; Haselton, H.H.; Nelson, W.D.

1993-11-01

In a microwave electron cyclotron resonance (ECR) plasma source, reactive plasmas of oxygen and its mixture with argon are used for plasma-cleaning experiments. Aluminum test samples (0.95 {times} 1.9 cm) were coated with thin films ({le} 20 {mu}m in thickness) of Shell Vitrea oil and cleaned by using such reactive plasmas. The plasma cleaning was done in various discharge conditions with fixed microwave power, rf power, biased potential, gas pressures (0.5 and 5 mtorr), and operating time up to 35 min. The status of plasma cleaning has been monitored by using mass spectroscopy. Mass loss of the samples after plasmamore » cleaning was measured to estimate cleaning rates. Measured clean rates of low pressure (0.5 mtorr) argon/oxygen plasmas were as high as 2.7 {mu}/min. X-ray photoelectron spectroscopy was used to determine cleanliness of the sample surfaces and confirm the effectiveness of plasma cleaning in achieving atomic levels of surface cleanliness. In this paper, significant results are reported and discussed.« less

Evaluation of dried blood spot as an alternative sample collection method for hepatitis C virus RNA quantitation and genotyping using a commercial system.

PubMed

Mahajan, Supriya; Choudhary, Manish Chandra; Kumar, Guresh; Gupta, Ekta

2018-06-01

Dried blood spot (DBS) is a minimally invasive sampling method suitable for sample collection, storage and transportation in resource limited areas. Aim of this study was to compare the diagnostic utility of DBS with plasma sample for HCV RNA quantitation and genotyping using commercial systems. Plasma and DBS card spotted samples were collected from 95 HCV seropositive patients. Both types of samples were subjected to HCV RNA by real-time PCR (Abbott m2000rt, USA). Genotyping was performed using Abbott HCV genotype II kit (Abbott diagnostics, USA) in samples with viral load > 3 log 10  IU/ml. In both plasma and DBS, 14 (14.7%) samples were negative and 81 (85.3%) were positive for HCV RNA. Median viral load in plasma (3.78; range 0-7.43) log 10  IU/ml was comparable to DBS (3.93; range 0-7.24) log 10  IU/ml. DBS demonstrated sensitivity and specificity of 97.5 and 85.7% respectively, with positive predictive value (PPV) of 97.5% and negative predictive value (NPV) of 85.7%. DBS showed good correlation (r 2  = 0.866) and agreement (93.5%) with plasma. Genotyping in 20 patients showed 100% concordance between DBS and plasma samples. DBS showed good sensitivity and specificity as a sampling method for HCV RNA quantitation and genotyping.

Characteristics and Hypothesized Functions of Challenging Behavior in a Community-Based Sample

ERIC Educational Resources Information Center

Petursdottir, Anna Ingeborg; Esch, John W.; Sautter, Rachael A.; Stewart, Kelise K.

2010-01-01

An archival study was conducted to document (a) types of challenging behavior, and (b) functional assessment outcomes, for a sample of persons with developmental disabilities who were referred to community-practicing behavior analysts for assessment and treatment of challenging behavior. Functional assessment reports, prepared by 17 behavior…

Linking two thousand years of European historical records with environmental change recorded in a high Alpine ice core

NASA Astrophysics Data System (ADS)

Bohleber, Pascal; Spaulding, Nicole; Mayewski, Paul; Kurbatov, Andrei; Hoffmann, Helene; Erhardt, Tobias; Fischer, Hubertus; More, Alexander; Loveluck, Christopher; Luongo, Matthew; Kabala, Jakub; McCormick, Michael

2016-04-01

Its extraordinary network of historical and archaeological records makes Europe exceptionally promising for investigating environmental change and human response over the last two thousand years. Among natural proxy archives, ice core records offer a wide range of environmental reconstructions including natural and human source histories of the chemistry of the atmosphere. To link these robust environmental records with historical evidence of past civilizations remains a great challenge, however. In central Europe the unique target for a comparison for environmental change recorded in ice cores and human activity is the small firn saddle of Colle Gnifetti (4550 m above sea level on the Italian-Swiss border). Its exceptionally low net accumulation make Colle Gnifetti (CG) the only feasible site in the Alps for retrieving a long-term ice core record beyond the last century. However, at CG rapid annual layer thinning eventually limits conventional cm-resolution analysis to multi-annual signals and hampers dating by annual layer counting beyond a few hundred years. Thereby, a crucial gap is introduced to the sub-seasonal time scale of events typically recorded in written archives. In our ongoing project we pioneer correlating the CG environmental ice core archive with a unique compilation of European historical records provided through the Harvard Initiative for the Science of the Human Past and the Digital Atlas of Roman and Medieval Civilization. For this purpose, state-of-the-art glacio-chemical analysis was performed on a newly recovered CG ice core, including continuous flow analysis chemistry and stable isotopes. A crucial contribution comes from the application of LA-ICP-MS (laser ablation ion coupled plasma mass spectrometry) to meter long sections of frozen ice samples, developed and operated by the University of Maine's Climate Change Institute, offering glacio-chemical records up to 100 μm in resolution. The new methods significantly improves sampling resolution and allows detection of annual layers even in highly compressed old sections of CG ice cores: A breakthrough not only for extending the ice core dating over the last two millennia but also for bridging the gap in time scales to historical records. Here we present first results from our ongoing efforts in bringing together ice core time series with historical evidence, focusing on the time period from 1 to 1400 C.E. Based on a thorough consideration of the glaciological constraints at CG we explore various ice core proxy signals for their significance to correlate with events recorded in human writing, such as dust storms, volcanic events, climate-induced crop failures and starvation as well as metal production levels. Distinct dust layers are frequently found in CG ice cores, representative for meteorological conditions that transported sand from the Sahara to Europe. At the same time, Saharan dust events were also frequently recorded by ancient and medieval observers as "blood rain". Ultimately we work towards using past extreme climate events from medieval Europe recorded as written evidence to constrain the ice core age scale and, vice versa, to investigate the response of human societies to environmental change recorded in the CG glacier archive.

Stability of Bovine viral diarrhea virus 1 nucleic acid in fetal bovine samples stored under different conditions.

PubMed

Ridpath, Julia F; Neill, John D; Chiang, Yu-Wei; Waldbillig, Jill

2014-01-01

Infection of pregnant cattle with both species of Bovine viral diarrhea virus (BVDV) can result in reproductive disease that includes fetal reabsorption, mummification, abortion, stillbirths, congenital defects affecting structural, neural, reproductive, and immune systems, and the birth of calves persistently infected with BVDV. Accurate diagnosis of BVDV-associated reproductive disease is important to control BVDV at the production unit level and assessment of the cost of BVDV infections in support of BVDV control programs. The purpose of the current study was to examine the stability of viral nucleic acid in fetal tissues exposed to different conditions, as measured by detection by polymerase chain reaction. Five different types of fetal tissue, including brain, skin and muscle, ear, and 2 different pooled organ samples, were subjected to conditions that mimicked those that might exist for samples collected after abortions in production settings or possible storage conditions after collection and prior to testing. In addition, tissues were archived for 36 months at -20°C and then retested, to mimic conditions that might occur in the case of retrospective surveillance studies. Brain tissue showed the highest stability under the conditions tested. The impact of fecal contamination was increased following archiving in all tissue types suggesting that, for long-term storage, effort should be made to reduce environmental contaminants before archiving.

Pharmaceuticals and Personal Care Products in Archived U.S. Biosolids from the 2001 EPA National Sewage Sludge Survey

PubMed Central

McClellan, Kristin; Halden, Rolf U.

2010-01-01

In response to the U.S. National Academies’ call for a better assessment of chemical pollutants contained in the approximately 6.9 million dry tons of digested municipal sludge produced annually in the United States, the mean concentration of 72 pharmaceuticals and personal care products (PPCP) were determined in 110 biosolids samples collected by the U.S. Environmental Protection Agency (EPA) in its 2001 National Sewage Sludge Survey. Composite samples of archived biosolids, collected at 94 U.S. wastewater treatment plants from 32 states and the District of Columbia, were analyzed by liquid chromatography tandem mass spectrometry using EPA Method 1694. Thirty-eight (54%) of the 72 analytes were detected in at least one composite sample at concentrations ranging from 0.002 to 48 mg kg−1 dry weight. Triclocarban and triclosan were the most abundant analytes with mean concentrations of 36 ± 8 and 12.6 ± 3.8 mg kg−1 (n = 5), respectively, accounting for 65% of the total PPCP mass found. The loading to U.S. soils from nationwide biosolids recycling was estimated at 210–250 metric tons per year for the sum of the 72 PPCPs investigated. The results of this nationwide reconnaissance of PPCPs in archived U.S. biosolids mirror in contaminant occurrences, frequencies and concentrations, those reported by the U.S. EPA for samples collected in 2006/07. This demonstrates that PPCP releases in U.S. biosolids have been ongoing for many years and the most abundant PPCPs appear to show limited fluctuations in mass over time when assessed on a nationwide basis. The here demonstrated use of five mega composite samples holds promise for conducting cost-effective, routine monitoring on a regional basis. PMID:20106500

Distribution of chemical elements in attic dust as reflection of their geogenic and anthropogenic sources in the vicinity of the copper mine and flotation plant.

PubMed

Balabanova, Biljana; Stafilov, Trajče; Sajn, Robert; Bačeva, Katerina

2011-08-01

The main aim of this article was to assess the atmospheric pollution with heavy metals due to copper mining Bučim near Radoviš, the Republic of Macedonia. The open pit and mine waste and flotation tailings are continually exposed to open air, which leads to winds carrying the fine particles into the atmosphere. Samples of attic dust were examined as historical archives of mine emissions, with the aim of elucidating the pathways of pollution. Dust was collected from the attics of 29 houses, built between 1920 and 1970. Nineteen elements (Ag, Al, As, Ba, Ca, Cd, Co, Cr, Cu, Li, Fe, K, Mg, Mn, Na, Ni, Pb, Sr, and Zn) were analyzed by atomic emission spectrometry with inductively coupled plasma. The obtained values of the investigated elements in attic dust samples were statistically processed using nonparametric and parametric analysis. Factor analysis revealed three factors governing the source of individual chemical elements. Two of them grouping Ca, Li, Mg, Mn, and Sr (Factor 1) and Co, Cr, and Ni (Factor 2) can be characterized as geogenic. The third factor grouping As, Cu, and Pb is anthropogenic and mirrors dust fallout from mining operation and from flotation tailings. Maps of areal deposition were prepared for this group of elements, from which correlation of these anthropogenic born elements was confirmed.

Use of Blood Smears and Dried Blood Spots for Polymerase Chain Reaction-Based Detection and Quantification of Bacterial Infection and Plasmodium falciparum in Severely Ill Febrile African Children.

PubMed

Wihokhoen, Benchawan; Dondorp, Arjen M; Turner, Paul; Woodrow, Charles J; Imwong, Mallika

2016-02-01

Molecular approaches offer a means of testing archived samples stored as dried blood spots in settings where standard blood cultures are not possible. Peripheral blood films are one suggested source of material, although the sensitivity of this approach has not been well defined. Thin blood smears and dried blood spots from a severe pediatric malaria study were assessed using specific polymerase chain reaction (PCR) primers to detect non-typhoidal Salmonella (NTS; MisL gene), Streptococcus pneumoniae (lytA), and Plasmodium falciparum (18S rRNA). Of 16 cases of NTS and S. pneumoniae confirmed on blood culture, none were positive by PCR using DNA extracts from blood films or dried blood spots. In contrast, four of 36 dried blood spots and two of 178 plasma samples were PCR positive for S. pneumoniae, despite negative bacterial blood cultures, suggesting false positives. Quantitative assessment revealed that the effective concentration of P. falciparum DNA in blood films was three log orders of magnitude lower than for dried blood spots. The P. falciparum kelch13 gene could not be amplified from blood films. These findings question the value of blood PCR-based approaches for detection of NTS and S. pneumoniae, and show that stored blood films are an inefficient method of studying P. falciparum. © The American Society of Tropical Medicine and Hygiene.

Use of Blood Smears and Dried Blood Spots for Polymerase Chain Reaction–Based Detection and Quantification of Bacterial Infection and Plasmodium falciparum in Severely Ill Febrile African Children

PubMed Central

Wihokhoen, Benchawan; Dondorp, Arjen M.; Turner, Paul; Woodrow, Charles J.; Imwong, Mallika

2016-01-01

Molecular approaches offer a means of testing archived samples stored as dried blood spots in settings where standard blood cultures are not possible. Peripheral blood films are one suggested source of material, although the sensitivity of this approach has not been well defined. Thin blood smears and dried blood spots from a severe pediatric malaria study were assessed using specific polymerase chain reaction (PCR) primers to detect non-typhoidal Salmonella (NTS; MisL gene), Streptococcus pneumoniae (lytA), and Plasmodium falciparum (18S rRNA). Of 16 cases of NTS and S. pneumoniae confirmed on blood culture, none were positive by PCR using DNA extracts from blood films or dried blood spots. In contrast, four of 36 dried blood spots and two of 178 plasma samples were PCR positive for S. pneumoniae, despite negative bacterial blood cultures, suggesting false positives. Quantitative assessment revealed that the effective concentration of P. falciparum DNA in blood films was three log orders of magnitude lower than for dried blood spots. The P. falciparum kelch13 gene could not be amplified from blood films. These findings question the value of blood PCR-based approaches for detection of NTS and S. pneumoniae, and show that stored blood films are an inefficient method of studying P. falciparum. PMID:26711525

Desizing of Starch Containing Cotton Fabrics Using Near Atmospheric Pressure, Cold DC Plasma Treatment

NASA Astrophysics Data System (ADS)

Prasath, A.; Sivaram, S. S.; Vijay Anand, V. D.; Dhandapani, Saravanan

2013-03-01

An attempt has been made to desize the starch containing grey cotton fabrics using the DC plasma with oxygen as the gaseous medium. Process conditions of the plasma reactor were optimized in terms of distance between the plates (3.2 cm), applied voltage (600 V) and applied pressure (0.01 bar) to obtain maximum desizing efficiency. No discolouration was observed in the hot water extracts of the desized sample in presence of iodine though relatively higher solvent extractable impurities (4.53 %) were observed in the plasma desized samples compared to acid desized samples (3.38 %). Also, significant weight loss, improvements in plasma desized samples were observed than that of grey fabrics in terms of drop absorbency.

Determination of benzocaine in rainbow trout plasma

USGS Publications Warehouse

Bernardy, Jeffery A.; Coleman, K.S.; Stehly, G.R.; Gingerich, William H.

1996-01-01

A liquid chromatographic method is described for analysis of benzocaine (BZ), a proposed fish anesthetic, in rainbow trout plasma, Mean recoveries of BZ from plasma samples fortified at 44-10 100 ng/mL were 96-100%. The method detection limit is 10 ng/mL, and the limit of quantitation is 37 ng/mL. Acetylation of BZ occurs in whole blood after storage at room temperature (i.e., 21 degrees C) for 10 min. However, no acetylation of BZ was detected in plasma samples held at room temperature for 4 h, Mean method precision for plasma samples with incurred BZ residue is similar to that for fortified samples in the same concentration range (relative standard deviations of 0.9 and 1.2%, respectively).

A random sampling approach for robust estimation of tissue-to-plasma ratio from extremely sparse data.

PubMed

Chu, Hui-May; Ette, Ene I

2005-09-02

his study was performed to develop a new nonparametric approach for the estimation of robust tissue-to-plasma ratio from extremely sparsely sampled paired data (ie, one sample each from plasma and tissue per subject). Tissue-to-plasma ratio was estimated from paired/unpaired experimental data using independent time points approach, area under the curve (AUC) values calculated with the naïve data averaging approach, and AUC values calculated using sampling based approaches (eg, the pseudoprofile-based bootstrap [PpbB] approach and the random sampling approach [our proposed approach]). The random sampling approach involves the use of a 2-phase algorithm. The convergence of the sampling/resampling approaches was investigated, as well as the robustness of the estimates produced by different approaches. To evaluate the latter, new data sets were generated by introducing outlier(s) into the real data set. One to 2 concentration values were inflated by 10% to 40% from their original values to produce the outliers. Tissue-to-plasma ratios computed using the independent time points approach varied between 0 and 50 across time points. The ratio obtained from AUC values acquired using the naive data averaging approach was not associated with any measure of uncertainty or variability. Calculating the ratio without regard to pairing yielded poorer estimates. The random sampling and pseudoprofile-based bootstrap approaches yielded tissue-to-plasma ratios with uncertainty and variability. However, the random sampling approach, because of the 2-phase nature of its algorithm, yielded more robust estimates and required fewer replications. Therefore, a 2-phase random sampling approach is proposed for the robust estimation of tissue-to-plasma ratio from extremely sparsely sampled data.

Performance Evaluation of the Operational Air Quality Monitor for Water Testing Aboard the International Space Station

NASA Technical Reports Server (NTRS)

Wallace, William T.; Limero, Thomas F.; Gazda, Daniel B.; Macatangay, Ariel V.; Dwivedi, Prabha; Fernandez, Facundo M.

2014-01-01

In the history of manned spaceflight, environmental monitoring has relied heavily on archival sampling. For short missions, this type of sample collection was sufficient; returned samples provided a snapshot of the presence of chemical and biological contaminants in the spacecraft air and water. However, with the construction of the International Space Station (ISS) and the subsequent extension of mission durations, soon to be up to one year, the need for enhanced, real-time environmental monitoring became more pressing. The past several years have seen the implementation of several real-time monitors aboard the ISS, complemented with reduced archival sampling. The station air is currently monitored for volatile organic compounds (VOCs) using gas chromatography-differential mobility spectrometry (Air Quality Monitor [AQM]). The water on ISS is analyzed to measure total organic carbon and biocide concentrations using the Total Organic Carbon Analyzer (TOCA) and the Colorimetric Water Quality Monitoring Kit (CWQMK), respectively. The current air and water monitors provide important data, but the number and size of the different instruments makes them impractical for future exploration missions. It is apparent that there is still a need for improvements in environmental monitoring capabilities. One such improvement could be realized by modifying a single instrument to analyze both air and water. As the AQM currently provides quantitative, compound-specific information for target compounds present in air samples, and many of the compounds are also targets for water quality monitoring, this instrument provides a logical starting point to evaluate the feasibility of this approach. In this presentation, we will discuss our recent studies aimed at determining an appropriate method for introducing VOCs from water samples into the gas phase and our current work, in which an electro-thermal vaporization unit has been interfaced with the AQM to analyze target analytes at the relevant concentrations at which they are routinely detected in archival water samples from the ISS.

ICE/ISEE plasma wave data analysis

NASA Technical Reports Server (NTRS)

Greenstadt, E. W.

1992-01-01

The interval reported on, from Jan. 1990 to Dec. 1991, has been one of continued processing and archiving of ICE plasma wave (pw) data and transition from analysis of ISEE 3 and ICE cometary data to ICE data taken along its cruise trajectory, where coronal mass ejections are the focus of attention. We have continued to examine with great interest the last year of ISEE 3's precomet phase, when it spent considerable time far downwind from Earth, recording conditions upstream, downstream, and across the very weak, distant flank bow shock. Among other motivations was the apparent similarity of some shock and post shock structures to the signatures of the bow wave surrounding comet Giacobini-Zinner, whose ICE-phase data was revisited. While pursuing detailed, second-order scientific inquiries still pending from the late ISEE 3 recordings, we have also sought to position ourselves for study of CME's by instituting a data processing format new to the ISEE 3/ICE pw detector. Processed detector output has always been summarized and archived in 24-hour segments, with all pw channels individually plotted and stacked one above the next down in frequency, with each channel calibrated separately to keep all data patterns equally visible in the plots, regardless of gross differences in energy content at the various frequencies. Since CME's, with their preceding and following solar wind plasmas, can take more than one day to pass by the spacecraft, a more condensed synoptic view of the pw data is required to identify, let alone assess, CME characteristics than has been afforded by the traditional routines. This requirement is addressed in a major new processing initiative in the past two years. Besides our own ongoing and fresh investigations, we have cooperated, within our resources, with studies conducted extramurally by distant colleagues irrespective of the phase of the ISEE 3/ICE mission under scrutiny. The remainder of this report summarizes our processing activities, our investigations, both internal and cooperative, our scientific results, and our publication activity.

A needle extraction utilizing a molecularly imprinted-sol-gel xerogel for on-line microextraction of the lung cancer biomarker bilirubin from plasma and urine samples.

PubMed

Moein, Mohammad Mahdi; Jabbar, Dunia; Colmsjö, Anders; Abdel-Rehim, Mohamed

2014-10-31

In the present work, a needle trap utilizing a molecularly imprinted sol-gel xerogel was prepared for the on-line microextraction of bilirubin from plasma and urine samples. Each prepared needle could be used for approximately one hundred extractions before it was discarded. Imprinted and non-imprinted sol-gel xerogel were applied for the extraction of bilirubin from plasma and urine samples. The produced molecularly imprinted sol-gel xerogel polymer showed high binding capacity and fast adsorption/desorption kinetics for bilirubin in plasma and urine samples. The adsorption capacity of molecularly imprinted sol-gel xerogel polymer was approximately 60% higher than that of non-imprinted polymer. The effect of the conditioning, washing and elution solvents, pH, extraction time, adsorption capacity and imprinting factor were investigated. The limit of detection and the lower limit of quantification were set to 1.6 and 5nmolL(-1), respectively using plasma or urine samples. The standard calibration curves were obtained within the concentration range of 5-1000nmolL(-1) in both plasma and urine samples. The coefficients of determination values (R(2)) were ≥0.998 for all runs. The extraction recovery was approximately 80% for BR in the human plasma and urine samples. Copyright © 2014 Elsevier B.V. All rights reserved.

The effects of RF plasma ashing on zinc orthotitanate/potassium silicate thermal control coatings

NASA Technical Reports Server (NTRS)

Dever, Joyce A.; Bruckner, Eric J.

1992-01-01

Samples of YB-71, a white thermal control coating composed of zinc orthotitanate pigment in a potassium silicate binder, were exposed in air plasma and in oxygen plasma to determine optical property and surface chemistry changes. Results show that YB-71 undergoes a significant reflectance decrease upon exposure to the simulated LEO atomic oxygen environment provided by an air plasma asher. YB-71 samples exposed to the same effective fluence in oxygen plasma, or in a UV screening Faraday cage in air or oxygen, do not undergo as severe reflectance decreases as the samples exposed in the air plasma asher environment. The UV and VUV radiation present in the plasma ashers affects the YB-71 degradation. It is noted that, when using plasma ashers to determine LEO degradation, it is necessary to take into account the sensitivity of the material to the synergistic effects of atomic oxygen and accelerated UV radiation.

Closed inductively coupled plasma cell

DOEpatents

Manning, Thomas J.; Palmer, Byron A.; Hof, Douglas E.

1990-01-01

A closed inductively coupled plasma cell generates a relatively high power, low noise plasma for use in spectroscopic studies. A variety of gases can be selected to form the plasma to minimize spectroscopic interference and to provide a electron density and temperature range for the sample to be analyzed. Grounded conductors are placed at the tube ends and axially displaced from the inductive coil, whereby the resulting electromagnetic field acts to elongate the plasma in the tube. Sample materials can be injected in the plasma to be excited for spectroscopy.

Comparison of serum and plasma measurements of Müllerian inhibiting substance.

PubMed

Merhi, Zaher O; Messerlian, Geralyn M; Minkoff, Howard; Eklund, Elizabeth E; Macura, Jerzy; Feldman, Joseph; Rodriguez, Carlos; Seifer, David B

2008-06-01

The authors sought to determine whether measurement of plasma Müllerian inhibiting substance (MIS) is a suitable substitute for measurement of serum MIS. Eighteen samples of serum and plasma were examined that were drawn simultaneously. Levels of MIS were measured with an ELISA kit, and plasma levels were studied in parallel to serum samples. A 98.5% correlation was found between serum and plasma MIS values.

Cortisol in saliva and plasma of cattle after ACTH administration and milking.

PubMed

Negrão, J A; Porcionato, M A; de Passillé, A M; Rushen, J

2004-06-01

Interest in the measurement of salivary cortisol has increased recently because saliva can be easily collected before and after an imposed stress. This study evaluated the relationship between plasma and salivary concentrations of cortisol following ACTH administration in calves (experiment 1) and machine milking of adult cows (experiment 2). A catheter was inserted into the jugular vein of all animals 72 h before the beginning of experiments. Blood and saliva samples were collected before and after ACTH administration (0.6 IU/kg BW) in calves or before and after machine milking of cows. Using a cotton swab, each saliva sample was taken immediately following the blood sample. In general, cortisol profiles were similar in plasma and saliva and correlated in both experiments; however, plasma concentrations were significantly higher than salivary concentrations. In addition, the differences between cortisol concentrations measured in saliva and plasma within each experiment varied substantially between animals and samples. Furthermore, in experiment 2, nearly 10% of salivary samples were below limits of detection. The sharp peaks in cortisol after ACTH administration in both the plasma and saliva were reflected adrenal stimulation. In addition, increases in cortisol in response to milking in both the plasma and saliva suggest that salivary sampling is a reliable option when studying cortisol responses to normal physiological events.

Capillary whole blood testing by a new portable monitor. Comparison with standard determination of the international normalized ratio.

PubMed

de Miguel, Dunia; Burgaleta, Carmen; Reyes, Eduardo; Pascual, Teresa

2003-07-01

We evaluated a new portable monitor (AvoSure PT PRO, Menarini Diagnostics, Firenze, Italy) developed to test the prothrombin time in capillary blood and plasma by comparing it with the standard laboratory determination. We studied 62 patients receiving acenocoumarol therapy. The international normalized ratio (INR) in capillary blood was analyzed by 2 methods: AvoSure PT PRO and Thrombotrack Nycomed Analyzer (Axis-Shield, Dundee, Scotland). Parallel studies were performed in plasma samples by a reference method using the Behring Coagulation Timer (Behring Diagnostics, Marburg, Germany). Plasma samples also were tested with the AvoSure PT PRO. Correlation was good for INR values for capillary blood and plasma samples by AvoSure PT PRO and our reference method (R2 = 0.8596) and for capillary blood samples tested by the AvoSure PT PRO and Thrombotrack Nycomed Analyzer (R2 = 0.8875). The correlation for INR in capillary blood and plasma samples by AvoSure PT PRO was 0.6939 (P < .0004). Capillary blood determinations are rapid and effective for monitoring oral anticoagulation therapy and have a high correlation to plasma determinations. AvoSure PT PRO is accurate for controlling INR in plasma and capillary blood samples, may be used in outpatient clinics, and has advantages over previous portable monitors.

Comparison of plasma and tissue samples in epidermal growth factor receptor mutation by ARMS in advanced non-small cell lung cancer.

PubMed

Ma, MeiLi; Shi, ChunLei; Qian, JiaLin; Teng, JiaJun; Zhong, Hua; Han, BaoHui

2016-10-10

The aim of this study was to assess the effectiveness and accuracy of blood-based circulating-free tumor DNA on testing epidermal growth factor receptor (EGFR) gene mutations. In total, 219 non-small cell lung cancer patients in stages III-IV were enrolled into this study. All patients had tissue samples and matched plasma DNA samples. EGFR gene mutations were detected by the Amplification Refractory Mutation System (ARMS). We compared the mutations in tumor tissue samples with matched plasma samples and determined the correlation between EGFR mutation status and clinical pathologic characteristics. The overall concordance rate of EGFR mutation status between the 219 matched plasma and tissue samples was 82% (179/219). The sensitivity and specificity for the ARMS EGFR mutation test in the plasma compared with tumor tissue were 60% (54/90) and 97% (125/129), respectively. The positive predictive value was 93% (54/58) and the negative predictive value was 78% (125/161). The median overall survival was longer for those with EGFR mutations than for those without EGFR mutations both in tissue samples (23.98 vs. 12.16months; P<0.001) and in plasma (19.96 vs. 13.63months; P=0.009). For the 68 patients treated with EGFR- tyrosine kinase inhibitors (TKIs), the median progression-free survival (PFS) was significantly prolonged in the EGFR mutant group compared to the non-mutation group in tumor tissue samples (12.26months vs. 2.40months, P<0.001). In plasma samples, the PFS of the mutant group was longer than that of the non-mutant group. However, there was no significant difference between the two groups (10.88months vs. 9.89months, P=0.411). The detection of EGFR mutations in plasma using ARMS is relatively sensitive and highly specific. However, EGFR mutation status tested by ARMS in plasma cannot replace a tumor tissue biopsy. Positive EGFR mutation results detected in plasma are fairly reliable, but negative results are hampered by a high rate of false negatives. Copyright © 2016. Published by Elsevier B.V.

The Use of Dried Blood Spots for Pharmacokinetic Monitoring of Vemurafenib Treatment in Melanoma Patients.

PubMed

Nijenhuis, Cynthia M; Huitema, Alwin D R; Marchetti, Serena; Blank, Christian; Haanen, John B A G; van Thienen, Johannes V; Rosing, Hilde; Schellens, Jan H M; Beijnen, Jos H

2016-10-01

Pharmacokinetic monitoring is increasingly becoming an important part of clinical care of tyrosine kinase inhibitor treatment. Vemurafenib is an oral tyrosine kinase inhibitor that inhibits mutated serine/threonine protein kinase B-Raf (BRAF) and is approved for the treatment of adult patients with BRAF V600 mutation-positive unresectable or metastatic melanoma. The aim of this study was to establish the relationship between dried blood spot (DBS) and plasma concentrations of vemurafenib to enable the use of DBS sampling, which is a minimally invasive form of sample collection. In total, 43 paired plasma and DBS samples (in duplicate) were obtained from 8 melanoma patients on vemurafenib therapy and were analyzed using high-performance liquid chromatography-tandem mass spectrometry. Plasma concentrations were predicted from the DBS concentrations using 2 methods: (1) individual hematocrit correction and blood cell-to-plasma partitioning and (2) the calculated slope explaining the relationship between DBS and plasma concentrations (without individual hematocrit correction). Vemurafenib DBS concentrations and plasma concentrations showed a strong correlation (r = 0.964), and the relationship could be described by ([vemurafenib]plasma = [vemurafenib]DBS /0.64). The predicted plasma concentrations were within ±20% of the analyzed plasma concentrations in 97% and 100% of the samples for the methods with and without hematocrit correction, respectively. In conclusion, DBS concentrations and plasma concentrations of vemurafenib are highly correlated. Plasma concentrations can be predicted from DBS concentration using the blood cell-to-plasma partition and the average hematocrit value of this cohort (0.40 L/L). DBS sampling for pharmacokinetic monitoring of vemurafenib treatment can be used in clinical practice. © 2016, The American College of Clinical Pharmacology.

Plasma discharge elemental detector for a mass spectrometer

NASA Astrophysics Data System (ADS)

Heppner, R. A.

1983-06-01

A material to be analyzed is injected into a mirowave-induced plasma discharge unit, in which the material is carried with a flow of buffer gas through an intense microwave energy field which produces a plasma discharge in the buffer gas. As the material exits from the plasma discharge, the material is sampled and conveyed along a capillary transfer tube to a mass spectrometer where it is analyzed. The plasma discharge causes dissociation of complex organic molecules into simpler molecules which return to the neutral ground state before they are analyzed in the mass spectrometer. The buffer gas is supplied to one end portion of the discharge tube and is withdrawn from the other end portion by a vacuum pump which maintains a subatmospheric pressure in the discharge tube. The sample material is injected by a capillary injection tube into the buffer gas flow as it enters the plasma discharge zone. The dissociated materials are sampled by an axial sampling tube having an entrance where the buffer gas exits from the plasma discharge zone. The sample material may be supplied by a gas chromatography having a capillary effluent line connected to the capillary injection tube, so that the effluent material is injected into the microwave induced plasma discharge. The microwave field is produced by a cavity resonator through which the discharge tube passes.

Modeling the Plasmasphere

NASA Technical Reports Server (NTRS)

Gallagher, Dennis L

1998-01-01

The plasmasphere has often been considered one of the more boring regions in the magnetosphere. Its low energy plasma doesn't begin to compete against the free sources of energy available in the ring current, auroral zone, or plasma sheet. Its best known feature is its relatively highly density, archived as a result of prolonged accumulation of ionospheric outflow onto corotating flux tubes. On second look, however, the plasmasphere can be found to exhibit a remarkable influence on its more energetic cousins and display convection behavior indicative of physical processes acting throughout the magnetosphere for which we have no explanation. Plasmaspheric plasma densities and composition of heavy ions are particularly sensitive to heating by processes active in the ionosphere and all along field lines. Wave propagation and instabilities, collisional losses in the ring current, and heat transport from superthermal electrons are all equally sensitive to dense, heavy plasmaspheric densities and density gradients. It is in this context that we seek to characterize plasmaspheric populations using event based, empirical, and physical modeling methods. The modeling approaches, the challenges, and some of the results of these efforts will be presented.

Evaluation of a Gas Chromatograph-Differential Mobility Spectrometer for Potential Water Monitoring on the International Space Station

NASA Technical Reports Server (NTRS)

Wallace, William T.; Limero, Thomas F.; Gazda, Daniel B.; Macatangay, Ariel V.; Dwivedi, Prabha; Fernandez, Facundo M.

2015-01-01

Environmental monitoring for manned spaceflight has long depended on archival sampling, which was sufficient for short missions. However, the longer mission durations aboard the International Space Station (ISS) have shown that enhanced, real-time monitoring capabilities are necessary in order to protect both the crewmembers and the spacecraft systems. Over the past several years, a number of real-time environmental monitors have been deployed on the ISS. Currently, volatile organic compounds (VOCs) in the station air are monitored by the Air Quality Monitor (AQM), a small, lightweight gas chromatograph-differential mobility spectrometer. For water monitoring, real-time monitors are used for total organic carbon (TOC) and biocide analysis. No information on the actual makeup of the TOC is provided presently, however. An improvement to the current state of environmental monitoring could be realized by modifying a single instrument to analyze both air and water. As the AQM currently provides quantitative, compound-specific information for VOCs in air samples, this instrument provides a logical starting point to evaluate the feasibility of this approach. The major hurdle for this effort lies in the liberation of the target analytes from the water matrix. In this presentation, we will discuss our recent studies, in which an electro-thermal vaporization unit has been interfaced with the AQM to analyze target VOCs at the concentrations at which they are routinely detected in archival water samples from the ISS. We will compare the results of these studies with those obtained from the instrumentation routinely used to analyze archival water samples.

National Aeronautics and Space Administration Biological Specimen Repository

NASA Technical Reports Server (NTRS)

McMonigal, Kathleen A.; Pietrzyk, Robert a.; Johnson, Mary Anne

2008-01-01

The National Aeronautics and Space Administration Biological Specimen Repository (Repository) is a storage bank that is used to maintain biological specimens over extended periods of time and under well-controlled conditions. Samples from the International Space Station (ISS), including blood and urine, will be collected, processed and archived during the preflight, inflight and postflight phases of ISS missions. This investigation has been developed to archive biosamples for use as a resource for future space flight related research. The International Space Station (ISS) provides a platform to investigate the effects of microgravity on human physiology prior to lunar and exploration class missions. The storage of crewmember samples from many different ISS flights in a single repository will be a valuable resource with which researchers can study space flight related changes and investigate physiological markers. The development of the National Aeronautics and Space Administration Biological Specimen Repository will allow for the collection, processing, storage, maintenance, and ethical distribution of biosamples to meet goals of scientific and programmatic relevance to the space program. Archiving of the biosamples will provide future research opportunities including investigating patterns of physiological changes, analysis of components unknown at this time or analyses performed by new methodologies.

Air plasma effect on dental disinfection

NASA Astrophysics Data System (ADS)

Duarte, S.; Kuo, S. P.; Murata, R. M.; Chen, C. Y.; Saxena, D.; Huang, K. J.; Popovic, S.

2011-07-01

A nonthermal low temperature air plasma jet is characterized and applied to study the plasma effects on oral pathogens and biofilms. Experiments were performed on samples of six defined microorganisms' cultures, including those of gram-positive bacteria and fungi, and on a cultivating biofilm sample of Streptococcus mutans UA159. The results show that the plasma jet creates a zone of microbial growth inhibition in each treated sample; the zone increases with the plasma treatment time and expands beyond the entire region directly exposed to the plasma jet. With 30s plasma treatment twice daily during 5 days of biofilm cultivation, its formation was inhibited. The viability of S. mutans cells in the treated biofilms dropped to below the measurable level and the killed bacterial cells concentrated to local regions as manifested by the fluorescence microscopy via the environmental scanning electron microscope. The emission spectroscopy of the jet indicates that its plasma effluent carries an abundance of reactive atomic oxygen, providing catalyst for the observed plasma effect.

Air plasma effect on dental disinfection

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

Duarte, S.; Murata, R. M.; Saxena, D.

2011-07-15

A nonthermal low temperature air plasma jet is characterized and applied to study the plasma effects on oral pathogens and biofilms. Experiments were performed on samples of six defined microorganisms' cultures, including those of gram-positive bacteria and fungi, and on a cultivating biofilm sample of Streptococcus mutans UA159. The results show that the plasma jet creates a zone of microbial growth inhibition in each treated sample; the zone increases with the plasma treatment time and expands beyond the entire region directly exposed to the plasma jet. With 30s plasma treatment twice daily during 5 days of biofilm cultivation, its formationmore » was inhibited. The viability of S. mutans cells in the treated biofilms dropped to below the measurable level and the killed bacterial cells concentrated to local regions as manifested by the fluorescence microscopy via the environmental scanning electron microscope. The emission spectroscopy of the jet indicates that its plasma effluent carries an abundance of reactive atomic oxygen, providing catalyst for the observed plasma effect.« less

Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive

PubMed Central

Nakazato, Takeru; Bono, Hidemasa

2017-01-01

Abstract It is important for public data repositories to promote the reuse of archived data. In the growing field of omics science, however, the increasing number of submissions of high-throughput sequencing (HTSeq) data to public repositories prevents users from choosing a suitable data set from among the large number of search results. Repository users need to be able to set a threshold to reduce the number of results to obtain a suitable subset of high-quality data for reanalysis. We calculated the quality of sequencing data archived in a public data repository, the Sequence Read Archive (SRA), by using the quality control software FastQC. We obtained quality values for 1 171 313 experiments, which can be used to evaluate the suitability of data for reuse. We also visualized the data distribution in SRA by integrating the quality information and metadata of experiments and samples. We provide quality information of all of the archived sequencing data, which enable users to obtain sufficient quality sequencing data for reanalyses. The calculated quality data are available to the public in various formats. Our data also provide an example of enhancing the reuse of public data by adding metadata to published research data by a third party. PMID:28449062

Geochemical signatures in fin rays provide a nonlethal method to distinguish the natal rearing streams of endangered juvenile Chinook Salmon Oncorhynchus tshawytscha in the Wenatchee River, Washington

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

Linley, Timothy J.; Krogstad, Eirik J.; Nims, Megan K.

Rebuilding fish populations that have undergone a major decline is a challenging task that can be made more complicated when estimates of abundance obtained from physical tags are biased or imprecise. Abundance estimates based on natural tags where each fish in the population is marked can help address these problems, but generally requires that the samples be obtained in a nonlethal manner. We evaluated the potential of using geochemical signatures in fin rays as a nonlethal method to determine the natal tributaries of endangered juvenile spring Chinook Salmon in the Wenatchee River, Washington. Archived samples of anal fin clips collectedmore » from yearling smolt in 2009, 2010 and 2011 were analyzed for Ba/Ca, Mn/Ba, Mg/Ca, Sr/Ca, Zn/Ca and 87Sr/86Sr by inductively coupled plasma mass spectrometry. Water samples collected from these same streams in 2012 were also quantified for geochemical composition. Fin ray and water Ba/Ca, Sr/Ca, and 87Sr/86Sr were highly correlated despite the samples having been collected in different years. Fin ray Ba/Ca, Mg/Ca, Sr/Ca, Zn/Ca and 87Sr/86Sr ratios differed significantly among the natal streams, but also among years within streams. A linear discriminant model that included Ba/Ca, Mg/Ca, Sr/Ca, and 87Sr/86Sr correctly classified 95% of the salmon to their natal stream. Our results suggest that fin ray geochemistry may provide an effective, nonlethal method to identify mixtures of Wenatchee River spring Chinook Salmon for recovery efforts when these involve the capture of juvenile fish to estimate population abundance.« less

Discovery and Identification of Dimethylsilanediol as a Contaminant in ISS Potable Water

NASA Technical Reports Server (NTRS)

Rutz, Jeffrey A.; Schultz, John R.; Kuo, C. Mike; Curtis, Matthew; Jones, Patrick R.; Sparkman, O. David; McCoy, J. Torin

2011-01-01

In September 2010, analysis of ISS potable water samples was undertaken to determine the contaminant(s) responsible for a rise of total organic carbon (TOC) in the Water Processor Assembly (WPA) product water. As analysis of the routine target list of organic compounds did not reveal the contaminant, efforts to look for unknown compounds were initiated, resulting in discovery of an unknown peak in the gas chromatography/mass spectrometry (GC/MS) analysis for glycols. A mass spectrum of the contaminant was then generated by concentrating one of the samples and analyzing it by GC/MS in full-scan mode. Although a computer match of the compound identity could not be obtained with the instrument database, a search with a more up-to-date mass spectral library yielded a good match with dimethylsilanediol (DMSD). Inductively coupled plasma/mass spectrometry (ICP/MS) analyses showed abnormally high silicon levels in the samples, confirming that the unknown compound(s) contained silicon. DMSD was then synthesized to confirm the identification and provide a standard to develop a calibration curve. Further confirmation was provided by external direct analysis in real time time of flight (DART TOF) mass spectrometry. To routinely test for DMSD in the future, a quantitative method was needed. A preliminary GC/MS method was developed and archived samples from various locations on ISS were analyzed to determine the extent of the contamination and provide data for troubleshooting. This paper describes these events in more detail as well as problems encountered in routine GC/MS analyses and the subsequent development of high performance liquid chromatography and LC/MS/MS methods for measuring DMSD.

BRAFV600E mutation in the diagnosis of unicystic ameloblastoma.

PubMed

Pereira, Núbia Braga; Pereira, Karuza Maria Alves; Coura, Bruna Pizziolo; Diniz, Marina Gonçalves; de Castro, Wagner Henriques; Gomes, Carolina Cavalieri; Gomez, Ricardo Santiago

2016-11-01

Unicystic ameloblastoma, an odontogenic neoplasm, presents clinical and radiographic similarities with dentigerous and radicular cysts, non-neoplastic lesions. It is not always possible to reach a final diagnosis with the incisional biopsy, leading to inappropriate treatment. The BRAFV600E activating mutation has been reported in a high proportion of ameloblastomas. The purpose of the study was to assess the utility of the detection of the BRAFV600E mutation in the differential diagnosis of unicystic ameloblastoma with dentigerous and radicular cysts. Twenty-six archival samples were included, comprising eight unicystic ameloblastomas (UAs), nine dentigerous and nine radicular cysts. The mutation was assessed in all samples by anti-BRAFV600E (clone VE1) immunohistochemistry (IHC) and by TaqMan mutation detection qPCR assay. Sanger sequencing was further carried out when samples showed conflicting results in the IHC and qPCR. Although all UAs (8/8) showed positive uniform BRAFV600E staining along the epithelial lining length, the mutation was not confirmed by qPCR and Sanger sequencing in three samples. Positive staining for the BRAFV600E protein was observed in one dentigerous cyst, but it was not confirmed by the molecular methods. Furthermore, 2/9 dentigerous cysts and 2/9 radicular cysts showed non-specific immunostaining of the epithelium or plasma cells. None of the dentigerous or radicular cysts cases presented the BRAFV600E mutation in the qPCR assay. The BRAFV600E antibody (clone VE1) IHC may show non-specific staining, but molecular assays may be useful for the diagnosis of unicystic ameloblastoma, in conjunction with clinical, radiological and histopathological features. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Opioid Concentrations in Oral Fluid and Plasma in Cancer Patients With Pain.

PubMed

Heiskanen, Tarja; Langel, Kaarina; Gunnar, Teemu; Lillsunde, Pirjo; Kalso, Eija A

2015-10-01

Measuring opioid concentrations in pain treatment is warranted in situations where optimal opioid analgesia is difficult to reach. To assess the usefulness of oral fluid (OFL) as an alternative to plasma in opioid concentration monitoring in cancer patients on chronic opioid therapy. We collected OFL and plasma samples from 64 cancer patients on controlled-release (CR) oral morphine, CR oral oxycodone, or transdermal (TD) fentanyl for pain. Samples were obtained on up to five separate days. A total of 213 OFL and plasma samples were evaluable. All patients had detectable amounts of the CR or TD opioid in both plasma and OFL samples. The plasma concentrations of oxycodone and fentanyl (determination coefficient R(2) = 0.628 and 0.700, respectively), but not morphine (R(2) = 0.292), were moderately well correlated to the daily opioid doses. In contrast to morphine and fentanyl (mean OFL/plasma ratio 2.0 and 3.0, respectively), the OFL oxycodone concentrations were significantly higher than the respective plasma concentrations (mean OFL/plasma ratio 14.9). An active transporter could explain the much higher OFL vs. plasma concentrations of oxycodone compared with morphine and fentanyl. OFL analysis is well suited for detecting the studied opioids. For morphine and fentanyl, an approximation of the plasma opioid concentrations is obtainable, whereas for oxycodone, the OFL/plasma concentration relationship is too variable for reliable approximation results. Copyright © 2015 American Academy of Hospice and Palliative Medicine. Published by Elsevier Inc. All rights reserved.

Avian plasma chemistry analysis using diluted samples.

PubMed

Waldoch, Jennifer; Wack, Raymund; Christopher, Mary

2009-12-01

Clinical chemistry tests are essential for the diagnosis and monitoring of disease in birds. The small volume of blood that can be obtained from many avian species limits the use of routine in-house chemistry analyzers. The aim of this study was to examine the accuracy and precision of avian plasma chemistry values obtained by use of a benchtop analyzer in samples diluted with sterile water, as compared with undiluted samples. Whole blood samples were collected from 13 clinically healthy thick-billed parrots (Rhynchopsitta pachyrhyncha). The samples were placed in lithium heparin tubes and centrifuged and the plasma decanted. One aliquot was analyzed immediately using a VetScan benchtop analyzer with an avian-reptile-specific rotor that included 12 analytes. The remainder of the plasma was divided into two aliquots and stored at -80 degrees C until analysis. One of these aliquots was diluted 1:1, 1:1.5, 1:2, and 1:2.5 with sterile water to give final dilutions of 1:2, 1:2.5, 1:3, and 1:3.5, respectively. The other aliquot was pooled with the 12 other samples to create a plasma pool. The undiluted plasma pool and two final dilutions (1:2 and 1:3) of the pooled plasma were analyzed in replicate (n = 20) to determine intra- and interassay imprecision. Each dilution was analyzed using the avian-reptile rotor and the results multiplied by the appropriate dilution factor to obtain the final result. Significant differences were observed in clinical chemistry results obtained from diluted plasma samples for all analytes except aspartate aminotransferase, creatine kinase, and glucose. Uric acid concentration was not significantly different at dilutions of up to 1:3. Bile acids, globulins, and sodium concentrations were below the limit of detection in all diluted samples and were not statistically analyzed. Based on these results, dilution with sterile water is not recommended for biochemical analysis of avian plasma using the VetScan benchtop analyzer.

Multiplex picodroplet digital PCR to detect KRAS mutations in circulating DNA from the plasma of colorectal cancer patients.

PubMed

Taly, Valerie; Pekin, Deniz; Benhaim, Leonor; Kotsopoulos, Steve K; Le Corre, Delphine; Li, Xinyu; Atochin, Ivan; Link, Darren R; Griffiths, Andrew D; Pallier, Karine; Blons, Hélène; Bouché, Olivier; Landi, Bruno; Hutchison, J Brian; Laurent-Puig, Pierre

2013-12-01

Multiplex digital PCR (dPCR) enables noninvasive and sensitive detection of circulating tumor DNA with performance unachievable by current molecular-detection approaches. Furthermore, picodroplet dPCR facilitates simultaneous screening for multiple mutations from the same sample. We investigated the utility of multiplex dPCR to screen for the 7 most common mutations in codons 12 and 13 of the KRAS (Kirsten rat sarcoma viral oncogene homolog) oncogene from plasma samples of patients with metastatic colorectal cancer. Fifty plasma samples were tested from patients for whom the primary tumor biopsy tissue DNA had been characterized by quantitative PCR. Tumor characterization revealed that 19 patient tumors had KRAS mutations. Multiplex dPCR analysis of the plasma DNA prepared from these samples identified 14 samples that matched the mutation identified in the tumor, 1 sample contained a different KRAS mutation, and 4 samples had no detectable mutation. Among the tumor samples that were wild type for KRAS, 2 KRAS mutations were identified in the corresponding plasma samples. Duplex dPCR (i.e., wild-type and single-mutation assay) was also used to analyze plasma samples from patients with KRAS-mutated tumors and 5 samples expected to contain the BRAF (v-raf murine sarcoma viral oncogene homolog B) V600E mutation. The results for the duplex analysis matched those for the multiplex analysis for KRAS-mutated samples and, owing to its higher sensitivity, enabled detection of 2 additional samples with low levels of KRAS-mutated DNA. All 5 samples with BRAF mutations were detected. This work demonstrates the clinical utility of multiplex dPCR to screen for multiple mutations simultaneously with a sensitivity sufficient to detect mutations in circulating DNA obtained by noninvasive blood collection.

Quantitative determination of metformin, glyburide and its metabolites in plasma and urine of pregnant patients by LC-MS/MS.

PubMed

Zhang, Xing; Wang, Xiaoming; Vernikovskaya, Daria I; Fokina, Valentina M; Nanovskaya, Tatiana N; Hankins, Gary D V; Ahmed, Mahmoud S

2015-04-01

This report describes the development and validation of an LC-MS/MS method for the quantitative determination of glyburide (GLB), its five metabolites (M1, M2a, M2b, M3 and M4) and metformin (MET) in plasma and urine of pregnant patients under treatment with a combination of the two medications. The extraction recovery of the analytes from plasma samples was 87-99%, and that from urine samples was 85-95%. The differences in retention times among the analytes and the wide range of the concentrations of the medications and their metabolites in plasma and urine patient samples required the development of three LC methods. The lower limit of quantitation (LLOQ) of the analytes in plasma samples was as follows: GLB, 1.02 ng/mL; its five metabolites, 0.100-0.113 ng/mL; and MET, 4.95 ng/mL. The LLOQ in urine samples was 0.0594 ng/mL for GLB, 0.984-1.02 ng/mL for its five metabolites and 30.0 µg/mL for MET. The relative deviation of this method was <14% for intra-day and inter-day assays in plasma and urine samples, and the accuracy was 86-114% in plasma, and 94-105% in urine. The method described in this report was successfully utilized for determining the concentrations of the two medications in patient plasma and urine. Copyright © 2014 John Wiley & Sons, Ltd.

Quantitative determination of metformin, glyburide and its metabolites in plasma and urine of pregnant patients by LC-MS/MS

PubMed Central

Zhang, Xing; Wang, Xiaoming; Vernikovskaya, Daria I.; Fokina, Valentina M.; Nanovskaya, Tatiana N.; Hankins, Gary D.V.; Ahmed, Mahmoud S.

2014-01-01

This report describes the development and validation of an LC-MS/MS method for the quantitative determination of glyburide (GLB), its five metabolites (M1, M2a, M2b, M3, and M4) and metformin (MET) in plasma and urine of pregnant patients under treatment with a combination of the two medications. The extraction recovery of the analytes from plasma samples ranged between 87% and 99%, and 85%–95% for urine samples. The differences in retention times among the analytes, and the wide range of the concentrations of the medications and their metabolites in plasma and urine patient samples required the development of three LC methods. The lower limit of quantitation (LLOQ) of the analytes in plasma samples was as follows: GLB, 1.02 ng/mL; its five metabolites, 0.100–0.113 ng/mL and 4.95 ng/mL for MET. LLOQ in urine samples was 0.0594 ng/mL for GLB, 0.984–1.02 ng/mL for its five metabolites and 30.0 μg/mL for MET. The relative deviation of this method was < 14% for intra-day and inter-day assays in plasma and urine samples, and the accuracy ranged between 86% and 114% in plasma, and 94% to 105% in urine. The method described in this report was successfully utilized for determining the concentrations of the two medications in patient plasma and urine. PMID:25164921

Matrix-Assisted Plasma Atomization Emission Spectrometry for Surface Sampling Elemental Analysis

PubMed Central

Yuan, Xin; Zhan, Xuefang; Li, Xuemei; Zhao, Zhongjun; Duan, Yixiang

2016-01-01

An innovative technology has been developed involving a simple and sensitive optical spectrometric method termed matrix-assisted plasma atomization emission spectrometry (MAPAES) for surface sampling elemental analysis using a piece of filter paper (FP) for sample introduction. MAPAES was carried out by direct interaction of the plasma tail plume with the matrix surface. The FP absorbs energy from the plasma source and releases combustion heating to the analytes originally present on its surface, thus to promote the atomization and excitation process. The matrix-assisted plasma atomization excitation phenomenon was observed for multiple elements. The FP matrix served as the partial energy producer and also the sample substrate to adsorb sample solution. Qualitative and quantitative determinations of metal ions were achieved by atomic emission measurements for elements Ba, Cu, Eu, In, Mn, Ni, Rh and Y. The detection limits were down to pg level with linear correlation coefficients better than 0.99. The proposed MAPAES provides a new way for atomic spectrometry which offers advantages of fast analysis speed, little sample consumption, less sample pretreatment, small size, and cost-effective. PMID:26762972

Stable Water Isotope Climate Archives in Springs from the Olympic Mountains, Washington

EPA Science Inventory

The ¹⁸O and ²H (HDO) compositions are summarized for sampled springs (n = 81) within the Elwha watershed (≈ 692 km²) on the northern Olympic Peninsula. Samples, collected during 2001–2009, of springs (n = 158), precipitation (n = 520), streams (n...

The possible role of soils in the global cycling of PCBs

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

Lead, W.A.; Jones, K.C.; Steinnes, E.

Archived soil and humus samples collected between 1950 and 1974 from 50 remote sites across the U.K. have been analyzed for a range of PCB congeners. The same sites have been revisited and contemporary samples taken. Results show increasing {Sigma}PCB concentrations up until the late 1960s after which there has been a dramatic reduction in the soil {Sigma}PCB concentration. These trends are indicative of the changes in use of these compounds over time. There are also temporal changes in the congener profiles, with the percentage contribution of the heavier homologue groups (hepta and octa -chlorinated) increasing. Samples of contemporary humusmore » from 12 rural Norwegian sites have also been screened for a range of congeners and the results compared with those of the U.K. soils and humus samples. Results for the Norway/U.K. comparison and the trends in the congener profiles for the archived/contemporary soil comparison suggest that PCBs are volatilizing from temperate areas and undergoing long range transport and subsequent global fractionation.« less

Device and method for automated separation of a sample of whole blood into aliquots

DOEpatents

Burtis, Carl A.; Johnson, Wayne F.

1989-01-01

A device and a method for automated processing and separation of an unmeasured sample of whole blood into multiple aliquots of plasma. Capillaries are radially oriented on a rotor, with the rotor defining a sample chamber, transfer channels, overflow chamber, overflow channel, vent channel, cell chambers, and processing chambers. A sample of whole blood is placed in the sample chamber, and when the rotor is rotated, the blood moves outward through the transfer channels to the processing chambers where the blood is centrifugally separated into a solid cellular component and a liquid plasma component. When the rotor speed is decreased, the plasma component backfills the capillaries resulting in uniform aliquots of plasma which may be used for subsequent analytical procedures.

Novel Insight for Organic Matter Sourcing: Interest of Time Resolved Fluorescence to Qualify and Quantify PAH Content of Solid Matrix at High Resolution

NASA Astrophysics Data System (ADS)

Quiers, M.; Perrette, Y.; Jacq, K.; Pousset, E.; Plassart, G.

2017-12-01

OM fluorescence is today a well-developed tool used to characterize and quantify organic matter (OM), but also to evaluate and discriminate OM fate and changes related to climate and environmental modifications. While fluorescence measurements on water and soils extracts provide information about organic fluxes today, solid phase fluorescence using natural archives allows to obtain high resolution records of OM evolution during time. These evolutions can be discussed in regards of climate and environmental perturbations detected in archives using different proxies, and thus provide keys for understanding factors driving carbon fluxes mechanisms. Among fluorescent organic species, Polycyclic Aromatic Hydrocarbons (PAH) have been used as probe molecules for organic contamination tracking. Moreover, monitoring studies have shown that PAH could also be used as markers to discriminates atmospheric and erosion factors leading to PAH and organic matter fluxes to the aquifer. PAH records in soils and natural archives appear as a promising proxy to follow both past atmospheric contamination and soil erosion. But, PAH fluorescence is difficult to discriminate from bulk OM fluorescence using steady-state fluorescence (SSF) technics as their fluorescence domains recover. Time resolved emission spectroscopy (TRES) increases the information provided by SSF technic, adding a time dimension to measurements and allowing to discriminate PAH fluorescence. We report here a first application of this technic on natural archives. The challenge is to obtain TRES signature along the sample, including for low PAH concentrations. This study aims to evaluate the reliability of high resolution TRES measurement as PAH carbon fluxes sources. Method is based on LIF instrument for solid phase fluorescence measurement. An instrument coupling an excitation system constituting by 2 pulsed lasers (266 and 355 nm) and a detection system was developed. This measurement provides high resolution record of PAH fluorescence. Preliminary results on stalagmite samples, lake sediments and soils will be reported. PAH content variations along the sample were compared with PAH concentration and with bulk OM content deduced from SSF records. The accuracy of the PAH fluorescence as source marker of fluxes will be discussed for each type of sample.

Improved method for analysis of RNA present in long-term preserved thyroid cancer tissue of atomic bomb survivors.

PubMed

Hamatani, Kiyohiro; Eguchi, Hidetaka; Mukai, Mayumi; Koyama, Kazuaki; Taga, Masataka; Ito, Reiko; Hayashi, Yuzo; Nakachi, Kei

2010-01-01

Since many thyroid cancer tissue samples from atomic bomb (A-bomb) survivors have been preserved for several decades as unbuffered formalin-fixed, paraffin-embedded specimens, molecular oncological analysis of such archival specimens is indispensable for clarifying the mechanisms of thyroid carcinogenesis in A-bomb survivors. Although RET gene rearrangements are the most important targets, it is a difficult task to examine all of the 13 known types of RET gene rearrangements with the use of the limited quantity of RNA that has been extracted from invaluable paraffin-embedded tissue specimens of A-bomb survivors. In this study, we established an improved 5' rapid amplification of cDNA ends (RACE) method using a small amount of RNA extracted from archival thyroid cancer tissue specimens. Three archival thyroid cancer tissue specimens from three different patients were used as in-house controls to determine the conditions for an improved switching mechanism at 5' end of RNA transcript (SMART) RACE method; one tissue specimen with RET/PTC1 rearrangement and one with RET/PTC3 rearrangement were used as positive samples. One other specimen, used as a negative sample, revealed no detectable expression of the RET gene tyrosine kinase domain. We established a 5' RACE method using an amount of RNA as small as 10 ng extracted from long-term preserved, unbuffered formalin-fixed, paraffin-embedded thyroid cancer tissue by application of SMART technology. This improved SMART RACE method not only identified common RET gene rearrangements, but also isolated a clone containing a 93-bp insert of rare RTE/PTC8 in RNA extracted from formalin-fixed, paraffin-embedded thyroid cancer specimens from one A-bomb survivor who had been exposed to a high radiation dose. In addition, in the papillary thyroid cancer of another high-dose A-bomb survivor, this method detected one novel type of RET gene rearrangement whose partner gene is acyl coenzyme A binding domain 5, located on chromosome 10p. We conclude that our improved SMART RACE method is expected to prove useful in molecular analyses using archival formalin-fixed, paraffin-embedded tissue samples of limited quantity.

Temporal stability and rates of post-depositional change in geochemical signatures of brown trout Salmo trutta scales.

PubMed

Ryan, D; Shephard, S; Kelly, F L

2016-09-01

This study investigates temporal stability in the scale microchemistry of brown trout Salmo trutta in feeder streams of a large heterogeneous lake catchment and rates of change after migration into the lake. Laser-ablation inductively coupled plasma mass spectrometry was used to quantify the elemental concentrations of Na, Mg, Mn, Cu, Zn, Ba and Sr in archived (1997-2002) scales of juvenile S. trutta collected from six major feeder streams of Lough Mask, County Mayo, Ireland. Water-element Ca ratios within these streams were determined for the fish sampling period and for a later period (2013-2015). Salmo trutta scale Sr and Ba concentrations were significantly (P < 0·05) correlated with stream water sample Sr:Ca and Ba:Ca ratios respectively from both periods, indicating multi-annual stability in scale and water-elemental signatures. Discriminant analysis of scale chemistries correctly classified 91% of sampled juvenile S. trutta to their stream of origin using a cross-validated classification model. This model was used to test whether assumed post-depositional change in scale element concentrations reduced correct natal stream classification of S. trutta in successive years after migration into Lough Mask. Fish residing in the lake for 1-3 years could be reliably classified to their most likely natal stream, but the probability of correct classification diminished strongly with longer lake residence. Use of scale chemistry to identify natal streams of lake S. trutta should focus on recent migrants, but may not require contemporary water chemistry data. © 2016 The Fisheries Society of the British Isles.

Comparison of plasma ctDNA and tissue/cytology-based techniques for the detection of EGFR mutation status in advanced NSCLC: Spanish data subset from ASSESS.

PubMed

Arriola, E; Paredes-Lario, A; García-Gomez, R; Diz-Tain, P; Constenla, M; García-Girón, C; Márquez, G; Reck, M; López-Vivanco, G

2018-04-05

The analysis of epidermal growth factor receptor (EGFR) mutations in many patients with advanced non-small-cell lung cancer (aNSCLC) has provided the opportunity for successful treatment with specific, targeted EGFR tyrosine kinase inhibitors. However, this therapeutic decision may be challenging when insufficient tumor tissue is available for EGFR mutation testing. Therefore, blood surrogate samples for EGFR mutation analysis have been suggested. Data were collected from the Spanish cohort of patients in the large, non-interventional, diagnostic ASSESS study (NCT01785888) evaluating the utility of circulating free tumor-derived DNA from plasma for EGFR mutation testing. The incidence of EGFR mutation in Spain and the level of concordance between matched tissue/cytology and plasma samples were evaluated. In a cohort of 154 eligible patients, EGFR mutations were identified in 15.1 and 11.0% of tumor and plasma samples, respectively. The most commonly used EGFR mutation testing method for the tumor tissue samples was the QIAGEN Therascreen ® EGFR RGQ PCR kit (52.1%). Fragment Length Analysis + PNA LNA Clamp was used for the plasma samples. The concordance rate for EGFR mutation status between the tissue/cytology and plasma samples was 88.8%; the sensitivity was 45.5%, and the specificity was 96.7%. The high concordance between the different DNA sources for EGFR mutation testing supports the use of plasma samples when tumor tissue is unavailable.

Manual modification and plasma exposure of boron nitride ceramic to study Hall effect thruster plasma channel material erosion

NASA Astrophysics Data System (ADS)

Satonik, Alexander J.

Worn Hall effect thrusters (HET) show a variety of unique microstructures and elemental compositions in the boron nitride thruster channel walls. Worn thruster channels are typically created by running test thrusters in vacuum chambers for hundreds of hours. Studies were undertaken to manually modify samples of boron nitride without the use of a hall effect thruster. Samples were manually abraded with an abrasive blaster and sandpaper, in addition to a vacuum heater. Some of these samples were further exposed to a xenon plasma in a magnetron sputter device. Sandpaper and abrasive blaster tests were used to modify surface roughness values of the samples from 10,000 A to 150,000 A, matching worn thruster values. Vacuum heat treatments were performed on samples. These treatments showed the ability to modify chemical compositions of boron nitride samples, but not in a manner matching changes seen in worn thruster channels. Plasma erosion rate was shown to depend on the grade of the BN ceramic and the preparation of the surface prior to plasma exposure. Abraded samples were shown to erode 43% more than their pristine counterparts. Unique surface features and elemental compositions on the worn thruster channel samples were overwritten by new surface features on the ceramic grains. The microscope images of the ceramic surface show that the magnetron plasma source rounded the edges of the ceramic grains to closely match the worn HET surface. This effect was not as pronounced in studies of ion beam bombardment of the surface and appears to be a result of the quasi-neutral plasma environment.

Overview of diagnostic implementation on Proto-MPEX at ORNL

NASA Astrophysics Data System (ADS)

Biewer, T. M.; Bigelow, T.; Caughman, J. B. O.; Fehling, D.; Goulding, R. H.; Gray, T. K.; Isler, R. C.; Martin, E. H.; Meitner, S.; Rapp, J.; Unterberg, E. A.; Dhaliwal, R. S.; Donovan, D.; Kafle, N.; Ray, H.; Shaw, G. C.; Showers, M.; Mosby, R.; Skeen, C.

2015-11-01

The Prototype Material Plasma Exposure eXperiment (Proto-MPEX) recently began operating with an expanded diagnostic set. Approximately 100 sightlines have been established, delivering the plasma light emission to a ``patch panel'' in the diagnostic room for distribution to a variety of instruments: narrow-band filter spectroscopy, Doppler spectroscopy, laser induced breakdown spectroscopy, optical emission spectroscopy, and Thomson scattering. Additional diagnostic systems include: IR camera imaging, in-vessel thermocouples, ex-vessel fluoroptic probes, fast pressure gauges, visible camera imaging, microwave interferometry, a retarding-field energy analyzer, rf-compensated and ``double'' Langmuir probes, and B-dot probes. A data collection and archival system has been initiated using the MDSplus format. This effort capitalizes on a combination of new and legacy diagnostic hardware at ORNL and was accomplished largely through student labor. This work was supported by the US. D.O.E. contract DE-AC05-00OR22725.

The Atmospheric Dynamics of alpha Tau (K5 III) - Clues to Understanding the Magnetic Dynamo in Late-Type Giant Stars

NASA Technical Reports Server (NTRS)

Carpenter, Kenneth G.; Airapetian, Vladimir

2008-01-01

Using HST/GHRS, HST/STIS and FUSE archival data for alpha Tau and the CHIANTI spectroscopic code, we have derived line shifts, volumetric emission measures, and plasma density estimates, and calculated filling factors for a number of UV lines forming between 10,000 K and 300,000 K in the outer atmosphere of this red giant star. The data suggest the presence of low-temperature extended regions and high-temperature compact regions, associated with magnetically open and closed structures in the stellar atmosphere, respectively. The signatures of UV lines from alpha Tau can be consistently understood via a model of upward-traveling Alfven waves in a gravitationally stratified atmosphere. These waves cause non-thermal broadening in UV lines due to unresolved wave motions and downward plasma motions in compact magnetic loops heated by resonant Alfven wave heating.

The Atmospheric Dynamics of Alpha Tau (K5 III) - Clues to Understanding the Magnetic Dynamo in Late-Type Giant Stars

NASA Technical Reports Server (NTRS)

Carpenter, Kenneth G.; Airapetian, Vladimir

2008-01-01

Using HST/GHRS, HST/STIS and FUSE archival data for a Tau and the CHIANTI spectroscopic code, we have derived line shifts, volumetric emission measures, and plasma density estimates, and calculated filling factors for a number of UV lines forming between 10,000 K and 300,000 K in the outer atmosphere of this red giant star. The data suggest the presence of low-temperature extended regions and high-temperature compact regions, associated with magnetically open and closed structures in the stellar atmosphere, respectively. The signatures of UV lines from a Tau can be consistently understood via a model of upward-traveling Alfv6n waves in a gravitationally stratified atmosphere. These waves cause nonthermal broadening in UV lines due to unresolved wave motions and downward plasma motions in compact magnetic loops heated by resonant Alfven wave heating.

Closed inductively coupled plasma cell

DOEpatents

Manning, T.J.; Palmer, B.A.; Hof, D.E.

1990-11-06

A closed inductively coupled plasma cell generates a relatively high power, low noise plasma for use in spectroscopic studies is disclosed. A variety of gases can be selected to form the plasma to minimize spectroscopic interference and to provide a electron density and temperature range for the sample to be analyzed. Grounded conductors are placed at the tube ends and axially displaced from the inductive coil, whereby the resulting electromagnetic field acts to elongate the plasma in the tube. Sample materials can be injected in the plasma to be excited for spectroscopy. 1 fig.

Whole Transcriptome Sequencing Enables Discovery and Analysis of Viruses in Archived Primary Central Nervous System Lymphomas

PubMed Central

DeBoever, Christopher; Reid, Erin G.; Smith, Erin N.; Wang, Xiaoyun; Dumaop, Wilmar; Harismendy, Olivier; Carson, Dennis; Richman, Douglas; Masliah, Eliezer; Frazer, Kelly A.

2013-01-01

Primary central nervous system lymphomas (PCNSL) have a dramatically increased prevalence among persons living with AIDS and are known to be associated with human Epstein Barr virus (EBV) infection. Previous work suggests that in some cases, co-infection with other viruses may be important for PCNSL pathogenesis. Viral transcription in tumor samples can be measured using next generation transcriptome sequencing. We demonstrate the ability of transcriptome sequencing to identify viruses, characterize viral expression, and identify viral variants by sequencing four archived AIDS-related PCNSL tissue samples and analyzing raw sequencing reads. EBV was detected in all four PCNSL samples and cytomegalovirus (CMV), JC polyomavirus (JCV), and HIV were also discovered, consistent with clinical diagnoses. CMV was found to express three long non-coding RNAs recently reported as expressed during active infection. Single nucleotide variants were observed in each of the viruses observed and three indels were found in CMV. No viruses were found in several control tumor types including 32 diffuse large B-cell lymphoma samples. This study demonstrates the ability of next generation transcriptome sequencing to accurately identify viruses, including DNA viruses, in solid human cancer tissue samples. PMID:24023918

Sample Preparation Report of the Fourth OPCW Confidence Building Exercise on Biomedical Sample Analysis

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

Udey, R. N.; Corzett, T. H.; Alcaraz, A.

Following the successful completion of the 3rd biomedical confidence building exercise (February 2013 – March 2013), which included the analysis of plasma and urine samples spiked at low ppb levels as part of the exercise scenario, another confidence building exercise was targeted to be conducted in 2014. In this 4th exercise, it was desired to focus specifically on the analysis of plasma samples. The scenario was designed as an investigation of an alleged use of chemical weapons where plasma samples were collected, as plasma has been reported to contain CWA adducts which remain present in the human body for severalmore » weeks (Solano et al. 2008). In the 3rd exercise most participants used the fluoride regeneration method to analyze for the presence of nerve agents in plasma samples. For the 4th biomedical exercise it was decided to evaluate the analysis of human plasma samples for the presence/absence of the VX adducts and aged adducts to blood proteins (e.g., VX-butyrylcholinesterase (BuChE) and aged BuChE adducts using a pepsin digest technique to yield nonapeptides; or equivalent). As the aging of VX-BuChE adducts is relatively slow (t1/2 = 77 hr at 37 °C [Aurbek et al. 2009]), soman (GD), which ages much more quickly (t1/2 = 9 min at 37 °C [Masson et al. 2010]), was used to simulate an aged VX sample. Additional objectives of this exercise included having laboratories assess novel OP-adducted plasma sample preparation techniques and analytical instrumentation methodologies, as well as refining/designating the reporting formats for these new techniques.« less

Differential Contributions of Intrinsic and Extrinsic Pathways to Thrombin Generation in Adult, Maternal and Cord Plasma Samples

PubMed Central

Rice, Nicklaus T.; Szlam, Fania; Varner, Jeffrey D.; Bernstein, Peter S.; Szlam, Arthur D.; Tanaka, Kenichi A.

2016-01-01

Background Thrombin generation (TG) is a pivotal process in achieving hemostasis. Coagulation profiles during pregnancy and early neonatal period are different from that of normal (non-pregnant) adults. In this ex vivo study, the differences in TG in maternal and cord plasma relative to normal adult plasma were studied. Methods Twenty consented pregnant women and ten consented healthy adults were included in the study. Maternal and cord blood samples were collected at the time of delivery. Platelet-poor plasma was isolated for the measurement of TG. In some samples, anti-FIXa aptamer, RB006, or a TFPI inhibitor, BAX499 were added to elucidate the contribution of intrinsic and extrinsic pathway to TG. Additionally, procoagulant and inhibitor levels were measured in maternal and cord plasma, and these values were used to mathematically simulate TG. Results Peak TG was increased in maternal plasma (393.6±57.9 nM) compared to adult and cord samples (323.2±38.9 nM and 209.9±29.5 nM, respectively). Inhibitory effects of RB006 on TG were less robust in maternal or cord plasma (52% vs. 12% respectively) than in adult plasma (81%). Likewise the effectiveness of BAX499 as represented by the increase in peak TG was much greater in adult (21%) than in maternal (10%) or cord plasma (12%). Further, BAX499 was more effective in reversing RB006 in adult plasma than in maternal or cord plasma. Ex vivo data were reproducible with the results of the mathematical simulation of TG. Conclusion Normal parturient plasma shows a large intrinsic pathway reserve for TG compared to adult and cord plasma, while TG in cord plasma is sustained by extrinsic pathway, and low levels of TFPI and AT. PMID:27196067

Mass spectrometric identification of diagnostic markers for chronic prostatitis in seminal plasma by analysis of seminal plasma protein clinical samples.

PubMed

Rokka, A; Mehik, A; Tonttila, P; Vaarala, M

2017-08-15

There are few specific diagnostic markers for chronic prostatitis. Therefore, we used mass spectrometry to evaluate differences in seminal plasma protein expression among patients with prostatitis and young and middle-aged healthy controls. We analysed pooled seminal plasma protein samples from four prostatitis patients (two pools), three young controls (one pool), and three middle-aged controls (one pool). The samples were analysed by liquid chromatography-tandem mass spectrometry. Of the 349 proteins identified, 16 were differentially expressed between the two control pools. Five proteins were up- or down-regulated in both of the prostatitis pools compared to middle-aged controls but not between young and middle-aged pools. Progestagen-associated endometrial protein (PAEP) was over-expressed in prostatitis samples compared to young and middle-aged controls. Our findings and those of previous studies indicate that PAEP is a potential seminal plasma marker for chronic prostatitis. In conclusion, we found age-related changes in seminal plasma protein expression. PAEP expression in seminal plasma should be investigated further to evaluate its potential as a diagnostic marker for chronic prostatitis.

Base rate of performance invalidity among non-clinical undergraduate research participants.

PubMed

Silk-Eglit, Graham M; Stenclik, Jessica H; Gavett, Brandon E; Adams, Jason W; Lynch, Julie K; Mccaffrey, Robert J

2014-08-01

Neuropsychological research frequently uses non-clinical undergraduate participants to evaluate neuropsychological tests. However, a recent study by An and colleagues (2012, Archives of Clinical Neuropsychology, 27, 849-857) called into question that the extent to which the interpretation of these participants' performance on neuropsychological tests is valid. This study found that in a sample of 36 participants, 55.6% exhibited performance invalidity at an initial session and 30.8% exhibited performance invalidity at a follow-up session. The current study attempted to replicate these findings in a larger, more representative sample using a more rigorous methodology. Archival data from 133 non-clinical undergraduate research participants were analyzed. Participants were classified as performance invalid if they failed any one PVT. In the current sample, only 2.26% of participants exhibited performance invalidity. Thus, concerns regarding insufficient effort and performance invalidity when using undergraduate research participants appear to be overstated. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Persistence of perfluoroalkyl acid precursors in AFFF-impacted groundwater and soil.

PubMed

Houtz, Erika F; Higgins, Christopher P; Field, Jennifer A; Sedlak, David L

2013-08-06

Several classes of polyfluorinated chemicals that are potential precursors to the perfluorinated carboxylates and sulfonates are present in aqueous film-forming foams (AFFF). To assess the persistence of these AFFF-derived precursors, groundwater, soil, and aquifer solids were obtained in 2011 from an unlined firefighter training area at a U.S. Air Force Base where AFFF was regularly used between 1970 and 1990. To measure the total concentration of perfluorinated carboxylate and sulfonate precursors in archived AFFF formulations and AFFF-impacted environmental samples, a previously developed assay that uses hydroxyl radical to oxidize precursors to perfluorinated carboxylates was adapted for these media. This assay was employed along with direct measurement of 22 precursors found in AFFF and a suite of other poly- and perfluoroalkyl substances (PFASs). On a molar basis, precursors accounted for 41-100% of the total concentration of PFASs in archived AFFF formulations. In the training area, precursors measured by the oxidation assay accounted for an average of 23% and 28% of total PFASs (i.e., precursors and perfluorinated carboxylates and sulfonates) in groundwater and solids samples, respectively. One precursor in AFFF, perfluorohexane sulfonamide amine, was observed on several highly contaminated soil and aquifer solids samples, but no other precursors present in AFFF formulations were detected in any samples at this field site. Suspected intermediate transformation products of precursors in AFFF that were directly measured accounted for approximately half of the total precursor concentration in samples from the training site. The fraction of PFASs consisting of perfluorinated carboxylates and sulfonates was greater in groundwater and solid samples than in any archived AFFF formulations, suggesting that much of the mass of precursors released at the site was converted to perfluorinated carboxylates and sulfonates. The precursors that have persisted at this site may generate significant amounts of additional perfluorinated carboxylates and sulfonates upon remediation of contaminated groundwater or aquifer solids.

Increase in the energy absorption of pulsed plasma by the formation of tungsten nanostructure

NASA Astrophysics Data System (ADS)

Sato, D.; Ohno, N.; Domon, F.; Kajita, S.; Kikuchi, Y.; Sakuma, I.

2017-06-01

The synergistic effects of steady-state and pulsed plasma irradiation to material have been investigated in the device NAGDIS-PG (NAGoya DIvertor Simulator with Plasma Gun). The duration of the pulsed plasma was ~0.25 ms. To investigate the pulsed plasma heat load on the materials, we developed a temperature measurement system using radiation from the sample in a high time resolution. The heat deposited in response to the transient plasma on a tungsten surface was revealed by using this system. When the nanostructures were formed by helium plasma irradiation, the temperature increase on the bulk sample was enhanced. The result suggested that the amount of absorbed energy on the surface was increased by the formation of nanostructures. The possible mechanisms causing the phenomena are discussed with the calculation of a sample temperature in response to the transient heat load.

Interlaboratory trial for the measurement of total cobalt in equine urine and plasma by ICP-MS.

PubMed

Popot, Marie-Agnes; Ho, Emmie N M; Stojiljkovic, Natali; Bagilet, Florian; Remy, Pierre; Maciejewski, Pascal; Loup, Benoit; Chan, George H M; Hargrave, Sabine; Arthur, Rick M; Russo, Charlie; White, James; Hincks, Pamela; Pearce, Clive; Ganio, George; Zahra, Paul; Batty, David; Jarrett, Mark; Brooks, Lydia; Prescott, Lise-Anne; Bailly-Chouriberry, Ludovic; Bonnaire, Yves; Wan, Terence S M

2017-09-01

Cobalt is an essential mineral micronutrient and is regularly present in equine nutritional and feed supplements. Therefore, cobalt is naturally present at low concentrations in biological samples. The administration of cobalt chloride is considered to be blood doping and is thus prohibited. To control the misuse of cobalt, it was mandatory to establish an international threshold for cobalt in plasma and/or in urine. To achieve this goal, an international collaboration, consisting of an interlaboratory comparison between 5 laboratories for the urine study and 8 laboratories for the plasma study, has been undertaken. Quantification of cobalt in the biological samples was performed by inductively coupled plasma-mass spectrometry (ICP-MS). Ring tests were based on the analysis of 5 urine samples supplemented at concentrations ranging from 5 up to 500 ng/mL and 5 plasma samples spiked at concentrations ranging from 0.5 up to 25 ng/mL. The results obtained from the different laboratories were collected, compiled, and compared to assess the reproducibility and robustness of cobalt quantification measurements. The statistical approach for the ring test for total cobalt in urine was based on the determination of percentage deviations from the calculated means, while robust statistics based on the calculated median were applied to the ring test for total cobalt in plasma. The inter-laboratory comparisons in urine and in plasma were successful so that 97.6% of the urine samples and 97.5% of the plasma samples gave satisfactory results. Threshold values for cobalt in plasma and urine were established from data only obtained by laboratories involved in the ring test. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Effects of fusion relevant transient energetic radiation, plasma and thermal load on PLANSEE double forged tungsten samples in a low-energy plasma focus device

NASA Astrophysics Data System (ADS)

Javadi, S.; Ouyang, B.; Zhang, Z.; Ghoranneviss, M.; Salar Elahi, A.; Rawat, R. S.

2018-06-01

Tungsten is the leading candidate for plasma facing component (PFC) material for thermonuclear fusion reactors and various efforts are ongoing to evaluate its performance or response to intense fusion relevant radiation, plasma and thermal loads. This paper investigates the effects of hot dense decaying pinch plasma, highly energetic deuterium ions and fusion neutrons generated in a low-energy (3.0 kJ) plasma focus device on the structure, morphology and hardness of the PLANSEE double forged tungsten (W) samples surfaces. The tungsten samples were provided by Forschungszentrum Juelich (FZJ), Germany via International Atomic Energy Agency, Vienna, Austria. Tungsten samples were irradiated using different number of plasma focus (PF) shots (1, 5 and 10) at a fixed axial distance of 5 cm from the anode top and also at various distances from the top of the anode (5, 7, 9 and 11 cm) using fixed number (5) of plasma focus shots. The virgin tungsten sample had bcc structure (α-W phase). After PF irradiation, the XRD analysis showed (i) the presence of low intensity new diffraction peak corresponding to β-W phase at (211) crystalline plane indicating the partial structural phase transition in some of the samples, (ii) partial amorphization, and (iii) vacancy defects formation and compressive stress in irradiated tungsten samples. Field emission scanning electron microscopy showed the distinctive changes to non-uniform surface with nanometer sized particles and particle agglomerates along with large surface cracks at higher number of irradiation shots. X-ray photoelectron spectroscopy analysis demonstrated the reduction in relative tungsten oxide content and the increase in metallic tungsten after irradiation. Hardness of irradiated samples initially increased for one shot exposure due to reduction in tungsten oxide phase, but then decreased with increasing number of shots due to increasing concentration of defects. It is demonstrated that the plasma focus device provides appropriate intense fusion relevant pulses for testing the structural, morphological and mechanical changes on irradiated tungsten samples.

Influence of sample temperature on the expansion dynamics of laser-induced germanium plasma

NASA Astrophysics Data System (ADS)

Yang, LIU; Yue, TONG; Ying, WANG; Dan, ZHANG; Suyu, LI; Yuanfei, JIANG; Anmin, CHEN; Mingxing, JIN

2017-12-01

In this paper, we investigated the influence of sample temperature on the expansion dynamics and the optical emission spectroscopy of laser-induced plasma, and Ge was selected as the test sample. The target was heated from room temperature (22 °C) to 300 °C, and excited in atmospheric environment by using a Q-Switched Nd:YAG pulse laser with the wavelength of 1064 nm. To study the plasma expansion dynamics, we observed the plasma plume at different laser energies (5.0, 7.4 and 9.4 mJ) and different sample temperatures by using time-resolved image. We found that the heated target temperature could accelerate the expansion of plasma plume. Moreover, we also measured the effect of target temperature on the optical emission spectroscopy and signal-to-noise ratio.

Deactivation of Escherichia coli by the plasma needle

NASA Astrophysics Data System (ADS)

Sladek, R. E. J.; Stoffels, E.

2005-06-01

In this paper we present a parameter study on deactivation of Escherichia coli (E. coli) by means of a non-thermal plasma (plasma needle). The plasma needle is a small-sized (1 mm) atmospheric glow sustained by radio-frequency excitation. This plasma will be used to disinfect heat-sensitive objects; one of the intended applications is in vivo deactivation of dental bacteria: destruction of plaque and treatment of caries. We use E. coli films plated on agar dishes as a model system to optimize the conditions for bacterial destruction. Plasma power, treatment time and needle-to-sample distance are varied. Plasma treatment of E. coli films results in formation of a bacteria-free void with a size up to 12 mm. 104-105 colony forming units are already destroyed after 10 s of treatment. Prolongation of treatment time and usage of high powers do not significantly improve the destruction efficiency: short exposure at low plasma power is sufficient. Furthermore, we study the effects of temperature increase on the survival of E. coli and compare it with thermal effects of the plasma. The population of E. coli heated in a warm water bath starts to decrease at temperatures above 40°C. Sample temperature during plasma treatment has been monitored. The temperature can reach up to 60°C at high plasma powers and short needle-to-sample distances. However, thermal effects cannot account for bacterial destruction at low power conditions. For safe and efficient in vivo disinfection, the sample temperature should be kept low. Thus, plasma power and treatment time should not exceed 150 mW and 60 s, respectively.

Visualization tool for three-dimensional plasma velocity distributions (ISEE_3D) as a plug-in for SPEDAS

NASA Astrophysics Data System (ADS)

Keika, Kunihiro; Miyoshi, Yoshizumi; Machida, Shinobu; Ieda, Akimasa; Seki, Kanako; Hori, Tomoaki; Miyashita, Yukinaga; Shoji, Masafumi; Shinohara, Iku; Angelopoulos, Vassilis; Lewis, Jim W.; Flores, Aaron

2017-12-01

This paper introduces ISEE_3D, an interactive visualization tool for three-dimensional plasma velocity distribution functions, developed by the Institute for Space-Earth Environmental Research, Nagoya University, Japan. The tool provides a variety of methods to visualize the distribution function of space plasma: scatter, volume, and isosurface modes. The tool also has a wide range of functions, such as displaying magnetic field vectors and two-dimensional slices of distributions to facilitate extensive analysis. The coordinate transformation to the magnetic field coordinates is also implemented in the tool. The source codes of the tool are written as scripts of a widely used data analysis software language, Interactive Data Language, which has been widespread in the field of space physics and solar physics. The current version of the tool can be used for data files of the plasma distribution function from the Geotail satellite mission, which are publicly accessible through the Data Archives and Transmission System of the Institute of Space and Astronautical Science (ISAS)/Japan Aerospace Exploration Agency (JAXA). The tool is also available in the Space Physics Environment Data Analysis Software to visualize plasma data from the Magnetospheric Multiscale and the Time History of Events and Macroscale Interactions during Substorms missions. The tool is planned to be applied to data from other missions, such as Arase (ERG) and Van Allen Probes after replacing or adding data loading plug-ins. This visualization tool helps scientists understand the dynamics of space plasma better, particularly in the regions where the magnetohydrodynamic approximation is not valid, for example, the Earth's inner magnetosphere, magnetopause, bow shock, and plasma sheet.

Biomarkers for lymphoma

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

Zangar, Richard C.; Varnum, Susan M.

A biomarker, method, test kit, and diagnostic system for detecting the presence of lymphoma in a person are disclosed. The lymphoma may be Hodgkin's lymphoma or non-Hodgkin's lymphoma. The person may be a high-risk subject. In one embodiment, a plasma sample from a person is obtained. The level of at least one protein listed in Table S3 in the plasma sample is measured. The level of at least one protein in the plasma sample is compared with the level in a normal or healthy subject. The lymphoma is diagnosed based upon the level of the at least one protein inmore » the plasma sample in comparison to the normal or healthy level.« less

The Index to Marine and Lacustrine Geological Samples (IMLGS): Linking Digital Data to Physical Samples for the Marine Community

NASA Astrophysics Data System (ADS)

Stroker, K. J.; Jencks, J. H.; Eakins, B.

2016-12-01

The Index to Marine and Lacustrine Geological Samples (IMLGS) is a community designed and maintained resource enabling researchers to locate and request seafloor and lakebed geologic samples curated by partner institutions. The Index was conceived in the dawn of the digital age by representatives from U.S. academic and government marine core repositories and the NOAA National Geophysical Data Center, now the National Centers for Environmental Information (NCEI), at a 1977 meeting convened by the National Science Foundation (NSF). The Index is based on core concepts of community oversight, common vocabularies, consistent metadata and a shared interface. The Curators Consortium, international in scope, meets biennially to share ideas and discuss best practices. NCEI serves the group by providing database access and maintenance, a list server, digitizing support and long-term archival of sample metadata, data and imagery. Over three decades, participating curators have performed the laborious task of creating and contributing metadata for over 205,000 sea floor and lake-bed cores, grabs, and dredges archived in their collections. Some partners use the Index for primary web access to their collections while others use it to increase exposure of more in-depth institutional systems. The IMLGS has a persistent URL/Digital Object Identifier (DOI), as well as DOIs assigned to partner collections for citation and to provide a persistent link to curator collections. The Index is currently a geospatially-enabled relational database, publicly accessible via Web Feature and Web Map Services, and text- and ArcGIS map-based web interfaces. To provide as much knowledge as possible about each sample, the Index includes curatorial contact information and links to related data, information and images : 1) at participating institutions, 2) in the NCEI archive, and 3) through a Linked Data interface maintained by the Rolling Deck to Repository R2R. Over 43,000 International GeoSample Numbers (IGSNs) linking to the System for Earth Sample Registration (SESAR) are included in anticipation of opportunities for interconnectivity with Integrated Earth Data Applications (IEDA) systems. The paper will discuss the database with a goal to increase the connections and links to related data at partner institutions.

EGFR mutation status of paired cerebrospinal fluid and plasma samples in EGFR mutant non-small cell lung cancer with leptomeningeal metastases.

PubMed

Zhao, Jing; Ye, Xin; Xu, Yan; Chen, Minjiang; Zhong, Wei; Sun, Yun; Yang, Zhenfan; Zhu, Guanshan; Gu, Yi; Wang, Mengzhao

2016-12-01

Central nervous system (CNS) is the prevalent site for metastases in epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI)-relapsed NSCLC patients. To understand the EGFR mutation status in paired cerebrospinal fluid (CSF) and plasma samples after EGFR-TKI treatment failure might be useful to guide the treatment of intra- and extracranial tumors in those patients. Paired CSF and plasma samples were collected from seven NSCLC patients with CNS metastases after EGFR-TKI failure. EGFR mutations were tested by amplification refractory mutation system (ARMS) and droplet digital PCR (ddPCR) methods. Gefitinib concentrations were evaluated by high-performance liquid chromatography-mass spectrometry (HPLC-MS/MS). EGFR mutations were detected in all seven CSF samples, including three of E19-Del, three of L858R and one of E19-Del&T790M by both methods. On the other hand, majority of the matched plasma samples (5/7) were negative for EGFR mutations by both methods. The other two plasma samples were positive for E19-Del&T790M by ddPCR, and one of them had undetectable T790M by ARMS. Gefitinib concentration in CSF was much lower than that in plasma (mean CSF/plasma ratio: 1.8 %). After EGFR-TKI failure, majority of the NSCLC patients with CNS metastases remained positive detection of EGFR sensitive mutations in CSF, but much less detection in the matched plasma. Significantly low exposure of gefitinib in CSF might explain the intracranial protection of the EGFR sensitive mutation positive tumor cells.

Characterizing the X-ray Emission in Small Magellanic Cloud Supernova Remnants

NASA Astrophysics Data System (ADS)

Man, Nicole; Auchettl, Katie; Lopez, Laura

2018-01-01

The Small Magellanic Cloud is a close, metal-poor galaxy with active star formation, and it has a diverse population of 24 supernova remnants (SNRs) that have been identified at several wavelengths. Past work has characterized the X-ray emission in these sources separately and aimed to constrain their explosive origins from observations with Chandra and XMM-Newton. Three SNRs have possible evidence for Type Ia explosions based on strong Fe-L emission in their X-ray spectra, although the environments and intermediate-mass element abundances are more consistent with those of core-collapse SNe. In this poster, we analyze the archival Chandra and XMM-Newton observations of the SMC SNR sample, and we model the sources' X-ray spectra in a systematic way to derive the plasma properties and to constrain the nature of the explosions. In one SNR, we note the presence of an X-ray binary near the source's geometric center, suggesting the compact object was produced in the SN explosion. As one of only three SNRs known in the Local Group to host a binary system, this source is worthy of follow-up investigations to probe explosions of massive stars in binary systems.

Successful Application of Microarray Technology to Microdissected Formalin-Fixed, Paraffin-Embedded Tissue

PubMed Central

Coudry, Renata A.; Meireles, Sibele I.; Stoyanova, Radka; Cooper, Harry S.; Carpino, Alan; Wang, Xianqun; Engstrom, Paul F.; Clapper, Margie L.

2007-01-01

The establishment of a reliable method for using RNA from formalin-fixed, paraffin-embedded (FFPE) tissue would provide an opportunity to obtain novel gene expression data from the vast amounts of archived tissue. A custom-designed 22,000 oligonucleotide array was used in the present study to compare the gene expression profile of colonic epithelial cells isolated by laser capture microdissection from FFPE-archived samples with that of the same cell population from matched frozen samples, the preferred source of RNA. Total RNA was extracted from FFPE tissues, amplified, and labeled using the Paradise Reagent System. The quality of the input RNA was assessed by the Bioanalyzer profile, reverse transcriptase-polymerase chain reaction, and agarose gel electrophoresis. The results demonstrate that it is possible to obtain reliable microarray data from FFPE samples using RNA acquired by laser capture microdissection. The concordance between matched FFPE and frozen samples was evaluated and expressed as a Pearson’s correlation coefficient, with values ranging from 0.80 to 0.97. The presence of ribosomal RNA peaks in FFPE-derived RNA was reflected by a high correlation with paired frozen samples. A set of practical recommendations for evaluating the RNA integrity and quality in FFPE samples is reported. PMID:17251338

Auto-antibodies in prostate cancer: humoral immune response to antigenic determinants coded by the differentially expressed transcripts FLJ23438 and VAMP3.

PubMed

Pontes, E R; Matos, L C; da Silva, E A; Xavier, L S; Diaz, B L; Small, I A; Reis, E M; Verjovski-Almeida, S; Barcinski, M A; Gimba, E R P

2006-10-01

Here we evaluate auto-antibody response against two potential antigenic determinants of genes highly expressed in low Gleason Score prostate cancer (PC) tumor samples, namely FLJ23438 and VAMP3. RT-PCR assays were used to analyze mRNA expression profiles of FLJ23438 and VAMP3 transcripts. The auto-antibody response against FLJ23438 and VAMP3 recombinant proteins was tested by immunoblot assays using PC, benign prostate hyperplasia (BPH), healthy donors (HD), and other human cancers plasma samples. Our data showed that 37% (10/27) and 7.4% (2/27) of PC plasma samples presented auto-antibodies against FLJ23438 and VAMP3, respectively. Only 8.3% (1/12) of BPH plasma samples were reactive for both auto-antibodies, while none (0/12) of HD plasma samples tested were reactive. The prevalence of 37% of positive PC plasma samples for anti-FLJ23438 antibodies suggests that humoral immune response against this antigenic determinant could be a potential serum marker for this cancer. (c) 2006 Wiley-Liss, Inc.

Nanotribological response of a plasma nitrided bio-steel.

PubMed

Samanta, Aniruddha; Chakraborty, Himel; Bhattacharya, Manjima; Ghosh, Jiten; Sreemany, Monjoy; Bysakh, Sandip; Rane, Ramkrishna; Joseph, Alphonsa; Jhala, Ghanshyam; Mukherjee, Subroto; Das, Mitun; Mukhopadhyay, Anoop K

2017-01-01

AISI 316L is a well known biocompatible, austenitic stainless steel (SS). It is thus a bio-steel. Considering its importance as a bio-prosthesis material here we report the plasma nitriding of AISI 316L (SS) followed by its microstructural and nanotribological characterization. Plasma nitriding of the SS samples was carried out in a plasma reactor with a hot wall vacuum chamber. For ease of comparison these plasma nitrided samples were termed as SSPN. The experimental results confirmed the formations of an embedded nitrided metal layer zone (ENMLZ) and an interface zone (IZ) between the ENMLZ and the unnitrided bulk metallic layer zone (BMLZ) in the SSPN sample. These ENMLZ and IZ in the SSPN sample were richer in iron nitride (FeN) chromium nitride (CrN) along with the austenite phase. The results from nanoindentation, microscratch, nanoscratch and sliding wear studies confirmed that the static contact deformation resistance, the microwear, nanowear and sliding wear resistance of the SSPN samples were much better than those of the SS samples. These results were explained in terms of structure-property correlations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Feasibility of Using Convalescent Plasma Immunotherapy for MERS-CoV Infection, Saudi Arabia.

PubMed

Arabi, Yaseen M; Hajeer, Ali H; Luke, Thomas; Raviprakash, Kanakatte; Balkhy, Hanan; Johani, Sameera; Al-Dawood, Abdulaziz; Al-Qahtani, Saad; Al-Omari, Awad; Al-Hameed, Fahad; Hayden, Frederick G; Fowler, Robert; Bouchama, Abderrezak; Shindo, Nahoko; Al-Khairy, Khalid; Carson, Gail; Taha, Yusri; Sadat, Musharaf; Alahmadi, Mashail

2016-09-01

We explored the feasibility of collecting convalescent plasma for passive immunotherapy of Middle East respiratory syndrome coronavirus (MERS-CoV) infection by using ELISA to screen serum samples from 443 potential plasma donors: 196 patients with suspected or laboratory-confirmed MERS-CoV infection, 230 healthcare workers, and 17 household contacts exposed to MERS-CoV. ELISA-reactive samples were further tested by indirect fluorescent antibody and microneutralization assays. Of the 443 tested samples, 12 (2.7%) had a reactive ELISA result, and 9 of the 12 had reactive indirect fluorescent antibody and microneutralization assay titers. Undertaking clinical trials of convalescent plasma for passive immunotherapy of MERS-CoV infection may be feasible, but such trials would be challenging because of the small pool of potential donors with sufficiently high antibody titers. Alternative strategies to identify convalescent plasma donors with adequate antibody titers should be explored, including the sampling of serum from patients with more severe disease and sampling at earlier points during illness.

GC-MS and LC-MS analysis of nerve agents in body fluids: intra-laboratory verification test using spiked plasma and urine samples.

PubMed

Koller, Marianne; Becker, Christian; Thiermann, Horst; Worek, Franz

2010-05-15

The purpose of this study was to check the applicability of different analytical methods for the identification of unknown nerve agents in human body fluids. Plasma and urine samples were spiked with nerve agents (plasma) or with their metabolites (urine) or were left blank. Seven random samples (35% of all samples) were selected for the verification test. Plasma was worked up for unchanged nerve agents and for regenerated nerve agents after fluoride-induced reactivation of nerve agent-inhibited butyrylcholinesterase. Both extracts were analysed by GC-MS. Metabolites were extracted from plasma and urine, respectively, and were analysed by LC-MS. The urinary metabolites and two blank samples could be identified without further measurements, plasma metabolites and blanks were identified in six of seven samples. The analysis of unchanged nerve agent provided five agents/blanks and the sixth agent after further investigation. The determination of the regenerated agents also provided only five clear findings during the first screening because of a rather noisy baseline. Therefore, the sample preparation was extended by a size exclusion step performed before addition of fluoride which visibly reduced baseline noise and thus improved identification of the two missing agents. The test clearly showed that verification should be performed by analysing more than one biomarker to ensure identification of the agent(s). Copyright (c) 2010 Elsevier B.V. All rights reserved.

Structural Changes in the Vanadium Sample Surface Induced by Pulsed High-Temperature Deuterium Plasma and Deuterium Ion Fluxes

NASA Astrophysics Data System (ADS)

Borovitskaya, I. V.; Pimenov, V. N.; Gribkov, V. A.; Padukh, M.; Bondarenko, G. G.; Gaidar, A. I.; Paramonova, V. V.; Morozov, E. V.

2017-11-01

The structural changes in the vanadium sample surface are studied as functions of the conditions of irradiation by pulsed high-temperature deuterium plasma and deuterium ion fluxes in the Plasma Focus installation. It is found that processes of partial evaporation, melting, and crystallization of the surface layer of vanadium samples take place in the plasma flux power density range q = 108-1010 W/cm2 and the ion flux density range q = 1010-1012 W/cm2. The surface relief is wavelike. There are microcracks, gas-filled bubbles (blisters), and traces of fracture on the surface. The blisters are failed in the solid state. The character of blister fracture is similar to that observed during usual ion irradiation in accelerators. The samples irradiated at relatively low power density ( q = 107-108 W/cm2) demonstrate the ejection of microparticles (surface fragments) on the side facing plasma. This process is assumed to be due to the fact that the unloading wave formed in the sample-target volume reaches its irradiated surface. Under certain irradiation conditions (sample-anode distance, the number of plasma pulses), a block microstructure with block sizes of several tens of microns forms on the sample surfaces. This structure is likely to form via directional crack propagation upon cooling of a thin melted surface layer.

Comparison of digoxin concentration in plastic serum tubes with clot activator and heparinized plasma tubes.

PubMed

Dukić, Lora; Simundić, Ana-Maria; Malogorski, Davorin

2014-01-01

Sample type recommended by the manufacturer for the digoxin Abbott assay is either serum collected in glass tubes or plasma (sodium heparin, lithium heparin, citrate, EDTA or oxalate as anticoagulant) collected in plastic tubes. In our hospital samples are collected in plastic tubes. Our hypothesis was that the serum sample collected in plastic serum tube can be used interchangeably with plasma sample for measurement of digoxin concentration. Our aim was verification of plastic serum tubes for determination of digoxin concentration. Concentration of digoxin was determined simultaneously in 26 venous blood plasma (plastic Vacuette, LH Lithium heparin) and serum (plastic Vacuette, Z Serum Clot activator; both Greiner Bio-One GmbH, Kremsmünster, Austria) samples, on Abbott AxSYM analyzer using the original Abbott Digoxin III assay (Abbott, Wiesbaden, Germany). Tube comparability was assessed using the Passing Bablok regression and Bland-Altman plot. Serum and plasma digoxin concentrations are comparable. Passing Bablok intercept (0.08 [95% CI = -0.10 to 0.20]) and slope (0.99 [95% CI = 0.92 to 1.11]) showed there is no constant or proportional error. Blood samples drawn in plastic serum tubes and plastic plasma tubes can be interchangeably used for determination of digoxin concentration.

Comparison of digoxin concentration in plastic serum tubes with clot activator and heparinized plasma tubes

PubMed Central

Dukić, Lora; Šimundić, Ana-Maria; Malogorski, Davorin

2014-01-01

Introduction: Sample type recommended by the manufacturer for the digoxin Abbott assay is either serum collected in glass tubes or plasma (sodium heparin, lithium heparin, citrate, EDTA or oxalate as anticoagulant) collected in plastic tubes. In our hospital samples are collected in plastic tubes. Our hypothesis was that the serum sample collected in plastic serum tube can be used interchangeably with plasma sample for measurement of digoxin concentration. Our aim was verification of plastic serum tubes for determination of digoxin concentration. Materials and methods: Concentration of digoxin was determined simultaneously in 26 venous blood plasma (plastic Vacuette, LH Lithium heparin) and serum (plastic Vacuette, Z Serum Clot activator; both Greiner Bio-One GmbH, Kremsmünster, Austria) samples, on Abbott AxSYM analyzer using the original Abbott Digoxin III assay (Abbott, Wiesbaden, Germany). Tube comparability was assessed using the Passing Bablok regression and Bland-Altman plot. Results: Serum and plasma digoxin concentrations are comparable. Passing Bablok intercept (0.08 [95% CI = −0.10 to 0.20]) and slope (0.99 [95% CI = 0.92 to 1.11]) showed there is no constant or proportional error. Conclusion: Blood samples drawn in plastic serum tubes and plastic plasma tubes can be interchangeably used for determination of digoxin concentration. PMID:24627723

ctDNA Determination of EGFR Mutation Status in European and Japanese Patients with Advanced NSCLC: The ASSESS Study.

PubMed

Reck, Martin; Hagiwara, Koichi; Han, Baohui; Tjulandin, Sergei; Grohé, Christian; Yokoi, Takashi; Morabito, Alessandro; Novello, Silvia; Arriola, Edurne; Molinier, Olivier; McCormack, Rose; Ratcliffe, Marianne; Normanno, Nicola

2016-10-01

To offer patients with EGFR mutation-positive advanced NSCLC appropriate EGFR tyrosine kinase inhibitor treatment, mutation testing of tumor samples is required. However, tissue/cytologic samples are not always available or evaluable. The large, noninterventional diagnostic ASSESS study (NCT01785888) evaluated the utility of circulating free tumor-derived DNA (ctDNA) from plasma for EGFR mutation testing. ASSESS was conducted in 56 centers (in Europe and Japan). Eligible patients (with newly diagnosed locally advanced/metastatic treatment-naive advanced NSCLC) provided diagnostic tissue/cytologic and plasma samples. DNA extracted from tissue/cytologic samples was subjected to EGFR mutation testing using local practices; designated laboratories performed DNA extraction/mutation testing of blood samples. The primary end point was level of concordance of EGFR mutation status between matched tissue/cytologic and plasma samples. Of 1311 patients enrolled, 1288 were eligible. Concordance of mutation status in 1162 matched samples was 89% (sensitivity 46%, specificity 97%, positive predictive value 78%, and negative predictive value 90%). A group of 25 patients with apparent false-positive plasma results was overrepresented for cytologic samples, use of less sensitive tissue testing methodologies, and smoking habits associated with high EGFR mutation frequency, indicative of false-negative tumor results. In cases in which plasma and tumor samples were tested with identical highly sensitive methods, positive predictive value/sensitivity were generally improved. These real-world data suggest that ctDNA is a feasible sample for EGFR mutation analysis. It is important to conduct mutation testing of both tumor and plasma samples in specialized laboratories, using robust/sensitive methods to ensure that patients receive appropriate treatments that target the molecular features of their disease. Copyright © 2016 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.

Juvenile Delinquency Recidivism: Are Black and White Youth Vulnerable to the Same Risk Factors?

ERIC Educational Resources Information Center

Barrett, David E.; Katsiyannis, Antonis

2015-01-01

Using large-sample, archival data from the state of South Carolina's juvenile justice agency, we examine the question of race differences in predictors of repeat offending for a sample of approximately 100,000 youth who had been referred for criminal offenses. Independent variables relating to background, adverse parenting, mental health,…

Preparation of serum and plasma samples for determination of tricyclic antidepressants: effects of blood collection tubes and storage.

PubMed

Nyberg, G; Mårtensson, E

1986-01-01

The effects were tested of eight common types of blood collection tubes and two types of "plasma separators" on the stability of the tricyclic antidepressants amitriptyline, imipramine, clomipramine, and their monodemethylated metabolites in venous blood samples. Although EDTA-containing Venoject lavender and Vacutainer lavender tubes seemed to give the most stable plasma samples, and Venoject red the most stable serum samples, the differences were too small to have practical consequences. Vacutainer royal blue collection tubes gave significant losses of greater than 20% of some of the substances. The tubes with serum separator gel or filter proved unsuitable, since they were responsible for losses of greater than 40%. The losses were not caused by redistribution between blood cells and plasma but occurred mainly as a result of contact between the contents and the caps of the tubes. Experiments with freezing, thawing, and storage of samples showed that freshly sampled blood could be stored at room temperature for 24 h in Venoject green tubes without significant losses. Serum samples could be stored at refrigerator temperature for 4 weeks without important losses. Freezing, thawing, and storage at -20 degrees C did not influence the serum or plasma concentrations.

Preparation of magnetic ODS-PAN thin-films for microextraction of quetiapine and clozapine in plasma and urine samples followed by HPLC-UV detection.

PubMed

Li, Dan; Zou, Juan; Cai, Pei-Shan; Xiong, Chao-Mei; Ruan, Jin-Lan

2016-06-05

In this study, conventional thin-film microextraction (TFME) was endowed with magnetic by introducing superparamagnetic SiO2@Fe3O4 nanoparticles in thin-films. Novel magnetic octadecylsilane (ODS)-polyacrylonitrile (PAN) thin-films were prepared by spraying, and used for the microextraction of quetiapine and clozapine in plasma and urine samples, followed by the detection of HPLC-UV. The influencing factors on the extraction efficiency of magnetic ODS-PAN TFME, including pH, extraction time, desorption solvent, desorption time, and ion strength were investigated systematically. Under the optimal conditions, both analytes showed good linearity over ranges of 0.070-9.000μgmL(-1) and 0.012-9.000μgmL(-1) in plasma and urine samples, respectively, with correlation coefficients (R(2)) above 0.9990. Limits of detection (LODs) for quetiapine in plasma and urine samples were 0.013 and 0.003μgmL(-1), respectively. LODs for clozapine in plasma and urine samples were 0.015 and 0.003μgmL(-1), respectively. The relative standard deviations (RSDs) for quetiapine and clozapine were less than 9.23%. After the validation, the protocol was successfully applied for the determination of quetiapine and clozapine in patients' plasma and urine samples with satisfactory recoveries between 99-110%. The proposed magnetic ODS-PAN TFME was very simple, fast and easy to handle. It showed high potential as a powerful pretreatment technology for routine therapeutic drug monitoring (TDM) in plasma and urine samples. Copyright © 2016 Elsevier B.V. All rights reserved.

NS3 protease resistance-associated substitutions in liver tissue and plasma samples from patients infected by hepatitis C virus genotype 1A or 1B.

PubMed

Morsica, Giulia; Andolina, Andrea; Merli, Marco; Messina, Emanuela; Hasson, Hamid; Lazzarin, Adriano; Uberti-Foppa, Caterina; Bagaglio, Sabrina

2017-08-01

The presence of naturally occurring resistance-associated substitutions (RASs) in the HCV-protease domain has been poorly investigated in the liver, the main site of HCV replication. We evaluated the natural resistance of the virus to NS3 protease inhibitors in liver tissue and plasma samples taken from HCV-infected patients. RASs were investigated by means of viral population sequencing in liver tissue samples from 18 HCV-infected patients harbouring genotype 1a or genotype 1b; plasma samples from 12 of these patients were also available for virological investigation. A discordant genotype was found in two of the 12 patients (16.6%) who provided samples from both compartments. Sequence analysis of the NS3 protease domain showed the presence of RASs in four of the 18 liver tissue samples (22.2%), two of which showed cross-resistance to protease inhibitors in clinical use or phase 2-3 trials. The analysis of the 12 paired tissues and plasma samples excluded the presence of RASs in the plasma compartment. The dominance of discordant genotypes in the paired liver and plasma samples of some HCV-infected patients suggests mixed infection possibly leading to the selective advantage of different genotype in the two compartments. The presence of RASs at intra-hepatic level is not uncommon and may lead to the early emergence of cross-resistant strains.

Verification of out-of-control situations detected by "average of normal" approach.

PubMed

Liu, Jiakai; Tan, Chin Hon; Loh, Tze Ping; Badrick, Tony

2016-11-01

"Average of normal" (AoN) or "moving average" is increasingly used as an adjunct quality control tool in laboratory practice. Little guidance exists on how to verify if an out-of-control situation in the AoN chart is due to a shift in analytical performance, or underlying patient characteristics. Through simulation based on clinical data, we examined 1) the location of the last apparently stable period in the AoN control chart after an analytical shift, and 2) an approach to verify if the observed shift is related to an analytical shift by repeat testing of archived patient samples from the stable period for 21 common analytes. The number of blocks of results to look back for the stable period increased with the duration of the analytical shift, and was larger when smaller AoN block sizes were used. To verify an analytical shift, 3 archived samples from the analytically stable period should be retested. In particular, the process is deemed to have shifted if a difference of >2 analytical standard deviations (i.e. 1:2s rejection rule) between the original and retested results are observed in any of the 3 samples produced. The probability of Type-1 error (i.e., false rejection) and power (i.e., detecting true analytical shift) of this rule are <0.1 and >0.9, respectively. The use of appropriately archived patient samples to verify an apparent analytical shift is preferred to quality control materials. Nonetheless, the above findings may also apply to quality control materials, barring matrix effects. Copyright © 2016 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Documenting of Geologic Field Activities in Real-Time in Four Dimensions: Apollo 17 as a Case Study for Terrestrial Analogues and Future Exploration

NASA Technical Reports Server (NTRS)

Feist, B.; Bleacher, J. E.; Petro, N. E.; Niles, P. B.

2018-01-01

During the Apollo exploration of the lunar surface, thousands of still images, 16 mm videos, TV footage, samples, and surface experiments were captured and collected. In addition, observations and descriptions of what was observed was radioed to Mission Control as part of standard communications and subsequently transcribed. The archive of this material represents perhaps the best recorded set of geologic field campaigns and will serve as the example of how to conduct field work on other planetary bodies for decades to come. However, that archive of material exists in disparate locations and formats with varying levels of completeness, making it not easily cross-referenceable. While video and audio exist for the missions, it is not time synchronized, and images taken during the missions are not time or location tagged. Sample data, while robust, is not easily available in a context of where the samples were collected, their descriptions by the astronauts are not connected to them, or the video footage of their collection (if available). A more than five year undertaking to reconstruct and reconcile the Apollo 17 mission archive, from launch through splashdown, has generated an integrated record of the entire mission, resulting in searchable, synchronized image, voice, and video data, with geologic context provided at the time each sample was collected. Through www.apollo17.org the documentation of the field investigation conducted by the Apollo 17 crew is presented in chronologic sequence, with additional context provided by high-resolution Lunar Reconnaissance Orbiter Camera (LROC) Narrow Angle Camera (NAC) images and a corresponding digital terrain model (DTM) of the Taurus-Littrow Valley.

Human papillomavirus DNA detection in plasma and cervical samples of women with a recent history of low grade or precancerous cervical dysplasia

PubMed Central

Sina, Federica; Piana, Andrea; Sotgiu, Giovanni; Dell’Anna, Tiziana; Musumeci, Rosario

2017-01-01

Circulating HPV DNA has been previously described in women with advanced stages of cervical cancer and has been suggested to be a prognostic marker of disease recurrences and metastases. Only a few studies have reported the presence of HPV DNA in bloodstream of patients with low grade or precancerous cervical lesions. This study aimed to define if HPV DNA could be detected in plasma samples of 120 women referred for a recent history of cervical dysplasia who presented with lesions ranging from High Squamous Intraepithelial Lesion (H-SIL) to regressed normal cytology. HPV DNA detection was carried out in both plasma and cervical samples using type-specific real-time quantitative PCR assays identifying oncogenic HPV 16, 18, 31, 33, 45, 51 and 52. Overall, 34.2% (41/120) of plasma samples were shown to be positive for HPV DNA detection; HPV 45 (46.3%), HPV-51 (29.6%), and HPV 16 (18.5%) were the most frequently identified genotypes. The rate of HPV detection in paired cervical and plasma samples increased with advancing disease stage, ranging from 15.4% in women with regressed lesions to 38.9% in women with HSIL; HPV 16 resulted the most common genotype identified in women found to be HPV DNA positive in both cervical and plasma samples. Moreover, HPV 16 showed the highest median viral load value in both cervical and plasma samples, with 48,313 copies/104 cells and 1,099 copies/ml, respectively. Results obtained in this study confirm that HPV DNA can be detected and quantified in plasma samples of women with asymptomatic cervical infection. Further knowledge on HPV dissemination through the blood stream of women with cervical lesions would be very important in better understanding the natural history of HPV infection as well as its potential role in other distant tumors. PMID:29182627

Factors associated with low vitamin D status of Australian alpacas.

PubMed

Judson, G J; McGregor, B A; Partington, D L

2008-12-01

To investigate factors associated with low vitamin D status of alpacas at pasture in southern Australia. A 2-year survey of alpacas from two farms in South Australia and three in Victoria. Blood samples were collected from 20 to 30 alpacas on each farm on five occasions each year. Breed, gender, age and fleece colour of animals were recorded. Blood samples were assayed for plasma 2.5-hydroxycholecalciferol (25-OH D(3)) and plasma inorganic phosphorus (Pi). Data sets from 802 animal samples were analysed by multiple regression to determine variables associated with low vitamin D status of alpacas. The relationship between plasma 25-OH D(3) and plasma Pi was also investigated. Vitamin D status was significantly affected by month of sampling, with low values in late winter and high values in summer. Plasma vitamin D concentrations increased with age, were higher in alpacas with light fleeces than in those with dark fleeces and were also higher in the Suri than in the Huacaya breed. Plasma Pi concentrations were generally lower in alpacas with plasma 25-OH D(3) values < 25 nmol/L. Young alpacas with dark fleeces are most at risk from vitamin D insufficiency in late winter in southern Australia. The present study indicates that plasma Pi values are not a reliable indicator of vitamin D status of alpacas as assessed by plasma 25-OH D(3) concentrations.

The MATISSE analysis of large spectral datasets from the ESO Archive

NASA Astrophysics Data System (ADS)

Worley, C.; de Laverny, P.; Recio-Blanco, A.; Hill, V.; Vernisse, Y.; Ordenovic, C.; Bijaoui, A.

2010-12-01

The automated stellar classification algorithm, MATISSE, has been developed at the Observatoire de la Côte d'Azur (OCA) in order to determine stellar temperatures, gravities and chemical abundances for large datasets of stellar spectra. The Gaia Data Processing and Analysis Consortium (DPAC) has selected MATISSE as one of the key programmes to be used in the analysis of the Gaia Radial Velocity Spectrometer (RVS) spectra. MATISSE is currently being used to analyse large datasets of spectra from the ESO archive with the primary goal of producing advanced data products to be made available in the ESO database via the Virtual Observatory. This is also an invaluable opportunity to identify and address issues that can be encountered with the analysis large samples of real spectra prior to the launch of Gaia in 2012. The analysis of the archived spectra of the FEROS spectrograph is currently underway and preliminary results are presented.

Enhanced chromium adsorption capacity via plasma modification of natural zeolites

NASA Astrophysics Data System (ADS)

Cagomoc, Charisse Marie D.; Vasquez, Magdaleno R., Jr.

2017-01-01

Natural zeolites such as mordenite are excellent adsorbents for heavy metals. To enhance the adsorption capacity of zeolite, sodium-exchanged samples were irradiated with 13.56 MHz capacitively coupled radio frequency (RF) argon gas discharge. Hexavalent chromium [Cr(VI)] was used as the test heavy metal. Pristine and plasma-treated zeolite samples were soaked in 50 mg/L Cr solution and the amount of adsorbed Cr(VI) on the zeolites was calculated at predetermined time intervals. Compared with untreated zeolite samples, initial Cr(VI) uptake was 70% higher for plasma-treated zeolite granules (50 W 30 min) after 1 h of soaking. After 24 h, all plasma-treated zeolites showed increased Cr(VI) uptake. For a 2- to 4-month period, Cr(VI) uptake increased about 130% compared with untreated zeolite granules. X-ray diffraction analyses between untreated and treated zeolite samples revealed no major difference in terms of its crystal structure. However, for plasma-treated samples, an increase in the number of surface defects was observed from scanning electron microscopy images. This increase in the number of surface defects induced by plasma exposure played a crucial role in increasing the number of active sorption sites on the zeolite surface.

Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive.

PubMed

Ohta, Tazro; Nakazato, Takeru; Bono, Hidemasa

2017-06-01

It is important for public data repositories to promote the reuse of archived data. In the growing field of omics science, however, the increasing number of submissions of high-throughput sequencing (HTSeq) data to public repositories prevents users from choosing a suitable data set from among the large number of search results. Repository users need to be able to set a threshold to reduce the number of results to obtain a suitable subset of high-quality data for reanalysis. We calculated the quality of sequencing data archived in a public data repository, the Sequence Read Archive (SRA), by using the quality control software FastQC. We obtained quality values for 1 171 313 experiments, which can be used to evaluate the suitability of data for reuse. We also visualized the data distribution in SRA by integrating the quality information and metadata of experiments and samples. We provide quality information of all of the archived sequencing data, which enable users to obtain sufficient quality sequencing data for reanalyses. The calculated quality data are available to the public in various formats. Our data also provide an example of enhancing the reuse of public data by adding metadata to published research data by a third party. © The Authors 2017. Published by Oxford University Press.

Planetary plasma data analysis and 3D visualisation tools of the CDPP in the IMPEx infrastructure

NASA Astrophysics Data System (ADS)

Gangloff, Michel; Génot, Vincent; Khodachenko, Maxim; Modolo, Ronan; Kallio, Esa; Alexeev, Igor; Al-Ubaidi, Tarek; Scherf, Manuel; André, Nicolas; Bourrel, Nataliya; Budnik, Elena; Bouchemit, Myriam; Dufourg, Nicolas; Beigbeder, Laurent

2015-04-01

The CDPP (Centre de Données de la Physique des Plasmas,(http://cdpp.eu/), the French data center for plasma physics, is engaged for more than a decade in the archiving and dissemination of plasma data products from space missions and ground observatories. Besides these activities, the CDPP developed services like AMDA (http://amda.cdpp.eu/) which enables in depth analysis of a large amount of data through dedicated functionalities such as: visualization, conditional search, cataloguing, and 3DView (http://3dview.cdpp.eu/) which provides immersive visualisations in planetary environments and is further developed to include simulation and observational data. Both tools provide an interface to the IMPEx infrastructure (http://impexfp7.oeaw.ac.at) which facilitates the joint access to outputs of simulations (MHD or Hybrid models) in planetary sciences from providers like LATMOS, FMI as well as planetary plasma observational data provided by the CDPP. Several magnetospheric models are implemented in 3Dview (e.g. Tsyganenko for the Earth, and Cain for Mars). Magnetospheric models provided by SINP for the Earth, Jupiter, Saturn and Mercury as well as Hess models for Jupiter can also be used in 3DView, through the IMPEx infrastructure. A use case demonstrating the new capabilities offered by these tools and their interaction, including magnetospheric models, will be presented together with the IMPEx simulation metadata model used for the interface to simulation databases and model providers.

Is it acceptable to use coagulation plasma samples stored at room temperature and 4°C for 24 hours for additional prothrombin time, activated partial thromboplastin time, fibrinogen, antithrombin, and D-dimer testing?

PubMed

Rimac, V; Coen Herak, D

2017-10-01

Coagulation laboratories are faced on daily basis with requests for additional testing in already analyzed fresh plasma samples. This prompted us to examine whether plasma samples stored at room temperature (RT), and 4°C for 24 hours can be accepted for additional prothrombin time (PT), activated partial thromboplastin time (aPTT), fibrinogen (Fbg), antithrombin (AT), and D-dimer testing. We measured PT, aPTT, Fbg in 50 and AT in 30 plasma samples with normal and pathological values, within 4 hours of blood collection (baseline results) and after 24-hours storage at RT (primary tubes), and 4°C (aliquots). D-dimer stability was investigated in 20 samples stored in primary tubes at 4°C. No statistically significant difference between baseline results and results in samples stored at RT and 4°C was observed for PT (P=.938), aPTT (P=.186), Fbg (P=.962), AT (P=.713), and D-dimers (P=.169). The highest median percentage changes were found for aPTT, being more pronounced for samples stored at 4°C (13.0%) than at RT (8.7%). Plasma samples stored both at RT and 4°C for 24 hours are acceptable for additional PT, Fbg, and AT testing. Plasma samples stored 24 hours in primary tubes at 4°C are suitable for D-dimer testing. © 2017 John Wiley & Sons Ltd.

Association of mutant EGFR L858R and exon 19 concentration in circulating cell-free DNA using droplet digital PCR with response to EGFR-TKIs in NSCLC

PubMed Central

Zhu, Yan-Juan; Zhang, Hai-Bo; Liu, Yi-Hong; Zhu, Ya-Zhen; Chen, Jun; Li, Yong; Bai, Jian-Ping; Liu, Li-Rong; Qu, Yan-Chun; Qu, Xin; Chen, Xian; Zheng, Guang-Juan

2017-01-01

The present study aimed to determine the diagnostic concordance of plasma epidermal growth factor receptor (EGFR) mutation using droplet digital polymerase chain reaction (ddPCR) with tumor tissue samples and the predictive clinical significance of plasma EGFR mutation concentration. Plasma DNA samples from patients with non-small cell lung cancer (NSCLC) were analyzed for EGFR exon 21 codon 858 (L858R) mutation, deletion of exon 19 (ex19del) and exon 20 codon 790 (T790M) mutation using ddPCR. Firstly, the mutations in the plasma samples were compared with the matched tumor samples to determine the concordance. Secondly, image examination follow-ups were analyzed to assess the association between plasma EGFR mutation concentration and patients' response to EGFR-tyrosine kinase inhibitors (TKIs). A total of 51 patients with NSCLC were enrolled, including 48 newly diagnosed patients. Compared with tumor tissue samples, the sensitivity and specificity of ddPCR were 76.19% (16/21) and 96.55% (28/29) for mutant L858R, and 88.89% (8/9) and 100% (41/41) for ex19del, respectively. No patient exhibited the T790M mutation in the tumor tissue or plasma samples. Furthermore, 5 patients with the L858R mutation and 4 patients with ex19del in plasma and tumor tissue samples had been followed up with image examination for ≥3 months following EGFR-TKI treatment. The baseline mutant EGFR concentrations were positively correlated with a reduction in tumor burden (Spearman's r=0.7000, P=0.0358). When analyzed separately, ex19del concentrations (Spearman's r=1.0000, P<0.0001) were also positively correlated with the reduction, while mutant L858R concentrations were not (Spearman's r=0.7000, P=0.1881). In the present study, detection of plasma EGFR mutations using ddPCR exhibited sufficient concordance with tumor tissue sample results. Baseline plasma mutant EGFR and ex19del concentrations were significantly and positively correlated with response to EGFR-TKIs. PMID:28789464

Modification of W surfaces by exposure to hollow cathode plasmas

NASA Astrophysics Data System (ADS)

Stancu, C.; Stokker-Cheregi, F.; Moldovan, A.; Dinescu, M.; Grisolia, C.; Dinescu, G.

2017-10-01

In this work, we assess the surface modifications induced on W samples following exposure to He and He/H2 radiofrequency plasmas in hollow cathode discharge configuration. Our study addresses issues that relate to the use of W in next-generation fusion reactors and, therefore, the investigation of W surface degradation following exposure and heating by plasmas to temperatures above 1000 °C is of practical importance. For these experiments, we used commercially available tungsten samples having areas of 30 × 15 mm and 0.1 mm thickness. The hollow cathode plasma was produced using a radiofrequency (RF) generator (13.56 MHz) between parallel plate electrodes. The W samples were mounted as one of the electrodes. The He and He/H2 plasma discharges had a combined effect of heating and bombardment of the W surfaces. The surface modifications were studied for discharge powers between 200 and 300 W, which resulted in the heating of the samples to temperatures between 950 and 1230 °C, respectively. The samples were weighed prior and after plasma exposure, and loss of mass was measured following plasma exposure times up to 90 min. The analysis of changes in surface morphology was carried out by optical microscopy, scanning electron microscopy and atomic force microscopy. Additionally, optical emission spectra of the respective plasmas were recorded from the region localized inside the hollow cathode gap. We discuss the influence of experimental parameters on the changes in surface morphology.

Resolution of plasma sample mix-ups through comparison of patient antibody patterns to E. coli.

PubMed

Vetter, Beatrice N; Orlowski, Vanessa; Schüpbach, Jörg; Böni, Jürg; Rühe, Bettina; Huder, Jon B

2015-12-01

Accidental sample mix-ups and the need for their swift resolution is a challenge faced by every analytical laboratory. To this end, we developed a simple immunoblot-based method, making use of a patient's characteristic plasma antibody profile to Escherichia coli (E. coli) proteins. Nitrocellulose strips of size-separated proteins from E. coli whole-cell lysates were incubated with patient plasma and visualised with an enzyme-coupled secondary antibody and substrate. Plasma samples of 20 random patients as well as five longitudinal samples of three patients were analysed for antibody band patterns, to evaluate uniqueness and consistency over time, respectively. For sample mix-ups, antibody band patterns of questionable samples were compared with samples of known identity. Comparison of anti-E. coli antibody patterns of 20 random patients showed a unique antibody profile for each patient. Antibody profiles remained consistent over time, as shown for three patients over several years. Three example cases demonstrate the use of this methodology in mis-labelling or -pipetting incidences. Our simple method for resolving plasma sample mix-ups between non-related individuals can be performed with basic laboratory equipment and thus can easily be adopted by analytical laboratories. Copyright © 2015 Elsevier B.V. All rights reserved.

76 FR 28421 - Marine Mammals; File No. 15646

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-17

... Rebecca Dickhut, Ph.D., Virginia Institute of Marine Science, P.O. Box 1346, Route 1208 Greate Road... following archived samples will be imported from the Swedish Museum of Natural History: fur, blood, and fat...

Mobile inductively coupled plasma system

DOEpatents

D'Silva, Arthur P.; Jaselskis, Edward J.

1999-03-30

A system for sampling and analyzing a material located at a hazardous site. A laser located remote from the hazardous site is connected to an optical fiber, which directs laser radiation proximate the material at the hazardous site. The laser radiation abates a sample of the material. An inductively coupled plasma is located remotely from the material. An aerosol transport system carries the ablated particles to a plasma, where they are dissociated, atomized and excited to provide characteristic optical reduction of the elemental constituents of the sample. An optical spectrometer is located remotely from the site. A second optical fiber is connected to the optical spectrometer at one end and the plasma source at the other end to carry the optical radiation from the plasma source to the spectrometer.

A simple method for plasma total vitamin C analysis suitable for routine clinical laboratory use.

PubMed

Robitaille, Line; Hoffer, L John

2016-04-21

In-hospital hypovitaminosis C is highly prevalent but almost completely unrecognized. Medical awareness of this potentially important disorder is hindered by the inability of most hospital laboratories to determine plasma vitamin C concentrations. The availability of a simple, reliable method for analyzing plasma vitamin C could increase opportunities for routine plasma vitamin C analysis in clinical medicine. Plasma vitamin C can be analyzed by high performance liquid chromatography (HPLC) with electrochemical (EC) or ultraviolet (UV) light detection. We modified existing UV-HPLC methods for plasma total vitamin C analysis (the sum of ascorbic and dehydroascorbic acid) to develop a simple, constant-low-pH sample reduction procedure followed by isocratic reverse-phase HPLC separation using a purely aqueous low-pH non-buffered mobile phase. Although EC-HPLC is widely recommended over UV-HPLC for plasma total vitamin C analysis, the two methods have never been directly compared. We formally compared the simplified UV-HPLC method with EC-HPLC in 80 consecutive clinical samples. The simplified UV-HPLC method was less expensive, easier to set up, required fewer reagents and no pH adjustments, and demonstrated greater sample stability than many existing methods for plasma vitamin C analysis. When compared with the gold-standard EC-HPLC method in 80 consecutive clinical samples exhibiting a wide range of plasma vitamin C concentrations, it performed equivalently. The easy set up, simplicity and sensitivity of the plasma vitamin C analysis method described here could make it practical in a normally equipped hospital laboratory. Unlike any prior UV-HPLC method for plasma total vitamin C analysis, it was rigorously compared with the gold-standard EC-HPLC method and performed equivalently. Adoption of this method could increase the availability of plasma vitamin C analysis in clinical medicine.

The Effects of Gas Composition on the Atmospheric Pressure Plasma Jet Modification of Polyethylene Films

NASA Astrophysics Data System (ADS)

Sun, Jie; Qiu, Yiping

2015-05-01

Polyethylene (PE) films are treated using an atmospheric pressure plasma jet (APPJ) with He or He/O2 gas for different periods of time. The influence of gas type on the plasma-polymer interactions is studied. The surface contact angle of the PE film can be effectively lowered to 58° after 20 s of He/O2 plasma treatment and then remains almost unchanged for longer treatment durations, while, for He plasma treatment, the film surface contact angle drops gradually to 47° when the time reaches 120 s. Atomic force microscopy (AFM) results show that the root mean square (RMS) roughness was significantly higher for the He/O2 plasma treated samples than for the He plasma treated counterparts, and the surface topography of the He/O2 plasma treated PE films displays evenly distributed dome-shaped small protuberances. Chemical composition analysis reveals that the He plasma treated samples have a higher oxygen content but a clearly lower percentage of -COO than the comparable He/O2 treated samples, suggesting that differences exist in the mode of incorporating oxygen between the two gas condition plasma treatments. Electron spin resonance (ESR) results show that the free radical concentrations of the He plasma treated samples were clearly higher than those of the He/O2 plasma treated ones with other conditions unchanged. supported by the Fundamental Research Funds for the Central Universities of China (Nos. JUSRP1044 and JUSRP1045), National Natural Science Foundation of China (Nos. 51203062 and 51302110), and the Cooperative Innovation Fund, Project of Jiangsu Province, China (Nos. BY2012064, BY2013015-31 and BY2013015-32)

A study on the antimicrobial efficacy of RF oxygen plasma and neem extract treated cotton fabrics

NASA Astrophysics Data System (ADS)

Vaideki, K.; Jayakumar, S.; Thilagavathi, G.; Rajendran, R.

2007-06-01

The paper deals with a thorough investigation on the antimicrobial activity of RF oxygen plasma and Azadirachtin (neem extract) treated cotton fabric. The hydrophilicity of cotton fabric was found to improve when treated with RF oxygen plasma. The process parameters such as electrode gap, time of exposure and oxygen pressure have been varied to study their effect on improving the hydrophilicity of the cotton fabric. The static immersion test has been carried out to assess the hydrophilicity of the oxygen plasma treated samples and the process parameters were optimized based on these test results. The formation of carbonyl group during surface modification in the plasma treated sample was analysed using FTIR studies. The surface morphology has been studied using SEM micrographs. The antimicrobial activity was imparted to the RF oxygen plasma treated samples using methanolic extract of neem leaves containing Azadirachtin. The antimicrobial activity of these samples has been analysed and compared with the activity of the cotton fabric treated with neem extract alone. The investigation reveals that the surface modification due to RF oxygen plasma was found to increase the hydrophilicity and hence the antimicrobial activity of the cotton fabric when treated with Azadirachtin.

Ex vivo spontaneous generation of 19-norandrostenedione and nandrolone detected in equine plasma and urine.

PubMed

Guan, Fuyu; Uboh, Cornelius E; Soma, Lawrence R; You, Youwen; Li, Xiaoqing; McDonnell, Sue

2012-01-01

19-Norandrostenedione (NAED) and nandrolone are anabolic-androgenic steroids (AASs). Nandrolone was regarded solely as a synthetic AAS until the 1980s when trace concentrations of apparently endogenous nandrolone were detected in urine samples obtained from intact male horses (stallions). Since then, its endogenous origin has been reported in boars and bulls; endogenous NAED and nandrolone have been identified in plasma and urine samples collected from stallions. More recently, however, it was suggested that NAED and nandrolone detected in urine samples from stallions are primarily artifacts due to the analytical procedure. The present study was undertaken to determine whether NAED and nandrolone detected in plasma and urine samples collected from stallions are truly endogenous or artifacts from sample processing. To answer this question, fresh plasma and urine samples from ≥8 stallions were analyzed for the two AASs, soon after collection, by liquid chromatography hyphenated to tandem mass spectrometry (LC-MS/MS). NAED and nandrolone were not detected in fresh plasma samples but detected in the same samples post storage. Concentrations of both AASs increased with storage time, and the increases were greater at a higher storage temperature (37°C versus 4°C, and ambient temperature versus 4°C). Although NAED was detected in some fresh stallion urine samples, its concentration (<407 pg/mL) was far lower (<0.4%) than that in the same samples post storage (at ambient temperature for 15 days). Nandrolone was not detected in most of fresh urine samples but detected in the same samples post storage. Based on these results, it is concluded that all NAED and nandrolone detected in stored plasma samples of stallions and most of them in the stored urine samples are not from endogenous origins but spontaneously generated during sample storage, most likely from spontaneous decarboxylation of androstenedione-19-oic acid and testosterone-19-oic acid. To our knowledge, it is the first time that all NAED and nandrolone detected in plasma of stallions and most of them detected in the urine have been shown to be spontaneously generated in vitro during sample storage. This finding would have significant implications with regard to the regulation of the two steroids in horse racing. Copyright © 2011 Elsevier Ltd. All rights reserved.

An Integrated Nonlinear Analysis library - (INA) for solar system plasma turbulence

NASA Astrophysics Data System (ADS)

Munteanu, Costel; Kovacs, Peter; Echim, Marius; Koppan, Andras

2014-05-01

We present an integrated software library dedicated to the analysis of time series recorded in space and adapted to investigate turbulence, intermittency and multifractals. The library is written in MATLAB and provides a graphical user interface (GUI) customized for the analysis of space physics data available online like: Coordinated Data Analysis Web (CDAWeb), Automated Multi Dataset Analysis system (AMDA), Planetary Science Archive (PSA), World Data Center Kyoto (WDC), Ulysses Final Archive (UFA) and Cluster Active Archive (CAA). Three main modules are already implemented in INA : the Power Spectral Density (PSD) Analysis, the Wavelet and Intemittency Analysis and the Probability Density Functions (PDF) analysis.The layered structure of the software allows the user to easily switch between different modules/methods while retaining the same time interval for the analysis. The wavelet analysis module includes algorithms to compute and analyse the PSD, the Scalogram, the Local Intermittency Measure (LIM) or the Flatness parameter. The PDF analysis module includes algorithms for computing the PDFs for a range of scales and parameters fully customizable by the user; it also computes the Flatness parameter and enables fast comparison with standard PDF profiles like, for instance, the Gaussian PDF. The library has been already tested on Cluster and Venus Express data and we will show relevant examples. Research supported by the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement no 313038/STORM, and a grant of the Romanian Ministry of National Education, CNCS UEFISCDI, project number PN-II-ID PCE-2012-4-0418.

Evaluation of positive Rift Valley fever virus formalin-fixed paraffin embedded samples as a source of sequence data for retrospective phylogenetic analysis.

PubMed

Mubemba, B; Thompson, P N; Odendaal, L; Coetzee, P; Venter, E H

2017-05-01

Rift Valley fever (RVF), caused by an arthropod borne Phlebovirus in the family Bunyaviridae, is a haemorrhagic disease that affects ruminants and humans. Due to the zoonotic nature of the virus, a biosafety level 3 laboratory is required for isolation of the virus. Fresh and frozen samples are the preferred sample type for isolation and acquisition of sequence data. However, these samples are scarce in addition to posing a health risk to laboratory personnel. Archived formalin-fixed, paraffin-embedded (FFPE) tissue samples are safe and readily available, however FFPE derived RNA is in most cases degraded and cross-linked in peptide bonds and it is unknown whether the sample type would be suitable as reference material for retrospective phylogenetic studies. A RT-PCR assay targeting a 490 nt portion of the structural G N glycoprotein encoding gene of the RVFV M-segment was applied to total RNA extracted from archived RVFV positive FFPE samples. Several attempts to obtain target amplicons were unsuccessful. FFPE samples were then analysed using next generation sequencing (NGS), i.e. Truseq ® (Illumina) and sequenced on the Miseq ® genome analyser (Illumina). Using reference mapping, gapped virus sequence data of varying degrees of shallow depth was aligned to a reference sequence. However, the NGS did not yield long enough contigs that consistently covered the same genome regions in all samples to allow phylogenetic analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

Plasma circulating tumor DNA as an alternative to metastatic biopsies for mutational analysis in breast cancer.

PubMed

Rothé, F; Laes, J-F; Lambrechts, D; Smeets, D; Vincent, D; Maetens, M; Fumagalli, D; Michiels, S; Drisis, S; Moerman, C; Detiffe, J-P; Larsimont, D; Awada, A; Piccart, M; Sotiriou, C; Ignatiadis, M

2014-10-01

Molecular screening programs use next-generation sequencing (NGS) of cancer gene panels to analyze metastatic biopsies. We interrogated whether plasma could be used as an alternative to metastatic biopsies. The Ion AmpliSeq™ Cancer Hotspot Panel v2 (Ion Torrent), covering 2800 COSMIC mutations from 50 cancer genes was used to analyze 69 tumor (primary/metastases) and 31 plasma samples from 17 metastatic breast cancer patients. The targeted coverage for tumor DNA was ×1000 and for plasma cell-free DNA ×25 000. Whole blood normal DNA was used to exclude germline variants. The Illumina technology was used to confirm observed mutations. Evaluable NGS results were obtained for 60 tumor and 31 plasma samples from 17 patients. When tumor samples were analyzed, 12 of 17 (71%, 95% confidence interval (CI) 44% to 90%) patients had ≥1 mutation (median 1 mutation per patient, range 0-2 mutations) in either p53, PIK3CA, PTEN, AKT1 or IDH2 gene. When plasma samples were analyzed, 12 of 17 (71%, 95% CI: 44-90%) patients had ≥1 mutation (median 1 mutation per patient, range 0-2 mutations) in either p53, PIK3CA, PTEN, AKT1, IDH2 and SMAD4. All mutations were confirmed. When we focused on tumor and plasma samples collected at the same time-point, we observed that, in four patients, no mutation was identified in either tumor or plasma; in nine patients, the same mutations was identified in tumor and plasma; in two patients, a mutation was identified in tumor but not in plasma; in two patients, a mutation was identified in plasma but not in tumor. Thus, in 13 of 17 (76%, 95% CI 50% to 93%) patients, tumor and plasma provided concordant results whereas in 4 of 17 (24%, 95% CI 7% to 50%) patients, the results were discordant, providing complementary information. Plasma can be prospectively tested as an alternative to metastatic biopsies in molecular screening programs. © The Author 2014. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Surface cracking and melting of different tungsten grades under transient heat and particle loads in a magnetized coaxial plasma gun

NASA Astrophysics Data System (ADS)

Kikuchi, Y.; Sakuma, I.; Iwamoto, D.; Kitagawa, Y.; Fukumoto, N.; Nagata, M.; Ueda, Y.

2013-07-01

Surface damage of pure tungsten (W), W alloys with 2 wt.% tantalum (W-Ta) and vacuum plasma spray (VPS) W coating on a reduced activation material of ferritic steel (F82H) due to repetitive ELM-like pulsed (˜0.3 ms) deuterium plasma irradiation has been investigated by using a magnetized coaxial plasma gun. Surface cracks appeared on a pure W sample exposed to 10 plasma pulses of ˜0.3 MJ m-2, while a W-Ta sample did not show surface cracks with similar pulsed plasma irradiation. The energy density threshold for surface cracking was significantly increased by the existence of the alloying element of tantalum. No surface morphology change of a VPS W coated F82H sample was observed under 10 plasma pulses of ˜0.3 MJ m-2, although surface melting and cracks in the resolidification layer occurred at higher energy density of ˜0.9 MJ m-2. There was no indication of exfoliation of the W coating from the substrate of F82H after the pulsed plasma exposures.

Developing New Epidemiologic Tools for Investigating Breast Cancer Risk

DTIC Science & Technology

1997-09-01

EGF and TGF- a levels to each other and to plasma levels of estradiol and progesterone. Breast fluid and plasma samples were obtained two to four...relationships between EGF and TGF- a levels or between either GF level and menstrual cycle phase or plasma hormone concentrations. However, in random...and TGF- a levels were related to the menstrual cycle phase, to plasma estradiol or progesterone levels, or to each other. By repeat sampling of

Plasma impregnation of wood with fire retardants

NASA Astrophysics Data System (ADS)

Pabeliña, Karel G.; Lumban, Carmencita O.; Ramos, Henry J.

2012-02-01

The efficacy of chemical and plasma treatments with phosphate and boric compounds, and nitrogen as flame retardants on wood are compared in this study. The chemical treatment involved the conventional method of spraying the solution over the wood surface at atmospheric condition and chemical vapor deposition in a vacuum chamber. The plasma treatment utilized a dielectric barrier discharge ionizing and decomposing the flame retardants into innocuous simple compounds. Wood samples are immersed in either phosphoric acid, boric acid, hydrogen or nitrogen plasmas or a plasma admixture of two or three compounds at various concentrations and impregnated by the ionized chemical reactants. Chemical changes on the wood samples were analyzed by Fourier transform infrared spectroscopy (FTIR) while the thermal changes through thermo gravimetric analysis (TGA). Plasma-treated samples exhibit superior thermal stability and fire retardant properties in terms of highest onset temperature, temperature of maximum pyrolysis, highest residual char percentage and comparably low total percentage weight loss.

Programmable calculator software for computation of the plasma binding of ligands.

PubMed

Conner, D P; Rocci, M L; Larijani, G E

1986-01-01

The computation of the extent of plasma binding of a ligand to plasma constituents using radiolabeled ligand and equilibrium dialysis is complex and tedious. A computer program for the HP-41C Handheld Computer Series (Hewlett-Packard) was developed to perform these calculations. The first segment of the program constructs a standard curve for quench correction of post-dialysis plasma and buffer samples, using either external standard ratio (ESR) or sample channels ratio (SCR) techniques. The remainder of the program uses the counts per minute, SCR or ESR, and post-dialysis volume of paired plasma and buffer samples generated from the dialysis procedure to compute the extent of binding after correction for background radiation, counting efficiency, and intradialytic shifts of fluid between plasma and buffer compartments during dialysis. This program greatly simplifies the analysis of equilibrium dialysis data and has been employed in the analysis of dexamethasone binding in normal and uremic sera.

Testing an aflatoxin B1 gene signature in rat archival tissues.

PubMed

Merrick, B Alex; Auerbach, Scott S; Stockton, Patricia S; Foley, Julie F; Malarkey, David E; Sills, Robert C; Irwin, Richard D; Tice, Raymond R

2012-05-21

Archival tissues from laboratory studies represent a unique opportunity to explore the relationship between genomic changes and agent-induced disease. In this study, we evaluated the applicability of qPCR for detecting genomic changes in formalin-fixed, paraffin-embedded (FFPE) tissues by determining if a subset of 14 genes from a 90-gene signature derived from microarray data and associated with eventual tumor development could be detected in archival liver, kidney, and lung of rats exposed to aflatoxin B1 (AFB1) for 90 days in feed at 1 ppm. These tissues originated from the same rats used in the microarray study. The 14 genes evaluated were Adam8, Cdh13, Ddit4l, Mybl2, Akr7a3, Akr7a2, Fhit, Wwox, Abcb1b, Abcc3, Cxcl1, Gsta5, Grin2c, and the C8orf46 homologue. The qPCR FFPE liver results were compared to the original liver microarray data and to qPCR results using RNA from fresh frozen liver. Archival liver paraffin blocks yielded 30 to 50 μg of degraded RNA that ranged in size from 0.1 to 4 kB. qPCR results from FFPE and fresh frozen liver samples were positively correlated (p ≤ 0.05) by regression analysis and showed good agreement in direction and proportion of change with microarray data for 11 of 14 genes. All 14 transcripts could be amplified from FFPE kidney RNA except the glutamate receptor gene Grin2c; however, only Abcb1b was significantly upregulated from control. Abundant constitutive transcripts, S18 and β-actin, could be amplified from lung FFPE samples, but the narrow RNA size range (25-500 bp length) prevented consistent detection of target transcripts. Overall, a discrete gene signature derived from prior transcript profiling and representing cell cycle progression, DNA damage response, and xenosensor and detoxication pathways was successfully applied to archival liver and kidney by qPCR and indicated that gene expression changes in response to subchronic AFB1 exposure occurred predominantly in the liver, the primary target for AFB1-induced tumors. We conclude that an evaluation of gene signatures in archival tissues can be an important toxicological tool for evaluating critical molecular events associated with chemical exposures.

Interaction of cold radiofrequency plasma with seeds of beans (Phaseolus vulgaris)

PubMed Central

Bormashenko, Edward; Shapira, Yekaterina; Grynyov, Roman; Whyman, Gene; Bormashenko, Yelena; Drori, Elyashiv

2015-01-01

The impact of cold radiofrequency air plasma on the wetting properties and water imbibition of beans (Phaseolus vulgaris) was studied. The influence of plasma on wetting of a cotyledon and seed coat (testa) was elucidated. It was established that cold plasma treatment leads to hydrophilization of the cotyledon and tissues constituting the testa when they are separately exposed to plasma. By contrast, when the entire bean is exposed to plasma treatment, only the external surface of the bean is hydrophilized by the cold plasma. Water imbibition by plasma-treated beans was studied. Plasma treatment markedly accelerates the water absorption. The crucial role of a micropyle in the process of water imbibition was established. It was established that the final percentage of germination was almost the same in the cases of plasma-treated, untreated, and vacuum-pumped samples. However, the speed of germination was markedly higher for the plasma-treated samples. The influence of the vacuum pumping involved in the cold plasma treatment on the germination was also clarified. PMID:25948708

Effect of plasma power on reduction of printable graphene oxide thin films on flexible substrates

NASA Astrophysics Data System (ADS)

Banerjee, Indrani; Mahapatra, Santosh K.; Pal, Chandana; Sharma, Ashwani K.; Ray, Asim K.

2018-05-01

Room temperature hydrogen plasma treatment on solution processed 300 nm graphene oxide (GO) films on flexible indium tin oxide (ITO) coated polyethylene terephthalate (PET) substrates has been performed by varying the plasma power between 20 W and 60 W at a constant exposure time of 30 min with a view to examining the effect of plasma power on reduction of GO. X-ray powder diffraction (XRD) and Raman spectroscopic studies show that high energy hydrogen species generated in the plasma assist fast exfoliation of the oxygenated functional groups present in the GO samples. Significant decrease in the optical band gap is observed from 4.1 eV for untreated samples to 0.5 eV for 60 W plasma treated samples. The conductivity of the films treated with 60 W plasma power is estimated to be six orders of magnitude greater than untreated GO films and this enhancement of conductivity on plasma reduction has been interpreted in terms of UV-visible absorption spectra and density functional based first principle computational calculations. Plasma reduction of GO/ITO/PET structures can be used for efficiently tuning the electrical and optical properties of reduced graphene oxide (rGO) for flexible electronics applications.

Interpretation of ANA Indirect Immunofluorescence Test Outside the Darkroom Using NOVA View Compared to Manual Microscopy

PubMed Central

Copple, Susan S.; Jaskowski, Troy D.; Giles, Rashelle; Hill, Harry R.

2014-01-01

Objective. To evaluate NOVA View with focus on reading archived images versus microscope based manual interpretation of ANA HEp-2 slides by an experienced, certified medical technologist. Methods. 369 well defined sera from: 44 rheumatoid arthritis, 50 systemic lupus erythematosus, 35 scleroderma, 19 Sjögren's syndrome, and 10 polymyositis patients as well as 99 healthy controls were examined. In addition, 12 defined sera from the Centers for Disease Control and 100 random patient sera sent to ARUP Laboratories for ANA HEp-2 IIF testing were included. Samples were read using the archived images on NOVA View and compared to results obtained from manual reading. Results. At a 1 : 40/1 : 80 dilution the resulting comparison demonstrated 94.8%/92.9% positive, 97.4%/97.4% negative, and 96.5%/96.2% total agreements between manual IIF and NOVA View archived images. Agreement of identifiable patterns between methods was 97%, with PCNA and mixed patterns undetermined. Conclusion. Excellent agreements were obtained between reading archived images on NOVA View and manually on a fluorescent microscope. In addition, workflow benefits were observed which need to be analyzed in future studies. PMID:24741573

The SAMI Galaxy Survey: A prototype data archive for Big Science exploration

NASA Astrophysics Data System (ADS)

Konstantopoulos, I. S.; Green, A. W.; Foster, C.; Scott, N.; Allen, J. T.; Fogarty, L. M. R.; Lorente, N. P. F.; Sweet, S. M.; Hopkins, A. M.; Bland-Hawthorn, J.; Bryant, J. J.; Croom, S. M.; Goodwin, M.; Lawrence, J. S.; Owers, M. S.; Richards, S. N.

2015-11-01

We describe the data archive and database for the SAMI Galaxy Survey, an ongoing observational program that will cover ≈3400 galaxies with integral-field (spatially-resolved) spectroscopy. Amounting to some three million spectra, this is the largest sample of its kind to date. The data archive and built-in query engine use the versatile Hierarchical Data Format (HDF5), which precludes the need for external metadata tables and hence the setup and maintenance overhead those carry. The code produces simple outputs that can easily be translated to plots and tables, and the combination of these tools makes for a light system that can handle heavy data. This article acts as a contextual companion to the SAMI Survey Database source code repository, samiDB, which is freely available online and written entirely in Python. We also discuss the decisions related to the selection of tools and the creation of data visualisation modules. It is our aim that the work presented in this article-descriptions, rationale, and source code-will be of use to scientists looking to set up a maintenance-light data archive for a Big Science data load.

Contemporary-use pesticides in personal air samples during pregnancy and blood samples at delivery among urban minority mothers and newborns.

PubMed Central

Whyatt, Robin M; Barr, Dana B; Camann, David E; Kinney, Patrick L; Barr, John R; Andrews, Howard F; Hoepner, Lori A; Garfinkel, Robin; Hazi, Yair; Reyes, Andria; Ramirez, Judyth; Cosme, Yesenia; Perera, Frederica P

2003-01-01

We have measured 29 pesticides in plasma samples collected at birth between 1998 and 2001 from 230 mother and newborn pairs enrolled in the Columbia Center for Children's Environmental Health prospective cohort study. Our prior research has shown widespread pesticide use during pregnancy among this urban minority cohort from New York City. We also measured eight pesticides in 48-hr personal air samples collected from the mothers during pregnancy. The following seven pesticides were detected in 48-83% of plasma samples (range, 1-270 pg/g): the organophosphates chlorpyrifos and diazinon, the carbamates bendiocarb and 2-isopropoxyphenol (metabolite of propoxur), and the fungicides dicloran, phthalimide (metabolite of folpet and captan), and tetrahydrophthalimide (metabolite of captan and captafol). Maternal and cord plasma levels were similar and, except for phthalimide, were highly correlated (p < 0.001). Chlorpyrifos, diazinon, and propoxur were detected in 100% of personal air samples (range, 0.7-6,010 ng/m(3)). Diazinon and propoxur levels were significantly higher in the personal air of women reporting use of an exterminator, can sprays, and/or pest bombs during pregnancy compared with women reporting no pesticide use or use of lower toxicity methods only. A significant correlation was seen between personal air level of chlorpyrifos, diazinon, and propoxur and levels of these insecticides or their metabolites in plasma samples (maternal and/or cord, p < 0.05). The fungicide ortho-phenylphenol was also detected in 100% of air samples but was not measured in plasma. The remaining 22 pesticides were detected in 0-45% of air or plasma samples. Chlorpyrifos, diazinon, propoxur, and bendiocarb levels in air and/or plasma decreased significantly between 1998 and 2001. Findings indicate that pesticide exposures are frequent but decreasing and that the pesticides are readily transferred to the developing fetus during pregnancy. PMID:12727605

Distribution of Dengue Virus Types 1 and 4 in Blood Components from Infected Blood Donors from Puerto Rico

PubMed Central

Añez, Germán; Heisey, Daniel A. R.; Chancey, Caren; Fares, Rafaelle C. G.; Espina, Luz M.; Souza, Kátia P. R.; Teixeira-Carvalho, Andréa; Krysztof, David E.; Foster, Gregory A.; Stramer, Susan L.; Rios, Maria

2016-01-01

Background Dengue is a mosquito-borne viral disease caused by the four dengue viruses (DENV-1 to 4) that can also be transmitted by blood transfusion and organ transplantation. The distribution of DENV in the components of blood from infected donors is poorly understood. Methods We used an in-house TaqMan qRT-PCR assay to test residual samples of plasma, cellular components of whole blood (CCWB), serum and clot specimens from the same collection from blood donors who were DENV-RNA-reactive in a parallel blood safety study. To assess whether DENV RNA detected by TaqMan was associated with infectious virus, DENV infectivity in available samples was determined by culture in mosquito cells. Results DENV RNA was detected by TaqMan in all tested blood components, albeit more consistently in the cellular components; 78.8% of CCWB, 73.3% of clots, 86.7% of sera and 41.8% of plasma samples. DENV-1 was detected in 48 plasma and 97 CCWB samples while DENV-4 was detected in 21 plasma and 31 CCWB samples. In mosquito cell cultures, 29/111 (26.1%) plasma and 32/97 (32.7%) CCWB samples were infectious. A subset of samples from 29 donors was separately analyzed to compare DENV viral loads in the available blood components. DENV viral loads did not differ significantly between components and ranged from 3–8 log10 PCR-detectable units/ml. Conclusions DENV was present in all tested components from most donors, and viral RNA was not preferentially distributed in any of the tested components. Infectious DENV was also present in similar proportions in cultured plasma, clot and CCWB samples, indicating that these components may serve as a resource when sample sizes are limited. However, these results suggest that the sensitivity of the nucleic acid tests (NAT) for these viruses would not be improved by testing whole blood or components other than plasma. PMID:26871560

Distribution of Dengue Virus Types 1 and 4 in Blood Components from Infected Blood Donors from Puerto Rico

DOE PAGES

Anez, German; Heisey, Daniel A. R.; Chancey, Caren; ...

2016-02-12

Dengue is a mosquito-borne viral disease caused by the four dengue viruses (DENV-1 to 4) that can also be transmitted by blood transfusion and organ transplantation. The distribution of DENV in the components of blood from infected donors is poorly understood. Here, we used an in-house TaqMan qRT-PCR assay to test residual samples of plasma, cellular components of whole blood (CCWB), serum and clot specimens from the same collection from blood donors who were DENV-RNA-reactive in a parallel blood safety study. To assess whether DENV RNA detected by TaqMan was associated with infectious virus, DENV infectivity in available samples wasmore » determined by culture in mosquito cells. As a result, DENV RNA was detected by TaqMan in all tested blood components, albeit more consistently in the cellular components; 78.8% of CCWB, 73.3% of clots, 86.7% of sera and 41.8% of plasma samples. DENV-1 was detected in 48 plasma and 97 CCWB samples while DENV-4 was detected in 21 plasma and 31 CCWB samples. In mosquito cell cultures, 29/111 (26.1%) plasma and 32/97 (32.7%) CCWB samples were infectious. A subset of samples from 29 donors was separately analyzed to compare DENV viral loads in the available blood components. DENV viral loads did not differ significantly between components and ranged from 3–8 log 10 PCR-detectable units/ml. In conclusion, DENV was present in all tested components from most donors, and viral RNA was not preferentially distributed in any of the tested components. Infectious DENV was also present in similar proportions in cultured plasma, clot and CCWB samples, indicating that these components may serve as a resource when sample sizes are limited. However, these results suggest that the sensitivity of the nucleic acid tests (NAT) for these viruses would not be improved by testing whole blood or components other than plasma.« less

Distribution of Dengue Virus Types 1 and 4 in Blood Components from Infected Blood Donors from Puerto Rico

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

Anez, German; Heisey, Daniel A. R.; Chancey, Caren

Dengue is a mosquito-borne viral disease caused by the four dengue viruses (DENV-1 to 4) that can also be transmitted by blood transfusion and organ transplantation. The distribution of DENV in the components of blood from infected donors is poorly understood. Here, we used an in-house TaqMan qRT-PCR assay to test residual samples of plasma, cellular components of whole blood (CCWB), serum and clot specimens from the same collection from blood donors who were DENV-RNA-reactive in a parallel blood safety study. To assess whether DENV RNA detected by TaqMan was associated with infectious virus, DENV infectivity in available samples wasmore » determined by culture in mosquito cells. As a result, DENV RNA was detected by TaqMan in all tested blood components, albeit more consistently in the cellular components; 78.8% of CCWB, 73.3% of clots, 86.7% of sera and 41.8% of plasma samples. DENV-1 was detected in 48 plasma and 97 CCWB samples while DENV-4 was detected in 21 plasma and 31 CCWB samples. In mosquito cell cultures, 29/111 (26.1%) plasma and 32/97 (32.7%) CCWB samples were infectious. A subset of samples from 29 donors was separately analyzed to compare DENV viral loads in the available blood components. DENV viral loads did not differ significantly between components and ranged from 3–8 log 10 PCR-detectable units/ml. In conclusion, DENV was present in all tested components from most donors, and viral RNA was not preferentially distributed in any of the tested components. Infectious DENV was also present in similar proportions in cultured plasma, clot and CCWB samples, indicating that these components may serve as a resource when sample sizes are limited. However, these results suggest that the sensitivity of the nucleic acid tests (NAT) for these viruses would not be improved by testing whole blood or components other than plasma.« less

Metabolomic Quality Assessment of EDTA Plasma and Serum Samples.

PubMed

Malm, Linus; Tybring, Gunnel; Moritz, Thomas; Landin, Britta; Galli, Joakim

2016-10-01

Handling and processing of blood can significantly alter the molecular composition and consistency of biobank samples and can have a major impact on the identification of biomarkers. It is thus crucial to identify tools to determine the quality of samples to be used in biomarker discovery studies. In this study, a non-targeted gas chromatography/time-of-flight mass spectrometry (GC-TOFMS) metabolomic strategy was used with the aim of identifying quality markers for serum and plasma biobank collections lacking proper documentation of preanalytical handling. The effect of postcentrifugation delay was examined in serum stored in tubes with gel separation plugs and ethylenediaminetetraacetic acid (EDTA) plasma in tubes with or without gel separation plugs. The change in metabolic pattern was negligible in all sample types processed within 3 hours after centrifugation regardless of whether the samples were kept at 4°C or 22°C. After 8 and 24 hours postcentrifugation delay before aliquoting, there was a pronounced increase in the number of affected metabolites, as well as in the magnitude of the observed changes. No protective effect on the metabolites was observed in gel-separated EDTA plasma samples. In a separate series of experiments, lactate and glucose levels were determined in plasma to estimate the effect of precentrifugation delay. This separate experiment indicates that the lactate to glucose ratio may serve as a marker to identify samples with delayed time to centrifugation. Although our data from the untargeted GC-TOFMS analysis did not identify any specific markers, we conclude that plasma and serum metabolic profiles remain quite stable when plasma and serum are centrifuged and separated from the blood cells within 3 hours.

Guidelines for Contracting Microfilming Services.

ERIC Educational Resources Information Center

Byrne, Sherry

1986-01-01

Outlines the process involved in selecting an outside filming agent for the purpose of preserving a library's or archive's holdings. Guidelines include project planning, selecting a filming agent, and contract preparation and maintenance. A sample contract is included. (Author/EM)

EBI metagenomics in 2016 - an expanding and evolving resource for the analysis and archiving of metagenomic data

PubMed Central

Mitchell, Alex; Bucchini, Francois; Cochrane, Guy; Denise, Hubert; Hoopen, Petra ten; Fraser, Matthew; Pesseat, Sebastien; Potter, Simon; Scheremetjew, Maxim; Sterk, Peter; Finn, Robert D.

2016-01-01

EBI metagenomics (https://www.ebi.ac.uk/metagenomics/) is a freely available hub for the analysis and archiving of metagenomic and metatranscriptomic data. Over the last 2 years, the resource has undergone rapid growth, with an increase of over five-fold in the number of processed samples and consequently represents one of the largest resources of analysed shotgun metagenomes. Here, we report the status of the resource in 2016 and give an overview of new developments. In particular, we describe updates to data content, a complete overhaul of the analysis pipeline, streamlining of data presentation via the website and the development of a new web based tool to compare functional analyses of sequence runs within a study. We also highlight two of the higher profile projects that have been analysed using the resource in the last year: the oceanographic projects Ocean Sampling Day and Tara Oceans. PMID:26582919

A novel freeze-dried storage and preparation method for the determination of mycophenolic acid in plasma by high-performance liquid chromatography.

PubMed

Wang, Lei; Qiang, Wei; Li, Ying; Cheng, Zeneng; Xie, Mengmeng

2017-09-01

Plasma samples were conventionally stored at freezing conditions until the time of detection. Such a technique, when carried out over an extended period, is energy consuming; in addition, preparation and transportation of stored samples is inconvenient. In this study, a freeze-dried storage and preparation method was proposed to determine the presence of mycophenolic acid (MPA) in plasma. Fresh plasma samples were freeze-dried using a device, and then stored at ambient temperature. After the stored samples were soaked with methanol spiked with the internal standard, high-performance liquid chromatography was conducted to detect MPA. The proposed method was demonstrated to be precise and accurate over the linear range of 0.5-50 μg mL -1 , with both intra- and inter-day precision being <7% and biases <10%. The freeze-dried samples were stable at ambient temperature for at least 40 days. This method was also successfully applied to the pharmacokinetic study of MPA in healthy volunteers. Pharmacokinetic parameters, such as maximum plasma concentration, time point of maximum plasma concentration and elimination half-life, among others, were consistent with the results in the published study. This proposed technique was proved to be simple, reproducible and energy saving. This approach could also simplify the storage and analysis of samples in clinical and scientific drug research. Copyright © 2017 John Wiley & Sons, Ltd.

Experimental study of atmospheric-pressure micro-plasmas for the ambient sampling of conductive materials

NASA Astrophysics Data System (ADS)

Duan, Zhengchao; He, Feng; Si, Xinlu; Bradley, James W.; Ouyang, Jiting

2018-02-01

Conductive solid material sampling by micro-plasma under ambient atmosphere was studied experimentally. A high-voltage pulse generator was utilized to drive discharge between a tungsten needle and metal samples. The effects of pulse width on discharge, micro-plasma and sampling were investigated. The electrical results show that two discharge current pulses can be formed in one voltage pulse. The duration of the first current pulse is of the order of 100 ns. The duration of the second current pulse depends on the width of the voltage pulse. The electrical results also show that arc micro-plasma was generated during both current pulses. The results of the emission spectra of different sampled materials indicate that the relative emission intensity of elemental metal ions will increase with pulse width. The excitation temperature and electron density of the arc micro-plasmas increase with the voltage pulse width, which contributes to the increase of relative emission intensity of metal ions. The optical images and energy dispersive spectroscopy results of the sampling spots on metal surfaces indicate that discharge with a short voltage pulse can generate a small sputtering crater.

Climatically driven loss of calcium in steppe soil as a sink for atmospheric carbon

Treesearch

A.G. Lapenis; G.B. Lawrence; S.W. Bailey; B.F. Aparin; A.I. Shiklomanov; N.A. Speranskaya; M.S. Torn; M. Calef

2008-01-01

During the last several thousand years the semi-arid, cold climate of the Russian steppe formed highly fertile soils rich in organic carbon and calcium (classified as Chernozems in the Russian system). Analysis of archived soil samples collected in Kemannaya Steppe Preserve in 1920, 1947, 1970, and fresh samples collected in 1998 indicated that the native steppe...

A study of hydrocarbons associated with brines from DOE geopressured wells. Final report

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

Keeley, D.F.

1993-07-01

Accomplishments are summarized on the following tasks: distribution coefficients and solubilities, DOE design well sampling, analysis of well samples, review of theoretical models of geopressured reservoir hydrocarbons, monitor for aliphatic hydrocarbons, development of a ph meter probe, DOE design well scrubber analysis, removal and disposition of gas scrubber equipment at Pleasant Bayou Well, and disposition of archived brines.

Archive of Samples for Long-Term Preservation of RNA and Other Nucleic Acids

DTIC Science & Technology

2016-05-15

shaker platform whi le making sure that the tubes are held solidly in the rack. 6.3.4 Transfer the sample from the RNA tubes to the corresponding...well polypropylene u-bottom plate (Final_1) onto position P15. - 25- 6.3.15 Click the green "Play" arrow at the bottom right of the RNAdvance method

A study of hydrocarbons associated with brines from DOE geopressured wells

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

Keeley, D.F.

1993-01-01

Accomplishments are summarized on the following tasks: distribution coefficients and solubilities, DOE design well sampling, analysis of well samples, review of theoretical models of geopressured reservoir hydrocarbons, monitor for aliphatic hydrocarbons, development of a ph meter probe, DOE design well scrubber analysis, removal and disposition of gas scrubber equipment at Pleasant Bayou Well, and disposition of archived brines.

An Improved LC-ESI-MS/MS Method to Quantify Pregabalin in Human Plasma and Dry Plasma Spot for Therapeutic Monitoring and Pharmacokinetic Applications.

PubMed

Dwivedi, Jaya; Namdev, Kuldeep K; Chilkoti, Deepak C; Verma, Surajpal; Sharma, Swapnil

2018-06-06

Therapeutic drug monitoring (TDM) of anti-epileptic drugs provides a valid clinical tool in optimization of overall therapy. However, TDM is challenging due to the high biological samples (plasma/blood) storage/shipment costs and the limited availability of laboratories providing TDM services. Sampling in the form of dry plasma spot (DPS) or dry blood spot (DBS) is a suitable alternative to overcome these issues. An improved, simple, rapid, and stability indicating method for quantification of pregabalin in human plasma and DPS has been developed and validated. Analyses were performed on liquid chromatography tandem mass spectrometer under positive ionization mode of electrospray interface. Pregabain-d4 was used as internal standard, and the chromatographic separations were performed on Poroshell 120 EC-C18 column using an isocratic mobile phase flow rate of 1 mL/min. Stability of pregabalin in DPS was evaluated under simulated real-time conditions. Extraction procedures from plasma and DPS samples were compared using statistical tests. The method was validated considering the FDA method validation guideline. The method was linear over the concentration range of 20-16000 ng/mL and 100-10000 ng/mL in plasma and DPS, respectively. DPS samples were found stable for only one week upon storage at room temperature and for at least four weeks at freezing temperature (-20 ± 5 °C). Method was applied for quantification of pregabalin in over 600 samples of a clinical study. Statistical analyses revealed that two extraction procedures in plasma and DPS samples showed statistically insignificant difference and can be used interchangeably without any bias. Proposed method involves simple and rapid steps of sample processing that do not require a pre- or post-column derivatization procedure. The method is suitable for routine pharmacokinetic analysis and therapeutic monitoring of pregabalin.

Mobile inductively coupled plasma system

DOEpatents

D`Silva, A.P.; Jaselskis, E.J.

1999-03-30

A system is described for sampling and analyzing a material located at a hazardous site. A laser located remotely from the hazardous site is connected to an optical fiber, which directs laser radiation proximate the material at the hazardous site. The laser radiation abates a sample of the material. An inductively coupled plasma is located remotely from the material. An aerosol transport system carries the ablated particles to a plasma, where they are dissociated, atomized and excited to provide characteristic optical reduction of the elemental constituents of the sample. An optical spectrometer is located remotely from the site. A second optical fiber is connected to the optical spectrometer at one end and the plasma source at the other end to carry the optical radiation from the plasma source to the spectrometer. 10 figs.

Development of 2024 AA-Yttrium composites by Spark Plasma Sintering

NASA Astrophysics Data System (ADS)

Vidyasagar, CH S.; Karunakar, D. B.

2018-04-01

The method of fabrication of MMNCs is quite a challenge, which includes advanced processing techniques like Spark Plasma Sintering (SPS), etc. The objective of the present work is to fabricate aluminium based MMNCs with the addition of small amounts of yttrium using Spark Plasma Sintering and to evaluate their mechanical and microstructure properties. Samples of 2024 AA with yttrium ranging from 0.1% to 0.5 wt% are fabricated by Spark Plasma Sintering (SPS). Hardness of the samples is determined using Vickers hardness testing machine. The metallurgical characterization of the samples is evaluated by Optical Microscopy (OM), Field Emission Scanning Electron Microscopy (FE-SEM). Unreinforced 2024 AA sample is also fabricated as a benchmark to compare its properties with those of the composite developed. It is found that the yttrium addition increases the above mentioned properties by altering the precipitation kinetics and intermetallic formation to some extent and then decreases gradually when yttrium wt% increases beyond 0.3 wt%. High density (˂ 99.75) is achieved in the samples and highest hardness achieved is 114 Hv, fabricated by spark plasma sintering and uniform distribution of yttrium is observed.

MRM validation of targeted nonglycosylated peptides from N-glycoprotein biomarkers using direct trypsin digestion of undepleted human plasma.

PubMed

Lee, Ju Yeon; Kim, Jin Young; Cheon, Mi Hee; Park, Gun Wook; Ahn, Yeong Hee; Moon, Myeong Hee; Yoo, Jong Shin

2014-02-26

A rapid, simple, and reproducible MRM-based validation method for serological glycoprotein biomarkers in clinical use was developed by targeting the nonglycosylated tryptic peptides adjacent to N-glycosylation sites. Since changes in protein glycosylation are known to be associated with a variety of diseases, glycoproteins have been major targets in biomarker discovery. We previously found that nonglycosylated tryptic peptides adjacent to N-glycosylation sites differed in concentration between normal and hepatocellular carcinoma (HCC) plasma due to differences in steric hindrance of the glycan moiety in N-glycoproteins to tryptic digestion (Lee et al., 2011). To increase the feasibility and applicability of clinical validation of biomarker candidates (nonglycosylated tryptic peptides), we developed a method to effectively monitor nonglycosylated tryptic peptides from a large number of plasma samples and to reduce the total analysis time with maximizing the effect of steric hindrance by the glycans during digestion of glycoproteins. The AUC values of targeted nonglycosylated tryptic peptides were excellent (0.955 for GQYCYELDEK, 0.880 for FEDGVLDPDYPR and 0.907 for TEDTIFLR), indicating that these could be effective biomarkers for hepatocellular carcinoma. This method provides the necessary throughput required to validate glycoprotein biomarkers, as well as quantitative accuracy for human plasma analysis, and should be amenable to clinical use. Difficulties in verifying and validating putative protein biomarkers are often caused by complex sample preparation procedures required to determine their concentrations in a large number of plasma samples. To solve the difficulties, we developed MRM-based protein biomarker assays that greatly reduce complex, time-consuming, and less reproducible sample pretreatment steps in plasma for clinical implementation. First, we used undepleted human plasma samples without any enrichment procedures. Using nanoLC/MS/MS, we targeted nonglycosylated tryptic peptides adjacent to N-linked glycosylation sites in N-linked glycoprotein biomarkers, which could be detected in human plasma samples without depleting highly abundant proteins. Second, human plasma proteins were digested with trypsin without reduction and alkylation procedures to minimize sample preparation. Third, trypsin digestion times were shortened so as to obtain reproducible results with maximization of the steric hindrance effect of the glycans during enzyme digestion. Finally, this rapid and simple sample preparation method was applied to validate targeted nonglycosylated tryptic peptides as liver cancer biomarker candidates for diagnosis in 40 normal and 41 hepatocellular carcinoma (HCC) human plasma samples. This strategy provided the necessary throughput required to monitor protein biomarkers, as well as quantitative accuracy in human plasma analysis. From biomarker discovery to clinical implementation, our method will provide a biomarker study platform that is suitable for clinical deployment, and can be applied to high-throughput approaches. Copyright © 2014 Elsevier B.V. All rights reserved.

Peptidomic analysis of endogenous plasma peptides from patients with pancreatic neuroendocrine tumours.

PubMed

Kay, Richard G; Challis, Benjamin G; Casey, Ruth T; Roberts, Geoffrey P; Meek, Claire L; Reimann, Frank; Gribble, Fiona M

2018-06-01

Diagnosis of pancreatic neuroendocrine tumours requires the study of patient plasma with multiple immunoassays, using multiple aliquots of plasma. The application of mass spectrometry based techniques could reduce the cost and amount of plasma required for diagnosis. Plasma samples from two patients with pancreatic neuroendocrine tumours were extracted using an established acetonitrile based plasma peptide enrichment strategy. The circulating peptidome was characterised using nano and high flow rate LC/MS analyses. To assess the diagnostic potential of the analytical approach, a large sample batch (68 plasmas) from control subjects, and aliquots from subjects harbouring two different types of pancreatic neuroendocrine tumour (insulinoma and glucagonoma) were analysed using a 10-minute LC/MS peptide screen. The untargeted plasma peptidomics approach identified peptides derived from the glucagon prohormone, chromogranin A, chromogranin B and other peptide hormones and proteins related to control of peptide secretion. The glucagon prohormone derived peptides that were detected were compared against putative peptides that were identified using multiple antibody pairs against glucagon peptides. Comparison of the plasma samples for relative levels of selected peptides showed clear separation between the glucagonoma and the insulinoma and control samples. The combination of the organic solvent extraction methodology with high flow rate analysis could potentially be used to aid diagnosis and monitor treatment of patients with functioning pancreatic neuroendocrine tumours. However, significant validation will be required before this approach can be clinically applied. This article is protected by copyright. All rights reserved.

Retrospective MicroRNA Sequencing: Complementary DNA Library Preparation Protocol Using Formalin-fixed Paraffin-embedded RNA Specimens.

PubMed

Loudig, Olivier; Liu, Christina; Rohan, Thomas; Ben-Dov, Iddo Z

2018-05-05

-Archived, clinically classified formalin-fixed paraffin-embedded (FFPE) tissues can provide nucleic acids for retrospective molecular studies of cancer development. By using non-invasive or pre-malignant lesions from patients who later develop invasive disease, gene expression analyses may help identify early molecular alterations that predispose to cancer risk. It has been well described that nucleic acids recovered from FFPE tissues have undergone severe physical damage and chemical modifications, which make their analysis difficult and generally requires adapted assays. MicroRNAs (miRNAs), however, which represent a small class of RNA molecules spanning only up to ~18-24 nucleotides, have been shown to withstand long-term storage and have been successfully analyzed in FFPE samples. Here we present a 3' barcoded complementary DNA (cDNA) library preparation protocol specifically optimized for the analysis of small RNAs extracted from archived tissues, which was recently demonstrated to be robust and highly reproducible when using archived clinical specimens stored for up to 35 years. This library preparation is well adapted to the multiplex analysis of compromised/degraded material where RNA samples (up to 18) are ligated with individual 3' barcoded adapters and then pooled together for subsequent enzymatic and biochemical preparations prior to analysis. All purifications are performed by polyacrylamide gel electrophoresis (PAGE), which allows size-specific selections and enrichments of barcoded small RNA species. This cDNA library preparation is well adapted to minute RNA inputs, as a pilot polymerase chain reaction (PCR) allows determination of a specific amplification cycle to produce optimal amounts of material for next-generation sequencing (NGS). This approach was optimized for the use of degraded FFPE RNA from specimens archived for up to 35 years and provides highly reproducible NGS data.

Effects of anesthesia and blood sampling techniques on plasma metabolites and corticosterone in the rat.

PubMed

Arnold, Myrtha; Langhans, Wolfgang

2010-04-19

Blood is routinely sampled from laboratory animals in biomedical research, and many of the commonly applied sampling techniques require anesthesia. Acute effects of many sampling and anesthesia procedures may confound the results, but those effects are incompletely characterized. We here compare the effects of four common anesthesia procedures (inhalation anesthesia with ether (EA) or isoflurane (IA) and intraperitoneal injection anesthesia with xylazin/ketamine (XKA) or medetomidine/midazolam/fentanyl (MMFA)) on plasma concentrations of glucose, lactate, non-esterified fatty acids (NEFAs), and corticosterone in blood obtained from a previously implanted jugular vein (JV) catheter with the effect of JV blood sampling from non-anesthetized, freely-moving rats (JV-NA). Also, we included in the comparison two other blood sampling procedures usually performed without anesthesia (NA), i.e., puncture of the saphenic vein (SV) and tail incision (TI). Whereas the control procedure (JV-NA) did not significantly affect any of the target parameters, plasma glucose increased from 14 (JV-IA) to 44 (JV-MMFA) % (all Ps=0.05 when compared with the control procedure) in all blood samples collected in anesthesia and was 12 and 14% lower (both Ps<0.05) in SV-NA and TI-NA samples, respectively. Plasma lactate increased from 74 (JV-IA) to 226% (SV-NA) (all Ps<0.05) with all sampling and anesthesia procedures except for JV-XKA and JV-MMF. Plasma NEFAs increased to 52% (P<0.05) with the TI-NA procedure and appeared to decrease with the JV-IA and JV-MMFA procedures (both Ps>0.05). Finally, only the JV-EA and the JV-MMFA procedures increased plasma corticosterone (+525 and +353%, respectively, both Ps< 0.05). The JV-IA and JV-XKA procedures appeared to increase it as well, but these differences did not reach statistical significance. Thus, anesthesia and blood sampling procedures can have profound acute effects on plasma metabolite and hormone concentrations. This must be considered for the design and interpretation of blood sampling experiments in laboratory animals. (c) 2010. Published by Elsevier Inc.

Determination of the Biological Form of Human Cytomegalovirus DNA in the Plasma of Solid-Organ Transplant Recipients.

PubMed

Tong, Yupin; Pang, Xiaoli L; Mabilangan, Curtis; Preiksaitis, Jutta K

2017-04-01

Whether cytomegalovirus (CMV) DNA exists in plasma as virion-associated or free DNA is uncertain. An assay combining DNase I digestion and CMV quantitative polymerase chain reaction (DNase-CMV-qPCR) was developed to differentiate free naked DNA from virion DNA. One hundred three frozen and 10 fresh CMV DNA-positive plasma samples from solid-organ transplant recipients (SOTRs) were tested. Three sets of paired qPCR (P-qPCR) assays with amplicons of variable length were used to study CMV DNA fragmentation in 20 SOTR plasma samples, viral stocks (Towne, Merlin, AD169) and the first World Health Organization (WHO) international standard (IS) for CMV DNA. In all plasma samples, 98.8%-100% of CMV DNA was free DNA; this was the only form in 93 of 103 (90.3%) frozen and all 10 fresh samples tested using DNase-CMV-qPCR. Low levels of virion CMV DNA were found in 10 of 103 (9.7%) samples with higher total DNA load. Cytomegalovirus DNA results were highly reproducible for 3 CMV virus stocks and WHO IS (P > .80), tested by three sets of paired q-PCR. However, for the 20 SOTR plasma samples, the smaller amplicon assay result was 2.6-fold, 3.4-fold, and 6.5-fold higher than the longer amplicion result (P < .001). Cytomegalovirus DNA in SOTR plasma is almost exclusively free DNA, highly fragmented, and not virion associated. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

Comparison of plasma ammonia results from seven different automated platforms in use throughout Central Australia.

PubMed

Markus, Corey; Metz, Michael

2017-04-01

The clinical catchment area for the Metabolic service at the Women's and Children's Hospital in Adelaide, South Australia, covers nearly 2.5millionkm 2 . Care of children with metabolic disorders in these remote areas is assisted from Adelaide, and at times, using plasma ammonia results from laboratories up to 3000km away. There are seven different platforms measuring plasma ammonia within this vast clinical catchment area. Hence, a correlation study was conducted to examine the relationship between plasma ammonia results from the seven different platforms in use throughout central Australia. Multiple aliquots of plasma from remainder EDTA samples for haematological investigations were frozen. Samples were then dispatched on dry ice to the laboratories being correlated. At an agreed date and time correlation samples were thawed and plasma ammonia measured. Passing-Bablok regression analysis showed slopes ranging from 1.00 to 1.10 and y-intercepts ranging from -10μmol/L to 1μmol/L. Despite the absence of a reference method or reference material and troublesome pre-analytical effects in ammonia measurement, plasma ammonia results from the different platforms in general compare well. The study also demonstrates that samples for ammonia measurement can be transported over great distances and still correlate well. Furthermore, a common reference interval for plasma ammonia may be a possibility. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

Fully automated methods for the determination of hydrochlorothiazide in human plasma and urine.

PubMed

Hsieh, J Y; Lin, C; Matuszewski, B K; Dobrinska, M R

1994-12-01

LC assays utilizing fully automated sample preparation procedures on Zymark PyTechnology Robot and BenchMate Workstation for the quantification of hydrochlorothiazide (HCTZ) in human plasma and urine have been developed. After aliquoting plasma and urine samples, and adding internal standard (IS) manually, the robot executed buffer and organic solvent addition, liquid-liquid extraction, solvent evaporation and on-line LC injection steps for plasma samples, whereas, BenchMate performed buffer and organic solvent addition, liquid-liquid and solid-phase extractions, and on-line LC injection steps for urine samples. Chromatographic separations were carried out on Beckman Octyl Ultrasphere column using the mobile phase composed of 12% (v/v) acetonitrile and 88% of either an ion-pairing reagent (plasma) or 0.1% trifluoroacetic acid (urine). The eluent from the column was monitored with UV detector (271 nm). Peak heights for HCTZ and IS were automatically processed using a PE-Nelson ACCESS*CHROM laboratory automation system. The assays have been validated in the concentration range of 2-100 ng ml-1 in plasma and 0.1-20 micrograms ml-1 in urine. Both plasma and urine assays have the sensitivity and specificity necessary to determine plasma and urine concentrations of HCTZ from low dose (6.25/12.5 mg) administration of HCTZ to human subjects in the presence or absence of losartan.

Plasma creatinine in dogs: intra- and inter-laboratory variation in 10 European veterinary laboratories

PubMed Central

2011-01-01

Background There is substantial variation in reported reference intervals for canine plasma creatinine among veterinary laboratories, thereby influencing the clinical assessment of analytical results. The aims of the study was to determine the inter- and intra-laboratory variation in plasma creatinine among 10 veterinary laboratories, and to compare results from each laboratory with the upper limit of its reference interval. Methods Samples were collected from 10 healthy dogs, 10 dogs with expected intermediate plasma creatinine concentrations, and 10 dogs with azotemia. Overlap was observed for the first two groups. The 30 samples were divided into 3 batches and shipped in random order by postal delivery for plasma creatinine determination. Statistical testing was performed in accordance with ISO standard methodology. Results Inter- and intra-laboratory variation was clinically acceptable as plasma creatinine values for most samples were usually of the same magnitude. A few extreme outliers caused three laboratories to fail statistical testing for consistency. Laboratory sample means above or below the overall sample mean, did not unequivocally reflect high or low reference intervals in that laboratory. Conclusions In spite of close analytical results, further standardization among laboratories is warranted. The discrepant reference intervals seem to largely reflect different populations used in establishing the reference intervals, rather than analytical variation due to different laboratory methods. PMID:21477356

Quantifying K, U, and Th contents of marine sediments using shipboard natural gamma radiation spectra measured on DV JOIDES Resolution

NASA Astrophysics Data System (ADS)

De Vleeschouwer, David; Dunlea, Ann G.; Auer, Gerald; Anderson, Chloe H.; Brumsack, Hans; de Loach, Aaron; Gurnis, Michael; Huh, Youngsook; Ishiwa, Takeshige; Jang, Kwangchul; Kominz, Michelle A.; März, Christian; Schnetger, Bernhard; Murray, Richard W.; Pälike, Heiko

2017-03-01

During International Ocean Discovery Program (IODP) expeditions, shipboard-generated data provide the first insights into the cored sequences. The natural gamma radiation (NGR) of the recovered material, for example, is routinely measured on the ocean drilling research vessel DV JOIDES Resolution. At present, only total NGR counts are readily available as shipboard data, although full NGR spectra (counts as a function of gamma-ray energy level) are produced and archived. These spectra contain unexploited information, as one can estimate the sedimentary contents of potassium (K), thorium (Th), and uranium (U) from the characteristic gamma-ray energies of isotopes in the 40K, 232Th, and 238U radioactive decay series. Dunlea et al. (2013) quantified K, Th, and U contents in sediment from the South Pacific Gyre by integrating counts over specific energy levels of the NGR spectrum. However, the algorithm used in their study is unavailable to the wider scientific community due to commercial proprietary reasons. Here, we present a new MATLAB algorithm for the quantification of NGR spectra that is transparent and accessible to future NGR users. We demonstrate the algorithm's performance by comparing its results to shore-based inductively coupled plasma-mass spectrometry (ICP-MS), inductively coupled plasma-emission spectrometry (ICP-ES), and quantitative wavelength-dispersive X-ray fluorescence (XRF) analyses. Samples for these comparisons come from eleven sites (U1341, U1343, U1366-U1369, U1414, U1428-U1430, and U1463) cored in two oceans during five expeditions. In short, our algorithm rapidly produces detailed high-quality information on sediment properties during IODP expeditions at no extra cost.

High survivorship after catch-and-release fishing suggests physiological resilience in the endothermic shortfin mako shark (Isurus oxyrinchus)

PubMed Central

Lyle, Jeremy; Tracey, Sean; Currie, Suzanne; Semmens, Jayson M

2015-01-01

Abstract The shortfin mako shark (Isurus oxyrinchus) is a species commonly targeted by commercial and recreational anglers in many parts of the developed world. In Australia, the species is targeted by recreational anglers only, under the assumption that most of the sharks are released and populations remain minimally impacted. If released sharks do not survive, the current management strategy will need to be revised. Shortfin mako sharks are commonly subjected to lengthy angling events; however, their endothermic physiology may provide an advantage over ectothermic fishes when recovering from exercise. This study assessed the post-release survival of recreationally caught shortfin mako sharks using Survivorship Pop-up Archival Transmitting (sPAT) tags and examined physiological indicators of capture stress from blood samples as well as any injuries that may be caused by hook selection. Survival estimates were based on 30 shortfin mako sharks captured off the south-eastern coast of Australia. Three mortalities were observed over the duration of the study, yielding an overall survival rate of 90%. All mortalities occurred in sharks angled for <30 min. Sharks experienced increasing plasma lactate with longer fight times and higher sea surface temperatures (SSTs), increased plasma glucose at higher SSTs and depressed expression of heat shock protein 70 and β-hydroxybutyrate at higher SSTs. Long fight times did not impact survival. Circle hooks significantly reduced foul hooking when compared with J hooks. Under the conditions of this study, we found that physical injury associated with hook choice is likely to have contributed to an increased likelihood of mortality, whereas the high aerobic scope associated with the species' endothermy probably enabled it to cope with long fight times and the associated physiological responses to capture. PMID:27303650

The AMBRE Project: Stellar parameterisation of the ESO:UVES archived spectra

NASA Astrophysics Data System (ADS)

Worley, C. C.; de Laverny, P.; Recio-Blanco, A.; Hill, V.; Bijaoui, A.

2016-06-01

Context. The AMBRE Project is a collaboration between the European Southern Observatory (ESO) and the Observatoire de la Côte d'Azur (OCA) that has been established to determine the stellar atmospheric parameters for the archived spectra of four ESO spectrographs. Aims: The analysis of the UVES archived spectra for their stellar parameters was completed in the third phase of the AMBRE Project. From the complete ESO:UVES archive dataset that was received covering the period 2000 to 2010, 51 921 spectra for the six standard setups were analysed. These correspond to approximately 8014 distinct targets (that comprise stellar and non-stellar objects) by radial coordinate search. Methods: The AMBRE analysis pipeline integrates spectral normalisation, cleaning and radial velocity correction procedures in order that the UVES spectra can then be analysed automatically with the stellar parameterisation algorithm MATISSE to obtain the stellar atmospheric parameters. The synthetic grid against which the MATISSE analysis is carried out is currently constrained to parameters of FGKM stars only. Results: Stellar atmospheric parameters are reported for 12 403 of the 51 921 UVES archived spectra analysed in AMBRE:UVES. This equates to ~23.9% of the sample and ~3708 stars. Effective temperature, surface gravity, metallicity, and alpha element to iron ratio abundances are provided for 10 212 spectra (~19.7%), while effective temperature at least is provided for the remaining 2191 spectra. Radial velocities are reported for 36 881 (~71.0%) of the analysed archive spectra. While parameters were determined for 32 306 (62.2%) spectra these parameters were not considered reliable (and thus not reported to ESO) for reasons such as very low S/N, too poor radial velocity determination, spectral features too broad for analysis, and technical issues from the reduction. Similarly the parameters of a further 7212 spectra (13.9%) were also not reported to ESO based on quality criteria and error analysis which were determined within the automated parameterisation process. Those tests lead us to expect that multi-component stellar systems will return high errors in radial velocity and fitting to the synthetic spectra and therefore will not have parameters reported to ESO. Typical external errors of σTeff ~ 110 dex, σlog g ~ 0.18 dex, σ[ M/H ] ~ 0.13 dex, and σ[ α/ Fe ] ~ 0.05 dex with some variation between giants and dwarfs and between setups are reported. Conclusions: UVES is used to observe an extensive collection of stellar and non-stellar objects all of which have been included in the archived dataset provided to OCA by ESO. The AMBRE analysis extracts those objects that lie within the FGKM parameter space of the AMBRE slow-rotating synthetic spectra grid. Thus by homogeneous blind analysis AMBRE has successfully extracted and parameterised the targeted FGK stars (23.9% of the analysed sample) from within the ESO:UVES archive.

The ethical use of existing samples for genome research.

PubMed

Bathe, Oliver F; McGuire, Amy L

2009-10-01

Modern biobanking efforts consist of prospective collections of tissues linked to clinical data for patients who have given informed consent for the research use of their specimens and data, including their DNA. In such efforts, patient autonomy and privacy are well respected because of the prospective nature of the informed consent process. However, one of the richest sources of tissue for research continues to be the millions of archived samples collected by pathology departments during normal clinical care or for research purposes without specific consent for future research or genetic analysis. Because specific consent was not obtained a priori, issues related to individual privacy and autonomy are much more complicated. A framework for accessing these existing samples and related clinical data for research is presented. Archival tissues may be accessed only when there is a reasonable likelihood of generating beneficial and scientifically valid information. To minimize risks, databases containing information related to the tissue and to clinical data should be coded, no personally identifying phenotypic information should be included, and access should be restricted to bona fide researchers for legitimate research purposes. These precautions, if implemented appropriately, should ensure that the research use of archival tissue and data are no more than minimal risk. A waiver of the requirement for informed consent would then be justified if reconsent is shown to be impracticable. A waiver of consent should not be granted, however, if there is a significant risk to privacy, if the proposed research use is inconsistent with the original consent (where there is one), or if the potential harm from a privacy breach is considerable.

Detecting oscillatory patterns and time lags from proxy records with non-uniform sampling: Some pitfalls and possible solutions

NASA Astrophysics Data System (ADS)

Donner, Reik

2013-04-01

Time series analysis offers a rich toolbox for deciphering information from high-resolution geological and geomorphological archives and linking the thus obtained results to distinct climate and environmental processes. Specifically, on various time-scales from inter-annual to multi-millenial, underlying driving forces exhibit more or less periodic oscillations, the detection of which in proxy records often allows linking them to specific mechanisms by which the corresponding drivers may have affected the archive under study. A persistent problem in geomorphology is that available records do not present a clear signal of the variability of environmental conditions, but exhibit considerable uncertainties of both the measured proxy variables and the associated age model. Particularly, time-scale uncertainty as well as the heterogeneity of sampling in the time domain are source of severe conceptual problems that may lead to false conclusions about the presence or absence of oscillatory patterns and their mutual phasing in different archives. In my presentation, I will discuss how one can cope with non-uniformly sampled proxy records to detect and quantify oscillatory patterns in one or more data sets. For this purpose, correlation analysis is reformulated using kernel estimates which are found superior to classical estimators based on interpolation or Fourier transform techniques. In order to characterize non-stationary or noisy periodicities and their relative phasing between different records, an extension of continuous wavelet transform is utilized. The performance of both methods is illustrated for different case studies. An extension to explicitly considering time-scale uncertainties by means of Bayesian techniques is briefly outlined.

Exploring the Potential of a Global Emerging Contaminant Early Warning Network through the Use of Retrospective Suspect Screening with High-Resolution Mass Spectrometry.

PubMed

Alygizakis, Nikiforos A; Samanipour, Saer; Hollender, Juliane; Ibáñez, María; Kaserzon, Sarit; Kokkali, Varvara; van Leerdam, Jan A; Mueller, Jochen F; Pijnappels, Martijn; Reid, Malcolm J; Schymanski, Emma L; Slobodnik, Jaroslav; Thomaidis, Nikolaos S; Thomas, Kevin V

2018-05-01

A key challenge in the environmental and exposure sciences is to establish experimental evidence of the role of chemical exposure in human and environmental systems. High resolution and accurate tandem mass spectrometry (HRMS) is increasingly being used for the analysis of environmental samples. One lauded benefit of HRMS is the possibility to retrospectively process data for (previously omitted) compounds that has led to the archiving of HRMS data. Archived HRMS data affords the possibility of exploiting historical data to rapidly and effectively establish the temporal and spatial occurrence of newly identified contaminants through retrospective suspect screening. We propose to establish a global emerging contaminant early warning network to rapidly assess the spatial and temporal distribution of contaminants of emerging concern in environmental samples through performing retrospective analysis on HRMS data. The effectiveness of such a network is demonstrated through a pilot study, where eight reference laboratories with available archived HRMS data retrospectively screened data acquired from aqueous environmental samples collected in 14 countries on 3 different continents. The widespread spatial occurrence of several surfactants (e.g., polyethylene glycols ( PEGs ) and C12AEO-PEGs ), transformation products of selected drugs (e.g., gabapentin-lactam, metoprolol-acid, carbamazepine-10-hydroxy, omeprazole-4-hydroxy-sulfide, and 2-benzothiazole-sulfonic-acid), and industrial chemicals (3-nitrobenzenesulfonate and bisphenol-S) was revealed. Obtaining identifications of increased reliability through retrospective suspect screening is challenging, and recommendations for dealing with issues such as broad chromatographic peaks, data acquisition, and sensitivity are provided.

Recovery and archiving key Arctic Alaska vegetation map and plot data for the Arctic-Boreal Vulnerability Field Experiment (ABoVE)

NASA Astrophysics Data System (ADS)

Walker, D. A.; Breen, A. L.; Broderson, D.; Epstein, H. E.; Fisher, W.; Grunblatt, J.; Heinrichs, T.; Raynolds, M. K.; Walker, M. D.; Wirth, L.

2013-12-01

Abundant ground-based information will be needed to inform remote-sensing and modeling studies of NASA's Arctic-Boreal Vulnerability Experiment (ABoVE). A large body of plot and map data collected by the Alaska Geobotany Center (AGC) and collaborators from the Arctic regions of Alaska and the circumpolar Arctic over the past several decades is being archived and made accessible to scientists and the public via the Geographic Information Network of Alaska's (GINA's) 'Catalog' display and portal system. We are building two main types of data archives: Vegetation Plot Archive: For the plot information we use a Turboveg database to construct the Alaska portion of the international Arctic Vegetation Archive (AVA) http://www.geobotany.uaf.edu/ava/. High quality plot data and non-digital legacy datasets in danger of being lost have highest priority for entry into the archive. A key aspect of the database is the PanArctic Species List (PASL-1), developed specifically for the AVA to provide a standard of species nomenclature for the entire Arctic biome. A wide variety of reports, documents, and ancillary data are linked to each plot's geographic location. Geoecological Map Archive: This database includes maps and remote sensing products and links to other relevant data associated with the maps, mainly those produced by the Alaska Geobotany Center. Map data include GIS shape files of vegetation, land-cover, soils, landforms and other categorical variables and digital raster data of elevation, multispectral satellite-derived data, and data products and metadata associated with these. The map archive will contain all the information that is currently in the hierarchical Toolik-Arctic Geobotanical Atlas (T-AGA) in Alaska http://www.arcticatlas.org, plus several additions that are in the process of development and will be combined with GINA's already substantial holdings of spatial data from northern Alaska. The Geoecological Atlas Portal uses GINA's Catalog tool to develop a web interface to view and access the plot and map data. The mapping portal allows visualization of GIS data, sample-point locations and imagery and access to the map data. Catalog facilitates the discovery and dissemination of science-based information products in support of analysis and decision-making concerned with development and climate change and is currently used by GINA in several similar archive/distribution portals.

Metabolomics: A Window for Understanding Long Term Physical Consequences of Distrubed Sleep and Hypothalamic Pituitary Adrenal Function in Posttraumatic Stress

DTIC Science & Technology

2017-09-01

performed on pre -collected plasma samples from a study that had a two- group cross-sectional design in which main comparisons were with medically...controls. Approach Metabolomic analysis will be performed on pre -collected plasma samples from a study that had a two- group cross-sectional design in...disturbances, and health. Metabolomic analysis will be performed on pre -collected plasma samples from a study that had a two- group cross-sectional

The effect of surface nanocrystallization on plasma nitriding behaviour of AISI 4140 steel

NASA Astrophysics Data System (ADS)

Li, Yang; Wang, Liang; Zhang, Dandan; Shen, Lie

2010-11-01

A plastic deformation surface layer with nanocrystalline grains was produced on AISI 4140 steel by means of surface mechanical attrition treatment (SMAT). Plasma nitriding of SMAT and un-SMAT AISI 4140 steel was carried out by a low-frequency pulse excited plasma unit. A series of nitriding experiments has been conducted at temperatures ranging from 380 to 500 °C for 8 h in an NH 3 gas. The samples were characterized using X-ray diffraction, scanning electron microscopy, optical microscopy and Vickers microhardness tester. The results showed that a much thicker compound layer with higher hardness was obtained for the SMAT samples when compared with un-SMAT samples after nitriding at the low temperature. In particular, plasma nitriding SMAT AISI 4140 steel at 380 °C for 8 h can produced a compound layer of 2.5 μm thickness with very high hardness on the surface, which is similar to un-SMAT samples were plasma nitrided at approximately 430 °C within the same time.

Solvent-modified solid-phase microextraction for the determination of diazepam in human plasma samples by capillary gas chromatography.

PubMed

Krogh, M; Grefslie, H; Rasmussen, K E

1997-02-21

This paper describes microextraction and gas chromatographic analysis of diazepam from human plasma. The method was based on immobilisation of 1.5 microliters of 1-octanol on a polyacrylate-coated fiber designed for solid-phase microextraction. The solvent-modified fibre was used to extract diazepam from the samples. The plasma sample was pre-treated to release diazepam from the protein binding. The fibre was inserted into the modified plasma sample, adjusted to pH 5.5 an internal standard was added and the mixture was carefully stirred for 4 min. The fibre with the immobilised solvent and the enriched analytes was injected into the capillary gas chromatograph. The solvent and the extracted analytes were evaporated at 300 degrees C in the split-splitless injection port of the gas chromatograph, separated on a methylsilicon capillary column and detected with a nitrogen-phosphorus detector. The method was shown to be reproducible with a detection limit of 0.10 nmol/ml in human plasma.

Quantitative evaluation of plasma after methylene blue and white light treatment in four Chinese blood centers.

PubMed

Chunhui, Yang; Guohui, Bian; Hong, Yang; Xiaopu, Xiao; Zherong, Bai; Mingyuan, Wang; Xinsheng, Zhang; Juanjuan, Wang; Changqing, Li; Wuping, Li

2013-12-01

Pathogen reduction technology is an important process in the blood safety system, including solvent/detergent treatment, filtration and methylene blue-photochemical technology (MB-PCT). To investigate the quality of MB-PCT-treated plasma, plasma samples from four Chinese blood centers were analyzed over 12 months of storage to determine the recovery of activities and levels of various plasma proteins. Ten plasma units each from the Suzhou, Yancheng, Chongqing and Shandong blood centers were divided into two aliquots. One was subjected to treatment with one of two methylene blue-photochemical technology instruments and the other was used as control. The treated and untreated sample pairs were stored at -30°C. The recovery rates of coagulation factors, inhibitor proteins, total protein, immunoglobulins, and complement proteins were measured at different time points after storage. The mean recovery of most proteins exceeded 80% after MB treatment. The exceptions were factor XI and fibrinogen, of which only 71.3-74% and 69.0-92.3% were retained during storage. The two equipment types differed in terms of residual MB concentration in the plasma samples (0.18 μM and 0.29 μM, respectively). They had similar protein recovery rates at 0.5 month but differed at later time points. The four blood centers differed significantly with regard to factor II, V, VIII and fibrinogen activities. Only the samples from the Shandong blood center met the methylene blue treated fresh frozen plasma requirement. The major factor that influenced the quality of the MB-FFP samples was the time taken between blood collection and storage. Methylene blue treated plasma showed reduced coagulation factor (CF) activity and protein levels. The MB treatment-induced damage to the proteins was acceptable at the four Chinese blood centers, but the quality of the MB-treated plasma in general was not satisfactory. The main factor affecting plasma quality may be the duration of the collection and processing. Copyright © 2013 Elsevier Ltd. All rights reserved.

Simple, miniaturized blood plasma extraction method.

PubMed

Kim, Jin-Hee; Woenker, Timothy; Adamec, Jiri; Regnier, Fred E

2013-12-03

A rapid plasma extraction technology that collects a 2.5 μL aliquot of plasma within three minutes from a finger-stick derived drop of blood was evaluated. The utility of the plasma extraction cards used was that a paper collection disc bearing plasma was produced that could be air-dried in fifteen minutes and placed in a mailing envelop for transport to an analytical laboratory. This circumvents the need for venipuncture and blood collection in specialized vials by a phlebotomist along with centrifugation and refrigerated storage. Plasma extraction was achieved by applying a blood drop to a membrane stack through which plasma was drawn by capillary action. During the course of plasma migration to a collection disc at the bottom of the membrane stack blood cells were removed by a combination of adsorption and filtration. After the collection disc filled with an aliquot of plasma the upper membranes were stripped from the collection card and the collection disc was air-dried. Intercard differences in the volume of plasma collected varied approximately 1% while volume variations of less than 2% were seen with hematocrit levels ranging from 20% to 71%. Dried samples bearing metabolites and proteins were then extracted from the disc and analyzed. 25-Hydroxy vitamin D was quantified by LC-MS/MS analysis following derivatization with a secosteroid signal enhancing tag that imparted a permanent positive charge to the vitamin and reduced the limit of quantification (LOQ) to 1 pg of collected vitamin on the disc; comparable to values observed with liquid-liquid extraction (LLE) of a venipuncture sample. A similar study using conventional proteomics methods and spectral counting for quantification was conducted with yeast enolase added to serum as an internal standard. The LOQ with extracted serum samples for enolase was 1 μM, linear from 1 to 40 μM, the highest concentration examined. In all respects protein quantification with extracted serum samples was comparable to that observed with serum samples obtained by venipuncture.

Museums and disease: using tissue archive and museum samples to study pathogens.

PubMed

Tsangaras, Kyriakos; Greenwood, Alex D

2012-01-20

Molecular studies of archival and fossil samples have traditionally focused on the nucleic acids derived from the host species. However, there has recently been an increase in ancient DNA research on the identification and characterization of infectious agents within the hosts. The study of pathogens from the past provides great opportunities for discovering the causes of historical infection events, characterizing host-microorganism co-evolution and directly investigating the evolution of specific pathogens. Several research teams have been able to isolate and characterize a variety of different bacterial, parasite and viral microorganisms. However, this emerging field is not without obstacles. The diagenetic processes that make ancient DNA research generally difficult are also impediments to ancient pathogen research and perhaps more so given that their DNA may represent an even rarer proportion of the remaining nucleic acids in a fossil sample than host DNA. However, studies performed under controlled conditions and following stringent ancient DNA protocols can and have yielded reliable and often surprising results. This article reviews the advantages, problems, and failures of ancient microbiological research. Copyright © 2011 Elsevier GmbH. All rights reserved.

Direct Formalin Fixation Induces Widespread Genomic Effects in Archival Tissues

EPA Science Inventory

Recent advances in next generation sequencing have dramatically improved transcriptional analysis of degraded RNA from formalin-fixed paraffin-embedded (FFPE) samples. However, little is known about potential genomic artifacts induced by formalin fixation, which could affect toxi...

TEAM Webinar Series | EGRP/DCCPS/NCI/NIH

Cancer.gov

View archived webinars from the Transforming Epidemiology through Advanced Methods (TEAM) Webinar Series, hosted by NCI's Epidemiology and Genomics Research Program. Topics include participant engagement, data coordination, mHealth tools, sample selection, and instruments for diet & physical activity assessment.

The Genome Austria Tissue Bank (GATiB).

PubMed

Asslaber, M; Abuja, P M; Stark, K; Eder, J; Gottweis, H; Trauner, M; Samonigg, H; Mischinger, H J; Schippinger, W; Berghold, A; Denk, H; Zatloukal, K

2007-01-01

In the context of the Austrian Genome Program, a tissue bank is being established (Genome Austria Tissue Bank, GATiB) which is based on a collection of diseased and corresponding normal tissues representing a great variety of diseases at their natural frequency of occurrence from a non-selected Central European population of more than 700,000 patients. Major emphasis is put on annotation of archival tissue with comprehensive clinical data, including follow-up data. A specific IT infrastructure supports sample annotation, tracking of sample usage as well as sample and data storage. Innovative data protection tools were developed which prevent sample donor re-identification, particularly if detailed medical and genetic data are combined. For quality control of old archival tissues, new techniques were established to check RNA quality and antigen stability. Since 2003, GATiB has changed from a population-based tissue bank to a disease-focused biobank comprising major cancers such as colon, breast, liver, as well as metabolic liver diseases and organs affected by the metabolic syndrome. Prospectively collected tissues are associated with blood samples and detailed data on the sample donor's disease, lifestyle and environmental exposure, following standard operating procedures. Major emphasis is also placed on ethical, legal and social issues (ELSI) related to biobanks. A specific research project and an international advisory board ensure the proper embedding of GATiB in society and facilitate international networking. (c) 2007 S. Karger AG, Basel.

Method and apparatus for chemical and topographical microanalysis

NASA Technical Reports Server (NTRS)

Kossakovski, Dmitri A. (Inventor); Baldeschwieler, John D. (Inventor); Beauchamp, Jesse L. (Inventor)

2002-01-01

A scanning probe microscope is combined with a laser induced breakdown spectrometer to provide spatially resolved chemical analysis of the surface correlated with the surface topography. Topographical analysis is achieved by scanning a sharp probe across the sample at constant distance from the surface. Chemical analysis is achieved by the means of laser induced breakdown spectroscopy by delivering pulsed laser radiation to the sample surface through the same sharp probe, and consequent collection and analysis of emission spectra from plasma generated on the sample by the laser radiation. The method comprises performing microtopographical analysis of the sample with a scanning probe, selecting a scanned topological site on the sample, generating a plasma plume at the selected scanned topological site, and measuring a spectrum of optical emission from the plasma at the selected scanned topological site. The apparatus comprises a scanning probe, a pulsed laser optically coupled to the probe, an optical spectrometer, and a controller coupled to the scanner, laser and spectrometer for controlling the operation of the scanner, laser and spectrometer. The probe and scanner are used for topographical profiling the sample. The probe is also used for laser radiation delivery to the sample for generating a plasma plume from the sample. Optical emission from the plasma plume is collected and delivered to the optical spectrometer so that analysis of emission spectrum by the optical spectrometer allows for identification of chemical composition of the sample at user selected sites.

Direct measurements of sample heating by a laser-induced air plasma in pre-ablation spark dual-pulse laser-induced breakdown spectroscopy (LIBS).

PubMed

Register, Janna; Scaffidi, Jonathan; Angel, S Michael

2012-08-01

Direct measurements of temperature changes were made using small thermocouples (TC), placed near a laser-induced air plasma. Temperature changes up to ~500 °C were observed. From the measured temperature changes, estimates were made of the amount of heat absorbed per unit area. This allowed calculations to be made of the surface temperature, as a function of time, of a sample heated by the air plasma that is generated during orthogonal pre-ablation spark dual-pulse (DP) LIBS measurements. In separate experiments, single-pulse (SP) LIBS emission and sample ablation rate measurements were performed on nickel at sample temperatures ranging from room temperature to the maximum surface temperature that was calculated using the TC measurement results (500 °C). A small, but real sample temperature-dependent increase in both SP LIBS emission and the rate of sample ablation was found for nickel samples heated up to 500 °C. Comparison of DP LIBS emission enhancement values for bulk nickel samples at room temperature versus the enhanced SP LIBS emission and sample ablation rates observed as a function of increasing sample temperature suggests that sample heating by the laser-induced air plasma plays only a minor role in DP LIBS emission enhancement.

A system of equations to approximate the pharmacokinetic parameters of lacosamide at steady state from one plasma sample.

PubMed

Cawello, Willi; Schäfer, Carina

2014-08-01

Frequent plasma sampling to monitor pharmacokinetic (PK) profile of antiepileptic drugs (AEDs), is invasive, costly and time consuming. For drugs with a well-defined PK profile, such as AED lacosamide, equations can accurately approximate PK parameters from one steady-state plasma sample. Equations were derived to approximate steady-state peak and trough lacosamide plasma concentrations (Cpeak,ss and Ctrough,ss, respectively) and area under concentration-time curve during dosing interval (AUCτ,ss) from one plasma sample. Lacosamide (ka: ∼2 h(-1); ke: ∼0.05 h(-1), corresponding to half-life of 13 h) was calculated to reach Cpeak,ss after ∼1 h (tmax,ss). Equations were validated by comparing approximations to reference PK parameters obtained from single plasma samples drawn 3-12h following lacosamide administration, using data from double-blind, placebo-controlled, parallel-group PK study. Values of relative bias (accuracy) between -15% and +15%, and root mean square error (RMSE) values≤15% (precision) were considered acceptable for validation. Thirty-five healthy subjects (12 young males; 11 elderly males, 12 elderly females) received lacosamide 100mg/day for 4.5 days. Equation-derived PK values were compared to reference mean Cpeak,ss, Ctrough,ss and AUCτ,ss values. Equation-derived PK data had a precision of 6.2% and accuracy of -8.0%, 2.9%, and -0.11%, respectively. Equation-derived versus reference PK values for individual samples obtained 3-12h after lacosamide administration showed correlation (R2) range of 0.88-0.97 for AUCτ,ss. Correlation range for Cpeak,ss and Ctrough,ss was 0.65-0.87. Error analyses for individual sample comparisons were independent of time. Derived equations approximated lacosamide Cpeak,ss, Ctrough,ss and AUCτ,ss using one steady-state plasma sample within validation range. Approximated PK parameters were within accepted validation criteria when compared to reference PK values. Copyright © 2014 Elsevier B.V. All rights reserved.

Comparison of Performance Characteristics of Aspergillus PCR in Testing a Range of Blood-Based Samples in Accordance with International Methodological Recommendations.

PubMed

Springer, Jan; White, P Lewis; Hamilton, Shanna; Michel, Denise; Barnes, Rosemary A; Einsele, Hermann; Löffler, Juergen

2016-03-01

Standardized methodologies for the molecular detection of invasive aspergillosis (IA) have been established by the European Aspergillus PCR Initiative for the testing of whole blood, serum, and plasma. While some comparison of the performance of Aspergillus PCR when testing these different sample types has been performed, no single study has evaluated all three using the recommended protocols. Standardized Aspergillus PCR was performed on 423 whole-blood pellets (WBP), 583 plasma samples, and 419 serum samples obtained from hematology patients according to the recommendations. This analysis formed a bicenter retrospective anonymous case-control study, with diagnosis according to the revised European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) consensus definitions (11 probable cases and 36 controls). Values for clinical performance using individual and combined samples were calculated. For all samples, PCR positivity was significantly associated with cases of IA (for plasma, P = 0.0019; for serum, P = 0.0049; and for WBP, P = 0.0089). Plasma PCR generated the highest sensitivity (91%); the sensitivities for serum and WBP PCR were 80% and 55%, respectively. The highest specificity was achieved when testing WBP (96%), which was significantly superior to the specificities achieved when testing serum (69%, P = 0.0238) and plasma (53%, P = 0.0002). No cases were PCR negative in all specimen types, and no controls were PCR positive in all specimens. This study confirms that Aspergillus PCR testing of plasma provides robust performance while utilizing commercial automated DNA extraction processes. Combining PCR testing of different blood fractions allows IA to be both confidently diagnosed and excluded. A requirement for multiple PCR-positive plasma samples provides similar diagnostic utility and is technically less demanding. Time to diagnosis may be enhanced by testing multiple contemporaneously obtained sample types. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Direct and rapid mass spectral fingerprinting of maternal urine for the detection of Down syndrome pregnancy.

PubMed

Iles, Ray K; Shahpari, Maryam E; Cuckle, Howard; Butler, Stephen A

2015-01-01

The established methods of antenatal screening for Down syndrome are based on immunoassay for a panel of maternal serum biomarkers together with ultrasound measures. Recently, genetic analysis of maternal plasma cell free (cf) DNA has begun to be used but has a number of limitations including excessive turn-around time and cost. We aimed to develop an alternative method based on urinalysis that is simple, affordable and accurate. 101 maternal urine samples sampled at 12-17 weeks gestation were taken from an archival collection of 2567 spot urines collected from women attending a prenatal screening clinic. 18 pregnancies in this set subsequently proved to be Down pregnancies. Samples were either neat urine or diluted between 10 to 1000 fold in dH2O and subjected to matrix assisted laser desorption ionization (MALDI), time of flight (ToF) mass spectrometry (MS). Data profiles were examined in the region 6,000 to 14,000 m/z. Spectral data was normalised and quantitative characteristics of the profile were compared between Down and controls. In Down cases there were additional spectral profile peaks at 11,000-12,000 m/z and a corresponding reduction in intensity at 6,000-8,000 m/z. The ratio of the normalised values at these two ranges completely separated the 8 Down syndrome from the 39 controls at 12-14 weeks. Discrimination was poorer at 15-17 weeks where 3 of the 10 Down syndrome cases had values within the normal range. Direct MALDI ToF mass spectral profiling of maternal urinary has the potential for an affordable, simple, accurate and rapid alternative to current Down syndrome screening protocols.

Impact of Pre-analytic Blood Sample Collection Factors on Metabolomics.

PubMed

Townsend, Mary K; Bao, Ying; Poole, Elizabeth M; Bertrand, Kimberly A; Kraft, Peter; Wolpin, Brian M; Clish, Clary B; Tworoger, Shelley S

2016-05-01

Many epidemiologic studies are using metabolomics to discover markers of carcinogenesis. However, limited data are available on the influence of pre-analytic blood collection factors on metabolite measurement. We quantified 166 metabolites in archived plasma from 423 Health Professionals Follow-up Study and Nurses' Health Study participants using liquid chromatography-tandem mass spectrometry (LC-MS). We compared multivariable-adjusted geometric mean metabolite LC-MS peak areas across fasting time, season of blood collection, and time of day of blood collection categories. The majority of metabolites (160 of 166 metabolites) had geometric mean peak areas that were within 15% comparing samples donated after fasting 9 to 12 versus ≥13 hours; greater differences were observed in samples donated after fasting ≤4 hours. Metabolite peak areas generally were similar across season of blood collection, although levels of certain metabolites (e.g., bile acids and purines/pyrimidines) tended to be different in the summer versus winter months. After adjusting for fasting status, geometric mean peak areas for bile acids and vitamins, but not other metabolites, differed by time of day of blood collection. Fasting, season of blood collection, and time of day of blood collection were not important sources of variability in measurements of most metabolites in our study. However, considering blood collection variables in the design or analysis of studies may be important for certain specific metabolites, particularly bile acids, purines/pyrimidines, and vitamins. These results may be useful for investigators formulating analysis plans for epidemiologic metabolomics studies, including determining which metabolites to a priori exclude from analyses. Cancer Epidemiol Biomarkers Prev; 25(5); 823-9. ©2016 AACR. ©2016 American Association for Cancer Research.

Tenofovir-based regimens associated with less drug resistance in HIV-1-infected Nigerians failing first-line antiretroviral therapy.

PubMed

Etiebet, Mary-Ann A; Shepherd, James; Nowak, Rebecca G; Charurat, Man; Chang, Harry; Ajayi, Samuel; Elegba, Olufunmilayo; Ndembi, Nicaise; Abimiku, Alashle; Carr, Jean K; Eyzaguirre, Lindsay M; Blattner, William A

2013-02-20

In resource-limited settings, HIV-1 drug resistance testing to guide antiretroviral therapy (ART) selection is unavailable. We retrospectively conducted genotypic analysis on archived samples from Nigerian patients who received targeted viral load testing to confirm treatment failure and report their drug resistance mutation patterns. Stored plasma from 349 adult patients on non-nucleoside reverse transcriptase inhibitor (NNRTI) regimens was assayed for HIV-1 RNA viral load, and samples with more than 1000 copies/ml were sequenced in the pol gene. Analysis for resistance mutations utilized the IAS-US 2011 Drug Resistance Mutation list. One hundred and seventy-five samples were genotyped; the majority of the subtypes were G (42.9%) and CRF02_AG (33.7%). Patients were on ART for a median of 27 months. 90% had the M184V/I mutation, 62% had at least one thymidine analog mutation, and 14% had the K65R mutation. 97% had an NNRTI resistance mutation and 47% had at least two etravirine-associated mutations. In multivariate analysis tenofovir-based regimens were less likely to have at least three nucleoside reverse transcriptase inhibitor (NRTI) mutations after adjusting for subtype, previous ART, CD4, and HIV viral load [P < 0.001, odds ratio (OR) 0.04]. 70% of patients on tenofovir-based regimens had at least two susceptible NRTIs to include in a second-line regimen compared with 40% on zidovudine-based regimens (P = 0.04, OR = 3.4). At recognition of treatment failure, patients on tenofovir-based first-line regimens had fewer NRTI drug-resistant mutations and more active NRTI drugs available for second-line regimens. These findings can inform strategies for ART regimen sequencing to optimize long-term HIV treatment outcomes in low-resource settings.

Rosetta Planetary Science Archive (PSA) Status

NASA Astrophysics Data System (ADS)

Wirth, Kristin R.; Cardesin, A.; Barthelemy, M.; Diaz del Rio, J.; Zender, J.; Arviset, C.

2006-09-01

The Planetary Science Archive (PSA) is an online database (accessible via http://www.rssd.esa.int/PSA) implemented by ESA/RSSD. Currently the PSA contains the science data from the Giotto (Halley), Mars Express and SMART-1 (Moon) missions, and the Rosetta Supplementary Archive (Wirtanen). The PSA user is offered a broad range of search possibilities. Search queries can be combined without restrictions and are executed across the whole database. The PSA utilizes the Planetary Data System (PDS) standard. In spring 2007 the PSA will provide the first science and engineering data collected by Rosetta. In preparation for the initial Peer Review to be performed before publication of these data, an Internal Review was held in March 2006, executed by staff internal to the organizations responsible for the Rosetta archiving (ESA, PDS, CNES). The Internal Reviewers identified shortcomings in documentation, data structures, and completeness of the data delivery. They recommended the usage of unified conventions and formats across different instruments. Work is ongoing to include standardized geometry information in the datasets. Rosetta was launched in March 2004 to rendezvous with comet 67P/Churyumov-Gerasimenko (C-G) in May 2014. After having placed a lander on the comet's surface, the Rosetta orbiter will continue to orbit C-G and accompany the comet through perihelion. Rosetta makes use of three Earth swingbys and one Mars swingby in order to reach C-G. Rosetta will also perform close flybys at two asteroids, namely 2867 Steins in September 2008 and 21 Lutetia in July 2010. In addition, Rosetta makes scientific observations of targets of opportunity, e.g. lightcurves of the flyby asteroids to study the rotation, and plasma measurements when passing through cometary ion tails or meteoroid streams. Rosetta continuously monitored the encounter of the Deep Impact probe with comet 9P/Tempel 1 over an extended period of 16 days around the impact on 4 July 2005.

Migrating the Dawn Data Archive to the PDS4 Standard

NASA Astrophysics Data System (ADS)

Joy, S. P.; Mafi, J. N.; King, T. A.; Raymond, C. A.; Russell, C. T.

2017-12-01

The Dawn mission was proposed prior to the development of the PDS4 standard and all of its data are archived at the PDS Small Bodies Node (SBN) using the older PDS3 standard. Plans to migrate the existing PDS archives to PDS4 have been discussed within PDS for some time, and have been reemphasized in the PDS Roadmap Study for 2017 - 2026 (https://pds.nasa.gov/roadmap/PlanetaryDataSystemRMS17-26_20jun17.pdf). Updating the Dawn metadata to PDS4 would enable users of those data to take advantage of new capabilities offered by PDS4, and insure the full compatibility of past archives with current and future PDS4 tools and services. The Dawn data themselves will not require any reformatting during the migration to PDS4. The data and documentation will need to be reorganized and the metadata enhanced to fill in the gaps in the PDS3 metadata. The planned migration to PDS4 would be primarily carried out at the Dawn Science Center (DSC) at UCLA but the activity will require close coordination with the PDS-SBN. The PDS4 standard allows individual nodes to customize the metadata through the use of optional parameters and local data dictionaries to satisfy discipline and mission specific search and retrieval requirements and support node tools and services. The DSC shares much of its staff with the Planetary Plasma Interactions (PPI) Node of the PDS. This sharing of personnel means that the DSC staff are well versed in the PDS4 standard, have actively participated in the development of this standard, and are fully trained in the use of PPI tools for PDS4 metadata migration and/or generation. The combination of PDS4 training and detailed understanding of the Dawn mission, instruments, and datasets makes the DSC the most cost-effective organization to migrate these data to PDS4.

Effect of new Vacutainer blood collection tubes on plasma lidocaine concentrations.

PubMed

Lopez, L M; Sen, A; Robinson, J D; Curry, R W

1987-12-01

This study was designed to establish whether plasma lidocaine concentrations changed subsequent to contact with a new formulation of rubber-stopper Vacutainer collection tubes. Plasma lidocaine concentrations from blood samples exposed to rubber stoppers for one hour were compared with concentrations from blood samples which were not exposed to rubber stoppers. Plasma lidocaine concentrations remained essentially unchanged following one-hour exposure to Vacutainer rubber stoppers. The new formulation of "red-top" Vacutainer may be used reliably in lidocaine therapeutic drug monitoring.

Investigation of the Transport of Solar Ions Through the Earth's Magnetosphere

NASA Technical Reports Server (NTRS)

Lennartsson, O. W.; Evans, David (Technical Monitor)

2000-01-01

The objective of this study has been to infer, by statistical means, the most probable mode of entry of solar wind plasma into Earth's magnetotail, using a particular set of archived data from the Lockheed Plasma Composition Experiment on the International Sun-Earth Explorer One (ISEE-1) satellite, jointly sponsored by the National Aeronautics and Space Administration (NASA) and the European Space Agency (ESA) in the 1970's and 80's. Despite their considerable age, the Lockheed ISEE-1 data are still, at the time of this report, the only substantial ion composition data in the sub-keV to keV energy range available from the magnetotail beyond 9 R(sub E), because of various technical problems with ion mass spectrometers on later missions, and are therefore a unique source of information about the mixing of solar and terrestrial origin plasmas in the tail, within the ISEE-1 apogee of almost 23 R(sub E). The entire set of archived data used in this study, covering the 4.5 years of operation of the instrument and comprising not only tail measurements but also data from the inner magnetosphere as well as data from outside the magnetopause, is now available to the public via the WorldWideWeb at the address: http://cis.spasci.com/ISEE_ions The fundamental assumption of this and other studies of magnetosphere ion composition is that He++ and O+ ions are virtually certain "tags" of solar and terrestrial origins, respectively. This is an assumption with strong theoretical basis and it is corroborated by observational evidence, including the often substantial differences between the velocity distribution functions of those two species. The H+ ions can have a dual origin, in principle, but the close resemblance in the ISEE-1 data between the dynamics of H+ and He++ ions indicates a predominantly solar origin of the H+ ions in the tail, at least. By the same token, the usually minor He+ ions are probably almost entirely of terrestrial origin, because of their similarity to the O+ ions.

NASA's Planetary Data System: Support for the Delivery of Derived Data Sets at the Atmospheres Node

NASA Astrophysics Data System (ADS)

Chanover, Nancy J.; Beebe, Reta; Neakrase, Lynn; Huber, Lyle; Rees, Shannon; Hornung, Danae

2015-11-01

NASA’s Planetary Data System is charged with archiving electronic data products from NASA planetary missions that are sponsored by NASA’s Science Mission Directorate. This archive, currently organized by science disciplines, uses standards for describing and storing data that are designed to enable future scientists who are unfamiliar with the original experiments to analyze the data, and to do this using a variety of computer platforms, with no additional support. These standards address the data structure, description contents, and media design. The new requirement in the NASA ROSES-2015 Research Announcement to include a Data Management Plan will result in an increase in the number of derived data sets that are being delivered to the PDS. These data sets may come from the Planetary Data Archiving, Restoration and Tools (PDART) program, other Data Analysis Programs (DAPs) or be volunteered by individuals who are publishing the results of their analysis. In response to this increase, the PDS Atmospheres Node is developing a set of guidelines and user tools to make the process of archiving these derived data products more efficient. Here we provide a description of Atmospheres Node resources, including a letter of support for the proposal stage, a communication schedule for the planned archive effort, product label samples and templates in extensible markup language (XML), documentation templates, and validation tools necessary for producing a PDS4-compliant derived data bundle(s) efficiently and accurately.

VizieR Online Data Catalog: Star formation in active and normal galaxies (Tsai+, 2015)

NASA Astrophysics Data System (ADS)

Tsai, M.; Hwang, C.-Y.

2015-11-01

We selected 104 active galaxies from the lists of Melendez et al. (2010MNRAS.406..493M), Condon et al. 1991 (cat. J/ApJ/378/65), and Ho & Ulvestad 2001 (cat. J/ApJS/133/77). Most of the sources are identified as Active Galactic Nuclei (AGNs), and a few of them are classified as Luminous InfraRed Galaxies (LIRGs). We obtained 3.6 and 8μm infrared images of these galaxies from the Spitzer Archive (http://sha.ipac.caltech.edu/applications/Spitzer/SHA/) and 8GHz images from the VLA archive (http://archive.nrao.edu/archive/archiveimage.html). We also selected a nearby AGN sub-sample containing 21 radio-selected AGNs for further spatial analysis. We selected 25 nearby AGNs exhibiting no detected radio emission in order to compare with the results of the radio-selected sources. For comparison, we also selected normal galaxies with distances less than 15Mpc from the catalog of Tully 1994 (see cat. VII/145). We only selected the galaxies that have Spitzer archive data and are not identified as AGNs in either the Veron-Cetty & Veron 2006 (see cat. VII/258) AGN catalog or in the NED database (http://ned.ipac.caltech.edu/). Our results for the radio-selected and the non-radio-selected active galaxies are listed in Table1, and those for the normal galaxies are listed in Table2. (2 data files).

Natural dyeing and UV protection of plasma treated cotton

NASA Astrophysics Data System (ADS)

Gorjanc, Marija; Mozetič, Miran; Vesel, Alenka; Zaplotnik, Rok

2018-03-01

Raw cotton fabrics have been exposed to low-pressure non-equilibrium gaseous plasma to improve the adsorption of natural dyes as well as ultraviolet (UV) protection factor. Plasma created in a glass tube by an electrodeless radiofrequency (RF) discharge was created either in oxygen or ammonia at the pressure of 50 Pa to stimulate formation of oxygen and nitrogen groups, respectively. The type and concentration of functional groups was determined by X-ray photoelectron spectroscopy (XPS) and morphological modifications by scanning electron microscopy (SEM). The colour yield for curcumin dye was improved significantly for samples treated with ammonia plasma what was explained by bonding of the dye to surface of amino groups. Contrary, the yield decreased when oxygen plasma treatment was applied due to the negatively charged surface that repels the negatively charged dye molecules. The effect was even more pronounced when using green tea extract as the colouring agent. The colour difference between the untreated and ammonia plasma treated sample increased linearly with plasma treatment time reaching the factor of 3.5 for treatment time of 300 s. The ultraviolet protection factor (UPF) was over 50 indicating excellent protection due to improved adsorption of the dye on the ammonia plasma treated samples.

Pulsed, atmospheric pressure plasma source for emission spectrometry

DOEpatents

Duan, Yixiang; Jin, Zhe; Su, Yongxuan

2004-05-11

A low-power, plasma source-based, portable molecular light emission generator/detector employing an atmospheric pressure pulsed-plasma for molecular fragmentation and excitation is described. The average power required for the operation of the plasma is between 0.02 W and 5 W. The features of the optical emission spectra obtained with the pulsed plasma source are significantly different from those obtained with direct current (dc) discharge higher power; for example, strong CH emission at 431.2 nm which is only weakly observed with dc plasma sources was observed, and the intense CN emission observed at 383-388 nm using dc plasma sources was weak in most cases. Strong CN emission was only observed using the present apparatus when compounds containing nitrogen, such as aniline were employed as samples. The present apparatus detects dimethylsulfoxide at 200 ppb using helium as the plasma gas by observing the emission band of the CH radical. When coupled with a gas chromatograph for separating components present in a sample to be analyzed, the present invention provides an apparatus for detecting the arrival of a particular component in the sample at the end of the chromatographic column and the identity thereof.

Effects of combined plasma chromizing and shot peening on the fatigue properties of a Ti6Al4V alloy

NASA Astrophysics Data System (ADS)

Yu, Shouming; Liu, Daoxin; Zhang, Xiaohua; Du, Dongxing

2015-10-01

A plasma chromizing treatment was conducted on Ti6Al4V samples by employing the recently developed double glow plasma surface alloying technology. The Cr-alloyed layer consisted of four sub-layers, namely the Cr deposition, Cr2Ti, CrTi4, and Cr-Ti solid-solution layers. The local hardness and moduli were determined via nanoindentation. In addition, the fatigue properties of the samples were evaluated by using a rotating-bending fatigue machine under a given load. The results showed that the hardness or elastic moduli of the adjacent sub-layers differed significantly and the fatigue properties of the Ti6Al4V alloy deteriorated with the plasma chromizing treatment. This deterioration stemmed mainly from cracks initiated at the interfaces between the sub-layers and the microstructural changes of the substrate; these changes were induced by the high temperature used in the plasma chromizing process. However, the fatigue life of the plasma-chromized samples was increased by a shot peening post-treatment. The fatigue life of the samples resulting from this combination of treatments was slightly higher than that of the single-shot-peened Ti6Al4V substrate. In fact, the sample retaining only the Cr-Ti solid-solution layer (that is, the first three sub-layers were removed), when shot-peened, exhibited the highest fatigue life among all the tested samples; this was attributed to that sample having the highest residual compressive stress, the significant work hardening, and the good hardness to toughness balance.

Plasma and Serum Metabolite Association Networks: Comparability within and between Studies Using NMR and MS Profiling.

PubMed

Suarez-Diez, Maria; Adam, Jonathan; Adamski, Jerzy; Chasapi, Styliani A; Luchinat, Claudio; Peters, Annette; Prehn, Cornelia; Santucci, Claudio; Spyridonidis, Alexandros; Spyroulias, Georgios A; Tenori, Leonardo; Wang-Sattler, Rui; Saccenti, Edoardo

2017-07-07

Blood is one of the most used biofluids in metabolomics studies, and the serum and plasma fractions are routinely used as a proxy for blood itself. Here we investigated the association networks of an array of 29 metabolites identified and quantified via NMR in the plasma and serum samples of two cohorts of ∼1000 healthy blood donors each. A second study of 377 individuals was used to extract plasma and serum samples from the same individual on which a set of 122 metabolites were detected and quantified using FIA-MS/MS. Four different inference algorithms (ARANCE, CLR, CORR, and PCLRC) were used to obtain consensus networks. The plasma and serum networks obtained from different studies showed different topological properties with the serum network being more connected than the plasma network. On a global level, metabolite association networks from plasma and serum fractions obtained from the same blood sample of healthy people show similar topologies, and at a local level, some differences arise like in the case of amino acids.

Plasma and Serum Metabolite Association Networks: Comparability within and between Studies Using NMR and MS Profiling

PubMed Central

2017-01-01

Blood is one of the most used biofluids in metabolomics studies, and the serum and plasma fractions are routinely used as a proxy for blood itself. Here we investigated the association networks of an array of 29 metabolites identified and quantified via NMR in the plasma and serum samples of two cohorts of ∼1000 healthy blood donors each. A second study of 377 individuals was used to extract plasma and serum samples from the same individual on which a set of 122 metabolites were detected and quantified using FIA–MS/MS. Four different inference algorithms (ARANCE, CLR, CORR, and PCLRC) were used to obtain consensus networks. The plasma and serum networks obtained from different studies showed different topological properties with the serum network being more connected than the plasma network. On a global level, metabolite association networks from plasma and serum fractions obtained from the same blood sample of healthy people show similar topologies, and at a local level, some differences arise like in the case of amino acids. PMID:28517934

Determination of initial fuel state and number of reactor shutdowns in archived low-burnup uranium targets

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

Byerly, Benjamin; Tandon, Lav; Hayes-Sterbenz, Anna

This article presents a method for destructive analysis of irradiated uranium (U) targets, with a focus on collection and measurement of long-lived (t 1/2 > ~10 years) and stable fission product isotopes of ruthenium and cesium. Long-lived and stable isotopes of these elements can provide information on reactor conditions (e.g. flux, irradiation time, cooling time) in old samples (> 5–10 years) whose short-lived fission products have decayed away. The separation and analytical procedures were tested on archived U reactor targets at Los Alamos National Laboratory as part of an effort to evaluate reactor models at low-burnup.

Determination of initial fuel state and number of reactor shutdowns in archived low-burnup uranium targets

DOE PAGES

Byerly, Benjamin; Tandon, Lav; Hayes-Sterbenz, Anna; ...

2015-10-26

This article presents a method for destructive analysis of irradiated uranium (U) targets, with a focus on collection and measurement of long-lived (t 1/2 > ~10 years) and stable fission product isotopes of ruthenium and cesium. Long-lived and stable isotopes of these elements can provide information on reactor conditions (e.g. flux, irradiation time, cooling time) in old samples (> 5–10 years) whose short-lived fission products have decayed away. The separation and analytical procedures were tested on archived U reactor targets at Los Alamos National Laboratory as part of an effort to evaluate reactor models at low-burnup.

Plasma catecholamines and plasma corticosterone following restraint stress in juvenile alligators.

PubMed

Lance, V A; Elsey, R M

1999-05-01

Ten juvenile alligators, mean body mass 793 g, hatched from artificially incubated eggs and raised under controlled conditions, were held out of water with their jaws held closed for 48 hr. An initial blood sample was taken and further samples collected at 1, 2, 4, 8, 24, and 48 hr. Epinephrine, norepinephrine, and dopamine were measured in plasma aliquots of 1.5 ml using high pressure liquid chromatography with electrochemical detection. Corticosterone was measured by radioimmunoassay. Plasma glucose was measured using the Trinder method and plasma calcium, cholesterol, and triglycerides were measured in an autoanalyzer. Epinephrine was about 4 ng/ml at the initial bleed, but declined steadily to < 0.4 ng/ml by 24 hr. Norepinephrine was also about 4 ng/ml at the initial bleed, but rose to over 8 ng/ml at 1 hr, and then declined to < 0.2 ng/ml at 24 hr. A second, but smaller increase in plasma norepinephrine was seen at 48 hr. Plasma dopamine was low at the initial bleed (< 0.7 ng/ml), rose to over 8 ng/ml at 1 hr, then declined to < 0.2 ng/ml. Plasma corticosterone rose progressively for the first 4 hr, declined at 8 hr and 24 hr, then rose again at 48 hr. Plasma glucose rose significantly by 24 hr and remained elevated for 48 hr. Plasma calcium increased at 1, 2, and 4 hr then returned to levels not significantly different from the initial sample at 24 and 48 hr. The white blood cells showed changes indicating immune system suppression. By the end of the treatment the hetorophil/lymphocyte ratio increased to 4.7. These results suggest that handling alligators, taking multiple blood samples, and keeping them restrained for more than 8 hr is a severe stress to the animals.

Concentration of platelets and growth factors in platelet-rich plasma from Goettingen minipigs.

PubMed

Jungbluth, Pascal; Grassmann, Jan-Peter; Thelen, Simon; Wild, Michael; Sager, Martin; Windolf, Joachim; Hakimi, Mohssen

2014-01-01

In minipigs little is known about the concentration of growth factors in plasma, despite their major role in several patho-physiological processes such as healing of fractures. This prompted us to study the concentration of platelets and selected growth factors in plasma and platelet-rich plasma (PRP) preparation of sixteen Goettingen minipigs. Platelet concentrations increased significantly in PRP in comparison to native blood plasma. Generally, significant increase in the concentration of all growth factors tested was observed in the PRP in comparison to the corresponding plasma or serum. Five of the plasma samples examined contained detectable levels of bone morphogenic protein 2 (BMP-2) whereas eleven of the plasma or serum samples contained minimal amounts of vascular endothelial growth factor (VEGF) and platelet-derived growth factor (PDGF-bb) respectively. On the other hand variable concentrations of bone morphogenic protein 7 (BMP-7) and transforming growth factor β1 (TGF-β1) were measured in all plasma samples. In contrast, all PRP samples contained significantly increased amounts of growth factors. The level of BMP-2, BMP-7, TGF-β1, VEGF and PDGF-bb increased by 17.6, 1.5, 7.1, 7.2 and 103.3 fold, in comparison to the corresponding non-enriched preparations. Moreover significant positive correlations were found between platelet count and the concentrations of BMP-2 (r=0.62, p<0.001), TGF-β1 (r=0.85, p<0.001), VEGF (r=0.46, p<0.01) and PDGF-bb (r=0.9, p<0.001). Our results demonstrate that selected growth factors are present in the platelet-rich plasma of minipigs which might thus serve as a source of autologous growth factors.

Salivary caffeine concentrations are comparable to plasma concentrations in preterm infants receiving extended caffeine therapy

PubMed Central

Liu, Xiaoxi; Rhein, Lawrence M.; Darnall, Robert A.; Corwin, Michael J.; McEntire, Betty L.; Ward, Robert M.; James, Laura P.; Sherwin, Catherine M. T.; Heeren, Timothy C.; Hunt, Carl E.

2016-01-01

Aims Caffeine concentrations in preterm infants are usually measured in the blood. However, salivary assays may provide a valid and practical alternative. The present study explored the validity and clinical utility of salivary caffeine concentrations as an alternative to blood concentrations and developed a novel plasma/salivary caffeine distribution model. Methods Paired salivary and plasma samples were obtained in 29 infants. Salivary samples were obtained using a commercially available salivary collection system. Caffeine concentrations in the saliva and plasma were determined using high‐performance liquid chromatography. A population pharmacokinetic (PK) model was developed using NONMEM 7.3. Results The mean (± standard deviation) gestational age (GA) at birth and birth weight were 27.9 ± 2.1 weeks and 1171.6 ± 384.9 g, respectively. Paired samples were obtained at a mean postmenstrual age (PMA) of 35.5 ± 1.1 weeks. The range of plasma caffeine concentrations was 9.5–54.1 μg ml−1, with a mean difference (95% confidence interval) between plasma and salivary concentrations of −0.18 μg ml−1 (−1.90, 1.54). Salivary and plasma caffeine concentrations were strongly correlated (Pearson's correlation coefficient = 0.87, P < 0.001). Caffeine PK in plasma and saliva was simultaneously described by a three‐compartment recirculation model. Current body weight, birth weight, GA, PMA and postnatal age were not significantly correlated with any PK parameter. Conclusions Salivary sampling provides an easy, non‐invasive method for measuring caffeine concentrations. Salivary concentrations correlate highly with plasma concentrations. Caffeine PK in saliva and plasma are well described by a three‐compartment recirculation model. PMID:27145974

Irradiation of silver and agar/silver nanoparticles with argon, oxygen glow discharge plasma, and mercury lamp.

PubMed

Ahmad, Mahmoud M; Abdel-Wahab, Essam A; El-Maaref, A A; Rawway, Mohammed; Shaaban, Essam R

2014-01-01

The irradiation effect of argon, oxygen glow discharge plasma, and mercury lamp on silver and agar/silver nanoparticle samples is studied. The irradiation time dependence of the synthesized silver and agar/silver nanoparticle absorption spectra and their antibacterial effect are studied and compared. In the agar/silver nanoparticle sample, as the irradiation time of argon glow discharge plasma or mercury lamp increases, the peak intensity and the full width at half maximum, FWHM, of the surface plasmon resonance absorption band is increased, however a decrease of the peak intensity with oxygen glow plasma has been observed. In the silver nanoparticle sample, as the irradiation time of argon, oxygen glow discharge plasma or mercury lamp increases, the peak intensity of the surface plasmon resonance absorption band is increased, however, there is no significant change in the FWHM of the surface plasmon resonance absorption band. The SEM results for both samples showed nanoparticle formation with mean size about 50 nm and 40 nm respectively. Throughout the irradiation time with the argon, oxygen glow discharge plasma or mercury lamp, the antibacterial activity of several kinds of Gram-positive and Gram-negative bacteria has been examined.

A survey of avian paramyxovirus type 1 infections among backyard poultry in New Zealand.

PubMed

Dunowska, M; Zheng, T; Perrott, M R; Christensen, N

2013-11-01

To determine the presence and the pathotype of avian paramyxovirus type 1 (APMV-1), as well as the prevalence of APMV-1 antibodies, among backyard flocks of poultry in selected New Zealand locations. Archival pooled (n = 162) tracheal and cloacal swabs collected from backyard poultry were tested for the presence of APMV-1 RNA by real-time and conventional reverse transcription (RT)-PCR assays. Archival blood samples (n = 240) from a subpopulation of the same birds were tested for the presence of the APMV-1 antibody using a commercial ELISA assay. The archival samples were collected from geographical areas close to bodies of water, in the Bay of Plenty or Wairarapa regions of the North Island of New Zealand, with the high likelihood of interactions between wild waterfowl and domestic poultry. Avian paramyxovirus type 1 RNA was not detected in any of the swabs tested. Antibodies to APMV-1 were detected on 18/19 farms, in 71/240 (29.5%) blood samples tested. The percentage of seropositive birds varied between seropositive farms and ranged from 8.3 to 100%. The percentage of seropositive birds on each farm was not statistically correlated with the flock size, the number of birds sampled, the number of farmed waterfowl, or with the distance to the closest lake/river. However, all chickens from the farm with the highest number of farmed ducks were seropositive for APMV-1. Lack of detection of APMV-1 in any of the samples indicates that APMV-1 was not circulating among the poultry at the time of sampling. However, detection of APMV-1 antibodies in a proportion of birds on each farm indicates that infection with APMV-1, or antigenically related APMV, is common among backyard poultry. On-going proactive surveillance and characterisation of circulating APMV-1 is important for monitoring changes in circulating genotypes of APMV-1 and for understanding the regional ecology of these viruses for the purpose of planning appropriate disease control and prevention strategies. Our data suggest that backyard flocks should be considered as potential reservoirs of APMV. Chickens from backyard farms with multiple bird species may provide good targets for surveillance purposes.

Development of alternative plasma sources for cavity ring-down measurements of mercury.

PubMed

Duan, Yixiang; Wang, Chuji; Scherrer, Susan T; Winstead, Christopher B

2005-08-01

We have been exploring innovative technologies for elemental and hyperfine structure measurements using cavity ring-down spectroscopy (CRDS) combined with various plasma sources. A laboratory CRDS system utilizing a tunable dye laser is employed in this work to demonstrate the feasibility of the technology. An in-house fabricated sampling system is used to generate aerosols from solution samples and introduce the aerosols into the plasma source. The ring-down signals are monitored using a photomultiplier tube and recorded using a digital oscilloscope interfaced to a computer. Several microwave plasma discharge devices are tested for mercury CRDS measurement. Various discharge tubes have been designed and tested to reduce background interference and increase the sample path length while still controlling turbulence generated from the plasma gas flow. Significant background reduction has been achieved with the implementation of the newly designed tube-shaped plasma devices, which has resulted in a detection limit of 0.4 ng/mL for mercury with the plasma source CRDS. The calibration curves obtained in this work readily show that linearity over 2 orders of magnitude can be obtained with plasma-CRDS for mercury detection. In this work, the hyperfine structure of mercury at the experimental plasma temperatures is clearly identified. We expect that plasma source cavity ring-down spectroscopy will provide enhanced capabilities for elemental and isotopic measurements.

Variation in plasma lipids during the reproductive cycle of male and female desert tortoises, Gopherus agassizii.

PubMed

Lance, Valentine A; Place, Allen R; Grumbles, Janice S; Rostal, David C

2002-12-01

Plasma triacylglycerol, phospholipid, cholesterol, cholesterol esters, fatty acids, and total lipids were measured in 30 female and 20 male desert tortoises (Gopherus agassizii) during the annual reproductive cycle in the eastern Mojave desert, Nevada. Blood samples were collected at monthly intervals from April to October. All lipid fractions, with the exception of free fatty acids, were significantly higher in female plasma than in male plasma in all months of the year. In contrast, free fatty acids were higher in male plasma than in female plasma in all months. The seasonal pattern in estradiol secretion mirrored that of triacylglycerol, phospholipid, cholesterol, and total lipid, all of which showed a significant correlation with the hormone. Estradiol and the vitellogenesis-associated lipids were all significantly higher in August, September, October, and April than in June. The seasonal variation in cholesterol ester levels in females did not correlate with any of the reproductive events and did not appear to be involved in yolk precursor formation. Total lipid in males showed a negative correlation with testosterone and spermatogenesis. Individual fatty acids in the June and August samples (at the highest and lowest estradiol levels) were compared in male and female plasma. The percent of C18:3n3, C18:2n6, C18:1n9, C20:5n3, and C22:5 were significantly higher in the June female plasma sample than in the August sample. Docosahexanoic (C22:6n3) acid was barely detectable in female plasma in either month. Copyright 2002 Wiley-Liss, Inc.

Methods for detecting and correcting inaccurate results in inductively coupled plasma-atomic emission spectrometry

DOEpatents

Chan, George C. Y. [Bloomington, IN; Hieftje, Gary M [Bloomington, IN

2010-08-03

A method for detecting and correcting inaccurate results in inductively coupled plasma-atomic emission spectrometry (ICP-AES). ICP-AES analysis is performed across a plurality of selected locations in the plasma on an unknown sample, collecting the light intensity at one or more selected wavelengths of one or more sought-for analytes, creating a first dataset. The first dataset is then calibrated with a calibration dataset creating a calibrated first dataset curve. If the calibrated first dataset curve has a variability along the location within the plasma for a selected wavelength, errors are present. Plasma-related errors are then corrected by diluting the unknown sample and performing the same ICP-AES analysis on the diluted unknown sample creating a calibrated second dataset curve (accounting for the dilution) for the one or more sought-for analytes. The cross-over point of the calibrated dataset curves yields the corrected value (free from plasma related errors) for each sought-for analyte.

Determination of efavirenz in human dried blood spots by reversed-phase high-performance liquid chromatography with UV detection.

PubMed

Hoffman, Justin T; Rossi, Steven S; Espina-Quinto, Rowena; Letendre, Scott; Capparelli, Edmund V

2013-04-01

Previously published methods for determination of efavirenz (EFV) in human dried blood spots (DBS) use costly and complex liquid chromatography/mass spectrometry. We describe the validation and evaluation of a simple and inexpensive high-performance liquid chromatography method for EFV quantification in human DBS and dried plasma spots (DPS), using ultraviolet detection appropriate for resource-limited settings. One hundred microliters of heparinized whole blood or plasma were spotted onto blood collection cards, dried, punched, and eluted. Eluates are injected onto a C-18 reversed phase high-performance liquid chromatography column. EFV is separated isocratically using a potassium phosphate and acetonitrile mobile phase. Ultraviolet detection is at 245 nm. Quantitation is by use of external calibration standards. Following validation, the method was evaluated using whole blood and plasma from HIV-positive patients undergoing EFV therapy. Mean recovery of drug from DBS is 91.5%. The method is linear over the validated concentration range of 0.3125-20.0 μg/mL. A good correlation (Spearman r = 0.96) between paired plasma and DBS EFV concentrations from the clinical samples was observed, and hematocrit level was not found to be a significant determinant of the EFV DBS level. The mean observed C DBS/C plasma ratio was 0.68. A good correlation (Spearman r = 0.96) between paired plasma and DPS EFV concentrations from the clinical samples was observed. The mean percent deviation of DPS samples from plasma samples is 1.68%. Dried whole blood spot or dried plasma spot sampling is well suited for monitoring EFV therapy in resource-limited settings, particularly when high sensitivity is not essential.

Comparison between dried blood spot and plasma sampling for therapeutic drug monitoring of antiepileptic drugs in children with epilepsy: A step towards home sampling.

PubMed

Linder, Camilla; Wide, Katarina; Walander, Malin; Beck, Olof; Gustafsson, Lars L; Pohanka, Anton

2017-05-01

To investigate if dried blood spots could be used for therapeutic drug monitoring of the antiepileptic drugs, carbamazepine, lamotrigine and valproic acid in children with epilepsy. Fingerprick blood samples from 46 children at a neuropediatric outpatient clinic was collected on filterpaper at the same time as capillary plasma sampling. A validated dried blood spot liquid chromatography tandem mass spectrometry method for carbamazepine, lamotrigine and valproic acid was compared with the routine plasma laboratory methods. Method agreement was evaluated and plasma concentrations were estimated by different conversion approaches. Strong correlation was shown between dried blood spot and plasma concentrations for all three drugs, with R2 values>0.89. Regression analysis showed a proportional bias with 35% lower dried blood spot concentrations for valproic acid (n=33) and concentrations were 18% higher for carbamazepine (n=17). A ratio approach was used to make a conversion from dried blood spots to estimated plasma for these two drugs. Dried blood spot concentrations were directly comparable with plasma for lamotrigine (n=20). This study supports that dried blood spot concentrations can be used as an alternative to plasma in a children population for three commonly used antiepileptic drugs with the possibility to expand by adding other antiepileptic drugs. Clinical decisions can be made based on converted (carbamazepine, valproic acid) or unconverted (lamotrigine) dried blood spot concentrations. Dried blood spot sampling, in the future taken at home, will simplify an effective therapeutic drug monitoring for this group of patients who often have concomitant disorders and also reduce costs for society. Copyright © 2016 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Stability of hemostatic proteins in canine fresh-frozen plasma thawed with a modified commercial microwave warmer or warm water bath.

PubMed

Pashmakova, Medora B; Barr, James W; Bishop, Micah A

2015-05-01

To compare stability of hemostatic proteins in canine fresh-frozen plasma (FFP) thawed with a modified commercial microwave warmer (MCM) or warm water bath (37°C; WWB) or at room temperature (22°C). Fresh-frozen plasma obtained from 8 canine donors of a commercial blood bank. A commercial microwave warmer was modified with a thermocouple to measure surface temperature of bags containing plasma. The MCM and a WWB were each used to concurrently thaw a 60-mL bag of plasma obtained from the same donor. Two 3-mL control aliquots of FFP from each donor were thawed to room temperature without use of a heating device. Concentrations of hemostatic proteins, albumin, and D-dimers; prothrombin time (PT); and activated partial thromboplastin time (aPTT) were determined for all samples. Significant decreases in concentrations of factors II, IX, X, XI, fibrinogen, von Willebrand factor, antithrombin, protein C, and albumin and significant increases in PT and aPTT were detected for plasma thawed with the MCM, compared with results for samples thawed with the WWB. Concentrations of factors VII, VIII, and XII were not significantly different between plasma thawed with the MCM and WWB. Concentrations of D-dimers were above the reference range for all thawed samples regardless of thawing method. No significant differences in factor concentrations were detected between control and WWB-thawed samples. Significant differences in hemostatic protein concentrations and coagulation times were detected for plasma thawed with an MCM but not between control and WWB-thawed samples. Clinical importance of these changes should be investigated.

Measurement of rivaroxaban and apixaban in serum samples of patients

PubMed Central

Harenberg, Job; Krämer, Sandra; Du, Shanshan; Zolfaghari, Shabnam; Schulze, Astrid; Krämer, Roland; Weiss, Christel; Wehling, Martin; Lip, Gregory Y H

2014-01-01

Background The determination of rivaroxaban and apixaban from serum samples of patients may be beneficial in specific clinical situations when additional blood sampling for plasma and thus the determination of factor Xa activity is not feasible or results are not plausible. Materials and methods The primary aim of this study was to compare the concentrations of rivaroxaban and apixaban in serum with those measured in plasma. Secondary aims were the performance of three different chromogenic methods and concentrations in patients on treatment with rivaroxaban 10 mg od (n = 124) or 20 mg od (n = 94) or apixaban 5 mg bid (n = 52) measured at different time. Results Concentrations of rivaroxaban and apixaban in serum were about 20–25% higher compared with plasma samples with a high correlation (r = 0·79775–0·94662) using all assays (all P < 0·0001). The intraclass correlation coefficients were about 0·90 for rivaroxaban and 0·55 for apixaban. Mean rivaroxaban concentrations were higher at 2 and 3 h compared with 1 and 12 h after administration measured from plasma and serum samples (all P-values < 0·05) and were not different between 1 vs. 12 h (plasma and serum). Conclusions The results indicate that rivaroxaban and apixaban concentrations can be determined specifically from serum samples. PMID:24931429

Clinical Validation of Therapeutic Drug Monitoring of Imipenem in Spent Effluent in Critically Ill Patients Receiving Continuous Renal Replacement Therapy: A Pilot Study.

PubMed

Wen, Aiping; Li, Zhe; Yu, Junxian; Li, Ren; Cheng, Sheng; Duan, Meili; Bai, Jing

2016-01-01

The primary objective of this pilot study was to investigate whether the therapeutic drug monitoring of imipenem could be performed with spent effluent instead of blood sampling collected from critically ill patients under continuous renal replacement therapy. A prospective open-label study was conducted in a real clinical setting. Both blood and effluent samples were collected pairwise before imipenem administration and 0.5, 1, 1.5, 2, 3, 4, 6, and 8 h after imipenem administration. Plasma and effluent imipenem concentrations were determined by reversed-phase high-performance liquid chromatography with ultraviolet detection. Pharmacokinetic and pharmacodynamic parameters of blood and effluent samples were calculated. Eighty-three paired plasma and effluent samples were obtained from 10 patients. The Pearson correlation coefficient of the imipenem concentrations in plasma and effluent was 0.950 (P<0.0001). The average plasma-to-effluent imipenem concentration ratio was 1.044 (95% confidence interval, 0.975 to 1.114) with Bland-Altman analysis. No statistically significant difference was found in the pharmacokinetic and pharmacodynamic parameters tested in paired plasma and effluent samples with Wilcoxon test. Spent effluent of continuous renal replacement therapy could be used for therapeutic drug monitoring of imipenem instead of blood sampling in critically ill patients.

Recombining Plasma and Gamma-Ray Emission in the Mixed-morphology Supernova Remnant 3C 400.2

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

Ergin, T.; Sezer, A.; Sano, H.

3C 400.2 belongs to the mixed-morphology supernova remnant class, showing center-filled X-ray and shell-like radio morphology. We present a study of 3C 400.2 with archival Suzaku and Fermi -LAT observations. We find recombining plasma (RP) in the Suzaku spectra of north–east and south–east regions. The spectra of these regions are well described by two-component thermal plasma models: the hard component is in RP, while the soft component is in collisional ionization equilibrium (CIE) conditions. The RP has enhanced abundances, indicating that the X-ray emission has an ejecta origin, while the CIE has solar abundances associated with the interstellar material. Themore » X-ray spectra of north–west and south–west regions are best fitted by a two-component thermal plasma model: an ionizing and a CIE plasma. We have detected GeV gamma-ray emission from 3C 400.2 at the level of ∼5 σ , assuming a point-like source model with a power-law (PL) type spectrum. We have also detected a new GeV source at the level of ∼13 σ, assuming a Gaussian extension model with a PL-type spectrum in the neighborhood of the supernova remnant. We report the analysis results of 3C 400.2 and the new extended gamma-ray source, and discuss the nature of gamma-ray emission of 3C 400.2 in the context of existing NANTEN CO data, Dominion Radio Astrophysical Observatory H i data, and the Suzaku X-ray analysis results.« less

Gains in efficiency and scientific potential of continental climate reconstruction provided by the LRC LacCore Facility, University of Minnesota

NASA Astrophysics Data System (ADS)

Noren, A.; Brady, K.; Myrbo, A.; Ito, E.

2007-12-01

Lacustrine sediment cores comprise an integral archive for the determination of continental paleoclimate, for their potentially high temporal resolution and for their ability to resolve spatial variability in climate across vast sections of the globe. Researchers studying these archives now have a large, nationally-funded, public facility dedicated to the support of their efforts. The LRC LacCore Facility, funded by NSF and the University of Minnesota, provides free or low-cost assistance to any portion of research projects, depending on the specific needs of the project. A large collection of field equipment (site survey equipment, coring devices, boats/platforms, water sampling devices) for nearly any lacustrine setting is available for rental, and Livingstone-type corers and drive rods may be purchased. LacCore staff can accompany field expeditions to operate these devices and curate samples, or provide training prior to device rental. The Facility maintains strong connections to experienced shipping agents and customs brokers, which vastly improves transport and importation of samples. In the lab, high-end instrumentation (e.g., multisensor loggers, high-resolution digital linescan cameras) provides a baseline of fundamental analyses before any sample material is consumed. LacCore staff provide support and training in lithological description, including smear-slide, XRD, and SEM analyses. The LRC botanical macrofossil reference collection is a valuable resource for both core description and detailed macrofossil analysis. Dedicated equipment and space for various subsample analyses streamlines these endeavors; subsamples for several analyses may be submitted for preparation or analysis by Facility technicians for a fee (e.g., carbon and sulfur coulometry, grain size, pollen sample preparation and analysis, charcoal, biogenic silica, LOI, freeze drying). The National Lacustrine Core Repository now curates ~9km of sediment cores from expeditions around the world, and stores metadata and analytical data for all cores processed at the facility. Any researcher may submit sample requests for material in archived cores. Supplies for field (e.g., polycarbonate pipe, endcaps), lab (e.g., sample containers, pollen sample spike), and curation (e.g., D-tubes) are sold at cost. In collaboration with facility users, staff continually develop new equipment, supplies, and procedures as needed in order to provide the best and most comprehensive set of services to the research community.

Developments in Seismic Data Quality Assessment Using MUSTANG at the IRIS DMC

NASA Astrophysics Data System (ADS)

Sharer, G.; Keyson, L.; Templeton, M. E.; Weertman, B.; Smith, K.; Sweet, J. R.; Tape, C.; Casey, R. E.; Ahern, T.

2017-12-01

MUSTANG is the automated data quality metrics system at the IRIS Data Management Center (DMC), designed to help characterize data and metadata "goodness" across the IRIS data archive, which holds 450 TB of seismic and related earth science data spanning the past 40 years. It calculates 46 metrics ranging from sample statistics and miniSEED state-of-health flag counts to Power Spectral Densities (PSDs) and Probability Density Functions (PDFs). These quality measurements are easily and efficiently accessible to users through the use of web services, which allows users to make requests not only by station and time period but also to filter the results according to metric values that match a user's data requirements. Results are returned in a variety of formats, including XML, JSON, CSV, and text. In the case of PSDs and PDFs, results can also be retrieved as plot images. In addition, there are several user-friendly client tools available for exploring and visualizing MUSTANG metrics: LASSO, MUSTANG Databrowser, and MUSTANGular. Over the past year we have made significant improvements to MUSTANG. We have nearly complete coverage over our archive for broadband channels with sample rates of 20-200 sps. With this milestone achieved, we are now expanding to include higher sample rate, short-period, and strong-motion channels. Data availability metrics will soon be calculated when a request is made which guarantees that the information reflects the current state of the archive and also allows for more flexibility in content. For example, MUSTANG will be able to return a count of gaps for any arbitrary time period instead of being limited to 24 hour spans. We are also promoting the use of data quality metrics beyond the IRIS archive through our recent release of ISPAQ, a Python command-line application that calculates MUSTANG-style metrics for users' local miniSEED files or for any miniSEED data accessible through FDSN-compliant web services. Finally, we will explore how researchers are using MUSTANG in real-world situations to select data, improve station data quality, anticipate station outages and servicing, and characterize site noise and environmental conditions.

Effect of solvent/detergent-treated pooled plasma on fibrinolysis in reconstituted whole blood.

PubMed

Saadah, Nicholas H; van der Meer, Pieter F; Brinkman, Herm Jan M; de Korte, Dirk; Bontekoe, Ido J; Korsten, Herbert H; Middelburg, Rutger A; van der Bom, Johanna G; Schipperus, Martin R

2017-10-01

Hyperfibrinolysis has been observed in patients heavily transfused with solvent/detergent-treated pooled plasma (S/D plasma). We compared coagulation and fibrinolytic variables in blood containing S/D plasma with blood containing fresh-frozen plasma (FFP), with and without α2-antiplasmin or tranexamic acid (TXA) supplementation. Whole blood samples were reconstituted from red blood cells, platelet (PLT) concentrates, and varying mixtures of FFP and S/D plasma. Hematocrit and PLT count of reconstituted whole blood samples were varied. For a subset of runs, α2-antiplasmin or TXA was added to S/D plasma whole blood samples. Thromboelastography (TEG) analysis was performed to assess 50% clot lysis time (CLT 50% ), maximum amplitude (MA), and initial clotting time (R-time). The change in CLT 50% of whole blood as the plasma compartment transitions from FFP to S/D plasma was -52% (95% confidence interval [CI], -60% to -45%; p < 0.001). PLT count strengthened the effect, leading to an additional change in CLT 50% of -8% (95% CI, -14% to -2%; p = 0.012) as PLT count increased from 10 × 10 9 to 150 × 10 9 /L. MA and R-time were not associated with fraction of S/D plasma in whole blood. α2-Antiplasmin and TXA restored clot lysis time in S/D plasma whole blood. Whole blood with S/D plasma has shorter clot lysis times in vitro compared to whole blood with FFP. α2-Antiplasmin and TXA restore clot lysis time of S/D plasma whole blood to that of FFP whole blood. Clinicians should be aware of the decreased clot lysis time associated with S/D plasma transfusion. © 2017 AABB.

The Atmospheric Dynamics of Alpha Tau (K5 III) -- Clues to Understanding the Magnetic Dynamo

NASA Technical Reports Server (NTRS)

Carpenter Kenneth G.

2008-01-01

Using HST/GHRS, HST/STIS and FUSE archival data for (alpha) Tau and the CHIANTI spectroscopic code, we have derived line shifts, volumetric emission measures, and plasma density estimates, and calculated filling factors for a number of UV lines forming between 10,000 K and 300,000 K in the outer atmosphere of this red giant star. The data suggest the presence of low-temperature extended regions and high-temperature compact regions, associated with magnetically open and closed structures in the stellar atmosphere, respectively. The signatures of UV lines from Alpha Tau can be consistently understood via a model of upward-traveling Alfven waves in a gravitationally stratified atmosphere. These wakes cause non-thermal broadening in UV lines due to unresolved wave motions and downward plasma motions in compact magnetic loops heated by resonant .4lf\\en wave heating. We discuss implications of this interpretation for understanding the nature of magnetic dynamos operating in late-type giants.

Determination of tafenoquine in dried blood spots and plasma using LC and fluorescence detection.

PubMed

Römsing, Susanne; Lindegardh, Niklas; Bergqvist, Yngve

2011-08-01

The growing problem of parasites developing resistance to the traditional antimalarial drugs makes the development of new effective and safe drugs crucial. Tafenoquine is a new promising antimalarial drug for prophylaxis and treatment. A bioanalytical method for the determination of tafenoquine in 100 µl of capillary blood applied onto sampling paper and in 100 µl of plasma has been developed and validated. The Whatman 31 ET Chr paper was treated with 0.6 mol/l tartaric acid to improve the extraction recovery and solid-phase extraction was used for cleanup procedure of the blood samples. Plasma samples were precipitated with methanol. Tafenoquine and internal standard were separated on a Zorbax SB-CN column by reversed-phase LC and detected with fluorescence detection at 262 and 470 nm. The within- and between-day variations were below 10 and 14%, respectively, over the range 50-200 nmol/l for capillary blood on sampling paper and below 6 and 10% for plasma samples. The LLOQ of the method was 50 nmol/l. The developed method has adequate sensitivity and is highly suitable for clinical studies in dried blood spots and plasma.

Dried blood spot analysis for therapeutic drug monitoring of pazopanib.

PubMed

de Wit, Djoeke; den Hartigh, Jan; Gelderblom, Hans; Qian, Yanwen; den Hollander, Margret; Verheul, Henk; Guchelaar, Henk-Jan; van Erp, Nielka P

2015-12-01

Dried blood spot (DBS) sampling is potentially a more patient-friendly and flexible alternative to venous sampling of pazopanib. This study determined the agreement between pazopanib DBS and plasma concentrations to facilitate implementation of pazopanib DBS sampling into clinical practice. Paired DBS and plasma samples were collected in 12 patients. Pazopanib plasma concentrations were calculated from DBS concentrations using the formula: plasma concentration = DBSconcentration /(1 - hematocrit). Passing-Bablok and Bland-Altman analyses were used to determine the agreement between calculated and measured plasma concentrations. We predefined a clinical acceptance limit of 25% for the Bland-Altman analysis. Passing-Bablok analysis showed a small constant (intercept estimate, -8.53 [95%CI, -12.22 to -4.41]) and slightly proportional (slope estimate, 1.15 [95%CI, 1.04-1.24]) bias between calculated and measured concentrations. This bias was clinically nonrelevant, as shown by Bland-Altman analysis; the mean ratio of calculated to measured concentrations was 0.94 (95%CI, 0.65-1.23). The clinical acceptance limits were well within these 95% limits of agreement. More specifically, 92.6% of the data points were within the predefined acceptance limits. Pazopanib plasma concentrations can be accurately calculated from DBS concentrations. Although validation of DBS cards prepared by patients themselves is required, these results show that DBS sampling can be used to monitor pazopanib therapy in clinical practice. © 2015, The American College of Clinical Pharmacology.

Difference in drug resistance patterns between minor HIV-1 populations in cerebrospinal fluid and plasma.

PubMed

Bergroth, T; Ekici, H; Gisslén, M; Hagberg, L; Sönnerborg, A

2009-02-01

The aim of the study was to determine to what extent unique drug resistance patterns appear in minor and major HIV-1 quasispecies in cerebrospinal fluid (CSF) as compared with blood. Forty-four plasma and CSF samples from 13 multi-treatment-experienced patients, seven of whom provided longitudinal samples, were included in the study. The subjects had failed antiretroviral therapy including lamivudine. The reverse transcriptase (RT) gene was examined by selective real-time polymerase chain reaction (SPCR), which can detect M184I/V mutants down to 0.2% of the viral population. SPCR revealed differences at amino acid position 184 in the plasma/CSF populations in 12 paired samples from eight patients. One plasma sample was positive by SPCR where direct sequencing showed wild-type M184. The other 11 paired samples showed quantitative differences in the mixed populations of the mutant or wild-type M184 quasispecies. Differences in other resistance-associated mutations between plasma and CSF viruses were also found by direct sequencing. In multi-treatment-experienced patients with therapy failure, differences in drug resistance patterns were found frequently between plasma and CSF in both minor and major viral populations. To what extent this was a true biological phenomenon remains to be established, and the clinical relevance of these findings is yet to be determined.

The Story Behind the Numbers: Lessons Learned from the Integration of Monitoring Resources in Addressing an ISS Water Quality Anomaly

NASA Technical Reports Server (NTRS)

McCoy, Torin; Flint, Stephanie; Straub, John, II; Gazda, Dan; Schultz, John

2011-01-01

Beginning in June of 2010 an environmental mystery was unfolding on the International Space Station (ISS). The U.S. Water Processor Assembly (WPA) began to produce water with increasing levels of total organic carbon (TOC). A surprisingly consistent upward TOC trend was observed through weekly in-flight total organic carbon analyzer (TOCA) monitoring. As TOC is a general organics indicator, return of water archive samples was needed to make better-informed crew health decisions and to aid in WPA troubleshooting. TOCA-measured TOC was more than halfway to its health-based screening limit before archive samples could be returned on Soyuz 22 and analyzed. Although TOC was confirmed to be elevated, somewhat surprisingly, none of the typical target compounds were the source. After some solid detective work, it was confirmed that the TOC was associated with a compound known as dimethylsilanediol (DMSD). DMSD is believed to be a breakdown product of silicon-containing compounds present on ISS. A toxicological limit was set for DMSD and a forward plan developed for operations given this new understanding of the source of the TOC. This required extensive coordination with ISS stakeholders and innovative use of available in-flight and archive monitoring resources. Behind the numbers and scientific detail surrounding this anomaly, there exists a compelling story of multi-disciplinary awareness, teamwork, and important environmental lessons learned.

Twenty years of Landsat data accessible through the national satellite land remote sensing data archive

USGS Publications Warehouse

Larsen, Dana M.

1993-01-01

The EROS Data Center has managed to National Satellite Land Remote Sensing Data Archive's (NSLRSDA) Landsat data since 1972. The NSLRSDA includes Landsat MSS data from 1972 through 1991 and T M data from 1982 through 1993. In response to many requests from multi-disciplined users for an enhanced insight into the availability and volume of Landsat data over specific worldwide land areas, numerous world plots and corresponding statical overviews have been prepared. These presentations include information related to image quality, cloud cover, various types of data overage (i.e. regions, countries, path, rows), acquisition station coverage areas, various archive media formats (i.e. wide band video tapes, computer compatible tapes, high density tapes, etc.) and acquisition time periods (i.e. years, seasons). Plans are to publish this information in a paper sample booklet at the Pecora 12 Symposium, in a USGS circular and on a Landsat CD-ROM; the data will be also be incorporated into GLIS.

Improving the security of international ISO container traffic by centralizing the archival of inspection results

NASA Astrophysics Data System (ADS)

Chalmers, Alex

2004-09-01

To increase the security and throughput of ISO traffic through international terminals more technology must be applied to the problem. A transnational central archive of inspection records is discussed that can be accessed by national agencies as ISO containers approach their borders. The intent is to improve the throughput and security of the cargo inspection process. A review of currently available digital media archiving technologies is presented and their possible application to the tracking of international ISO container shipments. Specific image formats employed by current x-ray inspection systems are discussed. Sample x-ray data from systems in use today are shown that could be entered into such a system. Data from other inspection technologies are shown to be easily integrated, as well as the creation of database records suitable for interfacing with other computer systems. Overall system performance requirements are discussed in terms of security, response time and capacity. Suggestions for pilot projects based on existing border inspection processes are made also.

Non-thermal dielectric barrier discharge plasma induces angiogenesis through reactive oxygen species.

PubMed

Arjunan, Krishna Priya; Friedman, Gary; Fridman, Alexander; Clyne, Alisa Morss

2012-01-07

Vascularization plays a key role in processes such as wound healing and tissue engineering. Non-thermal plasma, which primarily produces reactive oxygen species (ROS), has recently emerged as an efficient tool in medical applications including blood coagulation, sterilization and malignant cell apoptosis. Liquids and porcine aortic endothelial cells were treated with a non-thermal dielectric barrier discharge plasma in vitro. Plasma treatment of phosphate-buffered saline (PBS) and serum-free medium increased ROS concentration in a dose-dependent manner, with a higher concentration observed in serum-free medium compared with PBS. Species concentration inside cells peaked 1 h after treatment, followed by a decrease 3 h post treatment. Endothelial cells treated with a plasma dose of 4.2 J cm(-2) had 1.7 times more cells than untreated samples 5 days after plasma treatment. The 4.2 J cm(-2) plasma dose increased two-dimensional migration distance by 40 per cent compared with untreated control, while the number of cells that migrated through a three-dimensional collagen gel increased by 15 per cent. Tube formation was also enhanced by plasma treatment, with tube lengths in plasma-treated samples measuring 2.6 times longer than control samples. A fibroblast growth factor-2 (FGF-2) neutralizing antibody and ROS scavengers abrogated these angiogenic effects. These data indicate that plasma enhanced proliferation, migration and tube formation is due to FGF-2 release induced by plasma-produced ROS. Non-thermal plasma may be used as a potential tool for applying ROS in precise doses to enhance vascularization.

Non-thermal dielectric barrier discharge plasma induces angiogenesis through reactive oxygen species

PubMed Central

Arjunan, Krishna Priya; Friedman, Gary; Fridman, Alexander; Clyne, Alisa Morss

2012-01-01

Vascularization plays a key role in processes such as wound healing and tissue engineering. Non-thermal plasma, which primarily produces reactive oxygen species (ROS), has recently emerged as an efficient tool in medical applications including blood coagulation, sterilization and malignant cell apoptosis. Liquids and porcine aortic endothelial cells were treated with a non-thermal dielectric barrier discharge plasma in vitro. Plasma treatment of phosphate-buffered saline (PBS) and serum-free medium increased ROS concentration in a dose-dependent manner, with a higher concentration observed in serum-free medium compared with PBS. Species concentration inside cells peaked 1 h after treatment, followed by a decrease 3 h post treatment. Endothelial cells treated with a plasma dose of 4.2 J cm–2 had 1.7 times more cells than untreated samples 5 days after plasma treatment. The 4.2 J cm–2 plasma dose increased two-dimensional migration distance by 40 per cent compared with untreated control, while the number of cells that migrated through a three-dimensional collagen gel increased by 15 per cent. Tube formation was also enhanced by plasma treatment, with tube lengths in plasma-treated samples measuring 2.6 times longer than control samples. A fibroblast growth factor-2 (FGF-2) neutralizing antibody and ROS scavengers abrogated these angiogenic effects. These data indicate that plasma enhanced proliferation, migration and tube formation is due to FGF-2 release induced by plasma-produced ROS. Non-thermal plasma may be used as a potential tool for applying ROS in precise doses to enhance vascularization. PMID:21653568

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

Malik, Hitendra K., E-mail: hkmalik@physics.iitd.ac.in; Singh, Omveer; Dahiya, Raj P.

We have established a hot cathode arc discharge plasma system, where different stainless steel samples can be treated by monitoring the plasma parameters and nitriding parameters independently. In the present work, a mixture of 70% N{sub 2} and 30% H{sub 2} gases was fed into the plasma chamber and the treatment time and substrate temperature were optimized for treating 304L Stainless Steel samples. Various physical techniques such as x-ray diffraction, energy dispersive x-ray spectroscopy and micro-vickers hardness tester were employed to determine the structural, surface composition and surface hardness of the treated samples.

Plasma current collection of Z-93 thermal control paint as measured in the Lewis Research Center's plasma interaction facility

NASA Technical Reports Server (NTRS)

Hillard, G. Barry

1993-01-01

A sample of Z-93 thermal control paint was exposed to a simulated space environment in a plasma chamber. The sample was biased through a series of voltages ranging from -100 volts to +300 volts and electron and ion currents were measured. Currents were found to be in the micro-ampere range indicating that the material remains a reasonably good insulator under plasma conditions. As a second step, the sample was left in the chamber for six days and retested. Collected currents were reduced by from two to five times from the previous values indicating a substantial loss of conductivity. As a final test, the sample was removed, exposed to room conditions for two days, and returned to the chamber. Current measurements showed that the sample had partially recovered the lost conductivity. In addition to presenting these results, this report documents all of the experimental data as well as the statistical analyses performed.

Neutron-Irradiated Samples as Test Materials for MPEX

DOE PAGES

Ellis, Ronald James; Rapp, Juergen

2015-10-09

Plasma Material Interaction (PMI) is a major concern in fusion reactor design and analysis. The Material-Plasma Exposure eXperiment (MPEX) will explore PMI under fusion reactor plasma conditions. Samples with accumulated displacements per atom (DPA) damage produced by fast neutron irradiations in the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL) will be studied in the MPEX facility. This paper presents assessments of the calculated induced radioactivity and resulting radiation dose rates of a variety of potential fusion reactor plasma-facing materials (such as tungsten). The scientific code packages MCNP and SCALE were used to simulate irradiation of themore » samples in HFIR including the generation and depletion of nuclides in the material and the subsequent composition, activity levels, gamma radiation fields, and resultant dose rates as a function of cooling time. A challenge of the MPEX project is to minimize the radioactive inventory in the preparation of the samples and the sample dose rates for inclusion in the MPEX facility.« less

Exposures of tungsten nanostructures to divertor plasmas in DIII-D

DOE PAGES

Rudakov, D. L.; Wong, C. P. C.; Doerner, R. P.; ...

2016-01-22

Tungsten nanostructures (W-fuzz) prepared in the PISCES-A linear device have been found to survive direct exposure to divertor plasmas in DIII-D. W-fuzz was exposed in the lower divertor of DIII-D using the divertor material evaluation system. Two samples were exposed in lower single null (LSN) deuterium H-mode plasmas. The first sample was exposed in three discharges terminated by vertical displacement event disruptions, and the second in two discharges near the lowered X-point. More recently, three samples were exposed near the lower outer strike point in predominantly helium H-mode LSN plasmas. In all cases, the W-fuzz survived plasma exposure with littlemore » obvious damage except in the areas where unipolar arcing occurred. In conclusion, arcing is effective in W-fuzz removal, and it appears that surfaces covered with W-fuzz can be more prone to arcing than smooth W surfaces.« less

Ion sampling and transport in Inductively Coupled Plasma Mass Spectrometry

NASA Astrophysics Data System (ADS)

Farnsworth, Paul B.; Spencer, Ross L.

2017-08-01

Quantitative accuracy and high sensitivity in inductively coupled plasma mass spectrometry (ICP-MS) depend on consistent and efficient extraction and transport of analyte ions from an inductively coupled plasma to a mass analyzer, where they are sorted and detected. In this review we examine the fundamental physical processes that control ion sampling and transport in ICP-MS and compare the results of theory and computerized models with experimental efforts to characterize the flow of ions through plasma mass spectrometers' vacuum interfaces. We trace the flow of ions from their generation in the plasma, into the sampling cone, through the supersonic expansion in the first vacuum stage, through the skimmer, and into the ion optics that deliver the ions to the mass analyzer. At each stage we consider idealized behavior and departures from ideal behavior that affect the performance of ICP-MS as an analytical tool.

Effects of humidity on sterilization of Geobacillus stearothermophilus spores with plasma-excited neutral gas

NASA Astrophysics Data System (ADS)

Matsui, Kei; Ikenaga, Noriaki; Sakudo, Noriyuki

2015-06-01

We investigate the effects of relative humidity on the sterilization process using a plasma-excited neutral gas that uniformly sterilizes both the space and inner wall of the reactor chamber at atmospheric pressure. Only reactive neutral species such as plasma-excited gas molecules and radicals were separated from the plasma and sent to the reactor chamber for chemical sterilization. The plasma source gas is nitrogen mixed with 0.1% oxygen, and the relative humidity in the source gas is controlled by changing the mixing ratio of water vapor. The relative humidity near the sample in the reactor chamber is controlled by changing the sample temperature. As a result, the relative humidity near the sample should be kept in the range from 60 to 90% for the sterilization of Geobacillus stearothermophilus spores. When the relative humidity in the source gas increases from 30 to 90%, the sterilization effect is enhanced by the same degree.

Quantification and clinical application of carboplatin in plasma ultrafiltrate.

PubMed

Downing, Kim; Jensen, Berit Packert; Grant, Sue; Strother, Matthew; George, Peter

2017-05-10

Carboplatin is a chemotherapy drug used in a variety of cancers with the primary toxicity being exposure-dependant myelosuppression. We present the development and validation of a simple, robust inductively coupled plasma mass spectrometry (ICP-MS) method to measure carboplatin in plasma ultrafiltrate. Plasma ultrafiltrates samples were prepared using Amicon Ultra 30,000da cut-off filters and then diluted with ammonia EDTA before ICP-MS analysis. The assay was validated in the range 0.19-47.5mg/L carboplatin in ultrafiltrate. The assay was linear (r 2 >0.9999), accurate (<6% bias, 12% bias at LLOQ) and precise (intra- and inter-day precision of <3% coefficient of variation). No matrix effects were observed between plasma ultrafiltrate and aqueous platinum calibrators and recovery was complete. The assay was applied to 10 clinical samples from patients receiving carboplatin. Incurred sample reanalysis showed reproducible values over 3 analysis days (<6% CV). As plasma stability prior to ultrafiltration has been a major concern in previous clinical studies this was studied extensively at room temperature (22°C) over 24h. Carboplatin was found to be stable in both spiked plasma (n=3) and real patient samples (n=10) at room temperature for up to 8h before ultrafiltration. This makes routine measurement of carboplatin concentrations in clinical settings feasible. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantitative determination of famotidine in human maternal plasma, umbilical cord plasma and urine using high-performance liquid chromatography - mass spectrometry

PubMed Central

Wang, Xiaoming; Rytting, Erik; Abdelrahman, Doaa R.; Nanovskaya, Tatiana N.; Hankins, Gary D.V.; Ahmed, Mahmoud S.

2013-01-01

The liquid chromatography with electrospray ionization mass spectrometry for the quantitative determination of famotidine in human urine, maternal and umbilical cord plasma was developed and validated. The plasma samples were alkalized with ammonium hydroxide and extracted twice with ethyl acetate. The extraction recovery of famotidine in maternal and umbilical cord plasma ranged from 53% to 64% and 72% to 79%, respectively. Urine samples were directly diluted with the initial mobile phase then injected into the HPLC system. Chromatographic separation of famotidine was achieved by using a Phenomenex Synergi™ Hydro-RP™ column with a gradient elution of acetonitrile and 10 mM ammonium acetate aqueous solution (pH 8.3, adjusted with ammonium hydroxide). Mass Spectrometric detection of famotidine was set in the positive mode and used a selected ion monitoring method. Carbon-13-labeled famotidine was used as internal standard. The calibration curves were linear (r2> 0.99) in the concentration ranges of 0.631-252 ng/mL for umbilical and maternal plasma samples, and of 0.075-30.0 μg/mL for urine samples. The relative deviation of method was less than 14% for intra- and inter-day assays, and the accuracy ranged between 93% and 110%. The matrix effect of famotidine in human urine, maternal and umbilical cord plasma is less than 17%. PMID:23401067

A comparison of ARMS-Plus and droplet digital PCR for detecting EGFR activating mutations in plasma

PubMed Central

Zhang, Xinxin; Chang, Ning; Yang, Guohua; Zhang, Yong; Ye, Mingxiang; Cao, Jing; Xiong, Jie; Han, Zhiping; Wu, Shuo; Shang, Lei; Zhang, Jian

2017-01-01

In this study, we introduce a novel amplification refractory mutation system (ARMS)-based assay, namely ARMS-Plus, for the detection of epidermal growth factor receptor (EGFR) mutations in plasma samples. We evaluated the performance of ARMS-Plus in comparison with droplet digital PCR (ddPCR) and assessed the significance of plasma EGFR mutations in predicting efficacy of EGFR-tyrosine kinase inhibitor (TKI) regimen. A total of 122 advanced non-small cell lung cancer (NSCLC) patients were enrolled in this study. The tumor tissue samples from these patients were evaluated by conventional ARMS PCR method to confirm their EGFR mutation status. For the 116 plasma samples analyzed by ARMS-Plus, the sensitivity, specificity, and concordance rate were 77.27% (34/44), 97.22% (70/72), and 89.66% (104/116; κ=0.77, P<0.0001), respectively. Among the 71 plasma samples analyzed by both ARMS-Plus and ddPCR, ARMS-Plus showed a higher sensitivity than ddPCR (83.33% versus 70.83%). The presence of EGFR activating mutations in plasma was not associated with the response to EGFR-TKI, although further validation with a larger cohort is required to confirm the correlation. Collectively, the performance of ARMS-Plus and ddPCR are comparable. ARMS-Plus could be a potential alternative to tissue genotyping for the detection of plasma EGFR mutations in NSCLC patients. PMID:29340107

Effect of W self-implantation and He plasma exposure on early-stage defect and bubble formation in tungsten

NASA Astrophysics Data System (ADS)

Thompson, M.; Drummond, D.; Sullivan, J.; Elliman, R.; Kluth, P.; Kirby, N.; Riley, D.; Corr, C. S.

2018-06-01

To determine the effect of pre-existing defects on helium-vacancy cluster nucleation and growth, tungsten samples were self-implanted with 1 MeV tungsten ions at varying fluences to induce radiation damage, then subsequently exposed to helium plasma in the MAGPIE linear plasma device. Positron annihilation lifetime spectroscopy was performed both immediately after self-implantation, and again after plasma exposure. After self-implantation vacancies clusters were not observed near the sample surface (<30 nm). At greater depths (30–150 nm) vacancy clusters formed, and were found to increase in size with increasing W-ion fluence. After helium plasma exposure in the MAGPIE linear plasma device at ~300 K with a fluence of 1023 He-m‑2, deep (30–150 nm) vacancy clusters showed similar positron lifetimes, while shallow (<30 nm) clusters were not observed. The intensity of positron lifetime signals fell for most samples after plasma exposure, indicating that defects were filling with helium. The absence of shallow clusters indicates that helium requires pre-existing defects in order to drive vacancy cluster growth at 300 K. Further samples that had not been pre-damaged with W-ions were also exposed to helium plasma in MAGPIE across fluences from 1  ×  1022 to 1.2  ×  1024 He-m‑2. Samples exposed to fluences up to 1  ×  1023 He-m‑2 showed no signs of damage. Fluences of 5  ×  1023 He-m‑2 and higher showed significant helium-cluster formation within the first 30 nm, with positron lifetimes in the vicinity 0.5–0.6 ns. The sample temperature was significantly higher for these higher fluence exposures (~400 K) due to plasma heating. This higher temperature likely enhanced bubble formation by significantly increasing the rate interstitial helium clusters generate vacancies, which is we suspect is the rate-limiting step for helium-vacancy cluster/bubble nucleation in the absence of pre-existing defects.

Extractive alkylation of 6-mercaptopurine and determination in plasma by gas chromatography-mass spectrometry.

PubMed

Floberg, S; Hartvig, P; Lindström, B; Lönner-Holm, G; Odlind, B

1981-09-11

An analytical procedure was developed for the determination of 6-mercaptopurine in plasma. Owing to the polar character and low plasma concentration of the compound, extraction and derivatization was carried out directly from the plasma sample by extractive alkylation. Determination was made using gas chromatography-mass spectrometry with multiple-ion detection. Conditions with respect to the rate of formation and the stability of the derivative formed in the extractive alkylation step were evaluated. The selectively of the method to azathioprine and to metabolites was thoroughly investigated. No 6-mercaptopurine was formed from azathioprine added to water or plasma and run through the method. The method enables the detection of 2 ng of 6 mercaptopurine in a 1.0-ml plasma sample. Quantitative determinations were done down to 10 ng/ml 6 mercaptopurine in plasma.

Lack of reliability of nanotechnology in the of free plasma DNA in samples of patients with prostate cancer

PubMed Central

2013-01-01

Background Several studies seek biological markers that give diagnostic and degree of tumor development. The aim of this study was to validate the determination of plasma DNA using nanotechnology (Nanovue™-NV) in samples of 80 patients with prostate cancer. Methods Blood samples of 80 patients of the Urology Ambulatory of Faculdade de Medicina do ABC with prostate cancer confirmed by anatomical-pathology criteria were analyzed. DNA extraction was performed using a GFX TM kit (Amersham Pharmacia Biotech, Inc, USA) following the adapted protocol. Plasma was subjected to centrifugation. Results There was a big difference between the first and the second value obtained by NanoVue Only two samples had no differences between duplicates. Maximum difference between duplicates was 38 μg/mL. Average variation between 51 samples was 10.29 μg/mL, although 21 samples had differences above this average. No correlation was observed between pDNA obtained by traditional spectrophotometry and by nanotechnology. Conclusion Determination of plasma DNA by nanotechnology was not reproducible. PMID:23311763

Single-centre study of the diagnostic performance of plasma metanephrines with seated sampling for the diagnosis of phaeochromocytoma/paraganglioma.

PubMed

Boot, Christopher; Toole, Barry; Johnson, Sarah J; Ball, Stephen; Neely, Dermot

2017-01-01

Background Measurement of plasma metanephrines is regarded as one of the best screening tests for phaeochromocytoma/paraganglioma. Current guidelines recommend that samples are ideally collected in the supine position after 30 min rest and interpreted using supine reference ranges, in order to optimize the diagnostic performance of the test. Current practice in our centre is to collect samples for plasma metanephrines from seated patients. The aim of the study was to determine, if seated sampling for plasma metanephrines provides acceptable diagnostic performance in our centre. Methods Clinical and laboratory data of 113 patients, gathered over a four-year period 2010-2014, were reviewed. All had undergone preoperative plasma metanephrines measurement and had postoperative histopathology confirmation or exclusion of phaeochromocytoma/paraganglioma. Results Of 113 patients included in the study, 40 had a histological diagnosis of phaeochromocytoma/paraganglioma. The remaining 73 patients had an alternative adrenal pathology. The diagnostic sensitivity of normetanephrine or metanephrine above the upper limit of our in-house seated reference range was 93%. However, excluding three cases of paraganglioma determined clinically and biochemically to be non-functional raised the sensitivity to 100%. Diagnostic specificity was 90%. Applying published supine reference ranges made no difference to diagnostic sensitivity in this group of patients but decreased diagnostic specificity to 75%. Conclusions While these data are derived from a relatively small study population, they demonstrate acceptable diagnostic performance for seated plasma metanephrines as a screening test for phaeochromocytoma/paraganglioma. These data highlight a high diagnostic sensitivity for plasma metanephrines with seated sampling in our centre.

Influence of the collection tube on metabolomic changes in serum and plasma.

PubMed

López-Bascón, M A; Priego-Capote, F; Peralbo-Molina, A; Calderón-Santiago, M; Luque de Castro, M D

2016-04-01

Major threats in metabolomics clinical research are biases in sampling and preparation of biological samples. Bias in sample collection is a frequently forgotten aspect responsible for uncontrolled errors in metabolomics analysis. There is a great diversity of blood collection tubes for sampling serum or plasma, which are widely used in metabolomics analysis. Most of the existing studies dealing with the influence of blood collection on metabolomics analysis have been restricted to comparison between plasma and serum. However, polymeric gel tubes, which are frequently proposed to accelerate the separation of serum and plasma, have not been studied. In the present research, samples of serum or plasma collected in polymeric gel tubes were compared with those taken in conventional tubes from a metabolomics perspective using an untargeted GC-TOF/MS approach. The main differences between serum and plasma collected in conventional tubes affected to critical pathways such as the citric acid cycle, metabolism of amino acids, fructose and mannose metabolism and that of glycerolipids, and pentose and glucuronate interconversion. On the other hand, the polymeric gel only promoted differences at the metabolite level in serum since no critical differences were observed between plasma collected with EDTA tubes and polymeric gel tubes. Thus, the main changes were attributable to serum collected in gel and affected to the metabolism of amino acids such as alanine, proline and threonine, the glycerolipids metabolism, and two primary metabolites such as aconitic acid and lactic acid. Therefore, these metabolite changes should be taken into account in planning an experimental protocol for metabolomics analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

A Single and Comprehensive Helios Data Archive

NASA Astrophysics Data System (ADS)

Salem, C. S.

2017-12-01

Helios 1 & 2 rank amoung the most important missions in Heliophysics, and the more-than 11 years of data returned by its spacecraft remain of paramount interests to researchers. Their unique trajectories which brought them closer to the Sun than any spaceccraft before or since, enabled their diverse suite of in-situ instruments to return measurements of unprecedented scientific richness. There is however no comprehensive public repository of all Helios in-situ data. Currently, most of the highest resolution data can be obtained from a variety of places, although highly processed and with very little documentation, especially on calibration. Analysis of this data set requires overcoming a number of technical and instrumental issues, knowledge and expertise of which is only possessed by the original PI's of the Helios experiments. We present here a work funded by NASA of aggregating, analyzing, evaluating, documenting and archiving the available Helios 1 and 2 in-situ data. This work at the UC Berkeley Space Sciences Laboratory is being undertaken in close collaboration with colleagues at the University of Koln, at the University of Kiel, at the Imperial College in London and at the Paris Observatory. A careful, detailed, analysis of the Helios fluxgate and search coil magnetic field data as well as plasma data has revealed numerous issues and problems with the available, processed, datasets, that we are still working to solve. We anticipate this comprehensive single archive of all Helios in-situ data, beyond its inherent scientific value, will also be an invaluable asset to the both the Solar Probe Plus and Solar Orbiter missions.

Experimental investigation of vapor shielding effects induced by ELM-like pulsed plasma loads using the double plasma gun device

NASA Astrophysics Data System (ADS)

Sakuma, I.; Kikuchi, Y.; Kitagawa, Y.; Asai, Y.; Onishi, K.; Fukumoto, N.; Nagata, M.

2015-08-01

We have developed a unique experimental device of so-called double plasma gun, which consists of two magnetized coaxial plasma gun (MCPG) devices, in order to clarify effects of vapor shielding on material erosion due to transient events in magnetically confined fusion devices. Two ELM-like pulsed plasmas produced by the two MCPG devices were injected into a target chamber with a variable time difference. For generating ablated plasmas in front of a target material, an aluminum foil sample in the target chamber was exposed to a pulsed plasma produced by the 1st MCPG device. The 2nd pulsed plasma was produced with a time delay of 70 μs. It was found that a surface absorbed energy measured by a calorimeter was reduced to ∼66% of that without the Al foil sample. Thus, the reduction of the incoming plasma energy by the vapor shielding effect was successfully demonstrated in the present experiment.

Development of a Climatology of Vertically Complete Wind Profiles from Doppler Radar Wind Profiler Systems

NASA Technical Reports Server (NTRS)

Barbre, Robert, Jr.

2015-01-01

Assessment of space vehicle loads and trajectories during design requires a large sample of wind profiles at the altitudes where winds affect the vehicle. Traditionally, this altitude region extends from near 8-14 km to address maximum dynamic pressure upon ascent into space, but some applications require knowledge of measured wind profiles at lower altitudes. Such applications include crew capsule pad abort and plume damage analyses. Two Doppler Radar Wind Profiler (DRWP) systems exist at the United States Air Force (USAF) Eastern Range and at the National Aeronautics and Space Administration's Kennedy Space Center. The 50-MHz DRWP provides wind profiles every 3-5 minutes from roughly 2.5-18.5 km, and five 915-MHz DRWPs provide wind profiles every 15 minutes from approximately 0.2-3.0 km. Archived wind profiles from all systems underwent rigorous quality control (QC) processes, and concurrent measurements from the QC'ed 50- and 915-MHz DRWP archives were spliced into individual profiles that extend from about 0.2-18.5 km. The archive contains combined profiles from April 2000 to December 2009, and thousands of profiles during each month are available for use by the launch vehicle community. This paper presents the details of the QC and splice methodology, as well as some attributes of the archive.

Enhancement of spectral quality of archival aerial photographs using satellite imagery for detection of land cover

NASA Astrophysics Data System (ADS)

Siok, Katarzyna; Jenerowicz, Agnieszka; Woroszkiewicz, Małgorzata

2017-07-01

Archival aerial photographs are often the only reliable source of information about the area. However, these data are single-band data that do not allow unambiguous detection of particular forms of land cover. Thus, the authors of this article seek to develop a method of coloring panchromatic aerial photographs, which enable increasing the spectral information of such images. The study used data integration algorithms based on pansharpening, implemented in commonly used remote sensing programs: ERDAS, ENVI, and PCI. Aerial photos and Landsat multispectral data recorded in 1987 and 2016 were chosen. This study proposes the use of modified intensity-hue-saturation and Brovey methods. The use of these methods enabled the addition of red-green-blue (RGB) components to monochrome images, thus enhancing their interpretability and spectral quality. The limitations of the proposed method relate to the availability of RGB satellite imagery, the accuracy of mutual orientation of the aerial and the satellite data, and the imperfection of archival aerial photographs. Therefore, it should be expected that the results of coloring will not be perfect compared to the results of the fusion of recent data with a similar ground sampling resolution, but still, they will allow a more accurate and efficient classification of land cover registered on archival aerial photographs.

Fermilab Today - Related Content

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Flow-injection chemiluminescence determination of melamine in urine and plasma.

PubMed

Tang, Xiaoshuang; Shi, Xiyan; Tang, Yuhai; Yue, Zhongjin; He, Qiqi

2012-01-01

A novel flow-injection chemiluminescence method for the determination of melamine in urine and plasma was developed. It was found that melamine can remarkably enhance chemiluminescence emission from the luminol-K(3) Fe(CN)(6) system in an alkaline medium. Under the optimum conditions, chemiluminescence intensity had a good linear relationship with the concentration of melamine in the range 9.0 × 10(-9) -7.0 × 10(-6) g/mL, with a correlation coefficient of 0.9992. The detection limit (3σ) was 3.5 ng/mL. The method has been applied to determine the concentration of melamine in samples using liquid-liquid extraction. Average recoveries of melamine were 102.6% in urine samples and 95.1% in plasma samples. The method provided a reproducible and stable approach for the sensitive detection of melamine in urine and plasma samples. Copyright © 2011 John Wiley & Sons, Ltd.

Concentric micro-nebulizer for direct sample insertion

DOEpatents

Fassel, V.A.; Rice, G.W.; Lawrence, K.E.

1984-03-06

A concentric micro-nebulizer and method for introducing liquid samples into a plasma established in a plasma torch including a first tube connected to a source of plasma gas. The concentric micro-nebulizer has inner and outer concentric tubes extending upwardly within the torch for connection to a source of nebulizer gas and to a source of liquid solvent and to a source of sample liquid. The inner tube is connected to the source of liquid solvent and to the source of sample liquid and the outer tube is connected to the source of nebulizer gas. The outer tube has an orifice positioned slightly below the plasma when it is established, with the inner and outer tubes forming an annulus therebetween with the annular spacing between the tubes at said orifice being less than about 0.05mm. The dead volume of the inner tube is less than about 5 microliters.

Concentric micro-nebulizer for direct sample insertion

DOEpatents

Fassel, Velmer A.; Rice, Gary W.; Lawrence, Kimberly E.

1986-03-11

A concentric micro-nebulizer and method for introducing liquid samples into a plasma established in a plasma torch including a first tube connected to a source of plasma gas. The concentric micro-nebulizer has inner and outer concentric tubes extending upwardly within the torch for connection to a source of nebulizer gas and to a source of liquid solvent and to a source of sample liquid. The inner tube is connected to the source of liquid solvent and to the source of sample liquid and the outer tube is connected to the source of nebulizer gas. The outer tube has an orifice positioned slightly below the plasma when it is established, with the inner and outer tubes forming an annulus therebetween with the annular spacing between the tubes at said orifice being less than about 0.05 mm. The dead volume of the inner tube is less than about 5 microliters.

Treatment of carprofen overdose with therapeutic plasma exchange in a dog.

PubMed

Kjaergaard, Astrid B; Davis, Jennifer L; Acierno, Mark J

2018-06-13

To report the use of therapeutic plasma exchange (TPE) in a dog with carprofen toxicosis. A 6-year-old female neutered Bichon Frise weighing 6.9 kg was examined after it had ingested 72 mg/kg carprofen. Mild dehydration without azotemia and with a urine specific gravity of 1.050 was noted at presentation. Treatment consisted of induction of emesis, symptomatic medical therapy, and TPE. The TPE achieved 1.5 plasma volume exchanges over 3 hours. Blood samples and effluent samples were collected every 30 minutes during TPE and additional blood samples were collected 11 and 35 hours after treatment. Carprofen concentrations in these samples were determined by high-pressure liquid chromatography. A 51% reduction in serum carprofen concentration was achieved following TPE. This report describes the successful reduction of plasma carprofen concentration in a dog using TPE. Although recent studies suggest that this particular dog may not have received a toxic dose, a 51% reduction of plasma carprofen concentration was achieved over 180 minutes, and TPE may be beneficial for treatment of dogs that have ingested higher doses. © Veterinary Emergency and Critical Care Society 2018.

Stability of BDNF in Human Samples Stored Up to 6 Months and Correlations of Serum and EDTA-Plasma Concentrations.

PubMed

Polyakova, Maryna; Schlögl, Haiko; Sacher, Julia; Schmidt-Kassow, Maren; Kaiser, Jochen; Stumvoll, Michael; Kratzsch, Jürgen; Schroeter, Matthias L

2017-06-03

Brain-derived neurotrophic factor (BDNF), an important neural growth factor, has gained growing interest in neuroscience, but many influencing physiological and analytical aspects still remain unclear. In this study we assessed the impact of storage time at room temperature, repeated freeze/thaw cycles, and storage at -80 °C up to 6 months on serum and ethylenediaminetetraacetic acid (EDTA)-plasma BDNF. Furthermore, we assessed correlations of serum and plasma BDNF concentrations in two independent sets of samples. Coefficients of variations (CVs) for serum BDNF concentrations were significantly lower than CVs of plasma concentrations ( n = 245, p = 0.006). Mean serum and plasma concentrations at all analyzed time points remained within the acceptable change limit of the inter-assay precision as declared by the manufacturer. Serum and plasma BDNF concentrations correlated positively in both sets of samples and at all analyzed time points of the stability assessment ( r = 0.455 to r s = 0.596; p < 0.004). In summary, when considering the acceptable change limit, BDNF was stable in serum and in EDTA-plasma up to 6 months. Due to a higher reliability, we suggest favoring serum over EDTA-plasma for future experiments assessing peripheral BDNF concentrations.

In Vitro Dialysis of Cytokine-Rich Plasma With High and Medium Cut-Off Membranes Reduces Its Procalcific Activity.

PubMed

Willy, Kevin; Hulko, Michael; Storr, Markus; Speidel, Rose; Gauss, Julia; Schindler, Ralf; Zickler, Daniel

2017-09-01

Recently developed high-flux (HF) dialysis membranes with extended permeability provide better clearance of middle-sized molecules such as interleukins (ILs). Whether this modulation of inflammation influences the procalcific effects of septic plasma on vascular smooth muscle cells (VSMCs) is not known. To assess the effects of high cut-off (HCO) and medium cut-off (MCO) membranes on microinflammation and in vitro vascular calcification we developed a miniature dialysis model. Plasma samples from lipopolysaccharide-spiked blood were dialyzed with HF, HCO, and MCO membranes in an in vitro miniature dialysis model. Afterwards, IL-6 concentrations were determined in dialysate and plasma. Calcifying VSMCs were incubated with dialyzed plasma samples and vascular calcification was assessed. Osteopontin (OPN) and matrix Gla protein (MGP) were measured in VSMC supernatants. IL-6 plasma concentrations were markedly lower with HCO and MCO dialysis. VSMC calcification was significantly lower after incubation with MCO- and HCO-serum compared to HF plasma. MGP and OPN levels in supernatants were significantly lower in the MCO but not in the HCO group compared to HF. In vitro dialysis of cytokine-enriched plasma samples with MCO and HCO membranes reduces IL-6 levels. The induction of vascular calcification by cytokine-enriched plasma is reduced after HCO and MCO dialysis. © 2017 International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

Shotgun Proteomic Analysis of Plasma from Dairy Cattle Suffering from Footrot: Characterization of Potential Disease-Associated Factors

PubMed Central

Sun, Dongbo; Zhang, Hong; Guo, Donghua; Sun, Anguo; Wang, Hongbin

2013-01-01

The plasma proteome of healthy dairy cattle and those with footrot was investigated using a shotgun LC-MS/MS approach. In total, 648 proteins were identified in healthy plasma samples, of which 234 were non-redundant proteins and 123 were high-confidence proteins; 712 proteins were identified from footrot plasma samples, of which 272 were non-redundant proteins and 138 were high-confidence proteins. The high-confidence proteins showed significant differences between healthy and footrot plasma samples in molecular weight, isoelectric points and the Gene Ontology categories. 22 proteins were found that may differentiate between the two sets of plasma proteins, of which 16 potential differential expression (PDE) proteins from footrot plasma involved in immunoglobulins, innate immune recognition molecules, acute phase proteins, regulatory proteins, and cell adhesion and cytoskeletal proteins; 6 PDE proteins from healthy plasma involved in regulatory proteins, cytoskeletal proteins and coagulation factors. Of these PDE proteins, haptoglobin, SERPINA10 protein, afamin precursor, haptoglobin precursor, apolipoprotein D, predicted peptidoglycan recognition protein L (PGRP-L) and keratan sulfate proteoglycan (KS-PG) were suggested to be potential footrot-associated factors. The PDE proteins PGRP-L and KS-PG were highlighted as potential biomarkers of footrot in cattle. The resulting protein lists and potential differentially expressed proteins may provide valuable information to increase understanding of plasma protein profiles in cattle and to assist studies of footrot-associated factors. PMID:23418487

A 96-well screen filter plate for high-throughput biological sample preparation and LC-MS/MS analysis.

PubMed

Peng, Sean X; Cousineau, Martin; Juzwin, Stephen J; Ritchie, David M

2006-01-01

A novel 96-well screen filter plate (patent pending) has been invented to eliminate a time-consuming and labor-intensive step in preparation of in vivo study samples--to remove blood or plasma clots. These clots plug the pipet tips during a manual or automated sample-transfer step causing inaccurate pipetting or total pipetting failure. Traditionally, these blood and plasma clots are removed by picking them out manually one by one from each sample tube before any sample transfer can be made. This has significantly slowed the sample preparation process and has become a bottleneck for automated high-throughput sample preparation using robotic liquid handlers. Our novel screen filter plate was developed to solve this problem. The 96-well screen filter plate consists of 96 stainless steel wire-mesh screen tubes connected to the 96 openings of a top plate so that the screen filter plate can be readily inserted into a 96-well sample storage plate. Upon insertion, the blood and plasma clots are excluded from entering the screen tube while clear sample solutions flow freely into it. In this way, sample transfer can be easily completed by either manual or automated pipetting methods. In this report, three structurally diverse compounds were selected to evaluate and validate the use of the screen filter plate. The plasma samples of these compounds were transferred and processed in the presence and absence of the screen filter plate and then analyzed by LC-MS/MS methods. Our results showed a good agreement between the samples prepared with and without the screen filter plate, demonstrating the utility and efficiency of this novel device for preparation of blood and plasma samples. The device is simple, easy to use, and reusable. It can be employed for sample preparation of other biological fluids that contain floating particulates or aggregates.

The Cluster Science Archive: from Time Period to Physics Based Search

NASA Astrophysics Data System (ADS)

Masson, A.; Escoubet, C. P.; Laakso, H. E.; Perry, C. H.

2015-12-01

Since 2000, the Cluster spacecraft relay the most detailed information on how the solar wind affects our geospace in three dimensions. Science output from Cluster is a leap forward in our knowledge of space plasma physics: the science behind space weather. It has been key in improving the modeling of the magnetosphere and understanding its various physical processes. Cluster data have enabled the publication of more than 2000 refereed papers and counting. This substantial scientific return is often attributed to the online availability of the Cluster data archive, now called the Cluster Science Archive (CSA). It is being developed by the ESAC Science Data Center (ESDC) team and maintained alongside other science ESA archives at ESAC (ESA Space Astronomy Center, Madrid, Spain). CSA is a public archive, which contains the entire set of Cluster high-resolution data, and other related products in a standard format and with a complete set of metadata. Since May 2015, it also contains data from the CNSA/ESA Double Star mission (2003-2008), a mission operated in conjunction with Cluster. The total amount of data format now exceeds 100 TB. Accessing CSA requires to be registered to enable user profiles and CSA accounts more than 1,500 users. CSA provides unique tools for visualizing its data including - on-demand particle distribution functions visualization - fast data browsing with more than 15TB of pre-generated plots - inventory plots It also offers command line capabilities (e.g. data access via Matlab or IDL softwares, data streaming). Despite its reliability, users can only request data for a specific time period while scientists often focus on specific regions or data signatures. For these reasons, a data-mining tool is being developed to do just that. It offers an interface to select data based not only on a time period but on various criteria including: key physical parameters, regions of space and spacecraft constellation geometry. The output of this tool is a list of time periods that fits the criteria imposed by the user. Such a list enables to download any bunch of datasets for all these time periods in one go. We propose to present the state of development of this tool and interact with the scientific community to better fit its needs.

Enhanced analytical sensitivity of a quantitative PCR for CMV using a modified nucleic-acid extraction procedure.

PubMed

Ferreira-Gonzalez, A; Yanovich, S; Langley, M R; Weymouth, L A; Wilkinson, D S; Garrett, C T

2000-01-01

Accurate and rapid diagnosis of CMV disease in immunocompromised individuals remains a challenge. Quantitative polymerase chain reaction (QPCR) methods for detection of CMV in peripheral blood mononuclear cells (PBMC) have improved the positive and negative predictive value of PCR for diagnosis of CMV disease. However, detection of CMV in plasma has demonstrated a lower negative predictive value for plasma as compared with PBMC. To enhance the sensitivity of the QPCR assay for plasma specimens, plasma samples were centrifuged before nucleic-acid extraction and the extracted DNA resolubilized in reduced volume. Optimization of the nucleic-acid extraction focused on decreasing or eliminating the presence of inhibitors in the pelleted plasma. Quantitation was achieved by co-amplifying an internal quantitative standard (IS) with the same primer sequences as CMV. PCR products were detected by hybridization in a 96-well microtiter plate coated with a CMV or IS specific probe. The precision of the QPCR assay for samples prepared from untreated and from pelleted plasma was then assessed. The coefficient of variation for both types of samples was almost identical and the magnitude of the coefficient of variations was reduced by a factor of ten if the data were log transformed. Linearity of the QPCR assay extended over a 3.3-log range for both types of samples but the range of linearity for pelleted plasma was 20 to 40,000 viral copies/ml (vc/ml) in contrast to 300 to 400,000 vc/ml for plasma. Thus, centrifugation of plasma before nucleic-acid extraction and resuspension of extracted CMV DNA in reduced volume enhanced the analytical sensitivity approximately tenfold over the dynamic range of the assay. Copyright 2000 Wiley-Liss, Inc.

Screening for phaeochromocytoma and paraganglioma: impact of using supine reference intervals for plasma metanephrines with samples collected from fasted/seated patients.

PubMed

Casey, R; Griffin, T P; Wall, D; Dennedy, M C; Bell, M; O'Shea, P M

2017-01-01

Background The Endocrine Society Clinical Practice Guideline on Phaeochomocytoma and Paraganglioma recommends phlebotomy for plasma-free metanephrines with patients fasted and supine using appropriately defined reference intervals. Studies have shown higher diagnostic sensitivities using these criteria. Further, with seated-sampling protocols, for result interpretation, reference intervals that do not compromise diagnostic sensitivity should be employed. Objective To determine the impact on diagnostic performance and financial cost of using supine reference intervals for result interpretation with our current plasma-free metanephrines fasted/seated-sampling protocol. Methods We conducted a retrospective cohort study of patients who underwent screening for PPGL using plasma-free metanephrines from 2009 to 2014 at Galway University Hospitals. Plasma-free metanephrines were measured using liquid chromatography-tandem mass spectrometry. Supine thresholds for plasma normetanephrine and metanephrine set at 610 pmol/L and 310 pmol/L, respectively, were used. Results A total of 183 patients were evaluated. Mean age of participants was 53.4 (±16.3) years. Five of 183 (2.7%) patients had histologically confirmed PPGL (males, n=4). Using seated reference intervals for plasma-free metanephrines, diagnostic sensitivity and specificity were 100% and 98.9%, respectively, with two false-positive cases. Application of reference intervals established in subjects supine and fasted to this cohort gave diagnostic sensitivity of 100% with specificity of 74.7%. Financial analysis of each pretesting strategy demonstrated cost-equivalence (€147.27/patient). Conclusion Our cost analysis, together with the evidence that fasted/supine-sampling for plasma-free metanephrines, offers more reliable exclusion of PPGL mandates changing our current practice. This study highlights the important advantages of standardized diagnostic protocols for plasma-free metanephrines to ensure the highest diagnostic accuracy for investigation of PPGL.

Dried Blood Spot Methodology in Combination With Liquid Chromatography/Tandem Mass Spectrometry Facilitates the Monitoring of Teriflunomide

PubMed Central

Lunven, Catherine; Turpault, Sandrine; Beyer, Yann-Joel; O'Brien, Amy; Delfolie, Astrid; Boyanova, Neli; Sanderink, Ger-Jan; Baldinetti, Francesca

2016-01-01

Background: Teriflunomide, a once-daily oral immunomodulator approved for treatment of relapsing-remitting multiple sclerosis, is eliminated slowly from plasma. If necessary to rapidly lower plasma concentrations of teriflunomide, an accelerated elimination procedure using cholestyramine or activated charcoal may be used. The current bioanalytical assay for determination of plasma teriflunomide concentration requires laboratory facilities for blood centrifugation and plasma storage. An alternative method, with potential for greater convenience, is dried blood spot (DBS) methodology. Analytical and clinical validations are required to switch from plasma to DBS (finger-prick sampling) methodology. Methods: Using blood samples from healthy subjects, an LC-MS/MS assay method for quantification of teriflunomide in DBS over a range of 0.01–10 mcg/mL was developed and validated for specificity, selectivity, accuracy, precision, reproducibility, and stability. Results were compared with those from the current plasma assay for determination of plasma teriflunomide concentration. Results: Method was specific and selective relative to endogenous compounds, with process efficiency ∼88%, and no matrix effect. Inaccuracy and imprecision for intraday and interday analyses were <15% at all concentrations tested. Quantification of teriflunomide in DBS assay was not affected by blood deposit volume and punch position within spot, and hematocrit level had a limited but acceptable effect on measurement accuracy. Teriflunomide was stable for at least 4 months at room temperature, and for at least 24 hours at 37°C with and without 95% relative humidity, to cover sampling, drying, and shipment conditions in the field. The correlation between DBS and plasma concentrations (R2 = 0.97), with an average blood to plasma ratio of 0.59, was concentration independent and constant over time. Conclusions: DBS sampling is a simple and practical method for monitoring teriflunomide concentrations. PMID:27015245

The requirements for low-temperature plasma ionization support miniaturization of the ion source.

PubMed

Kiontke, Andreas; Holzer, Frank; Belder, Detlev; Birkemeyer, Claudia

2018-06-01

Ambient ionization mass spectrometry (AI-MS), the ionization of samples under ambient conditions, enables fast and simple analysis of samples without or with little sample preparation. Due to their simple construction and low resource consumption, plasma-based ionization methods in particular are considered ideal for use in mobile analytical devices. However, systematic investigations that have attempted to identify the optimal configuration of a plasma source to achieve the sensitive detection of target molecules are still rare. We therefore used a low-temperature plasma ionization (LTPI) source based on dielectric barrier discharge with helium employed as the process gas to identify the factors that most strongly influence the signal intensity in the mass spectrometry of species formed by plasma ionization. In this study, we investigated several construction-related parameters of the plasma source and found that a low wall thickness of the dielectric, a small outlet spacing, and a short distance between the plasma source and the MS inlet are needed to achieve optimal signal intensity with a process-gas flow rate of as little as 10 mL/min. In conclusion, this type of ion source is especially well suited for downscaling, which is usually required in mobile devices. Our results provide valuable insights into the LTPI mechanism; they reveal the potential to further improve its implementation and standardization for mobile mass spectrometry as well as our understanding of the requirements and selectivity of this technique. Graphical abstract Optimized parameters of a dielectric barrier discharge plasma for ionization in mass spectrometry. The electrode size, shape, and arrangement, the thickness of the dielectric, and distances between the plasma source, sample, and MS inlet are marked in red. The process gas (helium) flow is shown in black.

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

DOE Data Explorer

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

2015-01-01

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

Validity of the MMPI-2-RF (Restructured Form) L-r and K-r Scales in Detecting Underreporting in Clinical and Nonclinical Samples

ERIC Educational Resources Information Center

Sellbom, Martin; Bagby, R. Michael

2008-01-01

In the current investigation, the authors examined the validity of the L-r and K-r scales on the recently developed Minnesota Multiphasic Personality Inventory-2-Restructured Form (MMPI-2-RF; Y. S. Ben-Porath & A. Tellegen, in press) in measuring underreported response bias. Three archival samples previously collected for examining MMPI-2…

Quantitative, multiplexed workflow for deep analysis of human blood plasma and biomarker discovery by mass spectrometry.

PubMed

Keshishian, Hasmik; Burgess, Michael W; Specht, Harrison; Wallace, Luke; Clauser, Karl R; Gillette, Michael A; Carr, Steven A

2017-08-01

Proteomic characterization of blood plasma is of central importance to clinical proteomics and particularly to biomarker discovery studies. The vast dynamic range and high complexity of the plasma proteome have, however, proven to be serious challenges and have often led to unacceptable tradeoffs between depth of coverage and sample throughput. We present an optimized sample-processing pipeline for analysis of the human plasma proteome that provides greatly increased depth of detection, improved quantitative precision and much higher sample analysis throughput as compared with prior methods. The process includes abundant protein depletion, isobaric labeling at the peptide level for multiplexed relative quantification and ultra-high-performance liquid chromatography coupled to accurate-mass, high-resolution tandem mass spectrometry analysis of peptides fractionated off-line by basic pH reversed-phase (bRP) chromatography. The overall reproducibility of the process, including immunoaffinity depletion, is high, with a process replicate coefficient of variation (CV) of <12%. Using isobaric tags for relative and absolute quantitation (iTRAQ) 4-plex, >4,500 proteins are detected and quantified per patient sample on average, with two or more peptides per protein and starting from as little as 200 μl of plasma. The approach can be multiplexed up to 10-plex using tandem mass tags (TMT) reagents, further increasing throughput, albeit with some decrease in the number of proteins quantified. In addition, we provide a rapid protocol for analysis of nonfractionated depleted plasma samples analyzed in 10-plex. This provides ∼600 quantified proteins for each of the ten samples in ∼5 h of instrument time.

Single-Center Experience with a Targeted Next Generation Sequencing Assay for Assessment of Relevant Somatic Alterations in Solid Tumors.

PubMed

Paasinen-Sohns, Aino; Koelzer, Viktor H; Frank, Angela; Schafroth, Julian; Gisler, Aline; Sachs, Melanie; Graber, Anne; Rothschild, Sacha I; Wicki, Andreas; Cathomas, Gieri; Mertz, Kirsten D

2017-03-01

Companion diagnostics rely on genomic testing of molecular alterations to enable effective cancer treatment. Here we report the clinical application and validation of the Oncomine Focus Assay (OFA), an integrated, commercially available next-generation sequencing (NGS) assay for the rapid and simultaneous detection of single nucleotide variants, short insertions and deletions, copy number variations, and gene rearrangements in 52 cancer genes with therapeutic relevance. Two independent patient cohorts were investigated to define the workflow, turnaround times, feasibility, and reliability of OFA targeted sequencing in clinical application and using archival material. Cohort I consisted of 59 diagnostic clinical samples from the daily routine submitted for molecular testing over a 4-month time period. Cohort II consisted of 39 archival melanoma samples that were up to 15years old. Libraries were prepared from isolated nucleic acids and sequenced on the Ion Torrent PGM sequencer. Sequencing datasets were analyzed using the Ion Reporter software. Genomic alterations were identified and validated by orthogonal conventional assays including pyrosequencing and immunohistochemistry. Sequencing results of both cohorts, including archival formalin-fixed, paraffin-embedded material stored up to 15years, were consistent with published variant frequencies. A concordance of 100% between established assays and OFA targeted NGS was observed. The OFA workflow enabled a turnaround of 3½ days. Taken together, OFA was found to be a convenient tool for fast, reliable, broadly applicable and cost-effective targeted NGS of tumor samples in routine diagnostics. Thus, OFA has strong potential to become an important asset for precision oncology. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Lyman Limit Absorbers in GALEX Spectra

NASA Astrophysics Data System (ADS)

Williger, Gerard M.; Haberzettl, Lutz G.; Ribaudo, Joseph; Kuchner, Marc J.; Burchett, Joseph; Clowes, Roger G.; Lauroesch, James T.; Mills, Brianna; Borden, Jeremy

2018-01-01

We describe the method and early results for crowdsourcing a search for low-redshift partial and complete Lyman Limit Systems (pLLSs and LLSs) in the GALEX spectral archive. LLSs have been found in large numbers at z>3 and traced to lower redshift through a relatively small number of QSO spectra from spaced-based telescopes. From a sample of 44 pLLSs and 11 LLSs at 0.1 = -0.32 +/- 0.07 and the low-metallicity portion centered at <[X/H]> = -1.87 +/- 0.11.The GALEX spectral archive offers a vast dataset potentially containing hundreds of LLSs, which may be leveraged to search for such a bimodality and track its evolution within the unconstrained near-UV gap at 1

Accelerating the Development and Validation of New Value-Based Diagnostics by Leveraging Biobanks.

PubMed

Schneider, Daniel; Riegman, Peter H J; Cronin, Maureen; Negrouk, Anastassia; Moch, Holger; Balling, Rudi; Penault-Llorca, Frederiques; Zatloukal, Kurt; Horgan, Denis

The challenges faced in developing value-based diagnostics has resulted in few of these tests reaching the clinic, leaving many treatment modalities without matching diagnostics to select patients for particular therapies. Many patients receive therapies from which they are unlikely to benefit, resulting in worse outcomes and wasted health care resources. The paucity of value-based diagnostics is a result of the scientific challenges in developing predictive markers, specifically: (1) complex biology, (2) a limited research infrastructure supporting diagnostic development, and (3) the lack of incentives for diagnostic developers to invest the necessary resources. Better access to biospecimens can address some of these challenges. Methodologies developed to evaluate biomarkers from biospecimens archived from patients enrolled in randomized clinical trials offer the greatest opportunity to develop and validate high-value molecular diagnostics. An alternative opportunity is to access high-quality biospecimens collected from large public and private longitudinal observational cohorts such as the UK Biobank, the US Million Veteran Program, the UK 100,000 Genomes Project, or the French E3N cohort. Value-based diagnostics can be developed to work in a range of samples including blood, serum, plasma, urine, and tumour tissue, and better access to these high-quality biospecimens with clinical data can facilitate biomarker research. © 2016 S. Karger AG, Basel.

Effect of Plasma Surface Finish on Wettability and Mechanical Properties of SAC305 Solder Joints

NASA Astrophysics Data System (ADS)

Kim, Kyoung-Ho; Koike, Junichi; Yoon, Jeong-Won; Yoo, Sehoon

2016-12-01

The wetting behavior, interfacial reactions, and mechanical reliability of Sn-Ag-Cu solder on a plasma-coated printed circuit board (PCB) substrate were evaluated under multiple heat-treatments. Conventional organic solderability preservative (OSP) finished PCBs were used as a reference. The plasma process created a dense and highly cross-linked polymer coating on the Cu substrates. The plasma finished samples had higher wetting forces and shorter zero-cross times than those with OSP surface finish. The OSP sample was degraded after sequential multiple heat treatments and reflow processes, whereas the solderability of the plasma finished sample was retained after multiple heat treatments. After the soldering process, similar microstructures were observed at the interfaces of the two solder joints, where the development of intermetallic compounds was observed. From ball shear tests, it was found that the shear force for the plasma substrate was consistently higher than that for the OSP substrate. Deterioration of the OSP surface finish was observed after multiple heat treatments. Overall, the plasma surface finish was superior to the conventional OSP finish with respect to wettability and joint reliability, indicating that it is a suitable material for the fabrication of complex electronic devices.

Multistage plasma initiation process by pulsed CO2 laser irradiation of a Ti sample in an ambient gas (He, Ar, or N2)

NASA Astrophysics Data System (ADS)

Hermann, J.; Boulmer-Leborgne, C.; Mihailescu, I. N.; Dubreuil, B.

1993-02-01

New experimental results are reported on plasma initiation in front of a titanium sample irradiated by ir (λ=10.6 μm) laser pulses in an ambient gas (He, Ar, and N2) at pressures ranging from several Torr up to the atmosphere. The plasma is studied by space- and time-resolved emission spectroscopy, while sample vaporization is probed by laser-induced fluorescence spectroscopy. Threshold laser intensities leading to the formation of a plasma in the vapor and in the ambient gases are determined. Experimental results support the model of a vaporization mechanism for the plasma initiation (vaporization-initiated plasma breakdown). The plasma initiation is described by simple numerical criteria based on a two-stage process. Theoretical predictions are found to be in a reasonable agreement with the experiment. This study provides also a clear explanation of the influence of the ambient gas on the laser beam-metal surface energy transfer. Laser irradiation always causes an important vaporization when performed in He, while in the case of Ar or N2, the interaction is reduced in heating and vaporization of some surface defects and impurities.

Non-Thermal Plasma in Contact with Water: The Origin of Species.

PubMed

Gorbanev, Yury; O'Connell, Deborah; Chechik, Victor

2016-03-01

Non-thermal atmospheric pressure plasma has attracted considerable attention in recent years due to its potential for biomedical applications. Determining the mechanism of the formation of reactive species in liquid treated with plasma is thus of paramount importance for both fundamental and applied research. In this work, the origin of reactive species in plasma-treated aqueous solutions was investigated by using spin-trapping, hydrogen and oxygen isotopic labelling and electron paramagnetic resonance (EPR) spectroscopy. The species originating from molecules in the liquid phase and those introduced with the feed gas were differentiated by EPR and 1 H NMR analysis of liquid samples. The effects of water vapour and oxygen admixtures in the feed gas were investigated. All the reactive species detected in the liquid samples were shown to be formed largely in the plasma gas phase. It is suggested that hydrogen peroxide (determined by UV/Vis analysis) is formed primarily in the plasma tube, whereas the radical species ⋅OOH, ⋅OH and ⋅H are proposed to originate from the region between the plasma nozzle and the liquid sample. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Identification of extracellular miRNA in archived serum samples by next-generation sequencing from RNA extracted using multiple methods.

PubMed

Gautam, Aarti; Kumar, Raina; Dimitrov, George; Hoke, Allison; Hammamieh, Rasha; Jett, Marti

2016-10-01

miRNAs act as important regulators of gene expression by promoting mRNA degradation or by attenuating protein translation. Since miRNAs are stably expressed in bodily fluids, there is growing interest in profiling these miRNAs, as it is minimally invasive and cost-effective as a diagnostic matrix. A technical hurdle in studying miRNA dynamics is the ability to reliably extract miRNA as small sample volumes and low RNA abundance create challenges for extraction and downstream applications. The purpose of this study was to develop a pipeline for the recovery of miRNA using small volumes of archived serum samples. The RNA was extracted employing several widely utilized RNA isolation kits/methods with and without addition of a carrier. The small RNA library preparation was carried out using Illumina TruSeq small RNA kit and sequencing was carried out using Illumina platform. A fraction of five microliters of total RNA was used for library preparation as quantification is below the detection limit. We were able to profile miRNA levels in serum from all the methods tested. We found out that addition of nucleic acid based carrier molecules had higher numbers of processed reads but it did not enhance the mapping of any miRBase annotated sequences. However, some of the extraction procedures offer certain advantages: RNA extracted by TRIzol seemed to align to the miRBase best; extractions using TRIzol with carrier yielded higher miRNA-to-small RNA ratios. Nuclease free glycogen can be carrier of choice for miRNA sequencing. Our findings illustrate that miRNA extraction and quantification is influenced by the choice of methodologies. Addition of nucleic acid- based carrier molecules during extraction procedure is not a good choice when assaying miRNA using sequencing. The careful selection of an extraction method permits the archived serum samples to become valuable resources for high-throughput applications.

JAMSTEC DARWIN Database Assimilates GANSEKI and COEDO

NASA Astrophysics Data System (ADS)

Tomiyama, T.; Toyoda, Y.; Horikawa, H.; Sasaki, T.; Fukuda, K.; Hase, H.; Saito, H.

2017-12-01

Introduction: Japan Agency for Marine-Earth Science and Technology (JAMSTEC) archives data and samples obtained by JAMSTEC research vessels and submersibles. As a common property of the human society, JAMSTEC archive is open for public users with scientific/educational purposes [1]. For publicizing its data and samples online, JAMSTEC is operating NUUNKUI data sites [2], a group of several databases for various data and sample types. For years, data and metadata of JAMSTEC rock samples, sediment core samples and cruise/dive observation were publicized through databases named GANSEKI, COEDO, and DARWIN, respectively. However, because they had different user interfaces and data structures, these services were somewhat confusing for unfamiliar users. Maintenance costs of multiple hardware and software were also problematic for performing sustainable services and continuous improvements. Database Integration: In 2017, GANSEKI, COEDO and DARWIN were integrated into DARWIN+ [3]. The update also included implementation of map-search function as a substitute of closed portal site. Major functions of previous systems were incorporated into the new system; users can perform the complex search, by thumbnail browsing, map area, keyword filtering, and metadata constraints. As for data handling, the new system is more flexible, allowing the entry of variety of additional data types. Data Management: After the DARWIN major update, JAMSTEC data & sample team has been dealing with minor issues of individual sample data/metadata which sometimes need manual modification to be transferred to the new system. Some new data sets, such as onboard sample photos and surface close-up photos of rock samples, are getting available online. Geochemical data of sediment core samples will supposedly be added in the near future. Reference: [1] http://www.jamstec.go.jp/e/database/data_policy.html [2] http://www.godac.jamstec.go.jp/jmedia/portal/e/ [3] http://www.godac.jamstec.go.jp/darwin/e/

Plasma synthesis, Mössbauer spectroscopy and X-ray diffraction studies of nanosized iron oxides

NASA Astrophysics Data System (ADS)

Paneva, Daniela; Zaharieva, Katerina; Grabis, Janis; Mitov, Ivan; Vissokov, Gheorghi

2010-06-01

In this article synthesis and study of iron oxide nanopowders are described. The synthesis of sample 1 and sample 2—iron oxides—was carried out by electric arc plasma cutting of ordinary steel. The sample 3 was prepared by evaporation of Fe2O3/FeO mixture in radio-frequency nitrogen plasma. The characterization of the as prepared iron oxide nanoproducts was achieved by means of Mössbauer spectroscopy and X-ray diffraction analysis. The presence of different phases of iron oxide with a basic phase Fe3 - xO4 (magnetite), additional Fe1 - xO (wüstite) and α or γ-Fe2O3 (hematite or maghemite) with superparamagnetic particles for sample 1 and sample 2 and Fe3 - xO4 (magnetite) for sample 3 is observed.

VESPA: Developing the Planetary Science Virtual Observatory in H2020

NASA Astrophysics Data System (ADS)

Erard, S.; Cecconi, B.; Le Sidaner, P.; Capria, T.; Rossi, A. P.; Schmitt, B.; André, N.; Vandaele, A.-C.; Scherf, M.; Hueso, R.; Maattanen, A.; Thuillot, W.; Achilleos, N.; Marmo, C.; Santolik, O.; Benson, K.; Bollard, Ph.

2015-10-01

The Europlanet H2020 programme will develop a research infrastructure in Horizon 2020. The programme includes a follow-on to the FP7 activity aimed at developing the Planetary Science Virtual Observatory (VO). This activity is called VESPA, which stands for Virtual European Solar and Planetary Access. Building on the IDIS activity of Europlanet FP7, VESPA will distribute more data, will improve the connected tools and infrastructure, and will help developing a community of both users and data providers. One goal of the Europlanet FP7 programme was to set the basis for a European Virtual Observatory in Planetary Science. A prototype has been set up during FP7, most of the activity being dedicated to the definition of standards to handle data in this field. The aim was to facilitate searches in big archives as well as sparse databases, to make on-line data access and visualization possible, and to allow small data providers to make their data available in an interoperable environment with minimum effort. This system makes intensive use of studies and developments led in Astronomy (IVOA), Solar Science (HELIO), plasma physics (SPASE), and space archive services (IPDA). It remains consistent with extensions of IVOA standards.

VESPA: developing the planetary science Virtual Observatory in H2020

NASA Astrophysics Data System (ADS)

Erard, Stéphane; Cecconi, Baptiste; Le Sidaner, Pierre; Capria, Teresa; Rossi, Angelo Pio

2016-04-01

The Europlanet H2020 programme will develop a research infrastructure in Horizon 2020. The programme includes a follow-on to the FP7 activity aimed at developing the Planetary Science Virtual Observatory (VO). This activity is called VESPA, which stands for Virtual European Solar and Planetary Access. Building on the IDIS activity of Europlanet FP7, VESPA will distribute more data, will improve the connected tools and infrastructure, and will help developing a community of both users and data providers. One goal of the Europlanet FP7 programme was to set the basis for a European Virtual Observatory in Planetary Science. A prototype has been set up during FP7, most of the activity being dedicated to the definition of standards to handle data in this field. The aim was to facilitate searches in big archives as well as sparse databases, to make on-line data access and visualization possible, and to allow small data providers to make their data available in an interoperable environment with minimum effort. This system makes intensive use of studies and developments led in Astronomy (IVOA), Solar Science (HELIO), plasma physics (SPASE), and space archive services (IPDA). It remains consistent with extensions of IVOA standards.

Real-Time Data Streaming and Storing Structure for the LHD's Fusion Plasma Experiments

NASA Astrophysics Data System (ADS)

Nakanishi, Hideya; Ohsuna, Masaki; Kojima, Mamoru; Imazu, Setsuo; Nonomura, Miki; Emoto, Masahiko; Yoshida, Masanobu; Iwata, Chie; Ida, Katsumi

2016-02-01

The LHD data acquisition and archiving system, i.e., LABCOM system, has been fully equipped with high-speed real-time acquisition, streaming, and storage capabilities. To deal with more than 100 MB/s continuously generated data at each data acquisition (DAQ) node, DAQ tasks have been implemented as multitasking and multithreaded ones in which the shared memory plays the most important role for inter-process fast and massive data handling. By introducing a 10-second time chunk named “subshot,” endless data streams can be stored into a consecutive series of fixed length data blocks so that they will soon become readable by other processes even while the write process is continuing. Real-time device and environmental monitoring are also implemented in the same way with further sparse resampling. The central data storage has been separated into two layers to be capable of receiving multiple 100 MB/s inflows in parallel. For the frontend layer, high-speed SSD arrays are used as the GlusterFS distributed filesystem which can provide max. 2 GB/s throughput. Those design optimizations would be informative for implementing the next-generation data archiving system in big physics, such as ITER.

Stress-induced suppression of testosterone secretion in male alligators.

PubMed

Lance, V A; Elsey, R M

1986-08-01

In order to test the effect of acute stress on gonadal hormone secretion in reptiles, six mature male alligators were captured, and a blood sample was taken within 5 min of capture. Additional blood samples were taken at timed intervals for up to 41 hr, and plasma testosterone and corticosterone were measured by radioimmunoassay. Plasma testosterone declined to 50% of the initial value by 4 hr and dropped to less than 10% of initial by 24 hr. Plasma corticosterone increased during the first 12 hr, declined at 24 hr, and rose again at 40 hr. Blood samples from male alligators collected in North and South Carolina, south Florida, and in south Louisiana in two consecutive breeding seasons were also assayed for testosterone and corticosterone. In these populations there were significant differences in mean plasma testosterone and corticosterone levels. Elevated corticosterone levels were consistently seen in alligators caught in traps and from which a blood sample was taken several hours later. Plasma testosterone, although consistently lower in trapped alligators, did not show a negative correlation with plasma corticosterone. Farm-reared alligators bled once, released, and bled again at 24 hr also showed a highly significant suppression of testosterone secretion. These results demonstrate that stress has a rapid and dramatic effect on testicular steroid secretion in both farm-reared and wild alligators.

Exposure of infants to budesonide through breast milk of asthmatic mothers.

PubMed

Fält, Anette; Bengtsson, Thomas; Kennedy, Britt-Marie; Gyllenberg, Ann; Lindberg, Bengt; Thorsson, Lars; Stråndgarden, Kerstin

2007-10-01

Maintenance treatment with inhaled corticosteroids is often required for asthmatic nursing women. Data on the transfer of inhaled corticosteroids from plasma to breast milk and the subsequent exposure of the breast-feeding infant has been unavailable. We sought to assess budesonide concentrations in milk and plasma of asthmatic nursing women receiving maintenance treatment with the Pulmicort Turbuhaler and estimate the exposure of their breast-fed infants. Milk and plasma samples were collected up to 8 hours after dosing from 8 mothers receiving budesonide maintenance treatment (200 or 400 microg twice daily). Pharmacokinetic parameters were calculated from budesonide milk and plasma concentrations. Infant exposure was estimated based on average milk budesonide concentrations. A single blood sample was obtained from 5 infants close to expected infant maximum concentration. Budesonide concentrations in milk reflected those in maternal plasma, supporting passive diffusion of budesonide between plasma and milk, and was always lower than that in plasma. The mean milk/plasma ratio was 0.46. The estimated daily infant dose was 0.3% of the daily maternal dose for both dose levels, and the average plasma concentration in infants was estimated to be 1/600th of the concentrations observed in maternal plasma, assuming complete infant oral bioavailability. Budesonide concentrations in infant plasma samples were all less than the limit of quantification. Maintenance treatment with inhaled budesonide (200 or 400 microg twice daily) in asthmatic nursing women results in negligible systemic exposure to budesonide in breast-fed infants. These data support continued use of inhaled budesonide during breast-feeding.

Metagenomic Investigation of Plasma in Individuals with ME/CFS Highlights the Importance of Technical Controls to Elucidate Contamination and Batch Effects.

PubMed

Miller, Ruth R; Uyaguari-Diaz, Miguel; McCabe, Mark N; Montoya, Vincent; Gardy, Jennifer L; Parker, Shoshana; Steiner, Theodore; Hsiao, William; Nesbitt, Matthew J; Tang, Patrick; Patrick, David M

2016-01-01

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a debilitating disease causing indefinite fatigue. ME/CFS has long been hypothesised to have an infectious cause; however, no specific infectious agent has been identified. We used metagenomics to analyse the RNA from plasma samples from 25 individuals with ME/CFS and compare their microbial content to technical controls as well as three control groups: individuals with alternatively diagnosed chronic Lyme syndrome (N = 13), systemic lupus erythematosus (N = 11), and healthy controls (N = 25). We found that the majority of sequencing reads were removed during host subtraction, thus there was very low microbial RNA content in the plasma. The effects of sample batching and contamination during sample processing proved to outweigh the effects of study group on microbial RNA content, as the few differences in bacterial or viral RNA abundance we did observe between study groups were most likely caused by contamination and batch effects. Our results highlight the importance of including negative controls in all metagenomic analyses, since there was considerable overlap between bacterial content identified in study samples and control samples. For example, Proteobacteria, Firmicutes, Actinobacteria, and Bacteriodes were found in both study samples and plasma-free negative controls. Many of the taxonomic groups we saw in our plasma-free negative control samples have previously been associated with diseases, including ME/CFS, demonstrating how incorrect conclusions may arise if controls are not used and batch effects not accounted for.

Tumor and Plasma Met Levels in Non-Metastatic Prostate Cancer.

PubMed

Kaye, Deborah R; Pinto, Peter A; Cecchi, Fabiola; Reilly, Joseph; Semerjian, Alice; Rabe, Daniel C; Gupta, Gopal; Choyke, Peter L; Bottaro, Donald P

2016-01-01

To measure Met protein content in prostate biopsies guided by fused magnetic resonance and ultrasound imaging, and to measure soluble Met (sMet) protein concentration in plasma samples from patients presenting evidence of prostate cancer. 345 patients had plasma samples drawn prior to image-guided biopsy of the prostate. Of these, 32% had benign biopsies. Of the 236 that were positive for prostate adenocarcinoma (PCa), 132 treated by total prostatectomy had Gleason scores of 6 (17%), 7, (55%), 8 (16%), or 9-10 (12%). 23% had evidence of local invasion. Plasma samples were also obtained from 80 healthy volunteers. Tissue Met and plasma sMet were measured by two-site immunoassay; values were compared among clinically defined groups using non-parametric statistical tests to determine significant differences or correlations. PCa tumor Met correlated significantly with plasma sMet, but median values were similar among benign and malignant groups. Median plasma sMet values were also similar among those groups, although both medians were significantly above normal. Median Met content in primary PCa tumors and sMet concentrations were independent of Gleason score, final pathologic stage and age. Plasma sMet is not predictive of PCa or its severity in patients with organ-confined or locally invasive disease. Quantitative analysis of Met protein content and activation state in PCa tumor biopsy samples was highly feasible and may have value in follow-up to genomic and/or transcriptomic-based screens that show evidence of oncogenically relevant MET gene features that occur at relatively low frequency in non-metastatic PCa.

Porous Silicon Antibody Microarrays for Quantitative Analysis: Measurement of Free and Total PSA in Clinical Plasma Samples

PubMed Central

Tojo, Axel; Malm, Johan; Marko-Varga, György; Lilja, Hans; Laurell, Thomas

2014-01-01

The antibody microarrays have become widespread, but their use for quantitative analyses in clinical samples has not yet been established. We investigated an immunoassay based on nanoporous silicon antibody microarrays for quantification of total prostate-specific-antigen (PSA) in 80 clinical plasma samples, and provide quantitative data from a duplex microarray assay that simultaneously quantifies free and total PSA in plasma. To further develop the assay the porous silicon chips was placed into a standard 96-well microtiter plate for higher throughput analysis. The samples analyzed by this quantitative microarray were 80 plasma samples obtained from men undergoing clinical PSA testing (dynamic range: 0.14-44ng/ml, LOD: 0.14ng/ml). The second dataset, measuring free PSA (dynamic range: 0.40-74.9ng/ml, LOD: 0.47ng/ml) and total PSA (dynamic range: 0.87-295ng/ml, LOD: 0.76ng/ml), was also obtained from the clinical routine. The reference for the quantification was a commercially available assay, the ProStatus PSA Free/Total DELFIA. In an analysis of 80 plasma samples the microarray platform performs well across the range of total PSA levels. This assay might have the potential to substitute for the large-scale microtiter plate format in diagnostic applications. The duplex assay paves the way for a future quantitative multiplex assay, which analyses several prostate cancer biomarkers simultaneously. PMID:22921878

Effect of storage duration on cytokine stability in human serum and plasma.

PubMed

Vincent, Fabien B; Nim, Hieu T; Lee, Jacinta P W; Morand, Eric F; Harris, James

2018-06-14

Quantification of analytes such as cytokines in serum samples is intrinsic to translational research in immune diseases. Optimising pre-analytical conditions is critical for ensuring study quality, including evaluation of cytokine stability. We aimed to evaluate the effect on cytokine stability of storage duration prior to freezing of serum, and compare to plasma samples obtained from patients with systemic lupus erythematosus (SLE). Protein stability was analysed by simultaneously quantifying 18 analytes using a custom multi-analyte profile in SLE patient serum and plasma samples that had been prospectively stored at 4 °C for pre-determined periods between 0 and 30 days, prior to freezing. Six analytes were excluded from analysis, because most tested samples were above or below the limit of detection. Amongst the 12 analysed proteins, 11 did not show significant signal degradation. Significant signal degradation was observed from the fourth day of storage for a single analyte, CCL19. Proteins levels were more stable in unseparated serum compared to plasma for most analytes, with the exception of IL-37 which appears slightly more stable in plasma. Based on this, a maximum 3 days of storage at 4 °C for unseparated serum samples is recommended for biobanked samples intended for cytokine analysis in studies of human immune disease. Copyright © 2018 Elsevier Ltd. All rights reserved.

Clinical Validation of Therapeutic Drug Monitoring of Imipenem in Spent Effluent in Critically Ill Patients Receiving Continuous Renal Replacement Therapy: A Pilot Study

PubMed Central

Wen, Aiping; Li, Zhe; Yu, Junxian; Li, Ren; Cheng, Sheng; Duan, Meili; Bai, Jing

2016-01-01

Objectives The primary objective of this pilot study was to investigate whether the therapeutic drug monitoring of imipenem could be performed with spent effluent instead of blood sampling collected from critically ill patients under continuous renal replacement therapy. Methods A prospective open-label study was conducted in a real clinical setting. Both blood and effluent samples were collected pairwise before imipenem administration and 0.5, 1, 1.5, 2, 3, 4, 6, and 8 h after imipenem administration. Plasma and effluent imipenem concentrations were determined by reversed-phase high-performance liquid chromatography with ultraviolet detection. Pharmacokinetic and pharmacodynamic parameters of blood and effluent samples were calculated. Results Eighty-three paired plasma and effluent samples were obtained from 10 patients. The Pearson correlation coefficient of the imipenem concentrations in plasma and effluent was 0.950 (P<0.0001). The average plasma-to-effluent imipenem concentration ratio was 1.044 (95% confidence interval, 0.975 to 1.114) with Bland-Altman analysis. No statistically significant difference was found in the pharmacokinetic and pharmacodynamic parameters tested in paired plasma and effluent samples with Wilcoxon test. Conclusion Spent effluent of continuous renal replacement therapy could be used for therapeutic drug monitoring of imipenem instead of blood sampling in critically ill patients. PMID:27093294