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.

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

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.

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).

Lack of concordance in microarray gene expression responses to Phenobarbital in companion aged FFPE and Frozen liver samples

EPA Science Inventory

Despite the immense potential value of public and private biorepositories, direct utilization of archival tissues for molecular profiling has been limited. A major reason for this limited use is the difficulty in obtaining reliable transcriptomic profiles from formalin-fixed par...

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.

PRESENTATION TYPE: Round Table Discussion (80 minutes) TITLE: Unlocking the ‘Omics Archive: Enabling Toxicogenomic/Proteomic Investigation from Archival Samples

EPA Science Inventory

Formalin fixation and paraffin embedding (FFPE) is a cross-industry gold standard for preparing nonclinical and clinical samples for histopathological assessment which preserves tissue architecture and enables storage of tissue in archival banks. These archival banks are an untap...

NASA Global Atmospheric Sampling Program (GASP) data report for tape VL0014

NASA Technical Reports Server (NTRS)

Briehl, D.; Dudzinski, T. J.; Liu, D. C.

1980-01-01

The data currently available from GASP, including flight routes and dates, instrumentation, data processing procedures, and data tape specifications are described. Measurements of atmospheric ozone, cabin ozine, carbon monoxide, water vapor, particles, clouds, condensation nuclei, filter samples and related meteorological and flight information obtained during 562 flights of aircraft N533PA, N4711U, N655PA, and VH-EBE from October 3, 1977 through January 5, 1978 are reported. Data representing tropopause pressures obtained from time and space interpolation of National Meteorological Center archived data for the dates of the flights are included.

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.

NASA Global Atmospheric Sampling Program (GASP) data report for tape VL0005

NASA Technical Reports Server (NTRS)

Holdeman, J. D.; Humenik, F. M.

1977-01-01

Atmospheric ozone, water vapor, and related flight and meteorological data were obtained during 214 flights of a United Airlines B-747 and two Pan American World Airways B-747's from March through June 1976. In addition, trichlorofluoromethane data obtained from laboratory analysis of two whole air samples collected in flight are reported. These data are available on GASP tape VL0005 from the National Climatic Center, Asheville, North Carolina. In addition to the GASP data, tropopause pressure fields obtained from NMC archives for the dates of the GASP flights are included on the data tape. Flight routes and dates, instrumentation, data processing procedures, and data tape specifications are described in this report. Selected analyses including ozone and sample bottle data are also presented.

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

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.

Luminescence signal profiling: a new proxy for sedimentologically "invisible" marine Mass Transport Deposits (MTDs)

NASA Astrophysics Data System (ADS)

López, Gloria I.; Bialik, Or; Waldmann, Nicolas

2017-04-01

When dealing with fine-grained, organic-rich, colour-monotone, underwater marine sediment cores retrieved from the continental shelf or slope, the initial visual impression, upon split-opening the vessels, is often of a "disappointing" homogeneous, monotonous, continuous archive. Only after thorough, micro- to macro-scale, multi-parameter investigations the sediment reveals its treasures, initially by performing some measurements on the intact core itself, hence depicting for the first time its contents, and subsequently by carrying out the destructive, multi-proxy sample-based analyses. Usually, routine Multi-Sensor Core Logger (MSCL) measurements of petrophysical parameters (e.g. magnetic susceptibility, density, P-Wave velocity) on un-split sediment cores are the first undertaken while still on-board in the field or back at the laboratory. Less often done, but equally valuable, are continuous X-Ray and CT scan imaging of the same intact archives. Upon splitting, routine granulometry, micro- and macro-fossil and invertebrate identification, total organic / inorganic carbon content (TOC / TIC), amid other analyses take place. The geochronology component is also established usually by AMS 14C on selected organic-rich units, and less common is Optically Stimulated Luminescence (OSL) dating used on the coarser-grained, siliciclastic layers. A relatively new tool used in Luminescence, the Portable OSL Reader, employed to rapidly assess the luminescence signal of untreated poly-mineral samples to assist with targeted field sampling for full OSL dating, was used for the first time in marine sediment cores as a novel petrophysical characterization tool with astonishing results. In this study, two 2 m-long underwater piston sediment cores recovered from 200 m depths on the continental shelf off-southern Israel, were subjected to pulsed-photon stimulation (PPSL) obtaining favourable luminescence signals along their entire lengths. Astoundingly, luminescence signals were obtained on both, already split-opened cores. Both cores depicted the monotonous characteristics of homogeneousness down-core as per most of the results obtained from the non-destructive and destructive tests. One of the cores showed several small higher energy events, including a Mass Transport Deposit (MTD) within its first 10 cm, only fully visible on the CT scan imaging, the PPSL profile and particle size distribution plot. This initial investigation demonstrates the feasibility and usefulness of luminescence profiling as a new sedimentological and petrophysical proxy to better visualize homogeneous yet complex, fine-grained, underwater archives. Moreover, it helps to understand the continuity of the stratigraphy and linearity of deposition of the sediment, besides assisting on the estimation of relative ages provided that good OSL ages are obtained throughout the recovered archive.

Nosocomial Outbreak of Parechovirus 3 Infection among Newborns, Austria, 2014.

PubMed

Strenger, Volker; Diedrich, Sabine; Boettcher, Sindy; Richter, Susanne; Maritschnegg, Peter; Gangl, Dietmar; Fuchs, Simone; Grangl, Gernot; Resch, Bernhard; Urlesberger, Berndt

2016-09-01

In 2014, sepsis-like illness affected 9 full-term newborns in 1 hospital in Austria. Although results of initial microbiological testing were negative, electron microscopy identified picornavirus. Archived serum samples and feces obtained after discharge were positive by PCR for human parechovirus 3. This infection should be included in differential diagnoses of sepsis-like illness in newborns.

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

Duration of Untreated Psychosis Is Associated with More Negative Schizophrenia Symptoms after Acute Treatment for First-Episode Psychosis

ERIC Educational Resources Information Center

Grano, Niklas; Lindsberg, Jenni; Karjalainen, Marjaana; Gronroos, Peter; Blomberg, Ari-Pekka

2010-01-01

Evidence of association between duration of untreated psychosis (DUP) and negative symptoms of schizophrenia in first-episode psychosis (FEP) patients is inconsistent in the recent literature. In the present study, DUP, schizophrenia symptoms, duration of medication, and diagnosis were obtained from hospital archives in a sample of FEP patients.…

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

Rescue karyotyping: a case series of array-based comparative genomic hybridization evaluation of archival conceptual tissue

PubMed Central

2014-01-01

Background Determination of fetal aneuploidy is central to evaluation of recurrent pregnancy loss (RPL). However, obtaining this information at the time of a miscarriage is not always possible or may not have been ordered. Here we report on “rescue karyotyping”, wherein DNA extracted from archived paraffin-embedded pregnancy loss tissue from a prior dilation and curettage (D&C) is evaluated by array-based comparative genomic hybridization (aCGH). Methods A retrospective case series was conducted at an academic medical center. Patients included had unexplained RPL and a prior pregnancy loss for which karyotype information would be clinically informative but was unavailable. After extracting DNA from slides of archived tissue, aCGH with a reduced stringency approach was performed, allowing for analysis of partially degraded DNA. Statistics were computed using STATA v12.1 (College Station, TX). Results Rescue karyotyping was attempted on 20 specimens from 17 women. DNA was successfully extracted in 16 samples (80.0%), enabling analysis at either high or low resolution. The longest interval from tissue collection to DNA extraction was 4.2 years. There was no significant difference in specimen sufficiency for analysis in the collection-to-extraction interval (p = 0.14) or gestational age at pregnancy loss (p = 0.32). Eight specimens showed copy number variants: 3 trisomies, 2 partial chromosomal deletions, 1 mosaic abnormality and 2 unclassified variants. Conclusions Rescue karyotyping using aCGH on DNA extracted from paraffin-embedded tissue provides the opportunity to obtain critical fetal cytogenetic information from a prior loss, even if it occurred years earlier. Given the ubiquitous archiving of paraffin embedded tissue obtained during a D&C and the ease of obtaining results despite long loss-to-testing intervals or early gestational age at time of fetal demise, this may provide a useful technique in the evaluation of couples with recurrent pregnancy loss. PMID:24589081

Geochemical reanalysis of historical U.S. Geological Survey sediment samples from the Tonsina area, Valdez Quadrangle, Alaska

USGS Publications Warehouse

Werdon, Melanie B.; Granitto, Matthew; Azain, Jaime S.

2015-01-01

The State of Alaska’s Strategic and Critical Minerals (SCM) Assessment project, a State-funded Capital Improvement Project (CIP), is designed to evaluate Alaska’s statewide potential for SCM resources. The SCM Assessment is being implemented by the Alaska Division of Geological & Geophysical Surveys (DGGS), and involves obtaining new airborne-geophysical, geological, and geochemical data. As part of the SCM Assessment, thousands of historical geochemical samples from DGGS, U.S. Geological Survey (USGS), and U.S. Bureau of Mines archives are being reanalyzed by DGGS using modern, quantitative, geochemical-analytical methods. The objective is to update the statewide geochemical database to more clearly identify areas in Alaska with SCM potential. The USGS is also undertaking SCM-related geologic studies in Alaska through the federally funded Alaska Critical Minerals cooperative project. DGGS and USGS share the goal of evaluating Alaska’s strategic and critical minerals potential and together created a Letter of Agreement (signed December 2012) and a supplementary Technical Assistance Agreement (#14CMTAA143458) to facilitate the two agencies’ cooperative work. Under these agreements, DGGS contracted the USGS in Denver to reanalyze historical USGS sediment samples from Alaska. For this report, DGGS funded reanalysis of 128 historical USGS sediment samples from the statewide Alaska Geochemical Database Version 2.0 (AGDB2; Granitto and others, 2013). Samples were chosen from the Tonsina area in the Chugach Mountains, Valdez quadrangle, Alaska (fig. 1). The USGS was responsible for sample retrieval from the National Geochemical Sample Archive (NGSA) in Denver, Colorado through the final quality assurance/quality control (QA/QC) of the geochemical analyses obtained through the USGS contract lab. The new geochemical data are published in this report as a coauthored DGGS report, and will be incorporated into the statewide geochemical databases of both agencies

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...

In situ molecular identification of the Influenza A (H1N1) 2009 Neuraminidase in patients with severe and fatal infections during a pandemic in Mexico City

PubMed Central

2013-01-01

Background In April 2009, public health surveillance detected an increased number of influenza-like illnesses in Mexico City’s hospitals. The etiological agent was subsequently determined to be a spread of a worldwide novel influenza A (H1N1) triple reassortant. The purpose of the present study was to demonstrate that molecular detection of pandemic influenza A (H1N1) 2009 strains is possible in archival material such as paraffin-embedded lung samples. Methods In order to detect A (H1N1) virus sequences in archived biological samples, eight paraffin-embedded lung samples from patients who died of pneumonia and respiratory failure were tested for influenza A (H1N1) Neuraminidase (NA) RNA using in situ RT-PCR. Results We detected NA transcripts in 100% of the previously diagnosed A (H1N1)-positive samples as a cytoplasmic signal. No expression was detected by in situ RT-PCR in two Influenza-like Illness A (H1N1)-negative patients using standard protocols nor in a non-related cervical cell line. In situ relative transcription levels correlated with those obtained when in vitro RT-PCR assays were performed. Partial sequences of the NA gene from A (H1N1)-positive patients were obtained by the in situ RT-PCR-sequencing method. Sequence analysis showed 98% similarity with influenza viruses reported previously in other places. Conclusions We have successfully amplified specific influenza A (H1N1) NA sequences using stored clinical material; results suggest that this strategy could be useful when clinical RNA samples are quantity limited, or when poor quality is obtained. Here, we provide a very sensitive method that specifically detects the neuraminidase viral RNA in lung samples from patients who died from pneumonia caused by Influenza A (H1N1) outbreak in Mexico City. PMID:23327529

A far-ultraviolet atlas of symbiotic stars observed with IUE. 1. The SWP range

NASA Technical Reports Server (NTRS)

Meier, S. R.; Kafatos, M.; Fahey, R. P.; Michalitsianos, A. G.

1994-01-01

This atlas contains sample spectra from the far-ultraviolet observations of 32 symbiotic stars obtained with the International Ultraviolet Explorer (IUE) satellite. In all, 394 low-resolution spectra from the short-wavelength primary (SWP) camera covering the range 1200-2000 A have been extracted from the IUE archive, calibrated, and measured. Absolute line fluxes and wavelengths for the prominent emission lines have been tabulated. Tables of both the general properties of these symbiotics and of features specific to the spectrum of each are included. The spectra shown are representative of the different classes of symbiotic stars that are currently in the IUE archive. These include known eclipsing systems and those that have been observed in outburst (as well as quiescence).

Relationship between Family Functioning and Parenting Beliefs and Feelings among Women Who Have a History of Sexual Abuse

ERIC Educational Resources Information Center

Hernandez, Guadalupe; Lam, Brian Trung

2012-01-01

This study explored the relationship between family functioning and parenting beliefs and feelings among women with a history of child sexual abuse (CSA). This study utilized secondary data obtained in 2001 from the National Data Archive on Child Abuse and Neglect. The sample included 107 women. Most respondents had a highly functional family;…

VizieR Online Data Catalog: Update of INTEGRAL/IBIS AGN catalogue (Malizia+, 2016)

NASA Astrophysics Data System (ADS)

Malizia, A.; Landi, R.; Molina, M.; Bassani, L.; Bazzano, A.; Bird, A. J.; Ubertini, P.

2017-09-01

In this paper we present the X-ray and optical follow-up work on 107 new AGN recently detected by INTEGRAL. Luckily, we have been able to obtain full X-ray coverage of the entire sample making use of data from Swift/XRT, Newton-XMM and NuSTAR archives or through Swift/XRT follow up observations triggered by us. (2 data files).

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.

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.

Arm structure in normal spiral galaxies, 1: Multivariate data for 492 galaxies

NASA Technical Reports Server (NTRS)

Magri, Christopher

1994-01-01

Multivariate data have been collected as part of an effort to develop a new classification system for spiral galaxies, one which is not necessarily based on subjective morphological properties. A sample of 492 moderately bright northern Sa and Sc spirals was chosen for future statistical analysis. New observations were made at 20 and 21 cm; the latter data are described in detail here. Infrared Astronomy Satellite (IRAS) fluxes were obtained from archival data. Finally, new estimates of arm pattern radomness and of local environmental harshness were compiled for most sample objects.

NASA Global Atmospheric Sampling Program (GASP). Data report for tape VL0001. [data management and data retrieval of information from environmental surveys

NASA Technical Reports Server (NTRS)

Holdeman, J. D.; Lezberg, E. A.

1976-01-01

Atmospheric trace constituents in the upper troposphere and lower stratosphere are now being measured as part of the NASA Global Atmospheric Sampling Program (GASP), using fully automated air sampling systems on board commercial 747 aircraft in routine airline service. Measurements of atmospheric ozone and related meteorological and flight information obtained during several GASP flights in March 1975 are now available from the National Climatic Center, Asheville, North Carolina. In addition to the data from the aircraft, tropopause pressure data obtained from the National Meteorological Center (NMC) archives for the dates of the flights are included. This report is the first of a series of reports which describes the data currently available from GASP, including flight routes and dates, instrumentation, the data processing procedure used, and data tape specifications.

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

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...

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.

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…

36 CFR 1256.98 - Can I get access to and obtain copies of USIA audiovisual records transferred to the National...

Code of Federal Regulations, 2010 CFR

2010-07-01

... obtain copies of USIA audiovisual records transferred to the National Archives of the United States? 1256... United States Information Agency Audiovisual Materials in the National Archives of the United States § 1256.98 Can I get access to and obtain copies of USIA audiovisual records transferred to the National...

Geochemical reanalysis of historical U.S. Geological Survey sediment samples from the Haines area, Juneau and Skagway quadrangles, southeast Alaska

USGS Publications Warehouse

Werdon, Melanie B.; Granitto, Matthew; Azain, Jaime S.

2015-01-01

The State of Alaska’s Strategic and Critical Minerals (SCM) Assessment project, a State-funded Capital Improvement Project (CIP), is designed to evaluate Alaska’s statewide potential for SCM resources. The SCM Assessment is being implemented by the Alaska Division of Geological & Geophysical Surveys (DGGS), and involves obtaining new airborne-geophysical, geological, and geochemical data. As part of the SCM Assessment, thousands of historical geochemical samples from DGGS, U.S. Geological Survey (USGS), and U.S. Bureau of Mines archives are being reanalyzed by DGGS using modern, quantitative, geochemical-analytical methods. The objective is to update the statewide geochemical database to more clearly identify areas in Alaska with SCM potential. The USGS is also undertaking SCM-related geologic studies in Alaska through the federally funded Alaska Critical Minerals cooperative project. DGGS and USGS share the goal of evaluating Alaska’s strategic and critical minerals potential and together created a Letter of Agreement (signed December 2012) and a supplementary Technical Assistance Agreement (#14CMTAA143458) to facilitate the two agencies’ cooperative work. Under these agreements, DGGS contracted the USGS in Denver to reanalyze historical USGS sediment samples from Alaska. For this report, DGGS funded reanalysis of 212 historical USGS sediment samples from the statewide Alaska Geochemical Database Version 2.0 (AGDB2; Granitto and others, 2013). Samples were chosen from the Chilkat, Klehini, Tsirku, and Takhin river drainages, as well as smaller drainages flowing into Chilkat and Chilkoot Inlets near Haines, Skagway Quadrangle, Southeast Alaska. Additionally some samples were also chosen from the Juneau gold belt, Juneau Quadrangle, Southeast Alaska (fig. 1). The USGS was responsible for sample retrieval from the National Geochemical Sample Archive (NGSA) in Denver, Colorado through the final quality assurance/quality control (QA/QC) of the geochemical analyses obtained through the USGS contract lab. The new geochemical data are published in this report as a coauthored DGGS report, and will be incorporated into the statewide geochemical databases of both agencies.

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.

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.

Test Results for Caustic Demand Measurements on Tank 241-AX-101 and Tank 241-AX-103 Archive Samples

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

Doll, Stephanie R.; Bolling, Stacie D.

Caustic demand testing is used to determine the necessary amount of caustic required to neutralize species present in the Hanford tank waste and obtain a target molarity of free hydroxide for tank corrosion control. The presence and quantity of hydroxide-consuming analytes are just as important in determining the caustic demand as is the amount of free hydroxide present. No single data point can accurately predict whether a satisfactory hydroxide level is being met, as it is dependent on multiple factors (e.g., free hydroxide, buffers, amphoteric metal hydroxides, bicarbonate, etc.). This enclosure contains the caustic demand, scanning electron microscopy (SEM), polarizedmore » light microscopy (PLM), and X-ray diffraction (XRD) analysis for the tank 241-AX-101 (AX-101) and 241-AX-103 (AX-103) samples. The work was completed to fulfill a customer request outlined in the test plan, WRPS-1505529, “Test Plan and Procedure for Caustic Demand Testing on Tank 241-AX-101 and Tank 241-AX-103 Archive Samples.” The work results will provide a baseline to support planned retrieval of AX-101 and AX-103.« less

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).

RECOMMENDATIONS FOR SAMPLING OF TANK 18 IN F TANK FARM

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

Shine, G.

2009-12-14

Representative sampling is required for characterization of the residual floor material in Tank 18 prior to operational closure. Tank 18 is an 85-foot diameter, 34-foot high carbon steel tank with nominal operating volume of 1,300,000 gallons. It is a Type IV tank, and has been in service storing radioactive materials since 1959. Recent mechanical cleaning of the tank removed all mounds of material. Anticipating a low level of solids in the residual material, Huff and Thaxton [2009] developed a plan to sample the material during the final clean-up process while it would still be resident in sufficient quantities to supportmore » analytical determinations in four quadrants of the tank. Execution of the plan produced fewer solids than expected to support analytical determinations in all four quadrants. Huff and Thaxton [2009] then restructured the plan to characterize the residual floor material separately in the North and the South regions: two 'hemispheres.' This document provides sampling recommendations to complete the characterization of the residual material on the tank bottom following the guidance in Huff and Thaxton [2009] to split the tank floor into a North and a South hemisphere. The number of samples is determined from a modification of the formula previously published in Edwards [2001] and the sample characterization data for previous sampling of Tank 18 described by Oji [2009]. The uncertainty is quantified by an upper 95% confidence limit (UCL95%) on each analyte's mean concentration in Tank 18. The procedure computes the uncertainty in analyte concentration as a function of the number of samples, and the final number of samples is determined when the reduction in the uncertainty from an additional sample no longer has a practical impact on results. The characterization of the full suite of analytes in the North hemisphere is currently supported by a single Mantis rover sample obtained from a compact region near the center riser. A floor scrape sample was obtained from a compact region near the northeast riser and has been analyzed for a shortened list of key analytes. Since the unused portion of the floor scrape sample material is archived and available in sufficient quantity, additional analyses need to be performed to complete results for the full suite of constituents. The characterization of the full suite of analytes in the South hemisphere is currently supported by a single Mantis rover sample; there have been no floor scrape samples previously taken from the South hemisphere. The criterion to determine the number of additional samples was based on the practical reduction in the uncertainty when a new sample is added. This was achieved when five additional samples are obtained. In addition, two archived samples will be used if a contingency such as failing to demonstrate the comparability of the Mantis samples to the floor scrape samples occurs. To complete sampling of the Tank 18 residual floor material, three additional samples should be taken from the North hemisphere and four additional samples should be taken from the South hemisphere. One of the samples from each hemisphere will be archived in case of need. Two of the three additional samples from the North hemisphere and three of the four additional samples from the South hemisphere will be analyzed. Once the results are available, differences between the Mantis and three floor scrape samples (the sample previously obtained near NE riser plus the two additional samples that will be analyzed) results will be evaluated. If there are no statistically significant analyte concentration differences between the Mantis and floor scrape samples, those results will be combined and then UCL95%s will be calculated. If the analyte concentration differences between the Mantis and floor scrape samples are statistically significant, the UCL95%s will be calculated without the Mantis sample results. If further reduction in the upper confidence limits is needed and can be achieved by the addition of the archived samples, they will be analyzed and included in the statistical computations. Initially, the analyte concentrations in the residual material on the floor of Tank 18 will be determined separately in the North and the South hemispheres. However, if final sampling results show that differences between the North and South samples are consistent within sampling variation, then the final computations can be based on consolidating all sample results from the tank floor. Recommended locations may be subject to physical tank access and sampling constraints for the additional samples. The recommendations have been discussed in Section 4 and are based on partitioning the Tank 18 floor into an inner and an outer ring and six 60{sup o} sectors depicted in Figure 1. The location of the border between the inner and outer rings is based on dividing the residual material into two approximately equal volumes.« less

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.

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.

Geochemical reanalysis of historical U.S. Geological Survey sediment samples from the Zane Hills, Hughes and Shungnak quadrangles, Alaska

USGS Publications Warehouse

Werdon, Melanie B.; Granitto, Matthew; Azain, Jaime S.

2015-01-01

The State of Alaska’s Strategic and Critical Minerals (SCM) Assessment project, a State-funded Capital Improvement Project (CIP), is designed to evaluate Alaska’s statewide potential for SCM resources. The SCM Assessment is being implemented by the Alaska Division of Geological & Geophysical Surveys (DGGS), and involves obtaining new airborne-geophysical, geological, and geochemical data. As part of the SCM Assessment, thousands of historical geochemical samples from DGGS, U.S. Geological Survey (USGS), and U.S. Bureau of Mines archives are being reanalyzed by DGGS using modern, quantitative, geochemical-analytical methods. The objective is to update the statewide geochemical database to more clearly identify areas in Alaska with SCM potential.The USGS is also undertaking SCM-related geologic studies in Alaska through the federally funded Alaska Critical Minerals cooperative project. DGGS and USGS share the goal of evaluating Alaska’s strategic and critical minerals potential and together created a Letter of Agreement (signed December 2012) and a supplementary Technical Assistance Agreement (#14CMTAA143458) to facilitate the two agencies’ cooperative work. Under these agreements, DGGS contracted the USGS in Denver to reanalyze historical USGS sediment samples from Alaska.For this report, DGGS funded reanalysis of 105 historical USGS sediment samples from the statewide Alaska Geochemical Database Version 2.0 (AGDB2; Granitto and others, 2013). Samples were chosen from the Zane Hills area in the Hughes and Shungnak quadrangles, Alaska (fig. 1). The USGS was responsible for sample retrieval from the National Geochemical Sample Archive (NGSA) in Denver, Colorado through the final quality assurance/quality control (QA/QC) of the geochemical analyses obtained through the USGS contract lab. The new geochemical data are published in this report as a coauthored DGGS report, and will be incorporated into the statewide geochemical databases of both agencies.

Geochemical reanalysis of historical U.S. Geological Survey sediment samples from the Kougarok area, Bendeleben and Teller quadrangles, Seward Peninsula, Alaska

USGS Publications Warehouse

Werdon, Melanie B.; Granitto, Matthew; Azain, Jaime S.

2015-01-01

The State of Alaska’s Strategic and Critical Minerals (SCM) Assessment project, a State-funded Capital Improvement Project (CIP), is designed to evaluate Alaska’s statewide potential for SCM resources. The SCM Assessment is being implemented by the Alaska Division of Geological & Geophysical Surveys (DGGS), and involves obtaining new airborne-geophysical, geological, and geochemical data. As part of the SCM Assessment, thousands of historical geochemical samples from DGGS, U.S. Geological Survey (USGS), and U.S. Bureau of Mines archives are being reanalyzed by DGGS using modern, quantitative, geochemical-analytical methods. The objective is to update the statewide geochemical database to more clearly identify areas in Alaska with SCM potential. The USGS is also undertaking SCM-related geologic studies in Alaska through the federally funded Alaska Critical Minerals cooperative project. DGGS and USGS share the goal of evaluating Alaska’s strategic and critical minerals potential and together created a Letter of Agreement (signed December 2012) and a supplementary Technical Assistance Agreement (#14CMTAA143458) to facilitate the two agencies’ cooperative work. Under these agreements, DGGS contracted the USGS in Denver to reanalyze historical USGS sediment samples from Alaska. For this report, DGGS funded reanalysis of 302 historical USGS sediment samples from the statewide Alaska Geochemical Database Version 2.0 (AGDB2; Granitto and others, 2013). Samples were chosen from the Kougarok River drainage as well as smaller adjacent drainages in the Bendeleben and Teller quadrangles, Seward Peninsula, Alaska (fig. 1). The USGS was responsible for sample retrieval from the National Geochemical Sample Archive (NGSA) in Denver, Colorado through the final quality assurance/quality control (QA/QC) of the geochemical analyses obtained through the USGS contract lab. The new geochemical data are published in this report as a coauthored DGGS report, and will be incorporated into the statewide geochemical databases of both agencies.

Geochemical reanalysis of historical U.S. Geological Survey sediment samples from the northeastern Alaska Range, Healy, Mount Hayes, Nabesna, and Tanacross quadrangles, Alaska

USGS Publications Warehouse

Werdon, Melanie B.; Granitto, Matthew; Azain, Jaime S.

2015-01-01

The State of Alaska’s Strategic and Critical Minerals (SCM) Assessment project, a State-funded Capital Improvement Project (CIP), is designed to evaluate Alaska’s statewide potential for SCM resources. The SCM Assessment is being implemented by the Alaska Division of Geological & Geophysical Surveys (DGGS), and involves obtaining new airborne-geophysical, geological, and geochemical data. As part of the SCM Assessment, thousands of historical geochemical samples from DGGS, U.S. Geological Survey (USGS), and U.S. Bureau of Mines archives are being reanalyzed by DGGS using modern, quantitative, geochemical-analytical methods. The objective is to update the statewide geochemical database to more clearly identify areas in Alaska with SCM potential. The USGS is also undertaking SCM-related geologic studies in Alaska through the federally funded Alaska Critical Minerals cooperative project. DGGS and USGS share the goal of evaluating Alaska’s strategic and critical minerals potential and together created a Letter of Agreement (signed December 2012) and a supplementary Technical Assistance Agreement (#14CMTAA143458) to facilitate the two agencies’ cooperative work. Under these agreements, DGGS contracted the USGS in Denver to reanalyze historical USGS sediment samples from Alaska. For this report, DGGS funded reanalysis of 670 historical USGS sediment samples from the statewide Alaska Geochemical Database Version 2.0 (AGDB2; Granitto and others, 2013). Samples were chosen from the northeastern Alaska Range, in the Healy, Mount Hayes, Nabesna, and Tanacross quadrangles, Alaska (fig. 1). The USGS was responsible for sample retrieval from the National Geochemical Sample Archive (NGSA) in Denver, Colorado through the final quality assurance/quality control (QA/QC) of the geochemical analyses obtained through the USGS contract lab. The new geochemical data are published in this report as a coauthored DGGS report, and will be incorporated into the statewide geochemical databases of both agencies.

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…

Strain-specific and pooled genome sequences for populations of Drosophila melanogaster from three continents.

PubMed Central

Bergman, Casey M.; Haddrill, Penelope R.

2015-01-01

To contribute to our general understanding of the evolutionary forces that shape variation in genome sequences in nature, we have sequenced genomes from 50 isofemale lines and six pooled samples from populations of Drosophila melanogaster on three continents. Analysis of raw and reference-mapped reads indicates the quality of these genomic sequence data is very high. Comparison of the predicted and experimentally-determined Wolbachia infection status of these samples suggests that strain or sample swaps are unlikely to have occurred in the generation of these data. Genome sequences are freely available in the European Nucleotide Archive under accession ERP009059. Isofemale lines can be obtained from the Drosophila Species Stock Center. PMID:25717372

Strain-specific and pooled genome sequences for populations of Drosophila melanogaster from three continents.

PubMed

Bergman, Casey M; Haddrill, Penelope R

2015-01-01

To contribute to our general understanding of the evolutionary forces that shape variation in genome sequences in nature, we have sequenced genomes from 50 isofemale lines and six pooled samples from populations of Drosophila melanogaster on three continents. Analysis of raw and reference-mapped reads indicates the quality of these genomic sequence data is very high. Comparison of the predicted and experimentally-determined Wolbachia infection status of these samples suggests that strain or sample swaps are unlikely to have occurred in the generation of these data. Genome sequences are freely available in the European Nucleotide Archive under accession ERP009059. Isofemale lines can be obtained from the Drosophila Species Stock Center.

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.

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

PubMed

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

2007-01-01

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

The Emergence of Star Clusters

NASA Astrophysics Data System (ADS)

Calzetti, Daniela

2017-08-01

We propose to measure the timescale for the clearing of natal dust by young star clusters. We will augment existing archival UV-to-I imaging data with new WFC3/IR images at J, H, and Paschen-beta for a sample of six nearby star forming galaxies. Under the standard scenario that the clearing is performed by supernovae (> 3 Myr), simulations show that not enough ionizing photons can escape galaxies and reionize the Universe at z>6. However, the actual clearing timescale is poorly established. We will obtain accurate ages and extinctions for the embedded and emergent young clusters in our target galaxies, in order to: (1) determine whether dust clearing occurs before or after 3 Myr, (2) investigate environmental dependencies for the timescale, and (3) establish the principal mechanisms for enabling the escape of ionizing photons from galaxies. Our project provides the physical footing for future JWST observations aimed at determining the sources of reionization of the Universe. The combination of archival and new images will also equip the community with a lasting legacy of homogeneous UV-to-IR coverage for a sample of nearby galaxies.

Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI's RNA-seq archive

PubMed Central

Olarerin-George, Anthony O.; Hogenesch, John B.

2015-01-01

Mycoplasmas are notorious contaminants of cell culture and can have profound effects on host cell biology by depriving cells of nutrients and inducing global changes in gene expression. Over the last two decades, sentinel testing has revealed wide-ranging contamination rates in mammalian culture. To obtain an unbiased assessment from hundreds of labs, we analyzed sequence data from 9395 rodent and primate samples from 884 series in the NCBI Sequence Read Archive. We found 11% of these series were contaminated (defined as ≥100 reads/million mapping to mycoplasma in one or more samples). Ninety percent of mycoplasma-mapped reads aligned to ribosomal RNA. This was unexpected given 37% of contaminated series used poly(A)-selection for mRNA enrichment. Lastly, we examined the relationship between mycoplasma contamination and host gene expression in a single cell RNA-seq dataset and found 61 host genes (P < 0.001) were significantly associated with mycoplasma-mapped read counts. In all, this study suggests mycoplasma contamination is still prevalent today and poses substantial risk to research quality. PMID:25712092

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...

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

Starburst Galaxies: Hard X-ray spectra and contribution to the diffuse background

NASA Technical Reports Server (NTRS)

Gruber, Duane E.

1993-01-01

During the period of this grant two main tasks were performed: a determination of a selection criterion for starburst galaxies most likely to emit X-rays, and performance of a pilot study of the X-ray emission from nine such systems. Starburst galaxies may be expected to emit flat-spectrum X-ray at energies above 10 keV resulting from the various remnants of the short-lived massive stars which characterize the starburst. The investigation to determine the optimum sample resulted in a change from an X-ray selected (HEAO-2) sample to infrared selection based on the IRAS catalogue. A much broader sample thereby available for study, and selection could be limited to only the nearest objects and still obtain a reasonably large sample. A sample of 99 of the brightest infrared starburst galaxies was settled on for the X-ray survey. For a set of practical size, this was then reduced to a subset of 53, based on luminosity and nearness. X-ray emission from these objects was individually measured from the UCSD HEAO-1 all-sky survey in four energy bands between 13 keV to 160 keV. This data base consists of about 20 optical disk volumes. Net significance for the result was roughly two sigma, and a very hard spectral shape is indicated for the net spectrum of the surveyed galaxies. With the possibility of detection of the class, it was then felt worthwhile to examine fluxes from these sources in other archival data. This was performed with the HEAO-1 A2 data and the HEAO-2 (EINSTEIN) main archive and slew survey. Positive results were also obtained for the sample, but again at weak significance. With three independent measures of weak X-ray fluxes from nearby starburst galaxies, we wrote a letter to the Astrophysical Journal (enclosed) discussing these results and their likely significance, in particular, for the contribution to the cosmic diffuse x-ray background, perhaps as much as 25 percent.

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...

NASA Global Atmospheric Sampling Program (GASP) data report for tape VL0015, VL0016, VL0017, VL0018, VL0019, and VL0020

NASA Technical Reports Server (NTRS)

Papthakos, L. C.; Briehl, D.

1981-01-01

This is the twelfth of a series of reports which describes the data currently available from GASP, including flight routes and dates, instrumentation, data processing procedures, and data tape specifications. In-situ measurements of atmospheric ozone, cabin ozone, carbon monoxide, water vapor, particles, clouds, condensation nuclei, filter samples and related meteorological and flight information obtained during 1732 flights of aircraft N533PA, N4711U, N655PA, and VH-EBE from January 5, 1978 through October 9, 1978 are reported. These data are now available from the National Climatic Center, Asheville, NC, 22801. In addition to the GASP data, tropopause pressures obtained from time ans space interpolation of National Meteorological Center archived data for the dates of the flights are included.

Study of activation data of metal samples from LDEF-1 and Spacelab-2

NASA Technical Reports Server (NTRS)

Laird, C. E.

1994-01-01

Gamma-ray spectra obtained from samples flown aboard the Long Duration Exposure Facility have been analyzed to obtain the nuclear species produced in this material by the interaction of this material with protons and neutrons in this material by the interaction of this material with protons and neutrons encountered in its 69 month orbital flight as well as to quantify the specific activity (pCi/kg) of these nuclear species. This quantification requires accurate corrections of efficiency, self-attenuation, and background. Plans have been developed for archival of the spectra in a form readily accessible to the scientific, engineering and technical community engaged in space research and application. Work has been initiated in the process of estimating the flux of activating particles encountered by material at various locations of the spacecraft.

Primer development to obtain complete coding sequence of HA and NA genes of influenza A/H3N2 virus.

PubMed

Agustiningsih, Agustiningsih; Trimarsanto, Hidayat; Setiawaty, Vivi; Artika, I Made; Muljono, David Handojo

2016-08-30

Influenza is an acute respiratory illness and has become a serious public health problem worldwide. The need to study the HA and NA genes in influenza A virus is essential since these genes frequently undergo mutations. This study describes the development of primer sets for RT-PCR to obtain complete coding sequence of Hemagglutinin (HA) and Neuraminidase (NA) genes of influenza A/H3N2 virus from Indonesia. The primers were developed based on influenza A/H3N2 sequence worldwide from Global Initiative on Sharing All Influenza Data (GISAID) and further tested using Indonesian influenza A/H3N2 archived samples of influenza-like illness (ILI) surveillance from 2008 to 2009. An optimum RT-PCR condition was acquired for all HA and NA fragments designed to cover complete coding sequence of HA and NA genes. A total of 71 samples were successfully sequenced for complete coding sequence both of HA and NA genes out of 145 samples of influenza A/H3N2 tested. The developed primer sets were suitable for obtaining complete coding sequences of HA and NA genes of Indonesian samples from 2008 to 2009.

RNA analysis of inner ear cells from formalin fixed paraffin embedded (FFPE) archival human temporal bone section using laser microdissection--a technical report.

PubMed

Kimura, Yurika; Kubo, Sachiho; Koda, Hiroko; Shigemoto, Kazuhiro; Sawabe, Motoji; Kitamura, Ken

2013-08-01

Molecular analysis using archival human inner ear specimens is challenging because of the anatomical complexity, long-term fixation, and decalcification. However, this method may provide great benefit for elucidation of otological diseases. Here, we extracted mRNA for RT-PCR from tissues dissected from archival FFPE human inner ears by laser microdissection. Three human temporal bones obtained at autopsy were fixed in formalin, decalcified by EDTA, and embedded in paraffin. The samples were isolated into spiral ligaments, outer hair cells, spiral ganglion cells, and stria vascularis by laser microdissection. RNA was extracted and heat-treated in 10 mM citrate buffer to remove the formalin-derived modification. To identify the sites where COCH and SLC26A5 mRNA were expressed, semi-nested RT-PCR was performed. We also examined how long COCH mRNA could be amplified by semi-nested RT-PCR in archival temporal bone. COCH was expressed in the spiral ligament and stria vascularis. However, SLC26A5 was expressed only in outer hair cells. The maximum base length of COCH mRNA amplified by RT-PCR was 98 bp in 1 case and 123 bp in 2 cases. We detected COCH and SLC26A5 mRNA in specific structures and cells of the inner ear from archival human temporal bone. Our innovative method using laser microdissection and semi-nested RT-PCR should advance future RNA study of human inner ear diseases. Copyright © 2013 Elsevier B.V. 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.

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/

VizieR Online Data Catalog: ETGs sample for the Coma cluster (Riguccini+, 2015)

NASA Astrophysics Data System (ADS)

Riguccini, L.; Temi, P.; Amblard, A.; Fanelli, M.; Brighenti, F.

2017-10-01

For the Coma Cluster, we utilize the work of Mahajan et al. (2010, J/MNRAS/404/1745) to build our ETG sample. Mahajan et al. (2010, J/MNRAS/404/1745) used a combination of MIPS 24 μm observations and SDSS photometry and spectra to investigate the star formation history of galaxies in the Coma supercluster. All of their galaxies from the SDSS data in the Coma supercluster region are brighter than r~17.77, the completeness limit of the SDSS spectroscopic galaxy catalog. Their 24 μm fluxes are obtained from archival data covering 2x2 deg2 for Coma Cluster. Our final sample of 124 sources is composed of 49 ellipticals and 75 lenticulars. (1 data file).

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 ...

Development of an Alternative Treatment Scheme for Sr/TRU Removal: Permanganate Treatment of AN-107 Waste

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

RT Hallen; SA Bryan; FV Hoopes

A number of Hanford tanks received waste containing organic complexants, which increase the volubility of Sr-90 and transuranic (TRU) elements. Wastes from these tanks require additional pretreatment to remove Sr-90 and TRU for immobilization as low activity waste (Waste Envelope C). The baseline pretreatment process for Sr/TRU removal was isotopic exchange and precipitation with added strontium and iron. However, studies at both Battelle and Savannah River Technology Center (SRTC) have shown that the Sr/Fe precipitates were very difficult to filter. This was a result of the formation of poor filtering iron solids. An alternate treatment technology was needed for Sr/TRUmore » removal. Battelle had demonstrated that permanganate treatment was effective for decontaminating waste samples from Hanford Tank SY-101 and proposed that permanganate be examined as an alternative Sr/TRU removal scheme for complexant-containing tank wastes such as AW107. Battelle conducted preliminary small-scale experiments to determine the effectiveness of permanganate treatment with AN-107 waste samples that had been archived at Battelle from earlier studies. Three series of experiments were performed to evaluate conditions that provided adequate Sr/TRU decontamination using permanganate treatment. The final series included experiments with actual AN-107 diluted feed that had been obtained specifically for BNFL process testing. Conditions that provided adequate Sr/TRU decontamination were identified. A free hydroxide concentration of 0.5M provided adequate decontamination with added Sr of 0.05M and permanganate of 0.03M for archived AN-107. The best results were obtained when reagents were added in the sequence Sr followed by permanganate with the waste at ambient temperature. The reaction conditions for Sr/TRU removal will be further evaluated with a 1-L batch of archived AN-107, which will provide a large enough volume of waste to conduct crossflow filtration studies (Hallen et al. 2000a).« less

48 CFR 22.404-1 - Types of wage determinations.

Code of Federal Regulations, 2010 CFR

2010-10-01

... in the “Archived DB WD” database on WDOL for information purposes only. Contracting officers may not use an archived wage determination in a contract action without obtaining prior approval of the...

Phylogenetic Variants of Rickettsia africae, and Incidental Identification of "Candidatus Rickettsia Moyalensis" in Kenya.

PubMed

Kimita, Gathii; Mutai, Beth; Nyanjom, Steven Ger; Wamunyokoli, Fred; Waitumbi, John

2016-07-01

Rickettsia africae, the etiological agent of African tick bite fever, is widely distributed in sub-Saharan Africa. Contrary to reports of its homogeneity, a localized study in Asembo, Kenya recently reported high genetic diversity. The present study aims to elucidate the extent of this heterogeneity by examining archived Rickettsia africae DNA samples collected from different eco-regions of Kenya. To evaluate their phylogenetic relationships, archived genomic DNA obtained from 57 ticks a priori identified to contain R. africae by comparison to ompA, ompB and gltA genes was used to amplify five rickettsial genes i.e. gltA, ompA, ompB, 17kDa and sca4. The resulting amplicons were sequenced. Translated amino acid alignments were used to guide the nucleotide alignments. Single gene and concatenated alignments were used to infer phylogenetic relationships. Out of the 57 DNA samples, three were determined to be R. aeschlimanii and not R. africae. One sample turned out to be a novel rickettsiae and an interim name of "Candidatus Rickettsia moyalensis" is proposed. The bonafide R. africae formed two distinct clades. Clade I contained 9% of the samples and branched with the validated R. africae str ESF-5, while clade II (two samples) formed a distinct sub-lineage. This data supports the use of multiple genes for phylogenetic inferences. It is determined that, despite its recent emergence, the R. africae lineage is diverse. This data also provides evidence of a novel Rickettsia species, Candidatus Rickettsia moyalensis.

A MySQL Based EPICS Archiver

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

Christopher Slominski

2009-10-01

Archiving a large fraction of the EPICS signals within the Jefferson Lab (JLAB) Accelerator control system is vital for postmortem and real-time analysis of the accelerator performance. This analysis is performed on a daily basis by scientists, operators, engineers, technicians, and software developers. Archiving poses unique challenges due to the magnitude of the control system. A MySQL Archiving system (Mya) was developed to scale to the needs of the control system; currently archiving 58,000 EPICS variables, updating at a rate of 11,000 events per second. In addition to the large collection rate, retrieval of the archived data must also bemore » fast and robust. Archived data retrieval clients obtain data at a rate over 100,000 data points per second. Managing the data in a relational database provides a number of benefits. This paper describes an archiving solution that uses an open source database and standard off the shelf hardware to reach high performance archiving needs. Mya has been in production at Jefferson Lab since February of 2007.« less

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...

Development of an indirect ELISA for detection of antibody to wobbly possum disease virus in archival sera of Australian brushtail possums (Trichosurus vulpecula) in New Zealand.

PubMed

Giles, J C; Johnson, W; Jones, G; Heuer, C; Dunowska, M

2018-07-01

To develop an indirect ELISA based on recombinant nucleocapsid (rN) protein of wobbly possum disease (WPD) virus for investigation of the presence of WPD virus in Australian brushtail possums (Trichosurus vulpecula) in New Zealand. Pre- and post-infection sera (n=15 and 16, respectively) obtained from a previous experimental challenge study were used for ELISA development. Sera were characterised as positive or negative for antibody to WPD virus based on western-blot using WPD virus rN protein as antigen. An additional 215 archival serum samples, collected between 2000-2016 from five different regions of New Zealand, were also tested using the ELISA. Bayesian modelling of corrected optical density at 450 nm (OD 450 ) results from the ELISA was used to obtain estimates of receiver operating characteristic (ROC) curves to establish cut-off values for the ELISA, and to estimate the prevalence of antibody to WPD virus. Western blot analysis showed 5/14 (36%) pre-infection sera and 11/11 (100%) post-infection sera from experimentally infected possums were positive for antibodies to WPD virus. Bayesian estimates of the ROC curves established cut-off values of OD 450 ≥0.41 for samples positive, and OD 450 <0.28 for samples negative for antibody to WPD virus, for sera diluted 1:100 for the ELISA. Based on the model, the estimated proportion of samples with antibodies to WPD virus was 0.30 (95% probability interval=0.196-0.418). Of the 230 archival serum samples tested using the ELISA, 48 (20.9%) were positive for antibody to WPD virus, 155 (67.4%) were negative and 27 (11.7%) equivocal, using the established cut-off values. The proportion of samples positive for WPD virus antibody differed between geographical regions (p<0.001). The results suggested that WPD virus or a related virus has circulated among possums in New Zealand with differences in the proportion of antibody-positive samples from different geographical regions. Antibodies to WPD virus did not seem to protect possums from disease following experimental infection, as one third of possums from the previous challenge study showed evidence of pre-existing antibody at the time of challenge. These results provide further support for existence of different pathotypes of WPD virus, but the exact determinants of protection against WPD and epidemiology of infection in various regions of New Zealand remain to be established. Availability of the indirect ELISA for detection of WPD virus antibody will facilitate prospective epidemiological investigation of WPD virus circulation in wild possum populations in New Zealand.

Archival of aircraft scatterometer data from AAFE RADSCAT missions

NASA Technical Reports Server (NTRS)

Schroeder, L. C.; Mitchell, J. L.

1983-01-01

Aircraft scatterometer data obtained over the ocean with the Radiometer-Scatterometer (RADSCAT) instrument is documented. The normalized radar cross section data was obtained at 13.9 GHz for a variety of ocean surface wind conditions, which are also presented. All such valid RADSCAT ocean scatterometer data for which surface truth was obtained are included, except for ice research missions during the last year of RADSCAT's lifetime. Aircraft scatterometer data obtained for the SEASAT underflights were with a second instrument, the Airborne Microwave Scatterometer (AMSCAT). The RADSCAT data are archived on card image computer tapes and on microfiche.

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.

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.

Geochemical reanalysis of historical U.S. Geological Survey sediment samples from the Inmachuk, Kugruk, Kiwalik, and Koyuk River drainages, Granite Mountain, and the northern Darby Mountains, Bendeleben, Candle, Kotzebue, and Solomon quadrangles, Alaska

USGS Publications Warehouse

Werdon, Melanie B.; Granitto, Matthew; Azain, Jaime S.

2015-01-01

The State of Alaska’s Strategic and Critical Minerals (SCM) Assessment project, a State-funded Capital Improvement Project (CIP), is designed to evaluate Alaska’s statewide potential for SCM resources. The SCM Assessment is being implemented by the Alaska Division of Geological & Geophysical Surveys (DGGS), and involves obtaining new airborne-geophysical, geological, and geochemical data. As part of the SCM Assessment, thousands of historical geochemical samples from DGGS, U.S. Geological Survey (USGS), and U.S. Bureau of Mines archives are being reanalyzed by DGGS using modern, quantitative, geochemical-analytical methods. The objective is to update the statewide geochemical database to more clearly identify areas in Alaska with SCM potential. The USGS is also undertaking SCM-related geologic studies in Alaska through the federally funded Alaska Critical Minerals cooperative project. DGGS and USGS share the goal of evaluating Alaska’s strategic and critical minerals potential and together created a Letter of Agreement (signed December 2012) and a supplementary Technical Assistance Agreement (#14CMTAA143458) to facilitate the two agencies’ cooperative work. Under these agreements, DGGS contracted the USGS in Denver to reanalyze historical USGS sediment samples from Alaska. For this report, DGGS funded reanalysis of 653 historical USGS sediment samples from the statewide Alaska Geochemical Database Version 2.0 (AGDB2; Granitto and others, 2013). Samples were chosen from an area covering portions of the Inmachuk, Kugruk, Kiwalik, and Koyuk river drainages, Granite Mountain, and the northern Darby Mountains, located in the Bendeleben, Candle, Kotzebue, and Solomon quadrangles of eastern Seward Peninsula, Alaska (fig. 1). The USGS was responsible for sample retrieval from the National Geochemical Sample Archive (NGSA) in Denver, Colorado through the final quality assurance/quality control (QA/QC) of the geochemical analyses obtained through the USGS contract lab. The new geochemical data are published in this report as a coauthored DGGS report, and will be incorporated into the statewide geochemical databases of both agencies.

The Golosiiv on-line plate archive database, management and maintenance

NASA Astrophysics Data System (ADS)

Pakuliak, L.; Sergeeva, T.

2007-08-01

We intend to create online version of the database of the MAO NASU plate archive as VO-compatible structures in accordance with principles, developed by the International Virtual Observatory Alliance in order to make them available for world astronomical community. The online version of the log-book database is constructed by means of MySQL+PHP. Data management system provides a user with user interface, gives a capability of detailed traditional form-filling radial search of plates, obtaining some auxiliary sampling, the listing of each collection and permits to browse the detail descriptions of collections. The administrative tool allows database administrator the data correction, enhancement with new data sets and control of the integrity and consistence of the database as a whole. The VO-compatible database is currently constructing under the demands and in the accordance with principles of international data archives and has to be strongly generalized in order to provide a possibility of data mining by means of standard interfaces and to be the best fitted to the demands of WFPDB Group for databases of the plate catalogues. On-going enhancements of database toward the WFPDB bring the problem of the verification of data to the forefront, as it demands the high degree of data reliability. The process of data verification is practically endless and inseparable from data management owing to a diversity of data errors nature, that means to a variety of ploys of their identification and fixing. The current status of MAO NASU glass archive forces the activity in both directions simultaneously: the enhancement of log-book database with new sets of observational data as well as generalized database creation and the cross-identification between them. The VO-compatible version of the database is supplying with digitized data of plates obtained with MicroTek ScanMaker 9800 XL TMA. The scanning procedure is not total but is conducted selectively in the frames of special projects.

A feather precipitation hydrogen isoscape for New Zealand

NASA Astrophysics Data System (ADS)

Rogers, K. M.; Wassenaar, L. I.; Soto, D. X.; Bartle, J. A.

2012-04-01

Forensic isotopic assays of feathers from historical Maori cloaks are a potential tool to link historical artefacts back to their native locales (Iwi) in New Zealand. In order to test this approach, we sampled feathers from extant museum archived birds of known origin for their feather hydrogen isotopes (δyHf) to assign their regional origin and location over time. We obtained feathers from two non-migratory bird species widely distributed around New Zealand, tui (Prosthemadera novaeseelandiae) and quail (Callipepla californica). Feathers were sampled from archived birds collected between 1880-2002 held in 3 New Zealand museum collections. We determined regression coefficients of δ2H on location, latitude, δ2Hprecipitation, and age. The data showed that ground dwelling quail had higher regression coefficients with respect to latitude (r2=0.46) than the nectar feeding tui (r2=0.39). On the whole, both resident birds showed promise as regional geographical indicators of their habitat (r2=0.58). Year of collection had no meaningful effect on isotopic composition. We conclude that isotopic assays may therefore be used to aid in regional assignments relevant to the interpretation of historical artefacts.

Performance of Identifiler Direct and PowerPlex 16 HS on the Applied Biosystems 3730 DNA Analyzer for processing biological samples archived on FTA cards.

PubMed

Laurin, Nancy; DeMoors, Anick; Frégeau, Chantal

2012-09-01

Direct amplification of STR loci from biological samples collected on FTA cards without prior DNA purification was evaluated using Identifiler Direct and PowerPlex 16 HS in conjunction with the use of a high throughput Applied Biosystems 3730 DNA Analyzer. In order to reduce the overall sample processing cost, reduced PCR volumes combined with various FTA disk sizes were tested. Optimized STR profiles were obtained using a 0.53 mm disk size in 10 μL PCR volume for both STR systems. These protocols proved effective in generating high quality profiles on the 3730 DNA Analyzer from both blood and buccal FTA samples. Reproducibility, concordance, robustness, sample stability and profile quality were assessed using a collection of blood and buccal samples on FTA cards from volunteer donors as well as from convicted offenders. The new developed protocols offer enhanced throughput capability and cost effectiveness without compromising the robustness and quality of the STR profiles obtained. These results support the use of these protocols for processing convicted offender samples submitted to the National DNA Data Bank of Canada. Similar protocols could be applied to the processing of casework reference samples or in paternity or family relationship testing. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

STScI Archive Manual, Version 7.0

NASA Astrophysics Data System (ADS)

Padovani, Paolo

1999-06-01

The STScI Archive Manual provides information a user needs to know to access the HST archive via its two user interfaces: StarView and a World Wide Web (WWW) interface. It provides descriptions of the StarView screens used to access information in the database and the format of that information, and introduces the use to the WWW interface. Using the two interfaces, users can search for observations, preview public data, and retrieve data from the archive. Using StarView one can also find calibration reference files and perform detailed association searches. With the WWW interface archive users can access, and obtain information on, all Multimission Archive at Space Telescope (MAST) data, a collection of mainly optical and ultraviolet datasets which include, amongst others, the International Ultraviolet Explorer (IUE) Final Archive. Both interfaces feature a name resolver which simplifies searches based on target name.

Perinatal acquisition of drug-resistant HIV-1 infection: mechanisms and long-term outcome

PubMed Central

Delaugerre, Constance; Chaix, Marie-Laure; Blanche, Stephane; Warszawski, Josiane; Cornet, Dorine; Dollfus, Catherine; Schneider, Veronique; Burgard, Marianne; Faye, Albert; Mandelbrot, Laurent; Tubiana, Roland; Rouzioux, Christine

2009-01-01

Background Primary-HIV-1-infection in newborns that occurs under antiretroviral prophylaxis that is a high risk of drug-resistance acquisition. We examine the frequency and the mechanisms of resistance acquisition at the time of infection in newborns. Patients and Methods We studied HIV-1-infected infants born between 01 January 1997 and 31 December 2004 and enrolled in the ANRS-EPF cohort. HIV-1-RNA and HIV-1-DNA samples obtained perinatally from the newborn and mother were subjected to population-based and clonal analyses of drug resistance. If positive, serial samples were obtained from the child for resistance testing. Results Ninety-two HIV-1-infected infants were born during the study period. Samples were obtained from 32 mother-child pairs and from another 28 newborns. Drug resistance was detected in 12 newborns (20%): drug resistance to nucleoside reverse transcriptase inhibitors was seen in 10 cases, non-nucleoside reverse transcriptase inhibitors in two cases, and protease inhibitors in one case. For 9 children, the detection of the same resistance mutations in mothers' samples (6 among 10 available) and in newborn lymphocytes (6/8) suggests that the newborn was initially infected by a drug-resistant strain. Resistance variants were either transmitted from mother-to-child or selected during subsequent temporal exposure under suboptimal perinatal prophylaxis. Follow-up studies of the infants showed that the resistance pattern remained stable over time, regardless of antiretroviral therapy, suggesting the early cellular archiving of resistant viruses. The absence of resistance in the mother of the other three children (3/10) and neonatal lymphocytes (2/8) suggests that the newborns were infected by a wild-type strain without long-term persistence of resistance when suboptimal prophylaxis was stopped. Conclusion This study confirms the importance of early resistance genotyping of HIV-1-infected newborns. In most cases (75%), drug resistance was archived in the cellular reservoir and persisted during infancy, with or without antiretroviral treatment. This finding stresses the need for effective antiretroviral treatment of pregnant women. PMID:19765313

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.

A new archival infrastructure for highly-structured astronomical data

NASA Astrophysics Data System (ADS)

Dovgan, Erik; Knapic, Cristina; Sponza, Massimo; Smareglia, Riccardo

2018-03-01

With the advent of the 2020 Radio Astronomy Telescopes era, the amount and format of the radioastronomical data is becoming a massive and performance-critical challenge. Such an evolution of data models and data formats require new data archiving techniques that allow massive and fast storage of data that are at the same time also efficiently processed. A useful expertise for efficient archiviation has been obtained through data archiving of Medicina and Noto Radio Telescopes. The presented archival infrastructure named the Radio Archive stores and handles various formats, such as FITS, MBFITS, and VLBI's XML, which includes description and ancillary files. The modeling and architecture of the archive fulfill all the requirements of both data persistence and easy data discovery and exploitation. The presented archive already complies with the Virtual Observatory directives, therefore future service implementations will also be VO compliant. This article presents the Radio Archive services and tools, from the data acquisition to the end-user data utilization.

An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis

PubMed Central

Karsten, Stanislav L.; Van Deerlin, Vivianna M. D.; Sabatti, Chiara; Gill, Lisa H.; Geschwind, Daniel H.

2002-01-01

Archival formalin-fixed, paraffin-embedded and ethanol-fixed tissues represent a potentially invaluable resource for gene expression analysis, as they are the most widely available material for studies of human disease. Little data are available evaluating whether RNA obtained from fixed (archival) tissues could produce reliable and reproducible microarray expression data. Here we compare the use of RNA isolated from human archival tissues fixed in ethanol and formalin to frozen tissue in cDNA microarray experiments. Since an additional factor that can limit the utility of archival tissue is the often small quantities available, we also evaluate the use of the tyramide signal amplification method (TSA), which allows the use of small amounts of RNA. Detailed analysis indicates that TSA provides a consistent and reproducible signal amplification method for cDNA microarray analysis, across both arrays and the genes tested. Analysis of this method also highlights the importance of performing non-linear channel normalization and dye switching. Furthermore, archived, fixed specimens can perform well, but not surprisingly, produce more variable results than frozen tissues. Consistent results are more easily obtainable using ethanol-fixed tissues, whereas formalin-fixed tissue does not typically provide a useful substrate for cDNA synthesis and labeling. PMID:11788730

14C Analysis of protein extracts from Bacillus spores.

PubMed

Cappuccio, Jenny A; Falso, Miranda J Sarachine; Kashgarian, Michaele; Buchholz, Bruce A

2014-07-01

Investigators of bioagent incidents or interdicted materials need validated, independent analytical methods that will allow them to distinguish between recently made bioagent samples versus material drawn from the archives of a historical program. Heterotrophic bacteria convert the carbon in their food sources, growth substrate or culture media, into the biomolecules they need. The F(14)C (fraction modern radiocarbon) of a variety of media, Bacillus spores, and separated proteins from Bacillus spores was measured by accelerator mass spectrometry (AMS). AMS precisely measures F(14)C values of biological materials and has been used to date the synthesis of biomaterials over the bomb pulse era (1955 to present). The F(14)C of Bacillus spores reflects the radiocarbon content of the media in which they were grown. In a survey of commercial media we found that the F(14)C value indicated that carbon sources for the media were alive within about a year of the date of manufacture and generally of terrestrial origin. Hence, bacteria and their products can be dated using their (14)C signature. Bacillus spore samples were generated onsite with defined media and carbon free purification and also obtained from archived material. Using mechanical lysis and a variety of washes with carbon free acids and bases, contaminant carbon was removed from soluble proteins to enable accurate (14)C bomb-pulse dating. Since media is contemporary, (14)C bomb-pulse dating of isolated soluble proteins can be used to distinguish between historical archives of bioagents and those produced from recent media. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

14C Analysis of Protein Extracts from Bacillus Spores

PubMed Central

Cappucio, Jenny A.; Sarachine Falso, Miranda J.; Kashgarian, Michaele; Buchholz, Bruce A.

2014-01-01

Investigators of bioagent incidents or interdicted materials need validated, independent analytical methods that will allow them to distinguish between recently made bioagent samples versus material drawn from the archives of a historical program. Heterotrophic bacteria convert the carbon in their food sources, growth substrate or culture media, into the biomolecules they need. The F14C (fraction modern radiocarbon) of a variety of media, Bacillus spores, and separated proteins from Bacillus spores was measured by accelerator mass spectrometry (AMS). AMS precisely measures F14C values of biological materials and has been used to date the synthesis of biomaterials over the bomb pulse era (1955 to present). The F14C of Bacillus spores reflects the radiocarbon content of the media in which they were grown. In a survey of commercial media we found that the F14C value indicated that carbon sources for the media were alive within about a year of the date of manufacture and generally of terrestrial origin. Hence, bacteria and their products can be dated using their 14C signature. Bacillus spore samples were generated onsite with defined media and carbon free purification and also obtained from archived material. Using mechanical lysis and a variety of washes with carbon free acids and bases, contaminant carbon was removed from soluble proteins to enable accurate 14C bomb-pulse dating. Since media is contemporary, 14C bomb-pulse dating of isolated soluble proteins can be used to distinguish between historical archives of bioagents and those produced from recent media. PMID:24814329

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

Whole Air Sampling During NASA's March-April 1999 Pacific Exploratory Expedition (PEM-Tropics B)

NASA Technical Reports Server (NTRS)

Blake, Donald R.

2001-01-01

University of California, Irvine (UCI) collected more than 4500 samples whole air samples collected over the remote Pacific Ocean during NASA's Global Tropospheric Experiment (GTE) Pacific Exploratory Mission-Tropics B (PEM-Tropics B) in March and early April 1999. Approximately 140 samples during a typical 8-hour DC-8 flight, and 120 canisters for each 8-hour flight aboard the P-3B. These samples were obtained roughly every 3-7 min during horizontal flight legs and 1-3 min during vertical legs. The filled canisters were analyzed in the laboratory at UCI within ten days of collection. The mixing ratios of 58 trace gases comprising hydrocarbons, halocarbons, alkyl nitrates and DMS were reported (and archived) for each sample. Two identical analytical systems sharing the same standards were operated simultaneously around the clock to improve canister turn-around time and to keep our measurement precision optimal. This report presents a summary of the results for sample collected.

Probing the Jet Turnover Frequency Dependence on Mass and Mass Accretion Rate

NASA Astrophysics Data System (ADS)

Hammerstein, Erica; Gültekin, Kayhan; King, Ashley

2018-01-01

We have examined a sample of 15 sub-Eddington supermassive black holes (SMBHs) in a variety of galaxy classifications to further understand the proposed fundamental plane of black hole activity and scaling relations between black hole masses and their radio and X-ray luminosities. This plane describes black holes from stellar-mass to supermassive. The physics probed by these sub-Eddington systems is thought to be a radiatively inefficient, jet-dominated accretion flow. By studying black holes in this regime, we can learn important information on the disk-jet connection for accreting black holes.A key factor in studying the fundamental plane is the turnover frequency — the frequency at which emission transitions from optically thick at lower frequencies to optically thin at higher frequencies. This turnover point can be measured by observing the source in both radio and X-ray. Our project aims to test the dependence of the turnover frequency on mass and mass accretion rate.Radio observations of the sample were obtained using the Karl G. Jansky Very Large Array (VLA) in the range of 5-40 GHz across four different frequency bands in A configuration to give the highest spatial resolution to focus on the core emission. Our carefully chosen sample of SMBHs with dynamically measured masses consists of two sub-samples: those with approximately constant mass accretion rate (LX/LEdd ~ 10‑7) and those with approximately constant mass (MBH ~ 108 Msun). X-ray data were obtained from archival Chandra observations. To find the turnover frequency, we used Markov Chain Monte Carlo methods to fit two power laws to the radio data and the archival X-ray data. The intersection of the radio and X-ray fits is the turnover frequency.We present the results for both subsamples of SMBHs and their relationship between the turnover frequency and X-ray luminosity, which we take to scale with mass accretion rate, and jet power derived from both radio and X-ray properties.

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.

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.

Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves.

PubMed

Sprouffske, Kathleen; Wagner, Andreas

2016-04-19

Plate readers can measure the growth curves of many microbial strains in a high-throughput fashion. The hundreds of absorbance readings collected simultaneously for hundreds of samples create technical hurdles for data analysis. Growthcurver summarizes the growth characteristics of microbial growth curve experiments conducted in a plate reader. The data are fitted to a standard form of the logistic equation, and the parameters have clear interpretations on population-level characteristics, like doubling time, carrying capacity, and growth rate. Growthcurver is an easy-to-use R package available for installation from the Comprehensive R Archive Network (CRAN). The source code is available under the GNU General Public License and can be obtained from Github (Sprouffske K, Growthcurver sourcecode, 2016).

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

NASA Astrophysics Data System (ADS)

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

2001-12-01

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

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

Choquet, Élodie; Perrin, Marshall D.; Chen, Christine H.

We present the first images of four debris disks observed in scattered light around the young (4–250 Myr old) M dwarfs TWA 7 and TWA 25, the K6 star HD 35650, and the G2 star HD 377. We obtained these images by reprocessing archival Hubble Space Telescope NICMOS coronagraph data with modern post-processing techniques as part of the Archival Legacy Investigation of Circumstellar Environments program. All four disks appear faint and compact compared with other debris disks resolved in scattered light. The disks around TWA 25, HD 35650, and HD 377 appear very inclined, while TWA 7's disk is viewed nearly face-on. The surface brightness of HD 35650's diskmore » is strongly asymmetric. These new detections raise the number of disks resolved in scattered light around M and late-K stars from one (the AU Mic system) to four. This new sample of resolved disks enables comparative studies of heretofore scarce debris disks around low-mass stars relative to solar-type stars.« less

VizieR Online Data Catalog: SEDs of the radio continuum from KINGFISHER (Tabatabaei+, 2017)

NASA Astrophysics Data System (ADS)

Tabatabaei, F. S.; Schinnerer, E.; Krause, M.; Dumas, G.; Meidt, S.; Damas-Segovia, A.; Beck, R.; Murphy, E. J.; Mulcahy, D. D.; Groves, B.; Bolatto, A.; Dale, D.; Galametz, M.; Sandstrom, K.; Boquien, M.; Calzetti, D.; Kennicutt, R. C.; Hunt, L. K.; de Looze, I.; Pellegrini, E. W.

2017-10-01

The KINGFISH sample consists of 61 nearby galaxies of different morphological types. From this sample, we selected all galaxies with declinations >=-21° and named this subsample KINGFISHER (KINGFISH galaxies Emitting in Radio). These galaxies can be observed with the Effelsberg 100m single-dish telescope to obtain global measurements of the radio continuum at 20cm, 6cm, and 3.6cm. The non-KINGFISH galaxy, M51, is also included in this study. We observed 35 of these galaxies at 6cm, 10 galaxies at 20cm, and 7 at 3.6cm to complete already existing archival data during four observation runs (2008 Dec, 2009 Dec, 2010 Apr and 2010 Dec & 2012 Mar). (3 data files).

Germanium, Arsenic, and Selenium Abundances in Metal-poor Stars

NASA Astrophysics Data System (ADS)

Roederer, Ian U.

2012-09-01

The elements germanium (Ge, Z = 32), arsenic (As, Z = 33), and selenium (Se, Z = 34) span the transition from charged-particle or explosive synthesis of the iron-group elements to neutron-capture synthesis of heavier elements. Among these three elements, only the chemical evolution of germanium has been studied previously. Here we use archive observations made with the Space Telescope Imaging Spectrograph on board the Hubble Space Telescope and observations from several ground-based facilities to study the chemical enrichment histories of seven stars with metallicities -2.6 <= [Fe/H] <= -0.4. We perform a standard abundance analysis of germanium, arsenic, selenium, and several other elements produced by neutron-capture reactions. When combined with previous derivations of germanium abundances in metal-poor stars, our sample reveals an increase in the [Ge/Fe] ratios at higher metallicities. This could mark the onset of the weak s-process contribution to germanium. In contrast, the [As/Fe] and [Se/Fe] ratios remain roughly constant. These data do not directly indicate the origin of germanium, arsenic, and selenium at low metallicity, but they suggest that the weak and main components of the s-process are not likely sources. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained from the data archive at the Space Telescope Science Institute. STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. This research made use of StarCAT, hosted by the Mikulski Archive at the Space Telescope Science Institute (MAST). These data are associated with Programs GO-7348, GO-7433, GO-8197, GO-9048, GO-9455, and GO-9804.Based on data obtained from the European Southern Observatory (ESO) Science Archive Facility. These data are associated with Programs 67.D-0439(A), 074.C-0364(A), 076.B-0055(A), and 080.D-0347(A).This research has made use of the Keck Observatory Archive (KOA), which is operated by the W.M. Keck Observatory and the NASA Exoplanet Science Institute (NExScI), under contract with the National Aeronautics and Space Administration. These data are associated with Programs H2aH, H6aH, and H39aH (PI: Boesgaard), N01H (PI: Latham), and U11H (PI: Prochaska).This paper includes data taken at The McDonald Observatory of The University of Texas at Austin.

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.

Weak lensing study of 16 DAFT/FADA clusters: Substructures and filaments

NASA Astrophysics Data System (ADS)

Martinet, Nicolas; Clowe, Douglas; Durret, Florence; Adami, Christophe; Acebrón, Ana; Hernandez-García, Lorena; Márquez, Isabel; Guennou, Loic; Sarron, Florian; Ulmer, Mel

2016-05-01

While our current cosmological model places galaxy clusters at the nodes of a filament network (the cosmic web), we still struggle to detect these filaments at high redshifts. We perform a weak lensing study for a sample of 16 massive, medium-high redshift (0.4

76 FR 7591 - Agency Information Collection Activities: Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-10

... NATIONAL ARCHIVES AND RECORDS ADMINISTRATION Agency Information Collection Activities: Submission for OMB Review; Comment Request AGENCY: National Archives and Records Administration (NARA). ACTION... in a timely fashion the volume of requests received for these records and the need to obtain specific...

Tank 241-AY-101 Privatization Push Mode Core Sampling and Analysis Plan

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

TEMPLETON, A.M.

2000-05-19

This sampling and analysis plan (SAP) identifies characterization objectives pertaining to sample collection, laboratory analytical evaluation, and reporting requirements for samples obtained from tank 241-AY-101. The purpose of this sampling event is to obtain information about the characteristics of the contents of 241-AY-101 required to satisfy ''Data Quality Objectives For RPP Privatization Phase I: Confirm Tank T Is An Appropriate Feed Source For High-Level Waste Feed Batch X(HLW DQO)' (Nguyen 1999a), ''Data Quality Objectives For TWRS Privatization Phase I: Confirm Tank T Is An Appropriate Feed Source For Low-Activity Waste Feed Butch X (LAW DQO) (Nguyen 1999b)'', ''Low Activity Wastemore » and High-Level Waste Feed Data Quality Objectives (L&H DQO)'' (Patello et al. 1999), and ''Characterization Data Needs for Development, Design, and Operation of Retrieval Equipment Developed through the Data Quality Objective Process (Equipment DQO)'' (Bloom 1996). Special instructions regarding support to the LAW and HLW DQOs are provided by Baldwin (1999). Push mode core samples will be obtained from risers 15G and 150 to provide sufficient material for the chemical analyses and tests required to satisfy these data quality objectives. The 222-S Laboratory will extrude core samples; composite the liquids and solids; perform chemical analyses on composite and segment samples; archive half-segment samples; and provide sub-samples to the Process Chemistry Laboratory. The Process Chemistry Laboratory will prepare test plans and perform process tests to evaluate the behavior of the 241-AY-101 waste undergoing the retrieval and treatment scenarios defined in the applicable DQOs. Requirements for analyses of samples originating in the process tests will be documented in the corresponding test plans and are not within the scope of this SAP.« less

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.

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

Multiplex KRASG12/G13 mutation testing of unamplified cell-free DNA from the plasma of patients with advanced cancers using droplet digital polymerase chain reaction.

PubMed

Janku, F; Huang, H J; Fujii, T; Shelton, D N; Madwani, K; Fu, S; Tsimberidou, A M; Piha-Paul, S A; Wheler, J J; Zinner, R G; Naing, A; Hong, D S; Karp, D D; Cabrilo, G; Kopetz, E S; Subbiah, V; Luthra, R; Kee, B K; Eng, C; Morris, V K; Karlin-Neumann, G A; Meric-Bernstam, F

2017-03-01

Cell-free DNA (cfDNA) from plasma offers easily obtainable material for KRAS mutation analysis. Novel, multiplex, and accurate diagnostic systems using small amounts of DNA are needed to further the use of plasma cfDNA testing in personalized therapy. Samples of 16 ng of unamplified plasma cfDNA from 121 patients with diverse progressing advanced cancers were tested with a KRASG12/G13 multiplex assay to detect the seven most common mutations in the hotspot of exon 2 using droplet digital polymerase chain reaction (ddPCR). The results were retrospectively compared to mutation analysis of archival primary or metastatic tumor tissue obtained at different points of clinical care. Eighty-eight patients (73%) had KRASG12/G13 mutations in archival tumor specimens collected on average 18.5 months before plasma analysis, and 78 patients (64%) had KRASG12/G13 mutations in plasma cfDNA samples. The two methods had initial overall agreement in 103 (85%) patients (kappa, 0.66; ddPCR sensitivity, 84%; ddPCR specificity, 88%). Of the 18 discordant cases, 12 (67%) were resolved by increasing the amount of cfDNA, using mutation-specific probes, or re-testing the tumor tissue, yielding overall agreement in 115 patients (95%; kappa 0.87; ddPCR sensitivity, 96%; ddPCR specificity, 94%). The presence of ≥ 6.2% of KRASG12/G13 cfDNA in the wild-type background was associated with shorter survival (P = 0.001). Multiplex detection of KRASG12/G13 mutations in a small amount of unamplified plasma cfDNA using ddPCR has good sensitivity and specificity and good concordance with conventional clinical mutation testing of archival specimens. A higher percentage of mutant KRASG12/G13 in cfDNA corresponded with shorter survival. © The Author 2016. 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.

VizieR Online Data Catalog: Abundances in the local region. I. G and K giants (Luck, 2015)

NASA Astrophysics Data System (ADS)

Luck, R. E.

2015-10-01

At the start of this program, the observation list for giants was set to sample the G/K giants of the local region out to about 100pc from the Sun in all directions. The region was subdivided into cubes that were 25pc on a side; from each sub-volume, appropriate stars were selected north of declination -30°. This sample yielded the 286 G/K giants found in Luck et al. 2007 (cat. J/AJ/133/2464). This data set was also augmented by the addition of numerous G/K giants, increasing the number in the 100pc volume to 594 stars. Because the volume selection criteria used in Luck et al. 2007 (cat. J/AJ/133/2464) formally extended out to 115pc, a more precise comparison is that the current sample has 740 stars out to the older limit. Additional stars from the Bright Star Catalog (Hoffleit & Jaschek, 1991bsc..book.....H) were added, driving the sample out to about 200pc. The spectral database was supplemented using the ELODIE and ESO Archives. The ESO addition adds the southern sky. The bulk of the northern stars were observed using the McDonald Observatory Struve Telescope and Sandiford Cassegrain Echelle Spectrograph. For the ELODIE and ESO data archives, a list of all stars available was obtained and spectral type for each from SIMBAD was retrieved. Stars having a spectral type of F, G, or K III were then processed. The ESO data derives from the HARPS and UVES spectrographs. Basic observational data for the program stars can be found in Table1, along with some derived quantities, such as distance. The primary source of observational data for this study is a set of high signal-to-noise ratio (S/N) spectra obtained during numerous observing runs between 1997 and 2010 at McDonald Observatory using the 2.1m Struve Telescope and the Sandiford Cassegrain Echelle Spectrograph. The spectra continuously cover a wavelength range from about 484 to 700nm, with a resolving power of about 60000. Typical S/N values for the spectra are in excess of 150. To enable cancellation of telluric lines, broad-lined B stars were regularly observed with S/N exceeding that of the program stars. The 726 stars observed with the Sandiford spectrograph are marked with an "S" in column "Sce" of Table1. A further 120 spectra were obtained from the ELODIE Archive. These echelle spectra are fully processed through order co-addition with a continuous wavelength span from about 400 to 680 nm and a resolution of 42000. Only spectra with S/N>50 were utilized in this analysis. An "E" in Table1, column "Sce", marks these stars. The ESO Archive was used to obtain spectra from the ESO 3.6m telescope and HARPS spectrograph. The HARPS spectra cover a continuous wavelength range from about 400 to 680nm with a native resolving power of 120000. To match the resolution of the Sandiford data and to increase the S/N of the data, these spectra were co-added to a resolution of 60000. Typical maximum S/N values (per pixel) for the spectra are in excess of 150. In Table1, column "Sce", these stars are marked with an "H." Spectra from the UVES spectrograph and VLT/UT2 were also utilized. These spectra are rather heterogeneous, having resolutions of 40000-80000 and non-continuous spectral coverages in the range 400-700nm. A number of the spectra from UVES stop at about 625nm, meaning that [O I] 630nm and Li I 670nm were not observed. In Table 1, "U" denotes the stars observed with UVES spectrograph. (5 data files).

76 FR 43960 - NARA Records Reproduction Fees

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-22

... transferred to NARA and maintain its fee schedule on NARA's Web site http://www.archives.gov . The proposed... document is faint or too dark, it requires additional time to obtain a readable image. In TABLE 1 below... our Web site ( http://www.archives.gov ) annually when announcing that records reproduction fees will...

Tank 241-AY-101 Privatization Push Mode Core Sampling and Analysis Plan

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

TEMPLETON, A.M.

2000-01-12

This sampling and analysis plan (SAP) identifies characterization objectives pertaining to sample collection, laboratory analytical evaluation, and reporting requirements for samples obtained from tank 241-AY-101. The purpose of this sampling event is to obtain information about the characteristics of the contents of 241-AY-101 required to satisfy Data Quality Objectives For RPP Privatization Phase I: Confirm Tank T Is An Appropriate Feed Source For High-Level Waste Feed Batch X(HLW DQO) (Nguyen 1999a), Data Quality Objectives For TWRS Privatization Phase I : Confirm Tank T Is An Appropriate Feed Source For Low-Activity Waste Feed Batch X (LAW DQO) (Nguyen 1999b), Low Activitymore » Waste and High-Level Waste Feed Data Quality Objectives (L and H DQO) (Patello et al. 1999), and Characterization Data Needs for Development, Design, and Operation of Retrieval Equipment Developed through the Data Quality Objective Process (Equipment DQO) (Bloom 1996). Special instructions regarding support to the LAW and HLW DQOs are provided by Baldwin (1999). Push mode core samples will be obtained from risers 15G and 150 to provide sufficient material for the chemical analyses and tests required to satisfy these data quality objectives. The 222-S Laboratory will extrude core samples; composite the liquids and solids; perform chemical analyses on composite and segment samples; archive half-segment samples; and provide subsamples to the Process Chemistry Laboratory. The Process Chemistry Laboratory will prepare test plans and perform process tests to evaluate the behavior of the 241-AY-101 waste undergoing the retrieval and treatment scenarios defined in the applicable DQOs. Requirements for analyses of samples originating in the process tests will be documented in the corresponding test plans and are not within the scope of this SAP.« less

Historic CH4 Records from Antarctic and Greenland Ice Cores, Antarctic Firn Data, and Archived Air Samples from Cape Grim, Tasmania

DOE Data Explorer

Etheridge, D. M. [Division of Atmospheric Research, CSIRO, Aspendale, Victoria, Australia; Steele, L. P. [Division of Atmospheric Research, CSIRO, Aspendale, Victoria, Australia; Francey, R. J. [Division of Atmospheric Research, CSIRO, Aspendale, Victoria, Australia; Langenfelds, R. L. [Division of Atmospheric Research, CSIRO, Aspendale, Victoria, Australia

2002-01-01

The Antarctic CH4 records presented here are derived from three ice cores obtained at Law Dome, East Antarctica (66°44'S, 112°50'E, 1390 meters above mean sea level). Law Dome has many qualities of an ideal ice core site for the reconstruction of past concentrations of atmospheric gases; these qualities include: negligible melting of the ice sheet surface, low concentrations of impurities, regular stratigraphic layering undisturbed by wind stress at the surface or differential ice flow at depth, and a high snow accumulation rate. Further details on the site, drilling, and cores are provided by Etheridge et al. (1998), Etheridge et al. (1996), Etheridge and Wookey (1989), and Morgan et al. (1997). The two Greenland ice cores are from the Summit region (72°34' N, 37°37' W, 3200 meters above mean sea level). Lower snow accumulation rate there results in lower air-age resolution, and measurements presented here cover only the pre-industrial period (until 1885). More details about these measurements are presented in Etheridge et al. (1998). Additionally, this site contains firn data from Core DE08-2, and archived air samples from Cape Grim, Tasmania, for comparison.

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

X-Ray Properties of AGN in Brightest Cluster Galaxies. I. A Systematic Study of the Chandra Archive in the 0.2 < z < 0.3 and 0.55 < z < 0.75 Redshift Range

NASA Astrophysics Data System (ADS)

Yang, Lilan; Tozzi, Paolo; Yu, Heng; Lusso, Elisabeta; Gaspari, Massimo; Gilli, Roberto; Nardini, Emanuele; Risaliti, Guido

2018-05-01

We present a search for nuclear X-ray emission in the brightest cluster galaxies (BCGs) of a sample of groups and clusters of galaxies extracted from the Chandra archive. The exquisite angular resolution of Chandra allows us to obtain robust photometry at the position of the BCG, and to firmly identify unresolved X-ray emission when present, thanks to an accurate characterization of the extended emission at the BCG position. We consider two redshift bins (0.2 < z < 0.3 and 0.55 < z < 0.75) and analyze all the clusters observed by Chandra with exposure time larger than 20 ks. Our samples have 81 BCGs in 73 clusters and 51 BCGs in 49 clusters in the low- and high-redshift bins, respectively. X-ray emission in the soft (0.5–2 keV) or hard (2–7 keV) band is detected only in 14 and 9 BCGs (∼18% of the total samples), respectively. The X-ray photometry shows that at least half of the BCGs have a high hardness ratio, compatible with significant intrinsic absorption. This is confirmed by the spectral analysis with a power-law model plus intrinsic absorption. We compute the fraction of X-ray bright BCGs above a given hard X-ray luminosity, considering only sources with positive photometry in the hard band (12/5 sources in the low/high-z sample).

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.

Archive data base and handling system for the Orbiter flying qualities experiment program

NASA Technical Reports Server (NTRS)

Myers, T. T.; Dimarco, R.; Magdaleno, R. E.; Aponso, B. L.

1986-01-01

The OFQ archives data base and handling system assembled as part of the Orbiter Flying Qualities (OFQ) research of the Orbiter Experiments Program (EOX) are described. The purpose of the OFQ archives is to preserve and document shuttle flight data relevant to vehicle dynamics, flight control, and flying qualities in a form that permits maximum use for qualified users. In their complete form, the OFQ archives contain descriptive text (general information about the flight, signal descriptions and units) as well as numerical time history data. Since the shuttle program is so complex, the official data base contains thousands of signals and very complex entries are required to obtain data. The OFQ archives are intended to provide flight phase oriented data subsets with relevant signals which are easily identified for flying qualities research.

Cloud object store for archive storage of high performance computing data using decoupling middleware

DOEpatents

Bent, John M.; Faibish, Sorin; Grider, Gary

2015-06-30

Cloud object storage is enabled for archived data, such as checkpoints and results, of high performance computing applications using a middleware process. A plurality of archived files, such as checkpoint files and results, generated by a plurality of processes in a parallel computing system are stored by obtaining the plurality of archived files from the parallel computing system; converting the plurality of archived files to objects using a log structured file system middleware process; and providing the objects for storage in a cloud object storage system. The plurality of processes may run, for example, on a plurality of compute nodes. The log structured file system middleware process may be embodied, for example, as a Parallel Log-Structured File System (PLFS). The log structured file system middleware process optionally executes on a burst buffer node.

The Panchromatic STARBurst IRregular Dwarf Survey (STARBIRDS): Observations and Data Archive

NASA Astrophysics Data System (ADS)

McQuinn, Kristen B. W.; Mitchell, Noah P.; Skillman, Evan D.

2015-06-01

Understanding star formation in resolved low mass systems requires the integration of information obtained from observations at different wavelengths. We have combined new and archival multi-wavelength observations on a set of 20 nearby starburst and post-starburst dwarf galaxies to create a data archive of calibrated, homogeneously reduced images. Named the panchromatic “STARBurst IRregular Dwarf Survey” archive, the data are publicly accessible through the Mikulski Archive for Space Telescopes. This first release of the archive includes images from the Galaxy Evolution Explorer Telescope (GALEX), the Hubble Space Telescope (HST), and the Spitzer Space Telescope (Spitzer) Multiband Imaging Photometer instrument. The data sets include flux calibrated, background subtracted images, that are registered to the same world coordinate system. Additionally, a set of images are available that are all cropped to match the HST field of view. The GALEX and Spitzer images are available with foreground and background contamination masked. Larger GALEX images extending to 4 times the optical extent of the galaxies are also available. Finally, HST images convolved with a 5″ point spread function and rebinned to the larger pixel scale of the GALEX and Spitzer 24 μm images are provided. Future additions are planned that will include data at other wavelengths such as Spitzer IRAC, ground-based Hα, Chandra X-ray, and Green Bank Telescope H i imaging. Based on observations made with the NASA/ESA Hubble Space Telescope, and obtained from the Hubble Legacy Archive, which is a collaboration between the Space Telescope Science Institute (STScI/NASA), the Space Telescope European Coordinating Facility (ST-ECF/ESA), and the Canadian Astronomy Data Centre (CADC/NRC/CSA).

Student Press in American Archives, Fall/Winter 1973-74.

ERIC Educational Resources Information Center

National Council of Coll. Publications Advisers.

This issue of the "Student Press in America Archives List" contains 100 entries on current issues and information, as well as cases involving student press editors, advisers, student media, and the generic subject of the campus press, emphasizing censorship practices and principles. Information concerning how and where to obtain documents of…

76 FR 4634 - Proposed Information Collection; Comment Request; Implantation and Recovery of Archival Tags for...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-26

... tags in, or affix archival tags to, selected Atlantic Highly Migratory Species (tunas, sharks... for scientists researching the movements and behavior of individual fish. It is often necessary to retrieve the tags in order to obtain the collected data; therefore, persons catching tagged fish are...

Selection of Russian Plutonium Beryllium Sources for Inclusion in the Nuclear Mateirals Information Program Archive

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

Narlesky, Joshua E; Padilla, Dennis D; Watts, Joe

2009-01-01

Throughout the 1960s and 1970s, the former Soviet Union produced and exported Plutonium-Beryllium (PuBe) neutron sources to various Eastern European countries. The Russian sources consist of an intermetallic compound of plutonium and beryllium encapsulated in an inner welded, sealed capsule and consisting of a body and one or more covers. The amount of plutonium in the sources ranges from 0.002 g up to 15 g. A portion of the sources was originally exported to East Germany. A portion of these sources were acquired by Los Alamos National Laboratory (LANL) in the late 1990s for destruction in the Offsite Source Recoverymore » Program. When the OSRP was canceled, the remaining 88 PuBe neutron sources were packaged and stored in a 55-gal drum at T A-55. This storage configuration is no longer acceptable for PuBe sources, and the sources must either be repackaged or disposed of. Repackaging would place the sources into Hagan container, and depending on the dose rates, some sources may be packaged individually increasing the footprint and cost of storage. In addition, each source will be subject to leak-checking every six months. Leaks have already been detected in some of the sources, and due to the age of these sources, it is likely that additional leaks may be detected over time, which will increase the overall complexity of handling and storage. Therefore, it was decided that the sources would be disposed of at the Waste Isolation Pilot Plant (WIPP) due to the cost and labor associated with continued storage at TA-55. However, the plutonium in the sources is of Russian origin and needs to be preserved for research purposes. Therefore, it is important that a representative sample of the sources retained and archived for future studies. This report describes the criteria used to obtain a representative sample of the sources. Nine Russian PuBe neutron sources have been selected out of a collection of 77 sources for inclusion in the NMIP archive. Selection criteria were developed so that the largest sources that are representative of the collection are included. One representative source was chosen for every 20 sources in the collection, and effort was made to preserve sources unique to the collection. In total, four representative sources and five unique sources were selected for the archive. The archive samples contain 40 grams of plutonium with an isotopic composition similar to that of weapon grade material and three grams of plutonium with an isotopic composition similar to that of reactor grade plutonium.« less

Historical Archives in Italian Astronomical Observatories: The ``Specola 2000'' Project

NASA Astrophysics Data System (ADS)

Chinnici, I.; Mandrino, A.; Bònoli, F.

2006-12-01

Italy's well-consolidated tradition in astronomy is fully witnessed by its rich archival heritage. Astronomical records are stored in many observatories and universities, as well as in libraries and in private institutions. In 2000 a project was promoted to arrange and produce inventories of all material kept in Italian observatory archives. The project was planned by the Società Astronomica Italiana, and financial support was provided by the Italian Ministero per i Beni e le Attività Culturali. In this paper, the results obtained thus far are presented and commented on.

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...

Effect of storage time on gene expression data acquired from unfrozen archived newborn blood spots.

PubMed

Ho, Nhan T; Busik, Julia V; Resau, James H; Paneth, Nigel; Khoo, Sok Kean

2016-11-01

Unfrozen archived newborn blood spots (NBS) have been shown to retain sufficient messenger RNA (mRNA) for gene expression profiling. However, the effect of storage time at ambient temperature for NBS samples in relation to the quality of gene expression data is relatively unknown. Here, we evaluated mRNA expression from quantitative real-time PCR (qRT-PCR) and microarray data obtained from NBS samples stored at ambient temperature to determine the effect of storage time on the quality of gene expression. These data were generated in a previous case-control study examining NBS in 53 children with cerebral palsy (CP) and 53 matched controls. NBS sample storage period ranged from 3 to 16years at ambient temperature. We found persistently low RNA integrity numbers (RIN=2.3±0.71) and 28S/18S rRNA ratios (~0) across NBS samples for all storage periods. In both qRT-PCR and microarray data, the expression of three common housekeeping genes-beta cytoskeletal actin (ACTB), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and peptidylprolyl isomerase A (PPIA)-decreased with increased storage time. Median values of each microarray probe intensity at log 2 scale also decreased over time. After eight years of storage, probe intensity values were largely reduced to background intensity levels. Of 21,500 genes tested, 89% significantly decreased in signal intensity, with 13,551, 10,730, and 9925 genes detected within 5years, > 5 to <10years, and >10years of storage, respectively. We also examined the expression of two gender-specific genes (X inactivation-specific transcript, XIST and lysine-specific demethylase 5D, KDM5D) and seven gene sets representing the inflammatory, hypoxic, coagulative, and thyroidal pathways hypothesized to be related to CP risk to determine the effect of storage time on the detection of these biologically relevant genes. We found the gender-specific genes and CP-related gene sets detectable in all storage periods, but exhibited differential expression (between male vs. female or CP vs. control) only within the first six years of storage. We concluded that gene expression data quality deteriorates in unfrozen archived NBS over time and that differential gene expression profiling and analysis is recommended for those NBS samples collected and stored within six years at ambient temperature. Copyright © 2016 Elsevier Inc. All rights reserved.

The digital archive of the International Halley Watch

NASA Technical Reports Server (NTRS)

Klinglesmith, D. A., III; Niedner, M. B.; Grayzeck, E.; Aronsson, M.; Newburn, R. L.; Warnock, A., III

1992-01-01

The International Halley Watch was established to coordinate, collect, archive, and distribute the scientific data from Comet P/Halley that would be obtained from both the ground and space. This paper describes one of the end products of that effort, namely the IHW Digital Archive. The IHW Digital Archive consists of 26 CD-ROM's containing over 32 gigabytes of data from the 9 IHW disciplines as well as data from the 5 spacecraft missions flown to comet P/Haley and P/Giacobini-Zinner. The total archive contains over 50,000 observations by 1,500 observers from at least 40 countries. The first 24 CD's, which are currently available, contain data from the 9 IHW disciplines. The two remaining CD's will have the spacecraft data and should be available within the next year. A test CD-ROM of these data has been created and is currently under review.

EZH2 and CD79B mutational status over time in B-cell non-Hodgkin lymphomas detected by high-throughput sequencing using minimal samples

PubMed Central

Saieg, Mauro Ajaj; Geddie, William R; Boerner, Scott L; Bailey, Denis; Crump, Michael; da Cunha Santos, Gilda

2013-01-01

BACKGROUND: Numerous genomic abnormalities in B-cell non-Hodgkin lymphomas (NHLs) have been revealed by novel high-throughput technologies, including recurrent mutations in EZH2 (enhancer of zeste homolog 2) and CD79B (B cell antigen receptor complex-associated protein beta chain) genes. This study sought to determine the evolution of the mutational status of EZH2 and CD79B over time in different samples from the same patient in a cohort of B-cell NHLs, through use of a customized multiplex mutation assay. METHODS: DNA that was extracted from cytological material stored on FTA cards as well as from additional specimens, including archived frozen and formalin-fixed histological specimens, archived stained smears, and cytospin preparations, were submitted to a multiplex mutation assay specifically designed for the detection of point mutations involving EZH2 and CD79B, using MassARRAY spectrometry followed by Sanger sequencing. RESULTS: All 121 samples from 80 B-cell NHL cases were successfully analyzed. Mutations in EZH2 (Y646) and CD79B (Y196) were detected in 13.2% and 8% of the samples, respectively, almost exclusively in follicular lymphomas and diffuse large B-cell lymphomas. In one-third of the positive cases, a wild type was detected in a different sample from the same patient during follow-up. CONCLUSIONS: Testing multiple minimal tissue samples using a high-throughput multiplex platform exponentially increases tissue availability for molecular analysis and might facilitate future studies of tumor progression and the related molecular events. Mutational status of EZH2 and CD79B may vary in B-cell NHL samples over time and support the concept that individualized therapy should be based on molecular findings at the time of treatment, rather than on results obtained from previous specimens. Cancer (Cancer Cytopathol) 2013;121:377–386. © 2013 American Cancer Society. PMID:23361872

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.

On the construction of a time base and the elimination of averaging errors in proxy records

NASA Astrophysics Data System (ADS)

Beelaerts, V.; De Ridder, F.; Bauwens, M.; Schmitz, N.; Pintelon, R.

2009-04-01

Proxies are sources of climate information which are stored in natural archives (e.g. ice-cores, sediment layers on ocean floors and animals with calcareous marine skeletons). Measuring these proxies produces very short records and mostly involves sampling solid substrates, which is subject to the following two problems: Problem 1: Natural archives are equidistantly sampled at a distance grid along their accretion axis. Starting from these distance series, a time series needs to be constructed, as comparison of different data records is only meaningful on a time grid. The time series will be non-equidistant, as the accretion rate is non-constant. Problem 2: A typical example of sampling solid substrates is drilling. Because of the dimensions of the drill, the holes drilled will not be infinitesimally small. Consequently, samples are not taken at a point in distance, but rather over a volume in distance. This holds for most sampling methods in solid substrates. As a consequence, when the continuous proxy signal is sampled, it will be averaged over the volume of the sample, resulting in an underestimation of the amplitude. Whether this averaging effect is significant, depends on the volume of the sample and the variations of interest of the proxy signal. Starting from the measured signal, the continuous signal needs to be reconstructed in order eliminate these averaging errors. The aim is to provide an efficient identification algorithm to identify the non-linearities in the distance-time relationship, called time base distortions, and to correct for the averaging effects. Because this is a parametric method, an assumption about the proxy signal needs to be made: the proxy record on a time base is assumed to be harmonic, this is an obvious assumption because natural archives often exhibit a seasonal cycle. In a first approach the averaging effects are assumed to be in one direction only, i.e. the direction of the axis on which the measurements were performed. The measured averaged proxy signal is modeled by following signal model: -- Δ ∫ n+12Δδ- y(n,θ) = δ- 1Δ- y(m,θ)dm n-2 δ where m is the position, x(m) = Δm; θ are the unknown parameters and y(m,θ) is the proxy signal we want to identify (the proxy signal as found in the natural archive), which we model as: y(m, θ) = A +∑H [A sin(kωt(m ))+ A cos(kωt(m ))] 0 k=1 k k+H With t(m): t(m) = mTS + g(m )TS Here TS = 1/fS is the sampling period, fS the sampling frequency, and g(m) the unknown time base distortion (TBD). In this work a splines approximation of the TBD is chosen: ∑ g(m ) = b blφl(m ) l=1 where, b is a vector of unknown time base distortion parameters, and φ is a set of splines. The estimates of the unknown parameters were obtained with a nonlinear least squares algorithm. The vessel density measured in the mangrove tree R mucronata was used to illustrate the method. The vessel density is a proxy for the rain fall in tropical regions. The proxy data on the newly constructed time base showed a yearly periodicity, this is what we expected and the correction for the averaging effect increased the amplitude by 11.18%.

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.

In-depth investigation of archival and prospectively collected samples reveals no evidence for XMRV infection in prostate cancer.

PubMed

Lee, Deanna; Das Gupta, Jaydip; Gaughan, Christina; Steffen, Imke; Tang, Ning; Luk, Ka-Cheung; Qiu, Xiaoxing; Urisman, Anatoly; Fischer, Nicole; Molinaro, Ross; Broz, Miranda; Schochetman, Gerald; Klein, Eric A; Ganem, Don; Derisi, Joseph L; Simmons, Graham; Hackett, John; Silverman, Robert H; Chiu, Charles Y

2012-01-01

XMRV, or xenotropic murine leukemia virus (MLV)-related virus, is a novel gammaretrovirus originally identified in studies that analyzed tissue from prostate cancer patients in 2006 and blood from patients with chronic fatigue syndrome (CFS) in 2009. However, a large number of subsequent studies failed to confirm a link between XMRV infection and CFS or prostate cancer. On the contrary, recent evidence indicates that XMRV is a contaminant originating from the recombination of two mouse endogenous retroviruses during passaging of a prostate tumor xenograft (CWR22) in mice, generating laboratory-derived cell lines that are XMRV-infected. To confirm or refute an association between XMRV and prostate cancer, we analyzed prostate cancer tissues and plasma from a prospectively collected cohort of 39 patients as well as archival RNA and prostate tissue from the original 2006 study. Despite comprehensive microarray, PCR, FISH, and serological testing, XMRV was not detected in any of the newly collected samples or in archival tissue, although archival RNA remained XMRV-positive. Notably, archival VP62 prostate tissue, from which the prototype XMRV strain was derived, tested negative for XMRV on re-analysis. Analysis of viral genomic and human mitochondrial sequences revealed that all previously characterized XMRV strains are identical and that the archival RNA had been contaminated by an XMRV-infected laboratory cell line. These findings reveal no association between XMRV and prostate cancer, and underscore the conclusion that XMRV is not a naturally acquired human infection.

Community Exoplanet Follow-up Program

NASA Technical Reports Server (NTRS)

Howell, Steve

2017-01-01

During the Kepler mission, our team provided the community with the highest resolution images available anywhere of exoplanet host stars. Using speckle interferometry on the 3.5-m WIYN, and 8-m Gemini telescopes, thousands of observations have been obtained reaching the diffraction limit of the telescope. From these public data available at the NASA Exoplanet Archive, numerous publications have resulted and many scientific results have been obtained for exoplanets including the fact that high-resolution imaging is critical to fully characterize the planet host stars and the planets themselves (e.g., planet radius and incident flux). Exoplanet host star observations have also occurred (and continue) for K2 mission candidates with archival data available as well. Observational programs for TESS candidates, WFIRST program stars, and Zodiacal light candidates are currently on-going. Availability to propose or obtain such observations are possible through 1) collaboration with our team, 2) successfully proposing to WIYN or GEMINI for telescope time, or 3) using publically available archival data. This poster will highlight the observational program, how time is allocated and how our queue observational program works, and new features and observational modes that are available now.

Archiving 40+ Years of Planetary Mission Data - Lessons Learned

NASA Astrophysics Data System (ADS)

Simmons, K. E.

2012-12-01

NASA has invested billions of dollars and millions of man-hours in obtaining information about our planet and its neighbors. Will the data obtained from those investments be accessible in 50 years, nae 20 or even 10? Will scientists be able to look back at the record and understand what stayed the same or has changed? Saving the data is critical, we all understand that, and keeping it reformatted to maintain usability is a given. But what is easily more critical is saving the information that allows a future person to use these data. This work explores the difficul-ties, costs and heartaches encountered with archiving data from six major NASA missions spanning 40+ years: Mariner 6, 7 and 9, Pioneer Venus, Voyager and Galileo. Some of these lessons are a) a central archive for Mission documents needs to be established, b) metadata from the early stages of a mission are frequntly poorly recorded, c) instrument microprocessors improve science flexibility but make documenting harder, d) archiving observation de-signs improves data recovery, e) more post mission time and dollars need to be allocated to archiving, f) additional PDS node funding would support more timely data ingestion, faster peer review and quicker public access and g) trained archivists should be part of mission teams at all levels. This work is supported from ROSES grant NNX09AM04GS04.

CHEERS: Chemical enrichment of clusters of galaxies measured using a large XMM-Newton sample

NASA Astrophysics Data System (ADS)

de Plaa, J.; Mernier, F.; Kaastra, J.; Pinto, C.

2017-10-01

The Chemical Enrichment RGS Sample (CHEERS) is aimed to be a sample of the most optimal clusters of galaxies for observation with the Reflection Grating Spectrometer (RGS) aboard XMM-Newton. It consists of 5 Ms of deep cluster observations of 44 objects obtained through a very large program and archival observations. The main goal is to measure chemical abundances in the hot Intra-Cluster Medium (ICM) of clusters to provide constraints on chemical evolution models. Especially the origin and evolution of type Ia supernovae is still poorly known and X-ray observations could contribute to constrain models regarding the SNIa explosion mechanism. Due to the high quality of the data, the uncertainties on the abundances are dominated by systematic effects. By carefully treating each systematic effect, we increase the accuracy or estimate the remaining uncertainty on the measurement. The resulting abundances are then compared to supernova models. In addition, also radial abundance profiles are derived. In the talk, we present an overview of the results that the CHEERS collaboration obtained based on the CHEERS data. We focus on the abundance measurements. The other topics range from turbulence measurements through line broadening to cool gas in groups.

Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample

PubMed Central

Gilks, William P.; Pennell, Tanya M.; Flis, Ilona; Webster, Matthew T.; Morrow, Edward H.

2016-01-01

As part of a study into the molecular genetics of sexually dimorphic complex traits, we used high-throughput sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly ( Drosophila melanogaster) population. We successfully resequenced the whole genome of 220 hemiclonal females that were heterozygous for the same Berkeley reference line genome (BDGP6/dm6), and a unique haplotype from the outbred base population (LH M). The use of a static and known genetic background enabled us to obtain sequences from whole-genome phased haplotypes. We used a BWA-Picard-GATK pipeline for mapping sequence reads to the dm6 reference genome assembly, at a median depth-of coverage of 31X, and have made the resulting data publicly-available in the NCBI Short Read Archive (Accession number SRP058502). We used Haplotype Caller to discover and genotype 1,726,931 small genomic variants (SNPs and indels, <200bp). Additionally we detected and genotyped 167 large structural variants (1-100Kb in size) using GenomeStrip/2.0. Sequence and genotype data are publicly-available at the corresponding NCBI databases: Short Read Archive, dbSNP and dbVar (BioProject PRJNA282591). We have also released the unfiltered genotype data, and the code and logs for data processing and summary statistics ( https://zenodo.org/communities/sussex_drosophila_sequencing/). PMID:27928499

The potential of Lake Karakul in the eastern Pamirs as a long-term climate archive

NASA Astrophysics Data System (ADS)

Mischke, S.; Rajabov, I.; Mustaeva, N.; Zhang, C.; Boomer, I.; Sherlock, S. C.; Myrbo, A.; Noren, A.; Brady, K.; Herzschuh, U.; Schudack, M. E.; Ito, E.

2008-12-01

Lake Karakul is a large closed-basin lake in the eastern Pamirs (NE Tajikistan) at an altitude of 3930 m. The lake fills a large basin about 45 km in diameter which may originate from a meteorite impact in the late Neogene. Exposed lake sediments at the northwestern shore 20 m above the lake display a bizarre Yardang relief indicating higher water levels in the past. Eroded remnants of lake, playa and fluvial sediments can be found on the northeastern slopes of the basin 200 m above the lake but their depositional age remains unknown. A field survey of the Lake Karakul region was conducted in July 2008 as a first attempt to evaluate the potential of the lake as a long-term climate archive in Central Asia. Sediment samples from the lake's bottom, water samples from the lake and inflowing streams, aquatic and terrestrial plant samples, and rock samples were collected to enable an interdisciplinary investigation of the lake and its catchment. A 1.04 m sediment core was obtained near the centre of the more shallow and flat eastern sub-basin of the lake at 19 m water depth. Corresponding to the lack of outlet and the resulting high pH (9.1) and electrical conductivity of the lake (10.3 mS/cm), fine aragonite needles constitute most of the sediments. Additionally, ostracod shells, aquatic plant fragments, detrital grains and Radix (Gastropoda) shells were recorded. First results of AMS 14C dating and ostracod analysis will be used to infer the environmental and climatic evolution of Lake Karakul in the Late Holocene.

Chemically Dissected Rotation Curves of the Galactic Bulge from Main-sequence Proper Motions

NASA Astrophysics Data System (ADS)

Clarkson, William I.; Calamida, Annalisa; Sahu, Kailash C.; Brown, Thomas M.; Gennaro, Mario; Avila, Roberto J.; Valenti, Jeff; Debattista, Victor P.; Rich, R. Michael; Minniti, Dante; Zoccali, Manuela; Aufdemberge, Emily R.

2018-05-01

We report results from an exploratory study implementing a new probe of Galactic evolution using archival Hubble Space Telescope imaging observations. Precise proper motions are combined with photometric relative metallicity and temperature indices, to produce the proper-motion rotation curves of the Galactic bulge separately for metal-poor and metal-rich main-sequence samples. This provides a “pencil-beam” complement to large-scale wide-field surveys, which to date have focused on the more traditional bright giant branch tracers. We find strong evidence that the Galactic bulge rotation curves drawn from “metal-rich” and “metal-poor” samples are indeed discrepant. The “metal-rich” sample shows greater rotation amplitude and a steeper gradient against line-of-sight distance, as well as possibly a stronger central concentration along the line of sight. This may represent a new detection of differing orbital anisotropy between metal-rich and metal-poor bulge objects. We also investigate selection effects that would be implied for the longitudinal proper-motion cut often used to isolate a “pure-bulge” sample. Extensive investigation of synthetic stellar populations suggests that instrumental and observational artifacts are unlikely to account for the observed rotation curve differences. Thus, proper-motion-based rotation curves can be used to probe chemodynamical correlations for main-sequence tracer stars, which are orders of magnitude more numerous in the Galactic bulge than the bright giant branch tracers. We discuss briefly the prospect of using this new tool to constrain detailed models of Galactic formation and evolution. Based on observations made with the NASA/ESA Hubble Space Telescope and obtained from the data archive at the Space Telescope Science Institute. STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555.

Potential and limitation of combining terrestrial and marine growth records from Iceland

NASA Astrophysics Data System (ADS)

Piermattei, A.; Urbinati, C.; Tonelli, E.; Eggertsson, Ó.; Levanič, T.; Kaczka, R. J.; Andrew, C.; Schöne, B. R.; Büntgen, U.

2017-08-01

Seasonally formed, perennial growth increments of various organisms may possibly contain information about past environmental changes, well before instrumental measurements occurred. Such annually resolved proxy records have been mainly obtained from terrestrial archives, with a paucity of similar data originating from marine habitats. Iceland represents ideal conditions to develop both, tree ring (dendro) and bivalve shell (sclero) chronologies from adjacent sites. Here we introduce the first network of Icelandic birch (Betula pubescens Ehrh.) and rowan (Sorbus aucuparia) dendrochronologies, as well as ocean quahog (Arctica islandica L.) sclerochronologies. In order to identify the dominant external drivers of tree and shell growth, we assess the common growth trends and growth extremes within and between the terrestrial and marine records, as well as relationships of both archives with instrumental-based meteorological indices. Capturing a strong signal of June-August mean air temperature, the dendrochronologies are significantly positively correlated to each other. The sclerochronologies, however, reveal much lower growth coherency, which likely results from different sampling strategies and growth habitats. Disagreement between the dendro- and sclerochronologies possibly originates from unequal sample size, offset in the seasonal timing and rate of the growth, as well as varying sensitivities to different environmental factors. Our results emphasize the importance of considering a wide range of species and taxa to reconstruct a more complete picture of terrestrial and marine ecosystem functioning and productivity across various spatiotemporal scales.

The new European Hubble archive

NASA Astrophysics Data System (ADS)

De Marchi, Guido; Arevalo, Maria; Merin, Bruno

2016-01-01

The European Hubble Archive (hereafter eHST), hosted at ESA's European Space Astronomy Centre, has been released for public use in October 2015. The eHST is now fully integrated with the other ESA science archives to ensure long-term preservation of the Hubble data, consisting of more than 1 million observations from 10 different scientific instruments. The public HST data, the Hubble Legacy Archive, and the high-level science data products are now all available to scientists through a single, carefully designed and user friendly web interface. In this talk, I will show how the the eHST can help boost archival research, including how to search on sources in the field of view thanks to precise footprints projected onto the sky, how to obtain enhanced previews of imaging data and interactive spectral plots, and how to directly link observations with already published papers. To maximise the scientific exploitation of Hubble's data, the eHST offers connectivity to virtual observatory tools, easily integrates with the recently released Hubble Source Catalog, and is fully accessible through ESA's archives multi-mission interface.

Databases and archiving for cryoEM

PubMed Central

Patwardhan, Ardan; Lawson, Catherine L.

2017-01-01

Cryo-EM in structural biology is currently served by three public archives – EMDB for 3DEM reconstructions, PDB for models built from 3DEM reconstructions and EMPIAR for the raw 2D image data used to obtain the 3DEM reconstructions. These archives play a vital role for both the structural community and the wider biological community in making the data accessible so that results may be reused, reassessed and integrated with other structural and bioinformatics resources. The important role of the archives is underpinned by the fact that many journals mandate the deposition of data to PDB and EMDB on publication. The field is currently undergoing transformative changes where on the one hand high-resolution structures are becoming a routine occurrence while on the other hand electron tomography is enabling the study of macromolecules in the cellular context. Concomitantly the archives are evolving to best serve their stakeholder communities. In this chapter we describe the current state of the archives, resources available for depositing, accessing, searching, visualising and validating data, on-going community-wide initiatives and opportunities and challenges for the future. PMID:27572735

Diffuse Reflectance Spectroscopy for Total Carbon Analysis of Hawaiian Soils

NASA Astrophysics Data System (ADS)

McDowell, M. L.; Bruland, G. L.; Deenik, J. L.; Grunwald, S.; Uchida, R.

2010-12-01

Accurate assessment of total carbon (Ct) content is important for fertility and nutrient management of soils, as well as for carbon sequestration studies. The non-destructive analysis of soils by diffuse reflectance spectroscopy (DRS) is a potential supplement or alternative to the traditional time-consuming and costly combustion method of Ct analysis, especially in spatial or temporal studies where sample numbers are large. We investigate the use of the visible to near-infrared (VNIR) and mid-infrared (MIR) spectra of soils coupled with chemometric analysis to determine their Ct content. Our specific focus is on Hawaiian soils of agricultural importance. Though this technique has been introduced to the soil community, it has yet to be fully tested and used in practical applications for all soil types, and this is especially true for Hawaii. In short, DRS characterizes and differentiates materials based on the variation of the light reflected by a material at certain wavelengths. This spectrum is dependent on the material’s composition, structure, and physical state. Multivariate chemometric analysis unravels the information in a set of spectra that can help predict a property such as Ct. This study benefits from the remarkably diverse soils of Hawaii. Our sample set includes 216 soil samples from 145 pedons from the main Hawaiian Islands archived at the National Soil Survey Center in Lincoln, NE, along with more than 50 newly-collected samples from Kauai, Oahu, Molokai, and Maui. In total, over 90 series from 10 of the 12 soil orders are represented. The Ct values of these samples range from < 1% - 55%. We anticipate that the diverse nature of our sample set will ensure a model with applicability to a wide variety of soils, both in Hawaii and globally. We have measured the VNIR and MIR spectra of these samples and obtained their Ct values by dry combustion. Our initial analyses are conducted using only samples obtained from the Lincoln archive. In this preliminary case, we use Partial Least Squares (PLS) regression with cross validation to develop a prediction model for soils of unknown carbon content given only their spectral signature. We find R2 values of greater than 0.93 for the MIR spectra and 0.87 for the VNIR spectra, indicating a strong ability to correlate a soil’s spectrum with its Ct content. We build on these encouraging results by continuing chemometric analyses using the full data set, different data subsets, separate model calibration and validation groups, combined VNIR and MIR spectra, and exploring different data pretreatment options and variations to the PLS parameters.

New and revised 14C dates for Hawaiian surface lava flows: Paleomagnetic and geomagnetic implications

USGS Publications Warehouse

Pressline, N.; Trusdell, F.A.; Gubbins, David

2009-01-01

Radiocarbon dates have been obtained for 30 charcoal samples corresponding to 27 surface lava flows from the Mauna Loa and Kilauea volcanoes on the Island of Hawaii. The submitted charcoal was a mixture of fresh and archived material. Preparation and analysis was undertaken at the NERC Radiocarbon Laboratory in Glasgow, Scotland, and the associated SUERC Accelerator Mass Spectrometry facility. The resulting dates range from 390 years B.P. to 12,910 years B.P. with corresponding error bars an order of magnitude smaller than previously obtained using the gas-counting method. The new and revised 14C data set can aid hazard and risk assessment on the island. The data presented here also have implications for geomagnetic modelling, which at present is limited by large dating errors. Copyright 2009 by the American Geophysical Union.

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.

National Satellite Land Remote Sensing Data Archive

USGS Publications Warehouse

Faundeen, John L.; Kelly, Francis P.; Holm, Thomas M.; Nolt, Jenna E.

2013-01-01

The National Satellite Land Remote Sensing Data Archive (NSLRSDA) resides at the U.S. Geological Survey's (USGS) Earth Resources Observation and Science (EROS) Center. Through the Land Remote Sensing Policy Act of 1992, the U.S. Congress directed the Department of the Interior (DOI) to establish a permanent Government archive containing satellite remote sensing data of the Earth's land surface and to make this data easily accessible and readily available. This unique DOI/USGS archive provides a comprehensive, permanent, and impartial observational record of the planet's land surface obtained throughout more than five decades of satellite remote sensing. Satellite-derived data and information products are primary sources used to detect and understand changes such as deforestation, desertification, agricultural crop vigor, water quality, invasive plant species, and certain natural hazards such as flood extent and wildfire scars.

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.

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.

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

Comparison of parametric and bootstrap method in bioequivalence test.

PubMed

Ahn, Byung-Jin; Yim, Dong-Seok

2009-10-01

The estimation of 90% parametric confidence intervals (CIs) of mean AUC and Cmax ratios in bioequivalence (BE) tests are based upon the assumption that formulation effects in log-transformed data are normally distributed. To compare the parametric CIs with those obtained from nonparametric methods we performed repeated estimation of bootstrap-resampled datasets. The AUC and Cmax values from 3 archived datasets were used. BE tests on 1,000 resampled datasets from each archived dataset were performed using SAS (Enterprise Guide Ver.3). Bootstrap nonparametric 90% CIs of formulation effects were then compared with the parametric 90% CIs of the original datasets. The 90% CIs of formulation effects estimated from the 3 archived datasets were slightly different from nonparametric 90% CIs obtained from BE tests on resampled datasets. Histograms and density curves of formulation effects obtained from resampled datasets were similar to those of normal distribution. However, in 2 of 3 resampled log (AUC) datasets, the estimates of formulation effects did not follow the Gaussian distribution. Bias-corrected and accelerated (BCa) CIs, one of the nonparametric CIs of formulation effects, shifted outside the parametric 90% CIs of the archived datasets in these 2 non-normally distributed resampled log (AUC) datasets. Currently, the 80~125% rule based upon the parametric 90% CIs is widely accepted under the assumption of normally distributed formulation effects in log-transformed data. However, nonparametric CIs may be a better choice when data do not follow this assumption.

Comparison of Parametric and Bootstrap Method in Bioequivalence Test

PubMed Central

Ahn, Byung-Jin

2009-01-01

The estimation of 90% parametric confidence intervals (CIs) of mean AUC and Cmax ratios in bioequivalence (BE) tests are based upon the assumption that formulation effects in log-transformed data are normally distributed. To compare the parametric CIs with those obtained from nonparametric methods we performed repeated estimation of bootstrap-resampled datasets. The AUC and Cmax values from 3 archived datasets were used. BE tests on 1,000 resampled datasets from each archived dataset were performed using SAS (Enterprise Guide Ver.3). Bootstrap nonparametric 90% CIs of formulation effects were then compared with the parametric 90% CIs of the original datasets. The 90% CIs of formulation effects estimated from the 3 archived datasets were slightly different from nonparametric 90% CIs obtained from BE tests on resampled datasets. Histograms and density curves of formulation effects obtained from resampled datasets were similar to those of normal distribution. However, in 2 of 3 resampled log (AUC) datasets, the estimates of formulation effects did not follow the Gaussian distribution. Bias-corrected and accelerated (BCa) CIs, one of the nonparametric CIs of formulation effects, shifted outside the parametric 90% CIs of the archived datasets in these 2 non-normally distributed resampled log (AUC) datasets. Currently, the 80~125% rule based upon the parametric 90% CIs is widely accepted under the assumption of normally distributed formulation effects in log-transformed data. However, nonparametric CIs may be a better choice when data do not follow this assumption. PMID:19915699

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).

Identification and validation of differentially expressed transcripts by RNA-sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis.

PubMed

Vukmirovic, Milica; Herazo-Maya, Jose D; Blackmon, John; Skodric-Trifunovic, Vesna; Jovanovic, Dragana; Pavlovic, Sonja; Stojsic, Jelena; Zeljkovic, Vesna; Yan, Xiting; Homer, Robert; Stefanovic, Branko; Kaminski, Naftali

2017-01-12

Idiopathic Pulmonary Fibrosis (IPF) is a lethal lung disease of unknown etiology. A major limitation in transcriptomic profiling of lung tissue in IPF has been a dependence on snap-frozen fresh tissues (FF). In this project we sought to determine whether genome scale transcript profiling using RNA Sequencing (RNA-Seq) could be applied to archived Formalin-Fixed Paraffin-Embedded (FFPE) IPF tissues. We isolated total RNA from 7 IPF and 5 control FFPE lung tissues and performed 50 base pair paired-end sequencing on Illumina 2000 HiSeq. TopHat2 was used to map sequencing reads to the human genome. On average ~62 million reads (53.4% of ~116 million reads) were mapped per sample. 4,131 genes were differentially expressed between IPF and controls (1,920 increased and 2,211 decreased (FDR < 0.05). We compared our results to differentially expressed genes calculated from a previously published dataset generated from FF tissues analyzed on Agilent microarrays (GSE47460). The overlap of differentially expressed genes was very high (760 increased and 1,413 decreased, FDR < 0.05). Only 92 differentially expressed genes changed in opposite directions. Pathway enrichment analysis performed using MetaCore confirmed numerous IPF relevant genes and pathways including extracellular remodeling, TGF-beta, and WNT. Gene network analysis of MMP7, a highly differentially expressed gene in both datasets, revealed the same canonical pathways and gene network candidates in RNA-Seq and microarray data. For validation by NanoString nCounter® we selected 35 genes that had a fold change of 2 in at least one dataset (10 discordant, 10 significantly differentially expressed in one dataset only and 15 concordant genes). High concordance of fold change and FDR was observed for each type of the samples (FF vs FFPE) with both microarrays (r = 0.92) and RNA-Seq (r = 0.90) and the number of discordant genes was reduced to four. Our results demonstrate that RNA sequencing of RNA obtained from archived FFPE lung tissues is feasible. The results obtained from FFPE tissue are highly comparable to FF tissues. The ability to perform RNA-Seq on archived FFPE IPF tissues should greatly enhance the availability of tissue biopsies for research in IPF.

Back to the Future: Long-Term Seismic Archives Revisited

NASA Astrophysics Data System (ADS)

Waldhauser, F.; Schaff, D. P.

2007-12-01

Archives of digital seismic data recorded by seismometer networks around the world have grown tremendously over the last several decades helped by the deployment of seismic stations and their continued operation within the framework of monitoring seismic activity. These archives typically consist of waveforms of seismic events and associated parametric data such as phase arrival time picks and the location of hypocenters. Catalogs of earthquake locations are fundamental data in seismology, and even in the Earth sciences in general. Yet, these locations have notoriously low spatial resolution because of errors in both the picks and the models commonly used to locate events one at a time. This limits their potential to address fundamental questions concerning the physics of earthquakes, the structure and composition of the Earth's interior, and the seismic hazards associated with active faults. We report on the comprehensive use of modern waveform cross-correlation based methodologies for high- resolution earthquake location - as applied to regional and global long-term seismic databases. By simultaneous re-analysis of two decades of the digital seismic archive of Northern California, reducing pick errors via cross-correlation and model errors via double-differencing, we achieve up to three orders of magnitude resolution improvement over existing hypocenter locations. The relocated events image networks of discrete faults at seismogenic depths across various tectonic settings that until now have been hidden in location uncertainties. Similar location improvements are obtained for earthquakes recorded at global networks by re- processing 40 years of parametric data from the ISC and corresponding waveforms archived at IRIS. Since our methods are scaleable and run on inexpensive Beowulf clusters, periodic re-analysis of entire archives may thus become a routine procedure to continuously improve resolution in existing catalogs. We demonstrate the role of seismic archives in obtaining the precise location of new events in real-time. Such information has considerable social and economic impact in the evaluation and mitigation of seismic hazards, for example, and highlights the need for consistent long-term seismic monitoring and archiving of records.

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 Gaia Archive at ESAC: a VO-inside archive

NASA Astrophysics Data System (ADS)

Gonzalez-Nunez, J.

2015-12-01

The ESDC (ESAC Science Data Center) is one of the active members of the IVOA (International Virtual Observatory Alliance) that have defined a set of standards, libraries and concepts that allows to create flexible,scalable and interoperable architectures on the data archives development. In the case of astronomy science that involves the use of big catalogues, as in Gaia or Euclid, TAP, UWS and VOSpace standards can be used to create an architecture that allows the explotation of this valuable data from the community. Also, new challenges arise like the implementation of the new paradigm "move code close to the data", what can be partially obtained by the extension of the protocols (TAP+, UWS+, etc) or the languages (ADQL). We explain how we have used VO standards and libraries for the Gaia Archive that, not only have producing an open and interoperable archive but, also, minimizing the developement on certain areas. Also we will explain how we have extended these protocols and the future plans.

Sanger and Next-Generation Sequencing data for characterization of CTL epitopes in archived HIV-1 proviral DNA.

PubMed

Tumiotto, Camille; Riviere, Lionel; Bellecave, Pantxika; Recordon-Pinson, Patricia; Vilain-Parce, Alice; Guidicelli, Gwenda-Line; Fleury, Hervé

2017-01-01

One of the strategies for curing viral HIV-1 is a therapeutic vaccine involving the stimulation of cytotoxic CD8-positive T cells (CTL) that are Human Leucocyte Antigen (HLA)-restricted. The lack of efficiency of previous vaccination strategies may have been due to the immunogenic peptides used, which could be different from a patient's virus epitopes and lead to a poor CTL response. To counteract this lack of specificity, conserved epitopes must be targeted. One alternative is to gather as many data as possible from a large number of patients on their HIV-1 proviral archived epitope variants, taking into account their genetic background to select the best presented CTL epitopes. In order to process big data generated by Next-Generation Sequencing (NGS) of the DNA of HIV-infected patients, we have developed a software package called TutuGenetics. This tool combines an alignment derived either from Sanger or NGS files, HLA typing, target gene and a CTL epitope list as input files. It allows automatic translation after correction of the alignment obtained between the HxB2 reference and the reads, followed by automatic calculation of the MHC IC50 value for each epitope variant and the HLA allele of the patient by using NetMHCpan 3.0, resulting in a csv file as output result. We validated this new tool by comparing Sanger and NGS (454, Roche) sequences obtained from the proviral DNA of patients at success of ART included in the Provir Latitude 45 study and showed a 90% correlation between the quantitative results of NGS and Sanger. This automated analysis combined with complementary samples should yield more data regarding the archived CTL epitopes according to the patients' HLA alleles and will be useful for screening epitopes that in theory are presented efficiently to the HLA groove, thus constituting promising immunogenic peptides for a therapeutic vaccine.

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.

Three archives of the U. S. Geological Survey's Western Mineral Resources Team

USGS Publications Warehouse

Bolm, Karen Sue; Frank, David G.; Schneider, Jill L.

2000-01-01

The Western Mineral Resources Team of the U.S. Geological Survey (USGS) has three archives, which hold unpublished or difficult-to-obtain records and literature. The Technical Data Unit in Anchorage, Alaska, holds maps, field notes, and other records of the USGS work in Alaska. The USGS Field Office in Spokane, Washington, houses the more than 5,000 files from Federal government exploration programs that contracted to fund exploration for some commodities from 1950 until 1974. The Latin American Archive in Tucson, Arizona, holds material on Latin American mineral resources collected by the Center for Inter-American MineralResources Investigations.

Professional Acceptance Of Electronic Images In Radiologic Practice

NASA Astrophysics Data System (ADS)

Gitlin, Joseph N.; Curtis, David J.; Kerlin, Barbara D.; Olmsted, William W.

1983-05-01

During the past four years, a large number of radiographic images have been interpreted in both film and video modes in an effort to determine the utility of digital/analogue systems in general practice. With the cooperation of the Department of Defense, the MITRE Corporation, and several university-based radiology departments, the Public Health Service has participated in laboratory experiments and a teleradiology field trial to meet this objective. During the field trial, 30 radiologists participated in the interpretation of more than 4,000 diagnostic x-ray examinations that were performed at distant clinics, digitized, and transmitted to a medical center for interpretation on video monitors. As part of the evaluation, all of the participating radiologists and the attending physicians at the clinics were queried regarding the teleradiology system, particularly with respect to the diagnostic quality of the electronic images. The original films for each of the 4,000 examinations were read independently, and the findings and impressions from each mode were compared to identify discrepancies. In addition, a sample of 530 cases was reviewed and interpreted by a consensus panel to measure the accuracy of findings and impressions of both film and video readings. The sample has been retained in an automated archive for future study at the National Center of Devices and Radiological Health facilities in Rockville, Maryland. The studies include a comparison of diagnostic findings and impressions from 1024 x 1024 matrices with those obtained from the 512 x 512 format used in the field trial. The archive also provides a database for determining the effect of data compression techniques on diagnostic interpretations and establishing the utility of image processing algorithms. The paper will include an analysis of the final results of the field trial and preliminary findings from the ongoing studies using the archive of cases at the National Center for Devices and Radiological Health. This paper was not available at the time of printing of the Proceedings.

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.

VizieR Online Data Catalog: X-ray observations of HCG galaxies (Tzanavaris+, 2016)

NASA Astrophysics Data System (ADS)

Tzanavaris, P.; Hornschemeier, A. E.; Gallagher, S. C.; Lenkic, L.; Desjardins, T. D.; Walker, L. M.; Johnson, K. E.; Mulchaey, J. S.

2016-04-01

In this paper we study a sample of 15 compact groups (CGs) observed with Chandra/ACIS, Swift/UVOT and Spitzer/IRAC-MIPS for which archival data exist, allowing us to obtain SFRs, stellar masses, sSFRs and X-ray fluxes and luminosities. Table 1 shows the group sample, including redshifts, luminosity distances and group evolutionary types. Allowing for the fact that some galaxies do not fall in the field of view of all three instruments, the total number of CG galaxies analyzed is 47. Details on the Swift and Spitzer observations and data for systems in this sample can be found in Tzanavaris et al. (2010ApJ...716..556T) and (L. Lenkic et al. 2015, in preparation). For Chandra/ACIS observations we refer the reader to Tzanavaris et al. (2014, J/ApJS/212/9) and Desjardins et al. (2013ApJ...763..121D; 2014ApJ...790..132D). (2 data files).

X-ray and optical substructures of the DAFT/FADA survey clusters

NASA Astrophysics Data System (ADS)

Guennou, L.; Durret, F.; Adami, C.; Lima Neto, G. B.

2013-04-01

We have undertaken the DAFT/FADA survey with the double aim of setting constraints on dark energy based on weak lensing tomography and of obtaining homogeneous and high quality data for a sample of 91 massive clusters in the redshift range 0.4-0.9 for which there were HST archive data. We have analysed the XMM-Newton data available for 42 of these clusters to derive their X-ray temperatures and luminosities and search for substructures. Out of these, a spatial analysis was possible for 30 clusters, but only 23 had deep enough X-ray data for a really robust analysis. This study was coupled with a dynamical analysis for the 26 clusters having at least 30 spectroscopic galaxy redshifts in the cluster range. Altogether, the X-ray sample of 23 clusters and the optical sample of 26 clusters have 14 clusters in common. We present preliminary results on the coupled X-ray and dynamical analyses of these 14 clusters.

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.

Mega-precovery and data mining of near-Earth asteroids and other Solar System objects

NASA Astrophysics Data System (ADS)

Popescu, M.; Vaduvescu, O.; Char, F.; Curelaru, L.; Euronear Team

2014-07-01

The vast collection of CCD images and photographic plate archives available from the world-wide archives and telescopes is still insufficiently exploited. Within the EURONEAR project we designed two data mining software with the purpose to search very large collections of archives for images which serendipitously include known asteroids or comets in their field, with the main aims to extend the arc and improve the orbits. In this sense, ''Precovery'' (published in 2008, aiming to search all known NEAs in few archives via IMCCE's SkyBoT server) and ''Mega-Precovery'' (published in 2010, querying the IMCCE's Miriade server) were made available to the community via the EURONEAR website (euronear.imcce.fr). Briefly, Mega-Precovery aims to search one or a few known asteroids or comets in a mega-collection including millions of images from some of the largest observatory archives: ESO (15 instruments served by ESO Archive including VLT), NVO (8 instruments served by U.S. NVO Archive), CADC (11 instruments, including HST and Gemini), plus other important instrument archives: SDSS, CFHTLS, INT-WFC, Subaru-SuprimeCam and AAT-WFI, adding together 39 instruments and 4.3 million images (Mar 2014), and our Mega-Archive is growing. Here we present some of the most important results obtained with our data-mining software and some new planned search options of Mega-Precovery. Particularly, the following capabilities will be added soon: the ING archive (all imaging cameras) will be included and new search options will be made available (such as query by orbital elements and by observations) to be able to target new Solar System objects such as Virtual Impactors, bolides, planetary satellites, TNOs (besides the comets added recently). In order to better characterize the archives, we introduce the ''AOmegaA'' factor (archival etendue) proportional to the AOmega (etendue) and the number of images in an archive. With the aim to enlarge the Mega-Archive database, we invite the observatories (particularly those storing their images online and also those that own plate archives which could be scanned on request) to contact us in order to add their instrument archives (consisting of an ASCII file with telescope pointings in a simple format) to our Mega-Precovery open project. We intend for the future to synchronise our service with the Virtual Observatory.

VizieR Online Data Catalog: Carbon-enhanced metal-poor star BD+44493 EWs (Roederer+, 2016)

NASA Astrophysics Data System (ADS)

Roederer, I. U.; Placco, V. M.; Beers, T. C.

2016-08-01

We have obtained new observations of portions of the UV spectrum of BD+44493 using the Cosmic Origins Spectrograph (COS) on HST (13000

OUTFLOW AND METALLICITY IN THE BROAD-LINE REGION OF LOW-REDSHIFT ACTIVE GALACTIC NUCLEI

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

Shin, Jaejin; Woo, Jong-Hak; Nagao, Tohru

2017-01-20

Outflows in active galactic nuclei (AGNs) are crucial to understand in investigating the co-evolution of supermassive black holes (SMBHs) and their host galaxies since outflows may play an important role as an AGN feedback mechanism. Based on archival UV spectra obtained with the Hubble Space Telescope and IUE , we investigate outflows in the broad-line region (BLR) in low-redshift AGNs ( z < 0.4) through detailed analysis of the velocity profile of the C iv emission line. We find a dependence of the outflow strength on the Eddington ratio and the BLR metallicity in our low-redshift AGN sample, which ismore » consistent with earlier results obtained for high-redshift quasars. These results suggest that BLR outflows, gas accretion onto SMBHs, and past star formation activity in host galaxies are physically related in low-redshift AGNs as in powerful high-redshift quasars.« less

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 Prorating Method for Estimating MMPI-2-RF Scores From MMPI Responses: Examination of Score Fidelity and Illustration of Empirical Utility in the PERSEREC Police Integrity Study Sample.

PubMed

Tarescavage, Anthony M; Corey, David M; Ben-Porath, Yossef S

2016-04-01

The purpose of the current study was to identify Minnesota Multiphasic Personality Inventory-2-Restructured Form (MMPI-2-RF) correlates of police officer integrity violations and other problem behaviors in an archival database with original MMPI item responses and collateral information regarding integrity violations obtained for 417 male officers. In Study 1, we estimated MMPI-2-RF scores from the MMPI item pool (which includes approximately 80% of the MMPI-2-RF items) in a normative sample, a psychiatric inpatient sample, and a police officer sample, and conducted analyses that demonstrated the comparability of estimated and full scale scores for 41 of the 51 MMPI-2-RF scales. In Study 2, we correlated estimated MMPI-2-RF scores with information about subsequent integrity violations and problem behaviors from the integrity violation data set. Several meaningful associations were obtained, predominately with scales from the emotional, thought, and behavioral dysfunction domains of the MMPI-2-RF. Application of a correction for range restriction yielded substantially improved validity estimates. Finally, we calculated relative risk ratios for the statistically significant findings using cutoffs lower than 65T, which is traditionally used to identify clinically significant elevations, and found several meaningful relative risk ratios. © The Author(s) 2015.

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.

X-ray aspects of the DAFT/FADA clusters

NASA Astrophysics Data System (ADS)

Guennou, L.; Durret, F.; Lima Neto, G. B.; Adami, C.

2012-12-01

We have undertaken the DAFT/FADA survey with the aim of applying constraints on dark energy based on weak lensing tomography as well as obtaining homogeneous and high quality data for a sample of 91 massive clusters in the redshift range [0.4,0.9] for which there are HST archive data. We have analysed the XMM-Newton data available for 42 of these clusters to derive their X-ray temperatures and luminosities and search for substructures. This study was coupled with a dynamical analysis for the 26 clusters having at least 30 spectroscopic galaxy redshifts in the cluster range. We present preliminary results on the coupled X-ray and dynamical analyses of these clusters.

Micronuclei formation in liver fibrosis samples from patients infected by hepatitis C virus

PubMed Central

2010-01-01

Genetic research on fibrosis outset and its progression in chronic hepatitis (CH) by hepatitis C virus (HCV) are limited. The lack of cytogenetic data led us to investigate the presence of micronuclei (MNi), as a sign of genomic damage. Hepatocytes of hepatic parenchyma from 62 cases diagnosed with CH associated with HCV and displaying different degrees of fibrosis (F1-F4) were analyzed. These data were compared to 15 cases without fibrosis (F0). Twelve healthy liver parenchyma samples were included as control. All samples were obtained from paraffin-embedded archival material. Micronucleated hepatocytes (MN-Heps) were analyzed through Feulgen/Fast-green staining. Results showed that the rates of MN-Heps in the F4 group were statistically significant (p < 0.05) and higher than those in the control group. Like results were also obtained on comparing F4 with F0, F1, F2 and F3 cases. Conversely, differences were not significant (p > 0.05) on comparing F0, F1, F2, F3, one against the other, as well as individual versus control. Although chromosomal losses in CH were detected, it was shown that liver parenchyma with fibrosis in the initial stages (F1-F3) cannot be considered cytogenetically abnormal. PMID:21637406

On the Likely Utility of Hybrid Weights Optimized for Variances in Hybrid Error Covariance Models

NASA Astrophysics Data System (ADS)

Satterfield, E.; Hodyss, D.; Kuhl, D.; Bishop, C. H.

2017-12-01

Because of imperfections in ensemble data assimilation schemes, one cannot assume that the ensemble covariance is equal to the true error covariance of a forecast. Previous work demonstrated how information about the distribution of true error variances given an ensemble sample variance can be revealed from an archive of (observation-minus-forecast, ensemble-variance) data pairs. Here, we derive a simple and intuitively compelling formula to obtain the mean of this distribution of true error variances given an ensemble sample variance from (observation-minus-forecast, ensemble-variance) data pairs produced by a single run of a data assimilation system. This formula takes the form of a Hybrid weighted average of the climatological forecast error variance and the ensemble sample variance. Here, we test the extent to which these readily obtainable weights can be used to rapidly optimize the covariance weights used in Hybrid data assimilation systems that employ weighted averages of static covariance models and flow-dependent ensemble based covariance models. Univariate data assimilation and multi-variate cycling ensemble data assimilation are considered. In both cases, it is found that our computationally efficient formula gives Hybrid weights that closely approximate the optimal weights found through the simple but computationally expensive process of testing every plausible combination of weights.

Collection, analysis, and archival of LDEF activation data

NASA Technical Reports Server (NTRS)

Laird, C. E.; Harmon, B. A.; Fishman, G. J.; Parnell, T. A.

1993-01-01

The study of the induced radioactivity of samples intentionally placed aboard the Long Duration Exposure Facility (LDEF) and samples obtained from the LDEF structure is reviewed. The eight laboratories involved in the gamma-ray counting are listed and the scientists and the associated counting facilities are described. Presently, most of the gamma-ray counting has been completed and the spectra are being analyzed and corrected for efficiency and self absorption. The acquired spectra are being collected at Eastern Kentucky University for future reference. The results of these analyses are being compiled and reviewed for possible inconsistencies as well as for comparison with model calculations. These model calculations are being revised to include the changes in trapped-proton flux caused by the onset of the period of maximum solar activity and the rapidly decreasing spacecraft orbit. Tentative plans are given for the storage of the approximately 1000 gamma-ray spectra acquired in this study and the related experimental data.

A Database of Young Star Clusters for Five Hundred Galaxies

NASA Astrophysics Data System (ADS)

Evans, Jessica; Whitmore, B. C.; Lindsay, K.; Chandar, R.; Larsen, S.

2009-01-01

The study of young massive stellar clusters has faced a series of observational challenges, such as the use of inconsistent data sets and low number statistics. To rectify these shortcomings, this project will use the source lists developed as part of the Hubble Legacy Archive to obtain a large, uniform database of super star clusters in nearby star-forming galaxies in order to address two fundamental astronomical questions: 1) To what degree is the cluster luminosity (and mass) function of star clusters universal? 2) What fraction of super star clusters are "missing" in optical studies (i.e., are hidden by dust)? The archive's recent data release (Data Release 2 - September, 2008) will help us achieve the large sample necessary (N 50 galaxies for multi-wavelength, N 500 galaxies for ACS F814W). The uniform data set will comprise of ACS, WFPC2, and NICMOS data, with DAOphot used for object detection. This database will also support comparisons with new Monte-Carlo simulations that have independently been developed in the past few years, and will be used to test the Whitmore, Chandar, Fall (2007) framework designed to understand the demographics of star clusters in all star forming galaxies. The catalogs will increase the number of galaxies with measured mass and luminosity functions by an order of magnitude, and will provide a powerful new tool for comparative studies, both ours and the community's. The poster will describe our preliminary investigation for the first 30 galaxies in the sample.

High-resolution droplet-based fractionation of nano-LC separations onto microarrays for MALDI-MS analysis.

PubMed

Küster, Simon K; Pabst, Martin; Jefimovs, Konstantins; Zenobi, Renato; Dittrich, Petra S

2014-05-20

We present a robust droplet-based device, which enables the fractionation of ultralow flow rate nanoflow liquid chromatography (nano-LC) eluate streams at high frequencies and high peak resolution. This is achieved by directly interfacing the separation column to a micro T-junction, where the eluate stream is compartmentalized into picoliter droplets. This immediate compartmentalization prevents peak dispersion during eluate transport and conserves the chromatographic performance. Subsequently, nanoliter eluate fractions are collected at a rate of one fraction per second on a high-density microarray to retain the separation with high temporal resolution. Chromatographic separations of up to 45 min runtime can thus be archived on a single microarray possessing 2700 sample spots. The performance of this device is demonstrated by fractionating the separation of a tryptic digest of a known protein mixture onto the microarray chip and subsequently analyzing the sample archive using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Resulting peak widths are found to be significantly reduced compared to standard continuous flow spotting technologies as well as in comparison to a conventional nano-LC-electrospray ionization-mass spectrometry interface. Moreover, we demonstrate the advantage of our high-definition nanofractionation device by applying two different MALDI matrices to all collected fractions in an alternating fashion. Since the information that is obtained from a MALDI-MS measurement depends on the choice of MALDI matrix, we can extract complementary information from neighboring spots containing almost identical composition but different matrices.

Expression of FGFR3 and FGFR4 and clinical risk factors associated with progression-free survival in synovial sarcoma.

PubMed

Charbonneau, Bridget; Vogel, Rachel Isaksson; Manivel, J Carlos; Rizzardi, Anthony; Schmechel, Stephen C; Ognjanovic, Simona; Subramanian, Subbaya; Largaespada, David; Weigel, Brenda

2013-09-01

Although rare, synovial sarcoma (SS) is one of the most common soft tissue sarcomas affecting young adults. To investigate potential tumor markers related to synovial sarcoma prognosis, we carried out a single-institution retrospective analysis of 103 patients diagnosed with SS between 1980 and 2009. Clinical outcome data were obtained from medical records, and archived tissue samples were used to evaluate the relationship between progression-free survival (PFS) and several prognostic factors, including tumor expression of FGFR3 and FGFR4. No associations were found between PFS and gender, body mass index, tumor site, SS18-SSX translocation, or FGFR4 expression. As seen in previous studies, age at diagnosis (<35, 63% versus ≥35 years, 31% 10-year PFS; P = .033), histologic subtype (biphasic, 75% versus monophasic 34% 10-year PFS; P = .034), and tumor size (≤5 cm, 70% versus >5 cm, 22% 10-year PFS; P < .0001) were associated with PFS in SS patients. In addition, in a subset of patients with available archived tumor samples taken prior to chemotherapy or radiation (n = 34), higher FGFR3 expression was associated with improved PFS (P = .030). To the best of our knowledge, this is the largest study of SS to date to suggest a potential clinical role for FGFR3. While small numbers make this investigation somewhat exploratory, the findings merit future investigation on a larger scale. Copyright © 2013 Elsevier Inc. All rights reserved.

36 CFR 1227.14 - How do I obtain copies of the GRS?

Code of Federal Regulations, 2010 CFR

2010-07-01

... ADMINISTRATION RECORDS MANAGEMENT GENERAL RECORDS SCHEDULES § 1227.14 How do I obtain copies of the GRS? (a) The GRS and instructions for their use are available online at http://www.archives.gov/records-mgmt/ardor...

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 ...

National Satellite Land Remote Sensing Data Archive

USGS Publications Warehouse

Faundeen, John L.; Longhenry, Ryan

2018-06-13

The National Satellite Land Remote Sensing Data Archive is managed on behalf of the Secretary of the Interior by the U.S. Geological Survey’s Earth Resources Observation and Science Center. The Land Remote Sensing Policy Act of 1992 (51 U.S.C. §601) directed the U.S. Department of the Interior to establish a permanent global archive consisting of imagery over land areas obtained from satellites orbiting the Earth. The law also directed the U.S. Department of the Interior, delegated to the U.S. Geological Survey, to ensure proper storage and preservation of imagery, and timely access for all parties. Since 2008, these images have been available at no cost to the user.

NASA participation in the 1980 PEPE/NEROS project: Data archive

NASA Technical Reports Server (NTRS)

Brewer, D. A.; Remsberg, E. E.; Loar, G. R.; Bendura, R. J.

1982-01-01

Eight experimental air quality measurement systems were investigated during July and August 1980 as part of the EPA PEPE/NEROS fiel measurement program. Data from those efforts have been entered into an archive that may be accessed by other researchers. The data sets consists of airborne measurements of regional mixed layer heights and aerosol and ozone distributions as well as point measurements of meteorological parameters and ozone obtained during diurnal transitions in the planetary boundary layer. This report gives a discussion of each measurement system, a preliminary assessment of data quality, a description of the archive format for each data set, and a summary of several proposed scientific studies which will utilize these data.

Pixel-by-Pixel SED Fitting of Intermediate Redshift Galaxies

NASA Astrophysics Data System (ADS)

Cohen, Seth H.; Kim, Hwihyun; Petty, Sara M.; Farrah, Duncan

2015-01-01

We select intermediate redshift galaxies from the Hubble Space Telescope CANDELS and GOODS surveys to study their stellar populations on sub-kilo-parsec scales by fitting SED models on a pixel-by-pixel basis. Galaxies are chosen to have measured spectroscopic redshifts (z<1.5), to be bright (H_AB<21 mag), to be relatively face-on (b/a > 0.6), and have a minimum of ten individual resolution elements across the face of the galaxy, as defined by the broadest PSF (F160W-band) in the data. The sample contains ~200 galaxies with BViz(Y)JH band HST photometry. The main goal of the study is to better understand the effects of population blending when using a pixel-by-pixel SED fitting (pSED) approach. We outline our pSED fitting method which gives maps of stellar mass, age, star-formation rate, etc. Several examples of individual pSED-fit maps are presented in detail, as well as some preliminary results on the full sample. The pSED method is necessarily biased by the brightest population in a given pixel outshining the rest of the stars, and, therefore, we intend to study this apparent population blending in a set of artificially redshifted images of nearby galaxies, for which we have star-by-star measurements of their stellar populations. This local sample will be used to better interpret the measurements for the higher redshift galaxies.Based on observations made with the NASA/ESA Hubble Space Telescope, obtained from the Data Archive at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. This archival research is associated with program #13241.

Timing of fluid seepage on summits of Quaker and Conical serpentine mud volcanoes, Mariana forearc: Evidence from U/Th dating of carbonate chimneys

NASA Astrophysics Data System (ADS)

Tong, Hongpeng; Fryer, Patricia; Feng, Dong; Chen, Duofu

2017-04-01

Serpetinization of forearc mantle along deep faults in the Mariana convergent plate margin permits formation of large active serpentinite mud volcanoes on the overiding plate within 90 km of the trench. Fluid seepage on summits of the mud volcanoes lead to the formation of authigenic carbonate chimneys close to the seafloor. Such carbonate chimneys are unique archives of past fluid seepage and assciated envrionemtnal parameters. Here, we report U/Th dating and stable carbon and oxygen isotopes of the chimneys from Quaker and Conical serpentine mud volcanoes. The resulting U/Th ages of samples from Quaker Seamount show three time intervals of 11,081 to10,542 yBP, 5,857 to 5,583 yBP, and 781 to 164 yBP, respectively. By comparison, carbonates from Conical Seamount have U/Th ages between 3,070 yBP and 1,623 yBP. Our results suggest that fluid seepage on the summits of serpentine mud volcanoes are episodic and probably locally controlled. Samples from Quaker seamount show depletion of 13C (δ13C=-7.0-0.4‰ V-PDB), indicating contribution of carbon from anoxic oxidation of abiogenic methane. By contrast, samples from Conical seamount have positive δ18O values (0.6-6.3), suggesting enrichment of 18O in the seepage fluid. The data obtained provide time integrated variation of seepage fluids and seepage dynamics that are archived in authigenic carbonates. This finding adds to the ongoing multidisciplinary effort to better constrain the environment in the Mariana forearc region and to determine the locally dominant biogeochemical processes. Acknowlegment: This study was funded by the CAS (Grant No. XDB06030102).

Ocean Color Data at the Goddard Earth Sciences (GES) DAAC: CZCS, SeaWiFS, OCTS, MODIS-Terra, MODIS-Aqua

NASA Technical Reports Server (NTRS)

2002-01-01

The Goddard Earth Sciences Distributed Active Archive Center (DAAC) is the designated archive for all of the ocean color data produced by NASA satellite missions. The DAAC is a long-term, high volume, secure repository for many different kinds of environmental data. With respect to ocean color, the Goddard DAAC holds all the data obtained during the eight-year mission of the Coastal Zone Color Scanner (CZCS). The DAAC is currently receiving data from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS), and the MODIS-Terra instrument. The DAAC recently received reformatted data from the Ocean Color and Temperature Scanner (OCTS) and will also archive MODIS-Aqua Ocean products. In addition to its archive and distribution services, the Goddard DAAC strives to improve data access, ease-of-use, and data applicability for a broad spectrum of customers. The DAAC's data support teams practice dual roles, both insuring the integrity of the DAAC data archive and serving the user community with answers to user inquiries, online and print documentation, and customized data services.

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.

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

Development of public science archive system of Subaru Telescope

NASA Astrophysics Data System (ADS)

Baba, Hajime; Yasuda, Naoki; Ichikawa, Shin-Ichi; Yagi, Masafumi; Iwamoto, Nobuyuki; Takata, Tadafumi; Horaguchi, Toshihiro; Taga, Masatochi; Watanabe, Masaru; Okumura, Shin-Ichiro; Ozawa, Tomohiko; Yamamoto, Naotaka; Hamabe, Masaru

2002-09-01

We have developed a public science archive system, Subaru-Mitaka-Okayama-Kiso Archive system (SMOKA), as a successor of Mitaka-Okayama-Kiso Archive (MOKA) system. SMOKA provides an access to the public data of Subaru Telescope, the 188 cm telescope at Okayama Astrophysical Observatory, and the 105 cm Schmidt telescope at Kiso Observatory of the University of Tokyo. Since 1997, we have tried to compile the dictionary of FITS header keywords. The accomplishment of the dictionary enabled us to construct an unified public archive of the data obtained with various instruments at the telescopes. SMOKA has two kinds of user interfaces; Simple Search and Advanced Search. Novices can search data by simply selecting the name of the target with the Simple Search interface. Experts would prefer to set detailed constraints on the query, using the Advanced Search interface. In order to improve the efficiency of searching, several new features are implemented, such as archive status plots, calibration data search, an annotation system, and an improved Quick Look Image browsing system. We can efficiently develop and operate SMOKA by adopting a three-tier model for the system. Java servlets and Java Server Pages (JSP) are useful to separate the front-end presentation from the middle and back-end tiers.

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.

The Influence of Sampling Density on Bayesian Age-Depth Models and Paleoclimatic Reconstructions - Lessons Learned from Lake Titicaca - Bolivia/Peru

NASA Astrophysics Data System (ADS)

Salenbien, W.; Baker, P. A.; Fritz, S. C.; Guedron, S.

2014-12-01

Lake Titicaca is one of the most important archives of paleoclimate in tropical South America, and prior studies have elucidated patterns of climate variation at varied temporal scales over the past 0.5 Ma. Yet, slow sediment accumulation rates in the main deeper basin of the lake have precluded analysis of the lake's most recent history at high resolution. To obtain a paleoclimate record of the last few millennia at multi-decadal resolution, we obtained five short cores, ranging from 139 to 181 cm in length, from the shallower Wiñaymarka sub-basin of of Lake Titicaca, where sedimentation rates are higher than in the lake's main basin. Selected cores have been analyzed for their geochemical signature by scanning XRF, diatom stratigraphy, sedimentology, and for 14C age dating. A total of 72 samples were 14C-dated using a Gas Ion Source automated high-throughput method for carbonate samples (mainly Littoridina sp. and Taphius montanus gastropod shells) at NOSAMS (Woods Hole Oceanographic Institute) with an analytical precision higher than 2%. The method has lower analytical precision compared with traditional AMS radiocarbon dating, but the lower cost enables analysis of a larger number of samples, and the error associated with the lower precision is relatively small for younger samples (< ~8,000 years). A 172-cm-long core was divided into centimeter long sections, and 47 14C dates were obtained from 1-cm intervals, averaging one date every 3-4 cm. The other cores were radiocarbon dated with a sparser sampling density that focused on visual unconformities and shell beds. The high-resolution radiocarbon analysis reveals complex sedimentation patterns in visually continuous sections, with abundant indicators of bioturbated or reworked sediments and periods of very rapid sediment accumulation. These features are not evident in the sparser sampling strategy but have significant implications for reconstructing past lake level and paleoclimatic history.

Certification Archives

EPA Pesticide Factsheets

The requirements of this product certification system are applicable to EPA-approved accreditation bodies (approved accreditation bodies), licensed certifying bodies, and the manufacturers that are obtaining product certification.

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.

VizieR Online Data Catalog: Circumstellar-interacting supernovae (Taddia+, 2015)

NASA Astrophysics Data System (ADS)

Taddia, F.; Sollerman, J.; Fremling, C.; Pastorello, A.; Leloudas, G.; Fransson, C.; Nyholm, A.; Stritzinger, M. D.; Ergon, M.; Roy, R.; Migotto, K.

2015-11-01

In Table 1 we report the list of 60 transients included in our sample. Thirty-five of them are SNe IIn, six are SNe Ibn, one is a SN Ia-CSM, 18 are SN IMs (if we also count SN 2009ip in the SN IMs, then we have 19 of these transients). With the NOT, long-slit spectra were obtained for the host galaxies of 13 SNe IIn, five SNe Ibn, one SN Ia-CSM, and 16 SN IMs (the derived metallicity for SN 2007sv was published in Tartaglia et al. 2015MNRAS.447..117T). The host galaxies observed at the NOT are marked with the letter "o" in the third column of Table 1. With the NOT, we also obtained broad-band R and narrow-band Hα images for the SNe IIn (except for SN 1995G) and Ibn. We complemented our observed sample with host galaxies whose metallicities (at the center of the galaxy or at the SN position) were already available in the literature (marked with the letter "l" in the third column of Table 1) or whose spectra were available in public archives (marked with the letter "a" in the third column of Table 1). (7 data files).

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

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.

VizieR Online Data Catalog: Jame Clerk Maxwell Telescope Science Archive (CADC, 2003)

NASA Astrophysics Data System (ADS)

Canadian Astronomy Data, Centre

2018-01-01

The JCMT Science Archive (JSA), a collaboration between the CADC and EOA, is the official distribution site for observational data obtained with the James Clerk Maxwell Telescope (JCMT) on Mauna Kea, Hawaii. The JSA search interface is provided by the CADC Search tool, which provides generic access to the complete set of telescopic data archived at the CADC. Help on the use of this tool is provided via tooltips. For additional information on instrument capabilities and data reduction, please consult the SCUBA-2 and ACSIS instrument pages provided on the JAC maintained JCMT pages. JCMT-specific help related to the use of the CADC AdvancedSearch tool is available from the JAC. (1 data file).

Global lightning studies

NASA Technical Reports Server (NTRS)

Goodman, Steven J.; Wright, Pat; Christian, Hugh; Blakeslee, Richard; Buechler, Dennis; Scharfen, Greg

1991-01-01

The global lightning signatures were analyzed from the DMSP Optical Linescan System (OLS) imagery archived at the National Snow and Ice Data Center. Transition to analysis of the digital archive becomes available and compare annual, interannual, and seasonal variations with other global data sets. An initial survey of the quality of the existing film archive was completed and lightning signatures were digitized for the summer months of 1986 to 1987. The relationship is studied between: (1) global and regional lightning activity and rainfall, and (2) storm electrical development and environment. Remote sensing data sets obtained from field programs are used in conjunction with satellite/radar/lightning data to develop and improve precipitation estimation algorithms, and to provide a better understanding of the co-evolving electrical, microphysical, and dynamical structure of storms.

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.

VizieR Online Data Catalog: Spectroscopy of luminous compact blue galaxies (Crawford+, 2016)

NASA Astrophysics Data System (ADS)

Crawford, S. M.; Wirth, G. D.; Bershady, M. A.; Randriamampandry, S. M.

2017-10-01

Deep imaging data in UBRIz and two narrow bands were obtained with the Mini-Mosaic camera from the WIYN 3.5 m telescope for all five clusters between 1999 October and 2004 June. We obtained spectroscopic observations for a sample of cluster star-forming galaxies with the DEIMOS, Faber et al. 2003 on the Keck II Telescope during 2005 October and 2007 April. The narrow-band filters were specifically designed to detect [OII] λ3727 at the redshift of each cluster. All of the clusters have been the target of extensive observations with the HST, primarily using either WFPC2 or the Advanced Camera for Surveys (ACS). For all measurements, we have attempted to select data taken in a filter closest to the rest-frame B band. We have employed ACS imaging data whenever possible and substituted WFPC2 images only when required. For clusters observed in the far-infrared regime by the Spitzer Space Telescope, we extracted MIPS 24μm flux densities, S24, from images obtained through the Enhanced Imaging Products archive. (2 data files).

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...

Application of Remote Sensing for the Analysis of Environmental Changes in Albania

NASA Astrophysics Data System (ADS)

Frasheri, N.; Beqiraj, G.; Bushati, S.; Frasheri, A.

2016-08-01

In the paper there is presented a review of remote sensing studies carried out for investigation of environmental changes in Albania. Using, often simple methodologies and general purpose image processing software, and exploiting free Internet archives of satellite imagery, significant results were obtained for hot areas of environmental changes. Such areas include sea coasts experiencing sea transgression, temporal variations of vegetation and aerosols, lakes, landslides and regional tectonics. Internet archives of European Space Agency ESA and USA Geological Service USGS are used.

Characterizing Space Environments with Long-Term Space Plasma Archive Resources

NASA Technical Reports Server (NTRS)

Minow, Joseph I.; Miller, J. Scott; Diekmann, Anne M.; Parker, Linda N.

2009-01-01

A significant scientific benefit of establishing and maintaining long-term space plasma data archives is the ready access the archives afford to resources required for characterizing spacecraft design environments. Space systems must be capable of operating in the mean environments driven by climatology as well as the extremes that occur during individual space weather events. Long- term time series are necessary to obtain quantitative information on environment variability and extremes that characterize the mean and worst case environments that may be encountered during a mission. In addition, analysis of large data sets are important to scientific studies of flux limiting processes that provide a basis for establishing upper limits to environment specifications used in radiation or charging analyses. We present applications using data from existing archives and highlight their contributions to space environment models developed at Marshall Space Flight Center including the Chandra Radiation Model, ionospheric plasma variability models, and plasma models of the L2 space environment.

FTS Spectra from the Mayall 4-m Telescope, 1975-1995

NASA Astrophysics Data System (ADS)

Pilachowski, Catherine A.; Hinkle, Kenneth H.; Young, Michael; Dennis, Harold; Gopu, Arvind; Henschel, Robert; Hayashi, Soichi

2017-01-01

The complete archive of spectra obtained with the Fourier Transform Spectrometers in use at the Mayall 4m telescope at the Kitt Peak National Observatory from 1975 through 1995 is now available to the community. The archive is hosted at Indiana University Bloomington, and includes nearly 10,000 individual spectra of more than 800 different astronomical sources. The FTS produced spectra in the wavelength regime from roughly 0.9 to 5 microns (11,000 to 2000 cm-1), mostly at relatively high spectral resolution. The archive can be searched to identify specific spectra of interest, and the spectra can be viewed online and downloaded in FITS format for analysis. Once a spectrum of interest has been identified, all spectra taken on the same date are provided to allow users to identify appropriate hot star spectra for telluric line division.The archive can be accessed on the web at https://sparc.sca.iu.edu.

BAO plate archive digitization

NASA Astrophysics Data System (ADS)

Mickaelian, A. M.; Nikoghosyan, E. H.; Gigoyan, K. S.; Paronyan, G. M.; Abrahamyan, H. V.; Andreasyan, H. R.; Azatyan, N. M.; Kostandyan, G. R.; Khachatryan, K. G.; Vardanyan, A. V.; Gyulzadyan, M. V.; Mikayelyan, G. A.; Farmanyan, S. V.; Knyazyan, A. V.

Astronomical plate archives created on the basis of numerous observations at many observatories are important part of the astronomical heritage. Byurakan Astrophysical Observatory (BAO) plate archive consists of 37,000 photographic plates and films, obtained at 2.6m telescope, 1m and 0.5m Schmidt telescopes and other smaller ones during 1947-1991. In 2015, we have started a project on the whole BAO Plate Archive digitization, creation of electronic database and its scientific usage. A Science Program Board is created to evaluate the observing material, to investigate new possibilities and to propose new projects based on the combined usage of these observations together with other world databases. The Executing Team consists of 11 astronomers and 2 computer scientists and will use 2 EPSON Perfection V750 Pro scanners for the digitization. The project will run during 3 years in 2015-2017 and the final result will be an electronic database and online interactive sky map to be used for further research projects.

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.

Tissue-type plasminogen activator-induced fibrinolysis is enhanced in patients with breast, lung, pancreas and colon cancer.

PubMed

Nielsen, Vance G; Matika, Ryan W; Ley, Michele L B; Waer, Amy L; Gharagozloo, Farid; Kim, Samuel; Nfonsam, Valentine N; Ong, Evan S; Jie, Tun; Warneke, James A; Steinbrenner, Evangelina B

2014-04-01

Although cancer-mediated changes in hemostatic proteins unquestionably promote hypercoagulation, the effects of neoplasia on fibrinolysis in the circulation are less well defined. The goals of the present investigation were to determine if plasma obtained from patients with breast, lung, pancreas and colon cancer was less or more susceptible to lysis by tissue-type plasminogen activator (tPA) compared to plasma obtained from normal individuals. Archived plasma obtained from patients with breast (n = 18), colon/pancreas (n = 27) or lung (n = 19) was compared to normal individual plasma (n = 30) using a thrombelastographic assay that assessed fibrinolytic vulnerability to exogenously added tPA. Plasma samples were activated with tissue factor/celite, had tPA added, and had data collected until clot lysis occurred. Additional, similar samples had potato carboxypeptidase inhibitor added to assess the role played by thrombin-activatable fibrinolysis inhibitor in cancer-modulated fibrinolysis. Rather than inflicting a hypofibrinolytic state, the three groups of cancers demonstrated increased vulnerability to tPA (e.g. decreased time to lysis, increased speed of lysis, decreased clot lysis time). However, hypercoagulation manifested as increased speed of clot formation and strength compensated for enhanced fibrinolytic vulnerability, resulting in a clot residence time that was not different from normal individual thrombi. In sum, enhanced hypercoagulability associated with cancer was in part diminished by enhanced fibrinolytic vulnerability to tPA.

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.;

Direct-to-PCR tissue preservation for DNA profiling.

PubMed

Sorensen, Amy; Berry, Clare; Bruce, David; Gahan, Michelle Elizabeth; Hughes-Stamm, Sheree; McNevin, Dennis

2016-05-01

Disaster victim identification (DVI) often occurs in remote locations with extremes of temperatures and humidities. Access to mortuary facilities and refrigeration are not always available. An effective and robust DNA sampling and preservation procedure would increase the probability of successful DNA profiling and allow faster repatriation of bodies and body parts. If the act of tissue preservation also released DNA into solution, ready for polymerase chain reaction (PCR), the DVI process could be further streamlined. In this study, we explored the possibility of obtaining DNA profiles without DNA extraction, by adding aliquots of preservative solutions surrounding fresh human muscle and decomposing human muscle and skin tissue samples directly to PCR. The preservatives consisted of two custom preparations and two proprietary solutions. The custom preparations were a salt-saturated solution of dimethyl sulfoxide (DMSO) with ethylenediaminetetraacetic (EDTA) and TENT buffer (Tris, EDTA, NaCl, Tween 20). The proprietary preservatives were DNAgard (Biomatrica(®)) and Tissue Stabilising Kit (DNA Genotek). We obtained full PowerPlex(®) 21 (Promega) and GlobalFiler(®) (Life Technologies) DNA profiles from fresh and decomposed tissue preserved at 35 °C for up to 28 days for all four preservatives. The preservative aliquots removed from the fresh muscle tissue samples had been stored at -80 °C for 4 years, indicating that long-term archival does not diminish the probability of successful DNA typing. Rather, storage at -80 °C seems to reduce PCR inhibition.

THE PANCHROMATIC STARBURST IRREGULAR DWARF SURVEY (STARBIRDS): OBSERVATIONS AND DATA ARCHIVE

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

McQuinn, Kristen B. W.; Mitchell, Noah P.; Skillman, Evan D., E-mail: kmcquinn@astro.umn.edu

2015-06-22

Understanding star formation in resolved low mass systems requires the integration of information obtained from observations at different wavelengths. We have combined new and archival multi-wavelength observations on a set of 20 nearby starburst and post-starburst dwarf galaxies to create a data archive of calibrated, homogeneously reduced images. Named the panchromatic “STARBurst IRregular Dwarf Survey” archive, the data are publicly accessible through the Mikulski Archive for Space Telescopes. This first release of the archive includes images from the Galaxy Evolution Explorer Telescope (GALEX), the Hubble Space Telescope (HST), and the Spitzer Space Telescope (Spitzer) Multiband Imaging Photometer instrument. The datamore » sets include flux calibrated, background subtracted images, that are registered to the same world coordinate system. Additionally, a set of images are available that are all cropped to match the HST field of view. The GALEX and Spitzer images are available with foreground and background contamination masked. Larger GALEX images extending to 4 times the optical extent of the galaxies are also available. Finally, HST images convolved with a 5″ point spread function and rebinned to the larger pixel scale of the GALEX and Spitzer 24 μm images are provided. Future additions are planned that will include data at other wavelengths such as Spitzer IRAC, ground-based Hα, Chandra X-ray, and Green Bank Telescope H i imaging.« less

Stability and reproducibility of proteomic profiles measured with an aptamer-based platform.

PubMed

Kim, Claire H; Tworoger, Shelley S; Stampfer, Meir J; Dillon, Simon T; Gu, Xuesong; Sawyer, Sherilyn J; Chan, Andrew T; Libermann, Towia A; Eliassen, A Heather

2018-05-30

The feasibility of SOMAscan, a multiplex, high sensitivity proteomics platform, for use in studies using archived plasma samples has not yet been assessed. We quantified 1,305 proteins from plasma samples donated by 16 Nurses' Health Study (NHS) participants, 40 NHSII participants, and 12 local volunteers. We assessed assay reproducibility using coefficients of variation (CV) from duplicate samples and intra-class correlation coefficients (ICC) and Spearman correlation coefficients (r) of samples processed (i.e., centrifuged and aliquoted into separate components) immediately, 24, and 48 hours after collection, as well as those of samples collected from the same individuals 1 year apart. CVs were <20% for 99% of proteins overall and <10% for 92% of proteins in heparin samples compared to 66% for EDTA samples. We observed ICC or Spearman r (comparing immediate vs. 24-hour delayed processing) ≥0.75 for 61% of proteins, with some variation by anticoagulant (56% for heparin and 70% for EDTA) and protein class (ranging from 49% among kinases to 83% among hormones). Within-person stability over 1 year was good (ICC or Spearman r ≥ 0.4) for 91% of proteins. These results demonstrate the feasibility of SOMAscan for analyses of archived plasma samples.

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.

Modern pollen data from the Canadian Arctic, 1972-1973

NASA Astrophysics Data System (ADS)

Nichols, Harvey; Stolze, Susann

2017-05-01

This data descriptor reports results of a 1972-73 baseline study of modern pollen deposition in the Canadian Arctic to originally aid interpretation of Holocene pollen diagrams from that region, especially focussed on the arctic tree-line. The data set is geographically unique due to its extent, and allows the assessment of the effects of modern climate change on northern ecosystems, including fluctuations of the a arctic tree-line. Repeated sampling was conducted along an interior transect at 29 sites from the Boreal Forest to the High Arctic, with five additional coastal sites covering a total distance of 3,200 km. Static pollen samplers captured both local pollen and long-distance pollen wind-blown from the Boreal Forest. Moss and lichen polsters provided multi-year pollen fallout to assess the effectiveness of the static pollen samplers. The local vegetation was recorded at each site. This descriptor provides information on data archived at the World Data Center PANGAEA, which includes spreadsheets detailing site and sample information as well as raw and processed pollen data obtained on over 500 samples.

Modern pollen data from the Canadian Arctic, 1972-1973.

PubMed

Nichols, Harvey; Stolze, Susann

2017-05-16

This data descriptor reports results of a 1972-73 baseline study of modern pollen deposition in the Canadian Arctic to originally aid interpretation of Holocene pollen diagrams from that region, especially focussed on the arctic tree-line. The data set is geographically unique due to its extent, and allows the assessment of the effects of modern climate change on northern ecosystems, including fluctuations of the a arctic tree-line. Repeated sampling was conducted along an interior transect at 29 sites from the Boreal Forest to the High Arctic, with five additional coastal sites covering a total distance of 3,200 km. Static pollen samplers captured both local pollen and long-distance pollen wind-blown from the Boreal Forest. Moss and lichen polsters provided multi-year pollen fallout to assess the effectiveness of the static pollen samplers. The local vegetation was recorded at each site. This descriptor provides information on data archived at the World Data Center PANGAEA, which includes spreadsheets detailing site and sample information as well as raw and processed pollen data obtained on over 500 samples.

Modern pollen data from the Canadian Arctic, 1972–1973

PubMed Central

Nichols, Harvey; Stolze, Susann

2017-01-01

This data descriptor reports results of a 1972–73 baseline study of modern pollen deposition in the Canadian Arctic to originally aid interpretation of Holocene pollen diagrams from that region, especially focussed on the arctic tree-line. The data set is geographically unique due to its extent, and allows the assessment of the effects of modern climate change on northern ecosystems, including fluctuations of the a arctic tree-line. Repeated sampling was conducted along an interior transect at 29 sites from the Boreal Forest to the High Arctic, with five additional coastal sites covering a total distance of 3,200 km. Static pollen samplers captured both local pollen and long-distance pollen wind-blown from the Boreal Forest. Moss and lichen polsters provided multi-year pollen fallout to assess the effectiveness of the static pollen samplers. The local vegetation was recorded at each site. This descriptor provides information on data archived at the World Data Center PANGAEA, which includes spreadsheets detailing site and sample information as well as raw and processed pollen data obtained on over 500 samples. PMID:28509898

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).

Sensitivity of HER-2/neu antibodies in archival tissue samples: potential source of error in immunohistochemical studies of oncogene expression.

PubMed

Press, M F; Hung, G; Godolphin, W; Slamon, D J

1994-05-15

HER-2/neu oncogene amplification and overexpression of breast cancer tissue has been correlated with poor prognosis in women with both node-positive and node-negative disease. However, several studies have not confirmed this association. Review of these studies reveals the presence of considerable methodological variability including differences in study size, follow-up time, techniques and reagents. The majority of papers with clinical follow-up information are immunohistochemical studies using archival, paraffin-embedded breast cancers, and a variety of HER-2/neu antibodies have been used in these studies. Very little information, however, is available about the ability of the antibodies to detect overexpression following tissue processing for paraffin-embedding. Therefore, a series of antibodies, reported in the literature or commercially available, were evaluated to assess their sensitivity and specificity as immunohistochemical reagents. Paraffin-embedded samples of 187 breast cancers, previously characterized as frozen specimens for HER-2/neu amplification by Southern blot and for overexpression by Northern blot, Western blot, and immunohistochemistry, were used. Two multitumor paraffin-embedded tissue blocks were prepared from the previously analyzed breast cancers as a panel of cases to test a series of previously studied and/or commercially available anti-HER-2/neu antibodies. Immunohistochemical staining results obtained with 7 polyclonal and 21 monoclonal antibodies in sections from paraffin-embedded blocks of these breast cancers were compared. The ability of these antibodies to detect overexpression was extremely variable, providing an important explantation for the variable overexpression rate reported in the literature.

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

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

Environmental System Science Data Infrastructure for a Virtual Ecosystem (ESS-DIVE) - A New U.S. DOE Data Archive

NASA Astrophysics Data System (ADS)

Agarwal, D.; Varadharajan, C.; Cholia, S.; Snavely, C.; Hendrix, V.; Gunter, D.; Riley, W. J.; Jones, M.; Budden, A. E.; Vieglais, D.

2017-12-01

The ESS-DIVE archive is a new U.S. Department of Energy (DOE) data archive designed to provide long-term stewardship and use of data from observational, experimental, and modeling activities in the earth and environmental sciences. The ESS-DIVE infrastructure is constructed with the long-term vision of enabling broad access to and usage of the DOE sponsored data stored in the archive. It is designed as a scalable framework that incentivizes data providers to contribute well-structured, high-quality data to the archive and that enables the user community to easily build data processing, synthesis, and analysis capabilities using those data. The key innovations in our design include: (1) application of user-experience research methods to understand the needs of users and data contributors; (2) support for early data archiving during project data QA/QC and before public release; (3) focus on implementation of data standards in collaboration with the community; (4) support for community built tools for data search, interpretation, analysis, and visualization tools; (5) data fusion database to support search of the data extracted from packages submitted and data available in partner data systems such as the Earth System Grid Federation (ESGF) and DataONE; and (6) support for archiving of data packages that are not to be released to the public. ESS-DIVE data contributors will be able to archive and version their data and metadata, obtain data DOIs, search for and access ESS data and metadata via web and programmatic portals, and provide data and metadata in standardized forms. The ESS-DIVE archive and catalog will be federated with other existing catalogs, allowing cross-catalog metadata search and data exchange with existing systems, including DataONE's Metacat search. ESS-DIVE is operated by a multidisciplinary team from Berkeley Lab, the National Center for Ecological Analysis and Synthesis (NCEAS), and DataONE. The primarily data copies are hosted at DOE's NERSC supercomputing facility with replicas at DataONE nodes.

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.

Leukemia and brain tumors among children after radiation exposure from CT scans: design and methodological opportunities of the Dutch Pediatric CT Study.

PubMed

Meulepas, Johanna M; Ronckers, Cécile M; Smets, Anne M J B; Nievelstein, Rutger A J; Jahnen, Andreas; Lee, Choonsik; Kieft, Mariëtte; Laméris, Johan S; van Herk, Marcel; Greuter, Marcel J W; Jeukens, Cécile R L P N; van Straten, Marcel; Visser, Otto; van Leeuwen, Flora E; Hauptmann, Michael

2014-04-01

Computed tomography (CT) scans are indispensable in modern medicine; however, the spectacular rise in global use coupled with relatively high doses of ionizing radiation per examination have raised radiation protection concerns. Children are of particular concern because they are more sensitive to radiation-induced cancer compared with adults and have a long lifespan to express harmful effects which may offset clinical benefits of performing a scan. This paper describes the design and methodology of a nationwide study, the Dutch Pediatric CT Study, regarding risk of leukemia and brain tumors in children after radiation exposure from CT scans. It is a retrospective record-linkage cohort study with an expected number of 100,000 children who received at least one electronically archived CT scan covering the calendar period since the introduction of digital archiving until 2012. Information on all archived CT scans of these children will be obtained, including date of examination, scanned body part and radiologist's report, as well as the machine settings required for organ dose estimation. We will obtain cancer incidence by record linkage with external databases. In this article, we describe several approaches to the collection of data on archived CT scans, the estimation of radiation doses and the assessment of confounding. The proposed approaches provide useful strategies for data collection and confounder assessment for general retrospective record-linkage studies, particular those using hospital databases on radiological procedures for the assessment of exposure to ionizing or non-ionizing radiation.

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.

Environmental controls for the precipitation of different fibrous calcite cement fabrics

NASA Astrophysics Data System (ADS)

Ritter, Ann-Christine; Wiethoff, Felix; Neuser, Rolf D.; Richter, Detlev K.; Immenhauser, Adrian

2016-04-01

Abiogenic calcite cements are widely used as climate archives. They can yield information on environmental change and climate dynamics at the time when the sediment was lithified in a (marine) diagenetic environment. Radiaxial-fibrous (RFC) and fascicular-optic fibrous (FOFC) calcite cements are two very common and similar pore-filling cement fabrics in Palaeozoic and Mesozoic carbonate rocks (Richter et al., 2011) and in Holocene Mg-calcitic speleothems (Richter et al., 2015). Both fabrics are characterised by distinct crystallographic properties. Current research has shown that these fabrics are often underexplored and that a careful combination of conservative and innovative proxies allows for a better applicability of these carbonate archives to paleoenvironmental reconstructions (Ritter et al., 2015). A main uncertainty in this context is that it is still poorly understood which parameters lead to the formation of either RFC or FOFC and if differential crystallographic parameters affect proxy data from these fabrics. This study aims at a better understanding of the environmental factors that may control either RFC or FOFC precipitation. Therefore, suitable samples (a stalagmite and a Triassic marine cement succession), each with clearly differentiable layers of RFC and FOFC, were identified and analysed in high detail using a multi-proxy approach. Detailed thin section and cathodoluminescence analysis of the samples allowed for a precise identification of layers consisting solely of either RFC or FOFC. Isotopic (δ13C, δ18O) as well as trace elemental compositions have been determined and the comparison of data obtained from these different carbonate archives sheds light on changes in environmental parameters during RFC or FOFC precipitation. References: Richter, D.K., et al., 2011. Radiaxial-fibrous calcites: A new look at an old problem. Sedimentary Geology, 239, 26-36 Richter, D.K., et al., 2015. Radiaxial-fibrous and fascicular-optic Mg-calcitic cave cements: a characterization usig electron backscattered diffraction (EBSD). International Journal of Speleology, 44, 91-98 Ritter, A.-C., et al., 2015. Application of redox sensitive proxies and carbonate clumped isotopes to Mesozoic and Palaeozoic radiaxial fibrous calcite cements. Chemical Geology, 417, 306-321

Long Duration Exposure Facility experiment M0003 deintegration observation data base

NASA Technical Reports Server (NTRS)

Gyetvay, S. R.; Coggi, J. M.; Meshishnek, M. J.

1993-01-01

The four trays (2 leading edge and 2 trailing edge) of the M0003 materials experiment on the Long Duration Exposure Facility (LDEF) contained 1274 samples from 20 subexperiments. The complete sample complement represented a broad range of materials, including thin film optical coatings, paints, polymer sheets and tapes, adhesives, and composites, for use in various spacecraft applications, including thermal control, structures, optics, and solar power. Most subexperiments contained sets of samples exposed on both the leading and trailing edge trays of LDEF. Each individual sample was examined by high resolution optical microscope during the deintegration of the subexperiments from the M0003 trays. Observations of the post-flight condition of the samples made during this examination were recorded in a computer data base. The deintegration observation data base is available to requesters on floppy disk in 4th Dimension for the Macintosh format. Over 3,000 color macrographs and photomicrographs were shot to complement the observation records and to document the condition of the individual samples and of the M0003 trays. The photographs provide a visual comparison of the response of materials in leading and trailing edge LDEF environments. The Aerospace Corporate Archives is distributing photographs of the samples and hard copies of the database records to the general public upon request. Information on obtaining copies of the data base disks and for ordering photographs and records of specific samples or materials are given.

Airborne Lidar measurements of aerosols, mixed layer heights, and ozone during the 1980 PEPE/NEROS summer field experiment

NASA Technical Reports Server (NTRS)

Browell, E. V.; Shipley, S. T.; Butler, C. F.; Ismail, S.

1985-01-01

A detailed summary of the NASA Ultraviolet Differential Absorption Lidar (UV DIAL) data archive obtained during the EPA Persistent Elevated Pollution Episode/Northeast Regional Oxidant Study (PEPE/NEROS) Summer Field Experiment Program (July through August 1980) is presented. The UV dial data set consists of remote measurements of mixed layer heights, aerosol backscatter cross sections, and sequential ozone profiles taken during 14 long-range flights onboard the NASA Wallops Flight Center Electra aircraft. These data are presented in graphic and tabular form, and they have been submitted to the PEPE/NEROS data archive on digital magnetic tape. The derivation of mixing heights and ozone profiles from UV Dial signals is discussed, and detailed intercomparisons with measurements obtained by in situ sensors are presented.

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.

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…

CpG Methylation Analysis of HPV16 in Laser Capture Microdissected Archival Tissue and Whole Tissue Sections from High Grade Anal Squamous Intraepithelial Lesions: A Potential Disease Biomarker

PubMed Central

Molano, Monica; Tabrizi, Sepehr N.; Garland, Suzanne M.; Roberts, Jennifer M.; Machalek, Dorothy A.; Phillips, Samuel; Chandler, David; Hillman, Richard J.; Grulich, Andrew E.; Jin, Fengyi; Poynten, I. Mary; Templeton, David J.; Cornall, Alyssa M.

2016-01-01

Incidence and mortality rates of anal cancer are increasing globally. More than 90% of anal squamous cell carcinomas (ASCC) are associated with human papillomavirus (HPV). Studies on HPV-related anogenital lesions have shown that patterns of methylation of viral and cellular DNA targets could potentially be developed as disease biomarkers. Lesion-specific DNA isolated from formalin-fixed paraffin-embedded (FFPE) tissues from existing or prospective patient cohorts may constitute a valuable resource for methylation analysis. However, low concentrations of DNA make these samples technically challenging to analyse using existing methods. We therefore set out to develop a sensitive and reproducible nested PCR-pyrosequencing based method to accurately quantify methylation at 10 CpG sites within the E2BS1, E2BS2,3,4 and Sp1 binding sites in the viral upstream regulatory region of HPV16 genome. Methylation analyses using primary and nested PCR-pyrosequencing on 52 FFPE tissue [26 paired whole tissue sections (WTS) and laser capture microdissected (LCM) tissues] from patients with anal squamous intraepithelial lesions was performed. Using nested PCR, methylation results were obtained for the E2BS1, E2BS2,3,4 and Sp1 binding sites in 86.4% of the WTS and 81.8% of the LCM samples. Methylation patterns were strongly correlated within median values of matched pairs of WTS and LCM sections, but overall methylation was higher in LCM samples at different CpG sites. High grade lesions showed low methylation levels in the E2BS1 and E2BS2 regions, with increased methylation detected in the E2BS,3,4/Sp1 regions, showing the highest methylation at CpG site 37. The method developed is highly sensitive in samples with low amounts of DNA and demonstrated to be suitable for archival samples. Our data shows a possible role of specific methylation in the HPV16 URR for detection of HSIL. PMID:27529629

CpG Methylation Analysis of HPV16 in Laser Capture Microdissected Archival Tissue and Whole Tissue Sections from High Grade Anal Squamous Intraepithelial Lesions: A Potential Disease Biomarker.

PubMed

Molano, Monica; Tabrizi, Sepehr N; Garland, Suzanne M; Roberts, Jennifer M; Machalek, Dorothy A; Phillips, Samuel; Chandler, David; Hillman, Richard J; Grulich, Andrew E; Jin, Fengyi; Poynten, I Mary; Templeton, David J; Cornall, Alyssa M

2016-01-01

Incidence and mortality rates of anal cancer are increasing globally. More than 90% of anal squamous cell carcinomas (ASCC) are associated with human papillomavirus (HPV). Studies on HPV-related anogenital lesions have shown that patterns of methylation of viral and cellular DNA targets could potentially be developed as disease biomarkers. Lesion-specific DNA isolated from formalin-fixed paraffin-embedded (FFPE) tissues from existing or prospective patient cohorts may constitute a valuable resource for methylation analysis. However, low concentrations of DNA make these samples technically challenging to analyse using existing methods. We therefore set out to develop a sensitive and reproducible nested PCR-pyrosequencing based method to accurately quantify methylation at 10 CpG sites within the E2BS1, E2BS2,3,4 and Sp1 binding sites in the viral upstream regulatory region of HPV16 genome. Methylation analyses using primary and nested PCR-pyrosequencing on 52 FFPE tissue [26 paired whole tissue sections (WTS) and laser capture microdissected (LCM) tissues] from patients with anal squamous intraepithelial lesions was performed. Using nested PCR, methylation results were obtained for the E2BS1, E2BS2,3,4 and Sp1 binding sites in 86.4% of the WTS and 81.8% of the LCM samples. Methylation patterns were strongly correlated within median values of matched pairs of WTS and LCM sections, but overall methylation was higher in LCM samples at different CpG sites. High grade lesions showed low methylation levels in the E2BS1 and E2BS2 regions, with increased methylation detected in the E2BS,3,4/Sp1 regions, showing the highest methylation at CpG site 37. The method developed is highly sensitive in samples with low amounts of DNA and demonstrated to be suitable for archival samples. Our data shows a possible role of specific methylation in the HPV16 URR for detection of HSIL.

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.

77 FR 20639 - Shashikant Shah: Debarment Order

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-05

... investigate, log, and archive questionable, aberrant, and unacceptable laboratory results so that Able could... maintaining false, fraudulent, and inaccurate data and records to obtain FDA approval to market new product...

77 FR 20641 - Jose Concepcion: Debarment Order

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-05

... investigate, log, and archive questionable, aberrant, and unacceptable laboratory results so that Able could... maintaining false, fraudulent, and inaccurate data and records to obtain FDA approval to market new product...

36 CFR 1227.14 - How do I obtain copies of the GRS?

Code of Federal Regulations, 2014 CFR

2014-07-01

... Administration, Modern Records Programs (NWM), 8601 Adelphi Road, College Park, MD 20740-6001, phone number (301... GRS? 1227.14 Section 1227.14 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION RECORDS MANAGEMENT GENERAL RECORDS SCHEDULES § 1227.14 How do I obtain copies of the GRS? (a) The...

36 CFR 1227.14 - How do I obtain copies of the GRS?

Code of Federal Regulations, 2012 CFR

2012-07-01

... Administration, Modern Records Programs (NWM), 8601 Adelphi Road, College Park, MD 20740-6001, phone number (301... GRS? 1227.14 Section 1227.14 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION RECORDS MANAGEMENT GENERAL RECORDS SCHEDULES § 1227.14 How do I obtain copies of the GRS? (a) The...

36 CFR 1227.14 - How do I obtain copies of the GRS?

Code of Federal Regulations, 2011 CFR

2011-07-01

... Administration, Modern Records Programs (NWM), 8601 Adelphi Road, College Park, MD 20740-6001, phone number (301... GRS? 1227.14 Section 1227.14 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION RECORDS MANAGEMENT GENERAL RECORDS SCHEDULES § 1227.14 How do I obtain copies of the GRS? (a) The...

Image analysis of pubic bone for age estimation in a computed tomography sample.

PubMed

López-Alcaraz, Manuel; González, Pedro Manuel Garamendi; Aguilera, Inmaculada Alemán; López, Miguel Botella

2015-03-01

Radiology has demonstrated great utility for age estimation, but most of the studies are based on metrical and morphological methods in order to perform an identification profile. A simple image analysis-based method is presented, aimed to correlate the bony tissue ultrastructure with several variables obtained from the grey-level histogram (GLH) of computed tomography (CT) sagittal sections of the pubic symphysis surface and the pubic body, and relating them with age. The CT sample consisted of 169 hospital Digital Imaging and Communications in Medicine (DICOM) archives of known sex and age. The calculated multiple regression models showed a maximum R (2) of 0.533 for females and 0.726 for males, with a high intra- and inter-observer agreement. The method suggested is considered not only useful for performing an identification profile during virtopsy, but also for application in further studies in order to attach a quantitative correlation for tissue ultrastructure characteristics, without complex and expensive methods beyond image analysis.

Building A Cloud Based Distributed Active Data Archive Center

NASA Technical Reports Server (NTRS)

Ramachandran, Rahul; Baynes, Katie; Murphy, Kevin

2017-01-01

NASA's Earth Science Data System (ESDS) Program facilitates the implementation of NASA's Earth Science strategic plan, which is committed to the full and open sharing of Earth science data obtained from NASA instruments to all users. The Earth Science Data information System (ESDIS) project manages the Earth Observing System Data and Information System (EOSDIS). Data within EOSDIS are held at Distributed Active Archive Centers (DAACs). One of the key responsibilities of the ESDS Program is to continuously evolve the entire data and information system to maximize returns on the collected NASA data.

Chemical Release and Radiation Effects Satellite (CRRES) program archiving and Puerto Rican sounding rocket campaign

NASA Technical Reports Server (NTRS)

Miller, George P.

1992-01-01

The tasks undertaken as part of this contract included the continued coordination and documentation of the CRRES program and the development of an archive that details, in easily accessible form, the experimental results obtained by the CRRES Program. Details of the work undertaken and results achieved are summarized in the following sections. The achievement of this goal is clearly demonstrated in the appendices attached to this report and the success, in both scientific and public relation terms, of the El Coqui rocket campaign.

21 CFR 180.30 - Brominated vegetable oil.

Code of Federal Regulations, 2012 CFR

2012-04-01

... material incorporated by reference may be obtained from the National Academy Press, 2101 Constitution Ave...://www.archives.gov/federal_register/code_of_federal_regulations/ibr_locations.html. (b) The additive is...

77 FR 20638 - Ashish Macwan: Debarment Order

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-05

... Manufacturing Practices; violating Standards of Procedure by failing to properly investigate, log, and archive... inaccurate data and records to obtain FDA approval to market new product lines. In furtherance of the...

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

DeMott, Paul J.; Hill, Thomas C. J.

This campaign augmented measurements obtained via deployment of the Atmospheric Radiation Measurement (ARM) Climate Research Facility’s ARM Mobile Facility (AMF) in the Marine ARM GPCI1 Investigation of Clouds (MAGIC) field campaign. The measurements, comprised of shipboard aerosol collections obtained during the five legs of the summer 2013 cruises, were sent for offline processing to measure ice nucleating particle (INP) number concentrations. The forty-three sample periods each represented, nominally, 24-hour segments during outbound and inbound transits of the Horizon Spirit. The samples were collected at locations between Los Angeles and Hawaii. Eight samples have been analyzed for immersion freezing temperature spectramore » thus far, using funding from other grants. Remaining samples are being frozen until support for further processing is obtained. Future analyses will investigate the inorganic/organic proportions of ice nuclei, in addition to determining the genetic composition of the overall biological community associated with INPs. Resulting correlations will be compared with other archived aerosol quantities, meteorological and ocean data (e.g., temperature, wind speed, sea surface temperature, etc…) and satellite ocean color products. These findings will ultimately aid in parameterizing oceanic (e.g., sea spray) INP emissions in regional and global scale models, when illustrating aerosol connections to cloud phases and properties. Independent future analyses of frozen filter samples, as proposed by collaborating investigators at the time of this report, will include single particle analyses of marine boundary layer aerosol compositions and morphology. The MAGIC-IN data are considered representative of the oligotrophic, low Chlorophyll-a (with the exception of near-shore) ocean regions, which exist along the MAGIC transect. Current analyses suggest that INP numbers in the marine boundary layer over this region are typically low, compared to existing measurements over marine areas and those collected in the laboratory as the result of realistic sea spray particle generation. These findings, along with separate studies, confirm the existence of highly variable emission sources for INP from oceans, (though weaker than land-based emissions at modestly cooled temperatures).« less

NASA Data Archive Evaluation

NASA Technical Reports Server (NTRS)

Holley, Daniel C.; Haight, Kyle G.; Lindstrom, Ted

1997-01-01

The purpose of this study was to expose a range of naive individuals to the NASA Data Archive and to obtain feedback from them, with the goal of learning how useful people with varied backgrounds would find the Archive for research and other purposes. We processed 36 subjects in four experimental categories, designated in this report as C+R+, C+R-, C-R+ and C-R-, for computer experienced researchers, computer experienced non-researchers, non-computer experienced researchers, and non-computer experienced non-researchers, respectively. This report includes an assessment of general patterns of subject responses to the various aspects of the NASA Data Archive. Some of the aspects examined were interface-oriented, addressing such issues as whether the subject was able to locate information, figure out how to perform desired information retrieval tasks, etc. Other aspects were content-related. In doing these assessments, answers given to different questions were sometimes combined. This practice reflects the tendency of the subjects to provide answers expressing their experiences across question boundaries. Patterns of response are cross-examined by subject category in order to bring out deeper understandings of why subjects reacted the way they did to the archive. After the general assessment, there will be a more extensive summary of the replies received from the test subjects.

Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens

PubMed Central

Loudig, Olivier; Wang, Tao; Ye, Kenny; Lin, Juan; Wang, Yihong; Ramnauth, Andrew; Liu, Christina; Stark, Azadeh; Chitale, Dhananjay; Greenlee, Robert; Multerer, Deborah; Honda, Stacey; Daida, Yihe; Spencer Feigelson, Heather; Glass, Andrew; Couch, Fergus J.; Rohan, Thomas; Ben-Dov, Iddo Z.

2017-01-01

Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years. We then evaluated this cDNA library preparation protocol by performing a miRNA expression analysis of archived breast ductal carcinoma in situ (DCIS) specimens, selected for their relation to the risk of subsequent breast cancer development and obtained from six different institutions. Our analyses identified six miRNAs (miR-29a, miR-221, miR-375, miR-184, miR-363, miR-455-5p) differentially expressed between DCIS lesions from women who subsequently developed an invasive breast cancer (cases) and women who did not develop invasive breast cancer within the same time interval (control). Our thorough evaluation and application of this laboratory-based miRNA sequencing analysis indicates that the preparation of small RNA cDNA libraries can reliably be performed on older, archived, clinically-classified specimens. PMID:28335433

Accuracy assessment in the Large Area Crop Inventory Experiment

NASA Technical Reports Server (NTRS)

Houston, A. G.; Pitts, D. E.; Feiveson, A. H.; Badhwar, G.; Ferguson, M.; Hsu, E.; Potter, J.; Chhikara, R.; Rader, M.; Ahlers, C.

1979-01-01

The Accuracy Assessment System (AAS) of the Large Area Crop Inventory Experiment (LACIE) was responsible for determining the accuracy and reliability of LACIE estimates of wheat production, area, and yield, made at regular intervals throughout the crop season, and for investigating the various LACIE error sources, quantifying these errors, and relating them to their causes. Some results of using the AAS during the three years of LACIE are reviewed. As the program culminated, AAS was able not only to meet the goal of obtaining accurate statistical estimates of sampling and classification accuracy, but also the goal of evaluating component labeling errors. Furthermore, the ground-truth data processing matured from collecting data for one crop (small grains) to collecting, quality-checking, and archiving data for all crops in a LACIE small segment.

VizieR Online Data Catalog: Broadband photometry of Neptune from K2 (Rowe+, 2017)

NASA Astrophysics Data System (ADS)

Rowe, J. F.; Gaulme, P.; Lissauer, J. J.; Marley, M. S.; Simon, A. A.; Hammel, H. B.; Silva Aguirre, V.; Barclay, T.; Benomar, O.; Boumier, P.; Caldwell, D. A.; Casewell, S. L.; Chaplin, W. J.; Colon, K. D.; Corsaro, E.; Davies, G. R.; Fortney, J. J.; Garcia, R. A.; Gizis, J. E.; Haas, M. R.; Mosser, B.; Schmider, F.-X.

2017-08-01

The K2 C3 field provided the first opportunity to observe the planet Neptune for up to 80 days with short-cadence (1 minute) sampling (the C3 campaign had an actual duration of 69.2 days, limited by on-board data storage). We were awarded sufficient pixel allocation from Guest Observer Programs GO3060 (PI: Rowe) and GO3057 (PI: Gaulme) to continuously monitor Neptune for 49 days. Short-cadence target pixel files were obtained from Mikulski Archive for Space Telescopes (MAST). The Neptune short-cadence subraster was spread across 161 FITS files. Each file contained 1 column of time-series pixel data. Each target pixel file contains observations starting on 2014 November 15 and finishing on 2015 January 18. (1 data file).

Expression of p27Kip1 and E-cadherin in Head and Neck Squamous Cell Carcinoma of Indonesian Patients.

PubMed

E I, Auerkari; V, Joewono; D R, Handjari; A T, Sarwono; A W, Suhartono; K, Eto; M A, Ikeda

2014-01-01

Cancer cells exhibit characteristic damage of DNA and its expression. The expression of the tumor suppressors E-cadherin and p27(Kip1) has been tested on 57 head and neck squamous cell carcinomas (HNSCC) of Indonesian subjects. HNSCC tumor samples including both primary and (unrelated) nodal cases were obtained from the archives of Indonesian hospitals, in accordance with acknowledged ethical requirements. Only modest correlation was found between reduced expression of E-cadherin or p27(Kip1) with increased malignancy of primary and nodal growth. The observed strong correlation regardless of malignancy between the expressed levels of E-cadherin and p27(Kip1) suggests that also in combination these would not help to better predict the outcome of HNSCC.

VizieR Online Data Catalog: Hubble Legacy Archive ACS grism data (Kuemmel+, 2011)

NASA Astrophysics Data System (ADS)

Kuemmel, M.; Rosati, P.; Fosbury, R.; Haase, J.; Hook, R. N.; Kuntschner, H.; Lombardi, M.; Micol, A.; Nilsson, K. K.; Stoehr, F.; Walsh, J. R.

2011-09-01

A public release of slitless spectra, obtained with ACS/WFC and the G800L grism, is presented. Spectra were automatically extracted in a uniform way from 153 archival fields (or "associations") distributed across the two Galactic caps, covering all observations to 2008. The ACS G800L grism provides a wavelength range of 0.55-1.00um, with a dispersion of 40Å/pixel and a resolution of ~80Å for point-like sources. The ACS G800L images and matched direct images were reduced with an automatic pipeline that handles all steps from archive retrieval, alignment and astrometric calibration, direct image combination, catalogue generation, spectral extraction and collection of metadata. The large number of extracted spectra (73,581) demanded automatic methods for quality control and an automated classification algorithm was trained on the visual inspection of several thousand spectra. The final sample of quality controlled spectra includes 47919 datasets (65% of the total number of extracted spectra) for 32149 unique objects, with a median iAB-band magnitude of 23.7, reaching 26.5 AB for the faintest objects. Each released dataset contains science-ready 1D and 2D spectra, as well as multi-band image cutouts of corresponding sources and a useful preview page summarising the direct and slitless data, astrometric and photometric parameters. This release is part of the continuing effort to enhance the content of the Hubble Legacy Archive (HLA) with highly processed data products which significantly facilitate the scientific exploitation of the Hubble data. In order to characterize the slitless spectra, emission-line flux and equivalent width sensitivity of the ACS data were compared with public ground-based spectra in the GOODS-South field. An example list of emission line galaxies with two or more identified lines is also included, covering the redshift range 0.2-4.6. Almost all redshift determinations outside of the GOODS fields are new. The scope of science projects possible with the ACS slitless release data is large, from studies of Galactic stars to searches for high redshift galaxies. (3 data files).

The Hubble Legacy Archive ACS grism data

NASA Astrophysics Data System (ADS)

Kümmel, M.; Rosati, P.; Fosbury, R.; Haase, J.; Hook, R. N.; Kuntschner, H.; Lombardi, M.; Micol, A.; Nilsson, K. K.; Stoehr, F.; Walsh, J. R.

2011-06-01

A public release of slitless spectra, obtained with ACS/WFC and the G800L grism, is presented. Spectra were automatically extracted in a uniform way from 153 archival fields (or "associations") distributed across the two Galactic caps, covering all observations to 2008. The ACS G800L grism provides a wavelength range of 0.55-1.00 μm, with a dispersion of 40 Å/pixel and a resolution of ~80 Å for point-like sources. The ACS G800L images and matched direct images were reduced with an automatic pipeline that handles all steps from archive retrieval, alignment and astrometric calibration, direct image combination, catalogue generation, spectral extraction and collection of metadata. The large number of extracted spectra (73,581) demanded automatic methods for quality control and an automated classification algorithm was trained on the visual inspection of several thousand spectra. The final sample of quality controlled spectra includes 47 919 datasets (65% of the total number of extracted spectra) for 32 149 unique objects, with a median iAB-band magnitude of 23.7, reaching 26.5 AB for the faintest objects. Each released dataset contains science-ready 1D and 2D spectra, as well as multi-band image cutouts of corresponding sources and a useful preview page summarising the direct and slitless data, astrometric and photometric parameters. This release is part of the continuing effort to enhance the content of the Hubble Legacy Archive (HLA) with highly processed data products which significantly facilitate the scientific exploitation of the Hubble data. In order to characterize the slitless spectra, emission-line flux and equivalent width sensitivity of the ACS data were compared with public ground-based spectra in the GOODS-South field. An example list of emission line galaxies with two or more identified lines is also included, covering the redshift range 0.2 - 4.6. Almost all redshift determinations outside of the GOODS fields are new. The scope of science projects possible with the ACS slitless release data is large, from studies of Galactic stars to searches for high redshift galaxies.

The archiving of meteor research information

NASA Technical Reports Server (NTRS)

Nechitailenko, V. A.

1987-01-01

The results obtained over the past years under GLOBMET are not reviewed but some of the problems the solution of which will guide further development of meteor investigation and international cooperation in this field for the near term are discussed. The main attention is paid to problems which the meteor community itself can solve, or at least expedite. Most of them are more or less connected with the problem of information archiving. Information archiving deals with methods and techniques of solving two closely connected groups of problems. The first is the analysis of data and information as an integral part of meteor research and deals with the solution of certain methodological problems. The second deals with gathering data and information for the designing of models of the atmosphere and/or meteor complex and its utilization. These problem solutions are discussed.

Archive of radar observations of meteors in Tomsk in 1965-1966. (Russian Title: Архив радиолокационных наблюдений метеоров в Томске в 1965-1966 гг.)

NASA Astrophysics Data System (ADS)

Ryabova, G. O.

2010-12-01

The archive of data of radar observations of Geminid, Quadrantid, Daytime Arietid, Perseid, Ursid, Lyrid, Orionid and Leonid meteor showers in Tomsk in 1965-1966 is described. In certain cases registrations of the sporadic background before and after a shower exist. Primary data of echo registrations contain time of a registration, distance, duration and amplitude of an echo, allowing to obtain corresponding distributions essential for calculation of the incident flux density of meteors. Work on the archive digitization has been started.

RECOMMENDATIONS FOR SAMPLING OF TANK 19 IN F TANK FARM

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

Harris, S.; Shine, G.

2009-12-14

Representative sampling is required for characterization of the residual material in Tank 19 prior to operational closure. Tank 19 is a Type IV underground waste storage tank located in the F-Tank Farm. It is a cylindrical-shaped, carbon steel tank with a diameter of 85 feet, a height of 34.25 feet, and a working capacity of 1.3 million gallons. Tank 19 was placed in service in 1961 and initially received a small amount of low heat waste from Tank 17. It then served as an evaporator concentrate (saltcake) receiver from February 1962 to September 1976. Tank 19 also received the spentmore » zeolite ion exchange media from a cesium removal column that once operated in the Northeast riser of the tank to remove cesium from the evaporator overheads. Recent mechanical cleaning of the tank removed all mounds of material. Anticipating a low level of solids in the residual waste, Huff and Thaxton [2009] developed a plan to sample the waste during the final clean-up process while it would still be resident in sufficient quantities to support analytical determinations in four quadrants of the tank. Execution of the plan produced fewer solids than expected to support analytical determinations in all four quadrants. Huff and Thaxton [2009] then restructured the plan to characterize the residual separately in the North and the South regions: two 'hemispheres.' This document provides sampling recommendations to complete the characterization of the residual material on the tank bottom following the guidance in Huff and Thaxton [2009] to split the tank floor into a North and a South hemisphere. The number of samples is determined from a modification of the formula previously published in Edwards [2001] and the sample characterization data for previous sampling of Tank 19 described by Oji [2009]. The uncertainty is quantified by an upper 95% confidence limit (UCL95%) on each analyte's mean concentration in Tank 19. The procedure computes the uncertainty in analyte concentration as a function of the number of samples, and the final number of samples is determined when the reduction in the uncertainty from an additional sample no longer has a practical impact on results. The characterization of the full suite of analytes in the North and South hemispheres is currently supported by a single Mantis rover sample in each hemisphere. A floor scrape sample was obtained from a compact region near the center riser slightly in the South hemisphere and has been analyzed for a shortened list of key analytes. There is not enough additional material from the floor scrape sample material for completing the full suite of constituents. No floor scrape samples have been previously taken from the North hemisphere. The criterion to determine the number of additional samples was based on the practical reduction in the uncertainty when a new sample is added. This was achieved when five additional samples are obtained. In addition, two archived samples will be used if a contingency such as failing to demonstrate the comparability of the Mantis samples to the floor scrape samples occurs. To complete sampling of the Tank 19 residual floor material, four additional samples should be taken from the North hemisphere and four additional samples should be taken from the South hemisphere. One of the samples from each hemisphere will be archived in case of need. Three of the four additional samples from each hemisphere will be analyzed. Once the results are available, differences between the Mantis and three floor scrape sample results will be evaluated. If there are no statistically significant analyte concentration differences between the Mantis and floor scrape samples, those results will be combined and then UCL95%s will be calculated. If the analyte concentration differences between the Mantis and floor scrape samples are statistically significant, the UCL95%s will be calculated without the Mantis sample results. If further reduction in the upper confidence limits is needed and can be achieved by the addition of the archived samples, they will be analyzed and included in the statistical computations. Initially the analyte concentrations in the residual material on the floor of Tank 19 will be determined separately in the North and the South hemispheres. However, if final sampling results show that differences between the North and South samples are consistent within sampling variation, then the final computations can be based on consolidating all sample results from the tank floor. Recommended locations may be subject to physical tank access and sampling constraints for the additional samples. The recommendations have been discussed in Section 4 and are based on partitioning the Tank 19 floor into an inner and an outer ring and six 60{sup o} sectors depicted in Figure 1. The location of the border between the inner and outer rings is based on dividing the residual material into two approximately equal volumes.« less

VizieR Online Data Catalog: Spitzer MIR AGN survey. I. (Lacy+, 2013)

NASA Astrophysics Data System (ADS)

Lacy, M.; Ridgway, S. E.; Gates, E. L.; Nielsen, D. M.; Petric, A. O.; Sajina, A.; Urrutia, T.; Cox Drews, S.; Harrison, C.; Seymour, N.; Storrie-Lombardi, L. J.

2013-10-01

A wide range of optical facilities and instruments were used for spectroscopic follow-up of our AGN candidates. Most of the bright samples were followed up with 3-5m telescopes and longslit spectroscopy (Hale with COSMIC, SOAR with Goodman, and Shane with Kast), whereas the fainter samples were followed up with multifiber and/or 6-8m class telescopes (Blanco with Hydra, MMT with Hectospec, and Gemini-South with GMOS (program GS-2008B-C4)). We also obtained spectra of some of the bright candidates with a successful poor weather (scheduling band 4) program at Gemini-South (program GS-2008B-Q86). Some objects had spectra available in archives from the SDSS, 2dF, (Colless et al. 2001, Cat. VII/250) or 6dF (Jones et al. 2009, Cat. VII/259) surveys and some have redshifts and classifications in the literature, all found using the NASA Extragalactic Database (NED). Table 2 gives details of the spectroscopic observations or literature references as appropriate. For some high-redshift candidates with ambiguous or low signal-to-noise optical spectra, we were able to obtain near-infrared spectra with the IRTF using SpeX (2007 June), Gemini with NIRI (program GN2009B-C-8), and Triplespec (2008 July and 2011 July) on Palomar. (5 data files).

Electronic archival tags provide first glimpse of bathythermal habitat use by free-ranging adult lake sturgeon Acipenser fulvescens

USGS Publications Warehouse

Briggs, Andrew S.; Hondorp, Darryl W.; Quinlan, Henry R.; Boase, James C.; Mohr, Lloyd C.

2016-01-01

Information on lake sturgeon (Acipenser fulvescens) depth and thermal habitat use during non-spawning periods is unavailable due to the difficulty of observing lake sturgeon away from shallow water spawning sites. In 2002 and 2003, lake sturgeon captured in commercial trap nets near Sarnia, Ontario were implanted with archival tags and released back into southern Lake Huron. Five of the 40 tagged individuals were recaptured and were at large for 32, 57, 286, 301, and 880 days. Temperatures and depths recorded by archival tags ranged from 0 to 23.5 ºC and 0.1 to 42.4 m, respectively. For the three lake sturgeon that were at large for over 200 days, temperatures occupied emulated seasonal fluctuations. Two of these fish occupied deeper waters during winter than summer while the other occupied similar depths during non-spawning periods. This study provides important insight into depth and thermal habitat use of lake sturgeon throughout the calendar year along with exploring the feasibility of using archival tags to obtain important physical habitat attributes during non-spawning periods.

Extraction of Dems and Orthoimages from Archive Aerial Imagery to Support Project Planning in Civil Engineering

NASA Astrophysics Data System (ADS)

Cogliati, M.; Tonelli, E.; Battaglia, D.; Scaioni, M.

2017-12-01

Archive aerial photos represent a valuable heritage to provide information about land content and topography in the past years. Today, the availability of low-cost and open-source solutions for photogrammetric processing of close-range and drone images offers the chance to provide outputs such as DEM's and orthoimages in easy way. This paper is aimed at demonstrating somehow and to which level of accuracy digitized archive aerial photos may be used within a such kind of low-cost software (Agisoft Photoscan Professional®) to generate photogrammetric outputs. Different steps of the photogrammetric processing workflow are presented and discussed. The main conclusion is that this procedure may come to provide some final products, which however do not feature the high accuracy and resolution that may be obtained using high-end photogrammetric software packages specifically designed for aerial survey projects. In the last part a case study is presented about the use of four-epoch archive of aerial images to analyze the area where a tunnel has to be excavated.

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…

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

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.

Epidemiological situation of toxocariasis in Iran: meta-analysis and systematic review.

PubMed

Abdi, Jahangir; Darabi, Maryam; Sayehmiri, Kouresh

2012-11-15

Toxocariasis is the clinical terms applied to infection of human with ascarid nematodes in the order Ascaridida, named toxocara canis and toxocara cati. It is transmitted from dog and cat to humans. Accidental ingestion of parasite eggs causes ocular and visceral larva migrans in human. The aim of this study is to study epidemiology of toxocariasis in Iran using meta-analysis and systematic review. Using main key words of toxocariasis including epidemiology, Toxocara spp. Iran, dog and cat in databases such as SID, Google scholar, Pubmed, Magiran and Iranmedex, a number of 50 articles was extracted. A number of 27 articles of them were eligible for meta-analysis. Data extracted from articles and archived in excel software for analysis. Variance of each study obtained using binomial distribution. Heterogeny of studies surveyed using Cochrans Q test. Data analyzed using Random Effect Model test. Overall prevalence of toxocariasis obtained 21.6% in Iran. In total of 27 articles, 6911 samples including 1543 carnivores, (13 articles), 4569 human sera (10 articles) and 799 soil samples (4 articles) has been investigated. Seropositivity for human toxocariasis 15.8% (95%CI, 9.2-22.5), soil contamination for Txocara spp. eggs 21.6% (95%CI,-1.6-44.8) and dogs and cats infections with adult worm 26.8% (95%CI, 18.7-36.8) was obtained. Results of this study show that prevalence of toxocariasis has a growing trend in Iran. It could be decreased using education, culture making and giving information to people.

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.

Radiometric 81Kr dating identifies 120,000-year-old ice at Taylor Glacier, Antarctica

PubMed Central

Buizert, Christo; Baggenstos, Daniel; Jiang, Wei; Purtschert, Roland; Petrenko, Vasilii V.; Lu, Zheng-Tian; Müller, Peter; Kuhl, Tanner; Lee, James; Severinghaus, Jeffrey P.; Brook, Edward J.

2014-01-01

We present successful 81Kr-Kr radiometric dating of ancient polar ice. Krypton was extracted from the air bubbles in four ∼350-kg polar ice samples from Taylor Glacier in the McMurdo Dry Valleys, Antarctica, and dated using Atom Trap Trace Analysis (ATTA). The 81Kr radiometric ages agree with independent age estimates obtained from stratigraphic dating techniques with a mean absolute age offset of 6 ± 2.5 ka. Our experimental methods and sampling strategy are validated by (i) 85Kr and 39Ar analyses that show the samples to be free of modern air contamination and (ii) air content measurements that show the ice did not experience gas loss. We estimate the error in the 81Kr ages due to past geomagnetic variability to be below 3 ka. We show that ice from the previous interglacial period (Marine Isotope Stage 5e, 130–115 ka before present) can be found in abundance near the surface of Taylor Glacier. Our study paves the way for reliable radiometric dating of ancient ice in blue ice areas and margin sites where large samples are available, greatly enhancing their scientific value as archives of old ice and meteorites. At present, ATTA 81Kr analysis requires a 40–80-kg ice sample; as sample requirements continue to decrease, 81Kr dating of ice cores is a future possibility. PMID:24753606

Radiometric 81Kr dating identifies 120,000-year-old ice at Taylor Glacier, Antarctica.

PubMed

Buizert, Christo; Baggenstos, Daniel; Jiang, Wei; Purtschert, Roland; Petrenko, Vasilii V; Lu, Zheng-Tian; Müller, Peter; Kuhl, Tanner; Lee, James; Severinghaus, Jeffrey P; Brook, Edward J

2014-05-13

We present successful (81)Kr-Kr radiometric dating of ancient polar ice. Krypton was extracted from the air bubbles in four ∼350-kg polar ice samples from Taylor Glacier in the McMurdo Dry Valleys, Antarctica, and dated using Atom Trap Trace Analysis (ATTA). The (81)Kr radiometric ages agree with independent age estimates obtained from stratigraphic dating techniques with a mean absolute age offset of 6 ± 2.5 ka. Our experimental methods and sampling strategy are validated by (i) (85)Kr and (39)Ar analyses that show the samples to be free of modern air contamination and (ii) air content measurements that show the ice did not experience gas loss. We estimate the error in the (81)Kr ages due to past geomagnetic variability to be below 3 ka. We show that ice from the previous interglacial period (Marine Isotope Stage 5e, 130-115 ka before present) can be found in abundance near the surface of Taylor Glacier. Our study paves the way for reliable radiometric dating of ancient ice in blue ice areas and margin sites where large samples are available, greatly enhancing their scientific value as archives of old ice and meteorites. At present, ATTA (81)Kr analysis requires a 40-80-kg ice sample; as sample requirements continue to decrease, (81)Kr dating of ice cores is a future possibility.

The bivalve Glycymeris planicostalis as a high-resolution paleoclimate archive for the Rupelian (Early Oligocene) of central Europe

NASA Astrophysics Data System (ADS)

Walliser, E. O.; Schöne, B. R.; Tütken, T.; Zirkel, J.; Grimm, K. I.; Pross, J.

2015-04-01

Current global warming is likely to result in a unipolar glaciated world with unpredictable repercussions on atmospheric and oceanic circulation patterns. These changes are expected to affect seasonal extremes and the year-to-year variability of seasonality. To better constrain the mode and tempo of the anticipated changes, climatologists require ultra-high-resolution proxy data of time intervals in the past, e.g., the Oligocene, during which boundary conditions were similar to those predicted for the near future. In the present paper, we assess whether such information can be obtained from shells of the long-lived bivalve mollusk Glycymeris planicostalis from the late Rupelian of the Mainz Basin, Germany. Our results indicate that the studied shells are pristinely preserved and provide an excellent archive for reconstructing changes of sea surface temperature on seasonal to interannual timescales. Shells of G. planicostalis grew uninterruptedly during winter and summer and therefore recorded the full seasonal temperature amplitude that prevailed in the Mainz Basin ~ 30 Ma. Absolute sea surface temperature data were reconstructed from δ18Oshell values assuming a δ18Owater signature that was extrapolated from coeval sirenian tooth enamel. Reconstructed values range between 12.3 and 22.0 °C and agree well with previous estimates based on planktonic foraminifera and shark teeth. However, temperatures during seasonal extremes vary greatly on interannual timescales. Mathematically re-sampled (i.e., corrected for uneven number of samples per annual increment) winter and summer temperatures averaged over 40 annual increments of three specimens equal 13.6 ± 0.8 and 17.3 ± 1.2 °C, respectively. Such high-resolution paleoclimate information can be highly relevant for numerical climate studies aiming to predict possible future climates in a unipolar glaciated or, ultimately, polar-ice-free world.

36 CFR 1256.92 - What is the purpose of this subpart?

Code of Federal Regulations, 2010 CFR

2010-07-01

... Distribution of United States Information Agency Audiovisual Materials in the National Archives of the United... public to inspect and obtain copies of USIA audiovisual records and other materials in the United States...

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

A Routing Mechanism for Cloud Outsourcing of Medical Imaging Repositories.

PubMed

Godinho, Tiago Marques; Viana-Ferreira, Carlos; Bastião Silva, Luís A; Costa, Carlos

2016-01-01

Web-based technologies have been increasingly used in picture archive and communication systems (PACS), in services related to storage, distribution, and visualization of medical images. Nowadays, many healthcare institutions are outsourcing their repositories to the cloud. However, managing communications between multiple geo-distributed locations is still challenging due to the complexity of dealing with huge volumes of data and bandwidth requirements. Moreover, standard methodologies still do not take full advantage of outsourced archives, namely because their integration with other in-house solutions is troublesome. In order to improve the performance of distributed medical imaging networks, a smart routing mechanism was developed. This includes an innovative cache system based on splitting and dynamic management of digital imaging and communications in medicine objects. The proposed solution was successfully deployed in a regional PACS archive. The results obtained proved that it is better than conventional approaches, as it reduces remote access latency and also the required cache storage space.

Earth Radiation Budget Experiment (ERBE) validation

NASA Technical Reports Server (NTRS)

Barkstrom, Bruce R.; Harrison, Edwin F.; Smith, G. Louis; Green, Richard N.; Kibler, James F.; Cess, Robert D.

1990-01-01

During the past 4 years, data from the Earth Radiation Budget Experiment (ERBE) have been undergoing detailed examination. There is no direct source of groundtruth for the radiation budget. Thus, this validation effort has had to rely heavily upon intercomparisons between different types of measurements. The ERBE SCIENCE Team chose 10 measures of agreement as validation criteria. Late in August 1988, the Team agreed that the data met these conditions. As a result, the final, monthly averaged data products are being archived. These products, their validation, and some results for January 1986 are described. Information is provided on obtaining the data from the archive.

The X-ray spectra of blazars: Analysis of the complete EXOSAT archive

NASA Technical Reports Server (NTRS)

Sambruna, Rita M.; Barr, Paul; Giommi, Paolo; Maraschi, Laura; Tagliaferri, Gianpiero; Treves, Aldo

1994-01-01

We analyzed the 0.1-10 keV spectra of 26 blazars (21 BL Lac objects and 5 highly polarized quasars), on the basis of 93 exposures taken from the EXOSAT archives. Fits were performed first with a single power-law model. Indications are found that better fits can be obtained with models where the slope steepens at higher energies. We therefore considered a broken power law and found that in a large fraction of the spectra the fit is significantly improved. Fits with a power law + oxygen edge at 0.6 keV are also explored.

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.

The Operation and Architecture of the Keck Observatory Archive

NASA Astrophysics Data System (ADS)

Berriman, G. B.; Gelino, C. R.; Laity, A.; Kong, M.; Swain, M.; Holt, J.; Goodrich, R.; Mader, J.; Tran, H. D.

2014-05-01

The Infrared Processing and Analysis Center (IPAC) and the W. M. Keck Observatory (WMKO) are collaborating to build an archive for the twin 10-m Keck Telescopes, located near the summit of Mauna Kea. The Keck Observatory Archive (KOA) takes advantage of IPAC's long experience with managing and archiving large and complex data sets from active missions and serving them to the community; and of the Observatory's knowledge of the operation of its sophisticated instrumentation and the organization of the data products. By the end of 2013, KOA will contain data from all eight active observatory instruments, with an anticipated volume of 28 TB. The data include raw science and observations, quick look products, weather information, and, for some instruments, reduced and calibrated products. The goal of including data from all instruments is the cumulation of a rapid expansion of the archive's holdings, and already data from four new instruments have been added since October 2012. One more active instrument, the integral field spectrograph OSIRIS, is scheduled for ingestion in December 2013. After preparation for ingestion into the archive, the data are transmitted electronically from WMKO to IPAC for curation in the physical archive. This process includes validation of the science and content of the data and verification that data were not corrupted in transmission. The archived data include both newly-acquired observations and all previously acquired observations. The older data extends back to the date of instrument commissioning; for some instruments, such as HIRES, these data can extend as far back as 1994. KOA will continue to ingest all newly obtained observations, at an anticipated volume of 4 TB per year, and plans to ingest data from two decommissioned instruments. Access to these data is governed by a data use policy that guarantees Principal Investigators (PI) exclusive access to their data for at least 18 months, and allows for extensions as granted by institutional Selecting Officials. Approximately one-half of the data in the archive are public. The archive architecture takes advantage of existing software and is designed for sustainability. The data preparation and quality assurance software exploits the software infrastructure at WMKO, and the physical archive at IPAC re-uses the portable component based architecture developed originally for the Infrared Science Archive, with extensions custom to KOA as needed. We will discuss the science services available to end-users. These include web and program query interfaces, interactive tabulation of data and metadata, association of files with science files, and interactive visualization of data products. We will discuss how the growth in the archive holdings has led to to a growth in usage and published science results. Finally, we will discuss the future of KOA, including the provision of data reduction pipelines and interoperability with world-wide archives and data centers, including VO-compliant services.

Suspected myofibrillar myopathy in Arabian horses with a history of exertional rhabdomyolysis.

PubMed

Valberg, S J; McKenzie, E C; Eyrich, L V; Shivers, J; Barnes, N E; Finno, C J

2016-09-01

Although exertional rhabdomyolysis (ER) is common in Arabian horses, there are no dedicated studies describing histopathological characteristics of muscle from Arabian horses with ER. To prospectively identify distinctive histopathological features of muscle from Arabian endurance horses with a history of ER (pro-ER) and to retrospectively determine their prevalence in archived samples from Arabian horses with exertional myopathies (retro-ER). Prospective and retrospective histopathological description. Middle gluteal muscle biopsies obtained from Arabian controls (n = 14), pro-ER (n = 13) as well as archived retro-ER (n = 25) muscle samples previously classified with type 2 polysaccharide storage myopathy (15/25), recurrent exertional rhabdomyolysis (7/25) and no pathology (3/25) were scored for histopathology and immunohistochemical staining of cytoskeletal proteins. Glutaraldehyde-fixed samples (2 pro-ER, one control) were processed for electron microscopy. Pro-ER and retro-ER groups were compared with controls using Mann-Whitney U and Fisher's exact tests. Centrally located myonuclei in mature myofibres were found in significantly more (P<0.05) pro-ER (12/13) and retro-ER (21/25) horses than controls (4/14). Degenerating myofibres were not evident in any biopsies. Retro-ER horses had amylase-resistant polysaccharide (6/25, P<0.05) and higher scores for cytoplasmic glycogen, rimmed vacuoles and rod-like bodies. A few control horses (3/14) and significantly (P<0.05) more pro-ER (12/13) and retro-ER (18/25) horses had disrupted myofibrillar alignment and large desmin and αβ-crystallin positive cytoplasmic aggregates. Prominent Z-disc degeneration and focal myofibrillar disruption with regional accumulation of β-glycogen particles were identified on electron microscopy of the 2 pro-ER samples. In a subset of Arabian horses with intermittent episodes of exertional rhabdomyolysis, ectopic accumulation of cytoskeletal proteins and Z-disc degeneration bear a strong resemblance to a myofibrillar myopathy. While many of these horses were previously diagnosed with type 2 polysaccharide storage myopathy, pools of glycogen forming within disrupted myofibrils appeared to give the false appearance of a glycogen storage disorder. © 2015 EVJ Ltd.

Suspected myofibrillar myopathy in Arabian horses with a history of exertional rhabdomyolysis

PubMed Central

VALBERG, S. J.; McKENZIE, E. C.; EYRICH, L. V.; SHIVERS, J.; BARNES, N. E.; FINNO, C. J.

2016-01-01

Summary Reasons for performing study Although exertional rhabdomyolysis (ER) is common in Arabian horses, there are no dedicated studies describing histopathological characteristics of muscle from Arabian horses with ER. Objectives To prospectively identify distinctive histopathological features of muscle from Arabian endurance horses with a history of ER (pro-ER) and to retrospectively determine their prevalence in archived samples from Arabian horses with exertional myopathies (retro-ER). Study design Prospective and retrospective histopathological description. Methods Middle gluteal muscle biopsies obtained from Arabian controls (n = 14), pro-ER (n = 13) as well as archived retro-ER (n = 25) muscle samples previously classified with type 2 polysaccharide storage myopathy (15/25), recurrent exertional rhabdomyolysis (7/25) and no pathology (3/25) were scored for histopathology and immunohistochemical staining of cytoskeletal proteins. Glutaraldehyde-fixed samples (2 pro-ER, one control) were processed for electron microscopy. Pro-ER and retro-ER groups were compared with controls using Mann–Whitney U and Fisher's exact tests. Results Centrally located myonuclei in mature myofibres were found in significantly more (P<0.05) pro-ER (12/13) and retro-ER (21/25) horses than controls (4/14). Degenerating myofibres were not evident in any biopsies. Retro-ER horses had amylase-resistant polysaccharide (6/25, P<0.05) and higher scores for cytoplasmic glycogen, rimmed vacuoles and rod-like bodies. A few control horses (3/14) and significantly (P<0.05) more pro-ER (12/13) and retro-ER (18/25) horses had disrupted myofibrillar alignment and large desmin and αβ-crystallin positive cytoplasmic aggregates. Prominent Z-disc degeneration and focal myofibrillar disruption with regional accumulation of β-glycogen particles were identified on electron microscopy of the 2 pro-ER samples. Conclusions In a subset of Arabian horses with intermittent episodes of exertional rhabdomyolysis, ectopic accumulation of cytoskeletal proteins and Z-disc degeneration bear a strong resemblance to a myofibrillar myopathy. While many of these horses were previously diagnosed with type 2 polysaccharide storage myopathy, pools of glycogen forming within disrupted myofibrils appeared to give the false appearance of a glycogen storage disorder. PMID:26234161

36 CFR § 1227.14 - How do I obtain copies of the GRS?

Code of Federal Regulations, 2013 CFR

2013-07-01

... Administration, Modern Records Programs (NWM), 8601 Adelphi Road, College Park, MD 20740-6001, phone number (301... GRS? § 1227.14 Section § 1227.14 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION RECORDS MANAGEMENT GENERAL RECORDS SCHEDULES § 1227.14 How do I obtain copies of the GRS? (a) The...

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

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.

Degraded document image enhancement

NASA Astrophysics Data System (ADS)

Agam, G.; Bal, G.; Frieder, G.; Frieder, O.

2007-01-01

Poor quality documents are obtained in various situations such as historical document collections, legal archives, security investigations, and documents found in clandestine locations. Such documents are often scanned for automated analysis, further processing, and archiving. Due to the nature of such documents, degraded document images are often hard to read, have low contrast, and are corrupted by various artifacts. We describe a novel approach for the enhancement of such documents based on probabilistic models which increases the contrast, and thus, readability of such documents under various degradations. The enhancement produced by the proposed approach can be viewed under different viewing conditions if desired. The proposed approach was evaluated qualitatively and compared to standard enhancement techniques on a subset of historical documents obtained from the Yad Vashem Holocaust museum. In addition, quantitative performance was evaluated based on synthetically generated data corrupted under various degradation models. Preliminary results demonstrate the effectiveness of the proposed approach.

Identification of Interesting Objects in Large Spectral Surveys Using Highly Parallelized Machine Learning

NASA Astrophysics Data System (ADS)

Škoda, Petr; Palička, Andrej; Koza, Jakub; Shakurova, Ksenia

2017-06-01

The current archives of LAMOST multi-object spectrograph contain millions of fully reduced spectra, from which the automatic pipelines have produced catalogues of many parameters of individual objects, including their approximate spectral classification. This is, however, mostly based on the global shape of the whole spectrum and on integral properties of spectra in given bandpasses, namely presence and equivalent width of prominent spectral lines, while for identification of some interesting object types (e.g. Be stars or quasars) the detailed shape of only a few lines is crucial. Here the machine learning is bringing a new methodology capable of improving the reliability of classification of such objects even in boundary cases. We present results of Spark-based semi-supervised machine learning of LAMOST spectra attempting to automatically identify the single and double-peak emission of Hα line typical for Be and B[e] stars. The labelled sample was obtained from archive of 2m Perek telescope at Ondřejov observatory. A simple physical model of spectrograph resolution was used in domain adaptation to LAMOST training domain. The resulting list of candidates contains dozens of Be stars (some are likely yet unknown), but also a bunch of interesting objects resembling spectra of quasars and even blazars, as well as many instrumental artefacts. The verification of a nature of interesting candidates benefited considerably from cross-matching and visualisation in the Virtual Observatory environment.

Enhanced Endometriosis Archiving Software (ENEAS): An Application for Storing, Retrieving, Comparing, and Sharing Data of Patients Affected by Endometriosis Integrated in the Daily Practice.

PubMed

Centini, Gabriele; Zannoni, Letizia; Lazzeri, Lucia; Buiarelli, Paolo; Limatola, Gianluca; Petraglia, Felice; Seracchioli, Renato; Zupi, Errico

Endometriosis is a chronic benign disease affecting women of fertile age, associated with pelvic pain and subfertility, often with negative impacts on quality of life. Meetings involving 5 gynecologists skilled in endometriosis management and 2 informatics technology consultants competent in data management and website administration were enlisted to create an endometriosis databank known as ENEAS (Enhanced Endometriosis Archiving Software). This processing system allows users to store, retrieve, compare, and correlate all data collected in conjunction with different Italian endometriosis centers, with the collective objective of obtaining homogeneous data for a large population sample. ENEAS is a web-oriented application that can be based on any open-source database that can be installed locally on a server, allowing collection of data on approximately 700 items, providing standardized and homogeneous data for comparison and analysis. ENEAS is capable of generating a sheet incorporating all data on the management of endometriosis that is both accurate and suitable for each individual patient. ENEAS is an effective and universal web application that encourages providers in the field of endometriosis to use a common language and share data to standardize medical and surgical treatment, with the main benefits being improved patient satisfaction and quality of life. Copyright © 2016 AAGL. Published by Elsevier Inc. All rights reserved.

A System for Information Management in BioMedical Studies—SIMBioMS

PubMed Central

Krestyaninova, Maria; Zarins, Andris; Viksna, Juris; Kurbatova, Natalja; Rucevskis, Peteris; Neogi, Sudeshna Guha; Gostev, Mike; Perheentupa, Teemu; Knuuttila, Juha; Barrett, Amy; Lappalainen, Ilkka; Rung, Johan; Podnieks, Karlis; Sarkans, Ugis; McCarthy, Mark I; Brazma, Alvis

2009-01-01

Summary: SIMBioMS is a web-based open source software system for managing data and information in biomedical studies. It provides a solution for the collection, storage, management and retrieval of information about research subjects and biomedical samples, as well as experimental data obtained using a range of high-throughput technologies, including gene expression, genotyping, proteomics and metabonomics. The system can easily be customized and has proven to be successful in several large-scale multi-site collaborative projects. It is compatible with emerging functional genomics data standards and provides data import and export in accepted standard formats. Protocols for transferring data to durable archives at the European Bioinformatics Institute have been implemented. Availability: The source code, documentation and initialization scripts are available at http://simbioms.org. Contact: support@simbioms.org; mariak@ebi.ac.uk PMID:19633095

VizieR Online Data Catalog: Atlas of HST STIS spectra of Seyfert galaxies (Spinelli+, 2006)

NASA Astrophysics Data System (ADS)

Spinelli, P. F.; Storchi-Bergmann, T.; Brandt, C. H.; Calzetti, D.

2008-05-01

We present a compilation of spectra of 101 Seyfert galaxies obtained with the Hubble Space Telescope (HST) Space Telescope Imaging Spectrograph (STIS), covering the UV and/or optical spectral range. Information on all the available spectra have been collected in a Mastertable, which is a very useful tool for anyone interested in a quick glance at the existent STIS spectra for Seyfert galaxies in the HST archive, and it can be recovered electronically. Nuclear spectra of the galaxies have been extracted in windows of 0.2" for an optimized sampling (as this is the slit width in most cases) and combined in order to improve the signal-to-noise ratio and provide the widest possible wavelength coverage. These combined spectra are also available electronically, at http://www.if.ufrgs.br/~pat/atlas.htm . (3 data files).

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.

Data archive for NO(y) from observations and construction and testing of airborne instrument for simultaneous measurement of NO, NO2, NO(y), and O3

NASA Technical Reports Server (NTRS)

Carroll, Mary Anne; Emmons, Louisa

1995-01-01

The compilation and archiving of NO(x) and NO(y) measurements began in mid-March 1994. Since the submission of the first report, data summaries have been obtained for the TROPOZ 2, STRATOZ 3, OCTA and TOR/Schauinsland campaigns, and the full data sets will become a part of this archive in the near future. Climatologies of NO(x) and NO(y) have been developed from these and previously archived data sets, including the available GTE campaigns (ABLE-2A, B, -3A, B, CITE-2, -3, TRACE-A, PEM WEST-A) and AASE 1 and 2. The data have been grouped by season and altitude (boundary layer and 3 km ranges in the free troposphere). Maps showing median values of midday NO, NO(x) and NO(y) have been produced for each season for the boundary layer and 3 km ranges of the free troposphere. The statistics of the data (median, mean, and standard deviation, central 67% and 90%) have also been determined, and are shown in representative figures included in this report.

Electronic patient record and archive of records in Cardio.net system for telecardiology.

PubMed

Sierdziński, Janusz; Karpiński, Grzegorz

2003-01-01

In modern medicine the well structured patient data set, fast access to it and reporting capability become an important question. With the dynamic development of information technology (IT) such question is solved via building electronic patient record (EPR) archives. We then obtain fast access to patient data, diagnostic and treatment protocols etc. It results in more efficient, better and cheaper treatment. The aim of the work was to design a uniform Electronic Patient Record, implemented in cardio.net system for telecardiology allowing the co-operation among regional hospitals and reference centers. It includes questionnaires for demographic data and questionnaires supporting doctor's work (initial diagnosis, final diagnosis, history and physical, ECG at the discharge, applied treatment, additional tests, drugs, daily and periodical reports). The browser is implemented in EPR archive to facilitate data retrieval. Several tools for creating EPR and EPR archive were used such as: XML, PHP, Java Script and MySQL. The separate question is the security of data on WWW server. The security is ensured via Security Socket Layer (SSL) protocols and other tools. EPR in Cardio.net system is a module enabling the co-work of many physicians and the communication among different medical centers.

The Luminosity Function of Star Clusters in 20 Star-forming Galaxies Based on Hubble Legacy Archive Photometry

NASA Astrophysics Data System (ADS)

Whitmore, Bradley C.; Chandar, Rupali; Bowers, Ariel S.; Larsen, Soeren; Lindsay, Kevin; Ansari, Asna; Evans, Jessica

2014-04-01

Luminosity functions (LFs) have been determined for star cluster populations in 20 nearby (4-30 Mpc), star-forming galaxies based on Advanced Camera for Surveys source lists generated by the Hubble Legacy Archive (HLA). These cluster catalogs provide one of the largest sets of uniform, automatically generated cluster candidates available in the literature at present. Comparisons are made with other recently generated cluster catalogs demonstrating that the HLA-generated catalogs are of similar quality, but in general do not go as deep. A typical cluster LF can be approximated by a power law, dN/dLvpropL α, with an average value for α of -2.37 and rms scatter = 0.18 when using the F814W ("I") band. A comparison of fitting results based on methods that use binned and unbinned data shows good agreement, although there may be a systematic tendency for the unbinned (maximum likelihood) method to give slightly more negative values of α for galaxies with steeper LFs. We find that galaxies with high rates of star formation (or equivalently, with the brightest or largest numbers of clusters) have a slight tendency to have shallower values of α. In particular, the Antennae galaxy (NGC 4038/39), a merging system with a relatively high star formation rate (SFR), has the second flattest LF in the sample. A tentative correlation may also be present between Hubble type and values of α, in the sense that later type galaxies (i.e., Sd and Sm) appear to have flatter LFs. Hence, while there do appear to be some weak correlations, the relative similarity in the values of α for a large number of star-forming galaxies suggests that, to first order, the LFs are fairly universal. We examine the bright end of the LFs and find evidence for a downturn, although it only pertains to about 1% of the clusters. Our uniform database results in a small scatter (≈0.4 to 0.5 mag) in the correlation between the magnitude of the brightest cluster (M brightest) and log of the number of clusters brighter than MI = -9 (log N). We also examine the magnitude of the brightest cluster versus log SFR for a sample including both dwarf galaxies and ULIRGs. This shows that the correlation extends over roughly six orders of magnitude but with scatter that is larger than for our spiral sample, probably because of the high levels of extinction in many of the LIRGs. Based on observations with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26555. Also based on data obtained from the Hubble Legacy Archive, which is a collaboration between the Space Telescope Science Institute (STScI/NASA), the Space Telescope European Coordinating Facility (ST-ECF/ESA), and the Canadian Astronomy Data Centre (CADC/NRC/CSA). Support for Program number 11781 was provided by NASA through a grant from the Space Telescope Science Institute.

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,…

VizieR Online Data Catalog: Brown dwarfs with spectral type later than T6 (Leggett+, 2017)

NASA Astrophysics Data System (ADS)

Leggett, S. K.; Tremblin, P.; Esplin, T. L.; Luhman, K. L.; Morley, C. V.

2018-01-01

We present the new GNIRS and FLAMINGOS-2 spectra and the new NIRI photometry in section 4 (see also table 1). We obtained a 0.95<=λ(um)<=2.5 spectrum using GNIRS at Gemini North on 2016 December 24 and 25 via program GN-2016B-Q-46 for WISEAJ041022.75+150247.9 with R~700. We also obtained near-infrared spectra for WISEJ071322.55-291751.9 and WISEAJ114156.67-332635.5 using FLAMINGOS-2 at Gemini South on 2017 February 3 and 7, via program GS-2017A-FT-2. The JH grism was used giving R~600. We obtained photometry for WISE J085510.83-071442.5 on Gemini North using NIRI at Y and CH4(short) via program GN-2016A-Q-50, and at M' via program GN-2016A-FT-10 between 2015 December and 2016 March. The M' data for a sample of T and Y dwarfs was obtained via program GN-2016B-Q-46 using NIRI on Gemini North. Finally, we obtained H data for the Y1 WISEA J064723.24-623235.4 using FLAMINGOS-2 on Gemini South, which were presented in Leggett+ (2013ApJ...763..130L). We also obtained new photometry from HST/WFC3, ESO VLT HAWK-I and Spitzer/IRAC and WISE archives; see section 5 and tables 2 and 3. (7 data files).

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.

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.

Intrinsic, Narrow N V Absorption Reveals a Clumpy Outflow in z < 0.4 Radio-Loud Quasars

NASA Astrophysics Data System (ADS)

DeMarcy, Bryan; Serra, Viktoriah; Culliton, Chris; Ganguly, Rajib; Runnoe, Jessie; Charlton, Jane; Eracleous, Michael; Misawa, Toru; Narayanan, Anand

2018-01-01

Quasar outflows are often invoked in models for galaxy evolution to inject energy and momentum into the gas in the host galaxy and influence its star formation history. Thus, the study of quasar outflows is essential for understanding galaxy evolution. N V absorption systems within the associated region (|Δv| ≤ 5000 km s-1) of the quasar are thought to be intrinsic since many show evidence for partial covering of the quasar. A recent archival study of quasar spectra taken with COS/G130M or G160M found 39/181 radio-quiet quasars show intrinsic N V absorption, while none of the 31 radio-loud quasars have N V absorption detected (Culliton et al. 2017). Further investigation of these radio-loud quasars showed a clear bias towards compact morphologies as revealed by FIRST 1.4 GHz imaging and comparatively flat radio spectra. This suggests we are viewing more face-on orientations which prevent us from seeing absorption outflows. The cause for such bias within the HST archive is still unknown; however, it could explain the lack of radio-loud intrinsic N V absorption seen by Culliton et al. (2017). Alternatively, the quasar wind structure may be fundamentally different between radio-loud and radio-quiet objects. We used COS/G130M or G160M to obtain rest-frame UV spectra (1195 Å - 1250 Å) of 14 low-redshift SDSS radio-loud quasars which show lobe-dominated FIRST morphologies to distinguish between these possibilities. Intrinsic N V absorption was detected in 6 of our 14 quasars. This suggests the lack of detections in the archival study was a result of an orientation effect/sampling bias rather than to differences in wind structure between radio-loud and radio-quiet quasars. Interestingly, we find significant overlap in radio core fractions between quasars with and without N V detection. Quasars in our sample with N V detection span a range of core fractions from < 0.01 up to 0.89 while those without detected N V range from 0.04 up to 0.93. A laminar outflow with a small opening angle would be difficult to explain given this overlap in radio core fractions. Our observations suggest a clumpy, sporadic outflow is the more likely explanation.

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...

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

Development and Evaluation of a Novel Multicopy-Element-Targeting Triplex PCR for Detection of Mycobacterium avium subsp. paratuberculosis in Feces

PubMed Central

Garrido, Joseba M.; Molina, Elena; Geijo, María V.; Elguezabal, Natalia; Vázquez, Patricia; Juste, Ramón A.

2014-01-01

The enteropathy called paratuberculosis (PTB), which mainly affects ruminants and has a worldwide distribution, is caused by Mycobacterium avium subsp. paratuberculosis. This disease significantly reduces the cost-effectiveness of ruminant farms, and therefore, reliable and rapid detection methods are needed to control the spread of the bacterium in livestock and in the environment. The aim of this study was to identify a specific and sensitive combination of DNA extraction and amplification to detect M. avium subsp. paratuberculosis in feces. Negative bovine fecal samples were inoculated with increasing concentrations of two different bacterial strains (field and reference) to compare the performance of four extraction and five amplification protocols. The best results were obtained using the JohnePrep and MagMax extraction kits combined with an in-house triplex real-time PCR designed to detect IS900, ISMap02 (an insertion sequence of M. avium subsp. paratuberculosis present in 6 copies per genome), and an internal amplification control DNA simultaneously. These combinations detected 10 M. avium subsp. paratuberculosis cells/g of spiked feces. The triplex PCR detected 1 fg of genomic DNA extracted from the reference strain K10. The performance of the robotized version of the MagMax extraction kit combined with the IS900 and ISMap02 PCR was further evaluated using 615 archival fecal samples from the first sampling of nine Friesian cattle herds included in a PTB control program and followed up for at least 4 years. The analysis of the results obtained in this survey demonstrated that the diagnostic method was highly specific and sensitive for the detection of M. avium subsp. paratuberculosis in fecal samples from cattle and a very valuable tool to be used in PTB control programs. PMID:24727272

VizieR Online Data Catalog: Dwarf galaxies surface brightness profiles. II. (Herrmann+, 2016)

NASA Astrophysics Data System (ADS)

Herrmann, K. A.; Hunter, D. A.; Elmegreen, B. G.

2016-07-01

Our galaxy sample (see Table1) is derived from the survey of nearby (>30Mpc) late-type galaxies conducted by Hunter & Elmegreen 2006 (cat. J/ApJS/162/49). The full survey includes 94 dwarf Irregulars (dIms), 26 Blue Compact Dwarfs (BCDs), and 20 Magellanic-type spirals (Sms). The 141 dwarf sample presented in the first paper of the present series (Paper I; Herrmann et al. 2013, Cat. J/AJ/146/104) contains one fewer Sm galaxy and two additional dIm systems than the original survey. A multi-wavelength data set has been assembled for these galaxies. The data include Hα images (129 galaxies with detections) to trace star formation over the past 10Myr (Hunter & Elmegreen 2004, Cat. J/AJ/128/2170) and satellite UV images (61 galaxies observed) obtained with the Galaxy Evolution Explorer (GALEX) to trace star formation over the past ~200Myr. The GALEX data include images from two passbands with effective wavelengths of 1516Å (FUV) and 2267Å (NUV) and resolutions of 4'' and 5.6'', respectively. Three of the galaxies in our sample with NUV data do not have FUV data. To trace older stars we have UBV images, which are sensitive to stars formed over the past 1Gyr for on-going star formation, and images in at least one band of JHK for 40 galaxies in the sample, which integrates the star formation over the galaxy's lifetime. Note that nine dwarfs are missing UB data and three more are missing U-band data. In addition we made use of 3.6μm images (39 galaxies) obtained with the Infrared Array Camera (IRAC) in the Spitzer archives also to probe old stars. (3 data files).

Performance of a HRP-2/pLDH based rapid diagnostic test at the Bangladesh-India-Myanmar border areas for diagnosis of clinical malaria.

PubMed

Elahi, Rubayet; Mohon, Abu Naser; Khan, Wasif A; Haque, Rashidul; Alam, Mohammad Shafiul

2013-10-30

The rapid diagnostic test (RDT) has been adopted in contemporary malaria control and management programmes around the world as it represents a fast and apt alternative for malaria diagnosis in a resource-limited setting. This study assessed the performance of a HRP-2/pLDH based RDT (Parascreen® Pan/Pf) in a laboratory setting utilizing clinical samples obtained from the field. Whole blood samples were obtained from febrile patients referred for malaria diagnosis by clinicians from two different Upazila Health Complexes (UHCs) located near the Bangladesh-India and Bangladesh-Myanmar border where malaria is endemic. RDT was performed on archived samples and sensitivity and specificity evaluated with expert microscopy (EM) and quantitative PCR (qPCR). A total of 327 clinical samples were made available for the study, of which 153 were Plasmodium falciparum-positive and 54 were Plasmodium vivax-positive. In comparison with EM, for P. falciparum malaria, the RDT had sensitivity: 96.0% (95% CI, 91.2-98.3) and specificity: 98.2% (95% CI, 94.6-99.5) and for P. vivax, sensitivity: 90.7% (95% CI, 78.9-96.5) and specificity: 98.9% (95% CI, 96.5-99.7). Comparison with qPCR showed, for P. falciparum malaria, sensitivity: 95.4% (95% CI, 90.5-98.0) and specificity: 98.8% (95% CI, 95.4-99.7) and for P. vivax malaria, sensitivity: 89.0% (95% CI,77.0-95.4) and specificity: 98.8% (95% CI, 96.5-99.7). Sensitivity varied according to different parasitaemia for falciparum and vivax malaria diagnosis. Parascreen® Pan/Pf Rapid test for malaria showed acceptable sensitivity and specificity in border belt endemic areas of Bangladesh when compared with EM and qPCR.

MOJAVE. XV. VLBA 15 GHz Total Intensity and Polarization Maps of 437 Parsec-scale AGN Jets from 1996 to 2017

NASA Astrophysics Data System (ADS)

Lister, M. L.; Aller, M. F.; Aller, H. D.; Hodge, M. A.; Homan, D. C.; Kovalev, Y. Y.; Pushkarev, A. B.; Savolainen, T.

2018-01-01

We present 5321 mas-resolution total intensity and linear polarization maps of 437 active galactic nuclei (AGNs) obtained with the VLBA at 15 GHz as part of the MOJAVE survey, and also from the NRAO data archive. The former is a long-term program to study the structure and evolution of powerful parsec-scale outflows associated with AGNs. The targeted AGNs are drawn from several flux-limited radio and γ-ray samples, and all have correlated VLBA flux densities greater than ∼50 mJy at 15 GHz. Approximately 80% of these AGNs are associated with γ-ray sources detected by the Fermi LAT instrument. The vast majority were observed with the VLBA on 5–15 occasions between 1996 January 19 and 2016 December 26, at intervals ranging from a month to several years, with the most typical sampling interval being six months. A detailed analysis of the linear and circular polarization evolutions of these AGN jets is presented in the other papers in this series.

Geodetic Seamless Archive Centers Modernization - Information Technology for Exploiting the Data Explosion

NASA Astrophysics Data System (ADS)

Boler, F. M.; Blewitt, G.; Kreemer, C. W.; Bock, Y.; Noll, C. E.; McWhirter, J.; Jamason, P.; Squibb, M. B.

2010-12-01

Space geodetic science and other disciplines using geodetic products have benefited immensely from open sharing of data and metadata from global and regional archives Ten years ago Scripps Orbit and Permanent Array Center (SOPAC), the NASA Crustal Dynamics Data Information System (CDDIS), UNAVCO and other archives collaborated to create the GPS Seamless Archive Centers (GSAC) in an effort to further enable research with the expanding collections of GPS data then becoming available. The GSAC partners share metadata to facilitate data discovery and mining across participating archives and distribution of data to users. This effort was pioneering, but was built on technology that has now been rendered obsolete. As the number of geodetic observing technologies has expanded, the variety of data and data products has grown dramatically, exposing limitations in data product sharing. Through a NASA ROSES project, the three archives (CDDIS, SOPAC and UNAVCO) have been funded to expand the original GSAC capability for multiple geodetic observation types and to simultaneously modernize the underlying technology by implementing web services. The University of Nevada, Reno (UNR) will test the web services implementation by incorporating them into their daily GNSS data processing scheme. The effort will include new methods for quality control of current and legacy data that will be a product of the analysis/testing phase performed by UNR. The quality analysis by UNR will include a report of the stability of the stations coordinates over time that will enable data users to select sites suitable for their application, for example identifying stations with large seasonal effects. This effort will contribute to enhanced ability for very large networks to obtain complete data sets for processing.

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

PubMed

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

2016-01-01

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

Forensic Tools to Track and Connect Physical Samples to Related Data

NASA Astrophysics Data System (ADS)

Molineux, A.; Thompson, A. C.; Baumgardner, R. W.

2016-12-01

Identifiers, such as local sample numbers, are critical to successfully connecting physical samples and related data. However, identifiers must be globally unique. The International Geo Sample Number (IGSN) generated when registering the sample in the System for Earth Sample Registration (SESAR) provides a globally unique alphanumeric code associated with basic metadata, related samples and their current physical storage location. When registered samples are published, users can link the figured samples to the basic metadata held at SESAR. The use cases we discuss include plant specimens from a Permian core, Holocene corals and derived powders, and thin sections with SEM stubs. Much of this material is now published. The plant taxonomic study from the core is a digital pdf and samples can be directly linked from the captions to the SESAR record. The study of stable isotopes from the corals is not yet digitally available, but individual samples are accessible. Full data and media records for both studies are located in our database where higher quality images, field notes, and section diagrams may exist. Georeferences permit mapping in current and deep time plate configurations. Several aspects emerged during this study. The first, ensure adequate and consistent details are registered with SESAR. Second, educate and encourage the researcher to obtain IGSNs. Third, publish the archive numbers, assigned prior to publication, alongside the IGSN. This provides access to further data through an Integrated Publishing Toolkit (IPT)/aggregators/or online repository databases, thus placing the initial sample in a much richer context for future studies. Fourth, encourage software developers to customize community software to extract data from a database and use it to register samples in bulk. This would improve workflow and provide a path for registration of large legacy collections.

Handbook of sensor technical characteristics

NASA Astrophysics Data System (ADS)

Tanner, S.

1982-07-01

Space and terrestrial applications remote sensor systems are described. Each sensor is presented separately. Information is included on its objectives, description, technical characteristics, data products obtained, data archives location, period of operation, and measurement and potential derived parameters. Each sensor is cross indexed.

Handbook of sensor technical characteristics

NASA Technical Reports Server (NTRS)

Tanner, S.

1982-01-01

Space and terrestrial applications remote sensor systems are described. Each sensor is presented separately. Information is included on its objectives, description, technical characteristics, data products obtained, data archives location, period of operation, and measurement and potential derived parameters. Each sensor is cross indexed.

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.

Comparison of Air Impaction and Electrostatic Dust Collector Sampling Methods to Assess Airborne Fungal Contamination in Public Buildings.

PubMed

Normand, Anne-Cécile; Ranque, Stéphane; Cassagne, Carole; Gaudart, Jean; Sallah, Kankoé; Charpin, Denis-André; Piarroux, Renaud

2016-03-01

Many ailments can be linked to exposure to indoor airborne fungus. However, obtaining a precise measurement of airborne fungal levels is complicated partly due to indoor air fluctuations and non-standardized techniques. Electrostatic dust collector (EDC) sampling devices have been used to measure a wide range of airborne analytes, including endotoxins, allergens, β-glucans, and microbial DNA in various indoor environments. In contrast, viable mold contamination has only been assessed in highly contaminated environments such as farms and archive buildings. This study aimed to assess the use of EDCs, compared with repeated air-impactor measurements, to assess airborne viable fungal flora in moderately contaminated indoor environments. Indoor airborne fungal flora was cultured from EDCs and daily air-impaction samples collected in an office building and a daycare center. The quantitative fungal measurements obtained using a single EDC significantly correlated with the cumulative measurement of nine daily air impactions. Both methods enabled the assessment of fungal exposure, although a few differences were observed between the detected fungal species and the relative quantity of each species. EDCs were also used over a 32-month period to monitor indoor airborne fungal flora in a hospital office building, which enabled us to assess the impact of outdoor events (e.g. ground excavations) on the fungal flora levels on the indoor environment. In conclusion, EDC-based measurements provided a relatively accurate profile of the viable airborne flora present during a sampling period. In particular, EDCs provided a more representative assessment of fungal levels compared with single air-impactor sampling. The EDC technique is also simpler than performing repetitive air-impaction measures over the course of several consecutive days. EDC is a versatile tool for collecting airborne samples and was efficient for measuring mold levels in indoor environments. © The Author 2015. Published by Oxford University Press on behalf of the British Occupational Hygiene Society.

Reanalysis of historical U.S. Geological Survey sediment samples for geochemical data from the western part of the Wrangellia terrane, Anchorage, Gulkana, Healy, Mt. Hayes, Nabesna, and Talkeetna Mountains quadrangles, Alaska

USGS Publications Warehouse

Werdon, Melanie B.; Azain, Jaime S.; Granitto, Matthew

2014-01-01

The State of Alaska’s Strategic and Critical Minerals (SCM) Assessment project, a State-funded Capital Improvement Project (CIP), is designed to evaluate Alaska’s statewide potential for SCM resources. The SCM Assessment is being implemented by the Alaska Division of Geological & Geophysical Surveys (DGGS), and involves obtaining new airborne-geophysical, geological, and geochemical data. For the geochemical part of the SCM Assessment, thousands of historical geochemical samples from DGGS, U.S. Geological Survey (USGS), and U.S. Bureau of Mines archives are being reanalyzed by DGGS using modern, quantitative, geochemical-analytical methods. The objective is to update the statewide geochemical database to more clearly identify areas in Alaska with SCM potential. The USGS is also undertaking SCM-related geologic studies in Alaska through the federally funded Alaska Critical Minerals cooperative project. DGGS and USGS share the goal of evaluating Alaska’s strategic and critical minerals potential and together created a Letter of Agreement (signed December 2012) and a supplementary Technical Assistance Agreement (#14CMTAA143458) to facilitate the two agencies’ cooperative work. Under these agreements, DGGS contracted the USGS in Denver to reanalyze historical USGS sediment samples from Alaska. For this report, DGGS funded reanalysis of 1,682 historical USGS sediment samples from the statewide Alaska Geochemical Database Version 2.0 (AGDB2; Granitto and others, 2013). Samples were chosen from an area covering the western half of the Wrangellia Terrane in the Anchorage, Gulkana, Healy, Mt. Hayes, Nabesna, and Talkeetna Mountains quadrangles of south-central Alaska (fig. 1). USGS was responsible for sample retrieval from the Denver warehouse through the final quality assurance/quality control (QA/QC) of the geochemical analyses obtained through the USGS contract lab. The new geochemical data are published in this report as a coauthored DGGS report, and will be incorporated into the statewide geochemical databases of both agencies.

Exposing exposure: automated anatomy-specific CT radiation exposure extraction for quality assurance and radiation monitoring.

PubMed

Sodickson, Aaron; Warden, Graham I; Farkas, Cameron E; Ikuta, Ichiro; Prevedello, Luciano M; Andriole, Katherine P; Khorasani, Ramin

2012-08-01

To develop and validate an informatics toolkit that extracts anatomy-specific computed tomography (CT) radiation exposure metrics (volume CT dose index and dose-length product) from existing digital image archives through optical character recognition of CT dose report screen captures (dose screens) combined with Digital Imaging and Communications in Medicine attributes. This institutional review board-approved HIPAA-compliant study was performed in a large urban health care delivery network. Data were drawn from a random sample of CT encounters that occurred between 2000 and 2010; images from these encounters were contained within the enterprise image archive, which encompassed images obtained at an adult academic tertiary referral hospital and its affiliated sites, including a cancer center, a community hospital, and outpatient imaging centers, as well as images imported from other facilities. Software was validated by using 150 randomly selected encounters for each major CT scanner manufacturer, with outcome measures of dose screen retrieval rate (proportion of correctly located dose screens) and anatomic assignment precision (proportion of extracted exposure data with correctly assigned anatomic region, such as head, chest, or abdomen and pelvis). The 95% binomial confidence intervals (CIs) were calculated for discrete proportions, and CIs were derived from the standard error of the mean for continuous variables. After validation, the informatics toolkit was used to populate an exposure repository from a cohort of 54 549 CT encounters; of which 29 948 had available dose screens. Validation yielded a dose screen retrieval rate of 99% (597 of 605 CT encounters; 95% CI: 98%, 100%) and an anatomic assignment precision of 94% (summed DLP fraction correct 563 in 600 CT encounters; 95% CI: 92%, 96%). Patient safety applications of the resulting data repository include benchmarking between institutions, CT protocol quality control and optimization, and cumulative patient- and anatomy-specific radiation exposure monitoring. Large-scale anatomy-specific radiation exposure data repositories can be created with high fidelity from existing digital image archives by using open-source informatics tools.

Enriching Great Britain's National Landslide Database by searching newspaper archives

NASA Astrophysics Data System (ADS)

Taylor, Faith E.; Malamud, Bruce D.; Freeborough, Katy; Demeritt, David

2015-11-01

Our understanding of where landslide hazard and impact will be greatest is largely based on our knowledge of past events. Here, we present a method to supplement existing records of landslides in Great Britain by searching an electronic archive of regional newspapers. In Great Britain, the British Geological Survey (BGS) is responsible for updating and maintaining records of landslide events and their impacts in the National Landslide Database (NLD). The NLD contains records of more than 16,500 landslide events in Great Britain. Data sources for the NLD include field surveys, academic articles, grey literature, news, public reports and, since 2012, social media. We aim to supplement the richness of the NLD by (i) identifying additional landslide events, (ii) acting as an additional source of confirmation of events existing in the NLD and (iii) adding more detail to existing database entries. This is done by systematically searching the Nexis UK digital archive of 568 regional newspapers published in the UK. In this paper, we construct a robust Boolean search criterion by experimenting with landslide terminology for four training periods. We then apply this search to all articles published in 2006 and 2012. This resulted in the addition of 111 records of landslide events to the NLD over the 2 years investigated (2006 and 2012). We also find that we were able to obtain information about landslide impact for 60-90% of landslide events identified from newspaper articles. Spatial and temporal patterns of additional landslides identified from newspaper articles are broadly in line with those existing in the NLD, confirming that the NLD is a representative sample of landsliding in Great Britain. This method could now be applied to more time periods and/or other hazards to add richness to databases and thus improve our ability to forecast future events based on records of past events.

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.

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)

Use of Body-Mounted Cameras to Enhance Data Collection: An Evaluation of Two Arthropod Sampling Techniques.

PubMed

Hagler, James R; Thompson, Alison L; Stefanek, Melissa A; Machtley, Scott A

2018-03-01

A study was conducted that compared the effectiveness of a sweepnet versus a vacuum suction device for collecting arthropods in cotton. The study differs from previous research in that body-mounted action cameras (B-MACs) were used to record the activity of the person conducting the arthropod collections. The videos produced by the B-MACs were then analyzed with behavioral event recording software to quantify various aspects of the sampling process. The sampler's speed and the number of sampling sweeps or vacuum suctions taken over a fixed distance (12.2 m) of cotton were two of the more significant sampling characteristics quantified for each method. The arthropod counts obtained, combined with the analyses of the videos, enabled us to estimate arthropod sampling efficiency for each technique based on fixed distance, time, and sample unit measurements. Data revealed that the vacuuming was the most precise method for collecting arthropods in the relatively small cotton research plots. However, data also indicates that the sweepnet method would be more efficient for collecting most of the cotton-dwelling arthropod taxa, especially if the sampler could continuously sweep for at least 1 min or ≥80 m (e.g., in larger research plots). The B-MACs are inexpensive and non-cumbersome, the video images generated are outstanding, and they can be archived to provide permanent documentation of a research project. The methods described here could be useful for other types of field-based research to enhance data collection efficiency.

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

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.

Using facebook to recruit young adult veterans: online mental health research.

PubMed

Pedersen, Eric R; Helmuth, Eric D; Marshall, Grant N; Schell, Terry L; PunKay, Marc; Kurz, Jeremy

2015-06-01

Veteran research has primarily been conducted with clinical samples and those already involved in health care systems, but much is to be learned about veterans in the community. Facebook is a novel yet largely unexplored avenue for recruiting veteran participants for epidemiological and clinical studies. In this study, we utilized Facebook to recruit a sample of young adult veterans for the first phase of an online alcohol intervention study. We describe the successful Facebook recruitment process, including data collection from over 1000 veteran participants in approximately 3 weeks, procedures to verify participation eligibility, and comparison of our sample with nationally available norms. Participants were young adult veterans aged 18-34 recruited through Facebook as part of a large study to document normative drinking behavior among a large community sample of veterans. Facebook ads were targeted toward young veterans to collect information on demographics and military characteristics, health behaviors, mental health, and health care utilization. We obtained a sample of 1023 verified veteran participants over a period of 24 days for the advertising price of approximately US $7.05 per verified veteran participant. Our recruitment strategy yielded a sample similar to the US population of young adult veterans in most demographic areas except for race/ethnicity and previous branch of service, which when we weighted the sample on race/ethnicity and branch a sample better matched with the population data was obtained. The Facebook sample recruited veterans who were engaged in a variety of risky health behaviors such as binge drinking and marijuana use. One fourth of veterans had never since discharge been to an appointment for physical health care and about half had attended an appointment for service compensation review. Only half had attended any appointment for a mental health concern at any clinic or hospital. Despite more than half screening positive for current probable mental health disorders such as post-traumatic stress disorder, depression, anxiety, only about 1 in 3 received mental health care in the past year and only 1 in 50 received such care within the past month. This work expands on the work of other studies that have examined clinical samples of veterans only and suggests Facebook can be an adequate method of obtaining samples of veterans in need of care. Clinicaltrials.gov NCT02187887; http://clinicaltrials.gov/ct2/show/NCT02187887 (Archived by WebCite at http://www.webcitation.org/6YiUKRsXY).

Using Facebook to Recruit Young Adult Veterans: Online Mental Health Research

PubMed Central

2015-01-01

Background Veteran research has primarily been conducted with clinical samples and those already involved in health care systems, but much is to be learned about veterans in the community. Facebook is a novel yet largely unexplored avenue for recruiting veteran participants for epidemiological and clinical studies. Objective In this study, we utilized Facebook to recruit a sample of young adult veterans for the first phase of an online alcohol intervention study. We describe the successful Facebook recruitment process, including data collection from over 1000 veteran participants in approximately 3 weeks, procedures to verify participation eligibility, and comparison of our sample with nationally available norms. Methods Participants were young adult veterans aged 18-34 recruited through Facebook as part of a large study to document normative drinking behavior among a large community sample of veterans. Facebook ads were targeted toward young veterans to collect information on demographics and military characteristics, health behaviors, mental health, and health care utilization. Results We obtained a sample of 1023 verified veteran participants over a period of 24 days for the advertising price of approximately US $7.05 per verified veteran participant. Our recruitment strategy yielded a sample similar to the US population of young adult veterans in most demographic areas except for race/ethnicity and previous branch of service, which when we weighted the sample on race/ethnicity and branch a sample better matched with the population data was obtained. The Facebook sample recruited veterans who were engaged in a variety of risky health behaviors such as binge drinking and marijuana use. One fourth of veterans had never since discharge been to an appointment for physical health care and about half had attended an appointment for service compensation review. Only half had attended any appointment for a mental health concern at any clinic or hospital. Despite more than half screening positive for current probable mental health disorders such as post-traumatic stress disorder, depression, anxiety, only about 1 in 3 received mental health care in the past year and only 1 in 50 received such care within the past month. Conclusions This work expands on the work of other studies that have examined clinical samples of veterans only and suggests Facebook can be an adequate method of obtaining samples of veterans in need of care. Trial Registration Clinicaltrials.gov NCT02187887; http://clinicaltrials.gov/ct2/show/NCT02187887 (Archived by WebCite at http://www.webcitation.org/6YiUKRsXY). PMID:26033209

The factor structure of the Alcohol Use Disorders Identification Test (AUDIT).

PubMed

Doyle, Suzanne R; Donovan, Dennis M; Kivlahan, Daniel R

2007-05-01

Past research assessing the factor structure of the Alcohol Use Disorders Identification Test (AUDIT) with various exploratory and confirmatory factor analytic techniques has identified one-, two-, and three-factor solutions. Because different factor analytic procedures may result in dissimilar findings, we examined the factor structure of the AUDIT using the same factor analytic technique on two new large clinical samples and on archival data from six samples studied in previous reports. Responses to the AUDIT were obtained from participants who met Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV), criteria for alcohol dependence in two large randomized clinical trials: the COMBINE (Combining Medications and Behavioral Interventions) Study (N = 1,337; 69% men) and Project MATCH (Matching Alcoholism Treatments to Client Heterogeneity; N = 1,711; 76% men). Supplementary analyses involved six correlation matrices of AUDIT data obtained from five previously published articles. Confirmatory factor analyses based on one-, two-, and three-factor models were conducted on the eight correlation matrices to assess the factor structure of the AUDIT. Across samples, analyses supported a correlated, two-factor solution representing alcohol consumption and alcohol-related consequences. The three-factor solution fit the data equally well, but two factors (alcohol dependence and harmful alcohol use) were highly correlated. The one-factor solution did not provide a good fit to the data. These findings support a two-factor solution for the AUDIT (alcohol consumption and alcohol-related consequences). The results contradict the original three-factor design of the AUDIT and the prevalent use of the AUDIT as a one-factor screening instrument with a single cutoff score.

Optimal molecular profiling of tissue and tissue components: defining the best processing and microdissection methods for biomedical applications.

PubMed

Bova, G Steven; Eltoum, Isam A; Kiernan, John A; Siegal, Gene P; Frost, Andra R; Best, Carolyn J M; Gillespie, John W; Emmert-Buck, Michael R

2005-01-01

Isolation of well-preserved pure cell populations is a prerequisite for sound studies of the molecular basis of pancreatic malignancy and other biological phenomena. This chapter reviews current methods for obtaining anatomically specific signals from molecules isolated from tissues, a basic requirement for productive linking of phenotype and genotype. The quality of samples isolated from tissue and used for molecular analysis is often glossed-over or omitted from publications, making interpretation and replication of data difficult or impossible. Fortunately, recently developed techniques allow life scientists to better document and control the quality of samples used for a given assay, creating a foundation for improvement in this area. Tissue processing for molecular studies usually involves some or all of the following steps: tissue collection, gross dissection/identification, fixation, processing/embedding, storage/archiving, sectioning, staining, microdissection/annotation, and pure analyte labeling/identification. High-quality tissue microdissection does not necessarily mean high-quality samples to analyze. The quality of biomaterials obtained for analysis is highly dependent on steps upstream and downstream from tissue microdissection. We provide protocols for each of these steps, and encourage you to improve upon these. It is worth the effort of every laboratory to optimize and document its technique at each stage of the process, and we provide a starting point for those willing to spend the time to optimize. In our view, poor documentation of tissue and cell type of origin and the use of nonoptimized protocols is a source of inefficiency in current life science research. Even incremental improvement in this area will increase productivity significantly.

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.

Clinical Validation and Implementation of a Targeted Next-Generation Sequencing Assay to Detect Somatic Variants in Non-Small Cell Lung, Melanoma, and Gastrointestinal Malignancies

PubMed Central

Fisher, Kevin E.; Zhang, Linsheng; Wang, Jason; Smith, Geoffrey H.; Newman, Scott; Schneider, Thomas M.; Pillai, Rathi N.; Kudchadkar, Ragini R.; Owonikoko, Taofeek K.; Ramalingam, Suresh S.; Lawson, David H.; Delman, Keith A.; El-Rayes, Bassel F.; Wilson, Malania M.; Sullivan, H. Clifford; Morrison, Annie S.; Balci, Serdar; Adsay, N. Volkan; Gal, Anthony A.; Sica, Gabriel L.; Saxe, Debra F.; Mann, Karen P.; Hill, Charles E.; Khuri, Fadlo R.; Rossi, Michael R.

2017-01-01

We tested and clinically validated a targeted next-generation sequencing (NGS) mutation panel using 80 formalin-fixed, paraffin-embedded (FFPE) tumor samples. Forty non-small cell lung carcinoma (NSCLC), 30 melanoma, and 30 gastrointestinal (12 colonic, 10 gastric, and 8 pancreatic adenocarcinoma) FFPE samples were selected from laboratory archives. After appropriate specimen and nucleic acid quality control, 80 NGS libraries were prepared using the Illumina TruSight tumor (TST) kit and sequenced on the Illumina MiSeq. Sequence alignment, variant calling, and sequencing quality control were performed using vendor software and laboratory-developed analysis workflows. TST generated ≥500× coverage for 98.4% of the 13,952 targeted bases. Reproducible and accurate variant calling was achieved at ≥5% variant allele frequency with 8 to 12 multiplexed samples per MiSeq flow cell. TST detected 112 variants overall, and confirmed all known single-nucleotide variants (n = 27), deletions (n = 5), insertions (n = 3), and multinucleotide variants (n = 3). TST detected at least one variant in 85.0% (68/80), and two or more variants in 36.2% (29/80), of samples. TP53 was the most frequently mutated gene in NSCLC (13 variants; 13/32 samples), gastrointestinal malignancies (15 variants; 13/25 samples), and overall (30 variants; 28/80 samples). BRAF mutations were most common in melanoma (nine variants; 9/23 samples). Clinically relevant NGS data can be obtained from routine clinical FFPE solid tumor specimens using TST, benchtop instruments, and vendor-supplied bioinformatics pipelines. PMID:26801070

Investigation of the Effects of Solar and Geomagnetic Changes on the Total Electron Content: Mid-Latitude Region

NASA Astrophysics Data System (ADS)

Ulukavak, Mustafa; Yalcinkaya, Mualla

2016-04-01

The Global Positioning System (GPS) is used as an important tool for ionosphere monitoring and obtaining the Total Electron Content (TEC). GPS satellites, positioned in the Earth's orbit, are used as sensors to investigate the space weather conditions. In this study, solar and geomagnetic activity variations were investigated between the dates 1 March-30 June 2015 for the mid-latitude region. GPS-TEC variations were calculated for each selected International GNSS Service (IGS) station in Europe. GNSS data was obtained from Crustal Dynamics Data and Information System (CDDIS) archive. Solar and geomagnetic activity indices (Kp, F10.7 ve Dst) were obtained from the Oceanic and Atmospheric Administration (NOAA), the Canadian Space Weather Forecast Centre (CSWFC) and Data Analysis Center for geomagnetism and Space Magnetism Graduate School of Science, Kyoto University (WDC) archives. GPS-TEC variations were determined for the quiet periods of the solar and geomagnetic activities. GPS-TEC changes were then compared with respect to the quiet periods of the solar and geomagnetic activities. Global Ionosphere Maps (GIM) IONEX files, obtained from the IGS analysis center, was used to check the robustness of the GPS-TEC variations. The investigations revealed that it is possible to use the GPS-TEC data for monitoring the ionospheric disturbances.

36 CFR 1208.160 - Communications.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 36 Parks, Forests, and Public Property 3 2011-07-01 2011-07-01 false Communications. 1208.160 Section 1208.160 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION GENERAL... ensure that interested persons, including persons with impaired vision or hearing, can obtain information...

Method and system for the diagnosis of disease using retinal image content and an archive of diagnosed human patient data

DOEpatents

Tobin, Kenneth W; Karnowski, Thomas P; Chaum, Edward

2013-08-06

A method for diagnosing diseases having retinal manifestations including retinal pathologies includes the steps of providing a CBIR system including an archive of stored digital retinal photography images and diagnosed patient data corresponding to the retinal photography images, the stored images each indexed in a CBIR database using a plurality of feature vectors, the feature vectors corresponding to distinct descriptive characteristics of the stored images. A query image of the retina of a patient is obtained. Using image processing, regions or structures in the query image are identified. The regions or structures are then described using the plurality of feature vectors. At least one relevant stored image from the archive based on similarity to the regions or structures is retrieved, and an eye disease or a disease having retinal manifestations in the patient is diagnosed based on the diagnosed patient data associated with the relevant stored image(s).

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.

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.

The Digital Sample: Metadata, Unique Identification, and Links to Data and Publications

NASA Astrophysics Data System (ADS)

Lehnert, K. A.; Vinayagamoorthy, S.; Djapic, B.; Klump, J.

2006-12-01

A significant part of digital data in the Geosciences refers to physical samples of Earth materials, from igneous rocks to sediment cores to water or gas samples. The application and long-term utility of these sample-based data in research is critically dependent on (a) the availability of information (metadata) about the samples such as geographical location and time of sampling, or sampling method, (b) links between the different data types available for individual samples that are dispersed in the literature and in digital data repositories, and (c) access to the samples themselves. Major problems for achieving this include incomplete documentation of samples in publications, use of ambiguous sample names, and the lack of a central catalog that allows to find a sample's archiving location. The International Geo Sample Number IGSN, managed by the System for Earth Sample Registration SESAR, provides solutions for these problems. The IGSN is a unique persistent identifier for samples and other GeoObjects that can be obtained by submitting sample metadata to SESAR (www.geosamples.org). If data in a publication is referenced to an IGSN (rather than an ambiguous sample name), sample metadata can readily be extracted from the SESAR database, which evolves into a Global Sample Catalog that also allows to locate the owner or curator of the sample. Use of the IGSN in digital data systems allows building linkages between distributed data. SESAR is contributing to the development of sample metadata standards. SESAR will integrate the IGSN in persistent, resolvable identifiers based on the handle.net service to advance direct linkages between the digital representation of samples in SESAR (sample profiles) and their related data in the literature and in web-accessible digital data repositories. Technologies outlined by Klump et al. (this session) such as the automatic creation of ontologies by text mining applications will be explored for harvesting identifiers of publications and datasets that contain information about a specific sample in order to establish comprehensive data profiles for samples.

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.

PULSAR OBSERVATIONS USING THE FIRST STATION OF THE LONG WAVELENGTH ARRAY AND THE LWA PULSAR DATA ARCHIVE

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

Stovall, K.; Dowell, J.; Eftekhari, T.

2015-08-01

We present initial pulsar results from the first station of the Long Wavelength Array (LWA1) obtained during the commissioning period of LWA1 and in early science results. We present detections of periodic emission from 44 previously known pulsars, including 3 millisecond pulsars. The effects of the interstellar medium (ISM) on pulsar emission are significantly enhanced at the low frequencies of the LWA1 band (10–88 MHz), making LWA1 a very sensitive instrument for characterizing changes in the dispersion measure (DM) and other effects from the ISM. Pulsars also often have significant evolution in their pulse profile at low frequency and amore » break in their spectral index. We report DM measurements for 44 pulsars, mean flux density measurements for 36 pulsars, and multi-frequency component spacing and widths for 15 pulsars with more than one profile component. For 27 pulsars, we report spectral index measurements within our frequency range. We also introduce the LWA1 Pulsar Data Archive, which stores reduced data products from LWA1 pulsar observations. Reduced data products for the observations presented here can be found in the archive. Reduced data products from future LWA1 pulsar observations will also be made available through the archive.« less

The System for Quick Search of the Astronomical Objects and Events in the Digital Plate Archives.

NASA Astrophysics Data System (ADS)

Sergeev, A. V.; Sergeeva, T. P.

From the middle of the XIX century observatories all over the world have accumulated about three millions astronomical plates contained the unique information about the Universe which can not be obtained or restored with the help of any newest facilities and technologies but may be useful for many modern astronomical investigations. The threat of astronomical plate archives loss caused by economical, technical or some other causes have put before world astronomical community a problem: the preservation of the unique information kept on those plates. The problem can be solved by transformation of the information from plates to digital form and keeping it on electronic data medium. We began a creation of a system for quick search and analysing of astronomical events and objects in digital plate archive of the Ukrainian Main astronomical observatory of NAS. Connection of the system to Internet will allow a remote user (astronomer or observer) to have access to digital plate archive and to work with it. For providing of the high efficiency of this work the plate database (list of the plates with all information about them and access software) are preparing. Modular structure of the system basic software and standard format of the plate image files allow future development of problem-oriented software for special astronomical researches.

Content-based retrieval of historical Ottoman documents stored as textual images.

PubMed

Saykol, Ediz; Sinop, Ali Kemal; Güdükbay, Ugur; Ulusoy, Ozgür; Cetin, A Enis

2004-03-01

There is an accelerating demand to access the visual content of documents stored in historical and cultural archives. Availability of electronic imaging tools and effective image processing techniques makes it feasible to process the multimedia data in large databases. In this paper, a framework for content-based retrieval of historical documents in the Ottoman Empire archives is presented. The documents are stored as textual images, which are compressed by constructing a library of symbols occurring in a document, and the symbols in the original image are then replaced with pointers into the codebook to obtain a compressed representation of the image. The features in wavelet and spatial domain based on angular and distance span of shapes are used to extract the symbols. In order to make content-based retrieval in historical archives, a query is specified as a rectangular region in an input image and the same symbol-extraction process is applied to the query region. The queries are processed on the codebook of documents and the query images are identified in the resulting documents using the pointers in textual images. The querying process does not require decompression of images. The new content-based retrieval framework is also applicable to many other document archives using different scripts.

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.

Roosevelt Hot Springs, Utah FORGE Observation Well Data

DOE Data Explorer

Nash, Greg

2018-02-22

This archive contains temperature data for Roosevelt Hot Springs observation wells OH-1, OH-4, OH-5 and OH-7. There are also mud logs for OH-4. These are old datasets obtained from Rocky Mountain Power for use in the Utah FORGE project.

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.

A novel presenilin 1 mutation (Ala275Val) as cause of early-onset familial Alzheimer disease.

PubMed

Luedecke, Daniel; Becktepe, Jos S; Lehmbeck, Jan T; Finckh, Ulrich; Yamamoto, Raina; Jahn, Holger; Boelmans, Kai

2014-04-30

Mutations in the presenilin 1 (PS1) gene (PSEN1) are associated with familial Alzheimer disease (FAD). Here, we report on a 50-year-old patient presenting with progressive deterioration of his short-term memory and a family history of early-onset dementia. Diagnostic workup included a neuropsychological examination, structural magnetic resonance (MR) imaging, cerebrospinal fluid (CSF) biomarkers including total tau, phosphorylated tau, and Aβ42 levels, as well as sequencing relevant fragments of the genes PSEN1, PSEN2, and APP. Additionally, we were able to obtain archival paraffin-embedded cerebellar tissue from the patient's father for cosegregation analysis. Clinical, neuropsychological and MR imaging data were indicative of early-onset Alzheimer disease. Furthermore, CSF biomarkers showed a typical pattern for Alzheimer disease. DNA sequencing revealed a heterozygous nucleotide transition (c.824C>T) in exon 8 of PSEN1, leading to an amino acid change from alanine to valine at codon 275 (Ala275Val). The same mutation was found in an archival brain specimen of the patient's demented father, but not in a blood sample of the non-demented mother. This mutation alters a conserved residue in the large hydrophilic loop of PS1, suggesting pathogenic relevance. Cosegregegation analysis and the structural as well as the presumed functional role of the mutated and highly conserved residue suggest FAD causing characteristics of the novel PSEN1 mutation Ala275Val. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Neurophysiological correlates of suicidal ideation in major depressive disorder: Hyperarousal during sleep

PubMed Central

Dolsen, Michael R.; Cheng, Philip; Arnedt, J. Todd; Swanson, Leslie; Casement, Melynda D.; Kim, Hyang Sook; Goldschmied, Jennifer R.; Hoffmann, Robert F.; Armitage, Roseanne; Deldin, Patricia J.

2017-01-01

Background Suicide is a major public health concern, and a barrier to reducing the suicide rate is the lack of objective predictors of risk. The present study considers whether quantitative sleep electroencephalography (EEG) may be a neurobiological correlate of suicidal ideation. Methods Participants included 84 (45 female, mean age=26.6) adults diagnosed with major depressive disorder (MDD). The item that measures thoughts of death or suicide on the Quick Inventory of Depressive Symptomatology (QIDS) was used to classify 47 participants as low suicidal ideation (24 females, mean age=26.1) and 37 as high suicidal ideation (21 females, mean age=27.3). Data were obtained from archival samples collected at the University of Michigan and University of Texas Southwestern Medical Center between 2004 and 2012. Sleep EEG was quantified using power spectral analysis, and focused on alpha, beta, and delta frequencies. Results Results indicated that participants with high compared to low suicidal ideation experienced 1) increased fast frequency activity, 2) decreased delta activity, and 3) increased alpha-delta sleep after adjusting for age, sex, depression, and insomnia symptoms. Limitations Limitations include the exclusion of imminent suicidal intent, a single suicidal ideation item, and cross-sectional archival data. Conclusions This is one of the first studies to provide preliminary support that electrophysiological brain activity during sleep is associated with increased suicidal ideation in MDD, and may point toward central nervous system (CNS) hyperarousal during sleep as a neurobiological correlate of suicidal ideation. PMID:28192765

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.

Photometric Study of Intermediate Age Open Clusters

NASA Astrophysics Data System (ADS)

Contreras, Maria Eugenia; Michel, R.; Schuster, W.; Chavarria-Kleinhenn, C.; Olguin, L.

2011-05-01

We present the study of a sample of intermediate age open clusters (age 10-30 Myr) using optical (UBVRI) and infrared (JHK) photometric data. Optical photometry was obtained as part of the San Pedro Martir Open Clusters Project (SPM-OCP, Schuster et al. 2007; Michel et al. 2011, in preparation) while near-infrared photometry was retrieved from the 2MASS public data archive (ref). Most of the clusters included in SPM-OCP were selected from the Dias et al. (2002). catalog. On one hand, UVRI photometry was used to derive fundamental parameters of each cluster in the sample, such as age, distance and reddening. On the other hand, infrared photometry has allowed us to carry out a preliminary search of candidate stars to posses a circumstellar disk detected via its near-infrared excess. Observational data show that the number of infrared excess detection decreases with stellar age and actually this emission seems to completely disappear in stars with an age of 30 Myr (Strom et al. 1993; Muzerolle et al. 2000). One possible explanation for the lack of infrared emission has been proposed to be grain coagulation where small dust particles grow into larger and larger bodies until forming planetesimals and even planets. In this work we are aimed to analyze a sample of open clusters lying in this crucial age range.

Archival of Seasat-A satellite scatterometer data merged with in situ data at selected, illuminated sites over the ocean

NASA Technical Reports Server (NTRS)

Schroeder, Lyle C.; Sweet, Jon L.

1987-01-01

A large data base of Seasat-A Satellite Scatterometer (SASS) measurements merged with high-quality surface-truth wind, wave, and temperature data has been documented. The data base was developed for all times when selected in situ measurement sites were within the SASS footprint. Data were obtained from 42 sites located in the coastal waters of North America, Australia, Western Europe, and Japan and were assembled by correlating the SASS and surface-truth measurements in both time and distance. These data have been archived on a set of nine-track 6250 bpi ASCII coded magnetic tapes, which are available from the National Technical Information Service.

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.

BAO Plate Archive Project

NASA Astrophysics Data System (ADS)

Mickaelian, A. M.; Gigoyan, K. S.; Gyulzadyan, M. V.; Paronyan, G. M.; Abrahamyan, H. V.; Andreasyan, H. R.; Azatyan, N. M.; Kostandyan, G. R.; Samsonyan, A. L.; Mikayelyan, G. A.; Farmanyan, S. V.; Harutyunyan, V. L.

2017-12-01

We present the Byurakan Astrophysical Observatory (BAO) Plate Archive Project that is aimed at digitization, extraction and analysis of archival data and building an electronic database and interactive sky map. BAO Plate Archive consists of 37,500 photographic plates and films, obtained with 2.6m telescope, 1m and 0.5m Schmidt telescopes and other smaller ones during 1947-1991. The famous Markarian Survey (or the First Byurakan Survey, FBS) 2000 plates were digitized in 2002-2005 and the Digitized FBS (DFBS, www.aras.am/Dfbs/dfbs.html) was created. New science projects have been conducted based on this low-dispersion spectroscopic material. Several other smaller digitization projects have been carried out as well, such as part of Second Byurakan Survey (SBS) plates, photographic chain plates in Coma, where the blazar ON 231 is located and 2.6m film spectra of FBS Blue Stellar Objects. However, most of the plates and films are not digitized. In 2015, we have started a project on the whole BAO Plate Archive digitization, creation of electronic database and its scientific usage. Armenian Virtual Observatory (ArVO, www.aras.am/Arvo/arvo.htm) database will accommodate all new data. The project runs in collaboration with the Armenian Institute of Informatics and Automation Problems (IIAP) and will continues during 4 years in 2015-2018. The final result will be an Electronic Database and online Interactive Sky map to be used for further research projects. ArVO will provide all standards and tools for efficient usage of the scientific output and its integration in international databases.

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.

STATISTICAL ANALYSIS OF TANK 18F FLOOR SAMPLE RESULTS

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

Harris, S.

2010-09-02

Representative sampling has been completed for characterization of the residual material on the floor of Tank 18F as per the statistical sampling plan developed by Shine [1]. Samples from eight locations have been obtained from the tank floor and two of the samples were archived as a contingency. Six samples, referred to in this report as the current scrape samples, have been submitted to and analyzed by SRNL [2]. This report contains the statistical analysis of the floor sample analytical results to determine if further data are needed to reduce uncertainty. Included are comparisons with the prior Mantis samples resultsmore » [3] to determine if they can be pooled with the current scrape samples to estimate the upper 95% confidence limits (UCL{sub 95%}) for concentration. Statistical analysis revealed that the Mantis and current scrape sample results are not compatible. Therefore, the Mantis sample results were not used to support the quantification of analytes in the residual material. Significant spatial variability among the current sample results was not found. Constituent concentrations were similar between the North and South hemispheres as well as between the inner and outer regions of the tank floor. The current scrape sample results from all six samples fall within their 3-sigma limits. In view of the results from numerous statistical tests, the data were pooled from all six current scrape samples. As such, an adequate sample size was provided for quantification of the residual material on the floor of Tank 18F. The uncertainty is quantified in this report by an upper 95% confidence limit (UCL{sub 95%}) on each analyte concentration. The uncertainty in analyte concentration was calculated as a function of the number of samples, the average, and the standard deviation of the analytical results. The UCL{sub 95%} was based entirely on the six current scrape sample results (each averaged across three analytical determinations).« less

STATISTICAL ANALYSIS OF TANK 19F FLOOR SAMPLE RESULTS

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

Harris, S.

2010-09-02

Representative sampling has been completed for characterization of the residual material on the floor of Tank 19F as per the statistical sampling plan developed by Harris and Shine. Samples from eight locations have been obtained from the tank floor and two of the samples were archived as a contingency. Six samples, referred to in this report as the current scrape samples, have been submitted to and analyzed by SRNL. This report contains the statistical analysis of the floor sample analytical results to determine if further data are needed to reduce uncertainty. Included are comparisons with the prior Mantis samples resultsmore » to determine if they can be pooled with the current scrape samples to estimate the upper 95% confidence limits (UCL95%) for concentration. Statistical analysis revealed that the Mantis and current scrape sample results are not compatible. Therefore, the Mantis sample results were not used to support the quantification of analytes in the residual material. Significant spatial variability among the current scrape sample results was not found. Constituent concentrations were similar between the North and South hemispheres as well as between the inner and outer regions of the tank floor. The current scrape sample results from all six samples fall within their 3-sigma limits. In view of the results from numerous statistical tests, the data were pooled from all six current scrape samples. As such, an adequate sample size was provided for quantification of the residual material on the floor of Tank 19F. The uncertainty is quantified in this report by an UCL95% on each analyte concentration. The uncertainty in analyte concentration was calculated as a function of the number of samples, the average, and the standard deviation of the analytical results. The UCL95% was based entirely on the six current scrape sample results (each averaged across three analytical determinations).« less

Positions and proper motions of dwarf carbon stars

NASA Technical Reports Server (NTRS)

Deutsch, Eric W.

1994-01-01

Recent-epochs positions and proper motions of nine dwarf carbon star candidates are presented along with finding charts for each object. Measurements are obtained from digitized Palomar Observatory Sky Survey (POSS) and Quik V plate archives at the Space Telescope Science Institute, and from recent CCD images.

Does the endometrial gene expression of fertile women vary within and between cycles?

PubMed

Evans, Gloria E; Phillipson, Gregory T M; Sykes, Peter H; McNoe, Les A; Print, Cristin G; Evans, John J

2018-01-23

Does gene expression of putative endometrial implantation markers vary in expression between menstrual cycles? In fertile women the expression of certain genes exhibits a pattern of stable regulation.which is not affected even when sampled twice in one cycle. Successful implantation occurs in a minority of IVF embryo transfers. In contrast to knowledge regarding the ovulatory process, there is a sparse understanding of endometrial genes critical to implantation. This lack of knowledge hinders progress in this field. Endometrial pipelle samples were collected based on blood endocrinological markers at 2 and 7 days post initial LH surge. Five samples were collected over four cycles where the interval between collections ranged from sequential months to three years. Six fertile women attending an IVF clinic for male factor infertility, had samples collected. Global gene expression profiles were obtained from laser-microdissected, endometrial glands and stroma. Nineteen potential proliferation, cytokine and adhesion markers based on previous validated reports were studied. There was a significant modification between LH+2 and LH+7 of expression for 23 genes-11 in 8 in glands and stroma, 4 in stroma only and 3 in glands only suggesting stable, controlled regulation. Nevertheless, genes exhibited individual characteristics, e.g MKI67 exhibited lower expression at LH+7 than LH+2 and CCL4 higher, whereas TRO expressed limited difference in both cell types. Stability between cycles was demonstrated for gene expression at both LH+2-more than 60% of genes had <25% variation and at LH+7-60% had <30% variation. Further, effects of prior collection of an LH+2 sample on gene expression at LH+7 were not detected. The range of mRNA expression suggested that a clinical/diagnostic sample at LH+2 and LH+7 is likely to be a better index of endometrial function than a single sample. The possibility of redundancy suggests a panel would be more informative than a single marker. Raw and normalized microarray data have been deposited with the EMBL's European Genome-Phenome Archive for collaborative analysis, reference ega-box-815 (Lappalainen I, Almeida-King J, Kumanduri V, Senf A, Spalding JD, Ur-Rehman S, Saunders G, Kandasamy J, Caccamo M, Leinonen R et al. The European Genome-phenome Archive of human data consented for biomedical research. Nat Genet 2015;47:692-695.) [https://www.ebi.ac.uk/ega/home]. This type of research has difficulties of recruitment of fertile women for multiple blood testing and repeat endometrial biopsies. Therefore, these data had decreased statistical power due to the overall participant numbers. However, the inclusion of four cycles for each participant permitted the aim of obtaining information on intercycle and intracycle variability to be achieved. Our results support the feasibility of a clinical means of identification of a functional receptive endometrium. The robustness of data from individual women suggests that samples from one cycle can generally be applied to subsequent cycles. Funding was granted from the Tertiary Education Commission of New Zealand, Contract I.D.:UOOX06007. There are no competing interests. © The Author(s) 2018. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Quantitative Assessment of the Sensitivity of Various Commercial Reverse Transcriptases Based on Armored HIV RNA

PubMed Central

Okello, John B. A.; Rodriguez, Linda; Poinar, Debi; Bos, Kirsten; Okwi, Andrew L.; Bimenya, Gabriel S.; Sewankambo, Nelson K.; Henry, Kenneth R.; Kuch, Melanie; Poinar, Hendrik N.

2010-01-01

Background The in-vitro reverse transcription of RNA to its complementary DNA, catalyzed by the enzyme reverse transcriptase, is the most fundamental step in the quantitative RNA detection in genomic studies. As such, this step should be as analytically sensitive, efficient and reproducible as possible, especially when dealing with degraded or low copy RNA samples. While there are many reverse transcriptases in the market, all claiming to be highly sensitive, there is need for a systematic independent comparison of their applicability in quantification of rare RNA transcripts or low copy RNA, such as those obtained from archival tissues. Methodology/Principal Findings We performed RT-qPCR to assess the sensitivity and reproducibility of 11 commercially available reverse transcriptases in cDNA synthesis from low copy number RNA levels. As target RNA, we used a serially known number of Armored HIV RNA molecules, and observed that 9 enzymes we tested were consistently sensitive to ∼1,000 copies, seven of which were sensitive to ∼100 copies, while only 5 were sensitive to ∼10 RNA template copies across all replicates tested. Despite their demonstrated sensitivity, these five best performing enzymes (Accuscript, HIV-RT, M-MLV, Superscript III and Thermoscript) showed considerable variation in their reproducibility as well as their overall amplification efficiency. Accuscript and Superscript III were the most sensitive and consistent within runs, with Accuscript and Superscript II ranking as the most reproducible enzymes between assays. Conclusions/Significance We therefore recommend the use of Accuscript or Superscript III when dealing with low copy number RNA levels, and suggest purification of the RT reactions prior to downstream applications (eg qPCR) to augment detection. Although the results presented in this study were based on a viral RNA surrogate, and applied to nucleic acid lysates derived from archival formalin-fixed paraffin embedded tissue, their relative performance on RNA obtained from other tissue types may vary, and needs future evaluation. PMID:21085668

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

Science.gov Websites

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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.

International Ultraviolet Explorer Final Archive

NASA Technical Reports Server (NTRS)

1997-01-01

CSC processed IUE images through the Final Archive Data Processing System. Raw images were obtained from both NDADS and the IUEGTC optical disk platters for processing on the Alpha cluster, and from the IUEGTC optical disk platters for DECstation processing. Input parameters were obtained from the IUE database. Backup tapes of data to send to VILSPA were routinely made on the Alpha cluster. IPC handled more than 263 requests for priority NEWSIPS processing during the contract. Staff members also answered various questions and requests for information and sent copies of IUE documents to requesters. CSC implemented new processing capabilities into the NEWSIPS processing systems as they became available. In addition, steps were taken to improve efficiency and throughput whenever possible. The node TORTE was reconfigured as the I/O server for Alpha processing in May. The number of Alpha nodes used for the NEWSIPS processing queue was increased to a maximum of six in measured fashion in order to understand the dependence of throughput on the number of nodes and to be able to recognize when a point of diminishing returns was reached. With Project approval, generation of the VD FITS files was dropped in July. This action not only saved processing time but, even more significantly, also reduced the archive storage media requirements, and the time required to perform the archiving, drastically. The throughput of images verified through CDIVS and processed through NEWSIPS for the contract period is summarized below. The number of images of a given dispersion type and camera that were processed in any given month reflects several factors, including the availability of the required NEWSIPS software system, the availability of the corresponding required calibrations (e.g., the LWR high-dispersion ripple correction and absolute calibration), and the occurrence of reprocessing efforts such as that conducted to incorporate the updated SWP sensitivity-degradation correction in May.

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…

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

21 CFR 184.1206 - Calcium iodate.

Code of Federal Regulations, 2012 CFR

2012-04-01

... may be obtained from the National Academy Press, 2101 Constitution Ave. NW., Washington, DC 20418, or... availability of this material at NARA, call 202-741-6030, or go to: http://www.archives.gov/federal_register/code_of_federal_regulations/ibr_locations.html. (c) The ingredient is used as a dough strengthener as...

21 CFR 172.812 - Glycine.

Code of Federal Regulations, 2012 CFR

2012-04-01

... may be obtained from the National Academy Press, 2101 Constitution Ave. NW., Washington, DC 20418, or... availability of this material at NARA, call 202-741-6030, or go to: http://www.archives.gov/federal_register/code_of_federal_regulations/ibr_locations.html. (b) The additive is used or intended for use as follows...

36 CFR § 1226.26 - How do agencies donate temporary records?

Code of Federal Regulations, 2013 CFR

2013-07-01

... temporary records? § 1226.26 Section § 1226.26 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION RECORDS MANAGEMENT IMPLEMENTING DISPOSITION § 1226.26 How do agencies donate temporary records? (a) Agencies must obtain written approval from NARA before donating records eligible for...

36 CFR 1254.90 - What is the scope of this subpart?

Code of Federal Regulations, 2012 CFR

2012-07-01

... the use of privately owned microfilm equipment to film accessioned archival records and donated... permission from the originating agency to film those records (see § 1253.4). For information about procedures for obtaining permission from the originating agency to film records in the records center operation...

36 CFR 1254.90 - What is the scope of this subpart?

Code of Federal Regulations, 2011 CFR

2011-07-01

... the use of privately owned microfilm equipment to film accessioned archival records and donated... permission from the originating agency to film those records (see § 1253.4). For information about procedures for obtaining permission from the originating agency to film records in the records center operation...

CRRES experiments, data collection, analysis and publication

NASA Technical Reports Server (NTRS)

Miller, George P.

1992-01-01

The tasks undertaken to be performed under this contract included the continued coordination and documentation of the CRRES program and the development of an archive that details the experimental results obtained by the CRRES Program. Details of the work undertaken and results achieved are summarized in the following sections.

All Aboard the Internet.

ERIC Educational Resources Information Center

Descy, Don E.

1993-01-01

This introduction to the Internet with examples for Macintosh computer users demonstrates the ease of using e-mail, participating on discussion group listservs, logging in to remote sites using Telnet, and obtaining resources using the File Transfer Protocol (FTP). Included are lists of discussion groups, Telnet sites, and FTP Archive sites. (EA)

Student Mobility 2005. ACAATO Archive Document

ERIC Educational Resources Information Center

Colleges Ontario, 2005

2005-01-01

Several data sources indicate that the desire to obtain both a college and university credential in Ontario's postsecondary system is considerable. Aspirations at the start of college are high, with at least one quarter of college students having serious intentions of attaining a degree after a diploma. Data sources include the College Student…

The Career Course as a Factor in College Graduation

ERIC Educational Resources Information Center

Reardon, Robert C.; Melvin, Brittany; McClain, Mary-Catherine; Peterson, Gary W.; Bowman, William J.

2015-01-01

Conducting research and engaging in discussions with administrators and legislators can be important contributions toward alleviating the trend toward lower graduation rates among college students. This study used archival data obtained from the university registrar to examine how engagement in a credit-bearing undergraduate career course related…

Tank 241-AY-102 Leak Assessment Supporting Documentation: Miscellaneous Reports, Letters, Memoranda, And Data

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

Engeman, J. K.; Girardot, C. L.; Harlow, D. G.

2012-12-20

This report contains reference materials cited in RPP-ASMT -53793, Tank 241-AY-102 Leak Assessment Report, that were obtained from the National Archives Federal Records Repository in Seattle, Washington, or from other sources including the Hanford Site's Integrated Data Management System database (IDMS).

VizieR Online Data Catalog: 24um excesses in clusters & membership of NGC2244 (Meng+, 2017)

NASA Astrophysics Data System (ADS)

Meng, H. Y. A.; Rieke, G. H.; Su, K. Y. L.; Gaspar, A.

2017-09-01

We re-measured the Spitzer/MIPS 24um photometry for all the clusters except for a few noted in Appendix A. We obtained the 24um data from the Spitzer Heritage Archive between 2004 Jan 28 and 2008 Oct 23. (3 data files).

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.

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.

Imaging Spectrophotometry of the Jet/ISM Interaction in IC5063

NASA Technical Reports Server (NTRS)

Cecil, G.; Schuft, B.; Morse, J.; Bland-Hawthorn, J.

2004-01-01

IC5063 is a somewhat dusty z=0.0110 S0 galaxy with a Seyfert 2 nucleus. It has a triple radio source that spans 3 arcsec, mostly blueshifted H I absorption that spans 700 km/s, and ionization cones that extend for more than 2 arcmins. We obtained fully sampled [O III]\\lambda5007 grids at 0."9 and 70 km/s FWHM resolution using the Rutgers Fabry-Perot system on the Blanco 4m telescope. Complementary long-slit spectra using the RC spectrograph on the Blanco, and Taurus Tunable Filter spectral images in H\\alpha and [N II]\\lambda6583, were also obtained to assess gaseous ionization conditions. We present the results of our analysis, and correlate spectral structures to those visible in archival WFPC2 images. We find that, in the region near the radio triple, gaseous ionization and line velocity width is tightly correlated, in excellent quantitative agreement with the high-velocity shock regime in the diagnostic emission-line ratio diagrams of Dopita & Sutherland. We separate kinematically gas in normal disk rotation that is illuminated by the AGN in the ionization cones from that agitated mechanically by the jet, and assess the energy input from both processes.

New constraints on Lyman-α opacity with a sample of 62 quasars at z > 5.7

NASA Astrophysics Data System (ADS)

Bosman, Sarah E. I.; Fan, Xiaohui; Jiang, Linhua; Reed, Sophie; Matsuoka, Yoshiki; Becker, George; Haehnelt, Martin

2018-05-01

We present measurements of the mean and scatter of the IGM Lyman-α opacity at 4.9 < z < 6.1 along the lines of sight of 62 quasars at zsource > 5.7, the largest sample assembled at these redshifts to date by a factor of two. The sample size enables us to sample cosmic variance at these redshifts more robustly than ever before. The spectra used here were obtained by the SDSS, DES-VHS and SHELLQs collaborations, drawn from the ESI and X-Shooter archives, reused from previous studies or observed specifically for this work. We measure the effective optical depth of Lyman-α in bins of 10, 30, 50 and 70 cMpc h-1, construct cumulative distribution functions under two treatments of upper limits on flux and explore an empirical analytic fit to residual Lyman-α transmission. We verify the consistency of our results with those of previous studies via bootstrap re-sampling and confirm the existence of tails towards high values in the opacity distributions, which may persist down to z ˜ 5.2. Comparing our results with predictions from cosmological simulations, we find further strong evidence against models that include a spatially uniform ionizing background and temperature-density relation. We also compare to IGM models that include either a fluctuating UVB dominated by rare quasars or temperature fluctuations due to patchy reionization. Although both models produce better agreement with the observations, neither fully captures the observed scatter in IGM opacity. Our sample of 62 z > 5.7 quasar spectra opens many avenues for future study of the reionisation epoch.

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.

Use of electrospray ionization ion-trap tandem mass spectrometry and principal component analysis to directly distinguish monosaccharides.

PubMed

Xia, Bing; Zhou, Yan; Liu, Xin; Xiao, Juan; Liu, Qing; Gu, Yucheng; Ding, Lisheng

2012-06-15

Carbohydrates are good source of drugs and play important roles in metabolism processes and cellular interactions in organisms. Distinguishing monosaccharide isomers in saccharide derivates is an important and elementary work in investigating saccharides. It is important to develop a fast, simple and direct method for this purpose, which is described in this study. Stock solutions of monosaccharide with a concentration of 400 μM and sodium chloride at a concentration of 10 μM were made in water/methanol (50:50, v/v). The samples were subjected to electrospray ionization ion-trap tandem mass spectrometry (ESI-MS) and the detected [2M + Na - H(2)O](+) ions were further investigated by tandem mass spectrometry (MS/MS), followed by applying principal component analysis (PCA) on the obtained MS/MS data sets. The MS/MS spectra of the [2M + Na - H(2)O](+) ions at m/z 365 for hexoses and m/z 305 for pentoses yielded unambiguous fragment patterns, while rhamnose can be directly identified by its ESI-MS [M + Na](+) ion at m/z 187. PCA showed clustering of MS/MS data of identical monosaccharide samples obtained from different experiments. By using this method, the monosaccharide in daucosterol hydrolysate was successfully identified. A new strategy was developed for differentiation of the monosaccharides using ESI-MS/MS and PCA. In MS/MS spectra, the [2M + Na - H(2)O](+) ions yielded unambiguous distinction. PCA of the archived MS/MS data sets was applied to demonstrate the spatial resolution of the studied samples. This method presented a simple and reliable way for distinguishing monosaccharides by ESI-MS/MS. Copyright © 2012 John Wiley & Sons, Ltd.

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.

Whole Genome Amplification and Reduced-Representation Genome Sequencing of Schistosoma japonicum Miracidia.

PubMed

Shortt, Jonathan A; Card, Daren C; Schield, Drew R; Liu, Yang; Zhong, Bo; Castoe, Todd A; Carlton, Elizabeth J; Pollock, David D

2017-01-01

In areas where schistosomiasis control programs have been implemented, morbidity and prevalence have been greatly reduced. However, to sustain these reductions and move towards interruption of transmission, new tools for disease surveillance are needed. Genomic methods have the potential to help trace the sources of new infections, and allow us to monitor drug resistance. Large-scale genotyping efforts for schistosome species have been hindered by cost, limited numbers of established target loci, and the small amount of DNA obtained from miracidia, the life stage most readily acquired from humans. Here, we present a method using next generation sequencing to provide high-resolution genomic data from S. japonicum for population-based studies. We applied whole genome amplification followed by double digest restriction site associated DNA sequencing (ddRADseq) to individual S. japonicum miracidia preserved on Whatman FTA cards. We found that we could effectively and consistently survey hundreds of thousands of variants from 10,000 to 30,000 loci from archived miracidia as old as six years. An analysis of variation from eight miracidia obtained from three hosts in two villages in Sichuan showed clear population structuring by village and host even within this limited sample. This high-resolution sequencing approach yields three orders of magnitude more information than microsatellite genotyping methods that have been employed over the last decade, creating the potential to answer detailed questions about the sources of human infections and to monitor drug resistance. Costs per sample range from $50-$200, depending on the amount of sequence information desired, and we expect these costs can be reduced further given continued reductions in sequencing costs, improvement of protocols, and parallelization. This approach provides new promise for using modern genome-scale sampling to S. japonicum surveillance, and could be applied to other schistosome species and other parasitic helminthes.

VizieR Online Data Catalog: Kepler multiple transiting planet systems (Wang+, 2015)

NASA Astrophysics Data System (ADS)

Wang, J.; Fischer, D. A.; Xie, J.-W.; Ciardi, D. R.

2017-10-01

The sample of MTPSs remains the same as that in Wang et al. (2014, J/ApJ/783/4). From the NASA Exoplanet Archive (http://exoplanetarchive.ipac.caltech.edu), we select Kepler objects of interest (KOIs) that satisfy the following criteria: (1) disposition of either Candidate or Confirmed; (2) with at least two planet candidates; (3) Kepler magnitude (KP) brighter than 13.5. The above selection criteria resulted in 138 MTPSs in Wang et al. (2014, J/ApJ/783/4). With the updated Exoplanet Archive, the selection criteria resulted in 208 MTPSs. In this paper, we focus on the 138 MTPSs to be consistent with previous work. (4 data files).

Archive of sediment data from vibracores collected in 2010 offshore of the Mississippi barrier islands

USGS Publications Warehouse

Kelso, Kyle W.; Flocks, James G.

2015-01-01

Selection of the core site locations was based on geophysical surveys conducted around the islands from 2008 to 2010. The surveys, using acoustic systems to image and interpret the nearsurface stratigraphy, were conducted to investigate the geologic controls on island evolution. This data series serves as an archive of sediment data collected from August to September 2010, offshore of the Mississippi barrier islands. Data products, including descriptive core logs, core photographs, results of sediment grain-size analyses, sample location maps, and geographic information system (GIS) data files with accompanying formal Federal Geographic Data Committee (FDGC) metadata can be downloaded from the data products and downloads page.

Mitigation of formalin-induced RNA damage to advance whole transcriptomic analyses of archival tissues

EPA Science Inventory

Leveraging the use of biorepository samples for genomic analyses holds huge implications for human health, including applications in pathway identification, biomarker discovery, and tumor profiling for precision medicine. However, there is a need for better ways to reduce nucleic...

IMPACT OF SUBMERSIBLE PUMPS ON PB CONSTITUENTS IN RESIDENTIAL WELLS

EPA Science Inventory

Dissolved lead in 51 domestic wells screened from 18 m to 48 m in glacial tills and outwash deposits were examined, from archived samples collected during 2001-2004, in conjunction with respective submersible pump characteristics. Pb concentrations of these residential water supp...

30 CFR 784.14 - Hydrologic information.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 30 Mineral Resources 3 2012-07-01 2012-07-01 false Hydrologic information. 784.14 Section 784.14... Hydrologic information. (a) Sampling and analysis. All water quality analyses performed to meet the... at the National Archives and Records Administration (NARA). For information on the availability of...

30 CFR 784.14 - Hydrologic information.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 3 2011-07-01 2011-07-01 false Hydrologic information. 784.14 Section 784.14... Hydrologic information. (a) Sampling and analysis. All water quality analyses performed to meet the... at the National Archives and Records Administration (NARA). For information on the availability of...

The metagenomic data life-cycle: standards and best practices

PubMed Central

ten Hoopen, Petra; Finn, Robert D.; Bongo, Lars Ailo; Corre, Erwan; Meyer, Folker; Mitchell, Alex; Pelletier, Eric; Pesole, Graziano; Santamaria, Monica; Willassen, Nils Peder

2017-01-01

Abstract Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonized way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (i) material sampling, (ii) material sequencing, (iii) data analysis, and (iv) data archiving and publishing. Taking examples from marine research, we summarize essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment. These aspects of metagenomics dataset generation have been to some extent addressed by the scientific community, but greater awareness and adoption is still needed. We emphasize the lack of standards relating to reporting how metagenomics datasets are analysed and how the metagenomics data analysis outputs should be archived and published. We propose best practice as a foundation for a community standard to enable reproducibility and better sharing of metagenomics datasets, leading ultimately to greater metagenomics data reuse and repurposing. PMID:28637310

The metagenomic data life-cycle: standards and best practices

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

ten Hoopen, Petra; Finn, Robert D.; Bongo, Lars Ailo

Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonised way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (1) material sampling, (2) material sequencing (3) data analysis and (4) data archiving & publishing. Taking examples from marine research, we summarise essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment. These aspects of metagenomics dataset generation have been to some extent addressed by the scientific community but greater awareness and adoption is stillmore » needed. We emphasise the lack of standards relating to reporting how metagenomics datasets are analysed and how the metagenomics data analysis outputs should be archived and published. We propose best practice as a foundation for a community standard to enable reproducibility and better sharing of metagenomics datasets, leading ultimately to greater metagenomics data reuse and repurposing.« less

BAO Plate Archive Project: Digitization, Electronic Database and Research Programmes

NASA Astrophysics Data System (ADS)

Mickaelian, A. M.; Abrahamyan, H. V.; Andreasyan, H. R.; Azatyan, N. M.; Farmanyan, S. V.; Gigoyan, K. S.; Gyulzadyan, M. V.; Khachatryan, K. G.; Knyazyan, A. V.; Kostandyan, G. R.; Mikayelyan, G. A.; Nikoghosyan, E. H.; Paronyan, G. M.; Vardanyan, A. V.

2016-06-01

The most important part of the astronomical observational heritage are astronomical plate archives created on the basis of numerous observations at many observatories. Byurakan Astrophysical Observatory (BAO) plate archive consists of 37,000 photographic plates and films, obtained at 2.6m telescope, 1m and 0.5m Schmidt type and other smaller telescopes during 1947-1991. In 2002-2005, the famous Markarian Survey (also called First Byurakan Survey, FBS) 1874 plates were digitized and the Digitized FBS (DFBS) was created. New science projects have been conducted based on these low-dispersion spectroscopic material. A large project on the whole BAO Plate Archive digitization, creation of electronic database and its scientific usage was started in 2015. A Science Program Board is created to evaluate the observing material, to investigate new possibilities and to propose new projects based on the combined usage of these observations together with other world databases. The Executing Team consists of 11 astronomers and 2 computer scientists and will use 2 EPSON Perfection V750 Pro scanners for the digitization, as well as Armenian Virtual Observatory (ArVO) database will be used to accommodate all new data. The project will run during 3 years in 2015-2017 and the final result will be an electronic database and online interactive sky map to be used for further research projects, mainly including high proper motion stars, variable objects and Solar System bodies.

BAO Plate Archive digitization, creation of electronic database and its scientific usage

NASA Astrophysics Data System (ADS)

Mickaelian, Areg M.

2015-08-01

Astronomical plate archives created on the basis of numerous observations at many observatories are important part of the astronomical heritage. Byurakan Astrophysical Observatory (BAO) plate archive consists of 37,500 photographic plates and films, obtained at 2.6m telescope, 1m and 0.5m Schmidt telescopes and other smaller ones during 1947-1991. In 2002-2005, the famous Markarian Survey (First Byurakan Survey, FBS) 2000 plates were digitized and the Digitized FBS (DFBS, http://www.aras.am/Dfbs/dfbs.html) was created. New science projects have been conducted based on these low-dispersion spectroscopic material. In 2015, we have started a project on the whole BAO Plate Archive digitization, creation of electronic database and its scientific usage. A Science Program Board is created to evaluate the observing material, to investigate new possibilities and to propose new projects based on the combined usage of these observations together with other world databases. The Executing Team consists of 9 astronomers and 3 computer scientists and will use 2 EPSON Perfection V750 Pro scanners for the digitization, as well as Armenian Virtual Observatory (ArVO) database to accommodate all new data. The project will run during 3 years in 2015-2017 and the final result will be an electronic database and online interactive sky map to be used for further research projects.

The SpaceInn-SISMA Database: Characterization of a Large Sample of Variable and Active Stars by Means of Harps Spectra

NASA Astrophysics Data System (ADS)

Rainer, M.; Poretti, E.; Mistò, A.; Panzera, M. R.; Molinaro, M.; Cepparo, F.; Roth, M.; Michel, E.; Monteiro, M. J. P. F. G.

2016-12-01

We created a large database of physical parameters and variability indicators by fully reducing and analyzing the large number of spectra taken to complement the asteroseismic observations of the COnvection, ROtation and planetary Transits (CoRoT) satellite. 7103 spectra of 261 stars obtained with the ESO echelle spectrograph HARPS have been stored in the VO-compliant database Spectroscopic Indicators in a SeisMic Archive (SISMA), along with the CoRoT photometric data of the 72 CoRoT asteroseismic targets. The remaining stars belong to the same variable classes of the CoRoT targets and were observed to better characterize the properties of such classes. Several useful variability indicators (mean line profiles, indices of differential rotation, activity and emission lines) together with v\\sin I and radial-velocity measurements have been extracted from the spectra. The atmospheric parameters {T}{eff},{log}g, and [Fe/H] have been computed following a homogeneous procedure. As a result, we fully characterize a sample of new and known variable stars by computing several spectroscopic indicators, also providing some cases of simultaneous photometry and spectroscopy.

Gamma radiation effects on physical properties of parchment documents: Assessment of Dmax

NASA Astrophysics Data System (ADS)

Nunes, Inês; Mesquita, Nuno; Cabo Verde, Sandra; João Trigo, Maria; Ferreira, Armando; Manuela Carolino, Maria; Portugal, António; Luísa Botelho, Maria

2012-12-01

Parchments are important documents that give testimony for History; therefore these materials should be respected and preserved. Considering incremental biodeterioration problems that have to be faced daily, the Archive of the University of Coimbra (AUC) is involved in different scientific projects in order to evaluate and determine new methods for document decontamination and preservation. The aim of this study was to evaluate gamma radiation effects on the colour and texture of the AUC parchment documents. The assessment of these effects was used to estimate the maximum gamma radiation dose (Dmax) that could guarantee parchment documents' decontamination treatment, without significant alteration of their physical properties. Parchment samples were exposed to gamma radiation doses ranging from 10 to 30 kGy. The texture and colour of samples were assessed before and after the irradiation procedure, using a texture analyser and an electronic colorimeter. Hardness and springiness were determined based on texture spectra. Lightness (L*), Chroma (C), greenness vs. redness (a*) and yellowness vs. blueness (b*) values were obtained from colorimetric measures. Results indicate no significant effects of gamma radiation on the texture and colour of parchment for the studied doses.

An Extension of the EDGES Survey: Stellar Populations in Dark Matter Halos

NASA Astrophysics Data System (ADS)

van Zee, Liese

The formation and evolution of galactic disks is one of the key questions in extragalactic astronomy today. We plan to use archival data from GALEX, Spitzer, and WISE to investigate the growth and evolution of the stellar component in a statistical sample of nearby galaxies. Data covering a broad wavelength range are critical for measurement of current star formation activity, stellar populations, and stellar distributions in nearby galaxies. In order to investigate the timescales associated with the growth of galactic disks, we will (1) investigate the structure of the underlying stellar distribution, (2) measure the ratio of current-to-past star formation activity as a function of radius, and (3) investigate the growth of the stellar disk as a function of baryon fraction and total dynamical mass. The proposed projects leverage the existing deep wide field-of-view near infrared imaging observations obtained with the Spitzer Space Telescope as part of the EDGES Survey, a Cycle 8 Exploration Science Program. The proposed analysis of multiwavelength imaging observations of a well-defined statistical sample will place strong constraints on hierarchical models of galaxy formation and evolution and will further our understanding of the stellar component of nearby galaxies.

Extremely Soft X-Ray Flash as the Indicator of Off-axis Orphan GRB Afterglow

NASA Astrophysics Data System (ADS)

Urata, Yuji; Huang, Kuiyun; Yamazaki, Ryo; Sakamoto, Takanori

2015-06-01

We verified the off-axis jet model of X-ray flashes (XRFs) and examined a discovery of off-axis orphan gamma-ray burst (GRB) afterglows. The XRF sample was selected on the basis of the following three factors: (1) a constraint on the lower peak energy of the prompt spectrum {E}{obs}{src}, (2) redshift measurements, and (3) multicolor observations of an earlier (or brightening) phase. XRF 020903 was the only sample selected on the basis of these criteria. A complete optical multicolor afterglow light curve of XRF 020903 obtained from archived data and photometric results in the literature showed an achromatic brightening around 0.7 days. An off-axis jet model with a large observing angle (0.21 rad, which is twice the jet opening half-angle, {θ }{jet}) can naturally describe the achromatic brightening and the prompt X-ray spectral properties. This result indicates the existence of off-axis orphan GRB afterglow light curves. Events with a larger viewing angle (\\gt ∼ 2{θ }{jet}) could be discovered using an 8 m class telescope with wide-field imagers such as the Subaru Hyper-Suprime-Cam and the Large Synoptic Survey Telescope.

Access to Archived Astronaut Data for Human Research Program Researchers: Update on Progress and Process Improvements

NASA Technical Reports Server (NTRS)

Lee, L. R.; Montague, K. A.; Charvat, J. M.; Wear, M. L.; Thomas, D. M.; Van Baalen, M.

2016-01-01

Since the 2010 NASA directive to make the Life Sciences Data Archive (LSDA) and Lifetime Surveillance of Astronaut Health (LSAH) data archives more accessible by the research and operational communities, demand for astronaut medical data has increased greatly. LSAH and LSDA personnel are working with Human Research Program on many fronts to improve data access and decrease lead time for release of data. Some examples include the following: Feasibility reviews for NASA Research Announcement (NRA) data mining proposals; Improved communication, support for researchers, and process improvements for retrospective Institutional Review Board (IRB) protocols; Supplemental data sharing for flight investigators versus purely retrospective studies; Work with the Multilateral Human Research Panel for Exploration (MHRPE) to develop acceptable data sharing and crew consent processes and to organize inter-agency data coordinators to facilitate requests for international crewmember data. Current metrics on data requests crew consenting will be presented, along with limitations on contacting crew to obtain consent. Categories of medical monitoring data available for request will be presented as well as flow diagrams detailing data request processing and approval steps.

Possibilities of Processing Archival Photogrammetric Images Captured by Rollei 6006 Metric Camera Using Current Method

NASA Astrophysics Data System (ADS)

Dlesk, A.; Raeva, P.; Vach, K.

2018-05-01

Processing of analog photogrammetric negatives using current methods brings new challenges and possibilities, for example, creation of a 3D model from archival images which enables the comparison of historical state and current state of cultural heritage objects. The main purpose of this paper is to present possibilities of processing archival analog images captured by photogrammetric camera Rollei 6006 metric. In 1994, the Czech company EuroGV s.r.o. carried out photogrammetric measurements of former limestone quarry the Great America located in the Central Bohemian Region in the Czech Republic. All the negatives of photogrammetric images, complete documentation, coordinates of geodetically measured ground control points, calibration reports and external orientation of images calculated in the Combined Adjustment Program are preserved and were available for the current processing. Negatives of images were scanned and processed using structure from motion method (SfM). The result of the research is a statement of what accuracy is possible to expect from the proposed methodology using Rollei metric images originally obtained for terrestrial intersection photogrammetry while adhering to the proposed methodology.

infoRAD: computers for clinical practice and education in radiology. Teleradiology, information transfer, and PACS: implications for diagnostic imaging in the 1990s.

PubMed

Schilling, R B

1993-05-01

Picture archiving and communication systems (PACS) provide image viewing at diagnostic, reporting, consultation, and remote workstations; archival on magnetic or optical media by means of short- or long-term storage devices; communications by means of local or wide area networks or public communication services; and integrated systems with modality interfaces and gateways to health care facilities and departmental information systems. Research indicates three basic needs for image and report management: (a) improved communication and turnaround time between radiologists and other imaging specialists and referring physicians, (b) fast reliable access to both current and previously obtained images and reports, and (c) space-efficient archival support. Although PACS considerations are much more complex than those associated with single modalities, the same basic purchase criteria apply. These criteria include technical leadership, image quality, throughput, life cost (eg, initial cost, maintenance, upgrades, and depreciation), and total service. Because a PACS takes much longer to implement than a single modality, the customer and manufacturer must develop a closer working relationship than has been necessary in the past.

Unravelling environmental conditions during the Holocene in the Dead Sea region using multiple archives

NASA Astrophysics Data System (ADS)

Rambeau, Claire; van Leeuwen, Jacqueline; van der Knaap, Pim; Gobet, Erika

2016-04-01

For the most arid parts of the Southern Levant (roughly corresponding to modern Jordan, Israel and Palestine), environmental reconstructions are impeded by the limited number of archives, and the frequent contradictions between individual palaeoenvironmental records. The Southern Levant is characterised by steep climate gradients; local conditions presently range from arid to dry Mediterranean, with limits that may have fluctuated during the Holocene. This further complicates the determination of site-specific past environmental conditions. Understanding past climate and environmental evolution through time, at a local level, is however crucial to compare these with societal evolution during the Holocene, which features major cultural developments such as cereal cultivation, animal domestication, water management, as well as times of preferential settlement growth or site abandonment. This contribution proposes to examine the different archives available for the Dead Sea region, paying special attention to the most recent pollen data obtained from the area. It will particularly critically compare local to regional-scale information, and try to decipher the main evolutions of environmental conditions during the Holocene in arid and semi-arid Southern Levant.

Object classification and outliers analysis in the forthcoming Gaia mission

NASA Astrophysics Data System (ADS)

Ordóñez-Blanco, D.; Arcay, B.; Dafonte, C.; Manteiga, M.; Ulla, A.

2010-12-01

Astrophysics is evolving towards the rational optimization of costly observational material by the intelligent exploitation of large astronomical databases from both terrestrial telescopes and spatial mission archives. However, there has been relatively little advance in the development of highly scalable data exploitation and analysis tools needed to generate the scientific returns from these large and expensively obtained datasets. Among the upcoming projects of astronomical instrumentation, Gaia is the next cornerstone ESA mission. The Gaia survey foresees the creation of a data archive and its future exploitation with automated or semi-automated analysis tools. This work reviews some of the work that is being developed by the Gaia Data Processing and Analysis Consortium for the object classification and analysis of outliers in the forthcoming mission.

Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis

PubMed Central

2014-01-01

Background Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system. Results We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h2 ~ 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers. Conclusion The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of pedigree-based studies to address challenging ecological and evolutionary questions in free-living populations, where genealogies can be traced only using molecular tools, and that significant increases in pedigree assignment power can be achieved by using higher numbers of markers. PMID:24684698

Constitutive modeling of the human Anterior Cruciate Ligament (ACL) under uniaxial loading using viscoelastic prony series and hyperelastic five parameter Mooney-Rivlin model

NASA Astrophysics Data System (ADS)

Chakraborty, Souvik; Mondal, Debabrata; Motalab, Mohammad

2016-07-01

In this present study, the stress-strain behavior of the Human Anterior Cruciate Ligament (ACL) is studied under uniaxial loads applied with various strain rates. Tensile testing of the human ACL samples requires state of the art test facilities. Furthermore, difficulty in finding human ligament for testing purpose results in very limited archival data. Nominal Stress vs. deformation gradient plots for different strain rates, as found in literature, is used to model the material behavior either as a hyperelastic or as a viscoelastic material. The well-known five parameter Mooney-Rivlin constitutivemodel for hyperelastic material and the Prony Series model for viscoelastic material are used and the objective of the analyses comprises of determining the model constants and their variation-trend with strain rates for the Human Anterior Cruciate Ligament (ACL) material using the non-linear curve fitting tool. The relationship between the model constants and strain rate, using the Hyperelastic Mooney-Rivlin model, has been obtained. The variation of the values of each coefficient with strain rates, obtained using Hyperelastic Mooney-Rivlin model are then plotted and variation of the values with strain rates are obtained for all the model constants. These plots are again fitted using the software package MATLAB and a power law relationship between the model constants and strain rates is obtained for each constant. The obtained material model for Human Anterior Cruciate Ligament (ACL) material can be implemented in any commercial finite element software package for stress analysis.

Status of the TESS Science Processing Operations Center

NASA Astrophysics Data System (ADS)

Jenkins, Jon Michael; Caldwell, Douglas A.; Davies, Misty; Li, Jie; Morris, Robert L.; Rose, Mark; Smith, Jeffrey C.; Tenenbaum, Peter; Ting, Eric; Twicken, Joseph D.; Wohler, Bill

2018-06-01

The Transiting Exoplanet Survey Satellite (TESS) was selected by NASA’s Explorer Program to conduct a search for Earth’s closest cousins starting in 2018. TESS will conduct an all-sky transit survey of F, G and K dwarf stars between 4 and 12 magnitudes and M dwarf stars within 200 light years. TESS is expected to discover 1,000 small planets less than twice the size of Earth, and to measure the masses of at least 50 of these small worlds. The TESS science pipeline is being developed by the Science Processing Operations Center (SPOC) at NASA Ames Research Center based on the highly successful Kepler science pipeline. Like the Kepler pipeline, the TESS pipeline provides calibrated pixels, simple and systematic error-corrected aperture photometry, and centroid locations for all 200,000+ target stars observed over the 2-year mission, along with associated uncertainties. The pixel and light curve products are modeled on the Kepler archive products and will be archived to the Mikulski Archive for Space Telescopes (MAST). In addition to the nominal science data, the 30-minute Full Frame Images (FFIs) simultaneously collected by TESS will also be calibrated by the SPOC and archived at MAST. The TESS pipeline searches through all light curves for evidence of transits that occur when a planet crosses the disk of its host star. The Data Validation pipeline generates a suite of diagnostic metrics for each transit-like signature, and then extracts planetary parameters by fitting a limb-darkened transit model to each potential planetary signature. The results of the transit search are modeled on the Kepler transit search products (tabulated numerical results, time series products, and pdf reports) all of which will be archived to MAST. Synthetic sample data products are available at https://archive.stsci.edu/tess/ete-6.html.Funding for the TESS Mission has been provided by the NASA Science Mission Directorate.

Constraints on Rational Model Weighting, Blending and Selecting when Constructing Probability Forecasts given Multiple Models

NASA Astrophysics Data System (ADS)

Higgins, S. M. W.; Du, H. L.; Smith, L. A.

2012-04-01

Ensemble forecasting on a lead time of seconds over several years generates a large forecast-outcome archive, which can be used to evaluate and weight "models". Challenges which arise as the archive becomes smaller are investigated: in weather forecasting one typically has only thousands of forecasts however those launched 6 hours apart are not independent of each other, nor is it justified to mix seasons with different dynamics. Seasonal forecasts, as from ENSEMBLES and DEMETER, typically have less than 64 unique launch dates; decadal forecasts less than eight, and long range climate forecasts arguably none. It is argued that one does not weight "models" so much as entire ensemble prediction systems (EPSs), and that the marginal value of an EPS will depend on the other members in the mix. The impact of using different skill scores is examined in the limits of both very large forecast-outcome archives (thereby evaluating the efficiency of the skill score) and in very small forecast-outcome archives (illustrating fundamental limitations due to sampling fluctuations and memory in the physical system being forecast). It is shown that blending with climatology (J. Bröcker and L.A. Smith, Tellus A, 60(4), 663-678, (2008)) tends to increase the robustness of the results; also a new kernel dressing methodology (simply insuring that the expected probability mass tends to lie outside the range of the ensemble) is illustrated. Fair comparisons using seasonal forecasts from the ENSEMBLES project are used to illustrate the importance of these results with fairly small archives. The robustness of these results across the range of small, moderate and huge archives is demonstrated using imperfect models of perfectly known nonlinear (chaotic) dynamical systems. The implications these results hold for distinguishing the skill of a forecast from its value to a user of the forecast are discussed.

Fermilab History and Archives Project | Norman F. Ramsey

Science.gov Websites

Fermilab History and Archives Project Fermilab History and Archives Project Fermilab History and Archives Project Home About the Archives History and Archives Online Request Contact Us History & ; Archives Project Fermilab History and Archives Project Norman F. Ramsey Back to History and Archives

A seasonal comparison of surface sediment characteristics in Chincoteague Bay, Maryland and Virginia, USA

USGS Publications Warehouse

Ellis, Alisha M.; Marot, Marci E.; Wheaton, Cathryn J.; Bernier, Julie C.; Smith, Christopher G.

2016-02-03

This report is an archive for sedimentological data derived from the surface sediment of Chincoteague Bay. Data are available for the spring (March/April 2014) and fall (October 2014) samples collected. Downloadable data are provided as Excel spreadsheets and as JPEG files. Additional files include ArcGIS shapefiles of the sampling sites, detailed results of sediment grain-size analyses, and formal Federal Geographic Data Committee metadata (data downloads).

Psychiatric Correlates of Nonsuicidal Cutting Behaviors in an Adolescent Inpatient Sample

ERIC Educational Resources Information Center

Swenson, Lance P.; Spirito, Anthony; Dyl, Jennifer; Kittler, Jennifer; Hunt, Jeffrey I.

2008-01-01

This archival study of 288 adolescent psychiatric inpatients examined the psychiatric correlates of cutting behavior. Participants were categorized into Threshold cutters (n = 61), Subthreshold cutters (n = 43), and Noncutters (n = 184). Groups were compared on psychiatric diagnoses, suicidality, and self-reported impairment. Results demonstrated…

Physics of Galaxy Clusters and How it Affects Cosmological Tests

NASA Technical Reports Server (NTRS)

Vikhlinin, Alexey; Oliversen, Ronald J. (Technical Monitor)

2002-01-01

We have worked on the analysis of the Chandra observations of the nearby and distant clusters of galaxies, and on the expansion of the sample of distant X-ray clusters based on the archival ROSAT PSPC data. Some of the scientific results are discussed.

42 CFR 37.44 - Approval of radiographic facilities that use digital radiography systems.

Code of Federal Regulations, 2013 CFR

2013-10-01

... image acquisition, digitization, processing, compression, transmission, display, archiving, and... quality digital chest radiographs by submitting to NIOSH digital radiographic image files of a test object... digital radiographic image files from six or more sample chest radiographs that are of acceptable quality...

42 CFR 37.44 - Approval of radiographic facilities that use digital radiography systems.

Code of Federal Regulations, 2012 CFR

2012-10-01

... image acquisition, digitization, processing, compression, transmission, display, archiving, and... quality digital chest radiographs by submitting to NIOSH digital radiographic image files of a test object... digital radiographic image files from six or more sample chest radiographs that are of acceptable quality...

The cataclysmic variable AE Aquarii: orbital variability in V band

NASA Astrophysics Data System (ADS)

Zamanov, R.; Latev, G.

2017-07-01

We present 62.7 hours observations of the cataclysmic variable AE Aqr in Johnson V band. These are non-published archive electro-photometric data obtained during the time period 1993 to 1999. We construct the orbital variability in V band and obtain a Fourier fit to the double-wave quiescent light curve. The strongest flares in our data set are in phase interval 0.6 - 0.8. The data can be downloaded from http://www.astro.bas.bg/~rz/DATA/AEAqr.elphot.dat.

Medical image archive node simulation and architecture

NASA Astrophysics Data System (ADS)

Chiang, Ted T.; Tang, Yau-Kuo

1996-05-01

It is a well known fact that managed care and new treatment technologies are revolutionizing the health care provider world. Community Health Information Network and Computer-based Patient Record projects are underway throughout the United States. More and more hospitals are installing digital, `filmless' radiology (and other imagery) systems. They generate a staggering amount of information around the clock. For example, a typical 500-bed hospital might accumulate more than 5 terabytes of image data in a period of 30 years for conventional x-ray images and digital images such as Magnetic Resonance Imaging and Computer Tomography images. With several hospitals contributing to the archive, the storage required will be in the hundreds of terabytes. Systems for reliable, secure, and inexpensive storage and retrieval of digital medical information do not exist today. In this paper, we present a Medical Image Archive and Distribution Service (MIADS) concept. MIADS is a system shared by individual and community hospitals, laboratories, and doctors' offices that need to store and retrieve medical images. Due to the large volume and complexity of the data, as well as the diversified user access requirement, implementation of the MIADS will be a complex procedure. One of the key challenges to implementing a MIADS is to select a cost-effective, scalable system architecture to meet the ingest/retrieval performance requirements. We have performed an in-depth system engineering study, and developed a sophisticated simulation model to address this key challenge. This paper describes the overall system architecture based on our system engineering study and simulation results. In particular, we will emphasize system scalability and upgradability issues. Furthermore, we will discuss our simulation results in detail. The simulations study the ingest/retrieval performance requirements based on different system configurations and architectures for variables such as workload, tape access time, number of drives, number of exams per patient, number of Central Processing Units, patient grouping, and priority impacts. The MIADS, which could be a key component of a broader data repository system, will be able to communicate with and obtain data from existing hospital information systems. We will discuss the external interfaces enabling MIADS to communicate with and obtain data from existing Radiology Information Systems such as the Picture Archiving and Communication System (PACS). Our system design encompasses the broader aspects of the archive node, which could include multimedia data such as image, audio, video, and free text data. This system is designed to be integrated with current hospital PACS through a Digital Imaging and Communications in Medicine interface. However, the system can also be accessed through the Internet using Hypertext Transport Protocol or Simple File Transport Protocol. Our design and simulation work will be key to implementing a successful, scalable medical image archive and distribution system.

Validation of Marek's disease diagnosis and monitoring of Marek's disease vaccines from samples collected in FTA cards.

PubMed

Cortes, Aneg L; Montiel, Enrique R; Gimeno, Isabel M

2009-12-01

The use of Flinders Technology Associates (FTA) filter cards to quantify Marek's disease virus (MDV) DNA for the diagnosis of Marek's disease (MD) and to monitor MD vaccines was evaluated. Samples of blood (43), solid tumors (14), and feather pulp (FP; 36) collected fresh and in FTA cards were analyzed. MDV DNA load was quantified by real-time PCR. Threshold cycle (Ct) ratios were calculated for each sample by dividing the Ct value of the internal control gene (glyceraldehyde-3-phosphate dehydrogenase) by the Ct value of the MDV gene. Statistically significant correlation (P < 0.05) within Ct ratios was detected between samples collected fresh and in FTA cards by using Pearson's correlation test. Load of serotype 1 MDV DNA was quantified in 24 FP, 14 solid tumor, and 43 blood samples. There was a statistically significant correlation between FP (r = 0.95), solid tumor (r = 0.94), and blood (r = 0.9) samples collected fresh and in FTA cards. Load of serotype 2 MDV DNA was quantified in 17 FP samples, and the correlation between samples collected fresh and in FTA cards was also statistically significant (Pearson's coefficient, r = 0.96); load of serotype 3 MDV DNA was quantified in 36 FP samples, and correlation between samples taken fresh and in FTA cards was also statistically significant (r = 0.84). MDV DNA samples extracted 3 days (t0) and 8 months after collection (t1) were used to evaluate the stability of MDV DNA in archived samples collected in FTA cards. A statistically significant correlation was found for serotype 1 (r = 0.96), serotype 2 (r = 1), and serotype 3 (r = 0.9). The results show that FTA cards are an excellent media to collect, transport, and archive samples for MD diagnosis and to monitor MD vaccines. In addition, FTA cards are widely available, inexpensive, and adequate for the shipment of samples nationally and internationally.

A mass spectrometric line for tritium analysis of water and noble gas measurements from different water amounts in the range of microlitres and millilitres.

PubMed

Papp, Laszlo; Palcsu, Laszlo; Major, Zoltan; Rinyu, Laszlo; Tóth, Istvan

2012-01-01

This paper describes the procedure followed for noble gas measurements for litres, millilitres and microlitres of water samples in our laboratory, including sample preparation, mass spectrometric measurement procedure, and the complete calibrations. The preparation line extracts dissolved gases from water samples of volumes of 0.2 μ l to 3 l and it separates them as noble and other chemically active gases. Our compact system handles the following measurements: (i) determination of tritium concentration of environmental water samples by the (3)He ingrowth method; (ii) noble gas measurements from surface water and groundwater; and (iii) noble gas measurements from fluid inclusions of solid geological archives (e.g. speleothems). As a result, the tritium measurements have a detection limit of 0.012 TU, and the expectation value (between 1 and 20 TU) is within 0.2 % of the real concentrations with a standard deviation of 2.4 %. The reproducibility of noble gas measurements for water samples of 20-40 ml allows us to determine solubility temperatures by an uncertainty better than 0.5 °C. Moreover, noble gas measurements for tiny water amounts (in the microlitre range) show that the results of the performed calibration measurements for most noble gas isotopes occur with a deviation of less than 2 %. Theoretically, these precisions for noble gas concentrations obtained from measurements of waters samples of a few microlitres allow us to determine noble gas temperatures by an uncertainty of less than 1 °C. Here, we present the first noble gas measurements of tiny amounts of artificial water samples prepared under laboratory conditions.

Clean and Cold Sample Curation

NASA Technical Reports Server (NTRS)

Allen, C. C.; Agee, C. B.; Beer, R.; Cooper, B. L.

2000-01-01

Curation of Mars samples includes both samples that are returned to Earth, and samples that are collected, examined, and archived on Mars. Both kinds of curation operations will require careful planning to ensure that the samples are not contaminated by the instruments that are used to collect and contain them. In both cases, sample examination and subdivision must take place in an environment that is organically, inorganically, and biologically clean. Some samples will need to be prepared for analysis under ultra-clean or cryogenic conditions. Inorganic and biological cleanliness are achievable separately by cleanroom and biosafety lab techniques. Organic cleanliness to the <50 ng/sq cm level requires material control and sorbent removal - techniques being applied in our Class 10 cleanrooms and sample processing gloveboxes.

Database Resources of the BIG Data Center in 2018

PubMed Central

Xu, Xingjian; Hao, Lili; Zhu, Junwei; Tang, Bixia; Zhou, Qing; Song, Fuhai; Chen, Tingting; Zhang, Sisi; Dong, Lili; Lan, Li; Wang, Yanqing; Sang, Jian; Hao, Lili; Liang, Fang; Cao, Jiabao; Liu, Fang; Liu, Lin; Wang, Fan; Ma, Yingke; Xu, Xingjian; Zhang, Lijuan; Chen, Meili; Tian, Dongmei; Li, Cuiping; Dong, Lili; Du, Zhenglin; Yuan, Na; Zeng, Jingyao; Zhang, Zhewen; Wang, Jinyue; Shi, Shuo; Zhang, Yadong; Pan, Mengyu; Tang, Bixia; Zou, Dong; Song, Shuhui; Sang, Jian; Xia, Lin; Wang, Zhennan; Li, Man; Cao, Jiabao; Niu, Guangyi; Zhang, Yang; Sheng, Xin; Lu, Mingming; Wang, Qi; Xiao, Jingfa; Zou, Dong; Wang, Fan; Hao, Lili; Liang, Fang; Li, Mengwei; Sun, Shixiang; Zou, Dong; Li, Rujiao; Yu, Chunlei; Wang, Guangyu; Sang, Jian; Liu, Lin; Li, Mengwei; Li, Man; Niu, Guangyi; Cao, Jiabao; Sun, Shixiang; Xia, Lin; Yin, Hongyan; Zou, Dong; Xu, Xingjian; Ma, Lina; Chen, Huanxin; Sun, Yubin; Yu, Lei; Zhai, Shuang; Sun, Mingyuan; Zhang, Zhang; Zhao, Wenming; Xiao, Jingfa; Bao, Yiming; Song, Shuhui; Hao, Lili; Li, Rujiao; Ma, Lina; Sang, Jian; Wang, Yanqing; Tang, Bixia; Zou, Dong; Wang, Fan

2018-01-01

Abstract The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. PMID:29036542

The Protein Data Bank

PubMed Central

Berman, Helen M.; Westbrook, John; Feng, Zukang; Gilliland, Gary; Bhat, T. N.; Weissig, Helge; Shindyalov, Ilya N.; Bourne, Philip E.

2000-01-01

The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource. PMID:10592235

A Description of Sexual Offending Committed by Canadian Teachers

ERIC Educational Resources Information Center

Moulden, Heather M.; Firestone, Philip; Kingston, Drew A.; Wexler, Audrey F.

2010-01-01

The aim of this investigation was to describe teachers who sexually offend against youth and the circumstances related to these offenses. Archival Violent Crime Linkage Analysis System reports were obtained from the Royal Canadian Mounted Police, and demographic and criminal characteristics for the offender, as well as information about the victim…

21 CFR 184.1271 - L-Cysteine.

Code of Federal Regulations, 2012 CFR

2012-04-01

... be obtained from the National Academy Press, 2101 Constitution Ave. NW., Washington, DC 20418, or may... availability of this material at NARA, call 202-741-6030, or go to: http://www.archives.gov/federal_register/code_of_federal_regulations/ibr_locations.html. (c) The ingredient is used to supply up to 0.009 part...

21 CFR 184.1271 - L-Cysteine.

Code of Federal Regulations, 2013 CFR

2013-04-01

... be obtained from the National Academy Press, 2101 Constitution Ave. NW., Washington, DC 20418, or may... availability of this material at NARA, call 202-741-6030, or go to: http://www.archives.gov/federal_register/code_of_federal_regulations/ibr_locations.html. (c) The ingredient is used to supply up to 0.009 part...

From Artifacts to Archives: Digging into a Community's Past.

ERIC Educational Resources Information Center

Morgan, Judy

1991-01-01

Presents a two-month historical research project for use in a sixth grade social studies class. Includes student use of artifacts, photographs, news clippings, maps, and oral histories obtained by interviews. Suggests that children compile a chronological history of their community to analyze, organize, and record what they have learned. (DK)

Employing Persons with Severe Disabilities: Much Work Remains to Be Done

ERIC Educational Resources Information Center

Kennedy, R. Bryan; Harris, Nicole K.

2005-01-01

This article presents statistical data depicting the employment of persons with disabilities at a federal installation using a recruitment intervention designed to increase the presence of persons with disabilities. The data were obtained by reviewing archival recruitment accessions that span 5 years (1999-2003). The organization under study is a…

Big heart data: advancing health informatics through data sharing in cardiovascular imaging.

PubMed

Suinesiaputra, Avan; Medrano-Gracia, Pau; Cowan, Brett R; Young, Alistair A

2015-07-01

The burden of heart disease is rapidly worsening due to the increasing prevalence of obesity and diabetes. Data sharing and open database resources for heart health informatics are important for advancing our understanding of cardiovascular function, disease progression and therapeutics. Data sharing enables valuable information, often obtained at considerable expense and effort, to be reused beyond the specific objectives of the original study. Many government funding agencies and journal publishers are requiring data reuse, and are providing mechanisms for data curation and archival. Tools and infrastructure are available to archive anonymous data from a wide range of studies, from descriptive epidemiological data to gigabytes of imaging data. Meta-analyses can be performed to combine raw data from disparate studies to obtain unique comparisons or to enhance statistical power. Open benchmark datasets are invaluable for validating data analysis algorithms and objectively comparing results. This review provides a rationale for increased data sharing and surveys recent progress in the cardiovascular domain. We also highlight the potential of recent large cardiovascular epidemiological studies enabling collaborative efforts to facilitate data sharing, algorithms benchmarking, disease modeling and statistical atlases.

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.

Using 13C in cattle hair to trace back the maize level in the feeding regime-A field test.

PubMed

Hammes, Verena; Nüsse, Olaf; Isselstein, Johannes; Kayser, Manfred

2017-01-01

Sections from cattle hair serve as an isotopic archive-they contain information on the cattle diet from different time periods. We tested the reliability of 13C signatures (δ13C) in cattle tail switch hair to retrospectively trace back the annual dietary proportion of maize of different production systems without having to sample and analyze the feed. Furthermore, we investigated if differences in dietary proportion of maize during summer and winter feeding can be detected in a single tail switch hair by sampling hair only once a year. We sampled hair and obtained information on management and annual composition of diets on 23 cattle farms in northern Germany. Farms differed in dietary proportions of maize, grass and concentrates as well as in grazing regime (year-round grazing, summer grazing, no grazing). We found that the annual mean δ13C values (δ13CY) of two hair sections that contain the isotopic information of summer and winter feeding is a robust indicator for the annual proportion of maize in cattle diet on a farm. The grazing regimes could clearly be distinguished by analyzing seasonal mean δ13C values (δ13CS). We could also demonstrate short term changes in the diet changes by means of δ13CS. We conclude that the method can be used in different cattle production systems to check on dietary proportions of maize for a period of one year before sampling of hair.

Examination of the Triarchic Assessment Procedure for Inconsistent Responding in six non-English language samples.

PubMed

Kelley, Shannon E; van Dongen, Josanne D M; Donnellan, M Brent; Edens, John F; Eisenbarth, Hedwig; Fossati, Andrea; Howner, Katarina; Somma, Antonella; Sörman, Karolina

2018-05-01

The Triarchic Assessment Procedure for Inconsistent Responding (TAPIR; Mowle et al., 2016) was recently developed to identify inattentiveness or comprehension difficulties that may compromise the validity of responses on the Triarchic Psychopathy Measure (TriPM; Patrick, 2010). The TAPIR initially was constructed and cross-validated using exclusively English-speaking participants from the United States; however, research using the TriPM has been increasingly conducted internationally, with numerous foreign language translations of the measure emerging. The present study examined the cross-language utility of the TAPIR in German, Dutch, Swedish, and Italian translations of the TriPM using 6 archival samples of community members, university students, forensic psychiatric inpatients, forensic detainees, and adolescents residing outside the United States (combined N = 5,404). Findings suggest that the TAPIR effectively detects careless responding across these 4 translated versions of the TriPM without the need for language-specific modifications. The TAPIR total score meaningfully discriminated genuine participant responses from both fully and partially randomly generated data in every sample, and demonstrated further utility in detecting fixed "all true" or "all false" response patterns. In addition, TAPIR scores were reliably associated with inconsistent responding scores from another psychopathy inventory. Specificity for a range of tentative cut scores for assessing profile validity was modestly reduced among our samples relative to rates previously obtained with the English version of the TriPM; however, overall the TAPIR appears to demonstrate satisfactory cross-language generalizability. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Introducing the PRIDE Archive RESTful web services.

PubMed

Reisinger, Florian; del-Toro, Noemi; Ternent, Tobias; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-07-01

The PRIDE (PRoteomics IDEntifications) database is one of the world-leading public repositories of mass spectrometry (MS)-based proteomics data and it is a founding member of the ProteomeXchange Consortium of proteomics resources. In the original PRIDE database system, users could access data programmatically by accessing the web services provided by the PRIDE BioMart interface. New REST (REpresentational State Transfer) web services have been developed to serve the most popular functionality provided by BioMart (now discontinued due to data scalability issues) and address the data access requirements of the newly developed PRIDE Archive. Using the API (Application Programming Interface) it is now possible to programmatically query for and retrieve peptide and protein identifications, project and assay metadata and the originally submitted files. Searching and filtering is also possible by metadata information, such as sample details (e.g. species and tissues), instrumentation (mass spectrometer), keywords and other provided annotations. The PRIDE Archive web services were first made available in April 2014. The API has already been adopted by a few applications and standalone tools such as PeptideShaker, PRIDE Inspector, the Unipept web application and the Python-based BioServices package. This application is free and open to all users with no login requirement and can be accessed at http://www.ebi.ac.uk/pride/ws/archive/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Deep-Learning Convolutional Neural Networks Accurately Classify Genetic Mutations in Gliomas.

PubMed

Chang, P; Grinband, J; Weinberg, B D; Bardis, M; Khy, M; Cadena, G; Su, M-Y; Cha, S; Filippi, C G; Bota, D; Baldi, P; Poisson, L M; Jain, R; Chow, D

2018-05-10

The World Health Organization has recently placed new emphasis on the integration of genetic information for gliomas. While tissue sampling remains the criterion standard, noninvasive imaging techniques may provide complimentary insight into clinically relevant genetic mutations. Our aim was to train a convolutional neural network to independently predict underlying molecular genetic mutation status in gliomas with high accuracy and identify the most predictive imaging features for each mutation. MR imaging data and molecular information were retrospectively obtained from The Cancer Imaging Archives for 259 patients with either low- or high-grade gliomas. A convolutional neural network was trained to classify isocitrate dehydrogenase 1 ( IDH1 ) mutation status, 1p/19q codeletion, and O6-methylguanine-DNA methyltransferase ( MGMT ) promotor methylation status. Principal component analysis of the final convolutional neural network layer was used to extract the key imaging features critical for successful classification. Classification had high accuracy: IDH1 mutation status, 94%; 1p/19q codeletion, 92%; and MGMT promotor methylation status, 83%. Each genetic category was also associated with distinctive imaging features such as definition of tumor margins, T1 and FLAIR suppression, extent of edema, extent of necrosis, and textural features. Our results indicate that for The Cancer Imaging Archives dataset, machine-learning approaches allow classification of individual genetic mutations of both low- and high-grade gliomas. We show that relevant MR imaging features acquired from an added dimensionality-reduction technique demonstrate that neural networks are capable of learning key imaging components without prior feature selection or human-directed training. © 2018 by American Journal of Neuroradiology.

Montreal Archive of Sleep Studies: an open-access resource for instrument benchmarking and exploratory research.

PubMed

O'Reilly, Christian; Gosselin, Nadia; Carrier, Julie; Nielsen, Tore

2014-12-01

Manual processing of sleep recordings is extremely time-consuming. Efforts to automate this process have shown promising results, but automatic systems are generally evaluated on private databases, not allowing accurate cross-validation with other systems. In lacking a common benchmark, the relative performances of different systems are not compared easily and advances are compromised. To address this fundamental methodological impediment to sleep study, we propose an open-access database of polysomnographic biosignals. To build this database, whole-night recordings from 200 participants [97 males (aged 42.9 ± 19.8 years) and 103 females (aged 38.3 ± 18.9 years); age range: 18-76 years] were pooled from eight different research protocols performed in three different hospital-based sleep laboratories. All recordings feature a sampling frequency of 256 Hz and an electroencephalography (EEG) montage of 4-20 channels plus standard electro-oculography (EOG), electromyography (EMG), electrocardiography (ECG) and respiratory signals. Access to the database can be obtained through the Montreal Archive of Sleep Studies (MASS) website (http://www.ceams-carsm.ca/en/MASS), and requires only affiliation with a research institution and prior approval by the applicant's local ethical review board. Providing the research community with access to this free and open sleep database is expected to facilitate the development and cross-validation of sleep analysis automation systems. It is also expected that such a shared resource will be a catalyst for cross-centre collaborations on difficult topics such as improving inter-rater agreement on sleep stage scoring. © 2014 European Sleep Research Society.

The XMM Cluster Survey: X-ray analysis methodology

NASA Astrophysics Data System (ADS)

Lloyd-Davies, E. J.; Romer, A. Kathy; Mehrtens, Nicola; Hosmer, Mark; Davidson, Michael; Sabirli, Kivanc; Mann, Robert G.; Hilton, Matt; Liddle, Andrew R.; Viana, Pedro T. P.; Campbell, Heather C.; Collins, Chris A.; Dubois, E. Naomi; Freeman, Peter; Harrison, Craig D.; Hoyle, Ben; Kay, Scott T.; Kuwertz, Emma; Miller, Christopher J.; Nichol, Robert C.; Sahlén, Martin; Stanford, S. A.; Stott, John P.

2011-11-01

The XMM Cluster Survey (XCS) is a serendipitous search for galaxy clusters using all publicly available data in the XMM-Newton Science Archive. Its main aims are to measure cosmological parameters and trace the evolution of X-ray scaling relations. In this paper we describe the data processing methodology applied to the 5776 XMM observations used to construct the current XCS source catalogue. A total of 3675 > 4σ cluster candidates with >50 background-subtracted X-ray counts are extracted from a total non-overlapping area suitable for cluster searching of 410 deg2. Of these, 993 candidates are detected with >300 background-subtracted X-ray photon counts, and we demonstrate that robust temperature measurements can be obtained down to this count limit. We describe in detail the automated pipelines used to perform the spectral and surface brightness fitting for these candidates, as well as to estimate redshifts from the X-ray data alone. A total of 587 (122) X-ray temperatures to a typical accuracy of <40 (<10) per cent have been measured to date. We also present the methodology adopted for determining the selection function of the survey, and show that the extended source detection algorithm is robust to a range of cluster morphologies by inserting mock clusters derived from hydrodynamical simulations into real XMMimages. These tests show that the simple isothermal β-profiles is sufficient to capture the essential details of the cluster population detected in the archival XMM observations. The redshift follow-up of the XCS cluster sample is presented in a companion paper, together with a first data release of 503 optically confirmed clusters.

Swift X-ray monitoring of stellar coronal variability

NASA Astrophysics Data System (ADS)

Miller, Brendan; Hagen, Cedric; Gallo, Elena; Wright, Jason T.

2018-01-01

We used California Planet Search Ca II H and K core emission measurements to identify and characterize chromospheric activity cycles in a sample of main-sequence FGK stars. About a dozen of these with existing ROSAT archival data were targeted with Swift to obtain a current epoch X-ray flux. We find that coronal variability by a factor of several is common on decade-long timescales (we attempt to link to the chromospheric cycle phase) but can also occur on short timescales between Swift visits to a given target, presumably related to stellar rotation and coronal inhomogeneity or to small flares. Additionally, we present new Swift monitoring observations of two M dwarfs with known exoplanets: GJ 15A and GJ 674. GJ 15A b is around 5.3 Earth masses with an 11.4 day orbital period, while GJ 674 is around 11.1 Earth masses with a 4.7 day orbital period. GJ 15A was observed several times in late 2014 and then monitored at approximately weekly intervals for several months in early 2016, for a total exposure of 18 ks. GJ 674 was monitored at approximately weekly intervals for most of 2016, for a total exposure of 40 ks. We provide light curves and hardness ratios for both sources, and also compare to earlier archival X-ray data. Both sources show significant X-ray variability, including between consecutive observations. We quantify the energy distribution for coronal flaring, and compare to optical results for M dwarfs from Kepler. Finally, we discuss the implications of M dwarf coronal activity for exoplanets orbiting within the nominal habitable zone.

Swift X-ray monitoring of stellar coronal variability

NASA Astrophysics Data System (ADS)

Miller, Brendan P.; Gallo, Elena; Wright, Jason; Hagen, Cedric

2017-08-01

We used California Planet Search Ca II H and K core emission measurements to identify and characterize chromospheric activity cycles in a sample of main-sequence FGK stars. About a dozen of these with existing ROSAT archival data were targeted with Swift to obtain a current epoch X-ray flux. We find that coronal variability by a factor of several is common on decade-long timescales (we attempt to link to the chromospheric cycle phase) but can also occur on short timescales between Swift visits to a given target, presumably related to stellar rotation and coronal inhomogeneity or to small flares.Additionally, we present new Swift monitoring observations of two M dwarfs with known exoplanets: GJ 15A and GJ 674. GJ 15A b is around 5.3 Earth masses with an 11.4 day orbital period, while GJ 674 is around 11.1 Earth masses with a 4.7 day orbital period. GJ 15A was observed several times in late 2014 and then monitored at approximately weekly intervals for several months in early 2016, for a total exposure of 18 ks. GJ 674 was monitored at approximately weekly intervals for most of 2016, for a total exposure of 40 ks. We provide light curves and hardness ratios for both sources, and also compare to earlier archival X-ray data. Both sources show significant X-ray variability, including between consecutive observations. We quantify the energy distribution for coronal flaring, and compare to optical results for M dwarfs from Kepler. Finally, we discuss the implications of M dwarf coronal activity for exoplanets orbiting within the nominal habitable zone.

High-resolution characterization of individual flood deposits

NASA Astrophysics Data System (ADS)

Støren, Eivind; Paasche, Øyvind; Hirt, Ann

2014-05-01

In most fluvial landscapes rivers transport sediments within and across catchments throughout the year. During flood events the capacity and competence of the river manifolds, and consequently more sediment are eroded and transported within the catchment. Whenever such sediment-laden rivers reach lakes, sediments are deposited at rate much faster than background sedimentation. For this reason alone, lakes can provide exceptionally rich archives of paleofloods. Flood sediments carry information not only about frequency variability through time, but also about source area(s), the time of the deposit (on a seasonal scale), as well as the evolution of the flood. In order to scrutinize the information that can be extracted from such pristine lake records we have developed an approach where high-resolution data are compared to high-precision measurements of selected samples. More specifically, data from high-resolution X-ray fluorescence (XRF) scanning (Itrax) and magnetic susceptibility (Bartington MS2 point sensor) can potentially provide information on annual to decadal resolution. These fast and effective surface scanning methods are subjected to well-known uncertainties, which can impact the interpretation of individual layers. To overcome this challenge - and obtain the highest possible precision and resolution - precise quantitative analysis of discrete flood layers using magnetic hysteresis measurements and First-order reversal curves (FORCs) as well as conventional X-ray fluorescence spectrometer (Philips PW1404) have been conducted. FORCs are obtained with an Alternating Gradient Force Magnetometer and have exceptional high sensitivity (1 x 10-11 A m2) that allows samples smaller than 200 milligrams to be measured. This means that sediments representing a band of less than a couple of millimeters in the lake sediment cores can be sampled without notable contamination from adjacent non-flood sediments, and analyzed with a high degree of precision (analytical error ±2%). Analyses are carried out on a well-documented lake sediment flood-archive from Meringsdalsvatnet in Southern Norway, which is proven to contain the sedimentary imprint of over hundred floods during the last ca. 10 000 years, including well-known historical events. Preliminary results indicate only minor changes in magnetic mineralogy throughout the record, but notable changes are seen in saturation magnetization, which reflects variations in concentration of the ferromagnetic mineralogy. When these results are compared to corresponding concentration of iron (Fe) and rubidium (Rb) it becomes evident that the core contains two statistical populations, which may indicate two contrasting flood systems. There are at least three potential explanations for this pattern: (1) a dual source area; (2) different mechanisms that trigger floods (spring snowmelting versus intense summer rainstorms); (3) the magnitude of the floods, which influences the sedimentary composition; or 4) a combination of the above.

Assessing the use of 3H-3He dating to determine the subsurface transit time of cave drip waters.

PubMed

Kluge, Tobias; Wieser, Martin; Aeschbach-Hertig, Werner

2010-09-01

(3)H-(3)He measurements constitute a well-established method for the determination of the residence time of young groundwater. However, this method has rarely been applied to karstified aquifers and in particular to drip water in caves, despite the importance of the information which may be obtained. Besides the determination of transfer times of climate signals from the atmosphere through the epikarst to speleothems as climate archives, (3)H-(3)He together with Ne, Ar, Kr, Xe data may also help to give new insights into the local hydrogeology, e.g. the possible existence of a perched aquifer above a cave. In order to check the applicability of (3)H-(3)He dating to cave drips, we collected drip water samples from three adjacent caves in northwestern Germany during several campaigns. The noble gas data were evaluated by inverse modelling to obtain recharge temperature and excess air, supporting the calculation of the tritiogenic (3)He and hence the (3)H-(3)He age. Although atmospheric noble gases were often found to be close to equilibrium with the cave atmosphere, several drip water samples yielded an elevated (3)He/(4)He ratio, providing evidence for the accumulation of (3)He from the decay of (3)H. No significant contribution of radiogenic (4)He was found, corresponding to the low residence times mostly in the range of one to three years. Despite complications during sampling, conditions of a perched aquifer could be confirmed by replicate samples at one drip site. Here, the excess air indicator ΔNe was about 10 %, comparable to typical values found in aquifers in mid-latitudes. The mean (3)H-(3)He age of 2.1 years at this site presumably refers to the residence time in the perched aquifer and is lower than the entire transit time of 3.4 years estimated from the tritium data.

Yet More Visualized JAMSTEC Cruise and Dive Information

NASA Astrophysics Data System (ADS)

Tomiyama, T.; Hase, H.; Fukuda, K.; Saito, H.; Kayo, M.; Matsuda, S.; Azuma, S.

2014-12-01

Every year, JAMSTEC performs about a hundred of research cruises and numerous dive surveys using its research vessels and submersibles. JAMSTEC provides data and samples obtained during these cruises and dives to international users through a series of data sites on the Internet. The "DARWIN (http://www.godac.jamstec.go.jp/darwin/e)" data site disseminates cruise and dive information. On DARWIN, users can search interested cruises and dives with a combination search form or an interactive tree menu, and find lists of observation data as well as links to surrounding databases. Document catalog, physical sample databases, and visual archive of dive surveys (e. g. in http://www.godac.jamstec.go.jp/jmedia/portal/e) are directly accessible from the lists. In 2014, DARWIN experienced an update, which was arranged mainly for enabling on-demand data visualization. Using　login users' functions, users can put listed data items into the virtual basket and then trim, plot and download the data. The visualization tools help users to quickly grasp the quality and characteristics of observation data. Meanwhile, JAMSTEC launched a new data site named "JDIVES (http://www.godac.jamstec.go.jp/jdives/e)"　to visualize data and sample information obtained by dive surveys. JDIVES shows tracks of dive surveys on the "Google Earth Plugin" and diagrams of deep-sea environmental data such as temperature, salinity, and depth. Submersible camera images and links to associated databases are placed along the dive tracks. The JDVIES interface enables users to perform so-called virtual dive surveys, which can help users to understand local geometries of dive spots and geological settings of associated data and samples. It is not easy for individual researchers to organize a huge amount of information recovered from each cruise and dive. The improved visibility and accessibility of JAMSTEC databases are advantageous not only for second-hand users, but also for on-board researchers themselves.

Performance of a HRP-2/pLDH based rapid diagnostic test at the Bangladesh-India-Myanmar border areas for diagnosis of clinical malaria

PubMed Central

2013-01-01

Background The rapid diagnostic test (RDT) has been adopted in contemporary malaria control and management programmes around the world as it represents a fast and apt alternative for malaria diagnosis in a resource-limited setting. This study assessed the performance of a HRP-2/pLDH based RDT (Parascreen® Pan/Pf) in a laboratory setting utilizing clinical samples obtained from the field. Methods Whole blood samples were obtained from febrile patients referred for malaria diagnosis by clinicians from two different Upazila Health Complexes (UHCs) located near the Bangladesh-India and Bangladesh-Myanmar border where malaria is endemic. RDT was performed on archived samples and sensitivity and specificity evaluated with expert microscopy (EM) and quantitative PCR (qPCR). Results A total of 327 clinical samples were made available for the study, of which 153 were Plasmodium falciparum-positive and 54 were Plasmodium vivax-positive. In comparison with EM, for P. falciparum malaria, the RDT had sensitivity: 96.0% (95% CI, 91.2-98.3) and specificity: 98.2% (95% CI, 94.6-99.5) and for P. vivax, sensitivity: 90.7% (95% CI, 78.9-96.5) and specificity: 98.9% (95% CI, 96.5-99.7). Comparison with qPCR showed, for P. falciparum malaria, sensitivity: 95.4% (95% CI, 90.5-98.0) and specificity: 98.8% (95% CI, 95.4-99.7) and for P. vivax malaria, sensitivity: 89.0% (95% CI,77.0-95.4) and specificity: 98.8% (95% CI, 96.5-99.7). Sensitivity varied according to different parasitaemia for falciparum and vivax malaria diagnosis. Conclusion Parascreen® Pan/Pf Rapid test for malaria showed acceptable sensitivity and specificity in border belt endemic areas of Bangladesh when compared with EM and qPCR. PMID:24172045

Laboratory divergence of Methylobacterium extorquens AM1 through unintended domestication and past selection for antibiotic resistance

PubMed Central

2014-01-01

Background A common assumption of microorganisms is that laboratory stocks will remain genetically and phenotypically constant over time, and across laboratories. It is becoming increasingly clear, however, that mutations can ruin strain integrity and drive the divergence or “domestication” of stocks. Since its discovery in 1960, a stock of Methylobacterium extorquens AM1 (“AM1”) has remained in the lab, propagated across numerous growth and storage conditions, researchers, and facilities. To explore the extent to which this lineage has diverged, we compared our own “Modern” stock of AM1 to a sample archived at a culture stock center shortly after the strain’s discovery. Stored as a lyophilized sample, we hypothesized that this Archival strain would better reflect the first-ever isolate of AM1 and reveal ways in which our Modern stock has changed through laboratory domestication or other means. Results Using whole-genome re-sequencing, we identified some 29 mutations – including single nucleotide polymorphisms, small indels, the insertion of mobile elements, and the loss of roughly 36 kb of DNA - that arose in the laboratory-maintained Modern lineage. Contrary to our expectations, Modern was both slower and less fit than Archival across a variety of growth substrates, and showed no improvement during long-term growth and storage. Modern did, however, outperform Archival during growth on nutrient broth, and in resistance to rifamycin, which was selected for by researchers in the 1980s. Recapitulating selection for rifamycin resistance in replicate Archival populations showed that mutations to RNA polymerase B (rpoB) substantially decrease growth in the absence of antibiotic, offering an explanation for slower growth in Modern stocks. Given the large number of genomic changes arising from domestication (28), it is somewhat surprising that the single other mutation attributed to purposeful laboratory selection accounts for much of the phenotypic divergence between strains. Conclusions These results highlight the surprising degree to which AM1 has diverged through a combination of unintended laboratory domestication and purposeful selection for rifamycin resistance. Instances of strain divergence are important, not only to ensure consistency of experimental results, but also to explore how microbes in the lab diverge from one another and from their wild counterparts. PMID:24384040

30 CFR 780.21 - Hydrologic information.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 3 2011-07-01 2011-07-01 false Hydrologic information. 780.21 Section 780.21... Hydrologic information. (a) Sampling and analysis methodology. All water-quality analyses performed to meet... information on the availability of this material at NARA, call 202-741-6030, or go to: http://www.archives.gov...

30 CFR 780.21 - Hydrologic information.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 30 Mineral Resources 3 2012-07-01 2012-07-01 false Hydrologic information. 780.21 Section 780.21... Hydrologic information. (a) Sampling and analysis methodology. All water-quality analyses performed to meet... information on the availability of this material at NARA, call 202-741-6030, or go to: http://www.archives.gov...

9 CFR 113.209 - Rabies Vaccine, Killed Virus.

Code of Federal Regulations, 2010 CFR

2010-01-01

... immunogenicity of vaccine prepared with virus at the highest passage from the Master Seed shall be established in... the availability of this material at NARA, call 202-741-6030, or go to: http://www.archives.gov... observation period, the serial is unsatisfactory. (3) Potency test. Bulk or final container samples of...

Measuring stream temperature with digital data loggers: a user's guide

Treesearch

Jason Dunham; Gwynne Chandler; Bruce Rieman; Don Martin

2005-01-01

Digital data loggers (thermographs) are among the most widespread instruments in use for monitoring physical conditions in aquatic ecosystems. The intent of this protocol is to provide guidelines for selecting and programming data loggers, sampling water temperatures in the field, data screening and analysis, and data archiving.

PRECISION OF ATMOSPHERIC DRY DEPOSITION DATA FROM THE CLEAN AIR STATUS AND TRENDS NETWORK (CASTNET)

EPA Science Inventory

A collocated, dry deposition sampling program was begun in January 1987 by the US Environmental Protection Agency to provide ongoing estimates of the overall precision of dry deposition and supporting data entering the Clean Air Status and Trends Network (CASTNet) archives Duplic...

A Correlation Study of Secondary Education and Postsecondary Outcomes for Native Americans with Disabilities

ERIC Educational Resources Information Center

Graham, Deborah J.

2016-01-01

This nonexperimental quantitative correlation study examined relationships between select special education and standardized testing variables for a purposive homogeneous sample of Arizona secondary school districts with Native American populations, and the archival records for students with disabilities postsecondary outcomes between 2012 and…

BAPA Database: a Landslide Inventory in the Principality of Asturias (NW Spain) by Using Press Archives and Free Cartographic Servers

NASA Astrophysics Data System (ADS)

Valenzuela, P.; Domínguez-Cuesta, M. J.; Jiménez-Sánchez, M.; Mora García, M. A.

2015-12-01

Due to its geological and climatic conditions, landslides are very common and widespread phenomena in the Principality of Asturias (NW of Spain), causing economic losses and, sometimes, human victims. In this scenario, temporal prediction of instabilities becomes particularly important. Although previous knowledge indicates that rainfall is the main trigger, the lack of data hinders the proper temporal forecast of landslides in the region. To resolve this deficiency, a new landslide inventory is being developed: the BAPA (Base de datos de Argayos del Principado de Asturias-Principality of Asturias Landslide Database). Data collection is mainly performed through the gathering of local newspaper archives, with special emphasis on the registration of spatial and temporal information. Moreover, a BAPA App and a BAPA website (http://geol.uniovi.es/BAPA) have been developed to easily obtain additional information from authorities and private individuals. Presently, dataset covers the period 1980-2015, registering more than 2000 individual landslide events. Fifty-two per cent of the records provide accurate dates, showing the usefulness of press archives as temporal records. The use of free cartographic servers, such as Google Maps, Google Street View and Iberpix (Government of Spain), combined with the spatial descriptions and photographs contained in the press releases, makes it possible to determine the exact location in fifty-eight per cent of the records. Field work performed to date has allowed the validation of the methodology proposed to obtain spatial data. In addition, BAPA database contain information about: source, typology of landslides, triggers, damages and costs.

The amino acid's backup bone - storage solutions for proteomics facilities.

PubMed

Meckel, Hagen; Stephan, Christian; Bunse, Christian; Krafzik, Michael; Reher, Christopher; Kohl, Michael; Meyer, Helmut Erich; Eisenacher, Martin

2014-01-01

Proteomics methods, especially high-throughput mass spectrometry analysis have been continually developed and improved over the years. The analysis of complex biological samples produces large volumes of raw data. Data storage and recovery management pose substantial challenges to biomedical or proteomic facilities regarding backup and archiving concepts as well as hardware requirements. In this article we describe differences between the terms backup and archive with regard to manual and automatic approaches. We also introduce different storage concepts and technologies from transportable media to professional solutions such as redundant array of independent disks (RAID) systems, network attached storages (NAS) and storage area network (SAN). Moreover, we present a software solution, which we developed for the purpose of long-term preservation of large mass spectrometry raw data files on an object storage device (OSD) archiving system. Finally, advantages, disadvantages, and experiences from routine operations of the presented concepts and technologies are evaluated and discussed. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. Copyright © 2013. Published by Elsevier B.V.

Guidelines for collecting and maintaining archives for genetic monitoring

USGS Publications Warehouse

Jackson, Jennifer A.; Laikre, Linda; Baker, C. Scott; Kendall, Katherine C.; ,

2012-01-01

Rapid advances in molecular genetic techniques and the statistical analysis of genetic data have revolutionized the way that populations of animals, plants and microorganisms can be monitored. Genetic monitoring is the practice of using molecular genetic markers to track changes in the abundance, diversity or distribution of populations, species or ecosystems over time, and to follow adaptive and non-adaptive genetic responses to changing external conditions. In recent years, genetic monitoring has become a valuable tool in conservation management of biological diversity and ecological analysis, helping to illuminate and define cryptic and poorly understood species and populations. Many of the detected biodiversity declines, changes in distribution and hybridization events have helped to drive changes in policy and management. Because a time series of samples is necessary to detect trends of change in genetic diversity and species composition, archiving is a critical component of genetic monitoring. Here we discuss the collection, development, maintenance, and use of archives for genetic monitoring. This includes an overview of the genetic markers that facilitate effective monitoring, describes how tissue and DNA can be stored, and provides guidelines for proper practice.

PLANET HUNTERS. VIII. CHARACTERIZATION OF 41 LONG-PERIOD EXOPLANET CANDIDATES FROM KEPLER ARCHIVAL DATA

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

Wang, Ji; Fischer, Debra A.; Picard, Alyssa

2015-12-20

The census of exoplanets is incomplete for orbital distances larger than 1 AU. Here, we present 41 long-period planet candidates in 38 systems identified by Planet Hunters based on Kepler archival data (Q0–Q17). Among them, 17 exhibit only one transit, 14 have two visible transits, and 10 have more than three visible transits. For planet candidates with only one visible transit, we estimate their orbital periods based on transit duration and host star properties. The majority of the planet candidates in this work (75%) have orbital periods that correspond to distances of 1–3 AU from their host stars. We conduct follow-up imaging and spectroscopic observationsmore » to validate and characterize planet host stars. In total, we obtain adaptive optics images for 33 stars to search for possible blending sources. Six stars have stellar companions within 4″. We obtain high-resolution spectra for 6 stars to determine their physical properties. Stellar properties for other stars are obtained from the NASA Exoplanet Archive and the Kepler Stellar Catalog by Huber et al. We validate 7 planet candidates that have planet confidence over 0.997 (3σ level). These validated planets include 3 single-transit planets (KIC-3558849b, KIC-5951458b, and KIC-8540376c), 3 planets with double transits (KIC-8540376b, KIC-9663113b, and KIC-10525077b), and 1 planet with four transits (KIC-5437945b). This work provides assessment regarding the existence of planets at wide separations and the associated false positive rate for transiting observation (17%–33%). More than half of the long-period planets with at least three transits in this paper exhibit transit timing variations up to 41 hr, which suggest additional components that dynamically interact with the transiting planet candidates. The nature of these components can be determined by follow-up radial velocity and transit observations.« less

Exposing Exposure: Automated Anatomy-specific CT Radiation Exposure Extraction for Quality Assurance and Radiation Monitoring

PubMed Central

Warden, Graham I.; Farkas, Cameron E.; Ikuta, Ichiro; Prevedello, Luciano M.; Andriole, Katherine P.; Khorasani, Ramin

2012-01-01

Purpose: To develop and validate an informatics toolkit that extracts anatomy-specific computed tomography (CT) radiation exposure metrics (volume CT dose index and dose-length product) from existing digital image archives through optical character recognition of CT dose report screen captures (dose screens) combined with Digital Imaging and Communications in Medicine attributes. Materials and Methods: This institutional review board–approved HIPAA-compliant study was performed in a large urban health care delivery network. Data were drawn from a random sample of CT encounters that occurred between 2000 and 2010; images from these encounters were contained within the enterprise image archive, which encompassed images obtained at an adult academic tertiary referral hospital and its affiliated sites, including a cancer center, a community hospital, and outpatient imaging centers, as well as images imported from other facilities. Software was validated by using 150 randomly selected encounters for each major CT scanner manufacturer, with outcome measures of dose screen retrieval rate (proportion of correctly located dose screens) and anatomic assignment precision (proportion of extracted exposure data with correctly assigned anatomic region, such as head, chest, or abdomen and pelvis). The 95% binomial confidence intervals (CIs) were calculated for discrete proportions, and CIs were derived from the standard error of the mean for continuous variables. After validation, the informatics toolkit was used to populate an exposure repository from a cohort of 54 549 CT encounters; of which 29 948 had available dose screens. Results: Validation yielded a dose screen retrieval rate of 99% (597 of 605 CT encounters; 95% CI: 98%, 100%) and an anatomic assignment precision of 94% (summed DLP fraction correct 563 in 600 CT encounters; 95% CI: 92%, 96%). Patient safety applications of the resulting data repository include benchmarking between institutions, CT protocol quality control and optimization, and cumulative patient- and anatomy-specific radiation exposure monitoring. Conclusion: Large-scale anatomy-specific radiation exposure data repositories can be created with high fidelity from existing digital image archives by using open-source informatics tools. ©RSNA, 2012 Supplemental material: http://radiology.rsna.org/lookup/suppl/doi:10.1148/radiol.12111822/-/DC1 PMID:22668563

From 20 cm - 1 micron: Measuring the Gas and Dust in Massive Low Surface Brightness Galaxies

NASA Astrophysics Data System (ADS)

Kearsley, E.; O'Neil, K.

2005-12-01

Archival data from the IRAS, 2MASS, NVSS, and FIRST catalogs, supplemented with new measurements of HI, are used to analyze the relationship between the relative mass of the various components of galaxies (stars, atomic hydrogen, dust, and molecular gas) using a small sample of nearby (z<0.1), massive low surface brightness galaxies. The sample is compared to three sets of published data: a large collection of radio sources from the UGC having a radio continuum intensity >2.5 mJy (Condon, Cotton, & Broderick 2002 AJ 124, 675) ; a smaller sample of low surface brightness galaxies (Galaz, et al 2002 2002 AJ 124, 1360); and a collection of NIR low surface brightness galaxies (Monnier-Ragaigne, et al 2002 Ap&SS 281, 145). Overall, our sample properties are similar to the comparison samples in regard to NIR color, gas, stellar, and dynamic mass ratios, etc. Based off the galaxies' q-value (determined from the FIR/1.4 GHz ratio), it appears likely that at least two of the 28 galaxies studied harbor AGN. Notably, we also find that if we naively assume the ratio of the dust and molecular gas mass relative to the mass of HI is a constant we are unable to predict the observed ratio of stellar mass to HI mass, indicating that the HI mass ratio is a poor indicator of the total baryonic mass in the studied galaxies. HI measurements obtained during this study using the Green Bank Telescope also provide a correction to the velocity of UGC 11068.

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

King, W. D.

In order to appropriately model and predict the chemical integrity and performance of cementitious materials used for waste immobilization at the Savannah River Site (SRS), it is critical to understand the I-129 solubility and distribution within the tank farm. Iodine in radioactive waste and in environmental media is typically highly mobile and long lived. Iodine is ubiquitous in SRS tank waste and waste forms. The iodine is assumed to be soluble and present at low levels in Performance Assessments (PAs) for SRS Tank Farms, and is one of the dose drivers in the PAs for both the SRS Salt Disposalmore » Facility (SDF) and the H-Area Tank Farm (HTF). Analysis of tank waste samples is critical to understanding the Tank Farm iodine inventory and reducing disposal uncertainty. Higher than expected iodine levels have recently been observed in residual solids isolated from some SRS tanks prior to closure, indicating uncertainty regarding the chemical species involved. If the iodine inventory uncertainty is larger than anticipated, future work may be necessary to reduce the uncertainty. This memorandum satisfies a portion of the work scope identified in Task Plan SRNL-RP-2016-00651. A separate memorandum issued previously, reported historical unpublished I-129 data, a significant portion of which was below detectable analytical limits. This memorandum includes iodine and general chemical analysis results for six archived SRNL samples which were previously reported to have I-129 concentrations below detectable limits. Lower sample dilution factors were used for the current analyses in order to obtain concentrations above detection. The samples analyzed included surface and depth samples from SRS tanks 30, 32, and 39.« less

Archiving Spectral Libraries in the Planetary Data System

NASA Astrophysics Data System (ADS)

Slavney, S.; Guinness, E. A.; Scholes, D.; Zastrow, A.

2017-12-01

Spectral libraries are becoming popular candidates for archiving in PDS. With the increase in the number of individual investigators funded by programs such as NASA's PDART, the PDS Geosciences Node is receiving many requests for support from proposers wishing to archive various forms of laboratory spectra. To accommodate the need for a standardized approach to archiving spectra, the Geosciences Node has designed the PDS Spectral Library Data Dictionary, which contains PDS4 classes and attributes specifically for labeling spectral data, including a classification scheme for samples. The Reflectance Experiment Laboratory (RELAB) at Brown University, which has long been a provider of spectroscopy equipment and services to the science community, has provided expert input into the design of the dictionary. Together the Geosciences Node and RELAB are preparing the whole of the RELAB Spectral Library, consisting of many thousands of spectra collected over the years, to be archived in PDS. An online interface for searching, displaying, and downloading selected spectra is planned, using the Spectral Library metadata recorded in the PDS labels. The data dictionary and online interface will be extended to include spectral libraries submitted by other data providers. The Spectral Library Data Dictionary is now available from PDS at https://pds.nasa.gov/pds4/schema/released/. It can be used in PDS4 labels for reflectance spectra as well as for Raman, XRF, XRD, LIBS, and other types of spectra. Ancillary data such as images, chemistry, and abundance data are also supported. To help generate PDS4-compliant labels for spectra, the Geosciences Node provides a label generation program called MakeLabels (http://pds-geosciences.wustl.edu/tools/makelabels.html) which creates labels from a template, and which can be used for any kind of PDS4 label. For information, contact the Geosciences Node at geosci@wunder.wustl.edu.

Radio polarization properties of quasars and active galaxies at high redshifts

NASA Astrophysics Data System (ADS)

Vernstrom, T.; Gaensler, B. M.; Vacca, V.; Farnes, J. S.; Haverkorn, M.; O'Sullivan, S. P.

2018-04-01

We present the largest ever sample of radio polarization properties for z > 4 sources, with 14 sources having significant polarization detections. Using wide-band data from the Karl G. Jansky Very Large Array, we obtained the rest-frame total intensity and polarization properties of 37 radio sources, nine of which have spectroscopic redshifts in the range 1 ≤ z ≤ 1.4, with the other 28 having spectroscopic redshifts in the range 3.5 ≤ z ≤ 6.21. Fits are performed for the Stokes I and fractional polarization spectra, and Faraday rotation measures are derived using rotation measure synthesis and QU fitting. Using archival data of 476 polarized sources, we compare high-redshift (z > 3) source properties to a 15 GHz rest-frame luminosity matched sample of low-redshift (z < 3) sources to investigate if the polarization properties of radio sources at high redshifts are intrinsically different than those at low redshift. We find a mean of the rotation measure absolute values, corrected for Galactic rotation, of 50 ± 22 rad m-2 for z > 3 sources and 57 ± 4 rad m-2 for z < 3. Although there is some indication of lower intrinsic rotation measures at high-z possibly due to higher depolarization from the high-density environments, using several statistical tests we detect no significant difference between low- and high-redshift sources. Larger samples are necessary to determine any true physical difference.

Sample introducing apparatus and sample modules for mass spectrometer

DOEpatents

Thompson, Cyril V.; Wise, Marcus B.

1993-01-01

An apparatus for introducing gaseous samples from a wide range of environmental matrices into a mass spectrometer for analysis of the samples is described. Several sample preparing modules including a real-time air monitoring module, a soil/liquid purge module, and a thermal desorption module are individually and rapidly attachable to the sample introducing apparatus for supplying gaseous samples to the mass spectrometer. The sample-introducing apparatus uses a capillary column for conveying the gaseous samples into the mass spectrometer and is provided with an open/split interface in communication with the capillary and a sample archiving port through which at least about 90 percent of the gaseous sample in a mixture with an inert gas that was introduced into the sample introducing apparatus is separated from a minor portion of the mixture entering the capillary discharged from the sample introducing apparatus.

Influence of imaging resolution on color fidelity in digital archiving.

PubMed

Zhang, Pengchang; Toque, Jay Arre; Ide-Ektessabi, Ari

2015-11-01

Color fidelity is of paramount importance in digital archiving. In this paper, the relationship between color fidelity and imaging resolution was explored by calculating the color difference of an IT8.7/2 color chart with a CIELAB color difference formula for scanning and simulation images. Microscopic spatial sampling was used in selecting the image pixels for the calculations to highlight the loss of color information. A ratio, called the relative imaging definition (RID), was defined to express the correlation between image resolution and color fidelity. The results show that in order for color differences to remain unrecognizable, the imaging resolution should be at least 10 times higher than the physical dimension of the smallest feature in the object being studied.

Identifying a Robust and Practical Quasar Accretion-Rate Indicator Using the Chandra Archive

NASA Astrophysics Data System (ADS)

Shemmer, Ohad

2017-09-01

Understanding the rapid growth of supermassive black holes and the assembly of their host galaxies is severely limited by the lack of reliable estimates of black-hole mass and accretion rate in distant quasars. We propose to utilize the Chandra archive to identify the most reliable and practical Eddington-ratio indicator by investigating diagnostics of quasar accretion power in the hard-X-ray, C IV, and Hbeta spectral bands of a carefully-selected sample of optically-selected sources. We will perform a ``stress test'' to each of these diagnostics, relying critically on the hard-X-ray observable properties, and deliver a prescription for the most robust Eddington-ratio estimate that can be utilized economically at the highest accessible redshifts.

A user`s guide to LUGSAN II. A computer program to calculate and archive lug and sway brace loads for aircraft-carried stores

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

Dunn, W.N.

1998-03-01

LUG and Sway brace ANalysis (LUGSAN) II is an analysis and database computer program that is designed to calculate store lug and sway brace loads for aircraft captive carriage. LUGSAN II combines the rigid body dynamics code, SWAY85, with a Macintosh Hypercard database to function both as an analysis and archival system. This report describes the LUGSAN II application program, which operates on the Macintosh System (Hypercard 2.2 or later) and includes function descriptions, layout examples, and sample sessions. Although this report is primarily a user`s manual, a brief overview of the LUGSAN II computer code is included with suggestedmore » resources for programmers.« less

Diplodon shells from Northwest Patagonia as continental proxy archives: Oxygen isotopic results and sclerochronological analyses

NASA Astrophysics Data System (ADS)

Soldati, A. L.; Beierlein, L.; Jacob, D. E.

2009-04-01

Freshwater mussels of the genus Diplodon (Bivalvia, Hyriidae) are the most abundant bivalve (today and in the past) in freshwater bodies at both sides of the South-Andean Cordillera. There are about 25 different Diplodon genera in Argentina and Chile that could be assigned almost completely to the species Diplodon chilensis (Gray, 1828) and two subspecies: D. ch. chilensis and D. ch. patagonicus; this latter species is found in Argentina between Mendoza (32˚ 52' S; 68˚ 51' W) and Chubut (45˚ 51' S; 67˚ 28' W), including the lakes and rivers of the target area, the Nahuel Huapi National Park (Castellanos, 1960). Despite their wide geographic distribution, Diplodon species have only rarely been used as climate archives in the southern hemisphere. Kaandorp et al. (2005) demonstrated for Diplodon longulus (Conrad 1874) collected from the Peruvian Amazonas that oxygen isotopic patterns in the shells could be used in order to reconstruct the precipitation regime and dry/wet seasonal of the monsoonal system in Amazonia. Although this study demonstrated the potential of Diplodon in climatological and ecological reconstructions in the southern hemisphere, as of yet, no systematic study of Diplodon as a multi-proxy archive has been undertaken for the Patagonian region. In this work we present sclerochronological analyses supported by ^18Oshell in recent mussel of Diplodon chilensis patagonicus (D'Orbigny, 1835) collected at Laguna El Trébol (42°S-71°W, Patagonia Argentina), one of the best studied water bodies in the region for paleoclimate analysis. Water temperature was measured every six hours for one year using a temperature sensor (Starmon mini®) placed at 5m depth in the lake, close to a mussel bank. Additionally, ^18Owater was measured monthly for the same time range.g^18Oshell values obtained by micro-milling at high spatial resolution in the growth increments of three Diplodon shells were compared to these records, and to air temperature and precipitation records in the region (from the NOAA database, station: airport of S.C. de Bariloche: 41°S-71°W). D. ch. patagonicus exhibit very well developed annual growth lines, which allow calibrating a precise temporal scale with calendar years in the shell (Soldati et al., 2008). Extremely wide increments (e.g. years 2000-2001 and 1978-1979), related to distinct periods (so-called benchmark increments) are present in all specimens and can be used to anchor the growth curves in order to create a master curve for the lake. ^18Oshell varies seasonally, presenting minima during the warm season (November/March) and maxima in the austral autumn/winter (April/October), reproducing the temperature fluctuations in the region. The resolution of the ^18Oshell measurement varies for each year: samples obtained from larger annual increments (>1 mm, generally mussels younger than 10 years old) allow a resolution of ca. 2 months (5-7 samples per year), and sometimes even give a 5 weeks resolution, while thinner annual increments (between 1 and 0.1 mm, generally older than 10 years) allow only a 4-6 month resolution (2-3 points per sampled year). Because of their long live span of ca. 100 years, Diplodon shells are useful to construct an accurate climatological archive for Patagonia with time windows of around a century, resolving the environmental signal annually and even seasonally. References: CASTELLANOS Z.A. (1960). Almejas nacaríferas de la República Argentina. Género Diplodon. Secretaría de Agricultura, Publicación Miscelánea, 421: 1-40. KAANDORP R.J.G., VONHOF H.B., WESSELINGH F.P., PITTMAN L.R., KROON D. & HINTE J.E.V. (2005). Seasonal Amazonian rainfall variation in the Miocene Climate Optimum. Palaeogeography, Palaeoclimatology, Palaeoecology, 221: 1-6. SOLDATI A.L., JACOB D.E., SCHÖNE B.R., BIANCHI M.M., HAJDUK A. (2008). Seasonal periodicity of growth and composition in valves of Diplodon chilensis patagonicus (D'Orbigny, 1835). Journal of Molluscan Studies, doi:10.1093/mollus/eyn044.

Assessment of Contribution of Contemporary Carbon Sources to Size-Fractionated Particulate Matter and Time-Resolved Bulk Particulate Matter Using the Measurement of Radiocarbon

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

Hwang, H M; Young, T M; Buchholz, B A

2009-04-16

This study was motivated by a desire to improve understanding of the sources contributing to the carbon that is an important component of airborne particulate matter (PM). The ultimate goal of this project was to lay a ground work for future tools that might be easily implemented with archived or routinely collected samples. A key feature of this study was application of radiocarbon measurement that can be interpreted to indicate the relative contributions from fossil and non-fossil carbon sources of atmospheric PM. Size-resolved PM and time-resolved PM{sub 10} collected from a site in Sacramento, CA in November 2007 (Phase I)more » and March 2008 (Phase II) were analyzed for radiocarbon and source markers such as levoglucosan, cholesterol, and elemental carbon. Radiocarbon data indicates that the contributions of non-fossil carbon sources were much greater than that from fossil carbon sources in all samples. Radiocarbon and source marker measurements confirm that a greater contribution of non-fossil carbon sources in Phase I samples was highly likely due to residential wood combustion. The present study proves that measurement of radiocarbon and source markers can be readily applied to archived or routinely collected samples for better characterization of PM sources. More accurate source apportionment will support ARB in developing more efficient control strategies.« less

Creating and Searching a Local Inventory for Data Granules in a Remote Archive

NASA Astrophysics Data System (ADS)

Cornillon, P. C.

2016-12-01

More often than not, search capabilities for network accessible data do not exist or do not meet the requirements of the user. For large archives this can make finding data of interest tedious at best. This summer, the author encountered such a problem with regard to the two existing archives of VIIRS L2 sea surface temperature (SST) fields obtained with the new ACSPO retrieval algorithm; one at the Jet Propulsion Laboratory's PO-DAAC and the other at NOAA's National Centers for Environmental Information (NCEI). In both cases the data were available via ftp and OPeNDAP but there was no search capability at the PO-DAAC and the NCEI archive was incomplete. Furthermore, in order to meet the needs of a broad range of datasets and users, the beta version of the search engine at NCEI was cumbersome for the searches of interest. Although some of these problems have been resolved since (and may be described in other posters/presentations at this meeting), the solution described in this presentation offers the user the ability to develop a search capability for archives lacking a search capability and/or to configure searches more to his or her preferences than the generic searches offered by the data provider. The solution, a Matlab script, used html access to the PO-DAAC web site to locate all VIIRS 10 minute granules and OPeNDAP access to acquire the bounding box for each granule from the metadata bound to the file. This task required several hours of wall time to acquire the data and to write the bounding boxes to a local file with the associated ftp and OPeNDAP urls for the 110,000+ granule archive. A second Matlab script searched the local archive, seconds, for granules falling in a user defined space-time window and an ascii file of wget commands associated with these was generated. This file was then executed to acquire the data of interest. The wget commands can be configured to acquire the entire files via ftp or a subset of each file via OPeNDAP. Furthermore, the search capability, based on bounding boxes and rectangular regions, could easily be modified to further refine the search. Finally, the script that builds the inventory has been designed to update the local inventory, minutes per month rather than hours.

Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research

PubMed Central

Spjuth, Ola; Krestyaninova, Maria; Hastings, Janna; Shen, Huei-Yi; Heikkinen, Jani; Waldenberger, Melanie; Langhammer, Arnulf; Ladenvall, Claes; Esko, Tõnu; Persson, Mats-Åke; Heggland, Jon; Dietrich, Joern; Ose, Sandra; Gieger, Christian; Ried, Janina S; Peters, Annette; Fortier, Isabel; de Geus, Eco JC; Klovins, Janis; Zaharenko, Linda; Willemsen, Gonneke; Hottenga, Jouke-Jan; Litton, Jan-Eric; Karvanen, Juha; Boomsma, Dorret I; Groop, Leif; Rung, Johan; Palmgren, Juni; Pedersen, Nancy L; McCarthy, Mark I; van Duijn, Cornelia M; Hveem, Kristian; Metspalu, Andres; Ripatti, Samuli; Prokopenko, Inga; Harris, Jennifer R

2016-01-01

A wealth of biospecimen samples are stored in modern globally distributed biobanks. Biomedical researchers worldwide need to be able to combine the available resources to improve the power of large-scale studies. A prerequisite for this effort is to be able to search and access phenotypic, clinical and other information about samples that are currently stored at biobanks in an integrated manner. However, privacy issues together with heterogeneous information systems and the lack of agreed-upon vocabularies have made specimen searching across multiple biobanks extremely challenging. We describe three case studies where we have linked samples and sample descriptions in order to facilitate global searching of available samples for research. The use cases include the ENGAGE (European Network for Genetic and Genomic Epidemiology) consortium comprising at least 39 cohorts, the SUMMIT (surrogate markers for micro- and macro-vascular hard endpoints for innovative diabetes tools) consortium and a pilot for data integration between a Swedish clinical health registry and a biobank. We used the Sample avAILability (SAIL) method for data linking: first, created harmonised variables and then annotated and made searchable information on the number of specimens available in individual biobanks for various phenotypic categories. By operating on this categorised availability data we sidestep many obstacles related to privacy that arise when handling real values and show that harmonised and annotated records about data availability across disparate biomedical archives provide a key methodological advance in pre-analysis exchange of information between biobanks, that is, during the project planning phase. PMID:26306643