Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project.

PubMed

Omenn, Gilbert S; Lane, Lydie; Lundberg, Emma K; Overall, Christopher M; Deutsch, Eric W

2017-12-01

The Human Proteome Organization (HUPO) Human Proteome Project (HPP) continues to make progress on its two overall goals: (1) completing the protein parts list, with an annual update of the HUPO draft human proteome, and (2) making proteomics an integrated complement to genomics and transcriptomics throughout biomedical and life sciences research. neXtProt version 2017-01-23 has 17 008 confident protein identifications (Protein Existence [PE] level 1) that are compliant with the HPP Guidelines v2.1 ( https://hupo.org/Guidelines ), up from 13 664 in 2012-12 and 16 518 in 2016-04. Remaining to be found by mass spectrometry and other methods are 2579 "missing proteins" (PE2+3+4), down from 2949 in 2016. PeptideAtlas 2017-01 has 15 173 canonical proteins, accounting for nearly all of the 15 290 PE1 proteins based on MS data. These resources have extensive data on PTMs, single amino acid variants, and splice isoforms. The Human Protein Atlas v16 has 10 492 highly curated protein entries with tissue and subcellular spatial localization of proteins and transcript expression. Organ-specific popular protein lists have been generated for broad use in quantitative targeted proteomics using SRM-MS or DIA-SWATH-MS studies of biology and disease.

Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany.

PubMed

Orchard, Sandra; Albar, Juan Pablo; Binz, Pierre-Alain; Kettner, Carsten; Jones, Andrew R; Salek, Reza M; Vizcaino, Juan Antonio; Deutsch, Eric W; Hermjakob, Henning

2014-11-01

The Annual 2014 Spring Workshop of the Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) was held this year jointly with the metabolomics COordination of Standards in MetabOlomicS (COSMOS) group. The range of existing MS standards (mzML, mzIdentML, mzQuantML, mzTab, TraML) was reviewed and updated in the light of new methodologies and advances in technologies. Adaptations to meet the needs of the metabolomics community were incorporated and a new data format for NMR, nmrML, was presented. The molecular interactions workgroup began work on a new version of the existing XML data interchange format. PSI-MI XML3.0 will enable the capture of more abstract data types such as protein complex topology derived from experimental data, allosteric binding, and dynamic interactions. Further information about the work of the HUPO-PSI can be found at http://www.psidev.info. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Highlights of B/D-HPP and HPP Resource Pillar Workshops at 12th Annual HUPO World Congress of Proteomics: September 14-18, 2013, Yokohama, Japan.

PubMed

Aebersold, Ruedi; Bader, Gary D; Edwards, Aled M; van Eyk, Jennifer; Kussman, Martin; Qin, Jun; Omenn, Gilbert S

2014-05-01

At the 12th Annual HUPO World Congress of Proteomics in Japan, the Human Proteome Project (HPP) presented 16 scientific workshop sessions. Here we summarize highlights of ten workshops from the Biology and Disease-driven HPP (B/D-HPP) teams and three from the HPP Resource Pillars. Highlights of the three Chromosome-centric HPP sessions appeared in the many articles of the 2014 C-HPP special issue of the Journal of Proteome Research . © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Progress and pitfalls in finding the 'missing proteins' from the human proteome map.

PubMed

Segura, Victor; Garin-Muga, Alba; Guruceaga, Elizabeth; Corrales, Fernando J

2017-01-01

The Human Proteome Project was launched with two main goals: the comprehensive and systematic definition of the human proteome map and the development of ready to use analytical tools to measure relevant proteins in their biological context in health and disease. Despite the great progress in this endeavour, there is still a group of reluctant proteins with no, or scarce, experimental evidence supporting their existence. These are called the 'missing proteins' and represent one of the biggest challenges to complete the human proteome map. Areas covered: This review focuses on the description of the missing proteome based on the HUPO standards, the analysis of the reasons explaining the difficulty of detecting missing proteins and the strategies currently used in the search for missing proteins. The present and future of the quest for the missing proteins is critically revised hereafter. Expert commentary: An overarching multidisciplinary effort is currently being done under the HUPO umbrella to allow completion of the human proteome map. It is expected that the detection of missing proteins will grow in the coming years since the methods and the best tissue/cell type sample for their search are already on the table.

Guidelines for reporting quantitative mass spectrometry based experiments in proteomics.

PubMed

Martínez-Bartolomé, Salvador; Deutsch, Eric W; Binz, Pierre-Alain; Jones, Andrew R; Eisenacher, Martin; Mayer, Gerhard; Campos, Alex; Canals, Francesc; Bech-Serra, Joan-Josep; Carrascal, Montserrat; Gay, Marina; Paradela, Alberto; Navajas, Rosana; Marcilla, Miguel; Hernáez, María Luisa; Gutiérrez-Blázquez, María Dolores; Velarde, Luis Felipe Clemente; Aloria, Kerman; Beaskoetxea, Jabier; Medina-Aunon, J Alberto; Albar, Juan P

2013-12-16

Mass spectrometry is already a well-established protein identification tool and recent methodological and technological developments have also made possible the extraction of quantitative data of protein abundance in large-scale studies. Several strategies for absolute and relative quantitative proteomics and the statistical assessment of quantifications are possible, each having specific measurements and therefore, different data analysis workflows. The guidelines for Mass Spectrometry Quantification allow the description of a wide range of quantitative approaches, including labeled and label-free techniques and also targeted approaches such as Selected Reaction Monitoring (SRM). The HUPO Proteomics Standards Initiative (HUPO-PSI) has invested considerable efforts to improve the standardization of proteomics data handling, representation and sharing through the development of data standards, reporting guidelines, controlled vocabularies and tooling. In this manuscript, we describe a key output from the HUPO-PSI-namely the MIAPE Quant guidelines, which have developed in parallel with the corresponding data exchange format mzQuantML [1]. The MIAPE Quant guidelines describe the HUPO-PSI proposal concerning the minimum information to be reported when a quantitative data set, derived from mass spectrometry (MS), is submitted to a database or as supplementary information to a journal. The guidelines have been developed with input from a broad spectrum of stakeholders in the proteomics field to represent a true consensus view of the most important data types and metadata, required for a quantitative experiment to be analyzed critically or a data analysis pipeline to be reproduced. It is anticipated that they will influence or be directly adopted as part of journal guidelines for publication and by public proteomics databases and thus may have an impact on proteomics laboratories across the world. This article is part of a Special Issue entitled: Standardization and Quality Control. Copyright © 2013 Elsevier B.V. All rights reserved.

"Does understanding the brain need proteomics and does understanding proteomics need brains?"--Second HUPO HBPP Workshop hosted in Paris.

PubMed

Hamacher, Michael; Klose, Joachim; Rossier, Jean; Marcus, Katrin; Meyer, Helmut E

2004-07-01

The second Human Brain Proteome Project (HBPP) Workshop of the Human Proteome Organisation (HUPO) took place at the Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI) from April 23-24, 2004. During two days, more than 70 attendees from Europe, Asia and the US came together to decide basic strategic approaches, standards and the beginning of a pilot phase prior to further studies of the human brain proteome. The international consortium presented the technological and scientific portfolio and scheduled the time table for the next year.

Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data.

PubMed

Chamrad, Daniel C; Körting, Gerhard; Schäfer, Heike; Stephan, Christian; Thiele, Herbert; Apweiler, Rolf; Meyer, Helmut E; Marcus, Katrin; Blüggel, Martin

2006-09-01

A novel software tool named PTM-Explorer has been applied to LC-MS/MS datasets acquired within the Human Proteome Organisation (HUPO) Brain Proteome Project (BPP). PTM-Explorer enables automatic identification of peptide MS/MS spectra that were not explained in typical sequence database searches. The main focus was detection of PTMs, but PTM-Explorer detects also unspecific peptide cleavage, mass measurement errors, experimental modifications, amino acid substitutions, transpeptidation products and unknown mass shifts. To avoid a combinatorial problem the search is restricted to a set of selected protein sequences, which stem from previous protein identifications using a common sequence database search. Prior to application to the HUPO BPP data, PTM-Explorer was evaluated on excellently manually characterized and evaluated LC-MS/MS data sets from Alpha-A-Crystallin gel spots obtained from mouse eye lens. Besides various PTMs including phosphorylation, a wealth of experimental modifications and unspecific cleavage products were successfully detected, completing the primary structure information of the measured proteins. Our results indicate that a large amount of MS/MS spectra that currently remain unidentified in standard database searches contain valuable information that can only be elucidated using suitable software tools.

Analyzing large-scale proteomics projects with latent semantic indexing.

PubMed

Klie, Sebastian; Martens, Lennart; Vizcaíno, Juan Antonio; Côté, Richard; Jones, Phil; Apweiler, Rolf; Hinneburg, Alexander; Hermjakob, Henning

2008-01-01

Since the advent of public data repositories for proteomics data, readily accessible results from high-throughput experiments have been accumulating steadily. Several large-scale projects in particular have contributed substantially to the amount of identifications available to the community. Despite the considerable body of information amassed, very few successful analyses have been performed and published on this data, leveling off the ultimate value of these projects far below their potential. A prominent reason published proteomics data is seldom reanalyzed lies in the heterogeneous nature of the original sample collection and the subsequent data recording and processing. To illustrate that at least part of this heterogeneity can be compensated for, we here apply a latent semantic analysis to the data contributed by the Human Proteome Organization's Plasma Proteome Project (HUPO PPP). Interestingly, despite the broad spectrum of instruments and methodologies applied in the HUPO PPP, our analysis reveals several obvious patterns that can be used to formulate concrete recommendations for optimizing proteomics project planning as well as the choice of technologies used in future experiments. It is clear from these results that the analysis of large bodies of publicly available proteomics data by noise-tolerant algorithms such as the latent semantic analysis holds great promise and is currently underexploited.

Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

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

Omenn, Gilbert; States, David J.; Adamski, Marcin

2005-08-13

HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anticoagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics. med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasetsmore » had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs. We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches. This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan. These PPP results on complexity, dynamic range, incomplete sampling, false-positive matches, and integration of diverse datasets for plasma and serum proteins lay a foundation for development and validation of circulating protein biomarkers in health and disease.« less

HUPO BPP pilot study: a proteomics analysis of the mouse brain of different developmental stages.

PubMed

Wang, Jing; Gu, Yong; Wang, Lihong; Hang, Xingyi; Gao, Yan; Wang, Hangyan; Zhang, Chenggang

2007-11-01

This study is a part of the HUPO Brain Proteome Project (BPP) pilot study, which aims at obtaining a reliable database of mouse brain proteome, at the comparison of techniques, laboratories, and approaches as well as at preparing subsequent proteome studies of neurologic diseases. The C57/Bl6 mouse brains of three developmental stages at embryonic day 16 (E16), postnatal day 7 (P7), and 8 wk (P56) (n = 5 in each group) were provided by the HUPO BPP executive committee. The whole brain proteins of each animal were individually prepared using 2-DE coupled with PDQuest software analysis. The protein spots representing developmentally related or stably expressed proteins were then prepared with in-gel digestion followed with MALDI-TOF/TOF MS/MS and analyzed using the MASCOT search engines to search the Swiss-Prot or NCBInr database. The 2-DE gel maps of the mouse brains of all of the developmental stages were obtained and submitted to the Data Collection Centre (DCC). The proteins alpha-enolase, stathmin, actin, C14orf166 homolog, 28,000 kDa heat- and acid-stable phosphoprotein, 3-mercaptopyruvate sulfurtransferase and 40 S ribosomal protein S3a were successfully identified. A further Western blotting analysis demonstrated that enolase is a protein up-regulated in the mouse brain from embryonic stage to adult stage. These data are helpful for understanding the proteome changes in the development of the mouse brain.

Occurrence of Virulence Genes Associated with Human Pathogenic Vibrios Isolated from Two Commercial Dusky Kob (Argyrosmus japonicus) Farms and Kareiga Estuary in the Eastern Cape Province, South Africa

PubMed Central

Fri, Justine; Ndip, Roland Ndip; Njom, Henry Akum; Clarke, Anna Maria

2017-01-01

Background: Seafood-borne Vibrio infections, often linked to contaminated seafood and water, are of increasing global public health concern. The aim of this study was to evaluate the prevalence of human pathogenic vibrios and their associated virulence genes isolated from fish and water samples from 2 commercial dusky kob farms and Kareiga estuary, South Africa. Methods: A total of 200 samples including dusky kob fish (n = 120) and seawater (n = 80) were subjected to Vibrio screening on thiosulfate-citrate-bile salts-sucrose agar (TCBS). Presumptive isolates were confirmed and delineated to V. cholerae, V. parahaemolyticus, V. vulnificus, and V. fluvialis by PCR. Various pathogenic gene markers were screened: V. parahaemolyticus (trh and tdh), V. vulnificus (vcgE and vcgC) and V. fluvialis (stn, vfh, hupO, vfpA). Restriction Fragment Length Polymorphism (RFLP) of the vvhA gene of V. vulnificus strains was performed to determine the associated biotypes. Results: Total Vibrio prevalence was 59.4% (606/1020) of which V. fluvialis was the most predominant 193 (31.85%), followed by Vibrio vulnificus 74 (12.21%) and V. parahaemolyticus 33 (5.45%). No V. cholerae strain was detected. One of the V. parahaemolyticus strains possessed the trh gene 7 (9.46%) while most (91.9%; 68/74) V. vulnificus isolates were of the E-type genotype. V. fluvialis virulence genes detected were stn (13.5%), hupO (10.4%) and vfpA (1.0%). 12.16% (9/74) of V. vulnificus strains exhibited a biotype 3 RFLP pattern. Conclusions: This is the first report of potentially pathogenic vibrios from healthy marine fish in the study area, and therefore a public health concern. PMID:28946684

The HUPO proteomics standards initiative--easing communication and minimizing data loss in a changing world.

PubMed

Orchard, Sandra; Hermjakob, Henning

2008-03-01

The amount of data currently being generated by proteomics laboratories around the world is increasing exponentially, making it ever more critical that scientists are able to exchange, compare and retrieve datasets when re-evaluation of their original conclusions becomes important. Only a fraction of this data is published in the literature and important information is being lost every day as data formats become obsolete. The Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) was tasked with the creation of data standards and interchange formats to allow both the exchange and storage of such data irrespective of the hardware and software from which it was generated. This article will provide an update on the work of this group, the creation and implementation of these standards and the standards-compliant data repositories being established as result of their efforts.

The strategy, organization, and progress of the HUPO Human Proteome Project.

PubMed

Omenn, Gilbert S

2014-04-04

The Human Proteome Project is a major, comprehensive initiative of the Human Proteome Organization. This global collaborative effort aims to identify and characterize at least one protein product and many PTM, SAP, and splice variant isoforms from the 20,300 human protein-coding genes. The deliverables are an extensive parts list and an array of technology platforms, reagents, spectral libraries, and linked knowledge bases that advance the field and facilitate the use of proteomics by a much wider community of life scientists. Such enablement will help address the Grand Challenge of using proteomics to bridge major gaps between evidence of genomic variation and diverse phenotypes. The HUPO Human Proteome Project (HPP) has made an outstanding launch, including a special issue of the Journal of Proteome Research on the Chromosome-centric HPP with a total of 48 articles. This article is part of a Special Issue: Can Proteomics Fill the Gap Between Genomics and Phenotypes? © 2013.

Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions

PubMed Central

Kerrien, Samuel; Orchard, Sandra; Montecchi-Palazzi, Luisa; Aranda, Bruno; Quinn, Antony F; Vinod, Nisha; Bader, Gary D; Xenarios, Ioannis; Wojcik, Jérôme; Sherman, David; Tyers, Mike; Salama, John J; Moore, Susan; Ceol, Arnaud; Chatr-aryamontri, Andrew; Oesterheld, Matthias; Stümpflen, Volker; Salwinski, Lukasz; Nerothin, Jason; Cerami, Ethan; Cusick, Michael E; Vidal, Marc; Gilson, Michael; Armstrong, John; Woollard, Peter; Hogue, Christopher; Eisenberg, David; Cesareni, Gianni; Apweiler, Rolf; Hermjakob, Henning

2007-01-01

Background Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI) format in 2004 was a major step towards the establishment of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions. Results The HUPO-PSI has further developed the PSI-MI XML schema to enable the description of interactions between a wider range of molecular types, for example nucleic acids, chemical entities, and molecular complexes. Extensive details about each supported molecular interaction can now be captured, including the biological role of each molecule within that interaction, detailed description of interacting domains, and the kinetic parameters of the interaction. The format is supported by data management and analysis tools and has been adopted by major interaction data providers. Additionally, a simpler, tab-delimited format MITAB2.5 has been developed for the benefit of users who require only minimal information in an easy to access configuration. Conclusion The PSI-MI XML2.5 and MITAB2.5 formats have been jointly developed by interaction data producers and providers from both the academic and commercial sector, and are already widely implemented and well supported by an active development community. PSI-MI XML2.5 enables the description of highly detailed molecular interaction data and facilitates data exchange between databases and users without loss of information. MITAB2.5 is a simpler format appropriate for fast Perl parsing or loading into Microsoft Excel. PMID:17925023

A tutorial for software development in quantitative proteomics using PSI standard formats☆

PubMed Central

Gonzalez-Galarza, Faviel F.; Qi, Da; Fan, Jun; Bessant, Conrad; Jones, Andrew R.

2014-01-01

The Human Proteome Organisation — Proteomics Standards Initiative (HUPO-PSI) has been working for ten years on the development of standardised formats that facilitate data sharing and public database deposition. In this article, we review three HUPO-PSI data standards — mzML, mzIdentML and mzQuantML, which can be used to design a complete quantitative analysis pipeline in mass spectrometry (MS)-based proteomics. In this tutorial, we briefly describe the content of each data model, sufficient for bioinformaticians to devise proteomics software. We also provide guidance on the use of recently released application programming interfaces (APIs) developed in Java for each of these standards, which makes it straightforward to read and write files of any size. We have produced a set of example Java classes and a basic graphical user interface to demonstrate how to use the most important parts of the PSI standards, available from http://code.google.com/p/psi-standard-formats-tutorial. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. PMID:23584085

The HUPO proteomics standards initiative--overcoming the fragmentation of proteomics data.

PubMed

Hermjakob, Henning

2006-09-01

Proteomics is a key field of modern biomolecular research, with many small and large scale efforts producing a wealth of proteomics data. However, the vast majority of this data is never exploited to its full potential. Even in publicly funded projects, often the raw data generated in a specific context is analysed, conclusions are drawn and published, but little attention is paid to systematic documentation, archiving, and public access to the data supporting the scientific results. It is often difficult to validate the results stated in a particular publication, and even simple global questions like "In which cellular contexts has my protein of interest been observed?" can currently not be answered with realistic effort, due to a lack of standardised reporting and collection of proteomics data. The Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organisation (HUPO), defines community standards for data representation in proteomics to facilitate systematic data capture, comparison, exchange and verification. In this article we provide an overview of PSI organisational structure, activities, and current results, as well as ways to get involved in the broad-based, open PSI process.

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

PubMed

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

2015-09-08

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

PRIDE: new developments and new datasets.

PubMed

Jones, Philip; Côté, Richard G; Cho, Sang Yun; Klie, Sebastian; Martens, Lennart; Quinn, Antony F; Thorneycroft, David; Hermjakob, Henning

2008-01-01

The PRIDE (http://www.ebi.ac.uk/pride) database of protein and peptide identifications was previously described in the NAR Database Special Edition in 2006. Since this publication, the volume of public data in the PRIDE relational database has increased by more than an order of magnitude. Several significant public datasets have been added, including identifications and processed mass spectra generated by the HUPO Brain Proteome Project and the HUPO Liver Proteome Project. The PRIDE software development team has made several significant changes and additions to the user interface and tool set associated with PRIDE. The focus of these changes has been to facilitate the submission process and to improve the mechanisms by which PRIDE can be queried. The PRIDE team has developed a Microsoft Excel workbook that allows the required data to be collated in a series of relatively simple spreadsheets, with automatic generation of PRIDE XML at the end of the process. The ability to query PRIDE has been augmented by the addition of a BioMart interface allowing complex queries to be constructed. Collaboration with groups outside the EBI has been fruitful in extending PRIDE, including an approach to encode iTRAQ quantitative data in PRIDE XML.

Clinical initiatives linking Japanese and Swedish healthcare resources on cancer studies utilizing Biobank Repositories.

PubMed

Nishimura, Toshihide; Kawamura, Takeshi; Sugihara, Yutaka; Bando, Yasuhiko; Sakamoto, Shigeru; Nomura, Masaharu; Ikeda, Norihiko; Ohira, Tatsuo; Fujimoto, Junichiro; Tojo, Hiromasa; Hamakubo, Takao; Kodama, Tatsuhiko; Andersson, Roland; Fehniger, Thomas E; Kato, Harubumi; Marko-Varga, György

2014-12-01

The Tokyo Medical University Hospital in Japan and the Lund University hospital in Sweden have recently initiated a research program with the objective to impact on patient treatment by clinical disease stage characterization (phenotyping), utilizing proteomics sequencing platforms. By sharing clinical experiences, patient treatment principles, and biobank strategies, our respective clinical teams in Japan and Sweden will aid in the development of predictive and drug related protein biomarkers. Data from joint lung cancer studies are presented where protein expression from Neuro- Endocrine lung cancer (LCNEC) phenotype patients can be separated from Small cell- (SCLC) and Large Cell lung cancer (LCC) patients by deep sequencing and spectral counting analysis. LCNEC, a subtype of large cell carcinoma (LCC), is characterized by neuroendocrine differentiation that small cell lung carcinoma (SCLC) shares. Pre-therapeutic histological distinction between LCNEC and SCLC has so far been problematic, leading to adverse clinical outcome. An establishment of protein targets characteristic of LCNEC is quite helpful for decision of optimal therapeutic strategy by diagnosing individual patients. Proteoform annotation and clinical biobanking is part of the HUPO initiative (http://www.hupo.org) within chromosome 10 and chromosome 19 consortia.

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.

PubMed

Hermjakob, Henning; Montecchi-Palazzi, Luisa; Bader, Gary; Wojcik, Jérôme; Salwinski, Lukasz; Ceol, Arnaud; Moore, Susan; Orchard, Sandra; Sarkans, Ugis; von Mering, Christian; Roechert, Bernd; Poux, Sylvain; Jung, Eva; Mersch, Henning; Kersey, Paul; Lappe, Michael; Li, Yixue; Zeng, Rong; Rana, Debashis; Nikolski, Macha; Husi, Holger; Brun, Christine; Shanker, K; Grant, Seth G N; Sander, Chris; Bork, Peer; Zhu, Weimin; Pandey, Akhilesh; Brazma, Alvis; Jacq, Bernard; Vidal, Marc; Sherman, David; Legrain, Pierre; Cesareni, Gianni; Xenarios, Ioannis; Eisenberg, David; Steipe, Boris; Hogue, Chris; Apweiler, Rolf

2004-02-01

A major goal of proteomics is the complete description of the protein interaction network underlying cell physiology. A large number of small scale and, more recently, large-scale experiments have contributed to expanding our understanding of the nature of the interaction network. However, the necessary data integration across experiments is currently hampered by the fragmentation of publicly available protein interaction data, which exists in different formats in databases, on authors' websites or sometimes only in print publications. Here, we propose a community standard data model for the representation and exchange of protein interaction data. This data model has been jointly developed by members of the Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organization (HUPO), and is supported by major protein interaction data providers, in particular the Biomolecular Interaction Network Database (BIND), Cellzome (Heidelberg, Germany), the Database of Interacting Proteins (DIP), Dana Farber Cancer Institute (Boston, MA, USA), the Human Protein Reference Database (HPRD), Hybrigenics (Paris, France), the European Bioinformatics Institute's (EMBL-EBI, Hinxton, UK) IntAct, the Molecular Interactions (MINT, Rome, Italy) database, the Protein-Protein Interaction Database (PPID, Edinburgh, UK) and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING, EMBL, Heidelberg, Germany).

Highlights of the Biology and Disease-driven Human Proteome Project, 2015-2016.

PubMed

Van Eyk, Jennifer E; Corrales, Fernando J; Aebersold, Ruedi; Cerciello, Ferdinando; Deutsch, Eric W; Roncada, Paola; Sanchez, Jean-Charles; Yamamoto, Tadashi; Yang, Pengyuan; Zhang, Hui; Omenn, Gilbert S

2016-11-04

The Biology and Disease-driven Human Proteome Project (B/D-HPP) is aimed at supporting and enhancing the broad use of state-of-the-art proteomic methods to characterize and quantify proteins for in-depth understanding of the molecular mechanisms of biological processes and human disease. Based on a foundation of the pre-existing HUPO initiatives begun in 2002, the B/D-HPP is designed to provide standardized methods and resources for mass spectrometry and specific protein affinity reagents and facilitate accessibility of these resources to the broader life sciences research and clinical communities. Currently there are 22 B/D-HPP initiatives and 3 closely related HPP resource pillars. The B/D-HPP groups are working to define sets of protein targets that are highly relevant to each particular field to deliver relevant assays for the measurement of these selected targets and to disseminate and make publicly accessible the information and tools generated. Major developments are the 2016 publications of the Human SRM Atlas and of "popular protein sets" for six organ systems. Here we present the current activities and plans of the BD-HPP initiatives as highlighted in numerous B/D-HPP workshops at the 14th annual HUPO 2015 World Congress of Proteomics in Vancouver, Canada.

Bacterial genes involved in incorporation of nickel into a hydrogenase enzyme.

PubMed Central

Fu, C; Javedan, S; Moshiri, F; Maier, R J

1994-01-01

Nickel is an essential component of all H2-uptake hydrogenases. A fragment of DNA that complements a H2-uptake-deficient but nickel-cured mutant strain (JHK7) of Bradyrhizobium japonicum was isolated and sequenced. This 4.5-kb DNA fragment contains four open reading frames designated as ORF1, hupN, hupO, and hupP, which encode polypeptides with predicted masses of 17, 40, 19, and 63.5 kDa, respectively. The last three open reading frames (hupNOP) are most likely organized as an operon with a putative sigma 54-type promoter. Based on its hydropathy profile, HupN is predicted to be a transmembrane protein. It has 56% identity to the previously described HoxN (high-affinity nickel transport protein) of Alcaligenes eutrophus. A subclone (pJF23) containing the hupNOP genes excluding ORF1 completely complemented (in trans) strain JHK7 for hydrogenase activity in low nickel conditions. pJF26 containing only a functional hupN complemented the hydrogenase activity of mutant strain JHK7 to 30-55% of the wild-type level. Mutant strain JHK70, with a chromosomal deletion in hupP but with an intact hupNO, showed greater activities than pJF26-complemented JHK7 but still had lower activities than the wild type at all nickel levels tested. pJF25, containing the entire hupO and hupP, but without hupN (a portion of hupN was deleted), did not complement hydrogenase activity of mutant strain JHK7. The results suggest that the products of the hupNOP operon are all involved in nickel incorporation/metabolism into the hydrogenase apoprotein. Based on (previous) nickel transport studies of strain JHK7, the hupNOP genes appear not to be involved in nickel transport by whole cells. The deleterious effects on hydrogenase expression are most pronounced by lack of the HupN product. PMID:8197192

NCI Releases Video: Proteogenomics Research - On the Frontier of Precision Medicine | Office of Cancer Clinical Proteomics Research

Cancer.gov

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute (NCI), part of the National Institutes of Health, announces the release of an educational video titled “Proteogenomics Research: On the Frontier of Precision Medicine."  Launched at the HUPO2017 Global Leadership Gala Dinner, catalyzed in part by the Cancer Moonshot initiative and featuring as keynote speaker the 47th Vice President of the United States of America Joseph R.

Comparison of analytical methods for profiling N- and O-linked glycans from cultured cell lines

PubMed Central

Togayachi, Akira; Azadi, Parastoo; Ishihara, Mayumi; Geyer, Rudolf; Galuska, Christina; Geyer, Hildegard; Kakehi, Kazuaki; Kinoshita, Mitsuhiro; Karlsson, Niclas G.; Jin, Chunsheng; Kato, Koichi; Yagi, Hirokazu; Kondo, Sachiko; Kawasaki, Nana; Hashii, Noritaka; Kolarich, Daniel; Stavenhagen, Kathrin; Packer, Nicolle H.; Thaysen-Andersen, Morten; Nakano, Miyako; Taniguchi, Naoyuki; Kurimoto, Ayako; Wada, Yoshinao; Tajiri, Michiko; Yang, Pengyuan; Cao, Weiqian; Li, Hong; Rudd, Pauline M.; Narimatsu, Hisashi

2016-01-01

The Human Disease Glycomics/Proteome Initiative (HGPI) is an activity in the Human Proteome Organization (HUPO) supported by leading researchers from international institutes and aims at development of disease-related glycomics/glycoproteomics analysis techniques. Since 2004, the initiative has conducted three pilot studies. The first two were N- and O-glycan analyses of purified transferrin and immunoglobulin-G and assessed the most appropriate analytical approach employed at the time. This paper describes the third study, which was conducted to compare different approaches for quantitation of N- and O-linked glycans attached to proteins in crude biological samples. The preliminary analysis on cell pellets resulted in wildly varied glycan profiles, which was probably the consequence of variations in the pre-processing sample preparation methodologies. However, the reproducibility of the data was not improved dramatically in the subsequent analysis on cell lysate fractions prepared in a specified method by one lab. The study demonstrated the difficulty of carrying out a complete analysis of the glycome in crude samples by any single technology and the importance of rigorous optimization of the course of analysis from preprocessing to data interpretation. It suggests that another collaborative study employing the latest technologies in this rapidly evolving field will help to realize the requirements of carrying out the large-scale analysis of glycoproteins in complex cell samples. PMID:26511985

Variability of Phytoplankton Size Structure in Response to Changes in Coastal Upwelling Intensity in the Southwestern East Sea

NASA Astrophysics Data System (ADS)

Shin, Jung-Wook; Park, Jinku; Choi, Jang-Geun; Jo, Young-Heon; Kang, Jae Joong; Joo, HuiTae; Lee, Sang Heon

2017-12-01

The aim of this study was to examine the size structure of phytoplankton under varying coastal upwelling intensities and to determine the resulting primary productivity in the southwestern East Sea. Samples of phytoplankton assemblages were collected on five occasions from the Hupo Bank, off the east coast of Korea, during 2012-2013. Because two major surface currents have a large effect on water mass transport in this region, we first performed a Backward Particle Tracking Experiment (BPTE) to determine the coastal sea from which the collected samples originated according to advection time of BPTE particles, following which we used upwelling age (UA) to determine the intensity of coastal upwelling in the region of origin for each sample. Only samples that were affected by coastal upwelling in the region of origin were included in subsequent analyses. We found that as UA increased, there was a decreasing trend in the concentration of picophytoplankton, and increasing trends in the concentration of nanophytoplankton and microphytoplankton. We also examined the relationship between the size structure of phytoplankton and primary productivity in the Ulleung Basin (UB), which has experienced significant variation over the past decade. We found that primary productivity in UB was closely related to the strength of the southerly wind, which is the most important mechanism for coastal upwelling in the southwestern East Sea. Thus, the size structure of phytoplankton is determined by the intensity of coastal upwelling, which is regulated by the southerly wind, and makes an important contribution to primary productivity.

P19-S Managing Proteomics Data from Data Generation and Data Warehousing to Central Data Repository and Journal Reviewing Processes

PubMed Central

Thiele, H.; Glandorf, J.; Koerting, G.; Reidegeld, K.; Blüggel, M.; Meyer, H.; Stephan, C.

2007-01-01

In today’s proteomics research, various techniques and instrumentation bioinformatics tools are necessary to manage the large amount of heterogeneous data with an automatic quality control to produce reliable and comparable results. Therefore a data-processing pipeline is mandatory for data validation and comparison in a data-warehousing system. The proteome bioinformatics platform ProteinScape has been proven to cover these needs. The reprocessing of HUPO BPP participants’ MS data was done within ProteinScape. The reprocessed information was transferred into the global data repository PRIDE. ProteinScape as a data-warehousing system covers two main aspects: archiving relevant data of the proteomics workflow and information extraction functionality (protein identification, quantification and generation of biological knowledge). As a strategy for automatic data validation, different protein search engines are integrated. Result analysis is performed using a decoy database search strategy, which allows the measurement of the false-positive identification rate. Peptide identifications across different workflows, different MS techniques, and different search engines are merged to obtain a quality-controlled protein list. The proteomics identifications database (PRIDE), as a public data repository, is an archiving system where data are finally stored and no longer changed by further processing steps. Data submission to PRIDE is open to proteomics laboratories generating protein and peptide identifications. An export tool has been developed for transferring all relevant HUPO BPP data from ProteinScape into PRIDE using the PRIDE.xml format. The EU-funded ProDac project will coordinate the development of software tools covering international standards for the representation of proteomics data. The implementation of data submission pipelines and systematic data collection in public standards–compliant repositories will cover all aspects, from the generation of MS data in each laboratory to the conversion of all the annotating information and identifications to a standardized format. Such datasets can be used in the course of publishing in scientific journals.

The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community.

PubMed

Aebersold, Ruedi; Bader, Gary D; Edwards, Aled M; van Eyk, Jennifer E; Kussmann, Martin; Qin, Jun; Omenn, Gilbert S

2013-01-04

The biology and disease oriented branch of the Human Proteome Project (B/D-HPP) was established by the Human Proteome Organization (HUPO) with the main goal of supporting the broad application of state-of the-art measurements of proteins and proteomes by life scientists studying the molecular mechanisms of biological processes and human disease. This will be accomplished through the generation of research and informational resources that will support the routine and definitive measurement of the process or disease relevant proteins. The B/D-HPP is highly complementary to the C-HPP and will provide datasets and biological characterization useful to the C-HPP teams. In this manuscript we describe the goals, the plans, and the current status of the of the B/D-HPP.

Tandem mass spectrometry of human tryptic blood peptides calculated by a statistical algorithm and captured by a relational database with exploration by a general statistical analysis system.

PubMed

Bowden, Peter; Beavis, Ron; Marshall, John

2009-11-02

A goodness of fit test may be used to assign tandem mass spectra of peptides to amino acid sequences and to directly calculate the expected probability of mis-identification. The product of the peptide expectation values directly yields the probability that the parent protein has been mis-identified. A relational database could capture the mass spectral data, the best fit results, and permit subsequent calculations by a general statistical analysis system. The many files of the Hupo blood protein data correlated by X!TANDEM against the proteins of ENSEMBL were collected into a relational database. A redundant set of 247,077 proteins and peptides were correlated by X!TANDEM, and that was collapsed to a set of 34,956 peptides from 13,379 distinct proteins. About 6875 distinct proteins were only represented by a single distinct peptide, 2866 proteins showed 2 distinct peptides, and 3454 proteins showed at least three distinct peptides by X!TANDEM. More than 99% of the peptides were associated with proteins that had cumulative expectation values, i.e. probability of false positive identification, of one in one hundred or less. The distribution of peptides per protein from X!TANDEM was significantly different than those expected from random assignment of peptides.

We Are Not Alone: The iMOP Initiative and Its Roles in a Biology- and Disease-Driven Human Proteome Project.

PubMed

Tholey, Andreas; Taylor, Nicolas L; Heazlewood, Joshua L; Bendixen, Emøke

2017-12-01

Mapping of the human proteome has advanced significantly in recent years and will provide a knowledge base to accelerate our understanding of how proteins and protein networks can affect human health and disease. However, providing solutions to human health challenges will likely fail if insights are exclusively based on studies of human samples and human proteomes. In recent years, it has become evident that human health depends on an integrated understanding of the many species that make human life possible. These include the commensal microorganisms that are essential to human life, pathogens, and food species as well as the classic model organisms that enable studies of biological mechanisms. The Human Proteome Organization (HUPO) initiative on multiorganism proteomes (iMOP) works to support proteome research undertaken on nonhuman species that remain widely under-studied compared with the progress in human proteome research. This perspective argues the need for further research on multiple species that impact human life. We also present an update on recent progress in model organisms, microbiota, and food species, address the emerging problem of antibiotics resistance, and outline how iMOP activities could lead to a more inclusive approach for the human proteome project (HPP) to better support proteome research aimed at improving human health and furthering knowledge on human biology.

The International Proteomics Tutorial Programme--reaching out to the next generation proteome scientists.

PubMed

James, Peter; Marko-Varga, György A

2011-08-05

One of the most critical functions of the various Proteomics organizations is the training of young scientists and the dissemination of information to the general scientific community. The education committees of the Human Proteome Organisation (HUPO) and the European Proteomics Association (EuPA) together with the other local proteomics associations are therefore launching a joint Tutorial Program to meet these needs. The level is aimed at Masters/PhD level students with good basic training in biology, biochemistry, mathematics and statistics. The Tutorials will consist of a review/teaching article with an accompanying talk slide presentation for classroom teaching. The Tutorial Program will cover core techniques and basics as an introduction to scientists new to the field. The entire series of articles and slides will be made freely available for teaching use at the Journals and Organizations homepages.

imzML: Imaging Mass Spectrometry Markup Language: A common data format for mass spectrometry imaging.

PubMed

Römpp, Andreas; Schramm, Thorsten; Hester, Alfons; Klinkert, Ivo; Both, Jean-Pierre; Heeren, Ron M A; Stöckli, Markus; Spengler, Bernhard

2011-01-01

Imaging mass spectrometry is the method of scanning a sample of interest and generating an "image" of the intensity distribution of a specific analyte. The data sets consist of a large number of mass spectra which are usually acquired with identical settings. Existing data formats are not sufficient to describe an MS imaging experiment completely. The data format imzML was developed to allow the flexible and efficient exchange of MS imaging data between different instruments and data analysis software.For this purpose, the MS imaging data is divided in two separate files. The mass spectral data is stored in a binary file to ensure efficient storage. All metadata (e.g., instrumental parameters, sample details) are stored in an XML file which is based on the standard data format mzML developed by HUPO-PSI. The original mzML controlled vocabulary was extended to include specific parameters of imaging mass spectrometry (such as x/y position and spatial resolution). The two files (XML and binary) are connected by offset values in the XML file and are unambiguously linked by a universally unique identifier. The resulting datasets are comparable in size to the raw data and the separate metadata file allows flexible handling of large datasets.Several imaging MS software tools already support imzML. This allows choosing from a (growing) number of processing tools. One is no longer limited to proprietary software, but is able to use the processing software which is best suited for a specific question or application. On the other hand, measurements from different instruments can be compared within one software application using identical settings for data processing. All necessary information for evaluating and implementing imzML can be found at http://www.imzML.org .

The mzqLibrary--An open source Java library supporting the HUPO-PSI quantitative proteomics standard.

PubMed

Qi, Da; Zhang, Huaizhong; Fan, Jun; Perkins, Simon; Pisconti, Addolorata; Simpson, Deborah M; Bessant, Conrad; Hubbard, Simon; Jones, Andrew R

2015-09-01

The mzQuantML standard has been developed by the Proteomics Standards Initiative for capturing, archiving and exchanging quantitative proteomic data, derived from mass spectrometry. It is a rich XML-based format, capable of representing data about two-dimensional features from LC-MS data, and peptides, proteins or groups of proteins that have been quantified from multiple samples. In this article we report the development of an open source Java-based library of routines for mzQuantML, called the mzqLibrary, and associated software for visualising data called the mzqViewer. The mzqLibrary contains routines for mapping (peptide) identifications on quantified features, inference of protein (group)-level quantification values from peptide-level values, normalisation and basic statistics for differential expression. These routines can be accessed via the command line, via a Java programming interface access or a basic graphical user interface. The mzqLibrary also contains several file format converters, including import converters (to mzQuantML) from OpenMS, Progenesis LC-MS and MaxQuant, and exporters (from mzQuantML) to other standards or useful formats (mzTab, HTML, csv). The mzqViewer contains in-built routines for viewing the tables of data (about features, peptides or proteins), and connects to the R statistical library for more advanced plotting options. The mzqLibrary and mzqViewer packages are available from https://code.google.com/p/mzq-lib/. © 2015 The Authors. PROTEOMICS Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

JAMI: a Java library for molecular interactions and data interoperability.

PubMed

Sivade Dumousseau, M; Koch, M; Shrivastava, A; Alonso-López, D; De Las Rivas, J; Del-Toro, N; Combe, C W; Meldal, B H M; Heimbach, J; Rappsilber, J; Sullivan, J; Yehudi, Y; Orchard, S

2018-04-11

A number of different molecular interactions data download formats now exist, designed to allow access to these valuable data by diverse user groups. These formats include the PSI-XML and MITAB standard interchange formats developed by Molecular Interaction workgroup of the HUPO-PSI in addition to other, use-specific downloads produced by other resources. The onus is currently on the user to ensure that a piece of software is capable of read/writing all necessary versions of each format. This problem may increase, as data providers strive to meet ever more sophisticated user demands and data types. A collaboration between EMBL-EBI and the University of Cambridge has produced JAMI, a single library to unify standard molecular interaction data formats such as PSI-MI XML and PSI-MITAB. The JAMI free, open-source library enables the development of molecular interaction computational tools and pipelines without the need to produce different versions of software to read different versions of the data formats. Software and tools developed on top of the JAMI framework are able to integrate and support both PSI-MI XML and PSI-MITAB. The use of JAMI avoids the requirement to chain conversions between formats in order to reach a desired output format and prevents code and unit test duplication as the code becomes more modular. JAMI's model interfaces are abstracted from the underlying format, hiding the complexity and requirements of each data format from developers using JAMI as a library.

The Gel Electrophoresis Markup Language (GelML) from the Proteomics Standards Initiative

PubMed Central

Gibson, Frank; Hoogland, Christine; Martinez-Bartolomé, Salvador; Medina-Aunon, J. Alberto; Albar, Juan Pablo; Babnigg, Gyorgy; Wipat, Anil; Hermjakob, Henning; Almeida, Jonas S; Stanislaus, Romesh; Paton, Norman W; Jones, Andrew R

2011-01-01

The Human Proteome Organisation’s Proteomics Standards Initiative (HUPO-PSI) has developed the GelML data exchange format for representing gel electrophoresis experiments performed in proteomics investigations. The format closely follows the reporting guidelines for gel electrophoresis, which are part of the Minimum Information About a Proteomics Experiment (MIAPE) set of modules. GelML supports the capture of metadata (such as experimental protocols) and data (such as gel images) resulting from gel electrophoresis so that laboratories can be compliant with the MIAPE Gel Electrophoresis guidelines, while allowing such data sets to be exchanged or downloaded from public repositories. The format is sufficiently flexible to capture data from a broad range of experimental processes, and complements other PSI formats for mass spectrometry data and the results of protein and peptide identifications to capture entire gel-based proteome workflows. GelML has resulted from the open standardisation process of PSI consisting of both public consultation and anonymous review of the specifications. PMID:20677327

MRUniNovo: an efficient tool for de novo peptide sequencing utilizing the hadoop distributed computing framework.

PubMed

Li, Chuang; Chen, Tao; He, Qiang; Zhu, Yunping; Li, Kenli

2017-03-15

Tandem mass spectrometry-based de novo peptide sequencing is a complex and time-consuming process. The current algorithms for de novo peptide sequencing cannot rapidly and thoroughly process large mass spectrometry datasets. In this paper, we propose MRUniNovo, a novel tool for parallel de novo peptide sequencing. MRUniNovo parallelizes UniNovo based on the Hadoop compute platform. Our experimental results demonstrate that MRUniNovo significantly reduces the computation time of de novo peptide sequencing without sacrificing the correctness and accuracy of the results, and thus can process very large datasets that UniNovo cannot. MRUniNovo is an open source software tool implemented in java. The source code and the parameter settings are available at http://bioinfo.hupo.org.cn/MRUniNovo/index.php. s131020002@hnu.edu.cn ; taochen1019@163.com. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Proteomic approaches in brain research and neuropharmacology.

PubMed

Vercauteren, Freya G G; Bergeron, John J M; Vandesande, Frans; Arckens, Lut; Quirion, Rémi

2004-10-01

Numerous applications of genomic technologies have enabled the assembly of unprecedented inventories of genes, expressed in cells under specific physiological and pathophysiological conditions. Complementing the valuable information generated through functional genomics with the integrative knowledge of protein expression and function should enable the development of more efficient diagnostic tools and therapeutic agents. Proteomic analyses are particularly suitable to elucidate posttranslational modifications, expression levels and protein-protein interactions of thousands of proteins at a time. In this review, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) investigations of brain tissues in neurodegenerative diseases such as Alzheimer's disease, Down syndrome and schizophrenia, and the construction of 2D-PAGE proteome maps of the brain are discussed. The role of the Human Proteome Organization (HUPO) as an international coordinating organization for proteomic efforts, as well as challenges for proteomic technologies and data analysis are also addressed. It is expected that the use of proteomic strategies will have significant impact in neuropharmacology over the coming decade.

qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments*

PubMed Central

Walzer, Mathias; Pernas, Lucia Espona; Nasso, Sara; Bittremieux, Wout; Nahnsen, Sven; Kelchtermans, Pieter; Pichler, Peter; van den Toorn, Henk W. P.; Staes, An; Vandenbussche, Jonathan; Mazanek, Michael; Taus, Thomas; Scheltema, Richard A.; Kelstrup, Christian D.; Gatto, Laurent; van Breukelen, Bas; Aiche, Stephan; Valkenborg, Dirk; Laukens, Kris; Lilley, Kathryn S.; Olsen, Jesper V.; Heck, Albert J. R.; Mechtler, Karl; Aebersold, Ruedi; Gevaert, Kris; Vizcaíno, Juan Antonio; Hermjakob, Henning; Kohlbacher, Oliver; Martens, Lennart

2014-01-01

Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles of the related mzML, mzIdentML, mzQuantML, and TraML standards from the HUPO-PSI (Proteomics Standards Initiative). In addition to the XML format, we also provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible use cases and an illustrative example of the subsequent analysis possibilities. All information about qcML is available at http://code.google.com/p/qcml. PMID:24760958

qcML: an exchange format for quality control metrics from mass spectrometry experiments.

PubMed

Walzer, Mathias; Pernas, Lucia Espona; Nasso, Sara; Bittremieux, Wout; Nahnsen, Sven; Kelchtermans, Pieter; Pichler, Peter; van den Toorn, Henk W P; Staes, An; Vandenbussche, Jonathan; Mazanek, Michael; Taus, Thomas; Scheltema, Richard A; Kelstrup, Christian D; Gatto, Laurent; van Breukelen, Bas; Aiche, Stephan; Valkenborg, Dirk; Laukens, Kris; Lilley, Kathryn S; Olsen, Jesper V; Heck, Albert J R; Mechtler, Karl; Aebersold, Ruedi; Gevaert, Kris; Vizcaíno, Juan Antonio; Hermjakob, Henning; Kohlbacher, Oliver; Martens, Lennart

2014-08-01

Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles of the related mzML, mzIdentML, mzQuantML, and TraML standards from the HUPO-PSI (Proteomics Standards Initiative). In addition to the XML format, we also provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible use cases and an illustrative example of the subsequent analysis possibilities. All information about qcML is available at http://code.google.com/p/qcml. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

The jmzQuantML programming interface and validator for the mzQuantML data standard.

PubMed

Qi, Da; Krishna, Ritesh; Jones, Andrew R

2014-03-01

The mzQuantML standard from the HUPO Proteomics Standards Initiative has recently been released, capturing quantitative data about peptides and proteins, following analysis of MS data. We present a Java application programming interface (API) for mzQuantML called jmzQuantML. The API provides robust bridges between Java classes and elements in mzQuantML files and allows random access to any part of the file. The API provides read and write capabilities, and is designed to be embedded in other software packages, enabling mzQuantML support to be added to proteomics software tools (http://code.google.com/p/jmzquantml/). The mzQuantML standard is designed around a multilevel validation system to ensure that files are structurally and semantically correct for different proteomics quantitative techniques. In this article, we also describe a Java software tool (http://code.google.com/p/mzquantml-validator/) for validating mzQuantML files, which is a formal part of the data standard. © 2014 The Authors. Proteomics published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data.

PubMed

Reisinger, Florian; Krishna, Ritesh; Ghali, Fawaz; Ríos, Daniel; Hermjakob, Henning; Vizcaíno, Juan Antonio; Jones, Andrew R

2012-03-01

We present a Java application programming interface (API), jmzIdentML, for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data. The API combines the power of Java Architecture of XML Binding (JAXB) and an XPath-based random-access indexer to allow a fast and efficient mapping of extensible markup language (XML) elements to Java objects. The internal references in the mzIdentML files are resolved in an on-demand manner, where the whole file is accessed as a random-access swap file, and only the relevant piece of XMLis selected for mapping to its corresponding Java object. The APIis highly efficient in its memory usage and can handle files of arbitrary sizes. The APIfollows the official release of the mzIdentML (version 1.1) specifications and is available in the public domain under a permissive licence at http://www.code.google.com/p/jmzidentml/. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.

PubMed

Deutsch, Eric W; Overall, Christopher M; Van Eyk, Jennifer E; Baker, Mark S; Paik, Young-Ki; Weintraub, Susan T; Lane, Lydie; Martens, Lennart; Vandenbrouck, Yves; Kusebauch, Ulrike; Hancock, William S; Hermjakob, Henning; Aebersold, Ruedi; Moritz, Robert L; Omenn, Gilbert S

2016-11-04

Every data-rich community research effort requires a clear plan for ensuring the quality of the data interpretation and comparability of analyses. To address this need within the Human Proteome Project (HPP) of the Human Proteome Organization (HUPO), we have developed through broad consultation a set of mass spectrometry data interpretation guidelines that should be applied to all HPP data contributions. For submission of manuscripts reporting HPP protein identification results, the guidelines are presented as a one-page checklist containing 15 essential points followed by two pages of expanded description of each. Here we present an overview of the guidelines and provide an in-depth description of each of the 15 elements to facilitate understanding of the intentions and rationale behind the guidelines, for both authors and reviewers. Broadly, these guidelines provide specific directions regarding how HPP data are to be submitted to mass spectrometry data repositories, how error analysis should be presented, and how detection of novel proteins should be supported with additional confirmatory evidence. These guidelines, developed by the HPP community, are presented to the broader scientific community for further discussion.

Identification of ubiquitin/ubiquitin-like protein modification from tandem mass spectra with various PTMs

PubMed Central

2011-01-01

Background Various solutions have been introduced for the identification of post-translational modification (PTM) from tandem mass spectrometry (MS/MS) in proteomics field but the identification of peptide modifiers, such as Ubiquitin (Ub) and ubiquitin-like proteins (Ubls), is still a challenge. The fragmentation of peptide modifier produce complex shifted ion mass patterns in combination with other PTMs, which makes it difficult to identify and locate the PTMs on a protein sequence. Currently, most PTM identification methods do not consider the complex fragmentation of peptide modifier or deals it separately from the other PTMs. Results We developed an advanced PTM identification method that inspects possible ion patterns of the most known peptide modifiers as well as other known biological and chemical PTMs to make more comprehensive and accurate conclusion. The proposed method searches all detectable mass differences of measured peaks from their theoretical values and the mass differences within mass tolerance range are grouped as mass shift classes. The most possible locations of multiple PTMs including peptide modifiers can be determined by evaluating all possible scenarios generated by the combination of the qualified mass shift classes.The proposed method showed excellent performance in the test with simulated spectra having various PTMs including peptide modifiers and in the comparison with recently developed methods such as QuickMod and SUMmOn. In the analysis of HUPO Brain Proteome Project (BPP) datasets, the proposed method could find the ubiquitin modification sites that were not identified by other conventional methods. Conclusions This work presents a novel method for identifying bothpeptide modifiers that generate complex fragmentation patternsand PTMs that are not fragmented during fragmentation processfrom tandem mass spectra. PMID:22373085

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.

PubMed

Griss, Johannes; Reisinger, Florian; Hermjakob, Henning; Vizcaíno, Juan Antonio

2012-03-01

We here present the jmzReader library: a collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML (based on the already existing API jmzML). The library is optimized to be used in conjunction with mzIdentML, the recently released standard data format for reporting protein and peptide identifications, developed by the HUPO proteomics standards initiative (PSI). mzIdentML files do not contain spectra data but contain references to different kinds of external MS data files. As a key functionality, all parsers implement a common interface that supports the various methods used by mzIdentML to reference external spectra. Thus, when developing software for mzIdentML, programmers no longer have to support multiple MS data file formats but only this one interface. The library (which includes a viewer) is open source and, together with detailed documentation, can be downloaded from http://code.google.com/p/jmzreader/. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spectra, chromatograms, Metadata: mzML-the standard data format for mass spectrometer output.

PubMed

Turewicz, Michael; Deutsch, Eric W

2011-01-01

This chapter describes Mass Spectrometry Markup Language (mzML), an XML-based and vendor-neutral standard data format for storage and exchange of mass spectrometer output like raw spectra and peak lists. It is intended to replace its two precursor data formats (mzData and mzXML), which had been developed independently a few years earlier. Hence, with the release of mzML, the problem of having two different formats for the same purposes is solved, and with it the duplicated effort of maintaining and supporting two data formats. The new format has been developed by a broad-based consortium of major instrument vendors, software vendors, and academic researchers under the aegis of the Human Proteome Organisation (HUPO), Proteomics Standards Initiative (PSI), with full participation of the main developers of the precursor formats. This comprehensive approach helped mzML to become a generally accepted standard. Furthermore, the collaborative development insured that mzML has adopted the best features of its precursor formats. In this chapter, we discuss mzML's development history, its design principles and use cases, as well as its main building components. We also present the available documentation, an example file, and validation software for mzML.

PAnalyzer: a software tool for protein inference in shotgun proteomics.

PubMed

Prieto, Gorka; Aloria, Kerman; Osinalde, Nerea; Fullaondo, Asier; Arizmendi, Jesus M; Matthiesen, Rune

2012-11-05

Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryotes. Recently data independent acquisition (DIA) approaches have emerged as an alternative to the traditional data dependent acquisition (DDA) in shotgun proteomics experiments. MSE is the term used to name one of the DIA approaches used in QTOF instruments. MSE data require specialized software to process acquired spectra and to perform peptide and protein identifications. However the software available at the moment does not group the identified proteins in a transparent way by taking into account peptide evidence categories. Furthermore the inspection, comparison and report of the obtained results require tedious manual intervention. Here we report a software tool to address these limitations for MSE data. In this paper we present PAnalyzer, a software tool focused on the protein inference process of shotgun proteomics. Our approach considers all the identified proteins and groups them when necessary indicating their confidence using different evidence categories. PAnalyzer can read protein identification files in the XML output format of the ProteinLynx Global Server (PLGS) software provided by Waters Corporation for their MSE data, and also in the mzIdentML format recently standardized by HUPO-PSI. Multiple files can also be read simultaneously and are considered as technical replicates. Results are saved to CSV, HTML and mzIdentML (in the case of a single mzIdentML input file) files. An MSE analysis of a real sample is presented to compare the results of PAnalyzer and ProteinLynx Global Server. We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates integration. PAnalyzer is an easy to use multiplatform and free software tool.

PAnalyzer: A software tool for protein inference in shotgun proteomics

PubMed Central

2012-01-01

Background Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryotes. Recently data independent acquisition (DIA) approaches have emerged as an alternative to the traditional data dependent acquisition (DDA) in shotgun proteomics experiments. MSE is the term used to name one of the DIA approaches used in QTOF instruments. MSE data require specialized software to process acquired spectra and to perform peptide and protein identifications. However the software available at the moment does not group the identified proteins in a transparent way by taking into account peptide evidence categories. Furthermore the inspection, comparison and report of the obtained results require tedious manual intervention. Here we report a software tool to address these limitations for MSE data. Results In this paper we present PAnalyzer, a software tool focused on the protein inference process of shotgun proteomics. Our approach considers all the identified proteins and groups them when necessary indicating their confidence using different evidence categories. PAnalyzer can read protein identification files in the XML output format of the ProteinLynx Global Server (PLGS) software provided by Waters Corporation for their MSE data, and also in the mzIdentML format recently standardized by HUPO-PSI. Multiple files can also be read simultaneously and are considered as technical replicates. Results are saved to CSV, HTML and mzIdentML (in the case of a single mzIdentML input file) files. An MSE analysis of a real sample is presented to compare the results of PAnalyzer and ProteinLynx Global Server. Conclusions We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates integration. PAnalyzer is an easy to use multiplatform and free software tool. PMID:23126499

Mirion--a software package for automatic processing of mass spectrometric images.

PubMed

Paschke, C; Leisner, A; Hester, A; Maass, K; Guenther, S; Bouschen, W; Spengler, B

2013-08-01

Mass spectrometric imaging (MSI) techniques are of growing interest for the Life Sciences. In recent years, the development of new instruments employing ion sources that are tailored for spatial scanning allowed the acquisition of large data sets. A subsequent data processing, however, is still a bottleneck in the analytical process, as a manual data interpretation is impossible within a reasonable time frame. The transformation of mass spectrometric data into spatial distribution images of detected compounds turned out to be the most appropriate method to visualize the results of such scans, as humans are able to interpret images faster and easier than plain numbers. Image generation, thus, is a time-consuming and complex yet very efficient task. The free software package "Mirion," presented in this paper, allows the handling and analysis of data sets acquired by mass spectrometry imaging. Mirion can be used for image processing of MSI data obtained from many different sources, as it uses the HUPO-PSI-based standard data format imzML, which is implemented in the proprietary software of most of the mass spectrometer companies. Different graphical representations of the recorded data are available. Furthermore, automatic calculation and overlay of mass spectrometric images promotes direct comparison of different analytes for data evaluation. The program also includes tools for image processing and image analysis.

A new reference implementation of the PSICQUIC web service.

PubMed

del-Toro, Noemi; Dumousseau, Marine; Orchard, Sandra; Jimenez, Rafael C; Galeota, Eugenia; Launay, Guillaume; Goll, Johannes; Breuer, Karin; Ono, Keiichiro; Salwinski, Lukasz; Hermjakob, Henning

2013-07-01

The Proteomics Standard Initiative Common QUery InterfaCe (PSICQUIC) specification was created by the Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) to enable computational access to molecular-interaction data resources by means of a standard Web Service and query language. Currently providing >150 million binary interaction evidences from 28 servers globally, the PSICQUIC interface allows the concurrent search of multiple molecular-interaction information resources using a single query. Here, we present an extension of the PSICQUIC specification (version 1.3), which has been released to be compliant with the enhanced standards in molecular interactions. The new release also includes a new reference implementation of the PSICQUIC server available to the data providers. It offers augmented web service capabilities and improves the user experience. PSICQUIC has been running for almost 5 years, with a user base growing from only 4 data providers to 28 (April 2013) allowing access to 151 310 109 binary interactions. The power of this web service is shown in PSICQUIC View web application, an example of how to simultaneously query, browse and download results from the different PSICQUIC servers. This application is free and open to all users with no login requirement (http://www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml).

The International Proteomics Tutorial Programme (IPTP): a teaching tool box for the proteomics community.

PubMed

James, Peter

2011-09-01

The most critical functions of the various proteomics organisations are the training of young scientists and the dissemination of information to the general scientific community. The education committees of the Human Proteome Organisation (HUPO) and the European Proteomics Association (EuPA) together with their national counterparts are therefore launching the International Proteomics Tutorial Programme to meet these needs. The programme is being led by Peter James (Sweden), Thierry Rabilloud (France) and Kazuyuki Nakamura (Japan). It involves collaboration between the leading proteomics journals: Journal of Proteome Research, Journal of Proteomics, Molecular and Cellular Proteomics, and Proteomics. The overall level is aimed at Masters/PhD level students who are starting out their research and who would benefit from a solid grounding in the techniques used in modern protein-based research. The tutorial program will cover core techniques and basics as an introduction to scientists new to the field. At a later stage the programme may be expanded with a series of more advanced topics focussing on the application of proteomics techniques to biological problem solving. The entire series of articles and slides will be made freely available for teaching use at the Journals and Organisations homepages and at a special website, www.proteomicstutorials.org. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work

PubMed Central

2017-01-01

The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, cochairs, and other leadership positions, the PSI working groups are tasked with the development and maintenance of community standards via special workshops and ongoing work. Among the existing ratified standards, the PSI working groups continue to update PSI-MI XML, MITAB, mzML, mzIdentML, mzQuantML, mzTab, and the MIAPE (Minimum Information About a Proteomics Experiment) guidelines with the advance of new technologies and techniques. Furthermore, new standards are currently either in the final stages of completion (proBed and proBAM for proteogenomics results as well as PEFF) or in early stages of design (a spectral library standard format, a universal spectrum identifier, the qcML quality control format, and the Protein Expression Interface (PROXI) web services Application Programming Interface). In this work we review the current status of all of these aspects of the PSI, describe synergies with other efforts such as the ProteomeXchange Consortium, the Human Proteome Project, and the metabolomics community, and provide a look at future directions of the PSI. PMID:28849660

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

PubMed

Deutsch, Eric W; Orchard, Sandra; Binz, Pierre-Alain; Bittremieux, Wout; Eisenacher, Martin; Hermjakob, Henning; Kawano, Shin; Lam, Henry; Mayer, Gerhard; Menschaert, Gerben; Perez-Riverol, Yasset; Salek, Reza M; Tabb, David L; Tenzer, Stefan; Vizcaíno, Juan Antonio; Walzer, Mathias; Jones, Andrew R

2017-12-01

The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, cochairs, and other leadership positions, the PSI working groups are tasked with the development and maintenance of community standards via special workshops and ongoing work. Among the existing ratified standards, the PSI working groups continue to update PSI-MI XML, MITAB, mzML, mzIdentML, mzQuantML, mzTab, and the MIAPE (Minimum Information About a Proteomics Experiment) guidelines with the advance of new technologies and techniques. Furthermore, new standards are currently either in the final stages of completion (proBed and proBAM for proteogenomics results as well as PEFF) or in early stages of design (a spectral library standard format, a universal spectrum identifier, the qcML quality control format, and the Protein Expression Interface (PROXI) web services Application Programming Interface). In this work we review the current status of all of these aspects of the PSI, describe synergies with other efforts such as the ProteomeXchange Consortium, the Human Proteome Project, and the metabolomics community, and provide a look at future directions of the PSI.

A standardized framing for reporting protein identifications in mzIdentML 1.2

PubMed Central

Seymour, Sean L.; Farrah, Terry; Binz, Pierre-Alain; Chalkley, Robert J.; Cottrell, John S.; Searle, Brian C.; Tabb, David L.; Vizcaíno, Juan Antonio; Prieto, Gorka; Uszkoreit, Julian; Eisenacher, Martin; Martínez-Bartolomé, Salvador; Ghali, Fawaz; Jones, Andrew R.

2015-01-01

Inferring which protein species have been detected in bottom-up proteomics experiments has been a challenging problem for which solutions have been maturing over the past decade. While many inference approaches now function well in isolation, comparing and reconciling the results generated across different tools remains difficult. It presently stands as one of the greatest barriers in collaborative efforts such as the Human Proteome Project and public repositories like the PRoteomics IDEntifications (PRIDE) database. Here we present a framework for reporting protein identifications that seeks to improve capabilities for comparing results generated by different inference tools. This framework standardizes the terminology for describing protein identification results, associated with the HUPO-Proteomics Standards Initiative (PSI) mzIdentML standard, while still allowing for differing methodologies to reach that final state. It is proposed that developers of software for reporting identification results will adopt this terminology in their outputs. While the new terminology does not require any changes to the core mzIdentML model, it represents a significant change in practice, and, as such, the rules will be released via a new version of the mzIdentML specification (version 1.2) so that consumers of files are able to determine whether the new guidelines have been adopted by export software. PMID:25092112

neXtProt: organizing protein knowledge in the context of human proteome projects.

PubMed

Gaudet, Pascale; Argoud-Puy, Ghislaine; Cusin, Isabelle; Duek, Paula; Evalet, Olivier; Gateau, Alain; Gleizes, Anne; Pereira, Mario; Zahn-Zabal, Monique; Zwahlen, Catherine; Bairoch, Amos; Lane, Lydie

2013-01-04

About 5000 (25%) of the ~20400 human protein-coding genes currently lack any experimental evidence at the protein level. For many others, there is only little information relative to their abundance, distribution, subcellular localization, interactions, or cellular functions. The aim of the HUPO Human Proteome Project (HPP, www.thehpp.org ) is to collect this information for every human protein. HPP is based on three major pillars: mass spectrometry (MS), antibody/affinity capture reagents (Ab), and bioinformatics-driven knowledge base (KB). To meet this objective, the Chromosome-Centric Human Proteome Project (C-HPP) proposes to build this catalog chromosome-by-chromosome ( www.c-hpp.org ) by focusing primarily on proteins that currently lack MS evidence or Ab detection. These are termed "missing proteins" by the HPP consortium. The lack of observation of a protein can be due to various factors including incorrect and incomplete gene annotation, low or restricted expression, or instability. neXtProt ( www.nextprot.org ) is a new web-based knowledge platform specific for human proteins that aims to complement UniProtKB/Swiss-Prot ( www.uniprot.org ) with detailed information obtained from carefully selected high-throughput experiments on genomic variation, post-translational modifications, as well as protein expression in tissues and cells. This article describes how neXtProt contributes to prioritize C-HPP efforts and integrates C-HPP results with other research efforts to create a complete human proteome catalog.

The ProteoRed MIAPE web toolkit: A User-friendly Framework to Connect and Share Proteomics Standards*

PubMed Central

Medina-Aunon, J. Alberto; Martínez-Bartolomé, Salvador; López-García, Miguel A.; Salazar, Emilio; Navajas, Rosana; Jones, Andrew R.; Paradela, Alberto; Albar, Juan P.

2011-01-01

The development of the HUPO-PSI's (Proteomics Standards Initiative) standard data formats and MIAPE (Minimum Information About a Proteomics Experiment) guidelines should improve proteomics data sharing within the scientific community. Proteomics journals have encouraged the use of these standards and guidelines to improve the quality of experimental reporting and ease the evaluation and publication of manuscripts. However, there is an evident lack of bioinformatics tools specifically designed to create and edit standard file formats and reports, or embed them within proteomics workflows. In this article, we describe a new web-based software suite (The ProteoRed MIAPE web toolkit) that performs several complementary roles related to proteomic data standards. First, it can verify that the reports fulfill the minimum information requirements of the corresponding MIAPE modules, highlighting inconsistencies or missing information. Second, the toolkit can convert several XML-based data standards directly into human readable MIAPE reports stored within the ProteoRed MIAPE repository. Finally, it can also perform the reverse operation, allowing users to export from MIAPE reports into XML files for computational processing, data sharing, or public database submission. The toolkit is thus the first application capable of automatically linking the PSI's MIAPE modules with the corresponding XML data exchange standards, enabling bidirectional conversions. This toolkit is freely available at http://www.proteored.org/MIAPE/. PMID:21983993

Quantitative proteomics unravels that the post-transcriptional regulator Crc modulates the generation of vesicles and secreted virulence determinants of Pseudomonas aeruginosa.

PubMed

Reales-Calderón, Jose Antonio; Corona, Fernando; Monteoliva, Lucía; Gil, Concha; Martínez, Jose Luis

2015-09-08

Recent research indicates that the post-transcriptional regulator Crc modulates susceptibility to antibiotics and virulence in Pseudomonas aeruginosa. Several P. aeruginosa virulence factors are secreted or engulfed in vesicles. To decipher the Crc modulation of P. aeruginosa virulence, we constructed a crc deficient mutant and measure the proteome associated extracellular vesicles and the vesicle-free secretome using iTRAQ. Fifty vesicle-associated proteins were more abundant and 14 less abundant in the crc-defective strain, whereas 37 were more abundant and 17 less abundant in the vesicle-free secretome. Among them, virulence determinants, such as ToxA, protease IV, azurin, chitin-binding protein, PlcB and Hcp1, were less abundant in the crc-defective mutant. Transcriptomic analysis revealed that some of the observed changes were post-transcriptional and, thus, could be attributed to a direct Crc regulatory role; whereas, for other differentially secreted proteins, the regulatory role was likely indirect. We also observed that the crc mutant presented an impaired vesicle-associated secretion of quorum sensing signal molecules and less cytotoxicity than its wild-type strain. Our results offer new insights into the mechanisms by which Crc regulates P. aeruginosa virulence, through the modulation of vesicle formation and secretion of both virulence determinants and quorum sensing signals. This article is part of a Special Issue entitled: HUPO 2014. Published by Elsevier B.V.

ProCon - PROteomics CONversion tool.

PubMed

Mayer, Gerhard; Stephan, Christian; Meyer, Helmut E; Kohl, Michael; Marcus, Katrin; Eisenacher, Martin

2015-11-03

With the growing amount of experimental data produced in proteomics experiments and the requirements/recommendations of journals in the proteomics field to publicly make available data described in papers, a need for long-term storage of proteomics data in public repositories arises. For such an upload one needs proteomics data in a standardized format. Therefore, it is desirable, that the proprietary vendor's software will integrate in the future such an export functionality using the standard formats for proteomics results defined by the HUPO-PSI group. Currently not all search engines and analysis tools support these standard formats. In the meantime there is a need to provide user-friendly free-to-use conversion tools that can convert the data into such standard formats in order to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories. ProCon is such a conversion tool written in Java for conversion of proteomics identification data into standard formats mzIdentML and Pride XML. It allows the conversion of Sequest™/Comet .out files, of search results from the popular and often used ProteomeDiscoverer® 1.x (x=versions 1.1 to1.4) software and search results stored in the LIMS systems ProteinScape® 1.3 and 2.1 into mzIdentML and PRIDE XML. This article is part of a Special Issue entitled: Computational Proteomics. Copyright © 2015. Published by Elsevier B.V.

Mechanisms of antibiotic resistance to enrofloxacin in uropathogenic Escherichia coli in dog.

PubMed

Piras, Cristian; Soggiu, Alessio; Greco, Viviana; Martino, Piera Anna; Del Chierico, Federica; Putignani, Lorenza; Urbani, Andrea; Nally, Jarlath E; Bonizzi, Luigi; Roncada, Paola

2015-09-08

Escherichia coli (E. coli) urinary tract infections (UTIs) are becoming a serious problem both for pets and humans (zoonosis) due to the close contact and to the increasing resistance to antibiotics. This study has been performed in order to unravel the mechanism of induced enrofloxacin resistance in canine E. coli isolates that represent a good tool to study this pathology. The isolated E. coli has been induced with enrofloxacin and studied through 2D DIGE and shotgun MS. Discovered differentially expressed proteins are principally involved in antibiotic resistance and linked to oxidative stress response, to DNA protection and to membrane permeability. Moreover, since enrofloxacin is an inhibitor of DNA gyrase, the overexpression of DNA starvation/stationary phase protection protein (Dsp) could be a central point to discover the mechanism of this clone to counteract the effects of enrofloxacin. In parallel, the dramatic decrease of the synthesis of the outer membrane protein W, which represents one of the main gates for enrofloxacin entrance, could explain additional mechanism of E. coli defense against this antibiotic. All 2D DIGE and MS data have been deposited into the ProteomeXchange Consortium with identifier PXD002000 and DOI http://dx.doi.org/10.6019/PXD002000. This article is part of a Special Issue entitled: HUPO 2014. Copyright © 2015 Elsevier B.V. All rights reserved.

Knowledge Translation: Moving Proteomics Science to Innovation in Society.

PubMed

Holmes, Christina; McDonald, Fiona; Jones, Mavis; Graham, Janice

2016-06-01

Proteomics is one of the pivotal next-generation biotechnologies in the current "postgenomics" era. Little is known about the ways in which innovative proteomics science is navigating the complex socio-political space between laboratory and society. It cannot be assumed that the trajectory between proteomics laboratory and society is linear and unidirectional. Concerned about public accountability and hopes for knowledge-based innovations, funding agencies and citizens increasingly expect that emerging science and technologies, such as proteomics, are effectively translated and disseminated as innovation in society. Here, we describe translation strategies promoted in the knowledge translation (KT) and science communication literatures and examine the use of these strategies within the field of proteomics. Drawing on data generated from qualitative interviews with proteomics scientists and ethnographic observation of international proteomics conferences over a 5-year period, we found that proteomics science incorporates a variety of KT strategies to reach knowledge users outside the field. To attain the full benefit of KT, however, proteomics scientists must challenge their own normative assumptions and approaches to innovation dissemination-beyond the current paradigm relying primarily on publication for one's scientific peers within one's field-and embrace the value of broader (interdisciplinary) KT strategies in promoting the uptake of their research. Notably, the Human Proteome Organization (HUPO) is paying increasing attention to a broader range of KT strategies, including targeted dissemination, integrated KT, and public outreach. We suggest that increasing the variety of KT strategies employed by proteomics scientists is timely and would serve well the omics system sciences community.

LiverAtlas: a unique integrated knowledge database for systems-level research of liver and hepatic disease.

PubMed

Zhang, Yanqiong; Yang, Chunyuan; Wang, Shaochuang; Chen, Tao; Li, Mansheng; Wang, Xue; Li, Dongsheng; Wang, Kang; Ma, Jie; Wu, Songfeng; Zhang, Xueli; Zhu, Yunping; Wu, Jinsheng; He, Fuchu

2013-09-01

A large amount of liver-related physiological and pathological data exist in publicly available biological and bibliographic databases, which are usually far from comprehensive or integrated. Data collection, integration and mining processes pose a great challenge to scientific researchers and clinicians interested in the liver. To address these problems, we constructed LiverAtlas (http://liveratlas.hupo.org.cn), a comprehensive resource of biomedical knowledge related to the liver and various hepatic diseases by incorporating 53 databases. In the present version, LiverAtlas covers data on liver-related genomics, transcriptomics, proteomics, metabolomics and hepatic diseases. Additionally, LiverAtlas provides a wealth of manually curated information, relevant literature citations and cross-references to other databases. Importantly, an expert-confirmed Human Liver Disease Ontology, including relevant information for 227 types of hepatic disease, has been constructed and is used to annotate LiverAtlas data. Furthermore, we have demonstrated two examples of applying LiverAtlas data to identify candidate markers for hepatocellular carcinoma (HCC) at the systems level and to develop a systems biology-based classifier by combining the differential gene expression with topological features of human protein interaction networks to enhance the ability of HCC differential diagnosis. LiverAtlas is the most comprehensive liver and hepatic disease resource, which helps biologists and clinicians to analyse their data at the systems level and will contribute much to the biomarker discovery and diagnostic performance enhancement for liver diseases. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The Spanish biology/disease initiative within the human proteome project: Application to rheumatic diseases.

PubMed

Ruiz-Romero, Cristina; Calamia, Valentina; Albar, Juan Pablo; Casal, José Ignacio; Corrales, Fernando J; Fernández-Puente, Patricia; Gil, Concha; Mateos, Jesús; Vivanco, Fernando; Blanco, Francisco J

2015-09-08

The Spanish Chromosome 16 consortium is integrated in the global initiative Human Proteome Project, which aims to develop an entire map of the proteins encoded following a gene-centric strategy (C-HPP) in order to make progress in the understanding of human biology in health and disease (B/D-HPP). Chromosome 16 contains many genes encoding proteins involved in the development of a broad range of diseases, which have a significant impact on the health care system. The Spanish HPP consortium has developed a B/D platform with five programs focused on selected medical areas: cancer, obesity, cardiovascular, infectious and rheumatic diseases. Each of these areas has a clinical leader associated to a proteomic investigator with the responsibility to get a comprehensive understanding of the proteins encoded by Chromosome 16 genes. Proteomics strategies have enabled great advances in the area of rheumatic diseases, particularly in osteoarthritis, with studies performed on joint cells, tissues and fluids. In this manuscript we describe how the Spanish HPP-16 consortium has developed a B/D platform with five programs focused on selected medical areas: cancer, obesity, cardiovascular, infectious and rheumatic diseases. Each of these areas has a clinical leader associated to a proteomic investigator with the responsibility to get a comprehensive understanding of the proteins encoded by Chromosome 16 genes. We show how the Proteomic strategy has enabled great advances in the area of rheumatic diseases, particularly in osteoarthritis, with studies performed on joint cells, tissues and fluids. This article is part of a Special Issue entitled: HUPO 2014. Copyright © 2015 Elsevier B.V. All rights reserved.

Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline.

PubMed

Dowsey, Andrew W; Dunn, Michael J; Yang, Guang-Zhong

2008-04-01

The quest for high-throughput proteomics has revealed a number of challenges in recent years. Whilst substantial improvements in automated protein separation with liquid chromatography and mass spectrometry (LC/MS), aka 'shotgun' proteomics, have been achieved, large-scale open initiatives such as the Human Proteome Organization (HUPO) Brain Proteome Project have shown that maximal proteome coverage is only possible when LC/MS is complemented by 2D gel electrophoresis (2-DE) studies. Moreover, both separation methods require automated alignment and differential analysis to relieve the bioinformatics bottleneck and so make high-throughput protein biomarker discovery a reality. The purpose of this article is to describe a fully automatic image alignment framework for the integration of 2-DE into a high-throughput differential expression proteomics pipeline. The proposed method is based on robust automated image normalization (RAIN) to circumvent the drawbacks of traditional approaches. These use symbolic representation at the very early stages of the analysis, which introduces persistent errors due to inaccuracies in modelling and alignment. In RAIN, a third-order volume-invariant B-spline model is incorporated into a multi-resolution schema to correct for geometric and expression inhomogeneity at multiple scales. The normalized images can then be compared directly in the image domain for quantitative differential analysis. Through evaluation against an existing state-of-the-art method on real and synthetically warped 2D gels, the proposed analysis framework demonstrates substantial improvements in matching accuracy and differential sensitivity. High-throughput analysis is established through an accelerated GPGPU (general purpose computation on graphics cards) implementation. Supplementary material, software and images used in the validation are available at http://www.proteomegrid.org/rain/.

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience.

PubMed

Griss, Johannes; Jones, Andrew R; Sachsenberg, Timo; Walzer, Mathias; Gatto, Laurent; Hartler, Jürgen; Thallinger, Gerhard G; Salek, Reza M; Steinbeck, Christoph; Neuhauser, Nadin; Cox, Jürgen; Neumann, Steffen; Fan, Jun; Reisinger, Florian; Xu, Qing-Wei; Del Toro, Noemi; Pérez-Riverol, Yasset; Ghali, Fawaz; Bandeira, Nuno; Xenarios, Ioannis; Kohlbacher, Oliver; Vizcaíno, Juan Antonio; Hermjakob, Henning

2014-10-01

The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS)-based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics and metabolomics experiments in a simple tabular format. Many downstream analysis use cases are only concerned with the final results of an experiment and require an easily accessible format, compatible with tools such as Microsoft Excel or R. We developed the mzTab file format for MS-based proteomics and metabolomics results to meet this need. mzTab is intended as a lightweight supplement to the existing standard XML-based file formats (mzML, mzIdentML, mzQuantML), providing a comprehensive summary, similar in concept to the supplemental material of a scientific publication. mzTab files can contain protein, peptide, and small molecule identifications together with experimental metadata and basic quantitative information. The format is not intended to store the complete experimental evidence but provides mechanisms to report results at different levels of detail. These range from a simple summary of the final results to a representation of the results including the experimental design. This format is ideally suited to make MS-based proteomics and metabolomics results available to a wider biological community outside the field of MS. Several software tools for proteomics and metabolomics have already adapted the format as an output format. The comprehensive mzTab specification document and extensive additional documentation can be found online. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience*

PubMed Central

Griss, Johannes; Jones, Andrew R.; Sachsenberg, Timo; Walzer, Mathias; Gatto, Laurent; Hartler, Jürgen; Thallinger, Gerhard G.; Salek, Reza M.; Steinbeck, Christoph; Neuhauser, Nadin; Cox, Jürgen; Neumann, Steffen; Fan, Jun; Reisinger, Florian; Xu, Qing-Wei; del Toro, Noemi; Pérez-Riverol, Yasset; Ghali, Fawaz; Bandeira, Nuno; Xenarios, Ioannis; Kohlbacher, Oliver; Vizcaíno, Juan Antonio; Hermjakob, Henning

2014-01-01

The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS)-based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics and metabolomics experiments in a simple tabular format. Many downstream analysis use cases are only concerned with the final results of an experiment and require an easily accessible format, compatible with tools such as Microsoft Excel or R. We developed the mzTab file format for MS-based proteomics and metabolomics results to meet this need. mzTab is intended as a lightweight supplement to the existing standard XML-based file formats (mzML, mzIdentML, mzQuantML), providing a comprehensive summary, similar in concept to the supplemental material of a scientific publication. mzTab files can contain protein, peptide, and small molecule identifications together with experimental metadata and basic quantitative information. The format is not intended to store the complete experimental evidence but provides mechanisms to report results at different levels of detail. These range from a simple summary of the final results to a representation of the results including the experimental design. This format is ideally suited to make MS-based proteomics and metabolomics results available to a wider biological community outside the field of MS. Several software tools for proteomics and metabolomics have already adapted the format as an output format. The comprehensive mzTab specification document and extensive additional documentation can be found online. PMID:24980485

Message-adjusted network (MAN) hypothesis in gastro-entero-pancreatic (GEP) endocrine system.

PubMed

Aykan, N Faruk

2007-01-01

Several types of communication coordinate body functions to maintain homeostasis. Clarifying intercellular communication systems is as important as intracellular signal mechanisms. In this study, we propose an intercellular network model to establish novel targets in GEP-endocrine system, based on up-to-date information from medical publications. As materials, two physiologic events which are Pavlov's sham-feeding assay and bicarbonate secretion into the duodenum from pancreas were explored by new biologic data from the literature. Major key words used in Pub-Med were modes of regulations (autocrine, paracrine, endocrine, neurocrine, juxtacrine, lumencrine), GEP cells, hormones, peptides and neuro-transmitters. In these two examples of physiologic events, we can design a model of network to clarify transmission of a message. When we take a simple, unique message, we can observe a complete intercellular network. In our examples, these messages are "food is coming" and "hydrogen ions are increasing" in human language (humanese). We need to find molecular counterparts of these unique messages in cell language (cellese). In this network (message-adjusted network; MAN), message is an input which can affect the physiologic equilibrium, mission is an output to improve the disequilibrium and aim is always maintenance of homeostasis. If we orientate to a transmission of a unique message we can distinguish that different cells use different chemical messengers in different modes of regulations to transmit the same message. This study also supports Shannon's information theory and cell language theories such as von Neumann-Patte principles. After human genome project (HU-GO) and protein organisations (HU-PO), finding true messages and the establishment of their networks (in our model HU-MAN project) can be a novel and exciting field in cell biology. We established an intercellular network model to understand intercellular communication in the physiology of GEP endocrine system. This model could help to explain complex physiologic events as well as to generate new treatment concepts.

21 CFR 864.3260 - OTC test sample collection systems for drugs of abuse testing.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false OTC test sample collection systems for drugs of... Instrumentation and Accessories § 864.3260 OTC test sample collection systems for drugs of abuse testing. (a) Identification. An over-the-counter (OTC) test sample collection system for drugs of abuse testing is a device...

Microbiological baseline study of beef and pork carcasses from provincially inspected abattoirs in Alberta, Canada

PubMed Central

Bohaychuk, Valerie M.; Gensler, Gary E.; Barrios, Pablo Romero

2011-01-01

In 2006 and 2007 beef and pork carcass swabs from provincially inspected abattoirs in Alberta, Canada were tested to determine the levels of total aerobic bacteria, coliform bacteria, and generic Escherichia coli, and the prevalence of Salmonella spp., Campylobacter spp., and Shiga toxin-producing E. coli (STEC). Swabs from beef and pork carcasses from 48 and 34 facilities, respectively, were analyzed. All samples tested were positive for aerobic bacteria with 99.8% of beef and 96.0% of pork samples, having total counts of ≤ 100 000 CFU/cm2. Coliform bacteria were isolated from 22.4% and 42.0% of beef and pork carcass samples, respectively. Generic E. coli were recovered from 14.6% of beef and 33.7% of pork carcass samples. For beef carcasses, positive tests were obtained for 0.1% of 1036 samples tested for Salmonella spp., 1.5% of 1022 samples tested for Campylobacter spp. and 5.4% of 1018 samples tested for STEC. For pork carcasses, positive tests were obtained for 1.6 % of 1076 samples tested for Salmonella spp., 8.8% of 1070 samples tested for Campylobacter spp. and 4.8% of 1067 samples tested for STEC. PMID:22467964

30 CFR 15.5 - Test samples.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Test samples. 15.5 Section 15.5 Mineral... § 15.5 Test samples. (a) Submission of test samples. (1) The applicant shall not submit explosives or... magazine for at least 30 days before gallery tests are conducted. ...

30 CFR 15.5 - Test samples.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Test samples. 15.5 Section 15.5 Mineral... § 15.5 Test samples. (a) Submission of test samples. (1) The applicant shall not submit explosives or... magazine for at least 30 days before gallery tests are conducted. ...

30 CFR 15.5 - Test samples.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Test samples. 15.5 Section 15.5 Mineral... § 15.5 Test samples. (a) Submission of test samples. (1) The applicant shall not submit explosives or... magazine for at least 30 days before gallery tests are conducted. ...

40 CFR 86.237-08 - Dynamometer test run, gaseous emissions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... minutes of the end of the sample collection phase of the test. Obtain methanol and formaldehyde sample... collection phase of the test. Obtain methanol and formaldehyde sample analyses, if applicable, within 24... the sample collection phase of the test. Obtain methanol and formaldehyde sample analyses, if...

40 CFR 86.237-08 - Dynamometer test run, gaseous emissions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... minutes of the end of the sample collection phase of the test. Obtain methanol and formaldehyde sample... collection phase of the test. Obtain methanol and formaldehyde sample analyses, if applicable, within 24... the sample collection phase of the test. Obtain methanol and formaldehyde sample analyses, if...

40 CFR 205.57-2 - Test vehicle sample selection.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 25 2011-07-01 2011-07-01 false Test vehicle sample selection. 205.57... vehicle sample selection. (a) Vehicles comprising the batch sample which are required to be tested... test request from a batch of vehicles of the category or configuration specified in the test request...

40 CFR 90.706 - Engine sample selection.

Code of Federal Regulations, 2010 CFR

2010-07-01

... = emission test result for an individual engine. x = mean of emission test results of the actual sample. FEL... test with the last test result from the previous model year and then calculate the required sample size.... Test results used to calculate the variables in the following Sample Size Equation must be final...

Accuracy of human papillomavirus testing on self-collected versus clinician-collected samples: a meta-analysis.

PubMed

Arbyn, Marc; Verdoodt, Freija; Snijders, Peter J F; Verhoef, Viola M J; Suonio, Eero; Dillner, Lena; Minozzi, Silvia; Bellisario, Cristina; Banzi, Rita; Zhao, Fang-Hui; Hillemanns, Peter; Anttila, Ahti

2014-02-01

Screening for human papillomavirus (HPV) infection is more effective in reducing the incidence of cervical cancer than screening using Pap smears. Moreover, HPV testing can be done on a vaginal sample self-taken by a woman, which offers an opportunity to improve screening coverage. However, the clinical accuracy of HPV testing on self-samples is not well-known. We assessed whether HPV testing on self-collected samples is equivalent to HPV testing on samples collected by clinicians. We identified relevant studies through a search of PubMed, Embase, and CENTRAL. Studies were eligible for inclusion if they fulfilled all of the following selection criteria: a cervical cell sample was self-collected by a woman followed by a sample taken by a clinician; a high-risk HPV test was done on the self-sample (index test) and HPV-testing or cytological interpretation was done on the specimen collected by the clinician (comparator tests); and the presence or absence of cervical intraepithelial neoplasia grade 2 (CIN2) or worse was verified by colposcopy and biopsy in all enrolled women or in women with one or more positive tests. The absolute accuracy for finding CIN2 or worse, or CIN grade 3 (CIN3) or worse of the index and comparator tests as well as the relative accuracy of the index versus the comparator tests were pooled using bivariate normal models and random effect models. We included data from 36 studies, which altogether enrolled 154 556 women. The absolute accuracy varied by clinical setting. In the context of screening, HPV testing on self-samples detected, on average, 76% (95% CI 69-82) of CIN2 or worse and 84% (72-92) of CIN3 or worse. The pooled absolute specificity to exclude CIN2 or worse was 86% (83-89) and 87% (84-90) to exclude CIN3 or worse. The variation of the relative accuracy of HPV testing on self-samples compared with tests on clinician-taken samples was low across settings, enabling pooling of the relative accuracy over all studies. The pooled sensitivity of HPV testing on self-samples was lower than HPV testing on a clinician-taken sample (ratio 0·88 [95% CI 0·85-0·91] for CIN2 or worse and 0·89 [0·83-0·96] for CIN3 or worse). Also specificity was lower in self-samples versus clinician-taken samples (ratio 0·96 [0·95-0·97] for CIN2 or worse and 0·96 [0·93-0·99] for CIN3 or worse). HPV testing with signal-based assays on self-samples was less sensitive and specific than testing on clinician-based samples. By contrast, some PCR-based HPV tests generally showed similar sensitivity on both self-samples and clinician-based samples. In screening programmes using signal-based assays, sampling by a clinician should be recommended. However, HPV testing on a self-sample can be suggested as an additional strategy to reach women not participating in the regular screening programme. Some PCR-based HPV tests could be considered for routine screening after careful piloting assessing feasibility, logistics, population compliance, and costs. The 7th Framework Programme of the European Commission, the Belgian Foundation against Cancer, the International Agency for Research on Cancer, and the German Guideline Program in Oncology. Copyright © 2014 Elsevier Ltd. All rights reserved.

40 CFR 205.171-2 - Test exhaust system sample selection and preparation.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 26 2013-07-01 2013-07-01 false Test exhaust system sample selection... Systems § 205.171-2 Test exhaust system sample selection and preparation. (a)(1) Exhaust systems comprising the sample which are required to be tested under a test request in accordance with this subpart...

Determination of Pass/Fail Criteria for Promoted Combustion Testing

NASA Technical Reports Server (NTRS)

Sparks, Kyle M.; Stoltzfus, Joel M.; Steinberg, Theodore A.; Lynn, David

2009-01-01

Promoted ignition testing is used to determine the relative flammability of metal rods in oxygen-enriched atmospheres. In these tests, a promoter is used to ignite each metal rod to start the sample burning. Experiments were performed to better understand the promoted ignition test by obtaining insight into the effect a burning promoter has on the preheating of a test sample. Test samples of several metallic materials were prepared and coupled to fast-responding thermocouples along their length. Various ignition promoters were used to ignite the test samples. The thermocouple measurements and test video was synchronized to determine temperature increase with respect to time and length along each test sample. A recommended length of test sample that must be consumed to be considered a flammable material was determined based on the preheated zone measured from these tests. This length was determined to be 30 mm (1.18 in.). Validation of this length and its rationale are presented.

Heat Effects of Promoters and Determination of Burn Criterion in Promoted Combustion Testing

NASA Technical Reports Server (NTRS)

Sparks, Kyle M.; Stoltzfus, Joel M.; Steinberg, Theodore A.; Lynn, David

2010-01-01

Promoted ignition testing (NASA Test 17) [1] is used to determine the relative flammability of metal rods in oxygen-enriched atmospheres. A promoter is used to ignite a metal sample rod, initiating sample burning. If a predetermined length of the sample burns, beyond the promoter, the material is considered flammable at the condition tested. Historically, this burn length has been somewhat arbitrary. Experiments were performed to better understand this test by obtaining insight into the effect a burning promoter has on the preheating of a test sample. Test samples of several metallic materials were prepared and coupled to fast-responding thermocouples along their length. Thermocouple measurements and test video were synchronized to determine temperature increase with respect to time and length along each test sample. A recommended flammability burn length, based on a sample preheat of 500 F, was determined based on the preheated zone measured from these tests. This length was determined to be 30 mm (1.18 in.). Validation of this length and its rationale are presented.

The t-test: An Influential Inferential Tool in Chaplaincy and Other Healthcare Research.

PubMed

Jankowski, Katherine R B; Flannelly, Kevin J; Flannelly, Laura T

2018-01-01

The t-test developed by William S. Gosset (also known as Student's t-test and the two-sample t-test) is commonly used to compare one sample mean on a measure with another sample mean on the same measure. The outcome of the t-test is used to draw inferences about how different the samples are from each other. It is probably one of the most frequently relied upon statistics in inferential research. It is easy to use: a researcher can calculate the statistic with three simple tools: paper, pen, and a calculator. A computer program can quickly calculate the t-test for large samples. The ease of use can result in the misuse of the t-test. This article discusses the development of the original t-test, basic principles of the t-test, two additional types of t-tests (the one-sample t-test and the paired t-test), and recommendations about what to consider when using the t-test to draw inferences in research.

On two-sample McNemar test.

PubMed

Xiang, Jim X

2016-01-01

Measuring a change in the existence of disease symptoms before and after a treatment is examined for statistical significance by means of the McNemar test. When comparing two treatments, Feuer and Kessler (1989) proposed a two-sample McNemar test. In this article, we show that this test usually inflates the type I error in the hypothesis testing, and propose a new two-sample McNemar test that is superior in terms of preserving type I error. We also make the connection between the two-sample McNemar test and the test statistic for the equal residual effects in a 2 × 2 crossover design. The limitations of the two-sample McNemar test are also discussed.

Sample Holder for Cryogenic Adhesive Shear Test

NASA Technical Reports Server (NTRS)

Ledbetter, F. E.; Clemons, J. M.; White, W. T.; Penn, B.; Semmel, M. L.

1983-01-01

Five samples tested in one cooldown. Holder mounted in testing machine. Submerged in cryogenic liquid held in cryostat. Movable crosshead of testing machine moves gradually downward. Samples placed under tension, one after another, starting with top one; each sample fails in turn before next is stressed.

Phase II test plan for the evaluation of the performance of container filling systems

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

BOGER, R.M.

The PHMC will provide tank wastes for final treatment by BNFL from Hanford's waste tanks. Concerns about the ability for ''grab'' sampling to provide large volumes of representative waste samples has led to the development of a nested, fixed-depth sampling system. Preferred concepts for filling sample containers that meet RCRA organic sample criteria were identified by a PHMC Decision Board. These systems will replace the needle based sampling ''T'' that is currently on the sampling system. This test plan document identifies cold tests with simulants that will demonstrate the preferred bottle filling concepts abilities to provide representative waste samples andmore » will meet RCRA criteria. Additional tests are identified that evaluate the potential for cross-contamination between samples and the ability for the system to decontaminate surfaces which have contacted tank wastes. These tests will be performed with kaolid/water and sand/water slurry simulants in the test rig that was used by AEAT to complete Phase 1 tests in FY 1999.« less

40 CFR 133.104 - Sampling and test procedures.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 22 2011-07-01 2011-07-01 false Sampling and test procedures. 133.104 Section 133.104 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS SECONDARY TREATMENT REGULATION § 133.104 Sampling and test procedures. (a) Sampling and test procedures for...

40 CFR 133.104 - Sampling and test procedures.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 21 2010-07-01 2010-07-01 false Sampling and test procedures. 133.104 Section 133.104 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS SECONDARY TREATMENT REGULATION § 133.104 Sampling and test procedures. (a) Sampling and test procedures for...

40 CFR 133.104 - Sampling and test procedures.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 23 2012-07-01 2012-07-01 false Sampling and test procedures. 133.104 Section 133.104 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS SECONDARY TREATMENT REGULATION § 133.104 Sampling and test procedures. (a) Sampling and test procedures for...

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

DOEpatents

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

1997-01-01

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

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

DOEpatents

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

1997-10-14

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

Sensitivity and specificity of normality tests and consequences on reference interval accuracy at small sample size: a computer-simulation study.

PubMed

Le Boedec, Kevin

2016-12-01

According to international guidelines, parametric methods must be chosen for RI construction when the sample size is small and the distribution is Gaussian. However, normality tests may not be accurate at small sample size. The purpose of the study was to evaluate normality test performance to properly identify samples extracted from a Gaussian population at small sample sizes, and assess the consequences on RI accuracy of applying parametric methods to samples that falsely identified the parent population as Gaussian. Samples of n = 60 and n = 30 values were randomly selected 100 times from simulated Gaussian, lognormal, and asymmetric populations of 10,000 values. The sensitivity and specificity of 4 normality tests were compared. Reference intervals were calculated using 6 different statistical methods from samples that falsely identified the parent population as Gaussian, and their accuracy was compared. Shapiro-Wilk and D'Agostino-Pearson tests were the best performing normality tests. However, their specificity was poor at sample size n = 30 (specificity for P < .05: .51 and .50, respectively). The best significance levels identified when n = 30 were 0.19 for Shapiro-Wilk test and 0.18 for D'Agostino-Pearson test. Using parametric methods on samples extracted from a lognormal population but falsely identified as Gaussian led to clinically relevant inaccuracies. At small sample size, normality tests may lead to erroneous use of parametric methods to build RI. Using nonparametric methods (or alternatively Box-Cox transformation) on all samples regardless of their distribution or adjusting, the significance level of normality tests depending on sample size would limit the risk of constructing inaccurate RI. © 2016 American Society for Veterinary Clinical Pathology.

10 CFR 430.70 - Enforcement.

Code of Federal Regulations, 2010 CFR

2010-01-01

...), the Secretary may conduct testing of that covered product under this subpart by means of a test notice... be selected for testing, the method of selecting the test sample, the time at which testing shall be... shall select a batch, a batch sample, and test units from the batch sample in accordance with the...

Face recognition based on symmetrical virtual image and original training image

NASA Astrophysics Data System (ADS)

Ke, Jingcheng; Peng, Yali; Liu, Shigang; Li, Jun; Pei, Zhao

2018-02-01

In face representation-based classification methods, we are able to obtain high recognition rate if a face has enough available training samples. However, in practical applications, we only have limited training samples to use. In order to obtain enough training samples, many methods simultaneously use the original training samples and corresponding virtual samples to strengthen the ability of representing the test sample. One is directly using the original training samples and corresponding mirror samples to recognize the test sample. However, when the test sample is nearly symmetrical while the original training samples are not, the integration of the original training and mirror samples might not well represent the test samples. To tackle the above-mentioned problem, in this paper, we propose a novel method to obtain a kind of virtual samples which are generated by averaging the original training samples and corresponding mirror samples. Then, the original training samples and the virtual samples are integrated to recognize the test sample. Experimental results on five face databases show that the proposed method is able to partly overcome the challenges of the various poses, facial expressions and illuminations of original face image.

'Nano-immuno test' for the detection of live Mycobacterium avium subspecies paratuberculosis bacilli in the milk samples using magnetic nano-particles and chromogen.

PubMed

Singh, Manju; Singh, Shoor Vir; Gupta, Saurabh; Chaubey, Kundan Kumar; Stephan, Bjorn John; Sohal, Jagdip Singh; Dutta, Manali

2018-04-26

Early rapid detection of Mycobacterium avium subspecies paratuberculosis (MAP) bacilli in milk samples is the major challenge since traditional culture method is time consuming and laboratory dependent. We report a simple, sensitive and specific nano-technology based 'Nano-immuno test' capable of detecting viable MAP bacilli in the milk samples within 10 h. Viable MAP bacilli were captured by MAP specific antibody-conjugated magnetic nano-particles using resazurin dye as chromogen. Test was optimized using true culture positive (10-bovine and 12-goats) and true culture negative (16-bovine and 25-goats) raw milk samples. Domestic livestock species in India are endemically infected with MAP. After successful optimization, sensitivity and specificity of the 'nano-immuno test' in goats with respect to milk culture was 91.7% and 96.0%, respectively. Whereas, it was 90.0% (sensitivity) and 92.6% (specificity) with respect to IS900 PCR. In bovine milk samples, sensitivity and specificity of 'nano-immuno test' with respect to milk culture was 90.0% and 93.7%, respectively. However, with respect to IS900 PCR, the sensitivity and specificity was 88.9% and 94.1%, respectively. Test was validated with field raw milk samples (goats-258 and bovine-138) collected from domestic livestock species to detect live/viable MAP bacilli. Of 138 bovine raw milk samples screened by six diagnostic tests, 81 (58.7%) milk samples were positive for MAP infection in one or more than one diagnostic tests. Of 81 (58.7%) positive bovine raw milk samples, only 24 (17.4%) samples were detected positive for the presence of viable MAP bacilli. Of 258 goats raw milk samples screened by six diagnostic tests, 141 (54.6%) were positive for MAP infection in one or more than one test. Of 141 (54.6%) positive raw milk samples from goats, only 48 (34.0%) were detected positive for live MAP bacilli. Simplicity and efficiency of this novel 'nano-immuno test' makes it suitable for wide-scale screening of milk samples in the field. Standardization, validation and re-usability of functionalized nano-particles and the test was successfully achieved in field samples. Test was highly specific, simple to perform and easy to read by naked eyes and does not require laboratory support in the performance of test. Test has potential to be used as screening test to estimate bio-load of MAP in milk samples at National level.

Sample features associated with success rates in population-based EGFR mutation testing.

PubMed

Shiau, Carolyn J; Babwah, Jesse P; da Cunha Santos, Gilda; Sykes, Jenna R; Boerner, Scott L; Geddie, William R; Leighl, Natasha B; Wei, Cuihong; Kamel-Reid, Suzanne; Hwang, David M; Tsao, Ming-Sound

2014-07-01

Epidermal growth factor receptor (EGFR) mutation testing has become critical in the treatment of patients with advanced non-small-cell lung cancer. This study involves a large cohort and epidemiologically unselected series of EGFR mutation testing for patients with nonsquamous non-small-cell lung cancer in a North American population to determine sample-related factors that influence success in clinical EGFR testing. Data from consecutive cases of Canadian province-wide testing at a centralized diagnostic laboratory for a 24-month period were reviewed. Samples were tested for exon-19 deletion and exon-21 L858R mutations using a validated polymerase chain reaction method with 1% to 5% detection sensitivity. From 2651 samples submitted, 2404 samples were tested with 2293 samples eligible for analysis (1780 histology and 513 cytology specimens). The overall test-failure rate was 5.4% with overall mutation rate of 20.6%. No significant differences in the failure rate, mutation rate, or mutation type were found between histology and cytology samples. Although tumor cellularity was significantly associated with test-success or mutation rates in histology and cytology specimens, respectively, mutations could be detected in all specimen types. Significant rates of EGFR mutation were detected in cases with thyroid transcription factor (TTF)-1-negative immunohistochemistry (6.7%) and mucinous component (9.0%). EGFR mutation testing should be attempted in any specimen, whether histologic or cytologic. Samples should not be excluded from testing based on TTF-1 status or histologic features. Pathologists should report the amount of available tumor for testing. However, suboptimal samples with a negative EGFR mutation result should be considered for repeat testing with an alternate sample.

21 CFR 864.3260 - OTC test sample collection systems for drugs of abuse testing.

Code of Federal Regulations, 2013 CFR

2013-04-01

... abuse testing. 864.3260 Section 864.3260 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... Instrumentation and Accessories § 864.3260 OTC test sample collection systems for drugs of abuse testing. (a) Identification. An over-the-counter (OTC) test sample collection system for drugs of abuse testing is a device...

21 CFR 864.3260 - OTC test sample collection systems for drugs of abuse testing.

Code of Federal Regulations, 2011 CFR

2011-04-01

... abuse testing. 864.3260 Section 864.3260 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... Instrumentation and Accessories § 864.3260 OTC test sample collection systems for drugs of abuse testing. (a) Identification. An over-the-counter (OTC) test sample collection system for drugs of abuse testing is a device...

21 CFR 864.3260 - OTC test sample collection systems for drugs of abuse testing.

Code of Federal Regulations, 2012 CFR

2012-04-01

... abuse testing. 864.3260 Section 864.3260 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... Instrumentation and Accessories § 864.3260 OTC test sample collection systems for drugs of abuse testing. (a) Identification. An over-the-counter (OTC) test sample collection system for drugs of abuse testing is a device...

21 CFR 864.3260 - OTC test sample collection systems for drugs of abuse testing.

Code of Federal Regulations, 2014 CFR

2014-04-01

... abuse testing. 864.3260 Section 864.3260 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... Instrumentation and Accessories § 864.3260 OTC test sample collection systems for drugs of abuse testing. (a) Identification. An over-the-counter (OTC) test sample collection system for drugs of abuse testing is a device...

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

PubMed

Rummel, John D; Kminek, Gerhard

2018-04-01

The last time NASA envisioned a sample return mission from Mars, the development of a protocol to support the analysis of the samples in a containment facility resulted in a "Draft Test Protocol" that outlined required preparations "for the safe receiving, handling, testing, distributing, and archiving of martian materials here on Earth" (Rummel et al., 2002 ). This document comprised a specific protocol to be used to conduct a biohazard test for a returned martian sample, following the recommendations of the Space Studies Board of the US National Academy of Sciences. Given the planned launch of a sample-collecting and sample-caching rover (Mars 2020) in 2 years' time, and with a sample return planned for the end of the next decade, it is time to revisit the Draft Test Protocol to develop a sample analysis and biohazard test plan to meet the needs of these future missions. Key Words: Biohazard detection-Mars sample analysis-Sample receiving facility-Protocol-New analytical techniques-Robotic sample handling. Astrobiology 18, 377-380.

NASA GRC and MSFC Space-Plasma Arc Testing Procedures

NASA Technical Reports Server (NTRS)

Ferguson, Dale C.; Vayner, Boris V.; Galofaro, Joel T.; Hillard, G. Barry; Vaughn, Jason; Schneider, Todd

2007-01-01

Tests of arcing and current collection in simulated space plasma conditions have been performed at the NASA Glenn Research Center (GRC) in Cleveland, Ohio, for over 30 years and at the Marshall Space Flight Center (MSFC) in Huntsville, Alabama, for almost as long. During this period, proper test conditions for accurate and meaningful space simulation have been worked out, comparisons with actual space performance in spaceflight tests and with real operational satellites have been made, and NASA has achieved our own internal standards for test protocols. It is the purpose of this paper to communicate the test conditions, test procedures, and types of analysis used at NASA GRC and MSFC to the space environmental testing community at large, to help with international space-plasma arcing-testing standardization. Discussed herein are neutral gas conditions, plasma densities and uniformity, vacuum chamber sizes, sample sizes and Debye lengths, biasing samples versus self-generated voltages, floating samples versus grounded samples, test electrical conditions, arc detection, preventing sustained discharges during testing, real samples versus idealized samples, validity of LEO tests for GEO samples, extracting arc threshold information from arc rate versus voltage tests, snapover, current collection, and glows at positive sample bias, Kapton pyrolysis, thresholds for trigger arcs, sustained arcs, dielectric breakdown and Paschen discharge, tether arcing and testing in very dense plasmas (i.e. thruster plumes), arc mitigation strategies, charging mitigation strategies, models, and analysis of test results. Finally, the necessity of testing will be emphasized, not to the exclusion of modeling, but as part of a complete strategy for determining when and if arcs will occur, and preventing them from occurring in space.

Acceptability of unsupervised HPV self-sampling using written instructions.

PubMed

Waller, J; McCaffery, K; Forrest, S; Szarewski, A; Cadman, L; Austin, J; Wardle, J

2006-01-01

The study measured the acceptability of self-sampling for human papillomavirus (HPV) testing in the context of cervical cancer screening. Women carried out self-sampling unsupervised, using a written instruction sheet. Participants were women attending either a family planning clinic or a primary care trust for routine cervical screening. Women (n = 902) carried out self-sampling for HPV testing and then a clinician did a routine cervical smear and HPV test. Immediately after having the two tests, participants completed a measure of acceptability for both tests, and answered questions about ease of using the instruction sheet and willingness to use self-sampling in the future. The majority of women found self-sampling more acceptable than the clinician-administered test, but there was a lack of confidence that the test had been done correctly. Significant demographic differences in attitudes were found, with married women having more favourable attitudes towards self-sampling than single women, and Asian women having more negative attitudes than women in other ethnic groups. Intention to use self-sampling in the future was very high across all demographic groups. Self-sampling for HPV testing was highly acceptable in this large and demographically diverse sample, and women were able to carry out the test alone, using simple written instructions. Consistent with previous studies, women were concerned about doing the test properly and this issue will need to be addressed if self-sampling is introduced. More work is needed to see whether the demographic differences we found are robust and to identify reasons for lower acceptability among single women and those from Asian background.

An Experimental Study of Launch Vehicle Propellant Tank Fragmentation

NASA Technical Reports Server (NTRS)

Richardson, Erin; Jackson, Austin; Hays, Michael; Bangham, Mike; Blackwood, James; Skinner, Troy; Richman, Ben

2014-01-01

In order to better understand launch vehicle abort environments, Bangham Engineering Inc. (BEi) built a test assembly that fails sample materials (steel and aluminum plates of various alloys and thicknesses) under quasi-realistic vehicle failure conditions. Samples are exposed to pressures similar to those expected in vehicle failure scenarios and filmed at high speed to increase understanding of complex fracture mechanics. After failure, the fragments of each test sample are collected, catalogued and reconstructed for further study. Post-test analysis shows that aluminum samples consistently produce fewer fragments than steel samples of similar thickness and at similar failure pressures. Video analysis shows that there are several failure 'patterns' that can be observed for all test samples based on configuration. Fragment velocities are also measured from high speed video data. Sample thickness and material are analyzed for trends in failure pressure. Testing is also done with cryogenic and noncryogenic liquid loading on the samples. It is determined that liquid loading and cryogenic temperatures can decrease material fragmentation for sub-flight thicknesses. A method is developed for capture and collection of fragments that is greater than 97 percent effective in recovering sample mass, addressing the generation of tiny fragments. Currently, samples tested do not match actual launch vehicle propellant tank material thicknesses because of size constraints on test assembly, but test findings are used to inform the design and build of another, larger test assembly with the purpose of testing actual vehicle flight materials that include structural components such as iso-grid and friction stir welds.

Comparison of Clark's presence-absence test and the membrane filter method for coliform detection in potable water samples.

PubMed Central

Pipes, W O; Minnigh, H A; Moyer, B; Troy, M A

1986-01-01

A total of 2,601 water samples from six different water systems were tested for coliform bacteria by Clark's presence-absence (P-A) test and by the membrane filter (MF) method. There was no significant difference in the fraction of samples positive for coliform bacteria for any of the systems tested. It was concluded that the two tests are equivalent for monitoring purposes. However, 152 samples were positive for coliform bacteria by the MF method but negative by the P-A test, and 132 samples were positive by the P-A test but negative by the MF method. Many of these differences for individual samples can be explained by random dispersion of bacteria in subsamples when the coliform density is low. However, 15 samples had MF counts greater than 3 and gave negative P-A results. The only apparent explanation for most of these results is that coliform bacteria were present in the P-A test bottles but did not produce acid and gas. Two other studies have reported more samples positive by Clark's P-A test than by the MF method. PMID:3532953

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

PubMed

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

2006-09-01

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

Impact of grey zone sample testing by enzyme-linked immunosorbent assay in enhancing blood safety: Experience at a tertiary care hospital in North India.

PubMed

Solanki, Archana; Singh, Abhay; Chaudhary, Rajendra

2016-01-01

Enzyme-linked immunosorbent assay (ELISA) used for screening blood donors for transfusion transmitted infections (TTIs) can sometimes fail to detect blood donors who are recently infected or possessing the low strength of pathogen. Estimation of a grey zone in ELISA testing and repeat testing of grey zone samples can further help in reducing the risks of TTI in countries where nucleic acid amplification testing for TTIs is not feasible. Grey zone samples with optical density (OD) lying between cut-off OD and 10% below the cut-off OD (cut-off OD × 0.9) were identified during routine ELISA testing. On performing repeat ELISA testing on grey zone samples in duplicate, the samples showing both OD value below grey zone were marked nonreactive, and samples showing one or both OD value in the grey zone were marked indeterminate. The samples on repeat testing showing one or both OD above cut-off value were marked positive. About 119 samples (77 for hepatitis B virus [HBV], 23 for human immunodeficiency virus [HIV], and 19 for hepatitis C virus [HCV]) were found to be in grey zone. On repeat testing of these samples in duplicate, 70 (58.8%) samples (45 for HBV, 12 for HIV, and 13 for HCV) were found to be reactive. Six (5%) samples (four for HBV, one for HIV, and one for HCV) were found to be indeterminate. Seventy donors initially screened negative, were found out to be potentially infectious on repeat grey zone testing. Thus, estimation of grey zone samples with repeat testing can further enhance the safety of blood transfusion.

49 CFR 199.111 - Retention of samples and additional testing.

Code of Federal Regulations, 2011 CFR

2011-10-01

... SAFETY DRUG AND ALCOHOL TESTING Drug Testing § 199.111 Retention of samples and additional testing. (a... other than the unauthorized use of a prohibited drug, and if timely additional testing is requested by... 49 Transportation 3 2011-10-01 2011-10-01 false Retention of samples and additional testing. 199...

49 CFR 199.111 - Retention of samples and additional testing.

Code of Federal Regulations, 2013 CFR

2013-10-01

... SAFETY DRUG AND ALCOHOL TESTING Drug Testing § 199.111 Retention of samples and additional testing. (a... other than the unauthorized use of a prohibited drug, and if timely additional testing is requested by... 49 Transportation 3 2013-10-01 2013-10-01 false Retention of samples and additional testing. 199...

49 CFR 199.111 - Retention of samples and additional testing.

Code of Federal Regulations, 2012 CFR

2012-10-01

... SAFETY DRUG AND ALCOHOL TESTING Drug Testing § 199.111 Retention of samples and additional testing. (a... other than the unauthorized use of a prohibited drug, and if timely additional testing is requested by... 49 Transportation 3 2012-10-01 2012-10-01 false Retention of samples and additional testing. 199...

49 CFR 199.111 - Retention of samples and additional testing.

Code of Federal Regulations, 2010 CFR

2010-10-01

... SAFETY DRUG AND ALCOHOL TESTING Drug Testing § 199.111 Retention of samples and additional testing. (a... other than the unauthorized use of a prohibited drug, and if timely additional testing is requested by... 49 Transportation 3 2010-10-01 2010-10-01 false Retention of samples and additional testing. 199...

49 CFR 199.111 - Retention of samples and additional testing.

Code of Federal Regulations, 2014 CFR

2014-10-01

... SAFETY DRUG AND ALCOHOL TESTING Drug Testing § 199.111 Retention of samples and additional testing. (a... other than the unauthorized use of a prohibited drug, and if timely additional testing is requested by... 49 Transportation 3 2014-10-01 2014-10-01 false Retention of samples and additional testing. 199...

Oscillating-flow regenerator test rig

NASA Technical Reports Server (NTRS)

Wood, J. G.; Gedeon, D. R.

1994-01-01

This report summarizes work performed in setting up and performing tests on a regenerator test rig. An earlier status report presented test results, together with heat transfer correlations, for four regenerator samples (two woven screen samples and two felt metal samples). Lessons learned from this testing led to improvements to the experimental setup, mainly instrumentation as well as to the test procedure. Given funding and time constraints for this project it was decided to complete as much testing as possible while the rig was set up and operational, and to forego final data reduction and analysis until later. Additional testing was performed on several of the previously tested samples as well an on five newly fabricated samples. The following report is a summary of the work performed at OU, with many of the final test results included in raw data form.

Fragrance patch tests prepared in advance may give false-negative reactions.

PubMed

Mowitz, Martin; Svedman, Cecilia; Zimerson, Erik; Bruze, Magnus

2014-11-01

Several of the ingredients in fragrance mix I (FM I) have been shown to evaporate from petrolatum preparations applied in test chambers to an extent that can be suspected to affect the patch test result. To compare the reactivity towards FM I and fragrance mix II (FM II) when they are applied in test chambers in advance and immediately prior to the patch test occasion. Seven hundred and ninety-five consecutive patients were simultaneously patch tested with duplicate samples of FM I and FM II. One sample was applied in the test chamber 6 days in advance (6D sample), and the other sample was applied immediately before the patients were patch tested (fresh sample). Twenty-two (2.8%) patients reacted exclusively to the fresh sample of FM I, 6 (0.7%) reacted exclusively to the 6D sample, and 22 (2.8%) reacted to both samples. The corresponding numbers for FM II were 9 (1.1%) for the fresh sample, 6 (0.7%) for the 6D sample and 12 (1.5%) for both samples. There was a statistically significant difference between the numbers of patients reacting to the fresh and 6D samples of FM I. No corresponding difference was observed for FM II. This can probably be explained by differences in volatilities between the ingredients of FM I and FM II. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Warm-Up Effect in Panelist-Articulated-2-Alternative Forced Choice Test.

PubMed

Bloom, David J; Baik, Hwa-Young; Lee, Soo-Yeun

2018-01-01

Panelist performance in discrimination tests has been shown to increase when warm-up samples are provided prior to the actual test. Samples are used prior to the actual test for the attribute articulation process of a panelist-articulated-2-alternative forced choice (PA-2-AFC) procedure; however, it is yet unknown if the pretest articulation phase adds to the power of this testing method as with the warm-up. The goal of the study was to determine if a "warm-up" effect was displayed in the PA-2-AFC test resulting in greater power compared to the researcher-designated-2-AFC (RD-2-AFC) test. A RD-2-AFC test, with and without warm-up samples, and a PA-2-AFC test were performed by 61 panelists. A reduced calorie, citrus-flavored, and carbonated beverage was used in the tests. During RD-2-AFC testing, panelists were asked to identify which sample was more sour. For PA-2-AFC testing, panelists individually articulated the nature and direction of the difference between the 2 samples through a pretesting articulation procedure. The articulated difference was, then, used in standard 2-AFC test procedure. A warm-up effect was observed when comparing the standard RD-2-AFC with and without warm-up samples. The addition of warm up samples significantly increased the power of the test, in addition, the PA-2-AFC method had lower power than the RD-2-AFC method. The increase in power with the addition of warm-up samples for the RD-2-AFC procedure supports literature findings on the benefit of providing warm-up samples. No warm-up effect can be attributed to the PA-2-AFC method evidenced by the overall low power observed, which may be attributed to sample complexity. Selecting a specified discrimination testing method is advantageous and can reduce costs of sensory testing, but has been considered unpractical when samples may differ in unknown ways. This research explores the use of panelist derived terms to circumvent the need for researchers to identify these differences and compares the results to using research designated terms in discrimination testing. Results from this study can be utilized in creating ways to incorporate more powerful methods into sensory discrimination testing plans and provides researchers with a means for selecting terms for use in specified discrimination testing methods. © 2017 Institute of Food Technologists®.

Characteristics of the LacTek test as applied to tissue samples: assessment of performance using incurred field samples.

PubMed

Mitchell, J M; McNab, W B; Yee, A J; Griffiths, M W; McEwen, S A; Spilsbury, L; Boison, J O

1998-08-01

The Lactek test, marketed for antimicrobial residue detection in milk, was validated for the detection of antimicrobial residues in tissues. A previous study found that the LacTek test could confidently identify tissue samples spiked with antimicrobial residues. However, the test could not reliably distinguish violative from nonviolative spiked samples relative to Canadian maximum residue limits (MRLs). The objectives of this study were to assess and compare the performance of the LacTek tests for beta-lactams, tetracyclines, gentamicin, and sulfamethazine on samples containing naturally incurred residues by running the test in parallel with the standard microbial inhibition test (MIT) presently used for the routine testing of tissues at our facility and to assess the agreement with high pressure liquid chromatographic (HPLC) determinative methods. Parallel testing with the official MIT found that the Lactek tests could be confidently used for testing tissue samples containing incurred residues. Among 1,008 MIT-positive samples, the LacTek test found that 90% contained beta-lactams and/or tetracyclines. A further 7.3% of violative residues could not be identified to an antimicrobial class. In addition, 9% of samples testing negative on the MIT were found to contain an antimicrobial residue by the LacTek tests. Comparative testing with HPLC methods found that there was very good agreement between the two tests and that most violations were due to penicillin G and oxytetracycline. Although the LacTek test cannot be used to distinguish violative from nonviolative residue levels, it does offer several advantages over the present MIT. These include speed, ease of use, the ability to identify residues to a specific class, and an improved sensitivity at the MRL level for the most commonly found antimicrobials in tissue.

Determination of HIV Status in African Adults With Discordant HIV Rapid Tests.

PubMed

Fogel, Jessica M; Piwowar-Manning, Estelle; Donohue, Kelsey; Cummings, Vanessa; Marzinke, Mark A; Clarke, William; Breaud, Autumn; Fiamma, Agnès; Donnell, Deborah; Kulich, Michal; Mbwambo, Jessie K K; Richter, Linda; Gray, Glenda; Sweat, Michael; Coates, Thomas J; Eshleman, Susan H

2015-08-01

In resource-limited settings, HIV infection is often diagnosed using 2 rapid tests. If the results are discordant, a third tie-breaker test is often used to determine HIV status. This study characterized samples with discordant rapid tests and compared different testing strategies for determining HIV status in these cases. Samples were previously collected from 173 African adults in a population-based survey who had discordant rapid test results. Samples were classified as HIV positive or HIV negative using a rigorous testing algorithm that included two fourth-generation tests, a discriminatory test, and 2 HIV RNA tests. Tie-breaker tests were evaluated, including rapid tests (1 performed in-country), a third-generation enzyme immunoassay, and two fourth-generation tests. Selected samples were further characterized using additional assays. Twenty-nine samples (16.8%) were classified as HIV positive and 24 of those samples (82.8%) had undetectable HIV RNA. Antiretroviral drugs were detected in 1 sample. Sensitivity was 8.3%-43% for the rapid tests; 24.1% for the third-generation enzyme immunoassay; 95.8% and 96.6% for the fourth-generation tests. Specificity was lower for the fourth-generation tests than the other tests. Accuracy ranged from 79.5% to 91.3%. In this population-based survey, most HIV-infected adults with discordant rapid tests were virally suppressed without antiretroviral drugs. Use of individual assays as tie-breaker tests was not a reliable method for determining HIV status in these individuals. More extensive testing algorithms that use a fourth-generation screening test with a discriminatory test and HIV RNA test are preferable for determining HIV status in these cases.

40 CFR 86.137-94 - Dynamometer test run, gaseous and particulate emissions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... within 20 minutes of the end of the sample collection phase of the test. Obtain methanol and formaldehyde... the sample collection phase of the test. Obtain methanol and formaldehyde sample analyses, if... methanol-fueled vehicles, with the sample selector valves in the “standby” position, insert fresh sample...

40 CFR 86.137-94 - Dynamometer test run, gaseous and particulate emissions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... within 20 minutes of the end of the sample collection phase of the test. Obtain methanol and formaldehyde... the sample collection phase of the test. Obtain methanol and formaldehyde sample analyses, if... methanol-fueled vehicles, with the sample selector valves in the “standby” position, insert fresh sample...

Detection and identification of occult HBV in blood donors in Taiwan using a commercial, multiplex, multi-dye nucleic acid amplification technology screening test.

PubMed

Lin, K T; Chang, C L; Tsai, M H; Lin, K S; Saldanha, J; Hung, C M

2014-02-01

The ability of a new generation commercial, multiplex, multi-dye test from Roche, the cobas TaqScreen MPX test, version 2.0, to detect and identify occult HBV infections was evaluated using routine donor samples from Kaohsiung Blood Bank, Taiwan. A total of 5973 samples were tested by nucleic acid amplification technology (NAT); 5898 in pools of six, 66 in pools of less than six and nine samples individually. NAT-reactive samples were retested with alternative NAT tests, and follow-up samples from the donors were tested individually by NAT and for all the HBV serological markers. Eight NAT-only-reactive donors were identified, and follow-up samples were obtained from six of the donors. The results indicated that all eight donors had an occult HBV infection with viral loads <12 IU/ml. The cobas(®) TaqScreen MPX test, version 2.0, has an advantage over the current Roche blood screening test, the cobas TaqScreen MPX test, for screening donations in countries with a high prevalence of occult HBV infections since the uncertainty associated with identifying samples with very low viremia is removed by the ability of the test to identify the viral target in samples that are reactive with the cobas TaqScreen MPX test, version 2.0. © 2013 International Society of Blood Transfusion.

Formability analysis of sheet metals by cruciform testing

NASA Astrophysics Data System (ADS)

Güler, B.; Alkan, K.; Efe, M.

2017-09-01

Cruciform biaxial tests are increasingly becoming popular for testing the formability of sheet metals as they achieve frictionless, in-plane, multi-axial stress states with a single sample geometry. However, premature fracture of the samples during testing prevents large strain deformation necessary for the formability analysis. In this work, we introduce a miniature cruciform sample design (few mm test region) and a test setup to achieve centre fracture and large uniform strains. With its excellent surface finish and optimized geometry, the sample deforms with diagonal strain bands intersecting at the test region. These bands prevent local necking and concentrate the strains at the sample centre. Imaging and strain analysis during testing confirm the uniform strain distributions and the centre fracture are possible for various strain paths ranging from plane-strain to equibiaxial tension. Moreover, the sample deforms without deviating from the predetermined strain ratio at all test conditions, allowing formability analysis under large strains. We demonstrate these features of the cruciform test for three sample materials: Aluminium 6061-T6 alloy, DC-04 steel and Magnesium AZ31 alloy, and investigate their formability at both the millimetre scale and the microstructure scale.

Approximate sample size formulas for the two-sample trimmed mean test with unequal variances.

PubMed

Luh, Wei-Ming; Guo, Jiin-Huarng

2007-05-01

Yuen's two-sample trimmed mean test statistic is one of the most robust methods to apply when variances are heterogeneous. The present study develops formulas for the sample size required for the test. The formulas are applicable for the cases of unequal variances, non-normality and unequal sample sizes. Given the specified alpha and the power (1-beta), the minimum sample size needed by the proposed formulas under various conditions is less than is given by the conventional formulas. Moreover, given a specified size of sample calculated by the proposed formulas, simulation results show that Yuen's test can achieve statistical power which is generally superior to that of the approximate t test. A numerical example is provided.

[Evaluation of the diagnostic performance of Xpert MTB/RIF test for the detection of Mycobacterium tuberculosis and rifampin resistance in clinical samples].

PubMed

Gürsoy, Nafia Canan; Yakupoğulları, Yusuf; Tekerekoğlu, Mehmet Sait; Otlu, Barış

2016-04-01

Rapid and accurate detection of active tuberculosis (TB) cases is one of the most important goal of tuberculosis control programme. For this purpose, new methods are being developed to isolate, serotype and determine the drug resistance of the agent. Xpert MTB/RIF test (CepheidGeneXpert® System, USA) that has been recently developed, is a real-time polymerase chain reaction-based method which detects Mycobacterium tuberculosis complex and resistance of the strain to rifampicin (RIF) from the clinical sample directly within a couple of hours. However, there are not sufficient data about the performance of that test for extrapulmonary samples and pulmonary samples other than sputum. The aims of this study were to investigate the sensitivity, specificity, positive and negative predictive values of Xpert MTB/RIF test in detection of M. tuberculosis and the performance in the determination of rifampicin resistance of the isolates from pulmonary and extrapulmonary clinical samples. A total of 2160 clinical samples, in which 1141 (52.8%) were pulmonary and 1019 (47.2%) were extrapulmonary samples, sent to our laboratory between July 2013 to December 2014, were included in the study. Sixty seven of the evaluated samples (3.1%) were positive with microscopy (acid-fast stain; AFS), 116 samples (5.1%) were positive with culture and 98 samples (4.5%) were positive with Xpert MTB/RIF test. When the culture was considered as the reference method, the sensitivity and specificity of Xpert MTB/RIF test were determined as 73.3% and 99.3%, respectively for all samples; 77.5% and 99.5%, respectively for pulmonary samples and 63.9% and 99.2%, respectively for extrapulmonary samples. Among AFS positive samples, the sensitivity was 100% and specificity was 66.7%; whereas among AFS negative samples those values were 40.4% and 99.4%, respectively. Among all the samples involved in the study, RIF resistance was determined only in three samples with Xpert MTB/ RIF test and that was also proved phenotypically (100% concordance). According to mycobacterial culture results, positive and negative predictive values of Xpert MTB/RIF test were determined as 86.7% and 98.5%, respectively for all samples. Those were determined as 92.5% and 98.3%, respectively for extrapulmonary samples and were determined as 74.2 and 98.7%, respectively for pulmonary samples. According to the results obtained in our study, sensitivity of Xpert MTB/RIF test for extrapulmonary samples was found to be at moderate level; sensitivity of the test was found to be decreased especially in AFS negative samples with less bacilli load. Nonetheless, specificity of Xpert MTB/RIF test to the agent in all samples was found to be extremely high. In our study, although RIF-resistant strains were detected in few of the samples, Xpert MTB/ RIF test could differentiate all resistant and sensitive strains. Additionally, detection of M. tuberculosis and RIF resistance in our laboratory takes approximately 20.96 days with culture, this period decreases to a couple of hours with Xpert MTB/RIF test. Because of the advantages such as being practical, rapid and requiring minimal safety measures, it was concluded that Xpert MTB/RIF test may contribute to rapid diagnosis of TB also in extrapulmonary samples, with the confirmation of culture method.

The effects of transport by car on coagulation tests.

PubMed

Ergin, Merve; Erdogan, Serpil; Akturk, Onur; Erel, Ozcan

2017-10-26

This research investigated the effects of the transport of blood samples between centers/laboratories by car on coagulation tests. Five tubes of blood samples were taken from 20 healthy volunteers. The samples consisted of a baseline (control) group, centrifuged and noncentrifuged transported samples; centrifuged and noncentrifuged untransported samples. The groups of centrifuged and noncentrifuged samples were transported by car for 2 h. The centrifuged and noncentrifuged untransported samples were incubated in the laboratory until the transported samples arrived. Prothrombin time (PT) and activated partial thromboplastin time (APTT) tests were conducted for all samples. Significant differences between the baseline group and the centrifuged and noncentrifuged transported samples and the noncentrifuged untransported samples were found for APTT levels (p<0.05, for all). In addition, significant mean percentage differences in PT values were found between the baseline group and the noncentrifuged transported samples (p<0.001) and the noncentrifuged untransported samples (p=0.005). The mean level of PT in the noncentrifuged transported samples was outside the upper limit of the clinical decision level. Noncentrifuged transported samples showed clinically significant differences in PT test results that may have stemmed from mechanical agitation during transportation. Therefore, we recommend not transporting noncentrifuged specimens for PT testing by car.

Variations in the detection of anti-PEDV antibodies in serum samples using three diagnostic tests - short communication.

PubMed

Plut, Jan; Toplak, Ivan; Štukelj, Marina

2018-06-01

Over the last few years several porcine epidemic diarrhoea (PED) outbreaks have been discovered in Europe including the first PED case in Slovenia in January 2015. The aim of this study was to determine when PED virus (PEDV) infection started in Slovenia. Serum samples collected between 2012 and 2016 were tested. Three hundred and seventy-five serum samples were collected from 132 Slovenian small, one-site pig farms. Samples were tested for PEDV antibodies utilising three different serological methods: commercially-available indirect ELISA, in-house blocking ELISA test and Immunoperoxidase Monolayer Assay (IPMA) test. One hundred and seventy (45.33%) tested samples were found positive by the commercially-available ELISA test kit, and 10 (5.68%) of these 170 samples found positive were positive by the in-house blocking ELISA. Only these 10 samples were collected from a farm where clinical signs of PED infection had been observed and PEDV was confirmed by RT-PCR methodology; the other 160 samples were collected randomly. Thirty-two samples with the highest S/P value obtained with the commercial ELISA were all negative with IPMA. Reasons for the high variance in the results obtained remain unclear; more research is required to ensure higher sensitivity and specificity in terms of PEDV antibody tests and other PED diagnostic methods.

43 CFR 3601.30 - Pre-application activities-how and when may I sample and test mineral materials?

Code of Federal Regulations, 2013 CFR

2013-10-01

... Sampling and Testing § 3601.30 Pre-application activities—how and when may I sample and test mineral... 43 Public Lands: Interior 2 2013-10-01 2013-10-01 false Pre-application activities-how and when may I sample and test mineral materials? 3601.30 Section 3601.30 Public Lands: Interior Regulations...

43 CFR 3601.30 - Pre-application activities-how and when may I sample and test mineral materials?

Code of Federal Regulations, 2012 CFR

2012-10-01

... Sampling and Testing § 3601.30 Pre-application activities—how and when may I sample and test mineral... 43 Public Lands: Interior 2 2012-10-01 2012-10-01 false Pre-application activities-how and when may I sample and test mineral materials? 3601.30 Section 3601.30 Public Lands: Interior Regulations...

43 CFR 3601.30 - Pre-application activities-how and when may I sample and test mineral materials?

Code of Federal Regulations, 2011 CFR

2011-10-01

... Sampling and Testing § 3601.30 Pre-application activities—how and when may I sample and test mineral... 43 Public Lands: Interior 2 2011-10-01 2011-10-01 false Pre-application activities-how and when may I sample and test mineral materials? 3601.30 Section 3601.30 Public Lands: Interior Regulations...

43 CFR 3601.30 - Pre-application activities-how and when may I sample and test mineral materials?

Code of Federal Regulations, 2014 CFR

2014-10-01

... Sampling and Testing § 3601.30 Pre-application activities—how and when may I sample and test mineral... 43 Public Lands: Interior 2 2014-10-01 2014-10-01 false Pre-application activities-how and when may I sample and test mineral materials? 3601.30 Section 3601.30 Public Lands: Interior Regulations...

Grouping methods for estimating the prevalences of rare traits from complex survey data that preserve confidentiality of respondents.

PubMed

Hyun, Noorie; Gastwirth, Joseph L; Graubard, Barry I

2018-03-26

Originally, 2-stage group testing was developed for efficiently screening individuals for a disease. In response to the HIV/AIDS epidemic, 1-stage group testing was adopted for estimating prevalences of a single or multiple traits from testing groups of size q, so individuals were not tested. This paper extends the methodology of 1-stage group testing to surveys with sample weighted complex multistage-cluster designs. Sample weighted-generalized estimating equations are used to estimate the prevalences of categorical traits while accounting for the error rates inherent in the tests. Two difficulties arise when using group testing in complex samples: (1) How does one weight the results of the test on each group as the sample weights will differ among observations in the same group. Furthermore, if the sample weights are related to positivity of the diagnostic test, then group-level weighting is needed to reduce bias in the prevalence estimation; (2) How does one form groups that will allow accurate estimation of the standard errors of prevalence estimates under multistage-cluster sampling allowing for intracluster correlation of the test results. We study 5 different grouping methods to address the weighting and cluster sampling aspects of complex designed samples. Finite sample properties of the estimators of prevalences, variances, and confidence interval coverage for these grouping methods are studied using simulations. National Health and Nutrition Examination Survey data are used to illustrate the methods. Copyright © 2018 John Wiley & Sons, Ltd.

NASA GRC and MSFC Space-Plasma Arc Testing Procedures

NASA Technical Reports Server (NTRS)

Ferguson, Dale C.; Vayner, Boris V.; Galofaro, Joel T,; Hillard, G. Barry; Vaughn, Jason; Schneider, Todd

2005-01-01

Tests of arcing and current collection in simulated space plasma conditions have been performed at the NASA Glenn Research Center (GRC) in Cleveland, Ohio, for over 30 years and at the Marshall Space Flight Center (MSFC) in Huntsville, Alabama, for almost as long. During this period, proper test conditions for accurate and meaningful space simulation have been worked out, comparisons with actual space performance in spaceflight tests and with real operational satellites have been made, and NASA has achieved our own internal standards for test protocols. It is the purpose of this paper to communicate the test conditions, test procedures, and types of analysis used at NASA GRC and MSFC to the space environmental testing community at large, to help with international space-plasma arcing-testing standardization. To be discussed are: 1.Neutral pressures, neutral gases, and vacuum chamber sizes. 2. Electron and ion densities, plasma uniformity, sample sizes, and Debuy lengths. 3. Biasing samples versus self-generated voltages. Floating samples versus grounded. 4. Power supplies and current limits. Isolation of samples from power supplies during arcs. 5. Arc circuits. Capacitance during biased arc-threshold tests. Capacitance during sustained arcing and damage tests. Arc detection. Prevention sustained discharges during testing. 6. Real array or structure samples versus idealized samples. 7. Validity of LEO tests for GEO samples. 8. Extracting arc threshold information from arc rate versus voltage tests. 9. Snapover and current collection at positive sample bias. Glows at positive bias. Kapon (R) pyrolisis. 10. Trigger arc thresholds. Sustained arc thresholds. Paschen discharge during sustained arcing. 11. Testing for Paschen discharge threshold. Testing for dielectric breakdown thresholds. Testing for tether arcing. 12. Testing in very dense plasmas (ie thruster plumes). 13. Arc mitigation strategies. Charging mitigation strategies. Models. 14. Analysis of test results. Finally, the necessity of testing will be emphasized, not to the exclusion of modeling, but as part of a complete strategy for determining when and if arcs will occur, and preventing them from occurring in space.

NASA GRC and MSFC Space-Plasma Arc Testing Procedures

NASA Technical Reports Server (NTRS)

Ferguson, Dale C.a; Vayner, Boris V.; Galofaro, Joel T.; Hillard, G. Barry; Vaughn, Jason; Schneider, Todd

2005-01-01

Tests of arcing and current collection in simulated space plasma conditions have been performed at the NASA Glenn Research Center (GRC) in Cleveland, Ohio, for over 30 years and at the Marshall Space flight Center (MSFC) for almost as long. During this period, proper test conditions for accurate and meaningful space simulation have been worked out, comparisons with actual space performance in spaceflight tests and with real operational satellites have been made, and NASA has achieved our own internal standards for test protocols. It is the purpose of this paper to communicate the test conditions, test procedures, and types of analysis used at NASA GRC and MSFC to the space environmental testing community at large, to help with international space-plasma arcing testing standardization. To be discussed are: 1. Neutral pressures, neutral gases, and vacuum chamber sizes. 2. Electron and ion densities, plasma uniformity, sample sizes, and Debye lengths. 3. Biasing samples versus self-generated voltages. Floating samples versus grounded. 4. Power supplies and current limits. Isolation of samples from power supplies during arcs. Arc circuits. Capacitance during biased arc-threshold tests. Capacitance during sustained arcing and damage tests. Arc detection. Preventing sustained discharges during testing. 5. Real array or structure samples versus idealized samples. 6. Validity of LEO tests for GEO samples. 7. Extracting arc threshold information from arc rate versus voltage tests. 8 . Snapover and current collection at positive sample bias. Glows at positive bias. Kapton pyrolization. 9. Trigger arc thresholds. Sustained arc thresholds. Paschen discharge during sustained arcing. 10. Testing for Paschen discharge thresholds. Testing for dielectric breakdown thresholds. Testing for tether arcing. 11. Testing in very dense plasmas (ie thruster plumes). 12. Arc mitigation strategies. Charging mitigation strategies. Models. 13. Analysis of test results. Finally, the necessity of testing will be emphasized, not to the exclusion of modeling, but as part of a complete strategy for determining when and if arcs will occur, and preventing them from occurring in space.

Core Cutting Test with Vertical Rock Cutting Rig (VRCR)

NASA Astrophysics Data System (ADS)

Yasar, Serdar; Osman Yilmaz, Ali

2017-12-01

Roadheaders are frequently used machines in mining and tunnelling, and performance prediction of roadheaders is important for project economics and stability. Several methods were proposed so far for this purpose and, rock cutting tests are the best choice. Rock cutting tests are generally divided into two groups which are namely, full scale rock cutting tests and small scale rock cutting tests. These two tests have some superiorities and deficiencies over themselves. However, in many cases, where rock sampling becomes problematic, small scale rock cutting test (core cutting test) is preferred for performance prediction, since small block samples and core samples can be conducted to rock cutting testing. Common problem for rock cutting tests are that they can be found in very limited research centres. In this study, a new mobile rock cutting testing equipment, vertical rock cutting rig (VRCR) was introduced. Standard testing procedure was conducted on seven rock samples which were the part of a former study on cutting rocks with another small scale rock cutting test. Results showed that core cutting test can be realized successfully with VRCR with the validation of paired samples t-test.

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

Miller, D. H.; Reigel, M. M.

A full-scale formed core sampler was designed and functionally tested for use in the Saltstone Disposal Facility (SDF). Savannah River National Laboratory (SRNL) was requested to compare properties of the formed core samples and core drilled samples taken from adjacent areas in the full-scale sampler. While several physical properties were evaluated, the primary property of interest was hydraulic conductivity. Differences in hydraulic conductivity between the samples from the formed core sampler and those representing the bulk material were noted with respect to the initial handling and storage of the samples. Due to testing conditions, the site port samples were exposedmore » to uncontrolled temperature and humidity conditions prior to testing whereas the formed core samples were kept in sealed containers with minimal exposure to an uncontrolled environment prior to testing. Based on the results of the testing, no significant differences in porosity or density were found between the formed core samples and those representing the bulk material in the test stand.« less

Power of tests of normality for detecting contaminated normal samples

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

Thode, H.C. Jr.; Smith, L.A.; Finch, S.J.

1981-01-01

Seventeen tests of normality or goodness of fit were evaluated for power at detecting a contaminated normal sample. This study used 1000 replications each of samples of size 12, 17, 25, 33, 50, and 100 from six different contaminated normal distributions. The kurtosis test was the most powerful over all sample sizes and contaminations. The Hogg and weighted Kolmogorov-Smirnov tests were second. The Kolmogorov-Smirnov, chi-squared, Anderson-Darling, and Cramer-von-Mises tests had very low power at detecting contaminated normal random variables. Tables of the power of the tests and the power curves of certain tests are given.

Acute toxic tests of rainwater samples using Daphnia magna.

PubMed

Sakai, Manabu

2006-06-01

Rainwater samples were collected at Isogo Ward of Yokohama City, Japan, from 23 June to 31 July 2003. The toxic potency of pollutants present in 13 rainwater samples was tested using Daphnia magna. Most test animals died within 48 h in five test solutions that were prepared from rainwater samples. On the other hand, when nonpolar compounds such as pesticides were removed from rainwater samples before the toxic tests, mortalities in all test solutions were less than 10%. Eight kinds of pesticides were detected in rainwater samples. The highest concentration was of dichlorvos, at 0.74 microg/L. Results indicated that insecticides in rainwater sometimes lethally affected D. magna and that toxic potency of insecticides that are present in rainwater constitutes an important problem for environmental protection.

Assessing Acceptability of Self-Sampling Kits, Prevalence, and Risk Factors for Human Papillomavirus Infection in American Indian Women.

PubMed

Winer, Rachel L; Gonzales, Angela A; Noonan, Carolyn J; Cherne, Stephen L; Buchwald, Dedra S

2016-10-01

We evaluated the feasibility and acceptability of self-sampling for human papillomavirus (HPV) testing and calculated the prevalence of and risk factors for high-risk (hr) HPV infections in a community-based sample of American Indian women. To this end, we recruited 329 Hopi women aged 21-65 years to self-collect vaginal samples for hrHPV testing. Samples were tested by polymerase chain reaction for 14 hrHPV genotypes. We used Chi square tests to identify correlates of preference for clinician Pap testing versus HPV self-sampling, and age-adjusted Poisson regression to evaluate correlates of hrHPV prevalence. We found that satisfaction with HPV self-sampling was high, with 96 % of women reporting that the sample was easy to collect and 87 % reporting no discomfort. The majority (62 %) indicated that they preferred HPV self-sampling to receiving a Pap test from a clinician. Preference for Pap testing over HPV self-sampling was positively associated with adherence to Pap screening and employment outside the home. All samples evaluated were satisfactory for HPV testing, and 22 % were positive for hrHPV. HrHPV prevalence peaked in the late 20 s and declined with increasing age. HrHPV positivity was inversely associated with having children living the household. In conclusion, HPV self-sampling is feasible and acceptable to Hopi women, and could be effective in increasing rates of cervical cancer screening in Hopi communities. HrHPV prevalence was similar to estimates in the general United States population.

7 CFR 58.243 - Checking quality.

Code of Federal Regulations, 2012 CFR

2012-01-01

.... Periodically samples of product and environmental material shall be tested for salmonella. Test results shall be negative when samples are tested for salmonella. Line samples should be taken periodically as an...

7 CFR 58.243 - Checking quality.

Code of Federal Regulations, 2013 CFR

2013-01-01

.... Periodically samples of product and environmental material shall be tested for salmonella. Test results shall be negative when samples are tested for salmonella. Line samples should be taken periodically as an...

7 CFR 58.243 - Checking quality.

Code of Federal Regulations, 2014 CFR

2014-01-01

.... Periodically samples of product and environmental material shall be tested for salmonella. Test results shall be negative when samples are tested for salmonella. Line samples should be taken periodically as an...

7 CFR 58.243 - Checking quality.

Code of Federal Regulations, 2011 CFR

2011-01-01

.... Periodically samples of product and environmental material shall be tested for salmonella. Test results shall be negative when samples are tested for salmonella. Line samples should be taken periodically as an...

Evaluation of enzyme-linked immunosorbent assays performed on milk and serum samples for detection of neosporosis and leukosis in lactating dairy cows

PubMed Central

Walsh, Robert B.; Kelton, David F.; Hietala, Sharon K.; Duffield, Todd F.

2013-01-01

Serum and milk samples from 1229 cows on 22 Ontario dairy farms were individually tested for antibodies specific for bovine leukosis virus (BLV) and Neospora caninum by enzyme-linked immunosorbent assay (ELISA). Antibodies against BLV were present in 361 serum samples (29.4%) and 369 milk samples (30.0%). Comparing the 2 tests, agreement was almost perfect (k = 0.86; 95% CI = 0.83 to 0.90) and the proportions of samples positive were not significantly different (P = 0.56). Both tests identified the same 3 herds free of bovine leukosis virus. Antibodies against N. caninum were detected in 138 serum samples (11.2%), and 111 milk samples (9.0%). Agreement between the 2 tests was moderate (k = 0.52; 95% CI = 0.43 to 0.59). Four herds were free of neosporosis by the serum test, while 10 herds were negative by the milk test. The ELISA on milk samples facilitates sample collection to classify herds free of BLV; the milk N. caninum ELISA was less reliable in predicting herd-level infection. PMID:24082160

Hog Charm II tetracycline test screening results compared with a liquid chromatography tandem mass spectrometry 10-μg/kg method.

PubMed

Salter, Robert; Holmes, Steven; Legg, David; Coble, Joel; George, Bruce

2012-02-01

Pork tissue samples that tested positive and negative by the Charm II tetracycline test screening method in the slaughter plant laboratory were tested with the modified AOAC International liquid chromatography tandem mass spectrometry (LC-MS-MS) method 995.09 to determine the predictive value of the screening method at detecting total tetracyclines at 10 μg/kg of tissue, in compliance with Russian import regulations. There were 218 presumptive-positive tetracycline samples of 4,195 randomly tested hogs. Of these screening test positive samples, 83% (182) were positive, >10 μg/kg by LC-MS-MS; 12.8% (28) were false violative, greater than limit of detection (LOD) but <10 μg/kg; and 4.2% (8) were not detected at the LC-MS-MS LOD. The 36 false-violative and not-detected samples represent 1% of the total samples screened. Twenty-seven of 30 randomly selected tetracycline screening negative samples tested below the LC-MS-MS LOD, and 3 samples tested <3 μg/kg chlortetracycline. Results indicate that the Charm II tetracycline test is effective at predicting hogs containing >10 μg/kg total tetracyclines in compliance with Russian import regulations.

Quality of different in-clinic test systems for feline immunodeficiency virus and feline leukaemia virus infection.

PubMed

Hartmann, Katrin; Griessmayr, Pascale; Schulz, Bianka; Greene, Craig E; Vidyashankar, Anand N; Jarrett, Os; Egberink, Herman F

2007-12-01

Many new diagnostic in-house tests for identification of feline immunodeficiency virus (FIV) and feline leukaemia virus (FeLV) infection have been licensed for use in veterinary practice, and the question of the relative merits of these kits has prompted comparative studies. This study was designed to define the strengths and weaknesses of seven FIV and eight FeLV tests that are commercially available. In this study, 536 serum samples from randomly selected cats were tested. Those samples reacting FIV-positive in at least one of the tests were confirmed by Western blot, and those reacting FeLV-positive were confirmed by virus isolation. In addition, a random selection of samples testing negative in all test systems was re-tested by Western blot (100 samples) and by virus isolation (81 samples). Specificity, sensitivity, positive and negative predictive values of each test and the quality of the results were compared.

Diagnostic test accuracy and prevalence inferences based on joint and sequential testing with finite population sampling.

PubMed

Su, Chun-Lung; Gardner, Ian A; Johnson, Wesley O

2004-07-30

The two-test two-population model, originally formulated by Hui and Walter, for estimation of test accuracy and prevalence estimation assumes conditionally independent tests, constant accuracy across populations and binomial sampling. The binomial assumption is incorrect if all individuals in a population e.g. child-care centre, village in Africa, or a cattle herd are sampled or if the sample size is large relative to population size. In this paper, we develop statistical methods for evaluating diagnostic test accuracy and prevalence estimation based on finite sample data in the absence of a gold standard. Moreover, two tests are often applied simultaneously for the purpose of obtaining a 'joint' testing strategy that has either higher overall sensitivity or specificity than either of the two tests considered singly. Sequential versions of such strategies are often applied in order to reduce the cost of testing. We thus discuss joint (simultaneous and sequential) testing strategies and inference for them. Using the developed methods, we analyse two real and one simulated data sets, and we compare 'hypergeometric' and 'binomial-based' inferences. Our findings indicate that the posterior standard deviations for prevalence (but not sensitivity and specificity) based on finite population sampling tend to be smaller than their counterparts for infinite population sampling. Finally, we make recommendations about how small the sample size should be relative to the population size to warrant use of the binomial model for prevalence estimation. Copyright 2004 John Wiley & Sons, Ltd.

Growth hormone suppression test

MedlinePlus

GH suppression test; Glucose loading test; Acromegaly - blood test; Gigantism - blood test ... At least 3 blood samples are taken. The test is done in the following way: The first blood sample is collected between 6 ...

9 CFR 113.111 - Clostridium Perfringens Type C Toxoid and Bacterin-Toxoid.

Code of Federal Regulations, 2013 CFR

2013-01-01

... a prescribed test shall not be released. (a) Purity test. Final container samples of completed... § 113.26. (b) Safety test. Bulk or final container samples of completed product from each serial shall be tested for safety as provided in § 113.33(b). (c) Potency test. Bulk or final container samples of...

9 CFR 113.111 - Clostridium Perfringens Type C Toxoid and Bacterin-Toxoid.

Code of Federal Regulations, 2014 CFR

2014-01-01

... a prescribed test shall not be released. (a) Purity test. Final container samples of completed... § 113.26. (b) Safety test. Bulk or final container samples of completed product from each serial shall be tested for safety as provided in § 113.33(b). (c) Potency test. Bulk or final container samples of...

9 CFR 113.111 - Clostridium Perfringens Type C Toxoid and Bacterin-Toxoid.

Code of Federal Regulations, 2012 CFR

2012-01-01

... a prescribed test shall not be released. (a) Purity test. Final container samples of completed... § 113.26. (b) Safety test. Bulk or final container samples of completed product from each serial shall be tested for safety as provided in § 113.33(b). (c) Potency test. Bulk or final container samples of...

Sample Size Determination for One- and Two-Sample Trimmed Mean Tests

ERIC Educational Resources Information Center

Luh, Wei-Ming; Olejnik, Stephen; Guo, Jiin-Huarng

2008-01-01

Formulas to determine the necessary sample sizes for parametric tests of group comparisons are available from several sources and appropriate when population distributions are normal. However, in the context of nonnormal population distributions, researchers recommend Yuen's trimmed mean test, but formulas to determine sample sizes have not been…

40 CFR 86.537-90 - Dynamometer test runs.

Code of Federal Regulations, 2010 CFR

2010-07-01

... phase of the test. Obtain methanol and formaldehyde sample analyses, if applicable, within 24 hours of... minutes of the end of the sample collection phase of the test. Obtain methanol and formaldehyde sample... the dilute exhaust and dilution air sample collection systems. (4) For methanol-fueled vehicles, with...

40 CFR 86.537-90 - Dynamometer test runs.

Code of Federal Regulations, 2011 CFR

2011-07-01

... phase of the test. Obtain methanol and formaldehyde sample analyses, if applicable, within 24 hours of... minutes of the end of the sample collection phase of the test. Obtain methanol and formaldehyde sample... the dilute exhaust and dilution air sample collection systems. (4) For methanol-fueled vehicles, with...

A note on sample size calculation for mean comparisons based on noncentral t-statistics.

PubMed

Chow, Shein-Chung; Shao, Jun; Wang, Hansheng

2002-11-01

One-sample and two-sample t-tests are commonly used in analyzing data from clinical trials in comparing mean responses from two drug products. During the planning stage of a clinical study, a crucial step is the sample size calculation, i.e., the determination of the number of subjects (patients) needed to achieve a desired power (e.g., 80%) for detecting a clinically meaningful difference in the mean drug responses. Based on noncentral t-distributions, we derive some sample size calculation formulas for testing equality, testing therapeutic noninferiority/superiority, and testing therapeutic equivalence, under the popular one-sample design, two-sample parallel design, and two-sample crossover design. Useful tables are constructed and some examples are given for illustration.

30 CFR 14.5 - Test samples.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Test samples. 14.5 Section 14.5 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING, EVALUATION, AND APPROVAL OF... Test samples. Upon request by MSHA, the applicant must submit 3 precut, unrolled, flat conveyor belt...

30 CFR 14.5 - Test samples.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Test samples. 14.5 Section 14.5 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING, EVALUATION, AND APPROVAL OF... Test samples. Upon request by MSHA, the applicant must submit 3 precut, unrolled, flat conveyor belt...

30 CFR 14.5 - Test samples.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Test samples. 14.5 Section 14.5 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING, EVALUATION, AND APPROVAL OF... Test samples. Upon request by MSHA, the applicant must submit 3 precut, unrolled, flat conveyor belt...

Development of NASA's Sample Cartridge Assembly: Summary of GEDS Design, Development Testing, and Thermal Analyses

NASA Technical Reports Server (NTRS)

O'Connor, Brian; Hernandez, Deborah; Hornsby, Linda; Brown, Maria; Horton-Mullins, Kathryn

2017-01-01

Outline: Background of ISS (International Space Station) Material Science Research Rack; NASA SCA (Sample Cartridge Assembly) Design; GEDS (Gravitational Effects in Distortion in Sintering) Experiment Ampoule Design; Development Testing Summary; Thermal Modeling and Analysis. Summary: GEDS design development challenging (GEDS Ampoule design developed through MUGS (Microgravity) testing; Short duration transient sample processing; Unable to measure sample temperatures); MUGS Development testing used to gather data (Actual LGF (Low Gradient Furnace)-like furnace response; Provided sample for sintering evaluation); Transient thermal model integral to successful GEDS experiment (Development testing provided furnace response; PI (Performance Indicator) evaluation of sintering anchored model evaluation of processing durations; Thermal transient model used to determine flight SCA sample processing profiles).

Comparison of mine waste assessment methods at the Rattler mine site, Virginia Canyon, Colorado

USGS Publications Warehouse

Hageman, Phil L.; Smith, Kathleen S.; Wildeman, Thomas R.; Ranville, James F.

2005-01-01

In a joint project, the mine waste-piles at the Rattler Mine near Idaho Springs, Colorado, were sampled and analyzed by scientists from the U.S. Geological Survey (USGS) and the Colorado School of Mines (CSM). Separate sample collection, sample leaching, and leachate analyses were performed by both groups and the results were compared. For the study, both groups used the USGS sampling procedure and the USGS Field Leach Test (FLT). The leachates generated from these tests were analyzed for a suite of elements using ICP-AES (CSM) and ICP-MS (USGS). Leachate geochemical fingerprints produced by the two groups for composites collected from the same mine waste showed good agreement. In another set of tests, CSM collected another set of Rattler mine waste composite samples using the USGS sampling procedure. This set of composite samples was leached using the Colorado Division of Minerals and Geology (CDMG) leach test, and a modified Toxicity Characteristic Leaching Procedure (TCLP) leach test. Leachate geochemical fingerprints produced using these tests showed a variation of more than a factor of two from the geochemical fingerprints produced using the USGS FLT leach test. We have concluded that the variation in the results is due to the different parameters of the leaching tests and not due to the sampling or analytical methods.

46 CFR 160.055-7 - Sampling, tests, and inspections.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 6 2011-10-01 2011-10-01 false Sampling, tests, and inspections. 160.055-7 Section 160.055-7 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) EQUIPMENT, CONSTRUCTION, AND... and Child, for Merchant Vessels § 160.055-7 Sampling, tests, and inspections. (a) Production tests and...

46 CFR 160.005-5 - Sampling, tests, and inspections.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 6 2010-10-01 2010-10-01 false Sampling, tests, and inspections. 160.005-5 Section 160.005-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) EQUIPMENT, CONSTRUCTION, AND... (Jacket Type), Models 52 and 56 § 160.005-5 Sampling, tests, and inspections. (a) Production tests and...

46 CFR 160.055-7 - Sampling, tests, and inspections.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 6 2010-10-01 2010-10-01 false Sampling, tests, and inspections. 160.055-7 Section 160.055-7 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) EQUIPMENT, CONSTRUCTION, AND... and Child, for Merchant Vessels § 160.055-7 Sampling, tests, and inspections. (a) Production tests and...

46 CFR 160.002-5 - Sampling, tests, and inspections.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 6 2011-10-01 2011-10-01 false Sampling, tests, and inspections. 160.002-5 Section 160.002-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) EQUIPMENT, CONSTRUCTION, AND... Type), Models 3 and 5 § 160.002-5 Sampling, tests, and inspections. (a) Production tests and...

46 CFR 160.002-5 - Sampling, tests, and inspections.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 6 2010-10-01 2010-10-01 false Sampling, tests, and inspections. 160.002-5 Section 160.002-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) EQUIPMENT, CONSTRUCTION, AND... Type), Models 3 and 5 § 160.002-5 Sampling, tests, and inspections. (a) Production tests and...

46 CFR 160.005-5 - Sampling, tests, and inspections.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 6 2011-10-01 2011-10-01 false Sampling, tests, and inspections. 160.005-5 Section 160.005-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) EQUIPMENT, CONSTRUCTION, AND... (Jacket Type), Models 52 and 56 § 160.005-5 Sampling, tests, and inspections. (a) Production tests and...

40 CFR 86.607-84 - Sample selection.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 19 2010-07-01 2010-07-01 false Sample selection. 86.607-84 Section 86... selection. (a) Vehicles comprising a test sample which are required to be tested, pursuant to a test order... specified in the test order, an alternative selection procedure may be employed: Provided, That the...

40 CFR 204.51 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... tests. (m) Test sample means the collection of compressors from the same category or configuration which is randomly drawn from the batch sample and which will receive emissions tests. (n) Batch size means... category or configuration in a batch. (o) Test sample size means the number of compressors of the same...

Estimation of sample size and testing power (part 5).

PubMed

Hu, Liang-ping; Bao, Xiao-lei; Guan, Xue; Zhou, Shi-guo

2012-02-01

Estimation of sample size and testing power is an important component of research design. This article introduced methods for sample size and testing power estimation of difference test for quantitative and qualitative data with the single-group design, the paired design or the crossover design. To be specific, this article introduced formulas for sample size and testing power estimation of difference test for quantitative and qualitative data with the above three designs, the realization based on the formulas and the POWER procedure of SAS software and elaborated it with examples, which will benefit researchers for implementing the repetition principle.

Drinking water test methods in crisis-afflicted areas: comparison of methods under field conditions.

PubMed

Merle, Roswitha; Bleul, Ingo; Schulenburg, Jörg; Kreienbrock, Lothar; Klein, Günter

2011-11-01

To simplify the testing of drinking water in crisis-afflicted areas (as in Kosovo in 2007), rapid test methods were compared with the standard test. For Escherichia coli and coliform pathogens, rapid tests were made available: Colilert(®)-18, P/A test with 4-methylumbelliferyl-β-D-glucoronid, and m-Endo Broth. Biochemical differentiation was carried out by Enterotube™ II. Enterococci were determined following the standard ISO test and by means of Enterolert™. Four hundred ninety-nine water samples were tested for E. coli and coliforms using four methods. Following the standard method, 20.8% (n=104) of the samples contained E. coli, whereas the rapid tests detected between 19.6% (m-Endo Broth, 92.0% concordance) and 20.0% (concordance: 93.6% Colilert-18 and 94.8% P/A-test) positive samples. Regarding coliforms, the percentage of concordant results ranged from 98.4% (P/A-test) to 99.0% (Colilert-18). Colilert-18 and m-Endo Broth detected even more positive samples than the standard method did. Enterococci were detected in 93 of 573 samples by the standard method, but in 92 samples by Enterolert (concordance: 99.5%). Considering the high-quality equipment and time requirements of the standard method, the use of rapid tests in crisis-afflicted areas is sufficiently reliable.

System and method for measuring permeability of materials

DOEpatents

Hallman, Jr., Russell Louis; Renner, Michael John

2013-07-09

Systems and methods are provided for measuring the permeance of a material. The permeability of the material may also be derived. Systems typically provide a liquid or high concentration fluid bath on one side of a material test sample, and a gas flow across the opposing side of the material test sample. The mass flow rate of permeated fluid as a fraction of the combined mass flow rate of gas and permeated fluid is used to calculate the permeance of the material. The material test sample may be a sheet, a tube, or a solid shape. Operational test conditions may be varied, including concentration of the fluid, temperature of the fluid, strain profile of the material test sample, and differential pressure across the material test sample.

Fluid permeability measurement system and method

DOEpatents

Hallman, Jr., Russell Louis; Renner, Michael John [Oak Ridge, TN

2008-02-05

A system for measuring the permeance of a material. The permeability of the material may also be derived. The system provides a liquid or high concentration fluid bath on one side of a material test sample, and a gas flow across the opposing side of the material test sample. The mass flow rate of permeated fluid as a fraction of the combined mass flow rate of gas and permeated fluid is used to calculate the permeance of the material. The material test sample may be a sheet, a tube, or a solid shape. Operational test conditions may be varied, including concentration of the fluid, temperature of the fluid, strain profile of the material test sample, and differential pressure across the material test sample.

Material permeance measurement system and method

DOEpatents

Hallman, Jr., Russell Louis; Renner, Michael John [Oak Ridge, TN

2012-05-08

A system for measuring the permeance of a material. The permeability of the material may also be derived. The system provides a liquid or high concentration fluid bath on one side of a material test sample, and a gas flow across the opposing side of the material test sample. The mass flow rate of permeated fluid as a fraction of the combined mass flow rate of gas and permeated fluid is used to calculate the permeance of the material. The material test sample may be a sheet, a tube, or a solid shape. Operational test conditions may be varied, including concentration of the fluid, temperature of the fluid, strain profile of the material test sample, and differential pressure across the material test sample.

Predictive Service Life Tests for Roofing Membranes: Phase II Investigation of Accelerated Aging Tests for Tracking Degradation of Roofing Membrane Materials

DTIC Science & Technology

2002-09-01

bitumens, EPDM , and PVC. Most heat-driven aging tests for building materials use a temperature of 70 °C. Ultraviolet radiation exposure in the...of 0.85 mm/sec. These samples generated three types of load-strain curves. A relatively straight line was generated by each EPDM rubber sample...Mathey 1974) at -18 °C. Except for the EPDM rubber membranes and Sample H, all samples tested comply with this suggested requirement. Sample H is an

43 CFR 3593.1 - Core or test hole cores, samples, cuttings.

Code of Federal Regulations, 2014 CFR

2014-10-01

.... (d) When drilling on lands with potential for encountering high pressure oil, gas or geothermal... 43 Public Lands: Interior 2 2014-10-01 2014-10-01 false Core or test hole cores, samples, cuttings...) EXPLORATION AND MINING OPERATIONS Bore Holes and Samples § 3593.1 Core or test hole cores, samples, cuttings...

43 CFR 3593.1 - Core or test hole cores, samples, cuttings.

Code of Federal Regulations, 2012 CFR

2012-10-01

.... (d) When drilling on lands with potential for encountering high pressure oil, gas or geothermal... 43 Public Lands: Interior 2 2012-10-01 2012-10-01 false Core or test hole cores, samples, cuttings...) EXPLORATION AND MINING OPERATIONS Bore Holes and Samples § 3593.1 Core or test hole cores, samples, cuttings...

43 CFR 3593.1 - Core or test hole cores, samples, cuttings.

Code of Federal Regulations, 2013 CFR

2013-10-01

.... (d) When drilling on lands with potential for encountering high pressure oil, gas or geothermal... 43 Public Lands: Interior 2 2013-10-01 2013-10-01 false Core or test hole cores, samples, cuttings...) EXPLORATION AND MINING OPERATIONS Bore Holes and Samples § 3593.1 Core or test hole cores, samples, cuttings...

43 CFR 3593.1 - Core or test hole cores, samples, cuttings.

Code of Federal Regulations, 2011 CFR

2011-10-01

.... (d) When drilling on lands with potential for encountering high pressure oil, gas or geothermal... 43 Public Lands: Interior 2 2011-10-01 2011-10-01 false Core or test hole cores, samples, cuttings...) EXPLORATION AND MINING OPERATIONS Bore Holes and Samples § 3593.1 Core or test hole cores, samples, cuttings...

40 CFR 80.1347 - What are the sampling and testing requirements for refiners and importers?

Code of Federal Regulations, 2013 CFR

2013-07-01

... Benzene Sampling, Testing and Retention Requirements § 80.1347 What are the sampling and testing... benzene requirements of this subpart, except as modified by paragraphs (a)(2), (a)(3) and (a)(4) of this... benzene concentration for compliance with the requirements of this subpart. (ii) Independent sample...

40 CFR 80.1347 - What are the sampling and testing requirements for refiners and importers?

Code of Federal Regulations, 2011 CFR

2011-07-01

... Benzene Sampling, Testing and Retention Requirements § 80.1347 What are the sampling and testing... benzene requirements of this subpart, except as modified by paragraphs (a)(2), (a)(3) and (a)(4) of this... benzene concentration for compliance with the requirements of this subpart. (ii) Independent sample...

Mutagenicity in emissions from coal- and oil-fired boilers.

PubMed Central

Alfheim, I; Bergström, J G; Jenssen, D; Møller, M

1983-01-01

The mutagenicity of emission samples from three oil-fired and four coal-fired boilers have been compared by using the Salmonella/microsome assay. Very little or no mutagenic activity was observed in samples from five of these boilers. The sample from one oil-fired boiler showed mutagenic activity of about 500 revertants/MJ, and the sample from a coal-fired fluidized bed combustor had an activity of 58,000 revertants/MJ measured with strain TA 98 in the absence of metabolic activation. All samples contained substances that were cytotoxic to the test bacteria, thus making it difficult to obtain linear dose-response curves. Mutagenic activity at low levels may remain undetected due to this toxicity of the samples. Samples with mutagenic activity below the detection limit in the Salmonella test have also been tested for forward mutations at the HGPRT locus in V79 hamster cells. Weak mutagenic effects were detected in two of the samples, whereas the sample from one oil-fired boiler remained negative. In this test, as well as in the Salmonella test, a strong cytotoxic effect could be observed with all samples. PMID:6825617

Comparison of Schmallenberg virus antibody levels detected in milk and serum from individual cows.

PubMed

Daly, Janet M; King, Barnabas; Tarlinton, Rachael A; Gough, Kevin C; Maddison, Ben C; Blowey, Roger

2015-03-11

Schmallenberg virus (SBV) is a recently emerged virus of ruminants in Europe. Enzyme-linked immunosorbent assays (ELISA) are commonly used to detect SBV-specific antibodies in bulk tank milk samples to monitor herd exposure to infection. However, it has previously been shown that a bulk tank milk sample can test positive even though the majority of cows within the herd are seronegative for SBV antibodies. Development of a pen-side test to detect antibodies in individual milk samples would potentially provide a cheaper test (for which samples are obtained non-invasively) than testing individual serum samples by ELISA. Therefore, the aim of this study was to investigate the agreement between antibody levels measured in milk and serum. Corresponding milk and serum samples from 88 cows in two dairy herds in the UK were tested for presence of immunoglobulin G antibodies to SBV using a commercially-available indirect ELISA. A serum neutralisation test (NT) was also performed as a gold standard assay. The ELISA values obtained for the bulk tank milk samples corresponded with the mean values for individual milk samples from each herd (bulk tank milk values were 58% and 73% and mean individual milk values 50% and 63% for herds A and B, respectively). Of the 88 serum samples tested in the NT, 82 (93%) were positive. Although at higher antibody levels, the ELISA values tended to be higher for the individual milk samples than for the corresponding serum samples, the positive predictive value for milk samples was 98% and for serum samples 94%. The serum ELISA was more likely to give false positive results around the lower cut-off value of the assay. The results indicate that testing of individual milk samples for antibodies against SBV by ELISA could be used to inform decisions in the management of dairy herds such as which, if any, animals to vaccinate.

Method and apparatus for testing surface characteristics of a material

NASA Technical Reports Server (NTRS)

Johnson, David L. (Inventor); Kersker, Karl D. (Inventor); Stratton, Troy C. (Inventor); Richardson, David E. (Inventor)

2006-01-01

A method, apparatus and system for testing characteristics of a material sample is provided. The system includes an apparatus configured to house the material test sample while defining a sealed volume against a surface of the material test sample. A source of pressurized fluid is in communication with, and configured to pressurize, the sealed volume. A load applying apparatus is configured to apply a defined load to the material sample while the sealed volume is monitored for leakage of the pressurized fluid. Thus, the inducement of surface defects such as microcracking and crazing may be detected and their effects analyzed for a given material. The material test samples may include laminar structures formed of, for example, carbon cloth phenolic, glass cloth phenolic, silica cloth phenolic materials or carbon-carbon materials. In one embodiment the system may be configured to analyze the material test sample while an across-ply loading is applied thereto.

Detection of epidermal growth factor receptor gene T790M mutation in cytology samples using the cobas® EGFR mutation test.

PubMed

Satouchi, Miyako; Tanaka, Hiroshi; Yoshioka, Hiroshige; Shimokawaji, Tadasuke; Mizuno, Keiko; Takeda, Koji; Yoshino, Ichiro; Seto, Takashi; Kurata, Takayasu; Tashiro, Naoki; Hagiwara, Koichi

2017-09-01

Detection of epidermal growth factor receptor (EGFR) gene mutations is essential in deciding therapeutic strategy in non-small cell lung cancer (NSCLC) patients at initial diagnosis. Moreover, in EGFR mutation-positive (EGFRm) NSCLC patients, re-biopsy at disease progression to clarify resistance mechanisms is also important. However, collecting histology samples is often difficult because of inaccessibility and invasiveness. In some cases, only cytology samples can be collected, and studies have reported that cytology samples are appropriate for EGFR gene mutation testing. The cobas ® EGFR Mutation Test (Roche Molecular Systems Inc., Branchburg, New Jersey, USA) is approved as a companion diagnostic for osimertinib, a third-generation EGFR-tyrosine kinase inhibitor approved in Japan. However, it is not clear whether the EGFR T790M mutation can be detected in cytology samples using this test. The primary objective of this study was to assess concordance of EGFR T790M gene mutation detection between histology and matched cytology samples using the cobas ® EGFR Mutation Test. We conducted a multicenter, observational study in Japan. Overall, 41 EGFRm NSCLC patients who had both histology and cytology samples collected at the same time at re-biopsy and with the results of EGFR mutation test using histology samples were enrolled. The EGFR mutation status of both sample types was tested using the cobas ® EGFR Mutation Test and the concordance rates were calculated. The EGFR T790M mutation detection rate in histology and cytology samples was 42.5% and 37.5%, respectively. The overall percent agreement between the histology and cytology samples was 91.7%. These data demonstrate that the cobas ® EGFR Mutation Test can detect the EGFR T790M mutation in both cytology and histology samples. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Oxidative stress, d-ROMs test, and ceruloplasmin.

PubMed

Colombini, Francesco; Carratelli, Mauro; Alberti, Angelo

2016-01-01

Human serum samples were evaluated for oxidative stress with the d-ROMs test. The ceruloplasmin (CP) and copper contents of the samples was independently measured and compared to those calculated on the basis of the d-ROMs test results for pure CP solutions. The d-ROMs readings did not show any significant correlation with either the CP or copper contents of the samples. Critical interference of CP on the d-ROMs test was therefore excluded and the usefulness of the test in the evaluation of global oxidative status of a biological sample could be reassessed.

Differential auger spectrometry

DOEpatents

Strongin, Myron; Varma, Matesh Narayan; Anne, Joshi

1976-06-22

Differential Auger spectroscopy method for increasing the sensitivity of micro-Auger spectroanalysis of the surfaces of dilute alloys, by alternately periodically switching an electron beam back and forth between an impurity free reference sample and a test sample containing a trace impurity. The Auger electrons from the samples produce representative Auger spectrum signals which cancel to produce an Auger test sample signal corresponding to the amount of the impurity in the test samples.

NASA-STD-6001B Test 1 Upward Flame Propagation; Sample Length Impact on MOC Investigation

NASA Technical Reports Server (NTRS)

Harper, Susana Tapia; Juarez, Alfredo; Woods, Brenton L.; Beeson, Harold D.

2017-01-01

Understanding the combustion behavior of materials in the elevated oxygen environments of habitable spacecraft is of utmost importance to crew safety and mission success. Currently, certification for unrestricted flight usage of a material with respect to flammability involves passing the Upward Flame Propagation Test of NASA-STD-6001B (Test 1). This test evaluates materials in a standardized test configuration for two failure criteria: self-extinguishment within 15 cm (6 in.) and the propensity of flame propagation by means of flaming material transfer. By the NASA standard, full-length samples are 30 cm (12 in.) in length; however, factors independent of the test method such as limited material availability or various nonstandard test configurations limit the full pretest sample lengths available for test. This paper characterizes the dependence, if any, of pretest sample length on NASA-STD-6001B Test 1 results. Testing was performed using the Maximum Oxygen Concentration (MOC) Threshold Method to obtain a data set for each sample length tested. In addition, various material types, including cloth (Nomex), foam (TA-301) and solids (Ultem), were tested to investigate potential effects of test specimen types. Though additional data needs to be generated to provide statistical confidence, preliminary findings are that use of variable sample lengths has minimal impact on NASA-STD-6001B flammability performance and MOC determination.

Therapeutic Drug Monitoring of Asparaginase Activity-Method Comparison of MAAT and AHA Test Used in the International AIEOP-BFM ALL 2009 Trial.

PubMed

Lanvers-Kaminsky, Claudia; Rüffer, Andrea; Würthwein, Gudrun; Gerss, Joachim; Zucchetti, Massimo; Ballerini, Andrea; Attarbaschi, Andishe; Smisek, Petr; Nath, Christa; Lee, Samiuela; Elitzur, Sara; Zimmermann, Martin; Möricke, Anja; Schrappe, Martin; Rizzari, Carmelo; Boos, Joachim

2018-02-01

In the international AIEOP-BFM ALL 2009 trial, asparaginase (ASE) activity was monitored after each dose of pegylated Escherichia coli ASE (PEG-ASE). Two methods were used: the aspartic acid β-hydroxamate (AHA) test and medac asparaginase activity test (MAAT). As the latter method overestimates PEG-ASE activity because it calibrates using E. coli ASE, method comparison was performed using samples from the AIEOP-BFM ALL 2009 trial. PEG-ASE activities were determined using MAAT and AHA test in 2 sets of samples (first set: 630 samples and second set: 91 samples). Bland-Altman analysis was performed on ratios between MAAT and AHA tests. The mean difference between both methods, limits of agreement, and 95% confidence intervals were calculated and compared for all samples and samples grouped according to the calibration ranges of the MAAT and the AHA test. PEG-ASE activity determined using the MAAT was significantly higher than when determined using the AHA test (P < 0.001; Wilcoxon signed-rank test). Within the calibration range of the MAAT (30-600 U/L), PEG-ASE activities determined using the MAAT were on average 23% higher than PEG-ASE activities determined using the AHA test. This complies with the mean difference reported in the MAAT manual. With PEG-ASE activities >600 U/L, the discrepancies between MAAT and AHA test increased. Above the calibration range of the MAAT (>600 U/L) and the AHA test (>1000 U/L), a mean difference of 42% was determined. Because more than 70% of samples had PEG-ASE activities >600 U/L and required additional sample dilution, an overall mean difference of 37% was calculated for all samples (37% for the first and 34% for the second set). Comparison of the MAAT and AHA test for PEG-ASE activity confirmed a mean difference of 23% between MAAT and AHA test for PEG-ASE activities between 30 and 600 U/L. The discrepancy increased in samples with >600 U/L PEG-ASE activity, which will be especially relevant when evaluating high PEG-ASE activities in relation to toxicity, efficacy, and population pharmacokinetics.

Analysis of rabies diagnosis in dogs and cats in the state of São Paulo, Brazil.

PubMed

Castilho, Juliana Galera; Achkar, Samira Maria; de Novaes Oliveira, Rafael; Mori, Enio; Carnieli, Pedro; Macedo, Carla Isabel

2018-05-08

The genetic lineage of rabies virus (RABV) associated with dogs has not been found in the state of São Paulo since 1998, and all cases of rabies in domestic animals reported since then have involved the RABV lineage that circulates in bats. As there has been a change in the rabies transmission cycle in cats and dogs, we decided to analyze the tests used to diagnose rabies in these animals in the 15-year period from 2002 to 2016 in the state of São Paulo. During this period, 85,508 central nervous system (CNS) samples from dogs and cats were submitted to the Rabies Diagnosis Section at the Pasteur Institute of São Paulo for testing. All of the samples were tested by the fluorescent antibody test (FAT) and at least one of the following three tests: mouse inoculation test (MIT), rabies tissue culture infection test (RTCIT) and reverse transcription polymerase chain reaction (RT-PCR). Of all the samples tested, twenty were positive in at least one of these assays. Four other positive samples were identified at other institutions in the state of São Paulo. Of the twenty samples that tested positive at the Pasteur Institute of São Paulo, nine were tested by FAT, and the results were subsequently confirmed by other techniques; five gave inconclusive results, and therefore, other techniques had to be used as soon as possible in case the samples were positive; and six were negative by FAT and positive by one or more of the following tests: RTCIT, MIT and RT-PCR. Genetic typing of isolates from eighteen samples identified them as the lineage circulating in bats. In light of this finding, which indicates that genetic lineages associated with bats are circulating in domestic animals in the state of São Paulo, when the results of FAT carried out with samples from aggressive cats and dogs are inconclusive, complementary tests should be used. Decomposing samples and samples for which FAT was inconclusive should be tested using molecular techniques so that a definitive result can be obtained quickly and timely post-exposure prophylaxis can be administered to exposed individuals.

Characterization of Volatiles Loss from Soil Samples at Lunar Environments

NASA Technical Reports Server (NTRS)

Kleinhenz, Julie; Smith, Jim; Roush, Ted; Colaprete, Anthony; Zacny, Kris; Paulsen, Gale; Wang, Alex; Paz, Aaron

2017-01-01

Resource Prospector Integrated Thermal Vacuum Test Program A series of ground based dirty thermal vacuum tests are being conducted to better understand the subsurface sampling operations for RP Volatiles loss during sampling operations Hardware performance Sample removal and transfer Concept of operationsInstrumentation5 test campaigns over 5 years have been conducted with RP hardware with advancing hardware designs and additional RP subsystems Volatiles sampling 4 years Using flight-forward regolith sampling hardware, empirically determine volatile retention at lunar-relevant conditions Use data to improve theoretical predictions Determine driving variables for retention Bound water loss potential to define measurement uncertainties. The main goal of this talk is to introduce you to our approach to characterizing volatiles loss for RP. Introduce the facility and its capabilities Overview of the RP hardware used in integrated testing (most recent iteration) Summarize the test variables used thus farReview a sample of the results.

43 CFR 3162.4-2 - Samples, tests, and surveys.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 43 Public Lands: Interior 2 2014-10-01 2014-10-01 false Samples, tests, and surveys. 3162.4-2... for Operating Rights Owners and Operators § 3162.4-2 Samples, tests, and surveys. (a) During the... tests, run logs, and make other surveys reasonably necessary to determine the presence, quantity, and...

43 CFR 3162.4-2 - Samples, tests, and surveys.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 43 Public Lands: Interior 2 2011-10-01 2011-10-01 false Samples, tests, and surveys. 3162.4-2... for Operating Rights Owners and Operators § 3162.4-2 Samples, tests, and surveys. (a) During the... tests, run logs, and make other surveys reasonably necessary to determine the presence, quantity, and...

43 CFR 3162.4-2 - Samples, tests, and surveys.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 43 Public Lands: Interior 2 2013-10-01 2013-10-01 false Samples, tests, and surveys. 3162.4-2... for Operating Rights Owners and Operators § 3162.4-2 Samples, tests, and surveys. (a) During the... tests, run logs, and make other surveys reasonably necessary to determine the presence, quantity, and...

Synthesizing Information from Language Samples and Standardized Tests in School-Age Bilingual Assessment

ERIC Educational Resources Information Center

Ebert, Kerry Danahy; Pham, Giang

2017-01-01

Purpose: Although language samples and standardized tests are regularly used in assessment, few studies provide clinical guidance on how to synthesize information from these testing tools. This study extends previous work on the relations between tests and language samples to a new population--school-age bilingual speakers with primary language…

40 CFR 91.506 - Engine sample selection.

Code of Federal Regulations, 2010 CFR

2010-07-01

... paragraph (b)(2) of this section. It defines one-tail, 95 percent confidence intervals. σ=actual test sample... individual engine x=mean of emission test results of the actual sample FEL=Family Emission Limit n=The actual... carry-over engine families: After one engine is tested, the manufacturer will combine the test with the...

Retail Survey of Brazilian Milk and Minas Frescal Cheese and a Contaminated Dairy Plant To Establish Prevalence, Relatedness, and Sources of Listeria monocytogenes Isolates▿

PubMed Central

Brito, J. Renaldi F.; Santos, Emilia M. P.; Arcuri, Edna F.; Lange, Carla C.; Brito, Maria A. V. P.; Souza, Guilherme N.; Cerqueira, Mônica M. P. O.; Beltran, J. Marcela Soto; Call, Jeffrey E.; Liu, Yanhong; Porto-Fett, Anna C. S.; Luchansky, John B.

2008-01-01

A study was designed to recover Listeria monocytogenes from pasteurized milk and Minas frescal cheese (MFC) sampled at retail establishments (REs) and to identify the contamination source(s) of these products in the corresponding dairy processing plant. Fifty milk samples (9 brands) and 55 MFC samples (10 brands) were tested from REs located in Juiz de Fora, Minas Gerais, Brazil. All milk samples and 45 samples from 9 of 10 MFC brands tested negative for L. monocytogenes; however, “brand F” of MFC obtained from REs 119 and 159 tested positive. Thus, the farm/plant that produced brand F MFC was sampled; all samples from the milking parlor tested negative for L. monocytogenes, whereas several sites within the processing plant and the MFC samples tested positive. All 344 isolates recovered from retail MFC, plant F MFC, and plant F environmental samples were serotype 1/2a and displayed the same AscI or ApaI fingerprints. Since these results established that the storage coolers served as the contamination source of the MFC, plant F was closed so that corrective renovations could be made. Following renovation, samples from sites that previously tested positive for the pathogen were collected from the processing environment and from MFC on multiple visits; all tested negative for L. monocytogenes. In addition, on subsequent visits to REs 159 and 119, all MFC samples tested negative for the pathogen. Studies are ongoing to quantify the prevalence, levels, and types of L. monocytogenes in MFC and associated processing plants to lessen the likelihood of listeriosis in Brazil. PMID:18502929

A closer look at the effect of preliminary goodness-of-fit testing for normality for the one-sample t-test.

PubMed

Rochon, Justine; Kieser, Meinhard

2011-11-01

Student's one-sample t-test is a commonly used method when inference about the population mean is made. As advocated in textbooks and articles, the assumption of normality is often checked by a preliminary goodness-of-fit (GOF) test. In a paper recently published by Schucany and Ng it was shown that, for the uniform distribution, screening of samples by a pretest for normality leads to a more conservative conditional Type I error rate than application of the one-sample t-test without preliminary GOF test. In contrast, for the exponential distribution, the conditional level is even more elevated than the Type I error rate of the t-test without pretest. We examine the reasons behind these characteristics. In a simulation study, samples drawn from the exponential, lognormal, uniform, Student's t-distribution with 2 degrees of freedom (t(2) ) and the standard normal distribution that had passed normality screening, as well as the ingredients of the test statistics calculated from these samples, are investigated. For non-normal distributions, we found that preliminary testing for normality may change the distribution of means and standard deviations of the selected samples as well as the correlation between them (if the underlying distribution is non-symmetric), thus leading to altered distributions of the resulting test statistics. It is shown that for skewed distributions the excess in Type I error rate may be even more pronounced when testing one-sided hypotheses. ©2010 The British Psychological Society.

Integrating conventional and inverse representation for face recognition.

PubMed

Xu, Yong; Li, Xuelong; Yang, Jian; Lai, Zhihui; Zhang, David

2014-10-01

Representation-based classification methods are all constructed on the basis of the conventional representation, which first expresses the test sample as a linear combination of the training samples and then exploits the deviation between the test sample and the expression result of every class to perform classification. However, this deviation does not always well reflect the difference between the test sample and each class. With this paper, we propose a novel representation-based classification method for face recognition. This method integrates conventional and the inverse representation-based classification for better recognizing the face. It first produces conventional representation of the test sample, i.e., uses a linear combination of the training samples to represent the test sample. Then it obtains the inverse representation, i.e., provides an approximation representation of each training sample of a subject by exploiting the test sample and training samples of the other subjects. Finally, the proposed method exploits the conventional and inverse representation to generate two kinds of scores of the test sample with respect to each class and combines them to recognize the face. The paper shows the theoretical foundation and rationale of the proposed method. Moreover, this paper for the first time shows that a basic nature of the human face, i.e., the symmetry of the face can be exploited to generate new training and test samples. As these new samples really reflect some possible appearance of the face, the use of them will enable us to obtain higher accuracy. The experiments show that the proposed conventional and inverse representation-based linear regression classification (CIRLRC), an improvement to linear regression classification (LRC), can obtain very high accuracy and greatly outperforms the naive LRC and other state-of-the-art conventional representation based face recognition methods. The accuracy of CIRLRC can be 10% greater than that of LRC.

Efficient statistical tests to compare Youden index: accounting for contingency correlation.

PubMed

Chen, Fangyao; Xue, Yuqiang; Tan, Ming T; Chen, Pingyan

2015-04-30

Youden index is widely utilized in studies evaluating accuracy of diagnostic tests and performance of predictive, prognostic, or risk models. However, both one and two independent sample tests on Youden index have been derived ignoring the dependence (association) between sensitivity and specificity, resulting in potentially misleading findings. Besides, paired sample test on Youden index is currently unavailable. This article develops efficient statistical inference procedures for one sample, independent, and paired sample tests on Youden index by accounting for contingency correlation, namely associations between sensitivity and specificity and paired samples typically represented in contingency tables. For one and two independent sample tests, the variances are estimated by Delta method, and the statistical inference is based on the central limit theory, which are then verified by bootstrap estimates. For paired samples test, we show that the estimated covariance of the two sensitivities and specificities can be represented as a function of kappa statistic so the test can be readily carried out. We then show the remarkable accuracy of the estimated variance using a constrained optimization approach. Simulation is performed to evaluate the statistical properties of the derived tests. The proposed approaches yield more stable type I errors at the nominal level and substantially higher power (efficiency) than does the original Youden's approach. Therefore, the simple explicit large sample solution performs very well. Because we can readily implement the asymptotic and exact bootstrap computation with common software like R, the method is broadly applicable to the evaluation of diagnostic tests and model performance. Copyright © 2015 John Wiley & Sons, Ltd.

Mars Science Laboratory Sample Acquisition, Sample Processing and Handling: Subsystem Design and Test Challenges

NASA Technical Reports Server (NTRS)

Jandura, Louise

2010-01-01

The Sample Acquisition/Sample Processing and Handling subsystem for the Mars Science Laboratory is a highly-mechanized, Rover-based sampling system that acquires powdered rock and regolith samples from the Martian surface, sorts the samples into fine particles through sieving, and delivers small portions of the powder into two science instruments inside the Rover. SA/SPaH utilizes 17 actuated degrees-of-freedom to perform the functions needed to produce 5 sample pathways in support of the scientific investigation on Mars. Both hardware redundancy and functional redundancy are employed in configuring this sampling system so some functionality is retained even with the loss of a degree-of-freedom. Intentional dynamic environments are created to move sample while vibration isolators attenuate this environment at the sensitive instruments located near the dynamic sources. In addition to the typical flight hardware qualification test program, two additional types of testing are essential for this kind of sampling system: characterization of the intentionally-created dynamic environment and testing of the sample acquisition and processing hardware functions using Mars analog materials in a low pressure environment. The overall subsystem design and configuration are discussed along with some of the challenges, tradeoffs, and lessons learned in the areas of fault tolerance, intentional dynamic environments, and special testing

Optimum sample size allocation to minimize cost or maximize power for the two-sample trimmed mean test.

PubMed

Guo, Jiin-Huarng; Luh, Wei-Ming

2009-05-01

When planning a study, sample size determination is one of the most important tasks facing the researcher. The size will depend on the purpose of the study, the cost limitations, and the nature of the data. By specifying the standard deviation ratio and/or the sample size ratio, the present study considers the problem of heterogeneous variances and non-normality for Yuen's two-group test and develops sample size formulas to minimize the total cost or maximize the power of the test. For a given power, the sample size allocation ratio can be manipulated so that the proposed formulas can minimize the total cost, the total sample size, or the sum of total sample size and total cost. On the other hand, for a given total cost, the optimum sample size allocation ratio can maximize the statistical power of the test. After the sample size is determined, the present simulation applies Yuen's test to the sample generated, and then the procedure is validated in terms of Type I errors and power. Simulation results show that the proposed formulas can control Type I errors and achieve the desired power under the various conditions specified. Finally, the implications for determining sample sizes in experimental studies and future research are discussed.

Evaluation of an automated microplate technique in the Galileo system for ABO and Rh(D) blood grouping.

PubMed

Xu, Weiyi; Wan, Feng; Lou, Yufeng; Jin, Jiali; Mao, Weilin

2014-01-01

A number of automated devices for pretransfusion testing have recently become available. This study evaluated the Immucor Galileo System, a fully automated device based on the microplate hemagglutination technique for ABO/Rh (D) determinations. Routine ABO/Rh typing tests were performed on 13,045 samples using the Immucor automated instruments. Manual tube method was used to resolve ABO forward and reverse grouping discrepancies. D-negative test results were investigated and confirmed manually by the indirect antiglobulin test (IAT). The system rejected 70 tests for sample inadequacy. 87 samples were read as "No-type-determined" due to forward and reverse grouping discrepancies. 25 tests gave these results because of sample hemolysis. After further tests, we found 34 tests were caused by weakened RBC antibodies, 5 tests were attributable to weak A and/or B antigens, 4 tests were due to mixed-field reactions, and 8 tests had high titer cold agglutinin with blood qualifications which react only at temperatures below 34 degrees C. In the remaining 11 cases, irregular RBC antibodies were identified in 9 samples (seven anti-M and two anti-P) and two subgroups were identified in 2 samples (one A1 and one A2) by a reference laboratory. As for D typing, 2 weak D+ samples missed by automated systems gave negative results, but weak-positive reactions were observed in the IAT. The Immucor Galileo System is reliable and suited for ABO and D blood groups, some reasons may cause a discrepancy in ABO/D typing using a fully automated system. It is suggested that standardization of sample collection may improve the performance of the fully automated system.

The cost of large numbers of hypothesis tests on power, effect size and sample size.

PubMed

Lazzeroni, L C; Ray, A

2012-01-01

Advances in high-throughput biology and computer science are driving an exponential increase in the number of hypothesis tests in genomics and other scientific disciplines. Studies using current genotyping platforms frequently include a million or more tests. In addition to the monetary cost, this increase imposes a statistical cost owing to the multiple testing corrections needed to avoid large numbers of false-positive results. To safeguard against the resulting loss of power, some have suggested sample sizes on the order of tens of thousands that can be impractical for many diseases or may lower the quality of phenotypic measurements. This study examines the relationship between the number of tests on the one hand and power, detectable effect size or required sample size on the other. We show that once the number of tests is large, power can be maintained at a constant level, with comparatively small increases in the effect size or sample size. For example at the 0.05 significance level, a 13% increase in sample size is needed to maintain 80% power for ten million tests compared with one million tests, whereas a 70% increase in sample size is needed for 10 tests compared with a single test. Relative costs are less when measured by increases in the detectable effect size. We provide an interactive Excel calculator to compute power, effect size or sample size when comparing study designs or genome platforms involving different numbers of hypothesis tests. The results are reassuring in an era of extreme multiple testing.

21 CFR 211.110 - Sampling and testing of in-process materials and drug products.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 4 2012-04-01 2012-04-01 false Sampling and testing of in-process materials and... PHARMACEUTICALS Production and Process Controls § 211.110 Sampling and testing of in-process materials and drug... testing. (b) Valid in-process specifications for such characteristics shall be consistent with drug...

21 CFR 211.110 - Sampling and testing of in-process materials and drug products.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 4 2011-04-01 2011-04-01 false Sampling and testing of in-process materials and... PHARMACEUTICALS Production and Process Controls § 211.110 Sampling and testing of in-process materials and drug... testing. (b) Valid in-process specifications for such characteristics shall be consistent with drug...

21 CFR 211.110 - Sampling and testing of in-process materials and drug products.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 4 2013-04-01 2013-04-01 false Sampling and testing of in-process materials and... PHARMACEUTICALS Production and Process Controls § 211.110 Sampling and testing of in-process materials and drug... testing. (b) Valid in-process specifications for such characteristics shall be consistent with drug...

21 CFR 211.110 - Sampling and testing of in-process materials and drug products.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 4 2010-04-01 2010-04-01 false Sampling and testing of in-process materials and... PHARMACEUTICALS Production and Process Controls § 211.110 Sampling and testing of in-process materials and drug... testing. (b) Valid in-process specifications for such characteristics shall be consistent with drug...

21 CFR 211.110 - Sampling and testing of in-process materials and drug products.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 4 2014-04-01 2014-04-01 false Sampling and testing of in-process materials and... PHARMACEUTICALS Production and Process Controls § 211.110 Sampling and testing of in-process materials and drug... testing. (b) Valid in-process specifications for such characteristics shall be consistent with drug...

Analysis of Duplicated Multiple-Samples Rank Data Using the Mack-Skillings Test.

PubMed

Carabante, Kennet Mariano; Alonso-Marenco, Jose Ramon; Chokumnoyporn, Napapan; Sriwattana, Sujinda; Prinyawiwatkul, Witoon

2016-07-01

Appropriate analysis for duplicated multiple-samples rank data is needed. This study compared analysis of duplicated rank preference data using the Friedman versus Mack-Skillings tests. Panelists (n = 125) ranked twice 2 orange juice sets: different-samples set (100%, 70%, vs. 40% juice) and similar-samples set (100%, 95%, vs. 90%). These 2 sample sets were designed to get contrasting differences in preference. For each sample set, rank sum data were obtained from (1) averaged rank data of each panelist from the 2 replications (n = 125), (2) rank data of all panelists from each of the 2 separate replications (n = 125 each), (3) jointed rank data of all panelists from the 2 replications (n = 125), and (4) rank data of all panelists pooled from the 2 replications (n = 250); rank data (1), (2), and (4) were separately analyzed by the Friedman test, although those from (3) by the Mack-Skillings test. The effect of sample sizes (n = 10 to 125) was evaluated. For the similar-samples set, higher variations in rank data from the 2 replications were observed; therefore, results of the main effects were more inconsistent among methods and sample sizes. Regardless of analysis methods, the larger the sample size, the higher the χ(2) value, the lower the P-value (testing H0 : all samples are not different). Analyzing rank data (2) separately by replication yielded inconsistent conclusions across sample sizes, hence this method is not recommended. The Mack-Skillings test was more sensitive than the Friedman test. Furthermore, it takes into account within-panelist variations and is more appropriate for analyzing duplicated rank data. © 2016 Institute of Food Technologists®

Modification of the fluorescent antibody virus neutralisation test--elimination of the cytotoxic effect for the detection of rabies virus neutralising antibodies.

PubMed

Bedeković, Tomislav; Lemo, Nina; Lojkić, Ivana; Mihaljević, Zeljko; Jungić, Andreja; Cvetnić, Zeljko; Cač, Zeljko; Hostnik, Peter

2013-04-01

The virus neutralisation test is used for the quantitation of specific antibodies in serum samples. However, the success of the test depends on the quality of samples. In the case of poor quality samples, a cytotoxic effect can be observed and the results of the test can be compromised. Additionally, the cytotoxic effect limits the use of different substances, such as muscle extract or liquid from thoracic cavity (thoracic liquid), as a sample for the detection of rabies virus neutralising antibodies in the follow-up of fox oral vaccination campaigns. To eliminate the cytotoxic effect, a modified fluorescent antibody virus neutralisation (mFAVN) test was developed and evaluated. In the mFAVN test, inocula were removed after a 1h and the cytotoxic effect was prevented. According to the results obtained, the specificity of the mFAVN test compared to the FAVN test was 88.8% and the sensitivity was 94.4%. The diagnostic validity of the test was 0.99 (CI=0.98-1.00). To evaluate the possibility of using muscle extract and thoracic liquid as samples for the virus neutralisation test, 102 sera, muscle extract and thoracic liquid samples of dog origin were tested with the mFAVN test. The correlation between sera and muscle extracts was 87.9% (r=0.88, p<0.001). The correlation between sera and thoracic liquid was 94.2% (r=0.94, p<0.001). These findings indicated that both muscle extract and thoracic liquid could be used as samples for detection of rabies virus neutralising antibodies in the follow-up of oral vaccination campaigns. To evaluate the level of elimination of the cytotoxic effect, the 102 samples of sera, muscle extracts and thoracic liquid of dog origin were also tested in parallel using the mFAVN and FAVN tests. In the mFAVN test, no instance of cytotoxic effect was observed in the cells. In the FAVN test, two sera (1.9%), 35 muscle extracts (34.3%) and 56 thoracic liquid samples (54.9%) showed cytotoxic effect. The results of this study strongly suggest that cytotoxic effect can be eliminated completely from the rabies virus neutralising antibody detection tests used in the follow-up of oral vaccination campaigns and that very poor quality samples, such as muscle extract and thoracic liquid, can be used. Copyright © 2013 Elsevier B.V. All rights reserved.

Design, development, and testing of a hybrid in situ testing device for building joint sealant

Treesearch

C. White; N. Embree; C. Buch; R.S. Williams

2005-01-01

The testing of sealant samples has been restricted to devices that either focus on fatiguing multiple samples or quantifying the mechanical properties of a single sample. This manuscript describes a device that combines these two instrumental designs: the ability to both fatigue and characterize multiple sealant samples at the same time. This device employs precise...

16 CFR 1616.4 - Sampling and acceptance procedures.

Code of Federal Regulations, 2011 CFR

2011-01-01

... specimen to one of the three samples. Test each set of three samples and accept or reject each seam design... all the test criteria of § 1616.3(b), accept the seam design. If one or more of the three additional.... Test the sets of three samples and accept or reject the type of trim and design on the same basis as...

16 CFR 1616.4 - Sampling and acceptance procedures.

Code of Federal Regulations, 2012 CFR

2012-01-01

... specimen to one of the three samples. Test each set of three samples and accept or reject each seam design... all the test criteria of § 1616.3(b), accept the seam design. If one or more of the three additional.... Test the sets of three samples and accept or reject the type of trim and design on the same basis as...

16 CFR 1616.4 - Sampling and acceptance procedures.

Code of Federal Regulations, 2010 CFR

2010-01-01

... specimen to one of the three samples. Test each set of three samples and accept or reject each seam design... all the test criteria of § 1616.3(b), accept the seam design. If one or more of the three additional.... Test the sets of three samples and accept or reject the type of trim and design on the same basis as...

46 CFR 160.076-29 - Production oversight.

Code of Federal Regulations, 2010 CFR

2010-10-01

...) Samples selected for the indicated tests may not be used for more than one test. (iii) If a sample fails... 12 months. (iii) One sample of each means of marking on each type of fabric or finish used in PFD... if any sample fails one or more tests. (3) In lots of more than 200 PFDs, the lot must be rejected if...

19 CFR 151.52 - Sampling procedures.

Code of Federal Regulations, 2012 CFR

2012-04-01

.... Representative commercial moisture and assay samples shall be taken under Customs supervision for testing by the Customs laboratory. The samples used for the moisture test shall be representative of the shipment at the... verified commercial moisture sample and prepared assay sample certified to be representative of the...

Results of Performance Tests Performed on the John Watts WW Casing Connection on 7" Pipe

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

John D. Watts

2000-02-01

Stress Engineering Services (SES) was contracted by Mr. John Watts to test his ''WW'' threaded connection developed for oilfield oil and gas service. This work was a continuation of testing performed by SES as reported in August of 1999. The connection design tested was identified as ''WW''. The samples were all integral (no coupled connections) and contained a wedge thread form with 90{sup o} flank angles relative to the pipe centerline. The wedge thread form is a variable width thread that primarily engages on the flanks. This thread form provides very high torque capacity and good stabbing ability and makeup.more » The test procedure selected for one of the samples was the newly written ISO 13679 procedure for full scale testing of casing and tubing connections, which is currently going through the ISO acceptance process. The ISO procedure requires a variety of tests that includes makeup/breakout testing, internal gas sealability/external water sealability testing with axial tension, axial compression, bending, internal gas thermal cycle tests and limit load (failure) tests. This test procedure was performed with one sample. Four samples were tested to failure. Table 1 contains a summary of the tasks performed by SES. The project started with the delivery of test samples by Mr. Watts. Pipe from the previous round of tests was used for the new samples. Figure 1 shows the structural and sealing results relative to the pipe body. Sample 1 was used to determine the torque capacity of the connection. Torque was applied to the capacity of SES's equipment which was 28,424 ft-lbs. From this, an initial recommended torque range of 7,200 to 8,800 ft-lbs. was selected. The sample was disassembled and while there was no galling observed in the threads, the end of the pin had collapsed inward. Sample 2 received three makeups. Breakouts 1 and 2 also had collapsing of the pin end, with no thread galling. From these make/breaks, it was decided to reduce the amount of lubricant applied to the connection by applying it to the box or pin only and reducing the amount applied. Samples 3 and 4 received one makeup only. Sample 5 initially received two make/breaks to test for galling resistance before final makeup, No galling was observed. Later, three additional make/breaks were performed with no pin end collapse and galling over 1/2 a thread occurring on one of the breakouts. During the make/break tests, the stabbing and hand tight makeup of the WW connection was found to be very easy and trouble free. There was no tendency to crossthread, even when stabbed at an angle, and it screwed together very smoothly up to hand tight. During power tight makeup, there was no heat generated in the box (as checked by hand contact) and no jerkiness associated with any of the makeups or breakouts. Sample 2 was tested in pure compression. The maximum load obtained was 1,051 kips and the connection was beginning to significantly deform as the sample buckled. Actual pipe yield was 1,226 kips. Sample 3 was capped-end pressure tested to failure. The capped-end yield pressure of the pipe was 16,572 psi and the sample began to leak at 12,000 psi. Sample 4 was tested in pure tension. The maximum load obtained was 978 kips and the connection failed by fracture at the pin critical section. Actual pipe yield was 1,226 kips. Sample 5 was tested in combined tension/compression and internal gas pressure. The sample was assembled, setup and tested four times. The first time was with a torque of 7,298 ft-lbs and the connection leaked halfway to ISO Load Point 2 with loads of 693 kips and 4,312 psi. The second time the torque was increased to 14,488 ft-lbs and a leak occurred at 849 kips and 9,400 psi, which was ISO Load Point 2. The third time the makeup torque was again increased, to 20,456 ft-lbs, and a leak occurred at 716 kips and 11,342 psi, ISO Load Point 4. The fourth test was with the same torque as before, 20,617 ft-lbs, and the connection successfully tested up to load step 56, ISO Load Point 6 (second round) before leaking at 354 kips and 11,876 psi. At this point, time and funds prevented additional testing to be performed.« less

Report on Electrochemcial Corrosion Testing of 241-SY-102 Grab Samples from the 2012 Grab Sampling Campaign

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

Wyrwas, Richard B.; Lamothe, Margaret E.

2013-05-30

This report describes the results of the electrochemical testing performed on tank 241-SY-102 (SY-102) grab samples that were collected in support of corrosion mitigation. The objective of the work presented here was to determine corrosion resistance of tank SY-102 to the grab samples collected using electrochemical methods up to 50°C as well as to satisfy data quality objectives. Grab samples were collected at multiple elevations from Riser 003. The electrochemical corrosion testing was planned to consist of linear polarization resistance testing (LPR) and cyclic potentiodynamic polarization (CPP) testing at 50°C. The temperature would be lowered to 40 °C and themore » test repeated if the CPP curve indicated pitting corrosion at 50°C. Ifno pitting was indicated by the CPP curve, then a duplicate scan would be repeated at 50°C to confirm the first result. The testing would be complete if the duplicate CPP scan was consistent with the first. This report contains the CPP results of the testing of grab sample 2SY-12-03 and 2SY-12-03DUP composite sample tested under these conditions. There was no indication of pitting at 50°C, and the duplicate scan was in agreement with the first scan. Since no further testing was required, a third scan with a shorter rest time was performed and is present in this report.« less

Effect of microbiological testing on subsequent mid-infrared milk component analysis of the same milk sample.

PubMed

Wojciechowski, Karen L; Melilli, Caterina; Barbano, David M

2014-09-01

Our objectives were to determine if mixing and sampling of a raw milk sample at 4°C for determination of total bacteria count (TBC) and if incubation at 14°C for 18h and sampling for a preliminary incubation (PI) count influenced the accuracy of subsequent fat, protein, or lactose measurement by mid-infrared (IR) analysis of milk from the same sample container due to either nonrepresentative sampling or the presence of microbial metabolites produced by microbial growth in the milk from the incubation. Milks of 4 fat levels (2.2, 3, 4, and 5%) reflected the range of fat levels encountered in producer milks. If the portion of milk removed from a cold sample was not representative, then the effect on a milk component test would likely be larger as fat content increases. Within the milks at each fat level, 3 treatments were used: (1) 20 vials of the same milk sampled for testing TBC using a BactoScan FC and then used for a milk component test; (2) 20 vials for testing TBC plus PI count followed by component test; and (3) 20 vials to run for IR component test without a prior micro sampling and testing. This was repeated in 3 different weeks using a different batch of milk each week. No large effect on the accuracy of component milk testing [IR fat B (carbon hydrogen stretch) and fat A (carbonyl stretch)] due to the cold milk sample handling and mixing procedures used for TBC was detected, confirming the fact that the physical removal of milk from the vial by the BactoScan FC (Foss Electric, Hillerød, Denmark) was a representative portion of the milk. However, the representativeness of any other sampling procedure (manual or automated) of a cold milk sample before running milk component testing on the same container of milk should be demonstrated and verified periodically as a matter of routine laboratory quality assurance. Running TBC with a BactoScan FC first and then IR milk analysis after had a minimal effect on milk component tests by IR when milk bacteria counts were within pasteurized milk ordinance limits of <100,000 cfu/mL. Running raw milk PI counts (18h of incubation at 13-14°C) with the BactoScan FC before milk component testing by IR milk analysis had an effect on component tests. The effect was largest on fat test results and would decrease the accuracy of milk payment testing on individual producer milks. The effect was most likely due to the absorption of light by bacterial metabolites resulting from microbial growth or other chemical degradation processes occurring in the milk during the PI count incubation, not by the sampling procedure of the BactoScan. The direction of the effect on component test results will vary depending on the bacteria count and the type of bacteria that grew in the milk, and this could be different in every individual producer milk sample. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

40 CFR 86.1845-04 - Manufacturer in-use verification testing requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

... of test vehicles in the sample comply with the sample size requirements of this section. Any post... HDV must test, or cause to have tested, a specified number of vehicles. Such testing must be conducted... first test will be considered the official results for the test vehicle, regardless of any test results...

Comparison of the Abbott RealTime High Risk HPV test and the Roche cobas 4800 HPV test using urine samples.

PubMed

Lim, Myong Cheol; Lee, Do-Hoon; Hwang, Sang-Hyun; Hwang, Na Rae; Lee, Bomyee; Shin, Hye Young; Jun, Jae Kwan; Yoo, Chong Woo; Lee, Dong Ock; Seo, Sang-Soo; Park, Sang-Yoon; Joo, Jungnam

2017-05-01

Human papillomavirus (HPV) testing based on cervical samples is important for use in cervical cancer screening. However, cervical sampling is invasive. Therefore, non-invasive methods for detecting HPV, such as urine samples, are needed. For HPV detection in urine samples, two real-time PCR (RQ-PCR) tests, Roche cobas 4800 test (Roche_HPV; Roche Molecular Diagnostics) and Abbott RealTime High Risk HPV test (Abbott_HPV; Abbott Laboratories) were compared to standard cervical samples. The performance of Roche_HPV and Abbott_HPV for HPV detection was evaluated at the National Cancer Center using 100 paired cervical and urine samples. The tests were also compared using urine samples stored at various temperatures and for a range of durations. The overall agreement between the Roche_HPV and Abbott_HPV tests using urine samples for any hrHPV type was substantial (86.0% with a kappa value of 0.7173), and that for HPV 16/18 was nearly perfect (99.0% with a kappa value of 0.9668). The relative sensitivities (based on cervical samples) for HPV 16/18 detection using Roche_HPV and Abbott_HPV with urine samples were 79.2% (95% CI; 57.9-92.9%) and 81.8% (95% CI; 59.7-94.8%), respectively. When the cut-off C T value for Abbott_HPV was extended to 40 for urine samples, the relative sensitivity of Abbott_HPV increased to 91.7% from 81.8% for HPV16/18 detection and to 87.0% from 68.5% for other hrHPV detection. The specificity was not affected by the change in the C T threshold. Roche_HPV and Abbott_HPV showed high concordance. However, HPV DNA detection using urine samples was inferior to HPV DNA detection using cervical samples. Interestingly, when the cut-off C T value was set to 40, Abbott_HPV using urine samples showed high sensitivity and specificity, comparable to those obtained using cervical samples. Fully automated DNA extraction and detection systems, such as Roche_HPV and Abbott_HPV, could reduce the variability in HPV detection and accelerate the standardization of HPV detection in urine. Thus, urine samples may be an effective alternative for HPV detection in women who hesitate to participate in cervical cancer screening programs. Copyright © 2017 Elsevier B.V. All rights reserved.

Ultra-Gradient Test Cavity for Testing SRF Wafer Samples

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

N.J. Pogue, P.M. McIntyre, A.I. Sattarov, C. Reece

2010-11-01

A 1.3 GHz test cavity has been designed to test wafer samples of superconducting materials. This mushroom shaped cavity, operating in TE01 mode, creates a unique distribution of surface fields. The surface magnetic field on the sample wafer is 3.75 times greater than elsewhere on the Niobium cavity surface. This field design is made possible through dielectrically loading the cavity by locating a hemisphere of ultra-pure sapphire just above the sample wafer. The sapphire pulls the fields away from the walls so the maximum field the Nb surface sees is 25% of the surface field on the sample. In thismore » manner, it should be possible to drive the sample wafer well beyond the BCS limit for Niobium while still maintaining a respectable Q. The sapphire's purity must be tested for its loss tangent and dielectric constant to finalize the design of the mushroom test cavity. A sapphire loaded CEBAF cavity has been constructed and tested. The results on the dielectric constant and loss tangent will be presented« less

Directional spectral emissivity measurement system

NASA Technical Reports Server (NTRS)

Halyo, Nesim (Inventor); Pandey, Dhirendra K. (Inventor)

1992-01-01

Apparatus and process for determining the emissivity of a test specimen including an integrated sphere having two concentric walls with a coolant circulating therebetween, and disposed within a chamber which may be under ambient, vacuum or inert gas conditions. A reference sample is disposed within the sphere with a monochromatic light source in optical alignment therewith. A pyrometer is in optical alignment with the test sample for obtaining continuous test sample temperature measurements during a test. An arcuate slit port is provided through the spaced concentric walls of the integrating sphere with a movable monochromatic light source extending through and movable along the arcuate slit port. A detector system extends through the integrating sphere for continuously detecting an integrated signal indicative of all radiation within its field of view, as a function of the emissivity of the test specimen at various temperatures and various angle position of the monochromatic light source. A furnace for heating the test sample to approximately 3000 K. and control mechanism for transferring the heated sample from the furnace to the test sample port in the integrating sphere is also contained within the chamber.

49 CFR 178.606 - Stacking test.

Code of Federal Regulations, 2014 CFR

2014-10-01

... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) SPECIFICATIONS FOR PACKAGINGS Testing of Non-bulk.... (c) Test method—(1) Design qualification testing. The test sample must be subjected to a force... might be stacked on it during transport; where the contents of the test sample are non-hazardous liquids...

49 CFR 178.606 - Stacking test.

Code of Federal Regulations, 2012 CFR

2012-10-01

... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) SPECIFICATIONS FOR PACKAGINGS Testing of Non-bulk.... (c) Test method—(1) Design qualification testing. The test sample must be subjected to a force... might be stacked on it during transport; where the contents of the test sample are non-hazardous liquids...

49 CFR 178.606 - Stacking test.

Code of Federal Regulations, 2011 CFR

2011-10-01

... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) SPECIFICATIONS FOR PACKAGINGS Testing of Non-bulk.... (c) Test method—(1) Design qualification testing. The test sample must be subjected to a force... might be stacked on it during transport; where the contents of the test sample are non-hazardous liquids...

A Draft Protocol for Detecting Possible Biohazards in Martian Samples Returned to Earth

NASA Technical Reports Server (NTRS)

Viso, M.; DeVincenzi, D. L.; Race, M. S.; Schad, P. J.; Stabekis, P. D.; Acevedo, S. E.; Rummel, J. D.

2002-01-01

In preparation for missions to Mars that will involve the return of samples, it is necessary to prepare for the safe receiving, handling, testing, distributing, and archiving of martian materials here on Earth. Previous groups and committees have studied selected aspects of sample return activities, but a specific protocol for handling and testing of returned -=1 samples from Mars remained to be developed. To refine the requirements for Mars sample hazard testing and to develop criteria for the subsequent release of sample materials from precautionary containment, NASA Planetary Protection Officer, working in collaboration with CNES, convened a series of workshops to produce a Protocol by which returned martian sample materials could be assessed for biological hazards and examined for evidence of life (extant or extinct), while safeguarding the samples from possible terrestrial contamination. The Draft Protocol was then reviewed by an Oversight and Review Committee formed specifically for that purpose and composed of senior scientists. In order to preserve the scientific value of returned martian samples under safe conditions, while avoiding false indications of life within the samples, the Sample Receiving Facility (SRF) is required to allow handling and processing of the Mars samples to prevent their terrestrial contamination while maintaining strict biological containment. It is anticipated that samples will be able to be shipped among appropriate containment facilities wherever necessary, under procedures developed in cooperation with international appropriate institutions. The SRF will need to provide different types of laboratory environments for carrying out, beyond sample description and curation, the various aspects of the protocol: Physical/Chemical analysis, Life Detection testing, and Biohazard testing. The main principle of these tests will be described and the criteria for release will be discussed, as well as the requirements for the SRF and its personnel.

Coaxial test fixture

DOEpatents

Praeg, W.F.

1984-03-30

This invention pertains to arrangements for performing electrical tests on contact material samples, and in particular for testing contact material test samples in an evacuated environment under high current loads. Frequently, it is desirable in developing high-current separable contact material, to have at least a preliminary analysis of selected candidate conductor materials. Testing of material samples will hopefully identify materials unsuitable for high current electrical contact without requiring incorporation of the materials into a completed and oftentimes complex structure.

40 CFR 1065.805 - Sampling system.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 33 2011-07-01 2011-07-01 false Sampling system. 1065.805 Section 1065... ENGINE-TESTING PROCEDURES Testing With Oxygenated Fuels § 1065.805 Sampling system. (a) Dilute engine exhaust, and use batch sampling to collect proportional flow-weighted dilute samples of the applicable...

40 CFR 1065.805 - Sampling system.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 32 2010-07-01 2010-07-01 false Sampling system. 1065.805 Section 1065... ENGINE-TESTING PROCEDURES Testing With Oxygenated Fuels § 1065.805 Sampling system. (a) Dilute engine exhaust, and use batch sampling to collect proportional flow-weighted dilute samples of the applicable...

19 CFR 151.70 - Method of sampling by Customs.

Code of Federal Regulations, 2013 CFR

2013-04-01

... THE TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Wool and Hair § 151.70... feasible to obtain a representative general sample of the wool or hair in a sampling unit or to test such a...

19 CFR 151.70 - Method of sampling by Customs.

Code of Federal Regulations, 2012 CFR

2012-04-01

... THE TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Wool and Hair § 151.70... feasible to obtain a representative general sample of the wool or hair in a sampling unit or to test such a...

19 CFR 151.70 - Method of sampling by Customs.

Code of Federal Regulations, 2014 CFR

2014-04-01

... THE TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Wool and Hair § 151.70... feasible to obtain a representative general sample of the wool or hair in a sampling unit or to test such a...

19 CFR 151.70 - Method of sampling by Customs.

Code of Federal Regulations, 2010 CFR

2010-04-01

... THE TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Wool and Hair § 151.70... feasible to obtain a representative general sample of the wool or hair in a sampling unit or to test such a...

19 CFR 151.70 - Method of sampling by Customs.

Code of Federal Regulations, 2011 CFR

2011-04-01

... THE TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Wool and Hair § 151.70... feasible to obtain a representative general sample of the wool or hair in a sampling unit or to test such a...

Tests of Independence in Contingency Tables with Small Samples: A Comparison of Statistical Power.

ERIC Educational Resources Information Center

Parshall, Cynthia G.; Kromrey, Jeffrey D.

1996-01-01

Power and Type I error rates were estimated for contingency tables with small sample sizes for the following four types of tests: (1) Pearson's chi-square; (2) chi-square with Yates's continuity correction; (3) the likelihood ratio test; and (4) Fisher's Exact Test. Various marginal distributions, sample sizes, and effect sizes were examined. (SLD)

75 FR 16874 - Market Test of “Samples Co-Op Box” Experimental Product

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-02

... POSTAL SERVICE Market Test of ``Samples Co-Op Box'' Experimental Product AGENCY: Postal Service TM . ACTION: Notice. SUMMARY: The Postal Service gives notice of a market test of an experimental product in... pursuant to 39 U.S.C. 3641(c)(1) that it will begin a market test of its ``Samples Co-Op Box'' experimental...

Study samples are too small to produce sufficiently precise reliability coefficients.

PubMed

Charter, Richard A

2003-04-01

In a survey of journal articles, test manuals, and test critique books, the author found that a mean sample size (N) of 260 participants had been used for reliability studies on 742 tests. The distribution was skewed because the median sample size for the total sample was only 90. The median sample sizes for the internal consistency, retest, and interjudge reliabilities were 182, 64, and 36, respectively. The author presented sample size statistics for the various internal consistency methods and types of tests. In general, the author found that the sample sizes that were used in the internal consistency studies were too small to produce sufficiently precise reliability coefficients, which in turn could cause imprecise estimates of examinee true-score confidence intervals. The results also suggest that larger sample sizes have been used in the last decade compared with those that were used in earlier decades.

Evaluation of rapid diagnostic test kits for feline leukemia virus infection using samples from naturally infected cats.

PubMed

Liu, Jiayou; O'Connor, Thomas; Beall, Melissa; Chandrashekar, Ramaswamy; Lappin, Michael

2016-01-01

Feline leukemia virus (FeLV) is a potentially life-threatening oncogenic retrovirus. The p27 viral core protein is produced by the virus in infected feline cells, is found in the cytoplasm in several blood cells and can be free in the serum and plasma. ELISA or particle-based immunoassay are commonly used to detect the presence of the p27 core protein in samples obtained from blood. The objective of this study was to compare the performance of several in-clinic tests: the SNAP Feline Triple Test (IDEXX Laboratories), the WITNESS FeLV-FIV Test (Zoetis) and the VetScan Feline FeLV/FIV Rapid Test (Abaxis). The sample population (100 positive, 105 negative samples) consisted of serum and plasma samples submitted to IDEXX's worldwide reference laboratory for feline retrovirus testing. Virus isolation and reverse transcriptase PCR results were not available and so samples were judged to be positive or negative based on the results of the ViraCHEK FeLV (Zoetis) microtiter plate assay. The percentage of samples positive and negative for FeLV p27 antigen using the three in-clinic tests compared with the ViraCHEK method were as follows: IDEXX Feline Triple (positive 98.0%, negative 100%); Zoetis WITNESS (positive 79.0%, negative 97.1%); Abaxis VetScan (positive 73.0%, negative 97.1%). The SNAP Feline Triple Test demonstrated a high level of agreement for FeLV-positive and FeLV-negative samples when assessed in this model. Results of FeLV assays can vary among tests.

An Investigation of Measurement Invariance of the Key Stage 2 National Curriculum Science Sampling Test in England

ERIC Educational Resources Information Center

He, Qingping; Anwyll, Steve; Glanville, Matthew; Opposs, Dennis

2014-01-01

Since 2010, the whole national cohort Key Stage 2 (KS2) National Curriculum test in science in England has been replaced with a sampling test taken by pupils at the age of 11 from a nationally representative sample of schools annually. The study reported in this paper compares the performance of different subgroups of the samples (classified by…

16 CFR § 1616.4 - Sampling and acceptance procedures.

Code of Federal Regulations, 2013 CFR

2013-01-01

... specimen to one of the three samples. Test each set of three samples and accept or reject each seam design... all the test criteria of § 1616.3(b), accept the seam design. If one or more of the three additional.... Test the sets of three samples and accept or reject the type of trim and design on the same basis as...

Correcting Two-Sample "z" and "t" Tests for Correlation: An Alternative to One-Sample Tests on Difference Scores

ERIC Educational Resources Information Center

Zimmerman, Donald W.

2012-01-01

In order to circumvent the influence of correlation in paired-samples and repeated measures experimental designs, researchers typically perform a one-sample Student "t" test on difference scores. That procedure entails some loss of power, because it employs N - 1 degrees of freedom instead of the 2N - 2 degrees of freedom of the…

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

PubMed

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

2018-02-10

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

Estimation of infection prevalence and sensitivity in a stratified two-stage sampling design employing highly specific diagnostic tests when there is no gold standard.

PubMed

Miller, Ezer; Huppert, Amit; Novikov, Ilya; Warburg, Alon; Hailu, Asrat; Abbasi, Ibrahim; Freedman, Laurence S

2015-11-10

In this work, we describe a two-stage sampling design to estimate the infection prevalence in a population. In the first stage, an imperfect diagnostic test was performed on a random sample of the population. In the second stage, a different imperfect test was performed in a stratified random sample of the first sample. To estimate infection prevalence, we assumed conditional independence between the diagnostic tests and develop method of moments estimators based on expectations of the proportions of people with positive and negative results on both tests that are functions of the tests' sensitivity, specificity, and the infection prevalence. A closed-form solution of the estimating equations was obtained assuming a specificity of 100% for both tests. We applied our method to estimate the infection prevalence of visceral leishmaniasis according to two quantitative polymerase chain reaction tests performed on blood samples taken from 4756 patients in northern Ethiopia. The sensitivities of the tests were also estimated, as well as the standard errors of all estimates, using a parametric bootstrap. We also examined the impact of departures from our assumptions of 100% specificity and conditional independence on the estimated prevalence. Copyright © 2015 John Wiley & Sons, Ltd.

PERFORMANCE EVALUATION OF A PROTOTYPE ARCHITECT ANTIBODY ASSAY FOR BABESIA MICROTI.

PubMed

Cheng, Kevin; Coller, Kelly E; Marohnic, Christopher C; Pfeiffer, Zachary A; Fino, James R; Elsing, Randee R; Bergsma, Janet; Marcinkus, Marilee A; Kar, Alak K; Gumbs, Orlando H; Otis, Kathy S; Fishpaugh, Jeffrey; Schultz, Phillip W; Pope, Mark R; Narvaez, Alfredo R; Wong, Susan J; Madison-Antenucci, Susan; Leary, Thomas P; Dawson, George J

2018-05-09

The tick-borne protozoan Babesia microti is responsible for more than 200 cases of transfusion-transmitted babesiosis (TTB) infection in the United States over the last 30 years. Measures to mitigate the risk of TTB include nucleic acid testing (NAT) and B. microti antibody testing. A fully automated prototype B. microti antibody test was developed on the ARCHITECT instrument. The specificity was determined to be 99.98% in volunteer blood donors (n=28,740) from areas considered as low endemic for B. microti The sensitivity of the prototype test was studied in experimentally-infected macaques; a total of 128 samples were detected compared to 125 with the indirect fluorescent antibody test (IFA), additionally, 83 (89.2%) of the PCR positive samples were detected compared to 81 (87.1%) using the IFA test. All PCR positive samples that tested negative in the prototype antibody test were pre-seroconversion period samples. Following seroconversion, periods of intermittent parasitemia occurred; 17 PCR negative samples drawn in-between PCR positive bleed dates, tested positive both by the prototype test (robust reactivity) and IFA (marginal reactivity) prior to the administration of therapeutic drugs, indicating that the PCR test failed to detect samples from persistently infected macaques. The prototype assay detected 56 of 58 (96.6%) human subjects diagnosed with clinical babesiosis by both PCR and IFA testing. Overall, the prototype anti-babesia assay provides a highly sensitive and specific test for the diagnosis of B. microti infection. While PCR is preferred for detection of window period parasitemia, antibody tests detect infected subjects during periods of low level parasitemia. Copyright © 2018 Cheng et al.

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

PubMed

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

2016-10-01

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

Evaluation of a monoclonal antibody-based latex agglutination test for diagnosis of cryptococcosis: comparison with two tests using polyclonal antibodies.

PubMed Central

Temstet, A; Roux, P; Poirot, J L; Ronin, O; Dromer, F

1992-01-01

Cryptococcal antigen detection has become a routine biological test performed for patients with AIDS. The poor prognosis of cryptococcosis explains the need for reliable tests. We evaluated the performances of a newly commercialized agglutination test that uses a monoclonal antibody specific for cryptococcal capsular polysaccharide (Pastorex Cryptococcus; Sanofi-Diagnostics Pasteur, Marnes-la-Coquette, France) and compared them with those of tests that use polyclonal immune sera (Cryptococcal Antigen Latex Agglutination System, Meridian Diagnostics, Inc., Cincinnati, Ohio; and Crypto-LA, International Biological Labs Inc., Cranbury, N.J.). The sensitivities and specificities of the tests were compared by using purified polysaccharides and yeast suspensions. Clinical specimens (131 serum samples, 41 cerebrospinal fluid samples, 34 urine samples, and 19 bronchoalveolar lavage samples) from 87 human immunodeficiency virus-positive subjects with (40 patients) and without (47 patients) culture-proven cryptococcosis were retrospectively tested during a blinded study. The effect of pronase treatment of samples was assessed for Pastorex Cryptococcus and the Cryptococcal Antigen Latex Agglutination System, and the antigen titers were compared. Our results show that (i) during the screening, concordance among the three tests was 97%; (ii) the use of pronase enhanced both the sensitivities and specificities of the Pastorex Cryptococcus test; (iii) titers agreed for 67% of the cerebrospinal fluid samples and 60% of the serum samples; and (iv) cryptococcosis was detected equally well with Pastorex Cryptococcus and with the other tests, whatever the infecting serotype (A, B, or D). The meaning of in vitro sensitivity and the relationship between titers and sensitivity are discussed. The results show that Pastorex Cryptococcus is a rapid and reliable test for the detection of cryptococcal antigen in body fluids and suggest that kits cannot be used interchangeably to monitor antigen titers in patients. PMID:1400951

Type I error probabilities based on design-stage strategies with applications to noninferiority trials.

PubMed

Rothmann, Mark

2005-01-01

When testing the equality of means from two different populations, a t-test or large sample normal test tend to be performed. For these tests, when the sample size or design for the second sample is dependent on the results of the first sample, the type I error probability is altered for each specific possibility in the null hypothesis. We will examine the impact on the type I error probabilities for two confidence interval procedures and procedures using test statistics when the design for the second sample or experiment is dependent on the results from the first sample or experiment (or series of experiments). Ways for controlling a desired maximum type I error probability or a desired type I error rate will be discussed. Results are applied to the setting of noninferiority comparisons in active controlled trials where the use of a placebo is unethical.

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

27 CFR 19.749 - Samples.

Code of Federal Regulations, 2011 CFR

2011-04-01

... Samples. The following rules apply to the testing and analysis of samples of spirits and fuel alcohol for purposes of this subpart: (a) A proprietor may take samples of spirits and fuel alcohol for on-site testing and analysis at the proprietor's alcohol fuel plant; (b) A proprietor may not remove samples of...

40 CFR 86.1845-01 - Manufacturer in-use verification testing requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... of test vehicles in the sample comply with the sample size requirements of this section. Any post... vehicles, light-duty trucks, and complete heavy-duty vehicles shall test, or cause to have tested a...) Low mileage testing. [Reserved] (c) High-mileage testing—(1) Test groups. Testing must be conducted...

40 CFR 86.1845-01 - Manufacturer in-use verification testing requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... of test vehicles in the sample comply with the sample size requirements of this section. Any post... vehicles, light-duty trucks, and complete heavy-duty vehicles shall test, or cause to have tested a...) Low mileage testing. [Reserved] (c) High-mileage testing—(1) Test groups. Testing must be conducted...

40 CFR 86.1845-01 - Manufacturer in-use verification testing requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... of test vehicles in the sample comply with the sample size requirements of this section. Any post... vehicles, light-duty trucks, and complete heavy-duty vehicles shall test, or cause to have tested a...) Low mileage testing. [Reserved] (c) High-mileage testing—(1) Test groups. Testing must be conducted...

40 CFR 86.1845-01 - Manufacturer in-use verification testing requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

... of test vehicles in the sample comply with the sample size requirements of this section. Any post... vehicles, light-duty trucks, and complete heavy-duty vehicles shall test, or cause to have tested a...) Low mileage testing. [Reserved] (c) High-mileage testing—(1) Test groups. Testing must be conducted...

Apparatus for testing skin samples or the like

DOEpatents

Holland, J.M.

1982-08-31

An apparatus for testing the permeability of living skin samples has a flat base with a plurality of sample-holding cavities formed in its upper surface, the samples being placed in counterbores in the cavities with the epidermis uppermost. O-rings of Teflon washers are respectively placed on the samples and a flat cover is connected to the base to press the rings against the upper surfaces of the samples. Media to maintain tissue viability and recovery of metabolites is introduced into the lower portion of the sample-holding cavities through passages in the base. Test materials are introduced through holes in the cover plate after assembly of the chamber.

Formal Functional Test Designs: Bridging the Gap Between Test Requirements and Test Specifications

NASA Technical Reports Server (NTRS)

Hops, Jonathan

1993-01-01

This presentation describes the testing life cycle, the purpose of the test design phase, and test design methods and gives an example application. Also included is a description of Test Representation Language (TRL), a summary of the language, and an example of an application of TRL. A sample test requirement and sample test design are included.

Synthesizing Information From Language Samples and Standardized Tests in School-Age Bilingual Assessment

PubMed Central

Pham, Giang

2017-01-01

Purpose Although language samples and standardized tests are regularly used in assessment, few studies provide clinical guidance on how to synthesize information from these testing tools. This study extends previous work on the relations between tests and language samples to a new population—school-age bilingual speakers with primary language impairment—and considers the clinical implications for bilingual assessment. Method Fifty-one bilingual children with primary language impairment completed narrative language samples and standardized language tests in English and Spanish. Children were separated into younger (ages 5;6 [years;months]–8;11) and older (ages 9;0–11;2) groups. Analysis included correlations with age and partial correlations between language sample measures and test scores in each language. Results Within the younger group, positive correlations with large effect sizes indicated convergence between test scores and microstructural language sample measures in both Spanish and English. There were minimal correlations in the older group for either language. Age related to English but not Spanish measures. Conclusions Tests and language samples complement each other in assessment. Wordless picture-book narratives may be more appropriate for ages 5–8 than for older children. We discuss clinical implications, including a case example of a bilingual child with primary language impairment, to illustrate how to synthesize information from these tools in assessment. PMID:28055056

Performance Tested Method multiple laboratory validation study of ELISA-based assays for the detection of peanuts in food.

PubMed

Park, Douglas L; Coates, Scott; Brewer, Vickery A; Garber, Eric A E; Abouzied, Mohamed; Johnson, Kurt; Ritter, Bruce; McKenzie, Deborah

2005-01-01

Performance Tested Method multiple laboratory validations for the detection of peanut protein in 4 different food matrixes were conducted under the auspices of the AOAC Research Institute. In this blind study, 3 commercially available ELISA test kits were validated: Neogen Veratox for Peanut, R-Biopharm RIDASCREEN FAST Peanut, and Tepnel BioKits for Peanut Assay. The food matrixes used were breakfast cereal, cookies, ice cream, and milk chocolate spiked at 0 and 5 ppm peanut. Analyses of the samples were conducted by laboratories representing industry and international and U.S governmental agencies. All 3 commercial test kits successfully identified spiked and peanut-free samples. The validation study required 60 analyses on test samples at the target level 5 microg peanut/g food and 60 analyses at a peanut-free level, which was designed to ensure that the lower 95% confidence limit for the sensitivity and specificity would not be <90%. The probability that a test sample contains an allergen given a prevalence rate of 5% and a positive test result using a single test kit analysis with 95% sensitivity and 95% specificity, which was demonstrated for these test kits, would be 50%. When 2 test kits are run simultaneously on all samples, the probability becomes 95%. It is therefore recommended that all field samples be analyzed with at least 2 of the validated kits.

Chemical analysis of water samples and geophysical logs from cored test holes drilled in the central Oklahoma Aquifer, Oklahoma

USGS Publications Warehouse

Schlottmann, Jamie L.; Funkhouser, Ron A.

1991-01-01

Chemical analyses of water from eight test holes and geophysical logs for nine test holes drilled in the Central Oklahoma aquifer are presented. The test holes were drilled to investigate local occurrences of potentially toxic, naturally occurring trace substances in ground water. These trace substances include arsenic, chromium, selenium, residual alpha-particle activities, and uranium. Eight of the nine test holes were drilled near wells known to contain large concentrations of one or more of the naturally occurring trace substances. One test hole was drilled in an area known to have only small concentrations of any of the naturally occurring trace substances.Water samples were collected from one to eight individual sandstone layers within each test hole. A total of 28 water samples, including four duplicate samples, were collected. The temperature, pH, specific conductance, alkalinity, and dissolved-oxygen concentrations were measured at the sample site. Laboratory determinations included major ions, nutrients, dissolved organic carbon, and trace elements (aluminum, arsenic, barium, beryllium, boron, cadmium, chromium, hexavalent chromium, cobalt, copper, iron, lead, lithium, manganese, mercury, molybdenum, nickel, selenium, silver, strontium, vanadium and zinc). Radionuclide activities and stable isotope (5 values also were determined, including: gross-alpha-particle activity, gross-beta-particle activity, radium-226, radium-228, radon-222, uranium-234, uranium-235, uranium-238, total uranium, carbon-13/carbon-12, deuterium/hydrogen-1, oxygen-18/oxygen-16, and sulfur-34/sulfur-32. Additional analyses of arsenic and selenium species are presented for selected samples as well as analyses of density and iodine for two samples, tritium for three samples, and carbon-14 for one sample.Geophysical logs for most test holes include caliper, neutron, gamma-gamma, natural-gamma logs, spontaneous potential, long- and short-normal resistivity, and single-point resistance. Logs for test-hole NOTS 7 do not include long- and short-normal resistivity, spontaneous-potential, or single-point resistivity. Logs for test-hole NOTS 7A include only caliper and natural-gamma logs.

49 CFR 178.606 - Stacking test.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 3 2013-10-01 2013-10-01 false Stacking test. 178.606 Section 178.606... Packagings and Packages § 178.606 Stacking test. (a) General. All packaging design types other than bags must be subjected to a stacking test. (b) Number of test samples. Three test samples are required for each...

Routine screening of blood donations at Qingdao central blood bank, China, for hepatitis B virus (HBV) DNA with a real-time, multiplex nucleic acid test for HBV, hepatitis C virus, and human immunodeficiency virus Types 1 and 2.

PubMed

Yang, Zhongsi; Xu, Lei; Liu, Li; Feng, Qiuxia; Zhang, Longmu; Ma, Weijuan; Saldanha, John; Wang, Mingmin; Zhao, Lin

2013-10-01

The Roche cobas TaqScreen MPX test was used to evaluate the rate of hepatitis B surface antigen (HBsAg)-negative donations that were hepatitis B virus (HBV) DNA reactive from June 2010 to January 2011 in Qingdao, China. HBsAg-negative samples from 65,800 voluntary blood donors were tested with the cobas TaqScreen MPX test in pools of 6 on the Roche cobas s 201 blood screening platform. Samples positive for HBV DNA and negative for HBsAg were quantitated with the Roche COBAS AmpliPrep/COBAS TaqMan HBV test. In addition, serologic tests for HBsAg, hepatitis B surface antibody, anti-hepatitis B core antigen (anti-HBc), anti-hepatitis B e antigen (anti-HBe), and hepatitis B e antigen (HBe) were done using the Roche electrochemiluminescence immunoassay. A total of 80 nucleic acid amplification technology (NAT) test-reactive pools were identified and 59 pools (74%) resolved to a reactive sample. All samples were HBV DNA reactive and the viral load in each sample was quantitated. The viral loads of the samples ranged from less than 20 to 34,600 IU/mL; 13 samples (22%) had viral loads of more than 20 IU/mL, 27 samples (45.8%) had viral loads of less than 20 IU/mL, and 19 samples (32.2%) had undetectable viral loads. Of the 59 NAT-reactive samples, 40 (67.8%) were anti-HBc positive. Fifteen of the 59 samples could not be confirmed as NAT reactive either by an alternative NAT test or by serology. The HBV NAT yield in blood donors in Qingdao is 0.06% (38/65,800). This study confirmed the value of NAT for interdicting HBV-positive donations and preventing transfusion-transmitted HBV infections. © 2013 American Association of Blood Banks.

75 FR 43045 - Pistachios Grown in California, Arizona, and New Mexico; Modification of the Aflatoxin Regulations

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-23

.... SUMMARY: This rule modifies the aflatoxin sampling and testing regulations currently prescribed under the... Administrative Committee for Pistachios (Committee). This rule streamlines the aflatoxin sampling and testing... by providing a uniform and consistent aflatoxin sampling and testing procedure for pistachios shipped...

46 CFR 161.006-5 - Sampling, inspections and tests.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 6 2011-10-01 2011-10-01 false Sampling, inspections and tests. 161.006-5 Section 161.006-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) EQUIPMENT, CONSTRUCTION, AND... Vessels § 161.006-5 Sampling, inspections and tests. (a) General. Motor lifeboat searchlights specified by...

46 CFR 161.006-5 - Sampling, inspections and tests.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 6 2010-10-01 2010-10-01 false Sampling, inspections and tests. 161.006-5 Section 161.006-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) EQUIPMENT, CONSTRUCTION, AND... Vessels § 161.006-5 Sampling, inspections and tests. (a) General. Motor lifeboat searchlights specified by...

7 CFR 29.426 - Collection of pesticide test samples.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 2 2013-01-01 2013-01-01 false Collection of pesticide test samples. 29.426 Section... CONTAINER REGULATIONS TOBACCO INSPECTION Regulations Miscellaneous § 29.426 Collection of pesticide test samples. Any lot of tobacco not certified by the importer as being free of prohibited pesticide residues...

7 CFR 29.426 - Collection of pesticide test samples.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 2 2011-01-01 2011-01-01 false Collection of pesticide test samples. 29.426 Section... CONTAINER REGULATIONS TOBACCO INSPECTION Regulations Miscellaneous § 29.426 Collection of pesticide test samples. Any lot of tobacco not certified by the importer as being free of prohibited pesticide residues...

7 CFR 29.426 - Collection of pesticide test samples.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 2 2012-01-01 2012-01-01 false Collection of pesticide test samples. 29.426 Section... CONTAINER REGULATIONS TOBACCO INSPECTION Regulations Miscellaneous § 29.426 Collection of pesticide test samples. Any lot of tobacco not certified by the importer as being free of prohibited pesticide residues...

7 CFR 29.426 - Collection of pesticide test samples.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 2 2014-01-01 2014-01-01 false Collection of pesticide test samples. 29.426 Section... CONTAINER REGULATIONS TOBACCO INSPECTION Regulations Miscellaneous § 29.426 Collection of pesticide test samples. Any lot of tobacco not certified by the importer as being free of prohibited pesticide residues...

7 CFR 29.426 - Collection of pesticide test samples.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Collection of pesticide test samples. 29.426 Section... CONTAINER REGULATIONS TOBACCO INSPECTION Regulations Miscellaneous § 29.426 Collection of pesticide test samples. Any lot of tobacco not certified by the importer as being free of prohibited pesticide residues...

46 CFR 164.006-4 - Inspection and testing.

Code of Federal Regulations, 2013 CFR

2013-10-01

... attachments shall be incorporated in the samples. Each sample shall be heated in a furnace whose temperature... minutes—60 percent light transmission. 60 minutes—50 percent light transmission. (c) Fire resistance and integrity tests. (1) A sample of each thickness submitted shall be tested for fire resistance and integrity...

46 CFR 164.006-4 - Inspection and testing.

Code of Federal Regulations, 2012 CFR

2012-10-01

... attachments shall be incorporated in the samples. Each sample shall be heated in a furnace whose temperature... minutes—60 percent light transmission. 60 minutes—50 percent light transmission. (c) Fire resistance and integrity tests. (1) A sample of each thickness submitted shall be tested for fire resistance and integrity...

46 CFR 164.006-4 - Inspection and testing.

Code of Federal Regulations, 2011 CFR

2011-10-01

... attachments shall be incorporated in the samples. Each sample shall be heated in a furnace whose temperature... minutes—60 percent light transmission. 60 minutes—50 percent light transmission. (c) Fire resistance and integrity tests. (1) A sample of each thickness submitted shall be tested for fire resistance and integrity...

46 CFR 164.006-4 - Inspection and testing.

Code of Federal Regulations, 2014 CFR

2014-10-01

... attachments shall be incorporated in the samples. Each sample shall be heated in a furnace whose temperature... minutes—60 percent light transmission. 60 minutes—50 percent light transmission. (c) Fire resistance and integrity tests. (1) A sample of each thickness submitted shall be tested for fire resistance and integrity...

Journal: A Review of Some Tracer-Test Design Equations for Tracer-Mass Estimation and Sample Collection Frequency

EPA Science Inventory

Determination of necessary tracer mass, initial sample-collection time, and subsequent sample-collection frequency are the three most difficult aspects to estimate for a proposed tracer test prior to conducting the tracer test. To facilitate tracer-mass estimation, 33 mass-estima...

7 CFR 28.952 - Testing of samples.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Testing of samples. 28.952 Section 28.952 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... processing tests of the properties of cotton samples and report the results thereof to the persons from whom...

Credit Building in IDA Programs: Early Findings of a Longitudinal Study

ERIC Educational Resources Information Center

Birkenmaier, Julie; Curley, Jami; Kelly, Patrick

2012-01-01

Objective: This article reports on the impact of the Individual Development Account (IDA) program on credit. Method: Using a convenience sample of IDA participants (N = 165), data were analyzed using paired sample "t" tests, independent sample "t" test, one-way analysis of variance, Mann-Whitney "U" Tests, and…

Statistical Analysis Techniques for Small Sample Sizes

NASA Technical Reports Server (NTRS)

Navard, S. E.

1984-01-01

The small sample sizes problem which is encountered when dealing with analysis of space-flight data is examined. Because of such a amount of data available, careful analyses are essential to extract the maximum amount of information with acceptable accuracy. Statistical analysis of small samples is described. The background material necessary for understanding statistical hypothesis testing is outlined and the various tests which can be done on small samples are explained. Emphasis is on the underlying assumptions of each test and on considerations needed to choose the most appropriate test for a given type of analysis.

Microbial ecology measurement system

NASA Technical Reports Server (NTRS)

1972-01-01

The sensitivity and potential rapidity of the PIA test that was demonstrated during the feasibility study warranted continuing the effort to examine the possibility of adapting this test to an automated procedure that could be used during manned missions. The effort during this program has optimized the test conditions for two important respiratory pathogens, influenza virus and Mycoplasma pneumoniae, developed a laboratory model automated detection system, and investigated a group antigen concept for virus detection. Preliminary tests on the handling of oropharygeal clinical samples for PIA testing were performed using the adenovirus system. The results obtained indicated that the PIA signal is reduced in positive samples and is increased in negative samples. Treatment with cysteine appeared to reduce nonspecific agglutination in negative samples but did not maintain the signal in positive samples.

Identification of fecal contamination sources in water using host-associated markers.

PubMed

Krentz, Corinne A; Prystajecky, Natalie; Isaac-Renton, Judith

2013-03-01

In British Columbia, Canada, drinking water is tested for total coliforms and Escherichia coli, but there is currently no routine follow-up testing to investigate fecal contamination sources in samples that test positive for indicator bacteria. Reliable microbial source tracking (MST) tools to rapidly test water samples for multiple fecal contamination markers simultaneously are currently lacking. The objectives of this study were (i) to develop a qualitative MST tool to identify fecal contamination from different host groups, and (ii) to evaluate the MST tool using water samples with evidence of fecal contamination. Singleplex and multiplex polymerase chain reaction (PCR) were used to test (i) water from polluted sites and (ii) raw and drinking water samples for presence of bacterial genetic markers associated with feces from humans, cattle, seagulls, pigs, chickens, and geese. The multiplex MST assay correctly identified suspected contamination sources in contaminated waterways, demonstrating that this test may have utility for heavily contaminated sites. Most raw and drinking water samples analyzed using singleplex PCR contained at least one host-associated marker. Singleplex PCR was capable of detecting host-associated markers in small sample volumes and is therefore a promising tool to further analyze water samples submitted for routine testing and provide information useful for water quality management.

On sample size of the kruskal-wallis test with application to a mouse peritoneal cavity study.

PubMed

Fan, Chunpeng; Zhang, Donghui; Zhang, Cun-Hui

2011-03-01

As the nonparametric generalization of the one-way analysis of variance model, the Kruskal-Wallis test applies when the goal is to test the difference between multiple samples and the underlying population distributions are nonnormal or unknown. Although the Kruskal-Wallis test has been widely used for data analysis, power and sample size methods for this test have been investigated to a much lesser extent. This article proposes new power and sample size calculation methods for the Kruskal-Wallis test based on the pilot study in either a completely nonparametric model or a semiparametric location model. No assumption is made on the shape of the underlying population distributions. Simulation results show that, in terms of sample size calculation for the Kruskal-Wallis test, the proposed methods are more reliable and preferable to some more traditional methods. A mouse peritoneal cavity study is used to demonstrate the application of the methods. © 2010, The International Biometric Society.

Performance of OncoE6 cervical test with collection methods enabling self-sampling.

PubMed

Krings, Amrei; Dückelmann, Anna M; Moser, Lutz; Gollrad, Johannes; Wiegerinck, Maarten; Schweizer, Johannes; Kaufmann, Andreas M

2018-05-21

The paradigm shift from cytological screening to Human Papillomavirus (HPV)-based screening for cervical cancer allows the introduction of new technologies in sample collection and diagnostics. The OncoE6™ Cervical Test (OncoE6 Test) is a rapid, easy-to-use lateral flow method detecting HPV16/18 E6 oncoproteins that has proven to detect high-grade cervical lesions with high specificity. If compatible with self-collection samples, this technology might allow for decentralized screening of hard-to-reach populations. For technical validation, cervicovaginal lavages were collected from 20 patients with confirmed HPV16+ or HPV18+ invasive cervical cancer. Cervical smears were collected by polyester-tipped swabs and cytobrushes. All samples were applied to the OncoE6 Test and cytobrush samples additionally genotyped. Lavage, swab, and cytobrush revealed concordant outcome in 18/20 samples. HPV types corresponded with the HPV genotyping by GP5+/6+ PCR analyses. Due to a rare mutation found in the E6 antibody binding site one sample was not detected, another sample had very low cellularity. Overall, vaginal lavages are technically adequate for the OncoE6 Test. Combining self-sampling with oncoprotein rapid testing to detect women with highest risk for severe dysplasia or cancer may allow for secondary cancer prevention in settings where other screening modalities were unsuccessful to date.

Hematology and pathology devices; reclassification; restricted devices; OTC test sample collection systems for drugs of abuse testing. Food and Drug Administration, HHS. Final rule.

PubMed

2000-04-07

The Food and Drug Administration (FDA) is reclassifying over-the-counter (OTC) test sample collection systems for drugs of abuse testing from class III (premarket approval) into class I (general controls) and exempting them from premarket notification (510(k)) and current good manufacturing practice (CGMP) requirements. FDA is also designating OTC test sample collection systems for drugs of abuse testing as restricted devices under the Federal Food, Drug, and Cosmetic Act (the act) and establishing restrictions intended to assure consumers that: The underlying laboratory test(s) are accurate and reliable; the laboratory performing the test(s) has adequate expertise and competency; and the product has adequate labeling and methods of communicating test results to consumers. Finally, FDA is adding a conforming amendment to the existing classification regulation for specimen transport and storage containers to clarify that it does not apply to specimen transport and storage containers that are part of an OTC test sample collection system for the purpose of testing for the presence of drugs of abuse or their metabolites in a laboratory.

Stainless Steel to Titanium Bimetallic Transitions

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

Kaluzny, J. A.; Grimm, C.; Passarelli, D.

In order to use stainless steel piping in an LCLS-II (Linac Coherent Light Source Upgrade) cryomodule, stainless steel to titanium bimetallic transitions are needed to connect the stainless steel piping to the titanium cavity helium vessel. Explosion bonded stainless steel to titanium transition pieces and bimetallic transition material samples have been tested. A sample transition tube was subjected to tests and x-ray examinations between tests. Samples of the bonded joint material were impact and tensile tested at room temperature as well as liquid helium temperature. The joint has been used successfully in horizontal tests of LCLS-II cavity helium vessels andmore » is planned to be used in LCLS-II cryomodules. Results of material sample and transition tube tests will be presented.« less

Characterization of Friction Joints Subjected to High Levels of Random Vibration

NASA Technical Reports Server (NTRS)

deSantos, Omar; MacNeal, Paul

2012-01-01

This paper describes the test program in detail including test sample description, test procedures, and vibration test results of multiple test samples. The material pairs used in the experiment were Aluminum-Aluminum, Aluminum- Dicronite coated Aluminum, and Aluminum-Plasmadize coated Aluminum. Levels of vibration for each set of twelve samples of each material pairing were gradually increased until all samples experienced substantial displacement. Data was collected on 1) acceleration in all three axes, 2) relative static displacement between vibration runs utilizing photogrammetry techniques, and 3) surface galling and contaminant generation. This data was used to estimate the values of static friction during random vibratory motion when "stick-slip" occurs and compare these to static friction coefficients measured before and after vibration testing.

Soil contamination in landfills: a case study of a landfill in Czech Republic

NASA Astrophysics Data System (ADS)

Adamcová, D.; Vaverková, M. D.; Bartoň, S.; Havlíček, Z.; Břoušková, E.

2016-02-01

A phytotoxicity test was determined to assess ecotoxicity of landfill soil. Sinapis alba L. was used as a bioindicator of heavy metals. Soil samples 1-8, which were taken from the landfill body, edge of the landfill body, and its vicinity meet the limits for heavy metals Co, Cd, Pb, and Zn specified in the applicable legislation. Hg and Mn threshold values are not established in legislation, but values have been determined for the needs of the landfill operator. For heavy metals Cr, Cu, and Ni sample 2 exceeded the threshold values, which attained the highest values of all the samples tested for Cr, Cu, and Ni. For Cr and Ni the values were several times higher than values of the other samples. The second highest values for Cr, Cu, and Ni showed sample 6 and 7. Both samples exceeded the set limits. An increase in plant biomass was observed in plants growing on plates with soil samples, but no changes in appearance, slow growth, or necrotic lesions appeared. Ecotoxicity tests show that tested soils (concentration of 50 %) collected from the landfill body, edge of the landfill body, and its vicinity reach high percentage values of germination capacity of seeds of Sinapis alba L. (101-137 %). At a concentration of 25 %, tested soil samples exhibit lower values of germination capacity - in particular samples 3 to 8 - yet the seed germination capacity in all eight samples of tested soils ranges between 86 and 137 %.

Soil contaminations in landfill: a case study of the landfill in Czech Republic

NASA Astrophysics Data System (ADS)

Adamcová, D.; Vaverková, M. D.; Bartoň, S.; Havlíček, Z.; Břoušková, E.

2015-10-01

Phytotoxicity test was determined to assess ecotoxicity of landfill soil. Sinapis alba L. was used as heavy metals bioindicator. Soil samples 1-8, which were taken from the landfill body, edge of the landfill body and its vicinity meet the limits for heavy metals Co, Cd, Pb, and Zn specified in the applicable legislation. Hg and Mn threshold values are not established in legislation, but values have been determined for the needs of the landfill operator. For heavy metals Cr, Cu, and Ni sample 2 exceeded the threshold values, which attained the highest values of all the samples tested for Cr, Cu and Ni. For Cr and Ni the values were several times higher than values of the other samples. The second highest values for Cr, Cu, and Ni showed sample 6 and 7. Both samples exceeded the set limits. An increase in plant biomass was observed in plants growing on plates with soil samples, but no changes in appearance, slow growth or necrotic lesions appeared. Ecotoxicity tests show that tested soils (concentration of 50 %) collected from the landfill body, edge of the landfill body and its vicinity reach high percentage values of germination capacity of seeds of Sinapis alba L. (101-137 %). At a concentration of 25 %, tested soil samples exhibit lower values of germination capacity; in particular samples 3 to 8, yet the seed germination capacity in all 8 samples of tested soils range between 86 and 137 %.

Brief Report: Impact of Early Antiretroviral Therapy on the Performance of HIV Rapid Tests and HIV Incidence Assays.

PubMed

Fogel, Jessica M; Piwowar-Manning, Estelle; Debevec, Barbara; Walsky, Tamara; Schlusser, Katherine; Laeyendecker, Oliver; Wilson, Ethan A; McCauley, Marybeth; Gamble, Theresa; Tegha, Gerald; Soko, Dean; Kumwenda, Johnstone; Hosseinipour, Mina C; Chen, Ying Q; Cohen, Myron S; Eshleman, Susan H

2017-08-01

Antiretroviral therapy (ART) can downregulate antibody responses to HIV infection. We evaluated the impact of early vs. delayed ART on the performance of HIV diagnostic and incidence assays. Samples were obtained from 207 participants in the HPTN 052 trial, who were stably suppressed on ART for ≥4 years [Malawi sites; pre-ART CD4 cell count 350-550 cells/mm (early ART arm, N = 180) or <250 cells/mm or an AIDS-defining illness (delayed ART arm, N = 27)]. Samples were tested with 2 HIV rapid tests and 2 HIV incidence assays; selected samples were also tested with two fourth-generation immunoassays and a Western blot (WB) assay. A pre-ART sample was analyzed if the follow-up sample had a false-negative or weakly-reactive rapid test result, or had an incidence assay result indicative of recent infection (false-recent result). Ten (4.8%) samples had a nonreactive or weakly-reactive rapid test result (7/180 early ART arm, 3/27 delayed ART arm, P = 0.13); one sample had nonreactive fourth-generation assay results and 3 had indeterminate WBs. Forty (18.9%) samples had a false-recent incidence assay result; 16 (7.8%) had false-recent results with both incidence assays. Baseline samples had stronger rapid test and WB bands, higher fourth-generation assay signal-to-cutoff values, and fewer HIV incidence assay results indicative of recent infection. False-negative/weakly-reactive HIV rapid tests and false-recent HIV incidence assay results were observed in virally-suppressed individuals, regardless of pre-ART CD4 cell count. Downregulation of the antibody response to HIV infection in the setting of ART may impact population-level surveys of HIV prevalence and incidence.

Autoverification process improvement by Six Sigma approach: Clinical chemistry & immunoassay.

PubMed

Randell, Edward W; Short, Garry; Lee, Natasha; Beresford, Allison; Spencer, Margaret; Kennell, Marina; Moores, Zoë; Parry, David

2018-05-01

This study examines effectiveness of a project to enhance an autoverification (AV) system through application of Six Sigma (DMAIC) process improvement strategies. Similar AV systems set up at three sites underwent examination and modification to produce improved systems while monitoring proportions of samples autoverified, the time required for manual review and verification, sample processing time, and examining characteristics of tests not autoverified. This information was used to identify areas for improvement and monitor the impact of changes. Use of reference range based criteria had the greatest impact on the proportion of tests autoverified. To improve AV process, reference range based criteria was replaced with extreme value limits based on a 99.5% test result interval, delta check criteria were broadened, and new specimen consistency rules were implemented. Decision guidance tools were also developed to assist staff using the AV system. The mean proportion of tests and samples autoverified improved from <62% for samples and <80% for tests, to >90% for samples and >95% for tests across all three sites. The new AV system significantly decreased turn-around time and total sample review time (to about a third), however, time spent for manual review of held samples almost tripled. There was no evidence of compromise to the quality of testing process and <1% of samples held for exceeding delta check or extreme limits required corrective action. The Six Sigma (DMAIC) process improvement methodology was successfully applied to AV systems resulting in an increase in overall test and sample AV by >90%, improved turn-around time, reduced time for manual verification, and with no obvious compromise to quality or error detection. Copyright © 2018 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

[User's requests (from a practitioner's perspective)].

PubMed

Ohnishi, T

1997-08-01

As a practitioner, I have to rely on outside clinical laboratories and affiliated hospitals to perform laboratory tests. In this abstract, I describe specific problems I have encountered with third-party laboratories, and propose solutions for these problems to optimize use of laboratory tests. BLOOD TESTS: The most frequent problem in ordering blood tests is the lack of detailed information regarding sampling conditions. I often have to call laboratories to check whether the sample should be serum or plasma, what volume is needed, whether the sample should be cooled, etc. I propose that clinical laboratories should provide practitioners' manuals that describe specific sampling information. Most laboratories do not keep the data from ultrasonographic tests. The lack of these is most problematic when test results are interpreted differently by laboratories and by practitioners. Retaining the data would also help private laboratories improve the quality of the test by enabling them to compare their interpretations with others'. ANNUAL MEDICAL SCREENING: Even if an abnormal finding is detected at medical screening clinics, the final diagnosis is usually not sent back to the screening facilities. This is highly recommended to establish an official system that mediates the feedback to screening centers. MRI: Due to miscommunication between practitioners and radiologists, the test is sometimes performed inappropriately. A thorough consultation should occur before the test to clarify specific goals for each patient. PATHOLOGICAL TESTS: Interpretation of results is often inconsistent among laboratories. Independent clinical laboratories tend to report results without indicating sample problems, while pathology departments at affiliated hospitals tend to emphasize sample problems instead of diagnosis or suggesting ways to improve sample quality. Mutual communication among laboratories would help standardize the quality of pathological tests.

Evaluation of EMIT and RIA high volume test procedures for THC metabolites in urine utilizing GC/MS confirmation.

PubMed

Abercrombie, M L; Jewell, J S

1986-01-01

Results of EMIT, Abuscreen RIA, and GC/MS tests for THC metabolites in a high volume random urinalysis program are compared. Samples were field tested by non-laboratory personnel with an EMIT system using a 100 ng/mL cutoff. Samples were then sent to the Army Forensic Toxicology Drug Testing Laboratory (WRAMC) at Fort Meade, Maryland, where they were tested by RIA (Abuscreen) using a statistical 100 ng/mL cutoff. Confirmations of all RIA positives were accomplished using a GC/MS procedure. EMIT and RIA results agreed for 91% of samples. Data indicated a 4% false positive rate and a 10% false negative rate for EMIT field testing. In a related study, results for samples which tested positive by RIA for THC metabolites using a statistical 100 ng/mL cutoff were compared with results by GC/MS utilizing a 20 ng/mL cutoff for the THCA metabolite. Presence of THCA metabolite was detected in 99.7% of RIA positive samples. No relationship between quantitations determined by the two tests was found.

Static renewal tests using Pimephales promelas (fathead minnows) and Ceriodaphnia dubia (daphnids). Clinch River-Environmental Restoration Program (CR-ERP) study, ambient water toxicity

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

Simbeck, D.J.

1994-12-31

Clinch River-Environmental Restoration Program (CR-ERP) personnel and Tennessee Valley Authority (TVA) personnel conducted a study during the week of January 25--February 1, 1994. The organisms specified for testing were larval fathead minnows, Pimephales promelas, and the daphnid, Ceriodaphnia dubia. Surface water samples were collected from Clinch River Mile 9.0, Poplar Creek Mile 1.0, and Poplar Creek Mile 2.9 on January 24, 26, and 28. Samples were partitioned and provided to the CR-ERP and TVA toxicology laboratories for testing. Exposure of test organisms to these samples resulted in no toxicity (survival or growth) to fathead minnows; however, toxicity to daphnids wasmore » demonstrated in undiluted samples from Poplar Creek Mile 1.0 in testing conducted by TVA based on hypothesis testing of data. Point estimation (IC{sub 25}) analysis of the data, however, showed no toxicity in PCM 1.0 samples. Attachments to this report include: Chain of custody forms -- originals; Toxicity test bench sheets and statistical analyses; Meter calibrations; and Reference toxicant test information.« less

40 CFR 1065.245 - Sample flow meter for batch sampling.

Code of Federal Regulations, 2010 CFR

2010-07-01

... rates or total flow sampled into a batch sampling system over a test interval. You may use the... rates or total raw exhaust flow over a test interval. (b) Component requirements. We recommend that you... averaging Pitot tube, or a hot-wire anemometer. Note that your overall system for measuring sample flow must...

Valid statistical inference methods for a case-control study with missing data.

PubMed

Tian, Guo-Liang; Zhang, Chi; Jiang, Xuejun

2018-04-01

The main objective of this paper is to derive the valid sampling distribution of the observed counts in a case-control study with missing data under the assumption of missing at random by employing the conditional sampling method and the mechanism augmentation method. The proposed sampling distribution, called the case-control sampling distribution, can be used to calculate the standard errors of the maximum likelihood estimates of parameters via the Fisher information matrix and to generate independent samples for constructing small-sample bootstrap confidence intervals. Theoretical comparisons of the new case-control sampling distribution with two existing sampling distributions exhibit a large difference. Simulations are conducted to investigate the influence of the three different sampling distributions on statistical inferences. One finding is that the conclusion by the Wald test for testing independency under the two existing sampling distributions could be completely different (even contradictory) from the Wald test for testing the equality of the success probabilities in control/case groups under the proposed distribution. A real cervical cancer data set is used to illustrate the proposed statistical methods.

Bio-repository of post-clinical test samples at the national cancer center hospital (NCCH) in Tokyo.

PubMed

Furuta, Koh; Yokozawa, Karin; Takada, Takako; Kato, Hoichi

2009-08-01

We established the Bio-repository at the National Cancer Center Hospital in October 2002. The main purpose of this article is to show the importance and usefulness of a bio-repository of post-clinical test samples not only for translational cancer research but also for routine clinical oncology by introducing the experience of setting up such a facility. Our basic concept of a post-clinical test sample is not as left-over waste, but rather as frozen evidence of a patient's pathological condition at a particular point. We can decode, if not all, most of the laboratory data from a post-clinical test sample. As a result, the bio-repository is able to provide not only the samples, but potentially all related laboratory data upon request. The areas of sample coverage are the following: sera after routine blood tests; sera after cross-match tests for transfusion; serum or plasma submitted at a patient's clinically important time period by the physician; and samples collected by the individual investigator. The formats of stored samples are plasma or serum, dried blood spot (DBS) and buffy coat. So far, 150 218 plasmas or sera, 35 253 DBS and 536 buffy coats have been registered for our bio-repository system. We arranged to provide samples to various concerned parties under strict legal and ethical agreements. Although the number of the utilized samples was initially limited, the inquiries for sample utilization are now increasing steadily from both research and clinical sources. Further efforts to increase the benefits of the repository are intended.

Developing a Hypothetical Learning Trajectory for the Sampling Distribution of the Sample Means

NASA Astrophysics Data System (ADS)

Syafriandi

2018-04-01

Special types of probability distribution are sampling distributions that are important in hypothesis testing. The concept of a sampling distribution may well be the key concept in understanding how inferential procedures work. In this paper, we will design a hypothetical learning trajectory (HLT) for the sampling distribution of the sample mean, and we will discuss how the sampling distribution is used in hypothesis testing.

Impact of High Temperature Creep on the Buckling of Axially Compressed Steel Members

NASA Astrophysics Data System (ADS)

Włóka, Agata; Pawłowski, Kamil; Świerzko, Robert

2017-10-01

The paper presents results of the laboratory tests of the impact of creep on the buckling of axially compressed steel members at elevated temperatures. Tests were conducted on samples prepared of normal strength steel (S235JR) and high strength steel (S355J2). Samples were made in the form of a prismatic bar of a rectangular cross section 12 x 30 mm and a length of 500 mm. Support type of the specimens during tests was hinged on both ends. The tests were done at 600, 700 and 800°C. Experiments were carried out at static loads corresponding to values 0,8Ncr,T, 0,9Ncr,T, 1,0Ngr,T, where Ncr,T was theoretical value of Euler’s critical load at given temperature. Short-term creep analyses were performed in the universal testing machine Instron/Satec KN 600 equipped with a furnace for high-temperature testing type SF-16 2230, that enables testing at temperatures up to 1200°C. Temperature of the sample placed inside the furnace was verified and recorded with use of the compactRIO cRIO-9076 controller, equipped with a module for the connection of NI 9211 and K-type thermocouples. The system for the measurement and recording of the temperature of the analysed samples operated in the LabVIEW software environment. To measure lateral and longitudinal displacements LVTD Solatron ACR 100 displacement transducer was used. During the tests, the samples were heated to the given temperature (600, 700 or 800°C) and then subjected to a constant compressive load. During each test, for each sample following data was registered: the temperature on the surface of samples, longitudinal and lateral displacements in the middle of the sample. Basing on the conducted tests it was noted, for both analysed steel types, at the temperature of 800°C, growth of lateral displacements due to creep was very rapid, and tested elements were losing bearing capacity over the period of tens to hundreds of seconds, depending on stress level and the grade of the steel. At a temperature of 700°C growth of lateral displacements was much slower and the total loss of the bearing capacity of tested samples has occurred after 2 to 5 hours. At the temperature of 600°C samples did not show significant increments of lateral displacements at the test duration more than 6 hours, while maintaining throughout the test rectilinear form.

The special case of the 2 × 2 table: asymptotic unconditional McNemar test can be used to estimate sample size even for analysis based on GEE.

PubMed

Borkhoff, Cornelia M; Johnston, Patrick R; Stephens, Derek; Atenafu, Eshetu

2015-07-01

Aligning the method used to estimate sample size with the planned analytic method ensures the sample size needed to achieve the planned power. When using generalized estimating equations (GEE) to analyze a paired binary primary outcome with no covariates, many use an exact McNemar test to calculate sample size. We reviewed the approaches to sample size estimation for paired binary data and compared the sample size estimates on the same numerical examples. We used the hypothesized sample proportions for the 2 × 2 table to calculate the correlation between the marginal proportions to estimate sample size based on GEE. We solved the inside proportions based on the correlation and the marginal proportions to estimate sample size based on exact McNemar, asymptotic unconditional McNemar, and asymptotic conditional McNemar. The asymptotic unconditional McNemar test is a good approximation of GEE method by Pan. The exact McNemar is too conservative and yields unnecessarily large sample size estimates than all other methods. In the special case of a 2 × 2 table, even when a GEE approach to binary logistic regression is the planned analytic method, the asymptotic unconditional McNemar test can be used to estimate sample size. We do not recommend using an exact McNemar test. Copyright © 2015 Elsevier Inc. All rights reserved.

Impact of Different Visual Field Testing Paradigms on Sample Size Requirements for Glaucoma Clinical Trials.

PubMed

Wu, Zhichao; Medeiros, Felipe A

2018-03-20

Visual field testing is an important endpoint in glaucoma clinical trials, and the testing paradigm used can have a significant impact on the sample size requirements. To investigate this, this study included 353 eyes of 247 glaucoma patients seen over a 3-year period to extract real-world visual field rates of change and variability estimates to provide sample size estimates from computer simulations. The clinical trial scenario assumed that a new treatment was added to one of two groups that were both under routine clinical care, with various treatment effects examined. Three different visual field testing paradigms were evaluated: a) evenly spaced testing, b) United Kingdom Glaucoma Treatment Study (UKGTS) follow-up scheme, which adds clustered tests at the beginning and end of follow-up in addition to evenly spaced testing, and c) clustered testing paradigm, with clusters of tests at the beginning and end of the trial period and two intermediary visits. The sample size requirements were reduced by 17-19% and 39-40% using the UKGTS and clustered testing paradigms, respectively, when compared to the evenly spaced approach. These findings highlight how the clustered testing paradigm can substantially reduce sample size requirements and improve the feasibility of future glaucoma clinical trials.

Comparative evaluation of commercially available point-of-care heartworm antigen tests using well-characterized canine plasma samples.

PubMed

Starkey, Lindsay A; Bowles, Joy V; Payton, Mark E; Blagburn, Byron L

2017-11-09

Dirofilaria immitis is a worldwide parasite that is endemic in many parts of the United States. There are many commercial assays available for the detection of D. immitis antigen, one of which was modified and has reentered the market. Our objective was to compare the recently reintroduced Witness® Heartworm (HW) Antigen test Kit (Zoetis, Florham Park, NJ) and the SNAP® Heartworm RT (IDEXX Laboratories, Inc., Westbrook, ME) to the well-based ELISA DiroChek® Heartworm Antigen Test Kit (Zoetis, Florham Park, NJ). Canine plasma samples were either received at the Auburn Diagnostic Parasitology Laboratory from veterinarians submitting samples for additional heartworm testing (n = 100) from 2008 to 2016 or purchased from purpose-bred beagles (n = 50, presumed negative) in 2016. Samples were categorized as "positive," "borderline" or "negative" using our established spectrophotometric cutoff value with the DiroChek® assay when a sample was initially received and processed. Three commercially available heartworm antigen tests (DiroChek®, Witness® HW, and SNAP® RT) were utilized for simultaneous testing of the 150 samples in random order as per their package insert with the addition of spectrophotometric optical density (OD) readings of the DiroChek® assay. Any samples yielding discordant test results between assays were further evaluated by heat treatment of plasma and retesting. Chi-square tests for the equality of proportions were utilized for statistical analyses. Concordant results occurred in 140/150 (93.3%) samples. Discrepant results occurred in 10/150 samples tested (6.6%): 9/10 occurring in the borderline heartworm (HW) category and 1/10 occurring in the negative HW category. The sensitivity and specificity of each test compared to the DiroChek® read by spectrophotometer was similar to what has been reported previously (Witness®: sensitivity 97.0% [94.1-99.4%], specificity 96.4% [95.5-100.0%]; SNAP® RT: sensitivity 90.9% [78.0-100.0%], specificity 98.8% [96.0-100.0%]). There were significant differences detected when comparing the sensitivities of the SNAP® RT and the Witness® HW to the DiroChek® among the 150 total samples (p = 0.003) and the 50 "borderline" samples (p = 0.001). In this study, the sensitivity of the Witness® HW was higher than the sensitivity of the SNAP® RT when compared with the DiroChek® test results prior to heat treatment of samples.

The MISSE 7 Flexural Stress Effects Experiment After 1.5 Years of Wake Space Exposure

NASA Technical Reports Server (NTRS)

Snow, Kate E.; De Groh, Kim K.; Banks, Bruce A.

2017-01-01

Low Earth orbit space environment conditions, including ultraviolet radiation, thermal cycling, and atomic oxygen exposure, can cause degradation of exterior spacecraft materials over time. Radiation and thermal exposure often results in bond- breaking and embrittlement of polymers, reducing mechanical strength and structural integrity. An experiment called the Flexural Stress Effects Experiment (FSEE) was flown with the objective of determining the role of space environmental exposure on the degradation of polymers under flexural stress. The FSEE samples were flown in the wake orientation on the exterior of International Space Station for 1.5 years. Twenty-four samples were flown: 12 bent over a 0.375 in. mandrel and 12 were over a 0.25 in. mandrel. This was designed to simulate flight configurations of insulation blankets on spacecraft. The samples consisted of assorted polyimide and fluorinated polymers with various coatings. Half the samples were designated for bend testing and the other half will be tensile tested. A non-standard bend-test procedure was designed to determine the surface strain at which embrittled polymers crack. All ten samples designated for bend testing have been tested. None of the control samples' polymers cracked, even under surface strains up to 19.7%, although one coating cracked. Of the ten flight samples tested, seven show increased embrittlement through bend-test induced cracking at surface strains from 0.70%to 11.73%. These results show that most of the tested polymers are embrittled due to space exposure, when compared to their control samples. Determination of the extent of space induced embrittlement of polymers is important for designing durable spacecraft.

Clinical biochemistry laboratory rejection rates due to various types of preanalytical errors.

PubMed

Atay, Aysenur; Demir, Leyla; Cuhadar, Serap; Saglam, Gulcan; Unal, Hulya; Aksun, Saliha; Arslan, Banu; Ozkan, Asuman; Sutcu, Recep

2014-01-01

Preanalytical errors, along the process from the beginning of test requests to the admissions of the specimens to the laboratory, cause the rejection of samples. The aim of this study was to better explain the reasons of rejected samples, regarding to their rates in certain test groups in our laboratory. This preliminary study was designed on the rejected samples in one-year period, based on the rates and types of inappropriateness. Test requests and blood samples of clinical chemistry, immunoassay, hematology, glycated hemoglobin, coagulation and erythrocyte sedimentation rate test units were evaluated. Types of inappropriateness were evaluated as follows: improperly labelled samples, hemolysed, clotted specimen, insufficient volume of specimen and total request errors. A total of 5,183,582 test requests from 1,035,743 blood collection tubes were considered. The total rejection rate was 0.65 %. The rejection rate of coagulation group was significantly higher (2.28%) than the other test groups (P < 0.001) including insufficient volume of specimen error rate as 1.38%. Rejection rates of hemolysis, clotted specimen and insufficient volume of sample error were found to be 8%, 24% and 34%, respectively. Total request errors, particularly, for unintelligible requests were 32% of the total for inpatients. The errors were especially attributable to unintelligible requests of inappropriate test requests, improperly labelled samples for inpatients and blood drawing errors especially due to insufficient volume of specimens in a coagulation test group. Further studies should be performed after corrective and preventive actions to detect a possible decrease in rejecting samples.

Method of quantitating dsDNA

DOEpatents

Stark, Peter C.; Kuske, Cheryl R.; Mullen, Kenneth I.

2002-01-01

A method for quantitating dsDNA in an aqueous sample solution containing an unknown amount of dsDNA. A first aqueous test solution containing a known amount of a fluorescent dye-dsDNA complex and at least one fluorescence-attenutating contaminant is prepared. The fluorescence intensity of the test solution is measured. The first test solution is diluted by a known amount to provide a second test solution having a known concentration of dsDNA. The fluorescence intensity of the second test solution is measured. Additional diluted test solutions are similarly prepared until a sufficiently dilute test solution having a known amount of dsDNA is prepared that has a fluorescence intensity that is not attenuated upon further dilution. The value of the maximum absorbance of this solution between 200-900 nanometers (nm), referred to herein as the threshold absorbance, is measured. A sample solution having an unknown amount of dsDNA and an absorbance identical to that of the sufficiently dilute test solution at the same chosen wavelength is prepared. Dye is then added to the sample solution to form the fluorescent dye-dsDNA-complex, after which the fluorescence intensity of the sample solution is measured and the quantity of dsDNA in the sample solution is determined. Once the threshold absorbance of a sample solution obtained from a particular environment has been determined, any similarly prepared sample solution taken from a similar environment and having the same value for the threshold absorbance can be quantified for dsDNA by adding a large excess of dye to the sample solution and measuring its fluorescence intensity.

[Comparison of the Conventional Centrifuged and Filtrated Preparations in Urine Cytology].

PubMed

Sekita, Nobuyuki; Shimosakai, Hirofumi; Nishikawa, Rika; Sato, Hiroaki; Kouno, Hiroyoshi; Fujimura, Masaaki; Mikami, Kazuo

2016-03-01

The urine cytology test is one of the most important tools for the diagnosis of malignant urinary tract tumors. This test is also of great value for predicting malignancy. However, the sensitivity of this test is not high enough to screen for malignant cells. In our laboratory, we were able to attain a high sensitivity of urine cytology tests after changing the preparation method of urine samples. The differences in the cytodiagnosis between the two methods are discussed here. From January 2012 to June 2013, 2,031 urine samples were prepared using the conventional centrifuge method (C method) ; and from September 2013 to March 2015, 2,453 urine samples were prepared using the filtration method (F method) for the cytology test. When the samples included in category 4 or 5, were defined as cytological positive, the sensitivities of this test with samples prepared using the F method were significantly high compared with samples prepared using the C method (72% vs 28%, p＜0.001). The number of cells on the glass slides prepared by the F method was significantly higher than that of the samples prepared by the C method (p＜0.001). After introduction of the F method, the number of f alse negative cases was decreased in the urine cytology test because a larger number of cells was seen and easily detected as atypical or malignant epithelial cells. Therefore, this method has a higher sensitivity than the conventional C method as the sensitivity of urine cytology tests relies partially on the number of cells visualized in the prepared samples.

Application and Comparative Evaluation of Fluorescent Antibody, Immunohistochemistry and Reverse Transcription Polymerase Chain Reaction Tests for the Detection of Rabies Virus Antigen or Nucleic Acid in Brain Samples of Animals Suspected of Rabies in India.

PubMed

Prabhu, K Nithin; Isloor, Shrikrishna; Veeresh, B Hanchinal; Rathnamma, Doddamane; Sharada, R; Das, Lekshmi J; Satyanarayana, M L; Hegde, Nagendra R; Rahman, Sira Abdul

2018-02-28

Accurate and early diagnosis of animal rabies is critical for undertaking public health measures. Whereas the direct fluorescent antibody (DFA) technique is the recommended test, the more convenient, direct rapid immunochemistry test (dRIT), as well as the more sensitive, reverse transcription polymerase chain reaction (RT-PCR), have recently been employed for the laboratory diagnosis of rabies. We compared the three methods on brain samples from domestic (dog, cat, cattle, buffalo, horse, pig and goat) and wild (leopard, wolf and jackal) animals from various parts of India. Of the 257 samples tested, 167 were positive by all the three tests; in addition, 35 of the 36 decomposed samples were positive by RT-PCR. This is the first study in which such large number of animal samples have been subjected to the three tests simultaneously. The results confirm 100% corroboration between DFA and dRIT, buttress the applicability of dRIT in the simple and rapid diagnosis of rabies in animals, and reaffirm the suitability of RT-PCR for samples unfit for testing either by DFA or dRIT.

Quantifying Antimicrobial Resistance at Veal Calf Farms

PubMed Central

Bosman, Angela B.; Wagenaar, Jaap; Stegeman, Arjan; Vernooij, Hans; Mevius, Dik

2012-01-01

This study was performed to determine a sampling strategy to quantify the prevalence of antimicrobial resistance on veal calf farms, based on the variation in antimicrobial resistance within and between calves on five farms. Faecal samples from 50 healthy calves (10 calves/farm) were collected. From each individual sample and one pooled faecal sample per farm, 90 selected Escherichia coli isolates were tested for their resistance against 25 mg/L amoxicillin, 25 mg/L tetracycline, 0.5 mg/L cefotaxime, 0.125 mg/L ciprofloxacin and 8/152 mg/L trimethoprim/sulfamethoxazole (tmp/s) by replica plating. From each faecal sample another 10 selected E. coli isolates were tested for their resistance by broth microdilution as a reference. Logistic regression analysis was performed to compare the odds of testing an isolate resistant between both test methods (replica plating vs. broth microdilution) and to evaluate the effect of pooling faecal samples. Bootstrap analysis was used to investigate the precision of the estimated prevalence of resistance to each antimicrobial obtained by several simulated sampling strategies. Replica plating showed similar odds of E. coli isolates tested resistant compared to broth microdilution, except for ciprofloxacin (OR 0.29, p≤0.05). Pooled samples showed in general lower odds of an isolate being resistant compared to individual samples, although these differences were not significant. Bootstrap analysis showed that within each antimicrobial the various compositions of a pooled sample provided consistent estimates for the mean proportion of resistant isolates. Sampling strategies should be based on the variation in resistance among isolates within faecal samples and between faecal samples, which may vary by antimicrobial. In our study, the optimal sampling strategy from the perspective of precision of the estimated levels of resistance and practicality consists of a pooled faecal sample from 20 individual animals, of which 90 isolates are tested for their susceptibility by replica plating. PMID:22970313

Tube and column agglutination technology for autocontrol testing.

PubMed

Courtney, J E; Vincent, J L; Indrikovs, A J

2001-01-01

The incidence of positive autocontrol test results with column agglutination technology is a concern. This study investigates the incidence and significance of positive autocontrols in the ID Micro Typing System (gel) and the Gamma ReACT (ReACT). The study encompassed a total of 1021 randomly selected samples from patients and 95 samples from donors collected during 1 month. The autocontrol testing was carried out according to the manufacturer's instructions for the column agglutination tests. The tube method was carried out using low-ionic-strength solution (LISS). The direct antiglobulin test (DAT) was performed using the tube method, and further investigated with elution studies if warranted. Seventy-nine patient's samples (7.74%) had a positive autocontrol: the gel test, 72 (91.13%); ReACT, 21 (26.58%); and the tube method, 27 (34.18%). Of the 79 positive autocontrols, 44 samples had a negative DAT. Of the samples with positive DAT results, only one possessed a clinically significant antibody, anti-D. Moreover, the same sample also tested positive in all three methods. Column agglutination techniques have increased sensitivity for a positive autocontrol beyond the conventional tube method. However, ReACT and gel tests differ significantly in their frequency of positives. Investigation of the significance of a positive autocontrol in column agglutination technology when the conventional tube method is also positive is suggested.

46 CFR 164.006-4 - Inspection and testing.

Code of Federal Regulations, 2010 CFR

2010-10-01

... the Coast Guard. (b) Smoke tests. (1) A sample of each thickness submitted shall be tested for smoke... observations shall be made at intervals not greater than five minutes during the one-hour period of test. (2... integrity tests. (1) A sample of each thickness submitted shall be tested for fire resistance and integrity...

A weighted exact test for mutually exclusive mutations in cancer

PubMed Central

Leiserson, Mark D.M.; Reyna, Matthew A.; Raphael, Benjamin J.

2016-01-01

Motivation: The somatic mutations in the pathways that drive cancer development tend to be mutually exclusive across tumors, providing a signal for distinguishing driver mutations from a larger number of random passenger mutations. This mutual exclusivity signal can be confounded by high and highly variable mutation rates across a cohort of samples. Current statistical tests for exclusivity that incorporate both per-gene and per-sample mutational frequencies are computationally expensive and have limited precision. Results: We formulate a weighted exact test for assessing the significance of mutual exclusivity in an arbitrary number of mutational events. Our test conditions on the number of samples with a mutation as well as per-event, per-sample mutation probabilities. We provide a recursive formula to compute P-values for the weighted test exactly as well as a highly accurate and efficient saddlepoint approximation of the test. We use our test to approximate a commonly used permutation test for exclusivity that conditions on per-event, per-sample mutation frequencies. However, our test is more efficient and it recovers more significant results than the permutation test. We use our Weighted Exclusivity Test (WExT) software to analyze hundreds of colorectal and endometrial samples from The Cancer Genome Atlas, which are two cancer types that often have extremely high mutation rates. On both cancer types, the weighted test identifies sets of mutually exclusive mutations in cancer genes with fewer false positives than earlier approaches. Availability and Implementation: See http://compbio.cs.brown.edu/projects/wext for software. Contact: braphael@cs.brown.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27587696

77 FR 58313 - Revisions to the California State Implementation Plan, San Diego County, Antelope Valley and...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-20

..., closures and coils, from graphic arts operations, from the provision of sampling and testing facilities... Provision of Sampling and Revised 03/21/01....... 05/31/01 Testing Facilities. AVAQMD 1168 Adhesive and... District (1) Rule 205, ``Provision of Sampling and Testing Facilities,'' revised on March 21, 2001...

40 CFR 80.1349 - Alternative sampling and testing requirements for importers who import gasoline into the United...

Code of Federal Regulations, 2014 CFR

2014-07-01

... requirements for importers who import gasoline into the United States by truck. 80.1349 Section 80.1349... FUELS AND FUEL ADDITIVES Gasoline Benzene Sampling, Testing and Retention Requirements § 80.1349 Alternative sampling and testing requirements for importers who import gasoline into the United States by...

40 CFR 80.1347 - What are the sampling and testing requirements for refiners and importers?

Code of Federal Regulations, 2014 CFR

2014-07-01

... Benzene Sampling, Testing and Retention Requirements § 80.1347 What are the sampling and testing... benzene requirements of this subpart, except as modified by paragraphs (a)(2), (a)(3) and (a)(4) of this..., 2015, to determine its benzene concentration for compliance with the requirements of this subpart...

Western blotting method (TESAcruzi) as a supplemental test for confirming the presence of anti-Trypanosoma cruzi antibodies in finger prick blood samples from children aged 0-5 years in Brazil.

PubMed

Frade, Amanda Farage; Luquetti, Alejandro O; Prata, Aluísio; Ferreira, Antonio Walter

2011-01-01

Some Latin American countries have plans for total control and/or eradication of Chagas disease by the main vector (Triatoma infestans) and by blood transfusion. To achieve this, patients with Chagas disease must be identified. A Western blotting test, TESAcruzi, is described as a supplemental test for diagnosis of Chagas disease using samples collected from children <5 years living in different states of Brazil. Blood samples collected by finger prick on filter paper were sent to the test laboratory by a central laboratory to confirm results obtained previously. Ten percent of negative samples, all doubtful and all positive samples were received. Commercial reagents, IgG indirect immunofluorescence, enzyme immunoassay, and a recently introduced TESAcruzi test were used. From 8788 samples, 163 (1.85%) were reactive by IgG-ELISA and 312 (3.55%) by IgG IIF. From these, 77 (0.87%) were reactive in the TESAcruzi test. The results had high clinical value to identify those truly infected. Copyright © 2010 Elsevier B.V. All rights reserved.

The Sequential Probability Ratio Test: An efficient alternative to exact binomial testing for Clean Water Act 303(d) evaluation.

PubMed

Chen, Connie; Gribble, Matthew O; Bartroff, Jay; Bay, Steven M; Goldstein, Larry

2017-05-01

The United States's Clean Water Act stipulates in section 303(d) that states must identify impaired water bodies for which total maximum daily loads (TMDLs) of pollution inputs into water bodies are developed. Decision-making procedures about how to list, or delist, water bodies as impaired, or not, per Clean Water Act 303(d) differ across states. In states such as California, whether or not a particular monitoring sample suggests that water quality is impaired can be regarded as a binary outcome variable, and California's current regulatory framework invokes a version of the exact binomial test to consolidate evidence across samples and assess whether the overall water body complies with the Clean Water Act. Here, we contrast the performance of California's exact binomial test with one potential alternative, the Sequential Probability Ratio Test (SPRT). The SPRT uses a sequential testing framework, testing samples as they become available and evaluating evidence as it emerges, rather than measuring all the samples and calculating a test statistic at the end of the data collection process. Through simulations and theoretical derivations, we demonstrate that the SPRT on average requires fewer samples to be measured to have comparable Type I and Type II error rates as the current fixed-sample binomial test. Policymakers might consider efficient alternatives such as SPRT to current procedure. Copyright © 2017 Elsevier Ltd. All rights reserved.

Development of a biaxial compression device for biological samples: preliminary experimental results for a closed cell foam.

PubMed

Little, J P; Tevelen, G; Adam, C J; Evans, J H; Pearcy, M J

2009-07-01

Biological tissues are subjected to complex loading states in vivo and in order to define constitutive equations that effectively simulate their mechanical behaviour under these loads, it is necessary to obtain data on the tissue's response to multiaxial loading. Single axis and shear testing of biological tissues is often carried out, but biaxial testing is less common. We sought to design and commission a biaxial compression testing device, capable of obtaining repeatable data for biological samples. The apparatus comprised a sealed stainless steel pressure vessel specifically designed such that a state of hydrostatic compression could be created on the test specimen while simultaneously unloading the sample along one axis with an equilibrating tensile pressure. Thus a state of equibiaxial compression was created perpendicular to the long axis of a rectangular sample. For the purpose of calibration and commissioning of the vessel, rectangular samples of closed cell ethylene vinyl acetate (EVA) foam were tested. Each sample was subjected to repeated loading, and nine separate biaxial experiments were carried out to a maximum pressure of 204 kPa (30 psi), with a relaxation time of two hours between them. Calibration testing demonstrated the force applied to the samples had a maximum error of 0.026 N (0.423% of maximum applied force). Under repeated loading, the foam sample demonstrated lower stiffness during the first load cycle. Following this cycle, an increased stiffness, repeatable response was observed with successive loading. While the experimental protocol was developed for EVA foam, preliminary results on this material suggest that this device may be capable of providing test data for biological tissue samples. The load response of the foam was characteristic of closed cell foams, with consolidation during the early loading cycles, then a repeatable load-displacement response upon repeated loading. The repeatability of the test results demonstrated the ability of the test device to provide reproducible test data and the low experimental error in the force demonstrated the reliability of the test data.

Comparison of five diagnostic tests for Giardia duodenalis in fecal samples from young dogs.

PubMed

Uehlinger, Fabienne D; Naqvi, S Ali; Greenwood, Spencer J; McClure, J Trenton; Conboy, Gary; O'Handley, Ryan; Barkema, Herman W

2017-09-15

Five diagnostic tests were compared for the diagnosis of Giardia duodenalis in fecal samples of young dogs. Fecal samples were collected from 136 healthy dogs <1year old and examined using immunofluorescence antibody microscopy (IFA) after sucrose gradient centrifugation, zinc sulfate centrifugal flotation technique (ZSCT), SNAP ® Giardia test, and ProSpecT ® Giardia EZ Microplate assay. In addition, polymerase chain reaction (PCR) of the 16S rRNA gene was performed. Kappa (κ) statistic was calculated to assess diagnostic agreement between the IFA and each test. Using the IFA as the gold standard, the relative sensitivity and specificity of each test were determined. Subsequently, a Bayesian approach was used to estimate the sensitivity and specificity of each test in comparison to the IFA results. Giardia duodenalis was detected in 41% of the samples examined by IFA. The ZSCT resulted in 37% of positive samples, with a relative sensitivity and specificity of 86 and 98%, respectively. The SNAP ® Giardia test was positive in 40% of the samples, with a relative sensitivity and specificity of 91 and 96%, respectively. The ProSpecT ® test was positive in 51% of the samples, with a relative sensitivity and specificity of 100 and 83%, respectively. The relative sensitivity and specificity for PCR were 58 and 56%, respectively, with 55% of samples being PCR-positive. While the sensitivity and specificity estimates of each test in comparison to the IFA changed when using a Bayesian approach, the conclusions remained the same. While the ProSpecT ® test was the most sensitive test in this study, it is not designed for dogs and more costly than the other tests. The SNAP ® Giardia test performed similar to the ZSCT but may be more favorable because it is fast and easy to perform. Performance of the PCR was poor and the benefit of PCR may be in determining genotypes for evaluating zoonotic transfer between dogs and humans. Copyright © 2017 Elsevier B.V. All rights reserved.

Exploring the cause of initially reactive bovine brains on rapid tests for BSE

PubMed Central

Dudas, Sandor; James, Jace; Anderson, Renee; Czub, Stefanie

2015-01-01

ABSTRACT Bovine spongiform encephalopathy (BSE) is an invariably fatal prion disease of cattle. The identification of the zoonotic potential of BSE prompted safety officials to initiate surveillance testing for this disease. In Canada, BSE surveillance is primarily focused on high risk cattle including animals which are dead, down and unable to rise, diseased or distressed. This targeted surveillance results in the submission of brain samples with a wide range of tissue autolysis and associated contaminants. These contaminants have the potential to interfere with important steps of surveillance tests resulting in initially positive test results requiring additional testing to confirm the disease status of the animal. The current tests used for BSE screening in Canada utilize the relative protease resistance of the prion protein gained when it misfolds from PrPC to PrPSc as part of the disease process. Proteinase K completely digests PrPC in normal brains, but leaves most of the PrPSc in BSE positive brains intact which is detected using anti-prion antibodies. These tests are highly reliable but occasionally give rise to initially reactive/false positive results. Test results for these reactive samples were close to the positive/negative cut-off on a sub set of test platforms. This is in contrast to all of the previous Canadian positive samples whose numeric values on these same test platforms were 10 to 100 fold greater than the test positive/negative cut-off. Here we explore the potential reason why a sample is repeatedly positive on a sub-set of rapid surveillance tests, but negative on other test platforms. In order to better understand and identify what might cause these initial reactions, we have conducted a variety of rapid and confirmatory assays as well as bacterial isolation and identification on BSE positive, negative and initially reactive samples. We observed high levels of viable bacterial contamination in initially reactive samples suggesting that the reactivity may be related to bacterial factors. Several bacteria isolated from the initially reactive samples have characteristics of biofilm forming bacteria and this extracellular matrix might play a role in preventing complete digestion of PrPC in these samples. PMID:26689488

Microbial load monitor

NASA Technical Reports Server (NTRS)

Caplin, R. S.; Royer, E. R.

1978-01-01

Attempts are made to provide a total design of a Microbial Load Monitor (MLM) system flight engineering model. Activities include assembly and testing of Sample Receiving and Card Loading Devices (SRCLDs), operator related software, and testing of biological samples in the MLM. Progress was made in assembling SRCLDs with minimal leaks and which operate reliably in the Sample Loading System. Seven operator commands are used to control various aspects of the MLM such as calibrating and reading the incubating reading head, setting the clock and reading time, and status of Card. Testing of the instrument, both in hardware and biologically, was performed. Hardware testing concentrated on SRCLDs. Biological testing covered 66 clinical and seeded samples. Tentative thresholds were set and media performance listed.

The effect of carbon black filler to the mechanical properties of natural rubber as base isolation system

NASA Astrophysics Data System (ADS)

Ismail, R.; Mahadi, Z. A.; Ishak, I. S.

2018-04-01

This paper presented the study on the effect of carbon black as filler to the mechanical properties of natural rubber for base isolation system. This study used the five formulations with the different amount of carbon black filler for every sample. The samples were tested for tensile, hardness and resilience test. The samples were cured or vulcanized at 1500C for 23 minutes for every formulation. The filler used in this study was the carbon black filler with type N660. The tensile test was done to determine the ability of the sample in term of the elongation with the load at break. The hardness test, it has been done to determine the ability of the sample to resist the load. This hardness was measured in the unit of IRHD. The resilience test was being done to determine the properties of the sample in term of rebound characteristics. The finding of this study showed that, the high the loading of carbon black filler, the high the tensile strength of the sample and the high the hardness of the sample. In term of resilience, it was inversely proportional to the loading of the carbon black filler.

Analysis of small sample size studies using nonparametric bootstrap test with pooled resampling method.

PubMed

Dwivedi, Alok Kumar; Mallawaarachchi, Indika; Alvarado, Luis A

2017-06-30

Experimental studies in biomedical research frequently pose analytical problems related to small sample size. In such studies, there are conflicting findings regarding the choice of parametric and nonparametric analysis, especially with non-normal data. In such instances, some methodologists questioned the validity of parametric tests and suggested nonparametric tests. In contrast, other methodologists found nonparametric tests to be too conservative and less powerful and thus preferred using parametric tests. Some researchers have recommended using a bootstrap test; however, this method also has small sample size limitation. We used a pooled method in nonparametric bootstrap test that may overcome the problem related with small samples in hypothesis testing. The present study compared nonparametric bootstrap test with pooled resampling method corresponding to parametric, nonparametric, and permutation tests through extensive simulations under various conditions and using real data examples. The nonparametric pooled bootstrap t-test provided equal or greater power for comparing two means as compared with unpaired t-test, Welch t-test, Wilcoxon rank sum test, and permutation test while maintaining type I error probability for any conditions except for Cauchy and extreme variable lognormal distributions. In such cases, we suggest using an exact Wilcoxon rank sum test. Nonparametric bootstrap paired t-test also provided better performance than other alternatives. Nonparametric bootstrap test provided benefit over exact Kruskal-Wallis test. We suggest using nonparametric bootstrap test with pooled resampling method for comparing paired or unpaired means and for validating the one way analysis of variance test results for non-normal data in small sample size studies. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Clinical evaluation of high-risk HPV detection on self-samples using the indicating FTA-elute solid-carrier cartridge.

PubMed

Geraets, D T; van Baars, R; Alonso, I; Ordi, J; Torné, A; Melchers, W J G; Meijer, C J L M; Quint, W G V

2013-06-01

High-risk human papillomavirus (hrHPV) testing in cervical screening is usually performed on physician-taken cervical smears in liquid-based medium. However, solid-state specimen carriers allow easy, non-hazardous storage and transportation and might be suitable for self-collection by non-responders in screening and in low-resource settings. We evaluated the adequacy of self-collected cervicovaginal (c/v) samples using a Viba-brush stored on an Indicating FTA-elute cartridge (FTA-based self-sampling) for hrHPV testing in women referred to a gynecology clinic due to an abnormal smear. 182 women accepted to self-collect a c/v sample. After self-sampling, a physician obtained a conventional liquid-based cervical smear. Finally, women were examined by colposcopy and a biopsy was taken when clinically indicated. Self-samples required only simple DNA elution, and DNA was extracted from physician-obtained samples. Both samples were tested for 14 hrHPVs by GP5+/6+-EIA-LQ Test and SPF(10)-DEIA-LiPA(25). Both assays detected significantly more hrHPV in physician-collected specimens than in self-collected samples (75.3% and 67.6% by SPF(10); 63.3% and 53.3% by GP5+/6+, respectively). The combination of physician-collected specimen and GP5+/6+ testing demonstrated the optimal balance in sensitivity (98.0%) and specificity (48.1%) for CIN2+ detection in this referral population. A test system of FTA-based self-collection and SPF(10) hrHPV detection approached this sensitivity (95.9%) and specificity (42.9%). These results show that the clinical performance of hrHPV detection is determined by both the sample collection system and the test method. FTA-based self-collection with SPF(10) testing might be valuable when a liquid-based medium cannot be used, but requires further investigation in screening populations. Copyright © 2013 Elsevier B.V. All rights reserved.

Rapid Salmonella detection in experimentally inoculated equine faecal and veterinary hospital environmental samples using commercially available lateral flow immunoassays.

PubMed

Burgess, B A; Noyes, N R; Bolte, D S; Hyatt, D R; van Metre, D C; Morley, P S

2015-01-01

Salmonella enterica is the most commonly reported cause of outbreaks of nosocomial infections in large animal veterinary teaching hospitals and the closure of equine hospitals. Rapid detection may facilitate effective control practices in equine populations. Shipping and laboratory testing typically require ≥48 h to obtain results. Lateral flow immunoassays developed for use in food-safety microbiology provide an alternative that has not been evaluated for use with faeces or environmental samples. We aimed to identify enrichment methods that would allow commercially available rapid Salmonella detection systems (lateral flow immunoassays) to be used in clinical practice with equine faecal and environmental samples, providing test results in 18-24 h. In vitro experiment. Equine faecal and environmental samples were inoculated with known quantities of S. enterica serotype Typhimurium and cultured using 2 different enrichment techniques for faeces and 4 enrichment techniques for environmental samples. Samples were tested blindly using 2 different lateral flow immunoassays and plated on agar media for confirmatory testing. In general, commercial lateral flow immunoassays resulted in fewer false-negative test results with enrichment of 1 g faecal samples in tetrathionate for 18 h, while all environmental sample enrichment techniques resulted in similar detection rates. The limit of detection from spiked samples, ∼4 colony-forming units/g, was similar for all methods evaluated. The lateral flow immunoassays evaluated could reliably detect S. enterica within 18 h, indicating that they may be useful for rapid point-of-care testing in equine practice applications. Additional evaluation is needed using samples from naturally infected cases and the environment to gain an accurate estimate of test sensitivity and specificity and to substantiate further the true value of these tests in clinical practice. © 2014 EVJ Ltd.

Evaluation of adenosine triphosphate test for cleaning assessment of gastroscopes and the effect on workload in a busy endoscopy center.

PubMed

Schmitt, Cristiane; Pires Maciel, Amanda Luiz; Boszczowski, Icaro; da Silva, Thaís Pereira; Neves, Eliane Aparecida Job; Rossini, Giulio Fabio; Rizek, Camila; Costa, Silvia Figueiredo; Lourenço, Rogério Ferreira; Alfa, Michelle J

2018-05-18

Using adenosine triphosphate (ATP) tests to assess manual cleaning of gastroscopes and to determine the associated workload in a busy endoscopy unit. Patient-used gastroscopes were sampled before and after cleaning to assess ATP levels, bioburden, and protein. Samples were collected by flushing 20 mL of sterile water through the biopsy port to the distal end. Time spent for reprocessing and performing the ATP test was recorded. Twenty-four samples were collected from 10 gastroscopes. After manual cleaning, 14/24 (58.3%) samples had no microbial growth (mean, 21 colony-forming units/cm 2 ), and in 22/24 (91.7%) samples the protein was undetectable (mean, 0.04 µg/cm 2 ). ATP test was above the cutoff (200 relative light units [RLU]) in 17/24 (70.8%) samples (mean, 498 RLU). After the second cleaning, 11/17 (64.7%) gastroscopes still failed the ATP test (mean, 321.2 RLU). The mean time spent to perform manual cleaning and ATP tests was 16 and 8 minutes, respectively. Hence, each test increased the length of time for cleaning plus testing cleanliness by 50%. Further studies regarding the optimal cutoff for ATP tests are needed. ATP tests for cleaning monitoring are easy to perform and provide immediate feedback to the team. However, the increased workload needs to be considered. Copyright © 2018 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

ACT Test

MedlinePlus

... Sample Required? A blood sample drawn from a vein in your arm Test Preparation Needed? None Looking ... is obtained by inserting a needle into a vein in the arm. Is any test preparation needed ...

Burning of CP Titanium (Grade 2) in Oxygen-Enriched Atmospheres

NASA Technical Reports Server (NTRS)

Stoltzfus, Joel M.; Jeffers, Nathan; Gallus, Timothy D.

2012-01-01

The flammability in oxygen-enriched atmospheres of commercially pure (CP) titanium rods as a function of diameter and test gas pressure was determined. Test samples of varying diameters were ignited at the bottom and burned upward in 70% O2/balance N2 and in 99.5+% O2 at various pressures. The burning rate of each ignited sample was determined by observing the apparent regression rate of the melting interface (RRMI) of the burning samples. The burning rate or RRMI increased with decreasing test sample diameter and with increasing test gas pressure and oxygen concentration

Remote temperature-set-point controller

DOEpatents

Burke, W.F.; Winiecki, A.L.

1984-10-17

An instrument is described for carrying out mechanical strain tests on metallic samples with the addition of means for varying the temperature with strain. The instrument includes opposing arms and associated equipment for holding a sample and varying the mechanical strain on the sample through a plurality of cycles of increasing and decreasing strain within predetermined limits, circuitry for producing an output signal representative of the strain during the tests, apparatus including a a set point and a coil about the sample for providing a controlled temperature in the sample, and circuitry interconnected between the strain output signal and set point for varying the temperature of the sample linearly with strain during the tests.

Remote temperature-set-point controller

DOEpatents

Burke, William F.; Winiecki, Alan L.

1986-01-01

An instrument for carrying out mechanical strain tests on metallic samples with the addition of an electrical system for varying the temperature with strain, the instrument including opposing arms and associated equipment for holding a sample and varying the mechanical strain on the sample through a plurality of cycles of increasing and decreasing strain within predetermined limits, circuitry for producing an output signal representative of the strain during the tests, apparatus including a set point and a coil about the sample for providing a controlled temperature in the sample, and circuitry interconnected between the strain output signal and set point for varying the temperature of the sample linearly with strain during the tests.

Salmonella testing of pooled pre-enrichment broth cultures for screening multiple food samples.

PubMed

Price, W R; Olsen, R A; Hunter, J E

1972-04-01

A method has been described for testing multiple food samples for Salmonella without loss in sensitivity. The method pools multiple pre-enrichment broth cultures into single enrichment broths. The subsequent stages of the Salmonella analysis are not altered. The method was found applicable to several dry food materials including nonfat dry milk, dried egg albumin, cocoa, cottonseed flour, wheat flour, and shredded coconut. As many as 25 pre-enrichment broth cultures were pooled without apparent loss in the sensitivity of Salmonella detection as compared to individual sample analysis. The procedure offers a simple, yet effective, way to increase sample capacity in the Salmonella testing of foods, particularly where a large proportion of samples ordinarily is negative. It also permits small portions of pre-enrichment broth cultures to be retained for subsequent individual analysis if positive tests are found. Salmonella testing of pooled pre-enrichment broths provides increased consumer protection for a given amount of analytical effort as compared to individual sample analysis.

Relationship between substances in seminal plasma and Acrobeads Test results.

PubMed

Komori, Kazuhiko; Tsujimura, Akira; Okamoto, Yoshio; Matsuoka, Yasuhiro; Takao, Tetsuya; Miyagawa, Yasushi; Takada, Shingo; Nonomura, Norio; Okuyama, Akihiko

2009-01-01

To asses the effects of seminal plasma on sperm function. Retrospective case-control study. University hospital. One hundred fourteen infertile men. Acrobeads Test scores (0-4) and measurement of interleukin (IL)-6, soluble IL-6 receptor, epidermal growth factor, insulin-like growth factor-I (IGF-I), transforming growth factor-beta I, superoxide dismutase, calcitonin, and macrophage migration inhibitory factor (MIF) levels in seminal plasma. Kruskal-Wallis test to compare the concentrations of substances as a nonparametric test for differences among Acrobeads Test scores and a multivariable logistic regression model to find independent risk factors associated with abnormal Acrobeads Test results. The Acrobeads Test score was 0 for 7 samples, 1 for 20 samples, 2 for 18 samples, 3 for 28 samples, and 4 for 41 samples. Age, abstinence period, and semen parameters, except for sperm motility and percentage of sperm with abnormal morphology, had no effect on the Acrobeads Test results. Concentrations of IGF-I and MIF were significantly higher in patients with abnormal Acrobeads Test results. Multivariate analysis indicated that MIF and IGF-I were significantly associated with abnormal Acrobeads Test results (scores 0 to 1). Although further studies are needed, IGF-I and MIF in seminal plasma may have negative effects on sperm function.

Serological diagnosis of bovine brucellosis using B. melitensis strain B115.

PubMed

Corrente, Marialaura; Desario, Costantina; Parisi, Antonio; Grandolfo, Erika; Scaltrito, Domenico; Vesco, Gesualdo; Colao, Valeriana; Buonavoglia, Domenico

2015-12-01

Bovine brucellosis is diagnosed by official tests, such as Rose Bengal plate test (RBPT) and Complement Fixation test (CFT). Both tests detect antibodies directed against the lipolysaccharide (LPS) of Brucella cell wall. Despite their good sensitivity, those tests do not discriminate between true positive and false positive serological reactions (FPSR), the latter being generated by animals infected with other Gram negative microorganisms that share components of Brucella LPS. In this study, an antigenic extract from whole Brucella melitensis B115 strain was used to set up an ELISA assay for the serological diagnosis of bovine brucellosis. A total of 148 serum samples from five different groups of animals were tested: Group A: 28 samples from two calves experimentally infected with Yersinia enterocolitica O:9; Group B: 30 samples from bovines infected with Brucella abortus; Group C: 50 samples from brucellosis-free herds; Group D: 20 samples RBPT positive and CFT negative; Group E: 20 samples both RBPT and CFT positive. Group D and Group E serum samples were from brucellosis-free herds. Positive reactions were detected only by RBPT and CFT in calves immunized with Y. enterocolitica O:9. Sera from Group B animals tested positive also in the ELISA assay, whereas sera from the remaining groups were all negative. The results obtained encourage the use of the ELISA assay to implement the serological diagnosis of brucellosis. Copyright © 2015 Elsevier B.V. All rights reserved.

A Monte Carlo Program for Simulating Selection Decisions from Personnel Tests

ERIC Educational Resources Information Center

Petersen, Calvin R.; Thain, John W.

1976-01-01

Relative to test and criterion parameters and cutting scores, the correlation coefficient, sample size, and number of samples to be drawn (all inputs), this program calculates decision classification rates across samples and for combined samples. Several other related indices are also computed. (Author)

A proposal to standardize reporting units for fecal immunochemical tests for hemoglobin.

PubMed

Fraser, Callum G; Allison, James E; Halloran, Stephen P; Young, Graeme P

2012-06-06

Fecal immunochemical tests for hemoglobin are replacing traditional guaiac fecal occult blood tests in population screening programs for many reasons. However, the many available fecal immunochemical test devices use a range of sampling methods, differ with regard to hemoglobin stability, and report hemoglobin concentrations in different ways. The methods for sampling, the mass of feces collected, and the volume and characteristics of the buffer used in the sampling device also vary among fecal immunochemical tests, making comparisons of test performance characteristics difficult. Fecal immunochemical test results may be expressed as the hemoglobin concentration in the sampling device buffer and, sometimes, albeit rarely, as the hemoglobin concentration per mass of feces. The current lack of consistency in units for reporting hemoglobin concentration is particularly problematic because apparently similar hemoglobin concentrations obtained with different devices can lead to very different clinical interpretations. Consistent adoption of an internationally accepted method for reporting results would facilitate comparisons of outcomes from these tests. We propose a simple strategy for reporting fecal hemoglobin concentration that will facilitate the comparison of results between fecal immunochemical test devices and across clinical studies. Such reporting is readily achieved by defining the mass of feces sampled and the volume of sample buffer (with confidence intervals) and expressing results as micrograms of hemoglobin per gram of feces. We propose that manufacturers of fecal immunochemical tests provide this information and that the authors of research articles, guidelines, and policy articles, as well as pathology services and regulatory bodies, adopt this metric when reporting fecal immunochemical test results.

Serodiagnosis of infectious mononucleosis with a bovine erythrocyte glycoprotein.

PubMed

Fletcher, M A; Klimas, N G; Latif, Z A; Caldwell, K E

1983-09-01

A glycoprotein from bovine erythrocyte membrane was evaluated in two immunoassays as a reagent for the serodiagnosis of infectious mononucleosis (IM). We previously reported that a partially purified preparation of this glycoprotein, when attached to latex beads, agglutinated in the presence of IM heterophile antibody. In the present study, we used a highly purified form of the glycoprotein both as an agglutinating reagent, covalently bound to latex, and in a solid-phase sandwich-type radioimmunoassay (RIA) for IM antibody detection in a larger population of patients. We tested serum samples from college students with symptoms suggestive of IM with the latex reagent (143 samples) and with the RIA (245 samples). Correlation of these two tests, both with each other and with the classical differentially absorbed, agglutination tests for Paul-Bunnell antibody in IM sera, using fresh sheep or horse cells, was excellent (greater than 97% agreement). The new tests also corresponded in most cases with a rapid, unabsorbed preserved horse erythrocyte slide test. However, in this study of 245 samples, both apparent false-positives (5 samples) and apparent false-negatives (3 samples) were observed with this slide test. In conclusion, we found that the bovine glycoprotein as a reagent can facilitate the diagnosis of IM, giving results comparable to those with erythrocyte agglutination tests on differentially absorbed sera. The advantages are ease and speed of performance (latex test), potential for automation (RIA test), stability and uniformity of the glycoprotein reagent (latex and RIA tests), and most importantly, the ability to use unabsorbed sera (latex and RIA tests).

Using the Student's "t"-Test with Extremely Small Sample Sizes

ERIC Educational Resources Information Center

de Winter, J. C .F.

2013-01-01

Researchers occasionally have to work with an extremely small sample size, defined herein as "N" less than or equal to 5. Some methodologists have cautioned against using the "t"-test when the sample size is extremely small, whereas others have suggested that using the "t"-test is feasible in such a case. The present…

One-sided truncated sequential t-test: application to natural resource sampling

Treesearch

Gary W. Fowler; William G. O' Regan

1974-01-01

A new procedure for constructing one-sided truncated sequential t-tests and its application to natural resource sampling are described. Monte Carlo procedures were used to develop a series of one-sided truncated sequential t-tests and the associated approximations to the operating characteristic and average sample number functions. Different truncation points and...

9 CFR 147.8 - Procedures for preparing egg yolk samples for diagnostic tests.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 9 Animals and Animal Products 1 2014-01-01 2014-01-01 false Procedures for preparing egg yolk samples for diagnostic tests. 147.8 Section 147.8 Animals and Animal Products ANIMAL AND PLANT HEALTH... IMPROVEMENT PLAN Blood Testing Procedures § 147.8 Procedures for preparing egg yolk samples for diagnostic...

9 CFR 147.8 - Procedures for preparing egg yolk samples for diagnostic tests.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 9 Animals and Animal Products 1 2013-01-01 2013-01-01 false Procedures for preparing egg yolk samples for diagnostic tests. 147.8 Section 147.8 Animals and Animal Products ANIMAL AND PLANT HEALTH... IMPROVEMENT PLAN Blood Testing Procedures § 147.8 Procedures for preparing egg yolk samples for diagnostic...

9 CFR 147.8 - Procedures for preparing egg yolk samples for diagnostic tests.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 9 Animals and Animal Products 1 2012-01-01 2012-01-01 false Procedures for preparing egg yolk samples for diagnostic tests. 147.8 Section 147.8 Animals and Animal Products ANIMAL AND PLANT HEALTH... IMPROVEMENT PLAN Blood Testing Procedures § 147.8 Procedures for preparing egg yolk samples for diagnostic...

9 CFR 147.8 - Procedures for preparing egg yolk samples for diagnostic tests.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 9 Animals and Animal Products 1 2011-01-01 2011-01-01 false Procedures for preparing egg yolk samples for diagnostic tests. 147.8 Section 147.8 Animals and Animal Products ANIMAL AND PLANT HEALTH... IMPROVEMENT PLAN Blood Testing Procedures § 147.8 Procedures for preparing egg yolk samples for diagnostic...

36 CFR 9.42 - Well records and reports, plots and maps, samples, tests and surveys.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Well records and reports, plots and maps, samples, tests and surveys. Any technical data gathered... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Well records and reports, plots and maps, samples, tests and surveys. 9.42 Section 9.42 Parks, Forests, and Public Property...

[Concordance among invasive diagnostic procedures for Helicobacter pylori infection in adults].

PubMed

Sánchez-Cuén, Jaime Alberto; Canizalez-Román, Vicente Adrián; León-Sicairos, Nidia Maribel; Irineo-Cabrales, Ana Bertha; Bernal-Magaña, Gregorio

2015-01-01

Compare the strength of concordance between culture, histology, rapid urease test for diagnosis of Helicobacter pylori infection and histopathological findings relationship and frequency of positivity among such diagnostic procedures. Diagnostic test study. The study population were subjects with endoscopy and take samples of gastric antral. Rapid urease test (one sample), histology (two samples) and culture (two samples), and histopathological findings of gastric mucosa were performed. Statistical design with Student's t, Fisher exact test, Kappa coefficient. We reviewed 108 subjects, 28 (25.9%) men, 80 (74.1%) women, mean age was 49.1 years (SD 15.1). The Kappa coefficient was 0.729 and 0.377 between culture with histology and rapid urease test, respectively; likewise the Kappa coefficient was 0.565 between histology and rapid urease test. The strength of concordance was higher between histology with culture and rapid urease test; the most recommended being histology in clinical practice for the detection of Helicobacter pylori infection.

Comet sample acquisition for ROSETTA lander mission

NASA Astrophysics Data System (ADS)

Marchesi, M.; Campaci, R.; Magnani, P.; Mugnuolo, R.; Nista, A.; Olivier, A.; Re, E.

2001-09-01

ROSETTA/Lander is being developed with a combined effort of European countries, coordinated by German institutes. The commitment for such a challenging probe will provide a unique opportunity for in-situ analysis of a comet nucleus. The payload for coring, sampling and investigations of comet materials is called SD2 (Sampling Drilling and Distribution). The paper presents the drill/sampler tool and the sample transfer trough modeling, design and testing phases. Expected drilling parameters are then compared with experimental data; limited torque consumption and axial thrust on the tool constraint the operation and determine the success of tests. Qualification campaign involved the structural part and related vibration test, the auger/bit parts and drilling test, and the coring mechanism with related sampling test. Mechanical check of specimen volume is also reported, with emphasis on the measurement procedure and on the mechanical unit. The drill tool and all parts of the transfer chain were tested in the hypothetical comet environment, charcterized by frozen material at extreme low temperature and high vacuum (-160°C, 10-3 Pa).

Calculating p-values and their significances with the Energy Test for large datasets

NASA Astrophysics Data System (ADS)

Barter, W.; Burr, C.; Parkes, C.

2018-04-01

The energy test method is a multi-dimensional test of whether two samples are consistent with arising from the same underlying population, through the calculation of a single test statistic (called the T-value). The method has recently been used in particle physics to search for samples that differ due to CP violation. The generalised extreme value function has previously been used to describe the distribution of T-values under the null hypothesis that the two samples are drawn from the same underlying population. We show that, in a simple test case, the distribution is not sufficiently well described by the generalised extreme value function. We present a new method, where the distribution of T-values under the null hypothesis when comparing two large samples can be found by scaling the distribution found when comparing small samples drawn from the same population. This method can then be used to quickly calculate the p-values associated with the results of the test.

Clinical comparison of the Treponema pallidum CAPTIA syphilis-G enzyme immunoassay with the fluorescent treponemal antibody absorption immunoglobulin G assay for syphilis testing.

PubMed

Halling, V W; Jones, M F; Bestrom, J E; Wold, A D; Rosenblatt, J E; Smith, T F; Cockerill, F R

1999-10-01

Recently, a treponema-specific immunoglobulin G (IgG) enzyme immunoassay (EIA), the CAPTIA Syphilis-G (Trinity Biotech, Jamestown, N.Y.), has become available as a diagnostic test for syphilis. A total of 89 stored sera previously tested by the fluorescent treponemal antibody absorption (FTA-ABS) IgG assay were evaluated by the CAPTIA EIA. The FTA-ABS IgG procedure was performed by technologists unblinded to results of rapid plasmid reagin (RPR) testing of the same specimens. Borderline CAPTIA-positive samples (antibody indices of >/=0.650 and 0.900, the sample was considered positive. Thirteen of 89 (15%) samples had discrepant results. Compared to the FTA-ABS assay, the CAPTIA EIA had a sensitivity and specificity and positive and negative predictive values of 70.7, 97.9, 96.7, and 79.7%, respectively. In another analysis, discrepancies between results were resolved by repeated FTA-ABS testing (technologists were blinded to previous RPR results) and patient chart reviews. Seven CAPTIA-negative samples which were previously interpreted (unblinded) as minimally reactive by the FTA method were subsequently interpreted (blinded) as nonreactive. One other discrepant sample (CAPTIA negative and FTA-ABS positive [at an intensity of 3+], unblinded) was FTA negative with repeated testing (blinded). For the five remaining discrepant samples, chart reviews indicated that one patient (CAPTIA negative and FTA-ABS positive [minimally reactive], blinded) had possible syphilis. These five samples were also evaluated and found to be negative by another treponema-specific test, the Treponema pallidum microhemagglutination assay. Therefore, after repeated testing and chart reviews, 2 of the 89 (2%) samples had discrepant results; the adjusted sensitivity, specificity, and positive and negative predictive values were 96.7, 98.3, 96.7, and 98.3%, respectively. This study demonstrates that the CAPTIA IgG EIA is a reliable method for syphilis testing and that personnel performing tests which require subjective interpretation, like the FTA-ABS test, may be biased by RPR test results.

Clinical Comparison of the Treponema pallidum CAPTIA Syphilis-G Enzyme Immunoassay with the Fluorescent Treponemal Antibody Absorption Immunoglobulin G Assay for Syphilis Testing

PubMed Central

Halling, V. W.; Jones, M. F.; Bestrom, J. E.; Wold, A. D.; Rosenblatt, J. E.; Smith, T. F.; Cockerill, F. R.

1999-01-01

Recently, a treponema-specific immunoglobulin G (IgG) enzyme immunoassay (EIA), the CAPTIA Syphilis-G (Trinity Biotech, Jamestown, N.Y.), has become available as a diagnostic test for syphilis. A total of 89 stored sera previously tested by the fluorescent treponemal antibody absorption (FTA-ABS) IgG assay were evaluated by the CAPTIA EIA. The FTA-ABS IgG procedure was performed by technologists unblinded to results of rapid plasmid reagin (RPR) testing of the same specimens. Borderline CAPTIA-positive samples (antibody indices of ≥0.650 and ≤0.900) were retested; if the second analysis produced an index of >0.900, the sample was considered positive. Thirteen of 89 (15%) samples had discrepant results. Compared to the FTA-ABS assay, the CAPTIA EIA had a sensitivity and specificity and positive and negative predictive values of 70.7, 97.9, 96.7, and 79.7%, respectively. In another analysis, discrepancies between results were resolved by repeated FTA-ABS testing (technologists were blinded to previous RPR results) and patient chart reviews. Seven CAPTIA-negative samples which were previously interpreted (unblinded) as minimally reactive by the FTA method were subsequently interpreted (blinded) as nonreactive. One other discrepant sample (CAPTIA negative and FTA-ABS positive [at an intensity of 3+], unblinded) was FTA negative with repeated testing (blinded). For the five remaining discrepant samples, chart reviews indicated that one patient (CAPTIA negative and FTA-ABS positive [minimally reactive], blinded) had possible syphilis. These five samples were also evaluated and found to be negative by another treponema-specific test, the Treponema pallidum microhemagglutination assay. Therefore, after repeated testing and chart reviews, 2 of the 89 (2%) samples had discrepant results; the adjusted sensitivity, specificity, and positive and negative predictive values were 96.7, 98.3, 96.7, and 98.3%, respectively. This study demonstrates that the CAPTIA IgG EIA is a reliable method for syphilis testing and that personnel performing tests which require subjective interpretation, like the FTA-ABS test, may be biased by RPR test results. PMID:10488183

Efficacy of Cyto-Chex blood preservative for delayed manual CD4 testing using Dynal T4 Quant CD4 test among HIV-infected persons in Zambia.

PubMed

Truett, April A; Letizia, Andrew; Malyangu, Evans; Sinyangwe, Frank; Morales, Brandi N; Crum, Nancy F; Crowe, Suzanne M

2006-02-01

Manual CD4 tests such as Dynal T4 Quant (Dynabeads, Dynal Biotech, Oslo, Norway) are less expensive alternatives to flow cytometry in resource-limited countries. Whereas blood preservatives have proven useful for stabilizing blood samples to allow delayed CD4 testing by flow cytometry, they have not been verified for manual tests. A method for preservation of blood prior to manual CD4 testing is needed for long-distance transport or sample batching. Blood from HIV-positive Zambian military beneficiaries was mixed (1:1) with Cyto-Chex (Streck Laboratories, La Vista, NE) blood preservative, and the blood was stored at refrigerated, ambient, and incubator (37 degrees C) temperatures prior to Dynabeads CD4 testing at 0, 3, 6, and 9 days after collection. Baseline flow cytometry and Dynabeads testing without preservative were performed for comparison. Twenty-seven patient samples were analyzed. Dynabeads vs. flow cytometry had a correlation coefficient (r) of 0.84. There was excellent correlation (r = 0.96) between baseline Dynabeads testing and Cyto-Chex-preserved samples. Refrigerated samples showed strong correlation with baseline Dynabeads (r = 0.93-0.95) on days 3, 6, and 9 without decline in CD4 count (P = 0.73). Samples stored at ambient temperature yielded inferior results (r = 0.76-0.81), with a significant decline in CD4 count by day 3 (P < 0.001). The incubator arm had especially poor correlation (r = 0.30-0.49). Addition of Cyto-Chex to peripheral blood (1:1) adequately preserves refrigerated blood samples for up to 9 days for subsequent testing with Dynabeads CD4 test. Cyto-Chex, however, cannot be recommended for delayed Dynabeads CD4 testing with storage at 37 degrees C or ambient temperatures in tropical areas similar to the site of this study.

Accuracy of five serologic tests for the follow up of Strongyloides stercoralis infection.

PubMed

Buonfrate, Dora; Sequi, Marco; Mejia, Rojelio; Cimino, Ruben O; Krolewiecki, Alejandro J; Albonico, Marco; Degani, Monica; Tais, Stefano; Angheben, Andrea; Requena-Mendez, Ana; Muñoz, José; Nutman, Thomas B; Bisoffi, Zeno

2015-02-01

Traditional faecal-based methods have poor sensitivity for the detection of S. stercoralis, therefore are inadequate for post-treatment evaluation of infected patients who should be carefully monitored to exclude the persistence of the infection. In a previous study, we demonstrated high accuracy of five serology tests for the screening and diagnosis of strongyloidiasis. Aim of this study is to evaluate the performance of the same five tests for the follow up of patients infected with S. stercoralis. Retrospective study on anonymized, cryo-preserved samples available at the Centre for Tropical Diseases (Negrar, Verona, Italy). Samples were collected before and from 3 to 12 months after treatment. The samples were tested with two commercially-available ELISA tests (IVD, Bordier), two techniques based on a recombinant antigen (NIE-ELISA and NIE-LIPS) and one in-house IFAT. The results of each test were evaluated both in relation to the results of fecal examination and to those of a composite reference standard (classifying as positive a sample with positive stools and/or at least three positive serology tests). The associations between the independent variables age and time and the dependent variable value of serological test (for all five tests), were analyzed by linear mixed-effects regression model. A high proportion of samples demonstrated for each test a seroreversion or a relevant decline (optical density/relative light units halved or decrease of at least two titers for IFAT) at follow up, results confirmed by the linear mixed effects model that showed a trend to seroreversion over time for all tests. In particular, IVD-ELISA (almost 90% samples demonstrated relevant decline) and IFAT (almost 87%) had the best performance. Considering only samples with a complete negativization, NIE-ELISA showed the best performance (72.5% seroreversion). Serology is useful for the follow up of patients infected with S. stercoralis and determining test of cure.

Standardization and validation of a cytometric bead assay to assess antibodies to multiple Plasmodium falciparum recombinant antigens.

PubMed

Ondigo, Bartholomew N; Park, Gregory S; Gose, Severin O; Ho, Benjamin M; Ochola, Lyticia A; Ayodo, George O; Ofulla, Ayub V; John, Chandy C

2012-12-21

Multiplex cytometric bead assay (CBA) have a number of advantages over ELISA for antibody testing, but little information is available on standardization and validation of antibody CBA to multiple Plasmodium falciparum antigens. The present study was set to determine optimal parameters for multiplex testing of antibodies to P. falciparum antigens, and to compare results of multiplex CBA to ELISA. Antibodies to ten recombinant P. falciparum antigens were measured by CBA and ELISA in samples from 30 individuals from a malaria endemic area of Kenya and compared to known positive and negative control plasma samples. Optimal antigen amounts, monoplex vs multiplex testing, plasma dilution, optimal buffer, number of beads required were assessed for CBA testing, and results from CBA vs. ELISA testing were compared. Optimal amounts for CBA antibody testing differed according to antigen. Results for monoplex CBA testing correlated strongly with multiplex testing for all antigens (r = 0.88-0.99, P values from <0.0001 - 0.004), and antibodies to variants of the same antigen were accurately distinguished within a multiplex reaction. Plasma dilutions of 1:100 or 1:200 were optimal for all antigens for CBA testing. Plasma diluted in a buffer containing 0.05% sodium azide, 0.5% polyvinylalcohol, and 0.8% polyvinylpyrrolidone had the lowest background activity. CBA median fluorescence intensity (MFI) values with 1,000 antigen-conjugated beads/well did not differ significantly from MFI with 5,000 beads/well. CBA and ELISA results correlated well for all antigens except apical membrane antigen-1 (AMA-1). CBA testing produced a greater range of values in samples from malaria endemic areas and less background reactivity for blank samples than ELISA. With optimization, CBA may be the preferred method of testing for antibodies to P. falciparum antigens, as CBA can test for antibodies to multiple recombinant antigens from a single plasma sample and produces a greater range of values in positive samples and lower background readings for blank samples than ELISA.

Cryocooler based test setup for high current applications

NASA Astrophysics Data System (ADS)

Pradhan, Jedidiah; Das, Nisith Kr.; Roy, Anindya; Duttagupta, Anjan

2018-04-01

A cryo-cooler based cryogenic test setup has been designed, fabricated, and tested. The setup incorporates two numbers of cryo-coolers, one for sample cooling and the other one for cooling the large magnet coil. The performance and versatility of the setup has been tested using large samples of high-temperature superconductor magnet coil as well as short samples with high current. Several un-calibrated temperature sensors have been calibrated using this system. This paper presents the details of the system along with results of different performance tests.

40 CFR 91.606 - Sample selection.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Sample selection. 91.606 Section 91....606 Sample selection. (a) Engines comprising a test sample will be selected at the location and in the... in the manner specified in the test order, an alternative selection procedure may be employed...

40 CFR 90.507 - Sample selection.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Sample selection. 90.507 Section 90... Auditing § 90.507 Sample selection. (a) Engines comprising a test sample will be selected at the location... cannot be selected in the manner specified in the test order, an alternative selection procedure may be...

40 CFR 89.507 - Sample selection.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Sample selection. 89.507 Section 89... Auditing § 89.507 Sample selection. (a) Engines comprising a test sample will be selected at the location... cannot be selected in the manner specified in the test order, an alternative selection procedure may be...

40 CFR 63.7 - Performance testing requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

...) program. Data quality objectives are the pretest expectations of precision, accuracy, and completeness of... test data bias. Gaseous audit samples are designed to audit the performance of the sampling system as... just as the compliance samples are collected. If a liquid or solid audit sample is designed to audit...

40 CFR 63.7 - Performance testing requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

...) program. Data quality objectives are the pretest expectations of precision, accuracy, and completeness of... test data bias. Gaseous audit samples are designed to audit the performance of the sampling system as... just as the compliance samples are collected. If a liquid or solid audit sample is designed to audit...

40 CFR 63.7 - Performance testing requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

...) program. Data quality objectives are the pretest expectations of precision, accuracy, and completeness of... test data bias. Gaseous audit samples are designed to audit the performance of the sampling system as... just as the compliance samples are collected. If a liquid or solid audit sample is designed to audit...

40 CFR 63.7 - Performance testing requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

...) program. Data quality objectives are the pretest expectations of precision, accuracy, and completeness of... test data bias. Gaseous audit samples are designed to audit the performance of the sampling system as... just as the compliance samples are collected. If a liquid or solid audit sample is designed to audit...

Electrofracturing test system and method of determining material characteristics of electrofractured material samples

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

Bauer, Stephen J.; Glover, Steven F.; Pfeifle, Tom

A device for electrofracturing a material sample and analyzing the material sample is disclosed. The device simulates an in situ electrofracturing environment so as to obtain electrofractured material characteristics representative of field applications while allowing permeability testing of the fractured sample under in situ conditions.

Sample Size Estimation: The Easy Way

ERIC Educational Resources Information Center

Weller, Susan C.

2015-01-01

This article presents a simple approach to making quick sample size estimates for basic hypothesis tests. Although there are many sources available for estimating sample sizes, methods are not often integrated across statistical tests, levels of measurement of variables, or effect sizes. A few parameters are required to estimate sample sizes and…

Kolmogorov-Smirnov test for spatially correlated data

USGS Publications Warehouse

Olea, R.A.; Pawlowsky-Glahn, V.

2009-01-01

The Kolmogorov-Smirnov test is a convenient method for investigating whether two underlying univariate probability distributions can be regarded as undistinguishable from each other or whether an underlying probability distribution differs from a hypothesized distribution. Application of the test requires that the sample be unbiased and the outcomes be independent and identically distributed, conditions that are violated in several degrees by spatially continuous attributes, such as topographical elevation. A generalized form of the bootstrap method is used here for the purpose of modeling the distribution of the statistic D of the Kolmogorov-Smirnov test. The innovation is in the resampling, which in the traditional formulation of bootstrap is done by drawing from the empirical sample with replacement presuming independence. The generalization consists of preparing resamplings with the same spatial correlation as the empirical sample. This is accomplished by reading the value of unconditional stochastic realizations at the sampling locations, realizations that are generated by simulated annealing. The new approach was tested by two empirical samples taken from an exhaustive sample closely following a lognormal distribution. One sample was a regular, unbiased sample while the other one was a clustered, preferential sample that had to be preprocessed. Our results show that the p-value for the spatially correlated case is always larger that the p-value of the statistic in the absence of spatial correlation, which is in agreement with the fact that the information content of an uncorrelated sample is larger than the one for a spatially correlated sample of the same size. ?? Springer-Verlag 2008.

Comparison of Sofia Legionella FIA and BinaxNOW® Legionella urinary antigen card in two national reference centers.

PubMed

Beraud, L; Gervasoni, K; Freydiere, A M; Descours, G; Ranc, A G; Vandenesch, F; Lina, G; Gaia, V; Jarraud, S

2015-09-01

The Sofia Legionella Fluorescence Immunoassay (FIA; Quidel) is a recently introduced rapid immunochromatographic diagnostic test for Legionnaires' disease using immunofluorescence technology designed to enhance its sensitivity. The aim of this study was to evaluate its performance for the detection of urinary antigens for Legionella pneumophila serogroup 1 in two National Reference Centers for Legionella. The sensitivity and specificity of the Sofia Legionella FIA test were determined in concentrated and nonconcentrated urine samples, before and after boiling, in comparison with the BinaxNOW® Legionella Urinary Antigen Card (UAC; Alere). Compared with BinaxNOW® Legionella UAC, the sensitivity of the Sofia Legionella test was slightly higher in nonconcentrated urine samples and was identical in concentrated urine samples. The specificity of the Sofia Legionella FIA test was highly reduced by the concentration of urine samples. In nonconcentrated samples, a lack of specificity was observed in 2.3 % of samples, all of them resolved by heat treatment. The Sofia Legionella FIA is a sensitive test for detecting Legionella urinary antigens with no previous urine concentration. However, all positive samples have to be re-tested after boiling to reach a high specificity. The reading is automatized on the Sofia analyzer, which can be connected to laboratory information systems, facilitating accurate and rapid reporting of results.

Experimental investigation of fatigue behavior of carbon fiber composites using fully-reversed four-point bending test

NASA Astrophysics Data System (ADS)

Amiri, Ali

Carbon fiber reinforced polymers (CFRP) have become an increasingly notable material for use in structural engineering applications. Some of their advantages include high strength-to-weight ratio, high stiffness-to-weight ratio, and good moldability. Prediction of the fatigue life of composite laminates has been the subject of various studies due to the cyclic loading experienced in many applications. Both theoretical studies and experimental tests have been performed to estimate the endurance limit and fatigue life of composite plates. One of the main methods to predict fatigue life is the four-point bending test. In most previous works, the tests have been done in one direction (load ratio, R, > 0). In the current work, we have designed and manufactured a special fixture to perform a fully reversed bending test (R = -1). Static four-point bending tests were carried out on three (0°/90°)15 and (± 45°)15 samples to measure the mechanical properties of CFRP. Testing was displacement-controlled at the rate of 10 mm/min until failure. In (0°/90°)15 samples, all failed by cracking/buckling on the compressive side of the sample. While in (± 45°)15 all three tests, no visual fracture or failure of the samples was observed. 3.4 times higher stresses were reached during four-point static bending test of (0° /90°)15 samples compared to (± 45°)15. Same trend was seen in literature for similar tests. Four-point bending fatigue tests were carried out on (0° /90°)15 sample with stress ratio, R = -1 and frequency of 5 Hz. Applied maximum stresses were approximately 45%, 56%, 67%, 72% and 76% of the measured yield stress for (0° /90°)15 samples. There was visible cracking through the thickness of the samples. The expected downward trend in fatigue life with increasing maximum applied stress was observed in S-N curves of samples. There appears to be a threshold for ‘infinite’ life, defined as 1.7 million cycles in the current work, at a maximum stress of about 200 MPa. The decay in flexural modulus of the beam as it goes under cyclic loading was calculated and it was seen that flexural modulus shows an exponential decay which can be expressed as: E = E0e AN. Four-point bending fatigue tests were carried out on three (±45°)15 samples with stress ratio, R = -1 and frequency of 5 Hz. Maximum applied stress was 85% of the measured yield stress of (±45°)15 samples. None of the samples failed, nor any sign of crack was seen. Tests were stopped once the number of cycles passed 1.7×106. In general, current study provided additional insight into the fatigue and static behavior of polymer composites and effect of fiber orientation in their mechanical behavior.

The Bootstrap, the Jackknife, and the Randomization Test: A Sampling Taxonomy.

PubMed

Rodgers, J L

1999-10-01

A simple sampling taxonomy is defined that shows the differences between and relationships among the bootstrap, the jackknife, and the randomization test. Each method has as its goal the creation of an empirical sampling distribution that can be used to test statistical hypotheses, estimate standard errors, and/or create confidence intervals. Distinctions between the methods can be made based on the sampling approach (with replacement versus without replacement) and the sample size (replacing the whole original sample versus replacing a subset of the original sample). The taxonomy is useful for teaching the goals and purposes of resampling schemes. An extension of the taxonomy implies other possible resampling approaches that have not previously been considered. Univariate and multivariate examples are presented.

Self-sampling for cervical screening: could it overcome some of the barriers to the Pap test?

PubMed

Mullins, Robyn; Scalzo, Katherine; Sultana, Farhana

2014-12-01

To determine which groups of women would be most likely to take part in self-sampling for cervical screening, and what they perceive as the key barriers and benefits to self-sampling. A random sample of 3000 women aged 18-69 in Victoria, Australia, were asked questions about "taking their own Pap test" in a telephone survey about cervical screening; 2526 answered the questions about self-sampling. The terminology "Pap test" was used in questions, due to the very low understanding of HPV and its link to cervical cancer. One-third of women (34.0%) indicated they would prefer to self-sample, 57.2% would not and 8.7% were unsure. Preference for self-sampling was significantly stronger among women who had not had a Pap test for more than three years (64.8%, p < .001) or who had never had one (62.1%, p < .001), compared with those up-to-date (27.0%). Convenience was a key benefit (37.8%), as was less embarrassment (31.5%). For those who did not want to self-sample or were unsure, key factors included professionals being more skilled (53.4% and 28.2% respectively), and doubts about being able to do it properly (28.9% and 23.6%). Self-sampling was most popular among women who needed to have a Pap test, and could potentially reach some women who are not participating appropriately in cervical screening. Key barriers to participation could be addressed by providing information about the test being for HPV, and being easier to do properly than a Pap test. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Buoyant Effects on the Flammability of Silicone Samples Planned for the Spacecraft Fire Experiment (Saffire)

NASA Technical Reports Server (NTRS)

Niehaus, Justin E.; Ferkul, Paul V.; Gokoglu, Suleyman A.; Ruff, Gary A.

2015-01-01

Flammability experiments on silicone samples were conducted in anticipation of the Spacecraft Fire Experiment (Saffire). The sample geometry was chosen to match the NASA 6001 Test 1 specification, namely 5 cm wide by 30 cm tall. Four thicknesses of silicone (0.25, 0.36, 0.61 and 1.00 mm) were examined. Tests included traditional upward buoyant flame spread using Test 1 procedures, downward opposed-flow flame spread, horizontal and angled flame spread, and forced-flow upward and downward flame spread. In addition to these configurations, upward and downward tests were conducted in a chamber with varying oxygen concentrations. In the upward buoyant flame spread tests, the flame generally did not burn the entire sample. As thickness was increased, the flame spread distance decreased before flame extinguishment. For the thickest sample, ignition could not be achieved. In the downward tests, the two thinnest samples permitted the flame to burn the entire sample, but the spread rate was lower compared to the corresponding upward values. The other two thicknesses could not be ignited in the downward configuration. The increased flammability for downward spreading flames relative to upward ones is uncommon. The two thinnest samples also burned completely in the horizontal configuration, as well as at angles up to 75 degrees from the horizontal. Upward tests in air with an added forced flow were more flammable. The upward and downward flammability behavior was compared in atmospheres of varying oxygen concentration to determine a maximum oxygen concentration for each configuration. Complementary analyses using EDS, TGA, and SEM techniques suggest the importance of the silica layer deposited downstream onto the unburned sample surface.

Improved ASTM G72 Test Method for Ensuring Adequate Fuel-to-Oxidizer Ratios

NASA Technical Reports Server (NTRS)

Juarez, Alfredo; Harper, Susana A.

2016-01-01

The ASTM G72/G72M-15 Standard Test Method for Autogenous Ignition Temperature of Liquids and Solids in a High-Pressure Oxygen-Enriched Environment is currently used to evaluate materials for the ignition susceptibility driven by exposure to external heat in an enriched oxygen environment. Testing performed on highly volatile liquids such as cleaning solvents has proven problematic due to inconsistent test results (non-ignitions). Non-ignition results can be misinterpreted as favorable oxygen compatibility, although they are more likely associated with inadequate fuel-to-oxidizer ratios. Forced evaporation during purging and inadequate sample size were identified as two potential causes for inadequate available sample material during testing. In an effort to maintain adequate fuel-to-oxidizer ratios within the reaction vessel during test, several parameters were considered, including sample size, pretest sample chilling, pretest purging, and test pressure. Tests on a variety of solvents exhibiting a range of volatilities are presented in this paper. A proposed improvement to the standard test protocol as a result of this evaluation is also presented. Execution of the final proposed improved test protocol outlines an incremental step method of determining optimal conditions using increased sample sizes while considering test system safety limits. The proposed improved test method increases confidence in results obtained by utilizing the ASTM G72 autogenous ignition temperature test method and can aid in the oxygen compatibility assessment of highly volatile liquids and other conditions that may lead to false non-ignition results.

Typhoid fever in a Tertiary Hospital in Nigeria: Another look at the Widal agglutination test as a preferred option for diagnosis.

PubMed

Enabulele, Osahon; Awunor, Simeon Nyemike

2016-01-01

Single Widal agglutination test rather than blood culture, is commonly employed to diagnose typhoid fever in Nigeria. We took another look at the Widal agglutination test as a preferred option for diagnosis of typhoid fever by determining the specificity and sensitivity of Widal agglutination test in febrile adult patients. Two hundred and seventy-one blood samples from consecutive adults (>18 years) with febrile illness attending the General Practice Clinic of the University of Benin Teaching Hospital were tested using the Widal agglutination test, blood culture, and malaria parasite test on each sample to establish the diagnosis of typhoid fever. Of the 271 blood samples 124 (45.76%) were positive following a Widal agglutination test, 60 (22.10%) blood samples grew Salmonella organisms on blood culture while 55 (20.29%) blood samples showed a co-infection of typhoid fever and malaria. A sensitivity of 35%, specificity of 51%, positive predictive value of 17%, and a negative predictive value of 73% were observed for Widal agglutination test as a diagnostic modality for typhoid fever infection. A single Widal agglutination test is not a valid diagnostic option for typhoid fever while co-infection with malaria parasite is the preponderant microbiological finding in typhoid fever infections. The severity of malaria parasitemia is associated with positive titers on Widal test.

Typhoid fever in a Tertiary Hospital in Nigeria: Another look at the Widal agglutination test as a preferred option for diagnosis

PubMed Central

Enabulele, Osahon; Awunor, Simeon Nyemike

2016-01-01

Background: Single Widal agglutination test rather than blood culture, is commonly employed to diagnose typhoid fever in Nigeria. We took another look at the Widal agglutination test as a preferred option for diagnosis of typhoid fever by determining the specificity and sensitivity of Widal agglutination test in febrile adult patients. Materials and Methods: Two hundred and seventy-one blood samples from consecutive adults (>18 years) with febrile illness attending the General Practice Clinic of the University of Benin Teaching Hospital were tested using the Widal agglutination test, blood culture, and malaria parasite test on each sample to establish the diagnosis of typhoid fever. Results: Of the 271 blood samples 124 (45.76%) were positive following a Widal agglutination test, 60 (22.10%) blood samples grew Salmonella organisms on blood culture while 55 (20.29%) blood samples showed a co-infection of typhoid fever and malaria. A sensitivity of 35%, specificity of 51%, positive predictive value of 17%, and a negative predictive value of 73% were observed for Widal agglutination test as a diagnostic modality for typhoid fever infection. Conclusion: A single Widal agglutination test is not a valid diagnostic option for typhoid fever while co-infection with malaria parasite is the preponderant microbiological finding in typhoid fever infections. The severity of malaria parasitemia is associated with positive titers on Widal test. PMID:27397952

Development and application of a marine sediment pore-water toxicity test using Ulva fasciata zoospores

USGS Publications Warehouse

Hooten, Russell L.; Carr, R. Scott

1998-01-01

An acute (96 h) pore-water toxicity test protocol using germination and growth of Ulva fasciatazoospores as endpoints was developed to test the toxicity of marine and estuarine sediment pore-water samples. Tests with an organic toxicant (sodium dodecyl sulfate; SDS), three metals (Cd, Cu, and Zn), and ammonia (NH3) were conducted to determine zoospore sensitivity. Zoospore germination and gametophyte growth were as sensitive to SDS as sea urchin (Arbacia punctulata) fertilization and embryological development. Zoospore sensitivity to metals was greater than or comparable to that of adult macroalgae. Zoospores were less sensitive to NH3than were other commonly used toxicity test organisms. Test results using this algal assay with sediment pore-water samples with high NH3 concentrations were compared with results from sea urchin fertilization and embryological development tests for the same samples. Ulva fasciatazoospore germination was not affected by samples with high NH3 concentrations that were toxic in both sea urchin tests. Zoospore tolerance of NH3 and sensitivity to other contaminants indicate that their response may be useful in toxicity identification evaluation studies with pore-water samples that contain high concentrations of unionized NH3.

46 CFR 160.176-15 - Production tests and inspections.

Code of Federal Regulations, 2010 CFR

2010-10-01

... known weight and winch, (B) a scale, winch, and fixed anchor, or (C) a tensile test machine that is... laboratory inspector tests and inspects the lot; (ii) Perform required testing of each incoming lot of... produced the components used in the lifejacket. (d) Samples. (1) Samples used in testing and inspections...

A sample-to-result system for blood coagulation tests on a microfluidic disk analyzer

PubMed Central

Lin, Chia-Hui; Liu, Cheng-Yuan; Shih, Chih-Hsin; Lu, Chien-Hsing

2014-01-01

In this report, we describe in detail a microfluidic analyzer, which is able to conduct blood coagulation tests using whole blood samples. Sample preparation steps, such as whole blood aliquoting and metering, plasma separation, decanting, and mixing with reagents were performed in sequence through microfluidic functions integrated on a disk. Both prothrombin time (PT) and activated partial thromboplastin time (aPTT) were carried out on the same platform and the test results can be reported in 5 min. Fifty clinical samples were tested for both PT and aPTT utilizing the microfluidic disk analyzer and the instrument used in hospitals. The test results showed good correlation and agreement between the two instruments. PMID:25332733

Investigation of Hall Effect Thruster Channel Wall Erosion Mechanisms

DTIC Science & Technology

2016-08-02

pretest height and laser image, c, d) post - test height and laser image. On all the pre-roughened samples, a cell-pattern developed from the random...7.8: Pre and post - test sample microscopy: Fused silica sample SA6 (loaded), 20x, center of exposed surface, a, b) pretest height and laser image, c, d...stress on the surface features developed during plasma erosion. The experiment is also designed specifically to test the SRH. A test fixture is

Transistor step stress testing program for JANTX2N2905A

NASA Technical Reports Server (NTRS)

1979-01-01

The effect of power/temperature step stress when applied to the transistor JANTX2N2905A manufactured by Texas Instruments and Motorola is reported. A total of 48 samples from each manufacturer was submitted to the process outlined. In addition, two control sample units were maintained for verification of the electrical parametric testing. All test samples were subjected to the electrical tests outlined in Table 2 after completing the prior power/temperature step stress point.

Evaluation of the black light test for screening aflatoxin-contaminated maize in the Brazilian food industry.

PubMed

Gloria, E M; Fonseca, H; Calori-Domingues, M A; Souza, I M

1998-01-01

The results of the black light test for aflatoxin-contaminated maize carried out in a large food factory in the State of São Paulo was evaluated against bi-directional thin layer chromatography (TLC) analysis for 286 samples of maize. All 286 samples were accepted by the black light test (< 7 fluorescent points), however, the results from TLC analysis showed that 96 samples were contaminated and 14 showed aflatoxin B1 contamination levels higher than 20 micrograms/kg. There were 14 false negative results and no false positives and out of the 14 samples, six did not show visible fluorescent points. If the rejection criterion of one or more fluorescent points were applied, the six samples would be accepted by the black light test. But, in this case, 95 samples would be rejected and 87 results would be false positives because they did not have contamination levels over 20 micrograms/kg which is the acceptance limit of the black light test. The results indicate that the black light test, as utilized by this factory, was not able to indicate lots with possible contamination and the black light test, as recommended in the literature, would produce a high number of false positives. It is necessary to make more studies on the use of black light as a screening test for possible aflatoxin B1-contaminated maize.

Screening for tinea unguium by Dermatophyte Test Strip.

PubMed

Tsunemi, Y; Takehara, K; Miura, Y; Nakagami, G; Sanada, H; Kawashima, M

2014-02-01

The direct microscopy, fungal culture and histopathology that are necessary for the definitive diagnosis of tinea unguium are disadvantageous in that detection sensitivity is affected by the level of skill of the person who performs the testing, and the procedures take a long time. The Dermatophyte Test Strip, which was developed recently, can simply and easily detect filamentous fungi in samples in a short time, and there are expectations for its use as a method for tinea unguium screening. With this in mind, we examined the detection capacity of the Dermatophyte Test Strip for tinea unguium. The presence or absence of fungal elements was judged by direct microscopy and Dermatophyte Test Strip in 165 nail samples obtained from residents in nursing homes for the elderly. Moreover, the minimum sample amount required for positive determination was estimated using 32 samples that showed positive results by Dermatophyte Test Strip. The Dermatophyte Test Strip showed 98% sensitivity, 78% specificity, 84·8% positive predictive value, 97% negative predictive value and a positive and negative concordance rate of 89·1%. The minimum sample amount required for positive determination was 0·002-0·722 mg. The Dermatophyte Test Strip showed very high sensitivity and negative predictive value, and was considered a potentially useful method for tinea unguium screening. Positive determination was considered to be possible with a sample amount of about 1 mg. © 2013 British Association of Dermatologists.

The performance of multimodal hyperspectral spectroscopy in the detection of precancerous cervical lesions

NASA Astrophysics Data System (ADS)

Trahmono; Lusiana, N.; Indarti, J.

2017-08-01

The aim of this study was to compare the performance of multimodal hyperspectral spectroscopy (MHS), which combines fluorescence and reflectance spectroscopy, with that of conventional laboratory-based screening tests, such as the Papanicolaou (Pap) smear test and human papilloma virus (HPV) DNA test, for detecting precancerous lesions of the cervix. The study utilized a cross-sectional design, and the kappa test was used in the analytical assessment. MHS scans were obtained from a sample of 70 consecutive patients, followed by sample collection for Pap and HPV DNA analysis and colposcopy referral, if indicated. Of the 70 patients evaluated, the results of cervical spectroscopy were normal in 38 (54.3%) patients, and they were abnormal in 32 (45.7%) patients. Based on the cytology results, 45 (64.3%) samples were normal, and 25 (35.7%) samples were abnormal. According to the results of the HPV DNA test, 47 (67.14%) samples were normal, and 17 (24.28%) samples were abnormal. Based on the results of the kappa test, the agreement between MHS and cytology was 0.793 (p < 0.001). The agreement between MHS and the HPV DNA test was 0.195 (p = 0.086), and the agreement between MHS and colposcopy was 0.479 (p < 0.001).

A Passive Earth-Entry Capsule for Mars Sample Return

NASA Technical Reports Server (NTRS)

Mitcheltree, Robert A.; Kellas, Sotiris

1999-01-01

A combination of aerodynamic analysis and testing, aerothermodynamic analysis, structural analysis and testing, impact analysis and testing, thermal analysis, ground characterization tests, configuration packaging, and trajectory simulation are employed to determine the feasibility of an entirely passive Earth entry capsule for the Mars Sample Return mission. The design circumvents the potential failure modes of a parachute terminal descent system by replacing that system with passive energy absorbing material to cushion the Mars samples during ground impact. The suggested design utilizes a spherically blunted 45-degree half-angle cone forebody with an ablative heat shield. The primary structure is a hemispherical, composite sandwich enclosing carbon foam energy absorbing material. Though no demonstration test of the entire system is included, results of the tests and analysis presented indicate that the design is a viable option for the Mars Sample Return Mission.

Decision Models for Determining the Optimal Life Test Sampling Plans

NASA Astrophysics Data System (ADS)

Nechval, Nicholas A.; Nechval, Konstantin N.; Purgailis, Maris; Berzins, Gundars; Strelchonok, Vladimir F.

2010-11-01

Life test sampling plan is a technique, which consists of sampling, inspection, and decision making in determining the acceptance or rejection of a batch of products by experiments for examining the continuous usage time of the products. In life testing studies, the lifetime is usually assumed to be distributed as either a one-parameter exponential distribution, or a two-parameter Weibull distribution with the assumption that the shape parameter is known. Such oversimplified assumptions can facilitate the follow-up analyses, but may overlook the fact that the lifetime distribution can significantly affect the estimation of the failure rate of a product. Moreover, sampling costs, inspection costs, warranty costs, and rejection costs are all essential, and ought to be considered in choosing an appropriate sampling plan. The choice of an appropriate life test sampling plan is a crucial decision problem because a good plan not only can help producers save testing time, and reduce testing cost; but it also can positively affect the image of the product, and thus attract more consumers to buy it. This paper develops the frequentist (non-Bayesian) decision models for determining the optimal life test sampling plans with an aim of cost minimization by identifying the appropriate number of product failures in a sample that should be used as a threshold in judging the rejection of a batch. The two-parameter exponential and Weibull distributions with two unknown parameters are assumed to be appropriate for modelling the lifetime of a product. A practical numerical application is employed to demonstrate the proposed approach.

Stability of (13) C-Urea Breath Test Samples Over Time in the Diagnosis of Helicobacter pylori.

PubMed

Perets, Tsachi Tsadok; Shporn, Einav; Boltin, Doron; Dickman, Ram; Niv, Yaron

2016-05-01

The accuracy and repeatability of breath test in the diagnosis of Helicobacter pylori infection have not been adequately investigated. Although it has been shown that storage for long periods does not affect the analysis results, no data are available on the effect of repetitive testing. In this study, our aim was to evaluate the repeatability of the analyses of breath samples at room temperature. A total of 202 positive breath samples were collected in duplicates, before and after administration of 75 mg (13) C- urea dissolved in 100 ml of orange juice. Breath test results were expressed as delta (13) CO2 . The cut-off value was 3.5 parts per thousand. Each sample was analyzed in a mass spectrometer 7, 14, 21, and 28 days after collection. The accuracy calculation was based on the comparison of the delta (13) CO2 obtained in the three consecutive weeks following the first test run to the delta (13) CO2 obtained in the first test run. Two hundred (99%), 197 (97.52%), and 196 (97%) of the 202 samples tested positive in the second, third, and fourth test runs, respectively. The accuracy of the delta (13) CO2 was 98.6%, 99.2%, and 96.7% in the three consecutive runs, respectively. Short-term storage of 1 month does not affect sample stability or the results of (13) C-urea breath tests in up to three consecutive repeats. © 2015 Wiley Periodicals, Inc.

Evaluation of Nucleic Acid Preservation Cards for West Nile Virus Testing in Dead Birds

PubMed Central

Foss, Leslie; Reisen, William K.; Fang, Ying; Kramer, Vicki; Padgett, Kerry

2016-01-01

The California West Nile virus (WNV) Dead Bird Surveillance Program (DBSP) is an important component of WNV surveillance in the state. We evaluated FTA™ and RNASound™ cards as an alternative method for sampling dead birds for WNV molecular testing as these cards allow for more cost effective, rapid, and safer diagnostic sampling than the shipment of bird carcasses. To evaluate accuracy of results among avian sampling regimes, Reverse-Transcription Polymerase Chain Reaction (RT-PCR) results from FTA™ and RNASound™ cards were compared with results from kidney tissue, brain tissue, or oral swabs in lysis buffer in 2012–2013. In addition, RT-PCR results were compared with results from oral swabs tested by rapid antigen tests (RAMP™ and VecTOR™). While test results from the cards were not as sensitive as kidney tissue testing, they were more likely to provide accurate results than rapid antigen tests, and detected WNV in corvids as well as in other passerines, raptors, and waterfowl. Overall, WNV RT-PCR cycle threshold (Ct) scores from the cards were higher than those from tissue testing, but both card products displayed high sensitivity and specificity. American Crow samples provided the highest sensitivity. The cards also proved to be easier and more convenient vehicles for collecting and shipping samples, and in 2014 our program launched use of RNASound™ cards in the DBSP. Both FTA™ and RNASound™ products displayed 96% agreement with tissue results and are an adequate alternative sampling method for WNV dead bird testing. PMID:27341492

HNU-HANBY PCP IMMUNOASSAY TEST KIT - INNOVATIVE TECHNOLOGY EVALUATION REPORT

EPA Science Inventory

The HNU-Hanby pentachlorophenol (PCP) test kit rapidly analyzes for PCP in soil samples. The test kit can only detect those PCP carriers that contain aromatic compounds. The test kit estimates PCP concentrations in soil samples indirectly by measuring petroleum hydrocarbon carrie...

Investigation of an algorithm for anti HCV EIA reactivity in blood donor screening in Turkey in the absence of nucleic acid amplification screening.

PubMed

Karakoc, Ayse Esra; Berkem, Rukiye; Irmak, Hasan; Demiroz, Ali Pekcan; Yenicesu, Idil; Ertugrul, Nigar; Arslan, Önder; Kemahli, Sabri; Yilmaz, Sevinc; Ozcebe, Osman; Kara, Abdurrahman; Ozet, Gulsum; Acikgoz, Ziya Cibali; Acikgoz, Tulin

2017-10-01

In this study we aimed to propose an algorithm for initial anti HCV EIA reactive blood donations in Turkey where nucleic acid amplification tests are not yet obligatory for donor screening. A total of 416 anti HCV screening test reactive donor samples collected from 13 blood centers from three cities in Turkey were tested in duplicate by Ortho HCV Ab Version 3.0 and Radim HCV Ab. All the repeat reactive samples were tested by INNO-LIA HCV Ab 3.0 or Chiron RIBA HCV 3.0 and Abbott Real Time HCV. Intra-assay correlations were calculated with Pearson r test. ROC analysis was used to study the relationship between EIA tests and the confirmatory tests. The number of repeat reactive results with Ortho EIA were 221 (53.1%) whereas that of microEIA, 62 (14.9%). Confirmed positivity rate was 14.6% (33/226) by RIBA and 10.6% (24/226) by NAT. Reactive PCR results were predicted with 100% sensitivity and 95% specificity with S/CO levels of 8.1 with Ortho EIA and 3.4 with microEIA. Repeat reactivity rates declined with a second HCV antibody assay. Samples repeat reactive with one HCV antibody test and negative with the other were all NAT negative. All the NAT reactive samples were RIBA positive. None of the RIBA indeterminate or negative samples were NAT reactive. Considering the threshold values for EIA kits determined by ROC analysis NAT was decided to be performed for the samples above the threshold value and a validated supplemental HCV antibody test for the samples below. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Kolmogorov-Smirnov test for the molecular clock based on Bayesian ensembles of phylogenies

PubMed Central

Antoneli, Fernando; Passos, Fernando M.; Lopes, Luciano R.

2018-01-01

Divergence date estimates are central to understand evolutionary processes and depend, in the case of molecular phylogenies, on tests of molecular clocks. Here we propose two non-parametric tests of strict and relaxed molecular clocks built upon a framework that uses the empirical cumulative distribution (ECD) of branch lengths obtained from an ensemble of Bayesian trees and well known non-parametric (one-sample and two-sample) Kolmogorov-Smirnov (KS) goodness-of-fit test. In the strict clock case, the method consists in using the one-sample Kolmogorov-Smirnov (KS) test to directly test if the phylogeny is clock-like, in other words, if it follows a Poisson law. The ECD is computed from the discretized branch lengths and the parameter λ of the expected Poisson distribution is calculated as the average branch length over the ensemble of trees. To compensate for the auto-correlation in the ensemble of trees and pseudo-replication we take advantage of thinning and effective sample size, two features provided by Bayesian inference MCMC samplers. Finally, it is observed that tree topologies with very long or very short branches lead to Poisson mixtures and in this case we propose the use of the two-sample KS test with samples from two continuous branch length distributions, one obtained from an ensemble of clock-constrained trees and the other from an ensemble of unconstrained trees. Moreover, in this second form the test can also be applied to test for relaxed clock models. The use of a statistically equivalent ensemble of phylogenies to obtain the branch lengths ECD, instead of one consensus tree, yields considerable reduction of the effects of small sample size and provides a gain of power. PMID:29300759

Comparison of the Hologic Aptima HIV-1 Quant Dx Assay to the Roche COBAS Ampliprep/COBAS TaqMan HIV-1 Test v2.0 for the quantification of HIV-1 RNA in plasma samples.

PubMed

Schønning, Kristian; Johansen, Kim; Landt, Bodil; Benfield, Thomas; Westh, Henrik

2017-07-01

HIV-RNA is the most important parameter for monitoring antiviral treatment in individuals infected with HIV-1. Knowledge of the performance of different tests for the quantification of HIV-1 RNA is therefore important for clinical care. To compare the analytical performance of the Aptima HIV-1 Quant Dx Assay (Aptima) and the COBAS Ampliprep/COBAS TaqMan HIV-1 Test v2.0 (CAPCTMv2) for the quantification of HIV-1 RNA in plasma samples. The performance of the two tests was compared on 216 clinical plasma samples, on dilutions series in seven replicates of five clinical samples of known subtype and on ten replicates of the Acrometrix High and Low Positive Control. Bland-Altman analysis of 130 samples that quantified in both tests did not show indications of gross mis-quantification of either test. A tendency of the Aptima assay to quantify higher at high viral load compared to the CAPCTMv2 was observed in Bland-Altman analysis, by Deming regression (Slope 1.13) and in dilution series of clinical samples. Precision evaluated using the Acrometrix Positive Controls was similar for the High Control (CV: 1.2% vs. 1.3%; Aptima assay vs. CAPCTMv2 test, respectively), but differed for the Low control (CV: 17.9% vs. 7.1%; Aptima assay vs. CAPCTMv2 test, respectively). However, this did not impact clinical categorization of clinical samples at neither the 50 cp/mL nor 200 cp/mL level. The Aptima assay and the CAPCTMv2 test are highly correlated and are useful for monitoring HIV-infected individuals. Copyright © 2017 Elsevier B.V. All rights reserved.

Durability of building stones against artificial salt crystallization

NASA Astrophysics Data System (ADS)

Min, K.; Park, J.; Han, D.

2005-12-01

Salts have been known as the most powerful weathering agents, especially when combined with frost action. Salt crystallization test along with freezing-thawing test and acid immersion test was carried out to assess the durability of building stones against weathering. Granite, limestone, marble and basalt were sampled from different quarries in south Korea for this study. One cycle of artificial salt crystallization test was composed of immersion of cored rock specimens in oversaturated solutions of CaCl2, KCl, NaCl and Na2SO4, respectively for 15 hours and successive drying in an oven of 105°C for 3 hours and cooling at room temperature. Tests were performed up to 30 cycles, and specific gravity and ultrasonic velocity were measured after experiencing every 10 cycles and uniaxial compressive strength was measured only after 30 cycles. During the repeated Na2SO4 salt crystallization, some rock samples were gradually deformed excessively and burst after 20 to 30 cycles of test. The variation patterns of physical properties during the salt crystallization tests are too variable to generalize the effect of salt weathering on physical properties but limestone, marble and basalt samples showed relatively greater change of physical properties than granite samples. The recrystallized salts were well observed in the cracks of rock samples through the scanning electron microscope. In the all salt crystallization tests, apparent specific gravities for all tested samples increased generally but not so significantly due to recrystallization of salts. It can be inferred that filling the pores with salt crystals cause the increase of ultrasonic velocity during the early stage of salt crystallization and then in later stages the repeated cycles of salt crystallization result in development of cracks leading decrease of ultrasonic velocity for some rock samples.

Test Anxiety Prevalence and Gender Differences in a Sample of English Secondary School Students

ERIC Educational Resources Information Center

Putwain, Dave; Daly, Anthony L.

2014-01-01

The aim of this study was to estimate the proportion of students who report themselves as highly test anxious in a sample of English secondary schools and whether this proportion differed by gender. Self-report test anxiety data were collected from 2435 secondary school students in 11 schools. Results showed that 16.4% of the sample reported…

Factorial Structure of the New Ecological Paradigm Scale in Two French Samples

ERIC Educational Resources Information Center

Fleury-Bahi, Ghozlane; Marcouyeux, Aurore; Renard, Elise; Roussiau, Nicolas

2015-01-01

The principal objective of this research is to test the factorial structure of the New Ecological Paradigm scale on a population of men and women residing in France. The tested model is a second-order factorial model. This factorial structure is evaluated on two separate samples to test the stability of the solution (a first sample of 253…

40 CFR 53.57 - Test for filter temperature control during sampling and post-sampling periods.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 5 2011-07-01 2011-07-01 false Test for filter temperature control... Class I and Class II Equivalent Methods for PM2.5 or PM10â2.5 § 53.57 Test for filter temperature... candidate sampler's ability to prevent excessive overheating of the PM sample collection filter (or filters...

40 CFR 53.57 - Test for filter temperature control during sampling and post-sampling periods.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 6 2014-07-01 2014-07-01 false Test for filter temperature control... Class I and Class II Equivalent Methods for PM 2.5 or PM 10-2.5 § 53.57 Test for filter temperature... candidate sampler's ability to prevent excessive overheating of the PM sample collection filter (or filters...

40 CFR 53.57 - Test for filter temperature control during sampling and post-sampling periods.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 5 2010-07-01 2010-07-01 false Test for filter temperature control... Class I and Class II Equivalent Methods for PM2.5 or PM10â2.5 § 53.57 Test for filter temperature... candidate sampler's ability to prevent excessive overheating of the PM sample collection filter (or filters...

40 CFR 53.57 - Test for filter temperature control during sampling and post-sampling periods.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 6 2012-07-01 2012-07-01 false Test for filter temperature control... Class I and Class II Equivalent Methods for PM2.5 or PM10â2.5 § 53.57 Test for filter temperature... candidate sampler's ability to prevent excessive overheating of the PM sample collection filter (or filters...

40 CFR 53.57 - Test for filter temperature control during sampling and post-sampling periods.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 6 2013-07-01 2013-07-01 false Test for filter temperature control... Class I and Class II Equivalent Methods for PM 2.5 or PM 10-2,5 § 53.57 Test for filter temperature... candidate sampler's ability to prevent excessive overheating of the PM sample collection filter (or filters...

40 CFR 80.400 - What defenses apply to persons deemed liable for a violation of a prohibited act?

Code of Federal Regulations, 2010 CFR

2010-07-01

... sampling and testing program, as described in paragraph (d) of this section. A carrier may rely on the... sampling and testing by the branded refiner or importer to ensure compliance with such contractual... person must present evidence of the following: (1) A periodic sampling and testing program to ensure the...

tscvh R Package: Computational of the two samples test on microarray-sequencing data

NASA Astrophysics Data System (ADS)

Fajriyah, Rohmatul; Rosadi, Dedi

2017-12-01

We present a new R package, a tscvh (two samples cross-variance homogeneity), as we called it. This package is a software of the cross-variance statistical test which has been proposed and introduced by Fajriyah ([3] and [4]), based on the cross-variance concept. The test can be used as an alternative test for the significance difference between two means when sample size is small, the situation which is usually appeared in the bioinformatics research. Based on its statistical distribution, the p-value can be also provided. The package is built under a homogeneity of variance between samples.

Swab or biopsy samples for bioburden testing of allograft musculoskeletal tissue?

PubMed

Varettas, Kerry

2014-12-01

Swab and biopsy samples of allograft musculoskeletal tissue are most commonly collected by tissue banks for bacterial and fungal bioburden testing. An in vitro study was performed using the National Committee for Clinical Laboratory Standards standard 'Quality control of microbiological transport systems' (2003) to validate and evaluate the recovery of six challenge organisms from swab and biopsy samples of allograft musculoskeletal tissue. On average, 8.4 to >100 and 7.2 to >100 % of the inoculum was recovered from swab and biopsy samples respectively. A retrospective review of donor episodes was also performed, consisting of paired swab and biopsy samples received in this laboratory during the period 2001-2012. Samples of allograft femoral heads were collected from living donors during hip operations. From the 3,859 donor episodes received, 21 paired swab and biopsy samples each recovered an isolate, 247 swab samples only and 79 biopsy samples only were culture positive. Low numbers of challenge organisms were recovered from inoculated swab and biopsy samples in the in vitro study and validated their use for bioburden testing of allograft musculoskeletal tissue. Skin commensals were the most common group of organisms isolated during a 12-year retrospective review of paired swab and biopsy samples from living donor allograft femoral heads. Paired swab and biopsy samples are a suitable representative sample of allograft musculoskeletal tissue for bioburden testing.

Use of the binomial distribution to predict impairment: application in a nonclinical sample.

PubMed

Axelrod, Bradley N; Wall, Jacqueline R; Estes, Bradley W

2008-01-01

A mathematical model based on the binomial theory was developed to illustrate when abnormal score variations occur by chance in a multitest battery (Ingraham & Aiken, 1996). It has been successfully used as a comparison for obtained test scores in clinical samples, but not in nonclinical samples. In the current study, this model has been applied to demographically corrected scores on the Halstead-Reitan Neuropsychological Test Battery, obtained from a sample of 94 nonclinical college students. Results found that 15% of the sample had impairments suggested by the Halstead Impairment Index, using criteria established by Reitan and Wolfson (1993). In addition, one-half of the sample obtained impaired scores on one or two tests. These results were compared to that predicted by the binomial model and found to be consistent. The model therefore serves as a useful resource for clinicians considering the probability of impaired test performance.

Materials samples face rigors of space.

PubMed

Flinn, Edward D

2002-07-01

The Materials International Space Station Experiment (MISSE) is described. This project is designed to conduct long duration materials tests on samples attached to the ISS. A batch of 750 material samples were delivered on STS-105 and attached to the ISS airlock. They will be exposed to the space environment for 18 months and are slated to return on STS-114. A second batch of 750 samples is being prepared. The experiment containers were used originally for the Mir Environmental Effects Payload, which tested a variety of substances, including some slated for use on the ISS. Researchers are particularly interested in the effects of atomic oxygen on the samples. Some samples are being tested to determine their use in radiation protection. As part of the MISSE project, ultrathin tether materials are being tested for use on the Propulsive Small Expendable Depoloyer System (ProSEDS), which will use a tether system to change a satellite's orbital altitude.

Key considerations for the experimental training and evaluation of cancer odour detection dogs: lessons learnt from a double-blind, controlled trial of prostate cancer detection

PubMed Central

2014-01-01

Background Cancer detection using sniffer dogs is a potential technology for clinical use and research. Our study sought to determine whether dogs could be trained to discriminate the odour of urine from men with prostate cancer from controls, using rigorous testing procedures and well-defined samples from a major research hospital. Methods We attempted to train ten dogs by initially rewarding them for finding and indicating individual prostate cancer urine samples (Stage 1). If dogs were successful in Stage 1, we then attempted to train them to discriminate prostate cancer samples from controls (Stage 2). The number of samples used to train each dog varied depending on their individual progress. Overall, 50 unique prostate cancer and 67 controls were collected and used during training. Dogs that passed Stage 2 were tested for their ability to discriminate 15 (Test 1) or 16 (Tests 2 and 3) unfamiliar prostate cancer samples from 45 (Test 1) or 48 (Tests 2 and 3) unfamiliar controls under double-blind conditions. Results Three dogs reached training Stage 2 and two of these learnt to discriminate potentially familiar prostate cancer samples from controls. However, during double-blind tests using new samples the two dogs did not indicate prostate cancer samples more frequently than expected by chance (Dog A sensitivity 0.13, specificity 0.71, Dog B sensitivity 0.25, specificity 0.75). The other dogs did not progress past Stage 1 as they did not have optimal temperaments for the sensitive odour discrimination training. Conclusions Although two dogs appeared to have learnt to select prostate cancer samples during training, they did not generalise on a prostate cancer odour during robust double-blind tests involving new samples. Our study illustrates that these rigorous tests are vital to avoid drawing misleading conclusions about the abilities of dogs to indicate certain odours. Dogs may memorise the individual odours of large numbers of training samples rather than generalise on a common odour. The results do not exclude the possibility that dogs could be trained to detect prostate cancer. We recommend that canine olfactory memory is carefully considered in all future studies and rigorous double-blind methods used to avoid confounding effects. PMID:24575737

Experimental breakdown of selected anodized aluminum samples in dilute plasmas

NASA Technical Reports Server (NTRS)

Grier, Norman T.; Domitz, Stanley

1992-01-01

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

Sediment toxicity test results for the Urban Waters Study 2010, Bellingham Bay, Washington

USGS Publications Warehouse

Biedenbach, James M.

2011-01-01

The Washington Department of Ecology annually determines the quality of recently deposited sediments in Puget Sound as a part of Ecology's Urban Waters Initiative. The annual sediment quality studies use the Sediment Quality Triad (SQT) approach, thus relying on measures of chemical contamination, toxicity, and benthic in-faunal effects (Chapman, 1990). Since 2002, the studies followed a rotating sampling scheme, each year sampling a different region of the greater Puget Sound Basin. During the annual studies, samples are collected in locations selected with a stratified-random design, patterned after the designs previously used in baseline surveys completed during 1997-1999 (Long and others, 2003; Wilson and Partridge, 2007). Sediment samples were collected by personnel from the Washington Department of Ecology, in June of 2010 and shipped to the U. S. Geological Survey (USGS) laboratory in Corpus Christi, Texas (not shown), where the tests were performed. Sediment pore water was extracted with a pneumatic apparatus and was stored frozen. Just before testing, water-quality measurements were made and salinity adjusted, if necessary. Tests were performed on a dilution series of each sample consisting of 100-, 50-, and 25-percent pore-water concentrations. The specific objectives of this study were to: * Extract sediment pore water from a total of 30 sediment samples from the Bellingham Bay, Washington area within a day of receipt of the samples. * Measure water-quality parameters (salinity, dissolved oxygen, pH, sulfide, and ammonia) of thawed pore-water samples before testing and adjust salinity, temperature and dissolved oxygen, if necessary, to obtain optimal ranges for the test species. * Conduct the fertilization toxicity test with pore water using sea urchin (Stronylocentrotus purpuratus) (S. purpuratus) gametes. * Perform quality control assays with reference pore water, dilution blanks and a positive control dilution series with sodium dodecyl sulfate (SDS) in conjunction with each test. * Determine which samples caused a significant decrease in percent fertilization success relative to the negative control.

Analytical performance of the Hologic Aptima HBV Quant Assay and the COBAS Ampliprep/COBAS TaqMan HBV test v2.0 for the quantification of HBV DNA in plasma samples.

PubMed

Schønning, Kristian; Johansen, Kim; Nielsen, Lone Gilmor; Weis, Nina; Westh, Henrik

2018-07-01

Quantification of HBV DNA is used for initiating and monitoring antiviral treatment. Analytical test performance consequently impacts treatment decisions. To compare the analytical performance of the Aptima HBV Quant Assay (Aptima) and the COBAS Ampliprep/COBAS TaqMan HBV Test v2.0 (CAPCTMv2) for the quantification of HBV DNA in plasma samples. The performance of the two tests was compared on 129 prospective plasma samples, and on 63 archived plasma samples of which 53 were genotyped. Linearity of the two assays was assessed on dilutions series of three clinical samples (Genotype B, C, and D). Bland-Altman analysis of 120 clinical samples, which quantified in both tests, showed an average quantification bias (Aptima - CAPCTMv2) of -0.19 Log IU/mL (SD: 0.33 Log IU/mL). A single sample quantified more than three standard deviations higher in Aptima than in CAPCTMv2. Only minor differences were observed between genotype A (N = 4; average difference -0.01 Log IU/mL), B (N = 8; -0.13 Log IU/mL), C (N = 8; -0.31 Log IU/mL), D (N = 25; -0.22 Log IU/mL), and E (N = 7; -0.03 Log IU/mL). Deming regression showed that the two tests were excellently correlated (slope of the regression line 1.03; 95% CI: 0.998-1.068). Linearity of the tests was evaluated on dilution series and showed an excellent correlation of the two tests. Both tests were precise with %CV less than 3% for HBV DNA ≥3 Log IU/mL. The Aptima and CAPCTMv2 tests are highly correlated, and both tests are useful for monitoring patients chronically infected with HBV. Copyright © 2018 Elsevier B.V. All rights reserved.

HIV rapid diagnostic testing by lay providers in a key population-led health service programme in Thailand.

PubMed

Wongkanya, Rapeeporn; Pankam, Tippawan; Wolf, Shauna; Pattanachaiwit, Supanit; Jantarapakde, Jureeporn; Pengnongyang, Supabhorn; Thapwong, Prasopsuk; Udomjirasirichot, Apichat; Churattanakraisri, Yutthana; Prawepray, Nanthika; Paksornsit, Apiluk; Sitthipau, Thidadaow; Petchaithong, Sarayut; Jitsakulchaidejt, Raruay; Nookhai, Somboon; Lertpiriyasuwat, Cheewanan; Ongwandee, Sumet; Phanuphak, Praphan; Phanuphak, Nittaya

2018-01-01

Introduction:  Rapid diagnostic testing (RDT) for HIV has a quick turn-around time, which increases the proportion of people testing who receive their result. HIV RDT in Thailand has traditionally been performed only by medical technologists (MTs), which is a barrier to its being scaled up. We evaluated the performance of HIV RDT conducted by trained lay providers who were members of, or worked closely with, a group of men who have sex with men (MSM) and with transgender women (TG) communities, and compared it to tests conducted by MTs. Methods:  Lay providers received a 3-day intensive training course on how to perform a finger-prick blood collection and an HIV RDT as part of the Key Population-led Health Services (KPLHS) programme among MSM and TG. All the samples were tested by lay providers using Alere Determine HIV 1/2. HIV-reactive samples were confirmed by DoubleCheckGold Ultra HIV 1&2 and SD Bioline HIV 1/2. All HIV-positive and 10% of HIV-negative samples were re-tested by MTs using Serodia HIV 1/2. Results:  Of 1680 finger-prick blood samples collected and tested using HIV RDT by lay providers in six drop-in centres in Bangkok, Chiang Mai, Chonburi and Songkhla, 252 (15%) were HIV-positive. MTs re-tested these HIV-positive samples and 143 randomly selected HIV-negative samples with 100% concordant test results. Conclusion:  Lay providers in Thailand can be trained and empowered to perform HIV RDT as they were found to achieve comparable results in sample testing with MTs. Based on the task-shifting concept, this rapid HIV testing performed by lay providers as part of the KPLHS programme has great potential to enhance HIV prevention and treatment programmes among key at-risk populations.

Photometric and Colorimetric Assessment of LED Chip Scale Packages by Using a Step-Stress Accelerated Degradation Test (SSADT) Method.

PubMed

Qian, Cheng; Fan, Jiajie; Fang, Jiayi; Yu, Chaohua; Ren, Yi; Fan, Xuejun; Zhang, Guoqi

2017-10-16

By solving the problem of very long test time on reliability qualification for Light-emitting Diode (LED) products, the accelerated degradation test with a thermal overstress at a proper range is regarded as a promising and effective approach. For a comprehensive survey of the application of step-stress accelerated degradation test (SSADT) in LEDs, the thermal, photometric, and colorimetric properties of two types of LED chip scale packages (CSPs), i.e., 4000 °K and 5000 °K samples each of which was driven by two different levels of currents (i.e., 120 mA and 350 mA, respectively), were investigated under an increasing temperature from 55 °C to 150 °C and a systemic study of driving current effect on the SSADT results were also reported in this paper. During SSADT, junction temperatures of the test samples have a positive relationship with their driving currents. However, the temperature-voltage curve, which represents the thermal resistance property of the test samples, does not show significant variance as long as the driving current is no more than the sample's rated current. But when the test sample is tested under an overdrive current, its temperature-voltage curve is observed as obviously shifted to the left when compared to that before SSADT. Similar overdrive current affected the degradation scenario is also found in the attenuation of Spectral Power Distributions (SPDs) of the test samples. As used in the reliability qualification, SSADT provides explicit scenes on color shift and correlated color temperature (CCT) depreciation of the test samples, but not on lumen maintenance depreciation. It is also proved that the varying rates of the color shift and CCT depreciation failures can be effectively accelerated with an increase of the driving current, for instance, from 120 mA to 350 mA. For these reasons, SSADT is considered as a suitable accelerated test method for qualifying these two failure modes of LED CSPs.

Self-Sampling for Human Papillomavirus Testing: Increased Cervical Cancer Screening Participation and Incorporation in International Screening Programs

PubMed Central

Gupta, Sarah; Palmer, Christina; Bik, Elisabeth M.; Cardenas, Juan P.; Nuñez, Harold; Kraal, Laurens; Bird, Sara W.; Bowers, Jennie; Smith, Alison; Walton, Nathaniel A.; Goddard, Audrey D.; Almonacid, Daniel E.; Zneimer, Susan; Richman, Jessica; Apte, Zachary S.

2018-01-01

In most industrialized countries, screening programs for cervical cancer have shifted from cytology (Pap smear or ThinPrep) alone on clinician-obtained samples to the addition of screening for human papillomavirus (HPV), its main causative agent. For HPV testing, self-sampling instead of clinician-sampling has proven to be equally accurate, in particular for assays that use nucleic acid amplification techniques. In addition, HPV testing of self-collected samples in combination with a follow-up Pap smear in case of a positive result is more effective in detecting precancerous lesions than a Pap smear alone. Self-sampling for HPV testing has already been adopted by some countries, while others have started trials to evaluate its incorporation into national cervical cancer screening programs. Self-sampling may result in more individuals willing to participate in cervical cancer screening, because it removes many of the barriers that prevent women, especially those in low socioeconomic and minority populations, from participating in regular screening programs. Several studies have shown that the majority of women who have been underscreened but who tested HPV-positive in a self-obtained sample will visit a clinic for follow-up diagnosis and management. In addition, a self-collected sample can also be used for vaginal microbiome analysis, which can provide additional information about HPV infection persistence as well as vaginal health in general. PMID:29686981

40 CFR 61.54 - Sludge sampling.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 8 2011-07-01 2011-07-01 false Sludge sampling. 61.54 Section 61.54... sampling. (a) As an alternative means for demonstrating compliance with § 61.52(b), an owner or operator... days prior to a sludge sampling test, so that he may at his option observe the test. (c) Sludge shall...

40 CFR 61.54 - Sludge sampling.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 8 2010-07-01 2010-07-01 false Sludge sampling. 61.54 Section 61.54... sampling. (a) As an alternative means for demonstrating compliance with § 61.52(b), an owner or operator... days prior to a sludge sampling test, so that he may at his option observe the test. (c) Sludge shall...

A comparison of fitness-case sampling methods for genetic programming

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

Agreement of the Kato-Katz test established by the WHO with samples fixed with sodium acetate analyzed at 6 months to diagnose intestinal geohelminthes.

PubMed

Alfredo Fernández-Niño, Julián; David Ramírez, Juan; Consuelo López, Myriam; Inés Moncada, Ligia; Reyes, Patricia; Darío Heredia, Rubén

2015-06-01

The aim of this study was to evaluate the performance of the Kato-Katz test (WHO version) with stool samples from a rural area, fixed with sodium acetate (SAF). The Kato-Katz test was used to compare unfixed samples (conventional test) with the same samples containing SAF fixative at time 0 and at 6 months. The study included stools from 154 subjects. A marginally statistically significant decrease in prevalence was estimated only for hookworm, when comparing unfixed samples versus the SAF fixed samples read at 6 months (p=0.06). A significant reduction in parasite load was found for hookworm (p<0.01) and Trichuris trichiura (p<0.01) between the unfixed and the fixed sample read at 6 months, but not for Ascaris lumbricoides (p=0.10). This research suggests that the SAF fixative solution is a good option for transporting samples for diagnosis, especially in rural areas in developing countries. Copyright © 2015 Elsevier B.V. All rights reserved.

DEMONSTRATION BULLETIN: HNU-HANBY PCP IMMUNOASSAY TEST KIT - HNU - SYSTEMS, INC.

EPA Science Inventory

The HNU-Hanby test kit rapidly analyzes for petroleum hydrocarbons in soil and water samples. The test kit can be used to estimate pentachlorophenol (PCP) concentrations in samples when the carrier solvent is a petroleum hydrocarbon. The test kit estimates PCP concentrations in ...

Genotoxic response of Austrian groundwater samples treated under standardized UV (254 nm)--disinfection conditions in a combination of three different bioassays.

PubMed

Haider, Thomas; Sommer, Regina; Knasmüller, Siefried; Eckl, Peter; Pribil, Walter; Cabaj, Alexander; Kundi, Michael

2002-01-01

Ground water samples from different geographic areas in Austria, with different amounts of natural and anthropogenic organic compounds were treated with a standardized low pressure UV (254 nm)-irradiation laboratory flow-through system (UV fluence: 800 J/m2). The genotoxic activities of the water samples before and after the UV disinfection were investigated using a combination of three different bioassays which complement each other with regard to their sensitivity detecting different genotoxins. The test battery comprises the Salmonella/microsome assay (Ames test with TA98. TA 100 and TA 102, with and without S9 mix) and two micronucleus tests with the plant Tradescantia (clone #4430) and with primary rat hepatocytes. Overall, the tested Austrian groundwater samples used for human consumption caused only weak genotoxic activities compared to drinking water samples reported from other countries under similar experimental conditions. With the exception of one weak positive result in the Ames test (only in strain TA98 without S9 mix) with an induction factor of 1.9) all samples after UV disinfection were devoid of additional mutagenic and clastogenic activities compared to the samples before UV disinfection.

Critical tests for determination of microbiological quality and biological activity in commercial vermicompost samples of different origins.

PubMed

Grantina-Ievina, Lelde; Andersone, Una; Berkolde-Pīre, Dace; Nikolajeva, Vizma; Ievinsh, Gederts

2013-12-01

The aim of the present paper was to show that differences in biological activity among commercially produced vermicompost samples can be found by using a relatively simple test system consisting of microorganism tests on six microbiological media and soilless seedling growth tests with four vegetable crop species. Significant differences in biological properties among analyzed samples were evident both at the level of microbial load as well as plant growth-affecting activity. These differences were mostly manufacturer- and feedstock-associated, but also resulted from storage conditions of vermicompost samples. A mature vermicompost sample that was produced from sewage sludge still contained considerable number of Escherichia coli. Samples from all producers contained several potentially pathogenic fungal species such as Aspergillus fumigatus, Pseudallescheria boidii, Pseudallescheria fimeti, Pseudallescheria minutispora, Scedosporium apiospermum, Scedosporium prolificans, Scopulariopsis brevicaulis, Stachybotrys chartarum, Geotrichum spp., Aphanoascus terreus, and Doratomyces columnaris. In addition, samples from all producers contained plant growth-promoting fungi from the genera Trichoderma and Mortierella. The described system can be useful both for functional studies aiming at understanding of factors affecting quality characteristics of vermicompost preparations and for routine testing of microbiological quality and biological activity of organic waste-derived composts and vermicomposts.

Clinch River - Environmental Restoration Program (CR-ERP) study, ambient water toxicity

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

Simbeck, D.J.

1997-06-01

Clinch River - Environmental Restoration Program (CR-ERP) personnel and Tennessee Valley Authority (TVA) personnel conducted a study during the week of April 14-21, 1994, as described in the Statement of Work (SOW) document. The organisms specified for testing were larval fathead minnows, Pimephales promelas, and the daphnid, Ceriodaphnia dubia. Surface water samples were collected by TVA Field Engineering personnel from Poplar Creek Mile 4.3, Poplar Creek Mile 5.1, and Poplar Creek Mile 6.0 on April 13, 15, and 18. Samples were partitioned (split) and provided to the CR-ERP and TVA toxicology laboratories for testing. Exposure of test organisms to thesemore » samples resulted in no toxicity (survival or growth) to daphnids in undiluted samples; however, toxicity to fathead minnows (significantly reduced survival) was demonstrated in undiluted samples from Poplar Creek Miles 4.3 and 6.0 in testing conducted by TVA based on hypothesis testing of data. Daphnid reproduction was significantly less than controls in 50 percent dilutions of samples from Poplar Creek Miles 4.3 and 6.0, while no toxicity to fathead minnows was shown in diluted (50 percent) samples.« less

Urine melanin test

MedlinePlus

Thormahlen's test; Melanin - urine ... A clean-catch urine sample is needed. ... this substance that it shows up in the urine. ... Normally, melanin is not present in urine. Normal value ranges may ... measurements or test different samples. Talk to your health ...

A field test of point relascope sampling of down coarse woody material in managed stands in the Acadian Forest

Treesearch

John C. Brissette; Mark J. Ducey; Jeffrey H. Gove

2003-01-01

We field tested a new method for sampling down coarse woody material (CWM) using an angle gauge and compared it with the more traditional line intersect sampling (LIS) method. Permanent sample locations in stands managed with different silvicultural treatments within the Penobscot Experimental Forest (Maine, USA) were used as the sampling locations. Point relascope...

HPV self-sampling in Japanese women: A feasibility study in a population with limited experience of tampon use.

PubMed

Hanley, Sharon Jb; Fujita, Hiromasa; Yokoyama, Susumu; Kunisawa, Shiori; Tamakoshi, Akiko; Dong, Peixin; Kobayashi, Noriko; Watari, Hidemichi; Kudo, Masataka; Sakuragi, Noriaki

2016-09-01

Cervical cancer incidence and mortality is increasing in Japanese women under age 50. Screening uptake is low and proactive recommendations for human papillomavirus vaccination have been suspended. Other cervical cancer prevention initiatives are urgently needed. We assessed whether human papillomavirus self-sampling might be an acceptable alternative to physician-led screening, particularly in women with limited experience of tampon use. We also sought to identify any practical, logistical, or safety issues in women already attending for screening, before carrying out further large-scale studies in non-responders. In total, 203 women aged 20-49 attending their annual workplace healthcheck in Sapporo, northern Japan, performed unsupervised human papillomavirus self-sampling before undergoing a physician-led cervical smear and human papillomavirus test, and completing a measure of acceptability for both tests. Ninety per cent of participants stated they would use self-sampling again. They found instructions easy to follow and reported no issues with the usability of the self-sampling device. Compared with physician-led testing, women found self-sampling significantly less painful, less embarrassing and could relax more (p < 0.001), regardless of history of tampon use, which was associated with negative experiences in physician sampling (p = 0.034). Women lacked confidence the test had been performed correctly, despite no unsatisfactory samples. No safety issues were reported. Self-sampling was highly acceptable in this population of women. They could perform the test safely unsupervised, but lacked confidence the test has been carried out correctly. Japanese women need to be educated about the accuracy of human papillomavirus self-sampling and further large-scale studies are necessary in non-responders. © The Author(s) 2016.

Improved variance estimation of classification performance via reduction of bias caused by small sample size.

PubMed

Wickenberg-Bolin, Ulrika; Göransson, Hanna; Fryknäs, Mårten; Gustafsson, Mats G; Isaksson, Anders

2006-03-13

Supervised learning for classification of cancer employs a set of design examples to learn how to discriminate between tumors. In practice it is crucial to confirm that the classifier is robust with good generalization performance to new examples, or at least that it performs better than random guessing. A suggested alternative is to obtain a confidence interval of the error rate using repeated design and test sets selected from available examples. However, it is known that even in the ideal situation of repeated designs and tests with completely novel samples in each cycle, a small test set size leads to a large bias in the estimate of the true variance between design sets. Therefore different methods for small sample performance estimation such as a recently proposed procedure called Repeated Random Sampling (RSS) is also expected to result in heavily biased estimates, which in turn translates into biased confidence intervals. Here we explore such biases and develop a refined algorithm called Repeated Independent Design and Test (RIDT). Our simulations reveal that repeated designs and tests based on resampling in a fixed bag of samples yield a biased variance estimate. We also demonstrate that it is possible to obtain an improved variance estimate by means of a procedure that explicitly models how this bias depends on the number of samples used for testing. For the special case of repeated designs and tests using new samples for each design and test, we present an exact analytical expression for how the expected value of the bias decreases with the size of the test set. We show that via modeling and subsequent reduction of the small sample bias, it is possible to obtain an improved estimate of the variance of classifier performance between design sets. However, the uncertainty of the variance estimate is large in the simulations performed indicating that the method in its present form cannot be directly applied to small data sets.

Characterization of Estrogen and Androgen Activity of Food Contact Materials by Different In Vitro Bioassays (YES, YAS, ERα and AR CALUX) and Chromatographic Analysis (GC-MS, HPLC-MS)

PubMed Central

Osorio, Veronica; Grininger, Angelika; Richter, Alexander; Bergmair, Johannes; Pyerin, Michael; Washüttl, Michael; Tacker, Manfred

2014-01-01

Endocrine active substances (EAS) show structural similarities to natural hormones and are suspected to affect the human endocrine system by inducing hormone dependent effects. Recent studies with in vitro tests suggest that EAS can leach from packaging into food and may therefore pose a risk to human health. Sample migrates from food contact materials were tested for estrogen and androgen agonists and antagonists with different commonly used in vitro tests. Additionally, chemical trace analysis by GC-MS and HPLC-MS was used to identify potential hormone active substances in sample migrates. A GC-MS method to screen migrates for 29 known or potential endocrine active substances was established and validated. Samples were migrated according to EC 10/2011, concentrated by solid phase extraction and tested with estrogen and androgen responsive reporter gene assays based on yeast cells (YES and YAS) or human osteoblast cells (ERα and AR CALUX). A high level of agreement between the different bioassays could be observed by screening for estrogen agonists. Four out of 18 samples tested showed an estrogen activity in a similar range in both, YES and ERα CALUX. Two more samples tested positive in ERα CALUX due to the lower limits of detection in this assay. Androgen agonists could not be detected in any of the tested samples, neither with YAS nor with AR CALUX. When testing for antagonists, significant differences between yeast and human cell-based bioassays were noticed. Using YES and YAS many samples showed a strong antagonistic activity which was not observed using human cell-based CALUX assays. By GC-MS, some known or supposed EAS were identified in sample migrates that showed a biological activity in the in vitro tests. However, no firm conclusions about the sources of the observed hormone activity could be obtained from the chemical results. PMID:25000404

Sample Dimensionality Effects on d' and Proportion of Correct Responses in Discrimination Testing.

PubMed

Bloom, David J; Lee, Soo-Yeun

2016-09-01

Products in the food and beverage industry have varying levels of dimensionality ranging from pure water to multicomponent food products, which can modify sensory perception and possibly influence discrimination testing results. The objectives of the study were to determine the impact of (1) sample dimensionality and (2) complex formulation changes on the d' and proportion of correct response of the 3-AFC and triangle methods. Two experiments were conducted using 47 prescreened subjects who performed either triangle or 3-AFC test procedures. In Experiment I, subjects performed 3-AFC and triangle tests using model solutions with different levels of dimensionality. Samples increased in dimensionality from 1-dimensional sucrose in water solution to 3-dimensional sucrose, citric acid, and flavor in water solution. In Experiment II, subjects performed 3-AFC and triangle tests using 3-dimensional solutions. Sample pairs differed in all 3 dimensions simultaneously to represent complex formulation changes. Two forms of complexity were compared: dilution, where all dimensions decreased in the same ratio, and compensation, where a dimension was increased to compensate for a reduction in another. The proportion of correct responses decreased for both methods when the dimensionality was increased from 1- to 2-dimensional samples. No reduction in correct responses was observed from 2- to 3-dimensional samples. No significant differences in d' were demonstrated between the 2 methods when samples with complex formulation changes were tested. Results reveal an impact on proportion of correct responses due to sample dimensionality and should be explored further using a wide range of sample formulations. © 2016 Institute of Food Technologists®

Detection of Chlamydophila psittaci from feral pigeons in environmental samples: problems with currently available techniques.

PubMed

Geigenfeind, Ila; Haag-Wackernagel, Daniel

2010-03-01

Chlamydophila psittaci (Lillie, 1930) Everett et al., 1999, the pathogenic agent of human ornithosis, is widespread in feral pigeon populations and many cases of transmission from feral pigeons to humans have been reported. The aim of the present study was to detect C. psittaci in environmental samples to find out more about possible transmission routes and, therefore, to assess the zoonotic risk for humans. Fecal samples were collected from nest boxes in a feral pigeon loft. Additionally, samples were taken from the feather dust film covering the water surface of public fountains where pigeons regularly bathe. The samples were tested for the presence of chlamydial antigen using an antigen enzyme-linked immunosorbent assay to prove shedding of C. psittaci by feral pigeons. This test detects a genus specific lipopolysaccharide in the outer membrane of the chlamydial bacteria. Samples were tested using the IDEIA PCE Chlamydia Test kit (DakoCytomation) and positive results were verified with IDEIA Chlamydia Blocking Reagents (DakoCytomation). The IDEIA PCE Chlamydia Test yields a high proportion of positive results. However, when IDEIA Chlamydia Blocking was performed, most of the positive results turned out to be negative or could not be interpreted. We conclude that antigen-enzyme-linked immunosorbent assay tests are not suitable for detecting C. psittaci in environmental samples. Previous publications where no blocking test was used should be reconsidered critically. © 2010 ISZS, Blackwell Publishing and IOZ/CAS.

Plasma Septin9 versus fecal immunochemical testing for colorectal cancer screening: a prospective multicenter study.

PubMed

Johnson, David A; Barclay, Robert L; Mergener, Klaus; Weiss, Gunter; König, Thomas; Beck, Jürgen; Potter, Nicholas T

2014-01-01

Screening improves outcomes related to colorectal cancer (CRC); however, suboptimal participation for available screening tests limits the full benefits of screening. Non-invasive screening using a blood based assay may potentially help reach the unscreened population. To compare the performance of a new Septin9 DNA methylation based blood test with a fecal immunochemical test (FIT) for CRC screening. In this trial, fecal and blood samples were obtained from enrolled patients. To compare test sensitivity for CRC, patients with screening identified colorectal cancer (n = 102) were enrolled and provided samples prior to surgery. To compare test specificity patients were enrolled prospectively (n = 199) and provided samples prior to bowel preparation for screening colonoscopy. Plasma and fecal samples were analyzed using the Epi proColon and OC Fit-Check tests respectively. For all samples, sensitivity for CRC detection was 73.3% (95% CI 63.9-80.9%) and 68.0% (95% CI 58.2-76.5%) for Septin9 and FIT, respectively. Specificity of the Epi proColon test was 81.5% (95% CI 75.5-86.3%) compared with 97.4% (95% CI 94.1-98.9%) for FIT. For paired samples, the sensitivity of the Epi proColon test (72.2% -95% CI 62.5-80.1%) was shown to be statistically non-inferior to FIT (68.0%-95% CI 58.2-76.5%). When test results for Epi proColon and FIT were combined, CRC detection was 88.7% at a specificity of 78.8%. At a sensitivity of 72%, the Epi proColon test is non- inferior to FIT for CRC detection, although at a lower specificity. With negative predictive values of 99.8%, both methods are identical in confirming the absence of CRC. ClinicalTrials.gov NCT01580540.

Spatially Targeted Activation of a Shape Memory, Polymer-Based, Reconfigurable Skin System

DTIC Science & Technology

2014-02-01

bone samples described in ASTM Standard D638 using a CNC router. Compression test samples were cured in an aluminum cylinder mold treated with mold...release with Teflon end plugs and cut to length with a small lathe . 2.2 Tensile/Compressive Tests Tensile tests were conducted on a MTS QTest/1L...fixture with a CNC mill and a decal applied to the front surface for tracking by the DIC system. Figure 10: Shear Test Sample with DIC Decal 10

Validation of a hospital-laboratory workstation for immunohematologic methods.

PubMed

Schoenfeld, Helge; Pretzel, Karin J; von Heymann, Christian; Neuner, Bruno; Kalus, Ulrich; Kiesewetter, Holger; Pruss, Axel

2010-01-01

The FREELYS Nano system (Diagast) is a manual workstation for ABO/D grouping, Rh phenotyping, K typing, and antibody screening (ABS) for immunoglobulin G (IgG) antibodies only and works with the erythrocyte-magnetized technology (EMT). The principle of EMT is based on magnetization of red blood cells and avoids centrifugation and washing steps. A total of 304 samples were tested with our routine blood bank methods, 100 samples for ABO/D grouping, 196 samples (100 at first evaluation, 96 at second evaluation) for Rh phenotyping and K typing (PK7200, Olympus), and 108 samples for ABS (DiaMed). All samples were tested in parallel with the FREELYS Nano. We found a 100% concordance between the observed (FREELYS Nano) and the expected (Olympus PK7200) results for ABO/D grouping in all 100 samples. For Rh phenotyping and K tests, in 24 of 100 samples false-positive reactions were observed in the first evaluation by the FREELYS Nano. After changing the test kit batch for Rh phenotyping by the manufacturer, a complete concordance in Rh phenotyping and K tests was observed in a second evaluation. For ABS, the FREELYS Nano showed in 4 of 108 samples (3.7%) false-negative reactions for IgG antibodies (two anti-K, one anti-E, one anti-C(w)), and one (0.9%) false-positive reaction. The FREELYS Nano is reliably suited to ABO/D grouping, Rh phenotyping, and K testing. The rate of false-negative reactions for IgG antibodies should be reduced.

The value of Bayes' theorem for interpreting abnormal test scores in cognitively healthy and clinical samples.

PubMed

Gavett, Brandon E

2015-03-01

The base rates of abnormal test scores in cognitively normal samples have been a focus of recent research. The goal of the current study is to illustrate how Bayes' theorem uses these base rates--along with the same base rates in cognitively impaired samples and prevalence rates of cognitive impairment--to yield probability values that are more useful for making judgments about the absence or presence of cognitive impairment. Correlation matrices, means, and standard deviations were obtained from the Wechsler Memory Scale--4th Edition (WMS-IV) Technical and Interpretive Manual and used in Monte Carlo simulations to estimate the base rates of abnormal test scores in the standardization and special groups (mixed clinical) samples. Bayes' theorem was applied to these estimates to identify probabilities of normal cognition based on the number of abnormal test scores observed. Abnormal scores were common in the standardization sample (65.4% scoring below a scaled score of 7 on at least one subtest) and more common in the mixed clinical sample (85.6% scoring below a scaled score of 7 on at least one subtest). Probabilities varied according to the number of abnormal test scores, base rates of normal cognition, and cutoff scores. The results suggest that interpretation of base rates obtained from cognitively healthy samples must also account for data from cognitively impaired samples. Bayes' theorem can help neuropsychologists answer questions about the probability that an individual examinee is cognitively healthy based on the number of abnormal test scores observed.

Direct Competitive Enzyme-Linked Immunosorbent Assay (ELISA).

PubMed

Kohl, Thomas O; Ascoli, Carl A

2017-07-05

The competitive enzyme-linked immunosorbent assay (ELISA) (cELISA; also called an inhibition ELISA) is designed so that purified antigen competes with antigen in the test sample for binding to an antibody that has been immobilized in microtiter plate wells. The same concept works if the immobilized molecule is antigen and the competing molecules are purified labeled antibody versus antibody in a test sample. Direct cELISAs incorporate labeled antigen or antibody, whereas indirect assay configurations use reporter-labeled secondary antibodies. The cELISA is very useful for determining the concentration of small-molecule antigens in complex sample mixtures. In the direct cELISA, antigen-specific capture antibody is adsorbed onto the microtiter plate before incubation with either known standards or unknown test samples. Enzyme-linked antigen (i.e., labeled antigen) is also added, which can bind to the capture antibody only when the antibody's binding site is not occupied by either the antigen standard or antigen in the test samples. Unbound labeled and unlabeled antigens are washed away and substrate is added. The amount of antigen in the standard or the test sample determines the amount of reporter-labeled antigen bound to antibody, yielding a signal that is inversely proportional to antigen concentration within the sample. Thus, the higher the antigen concentration in the test sample, the less labeled antigen is bound to the capture antibody, and hence the weaker is the resultant signal. © 2017 Cold Spring Harbor Laboratory Press.

A cryogenic tensile testing apparatus for micro-samples cooled by miniature pulse tube cryocooler

NASA Astrophysics Data System (ADS)

Chen, L. B.; Liu, S. X.; Gu, K. X.; Zhou, Y.; Wang, J. J.

2015-12-01

This paper introduces a cryogenic tensile testing apparatus for micro-samples cooled by a miniature pulse tube cryocooler. At present, tensile tests are widely applied to measure the mechanical properties of materials; most of the cryogenic tensile testing apparatus are designed for samples with standard sizes, while for non-standard size samples, especially for microsamples, the tensile testing cannot be conducted. The general approach to cool down the specimens for tensile testing is by using of liquid nitrogen or liquid helium, which is not convenient: it is difficult to keep the temperature of the specimens at an arbitrary set point precisely, besides, in some occasions, liquid nitrogen, especially liquid helium, is not easily available. To overcome these limitations, a cryogenic tensile testing apparatus cooled by a high frequency pulse tube cryocooler has been designed, built and tested. The operating temperatures of the developed tensile testing apparatus cover from 20 K to room temperature with a controlling precision of ±10 mK. The apparatus configurations, the methods of operation and some cooling performance will be described in this paper.

Immunity to human cytomegalovirus measured and compared by complement fixation, indirect fluorescent-antibody, indirect hemagglutination, and enzyme-linked immunosorbent assays.

PubMed Central

Brandt, J A; Kettering, J D; Lewis, J E

1984-01-01

The complement fixation test is currently the test employed most frequently to determine the presence of antibody to human cytomegalovirus. Several other techniques have been adapted for this purpose. A comparison of cytomegalovirus antibody titers was made between the complement fixation test, a commercially available enzyme-linked immunosorbent assay, an indirect immunofluorescent technique, and a modified indirect hemagglutination test. Forty-three serum samples were tested for antibodies by each of the above procedures. The enzyme-linked immunosorbent, immunofluorescent, and indirect hemagglutination assays were in close agreement on all samples tested; the titers obtained with these methods were all equal to or greater than the complement fixation titer for 38 of the 41 samples (92.6%). Two samples were anticomplementary in the complement fixation test but gave readable results in the other tests. The complement fixation test was the least sensitive of the procedures examined. The commercial enzyme-linked immunosorbent assay system was the most practical method and offered the highest degree of sensitivity in detecting antibodies to cytomegalovirus. PMID:6321544

Test and evaluation of the Argonne BPAC10 Series air chamber calorimeter designed for 20 minute measurements

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

Perry, R.B.; Fiarman, S.; Jung, E.A.

1990-10-01

This paper is the final report on DOE-OSS Task ANLE88002 Fast Air Chamber Calorimetry.'' The task objective was to design, construct, and test an isothermal air chamber calorimeter for plutonium assay of bulk samples that would meet the following requirements for sample power measurement: average sample measurement time less than 20 minutes. Measurement of samples with power output up to 10 W. Precision of better than 1% RSD for sample power greater than 1 W. Precision better than 0.010 watt SD, for sample power less than 1 W. This report gives a description of the calorimeter hardware and software andmore » discusses the test results. The instrument operating procedure, included as an appendix, gives examples of typical input/output and explains the menu driven software. Sample measurement time of less than 20 minutes was attained by pre-equilibration of the samples in low cost precision preheaters and by prediction of equilibrium measurements. Tests at the TA55 Plutonium Facility at Los Alamos National Laboratory, on typical samples, indicates that the instrument meets all the measurement requirements.« less

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

PubMed

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

2016-09-07

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

Sample Containerization and Sealing Techniques for Contamination Prevention and Preservation of Science Value for Mars Sample Return

NASA Astrophysics Data System (ADS)

Younse, Paulo

Four sealing methods for encapsulating samples in 1 cm diameter thin-walled sample tubes were designed, along with a set of tests for characterization and evaluation of contamination prevention and sample preservation capability for the proposed Mars Sample Return (MSR) campaign. The sealing methods include a finned shape memory alloy (SMA) plug, expanding torque plug, contracting SMA ring cap, and expanding SMA ring plug. Mechanical strength and hermeticity of the seal were measured using a helium leak detector. Robustness of the seal to Mars simulant dust, surface abrasion, and pressure differentials were tested. Survivability tests were run to simulate thermal cycles on Mars, vibration from a Mars Ascent Vehicle (MAV), and shock from Earth Entry Vehicle (EEV) landing. Material compatibility with potential sample minerals and organic molecules were studied to select proper tube and seal materials that would not lead to adverse reactions nor contaminate the sample. Cleaning and sterilization techniques were executed on coupons made from the seal materials to assess compliance with planetary protection and contamination control. Finally, a method to cut a sealed tube for sample removal was designed and tested.

Swab2know: An HIV-Testing Strategy Using Oral Fluid Samples and Online Communication of Test Results for Men Who Have Sex With Men in Belgium.

PubMed

Platteau, Tom; Fransen, Katrien; Apers, Ludwig; Kenyon, Chris; Albers, Laura; Vermoesen, Tine; Loos, Jasna; Florence, Eric

2015-09-01

As HIV remains a public health concern, increased testing among those at risk for HIV acquisition is important. Men who have sex with men (MSM) are the most important group for targeted HIV testing in Europe. Several new strategies have been developed and implemented to increase HIV-testing uptake in this group, among them the Swab2know project. In this project, we aim to assess the acceptability and feasibility of outreach and online HIV testing using oral fluid samples as well as Web-based delivery of test results. Sample collection happened between December 2012 and April 2014 via outreach and online sampling among MSM. Test results were communicated through a secured website. HIV tests were executed in the laboratory. Each reactive sample needed to be confirmed using state-of-the-art confirmation procedures on a blood sample. Close follow-up of participants who did not pick up their results, and those with reactive results, was included in the protocol. Participants were asked to provide feedback on the methodology using a short survey. During 17 months, 1071 tests were conducted on samples collected from 898 men. Over half of the samples (553/1071, 51.63%) were collected during 23 outreach sessions. During an 8-month period, 430 samples out of 1071 (40.15%) were collected from online sampling. Additionally, 88 samples out of 1071 (8.22%) were collected by two partner organizations during face-to-face consultations with MSM and male sex workers. Results of 983 out of 1071 tests (91.78%) had been collected from the website. The pickup rate was higher among participants who ordered their kit online (421/430, 97.9%) compared to those participating during outreach activities (559/641, 87.2%; P<.001). MSM participating during outreach activities versus online participants were more likely to have never been tested before (17.3% vs 10.0%; P=.001) and reported more sexual partners in the 6 months prior to participation in the project (mean 7.18 vs 3.23; P<.001). A total of 20 participants out of 898 (2.2%) were confirmed HIV positive and were linked to care. Out of 1071 tests, 28 (2.61%) with a weak reactive result could not be confirmed, and were thereby classified as false reactive results. Most of the 388 participants who completed posttest surveys (388/983, 39.5%) were very positive about their experience. The vast majority (371/388, 95.6%) were very satisfied, while 17 out of 388 (4.4%) reported mixed feelings. Despite a high yield and a considerable number of false reactive results, satisfaction was high among participants. The project helped us to reach the target population, both in numbers of tests executed and in newly diagnosed HIV infections. Further optimization should be considered in the accuracy of the test, the functionalities of the website (including an online counseling tool), and in studying the cost effectiveness of the methodology.

Generating virtual training samples for sparse representation of face images and face recognition

NASA Astrophysics Data System (ADS)

Du, Yong; Wang, Yu

2016-03-01

There are many challenges in face recognition. In real-world scenes, images of the same face vary with changing illuminations, different expressions and poses, multiform ornaments, or even altered mental status. Limited available training samples cannot convey these possible changes in the training phase sufficiently, and this has become one of the restrictions to improve the face recognition accuracy. In this article, we view the multiplication of two images of the face as a virtual face image to expand the training set and devise a representation-based method to perform face recognition. The generated virtual samples really reflect some possible appearance and pose variations of the face. By multiplying a training sample with another sample from the same subject, we can strengthen the facial contour feature and greatly suppress the noise. Thus, more human essential information is retained. Also, uncertainty of the training data is simultaneously reduced with the increase of the training samples, which is beneficial for the training phase. The devised representation-based classifier uses both the original and new generated samples to perform the classification. In the classification phase, we first determine K nearest training samples for the current test sample by calculating the Euclidean distances between the test sample and training samples. Then, a linear combination of these selected training samples is used to represent the test sample, and the representation result is used to classify the test sample. The experimental results show that the proposed method outperforms some state-of-the-art face recognition methods.

9 CFR 113.110 - Clostridium Botulinum Type C Bacterin-Toxoid.

Code of Federal Regulations, 2012 CFR

2012-01-01

..., safety, and potency as prescribed in this section. A serial found unsatisfactory by any prescribed test shall not be released. (a) Purity test. Final container samples of completed product from each serial... test. Bulk or final container samples of completed product from each serial shall be tested for safety...

9 CFR 113.110 - Clostridium Botulinum Type C Bacterin-Toxoid.

Code of Federal Regulations, 2010 CFR

2010-01-01

..., safety, and potency as prescribed in this section. A serial found unsatisfactory by any prescribed test shall not be released. (a) Purity test. Final container samples of completed product from each serial... test. Bulk or final container samples of completed product from each serial shall be tested for safety...

10 CFR 429.11 - General sampling requirements for selecting units to be tested.

Code of Federal Regulations, 2012 CFR

2012-01-01

... tested. 429.11 Section 429.11 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION CERTIFICATION, COMPLIANCE, AND ENFORCEMENT FOR CONSUMER PRODUCTS AND COMMERCIAL AND INDUSTRIAL EQUIPMENT Certification § 429.11 General sampling requirements for selecting units to be tested. (a) When testing of covered products or...

Compilation of data on the uranium and equivalent uranium content of samples analyzed by U.S. Geological Survey during a program of sampling mine, mill, and smelter products

USGS Publications Warehouse

Hall, Marlene Louise; Butler, Arthur Pierce

1952-01-01

In 1942 the Geological Survey began to collect, in response to a request made by the War Production Board, samples of mine, mill, and smelter products. About 1,400 such samples were collected and analyzed spectrographically for about 20 elements that were of strategic importance, in order to determine whether any of the products analyzed might be possible sources of some of the needed elements. When attention was directed to radioactive elements in 1943, most of the samples were scanned for radioactivity. Part of the work was done on behalf of the Division of Raw Materials of the Atomic Energy Commission. The sources, mine mill, smelter, or prospect, from which these samples were collected, the kind of material sampled, i.e. ores, concentrates, middlings, tailings, flue dusts, and so forth, and the radioactivity of the samples are listed in this report. Samples of the materials collected in the course of the Geological Survey’s investigations for uranium are excluded, but about 500 such samples were analyzed spectrographically for some or all of the same 20 elements sought in the samples that are the subject of this report. Most of the samples were tested only for their radioactivity, but a few were analyzed chemically for uranium. The radioactivity of many of the samples tested in the early screening was determined only qualitatively. Several samples were tested at one time, and if the count obtained did not exceed a predetermined minimum above background, the samples were not tested individually. If the count was more than this minimum, the samples were tested individually to identify the radioactive sample or samples and to obtain a quantitative value for the radioactivity. In general, the rough screening served as a basis for separating samples in which the radioactivity amount to less than 0.003 percent equivalent uranium from those in which it exceeded that amount. Some aspects of various phases of the investigation of radioactivity in these samples have been reported in various other reports, as follows.

Laboratory Jet Erosion Tests on the Lower American River Soil Samples, Sacramento, CA- Phase 2

DTIC Science & Technology

2017-05-01

ER D C/ G SL T R- 17 -8 Laboratory Jet Erosion Tests on the Lower American River Soil Samples, Sacramento, CA – Phase 2 G eo te ch ni...Jet Erosion Tests on the Lower American River Soil Samples, Sacramento, CA – Phase 2 Johannes L. Wibowo and Bryant A. Robbins Geotechnical and...Appendix B: Soil Mechanics Data ........................................................................................................... 71

A Monte Carlo Study of Levene's Test of Homogeneity of Variance: Empirical Frequencies of Type I Error in Normal Distributions.

ERIC Educational Resources Information Center

Neel, John H.; Stallings, William M.

An influential statistics test recommends a Levene text for homogeneity of variance. A recent note suggests that Levene's test is upwardly biased for small samples. Another report shows inflated Alpha estimates and low power. Neither study utilized more than two sample sizes. This Monte Carlo study involved sampling from a normal population for…

The Magical Number 7

ERIC Educational Resources Information Center

Richardson, Mary; Reischman, Diann

2011-01-01

This article describes an interactive activity that involves students participating in a memory recall test. Data collected from the activity may be used to illustrate the one-sample t test or one-sample sign test. (Contains 1 table and 1 figure.)

Performance of asphalt mixture incorporating recycled waste

NASA Astrophysics Data System (ADS)

Hamid, Nor Baizura; Abdullah, Mohd Ezree; Sanik, Mohd Erwan; Mokhtar, Mardiha; Kaamin, Masiri; Raduan, Rasyidah; Ramli, Mohd Zakwan

2017-12-01

Nowadays, the amount of premix waste was increased every year, especially at the batching plants. Normally, the waste materials will be discarded without doing any innovative and effective research about those materials. This situation has become one of the global concerns due to the increasing number of premix waste produced every year. Therefore, the aim of this study is to evaluate the performance of hot mix asphalt (HMA) using premix waste on improving asphalt mixture fatigue behaviour. The method used in this study was Superpave mix design method. The sample conducted in this study were 0%, 10%, 20%, 30%, and 100% of premix waste respectively. For a binder test, the laboratory test conducted were penetration test, softening test and thin film oven test while for the performance test were resilient modulus test and indirect tensile fatigue test. From the laboratory test, the resilient modulus test was conducted with two different temperature which was 25°C and 40°C. The result from that test was 20% of premix waste had higher resilient modulus at that two different temperatures compared to another samples. From that test also shown that the sample at the lower temperature which was 25°C has higher resilient modulus compared to the temperature of 40°C. Indirect tensile fatigue test showed that the 30% of premix waste sample was suitable for the modified asphalt mixture with referring to the maximum deformation and strain for comparison control, 10%,20%, and 100% of premix waste samples. So, it can be concluded that premix waste inhibits great potential as road construction material and suitable for repeated traffic loading.

Internet cognitive testing of large samples needed in genetic research.

PubMed

Haworth, Claire M A; Harlaar, Nicole; Kovas, Yulia; Davis, Oliver S P; Oliver, Bonamy R; Hayiou-Thomas, Marianna E; Frances, Jane; Busfield, Patricia; McMillan, Andrew; Dale, Philip S; Plomin, Robert

2007-08-01

Quantitative and molecular genetic research requires large samples to provide adequate statistical power, but it is expensive to test large samples in person, especially when the participants are widely distributed geographically. Increasing access to inexpensive and fast Internet connections makes it possible to test large samples efficiently and economically online. Reliability and validity of Internet testing for cognitive ability have not been previously reported; these issues are especially pertinent for testing children. We developed Internet versions of reading, language, mathematics and general cognitive ability tests and investigated their reliability and validity for 10- and 12-year-old children. We tested online more than 2500 pairs of 10-year-old twins and compared their scores to similar internet-based measures administered online to a subsample of the children when they were 12 years old (> 759 pairs). Within 3 months of the online testing at 12 years, we administered standard paper and pencil versions of the reading and mathematics tests in person to 30 children (15 pairs of twins). Scores on Internet-based measures at 10 and 12 years correlated .63 on average across the two years, suggesting substantial stability and high reliability. Correlations of about .80 between Internet measures and in-person testing suggest excellent validity. In addition, the comparison of the internet-based measures to ratings from teachers based on criteria from the UK National Curriculum suggests good concurrent validity for these tests. We conclude that Internet testing can be reliable and valid for collecting cognitive test data on large samples even for children as young as 10 years.

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

Simbeck, D.J.

Clinch River - Environmental Restoration Program (CR-ERP) personnel and Tennessee Valley Authority (TVA) personnel conducted a study during the week of October 21-28, 1993, as described in the Statement of Work (SOW) document. The organisms specified for testing were larval fathead minnows, Pimephales promelas, and the daphnid, Ceriodaphnia dubia. Due to serious reproduction/embryo abortion problems with the TVA daphnid cultures, TVA conducted tests during this study period using only fathead minnows. A split sample test using daphnids only will be scheduled during 1994 as a substitute for this study period. Surface water samples were collected by TVA Field Engineering personnelmore » from Poplar Creek Mile 2.9, Mile 4.3, and Mile 5.1 on October 20, 22, and 25. Samples were split and provided to the CR-ERP and TVA toxicology laboratories for testing. Exposure of test organisms to these samples resulted in no toxicity (survival or growth) in testing conducted by TVA.« less

Performing a urine dipstick test with a clean-catch urine sample is an accurate screening method for urinary tract infections in young infants.

PubMed

Herreros, María Luisa; Tagarro, Alfredo; García-Pose, Araceli; Sánchez, Aida; Cañete, Alfonso; Gili, Pablo

2018-01-01

This study evaluated using urine dipstick tests with the clean-catch method to screen for urinary tract infection (UTI) in febrile infants under 90 days of age. We carried out a comparative diagnostic accuracy study of infants under 90 days old, who were studied for unexplained fever without any source, in the emergency room of a hospital in Madrid from January 2011 to January 2013. We obtained matched samples of urine using two different methods: a clean-catch, standardised stimulation technique and catheterisation collection. The results of the leucocyte esterase test and nitrite test were compared with their urine cultures. We obtained 60 pairs of matched samples. A combined analysis of leukocyte esterase and, or, nitrites yielded a sensitivity of 86% and a specificity of 80% for the diagnosis of UTIs in clean-catch samples. The sensitivity of leukocyte esterase and, or, nitrites in samples obtained by catheterisation were not statistically different to the clean-catch samples (p = 0.592). Performing urine dipstick tests using urine samples obtained by the clean-catch method was an accurate screening test for diagnosing UTIs in febrile infants of less than 90 days old. This provided a good alternative to bladder catheterisation when screening for UTIs. ©2017 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.

Sea urchin fertilization assay: an evaluation of assumptions related to sample salinity adjustment and use of natural and synthetic marine waters for testing.

PubMed

Jonczyk, E; Gilron, G; Zajdlik, B

2001-04-01

Most industrial effluents discharged into the marine coastal environment are freshwater in nature and therefore require manipulation prior to testing with marine organisms. The sea urchin fertilization test is a common marine bioassay used for routine environmental monitoring, investigative evaluations, and/or regulatory testing of effluents and sediment pore waters. The existing Canadian and U.S. Environmental Protection Agencies test procedures using sea urchin (and sand dollar) gametes allow for sample salinity adjustment using either brine or dry salts. Moreover, these procedures also allow for the use of either natural or synthetic marine water for culturing/holding test organisms and for full-scale testing. At present, it is unclear to what extent these variables affect test results for whole effluents. The test methods simply state that there are no data available and that the use of artificial dry sea salts should be considered provisional. We conducted a series of concurrent experiments aimed at comparing the two different treatments of sample salinity adjustment and the use of natural versus synthetic seawater in order to test these assumptions and evaluate effects on the estimated end points generated by the sea urchin fertilization sublethal toxicity test. Results from these experiments indicated that there is no significant difference in test end points when dry salts or brine are used for sample salinity adjustment. Similarly, results obtained from parallel (split-sample) industrial effluent tests with natural and artificial seawater suggest that both dilution waters produce similar test results. However, data obtained from concurrent tests with the reference toxicant, copper sulfate, showed higher variability and greater sensitivity when using natural seawater as control/dilution water.

Amelogenin test: From forensics to quality control in clinical and biochemical genomics.

PubMed

Francès, F; Portolés, O; González, J I; Coltell, O; Verdú, F; Castelló, A; Corella, D

2007-01-01

The increasing number of samples from the biomedical genetic studies and the number of centers participating in the same involves increasing risk of mistakes in the different sample handling stages. We have evaluated the usefulness of the amelogenin test for quality control in sample identification. Amelogenin test (frequently used in forensics) was undertaken on 1224 individuals participating in a biomedical study. Concordance between referred sex in the database and amelogenin test was estimated. Additional sex-error genetic detecting systems were developed. The overall concordance rate was 99.84% (1222/1224). Two samples showed a female amelogenin test outcome, being codified as males in the database. The first, after checking sex-specific biochemical and clinical profile data was found to be due to a codification error in the database. In the second, after checking the database, no apparent error was discovered because a correct male profile was found. False negatives in amelogenin male sex determination were discarded by additional tests, and feminine sex was confirmed. A sample labeling error was revealed after a new DNA extraction. The amelogenin test is a useful quality control tool for detecting sex-identification errors in large genomic studies, and can contribute to increase its validity.

Co-occurrence of Mycoplasma Species and Pigeon Herpesvirus-1 Infection in Racing Pigeons ( Columba livia).

PubMed

Hellebuyck, Tom; Göbel, Stephan; Pasmans, Frank; Adriaensen, Connie; Martel, An

2017-12-01

Oropharyngeal swab samples were collected from 438 live racing pigeons ( Columba livia), with and without signs of respiratory disease, that were housed in 220 lofts in 3 provinces in the western part of the Netherlands. Polymerase chain reaction (PCR) was used to identify Mycoplasma species and pigeon herpesvirus-1 (PHV-1) from the samples. In 8.6% of the pigeon lofts tested, signs of respiratory disease were present in pigeons at sampling, and in 30.9% of the sampled pigeon lofts, respiratory signs were observed in pigeons during the 6-month period immediately before sampling. A total of 39.8% of tested pigeons (54.5% of tested lofts) were positive for Mycoplasma species, and 30.6% of tested pigeons (48.6% of tested lofts) were positive for PHV-1. In 15.8% of the tested pigeons (26.8% of tested pigeon lofts), coinfection by Mycoplasma species and PHV-1 was identified. The number of pigeon lofts having pigeons coinfected by Mycoplasma species and PHV-1 was higher than that where only one of the infections was identified. Neither the presence of Mycoplasma species, PHV-1, nor the co-occurrence of both infections was significantly associated with signs of respiratory disease.

Chi-Squared Test of Fit and Sample Size-A Comparison between a Random Sample Approach and a Chi-Square Value Adjustment Method.

PubMed

Bergh, Daniel

2015-01-01

Chi-square statistics are commonly used for tests of fit of measurement models. Chi-square is also sensitive to sample size, which is why several approaches to handle large samples in test of fit analysis have been developed. One strategy to handle the sample size problem may be to adjust the sample size in the analysis of fit. An alternative is to adopt a random sample approach. The purpose of this study was to analyze and to compare these two strategies using simulated data. Given an original sample size of 21,000, for reductions of sample sizes down to the order of 5,000 the adjusted sample size function works as good as the random sample approach. In contrast, when applying adjustments to sample sizes of lower order the adjustment function is less effective at approximating the chi-square value for an actual random sample of the relevant size. Hence, the fit is exaggerated and misfit under-estimated using the adjusted sample size function. Although there are big differences in chi-square values between the two approaches at lower sample sizes, the inferences based on the p-values may be the same.

Analysis of particulate contamination on tape lift samples from the VETA optical surfaces

NASA Technical Reports Server (NTRS)

Germani, Mark S.

1992-01-01

Particulate contamination analysis was carried out on samples taken from the Verification Engineering Test Article (VETA) x-ray detection system. A total of eighteen tape lift samples were taken from the VETA optical surfaces. Initially, the samples were tested using a scanning electron microscope. Additionally, particle composition was determined by energy dispersive x-ray spectrometry. Results are presented in terms of particle loading per sample.

78 FR 14457 - Guidelines Establishing Test Procedures for the Analysis of Pollutants Under the Clean Water Act...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-06

... Establishing Test Procedures for the Analysis of Pollutants Under the Clean Water Act; Analysis and Sampling... for use as an alternative oil and grease method. Some comments were specific to the sampling...-side comparison using the specific procedures (e.g. sampling frequency, number of samples, QA/QC, and...

Terrestrial Eco-Toxicological Tests as Screening Tool to Assess Soil Contamination in Krompachy Area

NASA Astrophysics Data System (ADS)

Ol'ga, Šestinová; Findoráková, Lenka; Hančuľák, Jozef; Fedorová, Erika; Tomislav, Špaldon

2016-10-01

In this study, we present screening tool of heavy metal inputs to agricultural and permanent grass vegetation of the soils in Krompachy. This study is devoted to Ecotoxicity tests, Terrestrial Plant Test (modification of OECD 208, Phytotoxkit microbiotest on Sinapis Alba) and chronic tests of Earthworm (Dendrobaena veneta, modification of OECD Guidelines for the testing of chemicals 317, Bioaccumulation in Terrestrial Oligochaetes) as practical and sensitive screening method for assessing the effects of heavy metals in Krompachy soils. The total Cu, Zn, As, Pb and Hg concentrations and eco-toxicological tests of soils from the Krompachy area were determined of 4 sampling sites in 2015. An influence of the sampling sites distance from the copper smeltery on the absolutely concentrations of metals were recorded for copper, lead, zinc, arsenic and mercury. The highest concentrations of these metals were detected on the sampling sites up to 3 km from the copper smeltery. The samples of soil were used to assess of phytotoxic effect. Total mortality was established at earthworms using chronic toxicity test after 7 exposure days. The results of our study confirmed that no mortality was observed in any of the study soils. Based on the phytotoxicity testing, phytotoxic effects of the metals contaminated soils from the samples 3KR (7-9) S.alba seeds was observed.

Constant pressure high throughput membrane permeation testing system

DOEpatents

Albenze, Erik J.; Hopkinson, David P.; Luebke, David R.

2014-09-02

The disclosure relates to a membrane testing system for individual evaluation of a plurality of planar membranes subjected to a feed gas on one side and a sweep gas on a second side. The membrane testing system provides a pressurized flow of a feed and sweep gas to each membrane testing cell in a plurality of membrane testing cells while a stream of retentate gas from each membrane testing cell is ported by a retentate multiport valve for sampling or venting, and a stream of permeate gas from each membrane testing cell is ported by a permeate multiport valve for sampling or venting. Back pressure regulators and mass flow controllers act to maintain substantially equivalent gas pressures and flow rates on each side of the planar membrane throughout a sampling cycle. A digital controller may be utilized to position the retentate and permeate multiport valves cyclically, allowing for gas sampling of different membrane cells over an extended period of time.

Static renewal tests using Pimephales promelas (fathead minnows) and Ceriodaphnia dubia (daphnids). Clinch River-Environmental Restoration Program (CR-ERP) pilot study, ambient water toxicity

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

Simbeck, D.J.

1993-12-31

Clinch River-Environmental Restoration Program (CR-ERP) personnel and Tennessee Valley Authority (TVA) personnel conducted a pilot study during the week of April 22--29, 1993, prior to initiation of CR-ERP Phase 2 Sampling and Analysis activities. The organisms specified for testing were larval fathead minnows, Pimephales promelas, and the daphnid, Ceriodaphnia dubia. Surface water samples were collected by TVA Field Engineering personnel from Clinch River Mile 9.0 and Poplar Creek Kilometer 1.6 on April 21, 23, and 26. Samples were split and provided to the CR-ERP and TVA toxicology laboratories for testing. Exposure of test organisms to these samples resulted in nomore » toxicity (survival, growth, or reproduction) to either species in testing conducted by TVA. Attachments to this report include: Chain of custody forms -- originals; Toxicity test bench sheets and statistical analyses; Reference toxicant test information; and Personnel training documentation.« less

Women's views on human papillomavirus self-sampling: focus groups to assess acceptability, invitation letters and a test kit in the Australian setting.

PubMed

Sultana, Farhana; Mullins, Robyn; Murphy, Michael; English, Dallas R; Simpson, Julie A; Drennan, Kelly T; Heley, Stella; Wrede, C David; Brotherton, Julia M L; Saville, Marion; Gertig, Dorota M

2015-08-01

Background The study evaluated acceptability, invitation letters and the test kit for a trial of human papillomavirus (HPV) self-sampling among never- and under-screened women in Australia. Victorian women, 30-69 years, who had never had a Pap test or were overdue for one, participated. Four focus groups including eight to nine participants segmented by age (30-49 and 50-69 years) and screening history (never- and under-screened) were conducted in August 2013. Discussions were recorded and transcribed verbatim and data analysed using thematic content analysis. The response to the concept of HPV self-sampling was positive. Decision-making was largely influenced by the content of a pre-invitation letter. Appealing features of self-sampling were cost (free), convenience (home-based) and anticipated less discomfort (with a swab) than a Pap test. Small kits that fit in mailboxes were preferred over post office parcel collection. The perceived barriers include concerns about test accuracy and lack of confidence that a home-based test would give the same results as a physician administered test. Women wanted information on the timing of receipt of the results and information about the organisation providing the test. HPV self-sampling is a possible alternative for Australian women who are reluctant to have a Pap test and may increase the likelihood of participation in cervical cancer screening if women's concerns about it can be addressed. The findings of this study are relevant for researchers, policymakers and practitioners implementing self-sampling for under-screened women as part of cervical screening programs.

[Evaluation of cytomegalovirus quantification in blood by the R-gene real-time PCR test].

PubMed

Marque-Juillet, S; Touzard, A; Monnier, S; Fernand-Laurent, C; Therby, A; Rigaudeau, S; Harzic, M

2010-04-01

Diagnosing the presence of cytomegalovirus (CMV) in the blood of immunodepressed patients is often done by quantitative polymerase chain reaction (Q-PCR) even though the reference method remains the antigenemia pp65 (Ag-pp65) test. To define the predictive value of the Q-PCR in the diagnosis of CMV disease and assess treatment efficacy using the CMV R-gene test. To compare the Q-PCR results and feasibility with those of the Ag-pp65 test. The Q-PCR was performed in 34 whole blood samples (frozen at -80 degrees C until use) from five patients diagnosed with CMV disease, defined as the presence of clinical signs and Ag-pp65 in the nuclei of more than two cells. After extraction, viral DNA was quantified in each sample using the Q-PCR CMV R-gene kit according to the manufacturer's instructions. Immediately after blood was drawn, the Ag-pp65 test had been performed in 32 samples using CINAkit (Argene). The 16 samples positive by the Ag-pp65 test were also positive by PCR; six samples negative by the Ag-pp65 test were positive by PCR; and the remaining 10 samples were negative by both techniques. During treatment, the two markers' kinetics were similar. The CMV R-gene test has a predictive value as good as that of the Ag-pp65 test but is fast and easier to use. A prospective study with a greater number of patients is needed to define the prediction threshold for CMV disease. Copyright 2009 Elsevier Masson SAS. All rights reserved.

The microbiological quality of pasteurized milk sold by automatic vending machines.

PubMed

Angelidis, A S; Tsiota, S; Pexara, A; Govaris, A

2016-06-01

The microbiological quality of pasteurized milk samples (n = 39) collected during 13 weekly intervals from three automatic vending machines (AVM) in Greece was investigated. Microbiological counts (total aerobic (TAC), total psychrotrophic (TPC), Enterobacteriaceae (EC), and psychrotrophic aerobic bacterial spore counts (PABSC)) were obtained at the time of sampling and at the end of shelf-life (3 days) after storage of the samples at 4 or 8°C. TAC were found to be below the 10(7 ) CFU ml(-1) limit of pasteurized milk spoilage both during sampling as well as when milk samples were stored at either storage temperature for 3 days. Enterobacteriaceae populations were below 1 CFU ml(-1) in 69·2% of the samples tested at the time of sampling, whereas the remaining samples contained low numbers, typically less than 10 CFU ml(-1) . All samples tested negative for the presence of Listeria monocytogenes. Analogous microbiological data were also obtained by sampling and testing prepackaged, retail samples of pasteurized milk from two dairy companies in Greece (n = 26). From a microbiological standpoint, the data indicate that the AVM milk samples meet the quality standards of pasteurized milk. However, the prepackaged, retail milk samples yielded better results in terms of TAC, TPC and EC, compared to the AVM samples at the end of shelf-life. Recently, Greek dairy farmers organized in cooperatives launched the sale of pasteurized milk via AVM and this study reports on the microbiological quality of this product. The data show that AVM milk is sold at proper refrigeration temperatures and meets the quality standards of pasteurized milk throughout the manufacturer's specified shelf-life. However, based on the microbiological indicators tested, the keeping quality of the tested prepackaged, retail samples of pasteurized milk at the end of shelf-life upon storage under suboptimal refrigeration temperature (8°C) was better. © 2016 The Society for Applied Microbiology.

Screening for gonorrhoea using samples collected through the English National Chlamydia Screening Programme and risk of false positives: a national survey of Local Authorities

PubMed Central

Field, Nigel; Kennedy, Iain; Folkard, Kate; Duffell, Stephen; Town, Katy; Ison, Catherine A; Hughes, Gwenda

2014-01-01

Objectives To investigate use of dual tests for Chlamydia trachomatis and Neisseria gonorrhoeae on samples collected through the National Chlamydia Screening Programme (NCSP) in England. Design and setting During May–July 2013, we delivered an online survey to commissioners of sexual health services in the 152 upper-tier English Local Authorities (LAs) who were responsible for commissioning chlamydia screening in people aged 15–24 years. Main outcome measures (1) The proportion of English LAs using dual tests on samples collected by the NCSP; (2) The estimated number of gonorrhoea tests and false positives from samples collected by the NCSP, calculated using national surveillance data on the number of chlamydia tests performed, assuming the gonorrhoea prevalence to range between 0.1% and 1%, and test sensitivity and specificity of 99.5%. Results 64% (98/152) of LAs responded to this national survey; over half (53% (52/98)) reported currently using dual tests in community settings. There was no significant difference between LAs using and not using dual tests by chlamydia positivity, chlamydia diagnosis rate or population screening coverage. Although positive gonorrhoea results were confirmed with supplementary tests in 93% (38/41) of LAs, this occurred after patients were notified about the initial positive result in 63% (26/41). Approximately 450–4500 confirmed gonorrhoea diagnoses and 2300 false-positive screens might occur through use of dual tests on NCSP samples each year. Under reasonable assumptions, the positive predictive value of the screening test is 17–67%. Conclusions Over half of English LAs already commission dual tests for samples collected by the NCSP. Gonorrhoea screening has been introduced alongside chlamydia screening in many low prevalence settings without a national evidence review or change of policy. We question the public health benefit here, and suggest that robust testing algorithms and clinical management pathways, together with rigorous evaluation, be implemented wherever dual tests are deployed. PMID:25324326

An assessment of the feasibility of employing biochemical acidogenic potential tests for characterizing anaerobic biodegradability of raw and pretreated waste activated sludge.

PubMed

Kianmehr, Peiman; Parker, Wayne; Seto, Peter

2012-04-01

The potential to use the results of biochemical acid potential (BAP) tests to predict the ultimate digestibility of raw and pretreated waste activated sludge (WAS) was investigated. The ultimate methane production from biochemical methane potential (BMP) tests on raw and pretreated samples which spanned a range of biodegradability proved linearly related to the volatile fatty acid (VFA) and soluble chemical oxygen demand (COD) production in corresponding BAP tests. In addition, a linear relationship between NH4-N production in the BMP and BAP tests was observed. Despite the linear nature of the relationships, the ratio of the production of methane in the BMP tests to the production of VFAs in the BAP tests varied with the biodegradability of the sludge samples. Waste Activated Sludge samples with low digestibility had ultimate yields of CH4 that were greater than the VFA yields in BAP tests, whereas sludge samples with high digestibility had lower yields of CH4 than the corresponding VFA yields. This trend contrasted with the NH4 results, in which the yields in the BAP tests were consistently less than those observed in the BMP tests. It was hypothesized that the varying relationship between CH4 and VFA yields was because of the inhibition of anaerobic oxidation of long-chain fatty acids (LCFAs) in the BAP tests. Long-chain fatty acids would be converted to CH4 in BMP tests but produced as digestion intermediates in the BAP tests and were not measured as part of the VFA yield. Hydrogen and acetate were identified as the two most likely intermediates that would accumulate in the BAP tests (which would cause inhibition). A stoichiometric model to facilitate the development of an improved understanding of the biodegradation processes in the BAP and BMP tests was assembled. When the model was applied to the BAP tests the anaerobic oxidation of LCFAs and propionate and methanogenesis were excluded from the model. The model was employed to estimate the extent of degradation of lipids, carbohydrates, and proteins in the batch tests as a function of the ultimate biodegradability of the sludge samples. On the basis of model fitting, it was determined that the degradation of lipids in BMP tests decreased, whereas the degradation of carbohydrates and proteins increased as the digestibility of the sludge samples increased. The varying ratio of lipid to protein and carbohydrate degradability with increasing digestibility of the sludge samples describes the relationship between VFA production and CH4 production in the BAP, and BMP tests, respectively.

Arc Jet Testing of Carbon Phenolic for Mars Sample Return and Future NASA Missions

NASA Technical Reports Server (NTRS)

Laub, Bernard; Chen, Yih-Kanq; Skokova, Kristina; Delano, Chad

2004-01-01

The objective of the Mars Sample Return (MSR) Mission is to return a sample of MArtian soil to Earth. The Earth Entry Vehicle (EEV) brings te samples through the atmosphere to the ground.The program aims to: Model aerothermal environment during EEV flight; On the basis of results, select potential TPS materials for EEV forebody; Fabricate TPS materials; Test the materials in the arc jet environment representative of predicted flight environment;Evaluate material performance; Compare results of modeling predictions with test results.

A Preliminary Assessment of 3-Nitro-1,2,4-Triazol-5-One (NTO) as an Insensitive High Explosive

DTIC Science & Technology

1989-07-01

consisted of balled agglomerates of microfine NTO needles (Fig. 2b). Handling properties5 were poor. A final larger scale recrystallisation (20 g NTO...specification for the ERDE T of I test. Samples of 200 mg in glass test tubes were heated at 5"C/min till ignition occurred. Ignition was defined by...duplicate samples. Vacuum Thermal Stability 1251 The test procedure consisted of placing duplicate 5 g samples in glass sample tubes , attaching to a mercury

Development and Evaluation of a Rapid and Sensitive EBOV-RPA Test for Rapid Diagnosis of Ebola Virus Disease.

PubMed

Yang, Mingjuan; Ke, Yuehua; Wang, Xuesong; Ren, Hang; Liu, Wei; Lu, Huijun; Zhang, Wenyi; Liu, Shiwei; Chang, Guohui; Tian, Shuguang; Wang, Lihua; Huang, Liuyu; Liu, Chao; Yang, Ruifu; Chen, Zeliang

2016-06-01

Confirming Ebola virus disease (EVD), a deadly infectious disease, requires real-time RT-PCR, which takes up to a few hours to yield results. Therefore, a rapid diagnostic assay is imperative for EVD diagnosis. A rapid nucleic acid test based on recombinase polymerase amplification (EBOV-RPA) was developed to specifically detect the 2014 outbreak strains. The EBOV-RPA assay was evaluated by testing samples from suspected EVD patients in parallel with RT-PCR. An EBOV-RPA, which could be completed in 20 min, was successfully developed. Of 271 patients who tested positive for Ebola virus by RT-PCR, 264 (sensitivity: 97%, 95% CI: 95.5-99.3%) were positive by EBOV-RPA; 101 of 104 patients (specificity: 97%, 95% CI: 93.9-100%) who tested negative by RT-PCR were also negative by EBOV-RPA. The sensitivity values for samples with a Ct value of <34, which accounted for 95.59% of the samples, was 100%. Discordant samples positive by RT-PCR but negative by EBOV-RPA had significantly high Ct values. Results of external quality assessment samples with EBOV-RPA were 100%, consistent with those of RT-PCR. The EBOV-RPA assay showed 97% sensitivity and 97% specificity for all EVD samples tested, making it a rapid and sensitive test for EVD diagnosis.

Operability test report for the in SITU vapor sampling

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

Corbett, J.E., Westinghouse Hanford

1996-05-31

This report documents the successful completion of testing for the In Situ Vapor Sampling (ISVS) system. The report includes the test procedure (WHC-SD-WM-OTP-196, Rev OA), data sheets, exception resolutions, and a test report summary. This report conforms to the guidelines established in WHC-IP-1026, `Engineering Practice Guidelines,` Appendix L, `Operability Test Procedures and Reports.`

The Effects of Test Length and Sample Size on Item Parameters in Item Response Theory

ERIC Educational Resources Information Center

Sahin, Alper; Anil, Duygu

2017-01-01

This study investigates the effects of sample size and test length on item-parameter estimation in test development utilizing three unidimensional dichotomous models of item response theory (IRT). For this purpose, a real language test comprised of 50 items was administered to 6,288 students. Data from this test was used to obtain data sets of…

75 FR 22814 - Guidance for Industry: Nucleic Acid Testing (NAT) for Human Immunodeficiency Virus Type 1 (HIV-1...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-30

... Immunodeficiency Virus Type 1 (HIV-1) and Hepatitis C Virus (HCV): Testing, Product Disposition, and Donor Deferral... Industry: Nucleic Acid Testing (NAT) for Human Immunodeficiency Virus Type 1 (HIV-1) and Hepatitis C Virus... Acid Test (NAT) and Hepatitis C Virus (HCV) NAT, on testing individual samples or pooled samples from...

19 CFR 151.74 - Retest at port director's request.

Code of Federal Regulations, 2013 CFR

2013-04-01

... OF THE TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Wool and Hair § 151.74... results of such test, proceed to have another test made upon a suitable sample of the wool or hair at the...

19 CFR 151.74 - Retest at port director's request.

Code of Federal Regulations, 2011 CFR

2011-04-01

... OF THE TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Wool and Hair § 151.74... results of such test, proceed to have another test made upon a suitable sample of the wool or hair at the...

19 CFR 151.74 - Retest at port director's request.

Code of Federal Regulations, 2014 CFR

2014-04-01

... OF THE TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Wool and Hair § 151.74... results of such test, proceed to have another test made upon a suitable sample of the wool or hair at the...

19 CFR 151.74 - Retest at port director's request.

Code of Federal Regulations, 2010 CFR

2010-04-01

... OF THE TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Wool and Hair § 151.74... results of such test, proceed to have another test made upon a suitable sample of the wool or hair at the...

19 CFR 151.74 - Retest at port director's request.

Code of Federal Regulations, 2012 CFR

2012-04-01

... OF THE TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Wool and Hair § 151.74... results of such test, proceed to have another test made upon a suitable sample of the wool or hair at the...

23 CFR 637.209 - Laboratory and sampling and testing personnel qualifications.

Code of Federal Regulations, 2010 CFR

2010-04-01

... sampling and testing personnel. (c) Conflict of interest. In order to avoid an appearance of a conflict of interest, any qualified non-STD laboratory shall perform only one of the following types of testing on the...

Experimental Design for a Sponge-Wipe Study to Relate the Recovery Efficiency and False Negative Rate to the Concentration of a Bacillus anthracis Surrogate for Six Surface Materials

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

Piepel, Gregory F.; Amidan, Brett G.; Krauter, Paula

2011-05-01

Two concerns were raised by the Government Accountability Office following the 2001 building contaminations via letters containing Bacillus anthracis (BA). These included the: 1) lack of validated sampling methods, and 2) need to use statistical sampling to quantify the confidence of no contamination when all samples have negative results. Critical to addressing these concerns is quantifying the false negative rate (FNR). The FNR may depend on the 1) method of contaminant deposition, 2) surface concentration of the contaminant, 3) surface material being sampled, 4) sample collection method, 5) sample storage/transportation conditions, 6) sample processing method, and 7) sample analytical method.more » A review of the literature found 17 laboratory studies that focused on swab, wipe, or vacuum samples collected from a variety of surface materials contaminated by BA or a surrogate, and used culture methods to determine the surface contaminant concentration. These studies quantified performance of the sampling and analysis methods in terms of recovery efficiency (RE) and not FNR (which left a major gap in available information). Quantifying the FNR under a variety of conditions is a key aspect of validating sample and analysis methods, and also for calculating the confidence in characterization or clearance decisions based on a statistical sampling plan. A laboratory study was planned to partially fill the gap in FNR results. This report documents the experimental design developed by Pacific Northwest National Laboratory and Sandia National Laboratories (SNL) for a sponge-wipe method. The testing was performed by SNL and is now completed. The study investigated the effects on key response variables from six surface materials contaminated with eight surface concentrations of a BA surrogate (Bacillus atrophaeus). The key response variables include measures of the contamination on test coupons of surface materials tested, contamination recovered from coupons by sponge-wipe samples, RE, and FNR. The experimental design involves 16 test runs, performed in two blocks of eight runs. Three surface materials (stainless steel, vinyl tile, and ceramic tile) were tested in the first block, while three other surface materials (plastic, painted wood paneling, and faux leather) were tested in the second block. The eight surface concentrations of the surrogate were randomly assigned to test runs within each block. Some of the concentrations were very low and presented challenges for deposition, sampling, and analysis. However, such tests are needed to investigate RE and FNR over the full range of concentrations of interest. In each run, there were 10 test coupons of each of the three surface materials. A positive control sample was generated at the same time as each test sample. The positive control results will be used to 1) calculate RE values for the wipe sampling and analysis method, and 2) fit RE- and FNR-concentration equations, for each of the six surface materials. Data analyses will support 1) estimating the FNR for each combination of contaminant concentration and surface material, 2) estimating the surface concentrations and their uncertainties of the contaminant for each combination of concentration and surface material, 3) estimating RE (%) and their uncertainties for each combination of contaminant concentration and surface material, 4) fitting FNR-concentration and RE-concentration equations for each of the six surface materials, 5) assessing goodness-of-fit of the equations, and 6) quantifying the uncertainty in FNR and RE predictions made with the fitted equations.« less

Amphetamines and cannabinoids testing in hair: Evaluation of results from a two-year period.

PubMed

Burgueño, María José; Alonso, Amaya; Sánchez, Sergio

2016-08-01

This paper presents an overview of a set of amphetamines and cannabinoids tests performed on head hair samples from the Medico-Legal sector at the Madrid Department of the Spanish National Institute of Toxicology and Forensic Sciences during the years 2013 and 2014. The hair samples were tested for five stimulant phenylalkylamine derivatives -amphetamine (AP), methamphetamine (MA), 3,4-methylenedioxymethamphetamine (MDMA), 3,4-methylenedioxy-amphetamine (MDA), and 3,4-methylenedioxy-N-ethylamphetamine (MDEA)- and/or two cannabinoids-Δ(9)-tetrahydrocannabinol (THC) and cannabinol (CBN)- by gas chromatography equipped with mass spectrometry detection in selected-ion monitoring mode, applying a method accredited to ISO/IEC 17025 standards. The test results were interpreted according to the confirmation cut-offs proposed by the Society of Hair Testing (SoHT) to identify chronic drug use. The ratios of positive results were studied in relation to gender, age, hair colour, dyeing and length of the tested samples to assess the independence from these variables or the association with them. Low, medium and high ranges of concentration were also estimated for each drug. 21.94% of the 2954 hair samples tested for phenylalkylamine derivatives were positive for one or more substances. 16.38% of the samples were positive for AP, 12.09% for MDMA and only 0.44% for MA. 6.60% of the tested samples were positive for AP/MDMA combination. A total of 3178 samples were tested for cannabinoids, resulting in 53.40% positive for THC and CBN. Simultaneous tests for phenylalkylamine derivatives and cannabinoids were performed in 2931 of the samples; 14.94% of them were positive for THC, CBN, and one or more amphetamines. According to the results from the statistical analysis, the use of THC and MDMA vary with age and gender among the Medico-Legal sector in an extended area of Spain, while the use of AP appears to be independent of these variables. On the other hand, the results of THC in hair could be influenced by the length of the tested segment; therefore, a consensus regarding the hair length between 3.0 and 5.5cm for THC testing should be reached. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Methods for the field evaluation of quantitative G6PD diagnostics: a review.

PubMed

Ley, Benedikt; Bancone, Germana; von Seidlein, Lorenz; Thriemer, Kamala; Richards, Jack S; Domingo, Gonzalo J; Price, Ric N

2017-09-11

Individuals with glucose-6-phosphate dehydrogenase (G6PD) deficiency are at risk of severe haemolysis following the administration of 8-aminoquinoline compounds. Primaquine is the only widely available 8-aminoquinoline for the radical cure of Plasmodium vivax. Tafenoquine is under development with the potential to simplify treatment regimens, but point-of-care (PoC) tests will be needed to provide quantitative measurement of G6PD activity prior to its administration. There is currently a lack of appropriate G6PD PoC tests, but a number of new tests are in development and are likely to enter the market in the coming years. As these are implemented, they will need to be validated in field studies. This article outlines the technical details for the field evaluation of novel quantitative G6PD diagnostics such as sample handling, reference testing and statistical analysis. Field evaluation is based on the comparison of paired samples, including one sample tested by the new assay at point of care and one sample tested by the gold-standard reference method, UV spectrophotometry in an established laboratory. Samples can be collected as capillary or venous blood; the existing literature suggests that potential differences in capillary or venous blood are unlikely to affect results substantially. The collection and storage of samples is critical to ensure preservation of enzyme activity, it is recommended that samples are stored at 4 °C and testing occurs within 4 days of collection. Test results can be visually presented as scatter plot, Bland-Altman plot, and a histogram of the G6PD activity distribution of the study population. Calculating the adjusted male median allows categorizing results according to G6PD activity to calculate standard performance indicators and to perform receiver operating characteristic (ROC) analysis.

Comparison of initial stream urine samples and cervical samples for detection of human papillomavirus.

PubMed

Hagihara, Mao; Yamagishi, Yuka; Izumi, Koji; Miyazaki, Narimi; Suzuki, Takayoshi; Kato, Hideo; Nishiyama, Naoya; Koizumi, Yusuke; Suematsu, Hiroyuki; Mikamo, Hiroshige

2016-08-01

Uterine cervical cancer is a treatable and preventable cancer. Medical efforts to reduce rates of cervical cancer focus on the promotion of human papillomavirus (HPV) vaccination and the promotion of routine cervical cancer screening done by cervical cytology and cervical HPV testing. Urine-based HPV testing would be simple and noninvasive approach to screen for cervical cancer. Two biospecimens (clinician-taken sample from cervix and initial stream urine sample) were provided from a total of 240 healthy women attending for cancer screening provided for HPV testing. We have assessed the HPV detection rates among cervical samples and pellet fraction of urine samples using HPV test (Anyplex™ II HPV28 Detection kit, Seegene, Korea). Among 240 samples screened, HPV prevalence was 42.9% in pellet fractions of urine samples. The agreement between the two kinds of samples was 98.4%, k = 0.792. Discordant results were observed in 27 cases; 5 were positive only by urine samples and 22 were positive only by smear samples. Sensitivity and specificity for all HPV DNA in pellet fractions of urine using cervical samples as reference was 68.4% and 99.9%. Comparing methodologies of collection of samples for HPV detection, they showed the higher agreements for almost genotypes between cervical samples and pellet fractions of urine samples. These results suggest that urine could be a good noninvasive tool to monitor HPV infection in women. Additional research in a larger and general screening population would be needed. Copyright © 2016 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Eddy current nondestructive testing device for measuring variable characteristics of a sample utilizing Walsh functions

DOEpatents

Libby, Hugo L.; Hildebrand, Bernard P.

1978-01-01

An eddy current testing device for measuring variable characteristics of a sample generates a signal which varies with variations in such characteristics. A signal expander samples at least a portion of this generated signal and expands the sampled signal on a selected basis of square waves or Walsh functions to produce a plurality of signal components representative of the sampled signal. A network combines these components to provide a display of at least one of the characteristics of the sample.

A quarantine protocol for analysis of returned extraterrestrial samples

NASA Technical Reports Server (NTRS)

Bagby, J. R.; Sweet, H. C.; Devincenzi, D. L.

1983-01-01

A protocol is presented for the analysis at an earth-orbiting quarantine facility of return samples of extraterrestrial material that might contain (nonterrestrial) life forms. The protocol consists of a series of tests designed to determine whether the sample, conceptualized as a 1-kg sample of Martian soil, is free from nonterrestrial biologically active agents and so may safely be sent to a terrestrial containment facility, or it exhibits biological activity requiring further (second-order) testing outside the biosphere. The first-order testing procedure seeks to detect the presence of any replicating organisms or toxic substances through a series of experiments including gas sampling, analysis of radioactivity, stereomicroscopic inspection, chemical analysis, microscopic examination, the search for metabolic products under growth conditions, microbiologicl assays, and the challenge of cultured cells with any agents found or with the extraterrestrial material as is. Detailed plans for the second-order testing would be developed in response to the actual data received from primary testing.

Detecting Renibacterium salmoninarum in wild brown trout by use of multiple organ samples and diagnostic methods

USGS Publications Warehouse

Guomundsdottir, S.; Applegate, Lynn M.; Arnason, I.O.; Kristmundsson, A.; Purcell, Maureen K.; Elliott, Diane G.

2017-01-01

Renibacterium salmoninarum, the causative agent of salmonid bacterial kidney disease (BKD), is endemic in many wild trout species in northerly regions. The aim of the present study was to determine the optimal R. salmoninarum sampling/testing strategy for wild brown trout (Salmo trutta L.) populations in Iceland. Fish were netted in a lake and multiple organs—kidney, spleen, gills, oesophagus and mid-gut—were sampled and subjected to five detection tests i.e. culture, polyclonal enzyme-linked immunosorbent assay (pELISA) and three different PCR tests. The results showed that each fish had encountered R. salmoninarum but there were marked differences between results obtained depending on organ and test. The bacterium was not cultured from any kidney sample while all kidney samples were positive by pELISA. At least one organ from 92.9% of the fish tested positive by PCR. The results demonstrated that the choice of tissue and diagnostic method can dramatically influence the outcome of R. salmoninarum surveys.

A new low-cost procedure for detecting nucleic acids in low-incidence samples: a case study of detecting spores of Paenibacillus larvae from bee debris.

PubMed

Ryba, Stepan; Kindlmann, Pavel; Titera, Dalibor; Haklova, Marcela; Stopka, Pavel

2012-10-01

American foulbrood, because of its virulence and worldwide spread, is currently one of the most dangerous diseases of honey bees. Quick diagnosis of this disease is therefore vitally important. For its successful eradication, however, all the hives in the region must be tested. This is time consuming and costly. Therefore, a fast and sensitive method of detecting American foulbrood is needed. Here we present a method that significantly reduces the number of tests needed by combining batches of samples from different hives. The results of this method were verified by testing each sample. A simulation study was used to compare the efficiency of the new method with testing all the samples and to develop a decision tool for determining when best to use the new method. The method is suitable for testing large numbers of samples (over 100) when the incidence of the disease is low (10% or less).

Clinch River - Environmental Restoration Program (CR-ERP) study, Ambient water toxicity

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

Simbeck, D.J.

1997-06-01

Clinch River - Environmental Restoration Program (CR-ERP) personnel and Tennessee Valley Authority (TVA) personnel conducted a study during the week of January 25-February 1, 1994, as described in the Statement of Work (SOW) document. The organisms specified for testing were larval fathead minnows, Pimephales promelas, and the daphnid, Ceriodaphnia dubia. Surface water samples were collected by TVA Field Engineering personnel from Clinch River Mile 9.0, Poplar Creek Mile 1.0, and Poplar Creek Mile 2.9 on January 24, 26, and 28. Samples were partitioned (split) and provided to the CR-ERP and TVA toxicology laboratories for testing. Exposure of test organisms tomore » these samples resulted in no toxicity (survival or growth) to fathead minnows; however, toxicity to daphnids (significantly reduced reproduction) was demonstrated in undiluted samples from Poplar Creek Mile 1.0 in testing conducted by TVA based on hypothesis testing of data. Point estimation (IC{sub 25}) analysis of the data, however, showed no toxicity in PCM 1.0 samples.« less

Dilution testing using rapid diagnostic tests in a HIV diagnostic algorithm: a novel alternative for confirmation testing in resource limited settings.

PubMed

Shanks, Leslie; Siddiqui, M Ruby; Abebe, Almaz; Piriou, Erwan; Pearce, Neil; Ariti, Cono; Masiga, Johnson; Muluneh, Libsework; Wazome, Joseph; Ritmeijer, Koert; Klarkowski, Derryck

2015-05-14

Current WHO testing guidelines for resource limited settings diagnose HIV on the basis of screening tests without a confirmation test due to cost constraints. This leads to a potential risk of false positive HIV diagnosis. In this paper, we evaluate the dilution test, a novel method for confirmation testing, which is simple, rapid, and low cost. The principle of the dilution test is to alter the sensitivity of a rapid diagnostic test (RDT) by dilution of the sample, in order to screen out the cross reacting antibodies responsible for falsely positive RDT results. Participants were recruited from two testing centres in Ethiopia where a tiebreaker algorithm using 3 different RDTs in series is used to diagnose HIV. All samples positive on the initial screening RDT and every 10th negative sample underwent testing with the gold standard and dilution test. Dilution testing was performed using Determine™ rapid diagnostic test at 6 different dilutions. Results were compared to the gold standard of Western Blot; where Western Blot was indeterminate, PCR testing determined the final result. 2895 samples were recruited to the study. 247 were positive for a prevalence of 8.5 % (247/2895). A total of 495 samples underwent dilution testing. The RDT diagnostic algorithm misclassified 18 samples as positive. Dilution at the level of 1/160 was able to correctly identify all these 18 false positives, but at a cost of a single false negative result (sensitivity 99.6 %, 95 % CI 97.8-100; specificity 100 %, 95 % CI: 98.5-100). Concordance between the gold standard and the 1/160 dilution strength was 99.8 %. This study provides proof of concept for a new, low cost method of confirming HIV diagnosis in resource-limited settings. It has potential for use as a supplementary test in a confirmatory algorithm, whereby double positive RDT results undergo dilution testing, with positive results confirming HIV infection. Negative results require nucleic acid testing to rule out false negative results due to seroconversion or misclassification by the lower sensitivity dilution test. Further research is needed to determine if these results can be replicated in other settings. ClinicalTrials.gov, NCT01716299 .

Standardization and validation of a cytometric bead assay to assess antibodies to multiple Plasmodium falciparum recombinant antigens

PubMed Central

2012-01-01

Background Multiplex cytometric bead assay (CBA) have a number of advantages over ELISA for antibody testing, but little information is available on standardization and validation of antibody CBA to multiple Plasmodium falciparum antigens. The present study was set to determine optimal parameters for multiplex testing of antibodies to P. falciparum antigens, and to compare results of multiplex CBA to ELISA. Methods Antibodies to ten recombinant P. falciparum antigens were measured by CBA and ELISA in samples from 30 individuals from a malaria endemic area of Kenya and compared to known positive and negative control plasma samples. Optimal antigen amounts, monoplex vs multiplex testing, plasma dilution, optimal buffer, number of beads required were assessed for CBA testing, and results from CBA vs. ELISA testing were compared. Results Optimal amounts for CBA antibody testing differed according to antigen. Results for monoplex CBA testing correlated strongly with multiplex testing for all antigens (r = 0.88-0.99, P values from <0.0001 - 0.004), and antibodies to variants of the same antigen were accurately distinguished within a multiplex reaction. Plasma dilutions of 1:100 or 1:200 were optimal for all antigens for CBA testing. Plasma diluted in a buffer containing 0.05% sodium azide, 0.5% polyvinylalcohol, and 0.8% polyvinylpyrrolidone had the lowest background activity. CBA median fluorescence intensity (MFI) values with 1,000 antigen-conjugated beads/well did not differ significantly from MFI with 5,000 beads/well. CBA and ELISA results correlated well for all antigens except apical membrane antigen-1 (AMA-1). CBA testing produced a greater range of values in samples from malaria endemic areas and less background reactivity for blank samples than ELISA. Conclusion With optimization, CBA may be the preferred method of testing for antibodies to P. falciparum antigens, as CBA can test for antibodies to multiple recombinant antigens from a single plasma sample and produces a greater range of values in positive samples and lower background readings for blank samples than ELISA. PMID:23259607

Buoyant Effects on the Flammability of Silicone Samples Planned for the Spacecraft Fire Experiment (Saffire)

NASA Technical Reports Server (NTRS)

Niehaus, Justin; Ferkul, Paul V.; Gokoglu, Suleyman; Ruff, Gary

2015-01-01

Flammability experiments on silicone samples were conducted in anticipation of the Spacecraft Fire Experiment (Saffire). The sample geometry was chosen to match the NASA 6001 Test 1 specification, namely 5 cm wide by 30 cm tall. Four thicknesses of silicone (0.25, 0.36, 0.61 and 1.00 mm) were examined. Tests included traditional upward buoyant flame spread using Test 1 procedures, downward opposed flow flame spread, horizontal and angled flame spread, forced flow upward and downward flame spread. In addition to these configurations, upward and downward tests were also conducted in a chamber with varying oxygen concentrations. In the upward buoyant flame spread tests, the flame generally did not burn the entire sample. As thickness was increased, the flame spread distance decreased before flame extinguishment. For the thickest sample, ignition could not be achieved. In the downward tests, the two thinnest samples permitted the flame to burn the entire sample, but the spread rate was lower compared to the corresponding upward values. The other two thicknesses could not be ignited in the downward configuration. The increased flammability for downward spreading flames relative to upward ones is uncommon. The two thinnest samples also burned completely in the horizontal configuration, as well as at angles up to 75 degrees from the horizontal. The upward and downward flammability behavior was compared in atmospheres of varying oxygen concentration to determine a maximum oxygen concentration for each configuration. Upward tests in air with an added forced flow were more flammable. Complementary analyses using SEM and TGA techniques suggest the importance of the silica layer formed on the burned sample surface. As silicone burns upward, silica deposits downstream •If the silicone is ignited in the downward configuration, it burns the entire length of the sample •Burning upward at an angle increases the burn length in some cases possibly due to less silica deposition •Forced flow in the upward burning case increases flammability, likely due to an increase in convective flow preventing silica from depositing •Samples in upward configuration burning under forced flow self extinguish after forced flow is removed

CESIUM REMOVAL FROM TANKS 241-AN-103 & 241-SX-105 & 241-AZ-101/102 COMPOSITE FOR TESTING IN BENCH SCALE STEAM REFORMER

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

DUNCAN JB; HUBER HJ

2011-06-08

This report documents the preparation of three actual Hanford tank waste samples for shipment to the Savannah River National Laboratory (SRNL). Two of the samples were dissolved saltcakes from tank 241-AN-103 (hereafter AN-103) and tank 241-SX-105 (hereafter SX-105); one sample was a supernate composite from tanks 241-AZ-101 and 241-AZ-102 (hereafter AZ-101/102). The preparation of the samples was executed following the test plans LAB-PLAN-10-00006, Test Plan for the Preparation of Samples from Hanford Tanks 241-SX-105, 241-AN-103, 241-AN-107, and LAB-PLN-10-00014, Test Plan for the Preparation of a Composite Sample from Hanford Tanks 241-AZ-101 and 241-AZ-102 for Steam Reformer Testing at the Savannahmore » River National Laboratory. All procedural steps were recorded in laboratory notebook HNF-N-274 3. Sample breakdown diagrams for AN-103 and SX-105 are presented in Appendix A. The tank samples were prepared in support of a series of treatability studies of the Fluidized Bed Steam Reforming (FBSR) process using a Bench-Scale Reformer (BSR) at SRNL. Tests with simulants have shown that the FBSR mineralized waste form is comparable to low-activity waste glass with respect to environmental durability (WSRC-STI-2008-00268, Mineralization of Radioactive Wastes by Fluidized Bed Steam Reforming (FBSR): Comparisons to Vitreous Waste Forms and Pertinent Durability Testing). However, a rigorous assessment requires long-term performance data from FB SR product formed from actual Hanford tank waste. Washington River Protection Solutions, LLC (WRPS) has initiated a Waste Form Qualification Program (WP-S.2.1-20 1 0-00 1, Fluidized Bed Steam Reformer Low-level Waste Form Qualification) to gather the data required to demonstrate that an adequate FBSR mineralized waste form can be produced. The documentation of the selection process of the three tank samples has been separately reported in RPP-48824, 'Sample Selection Process for Bench-Scale Steam Reforming Treatability Studies Using Hanford Waste Samples.'« less

CESIUM REMOVAL FROM TANKS 241-AN-103 & 241-SX-105 & 241-AZ-101 & 241AZ-102 COMPOSITE FOR TESTING IN BENCH SCALE STEAM REFORMER

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

DUNCAN JB; HUBER HJ

2011-04-21

This report documents the preparation of three actual Hanford tank waste samples for shipment to the Savannah River National Laboratory (SRNL). Two of the samples were dissolved saltcakes from tank 241-AN-103 (hereafter AN-103) and tank 241-SX-105 (hereafter SX-105); one sample was a supernate composite from tanks 241-AZ-101 and 241-AZ-102 (hereafter AZ-101/102). The preparation of the samples was executed following the test plans LAB-PLAN-10-00006, Test Plan for the Preparation of Samples from Hanford Tanks 241-SX-105, 241-AN-103, 241-AN-107, and LAB-PLN-l0-00014, Test Plan for the Preparation of a Composite Sample from Hanford Tanks 241-AZ-101 and 241-AZ-102 for Steam Reformer Testing at the Savannahmore » River National Laboratory. All procedural steps were recorded in laboratory notebook HNF-N-274 3. Sample breakdown diagrams for AN-103 and SX-105 are presented in Appendix A. The tank samples were prepared in support of a series of treatability studies of the Fluidized Bed Steam Reforming (FBSR) process using a Bench-Scale Reformer (BSR) at SRNL. Tests with simulants have shown that the FBSR mineralized waste form is comparable to low-activity waste glass with respect to environmental durability (WSRC-STI-2008-00268, Mineralization of Radioactive Wastes by Fluidized Bed Steam Reforming (FBSR): Comparisons to Vitreous Waste Forms and Pertinent Durability Testing). However, a rigorous assessment requires long-term performance data from FBSR product formed from actual Hanford tank waste. Washington River Protection Solutions, LLC (WRPS) has initiated a Waste Form Qualification Program (WP-5.2.1-2010-001, Fluidized Bed Steam Reformer Low-level Waste Form Qualification) to gather the data required to demonstrate that an adequate FBSR mineralized waste form can be produced. The documentation of the selection process of the three tank samples has been separately reported in RPP-48824, Sample Selection Process for Bench-Scale Steam Reforming Treatability Studies Using Hanford Waste Samples.« less

Bayesian analysis of two diagnostic methods for paediatric ringworm infections in a teaching hospital.

PubMed

Rath, S; Panda, M; Sahu, M C; Padhy, R N

2015-09-01

Quantitatively, conventional methods of diagnosis of tinea capitis or paediatric ringworm, microscopic and culture tests were evaluated with Bayes rule. This analysis would help in quantifying the pervasive errors in each diagnostic method, particularly the microscopic method, as a long-term treatment would be involved to eradicate the infection by the use of a particular antifungal chemotherapy. Secondly, the analysis of clinical data would help in obtaining digitally the fallible standard of the microscopic test method, as the culture test method is taken as gold standard. Test results of 51 paediatric patients were of 4 categories: 21 samples were true positive (both tests positive), and 13 were true negative; the rest samples comprised both 14 false positive (microscopic test positivity with culture test negativity) and 3 false negative (microscopic test negativity with culture test positivity) samples. The prevalence of tinea infection was 47.01% in the population of 51 children. The microscopic test of a sample was efficient by 87.5%, in arriving at a positive result on diagnosis, when its culture test was positive; and, this test was efficient by 76.4%, in arriving at a negative result, when its culture test was negative. But, the post-test probability value of a sample with both microscopic and culture tests would be correct in distinguishing a sample from a sick or a healthy child with a chance of 71.5%. However, since the sensitivity of the analysis is 87.5%, the microscopic test positivity would be easier to detect in the presence of infection. In conclusion, it could be stated that Trychophyton rubrum was the most prevalent species; sensitivity and specificity of treating the infection, by antifungal therapy before ascertaining by the culture method remain as 0.8751 and 0.7642, respectively. A correct/coveted diagnostic method of fungal infection would be could be achieved by modern molecular methods (matrix-assisted laser desorption ionisation-time of flight mass spectrometry or fluorescence in situ hybridization or enzyme-linked immunosorbent assay [ELISA] or restriction fragment length polymorphism or DNA/RNA probes of known fungal taxa) in advanced laboratories. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Sample Size and Statistical Conclusions from Tests of Fit to the Rasch Model According to the Rasch Unidimensional Measurement Model (Rumm) Program in Health Outcome Measurement.

PubMed

Hagell, Peter; Westergren, Albert

Sample size is a major factor in statistical null hypothesis testing, which is the basis for many approaches to testing Rasch model fit. Few sample size recommendations for testing fit to the Rasch model concern the Rasch Unidimensional Measurement Models (RUMM) software, which features chi-square and ANOVA/F-ratio based fit statistics, including Bonferroni and algebraic sample size adjustments. This paper explores the occurrence of Type I errors with RUMM fit statistics, and the effects of algebraic sample size adjustments. Data with simulated Rasch model fitting 25-item dichotomous scales and sample sizes ranging from N = 50 to N = 2500 were analysed with and without algebraically adjusted sample sizes. Results suggest the occurrence of Type I errors with N less then or equal to 500, and that Bonferroni correction as well as downward algebraic sample size adjustment are useful to avoid such errors, whereas upward adjustment of smaller samples falsely signal misfit. Our observations suggest that sample sizes around N = 250 to N = 500 may provide a good balance for the statistical interpretation of the RUMM fit statistics studied here with respect to Type I errors and under the assumption of Rasch model fit within the examined frame of reference (i.e., about 25 item parameters well targeted to the sample).

Quality Control of Direct Molecular Diagnostics for Methicillin-Resistant Staphylococcus aureus▿

PubMed Central

van Belkum, Alex; Niesters, Hubert G. M.; MacKay, William G.; van Leeuwen, Willem B.

2007-01-01

Ten samples containing various amounts of methicillin-resistant Staphylococcus aureus (MRSA), methicillin-susceptible S. aureus, methicillin-resistant Staphylococcus epidermidis (MRSE), and combinations thereof were distributed to 51 laboratories for molecular diagnostics testing. Samples containing 102 to 103 MRSA cells were frequently reported to be negative. MRSE samples were scored as negative by all commercial tests but by only two out of three in-house tests. PMID:17581936

Operational Cyber Testing Recommendations- Version 1

DTIC Science & Technology

2014-05-02

be used to verify 5 representative pieces of the environment via sample test runs. Also, ideally, an early version of each test case can also be stood...extraneous effort). Comparing the sample results collected from the scripts with expected results can reveal deficiencies in the data collection techniques...the reporting mechanisms, and the system components themselves. The sample results can also be used for confirming that data is collected with high

Low-Pressure Testing of the Mars Science Laboratory’s Solid Sampling System: Test Methods and Preliminary Results

NASA Astrophysics Data System (ADS)

Mukherjee, S.; von der Heydt, M.; Hanson, C.; Jandura, L.

2009-12-01

The Mars Science Laboratory mission is scheduled to launch in 2011 with an extensive suite of in situ science instruments. Acquiring, processing and delivering appropriate samples of rock and martian regolith to the instruments is a critical component in realizing the science capability of these payload elements. However, there are a number of challenges in validating the design of these systems. In particular, differences in the environment (atmospheric pressure and composition, temperature, gravity), target materials (variation in rock and soil properties), and state of the hardware (electrical potential, particulate coatings) may effect sampling performance. To better understand the end-to-end system and allow development of mitigation strategies if necessary, early testing of high-fidelity engineering models of the hardware in the solid sample chain is being conducted. The components of the sample acquisition, processing & delivery chain that will be tested are the drill, scoop, sieves, portioners, and instrument inlet funnels. An evaluation of the environmental parameter space was conducted to identify a subset that may have significant effects on sampling performance and cannot be well bounded by analysis. Accordingly, support equipment to enable testing at Mars surface pressures (5-10 Torr), with carbon dioxide was designed and built. A description of the testing set-up, investigations, and preliminary results will be presented.

Relationships between narrative language samples and norm-referenced test scores in language assessments of school-age children.

PubMed

Danahy Ebert, Kerry; Scott, Cheryl M

2014-10-01

Both narrative language samples and norm-referenced language tests can be important components of language assessment for school-age children. The present study explored the relationship between these 2 tools within a group of children referred for language assessment. The study is a retrospective analysis of clinical records from 73 school-age children. Participants had completed an oral narrative language sample and at least one norm-referenced language test. Correlations between microstructural language sample measures and norm-referenced test scores were compared for younger (6- to 8-year-old) and older (9- to 12-year-old) children. Contingency tables were constructed to compare the 2 types of tools, at 2 different cutpoints, in terms of which children were identified as having a language disorder. Correlations between narrative language sample measures and norm-referenced tests were stronger for the younger group than the older group. Within the younger group, the level of language assessed by each measure contributed to associations among measures. Contingency analyses revealed moderate overlap in the children identified by each tool, with agreement affected by the cutpoint used. Narrative language samples may complement norm-referenced tests well, but age combined with narrative task can be expected to influence the nature of the relationship.

Efficacy of a lead based paint XRF analyzer and a commercially available colorimetric lead test kit as qualitative field tools for determining presence of lead in religious powders.

PubMed

Shah, Manthan P; Shendell, Derek G; Meng, Qingyu; Ohman-Strickland, Pamela; Halperin, William

2018-04-23

The performances of a portable X-Ray Fluorescence (XRF) lead paint analyzer (RMD LPA-1, Protec Instrument Corp., Waltham, MA) and a commercially available colorimetric lead test kit (First Alert Lead Test Kit, eAccess Solutions, Inc., Palatine, IL) were evaluated for use by local or state health departments as potential cost-effective rapid analysis or "spot test" field techniques for tentative identification of lead content in sindoor powders. For both field-sampling methods, sensitivity, specificity and predictive values varied widely for samples containing <300,000 μg/g lead. For samples containing ≥300,000 μg/g lead, the aforementioned metrics were 100% (however, the CIs had a wide range). In addition, both field sampling methods showed clear, consistent positive readings only for samples containing ≥300,000 μg/g lead. Even samples with lead content as high as 5,110 μg/g were not positively identified by either field analysis technique. The results of this study suggest the XRF analyzer and colorimetric lead test kit cannot be used as a rapid field test for sindoor by health department inspectors.