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Sample records for dna testing strategies

  1. Comparison of DNA testing strategies in monitoring human papillomavirus infection prevalence through simulation.

    Science.gov (United States)

    Lin, Carol Y; Li, Ling

    2016-11-07

    HPV DNA diagnostic tests for epidemiology monitoring (research purpose) or cervical cancer screening (clinical purpose) have often been considered separately. Women with positive Linear Array (LA) polymerase chain reaction (PCR) research test results typically are neither informed nor referred for colposcopy. Recently, a sequential testing by using Hybrid Capture 2 (HC2) HPV clinical test as a triage before genotype by LA has been adopted for monitoring HPV infections. Also, HC2 has been reported as a more feasible screening approach for cervical cancer in low-resource countries. Thus, knowing the performance of testing strategies incorporating HPV clinical test (i.e., HC2-only or using HC2 as a triage before genotype by LA) compared with LA-only testing in measuring HPV prevalence will be informative for public health practice. We conducted a Monte Carlo simulation study. Data were generated using mathematical algorithms. We designated the reported HPV infection prevalence in the U.S. and Latin America as the "true" underlying type-specific HPV prevalence. Analytical sensitivity of HC2 for detecting 14 high-risk (oncogenic) types was considered to be less than LA. Estimated-to-true prevalence ratios and percentage reductions were calculated. When the "true" HPV prevalence was designated as the reported prevalence in the U.S., with LA genotyping sensitivity and specificity of (0.95, 0.95), estimated-to-true prevalence ratios of 14 high-risk types were 2.132, 1.056, 0.958 for LA-only, HC2-only, and sequential testing, respectively. Estimated-to-true prevalence ratios of two vaccine-associated high-risk types were 2.359 and 1.063 for LA-only and sequential testing, respectively. When designated type-specific prevalence of HPV16 and 18 were reduced by 50 %, using either LA-only or sequential testing, prevalence estimates were reduced by 18 %. Estimated-to-true HPV infection prevalence ratios using LA-only testing strategy are generally higher than using HC2-only or

  2. Comparison of DNA testing strategies in monitoring human papillomavirus infection prevalence through simulation

    Directory of Open Access Journals (Sweden)

    Carol Y. Lin

    2016-11-01

    Full Text Available Abstract Background HPV DNA diagnostic tests for epidemiology monitoring (research purpose or cervical cancer screening (clinical purpose have often been considered separately. Women with positive Linear Array (LA polymerase chain reaction (PCR research test results typically are neither informed nor referred for colposcopy. Recently, a sequential testing by using Hybrid Capture 2 (HC2 HPV clinical test as a triage before genotype by LA has been adopted for monitoring HPV infections. Also, HC2 has been reported as a more feasible screening approach for cervical cancer in low-resource countries. Thus, knowing the performance of testing strategies incorporating HPV clinical test (i.e., HC2-only or using HC2 as a triage before genotype by LA compared with LA-only testing in measuring HPV prevalence will be informative for public health practice. Method We conducted a Monte Carlo simulation study. Data were generated using mathematical algorithms. We designated the reported HPV infection prevalence in the U.S. and Latin America as the “true” underlying type-specific HPV prevalence. Analytical sensitivity of HC2 for detecting 14 high-risk (oncogenic types was considered to be less than LA. Estimated-to-true prevalence ratios and percentage reductions were calculated. Results When the “true” HPV prevalence was designated as the reported prevalence in the U.S., with LA genotyping sensitivity and specificity of (0.95, 0.95, estimated-to-true prevalence ratios of 14 high-risk types were 2.132, 1.056, 0.958 for LA-only, HC2-only, and sequential testing, respectively. Estimated-to-true prevalence ratios of two vaccine-associated high-risk types were 2.359 and 1.063 for LA-only and sequential testing, respectively. When designated type-specific prevalence of HPV16 and 18 were reduced by 50 %, using either LA-only or sequential testing, prevalence estimates were reduced by 18 %. Conclusion Estimated-to-true HPV infection prevalence ratios using LA

  3. Comparison of DNA testing strategies in monitoring human papillomavirus infection prevalence through simulation

    OpenAIRE

    Lin, Carol Y.; Li, Ling

    2016-01-01

    Abstract Background HPV DNA diagnostic tests for epidemiology monitoring (research purpose) or cervical cancer screening (clinical purpose) have often been considered separately. Women with positive Linear Array (LA) polymerase chain reaction (PCR) research test results typically are neither informed nor referred for colposcopy. Recently, a sequential testing by using Hybrid Capture 2 (HC2) HPV clinical test as a triage before genotype by LA has been adopted for monitoring HPV infections. Als...

  4. The clinical utility of HPV DNA testing in cervical cancer screening strategies.

    Science.gov (United States)

    Bhatla, Neerja; Moda, Nidhi

    2009-09-01

    Cervical cancer continues to be the commonest cause of death among women in developing countries, largely due to the failure to the inability to sustain effective cytology-based screening programs. While this burden may come down following implementation of the human papillomavirus (HPV) vaccine, screening will still be required. HPV DNA testing is a promising new technology for cervical cancer prevention and is the most reproducible of all cervical cancer screening tests. Presently, the two assays most widely used for the detection of genital types are the polymerase chain reaction (PCR) and Hybrid Capture 2 assays (hc2). Rapid, affordable tests are expected to be available soon. HPV DNA testing can be used in a variety of clinical scenarios that include primary screening in women older than 30 yr; as an adjunctive test to cytology; in the triage of women with an equivocal cytologic report, e.g., ASC-US; or for follow-up post-treatment for cervical intraepithelial neoplasia (CIN). HPV DNA testing can also be performed on self-collected samples, which allows screening in remote areas and also in women who refuse gynecologic examination.

  5. Forensic DNA testing.

    Science.gov (United States)

    Butler, John M

    2011-12-01

    Forensic DNA testing has a number of applications, including parentage testing, identifying human remains from natural or man-made disasters or terrorist attacks, and solving crimes. This article provides background information followed by an overview of the process of forensic DNA testing, including sample collection, DNA extraction, PCR amplification, short tandem repeat (STR) allele separation and sizing, typing and profile interpretation, statistical analysis, and quality assurance. The article concludes with discussions of possible problems with the data and other forensic DNA testing techniques.

  6. HPV DNA test

    Science.gov (United States)

    ... test; Cancer of cervix - HPV DNA test References Hacker NF. Cervical dysplasia and cancer. In: Hacker NF, Gambone JC, Hobel CJ, eds. Hacker and Moore's Essentials of Obstetrics and Gynecology . 6th ...

  7. DNA testing in homicide investigations.

    Science.gov (United States)

    Prahlow, Joseph A; Cameron, Thomas; Arendt, Alexander; Cornelis, Kenneth; Bontrager, Anthony; Suth, Michael S; Black, Lisa; Tobey, Rebbecca; Pollock, Sharon; Stur, Shawn; Cotter, Kenneth; Gabrielse, Joel

    2017-10-01

    Objectives With the widespread use of DNA testing, police, death investigators, and attorneys need to be aware of the capabilities of this technology. This review provides an overview of scenarios where DNA evidence has played a major role in homicide investigations in order to highlight important educational issues for police, death investigators, forensic pathologists, and attorneys. Methods This was a nonrandom, observational, retrospective study. Data were obtained from the collective files of the authors from casework during a 15-year period, from 2000 through 2014. Results A series of nine scenarios, encompassing 11 deaths, is presented from the standpoint of the police and death investigation, the forensic pathology autopsy performance, the subsequent DNA testing of evidence, and, ultimately, the final adjudication of cases. Details of each case are presented, along with a discussion that focuses on important aspects of sample collection for potential DNA testing, especially at the crime scene and the autopsy. The presentation highlights the diversity of case and evidence types in which DNA testing played a valuable role in the successful prosecution of the case. Conclusions By highlighting homicides where DNA testing contributed to the successful adjudication of cases, police, death investigators, forensic pathologists, and attorneys will be better informed regarding the types of evidence and situations where such testing is of potential value.

  8. DNA testing in hereditary neuropathies.

    LENUS (Irish Health Repository)

    Murphy, Sinéad M

    2013-01-01

    The inherited neuropathies are a clinically and genetically heterogeneous group of disorders in which there have been rapid advances in the last two decades. Molecular genetic testing is now an integral part of the evaluation of patients with inherited neuropathies. In this chapter we describe the genes responsible for the primary inherited neuropathies. We briefly discuss the clinical phenotype of each of the known inherited neuropathy subgroups, describe algorithms for molecular genetic testing of affected patients and discuss genetic counseling. The basic principles of careful phenotyping, documenting an accurate family history, and testing the available genes in an appropriate manner should identify the vast majority of individuals with CMT1 and many of those with CMT2. In this chapter we also describe the current methods of genetic testing. As advances are made in molecular genetic technologies and improvements are made in bioinformatics, it is likely that the current time-consuming methods of DNA sequencing will give way to quicker and more efficient high-throughput methods, which are briefly discussed here.

  9. Strategies for online test security.

    Science.gov (United States)

    Hart, Leigh; Morgan, Lesley

    2009-01-01

    As online courses continue to increase, maintaining academic integrity in student evaluation is a challenge. The authors review several strategies, with varying degrees of cost and technology, to improve test security in the online classroom.

  10. Fetal DNA: strategies for optimal recovery

    NARCIS (Netherlands)

    Legler, Tobias J.; Heermann, Klaus-Hinrich; Liu, Zhong; Soussan, Aicha Ait; van der Schoot, C. Ellen

    2008-01-01

    For fetal DNA extraction, in principle each DNA extraction method can be used; however, because most methods have been optimized for genomic DNA from leucocytes, we describe here the methods that have been optimized for the extraction of fetal DNA from maternal plasma and validated for this purpose

  11. [Strategy for molecular testing in pulmonary carcinoma].

    Science.gov (United States)

    Penault-Llorca, Frédérique; Tixier, Lucie; Perrot, Loïc; Cayre, Anne

    2016-01-01

    Nowadays, the analysis of theranostic molecular markers is central in the management of lung cancer. As those tumors are diagnosed in two third of the cases at an advanced stage, molecular screening is frequently performed on "small samples". The screening strategy starts by an accurate histopathological characterization, including on biopsies or cytological specimens. WHO 2015 provided a new classification for small biopsy and cytology, defining categories such as non-small cell carcinoma (NSCC), favor adenocarcinoma (TTF1 positive), or favor squamous cell carcinoma (p40 positive). Only the NSCC tumors, non-squamous, are eligible to molecular testing. A strategy aiming at tissue sparing for the small biopsies has to be organized. Tests corresponding to available drugs are prioritized. Blank slides will be prepared for immunohistochemistry and in situ hybridization based tests such as ALK. DNA will then be extracted for the other tests, EGFR mutation screening first associated or not to KRAS. Then, the emerging biomarkers (HER2, ROS1, RET, BRAF…) as well as potentially other markers in case of clinical trials, can been tested. The spread of next generation sequencing technologies, with a very sensitive all-in-one approach will allow the identification of minority clones. Eventually, the development of liquid biopsies will provide the opportunity to monitor the apparition of resistance clones during treatment. This non-invasive approach allows patients with a contraindication to perform biopsy or with non-relevant biopsies to access to molecular screening. Copyright © 2016. Published by Elsevier Masson SAS.

  12. DNA Nanobiosensors: An Outlook on Signal Readout Strategies

    Directory of Open Access Journals (Sweden)

    Arun Richard Chandrasekaran

    2017-01-01

    Full Text Available A suite of functionalities and structural versatility makes DNA an apt material for biosensing applications. DNA-based biosensors are cost-effective and sensitive and have the potential to be used as point-of-care diagnostic tools. Along with robustness and biocompatibility, these sensors also provide multiple readout strategies. Depending on the functionality of DNA-based biosensors, a variety of output strategies have been reported: fluorescence- and FRET-based readout, nanoparticle-based colorimetry, spectroscopy-based techniques, electrochemical signaling, gel electrophoresis, and atomic force microscopy.

  13. DNA pooling strategies for categorical (ordinal) traits

    Science.gov (United States)

    Despite reduced genotyping costs in recent years, obtaining genotypes for all individuals in a population may still not be feasible when sample size is large. DNA pooling provides a useful alternative to determining genotype effects. Clustering algorithms allow for grouping of individuals (observati...

  14. KSHV strategies for host dsDNA sensing machinery.

    Science.gov (United States)

    Gao, Hang; Song, Yanyan; Liu, Chengrong; Liang, Qiming

    2016-12-01

    The innate immune system utilizes pattern recognition receptors cyclic GMP-AMP synthase (cGAS) to sense cytosolic double-stranded (ds) DNA and initiate type 1 interferon signaling and autophagy pathway, which collaborate to limit pathogen infections as well as alarm the adaptive immune response. The genomes of herpesviruses are large dsDNA, which represent a major class of pathogen signatures recognized by cellular DNA sensor cGAS. However, to successfully establish the persistent infection, herpesviruses have evolved their viral genes to modulate different aspects of host immune signaling. This review summarizes the evasion strategies of host cGAS DNA sensing pathway by Kaposi's Sarcoma-associated Herpesvirus (KSHV) and their contributions to KSHV life cycles.

  15. Next Generation Sequencing of Ancient DNA: Requirements, Strategies and Perspectives

    Directory of Open Access Journals (Sweden)

    Michael Knapp

    2010-07-01

    Full Text Available The invention of next-generation-sequencing has revolutionized almost all fields of genetics, but few have profited from it as much as the field of ancient DNA research. From its beginnings as an interesting but rather marginal discipline, ancient DNA research is now on its way into the centre of evolutionary biology. In less than a year from its invention next-generation-sequencing had increased the amount of DNA sequence data available from extinct organisms by several orders of magnitude. Ancient DNA  research is now not only adding a temporal aspect to evolutionary studies and allowing for the observation of evolution in real time, it also provides important data to help understand the origins of our own species. Here we review progress that has been made in next-generation-sequencing of ancient DNA over the past five years and evaluate sequencing strategies and future directions.

  16. Counting DNA: estimating the complexity of a test tube of DNA.

    Science.gov (United States)

    Faulhammer, D; Lipton, R J; Landweber, L F

    1999-10-01

    We consider the problem of estimation of the 'complexity' of a test tube of DNA. The complexity of a test tube is the number of different kinds of strands of DNA in the test tube. It is quite easy to estimate the number of total strands in a test tube, especially if the strands are all the same length. Estimation of the complexity is much less clear. We propose a simple kind of DNA computation that can estimate the complexity.

  17. Regional strategy tested in Caribbean.

    Science.gov (United States)

    1984-01-01

    Barbados, St. Vincent, and St. Lucia have joined forces in the world's 1st regional Contraceptive Social Marketing (CSM) effort -- the Caribbean CSM. The Barbados Family Planning Association (BFPS) is overseeing the operation, which begins selling 2 contraceptive pills and a condom in early February. Costs and start-up times were shaved by adopting brand names and advertising materials from Jamaica's highly successful CSM project. Jamaica's popular "Panther" condom and "Perle" oral contraceptive (OC) are being used by the Caribbean CSM project. Perle's 9-year-old package has been redesigned and the Caribbean CSM project also is selling a 2nd, low-dose version called "Perle-LD." The products are manufactured in the US by Syntex as Noriday and Norminest, respectively. But the regional approach's financial gains also had a debit side, most notably a tripling of bureaucratic procedures. Part of project difficulties stem from differences among the 3 Caribbean countries. While sharing a common cultural heritage, St. Lucians speak a patois dialect in addition to the English prevalent on the other islands. The biggest hurdle was overcoming an economic disparity between Barbados and its less affluent neighbors, St. Vincent and St. Lucia. The CSM project decided to try a 2-tier product pricing strategy. In US currency, prices run $1.75 per cycle for both OCs on Barbados, but $1.26 on St. Vincent and St. Lucia. A Panther 3-pack costs 75 cents on Barbados and 42 cents on the othe 2 islands. The project is being promoted with generic family planning media advertisements. The project also has held physician orientation seminars on each island. The pilot program will be accompanied by retailer training seminars. In addition the project may introduce a spermicidal foaming tablet, once the US Food and Drug Administration approvs a new American-made product. The unique Caribbean CSM project may spread an idea as potent as the family planning message. Its success could transmit the

  18. The strategies of DNA immobilization and hybridization detection mechanism in the construction of electrochemical DNA sensor: A review

    Directory of Open Access Journals (Sweden)

    Jahwarhar Izuan Abdul Rashid

    2017-11-01

    Full Text Available In recent years, electrochemical deoxyribonucleic acid (DNA sensor has recently emerged as promising alternative clinical diagnostic devices especially for infectious disease by exploiting DNA recognition events and converting them into an electrochemical signal. This is because the existing DNA diagnostic method possesses certain drawbacks such as time-consuming, expensive, laborious, low selectivity and sensitivity. DNA immobilization strategies and mechanism of electrochemical detection are two the most important aspects that should be considered before developing highly selective and sensitive electrochemical DNA sensor. Here, we focus on some recent strategies for DNA probes immobilization on the surface of electrochemical transducer such as adsorption, covalent bonding and Avidin/Streptavidin-Biotin interaction on the electrode surface for specific interaction with its complementary DNA target. A numerous approach for DNA hybridization detection based electrochemical technique that frequently used including direct DNA electrochemical detection and label based electrochemical (redox-active indicator, enzyme label and nanoparticles were also discussed in aiming to provide general guide for the design of electrochemical DNA sensor. We also discussed the challenges and suggestions to improve the application of electrochemical DNA sensor at point-care setting. Keywords: Electrochemical DNA sensor, DNA immobilization, DNA hybridization, Electrochemical mechanism

  19. Evaluation of Patients with an Apparent False Positive Stool DNA Test: The Role of Repeat Stool DNA Testing.

    Science.gov (United States)

    Cooper, Gregory S; Markowitz, Sanford D; Chen, Zhengyi; Tuck, Missy; Willis, Joseph E; Berger, Barry M; Brenner, Dean E; Li, Li

    2018-03-07

    There is uncertainty as to the appropriate follow-up of patients who test positive on multimarker stool DNA (sDNA) testing and have a colonoscopy without neoplasia. To determine the prevalence of missed colonic or occult upper gastrointestinal neoplasia in patients with an apparent false positive sDNA. We prospectively identified 30 patients who tested positive with a commercially available sDNA followed by colonoscopy without neoplastic lesions. Patients were invited to undergo repeat sDNA at 11-29 months after the initial test followed by repeat colonoscopy and upper endoscopy. We determined the presence of neoplastic lesions on repeat evaluation stratified by results of repeat sDNA. Twelve patients were restudied. Seven patients had a negative second sDNA test and a normal second colonoscopy and upper endoscopy. In contrast, 5 of 12 subjects had a persistently positive second sDNA test, and 3 had positive findings, including a 3-cm sessile transverse colon adenoma with high-grade dysplasia, a 2-cm right colon sessile serrated adenoma with dysplasia, and a nonadvanced colon adenoma (p = 0.045). These corresponded to a positive predictive value of 0.60 (95% CI 0.17-1.00) and a negative predictive value of 1.00 (95% CI 1.00-1.00) for the second sDNA test. In addition, the medical records of all 30 subjects with apparent false positive testing were reviewed and no documented cases of malignant tumors were recorded. Repeat positive sDNA testing may identify a subset of patients with missed or occult colorectal neoplasia after negative colonoscopy for an initially positive sDNA. High-quality colonoscopy with careful attention to the right colon in patients with positive sDNA is critically important and may avoid false negative colonoscopy.

  20. An integrated strategy combining DNA walking and NGS to detect GMOs.

    Science.gov (United States)

    Fraiture, Marie-Alice; Herman, Philippe; Papazova, Nina; De Loose, Marc; Deforce, Dieter; Ruttink, Tom; Roosens, Nancy H

    2017-10-01

    Recently, we developed a DNA walking system for the detection and characterization of a broad spectrum of GMOs in routine analysis of food/feed matrices. Here, we present a new version with improved throughput and sensitivity by coupling the DNA walking system to Pacific Bioscience® Next-generation sequencing technology. The performance of the new strategy was thoroughly assessed through several assays. First, we tested its detection and identification capability on grains with high or low GMO content. Second, the potential impacts of food processing were investigated using rice noodle samples. Finally, GMO mixtures and a real-life sample were analyzed to illustrate the applicability of the proposed strategy in routine GMO analysis. In all tested samples, the presence of multiple GMOs was unambiguously proven by the characterization of transgene flanking regions and the combinations of elements that are typical for transgene constructs. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  1. Building a successful board-test strategy

    CERN Document Server

    Scheiber, Stephen

    2001-01-01

    Written in a clear and thoughtful style, Building a Successful Board-Test Strategy, Second Edition offers an integrated approach to the complicated process of developing the test strategies most suited to a company's profile and philosophy. This book also provides comprehensive coverage of the specifics of electronic test equipment as well as those broader issues of management and marketing that shape a manufacturer's ""image of quality.""In this new edition, the author adds still more ""war stories,"" relevant examples from his own experience, which will guide his readers in their dec

  2. DNA nanotechnology from the test tube to the cell.

    Science.gov (United States)

    Chen, Yuan-Jyue; Groves, Benjamin; Muscat, Richard A; Seelig, Georg

    2015-09-01

    The programmability of Watson-Crick base pairing, combined with a decrease in the cost of synthesis, has made DNA a widely used material for the assembly of molecular structures and dynamic molecular devices. Working in cell-free settings, researchers in DNA nanotechnology have been able to scale up system complexity and quantitatively characterize reaction mechanisms to an extent that is infeasible for engineered gene circuits or other cell-based technologies. However, the most intriguing applications of DNA nanotechnology - applications that best take advantage of the small size, biocompatibility and programmability of DNA-based systems - lie at the interface with biology. Here, we review recent progress in the transition of DNA nanotechnology from the test tube to the cell. We highlight key successes in the development of DNA-based imaging probes, prototypes of smart therapeutics and drug delivery systems, and explore the future challenges and opportunities for cellular DNA nanotechnology.

  3. DNA nanotechnology from the test tube to the cell

    Science.gov (United States)

    Chen, Yuan-Jyue; Groves, Benjamin; Muscat, Richard A.; Seelig, Georg

    2015-09-01

    The programmability of Watson-Crick base pairing, combined with a decrease in the cost of synthesis, has made DNA a widely used material for the assembly of molecular structures and dynamic molecular devices. Working in cell-free settings, researchers in DNA nanotechnology have been able to scale up system complexity and quantitatively characterize reaction mechanisms to an extent that is infeasible for engineered gene circuits or other cell-based technologies. However, the most intriguing applications of DNA nanotechnology -- applications that best take advantage of the small size, biocompatibility and programmability of DNA-based systems -- lie at the interface with biology. Here, we review recent progress in the transition of DNA nanotechnology from the test tube to the cell. We highlight key successes in the development of DNA-based imaging probes, prototypes of smart therapeutics and drug delivery systems, and explore the future challenges and opportunities for cellular DNA nanotechnology.

  4. Development and validation of an integrated DNA walking strategy to detect GMO expressing cry genes.

    Science.gov (United States)

    Fraiture, Marie-Alice; Vandamme, Julie; Herman, Philippe; Roosens, Nancy H C

    2018-06-27

    Recently, an integrated DNA walking strategy has been proposed to prove the presence of GMO via the characterisation of sequences of interest, including their transgene flanking regions and the unnatural associations of elements in their transgenic cassettes. To this end, the p35S, tNOS and t35S pCAMBIA elements have been selected as key targets, allowing the coverage of most of GMO, EU authorized or not. In the present study, a bidirectional DNA walking method anchored on the CryAb/c genes is proposed with the aim to cover additional GMO and additional sequences of interest. The performance of the proposed bidirectional DNA walking method anchored on the CryAb/c genes has been evaluated in a first time for its feasibility using several GM events possessing these CryAb/c genes. Afterwards, its sensitivity has been investigated through low concentrations of targets (as low as 20 HGE). In addition, to illustrate its applicability, the entire workflow has been tested on a sample mimicking food/feed matrices analysed in GMO routine analysis. Given the successful assessment of its performance, the present bidirectional DNA walking method anchored on the CryAb/c genes can easily be implemented in GMO routine analysis by the enforcement laboratories and allows completing the entire DNA walking strategy in targeting an additional transgenic element frequently found in GMO.

  5. Surface-assisted DNA self-assembly: An enzyme-free strategy towards formation of branched DNA lattice

    International Nuclear Information System (INIS)

    Bhanjadeo, Madhabi M.; Nayak, Ashok K.; Subudhi, Umakanta

    2017-01-01

    DNA based self-assembled nanostructures and DNA origami has proven useful for organizing nanomaterials with firm precision. However, for advanced applications like nanoelectronics and photonics, large-scale organization of self-assembled branched DNA (bDNA) into periodic lattices is desired. In this communication for the first time we report a facile method of self-assembly of Y-shaped bDNA nanostructures on the cationic surface of Aluminum (Al) foil to prepare periodic two dimensional (2D) bDNA lattice. Particularly those Y-shaped bDNA structures having smaller overhangs and unable to self-assemble in solution, they are easily assembled on the surface of Al foil in the absence of ligase. Field emission scanning electron microscopy (FESEM) analysis shows homogenous distribution of two-dimensional bDNA lattices across the Al foil. When the assembled bDNA structures were recovered from the Al foil and electrophoresed in nPAGE only higher order polymeric bDNA structures were observed without a trace of monomeric structures which confirms the stability and high yield of the bDNA lattices. Therefore, this enzyme-free economic and efficient strategy for developing bDNA lattices can be utilized in assembling various nanomaterials for functional molecular components towards development of DNA based self-assembled nanodevices. - Highlights: • Al foil surface-assisted self-assembly of monomeric structures into larger branched DNA lattice. • FESEM study confirms the uniform distribution of two-dimensional bDNA lattice structures across the surface of Al foil. • Enzyme-free and economic strategy to prepare higher order structures from simpler DNA nanostructures have been confirmed by recovery assay. • Use of well proven sequences for the preparation of pure Y-shaped monomeric DNA nanostructure with high yield.

  6. DNA methylome profiling of maternal peripheral blood and placentas reveal potential fetal DNA markers for non-invasive prenatal testing.

    Science.gov (United States)

    Xiang, Yuqian; Zhang, Junyu; Li, Qiaoli; Zhou, Xinyao; Wang, Teng; Xu, Mingqing; Xia, Shihui; Xing, Qinghe; Wang, Lei; He, Lin; Zhao, Xinzhi

    2014-09-01

    Utilizing epigenetic (DNA methylation) differences to differentiate between maternal peripheral blood (PBL) and fetal (placental) DNA has been a promising strategy for non-invasive prenatal testing (NIPT). However, the differentially methylated regions (DMRs) have yet to be fully ascertained. In the present study, we performed genome-wide comparative methylome analysis between maternal PBL and placental DNA from pregnancies of first trimester by methylated DNA immunoprecipitation-sequencing (MeDIP-Seq) and Infinium HumanMethylation450 BeadChip assays. A total of 36 931 DMRs and 45 804 differentially methylated sites (DMSs) covering the whole genome, exclusive of the Y chromosome, were identified via MeDIP-Seq and Infinium 450k array, respectively, of which 3759 sites in 2188 regions were confirmed by both methods. Not only did we find the previously reported potential fetal DNA markers in our identified DMRs/DMSs but also we verified fully the identified DMRs/DMSs in the validation round by MassARRAY EpiTYPER. The screened potential fetal DNA markers may be used for NIPT on aneuploidies and other chromosomal diseases, such as cri du chat syndrome and velo-cardio-facial syndrome. In addition, these potential markers may have application in the early diagnosis of placental dysfunction, such as pre-eclampsia. © The Author 2014. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  7. Design and Test of an Oscillation-based System Architecture for DNA Sensor Arrays

    NARCIS (Netherlands)

    Liu, Hongyuan; Kerkhoff, Hans G.; Richardson, Andrew; Zhang, X.; Nouet, Pascal; Azais, Florence

    2005-01-01

    A DfT strategy for MEMS-based DNA sensors is investigated in this paper. Based on a fault-free and defect model developed for a single sensing element and the VHDL-AMS simulation results, it is implied that an oscillation-based interface might be a potential solution for both testing and read out of

  8. Value of DNA tests: a decision perspective.

    Science.gov (United States)

    Taroni, Franco; Bozza, Silvia; Bernard, Magali; Champod, Christophe

    2007-01-01

    Before a Court of Law testifying in DNA-evidence cases, scientists are often challenged with the idea that the more markers (loci) the better, i.e., why does the scientist not use 16 or more markers? This paper introduces a new perspective, decision analysis, to deal with the problem of the number of markers to type in a criminal context. The decision-making process, which plays a key role in the routine work of a forensic scientist, consists of the rational choice, given personal objectives, between two or more possible outcomes when the consequences of the choice are uncertain. Simulated results support the hypothesis that analytical added value does not increase with the number of markers.

  9. Large Liquid Rocket Testing: Strategies and Challenges

    Science.gov (United States)

    Rahman, Shamim A.; Hebert, Bartt J.

    2005-01-01

    development, the appropriate plan and strategy must be put in place at the outset of the development effort. A deferment of this test planning, or inattention to strategy, will compromise the ability of the development program to achieve its systems reliability requirements and/or its development milestones. It is important for the government leadership and support team, as well as the vehicle and propulsion development team, to give early consideration to this aspect of space propulsion and space transportation work.

  10. Block Copolymer Micellization as a Protection Strategy for DNA Origami.

    Science.gov (United States)

    Agarwal, Nayan P; Matthies, Michael; Gür, Fatih N; Osada, Kensuke; Schmidt, Thorsten L

    2017-05-08

    DNA nanotechnology enables the synthesis of nanometer-sized objects that can be site-specifically functionalized with a large variety of materials. For these reasons, DNA-based devices such as DNA origami are being considered for applications in molecular biology and nanomedicine. However, many DNA structures need a higher ionic strength than that of common cell culture buffers or bodily fluids to maintain their integrity and can be degraded quickly by nucleases. To overcome these deficiencies, we coated several different DNA origami structures with a cationic poly(ethylene glycol)-polylysine block copolymer, which electrostatically covered the DNA nanostructures to form DNA origami polyplex micelles (DOPMs). This straightforward, cost-effective, and robust route to protect DNA-based structures could therefore enable applications in biology and nanomedicine where unprotected DNA origami would be degraded. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. 32P-labeling test for DNA damage

    International Nuclear Information System (INIS)

    Randerath, K.; Reddy, M.V.; Gupta, R.C.

    1981-01-01

    Covalent adducts formed by the reaction of DNA with chemical carcinogens and mutagens may be detected by a 32 P-labeling test. DNA preparations exposed to chemicals known to bind covalently to DNA [N-methyl-N-nitrosourea, dimethyl sulfate, formaldehyde, β-propiolactone, propylene oxide, streptozotocin, nitrogen mustard, and 1,3-bis(2-chloroethyl)-1-nitrosourea] were digested to a mixture of deoxynucleoside 3'-monophosphates by incubation with micrococcal endonuclease (EC 3.1.31.1) and spleen exonuclease (EC 3.1.16.1). The digests were treated with [γ- 32 P]ATP and T4 polynucleotide kinase (ATP:5'-dephosphopolynucleotide 5'-phosphotransferase, EC 2.7.1.78) to convert the monophosphates to 5'- 32 P-labeled deoxynucleoside 3',5'-bis-phosphates. These compounds were then separated on polyethyl-eneimine-cellulose thin layers in ammonium formate and ammonium sulfate solutions. Autoradiograms of the chromatograms obtained by this high-resolution procedure showed the presence of nucleotides derived from chemically altered, as well as normal, DNA constituents. Maps from DNA exposed to any of the chemicals used exhibited a spot pattern typical for the particular chemical. This method detected a single adduct in 10 5 DNA nucleotides without requiring that the compound under investigation be radioactive and thus provides a useful test to screen chemicals for their capacity to damage DNA by covalent binding

  12. Antiphospholipid Syndrome Laboratory Testing and Diagnostic Strategies

    Science.gov (United States)

    Ortel, Thomas L.

    2016-01-01

    The Antiphospholipid Syndrome (APS) is diagnosed in patients with recurrent thromboembolic events and/or pregnancy loss in the presence of persistent laboratory evidence for antiphospholipid antibodies. Diagnostic tests for the detection of antiphospholipid antibodies include laboratory assays that detect anticardiolipin antibodies, lupus anticoagulants, and anti-β2-glycoprotein I antibodies. These assays have their origins beginning more than sixty years ago, with the identification of the biologic false positive test for syphilis, the observation of ‘circulating anticoagulants’ in certain patients with systemic lupus erythematosus, the identification of cardiolipin as a key component in the serologic test for syphilis, and the recognition and characterization of a ‘cofactor’ for antibody binding to phospholipids. Although these assays have been used clinically for many years, there are still problems with the accurate diagnosis of patients with this syndrome. For example, lupus anticoagulant testing can be difficult to interpret in patients receiving anticoagulant therapy, but most patients with a thromboembolic event will already be anticoagulated before the decision to perform the tests has been made. In addition to understanding limitations of the assays, clinicians also need to be aware of which patients should be tested and not obtain testing on patients unlikely to have APS. New tests and diagnostic strategies are in various stages of development and should help improve our ability to accurately diagnose this important clinical disorder. PMID:22473619

  13. A Fractual Mechanical Testing and Design Strategy for FRC Structures

    DEFF Research Database (Denmark)

    Stang, Henrik; Olesen, John Forbes

    1999-01-01

    A unified testing and design strategy for fibre reinforced concrete structures is summarised. The strategy is based on fracture mechanical concepts. Emphasis is placed on material characterisation and testing specifications.......A unified testing and design strategy for fibre reinforced concrete structures is summarised. The strategy is based on fracture mechanical concepts. Emphasis is placed on material characterisation and testing specifications....

  14. Noninvasive prenatal paternity testing (NIPAT) through maternal plasma DNA sequencing

    DEFF Research Database (Denmark)

    Jiang, Haojun; Xie, Yifan; Li, Xuchao

    2016-01-01

    developed a noninvasive prenatal paternity testing (NIPAT) based on SNP typing with maternal plasma DNA sequencing. We evaluated the influence factors (minor allele frequency (MAF), the number of total SNP, fetal fraction and effective sequencing depth) and designed three different selective SNP panels......Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) have been already used to perform noninvasive prenatal paternity testing from maternal plasma DNA. The frequently used technologies were PCR followed by capillary electrophoresis and SNP typing array, respectively. Here, we...... paternity test using STR multiplex system. Our study here proved that the maternal plasma DNA sequencing-based technology is feasible and accurate in determining paternity, which may provide an alternative in forensic application in the future....

  15. Polymerase chain reaction and conventional DNA tests in detection of HPV DNA in cytologically normal and abnormal cervical scrapes

    DEFF Research Database (Denmark)

    Kalia, A.; Jalava, T.; Nieminen, P.

    1992-01-01

    Med.mikrobiologi, polymerase chain reaction, DNA tests, human papillomavirus (HPV), cervical smear, hybridisation, cytologi, affiProbe HPV test, ViraType test......Med.mikrobiologi, polymerase chain reaction, DNA tests, human papillomavirus (HPV), cervical smear, hybridisation, cytologi, affiProbe HPV test, ViraType test...

  16. Suiformes conservation: a study case of strategies for DNA utilization

    Indian Academy of Sciences (India)

    However, the amount and quality of DNA obtained is a major concern and compar- .... and an improvement of the DNA purity observable in the. A260/280 ratio (the purity ratio ... facilities at The University of Arizona, Tucson, USA. Thanks also.

  17. False-positive Human Papillomavirus DNA tests in cervical screening

    DEFF Research Database (Denmark)

    Rebolj, Matejka; Pribac, Igor; Lynge, Elsebeth

    2011-01-01

    Based on data from randomised controlled trials (RCT) on primary cervical screening, it has been reported that the problem of more frequent false-positive tests in Human Papillomavirus (HPV) DNA screening compared to cytology could be overcome. However, these reports predominantly operated...

  18. Testing and development strategy for the tank waste remediation system

    International Nuclear Information System (INIS)

    Reddick, G.W.

    1994-12-01

    This document provides a strategy for performing radioactive (hot) and nonradioactive testing to support processing tank waste. It evaluates the need for hot pilot plant(s) to support pretreatment and other processing functions and presents a strategy for performing hot test work. A strategy also is provided for nonradioactive process and equipment testing. The testing strategy supports design, construction, startup, and operation of Tank Waste Remediation System (TWRS) facilities

  19. Testing and development strategy for the tank waste remediation system

    International Nuclear Information System (INIS)

    Reddick, G.W.

    1995-01-01

    This document provides a strategy for performing radioactive (hot) and nonradioactive testing to support processing tank waste. It evaluates the need for hot pilot plant(s) to support pretreatment and other processing functions and presents a strategy for performing hot test work. A strategy also is provided for nonradioactive process and equipment testing. The testing strategy supports design, construction, startup, and operation of Tank Waste Remediation System (TWRS) facilities

  20. Deep Borehole Field Test Laboratory and Borehole Testing Strategy

    Energy Technology Data Exchange (ETDEWEB)

    Kuhlman, Kristopher L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Brady, Patrick V. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); MacKinnon, Robert J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Heath, Jason E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Herrick, Courtney G. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Jensen, Richard P. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Gardner, W. Payton [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Sevougian, S. David [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Bryan, Charles R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Jang, Je-Hun [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Stein, Emily R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Bauer, Stephen J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Daley, Tom [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Freifeld, Barry M. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Birkholzer, Jens [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Spane, Frank A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-09-19

    Deep Borehole Disposal (DBD) of high-level radioactive wastes has been considered an option for geological isolation for many years (Hess et al. 1957). Recent advances in drilling technology have decreased costs and increased reliability for large-diameter (i.e., ≥50 cm [19.7”]) boreholes to depths of several kilometers (Beswick 2008; Beswick et al. 2014). These advances have therefore also increased the feasibility of the DBD concept (Brady et al. 2009; Cornwall 2015), and the current field test design will demonstrate the DBD concept and these advances. The US Department of Energy (DOE) Strategy for the Management and Disposal of Used Nuclear Fuel and High-Level Radioactive Waste (DOE 2013) specifically recommended developing a research and development plan for DBD. DOE sought input or expression of interest from States, local communities, individuals, private groups, academia, or any other stakeholders willing to host a Deep Borehole Field Test (DBFT). The DBFT includes drilling two boreholes nominally 200m [656’] apart to approximately 5 km [16,400’] total depth, in a region where crystalline basement is expected to begin at less than 2 km depth [6,560’]. The characterization borehole (CB) is the smaller-diameter borehole (i.e., 21.6 cm [8.5”] diameter at total depth), and will be drilled first. The geologic, hydrogeologic, geochemical, geomechanical and thermal testing will take place in the CB. The field test borehole (FTB) is the larger-diameter borehole (i.e., 43.2 cm [17”] diameter at total depth). Surface handling and borehole emplacement of test package will be demonstrated using the FTB to evaluate engineering feasibility and safety of disposal operations (SNL 2016).

  1. Development of novel vaccines using DNA shuffling and screening strategies.

    Science.gov (United States)

    Locher, Christopher P; Soong, Nay Wei; Whalen, Robert G; Punnonen, Juha

    2004-02-01

    DNA shuffling and screening technologies recombine and evolve genes in vitro to rapidly obtain molecules with improved biological activity and fitness. In this way, genes from related strains are bred like plants or livestock and their successive progeny are selected. These technologies have also been called molecular breeding-directed molecular evolution. Recent developments in bioinformatics-assisted computer programs have facilitated the design, synthesis and analysis of DNA shuffled libraries of chimeric molecules. New applications in vaccine development are among the key features of DNA shuffling and screening technologies because genes from several strains or antigenic variants of pathogens can be recombined to create novel molecules capable of inducing immune responses that protect against infections by multiple strains of pathogens. In addition, molecules such as co-stimulatory molecules and cytokines have been evolved to have improved T-cell proliferation and cytokine production compared with the wild-type human molecules. These molecules can be used to immunomodulate vaccine responsiveness and have multiple applications in infectious diseases, cancer, allergy and autoimmunity. Moreover, DNA shuffling and screening technologies can facilitate process development of vaccine manufacturing through increased expression of recombinant polypeptides and viruses. Therefore, DNA shuffling and screening technologies can overcome some of the challenges that vaccine development currently faces.

  2. Antiviral strategies to eliminate hepatitis B virus covalently closed circular DNA (cccDNA).

    Science.gov (United States)

    Revill, Peter; Locarnini, Stephen

    2016-10-01

    It has been over 50 years since the discovery of hepatitis B virus (HBV), yet 240 million people worldwide live with chronic HBV, resulting in up to 800000 deaths per year. A cure is yet to be achieved, due largely to a viral nuclear reservoir of transcriptionally active covalently closed circular DNA (cccDNA). While current antiviral therapies are effective at reducing viral replication, they have no impact on the existing cccDNA reservoir. Identifying mechanisms to either eliminate (complete cure) or inactivate (functional cure) HBV cccDNA are a major focus of HBV research worldwide. This review discusses recent advances in efforts to eliminate and/or regulate cccDNA, as well as future directions that may be considered in efforts to cure chronic HBV. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

  3. Cost-Effectiveness of Cervical Cancer Screening With Human Papillomavirus DNA Testing and HPV-16,18 Vaccination

    Science.gov (United States)

    Goldhaber-Fiebert, Jeremy D.; Stout, Natasha K.; Salomon, Joshua A.; Kuntz, Karen M.; Goldie, Sue J.

    2011-01-01

    Background The availability of human papillomavirus (HPV) DNA testing and vaccination against HPV types 16 and 18 (HPV-16,18) motivates questions about the cost-effectiveness of cervical cancer prevention in the United States for unvaccinated older women and for girls eligible for vaccination. Methods An empirically calibrated model was used to assess the quality-adjusted life years (QALYs), lifetime costs, and incremental cost-effectiveness ratios (2004 US dollars per QALY) of screening, vaccination of preadolescent girls, and vaccination combined with screening. Screening varied by initiation age (18, 21, or 25 years), interval (every 1, 2, 3, or 5 years), and test (HPV DNA testing of cervical specimens or cytologic evaluation of cervical cells with a Pap test). Testing strategies included: 1) cytology followed by HPV DNA testing for equivocal cytologic results (cytology with HPV test triage); 2) HPV DNA testing followed by cytology for positive HPV DNA results (HPV test with cytology triage); and 3) combined HPV DNA testing and cytology. Strategies were permitted to switch once at age 25, 30, or 35 years. Results For unvaccinated women, triennial cytology with HPV test triage, beginning by age 21 years and switching to HPV testing with cytology triage at age 30 years, cost $78 000 per QALY compared with the next best strategy. For girls vaccinated before age 12 years, this same strategy, beginning at age 25 years and switching at age 35 years, cost $41 000 per QALY with screening every 5 years and $188 000 per QALY screening triennially, each compared with the next best strategy. These strategies were more effective and cost-effective than screening women of all ages with cytology alone or cytology with HPV triage annually or biennially. Conclusions For both vaccinated and unvaccinated women, age-based screening by use of HPV DNA testing as a triage test for equivocal results in younger women and as a primary screening test in older women is expected to be more

  4. Testing of DNA isolation for the identification of hemp

    Directory of Open Access Journals (Sweden)

    Tomáš Vyhnánek

    2015-12-01

    Full Text Available Hemp is diploid organism (2n = 2x = 20, genome size 534 Mb with nine pairs of autosomes plus XX (♀ or XY (♂ chromosomes. Cannabis sativa L. is an important economic plant for the production of food, fibre, oils, and intoxicants. Genotypes (varieties or chemovar of hemp with low Δ9-tetrahydrocannabinol content are used for industrial applications. Varieties with high Δ9-tetrahydrocannabinol or high cannabidiol content are used for medicinal applications. Biochemical and molecular methods can be used for identification and classification. An important step for molecular biology methods is to obtain the matrix of the native and sufficiently pure DNA. We tested two different experimental variant of samples (20 mg and 100 mg of seeds, oilcake and dried flowers for analysis of the Italian variety Carmagnola for analysis (harvested in 2014, Hempoint Ltd., Czech Republic. The DNeasy® Plant Mini Kit (Qiagen, GE was used to isolate the DNA. The DNA concentration and purity was assessed by agarose electrophoresis and via a spectrophotometer. Samples of lower weight yielded lower values of DNA concentration (average 16.30 - 38.90 ng.µL-1, but with better purity than samples of higher weight (ratio A260nm/A280nm for low-weight samples was near 1.80. To test the applicability of DNA analysis, we used two SSR markers (CAN1347 and CAN2913. PCR products were separated on 1% agarose and on 8% polyacrylamide electrophoresis. DNA samples obtained from samples of higher weight exhibited less PCR amplification than samples of lower weight. We found no effect of sample weight on the formation of non-specific amplification products during the PCR reaction. Based on our results we can be recommended for practical isolation procedure using DNeasy® Plant Mini Kit with lower of sample weight (20 mg. In future work the procedure for DNA isolating from wheat-cannabis products, e. g. breads, rolls or pasta, will be optimized.

  5. Reading Test-taking Strategies in General Training IELTS

    OpenAIRE

    Vahede Nosrati

    2015-01-01

    The significance of gaining a better understanding of how test-taking strategies are used has been recognized by researchers. Considering this fact, this study aimed at investigating the test-taking strategies which were employed by IELTS candidates in reading comprehension test. Besides, it tried to take into account the differences among strategies used for different tasks. In order to gather data, two instruments were employed: the think-aloud protocol, and an IELTS reading test. The obtai...

  6. Tailoring DNA vaccines: designing strategies against HER2 positive cancers

    Directory of Open Access Journals (Sweden)

    Cristina eMarchini

    2013-05-01

    Full Text Available The crucial role of HER2 in epithelial transformation and its selective overexpression on cancer tissues makes it an ideal target for cancer immunotherapies such as passive immunotherapy with Trastuzumab. There are, however, a number of concerns regarding the use of monoclonal antibodies which include resistance, repeated treatments, considerable costs and side effects that make active immunotherapies against HER2 desirable alternative approaches. The efficacy of anti-HER2 DNA vaccination has been widely demonstrated in transgenic cancer-prone mice, which recapitulate several features of human breast cancers. Nonetheless, the rational design of a cancer vaccine able to trigger a long lasting immunity, and thus prevent tumor recurrence in patients, would require the understanding of how tolerance and immunosuppression regulate antitumor immune responses and, at the same time, the identification of the most immunogenic portions of the target protein. We herein retrace the findings that led to our most promising DNA vaccines that, by encoding human/rat chimeric forms of HER2, are able to circumvent peripheral tolerance. Preclinical data obtained with these chimeric DNA vaccines have provided the rationale for their use in an ongoing phase I clinical trial (EudraCT 2011-001104-34.

  7. Sensitive electrochemical assaying of DNA methyltransferase activity based on mimic-hybridization chain reaction amplified strategy.

    Science.gov (United States)

    Zhang, Linqun; Liu, Yuanjian; Li, Ying; Zhao, Yuewu; Wei, Wei; Liu, Songqin

    2016-08-24

    A mimic-hybridization chain reaction (mimic-HCR) amplified strategy was proposed for sensitive electrochemically detection of DNA methylation and methyltransferase (MTase) activity In the presence of methylated DNA, DNA-gold nanoparticles (DNA-AuNPs) were captured on the electrode by sandwich-type assembly. It then triggered mimic-HCR of two hairpin probes to produce many long double-helix chains for numerous hexaammineruthenium (III) chloride ([Ru(NH3)6](3+), RuHex) inserting. As a result, the signal for electrochemically detection of DNA MTase activity could be amplified. If DNA was non-methylated, however, the sandwich-type assembly would not form because the short double-stranded DNAs (dsDNA) on the Au electrode could be cleaved and digested by restriction endonuclease HpaII (HapII) and exonuclease III (Exo III), resulting in the signal decrement. Based on this, an electrochemical approach for detection of M.SssI MTase activity with high sensitivity was developed. The linear range for M.SssI MTase activity was from 0.05 U mL(-1) to 10 U mL(-1), with a detection limit down to 0.03 U mL(-1). Moreover, this detecting strategy held great promise as an easy-to-use and highly sensitive method for other MTase activity and inhibition detection by exchanging the corresponding DNA sequence. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Reading Test-Taking Strategies in General Training IELTS

    Science.gov (United States)

    Nosrati, Vahede

    2015-01-01

    The significance of gaining a better understanding of how test-taking strategies are used has been recognized by researchers. Considering this fact, this study aimed at investigating the test-taking strategies which were employed by IELTS candidates in reading comprehension test. Besides, it tried to take into account the differences among…

  9. Strategy for Alternative Occupant Volume Testing

    Science.gov (United States)

    2009-10-20

    This paper describes plans for a series of quasi-static : compression tests of rail passenger equipment. These tests are : designed to evaluate the strength of the occupant volume under : static loading conditions. The research plan includes a detail...

  10. Proteomics insights into DNA damage response and translating this knowledge to clinical strategies

    DEFF Research Database (Denmark)

    von Stechow, Louise; Olsen, Jesper V

    2017-01-01

    Genomic instability is a critical driver in the process of cancer formation. At the same time, inducing DNA damage by irradiation or genotoxic compounds constitutes a key therapeutic strategy to kill fast-dividing cancer cells. Sensing of DNA lesions initiates a complex set of signalling pathways......) in the DDR. Finally, we provide an outlook on how proteomics studies of the DDR could aid clinical developments on multiple levels. This article is protected by copyright. All rights reserved....

  11. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

    Science.gov (United States)

    Down, Thomas A.; Rakyan, Vardhman K.; Turner, Daniel J.; Flicek, Paul; Li, Heng; Kulesha, Eugene; Gräf, Stefan; Johnson, Nathan; Herrero, Javier; Tomazou, Eleni M.; Thorne, Natalie P.; Bäckdahl, Liselotte; Herberth, Marlis; Howe, Kevin L.; Jackson, David K.; Miretti, Marcos M.; Marioni, John C.; Birney, Ewan; Hubbard, Tim J. P.; Durbin, Richard; Tavaré, Simon; Beck, Stephan

    2009-01-01

    DNA methylation is an indispensible epigenetic modification of mammalian genomes. Consequently there is great interest in strategies for genome-wide/whole-genome DNA methylation analysis, and immunoprecipitation-based methods have proven to be a powerful option. Such methods are rapidly shifting the bottleneck from data generation to data analysis, necessitating the development of better analytical tools. Until now, a major analytical difficulty associated with immunoprecipitation-based DNA methylation profiling has been the inability to estimate absolute methylation levels. Here we report the development of a novel cross-platform algorithm – Bayesian Tool for Methylation Analysis (Batman) – for analyzing Methylated DNA Immunoprecipitation (MeDIP) profiles generated using arrays (MeDIP-chip) or next-generation sequencing (MeDIP-seq). The latter is an approach we have developed to elucidate the first high-resolution whole-genome DNA methylation profile (DNA methylome) of any mammalian genome. MeDIP-seq/MeDIP-chip combined with Batman represent robust, quantitative, and cost-effective functional genomic strategies for elucidating the function of DNA methylation. PMID:18612301

  12. Programmable DNA tile self-assembly using a hierarchical sub-tile strategy.

    Science.gov (United States)

    Shi, Xiaolong; Lu, Wei; Wang, Zhiyu; Pan, Linqiang; Cui, Guangzhao; Xu, Jin; LaBean, Thomas H

    2014-02-21

    DNA tile based self-assembly provides a bottom-up approach to construct desired nanostructures. DNA tiles have been directly constructed from ssDNA and readily self-assembled into 2D lattices and 3D superstructures. However, for more complex lattice designs including algorithmic assemblies requiring larger tile sets, a more modular approach could prove useful. This paper reports a new DNA 'sub-tile' strategy to easily create whole families of programmable tiles. Here, we demonstrate the stability and flexibility of our sub-tile structures by constructing 3-, 4- and 6-arm DNA tiles that are subsequently assembled into 2D lattices and 3D nanotubes according to a hierarchical design. Assembly of sub-tiles, tiles, and superstructures was analyzed using polyacrylamide gel electrophoresis and atomic force microscopy. DNA tile self-assembly methods provide a bottom-up approach to create desired nanostructures; the sub-tile strategy adds a useful new layer to this technique. Complex units can be made from simple parts. The sub-tile approach enables the rapid redesign and prototyping of complex DNA tile sets and tiles with asymmetric designs.

  13. Programmable DNA tile self-assembly using a hierarchical sub-tile strategy

    International Nuclear Information System (INIS)

    Shi, Xiaolong; Lu, Wei; Wang, Zhiyu; Pan, Linqiang; Cui, Guangzhao; Xu, Jin; LaBean, Thomas H

    2014-01-01

    DNA tile based self-assembly provides a bottom-up approach to construct desired nanostructures. DNA tiles have been directly constructed from ssDNA and readily self-assembled into 2D lattices and 3D superstructures. However, for more complex lattice designs including algorithmic assemblies requiring larger tile sets, a more modular approach could prove useful. This paper reports a new DNA ‘sub-tile’ strategy to easily create whole families of programmable tiles. Here, we demonstrate the stability and flexibility of our sub-tile structures by constructing 3-, 4- and 6-arm DNA tiles that are subsequently assembled into 2D lattices and 3D nanotubes according to a hierarchical design. Assembly of sub-tiles, tiles, and superstructures was analyzed using polyacrylamide gel electrophoresis and atomic force microscopy. DNA tile self-assembly methods provide a bottom-up approach to create desired nanostructures; the sub-tile strategy adds a useful new layer to this technique. Complex units can be made from simple parts. The sub-tile approach enables the rapid redesign and prototyping of complex DNA tile sets and tiles with asymmetric designs. (paper)

  14. High-speed and intercity passenger rail testing strategy.

    Science.gov (United States)

    2013-05-01

    This high-speed and intercity passenger rail (HSIPR) testing strategy addresses the requirements for testing of high-speed train sets and technology before introduction to the North American railroad system. The report documents the results of a surv...

  15. In-situ thermal testing program strategy

    International Nuclear Information System (INIS)

    1995-06-01

    In the past year the Yucca Mountain Site Characterization Project has implemented a new Program Approach to the licensing process. The Program Approach suggests a step-wise approach to licensing in which the early phases will require less site information than previously planned and necessitate a lesser degree of confidence in the longer-term performance of the repository. Under the Program Approach, the thermal test program is divided into two principal phases: (1) short-term in situ tests (in the 1996 to 2000 time period) and laboratory thermal tests to obtain preclosure information, parameters, and data along with bounding information for postclosure performance; and (2) longer-term in situ tests to obtain additional data regarding postclosure performance. This effort necessitates a rethinking of the testing program because the amount of information needed for the initial licensing phase is less than previously planned. This document proposes a revised and consolidated in situ thermal test program (including supporting laboratory tests) that is structured to meet the needs of the Program Approach. A customer-supplier model is used to define the Project data needs. These data needs, along with other requirements, were then used to define a set of conceptual experiments that will provide the required data within the constraints of the Program Approach schedule. The conceptual thermal tests presented in this document represent a consolidation and update of previously defined tests that should result in a more efficient use of Project resources. This document focuses on defining the requirements and tests needed to satisfy the goal of a successful license application in 2001, should the site be found suitable

  16. Listening Strategies of L2 Learners with Varied Test Tasks

    Science.gov (United States)

    Chang, Anna Ching-Shyang

    2008-01-01

    This article investigates the strategies that EFL students used and how they adjusted these strategies in response to various listening test tasks. The test tasks involved four forms of listening support: previewing questions, repeated input, background information preparation, and vocabulary instruction. Twenty-two participants were enlisted and…

  17. 78 FR 29698 - Availability of an Environmental Assessment for Field Testing a Canine Lymphoma Vaccine, DNA

    Science.gov (United States)

    2013-05-21

    ...] Availability of an Environmental Assessment for Field Testing a Canine Lymphoma Vaccine, DNA AGENCY: Animal and... Canine Lymphoma Vaccine, DNA. The environmental assessment, which is based on a risk analysis prepared to... biological product: Requester: Merial, Inc. Product: Canine Lymphoma Vaccine, DNA. Possible Field Test...

  18. Reading Test-taking Strategies in General Training IELTS

    Directory of Open Access Journals (Sweden)

    Vahede Nosrati

    2015-10-01

    Full Text Available The significance of gaining a better understanding of how test-taking strategies are used has been recognized by researchers. Considering this fact, this study aimed at investigating the test-taking strategies which were employed by IELTS candidates in reading comprehension test. Besides, it tried to take into account the differences among strategies used for different tasks. In order to gather data, two instruments were employed: the think-aloud protocol, and an IELTS reading test. The obtained data were analyzed and interpreted qualitatively by the researcher. The findings indicated that candidates employed 15 different strategies which were categorized in 3 stages, pre-reading, reading, and post-reading stages. Furthermore, it was revealed that test-takers used certain strategies differently, depending on the type of the task. The findings provide a better understanding of strategy use among IELTS candidates and help teachers to improve their approaches toward teaching and learning goals. Keywords: Test-taking Strategy, Test-taker, Reading Comprehension, Language Learning Strategy, IELTS

  19. Effects of direct-to-consumer advertising and clinical guidelines on appropriate use of human papillomavirus DNA tests.

    Science.gov (United States)

    Price, Rebecca Anhang; Frank, Richard G; Cleary, Paul D; Goldie, Sue J

    2011-02-01

    Both clinical guidelines and direct-to-consumer (DTC) advertising influence the use of new health care technologies, but little is known about their relative effects. The introduction of a cervical cancer screening test in 2000 offered a unique opportunity to assess the 2 strategies. To evaluate the effects of clinical guidelines and a targeted DTC advertising campaign on overall and appropriate use of human papillomavirus (HPV) DNA tests. Quasi-experimental study using difference-in-differences analysis. Data were MarketScan private insurance claims for 500,000 women aged 21 to 64 enrolled at least 12 consecutive months from January 2001 through December 2005. Both clinical guidelines and DTC advertising were associated with increases in overall HPV DNA test use. DTC advertising was associated with a statistically significant increase in HPV DNA test use in 2 groups of DTC cities (+5.57%, P advertising was associated with comparable increases in the probability of appropriate and inappropriate use of the HPV DNA test in primary screening. Clinical guideline releases from the American College of Obstetricians and Gynecologists, and by a cosponsored panel, were associated with greater increases in HPV DNA tests for appropriate primary screening than for inappropriate primary screening (β = 0.3347, P advertising was associated with increased overall use of a cervical cancer screening test, whereas clinical guidelines were differentially associated with increased appropriate use. These findings suggest distinct influences of consumer marketing and professional guidelines on the use of health care products and services.

  20. Inhibition of DNA2 nuclease as a therapeutic strategy targeting replication stress in cancer cells.

    Science.gov (United States)

    Kumar, S; Peng, X; Daley, J; Yang, L; Shen, J; Nguyen, N; Bae, G; Niu, H; Peng, Y; Hsieh, H-J; Wang, L; Rao, C; Stephan, C C; Sung, P; Ira, G; Peng, G

    2017-04-17

    Replication stress is a characteristic feature of cancer cells, which is resulted from sustained proliferative signaling induced by activation of oncogenes or loss of tumor suppressors. In cancer cells, oncogene-induced replication stress manifests as replication-associated lesions, predominantly double-strand DNA breaks (DSBs). An essential mechanism utilized by cells to repair replication-associated DSBs is homologous recombination (HR). In order to overcome replication stress and survive, cancer cells often require enhanced HR repair capacity. Therefore, the key link between HR repair and cellular tolerance to replication-associated DSBs provides us with a mechanistic rationale for exploiting synthetic lethality between HR repair inhibition and replication stress. DNA2 nuclease is an evolutionarily conserved essential enzyme in replication and HR repair. Here we demonstrate that DNA2 is overexpressed in pancreatic cancers, one of the deadliest and more aggressive forms of human cancers, where mutations in the KRAS are present in 90-95% of cases. In addition, depletion of DNA2 significantly reduces pancreatic cancer cell survival and xenograft tumor growth, suggesting the therapeutic potential of DNA2 inhibition. Finally, we develop a robust high-throughput biochemistry assay to screen for inhibitors of the DNA2 nuclease activity. The top inhibitors were shown to be efficacious against both yeast Dna2 and human DNA2. Treatment of cancer cells with DNA2 inhibitors recapitulates phenotypes observed upon DNA2 depletion, including decreased DNA double strand break end resection and attenuation of HR repair. Similar to genetic ablation of DNA2, chemical inhibition of DNA2 selectively attenuates the growth of various cancer cells with oncogene-induced replication stress. Taken together, our findings open a new avenue to develop a new class of anticancer drugs by targeting druggable nuclease DNA2. We propose DNA2 inhibition as new strategy in cancer therapy by targeting

  1. Strategy for the hemocompatibility testing of microparticles.

    Science.gov (United States)

    Braune, S; Basu, S; Kratz, K; Johansson, J Bäckemo; Reinthaler, M; Lendlein, A; Jung, F

    2016-01-01

    Polymer-based microparticles are applied as non-thrombogenic or thrombogenic materials in a wide variety of intra- or extra-corporeal medical devices. As demanded by the regulatory agencies, the hemocompatibility of these blood contacting biomaterials has to be evaluated in vitro to ensure that the particle systems appropriately fulfill the envisioned function without causing undesired events such as thrombosis or inflammation. Currently described in vitro assays for hemocompatibility testing of particles comprise tests with different single cell types (e.g. erythrocytes or leukocytes), varying concentrations/dilutions of the used blood cells or whole blood, which are not standardized.Here, we report about an in vitro dynamic test system for studying the hemocompatibility of polymeric microparticles utilizing fresh human whole blood from apparently healthy subjects, collected and processed under standardized conditions. Spherical poly(ether imide) microparticles with an average diameter of 140±30 μm were utilized as model systems. Reported as candidate materials for the removal of uremic toxins, these microparticles are anticipated to facilitate optimal flow conditions in a dialyzer with minimal backflow and blood cell damage. Pristine (PEI) and potassium hydroxide (PEI-KOH) functionalized microparticles exhibited similarly nanoporous surfaces (PEI: ØExternal pore = 90±60 nm; PEI-KOH ØExternal pore = 150±130 nm) but varying water wettabilities (PEI: θadv = 112±10° PEI-KOH θadv = 60±2°). The nanoporosity of the microparticle surfaces allows the exchange of toxic solutes from blood towards the interconnective pores in the particle core, while an immigration of the substantially larger blood cells is inhibited.Sterilized PEI microparticles were incorporated -air-free -in a syringe-based test system and exposed to whole blood for 60 minutes under gentle agitation. Thereafter, thrombi formation on the particles surfaces were analyzed

  2. Test Information Targeting Strategies for Adaptive Multistage Testing Designs.

    Science.gov (United States)

    Luecht, Richard M.; Burgin, William

    Adaptive multistage testlet (MST) designs appear to be gaining popularity for many large-scale computer-based testing programs. These adaptive MST designs use a modularized configuration of preconstructed testlets and embedded score-routing schemes to prepackage different forms of an adaptive test. The conditional information targeting (CIT)…

  3. Slim hole drilling and testing strategies

    Science.gov (United States)

    Nielson, Dennis L.; Garg, Sabodh K.; Goranson, Colin

    2017-12-01

    The financial and geologic advantages of drilling slim holes instead of large production wells in the early stages of geothermal reservoir assessment has been understood for many years. However, the practice has not been fully embraced by geothermal developers. We believe that the reason for this is that there is a poor understanding of testing and reservoir analysis that can be conducted in slim holes. In addition to reservoir engineering information, coring through the cap rock and into the reservoir provides important data for designing subsequent production well drilling and completion. Core drilling requires significantly less mud volume than conventional rotary drilling, and it is typically not necessary to cure lost circulation zones (LCZ). LCZs should be tested by either production or injection methods as they are encountered. The testing methodologies are similar to those conducted on large-diameter wells; although produced and/or injected fluid volumes are much less. Pressure, temperature and spinner (PTS) surveys in slim holes under static conditions can used to characterize temperature and pressure distribution in the geothermal reservoir. In many cases it is possible to discharge slim holes and obtain fluid samples to delineate the geochemical properties of the reservoir fluid. Also in the latter case, drawdown and buildup data obtained using a downhole pressure tool can be employed to determine formation transmissivity and well properties. Even if it proves difficult to discharge a slim hole, an injection test can be performed to obtain formation transmissivity. Given the discharge (or injection) data from a slimhole, discharge properties of a large-diameter well can be inferred using wellbore modeling. Finally, slim hole data (pressure, temperature, transmissivity, fluid properties) together with reservoir simulation can help predict the ability of the geothermal reservoir to sustain power production.

  4. Cost-Effectiveness Analysis of Different Genetic Testing Strategies for Lynch Syndrome in Taiwan.

    Directory of Open Access Journals (Sweden)

    Ying-Erh Chen

    Full Text Available Patients with Lynch syndrome (LS have a significantly increased risk of developing colorectal cancer (CRC and other cancers. Genetic screening for LS among patients with newly diagnosed CRC aims to identify mutations in the disease-causing genes (i.e., the DNA mismatch repair genes in the patients, to offer genetic testing for relatives of the patients with the mutations, and then to provide early prevention for the relatives with the mutations. Several genetic tests are available for LS, such as DNA sequencing for MMR genes and tumor testing using microsatellite instability and immunohistochemical analyses. Cost-effectiveness analyses of different genetic testing strategies for LS have been performed in several studies from different countries such as the US and Germany. However, a cost-effectiveness analysis for the testing has not yet been performed in Taiwan. In this study, we evaluated the cost-effectiveness of four genetic testing strategies for LS described in previous studies, while population-specific parameters, such as the mutation rates of the DNA mismatch repair genes and treatment costs for CRC in Taiwan, were used. The incremental cost-effectiveness ratios based on discounted life years gained due to genetic screening were calculated for the strategies relative to no screening and to the previous strategy. Using the World Health Organization standard, which was defined based on Taiwan's Gross Domestic Product per capita, the strategy based on immunohistochemistry as a genetic test followed by BRAF mutation testing was considered to be highly cost-effective relative to no screening. Our probabilistic sensitivity analysis results also suggest that the strategy has a probability of 0.939 of being cost-effective relative to no screening based on the commonly used threshold of $50,000 to determine cost-effectiveness. To the best of our knowledge, this is the first cost-effectiveness analysis for evaluating different genetic testing

  5. Vocabulary test Strategies used by the Students to answer Vocabulary Test the Reading Comprehension of TOEFL

    Directory of Open Access Journals (Sweden)

    Suyatman Suyatman

    2017-10-01

    Full Text Available Test of English as a foreign Language or TOEFL is a standardized test of English for non-native speaker. It consists of three parts or three sections of tests. In Reading Comprehension test, it consists of vocabulary test. To get better result of score, it needs strategies. The purposes of this study are to know the strategies used by the students to answer the vocabulary test on reading section of TOEFL, to know the most strategy used by the students, to know the least strategy used by the students and to know the distribution of strategies used by the students to answer the Vocabulary test of Reading Comprehension of the TOEFL. The researcher used descriptive qualitative research. The subject was twelve students. The instrument was questionnaire that consisted of thirty questions. Data analyzes technique was by using mean score. The result of the research showed that; (1 students used all strategies to answer the vocabulary test of reading comprehension of TOEFL. (2 the most strategies used by the students was ‘Looking for contextual clues to the meaning of unknown words.(3 the least strategy used by the students to answer vocabulary test was ‘Developing a new vocabulary study system, and (4 the distribution of the strategy number 1 was 3.88,strategy number 2 was 3.61, number 3 was 2.94, number four was 2.91, strategy number 5 was3.88, strategy number six was 3.47, strategy number seven was 3.69, strategy number eight was 3.02, strategy number nine was 3.00 and the last strategy was 3.13.

  6. Tungsten disulfide nanosheet and exonuclease III co-assisted amplification strategy for highly sensitive fluorescence polarization detection of DNA glycosylase activity

    International Nuclear Information System (INIS)

    Zhao, Jingjin; Ma, Yefei; Kong, Rongmei; Zhang, Liangliang; Yang, Wen; Zhao, Shulin

    2015-01-01

    Herein, we introduced a tungsten disulfide (WS 2 ) nanosheet and exonuclease III (Exo III) co-assisted signal amplification strategy for highly sensitive fluorescent polarization (FP) assay of DNA glycosylase activity. Two DNA glycosylases, uracil-DNA glycosylase (UDG) and human 8-oxoG DNA glycosylase 1 (hOGG1), were tested. A hairpin-structured probe (HP) which contained damaged bases in the stem was used as the substrate. The removal of damaged bases from substrate by DNA glycosylase would lower the melting temperature of HP. The HP was then opened and hybridized with a FAM dye-labeled single strand DNA (DP), generating a duplex with a recessed 3′-terminal of DP. This design facilitated the Exo III-assisted amplification by repeating the hybridization and digestion of DP, liberating numerous FAM fluorophores which could not be adsorbed on WS 2 nanosheet. Thus, the final system exhibited a small FP signal. However, in the absence of DNA glycosylases, no hybridization between DP and HP was occurred, hampering the hydrolysis of DP by Exo III. The intact DP was then adsorbed on the surface of WS 2 nanosheet that greatly amplified the mass of the labeled-FAM fluorophore, resulting in a large FP value. With the co-assisted amplification strategy, the sensitivity was substantially improved. In addition, this method was applied to detect UDG activity in cell extracts. The study of the inhibition of UDG was also performed. Furthermore, this method is simple in design, easy in implementation, and selective, which holds potential applications in the DNA glycosylase related mechanism research and molecular diagnostics. - Highlights: • A fluorescence polarization strategy for DNA glycosylase activity detection was developed. • The present method was based on WS 2 nanosheet and exonuclease III co-assisted signal amplification. • A high sensitivity and desirable selectivity were achieved. • This method provides a promising universal platform for DNA glycosylase

  7. Pydna: a simulation and documentation tool for DNA assembly strategies using python.

    Science.gov (United States)

    Pereira, Filipa; Azevedo, Flávio; Carvalho, Ângela; Ribeiro, Gabriela F; Budde, Mark W; Johansson, Björn

    2015-05-02

    Recent advances in synthetic biology have provided tools to efficiently construct complex DNA molecules which are an important part of many molecular biology and biotechnology projects. The planning of such constructs has traditionally been done manually using a DNA sequence editor which becomes error-prone as scale and complexity of the construction increase. A human-readable formal description of cloning and assembly strategies, which also allows for automatic computer simulation and verification, would therefore be a valuable tool. We have developed pydna, an extensible, free and open source Python library for simulating basic molecular biology DNA unit operations such as restriction digestion, ligation, PCR, primer design, Gibson assembly and homologous recombination. A cloning strategy expressed as a pydna script provides a description that is complete, unambiguous and stable. Execution of the script automatically yields the sequence of the final molecule(s) and that of any intermediate constructs. Pydna has been designed to be understandable for biologists with limited programming skills by providing interfaces that are semantically similar to the description of molecular biology unit operations found in literature. Pydna simplifies both the planning and sharing of cloning strategies and is especially useful for complex or combinatorial DNA molecule construction. An important difference compared to existing tools with similar goals is the use of Python instead of a specifically constructed language, providing a simulation environment that is more flexible and extensible by the user.

  8. A Closer Look at Chinese EFL Learners' Test-Wiseness Strategies in Reading Test

    Science.gov (United States)

    Haiyan, Miao; Rilong, Liu

    2016-01-01

    This paper reports on an investigation into the relationship of test-takers' use of test-wiseness strategies to Chinese EFL learners' reading test performance. A test-wiseness questionnaire was administered immediately after the final achievement test to probe into how learners thought while completing the reading section of the test. It was found…

  9. Using the noninformative families in family-based association tests : A powerful new testing strategy

    NARCIS (Netherlands)

    Lange, C; DeMeo, D; Silverman, EK; Weiss, ST; Laird, NM

    2003-01-01

    For genetic association studies with multiple phenotypes, we propose a new strategy for multiple testing with family-based association tests (FBATs). The strategy increases the power by both using all available family data and reducing the number of hypotheses tested while being robust against

  10. A test of the domain-specific acculturation strategy hypothesis.

    Science.gov (United States)

    Miller, Matthew J; Yang, Minji; Lim, Robert H; Hui, Kayi; Choi, Na-Yeun; Fan, Xiaoyan; Lin, Li-Ling; Grome, Rebekah E; Farrell, Jerome A; Blackmon, Sha'kema

    2013-01-01

    Acculturation literature has evolved over the past several decades and has highlighted the dynamic ways in which individuals negotiate experiences in multiple cultural contexts. The present study extends this literature by testing M. J. Miller and R. H. Lim's (2010) domain-specific acculturation strategy hypothesis-that individuals might use different acculturation strategies (i.e., assimilated, bicultural, separated, and marginalized strategies; J. W. Berry, 2003) across behavioral and values domains-in 3 independent cluster analyses with Asian American participants. Present findings supported the domain-specific acculturation strategy hypothesis as 67% to 72% of participants from 3 independent samples using different strategies across behavioral and values domains. Consistent with theory, a number of acculturation strategy cluster group differences emerged across generational status, acculturative stress, mental health symptoms, and attitudes toward seeking professional psychological help. Study limitations and future directions for research are discussed.

  11. RAMI strategies in the IFMIF Test Facilities design

    Energy Technology Data Exchange (ETDEWEB)

    Abal, Javier, E-mail: javier.abal@upc.edu [Fusion Energy Engineering Laboratory (FEEL), Technical University of Catalonia (UPC) Barcelona-Tech, Barcelona (Spain); Dies, Javier [Fusion Energy Engineering Laboratory (FEEL), Technical University of Catalonia (UPC) Barcelona-Tech, Barcelona (Spain); Arroyo, José Manuel [Laboratorio Nacional de Fusión por Confinamiento Magnético – CIEMAT, 28040 Madrid (Spain); Bargalló, Enric [Fusion Energy Engineering Laboratory (FEEL), Technical University of Catalonia (UPC) Barcelona-Tech, Barcelona (Spain); Casal, Natalia; García, Ángela [Laboratorio Nacional de Fusión por Confinamiento Magnético – CIEMAT, 28040 Madrid (Spain); Martínez, Gonzalo; Tapia, Carlos; De Blas, Alfredo [Fusion Energy Engineering Laboratory (FEEL), Technical University of Catalonia (UPC) Barcelona-Tech, Barcelona (Spain); Mollá, Joaquín; Ibarra, Ángel [Laboratorio Nacional de Fusión por Confinamiento Magnético – CIEMAT, 28040 Madrid (Spain)

    2013-10-15

    Highlights: • We have implemented fault tolerant design strategies so that the strong availability requirements are met. • The evolution to the present design of the signal and cooling lines inside the TTC has also been compared. • The RAMI analyses have demonstrated a strong capability in being a complementary tool in the design of IFMIF Test Facilities. -- Abstract: In this paper, a RAMI analysis of the different stages in Test Facilities (TF) design is described. The comparison between the availability results has been a milestone not only to evaluate the major unavailability contributors in the updates but also to implement fault tolerant design strategies when possible. These strategies encompass a wide range of design activities: from the definition of degraded modes of operation in the Test Facilities to specific modifications in the test modules in order to guarantee their fail safe operation.

  12. RAMI strategies in the IFMIF Test Facilities design

    International Nuclear Information System (INIS)

    Abal, Javier; Dies, Javier; Arroyo, José Manuel; Bargalló, Enric; Casal, Natalia; García, Ángela; Martínez, Gonzalo; Tapia, Carlos; De Blas, Alfredo; Mollá, Joaquín; Ibarra, Ángel

    2013-01-01

    Highlights: • We have implemented fault tolerant design strategies so that the strong availability requirements are met. • The evolution to the present design of the signal and cooling lines inside the TTC has also been compared. • The RAMI analyses have demonstrated a strong capability in being a complementary tool in the design of IFMIF Test Facilities. -- Abstract: In this paper, a RAMI analysis of the different stages in Test Facilities (TF) design is described. The comparison between the availability results has been a milestone not only to evaluate the major unavailability contributors in the updates but also to implement fault tolerant design strategies when possible. These strategies encompass a wide range of design activities: from the definition of degraded modes of operation in the Test Facilities to specific modifications in the test modules in order to guarantee their fail safe operation

  13. Positive view and increased likely uptake of follow-up testing with analysis of cell-free fetal DNA as alternative to invasive testing among Danish pregnant women

    DEFF Research Database (Denmark)

    Miltoft, Caroline B; Rode, Line; Tabor, Ann

    2018-01-01

    AND METHODS: Unselected and high-risk women attending first-trimester screening (Rigshospitalet, Copenhagen University Hospital) were invited to fill out the questionnaire Antenatal testing for Down syndrome as an online survey. RESULTS: The survey included 203 unselected and 50 high-risk women (response...... of follow-up testing without a corresponding rise in the termination rate of affected fetuses as some women test for information only. However, both unselected and high-risk women had overwhelmingly positive views underlining attention to avoid routinization.......INTRODUCTION: The aim of this study was to investigate the attitude (view, likely uptake and preferred strategy) towards cell-free fetal DNA (cfDNA) testing among pregnant women before a first-trimester risk assessment for trisomy 21 (unselected women) and after obtaining a high risk. MATERIAL...

  14. Testing and assessment strategies, including alternative and new approaches

    DEFF Research Database (Denmark)

    Meyer, Otto A.

    2003-01-01

    The object of toxicological testing is to predict possible adverse effect in humans when exposed to chemicals whether used as industrial chemicals, pharmaceuticals or pesticides. Animal models are predominantly used in identifying potential hazards of chemicals. The use of laboratory animals raises...... ethical concern. However, irrespective of animal welfare it is an important aspect of the discipline of toxicology that the primary object is human health. The ideal testing and assessment strategy is simple to use all the available test methods and preferably more in laboratory animal species from which...... uses and of the absence of health problems involved with their use. Thus, the regulatory toxicology is a cocktail of science and pragmatism added a crucial concern for animal welfare. Test methods are most often used in a testing sequence as bricks in a testing strategy. The main key driving forces...

  15. GMOtrack: generator of cost-effective GMO testing strategies.

    Science.gov (United States)

    Novak, Petra Krau; Gruden, Kristina; Morisset, Dany; Lavrac, Nada; Stebih, Dejan; Rotter, Ana; Zel, Jana

    2009-01-01

    Commercialization of numerous genetically modified organisms (GMOs) has already been approved worldwide, and several additional GMOs are in the approval process. Many countries have adopted legislation to deal with GMO-related issues such as food safety, environmental concerns, and consumers' right of choice, making GMO traceability a necessity. The growing extent of GMO testing makes it important to study optimal GMO detection and identification strategies. This paper formally defines the problem of routine laboratory-level GMO tracking as a cost optimization problem, thus proposing a shift from "the same strategy for all samples" to "sample-centered GMO testing strategies." An algorithm (GMOtrack) for finding optimal two-phase (screening-identification) testing strategies is proposed. The advantages of cost optimization with increasing GMO presence on the market are demonstrated, showing that optimization approaches to analytic GMO traceability can result in major cost reductions. The optimal testing strategies are laboratory-dependent, as the costs depend on prior probabilities of local GMO presence, which are exemplified on food and feed samples. The proposed GMOtrack approach, publicly available under the terms of the General Public License, can be extended to other domains where complex testing is involved, such as safety and quality assurance in the food supply chain.

  16. Problem-Solving Test: Analysis of DNA Damage Recognizing Proteins in Yeast and Human Cells

    Science.gov (United States)

    Szeberenyi, Jozsef

    2013-01-01

    The experiment described in this test was aimed at identifying DNA repair proteins in human and yeast cells. Terms to be familiar with before you start to solve the test: DNA repair, germline mutation, somatic mutation, inherited disease, cancer, restriction endonuclease, radioactive labeling, [alpha-[superscript 32]P]ATP, [gamma-[superscript…

  17. Injection molded nanofluidic chips: Fabrication method and functional tests using single-molecule DNA experiments

    DEFF Research Database (Denmark)

    Utko, Pawel; Persson, Karl Fredrik; Kristensen, Anders

    2011-01-01

    We demonstrate that fabrication of nanofluidic systems can be greatly simplified by injection molding of polymers. We functionally test our devices by single-molecule DNA experiments in nanochannels.......We demonstrate that fabrication of nanofluidic systems can be greatly simplified by injection molding of polymers. We functionally test our devices by single-molecule DNA experiments in nanochannels....

  18. Integrated testing strategies can be optimal for chemical risk classification.

    Science.gov (United States)

    Raseta, Marko; Pitchford, Jon; Cussens, James; Doe, John

    2017-08-01

    There is an urgent need to refine strategies for testing the safety of chemical compounds. This need arises both from the financial and ethical costs of animal tests, but also from the opportunities presented by new in-vitro and in-silico alternatives. Here we explore the mathematical theory underpinning the formulation of optimal testing strategies in toxicology. We show how the costs and imprecisions of the various tests, and the variability in exposures and responses of individuals, can be assembled rationally to form a Markov Decision Problem. We compute the corresponding optimal policies using well developed theory based on Dynamic Programming, thereby identifying and overcoming some methodological and logical inconsistencies which may exist in the current toxicological testing. By illustrating our methods for two simple but readily generalisable examples we show how so-called integrated testing strategies, where information of different precisions from different sources is combined and where different initial test outcomes lead to different sets of future tests, can arise naturally as optimal policies. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Improving enrichment of circulating fetal DNA for genetic testing: size fractionation followed by whole gene amplification.

    Science.gov (United States)

    Jorgez, Carolina J; Bischoff, Farideh Z

    2009-01-01

    Among the pitfalls of using cell-free fetal DNA in plasma for prenatal diagnosis is quality of the recovered DNA fragments and concomitant presence of maternal DNA (>95%). Our objective is to provide alternative methods for achieving enrichment and high-quality fetal DNA from plasma. Cell-free DNA from 31 pregnant women and 18 controls (10 males and 8 females) were size separated using agarose gel electrophoresis. DNA fragments of 100-300, 500-700 and 1,500-2,000 bp were excised and extracted, followed by whole genome amplification (WGA) of recovered fragments. Levels of beta-globin and DYS1 were measured. Distribution of beta-globin size fragments was similar among pregnant women and controls. Among control male cases, distribution of size fragments was the same for both beta-globin and DYS1. Among maternal cases confirmed to be male, the smallest size fragment (100-300 bp) accounted for nearly 50% (39.76 +/- 17.55%) of the recovered DYS1-DNA (fetal) and only 10% (10.40 +/- 6.49%) of beta-globin (total) DNA. After WGA of plasma fragments from pregnant women, DYS1 sequence amplification was best observed when using the 100-300 bp fragments as template. Combination of electrophoresis for size separation and WGA led to enriched fetal DNA from plasma. This novel combination of strategies is more likely to permit universal clinical applications of cell-free fetal DNA. Copyright 2009 S. Karger AG, Basel.

  20. The Five Immune Forces Impacting DNA-Based Cancer Immunotherapeutic Strategy

    Directory of Open Access Journals (Sweden)

    Suneetha Amara

    2017-03-01

    Full Text Available DNA-based vaccine strategy is increasingly realized as a viable cancer treatment approach. Strategies to enhance immunogenicity utilizing tumor associated antigens have been investigated in several pre-clinical and clinical studies. The promising outcomes of these studies have suggested that DNA-based vaccines induce potent T-cell effector responses and at the same time cause only minimal side-effects to cancer patients. However, the immune evasive tumor microenvironment is still an important hindrance to a long-term vaccine success. Several options are currently under various stages of study to overcome immune inhibitory effect in tumor microenvironment. Some of these approaches include, but are not limited to, identification of neoantigens, mutanome studies, designing fusion plasmids, vaccine adjuvant modifications, and co-treatment with immune-checkpoint inhibitors. In this review, we follow a Porter’s analysis analogy, otherwise commonly used in business models, to analyze various immune-forces that determine the potential success and sustainable positive outcomes following DNA vaccination using non-viral tumor associated antigens in treatment against cancer.

  1. Effects of Direct-to-Consumer Advertising and Clinical Guidelines on Appropriate Use of Human Papillomavirus DNA Tests

    Science.gov (United States)

    2011-01-01

    Background Both clinical guidelines and direct-to-consumer (DTC) advertising influence use of new health care technologies, but little is known about their relative effects. The introduction of a cervical cancer screening test in 2000 offered a unique opportunity to assess the two strategies. Objective To evaluate the effects of clinical guidelines and a targeted DTC advertising campaign on overall and appropriate use of human papillomavirus (HPV) DNA tests. Research Design Quasi-experimental study using difference-in-differences analysis. Data were MarketScan private insurance claims for 500,000 women ages 21 to 64 enrolled at least 12 consecutive months from January 2001 through December 2005. Results Both clinical guidelines and DTC advertising were associated with increases in overall HPV DNA test use. DTC advertising was associated with a statistically significant increase in HPV DNA test use in two groups of DTC cities (+5.57 percent, padvertising was associated with comparable increases in the probability of appropriate and inappropriate use of the HPV DNA test in primary screening. Clinical guideline releases from the American College of Obstetricians and Gynecologists, and by a co-sponsored panel, were associated with greater increases in HPV DNA tests for appropriate primary screening than for inappropriate primary screening (β=0.3347, padvertising was associated with increased overall use of a cervical cancer screening test, while clinical guidelines were differentially associated with increased appropriate use. These findings suggest distinct influences of consumer marketing and professional guidelines on the use of health care products and services. PMID:21150798

  2. Test-Taking Strategies in L2 Assessment: The Test of English for International Communication Speaking Test.

    Science.gov (United States)

    Huang, Heng-Tsung Danny

    2016-08-01

    This research explored the test-taking strategies associated with the Test of English for International Communication Speaking Test (TOEIC-S) and their relationship with test performance. Capitalizing on two sets of TOEIC-S and a custom-made strategy inventory, the researcher collected data from a total of 215 Taiwanese English learners consisting of 84 males and 131 females with an average age of 20.1 years (SD = 2.6). Quantitative data analysis gave rise to three major findings. First, TOEIC-S test-taking strategy use constituted a multi-faceted construct that involved multiple types of strategic behaviors. Second, these strategic behaviors matched those allowing test-takers to communicate both in real life and in the workplace. Third, communication strategy use and cognitive strategy use both contributed significantly to TOEIC-S performance. © The Author(s) 2016.

  3. Investigating CSI: portrayals of DNA testing on a forensic crime show and their potential effects.

    Science.gov (United States)

    Ley, Barbara L; Jankowski, Natalie; Brewer, Paul R

    2012-01-01

    The popularity of forensic crime shows such as CSI has fueled debate about their potential social impact. This study considers CSI's potential effects on public understandings regarding DNA testing in the context of judicial processes, the policy debates surrounding crime laboratory procedures, and the forensic science profession, as well as an effect not discussed in previous accounts: namely, the show's potential impact on public understandings of DNA and genetics more generally. To develop a theoretical foundation for research on the "CSI effect," it draws on cultivation theory, social cognitive theory, and audience reception studies. It then uses content analysis and textual analysis to illuminate how the show depicts DNA testing. The results demonstrate that CSI tends to depict DNA testing as routine, swift, useful, and reliable and that it echoes broader discourses about genetics. At times, however, the show suggests more complex ways of thinking about DNA testing and genetics.

  4. Primary ovary choriocarcinoma: individual DNA polymorphic analysis as a strategy to confirm diagnosis and treatment

    Directory of Open Access Journals (Sweden)

    Fernando Nalesso

    2013-04-01

    Full Text Available Primary choriocarcinoma of the ovary is rare. Furthermore, this tumor can arise from gestational tissue or pure germ cells of the ovary, with the latter resulting in non-gestational choriocarcinoma. While the clinical characteristics and histology of both tumor types are identical, differentiation of these tumors is necessary for effective treatment. One strategy for the differentiation of these tumors types is to assay for the presence of paternal DNA. Accordingly, in the present case, a patient with primary choriocarcinoma of the ovary with a non-gestational origin was confirmed by DNA analysis. The patient subsequently exhibited an excellent response to chemotherapy, and following surgery, achieved complete remission. A pathological analysis of surgical specimens further confirmed the absence of tumor.

  5. Positive cell-free fetal DNA testing for trisomy 13 reveals confined placental mosaicism.

    Science.gov (United States)

    Hall, April L; Drendel, Holli M; Verbrugge, Jennifer L; Reese, Angela M; Schumacher, Katherine L; Griffith, Christopher B; Weaver, David D; Abernathy, Mary P; Litton, Christian G; Vance, Gail H

    2013-09-01

    We report on a case in which cell-free fetal DNA was positive for trisomy 13 most likely due to confined placental mosaicism. Cell-free fetal DNA testing analyzes DNA derived from placental trophoblast cells and can lead to incorrect results that are not representative of the fetus. We sought to confirm commercial cell-free fetal DNA testing results by chorionic villus sampling and amniocentesis. These results were followed up by postnatal chromosome analysis of cord blood and placental tissue. First-trimester cell-free fetal DNA test results were positive for trisomy 13. Cytogenetic analysis of chorionic villus sampling yielded a mosaic karyotype of 47,XY,+13[10]/46,XY[12]. G-banded analysis of amniotic fluid was normal, 46,XY. Postnatal cytogenetic analysis of cord blood was normal. Karyotyping of tissues from four quadrants of the placenta demonstrated mosaicism for trisomy 13 in two of the quadrants and a normal karyotype in the other two. Our case illustrates several important aspects of this new testing methodology: that cell-free fetal DNA may not be representative of the fetal karyotype; that follow-up with diagnostic testing of chorionic villus sampling and/or amniotic fluid for abnormal test results should be performed; and that pretest counseling regarding the full benefits, limitations, and possible testing outcomes of cell-free fetal DNA screening is important.

  6. Impact of Laboratory Test Use Strategies in a Turkish Hospital.

    Directory of Open Access Journals (Sweden)

    Fatma Meriç Yılmaz

    Full Text Available Eliminating unnecessary laboratory tests is a good way to reduce costs while maintain patient safety. The aim of this study was to define and process strategies to rationalize laboratory use in Ankara Numune Training and Research Hospital (ANH and calculate potential savings in costs.A collaborative plan was defined by hospital managers; joint meetings with ANHTA and laboratory professors were set; the joint committee invited relevant staff for input, and a laboratory efficiency committee was created. Literature was reviewed systematically to identify strategies used to improve laboratory efficiency. Strategies that would be applicable in local settings were identified for implementation, processed, and the impact on clinical use and costs assessed for 12 months.Laboratory use in ANH differed enormously among clinics. Major use was identified in internal medicine. The mean number of tests per patient was 15.8. Unnecessary testing for chloride, folic acid, free prostate specific antigen, hepatitis and HIV testing were observed. Test panel use was pinpointed as the main cause of overuse of the laboratory and the Hospital Information System test ordering page was reorganized. A significant decrease (between 12.6-85.0% was observed for the tests that were taken to an alternative page on the computer screen. The one year study saving was equivalent to 371,183 US dollars.Hospital-based committees including laboratory professionals and clinicians can define hospital based problems and led to a standardized approach to test use that can help clinicians reduce laboratory costs through appropriate use of laboratory tests.

  7. Towards an alternative testing strategy for nanomaterials used in nanomedicine

    DEFF Research Database (Denmark)

    Dusinska, M; Boland, S; Saunders, M

    2015-01-01

    In spite of recent advances in describing the health outcomes of exposure to nanoparticles (NPs), it still remains unclear how exactly NPs interact with their cellular targets. Size, surface, mass, geometry, and composition may all play a beneficial role as well as causing toxicity. Concerns...... towards alternative testing strategies for hazard and risk assessment of nanomaterials, highlighting the adaptation of standard methods demanded by the special physicochemical features of nanomaterials and bioavailability studies. The work has assessed a broad range of toxicity tests, cell models and NP...... types and concentrations taking into account the inherent impact of NP properties and the effects of changes in experimental conditions using well-characterized NPs. The results of the studies have been used to generate recommendations for a suitable and robust testing strategy which can be applied...

  8. Hypothesis testing in students: Sequences, stages, and instructional strategies

    Science.gov (United States)

    Moshman, David; Thompson, Pat A.

    Six sequences in the development of hypothesis-testing conceptions are proposed, involving (a) interpretation of the hypothesis; (b) the distinction between using theories and testing theories; (c) the consideration of multiple possibilities; (d) the relation of theory and data; (e) the nature of verification and falsification; and (f) the relation of truth and falsity. An alternative account is then provided involving three global stages: concrete operations, formal operations, and a postformal metaconstructivestage. Relative advantages and difficulties of the stage and sequence conceptualizations are discussed. Finally, three families of teaching strategy are distinguished, which emphasize, respectively: (a) social transmission of knowledge; (b) carefully sequenced empirical experience by the student; and (c) self-regulated cognitive activity of the student. It is argued on the basis of Piaget's theory that the last of these plays a crucial role in the construction of such logical reasoning strategies as those involved in testing hypotheses.

  9. DNA-synthesis inhibition and repair DNA-synthesis in CHO Ade- C cells: An alternative approach to genotoxicity testing

    International Nuclear Information System (INIS)

    Slamenova, D.; Papsova, E.; Gabelova, A.; Dusinska, M.; Collins, A.; Wsolova, L.

    1997-01-01

    We describe an alternative assay to determine genotoxicity. Its main feature is that it combines two measures in a single experiment; the inhibition of replicative DNA synthesis together with the stimulation of DNA repair. We show that, in tests of four different genotoxic agents, the assay gives results that are entirely consistent with what is known about the mode of action of these agents. In addition, we have demonstrated that chemical carcinogens requiring metabolic activation can be examined using a standard procedure of incubation with a microsomal activating fraction. We consider the combined assay for DNA synthesis inhibition and repair synthesis to be a useful way for the rapid pre-screening of chemicals suspected of genotoxic activity on the level of mammalian cells. (author)

  10. Electrochemical DNA probe for Hg(2+) detection based on a triple-helix DNA and Multistage Signal Amplification Strategy.

    Science.gov (United States)

    Wang, Huan; Zhang, Yihe; Ma, Hongmin; Ren, Xiang; Wang, Yaoguang; Zhang, Yong; Wei, Qin

    2016-12-15

    In this work, an ultrasensitive electrochemical sensor was developed for detection of Hg(2+). Gold nanoparticles decorated bovine serum albumin reduction of graphene oxide (AuNP-BSA-rGO) were used as subsurface material for the immobilization of triple-helix DNA. The triple-helix DNA containing a thiol labelled single-stranded DNA (sDNA) and a thymine-rich DNA (T-rich DNA), which could be unwinded in the present of Hg(2+) to form more stable thymine-Hg(2+)-thymine (T-Hg(2+)-T) complex. T-Hg(2+)-T complex was then removed and the sDNA was left on the electrode. At this time, gold nanoparticle carrying thiol labelled cytosine-rich complementary DNA (cDNA-AuNP) could bind with the free sDNA. Meanwhile, the other free cDNA on AuNP could bind with each other in the present of Ag(+) to form the stable cytosine-Ag(+)-cytosine (C-Ag(+)-C) complex and circle amplification. Plenty of C-Ag(+)-C could form silver nanoclusters by electrochemical reduction and the striping signal of Ag could be measured for purpose of the final electrochemical detection of Hg(2+). This sensor could detect Hg(2+) over a wide concentration range from 0.1 to 130nM with a detection limit of 0.03nM. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Test strategies for industrial testers for converter controls equipment

    International Nuclear Information System (INIS)

    Oleniuk, P.; Kasampalis, V.; Cosmo, M. Di; Nisbet, D.; Todd, B.; Uznański, S.

    2017-01-01

    Power converters and their controls electronics are key elements for the operation of the CERN accelerator complex, having a direct impact on its availability. To prevent early-life failures and provide means to verify electronics, a set of industrial testers is used throughout the converters controls electronics' life cycle. The roles of the testers are to validate mass production during the manufacturing phase and to provide means to diagnose and repair failed modules that are brought back from operation. In the converter controls electronics section of the power converters group in the technology department of CERN (TE/EPC/CCE), two main test platforms have been adopted: a PXI platform for mixed analogue-digital functional tests and a JTAG Boundary-Scan platform for digital interconnection and functional tests. Depending on the functionality of the device under test, the appropriate test platforms are chosen. This paper is a follow-up to results presented at the TWEPP 2015 conference, adding the boundary scan test platform and the first results from exploitation of the test system. This paper reports on the test software, hardware design and test strategy applied for a number of devices that has resulted in maximizing test coverage and minimizing test design effort.

  12. Collaborative testing as a learning strategy in nursing education.

    Science.gov (United States)

    Sandahl, Sheryl S

    2010-01-01

    A primary goal of nursing education is to prepare nurses to work collaboratively as members of interprofessional health care teams on behalf of patients. Collaborative testing is a collaborative learning strategy used to foster knowledge development, critical thinking in decision making, and group processing skills. This study incorporated a quasi-experimental design with a comparison group to examine the effect of collaborative testing as a learning strategy on student learning and retention of course content as well as group process skills and student perceptions of their learning and anxiety. The setting was a baccalaureate nursing program; the sample consisted of two groups of senior students enrolled in Medical-Surgical Nursing II. Student learning, as measured by unit examination scores, was greater for students taking examinations collaboratively compared to individually. Retention of course content, as measured by final examination scores, was not greater for students taking examinations collaboratively compared to individually. Student perceptions were overwhelmingly positive, with students reporting increased learning as a result of the collaborative testing experiences. Despite the lack of data to support increased retention, collaborative testing may be a learning strategy worth implementing in nursing education. Students reported more positive interactions and collaboration with their peers, skills required by the professional nurse.

  13. Development of a codon optimization strategy using the efor RED reporter gene as a test case

    Science.gov (United States)

    Yip, Chee-Hoo; Yarkoni, Orr; Ajioka, James; Wan, Kiew-Lian; Nathan, Sheila

    2018-04-01

    Synthetic biology is a platform that enables high-level synthesis of useful products such as pharmaceutically related drugs, bioplastics and green fuels from synthetic DNA constructs. Large-scale expression of these products can be achieved in an industrial compliant host such as Escherichia coli. To maximise the production of recombinant proteins in a heterologous host, the genes of interest are usually codon optimized based on the codon usage of the host. However, the bioinformatics freeware available for standard codon optimization might not be ideal in determining the best sequence for the synthesis of synthetic DNA. Synthesis of incorrect sequences can prove to be a costly error and to avoid this, a codon optimization strategy was developed based on the E. coli codon usage using the efor RED reporter gene as a test case. This strategy replaces codons encoding for serine, leucine, proline and threonine with the most frequently used codons in E. coli. Furthermore, codons encoding for valine and glycine are substituted with the second highly used codons in E. coli. Both the optimized and original efor RED genes were ligated to the pJS209 plasmid backbone using Gibson Assembly and the recombinant DNAs were transformed into E. coli E. cloni 10G strain. The fluorescence intensity per cell density of the optimized sequence was improved by 20% compared to the original sequence. Hence, the developed codon optimization strategy is proposed when designing an optimal sequence for heterologous protein production in E. coli.

  14. Detection of complex hemoglobinopathies: recommendations on screening and DNA testing

    Directory of Open Access Journals (Sweden)

    E. Baysal

    2011-12-01

    Full Text Available The following recommendations should be taken into account during the evaluation and elucidation of the complex hemoglobinopathies: a in complex hemoglobinopathies performing DNA studies on all family members might be essential; b complex gene-gene interactions offer major diagnostic challenges both at the technical and clinical level; c hematological & DNA analyses must be run in parallel. Some cases may be straight forward but others may require indepth DNA work-up; d co-inheritance of a-thalassemia offers added challenge as it may affect phenotype significantly; e sickle cell anemia (SS, co-inherited with a-thal, can be a phenocopy of Sβ0-thal. The HbA2 increase can be mistaken for Sβ-thal. DNA Sequencing is imperative; f only a selected number of normal MCV, MCH, borderline HbA2 cases must be referred for DNA analysis. However, in certain cases, following hematological and family evaluation, the β and d genes may need to be sequenced; g DNA Sequencing will increasingly become the method of choice for screening and DNA mutation analysis. However, new methods like MLPA-which analyzes gene dosage- must be used more commonly to rule out deletion mutants to avoid false negative sequencing results; h these recommendations should be reviewed every 2-3 years reflecting new methods, new findings and new findings from ethnic groups. 诊断和说明复杂血红蛋白病时,建议考虑以下几点: a)针对复杂的血红蛋白病,有必要对所有家庭成员开展DNA研究;b 复杂的基因-基因交互作用可能使诊断在技术和临床层面上颇受挑战;c 血液和DNA分析须同时进行。 有些病例简单,但另外一些病例可能需要开展深层次的DNA检查;d 由于α型地中海贫血可能严重影响表型,α型地中海贫血的共同继承特征更具挑战;e 共同继承α型地中海贫血的镰状细胞贫血(SS),可以作为Sβ0型地中海贫血的显型。 HbA2增

  15. Progress and Strategies for Testing of Materials for Solar Panels

    Energy Technology Data Exchange (ETDEWEB)

    Kurtz, Sarah

    2017-04-25

    Accelerated testing is key to confident launch of a new product. However, for new products like solar panels, the best approach is not always clear. The challenge for materials manufacturers is that test times can be long. Also, small-coupon testing may not predict the behavior in the full-size module, but testing of the full-size module is too expensive. As a result, solar panel test standards like IEC 61215 are useful, but are not sufficient. Material manufacturers have needed to define their own test protocols. This presentation will review some historical data (e.g., data show that manufacturers are making great progress toward reducing encapsulant discoloration) and describe advances in material testing (for example, new techniques are being demonstrated on how to more quantitatively assess adhesion, detect tendency for delamination, and understand how encapsulant properties affect other properties like cracking of cells). The International PV Quality Assurance Task Force has been researching climate-specific weathering tests toward the goal of defining international standards that would simplify qualification and quality assurance testing for materials. The status of these tests and the strategies for how to organize these standards to best meet the needs of the industry will be discussed.

  16. Development of immunotoxicity testing strategies for immunomodulatory drugs.

    Science.gov (United States)

    Kawabata, Thomas T; Evans, Ellen W

    2012-01-01

    The ICH S8 immunotoxicity testing guideline for human pharmaceuticals was published in 2006 and was intended to provide guidance for assessing the immunotoxicity potential of low-molecular-weight drugs that are not intended to alter the immune system. For drugs intended to modulate the immune system, immunotoxicity testing strategies are generally developed on a case-by-case approach since the targets, intended patient population, and mechanisms of action of the test compound will determine the type of testing needed. Some of the general principles of ICH S8, however, may be applied to immunotoxicity testing strategies for immunomodulatory drugs. A weight-of-evidence approach using factors discussed in ICH S8 in concert with an assessment of the potential value of additional immunotoxicity testing should be considered. For most situations, immunotoxicity studies with immunomodulatory compounds evaluate off-target effects on the immune system and exaggerated pharmacology. The potential use of data from these studies and considerations such as translatability to humans are discussed.

  17. Testing possibilities for establishing nanodiamond-DNA-conjugates

    Science.gov (United States)

    Pohl, A.; Joch, S.; Michael, J.; Boschke, E.; Quenzel, P.; Schreiber, J.; Lapina, V.; Opitz, J.

    2011-07-01

    We report on the biofunctionalization of nanodiamond surfaces in a two step procedure: chemical modification, resulting in homogeneous and defined surface coating, with following addition of ssDNA. Carboxylation, thymidine coupling and amination methods for chemical modification of diamond surfaces for further functionalization experiments were applied. To enable the coupling process, biomolecules were also chemically modified with functional groups (-NH2). FTIR spectroscopy, fluorescence microscopy and gel electrophoresis were applied for characterizing modified ND particles and bioconjugates and for controlling the coupling success.

  18. Strategy for the development of EU Test Blanket Systems instrumentation

    Energy Technology Data Exchange (ETDEWEB)

    Calderoni, P., E-mail: Pattrick.Calderoni@f4e.europa.eu; Ricapito, I.; Poitevin, Y.

    2013-10-15

    Highlights: • We developed a strategy for the development of instrumentation for EU ITER TBSs. • TBSs instrumentation functions: safety, operation and scientific mission. • Described activities are in support of ITER design review process. -- Abstract: The instrumentation of the HCLL and HCPB Test Blanket System is fundamental in ensuring that ITER safety and operational requirements are satisfied as well as in enabling the scientific mission of the TBM program. It carries out three essential functions: (i) safety, intended as compliance with ITER requirements toward public and workers protection; (ii) system control, intended as compliance with ITER operational requirements and investment protection; and (iii) scientific mission, intended as validating technology and predictive tools for blanket concepts relevant to fusion energy systems. This paper describes the strategy for instrumentation development by providing details of the following five steps to be implemented in procured activities in the short to mid-term (3–4 years): (i) provide mapping of sensors requirements based on critical review of preliminary design data; (ii) develop functional specifications for TBS sensors based on the analysis of operative conditions in the various ITER buildings in which they are located; (iii) assess availability of commercial sensors against developed specifications; (iv) develop prototypes when no available solution is identified; and (v) perform single effect tests for the most critical solicitations and post-test examination of commercial products and prototypes. Examples of technology assessment in two technical areas are included to reinforce and complement the strategy description.

  19. Subsurface barrier demonstration test strategy and performance specification

    International Nuclear Information System (INIS)

    Treat, R.L.; Cruse, J.M.

    1994-05-01

    This document was developed to help specify a major demonstration test project of subsurface barrier systems supporting the Tank Waste Remediation System (TWRS) Program. The document focuses discussion on requirements applicable to demonstration of three subsurface barrier concepts: (1) Injected Material, (2) Cryogenic, and (3) Desiccant. Detailed requirements are provided for initial qualification of a technology proposal followed by the pre-demonstration and demonstration test requirements and specifications. Each requirement and specification is accompanied by a discussion of the rationale for it. The document also includes information on the Hanford Site tank farms and related data; the related and currently active technology development projects within the DOE's EM-50 Program; and the overall demonstration test strategy. Procurement activities and other preparations for actual demonstration testing are on hold until a decision is made regarding further development of subsurface barriers. Accordingly, this document is being issued for information only

  20. Tungsten disulfide nanosheet and exonuclease III co-assisted amplification strategy for highly sensitive fluorescence polarization detection of DNA glycosylase activity

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Jingjin; Ma, Yefei [Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources of Education Ministry, Guangxi Normal University, Guilin, 541004 (China); Kong, Rongmei [The Key Laboratory of Life-Organic Analysis, College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165 (China); Zhang, Liangliang, E-mail: liangzhang319@163.com [Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources of Education Ministry, Guangxi Normal University, Guilin, 541004 (China); Yang, Wen; Zhao, Shulin [Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources of Education Ministry, Guangxi Normal University, Guilin, 541004 (China)

    2015-08-05

    Herein, we introduced a tungsten disulfide (WS{sub 2}) nanosheet and exonuclease III (Exo III) co-assisted signal amplification strategy for highly sensitive fluorescent polarization (FP) assay of DNA glycosylase activity. Two DNA glycosylases, uracil-DNA glycosylase (UDG) and human 8-oxoG DNA glycosylase 1 (hOGG1), were tested. A hairpin-structured probe (HP) which contained damaged bases in the stem was used as the substrate. The removal of damaged bases from substrate by DNA glycosylase would lower the melting temperature of HP. The HP was then opened and hybridized with a FAM dye-labeled single strand DNA (DP), generating a duplex with a recessed 3′-terminal of DP. This design facilitated the Exo III-assisted amplification by repeating the hybridization and digestion of DP, liberating numerous FAM fluorophores which could not be adsorbed on WS{sub 2} nanosheet. Thus, the final system exhibited a small FP signal. However, in the absence of DNA glycosylases, no hybridization between DP and HP was occurred, hampering the hydrolysis of DP by Exo III. The intact DP was then adsorbed on the surface of WS{sub 2} nanosheet that greatly amplified the mass of the labeled-FAM fluorophore, resulting in a large FP value. With the co-assisted amplification strategy, the sensitivity was substantially improved. In addition, this method was applied to detect UDG activity in cell extracts. The study of the inhibition of UDG was also performed. Furthermore, this method is simple in design, easy in implementation, and selective, which holds potential applications in the DNA glycosylase related mechanism research and molecular diagnostics. - Highlights: • A fluorescence polarization strategy for DNA glycosylase activity detection was developed. • The present method was based on WS{sub 2} nanosheet and exonuclease III co-assisted signal amplification. • A high sensitivity and desirable selectivity were achieved. • This method provides a promising universal platform for DNA

  1. Toehold-mediated strand displacement reaction-dependent fluorescent strategy for sensitive detection of uracil-DNA glycosylase activity.

    Science.gov (United States)

    Wu, Yushu; Wang, Lei; Jiang, Wei

    2017-03-15

    Sensitive detection of uracil-DNA glycosylase (UDG) activity is beneficial for evaluating the repairing process of DNA lesions. Here, toehold-mediated strand displacement reaction (TSDR)-dependent fluorescent strategy was constructed for sensitive detection of UDG activity. A single-stranded DNA (ssDNA) probe with two uracil bases and a trigger sequence were designed. A hairpin probe with toehold domain was designed, and a reporter probe was also designed. Under the action of UDG, two uracil bases were removed from ssDNA probe, generating apurinic/apyrimidinic (AP) sites. Then, the AP sites could inhibit the TSDR between ssDNA probe and hairpin probe, leaving the trigger sequence in ssDNA probe still free. Subsequently, the trigger sequence was annealed with the reporter probe, initiating the polymerization and nicking amplification reaction. As a result, numerous G-quadruplex (G4) structures were formed, which could bind with N-methyl-mesoporphyrin IX (NMM) to generate enhanced fluorescent signal. In the absence of UDG, the ssDNA probe could hybridize with the toehold domain of the hairpin probe to initiate TSDR, blocking the trigger sequence, and then the subsequent amplification reaction would not occur. The proposed strategy was successfully implemented for detecting UDG activity with a detection limit of 2.7×10 -5 U/mL. Moreover, the strategy could distinguish UDG well from other interference enzymes. Furthermore, the strategy was also applied for detecting UDG activity in HeLa cells lysate with low effect of cellular components. These results indicated that the proposed strategy offered a promising tool for sensitive quantification of UDG activity in UDG-related function study and disease prognosis. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Cyber Security Test Strategy for Non-safety Display System

    International Nuclear Information System (INIS)

    Son, Han Seong; Kim, Hee Eun

    2016-01-01

    Cyber security has been a big issue since the instrumentation and control (I and C) system of nuclear power plant (NPP) is digitalized. A cyber-attack on NPP should be dealt with seriously because it might cause not only economic loss but also the radioactive material release. Researches on the consequences of cyber-attack onto NPP from a safety point of view have been conducted. A previous study shows the risk effect brought by initiation of event and deterioration of mitigation function by cyber terror. Although this study made conservative assumptions and simplifications, it gives an insight on the effect of cyber-attack. Another study shows that the error on a non-safety display system could cause wrong actions of operators. According to this previous study, the failure of the operator action caused by a cyber-attack on a display system might threaten the safety of the NPP by limiting appropriate mitigation actions. This study suggests a test strategy focusing on the cyber-attack on the information and display system, which might cause the failure of operator. The test strategy can be suggested to evaluate and complement security measures. Identifying whether a cyber-attack on the information and display system can affect the mitigation actions of operator, the strategy to obtain test scenarios is suggested. The failure of mitigation scenario is identified first. Then, for the test target in the scenario, software failure modes are applied to identify realistic failure scenarios. Testing should be performed for those scenarios to confirm the integrity of data and to assure effectiveness of security measures

  3. Cyber Security Test Strategy for Non-safety Display System

    Energy Technology Data Exchange (ETDEWEB)

    Son, Han Seong [Joongbu University, Geumsan (Korea, Republic of); Kim, Hee Eun [KAIST, Daejeon (Korea, Republic of)

    2016-10-15

    Cyber security has been a big issue since the instrumentation and control (I and C) system of nuclear power plant (NPP) is digitalized. A cyber-attack on NPP should be dealt with seriously because it might cause not only economic loss but also the radioactive material release. Researches on the consequences of cyber-attack onto NPP from a safety point of view have been conducted. A previous study shows the risk effect brought by initiation of event and deterioration of mitigation function by cyber terror. Although this study made conservative assumptions and simplifications, it gives an insight on the effect of cyber-attack. Another study shows that the error on a non-safety display system could cause wrong actions of operators. According to this previous study, the failure of the operator action caused by a cyber-attack on a display system might threaten the safety of the NPP by limiting appropriate mitigation actions. This study suggests a test strategy focusing on the cyber-attack on the information and display system, which might cause the failure of operator. The test strategy can be suggested to evaluate and complement security measures. Identifying whether a cyber-attack on the information and display system can affect the mitigation actions of operator, the strategy to obtain test scenarios is suggested. The failure of mitigation scenario is identified first. Then, for the test target in the scenario, software failure modes are applied to identify realistic failure scenarios. Testing should be performed for those scenarios to confirm the integrity of data and to assure effectiveness of security measures.

  4. Lay perceptions of predictive testing for diabetes based on DNA test results versus family history assessment: a focus group study.

    Science.gov (United States)

    Wijdenes-Pijl, Miranda; Dondorp, Wybo J; Timmermans, Danielle Rm; Cornel, Martina C; Henneman, Lidewij

    2011-07-05

    This study assessed lay perceptions of issues related to predictive genetic testing for multifactorial diseases. These perceived issues may differ from the "classic" issues, e.g. autonomy, discrimination, and psychological harm that are considered important in predictive testing for monogenic disorders. In this study, type 2 diabetes was used as an example, and perceptions with regard to predictive testing based on DNA test results and family history assessment were compared. Eight focus group interviews were held with 45 individuals aged 35-70 years with (n = 3) and without (n = 1) a family history of diabetes, mixed groups of these two (n = 2), and diabetes patients (n = 2). All interviews were transcribed and analysed using Atlas-ti. Most participants believed in the ability of a predictive test to identify people at risk for diabetes and to motivate preventive behaviour. Different reasons underlying motivation were considered when comparing DNA test results and a family history risk assessment. A perceived drawback of DNA testing was that diabetes was considered not severe enough for this type of risk assessment. In addition, diabetes family history assessment was not considered useful by some participants, since there are also other risk factors involved, not everyone has a diabetes family history or knows their family history, and it might have a negative influence on family relations. Respect for autonomy of individuals was emphasized more with regard to DNA testing than family history assessment. Other issues such as psychological harm, discrimination, and privacy were only briefly mentioned for both tests. The results suggest that most participants believe a predictive genetic test could be used in the prevention of multifactorial disorders, such as diabetes, but indicate points to consider before both these tests are applied. These considerations differ with regard to the method of assessment (DNA test or obtaining family history) and also differ from

  5. Lay perceptions of predictive testing for diabetes based on DNA test results versus family history assessment: a focus group study

    Directory of Open Access Journals (Sweden)

    Cornel Martina C

    2011-07-01

    Full Text Available Abstract Background This study assessed lay perceptions of issues related to predictive genetic testing for multifactorial diseases. These perceived issues may differ from the "classic" issues, e.g. autonomy, discrimination, and psychological harm that are considered important in predictive testing for monogenic disorders. In this study, type 2 diabetes was used as an example, and perceptions with regard to predictive testing based on DNA test results and family history assessment were compared. Methods Eight focus group interviews were held with 45 individuals aged 35-70 years with (n = 3 and without (n = 1 a family history of diabetes, mixed groups of these two (n = 2, and diabetes patients (n = 2. All interviews were transcribed and analysed using Atlas-ti. Results Most participants believed in the ability of a predictive test to identify people at risk for diabetes and to motivate preventive behaviour. Different reasons underlying motivation were considered when comparing DNA test results and a family history risk assessment. A perceived drawback of DNA testing was that diabetes was considered not severe enough for this type of risk assessment. In addition, diabetes family history assessment was not considered useful by some participants, since there are also other risk factors involved, not everyone has a diabetes family history or knows their family history, and it might have a negative influence on family relations. Respect for autonomy of individuals was emphasized more with regard to DNA testing than family history assessment. Other issues such as psychological harm, discrimination, and privacy were only briefly mentioned for both tests. Conclusion The results suggest that most participants believe a predictive genetic test could be used in the prevention of multifactorial disorders, such as diabetes, but indicate points to consider before both these tests are applied. These considerations differ with regard to the method of assessment

  6. A cDNA Immunization Strategy to Generate Nanobodies against Membrane Proteins in Native Conformation

    Science.gov (United States)

    Eden, Thomas; Menzel, Stephan; Wesolowski, Janusz; Bergmann, Philine; Nissen, Marion; Dubberke, Gudrun; Seyfried, Fabienne; Albrecht, Birte; Haag, Friedrich; Koch-Nolte, Friedrich

    2018-01-01

    Nanobodies (Nbs) are soluble, versatile, single-domain binding modules derived from the VHH variable domain of heavy-chain antibodies naturally occurring in camelids. Nbs hold huge promise as novel therapeutic biologics. Membrane proteins are among the most interesting targets for therapeutic Nbs because they are accessible to systemically injected biologics. In order to be effective, therapeutic Nbs must recognize their target membrane protein in native conformation. However, raising Nbs against membrane proteins in native conformation can pose a formidable challenge since membrane proteins typically contain one or more hydrophobic transmembrane regions and, therefore, are difficult to purify in native conformation. Here, we describe a highly efficient genetic immunization strategy that circumvents these difficulties by driving expression of the target membrane protein in native conformation by cells of the immunized camelid. The strategy encompasses ballistic transfection of skin cells with cDNA expression plasmids encoding one or more orthologs of the membrane protein of interest and, optionally, other costimulatory proteins. The plasmid is coated onto 1 µm gold particles that are then injected into the shaved and depilated skin of the camelid. A gene gun delivers a helium pulse that accelerates the DNA-coated particles to a velocity sufficient to penetrate through multiple layers of cells in the skin. This results in the exposure of the extracellular domains of the membrane protein on the cell surface of transfected cells. Repeated immunization drives somatic hypermutation and affinity maturation of target-specific heavy-chain antibodies. The VHH/Nb coding region is PCR-amplified from B cells obtained from peripheral blood or a lymph node biopsy. Specific Nbs are selected by phage display or by screening of Nb-based heavy-chain antibodies expressed as secretory proteins in transfected HEK cells. Using this strategy, we have successfully generated agonistic

  7. A cDNA Immunization Strategy to Generate Nanobodies against Membrane Proteins in Native Conformation

    Directory of Open Access Journals (Sweden)

    Thomas Eden

    2018-01-01

    Full Text Available Nanobodies (Nbs are soluble, versatile, single-domain binding modules derived from the VHH variable domain of heavy-chain antibodies naturally occurring in camelids. Nbs hold huge promise as novel therapeutic biologics. Membrane proteins are among the most interesting targets for therapeutic Nbs because they are accessible to systemically injected biologics. In order to be effective, therapeutic Nbs must recognize their target membrane protein in native conformation. However, raising Nbs against membrane proteins in native conformation can pose a formidable challenge since membrane proteins typically contain one or more hydrophobic transmembrane regions and, therefore, are difficult to purify in native conformation. Here, we describe a highly efficient genetic immunization strategy that circumvents these difficulties by driving expression of the target membrane protein in native conformation by cells of the immunized camelid. The strategy encompasses ballistic transfection of skin cells with cDNA expression plasmids encoding one or more orthologs of the membrane protein of interest and, optionally, other costimulatory proteins. The plasmid is coated onto 1 µm gold particles that are then injected into the shaved and depilated skin of the camelid. A gene gun delivers a helium pulse that accelerates the DNA-coated particles to a velocity sufficient to penetrate through multiple layers of cells in the skin. This results in the exposure of the extracellular domains of the membrane protein on the cell surface of transfected cells. Repeated immunization drives somatic hypermutation and affinity maturation of target-specific heavy-chain antibodies. The VHH/Nb coding region is PCR-amplified from B cells obtained from peripheral blood or a lymph node biopsy. Specific Nbs are selected by phage display or by screening of Nb-based heavy-chain antibodies expressed as secretory proteins in transfected HEK cells. Using this strategy, we have successfully

  8. Ethical, Legal and Social Issues in Japan on the Determination of Blood Relationship via DNA Testing.

    Science.gov (United States)

    Toya, Waki

    2017-01-01

    DNA paternity testing has recently become more widely available in Japan. The aim of this paper is to examine the issues surrounding (1) the implementing agency, whether the testing is conducted in a commercial direct-to-consumer (DTC) setting or a judicial non-DTC setting, and (2) the implementation conditions and more specifically the legal capacity of the proband (test subject). Literature research in Japanese and English was conducted. Some countries prohibit commercial DNA testing without the consent of the proband or her or his legally authorized representative. But as in some cases, the results of DTC paternity testing have proven to be unreliable. I propose a complete prohibition of DTC DNA paternity testing in Japan. In many cases of paternity testing, the proband is a minor. This has led to debate about whether proxy consent is sufficient for paternity testing or whether additional safeguards (such as a court order) are required. In cases where commercial DNA testing has been conducted and the test results are produced in court as evidence, the court must judge whether or not to admit these results as evidence. Another important issue is whether or not paternity testing should be legally mandated in certain cases. If we come to the conclusion that DNA test results are the only way to conclusively establish a parent-child relationship, then our society may prioritize even more genetic relatedness over other conceptions of a parent-child relationship. This prioritization could adversely affect families created through assisted reproductive technology (ART), especially in situations where children are not aware of their biological parentage. This paper argues for a complete prohibition of DTC DNA paternity testing in Japan, and highlights that broader ethical and legal deliberation on such genetic services is required.

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

    Science.gov (United States)

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

    2014-01-01

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

  10. Integrated testing strategy (ITS) for bioaccumulation assessment under REACH

    DEFF Research Database (Denmark)

    Lombardo, Anna; Roncaglioni, Alessandra; Benfentati, Emilio

    2014-01-01

    in a dossier. REACH promotes the use of alternative methods to replace, refine and reduce the use of animal (eco)toxicity testing. Within the EU OSIRIS project, integrated testing strategies (ITSs) have been developed for the rational use of non-animal testing approaches in chemical hazard assessment. Here we......REACH (registration, evaluation, authorisation and restriction of chemicals) regulation requires that all the chemicals produced or imported in Europe above 1 tonne/year are registered. To register a chemical, physicochemical, toxicological and ecotoxicological information needs to be reported...... present an ITS for evaluating the bioaccumulation potential of organic chemicals. The scheme includes the use of all available data (also the non-optimal ones), waiving schemes, analysis of physicochemical properties related to the end point and alternative methods (both in silico and in vitro). In vivo...

  11. Mendelian breeding units versus standard sampling strategies: mitochondrial DNA variation in southwest Sardinia

    Directory of Open Access Journals (Sweden)

    Daria Sanna

    2011-01-01

    Full Text Available We report a sampling strategy based on Mendelian Breeding Units (MBUs, representing an interbreeding group of individuals sharing a common gene pool. The identification of MBUs is crucial for case-control experimental design in association studies. The aim of this work was to evaluate the possible existence of bias in terms of genetic variability and haplogroup frequencies in the MBU sample, due to severe sample selection. In order to reach this goal, the MBU sampling strategy was compared to a standard selection of individuals according to their surname and place of birth. We analysed mitochondrial DNA variation (first hypervariable segment and coding region in unrelated healthy subjects from two different areas of Sardinia: the area around the town of Cabras and the western Campidano area. No statistically significant differences were observed when the two sampling methods were compared, indicating that the stringent sample selection needed to establish a MBU does not alter original genetic variability and haplogroup distribution. Therefore, the MBU sampling strategy can be considered a useful tool in association studies of complex traits.

  12. Test performance and acceptability of self- versus provider-collected swabs for high-risk HPV DNA testing in female-to-male trans masculine patients.

    Science.gov (United States)

    Reisner, Sari L; Deutsch, Madeline B; Peitzmeier, Sarah M; White Hughto, Jaclyn M; Cavanaugh, Timothy P; Pardee, Dana J; McLean, Sarah A; Panther, Lori A; Gelman, Marcy; Mimiaga, Matthew J; Potter, Jennifer E

    2018-01-01

    endorsed a preference for the self-collected vaginal swab over provider-collected cervical swab. Self-collected vaginal swabs are highly acceptable to TM as a means to test for hrHPV DNA. Test performance of this self-collection method for hrHPV detection in TM is consistent with previous studies in cisgender females. Self-collected vaginal swab testing for hrHPV DNA represents a reasonable and patient-centered strategy for primary cervical cancer screening in TM patients unwilling to undergo provider collection of specimens via speculum exam.

  13. Standing of nucleic acid testing strategies in veterinary diagnosis laboratories to uncover Mycobacterium tuberculosis complex members

    Science.gov (United States)

    Costa, Pedro; Botelho, Ana; Couto, Isabel; Viveiros, Miguel; Inácio, João

    2014-01-01

    Nucleic acid testing (NAT) designate any molecular approach used for the detection, identification, and characterization of pathogenic microorganisms, enabling the rapid, specific, and sensitive diagnostic of infectious diseases, such as tuberculosis. These assays have been widely used since the 90s of the last century in human clinical laboratories and, subsequently, also in veterinary diagnostics. Most NAT strategies are based in the polymerase chain reaction (PCR) and its several enhancements and variations. From the conventional PCR, real-time PCR and its combinations, isothermal DNA amplification, to the nanotechnologies, here we review how the NAT assays have been applied to decipher if and which member of the Mycobacterium tuberculosis complex is present in a clinical sample. Recent advances in DNA sequencing also brought new challenges and have made possible to generate rapidly and at a low cost, large amounts of sequence data. This revolution with the high-throughput sequencing (HTS) technologies makes whole genome sequencing (WGS) and metagenomics the trendiest NAT strategies, today. The ranking of NAT techniques in the field of clinical diagnostics is rising, and we provide a SWOT (Strengths, Weaknesses, Opportunities, and Threats) analysis with our view of the use of molecular diagnostics for detecting tuberculosis in veterinary laboratories, notwithstanding the gold standard being still the classical culture of the agent. The complementary use of both classical and molecular diagnostics approaches is recommended to speed the diagnostic, enabling a fast decision by competent authorities and rapid tackling of the disease. PMID:25988157

  14. Test of models for replication of SV40 DNA following UV irradiation

    International Nuclear Information System (INIS)

    Barnett, S.W.

    1983-01-01

    The replication of SV40 DNA immediately after irradiation of infected monkey cells has been examined. SV40 DNA synthesis is inhibited in a UV fluence-dependent fashion, and the synthesis of completely replicated (Form I) SV40 molecules is more severely inhibited than is total SV40 DNA synthesis. Two models for DNA replication-inhibition have been tested. Experimental results have been compared to those predicted by mathematical models derived to describe two possible molecular mechanisms of replication inhibition. No effect of UV irradiation on the uptake and phosphorylation of 3 H-thymidine nor on the size of the intracellular deoxythymidine triphosphate pool of SV40-infected cells have been observed, validating the use of 3 H-thymidine incorporation as a measure of DNA synthesis in this system. In vitro studies have been performed to further investigate the mechanism of dimer-specific inhibition of completion of SV40 DNA synthesis observed in in vivo. The results of these studies are consistent with a mechanism of discontinuous synthesis past dimer sites, but it is equally possible that the mechanism of DNA replication of UV-damaged DNA in the in vitro system is different from that which occurs in vivo

  15. High-Risk Palliative Care Patients' Knowledge and Attitudes about Hereditary Cancer Testing and DNA Banking.

    Science.gov (United States)

    Quillin, John M; Emidio, Oluwabunmi; Ma, Brittany; Bailey, Lauryn; Smith, Thomas J; Kang, In Guk; Yu, Brandon J; Owodunni, Oluwafemi Patrick; Abusamaan, Mohammed; Razzak, Rab; Bodurtha, Joann N

    2017-12-04

    Even at the end of life, testing cancer patients for inherited susceptibility may provide life-saving information to their relatives. Prior research suggests palliative care inpatients have suboptimal understanding of genetic importance, and testing may be underutilized in this clinical setting. These conclusions are based on limited research. This study aimed to estimate genetic testing prevalence among high-risk palliative care patients in a National Cancer Institute-designated comprehensive cancer center. We also aimed to understand these patients' understanding of, and attitudes toward, hereditary cancer testing and DNA banking. Palliative care in-patients with cancer completed structured interviews, and their medical records were reviewed. Among patients at high risk for hereditary cancer, we assessed history of genetic testing/DNA banking; and related knowledge and attitudes. Among 24 high-risk patients, 14 (58.3%) said they/their relatives had genetic testing or they had been referred for a genetics consultation. Of the remaining 10 patients, seven (70%) said they would "probably" or "definitely" get tested. Patients who had not had testing were least concerned about the impact of future testing on their family relationships; two (20%) said they were "extremely concerned" about privacy related to genetic testing. Of patients without prior testing, five (50%) said they had heard or read "a fair amount" about genetic testing. No high-risk patients had banked DNA. Overall, 23 (95.8%) said they had heard or read "almost nothing" or "relatively little" about DNA banking. Written materials and clinician discussion were most preferred ways to learn about genetic testing and DNA banking. Overall, this study demonstrates underutilization of genetics services at the end of life continues to be problematic, despite high patient interest.

  16. Evaluation of test intervals strategies with a risk monitor

    International Nuclear Information System (INIS)

    Soerman, J.

    2005-01-01

    The Swedish nuclear power utility Oskarshamn Power Group (OKG), is investigating how the use of a risk monitor can facilitate and improve risk-informed decision-making at their nuclear power plants. The intent is to evaluate if risk-informed decision-making can be accepted. A pilot project was initiated and carried out in 2004. The project included investigating if a risk monitor can be used for optimising test intervals for diesel- and gas turbine generators with regard to risk level. The Oskarhamn 2 (O2), PSA Level 1 model was converted into a risk monitor using RiskSpectrum RiskWatcher (RSRW) software. The converted PSA model included the complete PSA model for the power operation mode. RSRW then performs a complete requantification for every analysis. Time dependent reliability data are taken into account, i.e. a shorter test interval will increases the components availability (possibility to e.g. start on demand). The converted O2 model was then used to investigate whether it would be possible to balance longer test intervals for diesel generators, gas turbine generators and high pressure injection system with shorter test intervals for the low pressure injection system, while maintaining a low risk level at the plant. The results show that a new mixture of test intervals can be implemented with only marginally changes in the risk calculated with the risk monitor model. The results indicate that the total number of test activities for the systems included in the pilot study could be reduced by 20% with a maintained level of risk. A risk monitor taking into account the impact from test intervals in availability calculations for components is well suited for evaluation of test interval strategies. It also enables the analyst to evaluate the risk level over a period of time including the impact the actual status of the plant may have on the risk level. (author)

  17. Quantification of Plasmodiophora brassicae Using a DNA-Based Soil Test Facilitates Sustainable Oilseed Rape Production

    OpenAIRE

    Ann-Charlotte Wallenhammar; Albin Gunnarson; Fredrik Hansson; Anders Jonsson

    2016-01-01

    Outbreaks of clubroot disease caused by the soil-borne obligate parasite Plasmodiophora brassicae are common in oilseed rape (OSR) in Sweden. A DNA-based soil testing service that identifies fields where P. brassicae poses a significant risk of clubroot infection is now commercially available. It was applied here in field surveys to monitor the prevalence of P. brassicae DNA in field soils intended for winter OSR production and winter OSR field experiments. In 2013 in Scania, prior to plantin...

  18. Sequentially optimized reconstruction strategy: A meta-strategy for perimetry testing.

    Directory of Open Access Journals (Sweden)

    Şerife Seda Kucur

    Full Text Available Perimetry testing is an automated method to measure visual function and is heavily used for diagnosing ophthalmic and neurological conditions. Its working principle is to sequentially query a subject about perceived light using different brightness levels at different visual field locations. At a given location, this query-patient-feedback process is expected to converge at a perceived sensitivity, such that a shown stimulus intensity is observed and reported 50% of the time. Given this inherently time-intensive and noisy process, fast testing strategies are necessary in order to measure existing regions more effectively and reliably. In this work, we present a novel meta-strategy which relies on the correlative nature of visual field locations in order to strongly reduce the necessary number of locations that need to be examined. To do this, we sequentially determine locations that most effectively reduce visual field estimation errors in an initial training phase. We then exploit these locations at examination time and show that our approach can easily be combined with existing perceived sensitivity estimation schemes to speed up the examinations. Compared to state-of-the-art strategies, our approach shows marked performance gains with a better accuracy-speed trade-off regime for both mixed and sub-populations.

  19. A likelihood ratio test for species membership based on DNA sequence data

    DEFF Research Database (Denmark)

    Matz, Mikhail V.; Nielsen, Rasmus

    2005-01-01

    DNA barcoding as an approach for species identification is rapidly increasing in popularity. However, it remains unclear which statistical procedures should accompany the technique to provide a measure of uncertainty. Here we describe a likelihood ratio test which can be used to test if a sampled...... sequence is a member of an a priori specified species. We investigate the performance of the test using coalescence simulations, as well as using the real data from butterflies and frogs representing two kinds of challenge for DNA barcoding: extremely low and extremely high levels of sequence variability....

  20. Integrated testing strategies for toxicity employing new and existing technologies.

    Science.gov (United States)

    Combes, Robert D; Balls, Michael

    2011-07-01

    We have developed individual, integrated testing strategies (ITS) for predicting the toxicity of general chemicals, cosmetics, pharmaceuticals, inhaled chemicals, and nanoparticles. These ITS are based on published schemes developed previously for the risk assessment of chemicals to fulfil the requirements of REACH, which have been updated to take account of the latest developments in advanced in chemico modelling and in vitro technologies. In addition, we propose an ITS for neurotoxicity, based on the same principles, for incorporation in the other ITS. The technologies are deployed in a step-wise manner, as a basis for decision-tree approaches, incorporating weight-of-evidence stages. This means that testing can be stopped at the point where a risk assessment and/or classification can be performed, with labelling in accordance with the requirements of the regulatory authority concerned, rather than following a checklist approach to hazard identification. In addition, the strategies are intelligent, in that they are based on the fundamental premise that there is no hazard in the absence of exposure - which is why pharmacokinetic modelling plays a key role in each ITS. The new technologies include the use of complex, three-dimensional human cell tissue culture systems with in vivo-like structural, physiological and biochemical features, as well as dosing conditions. In this way, problems of inter-species extrapolation and in vitro/in vivo extrapolation are minimised. This is reflected in the ITS placing more emphasis on the use of volunteers at the whole organism testing stage, rather than on existing animal testing, which is the current situation. 2011 FRAME.

  1. Characterization of DNA repair phenotypes of Xeroderma pigmentosum cell lines by a paralleled in vitro test

    International Nuclear Information System (INIS)

    Raffin, A.L.

    2009-06-01

    DNA is constantly damaged modifying the genetic information for which it encodes. Several cellular mechanisms as the Base Excision Repair (BER) and the Nucleotide Excision Repair (NER) allow recovering the right DNA sequence. The Xeroderma pigmentosum is a disease characterised by a deficiency in the NER pathway. The aim of this study was to propose an efficient and fast test for the diagnosis of this disease as an alternative to the currently available UDS test. DNA repair activities of XP cell lines were quantified using in vitro miniaturized and paralleled tests in order to establish DNA repair phenotypes of XPA and XPC deficient cells. The main advantage of the tests used in this study is the simultaneous measurement of excision or excision synthesis (ES) of several lesions by only one cellular extract. We showed on one hand that the relative ES of the different lesions depend strongly on the protein concentration of the nuclear extract tested. Working at high protein concentration allowed discriminating the XP phenotype versus the control one, whereas it was impossible under a certain concentration's threshold. On the other hand, while the UVB irradiation of control cells stimulated their repair activities, this effect was not observed in XP cells. This study brings new information on the XPA and XPC protein roles during BER and NER and underlines the complexity of the regulations of DNA repair processes. (author)

  2. A test of the transcription model for biased inheritance of yeast mitochondrial DNA.

    Science.gov (United States)

    Lorimer, H E; Brewer, B J; Fangman, W L

    1995-09-01

    Two strand-specific origins of replication appear to be required for mammalian mitochondrial DNA (mtDNA) replication. Structural equivalents of these origins are found in the rep sequences of Saccharomyces cerevisiae mtDNA. These striking similarities have contributed to a universal model for the initiation of mtDNA replication in which a primer is created by cleavage of an origin region transcript. Consistent with this model are the properties of deletion mutants of yeast mtDNA ([rho-]) with a high density of reps (HS [rho-]). These mutant mtDNAs are preferentially inherited by the progeny resulting from the mating of HS [rho-] cells with cells containing wild-type mtDNA ([rho+]). This bias is presumed to result from a replication advantage conferred on HS [rho-] mtDNA by the high density of rep sequences acting as origins. To test whether transcription is indeed required for the preferential inheritance of HS [rho-] mtDNA, we deleted the nuclear gene (RPO41) for the mitochondrial RNA polymerase, reducing transcripts by at least 1000-fold. Since [rho-] genomes, but not [rho+] genomes, are stable when RPO41 is deleted, we examined matings between HS [rho-] and neutral [rho-] cells. Neutral [rho-] mtDNAs lack rep sequences and are not preferentially inherited in [rho-] x [rho+] crosses. In HS [rho-] x neutral [rho-] matings, the HS [rho-] mtDNA was preferentially inherited whether both parents were wild type or both were deleted for RPO41. Thus, transcription from the rep promoter does not appear to be necessary for biased inheritance. Our results, and analysis of the literature, suggest that priming by transcription is not a universal mechanism for mtDNA replication initiation.

  3. Clinico-laboratory aspects of anti-nuclear and anti-native DNA antibody tests.

    Science.gov (United States)

    Webb, J

    1978-01-01

    Available techniques for detection of anti-nuclear antibodies are here briefly reviewed. The relatively insensitive LE cell test has been largely supplanted by the indirect immunofluorescent ANA test which should be reported in terms of titre and pattern. Specific measurement of nDNA antibodies is now a regular technique in SLE diagnosis and management.

  4. Integrating non-animal test information into an adaptive testing strategy - skin sensitization proof of concept case.

    Science.gov (United States)

    Jaworska, Joanna; Harol, Artsiom; Kern, Petra S; Gerberick, G Frank

    2011-01-01

    There is an urgent need to develop data integration and testing strategy frameworks allowing interpretation of results from animal alternative test batteries. To this end, we developed a Bayesian Network Integrated Testing Strategy (BN ITS) with the goal to estimate skin sensitization hazard as a test case of previously developed concepts (Jaworska et al., 2010). The BN ITS combines in silico, in chemico, and in vitro data related to skin penetration, peptide reactivity, and dendritic cell activation, and guides testing strategy by Value of Information (VoI). The approach offers novel insights into testing strategies: there is no one best testing strategy, but the optimal sequence of tests depends on information at hand, and is chemical-specific. Thus, a single generic set of tests as a replacement strategy is unlikely to be most effective. BN ITS offers the possibility of evaluating the impact of generating additional data on the target information uncertainty reduction before testing is commenced.

  5. Comparison of DNA comet assay and germination test (half-embryo-test) in gamma-irradiated cherry seeds

    International Nuclear Information System (INIS)

    Todoroki, Setsuko; Hayashi, Toru

    2002-01-01

    Cherry fruits were irradiated with gamma-rays at doses up to 200Gy (effective dose for disinfestation of codling moth), and DNA strand break in seed embryos was investigated by using alkaline comet assay. Immediately after irradiation (≥100Gy), DNA from embryos produced comets with a long and wide tail due to fragmentation. In control cells, DNA relaxed and produced comet with very short tail (with few strand break). After 72h storage, DNA from fruits irradiated at 200 Gy showed comets with little tail and tail moment of comets was same as un-irradiated control. These results indicate that the strand breaks of DNA caused by irradiation in fresh seed embryo are repaired during storage. On the contrary, the ability of germination lost by irradiation did not restored, a dose of 100Gy and more retarded shoot elongation. In cherries irradiated at 100Gy, the shooting percentage was less than 50% at 4th day after incubation. Germination test (Half embryo test) can be discriminate between irradiated and un-irradiated cherries. (author)

  6. Label-free fluorescence strategy for sensitive detection of adenosine triphosphate using a loop DNA probe with low background noise.

    Science.gov (United States)

    Lin, Chunshui; Cai, Zhixiong; Wang, Yiru; Zhu, Zhi; Yang, Chaoyong James; Chen, Xi

    2014-07-15

    A simple, rapid, label-free, and ultrasensitive fluorescence strategy for adenosine triphosphate (ATP) detection was developed using a loop DNA probe with low background noise. In this strategy, a loop DNA probe, which is the substrate for both ligation and digestion enzyme reaction, was designed. SYBR green I (SG I), a double-stranded specific dye, was applied for the readout fluorescence signal. Exonuclease I (Exo I) and exonuclease III (Exo III), sequence-independent nucleases, were selected to digest the loop DNA probe in order to minimize the background fluorescence signal. As a result, in the absence of ATP, the loop DNA was completely digested by Exo I and Exo III, leading to low background fluorescence owing to the weak electrostatic interaction between SG I and mononucleotides. On the other hand, ATP induced the ligation of the nicking site, and the sealed loop DNA resisted the digestion of Exo I and ExoIII, resulting in a remarkable increase of fluorescence response. Upon background noise reduction, the sensitivity of the ATP determination was improved significantly, and the detection limitation was found to be 1.2 pM, which is much lower than that in almost all the previously reported methods. This strategy has promise for wide application in the determination of ATP.

  7. A pre-protective strategy for precise tumor targeting and efficient photodynamic therapy with a switchable DNA/upconversion nanocomposite.

    Science.gov (United States)

    Yu, Zhengze; Ge, Yegang; Sun, Qiaoqiao; Pan, Wei; Wan, Xiuyan; Li, Na; Tang, Bo

    2018-04-14

    Tumor-specific targeting based on folic acid (FA) is one of the most common and significant approaches in cancer therapy. However, the expression of folate receptors (FRs) in normal tissues will lead to unexpected targeting and unsatisfactory therapeutic effect. To address this issue, we develop a pre-protective strategy for precise tumor targeting and efficient photodynamic therapy (PDT) using a switchable DNA/upconversion nanocomposite, which can be triggered in the acidic tumor microenvironment. The DNA/upconversion nanocomposite is composed of polyacrylic acid (PAA) coated upconversion nanoparticles (UCNPs), the surface of which is modified using FA and chlorin e6 (Ce6) functionalized DNA sequences with different lengths. Initially, FA on the shorter DNA was protected by a longer DNA to prevent the bonding to FRs on normal cells. Once reaching the acidic tumor microenvironment, C base-rich longer DNA forms a C-quadruplex, resulting in the exposure of the FA groups and the bonding of FA and FRs on cancer cell membranes to achieve precise targeting. Simultaneously, the photosensitizer chlorin e6 (Ce6) gets close to the surface of UCNPs, enabling the excitation of Ce6 to generate singlet oxygen ( 1 O 2 ) under near infrared light via Förster resonance energy transfer (FRET). In vivo experiments indicated that higher tumor targeting efficiency was achieved and the tumor growth was greatly inhibited through the pre-protective strategy.

  8. Estrogen receptor testing and 10-year mortality from breast cancer: A model for determining testing strategy

    Directory of Open Access Journals (Sweden)

    Christopher Naugler

    2012-01-01

    Full Text Available Background: The use of adjuvant tamoxifen therapy in the treatment of estrogen receptor (ER expressing breast carcinomas represents a major advance in personalized cancer treatment. Because there is no benefit (and indeed there is increased morbidity and mortality associated with the use of tamoxifen therapy in ER-negative breast cancer, its use is restricted to women with ER expressing cancers. However, correctly classifying cancers as ER positive or negative has been challenging given the high reported false negative test rates for ER expression in surgical specimens. In this paper I model practice recommendations using published information from clinical trials to address the question of whether there is a false negative test rate above which it is more efficacious to forgo ER testing and instead treat all patients with tamoxifen regardless of ER test results. Methods: I used data from randomized clinical trials to model two different hypothetical treatment strategies: (1 the current strategy of treating only ER positive women with tamoxifen and (2 an alternative strategy where all women are treated with tamoxifen regardless of ER test results. The variables used in the model are literature-derived survival rates of the different combinations of ER positivity and treatment with tamoxifen, varying true ER positivity rates and varying false negative ER testing rates. The outcome variable was hypothetical 10-year survival. Results: The model predicted that there will be a range of true ER rates and false negative test rates above which it would be more efficacious to treat all women with breast cancer with tamoxifen and forgo ER testing. This situation occurred with high true positive ER rates and false negative ER test rates in the range of 20-30%. Conclusions: It is hoped that this model will provide an example of the potential importance of diagnostic error on clinical outcomes and furthermore will give an example of how the effect of that

  9. Stretching chimeric DNA: A test for the putative S-form

    Science.gov (United States)

    Whitelam, Stephen; Pronk, Sander; Geissler, Phillip L.

    2008-11-01

    Double-stranded DNA "overstretches" at a pulling force of about 65 pN, increasing in length by a factor of 1.7. The nature of the overstretched state is unknown, despite its considerable importance for DNA's biological function and technological application. Overstretching is thought by some to be a force-induced denaturation and by others to consist of a transition to an elongated, hybridized state called S-DNA. Within a statistical mechanical model, we consider the effect upon overstretching of extreme sequence heterogeneity. "Chimeric" sequences possessing halves of markedly different AT composition elongate under fixed external conditions via distinct, spatially segregated transitions. The corresponding force-extension data vary with pulling rate in a manner that depends qualitatively and strikingly upon whether the hybridized S-form is accessible. This observation implies a test for S-DNA that could be performed in experiment.

  10. Development of an efficient process intensification strategy for enhancing Pfu DNA polymerase production in recombinant Escherichia coli.

    Science.gov (United States)

    Hu, Jian-Hua; Wang, Feng; Liu, Chun-Zhao

    2015-04-01

    An efficient induction strategy that consisted of multiple additions of small doses of isopropyl-β-D-thiogalactopyranoside (IPTG) in the early cell growth phase was developed for enhancing Pfu DNA polymerase production in Escherichia coli. In comparison to the most commonly used method of a single induction of 1 mM IPTG, the promising induction strategy resulted in an increase in the Pfu activity of 13.5% in shake flasks, while simultaneously decreasing the dose of IPTG by nearly half. An analysis of the intracellular IPTG concentrations indicated that the cells need to maintain an optimum intracellular IPTG concentration after 6 h for efficient Pfu DNA polymerase production. A significant increase in the Pfu DNA polymerase activity of 31.5% under the controlled dissolved oxygen concentration of 30% in a 5 L fermentor was achieved using the multiple IPTG induction strategy in comparison with the single IPTG induction. The induction strategy using multiple inputs of IPTG also avoided over accumulation of IPTG and reduced the cost of Pfu DNA polymerase production.

  11. Controlled encoding strategies in memory tests in lithium patients.

    Science.gov (United States)

    Opgenoorth, E; Karlick-Bolten, E

    1986-03-01

    The "levels of processing" theory (Craik and Lockhart) and "dual coding" theory (Paivio) provide new aspects for clinical memory research work. Therefore, an incidental learning paradigm on the basis of these two theoretical approaches was chosen to test aspects of memory performances with lithium therapy. Results of two experiments, with controlled non-semantic processing (rating experiment "comparison of size") and additive semantic processing (rating "living--non-living") indicate a slight reduction in recall (Fig. 1) and recognition performance (Fig. 2) in lithium patients. Effects on encoding strategies are of equal quality in patients and healthy subjects (Tab. 1, 2) but performance differs between both groups: poorer systematic benefit from within code repetitions ("word-word" items, "picture-picture" items) and dual coding (repeated variable item presentation "picture-word") is obtained. The less efficient encoding strategies in the speeded task are discussed with respect to cognitive rigidity and slowing of performance by emotional states. This investigation of so-called "memory deficits" with lithium is an attempt to explore impairments at an early stage of processing; the characterization of the perceptual cognitive analysis seems useful for further clinical research work on this topic.

  12. Evaluation of different strategies for magnetic particle functionalization with DNA aptamers.

    Science.gov (United States)

    Pérez-Ruiz, Elena; Lammertyn, Jeroen; Spasic, Dragana

    2016-12-25

    The optimal bio-functionalization of magnetic particles is essential for developing magnetic particle-based bioassays. Whereas functionalization with antibodies is generally well established, immobilization of DNA probes, such as aptamers, is not yet fully explored. In this work, four different types of commercially available magnetic particles, coated with streptavidin, maleimide or carboxyl groups, were evaluated for their surface coverage with aptamer bioreceptors, efficiency in capturing target protein and non-specific protein adsorption on their surface. A recently developed aptamer against the peanut allergen, Ara h 1 protein, was used as a model system. Conjugation of biotinylated Ara h 1 aptamer to the streptavidin particles led to the highest surface coverage, whereas the coverage of maleimide particles was 25% lower. Carboxylated particles appeared to be inadequate for DNA functionalization. Streptavidin particles also showed the greatest target capturing efficiency, comparable to the one of particles functionalized with anti-Ara h 1 antibody. The performance of streptavidin particles was additionally tested in a sandwich assay with the aptamer as a capture receptor on the particle surface. While the limit of detection obtained was comparable to the same assay system with antibody as capture receptor, it was superior to previously reported values using the same aptamer in similar assay schemes with different detection platforms. These results point to the promising application of the Ara h 1 aptamer-functionalized particles in bioassay development. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Identifying insects with incomplete DNA barcode libraries, African fruit flies (Diptera: Tephritidae) as a test case.

    Science.gov (United States)

    Virgilio, Massimiliano; Jordaens, Kurt; Breman, Floris C; Backeljau, Thierry; De Meyer, Marc

    2012-01-01

    We propose a general working strategy to deal with incomplete reference libraries in the DNA barcoding identification of species. Considering that (1) queries with a large genetic distance with their best DNA barcode match are more likely to be misidentified and (2) imposing a distance threshold profitably reduces identification errors, we modelled relationships between identification performances and distance thresholds in four DNA barcode libraries of Diptera (n = 4270), Lepidoptera (n = 7577), Hymenoptera (n = 2067) and Tephritidae (n = 602 DNA barcodes). In all cases, more restrictive distance thresholds produced a gradual increase in the proportion of true negatives, a gradual decrease of false positives and more abrupt variations in the proportions of true positives and false negatives. More restrictive distance thresholds improved precision, yet negatively affected accuracy due to the higher proportions of queries discarded (viz. having a distance query-best match above the threshold). Using a simple linear regression we calculated an ad hoc distance threshold for the tephritid library producing an estimated relative identification error DNA barcodes and should be used as cut-off mark defining whether we can proceed identifying the query with a known estimated error probability (e.g. 5%) or whether we should discard the query and consider alternative/complementary identification methods.

  14. Hantavirus Gc induces long-term immune protection via LAMP-targeting DNA vaccine strategy.

    Science.gov (United States)

    Jiang, Dong-Bo; Zhang, Jin-Peng; Cheng, Lin-Feng; Zhang, Guan-Wen; Li, Yun; Li, Zi-Chao; Lu, Zhen-Hua; Zhang, Zi-Xin; Lu, Yu-Chen; Zheng, Lian-He; Zhang, Fang-Lin; Yang, Kun

    2018-02-01

    Hemorrhagic fever with renal syndrome (HFRS) occurs widely throughout Eurasia. Unfortunately, there is no effective treatment, and prophylaxis remains the best option against the major pathogenic agent, hantaan virus (HTNV), which is an Old World hantavirus. However, the absence of cellular immune responses and immunological memory hampers acceptance of the current inactivated HFRS vaccine. Previous studies revealed that a lysosome-associated membrane protein 1 (LAMP1)-targeting strategy involving a DNA vaccine based on the HTNV glycoprotein Gn successfully conferred long-term immunity, and indicated that further research on Gc, another HTNV antigen, was warranted. Plasmids encoding Gc and lysosome-targeted Gc, designated pVAX-Gc and pVAX-LAMP/Gc, respectively, were constructed. Proteins of interest were identified by fluorescence microscopy following cell line transfection. Five groups of 20 female BALB/c mice were subjected to the following inoculations: inactivated HTNV vaccine, pVAX-LAMP/Gc, pVAX-Gc, and, as the negative controls, pVAX-LAMP or the blank vector pVAX1. Humoral and cellular immunity were assessed by enzyme-linked immunosorbent assays (ELISAs) and 15-mer peptide enzyme-linked immunospot (ELISpot) epitope mapping assays. Repeated immunization with pVAX-LAMP/Gc enhanced adaptive immune responses, as demonstrated by the specific and neutralizing antibody titers and increased IFN-γ production. The inactivated vaccine induced a comparable humoral reaction, but the negative controls only elicited insignificant responses. Using a mouse model of HTNV challenge, the in vivo protection conferred by the inactivated vaccine and Gc-based constructs (with/without LAMP recombination) was confirmed. Evidence of pan-epitope reactions highlighted the long-term cellular response to the LAMP-targeting strategy, and histological observations indicated the safety of the LAMP-targeting vaccines. The long-term protective immune responses induced by pVAX-LAMP/Gc may be

  15. Efficacy Testing of H56 cDNA Tattoo Immunization against Tuberculosis in a Mouse Model.

    Science.gov (United States)

    Platteel, Anouk C M; Nieuwenhuizen, Natalie E; Domaszewska, Teresa; Schürer, Stefanie; Zedler, Ulrike; Brinkmann, Volker; Sijts, Alice J A M; Kaufmann, Stefan H E

    2017-01-01

    Tuberculosis (TB), caused by Mycobacterium tuberculosis ( Mtb ), remains a global threat. The only approved vaccine against TB, Mycobacterium bovis bacillus Calmette-Guérin (BCG), provides insufficient protection and, being a live vaccine, can cause disseminated disease in immunocompromised individuals. Previously, we found that intradermal cDNA tattoo immunization with cDNA of tetanus toxoid fragment C domain 1 fused to cDNA of the fusion protein H56, comprising the Mtb antigens Ag85B, ESAT-6, and Rv2660c, induced antigen-specific CD8 + T cell responses in vivo . As cDNA tattoo immunization would be safer than a live vaccine in immunocompromised patients, we tested the protective efficacy of intradermal tattoo immunization against TB with H56 cDNA, as well as with H56_E, a construct optimized for epitope processing in a mouse model. As Mtb antigens can be used in combination with BCG to boost immune responses, we also tested the protective efficacy of heterologous prime-boost, using dermal tattoo immunization with H56_E cDNA to boost BCG immunization in mice. Dermal H56 and H56_E cDNA immunization induced H56-specific CD4 + and CD8 + T cell responses and Ag85B-specific IgG antibodies, but did not reduce bacterial loads, although immunization with H56_E ameliorated lung pathology. Both subcutaneous and intradermal immunization with BCG resulted in broad cellular immune responses, with increased frequencies of CD4 + T effector memory cells, T follicular helper cells, and germinal center B cells, and resulted in reduced bacterial loads and lung pathology. Heterologous vaccination with BCG/H56_E cDNA induced increased H56-specific CD4 + and CD8 + T cell cytokine responses compared to vaccination with BCG alone, and lung pathology was significantly decreased in BCG/H56_E cDNA immunized mice compared to unvaccinated controls. However, bacterial loads were not decreased after heterologous vaccination compared to BCG alone. CD4 + T cells responding to Ag85B- and ESAT-6

  16. Detection of colorectal serrated polyps by stool DNA testing: comparison with fecal immunochemical testing for occult blood (FIT.

    Directory of Open Access Journals (Sweden)

    Russell I Heigh

    Full Text Available Precursors to 1/3 of colorectal cancer (CRC, serrated polyps have been under-detected by screening due to their inconspicuous, non-hemorrhagic, and proximal nature. A new multi-target stool DNA test (multi-target sDNA shows high sensitivity for both CRC and advanced adenomas. Screen detection of serrated polyps by this approach requires further validation. We sought to assess and compare noninvasive detection of sessile serrated polyps (SSP ≥ 1 cm by sDNA and an occult blood fecal immunochemical test (FIT.In a blinded prospective study, a single stool sample used for both tests was collected from 456 asymptomatic adults prior to screening or surveillance colonoscopy (criterion standard. All 29 patients with SSP ≥ 1 cm were included as cases and all 232 with no neoplastic findings as controls. Buffered stool samples were processed and frozen on receipt; Exact Sciences performed sDNA in batches using optimized analytical methods. The sDNA multi-marker panel targets methylated BMP3 (mBMP3 and NDRG4, mutant KRAS, β-actin, and hemoglobin. FIT (Polymedco OC-FIT Check was performed in separate lab ≤ 2 days post defecation and evaluated at cutoffs of 50 (FIT-50 and 100 ng/ml (FIT-100.MEDIAN AGES: cases 61 (range 57-77, controls 62 (52-70, p = NS. Women comprised 59% and 51%, p = NS, respectively. SSP median size was 1.2 cm (1-3 cm, 93% were proximal, and 64% had synchronous diminutive polyps. Among multi-target sDNA markers, mBMP3 proved highly discriminant for detection of SSP ≥ 1 cm (AUC = 0.87, p<0.00001; other DNA markers provided no incremental sensitivity. Hemoglobin alone showed no discrimination (AUC = 0.50, p = NS. At matched specificities, detection of SSP ≥ 1 cm by stool mBMP3 was significantly greater than by FIT-50 (66% vs 10%, p = 0.0003 or FIT-100 (63% vs 0%, p<0.0001.In a screening and surveillance setting, SSP ≥ 1 cm can be detected noninvasively by stool assay of exfoliated DNA markers, especially mBMP3. FIT appears to

  17. Shaping Vulnerable Bodies at the Thin Boundary between Environment and Organism: Skin, DNA Repair, and a Genealogy of DNA Care Strategies.

    Science.gov (United States)

    von Schwerin, Alexander

    2015-09-01

    This paper brings together the history of risk and the history of DNA repair, a biological phenomenon that emerged as a research field in between molecular biology, genetics, and radiation research in the 1960s. The case of xeroderma pigmentosum (XP), an inherited hypersensitivity to UV light and, hence, a disposition to skin cancer will be the starting point to argue that, in the 1970s and 1980s, DNA repair became entangled in the creation of new models of the human body at risk - what is here conceptually referred to as the vulnerability aspect of body history - and new attempts at cancer prevention and enhancement of the body associated with the new flourishing research areas of antimutagenesis and anticarcinogenesis. The aim will be to demonstrate that DNA repair created special attempts at disease prevention: molecular enhancement, seeking to identify means to increase the self-repair abilities of the body at the molecular level. Prevention in this sense meant enhancing the body's ability to cope with the environmental hazards of an already toxic world. This strategy has recently been adopted by the beauty industry, which introduced DNA care as a new target for skin care research and anti-aging formulas.

  18. Co-immunization with DNA and protein mixture: a safe and efficacious immunotherapeutic strategy for Alzheimer's disease in PDAPP mice.

    Science.gov (United States)

    Liu, Si; Shi, DanYang; Wang, Hai-Chao; Yu, Yun-Zhou; Xu, Qing; Sun, Zhi-Wei

    2015-01-14

    Active immunotherapy targeting β-amyloid (Aβ) is the most promising strategy to prevent or treat Alzheimer's disease (AD). Based on pre-clinical studies and clinical trials, a safe and effective AD vaccine requires a delicate balance between providing therapeutically adequate anti-Aβ antibodies and eliminating or suppressing unwanted adverse T cell-mediated inflammatory reactions. We describe here the immunological characterization and protective efficacy of co-immunization with a 6Aβ15-T DNA and protein mixture without adjuvant as an AD immunotherapeutic strategy. Impressively, this co-immunization induced robust Th2-polarized Aβ-specific antibodies while simultaneously suppressed unwanted inflammatory T cell reactions and avoiding Aβ42-specific T cell-mediated autoimmune responses in immunized mice. Co-immunization with the DNA + protein vaccine could overcome Aβ42-associated hypo-responsiveness and elicit long-term Aβ-specific antibody responses, which helped to maintain antibody-mediated clearance of amyloid and accordingly alleviated AD symptoms in co-immunized PDAPP mice. Our DNA and protein combined vaccine, which could induce an anti-inflammatory Th2 immune response with high level Aβ-specific antibodies and low level IFN-γ production, also demonstrated the capacity to inhibit amyloid accumulation and prevent cognitive dysfunction. Hence, co-immunization with antigen-matched DNA and protein may represent a novel and efficacious strategy for AD immunotherapy to eliminate T cell inflammatory reactions while retaining high level antibody responses.

  19. Integrating prior knowledge in multiple testing under dependence with applications to detecting differential DNA methylation.

    Science.gov (United States)

    Kuan, Pei Fen; Chiang, Derek Y

    2012-09-01

    DNA methylation has emerged as an important hallmark of epigenetics. Numerous platforms including tiling arrays and next generation sequencing, and experimental protocols are available for profiling DNA methylation. Similar to other tiling array data, DNA methylation data shares the characteristics of inherent correlation structure among nearby probes. However, unlike gene expression or protein DNA binding data, the varying CpG density which gives rise to CpG island, shore and shelf definition provides exogenous information in detecting differential methylation. This article aims to introduce a robust testing and probe ranking procedure based on a nonhomogeneous hidden Markov model that incorporates the above-mentioned features for detecting differential methylation. We revisit the seminal work of Sun and Cai (2009, Journal of the Royal Statistical Society: Series B (Statistical Methodology)71, 393-424) and propose modeling the nonnull using a nonparametric symmetric distribution in two-sided hypothesis testing. We show that this model improves probe ranking and is robust to model misspecification based on extensive simulation studies. We further illustrate that our proposed framework achieves good operating characteristics as compared to commonly used methods in real DNA methylation data that aims to detect differential methylation sites. © 2012, The International Biometric Society.

  20. Comparative evaluation of Amplicor HIV-1 DNA test, version 1.5, by ...

    African Journals Online (AJOL)

    Human immunodeficiency virus (HIV) DNA polymerase chain reaction (PCR) test using venous blood sample has been used for many years in low resource settings for early infant diagnosis of HIV infection in children less than 18 months. The aim of this study was to evaluate and compare the performance characteristics of ...

  1. Testing of Strategies for the Acceleration of the Cost Optimization

    Energy Technology Data Exchange (ETDEWEB)

    Ponciroli, Roberto [Argonne National Lab. (ANL), Argonne, IL (United States); Vilim, Richard B. [Argonne National Lab. (ANL), Argonne, IL (United States)

    2017-08-31

    one. The component physical dynamics are represented through suitable ramp constraints, which considerably simplify the numerical solving. In order to test the capabilities of the proposed approach, in the present report, the dispatch problem only is tackled, i.e. a reference unit configuration is assumed, and each one of the N-R HES unit components is assumed to have a fixed installed capacity. As for the next steps, the main improvement will concern the operation strategy of the ES facility. In particular, in order to describe a more realistic battery commitment strategy, the ES operation will be regulated according to the electricity price forecasts.

  2. A linear concatenation strategy to construct 5'-enriched amplified cDNA libraries using multiple displacement amplification.

    Science.gov (United States)

    Gadkar, Vijay J; Filion, Martin

    2013-06-01

    In various experimental systems, limiting available amounts of RNA may prevent a researcher from performing large-scale analyses of gene transcripts. One way to circumvent this is to 'pre-amplify' the starting RNA/cDNA, so that sufficient amounts are available for any downstream analysis. In the present study, we report the development of a novel protocol for constructing amplified cDNA libraries using the Phi29 DNA polymerase based multiple displacement amplification (MDA) system. Using as little as 200 ng of total RNA, we developed a linear concatenation strategy to make the single-stranded cDNA template amenable for MDA. The concatenation, made possible by the template switching property of the reverse transcriptase enzyme, resulted in the amplified cDNA library with intact 5' ends. MDA generated micrograms of template, allowing large-scale polymerase chain reaction analyses or other large-scale downstream applications. As the amplified cDNA library contains intact 5' ends, it is also compatible with 5' RACE analyses of specific gene transcripts. Empirical validation of this protocol is demonstrated on a highly characterized (tomato) and an uncharacterized (corn gromwell) experimental system.

  3. Pitfalls of establishing DNA barcoding systems in protists: the cryptophyceae as a test case.

    Science.gov (United States)

    Hoef-Emden, Kerstin

    2012-01-01

    A DNA barcode is a preferrably short and highly variable region of DNA supposed to facilitate a rapid identification of species. In many protistan lineages, a lack of species-specific morphological characters hampers an identification of species by light or electron microscopy, and difficulties to perform mating experiments in laboratory cultures also do not allow for an identification of biological species. Thus, testing candidate barcode markers as well as establishment of accurately working species identification systems are more challenging than in multicellular organisms. In cryptic species complexes the performance of a potential barcode marker can not be monitored using morphological characters as a feedback, but an inappropriate choice of DNA region may result in artifactual species trees for several reasons. Therefore a priori knowledge of the systematics of a group is required. In addition to identification of known species, methods for an automatic delimitation of species with DNA barcodes have been proposed. The Cryptophyceae provide a mixture of systematically well characterized as well as badly characterized groups and are used in this study to test the suitability of some of the methods for protists. As species identification method the performance of blast in searches against badly to well-sampled reference databases has been tested with COI-5P and 5'-partial LSU rDNA (domains A to D of the nuclear LSU rRNA gene). In addition the performance of two different methods for automatic species delimitation, fixed thresholds of genetic divergence and the general mixed Yule-coalescent model (GMYC), have been examined. The study demonstrates some pitfalls of barcoding methods that have to be taken care of. Also a best-practice approach towards establishing a DNA barcode system in protists is proposed.

  4. Pitfalls of establishing DNA barcoding systems in protists: the cryptophyceae as a test case.

    Directory of Open Access Journals (Sweden)

    Kerstin Hoef-Emden

    Full Text Available A DNA barcode is a preferrably short and highly variable region of DNA supposed to facilitate a rapid identification of species. In many protistan lineages, a lack of species-specific morphological characters hampers an identification of species by light or electron microscopy, and difficulties to perform mating experiments in laboratory cultures also do not allow for an identification of biological species. Thus, testing candidate barcode markers as well as establishment of accurately working species identification systems are more challenging than in multicellular organisms. In cryptic species complexes the performance of a potential barcode marker can not be monitored using morphological characters as a feedback, but an inappropriate choice of DNA region may result in artifactual species trees for several reasons. Therefore a priori knowledge of the systematics of a group is required. In addition to identification of known species, methods for an automatic delimitation of species with DNA barcodes have been proposed. The Cryptophyceae provide a mixture of systematically well characterized as well as badly characterized groups and are used in this study to test the suitability of some of the methods for protists. As species identification method the performance of blast in searches against badly to well-sampled reference databases has been tested with COI-5P and 5'-partial LSU rDNA (domains A to D of the nuclear LSU rRNA gene. In addition the performance of two different methods for automatic species delimitation, fixed thresholds of genetic divergence and the general mixed Yule-coalescent model (GMYC, have been examined. The study demonstrates some pitfalls of barcoding methods that have to be taken care of. Also a best-practice approach towards establishing a DNA barcode system in protists is proposed.

  5. Pitfalls of Establishing DNA Barcoding Systems in Protists: The Cryptophyceae as a Test Case

    Science.gov (United States)

    Hoef-Emden, Kerstin

    2012-01-01

    A DNA barcode is a preferrably short and highly variable region of DNA supposed to facilitate a rapid identification of species. In many protistan lineages, a lack of species-specific morphological characters hampers an identification of species by light or electron microscopy, and difficulties to perform mating experiments in laboratory cultures also do not allow for an identification of biological species. Thus, testing candidate barcode markers as well as establishment of accurately working species identification systems are more challenging than in multicellular organisms. In cryptic species complexes the performance of a potential barcode marker can not be monitored using morphological characters as a feedback, but an inappropriate choice of DNA region may result in artifactual species trees for several reasons. Therefore a priori knowledge of the systematics of a group is required. In addition to identification of known species, methods for an automatic delimitation of species with DNA barcodes have been proposed. The Cryptophyceae provide a mixture of systematically well characterized as well as badly characterized groups and are used in this study to test the suitability of some of the methods for protists. As species identification method the performance of blast in searches against badly to well-sampled reference databases has been tested with COI-5P and 5′-partial LSU rDNA (domains A to D of the nuclear LSU rRNA gene). In addition the performance of two different methods for automatic species delimitation, fixed thresholds of genetic divergence and the general mixed Yule-coalescent model (GMYC), have been examined. The study demonstrates some pitfalls of barcoding methods that have to be taken care of. Also a best-practice approach towards establishing a DNA barcode system in protists is proposed. PMID:22970104

  6. Internal Light Source-Driven Photoelectrochemical 3D-rGO/Cellulose Device Based on Cascade DNA Amplification Strategy Integrating Target Analog Chain and DNA Mimic Enzyme.

    Science.gov (United States)

    Lan, Feifei; Liang, Linlin; Zhang, Yan; Li, Li; Ren, Na; Yan, Mei; Ge, Shenguang; Yu, Jinghua

    2017-11-01

    In this work, a chemiluminescence-driven collapsible greeting card-like photoelectrochemical lab-on-paper device (GPECD) with hollow channel was demonstrated, in which target-triggering cascade DNA amplification strategy was ingeniously introduced. The GPECD had the functions of reagents storage and signal collection, and the change of configuration could control fluidic path, reaction time and alterations in electrical connectivity. In addition, three-dimentional reduced graphene oxide affixed Au flower was in situ grown on paper cellulose fiber for achieving excellent conductivity and biocompatibility. The cascade DNA amplification strategy referred to the cyclic formation of target analog chain and its trigger action to hybridization chain reaction (HCR), leading to the formation of numerous hemin/G-quadruplex DNA mimic enzyme with the presence of hemin. Subjected to the catalysis of hemin/G-quadruplex, the strong chemiluminiscence of luminol-H 2 O 2 system was obtained, which then was used as internal light source to excite photoactive materials realizing the simplification of instrument. In this analyzing process, thrombin served as proof-of-concept, and the concentration of target was converted into the DNA signal output by the specific recognition of aptamer-protein and target analog chain recycling. The target analog chain was produced in quantity with the presence of target, which further triggered abundant HCR and introduced hemin/G-quadruplex into the system. The photocurrent signal was obtained after the nitrogen-doped carbon dots sensitized ZnO was stimulated by chemiluminescence. The proposed GPECD exhibited excellent specificity and sensitivity toward thrombin with a detection limit of 16.7 fM. This judiciously engineered GPECD paved a luciferous way for detecting other protein with trace amounts in bioanalysis and clinical biomedicine.

  7. Quantification of Plasmodiophora brassicae Using a DNA-Based Soil Test Facilitates Sustainable Oilseed Rape Production.

    Science.gov (United States)

    Wallenhammar, Ann-Charlotte; Gunnarson, Albin; Hansson, Fredrik; Jonsson, Anders

    2016-04-22

    Outbreaks of clubroot disease caused by the soil-borne obligate parasite Plasmodiophora brassicae are common in oilseed rape (OSR) in Sweden. A DNA-based soil testing service that identifies fields where P. brassicae poses a significant risk of clubroot infection is now commercially available. It was applied here in field surveys to monitor the prevalence of P. brassicae DNA in field soils intended for winter OSR production and winter OSR field experiments. In 2013 in Scania, prior to planting, P. brassicae DNA was detected in 60% of 45 fields on 10 of 18 farms. In 2014, P. brassicae DNA was detected in 44% of 59 fields in 14 of 36 farms, in the main winter OSR producing region in southern Sweden. P. brassicae was present indicative of a risk for >10% yield loss with susceptible cultivars (>1300 DNA copies g soil(-1)) in 47% and 44% of fields in 2013 and 2014 respectively. Furthermore, P. brassicae DNA was indicative of sites at risk of complete crop failure if susceptible cultivars were grown (>50 000 copies g(-1) soil) in 14% and 8% of fields in 2013 and 2014, respectively. A survey of all fields at Lanna research station in western Sweden showed that P. brassicae was spread throughout the farm, as only three of the fields (20%) showed infection levels below the detection limit for P.brassicae DNA, while the level was >50,000 DNA copies g(-1) soil in 20% of the fields. Soil-borne spread is of critical importance and soil scraped off footwear showed levels of up to 682 million spores g(-1) soil. Soil testing is an important tool for determining the presence of P. brassicae and providing an indication of potential yield loss, e.g., in advisory work on planning for a sustainable OSR crop rotation. This soil test is gaining acceptance as a tool that increases the likelihood of success in precision agriculture and in applied research conducted in commercial oilseed fields and at research stations. The present application highlights the importance of prevention of

  8. Quantification of Plasmodiophora brassicae Using a DNA-Based Soil Test Facilitates Sustainable Oilseed Rape Production

    Directory of Open Access Journals (Sweden)

    Ann-Charlotte Wallenhammar

    2016-04-01

    Full Text Available Outbreaks of clubroot disease caused by the soil-borne obligate parasite Plasmodiophora brassicae are common in oilseed rape (OSR in Sweden. A DNA-based soil testing service that identifies fields where P. brassicae poses a significant risk of clubroot infection is now commercially available. It was applied here in field surveys to monitor the prevalence of P. brassicae DNA in field soils intended for winter OSR production and winter OSR field experiments. In 2013 in Scania, prior to planting, P. brassicae DNA was detected in 60% of 45 fields on 10 of 18 farms. In 2014, P. brassicae DNA was detected in 44% of 59 fields in 14 of 36 farms, in the main winter OSR producing region in southern Sweden. P. brassicae was present indicative of a risk for >10% yield loss with susceptible cultivars (>1300 DNA copies g soil−1 in 47% and 44% of fields in 2013 and 2014 respectively. Furthermore, P. brassicae DNA was indicative of sites at risk of complete crop failure if susceptible cultivars were grown (>50 000 copies g−1 soil in 14% and 8% of fields in 2013 and 2014, respectively. A survey of all fields at Lanna research station in western Sweden showed that P. brassicae was spread throughout the farm, as only three of the fields (20% showed infection levels below the detection limit for P.brassicae DNA, while the level was >50,000 DNA copies g−1 soil in 20% of the fields. Soil-borne spread is of critical importance and soil scraped off footwear showed levels of up to 682 million spores g−1 soil. Soil testing is an important tool for determining the presence of P. brassicae and providing an indication of potential yield loss, e.g., in advisory work on planning for a sustainable OSR crop rotation. This soil test is gaining acceptance as a tool that increases the likelihood of success in precision agriculture and in applied research conducted in commercial oilseed fields and at research stations. The present application highlights the importance of

  9. DNA vaccination protects mice against Zika virus-induced damage to the testes

    Science.gov (United States)

    Griffin, Bryan D.; Muthumani, Kar; Warner, Bryce M.; Majer, Anna; Hagan, Mable; Audet, Jonathan; Stein, Derek R.; Ranadheera, Charlene; Racine, Trina; De La Vega, Marc-Antoine; Piret, Jocelyne; Kucas, Stephanie; Tran, Kaylie N.; Frost, Kathy L.; De Graff, Christine; Soule, Geoff; Scharikow, Leanne; Scott, Jennifer; McTavish, Gordon; Smid, Valerie; Park, Young K.; Maslow, Joel N.; Sardesai, Niranjan Y.; Kim, J. Joseph; Yao, Xiao-jian; Bello, Alexander; Lindsay, Robbin; Boivin, Guy; Booth, Stephanie A.; Kobasa, Darwyn; Embury-Hyatt, Carissa; Safronetz, David; Weiner, David B.; Kobinger, Gary P.

    2017-01-01

    Zika virus (ZIKV) is an emerging pathogen causally associated with serious sequelae in fetuses, inducing fetal microcephaly and other neurodevelopment defects. ZIKV is primarily transmitted by mosquitoes, but can persist in human semen and sperm, and sexual transmission has been documented. Moreover, exposure of type-I interferon knockout mice to ZIKV results in severe damage to the testes, epididymis and sperm. Candidate ZIKV vaccines have shown protective efficacy in preclinical studies carried out in animal models, and several vaccines have entered clinical trials. Here, we report that administration of a synthetic DNA vaccine encoding ZIKV pre-membrane and envelope (prME) completely protects mice against ZIKV-associated damage to the testes and sperm and prevents viral persistence in the testes following challenge with a contemporary strain of ZIKV. These data suggest that DNA vaccination merits further investigation as a potential means to reduce ZIKV persistence in the male reproductive tract. PMID:28589934

  10. Price leadership strategy or branding strategy:an empirical test of indigenous Chinese exporters

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The effects of price leadership strategies and branding strategies on the export performance of indigenous Chinese exporters with a focus on developing country markets and developed country markets are examined based on the principles of strategy-environment co-alignment and marketing segmentation theory. Findings suggest that when focusing on developing country markets, the use of a branding strategy is more likely to enhance export performance. When focusing on developed country markets, neither the use o...

  11. Ultrasensitive electrochemical sensing platform based on graphene wrapping SnO2 nanocorals and autonomous cascade DNA duplication strategy.

    Science.gov (United States)

    Chen, Ying-Xu; Huang, Ke-Jing; Lin, Feng; Fang, Lin-Xia

    2017-12-01

    In this work, a sensitive, universal and reusable electrochemical biosensor based on stannic oxide nanocorals-graphene hybrids (SnO 2 NCs-Gr) is developed for target DNA detection by using two kinds of DNA enzymes for signal amplification through an autonomous cascade DNA duplication strategy. A hairpin probe is designed composing of a projecting part at the 3'-end as identification sequence for target, a recognition site for nicking endonuclease, and an 18-carbon shim to stop polymerization process. The designed DNA duplication-incision-replacement process is handled by KF polymerase and endonuclease, then combining with gold nanoparticles as signal carrier for further signal amplification. In the detection system, the electrochemical-chemical-chemical procedure, which uses ferrocene methanol, tris(2-carboxyethyl)phosphine and l-ascorbic acid 2-phosphate as oxidoreduction neurogen, deoxidizer and zymolyte, separately, is applied to amplify detection signal. Benefiting from the multiple signal amplification mechanism, the proposed sensor reveals a good linear connection between the peak current and logarithm of analyte concentration in range of 0.0001-1 × 10 -11 molL -1 with a detection limit of 1.25 × 10 -17 molL -1 (S/N=3). This assay also opens one promising strategy for ultrasensitive determination of other biological molecules for bioanalysis and biomedicine diagnostics. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Forensic individual age estimation with DNA: From initial approaches to methylation tests.

    Science.gov (United States)

    Freire-Aradas, A; Phillips, C; Lareu, M V

    2017-07-01

    Individual age estimation is a key factor in forensic science analysis that can provide very useful information applicable to criminal, legal, and anthropological investigations. Forensic age inference was initially based on morphological inspection or radiography and only later began to adopt molecular approaches. However, a lack of accuracy or technical problems hampered the introduction of these DNA-based methodologies in casework analysis. A turning point occurred when the epigenetic signature of DNA methylation was observed to gradually change during an individual´s lifespan. In the last four years, the number of publications reporting DNA methylation age-correlated changes has gradually risen and the forensic community now has a range of age methylation tests applicable to forensic casework. Most forensic age predictor models have been developed based on blood DNA samples, but additional tissues are now also being explored. This review assesses the most widely adopted genes harboring methylation sites, detection technologies, statistical age-predictive analyses, and potential causes of variation in age estimates. Despite the need for further work to improve predictive accuracy and establishing a broader range of tissues for which tests can analyze the most appropriate methylation sites, several forensic age predictors have now been reported that provide consistency in their prediction accuracies (predictive error of ±4 years); this makes them compelling tools with the potential to contribute key information to help guide criminal investigations. Copyright © 2017 Central Police University.

  13. A prime/boost strategy using DNA/fowlpox recombinants expressing the genetically attenuated E6 protein as a putative vaccine against HPV-16-associated cancers.

    Science.gov (United States)

    Bissa, Massimiliano; Illiano, Elena; Pacchioni, Sole; Paolini, Francesca; Zanotto, Carlo; De Giuli Morghen, Carlo; Massa, Silvia; Franconi, Rosella; Radaelli, Antonia; Venuti, Aldo

    2015-03-05

    Considering the high number of new cases of cervical cancer each year that are caused by human papilloma viruses (HPVs), the development of an effective vaccine for prevention and therapy of HPV-associated cancers, and in particular against the high-risk HPV-16 genotype, remains a priority. Vaccines expressing the E6 and E7 proteins that are detectable in all HPV-positive pre-cancerous and cancer cells might support the treatment of HPV-related lesions and clear already established tumors. In this study, DNA and fowlpox virus recombinants expressing the E6F47R mutant of the HPV-16 E6 oncoprotein were generated, and their correct expression verified by RT-PCR, Western blotting and immunofluorescence. Immunization protocols were tested in a preventive or therapeutic pre-clinical mouse model of HPV-16 tumorigenicity using heterologous (DNA/FP) or homologous (DNA/DNA and FP/FP) prime/boost regimens. The immune responses and therapeutic efficacy were evaluated by ELISA, ELISPOT assays, and challenge with TC-1* cells. In the preventive protocol, while an anti-E6-specific humoral response was just detectable, a specific CD8(+) cytotoxic T-cell response was elicited in immunized mice. After the challenge, there was a delay in cancer appearance and a significant reduction of tumor volume in the two groups of E6-immunized mice, thus confirming the pivotal role of the CD8(+) T-cell response in the control of tumor growth in the absence of E6-specific antibodies. In the therapeutic protocol, in-vivo experiments resulted in a higher number of tumor-free mice after the homologous DNA/DNA or heterologous DNA/FP immunization. These data establish a preliminary indication for the prevention and treatment of HPV-related tumors by the use of DNA and avipox constructs as safe and effective immunogens following a prime/boost strategy. The combined use of recombinants expressing both E6 and E7 proteins might improve the antitumor efficacy, and should represent an important approach to

  14. Comparison of potential protection conferred by three immunization strategies (protein/protein, DNA/DNA, and DNA/protein) against Brucella infection using Omp2b in BALB/c Mice.

    Science.gov (United States)

    Golshani, Maryam; Rafati, Sima; Nejati-Moheimani, Mehdi; Ghasemian, Melina; Bouzari, Saeid

    2016-12-25

    In the present study, immunogenicity and protective efficacy of the Brucella outer membrane protein 2b (Omp2b) was evaluated in BALB/c mice using Protein/Protein, DNA/DNA and DNA/Protein vaccine strategies. Immunization of mice with three vaccine regimens elicited a strong specific IgG response (higher IgG2a titers over IgG1 titers) and provided Th1-oriented immune response. Vaccination of BALB/c mice with the DNA/Pro regimen induced higher levels of IFN-γ/IL-2 and conferred more protection levels against B. melitenisis and B. abortus challenge than did the protein or DNA alone. In conclusion, Omp2b is able to stimulate specific immune responses and to confer cross protection against B. melitensis and B. abortus infection. Therefore, it could be introduced as a new potential candidate for the development of a subunit vaccine against Brucella infection. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. State of the art in non-animal approaches for skin sensitization testing: from individual test methods towards testing strategies.

    Science.gov (United States)

    Ezendam, Janine; Braakhuis, Hedwig M; Vandebriel, Rob J

    2016-12-01

    The hazard assessment of skin sensitizers relies mainly on animal testing, but much progress is made in the development, validation and regulatory acceptance and implementation of non-animal predictive approaches. In this review, we provide an update on the available computational tools and animal-free test methods for the prediction of skin sensitization hazard. These individual test methods address mostly one mechanistic step of the process of skin sensitization induction. The adverse outcome pathway (AOP) for skin sensitization describes the key events (KEs) that lead to skin sensitization. In our review, we have clustered the available test methods according to the KE they inform: the molecular initiating event (MIE/KE1)-protein binding, KE2-keratinocyte activation, KE3-dendritic cell activation and KE4-T cell activation and proliferation. In recent years, most progress has been made in the development and validation of in vitro assays that address KE2 and KE3. No standardized in vitro assays for T cell activation are available; thus, KE4 cannot be measured in vitro. Three non-animal test methods, addressing either the MIE, KE2 or KE3, are accepted as OECD test guidelines, and this has accelerated the development of integrated or defined approaches for testing and assessment (e.g. testing strategies). The majority of these approaches are mechanism-based, since they combine results from multiple test methods and/or computational tools that address different KEs of the AOP to estimate skin sensitization potential and sometimes potency. Other approaches are based on statistical tools. Until now, eleven different testing strategies have been published, the majority using the same individual information sources. Our review shows that some of the defined approaches to testing and assessment are able to accurately predict skin sensitization hazard, sometimes even more accurate than the currently used animal test. A few defined approaches are developed to provide an

  16. Validation of a sensitive DNA walking strategy to characterise unauthorised GMOs using model food matrices mimicking common rice products.

    Science.gov (United States)

    Fraiture, Marie-Alice; Herman, Philippe; Taverniers, Isabel; De Loose, Marc; Van Nieuwerburgh, Filip; Deforce, Dieter; Roosens, Nancy H

    2015-04-15

    To identify unauthorised GMOs in food and feed matrices, an integrated approach has recently been developed targeting pCAMBIA family vectors, highly present in transgenic plants. Their presence is first assessed by qPCR screening and is subsequently confirmed by characterising the transgene flanking regions, using DNA walking. Here, the DNA walking performance has been thoroughly tested for the first time, regarding the targeted DNA quality and quantity. Several assays, on model food matrices mimicking common rice products, have allowed to determine the limit of detection as well as the potential effects of food mixture and processing. This detection system allows the identification of transgenic insertions as low as 10 HGEs and was not affected by the presence of untargeted DNA. Moreover, despite the clear impact of food processing on DNA quality, this method was able to cope with degraded DNA. Given its specificity, sensitivity, reliability, applicability and practicability, the proposed approach is a key detection tool, easily implementable in enforcement laboratories. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  17. Determination of antinucleic factors and anti-DNA antibodies with immunefluorescence, radioimmunoassay and latex-test

    International Nuclear Information System (INIS)

    Lemmel, E.M.; Hoffmann, R.; Botzenhardt, U.; Mainz Univ.

    1976-01-01

    The results obtained with the 3 test methods are not completely equal. This is, on the one hand, based on the fact that at least in the fluorescence test other antibodies than in the DNS-compound test are also detected. Quantitatively, however, the two tests show a good correlation to the progress of the illness; strong positive DNA-compound is practically only found in SLE. The authors were able to prove that the addition of purified C1 or C1q components of the complementary system to the test can result in a DNA binding of over 50% and, consequently, in incorrect positive values in the compound test. The Latex test is less suitable for diagnosis and course observation since it relatively often renders negative results at established cases of SLE with distinct illness activity on the one hand, while on the other hand, quantitative evidence, which is desirable for assessing the illness activity, is not possible. (orig./GSE) [de

  18. Work Strategies: The Development and Testing of a Model.

    Science.gov (United States)

    1986-03-01

    strategies (e.g., Craik & Lockhart , 1972); hemispheric process - -7 ing differences (e.g., Seamon & Gazzaniga, 1973); problem-solving strategies (e.g...Charness, N. (1931). Aging and skilled problem solving. 3ournal of Experimental Psychology: General, 110, 21-38. Craik , F. I. \\., & Lockhart , R. S...1972). Levels of processing : A framework for memory research. Journal of Verbal Learning and Verbal Behavior, L1, 671-684. 3ansereau, D. F., McDonald

  19. Quantitative strategies to determine cisplatin adducts with DNA nucleotides in drosofila larvae and tumoral cell cultures

    International Nuclear Information System (INIS)

    Garcia Sar, D.; Montes-Bayon, M.; Hann, S.; Koellensperger, G.; Blanco-Gonzalez, E.; Sanz-Medel, A.

    2009-01-01

    Full text: The antitumoral effect of cisplatin [cis-diamminodichloroplatinum(II)] in mammals is related to its binding to DNA components. A novel sensitive and selective method is proposed to quantify cisplatin-DNA adducts induced in vivo in somatic cells of Drosophila melanogaster at biologically relevant concentrations. The method uses HPLC-ICPMS in combination with species-specific isotope dilution analysis (cisplatin enriched in 194 Pt). For the first time, a cisplatin-DNA adduct is quantified by this approach. The obtained results show the great potential of this system to advance our molecular understanding of the biological effects of cisplatin. (author)

  20. Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing.

    Directory of Open Access Journals (Sweden)

    Alexander William Eastman

    2015-01-01

    Full Text Available Advances in sequencing technology have drastically increased the depth and feasibility of bacterial genome sequencing. However, little information is available that details the specific techniques and procedures employed during genome sequencing despite the large numbers of published genomes. Shotgun approaches employed by second-generation sequencing platforms has necessitated the development of robust bioinformatics tools for in silico assembly, and complete assembly is limited by the presence of repetitive DNA sequences and multi-copy operons. Typically, re-sequencing with multiple platforms and laborious, targeted Sanger sequencing are employed to finish a draft bacterial genome. Here we describe a novel strategy based on the identification and targeted sequencing of repetitive rDNA operons to expedite bacterial genome assembly and finishing. Our strategy was validated by finishing the genome of Paenibacillus polymyxa strain CR1, a bacterium with potential in sustainable agriculture and bio-based processes. An analysis of the 38 contigs contained in the P. polymyxa strain CR1 draft genome revealed 12 repetitive rDNA operons with varied intragenic and flanking regions of variable length, unanimously located at contig boundaries and within contig gaps. These highly similar but not identical rDNA operons were experimentally verified and sequenced simultaneously with multiple, specially designed primer sets. This approach also identified and corrected significant sequence rearrangement generated during the initial in silico assembly of sequencing reads. Our approach reduces the required effort associated with blind primer walking for contig assembly, increasing both the speed and feasibility of genome finishing. Our study further reinforces the notion that repetitive DNA elements are major limiting factors for genome finishing. Moreover, we provided a step-by-step workflow for genome finishing, which may guide future bacterial genome finishing

  1. A versatile and highly sensitive homogeneous electrochemical strategy based on the split aptamer binding-induced DNA three-way junction and exonuclease III-assisted target recycling.

    Science.gov (United States)

    Hou, Ting; Li, Wei; Zhang, Lianfang; Li, Feng

    2015-08-21

    Herein, a highly sensitive and versatile homogeneous electrochemical biosensing strategy is proposed, based on the split aptamer-incorporated DNA three-way junction and the exonuclease (Exo) III-assisted target recycling. The aptamer of adenosine triphosphate (ATP, chosen as the model analyte) is split into two fragments and embedded in single-stranded DNA1 and DNA2, respectively. ATP specifically binds with the split aptamers, bringing DNA1 and DNA2 close to each other, thus inducing the DNA three-way junction formation through the partial hybridization among DNA1, DNA2 and the methylene blue-labelled MB-DNA. Subsequently, MB-DNA is specifically digested by Exo III, releasing a MB-labelled mononucleotide, as well as a DNA1-ATP-DNA2 complex, which acts as the recycled target and hybridizes with another intact MB-DNA to initiate the subsequent cycling cleavage process. As a result, large amounts of MB-labelled mononucleotides are released, generating a significantly amplified electrochemical signal toward the ATP assay. To the best of our knowledge, it is the first example to successfully incorporate split aptamers into DNA three-way junctions and to be adopted in a homogeneous electrochemical assay. In addition to high sensitivity, this strategy also exhibits the advantages of simplicity and convenience, because it is carried out in a homogeneous solution, and sophisticated electrode modification processes are avoided. By simply changing the sequences of the split aptamer fragments, this versatile strategy can be easily adopted to assay a large spectrum of targets. Due to its advantages of high sensitivity, excellent selectivity, versatility and simple operation, the as-proposed approach has great potential to be applied in biochemical research and clinical practices.

  2. DnaSAM: Software to perform neutrality testing for large datasets with complex null models.

    Science.gov (United States)

    Eckert, Andrew J; Liechty, John D; Tearse, Brandon R; Pande, Barnaly; Neale, David B

    2010-05-01

    Patterns of DNA sequence polymorphisms can be used to understand the processes of demography and adaptation within natural populations. High-throughput generation of DNA sequence data has historically been the bottleneck with respect to data processing and experimental inference. Advances in marker technologies have largely solved this problem. Currently, the limiting step is computational, with most molecular population genetic software allowing a gene-by-gene analysis through a graphical user interface. An easy-to-use analysis program that allows both high-throughput processing of multiple sequence alignments along with the flexibility to simulate data under complex demographic scenarios is currently lacking. We introduce a new program, named DnaSAM, which allows high-throughput estimation of DNA sequence diversity and neutrality statistics from experimental data along with the ability to test those statistics via Monte Carlo coalescent simulations. These simulations are conducted using the ms program, which is able to incorporate several genetic parameters (e.g. recombination) and demographic scenarios (e.g. population bottlenecks). The output is a set of diversity and neutrality statistics with associated probability values under a user-specified null model that are stored in easy to manipulate text file. © 2009 Blackwell Publishing Ltd.

  3. Testing strategies for digital picture processing of industrial X-ray images

    International Nuclear Information System (INIS)

    Filbert, D.; Klatte, R.

    1986-01-01

    Digital picture processing for difficult inspection work in general involves long and complex processing and much computer time. An adequate testing strategy can considerably reduce the testing time, which is shown by the example of a strategy for automated radiographic testing of castings. (orig./HP) [de

  4. Strategy for the extraction of yeast DNA from artisan agave must for quantitative PCR analysis.

    Science.gov (United States)

    Kirchmayr, Manuel Reinhart; Segura-Garcia, Luis Eduardo; Flores-Berrios, Ericka Patricia; Gschaedler, Anne

    2011-11-01

    An efficient method for the direct extraction of yeast genomic DNA from agave must was developed. The optimized protocol, which was based on silica-adsorption of DNA on microcolumns, included an enzymatic cell wall degradation step followed by prolonged lysis with hot detergent. The resulting extracts were suitable templates for subsequent qPCR assays that quantified mixed yeast populations in artisan Mexican mezcal fermentations. Copyright © 2011 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  5. Evolution of strategies to improve preclinical cardiac safety testing.

    Science.gov (United States)

    Gintant, Gary; Sager, Philip T; Stockbridge, Norman

    2016-07-01

    The early and efficient assessment of cardiac safety liabilities is essential to confidently advance novel drug candidates. This article discusses evolving mechanistically based preclinical strategies for detecting drug-induced electrophysiological and structural cardiotoxicity using in vitro human ion channel assays, human-based in silico reconstructions and human stem cell-derived cardiomyocytes. These strategies represent a paradigm shift from current approaches, which rely on simplistic in vitro assays that measure blockade of the Kv11.1 current (also known as the hERG current or IKr) and on the use of non-human cells or tissues. These new strategies have the potential to improve sensitivity and specificity in the early detection of genuine cardiotoxicity risks, thereby reducing the likelihood of mistakenly discarding viable drug candidates and speeding the progression of worthy drugs into clinical trials.

  6. Strategies for Ground Based Testing of Manned Lunar Surface Systems

    Science.gov (United States)

    Beyer, Jeff; Peacock, Mike; Gill, Tracy

    2009-01-01

    Integrated testing (such as Multi-Element Integrated Test (MEIT)) is critical to reducing risks and minimizing problems encountered during assembly, activation, and on-orbit operation of large, complex manned spacecraft. Provides the best implementation of "Test Like You Fly:. Planning for integrated testing needs to begin at the earliest stages of Program definition. Program leadership needs to fully understand and buy in to what integrated testing is and why it needs to be performed. As Program evolves and design and schedules mature, continually look for suitable opportunities to perform testing where enough components are together in one place at one time. The benefits to be gained are well worth the costs.

  7. Evaluating sampling strategy for DNA barcoding study of coastal and inland halo-tolerant Poaceae and Chenopodiaceae: A case study for increased sample size.

    Science.gov (United States)

    Yao, Peng-Cheng; Gao, Hai-Yan; Wei, Ya-Nan; Zhang, Jian-Hang; Chen, Xiao-Yong; Li, Hong-Qing

    2017-01-01

    Environmental conditions in coastal salt marsh habitats have led to the development of specialist genetic adaptations. We evaluated six DNA barcode loci of the 53 species of Poaceae and 15 species of Chenopodiaceae from China's coastal salt marsh area and inland area. Our results indicate that the optimum DNA barcode was ITS for coastal salt-tolerant Poaceae and matK for the Chenopodiaceae. Sampling strategies for ten common species of Poaceae and Chenopodiaceae were analyzed according to optimum barcode. We found that by increasing the number of samples collected from the coastal salt marsh area on the basis of inland samples, the number of haplotypes of Arundinella hirta, Digitaria ciliaris, Eleusine indica, Imperata cylindrica, Setaria viridis, and Chenopodium glaucum increased, with a principal coordinate plot clearly showing increased distribution points. The results of a Mann-Whitney test showed that for Digitaria ciliaris, Eleusine indica, Imperata cylindrica, and Setaria viridis, the distribution of intraspecific genetic distances was significantly different when samples from the coastal salt marsh area were included (P Imperata cylindrica and Chenopodium album, average intraspecific distance tended to reach stability. These results indicate that the sample size for DNA barcode of globally distributed species should be increased to 11-15.

  8. Testing - Smart strategy for safety and mission quality

    Science.gov (United States)

    Rodney, George A.

    The paper is concerned with the need for a comprehensive test plan for the Space Station Freedom (SST) that would fully verify specification compliance and be based on an error budget. In particular, attention is given to some lessons learned from other NASA programs and the principal challenges for SSF testing, including phase C/D/E agreements, testing parameters, phase testing, and the human element. The importance of close teamwork between the NASA/Contractor systems engineers and assurance engineers is emphasized.

  9. The Multiple Tasks Test: development and normal strategies.

    NARCIS (Netherlands)

    Bloem, B.R.; Valkenburg, V.V.; Slabbekoorn, M.; Willemsen, M.D.

    2001-01-01

    Simultaneous challenge of posture and cognition ("dual tasks") may predict falls better than tests of isolated components of postural control. We describe a new balance test (the Multiple Tasks Test, MTT) which (1) is based upon simultaneous assessment of multiple (>2) postural components; (2)

  10. Strategy for Extracting DNA from Clay Soil and Detecting a Specific Target Sequence via Selective Enrichment and Real-Time (Quantitative) PCR Amplification ▿

    Science.gov (United States)

    Yankson, Kweku K.; Steck, Todd R.

    2009-01-01

    We present a simple strategy for isolating and accurately enumerating target DNA from high-clay-content soils: desorption with buffers, an optional magnetic capture hybridization step, and quantitation via real-time PCR. With the developed technique, μg quantities of DNA were extracted from mg samples of pure kaolinite and a field clay soil. PMID:19633108

  11. Five essential tests of market strategy. Final report

    International Nuclear Information System (INIS)

    Buzzell, R.D.; George, S.S.; Leone, R.A.

    1996-04-01

    This report describes a diagnostic process for determining how well a utility's current market strategy meets the five key criteria and identifying areas requiring further attention. This process is based primarily on utility management and staff interviews but also examines existing information on customer perceptions of product/service offerings, utility and competitor characteristics, and other relevant issues

  12. Field testing of Schistosoma japonicum DNA vaccines in cattle in China.

    Science.gov (United States)

    Shi, Fuhui; Zhang, Yaobi; Lin, Jiaojiao; Zuo, Xin; Shen, Wei; Cai, Yiumin; Ye, Ping; Bickle, Quentin D; Taylor, Martin G

    2002-11-01

    Vaccines are needed to reduce the zoonotic reservoir of Schistosoma japonicum infection in bovines in China. We have developed two experimental DNA vaccines and have already shown these to be capable of inducing partial protection in water buffalo naturally exposed to the risk of S. japonicum infection in the field. We now report a similar field trial in cattle, the other major bovine reservoir host species in China. Groups of cattle were vaccinated with the VRSj28 vaccine or the VRSj23 vaccine, or, to test whether protection could be enhanced by combination vaccination, with both these DNA vaccines together. After vaccination, the cattle were exposed to natural infection in the field for a period of 54 days. Worm and egg counts carried out at the end of the experiment showed that each of the vaccine groups showed partial resistance, and that combined vaccination was not more effective than vaccination with the individual plasmids.

  13. Comparison of the cobas Human Papillomavirus (HPV) Test with the Hybrid Capture 2 and Linear Array HPV DNA Tests

    Science.gov (United States)

    Sadorra, Mark; LaMere, Brandon J.; Kail, Randi; Aldrich, Carrie; Kinney, Walter; Fetterman, Barbara; Lorey, Thomas; Schiffman, Mark; Castle, Philip E.

    2012-01-01

    The cobas human papillomavirus (HPV) test (cobas) was recently approved by the U.S. Food and Drug Administration (FDA) and identifies HPV16 and HPV18 separately as well as detecting a pool of 11 HR-HPV genotypes (HPV31, -33, -35, -39, -45, -51, -52, -56, -58, -59, -68) and also HPV66. We compared cobas, Linear Array (LA), and Hybrid Capture 2 (HC2) assays for detection of carcinogenic HPV DNA, and cobas and LA for detection of HPV16 and HPV18 DNA, among the first 1,852 women enrolled in the HPV Persistence and Progression Cohort (PaP Cohort) study. Specimens were tested by all 3 assays 1 year after an HC2-positive result. In 1,824 specimens with cobas results, cobas had an 85.9% agreement with HC2 and 91.0% agreement with LA for carcinogenic HPV detection. When results between cobas and HC2 disagreed, cobas tended to call more women HPV positive (P < 0.01). Categorizing cobas and LA results hierarchically according to cancer risk (HPV16, HPV18, other carcinogenic HPV genotypes, or carcinogen negative), there was a 90% agreement for all categories of HPV (n = 1,824). We found good agreement between the two U.S. FDA-approved HPV tests, with discrepancies between the two assays due to specific characteristics of the individual assays. Additional studies are needed to compare HC2 and cobas for detecting and predicting CIN3 to understand the clinical implications of the discrepant test results between the two tests. PMID:22075592

  14. Ada response - a strategy for repair of alkylated DNA in bacteria.

    Science.gov (United States)

    Mielecki, Damian; Grzesiuk, Elżbieta

    2014-06-01

    Alkylating agents are widespread in the environment and also occur endogenously. They can be cytotoxic or mutagenic to the cells introducing alkylated bases to DNA or RNA. All organisms have evolved multiple DNA repair mechanisms to counteract the effects of DNA alkylation: the most cytotoxic lesion, N(3)-methyladenine (3meA), is excised by AlkA glycosylase initiating base excision repair (BER); toxic N(1)-methyladenine (1meA) and N(3)-methylcytosine (3meC), induced in DNA and RNA, are removed by AlkB dioxygenase; and mutagenic and cytotoxic O(6)-methylguanine (O(6) meG) is repaired by Ada methyltransferase. In Escherichia coli, Ada response involves the expression of four genes, ada, alkA, alkB, and aidB, encoding respective proteins Ada, AlkA, AlkB, and AidB. The Ada response is conserved among many bacterial species; however, it can be organized differently, with diverse substrate specificity of the particular proteins. Here, an overview of the organization of the Ada regulon and function of individual proteins is presented. We put special effort into the characterization of AlkB dioxygenases, their substrate specificity, and function in the repair of alkylation lesions in DNA/RNA. © 2014 The Authors. FEMS Microbiology Letters published by John Wiley & Sons Ltd on behalf of Federation of European Microbiological Societies.

  15. Ada response – a strategy for repair of alkylated DNA in bacteria

    Science.gov (United States)

    Mielecki, Damian; Grzesiuk, Elżbieta

    2014-01-01

    Alkylating agents are widespread in the environment and also occur endogenously. They can be cytotoxic or mutagenic to the cells introducing alkylated bases to DNA or RNA. All organisms have evolved multiple DNA repair mechanisms to counteract the effects of DNA alkylation: the most cytotoxic lesion, N3-methyladenine (3meA), is excised by AlkA glycosylase initiating base excision repair (BER); toxic N1-methyladenine (1meA) and N3-methylcytosine (3meC), induced in DNA and RNA, are removed by AlkB dioxygenase; and mutagenic and cytotoxic O6-methylguanine (O6meG) is repaired by Ada methyltransferase. In Escherichia coli, Ada response involves the expression of four genes, ada, alkA, alkB, and aidB, encoding respective proteins Ada, AlkA, AlkB, and AidB. The Ada response is conserved among many bacterial species; however, it can be organized differently, with diverse substrate specificity of the particular proteins. Here, an overview of the organization of the Ada regulon and function of individual proteins is presented. We put special effort into the characterization of AlkB dioxygenases, their substrate specificity, and function in the repair of alkylation lesions in DNA/RNA. PMID:24810496

  16. Testing Strategies and Methodologies for the Max Launch Abort System

    Science.gov (United States)

    Schaible, Dawn M.; Yuchnovicz, Daniel E.

    2011-01-01

    The National Aeronautics and Space Administration (NASA) Engineering and Safety Center (NESC) was tasked to develop an alternate, tower-less launch abort system (LAS) as risk mitigation for the Orion Project. The successful pad abort flight demonstration test in July 2009 of the "Max" launch abort system (MLAS) provided data critical to the design of future LASs, while demonstrating the Agency s ability to rapidly design, build and fly full-scale hardware at minimal cost in a "virtual" work environment. Limited funding and an aggressive schedule presented a challenge for testing of the complex MLAS system. The successful pad abort flight demonstration test was attributed to the project s systems engineering and integration process, which included: a concise definition of, and an adherence to, flight test objectives; a solid operational concept; well defined performance requirements, and a test program tailored to reducing the highest flight test risks. The testing ranged from wind tunnel validation of computational fluid dynamic simulations to component ground tests of the highest risk subsystems. This paper provides an overview of the testing/risk management approach and methodologies used to understand and reduce the areas of highest risk - resulting in a successful flight demonstration test.

  17. Strategies for detection of transfusion-transmitted viruses eluding identification by conventional serologic tests. I

    International Nuclear Information System (INIS)

    Neurath, A.R.; Strick, N.

    1983-01-01

    The unavailability of serological tests for detection of several not yet characterized infectious agents transmitted by blood transfusion or by blood products prompted the development of alternative tests based on utilization of labeled nucleic acid probes specific for genomes of each of these agents. The prerequisite for the preparation of such probes is the demonstration in human plasma of nucleic acid sequences distinct from those present in host DNA or in genes of already characterized viruses occurring in plasma of infected individuals. To accomplish this, ultrasensitive tests for nucleic acids not dependent on their base sequence are needed. The authors describe a radioimmunoassay (RIA) for picogram quantities of DNA. Plasma (serum) specimens are treated with proteinase K in the presence of sodium dodecyl sulfate and extracted with phenol. Nucleic acids are precipitated with ethanol in the presence of dextran (mol.wt. approx. 5X10 5 ) as carrier. Subsequently, DNA from the redissolved samples is adsorbed onto polylysine-coated wells of microtiter plates and detected by a double-antibody RIA using anti-DNA autoantibodies from NZB/NZW mice and 125 I-labelled antibodies to mouse immunoglobulins. DNA which did not hybridize with human DNA was detected by this method in sera containing hepatitis B virus used as a model system. (Auth.)

  18. Screening Test for Shed Skin Cells by Measuring the Ratio of Human DNA to Staphylococcus epidermidis DNA.

    Science.gov (United States)

    Nakanishi, Hiroaki; Ohmori, Takeshi; Hara, Masaaki; Takahashi, Shirushi; Kurosu, Akira; Takada, Aya; Saito, Kazuyuki

    2016-05-01

    A novel screening method for shed skin cells by detecting Staphylococcus epidermidis (S. epidermidis), which is a resident bacterium on skin, was developed. Staphylococcus epidermidis was detected using real-time PCR. Staphylococcus epidermidis was detected in all 20 human skin surface samples. Although not present in blood and urine samples, S. epidermidis was detected in 6 of 20 saliva samples, and 5 of 18 semen samples. The ratio of human DNA to S. epidermidisDNA was significantly smaller in human skin surface samples than in saliva and semen samples in which S. epidermidis was detected. Therefore, although skin cells could not be identified by detecting only S. epidermidis, they could be distinguished by measuring the S. epidermidis to human DNA ratio. This method could be applied to casework touch samples, which suggests that it is useful for screening whether skin cells and human DNA are present on potential evidentiary touch samples. © 2016 American Academy of Forensic Sciences.

  19. Software-Supported USER Cloning Strategies for Site-Directed Mutagenesis and DNA Assembly

    DEFF Research Database (Denmark)

    Genee, Hans Jasper; Bonde, Mads Tvillinggaard; Bagger, Frederik Otzen

    2015-01-01

    USER cloning is a fast and versatile method for engineering of plasmid DNA. We have developed a user friendly Web server tool that automates the design of optimal PCR primers for several distinct USER cloning-based applications. Our Web server, named AMUSER (Automated DNA Modifications with USER...... cloning), facilitates DNA assembly and introduction of virtually any type of site-directed mutagenesis by designing optimal PCR primers for the desired genetic changes. To demonstrate the utility, we designed primers for a simultaneous two-position site-directed mutagenesis of green fluorescent protein...... (GFP) to yellow fluorescent protein (YFP), which in a single step reaction resulted in a 94% cloning efficiency. AMUSER also supports degenerate nucleotide primers, single insert combinatorial assembly, and flexible parameters for PCR amplification. AMUSER is freely available online at ....

  20. OPTIMAL STRATEGIES FOR REGIONAL CULTIVAR TESTING FOR VARIOUS CROPS

    OpenAIRE

    Kingwell, Ross S.

    1999-01-01

    Before a variety is released for adoption by farmers in a region it is subject to comparative field testing. An economic issue is how extensive and prolonged should be this field testing within the region; over how many locations, years and with what number of plot replications should testing occur? This paper addresses this issue for the main broadacre crops grown in Western Australia and shows through sensitivity analysis how robust are the findings for each crop type. Findings are contrast...

  1. Feasibility of testing DNA repair inhibitors for mutagenicity by a simple method

    International Nuclear Information System (INIS)

    Sideropoulos, A.S.; Specht, S.M.; Jones, M.T.

    1980-01-01

    A simple screening methodology for the determination of mutagenicity of DNA repair inhibitors has been tested in this laboratory. Radiation-resistant E. coli B/r and WP2 hcr + and hcr - are suitable strains for mutagenicity testing. In these strains irradiated with 40-60 ergs/mm 2 , chemicals which interfere with repair of ultraviolet-induced pre-mutational lesions can be shown to enhance significantly the frequency of mutations to streptomycin resistance. This phenomenon is termed 'mutational synergism' [18,20]. We have attempted to apply the procedure for securing data for 'mutational synergism' between ultraviolet (UV) radiation and a number of antimalarial drugs including quinine hydrochloride (50 μg/ml), quinine hydrobromide (50 μg/ml), primaquine diphosphate (50 μg/ml), chloroquine (50 μg/ml), quinine (50 μg/ml) and quinacrine dihydrochloride (25 μg/ml). All drugs tested give synergistic effects with UV light. The synergistic activity ranges from 3- to 35-fold. Quinine and quinacrine dihydrochloride have been found to be much more efficient enhancers of the mutagenic effect of UV than caffeine. In general, we have found that the expression of synergistic action occurs at a concentration well below the minimum inhibitory concentration (MIC) with the drugs tested. The implication of these observations in the establishment of a screening method for the evaluation of the mutagenicity of DNA repair inhibitors is discussed. (orig.)

  2. Feasibility of testing DNA repair inhibitors for mutagenicity by a simple method

    International Nuclear Information System (INIS)

    Sideropoulos, A.S.; Specht, S.M.; Jones, M.T.

    1980-01-01

    A simple screening methodology for the determination of mutagenictity of DNA repair inhibitors has been tested in this laboratory. Radiation-resistant E. coli B/r and WP2 hcr + and hcr - are suitable strains for mutagenicity testing. In these strains irradiated with 40-60 ergs/mm 2 , chemicals which interfere with repair of ultraviolet-induced pre-mutational lesions can be shown to enhance significantly the frequency of mutations to streptomycin resistance. This phenomenon is termed mutational synergism. We have attempted to apply the procedure for securing data for mutational synergism between ultraviolet (UV) radiation and a number of antimalarial drugs including quinine hydrochloride (50 μg/ml), quinine hydrobromide (50 μg/ml), primaquine diphosphate (50 μg/ml), chloroquine (50μg/ml) and quinacrine dihydrochloride (25 μg/ml). All drugs tested give synergistic effets with UV light. The synergistic activity ranges from 3- to 35-fold. Quinine and quinacrine dihydrochloride have been found to be much more efficient enhancers of the mutagenic effect of UV than caffeine. In general, we have found that the expression of synergistic action occurs at a concentration well below the minimum inhibitory concentration (MIC) with the drugs tested. The implication of these observations in the establishment of a screening method for the evaluation of the mutagenicity of DNA repair inhibitors is discussed. (orig.)

  3. Feasibility of testing DNA repair inhibitors for mutagenicity by a simple method

    Energy Technology Data Exchange (ETDEWEB)

    Sideropoulos, A S; Specht, S M; Jones, M T [Duquesne Univ., Pittsburgh, PA (USA). Dept. of Biological Sciences

    1980-04-01

    A simple screening methodology for the determination of mutagenictity of DNA repair inhibitors has been tested in this laboratory. Radiation-resistant E. coli B/r and WP2 hcr/sup +/ and hcr/sup -/ are suitable strains for mutagenicity testing. In these strains irradiated with 40-60 ergs/mm/sup 2/, chemicals which interfere with repair of ultraviolet-induced pre-mutational lesions can be shown to enhance significantly the frequency of mutations to streptomycin resistance. This phenomenon is termed mutational synergism. We have attempted to apply the procedure for securing data for mutational synergism between ultraviolet (uv) radiation and a number of antimalarial drugs including quinine hydrochloride (50 ..mu..g/ml), quinine hydrobromide (50 ..mu..g/ml), primaquine diphosphate (50 ..mu..g/ml), chloroquine (50..mu..g/ml) and quinacrine dihydrochloride (25 ..mu..g/ml). All drugs tested give synergistic effects with uv light. The synergistic activity ranges from 3- to 35-fold. Quinine and quinacrine dihydrochloride have been found to be much more efficient enhancers of the mutagenic effect of uv than caffeine. In general, we have found that the expression of synergistic action occurs at a concentration well below the minimum inhibitory concentration (MIC) with the drugs tested. The implication of these observations in the establishment of a screening method for the evaluation of the mutagenicity of DNA repair inhibitors is discussed.

  4. Feasibility of testing DNA repair inhibitors for mutagenicity by a simple method

    Energy Technology Data Exchange (ETDEWEB)

    Sideropoulos, A S; Specht, S M; Jones, M T [Duquesne Univ., Pittsburgh, PA (USA). Dept. of Biological Sciences

    1980-04-01

    A simple screening methodology for the determination of mutagenicity of DNA repair inhibitors has been tested in this laboratory. Radiation-resistant E. coli B/r and WP2 hcr/sup +/ and hcr/sup -/ are suitable strains for mutagenicity testing. In these strains irradiated with 40-60 ergs/mm/sup 2/, chemicals which interfere with repair of ultraviolet-induced pre-mutational lesions can be shown to enhance significantly the frequency of mutations to streptomycin resistance. This phenomenon is termed 'mutational synergism' (18,20). We have attempted to apply the procedure for securing data for 'mutational synergism' between ultraviolet (UV) radiation and a number of antimalarial drugs including quinine hydrochloride (50 ..mu..g/ml), quinine hydrobromide (50 ..mu..g/ml), primaquine diphosphate (50 ..mu..g/ml), chloroquine (50 ..mu..g/ml), quinine (50 ..mu..g/ml) and quinacrine dihydrochloride (25 ..mu..g/ml). All drugs tested give synergistic effects with UV light. The synergistic activity ranges from 3- to 35-fold. Quinine and quinacrine dihydrochloride have been found to be much more efficient enhancers of the mutagenic effect of UV than caffeine. In general, we have found that the expression of synergistic action occurs at a concentration well below the minimum inhibitory concentration (MIC) with the drugs tested. The implication of these observations in the establishment of a screening method for the evaluation of the mutagenicity of DNA repair inhibitors is discussed.

  5. A leukocyte activation test identifies food items which induce release of DNA by innate immune peripheral blood leucocytes.

    Science.gov (United States)

    Garcia-Martinez, Irma; Weiss, Theresa R; Yousaf, Muhammad N; Ali, Ather; Mehal, Wajahat Z

    2018-01-01

    Leukocyte activation (LA) testing identifies food items that induce a patient specific cellular response in the immune system, and has recently been shown in a randomized double blinded prospective study to reduce symptoms in patients with irritable bowel syndrome (IBS). We hypothesized that test reactivity to particular food items, and the systemic immune response initiated by these food items, is due to the release of cellular DNA from blood immune cells. We tested this by quantifying total DNA concentration in the cellular supernatant of immune cells exposed to positive and negative foods from 20 healthy volunteers. To establish if the DNA release by positive samples is a specific phenomenon, we quantified myeloperoxidase (MPO) in cellular supernatants. We further assessed if a particular immune cell population (neutrophils, eosinophils, and basophils) was activated by the positive food items by flow cytometry analysis. To identify the signaling pathways that are required for DNA release we tested if specific inhibitors of key signaling pathways could block DNA release. Foods with a positive LA test result gave a higher supernatant DNA content when compared to foods with a negative result. This was specific as MPO levels were not increased by foods with a positive LA test. Protein kinase C (PKC) inhibitors resulted in inhibition of positive food stimulated DNA release. Positive foods resulted in CD63 levels greater than negative foods in eosinophils in 76.5% of tests. LA test identifies food items that result in release of DNA and activation of peripheral blood innate immune cells in a PKC dependent manner, suggesting that this LA test identifies food items that result in release of inflammatory markers and activation of innate immune cells. This may be the basis for the improvement in symptoms in IBS patients who followed an LA test guided diet.

  6. Inappropriate Practices in Fitness Testing and Reporting: Alternative Strategies

    Science.gov (United States)

    Zhu, Xihe; Davis, Summer; Kirk, T. Nicole; Haegele, Justin A.; Knott, Stephen E.

    2018-01-01

    Fitness education is becoming an integrated component for many physical education programs. As such, many physical educators conduct health-related fitness tests on a regular basis. Some states even mandate certain types of physical fitness tests to be administered and reported annually or by semester. Yet, inappropriate practices have been…

  7. Automated detection of test fixture strategies and smells

    NARCIS (Netherlands)

    Greiler, M.S.; Van Deursen, A.; Storey, M.A.

    2013-01-01

    Paper accepted for publication in the Proceedings of the Sixth International Conference on Software Testing, Verification and Validation, IEEE Computer Society, 18-22 March 2013, ISBN 978-1-4673-5961-0, doi: 10.1109/ICST.2013.45 Designing automated tests is a challenging task. One important concern

  8. An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies

    Science.gov (United States)

    2012-01-01

    Background The combination of chromatin immunoprecipitation with two-channel microarray technology enables genome-wide mapping of binding sites of DNA-interacting proteins (ChIP-on-chip) or sites with methylated CpG di-nucleotides (DNA methylation microarray). These powerful tools are the gateway to understanding gene transcription regulation. Since the goals of such studies, the sample preparation procedures, the microarray content and study design are all different from transcriptomics microarrays, the data pre-processing strategies traditionally applied to transcriptomics microarrays may not be appropriate. Particularly, the main challenge of the normalization of "regulation microarrays" is (i) to make the data of individual microarrays quantitatively comparable and (ii) to keep the signals of the enriched probes, representing DNA sequences from the precipitate, as distinguishable as possible from the signals of the un-enriched probes, representing DNA sequences largely absent from the precipitate. Results We compare several widely used normalization approaches (VSN, LOWESS, quantile, T-quantile, Tukey's biweight scaling, Peng's method) applied to a selection of regulation microarray datasets, ranging from DNA methylation to transcription factor binding and histone modification studies. Through comparison of the data distributions of control probes and gene promoter probes before and after normalization, and assessment of the power to identify known enriched genomic regions after normalization, we demonstrate that there are clear differences in performance between normalization procedures. Conclusion T-quantile normalization applied separately on the channels and Tukey's biweight scaling outperform other methods in terms of the conservation of enriched and un-enriched signal separation, as well as in identification of genomic regions known to be enriched. T-quantile normalization is preferable as it additionally improves comparability between microarrays. In

  9. Robust joint score tests in the application of DNA methylation data analysis.

    Science.gov (United States)

    Li, Xuan; Fu, Yuejiao; Wang, Xiaogang; Qiu, Weiliang

    2018-05-18

    Recently differential variability has been showed to be valuable in evaluating the association of DNA methylation to the risks of complex human diseases. The statistical tests based on both differential methylation level and differential variability can be more powerful than those based only on differential methylation level. Anh and Wang (2013) proposed a joint score test (AW) to simultaneously detect for differential methylation and differential variability. However, AW's method seems to be quite conservative and has not been fully compared with existing joint tests. We proposed three improved joint score tests, namely iAW.Lev, iAW.BF, and iAW.TM, and have made extensive comparisons with the joint likelihood ratio test (jointLRT), the Kolmogorov-Smirnov (KS) test, and the AW test. Systematic simulation studies showed that: 1) the three improved tests performed better (i.e., having larger power, while keeping nominal Type I error rates) than the other three tests for data with outliers and having different variances between cases and controls; 2) for data from normal distributions, the three improved tests had slightly lower power than jointLRT and AW. The analyses of two Illumina HumanMethylation27 data sets GSE37020 and GSE20080 and one Illumina Infinium MethylationEPIC data set GSE107080 demonstrated that three improved tests had higher true validation rates than those from jointLRT, KS, and AW. The three proposed joint score tests are robust against the violation of normality assumption and presence of outlying observations in comparison with other three existing tests. Among the three proposed tests, iAW.BF seems to be the most robust and effective one for all simulated scenarios and also in real data analyses.

  10. Design of a testing strategy using non-animal based test methods: lessons learnt from the ACuteTox project.

    Science.gov (United States)

    Kopp-Schneider, Annette; Prieto, Pilar; Kinsner-Ovaskainen, Agnieszka; Stanzel, Sven

    2013-06-01

    In the framework of toxicology, a testing strategy can be viewed as a series of steps which are taken to come to a final prediction about a characteristic of a compound under study. The testing strategy is performed as a single-step procedure, usually called a test battery, using simultaneously all information collected on different endpoints, or as tiered approach in which a decision tree is followed. Design of a testing strategy involves statistical considerations, such as the development of a statistical prediction model. During the EU FP6 ACuteTox project, several prediction models were proposed on the basis of statistical classification algorithms which we illustrate here. The final choice of testing strategies was not based on statistical considerations alone. However, without thorough statistical evaluations a testing strategy cannot be identified. We present here a number of observations made from the statistical viewpoint which relate to the development of testing strategies. The points we make were derived from problems we had to deal with during the evaluation of this large research project. A central issue during the development of a prediction model is the danger of overfitting. Procedures are presented to deal with this challenge. Copyright © 2012 Elsevier Ltd. All rights reserved.

  11. Evaluating sampling strategy for DNA barcoding study of coastal and inland halo-tolerant Poaceae and Chenopodiaceae: A case study for increased sample size.

    Directory of Open Access Journals (Sweden)

    Peng-Cheng Yao

    Full Text Available Environmental conditions in coastal salt marsh habitats have led to the development of specialist genetic adaptations. We evaluated six DNA barcode loci of the 53 species of Poaceae and 15 species of Chenopodiaceae from China's coastal salt marsh area and inland area. Our results indicate that the optimum DNA barcode was ITS for coastal salt-tolerant Poaceae and matK for the Chenopodiaceae. Sampling strategies for ten common species of Poaceae and Chenopodiaceae were analyzed according to optimum barcode. We found that by increasing the number of samples collected from the coastal salt marsh area on the basis of inland samples, the number of haplotypes of Arundinella hirta, Digitaria ciliaris, Eleusine indica, Imperata cylindrica, Setaria viridis, and Chenopodium glaucum increased, with a principal coordinate plot clearly showing increased distribution points. The results of a Mann-Whitney test showed that for Digitaria ciliaris, Eleusine indica, Imperata cylindrica, and Setaria viridis, the distribution of intraspecific genetic distances was significantly different when samples from the coastal salt marsh area were included (P < 0.01. These results suggest that increasing the sample size in specialist habitats can improve measurements of intraspecific genetic diversity, and will have a positive effect on the application of the DNA barcodes in widely distributed species. The results of random sampling showed that when sample size reached 11 for Chloris virgata, Chenopodium glaucum, and Dysphania ambrosioides, 13 for Setaria viridis, and 15 for Eleusine indica, Imperata cylindrica and Chenopodium album, average intraspecific distance tended to reach stability. These results indicate that the sample size for DNA barcode of globally distributed species should be increased to 11-15.

  12. Practical aspects of mutagenicity testing strategy: an industrial perspective.

    Science.gov (United States)

    Gollapudi, B B; Krishna, G

    2000-11-20

    Genetic toxicology studies play a central role in the development and marketing of new chemicals for pharmaceutical, agricultural, industrial, and consumer use. During the discovery phase of product development, rapid screening tests that require minimal amounts of test materials are used to assist in the design and prioritization of new molecules. At this stage, a modified Salmonella reverse mutation assay and an in vitro micronucleus test with mammalian cell culture are frequently used for screening. Regulatory genetic toxicology studies are conducted with a short list of compounds using protocols that conform to various international guidelines. A set of four assays usually constitutes the minimum test battery that satisfies global requirements. This set includes a bacterial reverse mutation assay, an in vitro cytogenetic test with mammalian cell culture, an in vitro gene mutation assay in mammalian cell cultures, and an in vivo rodent bone marrow micronucleus test. Supplementary studies are conducted in certain instances either as a follow-up to the findings from this initial testing battery and/or to satisfy a regulatory requirement. Currently available genetic toxicology assays have helped the scientific and industrial community over the past several decades in evaluating the mutagenic potential of chemical agents. The emerging field of toxicogenomics has the potential to redefine our ability to study the response of cells to genetic damage and hence our ability to study threshold phenomenon.

  13. Strategies to enhance immunogenicity of cDNA vaccine encoded antigens by modulation of antigen processing

    NARCIS (Netherlands)

    Platteel, Anouk C M; Marit de Groot, A; Andersen, Peter; Ovaa, Huib; Kloetzel, Peter M; Mishto, Michele; Sijts, Alice J A M

    2016-01-01

    Most vaccines are based on protective humoral responses while for intracellular pathogens CD8(+) T cells are regularly needed to provide protection. However, poor processing efficiency of antigens is often a limiting factor in CD8(+) T cell priming, hampering vaccine efficacy. The multistage cDNA

  14. Novel extraction strategy of ribosomal RNA and genomic DNA from cheese for PCR-based investigations.

    Science.gov (United States)

    Bonaïti, Catherine; Parayre, Sandrine; Irlinger, Françoise

    2006-03-15

    Cheese microorganisms, such as bacteria and fungi, constitute a complex ecosystem that plays a central role in cheeses ripening. The molecular study of cheese microbial diversity and activity is essential but the extraction of high quality nucleic acid may be problematic: the cheese samples are characterised by a strong buffering capacity which negatively influenced the yield of the extracted rRNA. The objective of this study is to develop an effective method for the direct and simultaneous isolation of yeast and bacterial ribosomal RNA and genomic DNA from the same cheese samples. DNA isolation was based on a protocol used for nucleic acids isolation from anaerobic digestor, without preliminary washing step with the combined use of the action of chaotropic agent (acid guanidinium thiocyanate), detergents (SDS, N-lauroylsarcosine), chelating agent (EDTA) and a mechanical method (bead beating system). The DNA purification was carried out by two washing steps of phenol-chloroform. RNA was isolated successfully after the second acid extraction step by recovering it from the phenolic phase of the first acid extraction. The novel method yielded pure preparation of undegraded RNA accessible for reverse transcription-PCR. The extraction protocol of genomic DNA and rRNA was applicable to complex ecosystem of different cheese matrices.

  15. Diagnostic test strategies in children at increased risk of inflammatory bowel disease in primary care

    NARCIS (Netherlands)

    Holtman, Gea A.; Lisman-van Leeuwen, Yvonne; Kollen, Boudewijn J.; Norbruis, Obbe F.; Escher, Johanna C.; Walhout, Laurence C.; Kindermann, Angelika; de Rijke, Yolanda B.; van Rheenen, Patrick F.; Berger, Marjolein Y.

    2017-01-01

    In children with symptoms suggestive of inflammatory bowel disease (IBD) who present in primary care, the optimal test strategy for identifying those who require specialist care is unclear. We evaluated the following three test strategies to determine which was optimal for referring children with

  16. Diagnostic test strategies in children at increased risk of inflammatory bowel disease in primary care

    NARCIS (Netherlands)

    Holtman, Gea A.; Lisman-van Leeuwen, Yvonne; Kollen, Boudewijn J.; Norbruis, Obbe F.; Escher, Johanna C.; Walhout, Laurence C.; Kindermann, Angelika; de Rijke, Yolanda B.; van Rheenen, Patrick F.; Berger, Marjolein Y.

    2017-01-01

    Background: In children with symptoms suggestive of inflammatory bowel disease (IBD) who present in primary care, the optimal test strategy for identifying those who require specialist care is unclear. We evaluated the following three test strategies to determine which was optimal for referring

  17. Diagnostic test strategies in children at increased risk of inflammatory bowel disease in primary care

    NARCIS (Netherlands)

    G.A. Holtman (Gea A); Y. Lisman-van Leeuwen (Yvonne); B.J. Kollen (Boudewijn ); O.F. Norbruis (Obbe); J.C. Escher (Johanna); L.C. Walhout (Laurence); A. Kindermann; Y.B. de Rijke (Yolanda); P.F. van Rheenen (Patrick); M.Y. Berger (Marjolein)

    2017-01-01

    textabstractBackground: In children with symptoms suggestive of inflammatory bowel disease (IBD) who present in primary care, the optimal test strategy for identifying those who require specialist care is unclear. We evaluated the following three test strategies to determine which was optimal for

  18. An Investigation of the Learning Strategies as Bias Factors in Second Language Cloze Tests

    Science.gov (United States)

    Ajideh, Parviz; Yaghoubi-Notash, Massoud; Khalili, Abdolreza

    2017-01-01

    The present study investigated the contribution of the EFL students' learning strategies to the explanation of the variance in their results on language tests. More specifically, it examined the role of these strategies as bias factors in the results of English cloze tests. Based on this aim, first, 158 intermediate EFL learners were selected from…

  19. Dredging Research, Volume 3, No. 3. DNA Technology to Impact Dredged Material Projects through Faster, More Accurate Testing Methods

    National Research Council Canada - National Science Library

    McDonald, Allison

    2000-01-01

    .... Most people associate DNA with criminal cases and paternity testing, but thanks to research projects such as the Human Genome Project, which has isolated and identified thousands of genes, many...

  20. A Bayesian decision procedure for testing multiple hypotheses in DNA microarray experiments.

    Science.gov (United States)

    Gómez-Villegas, Miguel A; Salazar, Isabel; Sanz, Luis

    2014-02-01

    DNA microarray experiments require the use of multiple hypothesis testing procedures because thousands of hypotheses are simultaneously tested. We deal with this problem from a Bayesian decision theory perspective. We propose a decision criterion based on an estimation of the number of false null hypotheses (FNH), taking as an error measure the proportion of the posterior expected number of false positives with respect to the estimated number of true null hypotheses. The methodology is applied to a Gaussian model when testing bilateral hypotheses. The procedure is illustrated with both simulated and real data examples and the results are compared to those obtained by the Bayes rule when an additive loss function is considered for each joint action and the generalized loss 0-1 function for each individual action. Our procedure significantly reduced the percentage of false negatives whereas the percentage of false positives remains at an acceptable level.

  1. Determination of antinucleic factors and anti-DNA and antibodies with immunefluorescence, radioimmunoassay and latex-test

    Energy Technology Data Exchange (ETDEWEB)

    Lemmel, E M; Hoffmann, R; Botzenhardt, U

    1976-01-01

    The results obtained with the 3 test methods are not completely equal. This is, on the one hand, based on the fact that at least in the fluorescence test other antibodies than in the DNA-compound test are also detected. Quantitatively, however, the two tests show a good correlation to the progress of the illness; strong positive DNA-compound is practically only found in SLE. The authors were able to prove that the addition of purified C1 or C1q components of the complementary system to the test can result in a DNA binding of over 50% and, consequently, in incorrect positive values in the compound test. The Latex test is less suitable for diagnosis and course observation since it relatively often renders negative results at established cases of SLE with distinct illness activity on the one hand, while on the other hand, quantitative evidence, which is desirable for assessing the illness activity, is not possible.

  2. submitter Test strategies for industrial testers for converter controls equipment

    CERN Document Server

    Oleniuk, P; Kasampalis, V; Nisbet, D; Todd, B; Uznański, S

    2017-01-01

    Power converters and their controls electronics are key elements for the operation of the CERN accelerator complex, having a direct impact on its availability. To prevent early-life failures and provide means to verify electronics, a set of industrial testers is used throughout the converters controls electronics' life cycle. The roles of the testers are to validate mass production during the manufacturing phase and to provide means to diagnose and repair failed modules that are brought back from operation. In the converter controls electronics section of the power converters group in the technology department of CERN (TE/EPC/CCE), two main test platforms have been adopted: a PXI platform for mixed analogue-digital functional tests and a JTAG Boundary-Scan platform for digital interconnection and functional tests. Depending on the functionality of the device under test, the appropriate test platforms are chosen. This paper is a follow-up to results presented at the TWEPP 2015 conference, adding the boundary s...

  3. Integrated Testing Strategy (ITS) - Opportunities to better use existing data and guide future testing in toxicology.

    Science.gov (United States)

    Jaworska, Joanna; Hoffmann, Sebastian

    2010-01-01

    The topic of Integrated Testing Strategies (ITS) has attracted considerable attention, and not only because it is supposed to be a central element of REACH, the ambitious European chemical regulation effort. Although what ITSs are supposed to do seems unambiguous, i.e. speeding up hazard and risk assessment while reducing testing costs, not much has been said, except basic conceptual proposals, about the methodologies that would allow execution of these concepts. Although a pressing concern, the topic of ITS has drawn mostly general reviews, broad concepts, and the expression of a clear need for more research on ITS. Published research in the field remains scarce. Solutions for ITS design emerge slowly, most likely due to the methodological challenges of the task, and perhaps also to it its complexity and the need for multidisciplinary collaboration. Along with the challenge, ITS offer a unique opportunity to contribute to the Toxicology of the 21st century by providing frameworks and tools to actually implement 21st century toxicology data in the chemical management and decision making processes. Further, ITS have the potential to significantly contribute to a modernization of the science of risk assessment. Therefore, to advance ITS research we propose a methodical approach to their design and will discuss currently available approaches as well as challenges to overcome. To this end, we define a framework for ITS that will inform toxicological decisions in a systematic, transparent, and consistent way. We review conceptual requirements for ITS developed earlier and present a roadmap to an operational framework that should be probabilistic, hypothesis-driven, and adaptive. Furthermore, we define properties an ITS should have in order to meet the identified requirements and differentiate them from evidence synthesis. Making use of an ITS for skin sensitization, we demonstrate how the proposed ITS concepts can be implemented.

  4. Forgotten evidence: A mixed methods study of why sexual assault kits (SAKs) are not submitted for DNA forensic testing.

    Science.gov (United States)

    Campbell, Rebecca; Fehler-Cabral, Giannina; Bybee, Deborah; Shaw, Jessica

    2017-10-01

    Throughout the United States, hundreds of thousands of sexual assault kits (SAKs) (also termed "rape kits") have not been submitted by the police for forensic DNA testing. DNA evidence can help sexual assault investigations and prosecutions by identifying offenders, revealing serial offenders through DNA matches across cases, and exonerating those who have been wrongly accused. In this article, we describe a 5-year action research project conducted with 1 city that had large numbers of untested SAKs-Detroit, Michigan-and our examination into why thousands of rape kits in this city were never submitted for forensic DNA testing. This mixed methods study combined ethnographic observations and qualitative interviews to identify stakeholders' perspectives as to why rape kits were not routinely submitted for testing. Then, we quantitatively examined whether these factors may have affected police practices regarding SAK testing, as evidenced by predictable changes in SAK submission rates over time. Chronic resource scarcity only partially explained why the organizations that serve rape victims-the police, crime lab, prosecution, and victim advocacy-could not test all rape kits, investigate all reported sexual assaults, and support all rape survivors. SAK submission rates significantly increased once criminal justice professionals in this city had full access to the FBI DNA forensic database Combined DNA Index System (CODIS), but even then, most SAKs were still not submitted for DNA testing. Building crime laboratories' capacities for DNA testing and training police on the utility of forensic evidence and best practices in sexual assault investigations can help remedy, and possibly prevent, the problem of untested rape kits. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  5. Hydrogeologic testing strategy for the Basalt Waste Isolation Project site

    International Nuclear Information System (INIS)

    Logsdon, M.J.; Verma, T.R.

    1984-01-01

    At the time of licensing for a proposed deep geologic repository for high-level nuclear waste, the Department of Energy (DOE) has the responsibility to present and defend a complete licensing/performance assessment of the geologic repository system. As part of its responsibilities, the Nuclear Regulatory Commission (NRC) staff will be required to perform an independent assessment of the groundwater flow system with respect to the technical criteria of 10 Code of Federal Regulations (CFR) Part 60. Specifically, the staff expects to use mathematical models to predict pre-emplacement and post-emplacement groundwater flow paths and travel times. These predictive assessments will be used to reach findings on compliance with the proposed EPA Standards (10 CFR 60.112), which apply to post-emplacement groundwater travel time along the path of likely radionuclide travel (10 CFR 60.113(2)). Predictive modeling of groundwater flow will require defensible conceptual models of the flow system, defensible boundary conditions, and defensible values of hydraulic parameters. The purpose fo this technical position is to provide guidance to DOE on an approach that the NRC staff considers acceptable in determining what hydrogeologic testing (including types of tests, scale of tests, and number of tests) at the Hanford site will be required to produce the hydraulic data necessary and sufficient to perform rigorous, quantitative modeling to support predictions of repository performance. 2 figures

  6. Pilot Test of an Innovative Interprofessional Education Assessment Strategy

    Science.gov (United States)

    Emmert, Michelle Christine

    2011-01-01

    The primary goal of this study was to test an innovative way of assessing students' teamwork skills in a controlled environment. Twenty-four second year students from Western University of Health Sciences (WesternU) participated in the experimental group and 22 third year students from WesternU participated in the control group. Students in the…

  7. Adaptive and Qualitative Changes in Encoding Strategy With Experience: Evidence From the Test-Expectancy Paradigm

    Science.gov (United States)

    Finley, Jason R.; Benjamin, Aaron S.

    2012-01-01

    Three experiments demonstrated learners’ abilities to adaptively and qualitatively accommodate their encoding strategies to the demands of an upcoming test. Stimuli were word pairs. In Experiment 1, test expectancy was induced for either cued recall (of targets given cues) or free recall (of targets only) across 4 study–test cycles of the same test format, followed by a final critical cycle featuring either the expected or the unexpected test format. For final tests of both cued and free recall, participants who had expected that test format outperformed those who had not. This disordinal interaction, supported by recognition and self-report data, demonstrated not mere differences in effort based on anticipated test difficulty, but rather qualitative and appropriate differences in encoding strategies based on expected task demands. Participants also came to appropriately modulate metacognitive monitoring (Experiment 2) and study-time allocation (Experiment 3) across study–test cycles. Item and associative recognition performance, as well as self-report data, revealed shifts in encoding strategies across trials; these results were used to characterize and evaluate the different strategies that participants employed for cued versus free recall and to assess the optimality of participants’ metacognitive control of encoding strategies. Taken together, these data illustrate a sophisticated form of metacognitive control, in which learners qualitatively shift encoding strategies to match the demands of anticipated tests. PMID:22103783

  8. Strategies for improving approximate Bayesian computation tests for synchronous diversification.

    Science.gov (United States)

    Overcast, Isaac; Bagley, Justin C; Hickerson, Michael J

    2017-08-24

    Estimating the variability in isolation times across co-distributed taxon pairs that may have experienced the same allopatric isolating mechanism is a core goal of comparative phylogeography. The use of hierarchical Approximate Bayesian Computation (ABC) and coalescent models to infer temporal dynamics of lineage co-diversification has been a contentious topic in recent years. Key issues that remain unresolved include the choice of an appropriate prior on the number of co-divergence events (Ψ), as well as the optimal strategies for data summarization. Through simulation-based cross validation we explore the impact of the strategy for sorting summary statistics and the choice of prior on Ψ on the estimation of co-divergence variability. We also introduce a new setting (β) that can potentially improve estimation of Ψ by enforcing a minimal temporal difference between pulses of co-divergence. We apply this new method to three empirical datasets: one dataset each of co-distributed taxon pairs of Panamanian frogs and freshwater fishes, and a large set of Neotropical butterfly sister-taxon pairs. We demonstrate that the choice of prior on Ψ has little impact on inference, but that sorting summary statistics yields substantially more reliable estimates of co-divergence variability despite violations of assumptions about exchangeability. We find the implementation of β improves estimation of Ψ, with improvement being most dramatic given larger numbers of taxon pairs. We find equivocal support for synchronous co-divergence for both of the Panamanian groups, but we find considerable support for asynchronous divergence among the Neotropical butterflies. Our simulation experiments demonstrate that using sorted summary statistics results in improved estimates of the variability in divergence times, whereas the choice of hyperprior on Ψ has negligible effect. Additionally, we demonstrate that estimating the number of pulses of co-divergence across co-distributed taxon

  9. Utilization of DNA comet assay and half embryo test to identify irradiated lentil

    International Nuclear Information System (INIS)

    Romanelli, Maria Fernanda; Villavicencio, Anna Lucia C.H.

    2001-01-01

    Full text: Legumes make an important contribution to human nutrition on a worldwide basis. Insect infestation cause extensive damage to stored grains. Over the last few decades some countries adopted food irradiation as a safe food process. Radiation's processing on foods improves hygienic quality and extends their shelf life. The use of radiation treatment to reduce the microbial population and thereby extend the shelf life in legumes has been reported in many papers. Irradiation has been shown to be an effective pest control method for these commodities and a good alternative to prohibited methyl bromide. Radiation disinfestation can facilitate trade in foods that often harbor insect pests of quarantine importance. Although the wholesomeness of irradiated food is no longer a question there is a need for irradiation control in the international trade of foods, in order to enhance the consumer confidence in the regulation. As a screening methods to identify irradiated lentils, processed by e-beam as a food treatment to disinfestation, the DNA Comet Assay and Half Embryo tests were performed. The methodologies used in this work are based upon biological changes that occur in Brazilian lentils. The samples were irradiated in an electron beam accelerator facility of Radiation Dynamics Inc., USA (E=1,5 MeV, l=25 mA). The irradiation doses were 0,7; 1,4 and 3,0 kGy at dry conditions. The thickness of samples was less than 0,5 cm. A sensitive technique to detect DNA fragmentation is the microgel electrophoresis of single cells or nuclei, also called 'comet assay'. Since the large molecule of DNA is an easy target for ionizing radiation, changes in DNA offer potential as a detection method. It is restricted to foods that have not been subjected to heat or other treatments, which also cause DNA fragmentation. Lentil samples were crushed with a mortar and pestle and was transferred to 3ml ice-cold PBS. This suspension was stirred for 5 minutes and filtered. 100μl cell

  10. AOF LTAO mode: reconstruction strategy and first test results

    Science.gov (United States)

    Oberti, Sylvain; Kolb, Johann; Le Louarn, Miska; La Penna, Paolo; Madec, Pierre-Yves; Neichel, Benoit; Sauvage, Jean-François; Fusco, Thierry; Donaldson, Robert; Soenke, Christian; Suárez Valles, Marcos; Arsenault, Robin

    2016-07-01

    GALACSI is the Adaptive Optics (AO) system serving the instrument MUSE in the framework of the Adaptive Optics Facility (AOF) project. Its Narrow Field Mode (NFM) is a Laser Tomography AO (LTAO) mode delivering high resolution in the visible across a small Field of View (FoV) of 7.5" diameter around the optical axis. From a reconstruction standpoint, GALACSI NFM intends to optimize the correction on axis by estimating the turbulence in volume via a tomographic process, then projecting the turbulence profile onto one single Deformable Mirror (DM) located in the pupil, close to the ground. In this paper, the laser tomographic reconstruction process is described. Several methods (virtual DM, virtual layer projection) are studied, under the constraint of a single matrix vector multiplication. The pseudo-synthetic interaction matrix model and the LTAO reconstructor design are analysed. Moreover, the reconstruction parameter space is explored, in particular the regularization terms. Furthermore, we present here the strategy to define the modal control basis and split the reconstruction between the Low Order (LO) loop and the High Order (HO) loop. Finally, closed loop performance obtained with a 3D turbulence generator will be analysed with respect to the most relevant system parameters to be tuned.

  11. Modeling Test and Treatment Strategies for Presymptomatic Alzheimer Disease

    Science.gov (United States)

    Burke, James F.; Langa, Kenneth M.; Hayward, Rodney A.; Albin, Roger L.

    2014-01-01

    Objectives In this study, we developed a model of presymptomatic treatment of Alzheimer disease (AD) after a screening diagnostic evaluation and explored the circumstances required for an AD prevention treatment to produce aggregate net population benefit. Methods Monte Carlo simulation methods were used to estimate outcomes in a simulated population derived from data on AD incidence and mortality. A wide variety of treatment parameters were explored. Net population benefit was estimated in aggregated QALYs. Sensitivity analyses were performed by individually varying the primary parameters. Findings In the base-case scenario, treatment effects were uniformly positive, and net benefits increased with increasing age at screening. A highly efficacious treatment (i.e. relative risk 0.6) modeled in the base-case is estimated to save 20 QALYs per 1000 patients screened and 221 QALYs per 1000 patients treated. Conclusions Highly efficacious presymptomatic screen and treat strategies for AD are likely to produce substantial aggregate population benefits that are likely greater than the benefits of aspirin in primary prevention of moderate risk cardiovascular disease (28 QALYS per 1000 patients treated), even in the context of an imperfect treatment delivery environment. PMID:25474698

  12. Potential of Environmental DNA to Evaluate Northern Pike (Esox lucius) Eradication Efforts: An Experimental Test and Case Study.

    Science.gov (United States)

    Dunker, Kristine J; Sepulveda, Adam J; Massengill, Robert L; Olsen, Jeffrey B; Russ, Ora L; Wenburg, John K; Antonovich, Anton

    2016-01-01

    Determining the success of invasive species eradication efforts is challenging because populations at very low abundance are difficult to detect. Environmental DNA (eDNA) sampling has recently emerged as a powerful tool for detecting rare aquatic animals; however, detectable fragments of DNA can persist over time despite absence of the targeted taxa and can therefore complicate eDNA sampling after an eradication event. This complication is a large concern for fish eradication efforts in lakes since killed fish can sink to the bottom and slowly decay. DNA released from these carcasses may remain detectable for long periods. Here, we evaluated the efficacy of eDNA sampling to detect invasive Northern pike (Esox lucius) following piscicide eradication efforts in southcentral Alaskan lakes. We used field observations and experiments to test the sensitivity of our Northern pike eDNA assay and to evaluate the persistence of detectable DNA emitted from Northern pike carcasses. We then used eDNA sampling and traditional sampling (i.e., gillnets) to test for presence of Northern pike in four lakes subjected to a piscicide-treatment designed to eradicate this species. We found that our assay could detect an abundant, free-roaming population of Northern pike and could also detect low-densities of Northern pike held in cages. For these caged Northern pike, probability of detection decreased with distance from the cage. We then stocked three lakes with Northern pike carcasses and collected eDNA samples 7, 35 and 70 days post-stocking. We detected DNA at 7 and 35 days, but not at 70 days. Finally, we collected eDNA samples ~ 230 days after four lakes were subjected to piscicide-treatments and detected Northern pike DNA in 3 of 179 samples, with a single detection at each of three lakes, though we did not catch any Northern pike in gillnets. Taken together, we found that eDNA can help to inform eradication efforts if used in conjunction with multiple lines of inquiry and sampling

  13. Potential of Environmental DNA to Evaluate Northern Pike (Esox lucius Eradication Efforts: An Experimental Test and Case Study.

    Directory of Open Access Journals (Sweden)

    Kristine J Dunker

    Full Text Available Determining the success of invasive species eradication efforts is challenging because populations at very low abundance are difficult to detect. Environmental DNA (eDNA sampling has recently emerged as a powerful tool for detecting rare aquatic animals; however, detectable fragments of DNA can persist over time despite absence of the targeted taxa and can therefore complicate eDNA sampling after an eradication event. This complication is a large concern for fish eradication efforts in lakes since killed fish can sink to the bottom and slowly decay. DNA released from these carcasses may remain detectable for long periods. Here, we evaluated the efficacy of eDNA sampling to detect invasive Northern pike (Esox lucius following piscicide eradication efforts in southcentral Alaskan lakes. We used field observations and experiments to test the sensitivity of our Northern pike eDNA assay and to evaluate the persistence of detectable DNA emitted from Northern pike carcasses. We then used eDNA sampling and traditional sampling (i.e., gillnets to test for presence of Northern pike in four lakes subjected to a piscicide-treatment designed to eradicate this species. We found that our assay could detect an abundant, free-roaming population of Northern pike and could also detect low-densities of Northern pike held in cages. For these caged Northern pike, probability of detection decreased with distance from the cage. We then stocked three lakes with Northern pike carcasses and collected eDNA samples 7, 35 and 70 days post-stocking. We detected DNA at 7 and 35 days, but not at 70 days. Finally, we collected eDNA samples ~ 230 days after four lakes were subjected to piscicide-treatments and detected Northern pike DNA in 3 of 179 samples, with a single detection at each of three lakes, though we did not catch any Northern pike in gillnets. Taken together, we found that eDNA can help to inform eradication efforts if used in conjunction with multiple lines of

  14. Potential of environmental DNA to evaluate Northern pike (Esox lucius) eradication efforts: An experimental test and case study

    Science.gov (United States)

    Dunker, Kristine J.; Sepulveda, Adam; Massengill, Robert L.; Olsen, Jeffrey B.; Russ, Ora L.; Wenburg, John K.; Antonovich, Anton

    2016-01-01

    Determining the success of invasive species eradication efforts is challenging because populations at very low abundance are difficult to detect. Environmental DNA (eDNA) sampling has recently emerged as a powerful tool for detecting rare aquatic animals; however, detectable fragments of DNA can persist over time despite absence of the targeted taxa and can therefore complicate eDNA sampling after an eradication event. This complication is a large concern for fish eradication efforts in lakes since killed fish can sink to the bottom and slowly decay. DNA released from these carcasses may remain detectable for long periods. Here, we evaluated the efficacy of eDNA sampling to detect invasive Northern pike (Esox lucius) following piscicide eradication efforts in southcentral Alaskan lakes. We used field observations and experiments to test the sensitivity of our Northern pike eDNA assay and to evaluate the persistence of detectable DNA emitted from Northern pike carcasses. We then used eDNA sampling and traditional sampling (i.e., gillnets) to test for presence of Northern pike in four lakes subjected to a piscicide-treatment designed to eradicate this species. We found that our assay could detect an abundant, free-roaming population of Northern pike and could also detect low-densities of Northern pike held in cages. For these caged Northern pike, probability of detection decreased with distance from the cage. We then stocked three lakes with Northern pike carcasses and collected eDNA samples 7, 35 and 70 days post-stocking. We detected DNA at 7 and 35 days, but not at 70 days. Finally, we collected eDNA samples ~ 230 days after four lakes were subjected to piscicide-treatments and detected Northern pike DNA in 3 of 179 samples, with a single detection at each of three lakes, though we did not catch any Northern pike in gillnets. Taken together, we found that eDNA can help to inform eradication efforts if used in conjunction with multiple lines of inquiry and sampling

  15. Evaluation of tests using DNA repair-deficient bacteria for predicting genotoxicity and carcinogenicity

    Energy Technology Data Exchange (ETDEWEB)

    Leifer, Z.; Kada, T.; Mandel, M.; Zeiger, E.; Stafford, R.; Rosenkranz, H.S.

    1981-01-01

    The detection of DNA-damaging agents by repair-deficient bacterial assays is based on the differential inhibition of growth of repair-proficient and repair-deficient bacterial pairs. The various methodologies used are described and recommendations are made for their improved use. In a survey of the literature through April 1979, 91 of 276 papers evaluated contained usable data, resulting in an analysis of 611 compounds that had been assayed in 1 or more of 55 pairs of repair-proficient and repair-deficient strains. The results indicate that a liquid suspension assay is more sensitive than a spot (diffusion) test. There was a 78% correspondence between results obtained with E. coli polA and Bacillus subtilis (H17/M45, 17A/45T) rec assay and between E. coli polA and Proteus mirabilis. In a comparison of test results with carcinogenicity data, 44 of 71 (62%) carcinogenic compounds assayed by the polA system were positive, 10 (14%) were negative, and 17 (24%) gave No Test or doubtful results. The results were analyzed with respect to chemical classes. E. coli polA detected the highest percentage of hydroxylamines and alkyl epoxides. The B. subtilis rec assay detected the highest percentage of nitrosamines and sulfur and nitrogen oxides. It is concluded that some of these test systems are effective tools for the detection of DNA-damaging and potentially carcinogenic compounds, especially if the assay is done in liquid suspension and if more than 1 pair of tester strains is used. Advantages and disadvantages of the assay are discussed and suggestions are made for improvements in the system.

  16. Testing the Efficacy of DNA Barcodes for Identifying the Vascular Plants of Canada.

    Science.gov (United States)

    Braukmann, Thomas W A; Kuzmina, Maria L; Sills, Jesse; Zakharov, Evgeny V; Hebert, Paul D N

    2017-01-01

    Their relatively slow rates of molecular evolution, as well as frequent exposure to hybridization and introgression, often make it difficult to discriminate species of vascular plants with the standard barcode markers (rbcL, matK, ITS2). Previous studies have examined these constraints in narrow geographic or taxonomic contexts, but the present investigation expands analysis to consider the performance of these gene regions in discriminating the species in local floras at sites across Canada. To test identification success, we employed a DNA barcode reference library with sequence records for 96% of the 5108 vascular plant species known from Canada, but coverage varied from 94% for rbcL to 60% for ITS2 and 39% for matK. Using plant lists from 27 national parks and one scientific reserve, we tested the efficacy of DNA barcodes in identifying the plants in simulated species assemblages from six biogeographic regions of Canada using BLAST and mothur. Mean pairwise distance (MPD) and mean nearest taxon distance (MNTD) were strong predictors of barcode performance for different plant families and genera, and both metrics supported ITS2 as possessing the highest genetic diversity. All three genes performed strongly in assigning the taxa present in local floras to the correct genus with values ranging from 91% for rbcL to 97% for ITS2 and 98% for matK. However, matK delivered the highest species discrimination (~81%) followed by ITS2 (~72%) and rbcL (~44%). Despite the low number of plant taxa in the Canadian Arctic, DNA barcodes had the least success in discriminating species from this biogeographic region with resolution ranging from 36% with rbcL to 69% with matK. Species resolution was higher in the other settings, peaking in the Woodland region at 52% for rbcL and 87% for matK. Our results indicate that DNA barcoding is very effective in identifying Canadian plants to a genus, and that it performs well in discriminating species in regions where floristic diversity is

  17. A Short Review on the Synthetic Strategies of Duocarmycin Analogs that are Powerful DNA Alkylating Agents.

    Science.gov (United States)

    Patil, Pravin C; Satam, Vijay; Lee, Moses

    2015-01-01

    The duocarmycins and CC-1065 are members of a class of DNA minor groove, AT-sequence selective, and adenine-N3 alkylating agents, isolated from Streptomyces sp. that exhibit extremely potent cytotoxicity against the growth of cancer cells grown in culture. Initial synthesis and structural modification of the cyclopropa[c] pyrrolo[3,2-e]indole (CPI) DNA-alkylating motif as well as the indole non-covalent binding region in the 1980s have led to several compounds that entered clinical trials as potential anticancer drugs. However, due to significant systemic toxicity none of the analogs have passed clinical evaluation. As a result, the intensity in the design, synthesis, and development of novel analogs of the duocarmycins has continued. Accordingly, in this review, which covers a period from the 1990s through the present time, the design and synthesis of duocarmycin SA are described along with the synthesis of novel and highly cytotoxic analogs that lack the chiral center. Examples of achiral analogs of duocarmycin SA described in this review include seco-DUMSA (39 and 40), seco-amino-CBI-TMI (13, Centanamycin), and seco-hydroxy-CBI-TMI (14). In addition, another novel class of biologically active duocarmycin SA analogs that contained the seco-iso-cyclopropylfurano[2,3-e]indoline (seco-iso-CFI) and seco-cyclopropyltetrahydrofurano[2,3-f]quinoline (seco-CFQ) DNA alkylating submit was also designed and synthesized. The synthesis of seco-iso-CFI-TMI (10, Tafuramycin A) and seco-CFQ-TMI (11, Tafuramycin B) is included in this review.

  18. HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy

    Science.gov (United States)

    Yan, Yumeng; Zhang, Di; Zhou, Pei; Li, Botong

    2017-01-01

    Abstract Protein–protein and protein–DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, here we have presented HDOCK, a novel web server of our hybrid docking algorithm of template-based modeling and free docking, in which cases with misleading templates can be rescued by the free docking protocol. The server supports protein–protein and protein–DNA/RNA docking and accepts both sequence and structure inputs for proteins. The docking process is fast and consumes about 10–20 min for a docking run. Tested on the cases with weakly homologous complexes of server. The HDOCK web server is available at http://hdock.phys.hust.edu.cn/. PMID:28521030

  19. Characteristics of test anxiety among medical students and congruence of strategies to address it

    Directory of Open Access Journals (Sweden)

    John Encandela

    2014-08-01

    Full Text Available Introduction: Medical students may experience test anxiety associated with ‘high stakes’ exams, such as Step 1 of the United States Medical Licensing Examination. Methods: We collected qualitative responses about test anxiety at three points in time from 93 second-year medical students engaged in studying for and taking Step 1. Results: Causes of test anxiety as reported by students were related to negative self-talk during preparation for the exam. Effects of anxiety had to do with emotional well-being, cognitive functioning, and physical well-being. Strategies included socializing with others and a variety of cognitive and physical approaches. Comparison of individuals’ strategies with causes and effects showed some congruence, but substantial incongruence between the types of strategies chosen and the reported causes and effects of test anxiety. Discussion: Students’ adoption of a ‘menu’ of strategies rather than one or two carefully selected strategies suggest inefficiencies that might be addressed by interventions, such as advisor-directed conversations with students and incorporating student self-assessment and strategies for managing anxiety within courses on test-taking. Such interventions are in need of further study. An annotated list of evidence-based strategies would be helpful to students and educators. Most important, test anxiety should be viewed by medical educators as a ‘real’ experience, and students would benefit from educator support.

  20. New strategy for stable-isotope-aided, multidimensional NMR spectroscopy of DNA oligomers

    Energy Technology Data Exchange (ETDEWEB)

    Ono, Okira; Tate, Shin-Ichi; Kainosho, Masatsune [Tokyo Metropolitan Univ., Tokyo (Japan)

    1994-12-01

    Nuclear Magnetic Resonance (NMR) is the most efficient method for determining the solution structures of biomolecules. By applying multidimensional heteronuclear NMR techniques to {sup 13}C/{sup 15}N-labeled proteins, we can determine the solution structures of proteins with molecular mass of 20 to 30kDa at an accuracy similar to that of x-ray crystallography. Improvements in NMR instrumentation and techniques as well as the development of protein engineering methods for labeling proteins have rapidly advanced multidimensional heteronuclear NMR of proteins. In contrast, multidimensional heteronuclear NMR studies of nucleic acids is less advanced because there were no efficient methods for preparing large amounts of labeled DNA/RNA oligomers. In this report, we focused on the chemical synthesis of DNA oligomers labeled at specific residue(s). RNA oligomers with specific labels, which are difficult to synthesize by the enzyme method, can be synthesized by the chemical method. The specific labels are useful for conformational analysis of larger molecules such as protein-nucleic acid complexes.

  1. Design of different strategies of multivalent DNA-based vaccination against rabies and canine distemper in mice and dogs

    Directory of Open Access Journals (Sweden)

    Touihri Leila

    2012-12-01

    Full Text Available Abstract Background During the vaccination campaigns, puppies younger than 3 months old are not targeted and remain unvaccinated for at least the first year of their lives. Almost half of the reported rabid dogs are 6 months or younger. Hence, we should recommend the vaccination against rabies of young puppies. Unfortunately, owing to the exposure of puppies to infections with either canine parvovirus (CPV or distemper virus (CDV after the intervention of the vaccinators, owners are reluctant to vaccinate puppies against rabies. Therefore, it is necessary to include the CPV and CDV valences in the vaccine against rabies. Multivalent DNA-based vaccination in dogs, including rabies and distemper valences, could help in raising vaccine coverage. Methods We have designed monovalent and multivalent DNA-based vaccine candidates for in vitro and in vivo assays. These plasmids encode to the rabies virus glycoprotein and/or the canine distemper virus hemagglutinin. The first strategy of multivalent DNA-based vaccination is by mixing plasmids encoding to a single antigen each. The second is by simply fusing the genes of the antigens together. The third is by adding the foot and mouth disease virus (FMDV 2A oligopeptide gene into the antigen genes. The last strategy is by the design and use of a bicistronic plasmid with an “Internal Ribosome Entry Site” (IRES domain. Results The monovalent construct against canine distemper was efficiently validated by inducing higher humoral immune responses compared to cell-culture-derived vaccine both in mice and dogs. All multivalent plasmids efficiently expressed both valences after in vitro transfection of BHK-21 cells. In BALB/c mice, the bicistronic IRES-dependant construct was the most efficient inducer of virus-neutralizing antibodies against both valences. It was able to induce better humoral immune responses compared to the administration of either cell-culture-derived vaccines or monovalent plasmids. The

  2. Design of different strategies of multivalent DNA-based vaccination against rabies and canine distemper in mice and dogs.

    Science.gov (United States)

    Touihri, Leila; Ahmed, Sami Belhaj; Chtourou, Yacine; Daoud, Rahma; Bahloul, Chokri

    2012-12-27

    During the vaccination campaigns, puppies younger than 3 months old are not targeted and remain unvaccinated for at least the first year of their lives. Almost half of the reported rabid dogs are 6 months or younger. Hence, we should recommend the vaccination against rabies of young puppies. Unfortunately, owing to the exposure of puppies to infections with either canine parvovirus (CPV) or distemper virus (CDV) after the intervention of the vaccinators, owners are reluctant to vaccinate puppies against rabies. Therefore, it is necessary to include the CPV and CDV valences in the vaccine against rabies. Multivalent DNA-based vaccination in dogs, including rabies and distemper valences, could help in raising vaccine coverage. We have designed monovalent and multivalent DNA-based vaccine candidates for in vitro and in vivo assays. These plasmids encode to the rabies virus glycoprotein and/or the canine distemper virus hemagglutinin. The first strategy of multivalent DNA-based vaccination is by mixing plasmids encoding to a single antigen each. The second is by simply fusing the genes of the antigens together. The third is by adding the foot and mouth disease virus (FMDV) 2A oligopeptide gene into the antigen genes. The last strategy is by the design and use of a bicistronic plasmid with an "Internal Ribosome Entry Site" (IRES) domain. The monovalent construct against canine distemper was efficiently validated by inducing higher humoral immune responses compared to cell-culture-derived vaccine both in mice and dogs. All multivalent plasmids efficiently expressed both valences after in vitro transfection of BHK-21 cells. In BALB/c mice, the bicistronic IRES-dependant construct was the most efficient inducer of virus-neutralizing antibodies against both valences. It was able to induce better humoral immune responses compared to the administration of either cell-culture-derived vaccines or monovalent plasmids. The FMDV 2A was also efficient in the design of multivalent

  3. Value of high-risk HPV-DNA testing in the triage of ASCUS.

    Science.gov (United States)

    Silverloo, Iréne; Andrae, Bengt; Wilander, Erik

    2009-01-01

    OBJECTIVE. Atypical squamous cells of undetermined significance (ASCUS) cells, occurring in organized cytological screening, may be either high-risk human papillomavirus (HPV) positive or negative. To refine the assessment of women with ASCUS, a high-risk HPV-DNA test is recommended as triage in Sweden. A total of 197 consecutive women (mean age 39 years, range 21-60) with a diagnosis of ASCUS from the primary screening were selected for triage. Their cervical smears were collected and evaluated by using conventional cytological examination in combination with a high-risk HPV-DNA test (hybrid capture 2). The women were categorized into four groups: Group A, Cytology + /HPV + ; Group B, Cytology-/HPV + ; Group C, Cytology + /HPV-; and Group D, Cytology-/ HPV-. Women within Groups A-C were admitted for colposcopy and cervical biopsy. The women in Group D were considered as a low-risk group for tumor development, and were re-examined after three years in the next round of the organized screening. In women in Group A (n=58) the prevalence of histological verified CIN2-3 was 41%, in Group B (n=41) 20%, and in Group C (n=9) 0%. In Group D (n=89), repeated primary screening three years later revealed CIN2-3 in two biopsies from 74 women studied (age in women with ASCUS. It was 74% in women or =50 years. Adding a high-risk HPV test in secondary screening increased the identification of women with CIN2-3 lesions by 33% in comparison with repeat cytology (p=0.01). The clinical significance of the ASCUS diagnosis varied with age of the women.

  4. The DNA comet assay and the germination test in detection of food treated by ionizing radiation

    International Nuclear Information System (INIS)

    Huachaca, Nelida Simona Marin

    2002-01-01

    Two methods of irradiated food detection, one biochemical, the comet assay and, other biological, the germination test, were applied in bovine meat and fruit samples. The comet assay detects the damage on DNA caused by ionizing radiation. The germination test evaluates the sensitivity to radiation of seeds as for germination ability, shooting and, rooting. The samples were irradiated in gamma font and electron accelerator. For bovine meat samples, the doses were 0.0; 2.5; 4.5 e 7.0 kGy at chilled condition and, 0.0; 2.5; 4.5; 7.0 e 8.5 kGy at frozen conditions. For fruit samples such as melon, watermelon, apple, orange, papaya and, tomato, the doses were: 0.0; 0.5; 0.75; 1.0; 2.0 e 4.0 kGy. The differences between the gamma rays and the electron beam effects on extent of DNA migration and, on shooting and rooting, showed to be similar. The comet assay, under neutral conditions, permitted to discriminate between irradiated and unirradiated bovine meat samples, until one month of storage. Also, it was possible to distinguish, by the comet assay, the control sample with regard to irradiated fruit, at doses as low as 0,5 kGy. In the germination test, the root length was the best parameter to discriminate irradiated and unirradiated samples of melon, watermelon and tomato, while the germination percent was the best parameter for apple and orange. (author)

  5. The Role of Alternative Testing Strategies in Environmental Risk Assessment of Engineered Nanomaterials

    OpenAIRE

    Hjorth, Rune; Holden, Patricia; Hansen, Steffen Foss; Colman, Ben; Grieger, Khara; Hendren, Christine

    2017-01-01

    Within toxicology there is a pressure to find new test systems and organisms to replace, reduce and refine animal testing. In nanoecotoxicology the need for alternative testing strategies (ATS) is further emphasized as the validity of tests and risk assessment practices developed for dissolved chemicals are challenged. Nonetheless, standardized whole organism animal testing is still considered the gold standard for environmental risk assessment. Advancing risk analysis of engineered nanomater...

  6. TOXICITY TESTING IN THE 21ST CENTURY: A VISION AND A STRATEGY

    DEFF Research Database (Denmark)

    Krewski, D.; Acosta, D.; Andersen, M.

    2010-01-01

    With the release of the landmark report Toxicity Testing in the 21st Century: A Vision and a Strategy, the U. S. National Academy of Sciences, in 2007, precipitated a major change in the way toxicity testing is conducted. It envisions increased efficiency in toxicity testing and decreased animal ...

  7. Teaching Study Skills and Test-Taking Strategies to Elementary School Students.

    Science.gov (United States)

    Beidel, Deborah C.; Turner, Samuel M.; Taylor-Ferreira, Jill C.

    1999-01-01

    Presents and evaluates a pilot program to reduce test anxiety and related social-evaluative concerns. The Testbusters program teaches effective study habits, study skills, and test-taking strategies for children in grades 4 through 7. Results indicate that Testbusters decreased general levels of test anxiety and improved overall grade point…

  8. Adaptive and Qualitative Changes in Encoding Strategy with Experience: Evidence from the Test-Expectancy Paradigm

    Science.gov (United States)

    Finley, Jason R.; Benjamin, Aaron S.

    2012-01-01

    Three experiments demonstrated learners' abilities to adaptively and qualitatively accommodate their encoding strategies to the demands of an upcoming test. Stimuli were word pairs. In Experiment 1, test expectancy was induced for either cued recall (of targets given cues) or free recall (of targets only) across 4 study-test cycles of the same…

  9. Test Takers' Performance Appraisals, Appraisal Calibration, and Cognitive and Metacognitive Strategy Use

    Science.gov (United States)

    Phakiti, Aek

    2016-01-01

    The current study explores the nature and relationships among test takers' performance appraisals, appraisal calibration, and reported cognitive and metacognitive strategy use in a language test situation. Performance appraisals are executive processes of strategic competence for judging test performance (e.g., evaluating the correctness or…

  10. Targeting the Parasite's DNA with Methyltriazenyl Purine Analogs Is a Safe, Selective, and Efficacious Antitrypanosomal Strategy

    NARCIS (Netherlands)

    Rodenko, B.; Wanner, M.J.; Alkhaldi, A.A.M.; Ebiloma, G.U.; Barnes, R.L.; Kaiser, M.; Brun, R.; McCulloch, R.; Koomen, G.J.; de Koning, H.P.

    2015-01-01

    The human and veterinary disease complex known as African trypanosomiasis continues to inflict significant global morbidity, mortality, and economic hardship. Drug resistance and toxic side effects of old drugs call for novel and unorthodox strategies for new and safe treatment options. We designed

  11. Listening Strategies in the L2 Classroom: More Practice, Less Testing

    Science.gov (United States)

    Aponte-de-Hanna, Cecilia

    2012-01-01

    This paper looks at the history of listening strategies development from the first studies on strategies used by L2 learners to the most current studies specific to L2 listening, and how this theory can be incorporated into classroom teaching that fosters practice, not testing. This paper also examines the type of needs analysis and diagnostic…

  12. A pilot study to evaluate an efficient testing strategy for surveillance ...

    African Journals Online (AJOL)

    Introduction: Control strategies for schistosomiasis depend on the understanding of the population specific magnitude of the infection. We present pilot results of a testing strategy suggested by theoretical statistical investigation that lowers cost yet retains similar accuracy profile as the standard Kato-Katz technique.

  13. Development of Software and Strategies for Battery Management System Testing on HIL Simulator

    DEFF Research Database (Denmark)

    Fleischer, Christian; Sauer, Dirk Uwe; Barreras, Jorge Varela

    2016-01-01

    of complexity of the tests, the higher the demands for ad hoc development of SW and strategies. With regard to the latter, there is not a universal definition and there are different points of view. Therefore different strategies may be followed, which can be classified into many different ways according...

  14. Validation of a Human Papillomavirus (HPV) DNA Cervical Screening Test That Provides Expanded HPV Typing.

    Science.gov (United States)

    Demarco, Maria; Carter-Pokras, Olivia; Hyun, Noorie; Castle, Philip E; He, Xin; Dallal, Cher M; Chen, Jie; Gage, Julia C; Befano, Brian; Fetterman, Barbara; Lorey, Thomas; Poitras, Nancy; Raine-Bennett, Tina R; Wentzensen, Nicolas; Schiffman, Mark

    2018-05-01

    As cervical cancer screening shifts from cytology to human papillomavirus (HPV) testing, a major question is the clinical value of identifying individual HPV types. We aimed to validate Onclarity (Becton Dickinson Diagnostics, Sparks, MD), a nine-channel HPV test recently approved by the FDA, by assessing (i) the association of Onclarity types/channels with precancer/cancer; (ii) HPV type/channel agreement between the results of Onclarity and cobas (Roche Molecular Systems, Pleasanton, CA), another FDA-approved test; and (iii) Onclarity typing for all types/channels compared to typing results from a research assay (linear array [LA]; Roche). We compared Onclarity to histopathology, cobas, and LA. We tested a stratified random sample ( n = 9,701) of discarded routine clinical specimens that had tested positive by Hybrid Capture 2 (HC2; Qiagen, Germantown, MD). A subset had already been tested by cobas and LA ( n = 1,965). Cervical histopathology was ascertained from electronic health records. Hierarchical Onclarity channels showed a significant linear association with histological severity. Onclarity and cobas had excellent agreement on partial typing of HPV16, HPV18, and the other 12 types as a pool (sample-weighted kappa value of 0.83); cobas was slightly more sensitive for HPV18 and slightly less sensitive for the pooled high-risk types. Typing by Onclarity showed excellent agreement with types and groups of types identified by LA (kappa values from 0.80 for HPV39/68/35 to 0.97 for HPV16). Onclarity typing results corresponded well to histopathology and to an already validated HPV DNA test and could provide additional clinical typing if such discrimination is determined to be clinically desirable. This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.

  15. Putting it all behind: long-term psychological impact of an inconclusive DNA test result for breast cancer.

    Science.gov (United States)

    van Dijk, Sandra; Otten, Wilma; Tollenaar, Rob A E M; van Asperen, Christi J; Tibben, Aad

    2008-10-01

    An inconclusive DNA-result for breast cancer may leave women with uncertainty that cannot be relieved. We assessed the influence of beliefs women held about their inconclusive DNA-result on psychological well-being and whether women had been able to put the period of DNA testing behind them. In total, 215 women completed a baseline and a follow-up questionnaire 2.5 till 7 years after DNA test disclosure. Within the group of 147 women who received an inconclusive result (either a personal result or the result of an affected family member) multiple regression analyses were applied to investigate the relevance of women's personal beliefs. Personal beliefs and ambivalence about an inconclusive DNA-result were associated with cancer-related worry and distress (P testing behind them, even after controlling for all measures of psychological distress (P Psychological distress measures may provide an important but incomplete picture of how women make sense of an inconclusive DNA-result. These findings underscore the importance of discussing counselees' beliefs and expectations openly to enhance well-being and adaptation on the long term.

  16. A simple strategy for subcloning and amplifying random multimegabase subchromosomal acentric DNA fragments as double minute chromosomes

    International Nuclear Information System (INIS)

    Hahn, P.J.; Giddings, L.; Lane, M.J.

    1989-01-01

    Restriction mapping of relatively large genomes (e.g. human) utilizing randomly generated DNA segments requires high mapping redundancy to successfully organize 'contigs' to represent the entire genome. The number of independent DNA segment maps required is dependent on the average size of a mapping segment; the larger the segment, the fewer required. The authors have developed a strategy for subcloning intact multimegabase subchromosomal fragments as double minute chromosomes. Such fragments could serve as primary mapping elements or as adjunct (linking) fragments to rapidly connect already existent contigs generated using yeast artificial chromosomes or cosmids. They present several lines of evidence supporting the viability of this approach. (1) X-ray treated EMT-6 mouse cells (7.5 Gr.) which are selected over several months with increasing levels of methotrexate (MTX) contain highly amplified circular DNA molecules (double minutes) which include the dihydrofolate reductase (DHFR) gene in a size range between 1,000 and 3,500 kilobases as determined by pulsed-field gel electrophoresis and these acentric chromosomal fragments have been stably maintained in culture for at least a year. (2) Preliminary data based on experiments involving fusion of X-irradiated Chinese Hamster Ovary (CH0 DG44) cells containing randomly inserted cotransfected Neomycin resistance and DHFR genes to mouse EMT-6 cells shows that the linked genes can be readily cotransferred as acentric subchromosomal fragment(s) suitable for gene amplification. (3) The studies of CHO cells with cell fusion transferred X-ray induced chromosomal fragments containing the natural CHO DHFR gene suggest that transferred chromosome fragments undergo gene amplification much more readily than nonfragmented endogenous DHFR genes

  17. Alternative Testing Strategies for Nanomaterials: State of the Science and Considerations for Risk Analysis.

    Science.gov (United States)

    Shatkin, J A; Ong, K J

    2016-08-01

    The rapid growth of the nanotechnology industry has warranted equal progress in the nanotoxicology and risk assessment fields. In vivo models have traditionally been used to determine human and environmental risk for chemicals; however, the use of these tests has limitations, and there are global appeals to develop reliable alternatives to animal testing. Many have investigated the use of alternative (nonanimal) testing methods and strategies have quickly developed and resulted in the generation of large toxicological data sets for numerous nanomaterials (NMs). Due to the novel physicochemical properties of NMs that are related to surface characteristics, the approach toward toxicity test development has distinct considerations from traditional chemicals, bringing new requirements for adapting these approaches for NMs. The methodical development of strategies that combine multiple alternative tests can be useful for predictive NM risk assessment and help screening-level decision making. This article provides an overview of the main developments in alternative methods and strategies for reducing uncertainty in NM risk assessment, including advantages and disadvantages of in vitro, ex vivo, and in silico methods, and examples of existing comprehensive strategies. In addition, knowledge gaps are identified toward improvements for experimental and strategy design, specifically highlighting the need to represent realistic exposure scenarios and to consider NM-specific concerns such as characterization, assay interferences, and standardization. Overall, this article aims to improve the reliability and utility of alternative testing methods and strategies for risk assessment of manufactured NMs. © 2016 Society for Risk Analysis.

  18. Recent advances in therapeutic recruitment of mammalian RNAi and bacterial CRISPR-Cas DNA interference pathways as emerging antiviral strategies.

    Science.gov (United States)

    Chin, Wei-Xin; Ang, Swee Kim; Chu, Justin Jang Hann

    2017-01-01

    In invertebrate eukaryotes and prokaryotes, respectively, the RNAi and clustered regularly interspaced short palindromic repeats-CRISPR-associated (CRISPR-Cas) pathways are highly specific and efficient RNA and DNA interference systems, and are well characterised as potent antiviral systems. It has become possible to recruit or reconstitute these pathways in mammalian cells, where they can be directed against desired host or viral targets. The RNAi and CRISPR-Cas systems can therefore yield ideal antiviral therapeutics, capable of specific and efficient viral inhibition with minimal off-target effects, but development of such therapeutics can be slow. This review covers recent advances made towards developing RNAi or CRISPR-Cas strategies for clinical use. These studies address the delivery, toxicity or target design issues that typically plague the in vivo or clinical use of these technologies. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Analysis of fingerprint samples, testing various conditions, for forensic DNA identification.

    Science.gov (United States)

    Ostojic, Lana; Wurmbach, Elisa

    2017-01-01

    Fingerprints can be of tremendous value for forensic biology, since they can be collected from a wide variety of evident types, such as handles of weapons, tools collected in criminal cases, and objects with no apparent staining. DNA obtained from fingerprints varies greatly in quality and quantity, which ultimately affects the quality of the resulting STR profiles. Additional difficulties can arise when fingerprint samples show mixed STR profiles due to the handling of multiple persons. After applying a tested protocol for sample collection (swabbing with 5% Triton X-100), DNA extraction (using an enzyme that works at elevated temperatures), and PCR amplification (AmpFlSTR® Identifiler® using 31cycles) extensive analysis was performed to better understand the challenges inherent to fingerprint samples, with the ultimate goal of developing valuable profiles (≥50% complete). The impact of time on deposited fingerprints was investigated, revealing that while the quality of profiles deteriorated, full STR profiles could still be obtained from samples after 40days of storage at room temperature. By comparing the STR profiles from fingerprints of the dominant versus the non-dominant hand, we found a slightly better quality from the non-dominant hand, which was not always significant. Substrates seem to have greater effects on fingerprints. Tests on glass, plastic, paper and metal (US Quarter dollar, made of Cu and Ni), common substrates in offices and homes, showed best results for glass, followed by plastic and paper, while almost no profiles were obtained from a Quarter dollar. Important for forensic casework, we also assessed three-person mixtures of touched fingerprint samples. Unlike routinely used approaches for sampling evidence, the surface of an object (bottle) was sectioned into six equal parts and separate samples were taken from each section. The samples were processed separately for DNA extraction and STR amplification. The results included a few single

  20. How Human Papillomavirus Replication and Immune Evasion Strategies Take Advantage of the Host DNA Damage Repair Machinery.

    Science.gov (United States)

    Bordignon, Valentina; Di Domenico, Enea Gino; Trento, Elisabetta; D'Agosto, Giovanna; Cavallo, Ilaria; Pontone, Martina; Pimpinelli, Fulvia; Mariani, Luciano; Ensoli, Fabrizio

    2017-12-19

    The DNA damage response (DDR) is a complex signalling network activated when DNA is altered by intrinsic or extrinsic agents. DDR plays important roles in genome stability and cell cycle regulation, as well as in tumour transformation. Viruses have evolved successful life cycle strategies in order to ensure a chronic persistence in the host, virtually avoiding systemic sequelae and death. This process promotes the periodic shedding of large amounts of infectious particles to maintain a virus reservoir in individual hosts, while allowing virus spreading within the community. To achieve such a successful lifestyle, the human papilloma virus (HPV) needs to escape the host defence systems. The key to understanding how this is achieved is in the virus replication process that provides by itself an evasion mechanism by inhibiting and delaying the host immune response against the viral infection. Numerous studies have demonstrated that HPV exploits both the ataxia-telangiectasia mutated (ATM) and ataxia-telangiectasia and rad3-related (ATR) DDR pathways to replicate its genome and maintain a persistent infection by downregulating the innate and cell-mediated immunity. This review outlines how HPV interacts with the ATM- and ATR-dependent DDR machinery during the viral life cycle to create an environment favourable to viral replication, and how the interaction with the signal transducers and activators of transcription (STAT) protein family and the deregulation of the Janus kinase (JAK)-STAT pathways may impact the expression of interferon-inducible genes and the innate immune responses.

  1. Proof-testing strategies induced by dangerous detected failures of safety-instrumented systems

    International Nuclear Information System (INIS)

    Liu, Yiliu; Rausand, Marvin

    2016-01-01

    Some dangerous failures of safety-instrumented systems (SISs) are detected almost immediately by diagnostic self-testing as dangerous detected (DD) failures, whereas other dangerous failures can only be detected by proof-testing, and are therefore called dangerous undetected (DU) failures. Some items may have a DU- and a DD-failure at the same time. After the repair of a DD-failure is completed, the maintenance team has two options: to perform an insert proof test for DU-failure or not. If an insert proof test is performed, it is necessary to decide whether the next scheduled proof test should be postponed or performed at the scheduled time. This paper analyzes the effects of different testing strategies on the safety performance of a single channel of a SIS. The safety performance is analyzed by Petri nets and by approximation formulas and the results obtained by the two approaches are compared. It is shown that insert testing improves the safety performance of the channel, but the feasibility and cost of the strategy may be a hindrance to recommend insert testing. - Highlights: • Identify the tests induced by detected failures. • Model the testing strategies following DD-failures. • Propose analytical formulas for effects of strategies. • Simulate and verify the proposed models.

  2. Implementing a Standardized Social Networks Testing Strategy in a Low HIV Prevalence Jurisdiction.

    Science.gov (United States)

    Schumann, Casey; Kahn, Danielle; Broaddus, Michelle; Dougherty, Jacob; Elderbrook, Megan; Vergeront, James; Westergaard, Ryan

    2018-05-15

    Alternative HIV testing strategies are needed to engage individuals not reached by traditional clinical or non-clinical testing programs. A social networks recruitment strategy, in which people at risk for or living with HIV are enlisted and trained by community-based agencies to recruit individuals from their social, sexual, or drug-using networks for HIV testing, demonstrates higher positivity rates compared to other non-clinical recruitment strategies in some jurisdictions. During 2013-2015, a social networks testing protocol was implemented in Wisconsin to standardize an existing social networks testing program. Six community-based, non-clinical agencies with multiple sites throughout the state implemented the protocol over the 2-year period. Both quantitative and qualitative data were collected. The new positivity rate (0.49%) through social networks testing did not differ from that of traditional counseling, testing, and referral recruitment methods (0.48%). Although social networks testing did not yield a higher new positivity rate compared to other testing strategies, it proved to be successful at reaching high risk individuals who may not otherwise engage in HIV testing.

  3. Effectiveness comparison of partially executed t-way test suite based generated by existing strategies

    Science.gov (United States)

    Othman, Rozmie R.; Ahmad, Mohd Zamri Zahir; Ali, Mohd Shaiful Aziz Rashid; Zakaria, Hasneeza Liza; Rahman, Md. Mostafijur

    2015-05-01

    Consuming 40 to 50 percent of software development cost, software testing is one of the most resource consuming activities in software development lifecycle. To ensure an acceptable level of quality and reliability of a typical software product, it is desirable to test every possible combination of input data under various configurations. Due to combinatorial explosion problem, considering all exhaustive testing is practically impossible. Resource constraints, costing factors as well as strict time-to-market deadlines are amongst the main factors that inhibit such consideration. Earlier work suggests that sampling strategy (i.e. based on t-way parameter interaction or called as t-way testing) can be effective to reduce number of test cases without effecting the fault detection capability. However, for a very large system, even t-way strategy will produce a large test suite that need to be executed. In the end, only part of the planned test suite can be executed in order to meet the aforementioned constraints. Here, there is a need for test engineers to measure the effectiveness of partially executed test suite in order for them to assess the risk they have to take. Motivated by the abovementioned problem, this paper presents the effectiveness comparison of partially executed t-way test suite generated by existing strategies using tuples coverage method. Here, test engineers can predict the effectiveness of the testing process if only part of the original test cases is executed.

  4. Rapid diagnostic tests as a source of DNA for Plasmodium species-specific real-time PCR

    Directory of Open Access Journals (Sweden)

    Van Esbroeck Marjan

    2011-03-01

    Full Text Available Abstract Background This study describes the use of malaria rapid diagnostic tests (RDTs as a source of DNA for Plasmodium species-specific real-time PCR. Methods First, the best method to recover DNA from RDTs was investigated and then the applicability of this DNA extraction method was assessed on 12 different RDT brands. Finally, two RDT brands (OptiMAL Rapid Malaria Test and SDFK60 malaria Ag Plasmodium falciparum/Pan test were comprehensively evaluated on a panel of clinical samples submitted for routine malaria diagnosis at ITM. DNA amplification was done with the 18S rRNA real-time PCR targeting the four Plasmodium species. Results of PCR on RDT were compared to those obtained by PCR on whole blood samples. Results Best results were obtained by isolating DNA from the proximal part of the nitrocellulose component of the RDT strip with a simple DNA elution method. The PCR on RDT showed a detection limit of 0.02 asexual parasites/μl, which was identical to the same PCR on whole blood. For all 12 RDT brands tested, DNA was detected except for one brand when a low parasite density sample was applied. In RDTs with a plastic seal covering the nitrocellulose strip, DNA extraction was hampered. PCR analysis on clinical RDT samples demonstrated correct identification for single species infections for all RDT samples with asexual parasites of P. falciparum (n = 60, Plasmodium vivax (n = 10, Plasmodium ovale (n = 10 and Plasmodium malariae (n = 10. Samples with only gametocytes were detected in all OptiMAL and in 10 of the 11 SDFK60 tests. None of the negative samples (n = 20 gave a signal by PCR on RDT. With PCR on RDT, higher Ct-values were observed than with PCR on whole blood, with a mean difference of 2.68 for OptiMAL and 3.53 for SDFK60. Mixed infections were correctly identified with PCR on RDT in 4/5 OptiMAL tests and 2/5 SDFK60 tests. Conclusions RDTs are a reliable source of DNA for Plasmodium real-time PCR. This study demonstrates the

  5. Conceptual design and testing strategy of a dual functional lithium-lead test blanket module in ITER and EAST

    International Nuclear Information System (INIS)

    Wu, Y.

    2007-01-01

    A dual functional lithium-lead (DFLL) test blanket module (TBM) concept has been proposed for testing in the International Thermonuclear Experimental Reactor (ITER) and the Experimental Advanced Superconducting Tokamak (EAST) in China to demonstrate the technologies of the liquid lithium-lead breeder blankets with emphasis on the balance between the risks and the potential attractiveness of blanket technology development. The design of DFLL-TBM concept has the flexibility of testing both the helium-cooled quasi-static lithium-lead (SLL) blanket concept and the He/PbLi dual-cooled lithium-lead (DLL) blanket concept. This paper presents an effective testing strategy proposed to achieve the testing target of SLL and DLL DEMO blankets relevant conditions, which includes three parts: materials R and D and small-scale out-of-pile mockups testing in loops, middle-scale TBMs pre-testing in EAST and full-scale consecutive TBMs testing corresponding to different operation phases of ITER during the first 10 years. The design of the DFLL-TBM concept and the testing strategy ability to test TBMs for both blanket concepts in sequence and or in parallel for both ITER and EAST are discussed

  6. Characterization of the human DNA gut virome across populations with different subsistence strategies and geographical origin.

    Science.gov (United States)

    Rampelli, Simone; Turroni, Silvia; Schnorr, Stephanie L; Soverini, Matteo; Quercia, Sara; Barone, Monica; Castagnetti, Andrea; Biagi, Elena; Gallinella, Giorgio; Brigidi, Patrizia; Candela, Marco

    2017-11-01

    It is a matter of fact that the human gut microbiome also includes a non-bacterial fraction represented by eukaryotic cells and viruses. To further explore the gut microbiome variation in human populations, here we characterized the human DNA viral community from publicly available gut metagenome data sets from human populations with different geographical origin and lifestyle. In particular, such data sets encompass microbiome information from two western urban societies (USA and Italy), as well as two traditional hunter-gatherer communities (the Hadza from Tanzania and Matses from Peru) and one pre-agricultural tribe (Tunapuco from Peru). Our results allowed for the first taxonomic reconstruction of the complex viral metacommunities within the human gut. The core virome structure included herpesviruses, papillomaviruses, polyomaviruses, adenoviruses and anelloviruses. Using Random Forests and a co-occurrence analysis approach, we identified the viruses that distinguished populations according to their geographical origin and/or lifestyle. This paves the way for new research aimed at investigating the biological role of the gut virome in human physiology, and the importance of our viral counterpart in the microbiome-host co-evolutionary process. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  7. Assessing the geographic origin of the invasive grey squirrel using DNA sequencing: Implications for management strategies

    Directory of Open Access Journals (Sweden)

    Claire D. Stevenson-Holt

    2015-01-01

    Full Text Available The invasive grey squirrel Sciurus carolinensis has become a major pest species causing negative effects to forestry and biodiversity. This study aims to assess the origin of grey squirrel within Cumbria using phylogeographic analysis to aid in management and control. The work reported analysed mitochondrial DNA sequences in the D-Loop gene of 73 grey squirrel individuals from multiple locations in the UK. The results indicate that individuals in north Cumbria are derived from individuals from Scotland and North East England. Other individuals in north Cumbria share a unique haplotype with south Cumbria and Lancashire suggesting a southerly origin and movement around or over the Cumbrian Mountain range which is thought of as a barrier to movements. The assessment of invasive species geographical origin and the identification of potential wildlife transit corridors through natural barriers are becoming more important as species shift range in response to environmental and ecological changes. With the grey squirrel population expansion also occurring in Italy, the European red squirrel may become threatened across its entire range. It is crucial to understand the population origins of the invasive grey squirrel and landscape usage to successfully manage the incursion routes and control the population.

  8. An Effective Strategy to Build Up a Balanced Test Suite for Spectrum-Based Fault Localization

    Directory of Open Access Journals (Sweden)

    Ning Li

    2016-01-01

    Full Text Available During past decades, many automated software faults diagnosis techniques including Spectrum-Based Fault Localization (SBFL have been proposed to improve the efficiency of software debugging activity. In the field of SBFL, suspiciousness calculation is closely related to the number of failed and passed test cases. Studies have shown that the ratio of the number of failed and passed test case has more significant impact on the accuracy of SBFL than the total number of test cases, and a balanced test suite is more beneficial to improving the accuracy of SBFL. Based on theoretical analysis, we proposed an PNF (Passed test cases, Not execute Faulty statement strategy to reduce test suite and build up a more balanced one for SBFL, which can be used in regression testing. We evaluated the strategy making experiments using the Siemens program and Space program. Experiments indicated that our PNF strategy can be used to construct a new test suite effectively. Compared with the original test suite, the new one has smaller size (average 90% test case was reduced in experiments and more balanced ratio of failed test cases to passed test cases, while it has the same statement coverage and fault localization accuracy.

  9. Design and performance testing of a DNA extraction assay for sensitive and reliable quantification of acetic acid bacteria directly in red wine using real time PCR

    Directory of Open Access Journals (Sweden)

    Cédric eLONGIN

    2016-06-01

    Full Text Available Although strategies exist to prevent AAB contamination, the increased interest for wines with low sulfite addition leads to greater AAB spoilage. Hence there is a real need for a rapid, specific, sensitive and reliable method for detecting these spoilage bacteria. All these requirements are met by real time Polymerase Chain Reaction (or quantitative PCR; qPCR. Here, we compare existing methods of isolating DNA and their adaptation to a red wine matrix. Two different protocols for isolating DNA and three PCR mix compositions were tested to select the best method. The addition of insoluble polyvinylpolypyrrolidone (PVPP at 1% (v/v during DNA extraction using a protocol succeeded in eliminating PCR inhibitors from red wine. We developed a bacterial internal control which was efficient in avoiding false negative results due to decreases in the efficiency of DNA isolation and/or amplification. The specificity, linearity, repeatability and reproducibility of the method were evaluated. A standard curve was established for the enumeration of AAB inoculated into red wines. The limit of quantification in red wine was 3.7 log AAB/mL and about 2.8 log AAB/mL when the volume of the samples was increased from 1 mL to 10 mL. Thus the DNA extraction method developed in this paper allows sensitive and reliable AAB quantification without underestimation thanks to the presence of an internal control. Moreover, monitoring of both the AAB population and the amount of acetic acid in ethanol medium and red wine highlighted that a minimum about 6.0 log cells/mL of AAB is needed to significantly increase the production of acetic acid leading to spoilage.

  10. Effectiveness of a Test-Taking Strategy on Achievement in Essay Tests for Students with Learning Disabilities

    Science.gov (United States)

    Therrien, William J.; Hughes, Charles; Kapelski, Cory; Mokhtari, Kouider

    2009-01-01

    Research was conducted to ascertain if an essay-writing strategy was effective at improving the achievement on essay tests for 7th- and 8th-grade students with reading and writing disabilities. Students were assigned via a stratified random sample to treatment or control group. Student scores were also compared to students without learning…

  11. Decision making about healthcare-related tests and diagnostic test strategies. Paper 2: a review of methodological and practical challenges

    NARCIS (Netherlands)

    Mustafa, Reem A.; Wiercioch, Wojtek; Cheung, Adrienne; Prediger, Barbara; Brozek, Jan; Bossuyt, Patrick; Garg, Amit X.; Lelgemann, Monika; Büehler, Diedrich; Schünemann, Holger J.

    2017-01-01

    Objectives: In this first of a series of five articles, we provide an overview of how and why healthcare-related tests and diagnostic strategies are currently applied. We also describe how our findings can be integrated with existing frameworks for making decisions that guide the use of

  12. How'd they do it? Malingering strategies on symptom validity tests.

    Science.gov (United States)

    Tan, Jing Ee; Slick, Daniel J; Strauss, Esther; Hultsch, David F

    2002-12-01

    Twenty-five undergraduate students were instructed to feign believable impairment following a brain injury from a car accident and 27 students were told to perform like they had recovered from such an injury. Three forced-choice tests, the Test of Memory Malingering (TOMM), Victoria Symptom Validity Test (VSVT), and Word Memory Test (WMT) were given. Test-taking strategies were evaluated by means of a questionnaire given at the end of the test session. The results revealed that all the tasks differentiated between groups. Using conventional cut-scores, the WMT proved most efficient while the VSVT captured the most participants in the definitive below-chance category. Individuals instructed to feign injury were more likely to prepare prior to the experiment, with feigning of memory loss as the most frequently reported strategy. Regardless, preparation effort did not translate into believable performance on the tests.

  13. Using rapid diagnostic tests as source of malaria parasite DNA for molecular analyses in the era of declining malaria prevalence

    DEFF Research Database (Denmark)

    Ishengoma, Deus S; Lwitiho, Sudi; Madebe, Rashid A

    2011-01-01

    was conducted to examine if sufficient DNA could be successfully extracted from malaria rapid diagnostic tests (RDTs), used and collected as part of routine case management services in health facilities, and thus forming the basis for molecular analyses, surveillance and quality control (QC) testing of RDTs....... continued molecular surveillance of malaria parasites is important to early identify emerging anti-malarial drug resistance, it is becoming increasingly difficult to obtain parasite samples from ongoing studies, such as routine drug efficacy trials. To explore other sources of parasite DNA, this study...

  14. Developing test for experimental study: the effectiveness of hedwig strategy in english education department universitas brawijaya

    Directory of Open Access Journals (Sweden)

    Devinta Puspita Ratri

    2017-04-01

    Having a big number of students in content subject of a language class is a challenge for teacher since it is quite difficult to accommodate students’ critical thinking and active participation at the same time. Therefore, Hedwig strategy is aimed to give room for students to explore themselves and get involved in the materials delivered in the class. Furthermore, by having group and regroup to deliver message in Hedwig strategy, students are forced to be active participated in classroom activities. The idea of Hedwig strategy is inspired by Jigsaw and Think-Pair-Share which have existed before. To know whether Hedwig strategy is effectively applied in content subject in large language class, it is proposed to do quasi experimental study with one class as an experimental group and one class as a control group. The experimental group is treated by using Hedwig strategy. Prior to the experimental study, it is performed research and development to develop the test for pre-test and post-test. For that reason, the research problem is what test is valid and reliable for an experimental study on the effectiveness of Hedwig strategy for the 4th semester students in Language Teaching Methodology class in English Education Department Universitas Brawijaya. This research reports half of the whole plan where the researchers developed test for pre-test and posttest to measure students’ improvement in understanding Language Teaching Methodology. In short, the test developed in this study will be used to carry out experimental study as pre-test and post-test

  15. A simple and accurate two-step long DNA sequences synthesis strategy to improve heterologous gene expression in pichia.

    Directory of Open Access Journals (Sweden)

    Jiang-Ke Yang

    Full Text Available In vitro gene chemical synthesis is a powerful tool to improve the expression of gene in heterologous system. In this study, a two-step gene synthesis strategy that combines an assembly PCR and an overlap extension PCR (AOE was developed. In this strategy, the chemically synthesized oligonucleotides were assembled into several 200-500 bp fragments with 20-25 bp overlap at each end by assembly PCR, and then an overlap extension PCR was conducted to assemble all these fragments into a full length DNA sequence. Using this method, we de novo designed and optimized the codon of Rhizopus oryzae lipase gene ROL (810 bp and Aspergillus niger phytase gene phyA (1404 bp. Compared with the original ROL gene and phyA gene, the codon-optimized genes expressed at a significantly higher level in yeasts after methanol induction. We believe this AOE method to be of special interest as it is simple, accurate and has no limitation with respect to the size of the gene to be synthesized. Combined with de novo design, this method allows the rapid synthesis of a gene optimized for expression in the system of choice and production of sufficient biological material for molecular characterization and biotechnological application.

  16. Test-Taking Strategies and Task-based Assessment: The Case of Iranian EFL Learners

    Directory of Open Access Journals (Sweden)

    Hossein Barati

    2012-01-01

    Full Text Available The present study examined the effect of task-based assessment on the type and frequency of test-taking strategies that three proficiency groups of Iranian adult EFL learners used when completing the First Certificate in English FCE reading paper. A total of 70 EFL university undergraduates (53 females and 17 males took part in the main phase of this study. They were divided into three proficiency groups: high, intermediate, and low. A set of Chi-square analyses was used to explore the type and frequency of test-taking strategies used by participants. The results suggested that the intermediate group test takers used the strategies significantly different after completing each task (sub-test in the FCE reading paper. However, the high and low proficient test takers› use of strategies was only significant after completing the third task of the FCE reading paper. The findings also revealed that a pattern could be drawn of the type of strategies used by the three proficiency groups who participated in this study. Nonetheless, such a pattern shifted at times depending on the ability of the test takers and/or the task under study.

  17. Regulating approaches to learning: Testing learning strategy convergences across a year at university.

    Science.gov (United States)

    Fryer, Luke K; Vermunt, Jan D

    2018-03-01

    Contemporary models of student learning within higher education are often inclusive of processing and regulation strategies. Considerable research has examined their use over time and their (person-centred) convergence. The longitudinal stability/variability of learning strategy use, however, is poorly understood, but essential to supporting student learning across university experiences. Develop and test a person-centred longitudinal model of learning strategies across the first-year university experience. Japanese university students (n = 933) completed surveys (deep and surface approaches to learning; self, external, and lack of regulation) at the beginning and end of their first year. Following invariance and cross-sectional tests, latent profile transition analysis (LPTA) was undertaken. Initial difference testing supported small but significant differences for self-/external regulation. Fit indices supported a four-group model, consistent across both measurement points. These subgroups were labelled Low Quality (low deep approaches and self-regulation), Low Quantity (low strategy use generally), Average (moderate strategy use), and High Quantity (intense use of all strategies) strategies. The stability of these groups ranged from stable to variable: Average (93% stayers), Low Quality (90% stayers), High Quantity (72% stayers), and Low Quantity (40% stayers). The three largest transitions presented joint shifts in processing/regulation strategy preference across the year, from adaptive to maladaptive and vice versa. Person-centred longitudinal findings presented patterns of learning transitions that different students experience during their first year at university. Stability/variability of students' strategy use was linked to the nature of initial subgroup membership. Findings also indicated strong connections between processing and regulation strategy changes across first-year university experiences. Implications for theory and practice are discussed.

  18. Voices of University Students with ADHD about Test-Taking: Behaviors, Needs, and Strategies

    Science.gov (United States)

    Ofiesh, Nicole; Moniz, Erin; Bisagno, Joan

    2015-01-01

    In order to understand the test-taking behavior, needs, and strategies of postsecondary students with Attention Deficit Hyperactivity Disorder (ADHD), focus group comments from 17 university students with ADHD were analyzed. These comments formed the basis for a series of research studies that are in progress regarding test-taking and individuals…

  19. Strategies for Controlling Item Exposure in Computerized Adaptive Testing with the Generalized Partial Credit Model

    Science.gov (United States)

    Davis, Laurie Laughlin

    2004-01-01

    Choosing a strategy for controlling item exposure has become an integral part of test development for computerized adaptive testing (CAT). This study investigated the performance of six procedures for controlling item exposure in a series of simulated CATs under the generalized partial credit model. In addition to a no-exposure control baseline…

  20. Efficient strategies to find diagnostic test accuracy studies in kidney journals.

    Science.gov (United States)

    Rogerson, Thomas E; Ladhani, Maleeka; Mitchell, Ruth; Craig, Jonathan C; Webster, Angela C

    2015-08-01

    Nephrologists looking for quick answers to diagnostic clinical questions in MEDLINE can use a range of published search strategies or Clinical Query limits to improve the precision of their searches. We aimed to evaluate existing search strategies for finding diagnostic test accuracy studies in nephrology journals. We assessed the accuracy of 14 search strategies for retrieving diagnostic test accuracy studies from three nephrology journals indexed in MEDLINE. Two investigators hand searched the same journals to create a reference set of diagnostic test accuracy studies to compare search strategy results against. We identified 103 diagnostic test accuracy studies, accounting for 2.1% of all studies published. The most specific search strategy was the Narrow Clinical Queries limit (sensitivity: 0.20, 95% CI 0.13-0.29; specificity: 0.99, 95% CI 0.99-0.99). Using the Narrow Clinical Queries limit, a searcher would need to screen three (95% CI 2-6) articles to find one diagnostic study. The most sensitive search strategy was van der Weijden 1999 Extended (sensitivity: 0.95; 95% CI 0.89-0.98; specificity 0.55, 95% CI 0.53-0.56) but required a searcher to screen 24 (95% CI 23-26) articles to find one diagnostic study. Bachmann 2002 was the best balanced search strategy, which was sensitive (0.88, 95% CI 0.81-0.94), but also specific (0.74, 95% CI 0.73-0.75), with a number needed to screen of 15 (95% CI 14-17). Diagnostic studies are infrequently published in nephrology journals. The addition of a strategy for diagnostic studies to a subject search strategy in MEDLINE may reduce the records needed to screen while preserving adequate search sensitivity for routine clinical use. © 2015 Asian Pacific Society of Nephrology.

  1. Agent based models for testing city evacuation strategies under a flood event as strategy to reduce flood risk

    Science.gov (United States)

    Medina, Neiler; Sanchez, Arlex; Nokolic, Igor; Vojinovic, Zoran

    2016-04-01

    This research explores the uses of Agent Based Models (ABM) and its potential to test large scale evacuation strategies in coastal cities at risk from flood events due to extreme hydro-meteorological events with the final purpose of disaster risk reduction by decreasing human's exposure to the hazard. The first part of the paper corresponds to the theory used to build the models such as: Complex adaptive systems (CAS) and the principles and uses of ABM in this field. The first section outlines the pros and cons of using AMB to test city evacuation strategies at medium and large scale. The second part of the paper focuses on the central theory used to build the ABM, specifically the psychological and behavioral model as well as the framework used in this research, specifically the PECS reference model is cover in this section. The last part of this section covers the main attributes or characteristics of human beings used to described the agents. The third part of the paper shows the methodology used to build and implement the ABM model using Repast-Symphony as an open source agent-based modelling and simulation platform. The preliminary results for the first implementation in a region of the island of Sint-Maarten a Dutch Caribbean island are presented and discussed in the fourth section of paper. The results obtained so far, are promising for a further development of the model and its implementation and testing in a full scale city

  2. 78 FR 68076 - Request for Information on Alternative Skin Sensitization Test Methods and Testing Strategies and...

    Science.gov (United States)

    2013-11-13

    ... Laboratory for Alternatives to Animal Testing (EURL ECVAM), and by the industry organization Cosmetics Europe... products. Pesticides and other marketed chemicals, including cosmetic ingredients, are routinely tested for... sensitization. NICEATM collaboration with industry scientists to develop an open-source Bayesian network as an...

  3. Is retrieval the key? Metamemory judgment and testing as learning strategies.

    Science.gov (United States)

    Akdoğan, Elçin; Izaute, Marie; Danion, Jean-Marie; Vidailhet, Pierre; Bacon, Elisabeth

    2016-11-01

    Re-reading is the most common learning strategy, albeit not a very efficient one. Testing is highly efficient, but not perceived by students as a learning strategy. Prospective judgment-of-learning (JOL) reflect the learner's impression of subsequently being able to retrieve the ongoing learning in a cued-recall task. Estimating JOL involves attempting to retrieve the information, as in testing. The few studies that have explored the potential mnemonic benefit of JOL have yielded contradictory results. Our aim was to compare JOL and testing with re-study and to examine the impact of these strategies according to the relative difficulty of the material (cue-target association strength) in two experiments. After a first encoding phase, participants re-studied, provided JOL, or took a test. Forty-eight hours later, they participated in a final cued-recall test, during which their confidence level judgments were collected. The main result was that delayed JOL behaved in the same way as testing, and both yielded better performances than re-study when material was of moderate difficulty. The easy or very difficult material revealed no differences between these strategies. JOL is proposed as an alternative to testing when faced with difficult material.

  4. Strategy for phase 2 whole element furnace testing K West fuel

    International Nuclear Information System (INIS)

    Lawrence, L.A.

    1998-01-01

    A strategy was developed for the second phase of the whole element furnace testing of damaged fuel removed from the K West Basin. The Phase 2 testing can be divided into three groups covering oxidation of whole element in moist inert atmospheres, drying elements for post Cold Vacuum Drying staging tests, and drying additional K West elements to provide confirmation of the results from the first series of damaged K West fuel drying studies

  5. Single molecule measurements of DNA helicase activity with magnetic tweezers and t-test based step-finding analysis

    Science.gov (United States)

    Seol, Yeonee; Strub, Marie-Paule; Neuman, Keir C.

    2016-01-01

    Magnetic tweezers is a versatile and easy to implement single-molecule technique that has become increasingly prevalent in the study of nucleic acid based molecular motors. Here, we provide a description of the magnetic tweezers instrument and guidelines for measuring and analyzing DNA helicase activity. Along with experimental methods, we describe a robust method of single-molecule trajectory analysis based on the Student’s t-test that accommodates continuous transitions in addition to the discrete transitions assumed in most widely employed analysis routines. To illustrate the single-molecule unwinding assay and the analysis routine, we provide DNA unwinding measurements of Escherichia coli RecQ helicase under a variety of conditions (Na+, ATP, temperature, and DNA substrate geometry). These examples reveal that DNA unwinding measurements under various conditions can aid in elucidating the unwinding mechanism of DNA helicase but also emphasize that environmental effects on DNA helicase activity must be considered in relation to in vivo activity and mechanism. PMID:27131595

  6. Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification.

    Directory of Open Access Journals (Sweden)

    Bonita J Brewer

    2015-12-01

    Full Text Available DNA replication errors are a major driver of evolution--from single nucleotide polymorphisms to large-scale copy number variations (CNVs. Here we test a specific replication-based model to explain the generation of interstitial, inverted triplications. While no genetic information is lost, the novel inversion junctions and increased copy number of the included sequences create the potential for adaptive phenotypes. The model--Origin-Dependent Inverted-Repeat Amplification (ODIRA-proposes that a replication error at pre-existing short, interrupted, inverted repeats in genomic sequences generates an extrachromosomal, inverted dimeric, autonomously replicating intermediate; subsequent genomic integration of the dimer yields this class of CNV without loss of distal chromosomal sequences. We used a combination of in vitro and in vivo approaches to test the feasibility of the proposed replication error and its downstream consequences on chromosome structure in the yeast Saccharomyces cerevisiae. We show that the proposed replication error-the ligation of leading and lagging nascent strands to create "closed" forks-can occur in vitro at short, interrupted inverted repeats. The removal of molecules with two closed forks results in a hairpin-capped linear duplex that we show replicates in vivo to create an inverted, dimeric plasmid that subsequently integrates into the genome by homologous recombination, creating an inverted triplication. While other models have been proposed to explain inverted triplications and their derivatives, our model can also explain the generation of human, de novo, inverted amplicons that have a 2:1 mixture of sequences from both homologues of a single parent--a feature readily explained by a plasmid intermediate that arises from one homologue and integrates into the other homologue prior to meiosis. Our tests of key features of ODIRA lend support to this mechanism and suggest further avenues of enquiry to unravel the origins

  7. Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification.

    Science.gov (United States)

    Brewer, Bonita J; Payen, Celia; Di Rienzi, Sara C; Higgins, Megan M; Ong, Giang; Dunham, Maitreya J; Raghuraman, M K

    2015-12-01

    DNA replication errors are a major driver of evolution--from single nucleotide polymorphisms to large-scale copy number variations (CNVs). Here we test a specific replication-based model to explain the generation of interstitial, inverted triplications. While no genetic information is lost, the novel inversion junctions and increased copy number of the included sequences create the potential for adaptive phenotypes. The model--Origin-Dependent Inverted-Repeat Amplification (ODIRA)-proposes that a replication error at pre-existing short, interrupted, inverted repeats in genomic sequences generates an extrachromosomal, inverted dimeric, autonomously replicating intermediate; subsequent genomic integration of the dimer yields this class of CNV without loss of distal chromosomal sequences. We used a combination of in vitro and in vivo approaches to test the feasibility of the proposed replication error and its downstream consequences on chromosome structure in the yeast Saccharomyces cerevisiae. We show that the proposed replication error-the ligation of leading and lagging nascent strands to create "closed" forks-can occur in vitro at short, interrupted inverted repeats. The removal of molecules with two closed forks results in a hairpin-capped linear duplex that we show replicates in vivo to create an inverted, dimeric plasmid that subsequently integrates into the genome by homologous recombination, creating an inverted triplication. While other models have been proposed to explain inverted triplications and their derivatives, our model can also explain the generation of human, de novo, inverted amplicons that have a 2:1 mixture of sequences from both homologues of a single parent--a feature readily explained by a plasmid intermediate that arises from one homologue and integrates into the other homologue prior to meiosis. Our tests of key features of ODIRA lend support to this mechanism and suggest further avenues of enquiry to unravel the origins of interstitial

  8. More than friendship is required : an empirical test of cooperative firm strategies

    OpenAIRE

    Pesämaa, Ossi; Hair Jr, Joseph F

    2006-01-01

    Purpose - The purpose of this paper is to examine a proposed six-construct theoretical model of factors influencing successful cooperative relationships and strategy development. Design/methodology/approach - A theoretical model of strategy development and cooperative relationships was tested. Qualitative research among key experts identified 15 successful regional tourism networks. Two successful cooperative networks were selected based on annual revenues. A sample of 254 small and mediu...

  9. Decision making about healthcare-related tests and diagnostic test strategies. Paper 2: a review of methodological and practical challenges.

    Science.gov (United States)

    Mustafa, Reem A; Wiercioch, Wojtek; Cheung, Adrienne; Prediger, Barbara; Brozek, Jan; Bossuyt, Patrick; Garg, Amit X; Lelgemann, Monika; Büehler, Diedrich; Schünemann, Holger J

    2017-12-01

    In this first of a series of five articles, we provide an overview of how and why healthcare-related tests and diagnostic strategies are currently applied. We also describe how our findings can be integrated with existing frameworks for making decisions that guide the use of healthcare-related tests and diagnostic strategies. We searched MEDLINE, references of identified articles, chapters in relevant textbooks, and identified articles citing classic literature on this topic. We provide updated frameworks for the potential roles and applications of tests with suggested definitions and practical examples. We also discuss study designs that are commonly used to assess tests' performance and the effects of tests on people's health. These designs include diagnostic randomized controlled trials and retrospective validation. We describe the utility of these and other currently suggested designs, which questions they can answer and which ones they cannot. In addition, we summarize the challenges unique to decision-making resulting from the use of tests. This overview highlights current challenges in the application of tests in decision-making in healthcare, provides clarifications, and informs the proposed solutions. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy.

    Science.gov (United States)

    Yan, Yumeng; Zhang, Di; Zhou, Pei; Li, Botong; Huang, Sheng-You

    2017-07-03

    Protein-protein and protein-DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, here we have presented HDOCK, a novel web server of our hybrid docking algorithm of template-based modeling and free docking, in which cases with misleading templates can be rescued by the free docking protocol. The server supports protein-protein and protein-DNA/RNA docking and accepts both sequence and structure inputs for proteins. The docking process is fast and consumes about 10-20 min for a docking run. Tested on the cases with weakly homologous complexes of server. The HDOCK web server is available at http://hdock.phys.hust.edu.cn/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. Targeted ultrasound examination and DNA testing for Noonan syndrome, in fetuses with increased nuchal translucency and normal karyotype

    NARCIS (Netherlands)

    Bakker, M.; Pajkrt, E.; Mathijssen, I. B.; Bilardo, C. M.

    2011-01-01

    OBJECTIVE: To define sonographic criteria that may improve the prenatal diagnosis of Noonan syndrome by targeted DNA testing. METHODS: We searched our Fetal Medicine Unit records for all cases with a final diagnosis of Noonan syndrome. A literature review was undertaken to identify the sonographic

  12. Targeted ultrasound examination and DNA testing for Noonan syndrome, in fetuses with increased nuchal translucency and normal karyotype

    NARCIS (Netherlands)

    Bakker, Merel; Pajkrt, E.; Mathijssen, I. B.; Bilardo, C. M.

    Objective To define sonographic criteria that may improve the prenatal diagnosis of Noonan syndrome by targeted DNA testing. Methods We searched our Fetal Medicine Unit records for all cases with a final diagnosis of Noonan syndrome. A literature review was undertaken to identify the sonographic

  13. Nonparametric testing for DNA copy number induced differential mRNA gene expression

    NARCIS (Netherlands)

    van Wieringen, W.N.; van de Wiel, M.A.

    2009-01-01

    The central dogma of molecular biology relates DNA with mRNA. Array CGH measures DNA copy number and gene expression microarrays measure the amount of mRNA. Methods that integrate data from these two platforms may uncover meaningful biological relationships that further our understanding of cancer.

  14. Optimal Sequential Diagnostic Strategy Generation Considering Test Placement Cost for Multimode Systems

    Directory of Open Access Journals (Sweden)

    Shigang Zhang

    2015-10-01

    Full Text Available Sequential fault diagnosis is an approach that realizes fault isolation by executing the optimal test step by step. The strategy used, i.e., the sequential diagnostic strategy, has great influence on diagnostic accuracy and cost. Optimal sequential diagnostic strategy generation is an important step in the process of diagnosis system construction, which has been studied extensively in the literature. However, previous algorithms either are designed for single mode systems or do not consider test placement cost. They are not suitable to solve the sequential diagnostic strategy generation problem considering test placement cost for multimode systems. Therefore, this problem is studied in this paper. A formulation is presented. Two algorithms are proposed, one of which is realized by system transformation and the other is newly designed. Extensive simulations are carried out to test the effectiveness of the algorithms. A real-world system is also presented. All the results show that both of them have the ability to solve the diagnostic strategy generation problem, and they have different characteristics.

  15. Optimal Sequential Diagnostic Strategy Generation Considering Test Placement Cost for Multimode Systems

    Science.gov (United States)

    Zhang, Shigang; Song, Lijun; Zhang, Wei; Hu, Zheng; Yang, Yongmin

    2015-01-01

    Sequential fault diagnosis is an approach that realizes fault isolation by executing the optimal test step by step. The strategy used, i.e., the sequential diagnostic strategy, has great influence on diagnostic accuracy and cost. Optimal sequential diagnostic strategy generation is an important step in the process of diagnosis system construction, which has been studied extensively in the literature. However, previous algorithms either are designed for single mode systems or do not consider test placement cost. They are not suitable to solve the sequential diagnostic strategy generation problem considering test placement cost for multimode systems. Therefore, this problem is studied in this paper. A formulation is presented. Two algorithms are proposed, one of which is realized by system transformation and the other is newly designed. Extensive simulations are carried out to test the effectiveness of the algorithms. A real-world system is also presented. All the results show that both of them have the ability to solve the diagnostic strategy generation problem, and they have different characteristics. PMID:26457709

  16. Analysis of failure dependent test, repair and shutdown strategies for redundant trains

    International Nuclear Information System (INIS)

    Uryasev, S.; Samanta, P.

    1994-09-01

    Failure-dependent testing implies a test of a redundant components (or trains) when failure of one component has been detected. The purpose of such testing is to detect any common cause failures (CCFs) of multiple components so that a corrective action such as repair or plant shutdown can be taken to reduce the residence time of multiple failures, given a failure has been detected. This type of testing focuses on reducing the conditional risk of CCFs. Formulas for calculating the conditional failure probability of a two train system with different test, repair and shutdown strategies are developed. A methodology is presented with an example calculation showing the risk-effectiveness of failure-dependent strategies for emergency diesel generators (EDGs) in nuclear power plants (NPPs)

  17. Identification of irradiated wheat by germination test, DNA comet assay and electron spin resonance

    Science.gov (United States)

    Barros, Adilson C.; Freund, Maria Teresa L.; Villavicencio, Ana Lúcia C. H.; Delincée, Henry; Arthur, Valter

    2002-03-01

    In several countries, there has been an increase in the use of radiation for food processing thus improving the quality and sanitary conditions, inhibiting pathogenic microorganisms, delaying the natural aging process and so extending product lifetime. The need to develop analytical methods to detect these irradiated products is also increasing. The goal of this research was to identify wheat irradiated using different radiation doses. Seeds were irradiated with a gamma 60Co source (Gammacell 220 GC) in the Centro de Energia Nuclear na Agricultura and the Instituto de Pesquisas Energéticas e Nucleares. Dose rate used were 1.6 and 5.8kGy/h. Applied doses were 0.0, 0.10, 0.25, 0.50, 0.75, 1.0, and 2.0kGy. After irradiation, seeds were analysed over a 6 month period. Three different detection methods were employed to determine how irradiation had modified the samples. Screening methods consisted of a germination test measuring the inhibition of shooting and rooting and analysis of DNA fragmentation. The method of electron spin resonance spectroscopy allowed a better dosimetric evaluation. These techniques make the identification of irradiated wheat with different doses possible.

  18. Horses for courses: a DNA-based test for race distance aptitude in thoroughbred racehorses.

    Science.gov (United States)

    Hill, Emmeline W; Ryan, Donal P; MacHugh, David E

    2012-12-01

    Variation at the myostatin (MSTN) gene locus has been shown to influence racing phenotypes in Thoroughbred horses, and in particular, early skeletal muscle development and the aptitude for racing at short distances. Specifically, a single nucleotide polymorphism (SNP) in the first intron of MSTN (g.66493737C/T) is highly predictive of best race distance among Flat racing Thoroughbreds: homozygous C/C horses are best suited to short distance races, heterozygous C/T horses are best suited to middle distance races, and homozygous T/T horses are best suited to longer distance races. Patent applications for this gene marker association, and other linked markers, have been filed. The information contained within the patent applications is exclusively licensed to the commercial biotechnology company Equinome Ltd, which provides a DNA-based test to the international Thoroughbred horse racing and breeding industry. The application of this information in the industry enables informed decision making in breeding and racing and can be used to assist selection to accelerate the rate of change of genetic types among distinct populations (Case Study 1) and within individual breeding operations (Case Study 2).

  19. Pen-on-paper strategy for point-of-care testing: Rapid prototyping of fully written microfluidic biosensor.

    Science.gov (United States)

    Li, Zedong; Li, Fei; Xing, Yue; Liu, Zhi; You, Minli; Li, Yingchun; Wen, Ting; Qu, Zhiguo; Ling Li, Xiao; Xu, Feng

    2017-12-15

    Paper-based microfluidic biosensors have recently attracted increasing attentions in point-of-care testing (POCT) territories benefiting from their affordable, accessible and eco-friendly features, where technologies for fabricating such biosensors are preferred to be equipment free, easy-to-operate and capable of rapid prototyping. In this work, we developed a pen-on-paper (PoP) strategy based on two custom-made pens, i.e., a wax pen and a conductive-ink pen, to fully write paper-based microfluidic biosensors through directly writing both microfluidic channels and electrodes. Particularly, the proposed wax pen is competent to realize one-step fabrication of wax channels on paper, as the melted wax penetrates into paper during writing process without any post-treatments. The practical applications of the fabricated paper-based microfluidic biosensors are demonstrated by both colorimetric detection of Salmonella typhimurium DNA with detection limit of 1nM and electrochemical measurement of glucose with detection limit of 1mM. The developed PoP strategy for making microfluidic biosensors on paper characterized by true simplicity, prominent portability and excellent capability for rapid prototyping shows promising prospect in POCT applications. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Collaborative testing as a learning strategy in nursing education: a review of the literature.

    Science.gov (United States)

    Sandahl, Sheryl S

    2009-01-01

    Nurses are important members of a patient's interprofessional health care team. A primary goal of nursing education is to prepare nursing professionals who can work collaboratively with other team members for the benefit of the patient. Collaborative learning strategies provide students with opportunities to learn and practice collaboration. Collaborative testing is a collaborative learning strategy used to foster knowledge development, critical thinking in decision-making, and group processing skills. This article reviews the theoretical basis for collaborative learning and research on collaborative testing in nursing education.

  1. Advanced power cycler with intelligent monitoring strategy of IGBT module under test

    DEFF Research Database (Denmark)

    Choi, U. M.; Blaabjerg, F.; Iannuzzo, F.

    2017-01-01

    and diode, which for the wear-out condition monitoring are presented. This advanced power cycler allows to perform power cycling test cost-effectively under conditions close to real power converter applications. In addition, an intelligent monitoring strategy for the separation of package-related wear......-out failure mechanisms has been proposed. By means of the proposed method, the wear-out failure mechanisms of an IGBT module can be separated without any additional efforts during the power cycling tests. The validity and effectiveness of the proposed monitoring strategy are also verified by experiments....

  2. The roles of encoding strategies and retrieval practice in test-expectancy effects.

    Science.gov (United States)

    Cho, Kit W; Neely, James H

    2017-05-01

    We investigated whether expectations for different kinds of memory tests induce qualitatively different encoding strategies. In Experiment 1, participants studied four lists of words and after each list completed a cued-recall test that contained either all semantic or all orthographic cues so as to build up an expectancy for receiving the same type of test for the fifth critical study list. To rule out that the test-expectancy effects in Experiment 1 were due to differences in retrieval practice, in Experiment 2, participants received three practice tests each for both cue-types. Participants' test expectancy for all lists was induced by telling them before each list the type of cue they would receive for the upcoming study list. In both experiments, the critical test contained both expected and unexpected cues. In Experiment 1, participants who expected semantic cues had better recall to the semantic cues than to the orthographic cues and vice versa for those who expected orthographic cues. However, in Experiment 2, there was no effect of test expectancy. These findings suggest that the test-expectancy effects in Experiment 1 were due to more retrieval practice on the expected than unexpected tests rather than to qualitatively different test-expectancy-induced encoding strategies.

  3. End-specific strategies of attachment of long double stranded DNA onto gold-coated nanofiber arrays

    International Nuclear Information System (INIS)

    Peckys, Diana B; De Jonge, Niels; Simpson, Michael L; McKnight, Timothy E

    2008-01-01

    We report the effective and site-specific binding of long double stranded (ds)DNA to high aspect ratio carbon nanofiber arrays. The carbon nanofibers were first coated with a thin gold layer to provide anchorage for two controllable binding methods. One method was based on the direct binding of thiol end-labeled dsDNA. The second and enhanced method used amine end-labeled dsDNA bound with crosslinkers to a carboxyl-terminated self-assembled monolayer. The bound dsDNA was first visualized with a fluorescent, dsDNA-intercalating dye. The specific binding onto the carbon nanofiber was verified by a high resolution detection method using scanning electron microscopy in combination with the binding of neutravidin-coated fluorescent microspheres to the immobilized and biotinylated dsDNA. Functional activity of thiol end-labeled dsDNA on gold-coated nanofiber arrays was verified with a transcriptional assay, whereby Chinese hamster lung cells (V79) were impaled upon the DNA-modified nanofibers and scored for transgene expression of the tethered template. Thiol end-labeled dsDNA demonstrated significantly higher expression levels than nanofibers prepared with control dsDNA that lacked a gold-binding end-label. Employing these site-specific and robust techniques of immobilization of dsDNA onto nanodevices can be of advantage for the study of DNA/protein interactions and for gene delivery applications.

  4. Factors Affecting Result in Chinese Proficiency Test (HSK Level 6: Reading Section and Preparation Strategies

    Directory of Open Access Journals (Sweden)

    Sri Haryanti

    2013-11-01

    Full Text Available Chinese Proficiency Test (HSK is an internationally standardized exam which tests and rates Chinese language proficiency. The highest level in this test is level 6. The writing part of the test consists of 3 (three parts, namely, (1 listening, (2 reading, (3 writing. Furthermore, the reading part is made of 4 components. Level 6 of this test implies a high degree of difficulty. This paper specifically looked on how to prepare effectively for participants to be able to work on the reading part in order to achieve best result. This article used the methods of literature review and observational study as well as field research and would also incorporate the author’s personal experience in taking the test into recommending strategies for doing the reading part in a level 6 HSK test. Finally, research suggested several techniques and tips that might assist participants in achieving maximum scores in handling the reading part of level 6 HSK test.

  5. Redesigning pH optimum of Geobacillus sp. TF16 endoxylanase through in silico designed DNA swapping strategy.

    Science.gov (United States)

    Uzuner, Ugur; Canakci, Sabriye; Bektas, Kadriye Inan; Sapmaz, Merve Tuncel; Belduz, Ali Osman

    2017-06-01

    Thermoalkaliphilic xylanases are highly desired and of great importance due to their vast potential in paper pulp and bleaching processes. Here, we report rapid, cost-effective, and result-oriented combinatorial potential of in silico DNA swapping strategy to engineer the pH optimum of industrially crucial enzymes, particularly engineering of Geobacillus sp. TF16 endoxylanase for alkaline environments. The 3D structures of Geobacillus sp. TF16 and donor Bacillus halodurans C-125 endoxylanases were firstly predicted, analyzed, and compared for their similarities before any in silico design of mutants. Reasonably, to improve its alkaline pH tolerance, the corresponding regions in Geobacillus sp.TF16 endoxylanase were further engineered by swapping with negatively-charged amino acid-rich regions from B. halodurans C-125 endoxylanase. Through only two of four in silico-designed mutants, the optimum pH of GeoTF16 endoxylanase was improved from 8.5 to 10.0. Moreover, as compared to GeoTF16 parental enzyme, both GeoInt3 and GeoInt4 mutants revealed (i) enhanced biobleaching performance, (ii) improved adaptability to alkaline conditions, and (iii) better activity for broader pH range. Unlike GeoTF16 losing activity at pH 11.0 completely, GeoInt4 retained 60% and 40% of its activity at pH 11.0 and 12.0, respectively. Thus, GeoInt4 stands out as a more competent biocatalyst that is suitable for alkaline environments of diverse industrial applications. The current study represents an efficient protein engineering strategy to adapt industrial catalysts to diverse processing conditions. Further comprehensive and fine-tuned research efforts may result in biotechnologically more promising outcomes. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  6. Human papillomavirus mRNA and DNA testing in women with atypical squamous cells of undetermined significance

    DEFF Research Database (Denmark)

    Thomsen, Louise T; Dehlendorff, Christian; Junge, Jette

    2016-01-01

    In this prospective cohort study, we compared the performance of human papillomavirus (HPV) mRNA and DNA testing of women with atypical squamous cells of undetermined significance (ASC-US) during cervical cancer screening. Using a nationwide Danish pathology register, we identified women aged 30......-65 years with ASC-US during 2005-2011 who were tested for HPV16/18/31/33/45 mRNA using PreTect HPV-Proofer (n = 3,226) or for high-risk HPV (hrHPV) DNA using Hybrid Capture 2 (HC2) (n = 9,405) or Linear Array HPV-Genotyping test (LA) (n = 1,533). Women with ≥1 subsequent examination in the register (n = 13...... those testing HC2 negative (3.2% [95% CI: 2.2-4.2%] versus 0.5% [95% CI: 0.3-0.7%]). Patterns were similar after 18 months and 5 years'; follow-up; for CIN2+ and cancer as outcomes; across all age groups; and when comparing mRNA testing to hrHPV DNA testing using LA. In conclusion, the HPV16...

  7. Immunotoxicity, genotoxicity and epigenetic toxicity of nanomaterials: New strategies for toxicity testing?

    Science.gov (United States)

    Dusinska, Maria; Tulinska, Jana; El Yamani, Naouale; Kuricova, Miroslava; Liskova, Aurelia; Rollerova, Eva; Rundén-Pran, Elise; Smolkova, Bozena

    2017-11-01

    The unique properties of nanomaterials (NMs) are beneficial in numerous industrial and medical applications. However, they could also induce unintended effects. Thus, a proper strategy for toxicity testing is essential in human hazard and risk assessment. Toxicity can be tested in vivo and in vitro; in compliance with the 3Rs, alternative strategies for in vitro testing should be further developed for NMs. Robust, standardized methods are of great importance in nanotoxicology, with comprehensive material characterization and uptake as an integral part of the testing strategy. Oxidative stress has been shown to be an underlying mechanism of possible toxicity of NMs, causing both immunotoxicity and genotoxicity. For testing NMs in vitro, a battery of tests should be performed on cells of human origin, either cell lines or primary cells, in conditions as close as possible to an in vivo situation. Novel toxicity pathways, particularly epigenetic modification, should be assessed along with conventional toxicity testing methods. However, to initiate epigenetic toxicity screens for NM exposure, there is a need to better understand their adverse effects on the epigenome, to identify robust and reproducible causal links between exposure, epigenetic changes and adverse phenotypic endpoints, and to develop improved assays to monitor epigenetic toxicity. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  8. The price of performance: a cost and performance analysis of the implementation of cell-free fetal DNA testing for Down syndrome in Ontario, Canada.

    Science.gov (United States)

    Okun, N; Teitelbaum, M; Huang, T; Dewa, C S; Hoch, J S

    2014-04-01

    To examine the cost and performance implications of introducing cell-free fetal DNA (cffDNA) testing within modeled scenarios in a publicly funded Canadian provincial Down syndrome (DS) prenatal screening program. Two clinical algorithms were created: the first to represent the current screening program and the second to represent one that incorporates cffDNA testing. From these algorithms, eight distinct scenarios were modeled to examine: (1) the current program (no cffDNA), (2) the current program with first trimester screening (FTS) as the nuchal translucency-based primary screen (no cffDNA), (3) a program substituting current screening with primary cffDNA, (4) contingent cffDNA with current FTS performance, (5) contingent cffDNA at a fixed price to result in overall cost neutrality,(6) contingent cffDNA with an improved detection rate (DR) of FTS, (7) contingent cffDNA with higher uptake of FTS, and (8) contingent cffDNA with optimized FTS (higher uptake and improved DR). This modeling study demonstrates that introducing contingent cffDNA testing improves performance by increasing the number of cases of DS detected prenatally, and reducing the number of amniocenteses performed and concomitant iatrogenic pregnancy loss of pregnancies not affected by DS. Costs are modestly increased, although the cost per case of DS detected is decreased with contingent cffDNA testing. Contingent models of cffDNA testing can improve overall screening performance while maintaining the provision of an 11- to 13-week scan. Costs are modestly increased, but cost per prenatally detected case of DS is decreased. © 2013 John Wiley & Sons, Ltd.

  9. The effects of emotion regulation on explicit memory depend on strategy and testing method.

    Science.gov (United States)

    Knight, Marisa; Ponzio, Allison

    2013-12-01

    Although previous work has shown that emotion regulation strategies can influence memory, the mechanisms through which different strategies produce different memory outcomes are not well understood. We examined how two cognitive reappraisal strategies with similar elaboration demands but diverging effects on visual attention and emotional arousal influenced explicit memory for emotional stimuli and for the strategies used to evaluate the stimuli. At encoding, participants used reappraisal to increase and decrease the personal relevance of neutral and emotional pictures. In two experiments, recall accuracy was highest for emotional pictures featured on increase trials, intermediate for emotional pictures featured on look (respond naturally) trials, and lowest for emotional pictures featured on decrease trials. This recall pattern emerged after a short delay (15 min) and persisted over a longer delay (48 hr). Memory accuracy for the strategies used to evaluate the pictures showed a different pattern: Strategy memory was better for emotional pictures featured on decrease and increase trials than for pictures featured on look trials. Our findings show that the effects of emotion regulation on memory depend both on the particular strategy engaged and the particular aspect of memory being tested.

  10. Expanded HIV Testing Strategy Leveraging the Electronic Medical Record Uncovers Undiagnosed Infection Among Hospitalized Patients.

    Science.gov (United States)

    Felsen, Uriel R; Cunningham, Chinazo O; Heo, Moonseong; Futterman, Donna C; Weiss, Jeffrey M; Zingman, Barry S

    2017-05-01

    Routine HIV testing of hospitalized patients is recommended, but few strategies to expand testing in the hospital setting have been described. We assessed the impact of an electronic medical record (EMR) prompt on HIV testing for hospitalized patients. We performed a pre-post study at 3 hospitals in the Bronx, NY. We compared the proportion of admissions of patients 21-64 years old with an HIV test performed, characteristics of patients tested, and rate of new HIV diagnoses made by screening while an EMR prompt recommending HIV testing was inactive vs. active. The prompt appeared for patients with no previous HIV test or a high-risk diagnosis after their last HIV test. Among 36,610 admissions while the prompt was inactive, 9.5% had an HIV test performed. Among 18,943 admissions while the prompt was active, 21.8% had an HIV test performed. Admission while the prompt was active was associated with increased HIV testing among total admissions [adjusted odds ratio (aOR) 2.78, 95% confidence interval (CI): 2.62 to 2.96], those without a previous HIV test (aOR 4.03, 95% CI: 3.70 to 4.40), and those with a previous negative test (aOR 1.52, 95% CI: 1.37 to 1.68) (P diversification of patients tested, and an increase in diagnoses made by screening.

  11. The role of spent fuel test facilities in the fuel cycle strategy

    International Nuclear Information System (INIS)

    Huang, S. T.; Gross, D. L.; Snyder, N. W.; Woods, W. D.

    1988-01-01

    Disposal of commercial spent nuclear fuels in the major industrialized countries may be categorized into two broad approaches: a once-through policy which will dispose of spent fuels and recycle fissile materials. Within reprocess spent fuels and recycle fissile materials. Within each policy, various technical, licensing, institutional and public issues exist. These issues tend to complicate the formulation of an effective and acceptable fuel cycle strategy which will meet various cost, schedule, and legislative constraints. This paper examines overall fuel cycle strategies from the viewpoint of these underlying technical issues and assesses the roles of spent fuel test facilities in the overall fuel cycles steps. Basic functions of such test facilities are also discussed. The main emphasis is placed on the once-through policy although the reprocessing / recycle policy is also discussed. Benefits of utilizing test facilities in the fuel cycle strategies are explored. The results indicate that substantial benefits may be obtained in terms of minimizing programmatic risks, increasing public confidence, and more effective utilization of overall budgetary resources by structuring and highlighting the test facilities as an important element in the overall strategy

  12. Integrated testing strategies (ITS) for bioaccumulation: hierarchical scheme of chemistrydriven modules and definition of applicability domains

    DEFF Research Database (Denmark)

    Nendza, M.; Scheringer, M.; Strempel, S.

    2011-01-01

    The efficient assessment of the bioaccumulation potential of chemicals under REACH with integrated test strategies (ITS) requires multiple tools. Existing data have to be searched and information from chemical structures and physico-chemical properties need to be evaluated prior to considering to...

  13. Recall strategies for the verbal fluency test in patients with multiple sclerosis.

    Science.gov (United States)

    Velázquez-Cardoso, J; Marosi-Holczberger, E; Rodríguez-Agudelo, Y; Yañez-Tellez, G; Chávez-Oliveros, M

    2014-04-01

    Multiple sclerosis (MS) is a neurodegenerative disease characterised by inflammation and demyelination. It generates irreversible myelin changes, which in turn give rise to physical and cognitive disorders. The verbal fluency test (VF) has been shown to be a sensitive tool for detecting cognitive impairment in these patients. To compare quantitative and qualitative aspects of performance on semantic and phonological fluency tests between MS patients and healthy controls by analysing total words produced and strategies used (clusters and switching). We evaluated 46 patients with MS and 33 healthy controls using the VF test. The semantic VF task revealed no significant differences between groups; for the phonological task, patients demonstrated reduced word production (F [77]=2.286 P<.001) and poorer use of grouping strategies, resulting in more frequent switching (F [77]=3.808 P<.005). These results support using qualitative analysis for recall strategies, since the technique provides data about which components of the task are affected by brain damage. Clusters depend on the integrity of semantic memory, while switching has to do with developing effective search strategies, cognitive flexibility, and the ability to modify responses. Frontal lobe damage has been reported in MS, and this is consistent with results from the phonological VF test. Copyright © 2012 Sociedad Española de Neurología. Published by Elsevier Espana. All rights reserved.

  14. Cognitive Learning Strategy as a Partial Effect on Major Field Test in Business Results

    Science.gov (United States)

    Strang, Kenneth David

    2014-01-01

    An experiment was developed to determine if cognitive learning strategies improved standardized university business exam results. Previous studies revealed that factors such as prior ability, age, gender, and culture predicted a student's Major Field Test in Business (MFTB) score better than course content. The experiment control consisted of…

  15. Quantitative Field Testing Rotylenchulus reniformis DNA from Metagenomic Samples Isolated Directly from Soil

    Science.gov (United States)

    Showmaker, Kurt; Lawrence, Gary W.; Lu, Shien; Balbalian, Clarissa; Klink, Vincent P.

    2011-01-01

    A quantitative PCR procedure targeting the β-tubulin gene determined the number of Rotylenchulus reniformis Linford & Oliveira 1940 in metagenomic DNA samples isolated from soil. Of note, this outcome was in the presence of other soil-dwelling plant parasitic nematodes including its sister genus Helicotylenchus Steiner, 1945. The methodology provides a framework for molecular diagnostics of nematodes from metagenomic DNA isolated directly from soil. PMID:22194958

  16. Statistical Modeling for Quality Assurance of Human Papillomavirus DNA Batch Testing.

    Science.gov (United States)

    Beylerian, Emily N; Slavkovsky, Rose C; Holme, Francesca M; Jeronimo, Jose A

    2018-03-22

    Our objective was to simulate the distribution of human papillomavirus (HPV) DNA test results from a 96-well microplate assay to identify results that may be consistent with well-to-well contamination, enabling programs to apply specific quality assurance parameters. For this modeling study, we designed an algorithm that generated the analysis population of 900,000 to simulate the results of 10,000 microplate assays, assuming discrete HPV prevalences of 12%, 13%, 14%, 15%, and 16%. Using binomial draws, the algorithm created a vector of results for each prevalence and reassembled them into 96-well matrices for results distribution analysis of the number of positive cells and number and size of cell clusters (≥2 positive cells horizontally or vertically adjacent) per matrix. For simulation conditions of 12% and 16% HPV prevalence, 95% of the matrices displayed the following characteristics: 5 to 17 and 8 to 22 total positive cells, 0 to 4 and 0 to 5 positive cell clusters, and largest cluster sizes of up to 5 and up to 6 positive cells, respectively. Our results suggest that screening programs in regions with an oncogenic HPV prevalence of 12% to 16% can expect 5 to 22 positive results per microplate in approximately 95% of assays and 0 to 5 positive results clusters with no cluster larger than 6 positive results. Results consistently outside of these ranges deviate from what is statistically expected and could be the result of well-to-well contamination. Our results provide guidance that laboratories can use to identify microplates suspicious for well-to-well contamination, enabling improved quality assurance.This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal.

  17. Free recall test experience potentiates strategy-driven effects of value on memory.

    Science.gov (United States)

    Cohen, Michael S; Rissman, Jesse; Hovhannisyan, Mariam; Castel, Alan D; Knowlton, Barbara J

    2017-10-01

    People tend to show better memory for information that is deemed valuable or important. By one mechanism, individuals selectively engage deeper, semantic encoding strategies for high value items (Cohen, Rissman, Suthana, Castel, & Knowlton, 2014). By another mechanism, information paired with value or reward is automatically strengthened in memory via dopaminergic projections from midbrain to hippocampus (Shohamy & Adcock, 2010). We hypothesized that the latter mechanism would primarily enhance recollection-based memory, while the former mechanism would strengthen both recollection and familiarity. We also hypothesized that providing interspersed tests during study is a key to encouraging selective engagement of strategies. To test these hypotheses, we presented participants with sets of words, and each word was associated with a high or low point value. In some experiments, free recall tests were given after each list. In all experiments, a recognition test was administered 5 minutes after the final word list. Process dissociation was accomplished via remember/know judgments at recognition, a recall test probing both item memory and memory for a contextual detail (word plurality), and a task dissociation combining a recognition test for plurality (intended to probe recollection) with a speeded item recognition test (to probe familiarity). When recall tests were administered after study lists, high value strengthened both recollection and familiarity. When memory was not tested after each study list, but rather only at the end, value increased recollection but not familiarity. These dual process dissociations suggest that interspersed recall tests guide learners' use of metacognitive control to selectively apply effective encoding strategies. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  18. Design and validation of an ontology-driven animal-free testing strategy for developmental neurotoxicity testing.

    Science.gov (United States)

    Hessel, Ellen V S; Staal, Yvonne C M; Piersma, Aldert H

    2018-03-13

    Developmental neurotoxicity entails one of the most complex areas in toxicology. Animal studies provide only limited information as to human relevance. A multitude of alternative models have been developed over the years, providing insights into mechanisms of action. We give an overview of fundamental processes in neural tube formation, brain development and neural specification, aiming at illustrating complexity rather than comprehensiveness. We also give a flavor of the wealth of alternative methods in this area. Given the impressive progress in mechanistic knowledge of human biology and toxicology, the time is right for a conceptual approach for designing testing strategies that cover the integral mechanistic landscape of developmental neurotoxicity. The ontology approach provides a framework for defining this landscape, upon which an integral in silico model for predicting toxicity can be built. It subsequently directs the selection of in vitro assays for rate-limiting events in the biological network, to feed parameter tuning in the model, leading to prediction of the toxicological outcome. Validation of such models requires primary attention to coverage of the biological domain, rather than classical predictive value of individual tests. Proofs of concept for such an approach are already available. The challenge is in mining modern biology, toxicology and chemical information to feed intelligent designs, which will define testing strategies for neurodevelopmental toxicity testing. Copyright © 2018 Elsevier Inc. All rights reserved.

  19. Diagnostic test strategies in children at increased risk of inflammatory bowel disease in primary care.

    Directory of Open Access Journals (Sweden)

    Gea A Holtman

    Full Text Available In children with symptoms suggestive of inflammatory bowel disease (IBD who present in primary care, the optimal test strategy for identifying those who require specialist care is unclear. We evaluated the following three test strategies to determine which was optimal for referring children with suspected IBD to specialist care: 1 alarm symptoms alone, 2 alarm symptoms plus c-reactive protein, and 3 alarm symptoms plus fecal calprotectin.A prospective cohort study was conducted, including children with chronic gastrointestinal symptoms referred to pediatric gastroenterology. Outcome was defined as IBD confirmed by endoscopy, or IBD ruled out by either endoscopy or unremarkable clinical 12 month follow-up with no indication for endoscopy. Test strategy probabilities were generated by logistic regression analyses and compared by area under the receiver operating characteristic curves (AUC and decision curves.We included 90 children, of whom 17 (19% had IBD (n = 65 from primary care physicians, n = 25 from general pediatricians. Adding fecal calprotectin to alarm symptoms increased the AUC significantly from 0.80 (0.67-0.92 to 0.97 (0.93-1.00, but adding c-reactive protein to alarm symptoms did not increase the AUC significantly (p > 0.05. Decision curves confirmed these patterns, showing that alarm symptoms combined with fecal calprotectin produced the diagnostic test strategy with the highest net benefit at reasonable threshold probabilities.In primary care, when children are identified as being at high risk for IBD, adding fecal calprotectin testing to alarm symptoms was the optimal strategy for improving risk stratification.

  20. Quantification of intrahepatic total HBV DNA in liver biopsies of HBV-infected patients by a modified version of COBAS® Ampliprep/COBAS®TaqMan HBV test v2.0.

    Science.gov (United States)

    Salpini, Romina; Piermatteo, Lorenzo; Gill, Upkar; Battisti, Arianna; Stazi, Francesca; Guenci, Tania; Giannella, Sara; Serafini, Valentina; Kennedy, Patrick T F; Perno, Carlo Federico; Svicher, Valentina; Ciotti, Marco

    2017-08-01

    Intrahepatic total HBV DNA (it-HBV DNA) level might reflect the size of virus reservoir and correlate with the histological status of the liver. To quantitate it-HBV DNA in a series of 70 liver biopsies obtained from hepatitis B chronic patients, a modified version of the COBAS ® Ampliprep/COBAS ® TaqMan HBV test v2.0 was used for this purpose. The linearity and reproducibility of the modified protocol was tested by quantifying serial dilutions of a full-length HBV containing plasmid and it-HBV DNA from a reference patient. A good linear trend between the expected values and those generated by the assay was observed at different concentrations of both plasmid and reference patient (R 2  = 0.994 and 0.962, respectively). Differences between the values obtained in two independent runs were ≤0.3 log IU for the plasmid and ≤0.6 log IU/mg for the reference patient, showing a high inter-run reproducibility. In the 70 liver biopsies, it-HBV DNA level ranged from 1.4 to 5.4 log IU/mg, with a good linearity and reproducibility between the values obtained in two runs [R 2  = 0.981; median (IQR) difference of it-HBV DNA 0.05 (0.02-0.09) IU/mg]. The modified COBAS ® Ampliprep/COBAS ® TaqMan HBV test v2.0 allows an accurate quantitation of it-HBV DNA. Its determination may have prognostic value and may be a useful tool for the new therapeutic strategies aimed at eradicating the HBV infection.

  1. A simple and cost-effective method of DNA extraction from small formalin-fixed paraffin-embedded tissue for molecular oncologic testing.

    Science.gov (United States)

    Snow, Anthony N; Stence, Aaron A; Pruessner, Jonathan A; Bossler, Aaron D; Ma, Deqin

    2014-01-01

    Extraction of DNA from formalin-fixed, paraffin-embedded (FFPE) tissue is a critical step in molecular oncologic testing. As molecular oncology testing becomes more important for prognostic and therapeutic decision making and tissue specimens become smaller due to earlier detection of suspicious lesions and the use of fine needle aspiration methods for tissue collection, it becomes more challenging for the typical molecular pathology laboratory to obtain reliable test results. We developed a DNA extraction method to obtain sufficient quantity and high quality genomic DNA from limited FFPE tissue for molecular oncology testing using a combination of H&E stained slides, a matrix capture method and the Qiagen DNA column. THREE DNA EXTRACTION METHODS WERE COMPARED: our standard procedure of manually scraping tissue from unstained slides followed by DNA extraction using the QIAamp FFPE column (Qiagen, Valencia, CA), a glue capture method (Pinpoint Solution, Zymo Research Corp, Inc) on H&E stained slides followed by DNA extraction using either the QIAamp column or the column included with the Pinpoint kit (Zymo Research). The DNA extraction protocol was optimized. Statistical analysis was performed using the paired two-sample student's t-test. The combination of the matrix capture method with the QIAamp column gave an equivalent amount of DNA as our standard extraction method using the unstained slides and a 4.6-fold higher DNA yield than using the Zymo column included in the Pinpoint Slide Solution kit. Several molecular tests were performed and DNA purified using the new method gave the same results as for the previous methods. Using H&E stained slides allows visual confirmation of tumor cells during microdissection. The Pinpoint solution made removal of specific tissue from the slides easier and reduced the risk of contamination and tissue loss. This DNA extraction method is simple, cost-effective, and blends with our current workflow requiring no additional equipment.

  2. Long span DNA paired-end-tag (DNA-PET sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons.

    Directory of Open Access Journals (Sweden)

    Fei Yao

    Full Text Available Structural variations (SVs contribute significantly to the variability of the human genome and extensive genomic rearrangements are a hallmark of cancer. While genomic DNA paired-end-tag (DNA-PET sequencing is an attractive approach to identify genomic SVs, the current application of PET sequencing with short insert size DNA can be insufficient for the comprehensive mapping of SVs in low complexity and repeat-rich genomic regions. We employed a recently developed procedure to generate PET sequencing data using large DNA inserts of 10-20 kb and compared their characteristics with short insert (1 kb libraries for their ability to identify SVs. Our results suggest that although short insert libraries bear an advantage in identifying small deletions, they do not provide significantly better breakpoint resolution. In contrast, large inserts are superior to short inserts in providing higher physical genome coverage for the same sequencing cost and achieve greater sensitivity, in practice, for the identification of several classes of SVs, such as copy number neutral and complex events. Furthermore, our results confirm that large insert libraries allow for the identification of SVs within repetitive sequences, which cannot be spanned by short inserts. This provides a key advantage in studying rearrangements in cancer, and we show how it can be used in a fusion-point-guided-concatenation algorithm to study focally amplified regions in cancer.

  3. Modelling and operation strategies of DLR's large scale thermocline test facility (TESIS)

    Science.gov (United States)

    Odenthal, Christian; Breidenbach, Nils; Bauer, Thomas

    2017-06-01

    In this work an overview of the TESIS:store thermocline test facility and its current construction status will be given. Based on this, the TESIS:store facility using sensible solid filler material is modelled with a fully transient model, implemented in MATLAB®. Results in terms of the impact of filler site and operation strategies will be presented. While low porosity and small particle diameters for the filler material are beneficial, operation strategy is one key element with potential for optimization. It is shown that plant operators have to ponder between utilization and exergetic efficiency. Different durations of the charging and discharging period enable further potential for optimizations.

  4. Dental Student Study Strategies: Are Self-Testing and Scheduling Related to Academic Performance?

    Science.gov (United States)

    McAndrew, Maureen; Morrow, Christina S; Atiyeh, Lindsey; Pierre, Gaëlle C

    2016-05-01

    Self-testing, a strategy wherein a student actively engages in creating questions and answers from study materials to assist with studying, has been found to be especially advantageous because it enhances future retrieval of information. Studies have found correlations among students' grade point averages (GPAs), self-testing, and rereading study strategies, as well as the spacing of study sessions over time. The aim of this study was to assess relationships among dental students' study strategies, scheduling of study time, and academic achievement. A 16-item survey requesting information on study habits, study schedules, and GPAs was distributed to 358 second-year dental students at New York University College of Dentistry. Additionally, the survey asked students to report the average number of hours per week they devoted to studying for didactic courses and preparing for hands-on preclinical courses. Of the 358 students, 94 (26%) responded to the survey. The vast majority of the respondents reported utilizing self-testing and rereading study strategies. High performers (with higher GPAs) were more likely to use self-testing, especially with flashcards, and to space their studying over multiple sessions. Lower performing students were more likely to highlight or underline their notes and to mass their study sessions or cram. Longer hours devoted to studying and practicing for simulation courses were associated with stronger performance; lower performers reported spending significantly fewer hours practicing for simulation courses. Half of the dental students surveyed said that they felt their studying would be more productive in the morning, although 84% reported doing most of their studying in the evening or late night. Sound study decisions depend on accurate regulation of ongoing learning and appropriate use and timing of evidence-based study strategies, so these results suggest that dental students may require guidance in these areas.

  5. Economic Evaluation of Laboratory Testing Strategies for Hospital-Associated Clostridium difficile Infection

    Science.gov (United States)

    Robilotti, Elizabeth; Peterson, Lance R.; Banaei, Niaz; Dowdy, David W.

    2014-01-01

    Clostridium difficile infection (CDI) is the most common cause of infectious diarrhea in health care settings, and for patients presumed to have CDI, their isolation while awaiting laboratory results is costly. Newer rapid tests for CDI may reduce this burden, but the economic consequences of different testing algorithms remain unexplored. We used decision analysis from the hospital perspective to compare multiple CDI testing algorithms for adult inpatients with suspected CDI, assuming patient management according to laboratory results. CDI testing strategies included combinations of on-demand PCR (odPCR), batch PCR, lateral-flow diagnostics, plate-reader enzyme immunoassay, and direct tissue culture cytotoxicity. In the reference scenario, algorithms incorporating rapid testing were cost-effective relative to nonrapid algorithms. For every 10,000 symptomatic adults, relative to a strategy of treating nobody, lateral-flow glutamate dehydrogenase (GDH)/odPCR generated 831 true-positive results and cost $1,600 per additional true-positive case treated. Stand-alone odPCR was more effective and more expensive, identifying 174 additional true-positive cases at $6,900 per additional case treated. All other testing strategies were dominated by (i.e., more costly and less effective than) stand-alone odPCR or odPCR preceded by lateral-flow screening. A cost-benefit analysis (including estimated costs of missed cases) favored stand-alone odPCR in most settings but favored odPCR preceded by lateral-flow testing if a missed CDI case resulted in less than $5,000 of extended hospital stay costs and 93%, or if the symptomatic carrier proportion among the toxigenic culture-positive cases was >80%. These results can aid guideline developers and laboratory directors who are considering rapid testing algorithms for diagnosing CDI. PMID:24478478

  6. Economic evaluation of laboratory testing strategies for hospital-associated Clostridium difficile infection.

    Science.gov (United States)

    Schroeder, Lee F; Robilotti, Elizabeth; Peterson, Lance R; Banaei, Niaz; Dowdy, David W

    2014-02-01

    Clostridium difficile infection (CDI) is the most common cause of infectious diarrhea in health care settings, and for patients presumed to have CDI, their isolation while awaiting laboratory results is costly. Newer rapid tests for CDI may reduce this burden, but the economic consequences of different testing algorithms remain unexplored. We used decision analysis from the hospital perspective to compare multiple CDI testing algorithms for adult inpatients with suspected CDI, assuming patient management according to laboratory results. CDI testing strategies included combinations of on-demand PCR (odPCR), batch PCR, lateral-flow diagnostics, plate-reader enzyme immunoassay, and direct tissue culture cytotoxicity. In the reference scenario, algorithms incorporating rapid testing were cost-effective relative to nonrapid algorithms. For every 10,000 symptomatic adults, relative to a strategy of treating nobody, lateral-flow glutamate dehydrogenase (GDH)/odPCR generated 831 true-positive results and cost $1,600 per additional true-positive case treated. Stand-alone odPCR was more effective and more expensive, identifying 174 additional true-positive cases at $6,900 per additional case treated. All other testing strategies were dominated by (i.e., more costly and less effective than) stand-alone odPCR or odPCR preceded by lateral-flow screening. A cost-benefit analysis (including estimated costs of missed cases) favored stand-alone odPCR in most settings but favored odPCR preceded by lateral-flow testing if a missed CDI case resulted in less than $5,000 of extended hospital stay costs and 93%, or if the symptomatic carrier proportion among the toxigenic culture-positive cases was >80%. These results can aid guideline developers and laboratory directors who are considering rapid testing algorithms for diagnosing CDI.

  7. A new O6-alkylguanine-DNA alkyltransferase inhibitor associated with a nitrosourea (cystemustine) validates a strategy of melanoma-targeted therapy in murine B16 and human-resistant M4Beu melanoma xenograft models.

    Science.gov (United States)

    Rapp, Maryse; Maurizis, Jean C; Papon, Janine; Labarre, Pierre; Wu, Ting-Di; Croisy, Alain; Guerquin-Kern, Jean L; Madelmont, Jean C; Mounetou, Emmanuelle

    2008-07-01

    Chemoresistance to O(6)-alkylating agents is a major barrier to successful treatment of melanoma. It is mainly due to a DNA repair suicide protein, O(6)-alkylguanine-DNA alkyltransferase (AGT). Although AGT inactivation is a powerful clinical strategy for restoring tumor chemosensitivity, it was limited by increased toxicity to nontumoral cells resulting from a lack of tumor selectivity. Achieving enhanced chemosensitization via AGT inhibition preferably in the tumor should protect normal tissue. To this end, we have developed a strategy to target AGT inhibitors. In this study, we tested a new potential melanoma-directed AGT inhibitor [2-amino-6-(4-iodobenzyloxy)-9-[4-(diethylamino) ethylcarbamoylbenzyl] purine; IBgBZ] designed as a conjugate of O(6)-(4-iododbenzyl)guanine (IBg) as the AGT inactivator and a N,N-diethylaminoethylenebenzamido (BZ) moiety as the carrier to the malignant melanocytes. IBgBZ demonstrated AGT inactivation ability and potentiation of O(6)-alkylating agents (cystemustine, a chloroethylnitrosourea) in M4Beu highly chemoresistant human melanoma cells both in vitro and in tumor models. The biodisposition study on mice bearing B16 melanoma, the standard model for the evaluation of melanoma-directed agents, and the secondary ion mass spectrometry imaging confirmed the concentration of IBgBZ in the tumor and in particular in the intracytoplasmic melanosomes. These results validate the potential of IBgBZ as a new, more tumor-selective, AGT inhibitor in a strategy of melanoma-targeted therapy.

  8. Detection of Toxoplasma gondii DNA in horse meat from supermarkets in France and performance evaluation of two serological tests

    Directory of Open Access Journals (Sweden)

    Aroussi Abdelkrim

    2015-01-01

    Full Text Available In France, some cases of severe toxoplasmosis have been linked to the consumption of horse meat that had been imported from the American continent where atypical strains of Toxoplasma gondii are more common than in Europe. Many seroprevalence studies are presented in the literature but risk assessment of T. gondii infection after horse meat consumption is not possible in the absence of validated serological tests and the unknown correlation between detection of antibodies against T. gondii and presence of tissue cysts. We performed magnetic-capture polymerase chain reaction (MC-PCR to detect T. gondii DNA in 231 horse meat samples purchased in supermarkets in France and evaluated the performance and level of agreement of the modified agglutination test (MAT and enzyme-linked immunosorbent assay (ELISA in the meat juices. The serological tests lacked sensitivity, specificity, and agreement between them, and there was no correlation with the presence of T. gondii DNA in horse meat, raising concerns about the reliability of T. gondii seroprevalence data in horses from the literature. T. gondii DNA was detected in 43% of horse meat samples but the absence of strain isolation in mice following inoculation of more than 100 horse meat samples suggests a low distribution of cysts in skeletal muscles and a low risk of T. gondii infection associated with horse meat consumption. However, to avoid any risk of toxoplasmosis, thorough cooking of horse meat is recommended.

  9. Detection of Toxoplasma gondii DNA in horse meat from supermarkets in France and performance evaluation of two serological tests.

    Science.gov (United States)

    Aroussi, Abdelkrim; Vignoles, Philippe; Dalmay, François; Wimel, Laurence; Dardé, Marie-Laure; Mercier, Aurélien; Ajzenberg, Daniel

    2015-01-01

    In France, some cases of severe toxoplasmosis have been linked to the consumption of horse meat that had been imported from the American continent where atypical strains of Toxoplasma gondii are more common than in Europe. Many seroprevalence studies are presented in the literature but risk assessment of T. gondii infection after horse meat consumption is not possible in the absence of validated serological tests and the unknown correlation between detection of antibodies against T. gondii and presence of tissue cysts. We performed magnetic-capture polymerase chain reaction (MC-PCR) to detect T. gondii DNA in 231 horse meat samples purchased in supermarkets in France and evaluated the performance and level of agreement of the modified agglutination test (MAT) and enzyme-linked immunosorbent assay (ELISA) in the meat juices. The serological tests lacked sensitivity, specificity, and agreement between them, and there was no correlation with the presence of T. gondii DNA in horse meat, raising concerns about the reliability of T. gondii seroprevalence data in horses from the literature. T. gondii DNA was detected in 43% of horse meat samples but the absence of strain isolation in mice following inoculation of more than 100 horse meat samples suggests a low distribution of cysts in skeletal muscles and a low risk of T. gondii infection associated with horse meat consumption. However, to avoid any risk of toxoplasmosis, thorough cooking of horse meat is recommended. © A. Aroussi et al., published by EDP Sciences, 2015.

  10. On the effects of sampling, analysis and interpretation strategies for complex forensic DNA research with focus on sexual assault cases

    NARCIS (Netherlands)

    Benschop, C.C.G.

    2012-01-01

    Forensisch DNA-onderzoek kan een grote bijdrage leveren aan het oplossen van diverse soorten misdrijven. Dit DNA-onderzoek kan complex zijn, bijvoorbeeld als de hoeveelheid celmateriaal minimaal is of als het biologische spoor celmateriaal bevat van meerdere (aan elkaar verwante) donoren. Corina

  11. Data from complete mtDNA sequencing of Tunisian centenarians: testing haplogroup association and the "golden mean" to longevity.

    Science.gov (United States)

    Costa, Marta D; Cherni, Lotfi; Fernandes, Verónica; Freitas, Fernando; Ammar El Gaaied, Amel Ben; Pereira, Luísa

    2009-04-01

    Since the mitochondrial theory of ageing was proposed, mitochondrial DNA (mtDNA) diversity has been largely studied in old people, however complete genomes are still rare, being limited to Japanese and UK/US samples. In this work, we evaluated possible longevity associated polymorphisms/haplogroups in an African population, from Tunisia, by performing complete mtDNA sequencing. This population has a mixed Eurasian/sub-Saharan mtDNA gene pool, which could potentially facilitate the evaluation of association for sub-Saharan lineages. Sub-Saharan haplogroups were shown to be significantly less represented in centenarians (9.5%) than in controls (54.5%), but it is not possible to rule out an influence of population structure, which is high in these populations. No recurrent polymorphism were more frequent in centenarians than in controls, and although the Tunisian centenarians presented less synonymous and replacement polymorphisms than controls, this difference was not statistically significant. So far, it does not seem that centenarians have significantly less mildly deleterious substitutions, not only in Tunisia but also in Japanese and UK/US samples, as tested here, not favouring a "golden mean" to longevity.

  12. A dual amplification strategy for DNA detection combining bio-barcode assay and metal-enhanced fluorescence modality.

    Science.gov (United States)

    Zhou, Zhenpeng; Li, Tian; Huang, Hongduan; Chen, Yang; Liu, Feng; Huang, Chengzhi; Li, Na

    2014-11-11

    Silver-enhanced fluorescence was coupled with a bio-barcode assay to facilitate a dual amplification assay to demonstrate a non-enzymatic approach for simple and sensitive detection of DNA. In the assay design, magnetic nanoparticles seeded with silver nanoparticles were modified with the capture DNA, and silver nanoparticles were modified with the binding of ssDNA and the fluorescently labeled barcode dsDNA. Upon introduction of the target DNA, a sandwich structure was formed because of the hybridization reaction. By simple magnetic separation, silver-enhanced fluorescence of barcode DNAs could be readily measured without the need of a further step to liberate barcode DNAs from silver nanoparticles, endowing the method with simplicity and high sensitivity with a detection limit of 1 pM.

  13. Coping strategies as mediators in the relationship between test anxiety and academic achievement

    Directory of Open Access Journals (Sweden)

    Genc Ana

    2017-01-01

    Full Text Available In most modern societies, nearly every realm of life involves some form of evaluation of our knowledge, abilities and skills. Given the potentially significant consequences of exams, it is not surprising that they are often very stressful. This study aimed to determine the existence and nature of the relationships between level of test anxiety, coping strategies, and achieved success on a mid-term test. As well as examining the direct relations between the given variables, our primary interest was to investigate the potential mediating role of coping mechanisms between the input and output variables of the examined stressful transaction. The study was conducted on a sample of 263 students from the Psychology and German Studies Departments of the Faculty of Philosophy at the University of Novi Sad. According to our results, only emotion-focused coping mechanisms were statistically significant mediators in the relationship between level of test anxiety and mid-term test achievement. The results indicate that students with high test anxiety who employ predominantly emotion-focused coping strategies score lower on a pre-exam knowledge test.

  14. Testing the utility of matK and ITS DNA regions for discrimination of Allium species

    Science.gov (United States)

    Molecular phylogenetic analysis of the genus Allium L. has been mainly based on the nucleotide sequences of ITS region. In 2009 matK and rbcL were accepted as a two-locus DNA barcode to classify plant species by the Consortium for the Barcode of Life (CBOL) Plant Working Group. MatK region has been ...

  15. Cost-Effectiveness of HIV Testing Referral Strategies among Tuberculosis Patients in India

    Science.gov (United States)

    Uhler, Lauren M.; Kumarasamy, Nagalingeswaran; Mayer, Kenneth H.; Saxena, Anjali; Losina, Elena; Muniyandi, Malaisamy; Stoler, Adam W.; Lu, Zhigang; Walensky, Rochelle P.; Flanigan, Timothy P.; Bender, Melissa A.; Freedberg, Kenneth A.; Swaminathan, Soumya

    2010-01-01

    Background Indian guidelines recommend routine referral for HIV testing of all tuberculosis (TB) patients in the nine states with the highest HIV prevalence, and selective referral for testing elsewhere. We assessed the clinical impact and cost-effectiveness of alternative HIV testing referral strategies among TB patients in India. Methods and Findings We utilized a computer model of HIV and TB disease to project outcomes for patients with active TB in India. We compared life expectancy, cost, and cost-effectiveness for three HIV testing referral strategies: 1) selective referral for HIV testing of those with increased HIV risk, 2) routine referral of patients in the nine highest HIV prevalence states with selective referral elsewhere (current standard), and 3) routine referral of all patients for HIV testing. TB-related data were from the World Health Organization. HIV prevalence among TB patients was 9.0% in the highest prevalence states, 2.9% in the other states, and 4.9% overall. The selective referral strategy, beginning from age 33.50 years, had a projected discounted life expectancy of 16.88 years and a mean lifetime HIV/TB treatment cost of US$100. The current standard increased mean life expectancy to 16.90 years with additional per-person cost of US$10; the incremental cost-effectiveness ratio was US$650/year of life saved (YLS) compared to selective referral. Routine referral of all patients for HIV testing increased life expectancy to 16.91 years, with an incremental cost-effectiveness ratio of US$730/YLS compared to the current standard. For HIV-infected patients cured of TB, receiving antiretroviral therapy increased survival from 4.71 to 13.87 years. Results were most sensitive to the HIV prevalence and the cost of second-line antiretroviral therapy. Conclusions Referral of all patients with active TB in India for HIV testing will be both effective and cost-effective. While effective implementation of this strategy would require investment, routine

  16. Diagnostic value of stool DNA testing for multiple markers of colorectal cancer and advanced adenoma: a meta-analysis.

    Science.gov (United States)

    Yang, Hua; Xia, Bing-Qing; Jiang, Bo; Wang, Guozhen; Yang, Yi-Peng; Chen, Hao; Li, Bing-Sheng; Xu, An-Gao; Huang, Yun-Bo; Wang, Xin-Ying

    2013-08-01

    The diagnostic value of stool DNA (sDNA) testing for colorectal neoplasms remains controversial. To compensate for the lack of large-scale unbiased population studies, a meta-analysis was performed to evaluate the diagnostic value of sDNA testing for multiple markers of colorectal cancer (CRC) and advanced adenoma. The PubMed, Science Direct, Biosis Review, Cochrane Library and Embase databases were systematically searched in January 2012 without time restriction. Meta-analysis was performed using a random-effects model using sensitivity, specificity, diagnostic OR (DOR), summary ROC curves, area under the curve (AUC), and 95% CIs as effect measures. Heterogeneity was measured using the χ(2) test and Q statistic; subgroup analysis was also conducted. A total of 20 studies comprising 5876 individuals were eligible. There was no heterogeneity for CRC, but adenoma and advanced adenoma harboured considerable heterogeneity influenced by risk classification and various detection markers. Stratification analysis according to risk classification showed that multiple markers had a high DOR for the high-risk subgroups of both CRC (sensitivity 0.759 [95% CI 0.711 to 0.804]; specificity 0.883 [95% CI 0.846 to 0.913]; AUC 0.906) and advanced adenoma (sensitivity 0.683 [95% CI 0.584 to 0.771]; specificity 0.918 [95% CI 0.866 to 0.954]; AUC 0.946) but not for the average-risk subgroups of either. In the methylation subgroup, sDNA testing had significantly higher DOR for CRC (sensitivity 0.753 [95% CI 0.685 to 0.812]; specificity 0.913 [95% CI 0.860 to 0.950]; AUC 0.918) and advanced adenoma (sensitivity 0.623 [95% CI 0.527 to 0.712]; specificity 0.926 [95% CI 0.882 to 0.958]; AUC 0.910) compared with the mutation subgroup. There was no significant heterogeneity among studies for subgroup analysis. sDNA testing for multiple markers had strong diagnostic significance for CRC and advanced adenoma in high-risk subjects. Methylation makers had more diagnostic value than mutation

  17. Barriers to, and emerging strategies for, HIV testing among adolescents in sub-Saharan Africa.

    Science.gov (United States)

    Chikwari, Chido D; Dringus, Stefanie; Ferrand, Rashida A

    2018-05-01

    HIV/AIDS is one of the leading causes of death among adolescents in sub-Saharan Africa and 40% of new HIV infections worldwide occur in this group. HIV testing and counselling (HTC) is the critical first step to accessing HIV treatment. The prevalence of undiagnosed HIV infection is substantially higher in adolescents compared with adults. We review barriers to HTC for adolescents and emerging HTC strategies appropriate to adolescents in sub-Saharan Africa. There are substantial individual, health system and legal barriers to HTC among adolescents, and stigma by providers and communities remains an important obstacle. There has been progress made in recent years in developing strategies that address some of these barriers, increase uptake of HTC and yield of HIV. These include targeted approaches focused on provision of HTC among those higher risk of being infected, for example, index-linked HTC and use of screening tools to identify those at risk of HIV. Community-based HIV-testing approaches including HIV self-testing and incentives have also been shown to increase uptake of HTC. In implementing HTC strategies, consideration must be given to scalability and cost-effectiveness. HTC approaches must be coupled with linkage to appropriate care and prevention services.

  18. Strategy for 90% autoverification of clinical chemistry and immunoassay test results using six sigma process improvement.

    Science.gov (United States)

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

    2018-06-01

    Six Sigma involves a structured process improvement strategy that places processes on a pathway to continued improvement. The data presented here summarizes a project that took three clinical laboratories from autoverification processes that allowed between about 40% to 60% of tests being auto-verified to more than 90% of tests and samples auto-verified. The project schedule, metrics and targets, a description of the previous system and detailed information on the changes made to achieve greater than 90% auto-verification is presented for this Six Sigma DMAIC (Design, Measure, Analyze, Improve, Control) process improvement project.

  19. Comparison of strategies for the isolation of PCR-compatible, genomic DNA from a municipal biogas plants.

    Science.gov (United States)

    Weiss, Agnes; Jérôme, Valérie; Freitag, Ruth

    2007-06-15

    The goal of the project was the extraction of PCR-compatible genomic DNA representative of the entire microbial community from municipal biogas plant samples (mash, bioreactor content, process water, liquid fertilizer). For the initial isolation of representative DNA from the respective lysates, methods were used that employed adsorption, extraction, or precipitation to specifically enrich the DNA. Since no dedicated method for biogas plant samples was available, preference was given to kits/methods suited to samples that resembled either the bioreactor feed, e.g. foodstuffs, or those intended for environmental samples including wastewater. None of the methods succeeded in preparing DNA that was directly PCR-compatible. Instead the DNA was found to still contain considerable amounts of difficult-to-remove enzyme inhibitors (presumably humic acids) that hindered the PCR reaction. Based on the isolation method that gave the highest yield/purity for all sample types, subsequent purification was attempted by agarose gel electrophoresis followed by electroelution, spermine precipitation, or dialysis through nitrocellulose membrane. A combination of phenol/chloroform extraction followed by purification via dialysis constituted the most efficient sample treatment. When such DNA preparations were diluted 1:100 they did no longer inhibit PCR reactions, while they still contained sufficient genomic DNA to allow specific amplification of specific target sequences.

  20. Increased adolescent HIV testing with a hybrid mobile strategy in Uganda and Kenya.

    Science.gov (United States)

    Kadede, Kevin; Ruel, Theodore; Kabami, Jane; Ssemmondo, Emmanuel; Sang, Norton; Kwarisiima, Dalsone; Bukusi, Elizabeth; Cohen, Craig R; Liegler, Teri; Clark, Tamara D; Charlebois, Edwin D; Petersen, Maya L; Kamya, Moses R; Havlir, Diane V; Chamie, Gabriel

    2016-09-10

    We sought to increase adolescent HIV testing across rural communities in east Africa and identify predictors of undiagnosed HIV. Hybrid mobile testing. We enumerated 116 326 adolescents (10-24 years) in 32 communities of Uganda and Kenya ( NCT01864603): 98 694 (85%) reported stable (≥6 months of prior year) residence. In each community we performed hybrid testing: 2-week multidisease community health campaign that included HIV testing, followed by home-based testing of community health campaign nonparticipants. We measured adolescent HIV testing coverage and prevalence, and determined predictors of newly diagnosed HIV among HIV-infected adolescents using multivariable logistic regression. A total of 86 421 (88%) stable adolescents tested for HIV; coverage was 86, 90, and 88% in early (10-14), mid (15-17), and late (18-24) adolescents, respectively. Self-reported prior testing was 9, 26, and 55% in early, mid, and late adolescents tested, respectively. HIV prevalence among adolescents tested was 1.6 and 0.6% in Ugandan women and men, and 7.1 and 1.5% in Kenyan women and men, respectively. Prevalence increased in mid-adolescence for women and late adolescence for men. Among HIV-infected adolescents, 58% reported newly diagnosed HIV. In multivariate analysis of HIV-infected adolescents, predictors of newly diagnosed HIV included male sex [odds ratio (OR) = 1.97 (95% confidence interval (CI): 1.42-2.73)], Ugandan residence [OR = 2.63 (95% CI: 2.08-3.31)], and single status [OR = 1.62 (95% CI: 1.23-2.14) vs. married)]. The SEARCH hybrid strategy tested 88% of stable adolescents for HIV, a substantial increase over the 28% reporting prior testing. The majority (57%) of HIV-infected adolescents were new diagnoses. Mobile HIV testing for adults should be leveraged to reach adolescents for HIV treatment and prevention.

  1. Detection of Circulating Mucorales DNA in Critically Ill Burn Patients: Preliminary Report of a Screening Strategy for Early Diagnosis and Treatment.

    Science.gov (United States)

    Legrand, Matthieu; Gits-Muselli, Maud; Boutin, Louis; Garcia-Hermoso, Dea; Maurel, Véronique; Soussi, Sabri; Benyamina, Mourad; Ferry, Axelle; Chaussard, Maïté; Hamane, Samia; Denis, Blandine; Touratier, Sophie; Guigue, Nicolas; Fréalle, Emilie; Jeanne, Mathieu; Shaal, Jean-Vivien; Soler, Charles; Mimoun, Maurice; Chaouat, Marc; Lafaurie, Matthieu; Mebazaa, Alexandre; Bretagne, Stéphane; Alanio, Alexandre

    2016-11-15

     Invasive wound mucormycosis (IWM) is associated with an extremely poor outcome among critically ill burn patients. We describe the detection of circulating Mucorales DNA (cmDNA) for the early diagnosis of IWM in those patients and report the potential value of detecting cmDNA for treatment guidance.  Severely ill burn patients admitted to our tertiary referral center between October 2013 and February 2016 were included. Retrospective plasma samples were tested for the presence of cmDNA by quantitative real-time polymerase chain reaction (qPCR). Patients were then prospectively screened twice a week, and liposomal amphotericin-B therapy initiated based on a positive qPCR. The primary endpoint was the time between cmDNA detection and standard diagnosis. Secondary endpoints were the time from cmDNA detection and treatment initiation and mortality.  Seventy-seven patients (418 samples) were included. The average age was 46 (28-60) years, abbreviated burn severity index was 8 (7-10), and simplified acute physiology score was 33 (23-46). The total body surface area was 33% (22%-52%). cmDNA was detected 11 (4.5-15) days before standard diagnosis. The in-hospital mortality was 62% for patients with IWM and 24% for those without (P = .03). The mortality due to IWM was 80% during period A and 33% during period B (P = .46).  This study suggests that the detection of cmDNA allows earlier diagnosis of IWM in severely ill burn patients and earlier initiation of treatment. Further studies are needed to confirm the impact of earlier treatment initiation on patient outcome. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

  2. Development and applications of Bacillus subtilis test systems for mutagens, involving DNA-repair deficiency and suppressible auxotrophic mutations

    International Nuclear Information System (INIS)

    Tanooka, H.

    1977-01-01

    A mutagen-tester of Bacillus subtilis was constructed and tested with known carcinogens. The parental strain HA101 of Okubo and Yanagida carrying suppressible nonsense mutations in his and met genes was transformed to carry an excision-repair deficiency mutation. The constructed strain TKJ5211 showed a 20-30-fold higher sensitivity for His + reversion than the parental strain when treated with UV and UV-mimetic chemicals but unchanged mutation frequency with X-rays and methyl methanesulfonate. The tester strain was used in a spot test of 30 selected chemicals and also for testing with liver homogenate activation. The results showed an almost equivalent but somewhat broader detection spectrum than the Salmonella typhimurium TA100 system. Another test method used a pair of B. subtilis strains differing in their DNA-repair capacity, i.e. the most UV-sensitive mutant HJ-15 and a wild-type strain, to detect repair-dependent DNA damage produced by chemicals. Spores could be used in either test

  3. Informed decision making about predictive DNA tests: arguments for more public visibility of personal deliberations about the good life.

    Science.gov (United States)

    Boenink, Marianne; van der Burg, Simone

    2010-05-01

    Since its advent, predictive DNA testing has been perceived as a technology that may have considerable impact on the quality of people's life. The decision whether or not to use this technology is up to the individual client. However, to enable well considered decision making both the negative as well as the positive freedom of the individual should be supported. In this paper, we argue that current professional and public discourse on predictive DNA-testing is lacking when it comes to supporting positive freedom, because it is usually framed in terms of risk and risk management. We show how this 'risk discourse' steers thinking on the good life in a particular way. We go on to argue that empirical research into the actual deliberation and decision making processes of individuals and families may be used to enrich the environment of personal deliberation in three ways: (1) it points at a richer set of values that deliberators can take into account, (2) it acknowledges the shared nature of genes, and (3) it shows how one might frame decisions in a non-binary way. We argue that the public sharing and discussing of stories about personal deliberations offers valuable input for others who face similar choices: it fosters their positive freedom to shape their view of the good life in relation to DNA-diagnostics. We conclude by offering some suggestions as to how to realize such public sharing of personal stories.

  4. Direct-to-consumer DNA testing: the fallout for individuals and their families unexpectedly learning of their donor conception origins.

    Science.gov (United States)

    Crawshaw, Marilyn

    2017-07-11

    Increasing numbers of donor-conceived individuals (and/or parents) are seeking individuals genetically related through donor conception. One route is through 'direct-to-consumer' (DTC) DNA testing, prompting calls for fertility services to alert donors and prospective parents to the increasing unsustainability of anonymity and secrecy. The complexity of interpreting DNA results in this context has also been discussed, including their lack of absolute certainty, as has the need for professional and peer support. This commentary highlights a different 'threat', from individuals learning of their donor-conception origins through the use of such tests by themselves or relatives for such purposes as genealogy or health checks. It illustrates the personal complexities faced by three older women and their families on learning not only of their genetic relationship to each other but also to 15 more donor-related siblings. DTC DNA services are a growing feature of modern life. This commentary raises ethical questions about their responsibilities towards those inadvertently learning of donor conception origins and the responsibilities of fertility services to inform prospective parents and donors of this new phenomenon. Considerations of how and when parents should tell their children of their donor-conception origins here instead become how and when children should inform their parents.

  5. High School Students' Performance on Vandenberg's Mental Rotations Test: Art Ability, Gender, Activities, Academic Performance, Strategies, and Ease of Taking the Test.

    Science.gov (United States)

    Gurny, Helen Graham

    This study tested whether mental rotation performance of 186 high school students (80 males and 106 females) in grades 9 through 12 in art and nonart classes on Vandenbergs Mental Rotations test (S. Vandenberg and Kuse, 1978) was affected by gender, visual-spatial activities, strategies used while performing the test, and the ease of test taking.…

  6. Target-induced formation of gold amalgamation on DNA-based sensing platform for electrochemical monitoring of mercury ion coupling with cycling signal amplification strategy

    International Nuclear Information System (INIS)

    Chen, Jinfeng; Tang, Juan; Zhou, Jun; Zhang, Lan; Chen, Guonan; Tang, Dianping

    2014-01-01

    Graphical abstract: -- Highlights: •We report a new electrochemical sensing protocol for the detection of mercury ion. •Gold amalgamation on DNA-based sensing platform was used as nanocatalyst. •The signal was amplified by cycling signal amplification strategy. -- Abstract: Heavy metal ion pollution poses severe risks in human health and environmental pollutant, because of the likelihood of bioaccumulation and toxicity. Driven by the requirement to monitor trace-level mercury ion (Hg 2+ ), herein we construct a new DNA-based sensor for sensitive electrochemical monitoring of Hg 2+ by coupling target-induced formation of gold amalgamation on DNA-based sensing platform with gold amalgamation-catalyzed cycling signal amplification strategy. The sensor was simply prepared by covalent conjugation of aminated poly-T (25) oligonucleotide onto the glassy carbon electrode by typical carbodiimide coupling. Upon introduction of target analyte, Hg 2+ ion was intercalated into the DNA polyion complex membrane based on T–Hg 2+ –T coordination chemistry. The chelated Hg 2+ ion could induce the formation of gold amalgamation, which could catalyze the p-nitrophenol with the aid of NaBH 4 and Ru(NH 3 ) 6 3+ for cycling signal amplification. Experimental results indicated that the electronic signal of our system increased with the increasing Hg 2+ level in the sample, and has a detection limit of 0.02 nM with a dynamic range of up to 1000 nM Hg 2+ . The strategy afforded exquisite selectivity for Hg 2+ against other environmentally related metal ions. In addition, the methodology was evaluated for the analysis of Hg 2+ in spiked tap-water samples, and the recovery was 87.9–113.8%

  7. Target-induced formation of gold amalgamation on DNA-based sensing platform for electrochemical monitoring of mercury ion coupling with cycling signal amplification strategy

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Jinfeng; Tang, Juan; Zhou, Jun; Zhang, Lan; Chen, Guonan; Tang, Dianping, E-mail: dianping.tang@fzu.edu.cn

    2014-01-31

    Graphical abstract: -- Highlights: •We report a new electrochemical sensing protocol for the detection of mercury ion. •Gold amalgamation on DNA-based sensing platform was used as nanocatalyst. •The signal was amplified by cycling signal amplification strategy. -- Abstract: Heavy metal ion pollution poses severe risks in human health and environmental pollutant, because of the likelihood of bioaccumulation and toxicity. Driven by the requirement to monitor trace-level mercury ion (Hg{sup 2+}), herein we construct a new DNA-based sensor for sensitive electrochemical monitoring of Hg{sup 2+} by coupling target-induced formation of gold amalgamation on DNA-based sensing platform with gold amalgamation-catalyzed cycling signal amplification strategy. The sensor was simply prepared by covalent conjugation of aminated poly-T{sub (25)} oligonucleotide onto the glassy carbon electrode by typical carbodiimide coupling. Upon introduction of target analyte, Hg{sup 2+} ion was intercalated into the DNA polyion complex membrane based on T–Hg{sup 2+}–T coordination chemistry. The chelated Hg{sup 2+} ion could induce the formation of gold amalgamation, which could catalyze the p-nitrophenol with the aid of NaBH{sub 4} and Ru(NH{sub 3}){sub 6}{sup 3+} for cycling signal amplification. Experimental results indicated that the electronic signal of our system increased with the increasing Hg{sup 2+} level in the sample, and has a detection limit of 0.02 nM with a dynamic range of up to 1000 nM Hg{sup 2+}. The strategy afforded exquisite selectivity for Hg{sup 2+} against other environmentally related metal ions. In addition, the methodology was evaluated for the analysis of Hg{sup 2+} in spiked tap-water samples, and the recovery was 87.9–113.8%.

  8. Anxiety in voluntary HIV-antibody testing in pregnancy and its implications for preventive strategies.

    Science.gov (United States)

    Foldspang, A; Hedegaard, M

    1991-06-01

    During a three-month period in 1989, 820 pregnant women attending the antenatal clinic of the Aarhus University Hospital, Denmark, were offered a HIV-antibody test and asked to fill out an anonymous questionnaire about attitudes to HIV-antibody testing; 779 (95.0%) agreed to do so. One hundred and fifty-six women (20.0% of the participants) had been tested on a previous occasion, and 629 (80.7%) accepted the present offer to be tested. The most prevalent reasons to decline testing were indifference to the epidemic (45.3% of those declining), refusal of (further) blood testing (34.7%) and fear of being infected (16.7%). Women who consented to be tested most often expressed fear of being infected (21.8%). Fear of registration worried less than 5% of study group members; only 1% declined to be tested because of such worry. The pattern of worries expressed by the pregnant women is interpreted as one of anxiety and, in part at least, perplexity as concerns how to take rational consequences of public messages about the HIV epidemic. It is suggested that future surveillance be based primarily on voluntary testing and, whenever needed and possible, supplied with anonymous unlinked testing of existing blood samples from groups and persons declining to be tested. Such surveillance strategies should be supported in individual patient contacts and public health educational campaigns underscoring the risk of heterosexual transmission of HIV and the need for repeated HIV-antibody testing of selected groups and individuals.

  9. Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects

    Directory of Open Access Journals (Sweden)

    Vasco Elbrecht

    2016-04-01

    Full Text Available Cytochrome c oxidase I (COI is a powerful marker for DNA barcoding of animals, with good taxonomic resolution and a large reference database. However, when used for DNA metabarcoding, estimation of taxa abundances and species detection are limited due to primer bias caused by highly variable primer binding sites across the COI gene. Therefore, we explored the ability of the 16S ribosomal DNA gene as an alternative metabarcoding marker for species level assessments. Ten bulk samples, each containing equal amounts of tissue from 52 freshwater invertebrate taxa, were sequenced with the Illumina NextSeq 500 system. The 16S primers amplified three more insect species than the Folmer COI primers and amplified more equally, probably due to decreased primer bias. Estimation of biomass might be less biased with 16S than with COI, although variation in read abundances of two orders of magnitudes is still observed. According to these results, the marker choice depends on the scientific question. If the goal is to obtain a taxonomic identification at the species level, then COI is more appropriate due to established reference databases and known taxonomic resolution of this marker, knowing that a greater proportion of insects will be missed using COI Folmer primers. If the goal is to obtain a more comprehensive survey the 16S marker, which requires building a local reference database, or optimised degenerated COI primers could be more appropriate.

  10. DNA Barcoding for Species Identification of Insect Skins: A Test on Chironomidae (Diptera) Pupal Exuviae

    Science.gov (United States)

    Ekrem, Torbjørn; Stur, Elisabeth

    2017-01-01

    Abstract Chironomidae (Diptera) pupal exuviae samples are commonly used for biological monitoring of aquatic habitats. DNA barcoding has proved useful for species identification of chironomid life stages containing cellular tissue, but the barcoding success of chironomid pupal exuviae is unknown. We assessed whether standard DNA barcoding could be efficiently used for species identification of chironomid pupal exuviae when compared with morphological techniques and if there were differences in performance between temperate and tropical ecosystems, subfamilies, and tribes. PCR, sequence, and identification success differed significantly between geographic regions and taxonomic groups. For Norway, 27 out of 190 (14.2%) of pupal exuviae resulted in high-quality chironomid sequences that match species. For Costa Rica, 69 out of 190 (36.3%) Costa Rican pupal exuviae resulted in high-quality sequences, but none matched known species. Standard DNA barcoding of chironomid pupal exuviae had limited success in species identification of unknown specimens due to contaminations and lack of matching references in available barcode libraries, especially from Costa Rica. Therefore, we recommend future biodiversity studies that focus their efforts on understudied regions, to simultaneously use morphological and molecular identification techniques to identify all life stages of chironomids and populate the barcode reference library with identified sequences.

  11. Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China.

    Science.gov (United States)

    Chen, Juan; Zhao, Jietang; Erickson, David L; Xia, Nianhe; Kress, W John

    2015-03-01

    The genus Curcuma L. is commonly used as spices, medicines, dyes and ornamentals. Owing to its economic significance and lack of clear-cut morphological differences between species, this genus is an ideal case for developing DNA barcodes. In this study, four chloroplast DNA regions (matK, rbcL, trnH-psbA and trnL-F) and one nuclear region (ITS2) were generated for 44 Curcuma species and five species from closely related genera, represented by 96 samples. PCR amplification success rate, intra- and inter-specific genetic distance variation and the correct identification percentage were taken into account to assess candidate barcode regions. PCR and sequence success rate were high in matK (89.7%), rbcL (100%), trnH-psbA (100%), trnL-F (95.7%) and ITS2 (82.6%) regions. The results further showed that four candidate chloroplast barcoding regions (matK, rbcL, trnH-psbA and trnL-F) yield no barcode gaps, indicating that the genus Curcuma represents a challenging group for DNA barcoding. The ITS2 region presented large interspecific variation and provided the highest correct identification rates (46.7%) based on BLASTClust method among the five regions. However, the ITS2 only provided 7.9% based on NJ tree method. An increase in discriminatory power needs the development of more variable markers. © 2014 John Wiley & Sons Ltd.

  12. Single cells for forensic DNA analysis--from evidence material to test tube.

    Science.gov (United States)

    Brück, Simon; Evers, Heidrun; Heidorn, Frank; Müller, Ute; Kilper, Roland; Verhoff, Marcel A

    2011-01-01

    The purpose of this project was to develop a method that, while providing morphological quality control, allows single cells to be obtained from the surfaces of various evidence materials and be made available for DNA analysis in cases where only small amounts of cell material are present or where only mixed traces are found. With the SteREO Lumar.V12 stereomicroscope and UV unit from Zeiss, it was possible to detect and assess single epithelial cells on the surfaces of various objects (e.g., glass, plastic, metal). A digitally operated micromanipulator developed by aura optik was used to lift a single cell from the surface of evidence material and to transfer it to a conventional PCR tube or to an AmpliGrid(®) from Advalytix. The actual lifting of the cells was performed with microglobes that acted as carriers. The microglobes were held with microtweezers and were transferred to the DNA analysis receptacles along with the adhering cells. In a next step, the PCR can be carried out in this receptacle without removing the microglobe. Our method allows a single cell to be isolated directly from evidence material and be made available for forensic DNA analysis. © 2010 American Academy of Forensic Sciences.

  13. Detection of anti-dsDNA by IgG ELISA test using two different sources of antigens: calf thymus versus E.coli

    Directory of Open Access Journals (Sweden)

    Mohammadi M

    2009-04-01

    Full Text Available "nBackground: Anti-dsDNA antibodies frequently found in the sera Systemic Lupus Erythematosus patients, particularly in active disease stage. Nowadays exploit different eukaryotic and prokaryotic dsDNA as antigen source and different reagents as binder. The aim of this study to compared two dsDNA different sources and tow different kinds of reagents for binder in ELISA test. "nMethods: In this study bacterial genomic DNA from E.coli (ATCC 25922 and genomic DNA from calf thymus extracted with high purity and were used as antigens for IgG anti-dsDNA detection by ELISA. To coat dsDNA in microtiter wells, tow different kinds of reagents including methylated -BSA and poly-l-lysine (for pre-coating are used. Sera from systemic lupus erythematosus patients and from normal blood donors are used to assess sensitivity and specificity of our ELISA test in compared with IF test and commercial kits. "nResults: Our results displayed pre-coating of microtiter plates with methylated -BSA reduce nonspecific binding reaction and the relative sensitivity and specificity of ELISA increased when calf thymus DNA is employed as antigenic source in compared with IF test and commercial kits 80%, 88% and 100%, 98% respectively, but when E.coli DNA is used 73%, 69% and 85%, 79%, respectively. "nConclusion: The genomic DNA from calf thymus is a potentially useful source of antigen for detection of anti-dsDNA by ELISA. Also the use of methylatted- BSA could have an effective role in reducing of nonspecific binding reactions.

  14. Real-time ed end-point Polymerase Chain Reaction per la quantizzazione del DNA di Citomegalovirus: confronto tra metodi e con il test per l’antigene pp65

    Directory of Open Access Journals (Sweden)

    Tiziano Allice

    2006-03-01

    Full Text Available Quantitave Polymerase Chain Reaction (PCR for Cytomegalovirus (CMV DNA provides highly sensitive and specific data for detecting CMV as well as monitoring the infection and determining the appropriate antiviral strategy.To determine the clinical application of a recently introduced real-time (RT PCR assay for CMV DNA quantitation in peripheral blood leukocytes (PBLs and defining its correlation with the commercial quantitative end-point (EP PCR method COBAS AMPLICOR CMV Monitor and pp65 antigen test. Sequential PBL samples (n=158 from 32 liver transplanted patients with CMV asymptomatic infection and positive for CMV DNA by EP-PCR were retrospectively analysed with RT-PCR and studied according to pp65 antigen levels. A good correlation was found between RT-PCR and pp65 antigen test (r=0.691 and between the two PCR assays (r=0.761. RT-PCR data were significantly higher in pre-emptive treated patients (those with >20 pp65+positive cells, median value: 3.8 log10 copies/500,000 PBLs than in not-treated ones (2.9 logs.According to pp65 levels of 0, 1-10, 11-20, 21-50, 51-100 and >100 positive cells/200,000 PBLs, median CMV DNA load by RT-PCR was 2.6, 3.0, 3.6, 4.0. 4.2 and 4.8, log10 copies/ 500,000 PBLs, respectively (EP-PCR CMV DNA levels: 2. 8, 2.9, 3.8, 3.7, 3.9 and 4.0 logs. For samples with >20 pp65+cells, that is above the level at which pre-emptive therapy was started, RT-PCR values were significantly higher than in groups with less than 20 pp65+cells, whereas EP-PCR values did not significantly differ and showed a slower progression rate. Dilutions of DNA from CMV AD169 strain were used to probe RT-PCR reproducibility (between and intra-assay variability < 2% and sensitivity (100% detection rate at 10 copies/reaction, 28.5% with EP-PCR. A significant improvement is coming from the introduction of RT-PCR to the study of CMV DNA dynamics in differently CMV infected patients due to a more reliable quantitation of CMV DNA for moderate and high

  15. Effect of stigma reduction intervention strategies on HIV test uptake in low- and middle-income countries

    DEFF Research Database (Denmark)

    Thapa, Subash; Hannes, Karin; Cargo, Margaret

    2015-01-01

    BACKGROUND: Several stigma reduction intervention strategies have been developed and tested for effectiveness in terms of increasing human immunodeficiency virus (HIV) test uptake. These strategies have been more effective in some contexts and less effective in others. Individual factors......, such as lack of knowledge and fear of disclosure, and social-contextual factors, such as poverty and illiteracy, might influence the effect of stigma reduction intervention strategies on HIV test uptake in low- and middle-income countries. So far, it is not clearly known how the stigma reduction intervention...... strategies interact with these contextual factors to increase HIV test uptake. Therefore, we will conduct a review that will synthesize existing studies on stigma reduction intervention strategies to increase HIV test uptake to better understand the mechanisms underlying this process in low- and middle...

  16. Utilizing constructivism learning theory in collaborative testing as a creative strategy to promote essential nursing skills.

    Science.gov (United States)

    Duane, Barbara T; Satre, Maria E

    2014-01-01

    In nursing education, students participate in individual learner testing. This process follows the instructionist learning theory of a system model. However, in the practice of nursing, success depends upon collaboration with numerous people in different capacities, critical thinking, clinical reasoning, and the ability to communicate with others. Research has shown that collaborative testing, a constructivism learning activity and a form of collaborative learning, enhances students' abilities to master these areas. Collaborative testing is a clear, creative strategy which constructivists would say supports the socio-linguistic base of their learning theory. The test becomes an active implementation of peer-mediated learning where individual knowledge is enhanced through problem solving or defense of an individual position with the collaborative method. There is criticism for the testing method's potential of grade inflation and for students to receive grade benefits with little effort. After a review of various collaborative testing methods, this nursing faculty implemented a collaborative testing format that addresses both the positive and negative aspects of the process. Copyright © 2013 Elsevier Ltd. All rights reserved.

  17. Reliability and Validity of the Turkish Language Version of the Test of Performance Strategies

    Directory of Open Access Journals (Sweden)

    Miçooğulları Bülent Okan

    2017-03-01

    Full Text Available The aim of the present study was to examine the psychometric properties of the Test of Performance Strategies (TOPS; Thomas et al., 1999 on the Turkish population. The TOPS was designed to assess eight psychological skills and strategies used by athletes in competition (activation, automaticity, emotional control, goal-setting, imagery, relaxation, self-talk, and negative thinking and the same strategies, except negative thinking is replaced by attentional control used in training. The sample of the study included athletes who were training and competing in a wide variety of sports across a broad range of performance standards. The final sample consisted of 433 males (mean ± s: age 22.47 ± 5.30 years and 187 females (mean ± s: age 20.97 ± 4.78 years, 620 athletes in total (mean ± s: age 21.25 ± 4.87 years who voluntarily participated; TOPS was administered to all participants. Afterward, Confirmatory Factor Analysis (CFA was conducted by Analysis Moments of Structures (AMOS 18. Comparative fit index (CFI, non-normed fit index (NNFI and root mean square error of approximation (RMSEA were used to verify whether the model fit the data. Goodness-of-fit statistics were CFI= .91, NNFI= .92 and RMSEA= .056. These values showed that the tested model is coherent at a satisfactory level. Moreover, results of confirmatory factor analyses revealed that a total of four items (two items from competition and two from practice within the subscale of automaticity have been removed. The 28 items within the remaining seven subscales have been validated. In conclusion, Turkish version of TOPS is a valid and reliable instrument to assess the psychological skills and strategies used by athletes in competition and practices.

  18. Assessment of the stability of DNA in specimens collected under conditions for drug testing-A pilot study.

    Science.gov (United States)

    White, Robert M; Mitchell, John M; Hart, E Dale; Evans, Amy; Meaders, Meredith; Norsworthy, Sarah E; Hayes, Eugene D; Flegel, Ron; Maha, George C; Shaffer, Megan D; Hall, Erin M; Rogers, Kelley

    2018-02-01

    For forensic biological sample collections, the specimen donor is linked solidly to his or her specimen through a chain of custody (CoC) sometimes referenced as a chain of evidence. Rarely, a donor may deny that a urine or oral fluid (OF) specimen is his or her specimen even with a patent CoC. The goal of this pilot study was to determine the potential effects of short-term storage on the quality and quantity of DNA in both types of specimen under conditions that may be encountered with employment-related drug testing specimens. Fresh urine and freshly collected oral fluid all produced complete STR profiles. For the "pad" type OF collectors, acceptable DNA was extractable both from the buffer/preservative and the pad. Although fresh urine and OF produced complete STR profiles, partial profiles were obtained after storage for most samples. An exception was the DNA in the Quantisal OF collector, from which a complete profile was obtained for both freshly collected OF and stored OF. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. The construction and use of bacterial DNA microarrays based on an optimized two-stage PCR strategy

    Directory of Open Access Journals (Sweden)

    Pesta David

    2003-06-01

    Full Text Available Abstract Background DNA microarrays are a powerful tool with important applications such as global gene expression profiling. Construction of bacterial DNA microarrays from genomic sequence data using a two-stage PCR amplification approach for the production of arrayed DNA is attractive because it allows, in principal, the continued re-amplification of DNA fragments and facilitates further utilization of the DNA fragments for additional uses (e.g. over-expression of protein. We describe the successful construction and use of DNA microarrays by the two-stage amplification approach and discuss the technical challenges that were met and resolved during the project. Results Chimeric primers that contained both gene-specific and shared, universal sequence allowed the two-stage amplification of the 3,168 genes identified on the genome of Synechocystis sp. PCC6803, an important prokaryotic model organism for the study of oxygenic photosynthesis. The gene-specific component of the primer was of variable length to maintain uniform annealing temperatures during the 1st round of PCR synthesis, and situated to preserve full-length ORFs. Genes were truncated at 2 kb for efficient amplification, so that about 92% of the PCR fragments were full-length genes. The two-stage amplification had the additional advantage of normalizing the yield of PCR products and this improved the uniformity of DNA features robotically deposited onto the microarray surface. We also describe the techniques utilized to optimize hybridization conditions and signal-to-noise ratio of the transcription profile. The inter-lab transportability was demonstrated by the virtual error-free amplification of the entire genome complement of 3,168 genes using the universal primers in partner labs. The printed slides have been successfully used to identify differentially expressed genes in response to a number of environmental conditions, including salt stress. Conclusions The technique detailed

  20. Selective deficit in spatial memory strategies contrast to intact response strategies in patients with schizophrenia spectrum disorders tested in a virtual navigation task.

    Science.gov (United States)

    Wilkins, Leanne K; Girard, Todd A; Konishi, Kyoko; King, Matthew; Herdman, Katherine A; King, Jelena; Christensen, Bruce; Bohbot, Veronique D

    2013-11-01

    Spatial memory is impaired among persons with schizophrenia (SCZ). However, different strategies may be used to solve most spatial memory and navigation tasks. This study investigated the hypothesis that participants with schizophrenia-spectrum disorders (SSD) would demonstrate differential impairment during acquisition and retrieval of target locations when using a hippocampal-dependent spatial strategy, but not a response strategy, which is more associated with caudate function. Healthy control (CON) and SSD participants were tested using the 4-on-8 virtual maze (4/8VM), a virtual navigation task designed to differentiate between participants' use of spatial and response strategies. Consistent with our predictions, SSD participants demonstrated a differential deficit such that those who navigated using a spatial strategy made more errors and took longer to locate targets. In contrast, SSD participants who spontaneously used a response strategy performed as well as CON participants. The differential pattern of spatial-memory impairment in SSD provides only indirect support for underlying hippocampal dysfunction. These findings emphasize the importance of considering individual strategies when investigating SSD-related memory and navigation performance. Future cognitive intervention protocols may harness SSD participants' intact ability to navigate using a response strategy and/or train the deficient ability to navigate using a spatial strategy to improve navigation and memory abilities in participants with SSD. Copyright © 2013 Wiley Periodicals, Inc.

  1. A Strengths-Weaknesses-Opportunities-Threats (SWOT) analysis on the clinical utility of sperm DNA fragmentation testing in specific male infertility scenarios.

    Science.gov (United States)

    Esteves, Sandro C; Agarwal, Ashok; Cho, Chak-Lam; Majzoub, Ahmad

    2017-09-01

    Sperm DNA fragmentation (SDF) is recognized as a leading cause of male infertility because it can impair the paternal genome through distinct pathophysiological mechanisms. Current evidence supports SDF as a major factor in the pathophysiology of several conditions, including varicocele, unexplained infertility, assisted reproductive technology failure, and environmental lifestyle factors, although the mechanisms involved have not been fully described yet. Measurement of the levels of DNA fragmentation in semen provides valuable information on the integrity of paternal chromatin and may guide therapeutic strategies. A recently published clinical practice guideline (CPG) highlighted how to use the information provided by SDF testing in daily practice, which triggered a series of commentaries by leading infertility experts. These commentaries contained an abundance of information and conflicting views about the clinical utility of SDF testing, which underline the complex nature of SDF. A search of papers published in response to the CPG entitled "Clinical utility of sperm DNA fragmentation testing: practice recommendations based on clinical scenarios" was performed within the Translational Andrology and Urology ( TAU ) website (http://tau.amegroups.com/). The start and end dates for the search were May 2017 and August 2017, respectively. Each commentary meeting our inclusion criteria was rated as "supportive without reservation", "supportive with reservation", "not supportive" or "neutral". We recorded whether articles discussed either SDF characteristics as a laboratory test method or clinical scenarios, or both. Subsequently, we extracted the particulars from each commentary and utilized the 'Strengths-Weaknesses-Opportunities-Threats' (SWOT) analysis to understand the perceived advantages and drawbacks of SDF as a specialized sperm function method in clinical practice. Fifty-eight fertility experts from six continents and twenty-two countries contributed

  2. High-throughput strategy for molecular identification of Vel- blood donors employing nucleic acids extracted from plasma pools used for viral nucleic acid test screening.

    Science.gov (United States)

    Dezan, Marcia R; Dinardo, Carla L; Bosi, Silvia R A; Vega, Sileni; Salles, Nanci A; Mendrone-Júnior, Alfredo; Levi, José E

    2016-06-01

    Serologic methods to determine the Vel- phenotype require the use of rare human antisera and do not allow for many samples to be tested simultaneously, which limits their application as a tool to search for rare donors. This study developed a low-cost molecular screening strategy using real-time polymerase chain reaction (PCR) and DNA, extracted from plasma pools for viral nucleic acid test (NAT) screening, to identify Vel- and Vel+(W) donors. A total of 4680 blood donors from the Brazilian southeast region were genotyped through real-time PCR targeting the 17-nucleotide (c.64_80del) deletion in the SMIM1 gene, which determines the Vel- phenotype, by using remaining nucleic acid from plasma pools of six donors, routinely discarded after the release of viral NAT results. Twenty pools tested reactive and individual testing of samples from reactive pools identified 19 heterozygous donors with the SMIM1*64_80del deletion (0.40%) and one homozygous donor (0.02%). Fourteen of the 19 donors were confirmed as Vel- or Vel+(W) using anti-Vel human antiserum. The DNA pool genotyping strategy using real-time PCR designed to detect the deletion in the SMIM1 gene proved effective and accurate in identifying donors with the Vel- and Vel+(W) phenotypes. The fact that remaining nucleic acid from routine viral NAT screening was used makes this technique economically attractive and definitely superior to the serologic techniques available to search for this rare phenotype. © 2016 AABB.

  3. The problem of false-positive human papillomavirus DNA tests in cervical screening

    DEFF Research Database (Denmark)

    Rebolj, Matejka; Pribac, Igor; Frederiksen, Maria Eiholm

    2013-01-01

    Human Papillomavirus (HPV) testing has been extensively studied in randomized controlled trials of primary cervical screening. Based on encouraging results concerning its high detection rates and a high negative predictive value for high-grade cervical intraepithelial neoplasia (CIN), HPV testing...... will probably replace cytology in future primary cervical screening. However, HPV testing is associated with more frequent false-positive tests compared to cytology. False-positive tests are defined as positive screening tests which are not subsequently confirmed with high-grade CIN. Several authors have...

  4. DNA testing for parentage verification in a conservation nucleus of Pantaneiro horse

    Directory of Open Access Journals (Sweden)

    Fabiana Tavares Pires de Souza Sereno

    2008-01-01

    Full Text Available We investigated the genealogy of the in situ conservation nucleus of the Pantaneiro horse using DNA microsatellites by evaluating 101 horses, the group consisting of 71 adult horses (3 stallions, 40 male and 31 mares and 27 foals (14 colts and 13 fillies. Genomic DNA was extracted from hair roots and genotyped using 12 microsatellite markers (AHT4, AHT5, ASB2, ASB17, ASB23, HMS3 HMS6, HMS7, HTG4, HTG10, LEX33 and VHL20. The number of alleles per locus varied from 6 to 13, with a mean of 7.8 and the expected heterozygosity ranged from 0.544 to 0.734 (mean 0.644. The VLH20, ASB2, HTG10, ASB23 markers had a high (> 0.8 polymorphism information content and the total exclusion probability of the 12 microsatellite loci was 0.99. The genealogical study of the Pantaneiro horse using genetic markers was efficient in detecting mistakes during paternity and maternity designation and is an important tool which can be used together with traditional systems of animal identification. The use of genetic markers is recommended in the systematic control of the genealogical registrations and conservation plans to improve genetic aspects of the Pantaneiro horse.

  5. Mud Pit Risk-Based Closure Strategy Report, Nevada Test Site, Nevada, Revision 0

    Energy Technology Data Exchange (ETDEWEB)

    Brain Hoenes

    2004-08-01

    This report presents the findings of the human and ecological risk assessment for the NTS mud pits. The risk assessment utilizes data from 52 of the 270 NTS mud pits in conjunction with corroborative data from 87 other DOE mud pits associated with nuclear testing (at locations on the NTS, in the western United States, and Alaska) as well as relevant process knowledge. Based on the risk assessment findings, the report provides a strategy for further evaluation, characterization, and closure of all 270 NTS mud pit CASs using the Streamlined Approach for Environmental Restoration (SAFER).

  6. Evaluation of testing strategies to identify infected animals at a single round of testing within dairy herds known to be infected with Mycobacterium avium ssp. paratuberculosis.

    Science.gov (United States)

    More, S J; Cameron, A R; Strain, S; Cashman, W; Ezanno, P; Kenny, K; Fourichon, C; Graham, D

    2015-08-01

    As part of a broader control strategy within herds known to be infected with Mycobacterium avium ssp. paratuberculosis (MAP), individual animal testing is generally conducted to identify infected animals for action, usually culling. Opportunities are now available to quantitatively compare different testing strategies (combinations of tests) in known infected herds. This study evaluates the effectiveness, cost, and cost-effectiveness of different testing strategies to identify infected animals at a single round of testing within dairy herds known to be MAP infected. A model was developed, taking account of both within-herd infection dynamics and test performance, to simulate the use of different tests at a single round of testing in a known infected herd. Model inputs included the number of animals at different stages of infection, the sensitivity and specificity of each test, and the costs of testing and culling. Testing strategies included either milk or serum ELISA alone or with fecal culture in series. Model outputs included effectiveness (detection fraction, the proportion of truly infected animals in the herd that are successfully detected by the testing strategy), cost, and cost-effectiveness (testing cost per true positive detected, total cost per true positive detected). Several assumptions were made: MAP was introduced with a single animal and no management interventions were implemented to limit within-herd transmission of MAP before this test. In medium herds, between 7 and 26% of infected animals are detected at a single round of testing, the former using the milk ELISA and fecal culture in series 5 yr after MAP introduction and the latter using fecal culture alone 15 yr after MAP introduction. The combined costs of testing and culling at a single round of testing increases with time since introduction of MAP infection, with culling costs being much greater than testing costs. The cost-effectiveness of testing varied by testing strategy. It was also

  7. Calculation of Core Damage Frequency for the Change of the Common Cause Failure Parameters According to the Testing Strategies

    International Nuclear Information System (INIS)

    Kang, Dae Il; Kim, Kil You; Jin, Young Ho; Kim, Tae Woon

    2011-01-01

    Common cause failure (CCF) probabilities are differently estimated according to testing strategies. There are two representative testing schemes; staggered testing and non-staggered testing schemes. For the cases where trains or channels of standby safety systems consisting of more than two redundant components are tested in a staggered manner, the standby safety components within a train can be tested simultaneously or consecutively. In this case, mixed testing scheme, staggered and non-staggered testing schemes, are used for testing the components. Kang et al. derived the formulas for the estimations of the CCF probabilities of the components under the mixed testing scheme. This paper presents the sensitivity study results on the core damage frequency (CDF) of the SMART (System-integrated Modular Advanced Reactor) for the changes of the CCF parameters according to the testing strategies

  8. Operational Testing of a Combined Hardware-Software Strategy for Triage of Radiologically-Contaminated Persons.

    Science.gov (United States)

    Waller, Edward J

    2015-08-01

    After a radiological dispersal device (RDD) event, it is possible for radionuclides to enter the human body through inhalation, ingestion, and skin and wound absorption. The dominant pathway will be through inhalation. From a health physics perspective, it is important to know the magnitude of the intake to perform dosimetric assessments. From a medical perspective, removal of radionuclides leading to dose (hence risk) aversion is of high importance. The efficacy of medical decorporation strategies is extremely dependent upon the time of treatment delivery after intake. The "golden hour," or more realistically 3-4 h, is imperative when attempting to increase removal of radionuclides from extracellular fluids prior to cellular incorporation. To assist medical first response personnel in making timely decisions regarding appropriate treatment delivery modes, a software tool has been developed which compiles existing radionuclide decorporation therapy data and allows a user to perform simple triage leading to potential appropriate decorporation treatment strategies. Three triage algorithms were included: (1) multi-parameter model (MPM), (2) clinical decision guidance (CDG) model, and (3) annual limit on intake (ALI) model. A radiation triage mask (RTM) has simultaneously been developed to provide a simple and rapid hardware solution for first responders to triage internally exposed personnel in the field. The hardware/software strategy was field tested with a military medical unit and was found by end-users to be relatively simple to learn and use.

  9. Single-stranded DNA aptamer targeting and neutralization of anti-D alloantibody: a potential therapeutic strategy for haemolytic diseases caused by Rhesus alloantibody.

    Science.gov (United States)

    Zhang, Yinze; Wu, Fan; Wang, Manni; Zhuang, Naibao; Zhou, Huayou; Xu, Hua

    2018-02-01

    Rhesus (Rh) D antigen is the most important antigen in the Rh blood group system because of its strong immunogenicity. When RhD-negative individuals are exposed to RhD-positive blood, they may produce anti-D alloantibody, potentially resulting in delayed haemolytic transfusion reactions and Rh haemolytic disease of the foetus and newborn, which are difficult to treat. Inhibition of the binding of anti-D antibody with RhD antigens on the surface of red blood cells may effectively prevent immune haemolytic diseases. In this study, single-stranded (ss) DNA aptamers, specifically binding to anti-D antibodies, were selected via systematic evolution of ligands by exponential enrichment (SELEX) technology. After 14 rounds of selection, the purified ssDNA was sequenced using a Personal Genome Machine system. Haemagglutination inhibition assays were performed to screen aptamers for biological activity in terms of blocking antigen-antibody reactions: the affinity and specificity of the aptamers were also determined. In addition to high specificity, the aptamers which were selected showed high affinity for anti-D antibodies with dissociation constant (K d ) values ranging from 51.46±14.90 to 543.30±92.59 nM. By the combined use of specific ssDNA aptamer 7 and auxiliary ssDNA aptamer 2, anti-D could be effectively neutralised at low concentrations of the aptamers. Our results demonstrate that ssDNA aptamers may be a novel, promising strategy for the treatment of delayed haemolytic transfusion reactions and Rh haemolytic disease of the foetus and newborn.

  10. A strategy for in vitro safety testing of nanotitania-modified textile products

    International Nuclear Information System (INIS)

    Roszak, Joanna; Stępnik, Maciej; Nocuń, Marek; Ferlińska, Magdalena; Smok-Pieniążek, Anna; Grobelny, Jarosław; Tomaszewska, Emilia; Wąsowicz, Wojciech; Cieślak, Małgorzata

    2013-01-01

    Highlights: • Commercially available TiO 2 /Ag nanomaterials (NMs) showed higher cytotoxic effect than TiO 2 NMs. • Both titania NMs in pristine form induced a weak genotoxic effect in in vitro studies. • Cytotoxic effect of textile materials modified with TiO 2 /Ag NMs depended on the mode of the fiber manufacturing. • The strategy of in vitro testing of textile materials modified with NMs was proposed. -- Abstract: Titanium dioxide nanomaterials are extensively used in many applications, also for modification of textile materials. Toxicological assessment of such textile materials is currently seldom performed, mainly because of lack of appropriate guidelines. The aim of the study was to assess cytotoxic and genotoxic potential of commercially available TiO 2 and TiO 2 /Ag NMs in pristine form as well as polypropylene fibers modified with the NMs. Both titania NMs showed a cytotoxic effect on BALB/3T3 clone A31 and V79 fibroblasts after 72-h exposure. Both NMs induced a weak genotoxic effect in comet assay, with TiO 2 /Ag being more active. In vitro micronucleus test on human lymphocytes revealed a weak mutagenic effect of both materials after 24 h of exposure. In contrast, no significant increase in micronuclei frequency was observed in the in vitro micronucleus test on V79 fibroblasts. The 24-h extracts prepared from polypropylene fibers modified with TiO 2 /Ag induced a cytotoxic effect on BALB/3T3 cells which strongly depended on the mode of the fibers manufacturing. The study presents a comprehensive approach to toxicity assessment of textile fibers modified with NMs. Proposed approach may form a good “starting point” for improved future testing strategies

  11. A strategy for in vitro safety testing of nanotitania-modified textile products

    Energy Technology Data Exchange (ETDEWEB)

    Roszak, Joanna; Stępnik, Maciej; Nocuń, Marek; Ferlińska, Magdalena; Smok-Pieniążek, Anna [Nofer Institute of Occupational Medicine, 8 St Teresy St., 91-348 Łódź (Poland); Grobelny, Jarosław; Tomaszewska, Emilia [University of Lodz, Faculty of Chemistry, 163 Pomorska St, 90-236 Łódź (Poland); Wąsowicz, Wojciech [Nofer Institute of Occupational Medicine, 8 St Teresy St., 91-348 Łódź (Poland); Cieślak, Małgorzata, E-mail: cieslakm@iw.lodz.pl [Textile Research Institute, 118 Gdańska St., 90-520, Łódź (Poland)

    2013-07-15

    Highlights: • Commercially available TiO{sub 2}/Ag nanomaterials (NMs) showed higher cytotoxic effect than TiO{sub 2} NMs. • Both titania NMs in pristine form induced a weak genotoxic effect in in vitro studies. • Cytotoxic effect of textile materials modified with TiO{sub 2}/Ag NMs depended on the mode of the fiber manufacturing. • The strategy of in vitro testing of textile materials modified with NMs was proposed. -- Abstract: Titanium dioxide nanomaterials are extensively used in many applications, also for modification of textile materials. Toxicological assessment of such textile materials is currently seldom performed, mainly because of lack of appropriate guidelines. The aim of the study was to assess cytotoxic and genotoxic potential of commercially available TiO{sub 2} and TiO{sub 2}/Ag NMs in pristine form as well as polypropylene fibers modified with the NMs. Both titania NMs showed a cytotoxic effect on BALB/3T3 clone A31 and V79 fibroblasts after 72-h exposure. Both NMs induced a weak genotoxic effect in comet assay, with TiO{sub 2}/Ag being more active. In vitro micronucleus test on human lymphocytes revealed a weak mutagenic effect of both materials after 24 h of exposure. In contrast, no significant increase in micronuclei frequency was observed in the in vitro micronucleus test on V79 fibroblasts. The 24-h extracts prepared from polypropylene fibers modified with TiO{sub 2}/Ag induced a cytotoxic effect on BALB/3T3 cells which strongly depended on the mode of the fibers manufacturing. The study presents a comprehensive approach to toxicity assessment of textile fibers modified with NMs. Proposed approach may form a good “starting point” for improved future testing strategies.

  12. DNA Barcoding Meets Nanotechnology: Development of a Universal Colorimetric Test for Food Authentication.

    Science.gov (United States)

    Valentini, Paola; Galimberti, Andrea; Mezzasalma, Valerio; De Mattia, Fabrizio; Casiraghi, Maurizio; Labra, Massimo; Pompa, Pier Paolo

    2017-07-03

    Food trade globalization and the growing demand for selected food varieties have led to the intensification of adulteration cases, especially in the form of species substitution and mixing with cheaper taxa. This phenomenon has huge economic impact and sometimes even public health implications. DNA barcoding represents a well-proven molecular approach to assess the authenticity of food items, although its use is hampered by analytical constraints and timeframes that are often prohibitive for the food market. To address such issues, we have introduced a new technology, named NanoTracer, that allows for rapid and naked-eye molecular traceability of any food and requires limited instrumentation and cost-effective reagents. Moreover, unlike sequencing, this method can be used to identify not only the substitution of a fine ingredient, but also its dilution with cheaper ones. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Introduction to Special Issue: The Human, Human Rights and DNA Identity Tests

    DEFF Research Database (Denmark)

    Vaisman, Noa

    2018-01-01

    might these new ways of imagining the subject shape present and future human rights law and practice? The papers examine a variety of scientific technologies—personalized medicine and organ transplant, mitochondrial DNA replacement, and scaffolds and regenerative medicine—and their implications for our......This special issue examines the diverse realities created by the intersection of emerging technologies, new scientific knowledge, and the human being. It engages with two key questions: how is the human being shaped and constructed in new ways through advances in science and technology? and how...... conceptualization of the human subject. Each is then followed by a commentary that both brings to light new dimensions of the original paper and presents a new theoretical take on the topic. Together these papers offer a serious challenge to the vision of the human subject at the root of human rights law. Instead...

  14. An educational strategy for treating chronic, noncancer pain with opioids: a pilot test.

    Science.gov (United States)

    Elhwairis, Huda; Reznich, Christopher B

    2010-12-01

    Chronic pain is common and can be devastating to the patient and challenging to the health care provider. Despite the importance of the topic, pain management curricula are incomplete in health professionals' training. We developed a longitudinal curriculum to teach therapy for chronic noncancer pain over four units and pilot-tested the teaching of one unit (opioids) to internal medicine residents. The educational strategies we used included didactic sessions, write-up of a management plan following a model, case discussions, and role-play group activities. We pilot-tested one unit (opioid therapy) in March 2008. We performed learner evaluations, using a pretest and posttest, a write-up plan following a model, and a learner knowledge questionnaire. Results showed significant improvement in knowledge. Residents found the sessions and educational strategy to be excellent and reported higher confidence levels in managing patients with chronic noncancer pain. This article demonstrates that multiple teaching modalities-including didactic lectures, case discussions, write-up of a management plan following a model, and role-play group activities-are effective methods of teaching internal medicine residents how to use opioids to manage chronic noncancer pain. Copyright © 2010 American Pain Society. Published by Elsevier Inc. All rights reserved.

  15. Marketing-oriented strategy concept and its empirical testing with large sawmills.

    OpenAIRE

    Niemelä, Juha S.

    1993-01-01

    The objectives of this study are both theoretical and empirical. On the theoretical level strategy concept, its operationalization and measurement are analyzed and clarified. On the empirical level marketing strategies and competitive strategies are described by country, and the study also identifies the strategic marketing decisions characterizing different countries or competitive strategies. Furthermore, the relationships between strategies and marketing structures and functions are analyz...

  16. Impact of Breast Reader Assessment Strategy on mammographic radiologists' test reading performance.

    Science.gov (United States)

    Suleiman, Wasfi I; Rawashdeh, Mohammad A; Lewis, Sarah J; McEntee, Mark F; Lee, Warwick; Tapia, Kriscia; Brennan, Patrick C

    2016-06-01

    The detection of breast cancer is somewhat limited by human factors, and thus there is a need to improve reader performance. This study assesses whether radiologists who regularly undertake the education in the form of the Breast Reader Assessment Strategy (BREAST) demonstrate any changes in mammography interpretation performance over time. In 2011, 2012 and 2013, 14 radiologists independently assessed a year-specific BREAST mammographic test-set. Radiologists read a different single test-set once each year, with each comprising 60 digital mammogram cases. Radiologists marked the location of suspected lesions without computer-aided diagnosis (CAD) and assigned a confidence rating of 2 for benign and 3-5 for malignant lesions. The mean sensitivity, specificity, location sensitivity, JAFROC FOM and ROC AUC were calculated. A Kruskal-Wallis test was used to compare the readings for the 14 radiologists across the 3 years. Wilcoxon signed rank test was used to assess comparison between pairs of years. Relationships between changes in performance and radiologist characteristics were examined using a Spearman's test. Significant increases were noted in mean sensitivity (P = 0.01), specificity (P = 0.01), location sensitivity (P = 0.001) and JAFROC FOM (P = 0.001) between 2011 and 2012. Between 2012 and 2013, significant improvements were noted in mean sensitivity (P = 0.003), specificity (P = 0.002), location sensitivity (P = 0.02), JAFROC FOM (P = 0.005) and ROC AUC (P = 0.008). No statistically significant correlations were shown between the levels of improvement and radiologists' characteristics. Radiologists' who undertake the BREAST programme demonstrate significant improvements in test-set performance during a 3-year period, highlighting the value of ongoing education through the use of test-set. © 2016 The Royal Australian and New Zealand College of Radiologists.

  17. A molecular phylogeny of the Cephinae (Hymenoptera, Cephidae based on mtDNA COI gene: a test of traditional classification

    Directory of Open Access Journals (Sweden)

    Mahir Budak

    2011-09-01

    Full Text Available Cephinae is traditionally divided into three tribes and about 24 genera based on morphology and host utilization. There has been no study testing the monophyly of taxa under a strict phylogenetic criterion. A molecular phylogeny of Cephinae based on a total of 68 sequences of mtDNA COI gene, representing seven genera of Cephinae, is reconstructed to test the traditional limits and relationships of taxa. Monophyly of the traditional tribes is not supported. Monophyly of the genera are largely supported except for Pachycephus. A few host shift events are suggested based on phylogenetic relationships among taxa. These results indicate that a more robust phylogeny is required for a more plausible conclusion. We also report two species of Cephus for the first time from Turkey.

  18. Operation and control strategies in pre-series testing of cold circulating pumps for ITER

    International Nuclear Information System (INIS)

    Bhattacharya, R.; Vaghela, H.; Sarkar, B.; Srinivas, M.; Choukekar, K.

    2013-01-01

    Cryo-distribution system of ITER is responsible for the distribution and control of forced-flow supercritical helium for cooling of the superconducting magnets and the cryo-pumps. The requirements of cold circulating pumps (CCP) for mass flow rates and performance are much higher than presently existing and commercially available one used at 4.0 K helium. Design up-scaling with pre-series test of CCP has been proposed including test infrastructure. Operation and control strategies for the test distribution box (TDB) of test infrastructure have been developed and analyzed using steady state and dynamic process simulation to cope with the functional requirements of CCPs. Off-normal scenario with CCP inlet pressure variation is an important concern, dynamic process responses during such scenario have been evaluated to verify the operability of CCP. The paper describes process simulation to cope with the functional requirements of CCPs along with evaluation of off-normal scenario to verify the operability of CCP. (author)

  19. Restriction of human papillomavirus DNA testing in primary cervical screening to women above age 30

    DEFF Research Database (Denmark)

    Rebolj, Matejka; Njor, Sisse H; Lynge, Elsebeth

    2012-01-01

    Cervical screening with human papillomavirus (HPV) testing is less specific for high-grade cervical intraepithelial neoplasia (=CIN3) than cytology. The aim of this systematic review was to determine whether a restriction of HPV testing to women aged at least 30 years would eliminate the problem...

  20. A prime/boost strategy by DNA/fowlpox recombinants expressing a mutant E7 protein for the immunotherapy of HPV-associated cancers.

    Science.gov (United States)

    Radaelli, Antonia; De Giuli Morghen, Carlo; Zanotto, Carlo; Pacchioni, Sole; Bissa, Massimiliano; Franconi, Rosella; Massa, Silvia; Paolini, Francesca; Muller, Antonio; Venuti, Aldo

    2012-12-01

    Development of effective therapeutic vaccines against human papilloma virus (HPV) infections remains a priority, considering the high number of new cases of cervical cancer each year by high-risk HPVs, in particular by HPV-16. Vaccines expressing the E7 oncoprotein, which is detectable in all HPV-positive pre-cancerous and cancer cells, might clear already established tumors and support the treatment of HPV-related lesions. In this study, DNA or fowlpox virus recombinants expressing the harmless variant E7GGG of the HPV-16 E7 oncoprotein (DNA(E7GGG) and FP(E7GGG)) were generated. Two immunization regimens were tested in a pre-clinical mouse model by homologous (FP/FP) or heterologous (DNA/FP) prime-boost protocols to evaluate the immune response and therapeutic efficacy of the proposed HPV-16 vaccine. Low levels of anti-E7-specific antibodies were elicited after immunization, and in vivo experiments resulted in a higher number of tumor-free mice after the heterologous immunization. These results establish a preliminary indication for therapy of HPV-related tumors by the combined use of DNA and avipox recombinants, which might represent safer immunogens than vaccinia-based vaccines. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. The DNA-instability test as a specific marker of malignancy and its application to detect cancer clones in borderline malignancy

    Directory of Open Access Journals (Sweden)

    M Fukuda

    2009-06-01

    Full Text Available Recent progress in cytogenetic and biochemical mutator assay technologies has enabled us to detect single gene alterations and gross chromosomal rearrangements, and it became clear that all cancer cells are genetically unstable. In order to detect the genome-wide instability of cancer cells, a new simple method, the DNA-instability test, was developed. The methods to detect genomic instability so far reported have only demonstrated the presence of qualitative and quantitative alterations in certain specific genomic loci. In contrast to these commonly used methods to reveal the genomic instability at certain specific DNA regions, the newly introduced DNA-instability test revealed the presence of physical DNA-instability in the entire DNA molecule of a cancer cell nucleus as revealed by increased liability to denature upon HCl hydrolysis or formamide exposure. When this test was applied to borderline malignancies, cancer clones were detected in all cases at an early-stage of cancer progression. We proposed a new concept of “procancer” clones to define those cancer clones with “functional atypia” showing positivities for various cancer markers, as well as DNA-instability testing, but showing no remarkable ordinary “morphological atypia” which is commonly used as the basis of histopathological diagnosis of malignancy.

  2. Target-induced formation of gold amalgamation on DNA-based sensing platform for electrochemical monitoring of mercury ion coupling with cycling signal amplification strategy.

    Science.gov (United States)

    Chen, Jinfeng; Tang, Juan; Zhou, Jun; Zhang, Lan; Chen, Guonan; Tang, Dianping

    2014-01-31

    Heavy metal ion pollution poses severe risks in human health and environmental pollutant, because of the likelihood of bioaccumulation and toxicity. Driven by the requirement to monitor trace-level mercury ion (Hg(2+)), herein we construct a new DNA-based sensor for sensitive electrochemical monitoring of Hg(2+) by coupling target-induced formation of gold amalgamation on DNA-based sensing platform with gold amalgamation-catalyzed cycling signal amplification strategy. The sensor was simply prepared by covalent conjugation of aminated poly-T(25) oligonucleotide onto the glassy carbon electrode by typical carbodiimide coupling. Upon introduction of target analyte, Hg(2+) ion was intercalated into the DNA polyion complex membrane based on T-Hg(2+)-T coordination chemistry. The chelated Hg(2+) ion could induce the formation of gold amalgamation, which could catalyze the p-nitrophenol with the aid of NaBH4 and Ru(NH3)6(3+) for cycling signal amplification. Experimental results indicated that the electronic signal of our system increased with the increasing Hg(2+) level in the sample, and has a detection limit of 0.02nM with a dynamic range of up to 1000nM Hg(2+). The strategy afforded exquisite selectivity for Hg(2+) against other environmentally related metal ions. In addition, the methodology was evaluated for the analysis of Hg(2+) in spiked tap-water samples, and the recovery was 87.9-113.8%. Copyright © 2013 Elsevier B.V. All rights reserved.

  3. Asexual populations of the human malaria parasite, Plasmodium falciparum, use a two-step genomic strategy to acquire accurate, beneficial DNA amplifications.

    Directory of Open Access Journals (Sweden)

    Jennifer L Guler

    Full Text Available Malaria drug resistance contributes to up to a million annual deaths. Judicious deployment of new antimalarials and vaccines could benefit from an understanding of early molecular events that promote the evolution of parasites. Continuous in vitro challenge of Plasmodium falciparum parasites with a novel dihydroorotate dehydrogenase (DHODH inhibitor reproducibly selected for resistant parasites. Genome-wide analysis of independently-derived resistant clones revealed a two-step strategy to evolutionary success. Some haploid blood-stage parasites first survive antimalarial pressure through fortuitous DNA duplications that always included the DHODH gene. Independently-selected parasites had different sized amplification units but they were always flanked by distant A/T tracks. Higher level amplification and resistance was attained using a second, more efficient and more accurate, mechanism for head-to-tail expansion of the founder unit. This second homology-based process could faithfully tune DNA copy numbers in either direction, always retaining the unique DNA amplification sequence from the original A/T-mediated duplication for that parasite line. Pseudo-polyploidy at relevant genomic loci sets the stage for gaining additional mutations at the locus of interest. Overall, we reveal a population-based genomic strategy for mutagenesis that operates in human stages of P. falciparum to efficiently yield resistance-causing genetic changes at the correct locus in a successful parasite. Importantly, these founding events arise with precision; no other new amplifications are seen in the resistant haploid blood stage parasite. This minimizes the need for meiotic genetic cleansing that can only occur in sexual stage development of the parasite in mosquitoes.

  4. An Economic Analysis of Cell-Free DNA Non-Invasive Prenatal Testing in the US General Pregnancy Population.

    Directory of Open Access Journals (Sweden)

    Peter Benn

    Full Text Available Analyze the economic value of replacing conventional fetal aneuploidy screening approaches with non-invasive prenatal testing (NIPT in the general pregnancy population.Using decision-analysis modeling, we compared conventional screening to NIPT with cell-free DNA (cfDNA analysis in the annual US pregnancy population. Sensitivity and specificity for fetal aneuploidies, trisomy 21, trisomy 18, trisomy 13, and monosomy X, were estimated using published data and modeling of both first- and second trimester screening. Costs were assigned for each prenatal test component and for an affected birth. The overall cost to the healthcare system considered screening costs, the number of aneuploid cases detected, invasive procedures performed, procedure-related euploid losses, and affected pregnancies averted. Sensitivity analyses evaluated the effect of variation in parameters. Costs were reported in 2014 US Dollars.Replacing conventional screening with NIPT would reduce healthcare costs if it can be provided for $744 or less in the general pregnancy population. The most influential variables were timing of screening entry, screening costs, and pregnancy termination rates. Of the 13,176 affected pregnancies undergoing screening, NIPT detected 96.5% (12,717/13,176 of cases, compared with 85.9% (11,314/13,176 by conventional approaches. NIPT reduced invasive procedures by 60.0%, with NIPT and conventional methods resulting in 24,596 and 61,430 invasive procedures, respectively. The number of procedure-related euploid fetal losses was reduced by 73.5% (194/264 in the general screening population.Based on our analysis, universal application of NIPT would increase fetal aneuploidy detection rates and can be economically justified. Offering this testing to all pregnant women is associated with substantial prenatal healthcare benefits.

  5. A Comparison of Single-Cycle Versus Multiple-Cycle Proof Testing Strategies

    Science.gov (United States)

    McClung, R. C.; Chell, G. G.; Millwater, H. R.; Russell, D. A.; Millwater, H. R.

    1999-01-01

    Single-cycle and multiple-cycle proof testing (SCPT and MCPT) strategies for reusable aerospace propulsion system components are critically evaluated and compared from a rigorous elastic-plastic fracture mechanics perspective. Earlier MCPT studies are briefly reviewed. New J-integral estimation methods for semielliptical surface cracks and cracks at notches are derived and validated. Engineering methods are developed to characterize crack growth rates during elastic-plastic fatigue crack growth (FCG) and the tear-fatigue interaction near instability. Surface crack growth experiments are conducted with Inconel 718 to characterize tearing resistance, FCG under small-scale yielding and elastic-plastic conditions, and crack growth during simulated MCPT. Fractography and acoustic emission studies provide additional insight. The relative merits of SCPT and MCPT are directly compared using a probabilistic analysis linked with an elastic-plastic crack growth computer code. The conditional probability of failure in service is computed for a population of components that have survived a previous proof test, based on an assumed distribution of initial crack depths. Parameter studies investigate the influence of proof factor, tearing resistance, crack shape, initial crack depth distribution, and notches on the MCPT versus SCPT comparison. The parameter studies provide a rational basis to formulate conclusions about the relative advantages and disadvantages of SCPT and MCPT. Practical engineering guidelines are proposed to help select the optimum proof test protocol in a given application.

  6. Community-engaged strategies to promote hepatitis B testing and linkage to care in immigrants

    Directory of Open Access Journals (Sweden)

    Jevetta Stanford

    2016-12-01

    Full Text Available To improve early identification and linkage to treatment and preventive services for hepatitis B virus (HBV in persons born in countries with intermediate or high (>2% HBV prevalence, the University of Florida Center for HIV/AIDS Research, Education, and Services (UF CARES employed community-engaged strategies to implement the Hepatitis B Awareness and Service Linkage (HBASL program. In this brief report, we present a summary of program components, challenges, and successes. Faith and community-based networks were established to improve HBV testing and screening and to increase foreign born nationals (FBNs access to HBV care. A total of 1516 FBNs were tested and screened for hepatitis B. The majority were females (50.4%, Asians (62.8%, non-Hispanic (87.2%, and they also received post-test counseling (54.8%. Noted program advantages included the development of community networks and outreach to a large population of FBNs. The major challenges were institutional delays, pressures related to meeting program deliverables, and diversity within FBNs populations. Community health workers in the United States can replicate this program in their respective communities and ensure success by maintaining a strong community presence, establishing partnerships and linkage processes, developing a sustainability plan, and ensuring the presence of dedicated program staff.

  7. "It's our DNA, we deserve the right to test!" A content analysis of a petition for the right to access direct-to-consumer genetic testing.

    Science.gov (United States)

    Su, Yeyang; Borry, Pascal; Otte, Ina C; Howard, Heidi C

    2013-09-01

    Various companies are currently advertising or selling genetic tests over the internet using a model of provision referred to as 'direct-to-consumer' (DTC). This commercial offer of DTC genetic testing (GT) has fueled a number of scientific, ethical and policy debates. To date there have been few studies published regarding the users' perspective. This study aimed to obtain information regarding the issues raised by individuals who signed a petition in support of DTC GT and the 'unrestricted' access to their genetic information. We conducted qualitative content analysis of comments written by individuals who signed a public online petition initiated by DIYgenomics (CA, USA) to support "personal access to genetic information". Of the 523 individuals who signed the petition sponsored by DIYgenomics, 247 individuals also wrote individual comments. A content analysis of these comments reveals that petitioners raised six main issues in support of unrestricted access to DTC GT: that their ownership of their DNA should allow them to have unrestricted access to their genomic information; that they should have the right to their genomic information; that the government has no place in (further) regulating DTC GT; that healthcare professionals should not be placed as intermediaries when purchasing DTC GT services; that many petioners who had already obtained DTC GT had positive experiences with this model of provision; and that genealogy or ancestry DNA testing is one of the main activities petitioners wish to have 'unrestricted' or 'direct' access. These results give insight into why individuals may support unrestricted access to their genomic information and confirm some of the motivations of users for purchasing DTC GT. Our analysis also brings to the forefront themes that have been raised less often in empirical studies involving motivations to purchase DTC GT services; these include the strongly held beliefs of some petitioners that, since they own their DNA, they

  8. Nuclear test - The French nuclear strike force in the 21. century: challenges, ambitions and strategy

    International Nuclear Information System (INIS)

    Wodka-Gallien, Philippe

    2014-01-01

    This bibliographical note presents a book in which the author, after having recalled the history of the French nuclear force since the first nuclear test in 1960, and outlined the fact that France has been living under the protection of its own nuclear deterrence force since that date, presents the components of this nuclear strike force with its four nuclear submarines equipped to launch new generation missiles, its fifty fighter bomber aircraft equipped with the ASMP-A missile. He presents and discusses the mission of this nuclear force, discusses the relevancy of the deterrence strategy in the present context, and the significance of such a strategy for a European country like France. He wanders whether this strike force is still affordable for our country, which can be its benefits, whether this arsenal remains useful as it has been designed in the Cold War context. He also discusses the disarmament perspectives in an unsteady international environment where power and arms race logics prevail again

  9. In vitro test systems for the identification of gentoxic chemicals in the human environment: The proof of DNA repair synthesis in liver cells

    International Nuclear Information System (INIS)

    Rossberger, S.

    1986-01-01

    This work examines the possibilities of proving a DNA repair by gentoxic chemicals in primary hepatozytes and 2sFou liver cells of rates. Two different processes used for the in vitro mutagenic testing of alien substances for determining the DNA repair synthesis in primary hepatozytes, in the autoradiographic method and the gradient centrifuging method, are compared regarding their reliability and sensitivity. The rat hepatom cell line 2sFou was examined for its suitability for proving chemically induced DNA repair, instead of primary hepatozytes. (orig./MG) [de

  10. An economic evaluation of preclinical testing strategies compared to the compulsory scrapie flock scheme in the control of classical scrapie.

    Directory of Open Access Journals (Sweden)

    Lisa Boden

    Full Text Available Cost-benefit is rarely combined with nonlinear dynamic models when evaluating control options for infectious diseases. The current strategy for scrapie in Great Britain requires that all genetically susceptible livestock in affected flocks be culled (Compulsory Scrapie Flock Scheme or CSFS. However, this results in the removal of many healthy sheep, and a recently developed pre-clinical test for scrapie now offers a strategy based on disease detection. We explore the flock level cost-effectiveness of scrapie control using a deterministic transmission model and industry estimates of costs associated with genotype testing, pre-clinical tests and the value of a sheep culled. Benefit was measured in terms of the reduction in the number of infected sheep sold on, compared to a baseline strategy of doing nothing, using Incremental Cost Effectiveness analysis to compare across strategies. As market data was not available for pre-clinical testing, a threshold analysis was used to set a unit-cost giving equal costs for CSFS and multiple pre-clinical testing (MT, one test each year for three consecutive years. Assuming a 40% within-flock proportion of susceptible genotypes and a test sensitivity of 90%, a single test (ST was cheaper but less effective than either the CSFS or MT strategies (30 infected-sales-averted over the lifetime of the average epidemic. The MT strategy was slightly less effective than the CSFS and would be a dominated strategy unless preclinical testing was cheaper than the threshold price of £6.28, but may be appropriate for flocks with particularly valuable livestock. Though the ST is not currently recommended, the proportion of susceptible genotypes in the national flock is likely to continue to decrease; this may eventually make it a cost-effective alternative to the MT or CSFS.

  11. Studies of brain and cognitive maturation through childhood and adolescence: a strategy for testing neurodevelopmental hypotheses.

    Science.gov (United States)

    Luna, B; Sweeney, J A

    2001-01-01

    Although neurodevelopmental models of schizophrenia are now widely accepted, there is minimal direct human evidence of dysmaturation in schizophrenia to support this theory. This is especially the case regarding maturational changes during late childhood and adolescence, which immediately precede the typical age of onset of the disorder. By integrating new noninvasive methods of functional magnetic resonance imaging with techniques of developmental cognitive neuroscience, it is now possible to begin systematic research programs to directly test hypotheses of neurodevelopmental abnormalities in schizophrenia. In this article, we describe strategies for characterizing developmental changes taking place during the critical period of adolescence that can elucidate dysmaturation processes in schizophrenia. We emphasize the need for studies characterizing normal development before examining at-risk or clinical populations, and the potential value of using neurobehavioral and neuroimaging approaches to directly characterize the dysmaturation associated with schizophrenia.

  12. ITS-NANO - Prioritising nanosafety research to develop a stakeholder driven intelligent testing strategy

    DEFF Research Database (Denmark)

    Stone, V.; Pozzi-Mucelli, S.; Tran, L.

    2014-01-01

    of the current and future risk assessment of NMs. RESULTS: The framework for future research has been developed from the opinions of over 80 stakeholders, that describes the research priorities for effective development of an intelligent testing strategy (ITS) to allow risk evaluation of NMs. In this context......BACKGROUND: To assess the risk of all nanomaterials (NMs) on a case-by-case basis is challenging in terms of financial, ethical and time resources. Instead a more intelligent approach to knowledge gain and risk assessment is required. METHODS: A framework of future research priorities was developed......-priority research areas are described via a series of stepping stones, or hexagon diagrams structured into a time perspective. Importantly, this framework is flexible, allowing individual stakeholders to identify where their own activities and expertise are positioned within the prioritisation pathway...

  13. Tracing the geographic origin of traded leopard body parts in the indian subcontinent with DNA-based assignment tests.

    Science.gov (United States)

    Mondol, Samrat; Sridhar, Vanjulavalli; Yadav, Prasanjeet; Gubbi, Sanjay; Ramakrishnan, Uma

    2015-04-01

    Illicit trade in wildlife products is rapidly decimating many species across the globe. Such trade is often underestimated for wide-ranging species until it is too late for the survival of their remaining populations. Policing this trade could be vastly improved if one could reliably determine geographic origins of illegal wildlife products and identify areas where greater enforcement is needed. Using DNA-based assignment tests (i.e., samples are assigned to geographic locations), we addressed these factors for leopards (Panthera pardus) on the Indian subcontinent. We created geography-specific allele frequencies from a genetic reference database of 173 leopards across India to infer geographic origins of DNA samples from 40 seized leopard skins. Sensitivity analyses of samples of known geographic origins and assignments of seized skins demonstrated robust assignments for Indian leopards. We found that confiscated pelts seized in small numbers were not necessarily from local leopards. The geographic footprint of large seizures appeared to be bigger than the cumulative footprint of several smaller seizures, indicating widespread leopard poaching across the subcontinent. Our seized samples had male-biased sex ratios, especially the large seizures. From multiple seized sample assignments, we identified central India as a poaching hotspot for leopards. The techniques we applied can be used to identify origins of seized illegal wildlife products and trade routes at the subcontinent scale and beyond. © 2014 Society for Conservation Biology.

  14. Modification of Kolmogorov-Smirnov test for DNA content data analysis through distribution alignment.

    Science.gov (United States)

    Huang, Shuguang; Yeo, Adeline A; Li, Shuyu Dan

    2007-10-01

    The Kolmogorov-Smirnov (K-S) test is a statistical method often used for comparing two distributions. In high-throughput screening (HTS) studies, such distributions usually arise from the phenotype of independent cell populations. However, the K-S test has been criticized for being overly sensitive in applications, and it often detects a statistically significant difference that is not biologically meaningful. One major reason is that there is a common phenomenon in HTS studies that systematic drifting exists among the distributions due to reasons such as instrument variation, plate edge effect, accidental difference in sample handling, etc. In particular, in high-content cellular imaging experiments, the location shift could be dramatic since some compounds themselves are fluorescent. This oversensitivity of the K-S test is particularly overpowered in cellular assays where the sample sizes are very big (usually several thousands). In this paper, a modified K-S test is proposed to deal with the nonspecific location-shift problem in HTS studies. Specifically, we propose that the distributions are "normalized" by density curve alignment before the K-S test is conducted. In applications to simulation data and real experimental data, the results show that the proposed method has improved specificity.

  15. Non-invasive prenatal cell-free fetal DNA testing for down syndrome and other chromosomal abnormalities

    Directory of Open Access Journals (Sweden)

    Darija Strah

    2015-12-01

    Full Text Available Background: Chorionic villus sampling and amniocentesis as definitive diagnostic procedures represent a gold standard for prenatal diagnosis of chromosomal abnormalities. The methods are invasive and lead to a miscarriage and fetal loss in approximately 0.5–1 %. Non-invasive prenatal DNA testing (NIPT is based on the analysis of cell-free fetal DNA from maternal blood. It represents a highly accurate screening test for detecting the most common fetal chromosomal abnormalities. In our study we present the results of NIPT testing in the Diagnostic Center Strah, Slovenia, over the last 3 years.Methods: In our study, 123 pregnant women from 11th to 18th week of pregnancy were included. All of them had First trimester assessment of risk for trisomy 21, done before NIPT testing.Results: 5 of total 6 high-risk NIPT cases (including 3 cases of Down syndrome and 2 cases of Klinefelter’s syndrome were confirmed by fetal karyotyping. One case–Edwards syndrome was false positive. Patau syndrome, triple X syndrome or Turner syndrome were not observed in any of the cases. Furthermore, there were no false negative cases reported. In general, NIPT testing had 100 % sensitivity (95 % confidence interval: 46.29 %–100.00 % and 98.95 % specificity (95 % confidence interval: 93.44 %–99.95 %. In determining Down syndrome alone, specificity (95 % confidence interval: 95.25 %- 100.00 % and sensitivity (95 % confidence interval: 31.00 %–100.00 % turned out to be 100 %. In 2015, the average turnaround time for analysis was 8.3 days from the day when the sample was taken. Repeated blood sampling was required in 2 cases (redraw rate = 1.6 %.Conclusions: Our results confirm that NIPT represents a fast, safe and highly accurate advanced screening test for most common chromosomal abnormalities. In current clinical practice, NIPT would significantly decrease the number of unnecessary invasive procedures and the rate of fetal

  16. Validation of liquid biopsy: plasma cell-free DNA testing in clinical management of advanced non-small cell lung cancer

    Directory of Open Access Journals (Sweden)

    Veldore VH

    2018-01-01

    Full Text Available Vidya H Veldore,1,* Anuradha Choughule,2,* Tejaswi Routhu,1 Nitin Mandloi,1 Vanita Noronha,2 Amit Joshi,2 Amit Dutt,3 Ravi Gupta,1 Ramprasad Vedam,1 Kumar Prabhash2 1MedGenome Labs Private Ltd,, Bangalore, India; 2Tata Memorial Centre, Parel, Mumbai, India; 3The Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, India *These authors contributed equally to this work Abstract: Plasma cell-free tumor DNA, or circulating tumor DNA (ctDNA, from liquid biopsy is a potential source of tumor genetic material, in the absence of tissue biopsy, for EGFR testing. Our validation study reiterates the clinical utility of ctDNA next generation sequencing (NGS for EGFR mutation testing in non-small cell lung cancer (NSCLC. A total of 163 NSCLC cases were included in the validation, of which 132 patients had paired tissue biopsy and ctDNA. We chose to validate ctDNA using deep sequencing with custom designed bioinformatics methods that could detect somatic mutations at allele frequencies as low as 0.01%. Benchmarking allele specific real time PCR as one of the standard methods for tissue-based EGFR mutation testing, the ctDNA NGS test was validated on all the plasma derived cell-free DNA samples. We observed a high concordance (96.96% between tissue biopsy and ctDNA for oncogenic driver mutations in Exon 19 and Exon 21 of the EGFR gene. The sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy of the assay were 91.1%, 100% 100%, 95.6%, and 97%, respectively. A false negative rate of 3% was observed. A subset of mutations was also verified on droplet digital PCR. Sixteen percent EGFR mutation positivity was observed in patients where only liquid biopsy was available, thus creating options for targeted therapy. This is the first and largest study from India, demonstrating successful validation of circulating cell-free DNA as a clinically

  17. One or two serological assay testing strategy for diagnosis of HBV and HCV infection? The use of predictive modelling.

    Science.gov (United States)

    Parry, John V; Easterbrook, Philippa; Sands, Anita R

    2017-11-01

    Initial serological testing for chronic hepatitis B virus (HBV) and hepatitis C virus (HCV) infection is conducted using either rapid diagnostic tests (RDT) or laboratory-based enzyme immunoassays (EIA)s for detection of hepatitis B surface antigen (HBsAg) or antibodies to HCV (anti-HCV), typically on serum or plasma specimens and, for certain RDTs, capillary whole blood. WHO recommends the use of standardized testing strategies - defined as a sequence of one or more assays to maximize testing accuracy while simplifying the testing process and ideally minimizing cost. Our objective was to examine the diagnostic outcomes of a one- versus two-assay serological testing strategy. These data were used to inform recommendations in the 2017 WHO Guidelines on hepatitis B and C testing. Few published studies have compared diagnostic outcomes for one-assay versus two-assay serological testing strategies for HBsAg and anti-HCV. Therefore, the principles of Bayesian statistics were used to conduct a modelling exercise to examine the outcomes of a one-assay versus two-assay testing strategy when applied to a hypothetical population of 10,000 individuals. The resulting model examined the diagnostic outcomes (true and false positive diagnoses; true and false negative diagnoses; positive and negative predictive values as a function of prevalence; and total tests required) for both one-assay and two-assay testing strategies. The performance characteristics assumed for assays used within the testing strategies were informed by WHO prequalification assessment findings and systematic reviews for diagnostic accuracy studies. Each of the presumptive testing strategies (one-assay or two-assay) was modelled at varying prevalences of HBsAg (10%, 2% and 0.4%) and of anti-HCV (40%, 10%, 2% and 0.4%), aimed at representing the range of testing populations typically encountered in WHO Member States. When the two-assay testing strategy was considered, the model assumed the independence of the

  18. Problem-Based Test: Replication of Mitochondrial DNA during the Cell Cycle

    Science.gov (United States)

    Setalo, Gyorgy, Jr.

    2013-01-01

    Terms to be familiar with before you start to solve the test: cell cycle, generation time, S-phase, cell culture synchronization, isotopic pulse-chase labeling, density labeling, equilibrium density-gradient centrifugation, buoyant density, rate-zonal centrifugation, nucleoside, nucleotide, kinase enzymes, polymerization of nucleic acids,…

  19. Testing the implementation and sustainment facilitation (ISF) strategy as an effective adjunct to the Addiction Technology Transfer Center (ATTC) strategy: study protocol for a cluster randomized trial.

    Science.gov (United States)

    Garner, Bryan R; Zehner, Mark; Roosa, Mathew R; Martino, Steve; Gotham, Heather J; Ball, Elizabeth L; Stilen, Patricia; Speck, Kathryn; Vandersloot, Denna; Rieckmann, Traci R; Chaple, Michael; Martin, Erika G; Kaiser, David; Ford, James H

    2017-11-17

    Improving the extent to which evidence-based practices (EBPs)-treatments that have been empirically shown to be efficacious or effective-are integrated within routine practice is a well-documented challenge across numerous areas of health. In 2014, the National Institute on Drug Abuse funded a type 2 effectiveness-implementation hybrid trial titled the substance abuse treatment to HIV Care (SAT2HIV) Project. Aim 1 of the SAT2HIV Project tests the effectiveness of a motivational interviewing-based brief intervention (MIBI) for substance use as an adjunct to usual care within AIDS service organizations (ASOs) as part of its MIBI Experiment. Aim 2 of the SAT2HIV Project tests the effectiveness of implementation and sustainment facilitation (ISF) as an adjunct to the Addiction Technology Transfer Center (ATTC) model for training staff in motivational interviewing as part of its ISF Experiment. The current paper describes the study protocol for the ISF Experiment. Using a cluster randomized design, case management and leadership staff from 39 ASOs across the United States were randomized to receive either the ATTC strategy (control condition) or the ATTC + ISF strategy (experimental condition). The ATTC strategy is staff-focused and includes 10 discrete strategies (e.g., provide centralized technical assistance, conduct educational meetings, provide ongoing consultation). The ISF strategy is organization-focused and includes seven discrete strategies (e.g., use an implementation advisor, organize implementation team meetings, conduct cyclical small tests of change). Building upon the exploration-preparation-implementation-sustainment (EPIS) framework, the effectiveness of the ISF strategy is examined via three staff-level measures: (1) time-to-proficiency (i.e., preparation phase outcome), (2) implementation effectiveness (i.e., implementation phase outcome), and (3) level of sustainment (i.e., sustainment phase outcome). Although not without limitations, the ISF

  20. Testing the implementation and sustainment facilitation (ISF strategy as an effective adjunct to the Addiction Technology Transfer Center (ATTC strategy: study protocol for a cluster randomized trial

    Directory of Open Access Journals (Sweden)

    Bryan R. Garner

    2017-11-01

    Full Text Available Abstract Background Improving the extent to which evidence-based practices (EBPs—treatments that have been empirically shown to be efficacious or effective—are integrated within routine practice is a well-documented challenge across numerous areas of health. In 2014, the National Institute on Drug Abuse funded a type 2 effectiveness–implementation hybrid trial titled the substance abuse treatment to HIV Care (SAT2HIV Project. Aim 1 of the SAT2HIV Project tests the effectiveness of a motivational interviewing-based brief intervention (MIBI for substance use as an adjunct to usual care within AIDS service organizations (ASOs as part of its MIBI Experiment. Aim 2 of the SAT2HIV Project tests the effectiveness of implementation and sustainment facilitation (ISF as an adjunct to the Addiction Technology Transfer Center (ATTC model for training staff in motivational interviewing as part of its ISF Experiment. The current paper describes the study protocol for the ISF Experiment. Methods Using a cluster randomized design, case management and leadership staff from 39 ASOs across the United States were randomized to receive either the ATTC strategy (control condition or the ATTC + ISF strategy (experimental condition. The ATTC strategy is staff-focused and includes 10 discrete strategies (e.g., provide centralized technical assistance, conduct educational meetings, provide ongoing consultation. The ISF strategy is organization-focused and includes seven discrete strategies (e.g., use an implementation advisor, organize implementation team meetings, conduct cyclical small tests of change. Building upon the exploration–preparation–implementation–sustainment (EPIS framework, the effectiveness of the ISF strategy is examined via three staff-level measures: (1 time-to-proficiency (i.e., preparation phase outcome, (2 implementation effectiveness (i.e., implementation phase outcome, and (3 level of sustainment (i.e., sustainment phase outcome

  1. A Novel Experimental and Modelling Strategy for Nanoparticle Toxicity Testing Enabling the Use of Small Quantities

    Directory of Open Access Journals (Sweden)

    Marinda van Pomeren

    2017-11-01

    Full Text Available Metallic nanoparticles (NPs differ from other metal forms with respect to their large surface to volume ratio and subsequent inherent reactivity. Each new modification to a nanoparticle alters the surface to volume ratio, fate and subsequently the toxicity of the particle. Newly-engineered NPs are commonly available only in low quantities whereas, in general, rather large amounts are needed for fate characterizations and effect studies. This challenge is especially relevant for those NPs that have low inherent toxicity combined with low bioavailability. Therefore, within our study, we developed new testing strategies that enable working with low quantities of NPs. The experimental testing method was tailor-made for NPs, whereas we also developed translational models based on different dose-metrics allowing to determine dose-response predictions for NPs. Both the experimental method and the predictive models were verified on the basis of experimental effect data collected using zebrafish embryos exposed to metallic NPs in a range of different chemical compositions and shapes. It was found that the variance in the effect data in the dose-response predictions was best explained by the minimal diameter of the NPs, whereas the data confirmed that the predictive model is widely applicable to soluble metallic NPs. The experimental and model approach developed in our study support the development of (ecotoxicity assays tailored to nano-specific features.

  2. Frameshift mutations in infectious cDNA clones of Citrus tristeza virus: a strategy to minimize the toxicity of viral sequences to Escherichia coli

    International Nuclear Information System (INIS)

    Satyanarayana, Tatineni; Gowda, Siddarame; Ayllon, Maria A.; Dawson, William O.

    2003-01-01

    The advent of reverse genetics revolutionized the study of positive-stranded RNA viruses that were amenable for cloning as cDNAs into high-copy-number plasmids of Escherichia coli. However, some viruses are inherently refractory to cloning in high-copy-number plasmids due to toxicity of viral sequences to E. coli. We report a strategy that is a compromise between infectivity of the RNA transcripts and toxicity to E. coli effected by introducing frameshift mutations into 'slippery sequences' near the viral 'toxicity sequences' in the viral cDNA. Citrus tristeza virus (CTV) has cDNA sequences that are toxic to E. coli. The original full-length infectious cDNA of CTV and a derivative replicon, CTV-ΔCla, cloned into pUC119, resulted in unusually limited E. coli growth. However, upon sequencing of these cDNAs, an additional uridinylate (U) was found in a stretch of U's between nts 3726 and 3731 that resulted in a change to a reading frame with a stop codon at nt 3734. Yet, in vitro produced RNA transcripts from these clones infected protoplasts, and the resulting progeny virus was repaired. Correction of the frameshift mutation in the CTV cDNA constructs resulted in increased infectivity of in vitro produced RNA transcripts, but also caused a substantial increase of toxicity to E. coli, now requiring 3 days to develop visible colonies. Frameshift mutations created in sequences not suspected to facilitate reading frame shifting and silent mutations introduced into oligo(U) regions resulted in complete loss of infectivity, suggesting that the oligo(U) region facilitated the repair of the frameshift mutation. Additional frameshift mutations introduced into other oligo(U) regions also resulted in transcripts with reduced infectivity similarly to the original clones with the +1 insertion. However, only the frameshift mutations introduced into oligo(U) regions that were near and before the toxicity region improved growth and stability in E. coli. These data demonstrate that

  3. Comparison of Different Test Construction Strategies in the Development of a Gender Fair Interest Inventory Using Verbs

    Science.gov (United States)

    Wetzel, Eunike; Hell, Benedikt; Passler, Katja

    2012-01-01

    Three test construction strategies are described and illustrated in the development of the Verb Interest Test (VIT), an inventory that assesses vocational interests using verbs. Verbs might be a promising alternative to the descriptions of occupational activities used in most vocational interest inventories because they are context-independent,…

  4. Comparison of human papillomavirus DNA tests, liquid-based cytology and conventional cytology for the early detection of cervix uteri cancer.

    Science.gov (United States)

    Girianelli, Vania R; Thuler, Luiz Claudio S; Szklo, Moyses; Donato, Alexandre; Zardo, Lucilia M G; Lozana, José A; Almeida Neto, Olimpio F; Carvalho, Aurenice C L; Matos, Jorge H; Figueiredo, Valeska

    2006-12-01

    To compare the performance of human papillomavirus DNA tests (samples collected by a healthcare professional and self-collected) and liquid-based cytology with conventional cytology in the detection of cervix uteri cancer and its precursor lesions. A cross-sectional study was carried out in 1777 women living in poor communities in Rio de Janeiro State, Brazil. Eligibility criteria included ages 25-59 years and not having had a Papanicolau test within at least 3 years prior to the study. Cytology (conventional or liquid-based) and human papillomavirus DNA (collected by a healthcare professional or self-collected) tests were performed using samples collected in a single visit. Women with abnormalities in at least one test and a systematic sample of 70 women with negative test results were referred to a colposcopic examination. Test readings were double-masked, and the outcome of interest was high-grade squamous intraepithelial lesion or worse. The pathology report was used as the gold standard. The prevalence of high-grade squamous intraepithelial lesion or worse was 2.0%. Human papillomavirus DNA test collected by a health professional alone or combined with conventional cytology had the highest sensitivity (91.4 and 97.1%, respectively). The highest specificity was found for conventional cytology (91.6%) and for a human papillomavirus DNA test collected by a healthcare professional (90.2%). On the basis of only test performance, the use of human papillomavirus DNA tests, alone or combined with cytology, would seem to be recommended. Its population-wide implementation, however, is conditional on a cost-effectiveness analysis.

  5. Evaluating the enforceability of texting laws: strategies tested in Connecticut and Massachusetts.

    Science.gov (United States)

    2017-03-01

    The purpose of this research was to explore alternative strategies for increasing seat belt use. Researchers examined behavior : change strategies proven effective in education, healthcare, advertising, and marketing, and they considered how these : ...

  6. New vaccine strategies against enterotoxigenic Escherichia coli: II: Enhanced systemic and secreted antibody responses against the CFA/I fimbriae by priming with DNA and boosting with a live recombinant Salmonella vaccine

    Directory of Open Access Journals (Sweden)

    M.O. Lásaro

    1999-02-01

    Full Text Available The induction of systemic (IgG and mucosal (IgA antibody responses against the colonization factor I antigen (CFA/I of enterotoxigenic Escherichia coli (ETEC was evaluated in mice primed with an intramuscularly delivered CFA/I-encoding DNA vaccine followed by two oral immunizations with a live recombinant Salmonella typhimurium vaccine strain expressing the ETEC antigen. The booster effect induced by the oral immunization was detected two weeks and one year after the administration of the DNA vaccine. The DNA-primed/Salmonella-boosted vaccination regime showed a synergistic effect on the induced CFA/I-specific systemic and secreted antibody levels which could not be attained by either immunization strategy alone. These results suggest that the combined use of DNA vaccines and recombinant Salmonella vaccine strains can be a useful immunization strategy against enteric pathogens.

  7. Invasive Candidiasis in Various Patient Populations: Incorporating Non-Culture Diagnostic Tests into Rational Management Strategies

    Science.gov (United States)

    Clancy, Cornelius J.; Shields, Ryan K.; Nguyen, M. Hong

    2016-01-01

    Mortality rates due to invasive candidiasis remain unacceptably high, in part because the poor sensitivity and slow turn-around time of cultures delay the initiation of antifungal treatment. β-d-glucan (Fungitell) and polymerase chain reaction (PCR)-based (T2Candida) assays are FDA-approved adjuncts to cultures for diagnosing invasive candidiasis, but their clinical roles are unclear. We propose a Bayesian framework for interpreting non-culture test results and developing rational patient management strategies, which considers test performance and types of invasive candidiasis that are most common in various patient populations. β-d-glucan sensitivity/specificity for candidemia and intra-abdominal candidiasis is ~80%/80% and ~60%/75%, respectively. In settings with 1%–10% likelihood of candidemia, anticipated β-d-glucan positive and negative predictive values are ~4%–31% and ≥97%, respectively. Corresponding values in settings with 3%–30% likelihood of intra-abdominal candidiasis are ~7%–51% and ~78%–98%. β-d-glucan is predicted to be useful in guiding antifungal treatment for wide ranges of populations at-risk for candidemia (incidence ~5%–40%) or intra-abdominal candidiasis (~7%–20%). Validated PCR-based assays should broaden windows to include populations at lower-risk for candidemia (incidence ≥~2%) and higher-risk for intra-abdominal candidiasis (up to ~40%). In the management of individual patients, non-culture tests may also have value outside of these windows. The proposals we put forth are not definitive treatment guidelines, but rather represent starting points for clinical trial design and debate by the infectious diseases community. The principles presented here will be applicable to other assays as they enter the clinic, and to existing assays as more data become available from different populations. PMID:29376927

  8. Invasive Candidiasis in Various Patient Populations: Incorporating Non-Culture Diagnostic Tests into Rational Management Strategies

    Directory of Open Access Journals (Sweden)

    Cornelius J. Clancy

    2016-02-01

    Full Text Available Mortality rates due to invasive candidiasis remain unacceptably high, in part because the poor sensitivity and slow turn-around time of cultures delay the initiation of antifungal treatment. β-d-glucan (Fungitell and polymerase chain reaction (PCR-based (T2Candida assays are FDA-approved adjuncts to cultures for diagnosing invasive candidiasis, but their clinical roles are unclear. We propose a Bayesian framework for interpreting non-culture test results and developing rational patient management strategies, which considers test performance and types of invasive candidiasis that are most common in various patient populations. β-d-glucan sensitivity/specificity for candidemia and intra-abdominal candidiasis is ~80%/80% and ~60%/75%, respectively. In settings with 1%–10% likelihood of candidemia, anticipated β-d-glucan positive and negative predictive values are ~4%–31% and ≥97%, respectively. Corresponding values in settings with 3%–30% likelihood of intra-abdominal candidiasis are ~7%–51% and ~78%–98%. β-d-glucan is predicted to be useful in guiding antifungal treatment for wide ranges of populations at-risk for candidemia (incidence ~5%–40% or intra-abdominal candidiasis (~7%–20%. Validated PCR-based assays should broaden windows to include populations at lower-risk for candidemia (incidence ≥~2% and higher-risk for intra-abdominal candidiasis (up to ~40%. In the management of individual patients, non-culture tests may also have value outside of these windows. The proposals we put forth are not definitive treatment guidelines, but rather represent starting points for clinical trial design and debate by the infectious diseases community. The principles presented here will be applicable to other assays as they enter the clinic, and to existing assays as more data become available from different populations.

  9. Use of genotoxicity information in the development of integrated testing strategies (ITS) for skin sensitization.

    Science.gov (United States)

    Mekenyan, Ovanes; Patlewicz, Grace; Dimitrova, Gergana; Kuseva, Chanita; Todorov, Milen; Stoeva, Stoyanka; Kotov, Stefan; Donner, E Maria

    2010-10-18

    Skin sensitization is an end point of concern for various legislation in the EU, including the seventh Amendment to the Cosmetics Directive and Registration Evaluation, Authorisation and Restriction of Chemicals (REACH). Since animal testing is a last resort for REACH or banned (from 2013 onward) for the Cosmetics Directive, the use of intelligent/integrated testing strategies (ITS) as an efficient means of gathering necessary information from alternative sources (e.g., in vitro, (Q)SARs, etc.) is gaining widespread interest. Previous studies have explored correlations between mutagenicity data and skin sensitization data as a means of exploiting information from surrogate end points. The work here compares the underlying chemical mechanisms for mutagenicity and skin sensitization in an effort to evaluate the role mutagenicity information can play as a predictor of skin sensitization potential. The Tissue Metabolism Simulator (TIMES) hybrid expert system was used to compare chemical mechanisms of both end points since it houses a comprehensive set of established structure-activity relationships for both skin sensitization and mutagenicity. The evaluation demonstrated that there is a great deal of overlap between skin sensitization and mutagenicity structural alerts and their underlying chemical mechanisms. The similarities and differences in chemical mechanisms are discussed in light of available experimental data. A number of new alerts for mutagenicity were also postulated for inclusion into TIMES. The results presented show that mutagenicity information can provide useful insights on skin sensitization potential as part of an ITS and should be considered prior to any in vivo skin sensitization testing being initiated.

  10. Testing the effectiveness of simplified search strategies for updating systematic reviews.

    Science.gov (United States)

    Rice, Maureen; Ali, Muhammad Usman; Fitzpatrick-Lewis, Donna; Kenny, Meghan; Raina, Parminder; Sherifali, Diana

    2017-08-01

    The objective of the study was to test the overall effectiveness of a simplified search strategy (SSS) for updating systematic reviews. We identified nine systematic reviews undertaken by our research group for which both comprehensive and SSS updates were performed. Three relevant performance measures were estimated, that is, sensitivity, precision, and number needed to read (NNR). The update reference searches for all nine included systematic reviews identified a total of 55,099 citations that were screened resulting in final inclusion of 163 randomized controlled trials. As compared with reference search, the SSS resulted in 8,239 hits and had a median sensitivity of 83.3%, while precision and NNR were 4.5 times better. During analysis, we found that the SSS performed better for clinically focused topics, with a median sensitivity of 100% and precision and NNR 6 times better than for the reference searches. For broader topics, the sensitivity of the SSS was 80% while precision and NNR were 5.4 times better compared with reference search. SSS performed well for clinically focused topics and, with a median sensitivity of 100%, could be a viable alternative to a conventional comprehensive search strategy for updating this type of systematic reviews particularly considering the budget constraints and the volume of new literature being published. For broader topics, 80% sensitivity is likely to be considered too low for a systematic review update in most cases, although it might be acceptable if updating a scoping or rapid review. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. Transition from blastomere to trophectoderm biopsy: comparing two preimplantation genetic testing for aneuploidies strategies.

    Science.gov (United States)

    Coll, Lluc; Parriego, Mònica; Boada, Montserrat; Devesa, Marta; Arroyo, Gemma; Rodríguez, Ignacio; Coroleu, Bonaventura; Vidal, Francesca; Veiga, Anna

    2018-05-25

    SummaryShortly after the implementation of comprehensive chromosome screening (CCS) techniques for preimplantation genetic testing for aneuploidies (PGT-A), the discussion about the transition from day 3 to blastocyst stage biopsy was initiated. Trophectoderm biopsy with CCS is meant to overcome the limitations of cleavage-stage biopsy and single-cell analysis. The aim of this study was to assess the results obtained in our PGT-A programme after the implementation of this new strategy. Comparisons between the results obtained in 179 PGT-A cycles with day 3 biopsy (D+3) and fresh embryo transfer, and 204 cycles with trophectoderm biopsy and deferred (frozen-thawed) embryo transfer were established. Fewer embryos were biopsied and a higher euploidy rate was observed in the trophectoderm biopsy group. No differences in implantation (50.3% vs. 61.4%) and clinical pregnancy rate per transfer (56.1% vs. 65.3%) were found. Although the mean number of euploid embryos per cycle did not differ between groups (1.5 ± 1.7 vs. 1.7 ± 1.8), the final number of euploid blastocysts available for transfer per cycle was significantly higher in the trophectoderm biopsy group (1.1 ± 1.3 vs. 1.7 ± 1.8). This factor led to an increased cumulative live birth rate in this last group (34.1% vs. 44.6%). Although both strategies can offer good results, trophectoderm biopsy offers a more robust diagnosis and the intervention is less harmful for the embryos so more euploid blastocysts are finally available for transfer and/or vitrification.

  12. Loop-Mediated Isothermal Amplification on Crude DNA as a Point-of-Care Test for the Diagnosis of Mycoplasma-Related Vaginitis During Early Pregnancy.

    Science.gov (United States)

    Wang, Yichao; Zhang, Bumei; Sun, Yan; Liu, Yunde; Gu, Yajun

    2017-12-20

    Mycoplasma-related vaginitis gradually has been growing as a threat in adults-genitourinary infection contributes to funisitis, spontaneous abortion, and low birth weight. Until now, use of loop-mediated isothermal amplification (LAMP) to detect Ureaplasma urealyticum (UU), Mycoplasma hominis (MH), or Mycoplasma genitalium (MG) has been reported by some researchers. However, previous studies focused on purified DNA as the template for LAMP assay, which is usually extracted via commercial kit. We developed a LAMP assay for rapid detection of UU, MH, and MG genital mycoplasmas using a simple boiling method for DNA extraction, in a cohort of pregnant women with mycoplasma-related vaginitis. We monitored amplicons with the naked eye using SYBR Green I. The cohort in our study showed a prevalence of 22.6% in pregnant women, as detected by UU-LAMP assay. Compared to the polymerase chain reaction (PCR) test with purified DNA, the sensitivity of the UU-LAMP in clinical specimens with crude DNA was 87.5% (95% confidence interval [CI], 64.6%->99.9). For crude DNA specimens, UU-LAMP was more sensitive and reliable than PCR, with a higher agreement rate (96.8%) and Youden index value (0.88). As a point-of-care test, LAMP is a useful, specific, and efficient way to detect genital mycoplasmas in resource-limited settings, especially for crude DNA. © American Society for Clinical Pathology 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

  13. Development and validation of a multiplex reaction analyzing eight miniSTRs of the X chromosome for identity and kinship testing with degraded DNA.

    Science.gov (United States)

    Castañeda, María; Odriozola, Adrián; Gómez, Javier; Zarrabeitia, María T

    2013-07-01

    We report the development of an effective system for analyzing X chromosome-linked mini short tandem repeat loci with reduced-size amplicons (less than 220 bp), useful for analyzing highly degraded DNA samples. To generate smaller amplicons, we redesigned primers for eight X-linked microsatellites (DXS7132, DXS10079, DXS10074, DXS10075, DXS6801, DXS6809, DXS6789, and DXS6799) and established efficient conditions for a multiplex PCR system (miniX). The validation tests confirmed that it has good sensitivity, requiring as little as 20 pg of DNA, and performs well with DNA from paraffin-embedded tissues, thus showing potential for improved analysis and identification of highly degraded and/or very limited DNA samples. Consequently, this system may help to solve complex forensic cases, particularly when autosomal markers convey insufficient information.

  14. Variation in Research Designs Used to Test the Effectiveness of Dissemination and Implementation Strategies: A Review.

    Science.gov (United States)

    Mazzucca, Stephanie; Tabak, Rachel G; Pilar, Meagan; Ramsey, Alex T; Baumann, Ana A; Kryzer, Emily; Lewis, Ericka M; Padek, Margaret; Powell, Byron J; Brownson, Ross C

    2018-01-01

    The need for optimal study designs in dissemination and implementation (D&I) research is increasingly recognized. Despite the wide range of study designs available for D&I research, we lack understanding of the types of designs and methodologies that are routinely used in the field. This review assesses the designs and methodologies in recently proposed D&I studies and provides resources to guide design decisions. We reviewed 404 study protocols published in the journal Implementation Science from 2/2006 to 9/2017. Eligible studies tested the efficacy or effectiveness of D&I strategies (i.e., not effectiveness of the underlying clinical or public health intervention); had a comparison by group and/or time; and used ≥1 quantitative measure. Several design elements were extracted: design category (e.g., randomized); design type [e.g., cluster randomized controlled trial (RCT)]; data type (e.g., quantitative); D&I theoretical framework; levels of treatment assignment, intervention, and measurement; and country in which the research was conducted. Each protocol was double-coded, and discrepancies were resolved through discussion. Of the 404 protocols reviewed, 212 (52%) studies tested one or more implementation strategy across 208 manuscripts, therefore meeting inclusion criteria. Of the included studies, 77% utilized randomized designs, primarily cluster RCTs. The use of alternative designs (e.g., stepped wedge) increased over time. Fewer studies were quasi-experimental (17%) or observational (6%). Many study design categories (e.g., controlled pre-post, matched pair cluster design) were represented by only one or two studies. Most articles proposed quantitative and qualitative methods (61%), with the remaining 39% proposing only quantitative. Half of protocols (52%) reported using a theoretical framework to guide the study. The four most frequently reported frameworks were Consolidated Framework for Implementing Research and RE-AIM ( n  = 16 each), followed by

  15. Variation in Research Designs Used to Test the Effectiveness of Dissemination and Implementation Strategies: A Review

    Directory of Open Access Journals (Sweden)

    Stephanie Mazzucca

    2018-02-01

    Full Text Available BackgroundThe need for optimal study designs in dissemination and implementation (D&I research is increasingly recognized. Despite the wide range of study designs available for D&I research, we lack understanding of the types of designs and methodologies that are routinely used in the field. This review assesses the designs and methodologies in recently proposed D&I studies and provides resources to guide design decisions.MethodsWe reviewed 404 study protocols published in the journal Implementation Science from 2/2006 to 9/2017. Eligible studies tested the efficacy or effectiveness of D&I strategies (i.e., not effectiveness of the underlying clinical or public health intervention; had a comparison by group and/or time; and used ≥1 quantitative measure. Several design elements were extracted: design category (e.g., randomized; design type [e.g., cluster randomized controlled trial (RCT]; data type (e.g., quantitative; D&I theoretical framework; levels of treatment assignment, intervention, and measurement; and country in which the research was conducted. Each protocol was double-coded, and discrepancies were resolved through discussion.ResultsOf the 404 protocols reviewed, 212 (52% studies tested one or more implementation strategy across 208 manuscripts, therefore meeting inclusion criteria. Of the included studies, 77% utilized randomized designs, primarily cluster RCTs. The use of alternative designs (e.g., stepped wedge increased over time. Fewer studies were quasi-experimental (17% or observational (6%. Many study design categories (e.g., controlled pre–post, matched pair cluster design were represented by only one or two studies. Most articles proposed quantitative and qualitative methods (61%, with the remaining 39% proposing only quantitative. Half of protocols (52% reported using a theoretical framework to guide the study. The four most frequently reported frameworks were Consolidated Framework for Implementing Research and RE

  16. Reducing AD-like pathology in 3xTg-AD mouse model by DNA epitope vaccine - a novel immunotherapeutic strategy.

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    Nina Movsesyan

    Full Text Available BACKGROUND: The development of a safe and effective AD vaccine requires a delicate balance between providing an adequate anti-Abeta antibody response sufficient to provide therapeutic benefit, while eliminating an adverse T cell-mediated proinflammatory autoimmune response. To achieve this goal we have designed a prototype chemokine-based DNA epitope vaccine expressing a fusion protein that consists of 3 copies of the self-B cell epitope of Abeta(42 (Abeta(1-11 , a non-self T helper cell epitope (PADRE, and macrophage-derived chemokine (MDC/CCL22 as a molecular adjuvant to promote a strong anti-inflammatory Th2 phenotype. METHODS AND FINDINGS: We generated pMDC-3Abeta(1-11-PADRE construct and immunized 3xTg-AD mouse model starting at age of 3-4 months old. We demonstrated that prophylactic immunizations with the DNA epitope vaccine generated a robust Th2 immune response that induced high titers of anti-Abeta antibody, which in turn inhibited accumulation of Abeta pathology in the brains of older mice. Importantly, vaccination reduced glial activation and prevented the development of behavioral deficits in aged animals without increasing the incidence of microhemorrhages. CONCLUSIONS: Data from this transitional pre-clinical study suggest that our DNA epitope vaccine could be used as a safe and effective strategy for AD therapy. Future safety and immunology studies in large animals with the goal to achieve effective humoral immunity without adverse effects should help to translate this study to human clinical trials.

  17. Sensitivity, Specificity, and Clinical Value of Human Papillomavirus (HPV) E6/E7 mRNA Assay as a Triage Test for Cervical Cytology and HPV DNA Test

    Science.gov (United States)

    Benevolo, Maria; Vocaturo, Amina; Caraceni, Donatella; French, Deborah; Rosini, Sandra; Zappacosta, Roberta; Terrenato, Irene; Ciccocioppo, Lucia; Frega, Antonio; Rossi, Paolo Giorgi

    2011-01-01

    There is evidence that testing for human papillomavirus (HPV) E6/E7 mRNA is more specific than testing for HPV DNA. A retrospective study was carried out to evaluate the performance of the PreTect HPV-Proofer E6/E7 mRNA assay (Norchip) as a triage test for cytology and HPV DNA testing. This study analyzed 1,201 women, 688 of whom had a colposcopy follow-up and 195 of whom had histology-confirmed high-grade intraepithelial neoplasia or worse (CIN2+). The proportion of positive results and the sensitivity and specificity for CIN2+ were determined for HPV mRNA in comparison to HPV DNA and cytology. All data were adjusted for follow-up completeness. Stratified by cytological grades, the HPV mRNA sensitivity was 83% (95% confidence interval [CI] = 63 to 94%) in ASC-US (atypical squamous cells of undetermined significance), 62% (95% CI = 47 to 75%) in L-SIL (low-grade squamous intraepithelial lesion), and 67% (95% CI = 57 to 76%) in H-SIL (high-grade squamous intraepithelial lesion). The corresponding figures were 99, 91, and 96%, respectively, for HPV DNA. The specificities were 82, 76, and 45%, respectively, for HPV mRNA and 29, 13, and 4%, respectively, for HPV DNA. Used as a triage test for ASC-US and L-SIL, mRNA reduced colposcopies by 79% (95% CI = 74 to 83%) and 69% (95% CI = 65 to 74%), respectively, while HPV DNA reduced colposcopies by 38% (95% CI = 32 to 44%) and by 15% (95% CI = 12 to 19%), respectively. As a HPV DNA positivity triage test, mRNA reduced colposcopies by 63% (95% CI = 60 to 66%), having 68% sensitivity (95% CI = 61 to 75%), whereas cytology at the ASC-US+ threshold reduced colposcopies by 23% (95% CI = 20 to 26%), showing 92% sensitivity (95% CI = 87 to 95%). In conclusion, PreTect HPV-Proofer mRNA can serve as a better triage test than HPV DNA to reduce colposcopy referral in both ASC-US and L-SIL. It is also more efficient than cytology for the triage of HPV DNA-positive women. Nevertheless, its low sensitivity demands a strict follow-up of

  18. Human Papillomavirus Infection Among 2460 Men in Denmark: Prevalence in Relation to Age Using 2 Human Papillomavirus DNA Testing Methods.

    Science.gov (United States)

    Hebnes, Julie Buchholt; Munk, Christian; Nøhr, Bugge; Nielsen, Ann; Jørgensen, Hans Ole; Iftner, Thomas; Kjaer, Susanne Krüger

    2015-08-01

    It is crucial to understand the epidemiology and natural history of human papillomavirus (HPV) infection in both men and women, to prevent the increasing HPV-related disease burden in men. Data on HPV prevalence among men in the general population are limited. In this cross-sectional population-based study, we aimed to estimate genital HPV infection prevalence in Danish men using 2 different test methods. Penile swab samples from 2460 male employees and conscripts at military barracks in Denmark were tested for HPV DNA with the hybrid capture 2 (HC2) method, and a polymerase chain reaction (PCR) assay, Inno-LiPA. The overall and age- and type-specific prevalence of HPV infection with 95% confidence intervals (CIs) were estimated, and the correlation between the 2 assays was assessed. The overall HPV prevalence was 22.2% (95% CI, 20.6-23.9) in the HC2 test and 41.8% (95% CI, 39.9-43.8) with PCR. Of the PCR-positive samples, 50.9% were negative in the HC2 test. Of 183 PCR-positive samples that could not be genotyped (HPVX), 88.0% (95% CI, 83.2-92.7) were HC2 negative. The most prevalent types were HPV-51, HPV-16, HPV-66, HPV-53, and HPV-6. The prevalence of high-risk and low-risk HPV peaked among men aged 20 to 29 years, whereas the HPVX prevalence increased with age. Human papillomavirus is highly prevalent in the general male population of Denmark, with HPV-16 and HPV-51 being the most prevalent. Polymerase chain reaction detects twice as many positive samples as HC2 but includes HPVX, possibly representing cutaneous HPV types found on normal genital skin.

  19. Distribution of Plasmodium species on the island of Grande Comore on the basis of DNA extracted from rapid diagnostic tests

    Directory of Open Access Journals (Sweden)

    Papa Mze Nasserdine

    2016-01-01

    Full Text Available In the Union of Comoros, interventions for combating malaria have contributed to a spectacular decrease in the prevalence of the disease. We studied the current distribution of Plasmodium species on the island of Grande Comore using nested PCR. The rapid diagnostic tests (RDTs currently used in the Comoros are able to identify Plasmodium falciparum but no other Plasmodium species. In this study, we tested 211 RDTs (158 positive and 53 negative. Among the 158 positive RDTs, 22 were positive for HRP2, 3 were positive only for pLDH, and 133 were positive for HRP2 and pLDH. DNA was extracted from a proximal part of the nitrocellulose membrane of RDTs. A total of 159 samples were positive by nested PCR. Of those, 156 (98.11% were positive for P. falciparum, 2 (1.25% were positive for P. vivaxI, and 1 (0.62% was positive for P. malariae. None of the samples were positive for P. ovale. Our results show that P. falciparum is still the most dominant species on the island of Grande Comore, but P. vivax and P. malariae are present at a low prevalence.

  20. Integrating feeding behavior, ecological data, and DNA barcoding to identify developmental differences in invertebrate foraging strategies in wild white-faced capuchins (Cebus capucinus).

    Science.gov (United States)

    Mallott, Elizabeth K; Garber, Paul A; Malhi, Ripan S

    2017-02-01

    Invertebrate foraging strategies in nonhuman primates often require complex extractive foraging or prey detection techniques. As these skills take time to master, juveniles may have reduced foraging efficiency or concentrate their foraging efforts on easier to acquire prey than adults. We use DNA barcoding, behavioral observations, and ecological data to assess age-based differences in invertebrate prey foraging strategies in a group of white-faced capuchins (Cebus capucinus) in northeastern Costa Rica. Invertebrate availability was monitored using canopy traps and sweep netting. Fecal samples were collected from adult female, adult male, and juvenile white-faced capuchins (n = 225). COI mtDNA sequences were compared with known sequences in GenBank and the Barcode of Life Database. Frequencies of Lepidoptera and Hymenoptera consumption were higher in juveniles than in adults. A significantly smaller proportion of juvenile fecal samples contained Gryllidae and Cercopidae sequences, compared with adults (0% and 4.2% vs. 4.6% and 12.5%), and a significantly larger proportion contained Tenthredinidae, Culicidae, and Crambidae (5.6%, 9.7%, and 5.6% vs. 1.3%, 0.7%, and 1.3%). Juveniles spent significantly more time feeding and foraging than adults, and focused their foraging efforts on prey that require different skills to capture or extract. Arthropod availability was not correlated with foraging efficiency, and the rate of consumption of specific orders of invertebrates was not correlated with the availability of those same taxa. Our data support the hypothesis that juveniles are concentrating their foraging efforts on different prey than adults, potentially focusing their foraging efforts on more easily acquired types of prey. © 2016 Wiley Periodicals, Inc.

  1. Development and testing of an implementation strategy for a complex housing intervention: protocol for a mixed methods study.

    Science.gov (United States)

    Watson, Dennis P; Young, Jeani; Ahonen, Emily; Xu, Huiping; Henderson, Macey; Shuman, Valery; Tolliver, Randi

    2014-10-17

    There is currently a lack of scientifically designed and tested implementation strategies. Such strategies are particularly important for highly complex interventions that require coordination between multiple parts to be successful. This paper presents a protocol for the development and testing of an implementation strategy for a complex intervention known as the Housing First model (HFM). Housing First is an evidence-based practice for chronically homeless individuals demonstrated to significantly improve a number of outcomes. Drawing on practices demonstrated to be useful in implementation and e-learning theory, our team is currently adapting a face-to-face implementation strategy so that it can be delivered over a distance. Research activities will be divided between Chicago and Central Indiana, two areas with significantly different barriers to HFM implementation. Ten housing providers (five from Chicago and five from Indiana) will be recruited to conduct an alpha test of each of four e-learning modules as they are developed. Providers will be requested to keep a detailed log of their experience completing the modules and participate in one of two focus groups. After refining the modules based on alpha test results, we will test the strategy among a sample of four housing organizations (two from Chicago and two from Indiana). We will collect and analyze both qualitative and quantitative data from administration and staff. Measures of interest include causal factors affecting implementation, training outcomes, and implementation outcomes. This project is an important first step in the development of an evidence-based implementation strategy to increase scalability and impact of the HFM. The project also has strong potential to increase limited scientific knowledge regarding implementation strategies in general.

  2. Development of a dual test procedure for DNA typing and methamphetamine detection using a trace amount of stimulant-containing blood.

    Science.gov (United States)

    Irii, Toshiaki; Maebashi, Kyoko; Fukui, Kenji; Sohma, Ryoko; Matsumoto, Sari; Takasu, Shojiro; Iwadate, Kimiharu

    2016-05-01

    Investigation of drug-related crimes, such as violation of the Stimulant Drug Control Law, requires identifying the used drug (mainly stimulant drugs, methamphetamine hydrochloride) from a drug solution and the DNA type of the drug user from a trace of blood left in the syringe used to inject the drug. In current standard test procedures, DNA typing and methamphetamine detection are performed as independent tests that use two separate portions of a precious sample. The sample can be entirely used up by either analysis. Therefore, we developed a new procedure involving partial lysis of a stimulant-containing blood sample followed by separation of the lysate into a precipitate for DNA typing and a liquid-phase fraction for methamphetamine detection. The method enables these two tests to be run in parallel using a single portion of sample. Samples were prepared by adding methamphetamine hydrochloride water solution to blood. Samples were lysed with Proteinase K in PBS at 56°C for 20min, cooled at -20°C after adding methanol, and then centrifuged at 15,000rpm. Based on the biopolymer-precipitating ability of alcohol, the precipitate was used for DNA typing and the liquid-phase fraction for methamphetamine detection. For DNA typing, the precipitate was dissolved and DNA was extracted, quantified, and subjected to STR analysis using the AmpFℓSTR® Identifiler® Plus PCR Amplification Kit. For methamphetamine detection, the liquid-phase fraction was evaporated with N2 gas after adding 20μL acetic acid and passed through an extraction column; the substances captured in the column were eluted with a solvent, derivatized, and quantitatively detected using gas chromatograph/mass spectrometry. This method was simple and could be completed in approximately 2h. Both DNA typing and methamphetamine detection were possible, which suggests that this method may be valuable for use in criminal investigations. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  3. Safety Design Strategy for the Advanced Test Reactor Diesel Bus (E-3) and Switchgear Replacement Project

    International Nuclear Information System (INIS)

    Duckwitz, Noel

    2011-01-01

    In accordance with the requirements of U.S. Department of Energy (DOE) Order 413.3B, 'Program and Project Management for the Acquisition of Capital Assets,' safety must be integrated into the design process for new or major modifications to DOE Hazard Category 1, 2, and 3 nuclear facilities. The intended purpose of this requirement involves the handling of hazardous materials, both radiological and chemical, in a way that provides adequate protection to the public, workers, and the environment. Requirements provided in DOE Order 413.3B and DOE Order 420.1B, 'Facility Safety,' and the expectations of DOE-STD-1189-2008, 'Integration of Safety into the Design Process,' provide for identification of hazards early in the project and use of an integrated team approach to design safety into the facility. This safety design strategy provides the basic safety-in-design principles and concepts that will be used for the Advanced Test Reactor Reliability Sustainment Project. While this project does not introduce new hazards to the ATR, it has the potential for significant impacts to safety-related systems, structures, and components that are credited in the ATR safety basis and are being replaced. Thus the project has been determined to meet the definition of a major modification and is being managed accordingly.

  4. Safety Design Strategy for the Advanced Test Reactor Emergency Firewater Injection System Replacement Project

    International Nuclear Information System (INIS)

    Duckwitz, Noel

    2011-01-01

    In accordance with the requirements of U.S. Department of Energy (DOE) Order 413.3B, 'Program and Project Management for the Acquisition of Capital Assets,' safety must be integrated into the design process for new or major modifications to DOE Hazard Category 1, 2, and 3 nuclear facilities. The intended purpose of this requirement involves the handling of hazardous materials, both radiological and chemical, in a way that provides adequate protection to the public, workers, and the environment. Requirements provided in DOE Order 413.3B and DOE Order 420.1B, 'Facility Safety,' and the expectations of DOE-STD-1189-2008, 'Integration of Safety into the Design Process,' provide for identification of hazards early in the project and use of an integrated team approach to design safety into the facility. This safety design strategy provides the basic safety-in-design principles and concepts that will be used for the Advanced Test Reactor Reliability Sustainment Project. While this project does not introduce new hazards to the ATR, it has the potential for significant impacts to safety-related systems, structures, and components that are credited in the ATR safety basis and are being replaced. Thus the project has been determined to meet the definition of a major modification and is being managed accordingly.

  5. Optimizing Oral Bioavailability in Drug Discovery: An Overview of Design and Testing Strategies and Formulation Options.

    Science.gov (United States)

    Aungst, Bruce J

    2017-04-01

    For discovery teams working toward new, orally administered therapeutic agents, one requirement is to attain adequate systemic exposure after oral dosing, which is best accomplished when oral bioavailability is optimized. This report summarizes the bioavailability challenges currently faced in drug discovery, and the design and testing methods and strategies currently utilized to address the challenges. Profiling of discovery compounds usually includes separate assessments of solubility, permeability, and susceptibility to first-pass metabolism, which are the 3 most likely contributors to incomplete oral bioavailability. An initial assessment of absorption potential may be made computationally, and high throughput in vitro assays are typically performed to prioritize compounds for in vivo studies. The initial pharmacokinetic study is a critical decision point in compound evaluation, and the importance of the effect the dosing vehicle or formulation can have on oral bioavailability, especially for poorly water soluble compounds, is emphasized. Dosing vehicles and bioavailability-enabling formulations that can be used for discovery and preclinical studies are described. Optimizing oral bioavailability within a chemical series or for a lead compound requires identification of the barrier limiting bioavailability, and methods used for this purpose are outlined. Finally, a few key guidelines are offered for consideration when facing the challenges of optimizing oral bioavailability in drug discovery. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

  6. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  7. Characterization of DNA repair phenotypes of Xeroderma pigmentosum cell lines by a paralleled in vitro test; Phenotypage de la reparation de l'ADN de lignees Xeroderma pigmentosum, par un test in vitro multiparametrique

    Energy Technology Data Exchange (ETDEWEB)

    Raffin, A.L.

    2009-06-15

    DNA is constantly damaged modifying the genetic information for which it encodes. Several cellular mechanisms as the Base Excision Repair (BER) and the Nucleotide Excision Repair (NER) allow recovering the right DNA sequence. The Xeroderma pigmentosum is a disease characterised by a deficiency in the NER pathway. The aim of this study was to propose an efficient and fast test for the diagnosis of this disease as an alternative to the currently available UDS test. DNA repair activities of XP cell lines were quantified using in vitro miniaturized and paralleled tests in order to establish DNA repair phenotypes of XPA and XPC deficient cells. The main advantage of the tests used in this study is the simultaneous measurement of excision or excision synthesis (ES) of several lesions by only one cellular extract. We showed on one hand that the relative ES of the different lesions depend strongly on the protein concentration of the nuclear extract tested. Working at high protein concentration allowed discriminating the XP phenotype versus the control one, whereas it was impossible under a certain concentration's threshold. On the other hand, while the UVB irradiation of control cells stimulated their repair activities, this effect was not observed in XP cells. This study brings new information on the XPA and XPC protein roles during BER and NER and underlines the complexity of the regulations of DNA repair processes. (author)

  8. Comparison of the clinical performance of an HPV mRNA test and an HPV DNA test in triage of atypical squamous cells of undetermined significance (ASC-US)

    DEFF Research Database (Denmark)

    Waldstrom, M; Ornskov, D

    2012-01-01

    The effect of triaging women with atypical squamous cells of undetermined significance (ASC-US) with human papillomavirus (HPV) DNA testing has been well documented. New tests detecting HPV E6/E7 mRNA are emerging, claiming to be more specific for detecting high-grade disease. We evaluated the cl...

  9. Efficient reading in standardized tests for EFL learners : a case study of reading strategies used by Chinese English major students in TEM-4

    OpenAIRE

    Xia, Yan

    2011-01-01

    The aim of this study is to investigate the reading strategies used by Chinese English major students in the reading component in standardized national tests of TEM-4 with regard to reading efficiency. The research questions include: 1) what strategies are used by the students in TEM-4 test context; 2) whether there is a significant correlation between strategy use and efficient reading in the test; 3) what kinds of reading problems are revealed in the students’ use of processing strategies; ...

  10. Development of an alternative testing strategy for the fish early life-stage (FELS) test using the AOP framework

    Science.gov (United States)

    Currently, the fish early life-stage (FELS) test (OECD 210) is the primary guideline used to estimate chronic toxicity of regulated chemicals. Although already more cost-efficient than adult fish tests, the FELS test has some important drawbacks. Both industry and regulatory inst...

  11. Ameliorative effect of riboflavin on hyperglycemia, oxidative stress and DNA damage in type-2 diabetic mice: Mechanistic and therapeutic strategies.

    Science.gov (United States)

    Alam, Md Maroof; Iqbal, Sarah; Naseem, Imrana

    2015-10-15

    Increasing evidence in both experimental and clinical studies suggests that oxidative stress play a major role in the pathogenesis of type-2 diabetes mellitus (T2DM). Abnormally high levels of free radicals and the simultaneous decline of antioxidant defence mechanisms can lead to damage of cellular organelles and enzymes. Riboflavin constitutes an essential nutrient for humans and is also an important food additive for animals. It is a precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which serves as a coenzyme for several enzymes. The aim of this study was to observe the effects of illuminated and non-illuminated riboflavin in a diabetic mice model. The protocol included treatment of diabetic mice with illuminated RF and a control set without light. To our surprise, group receiving RF without light gave better results in a dose dependent manner. Significant amelioration of oxidative stress was observed with an increased glucose uptake in skeletal muscles and white adipose tissue. Histological studies showed recovery in the liver and kidney tissue injury. Cellular DNA damage was also recovered. Therefore, it is suggested that supplementation with dietary riboflavin might help in the reduction of diabetic complications. A possible mechanism of action is also proposed. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. "I think we've got too many tests!": Prenatal providers' reflections on ethical and clinical challenges in the practice integration of cell-free DNA screening.

    Science.gov (United States)

    Gammon, B L; Kraft, S A; Michie, M; Allyse, M

    2016-01-01

    The recent introduction of cell-free DNA-based non-invasive prenatal screening (cfDNA screening) into clinical practice was expected to revolutionize prenatal testing. cfDNA screening for fetal aneuploidy has demonstrated higher test sensitivity and specificity for some conditions than conventional serum screening and can be conducted early in the pregnancy. However, it is not clear whether and how clinical practices are assimilating this new type of testing into their informed consent and counselling processes. Since the introduction of cfDNA screening into practice in 2011, the uptake and scope have increased dramatically. Prenatal care providers are under pressure to stay up to date with rapidly changing cfDNA screening panels, manage increasing patient demands, and keep up with changing test costs, all while attempting to use the technology responsibly and ethically. While clinical literature on cfDNA screening has shown benefits for specific patient populations, it has also identified significant misunderstandings among providers and patients alike about the power of the technology. The unique features of cfDNA screening, in comparison to established prenatal testing technologies, have implications for informed decision-making and genetic counselling that must be addressed to ensure ethical practice. This study explored the experiences of prenatal care providers at the forefront of non-invasive genetic screening in the United States to understand how this testing changes the practice of prenatal medicine. We aimed to learn how the experience of providing and offering this testing differs from established prenatal testing methodologies. These differences may necessitate changes to patient education and consent procedures to maintain ethical practice. We used the online American Congress of Obstetricians and Gynecologists Physician Directory to identify a systematic sample of five prenatal care providers in each U.S. state and the District of Columbia. Beginning

  13. Framework for Testing the Effectiveness of Bat and Eagle Impact-Reduction Strategies at Wind Energy Projects

    Energy Technology Data Exchange (ETDEWEB)

    Sinclair, Karin [National Renewable Energy Lab. (NREL), Golden, CO (United States); DeGeorge, Elise [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2016-04-13

    The objectives of this framework are to facilitate the study design and execution to test the effectiveness of bat and eagle impact-reduction strategies at wind energy sites. Through scientific field research, the wind industry and its partners can help determine if certain strategies are ready for operational deployment or require further development. This framework should be considered a living document to be improved upon as fatality-reduction technologies advance from the initial concepts to proven readiness (through project- and technology-specific testing) and as scientific field methods improve.

  14. Clinical experience of laboratory follow-up with noninvasive prenatal testing using cell-free DNA and positive microdeletion results in 349 cases.

    Science.gov (United States)

    Schwartz, S; Kohan, M; Pasion, R; Papenhausen, P R; Platt, L D

    2018-02-01

    Screening via noninvasive prenatal testing (NIPT) involving the analysis of cell-free DNA (cfDNA) from plasma has become readily available to screen for chromosomal and DNA aberrations through maternal blood. This report reviews a laboratory's experience with follow-up of positive NIPT screens for microdeletions. Patients that were screened positive by NIPT for a microdeletion involving 1p, 4p, 5p, 15q, or 22q who underwent diagnostic studies by either chorionic villus sampling or amniocentesis were evaluated. The overall positive predictive value for 349 patients was 9.2%. When a microdeletion was confirmed, 39.3% of the cases had additional abnormal microarray findings. Unrelated abnormal microarray findings were detected in 11.8% of the patients in whom the screen positive microdeletion was not confirmed. Stretches of homozygosity in the microdeletion were frequently associated with a false positive cfDNA microdeletion result. Overall, this report reveals that while cfDNA analysis will screen for microdeletions, the positive predictive value is low; in our series it is 9.2%. Therefore, the patient should be counseled accordingly. Confirmatory diagnostic microarray studies are imperative because of the high percentage of false positives and the frequent additional abnormalities not delineated by cfDNA analysis. © 2018 John Wiley & Sons, Ltd.

  15. Development of a microarray-based assay for efficient testing of new HSP70/DnaK inhibitors.

    Science.gov (United States)

    Mohammadi-Ostad-Kalayeh, Sona; Hrupins, Vjaceslavs; Helmsen, Sabine; Ahlbrecht, Christin; Stahl, Frank; Scheper, Thomas; Preller, Matthias; Surup, Frank; Stadler, Marc; Kirschning, Andreas; Zeilinger, Carsten

    2017-12-15

    A facile method for testing ATP binding in a highly miniaturized microarray environment using human HSP70 and DnaK from Mycobacterium tuberculosis as biological targets is reported. Supported by molecular modelling studies we demonstrate that the position of the fluorescence label on ATP has a strong influence on the binding to human HSP70. Importantly, the label has to be positioned on the adenine ring and not to the terminal phosphate group. Unlabelled ATP displaced bound Cy5-ATP from HSP70 in the micromolar range. The affinity of a well-known HSP70 inhibitor VER155008 for the ATP binding site in HSP70 was determined, with a EC 50 in the micromolar range, whereas reblastin, a HSP90-inhibitor, did not compete for ATP in the presence of HSP70. The applicability of the method was demonstrated by screening a small compound library of natural products. This unraveled that terphenyls rickenyl A and D, recently isolated from cultures of the fungus Hypoxylon rickii, are inhibitors of HSP70. They compete with ATP for the chaperone in the range of 29 µM (Rickenyl D) and 49 µM (Rickenyl A). Furthermore, the microarray-based test system enabled protein-protein interaction analysis using full-length HSP70 and HSP90 proteins. The labelled full-length human HSP90 binds with a half-maximal affinity of 5.5 µg/ml (∼40 µM) to HSP70. The data also demonstrate that the microarray test has potency for many applications from inhibitor screening to target-oriented interaction studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. An efficient cDNA-AFLP-based strategy for the identification of putative pathogenicity factors from the potato cyst nematode Globodera rostochiensis.

    Science.gov (United States)

    Qin, L; Overmars, H; Helder, J; Popeijus, H; van der Voort, J R; Groenink, W; van Koert, P; Schots, A; Bakker, J; Smant, G

    2000-08-01

    A new strategy has been designed to identify putative pathogenicity factors from the dorsal or subventral esophageal glands of the potato cyst nematode Globodera rostochiensis. Three independent criteria were used for selection. First, genes of interest should predominantly be expressed in infective second-stage juveniles, and not, or to a far lesser extent, in younger developmental stages. For this, gene expression profiles from five different developmental stages were generated with cDNA-AFLP (amplified fragment length polymorphism). Secondly, the mRNA corresponding to such a putative pathogenicity factor should predominantly be present in the esophageal glands of pre-parasitic juveniles. This was checked by in situ hybridization. As a third criterion, these proteinaceous factors should be preceded by a signal peptide for secretion. Expression profiles of more than 4,000 genes were generated and three up-regulated, dorsal gland-specific proteins preceded by signal peptide for secretion were identified. No dorsal gland genes have been cloned before from plant-parasitic nematodes. The partial sequence of these three factors, A4, A18, and A41, showed no significant homology to any known gene. Their presence in the dorsal glands of infective juveniles suggests that these proteins could be involved in feeding cell initiation, and not in migration in the plant root or in protection against plant defense responses. Finally, the applicability of this new strategy in other plant-microbe interactions is discussed.

  17. Frequency of intron loss correlates with processed pseudogene abundance: a novel strategy to test the reverse transcriptase model of intron loss.

    Science.gov (United States)

    Zhu, Tao; Niu, Deng-Ke

    2013-03-05

    Although intron loss in evolution has been described, the mechanism involved is still unclear. Three models have been proposed, the reverse transcriptase (RT) model, genomic deletion model and double-strand-break repair model. The RT model, also termed mRNA-mediated intron loss, suggests that cDNA molecules reverse transcribed from spliced mRNA recombine with genomic DNA causing intron loss. Many studies have attempted to test this model based on its predictions, such as simultaneous loss of adjacent introns, 3'-side bias of intron loss, and germline expression of intron-lost genes. Evidence either supporting or opposing the model has been reported. The mechanism of intron loss proposed in the RT model shares the process of reverse transcription with the formation of processed pseudogenes. If the RT model is correct, genes that have produced more processed pseudogenes are more likely to undergo intron loss. In the present study, we observed that the frequency of intron loss is correlated with processed pseudogene abundance by analyzing a new dataset of intron loss obtained in mice and rats. Furthermore, we found that mRNA molecules of intron-lost genes are mostly translated on free cytoplasmic ribosomes, a feature shared by mRNA molecules of the parental genes of processed pseudogenes and long interspersed elements. This feature is likely convenient for intron-lost gene mRNA molecules to be reverse transcribed. Analyses of adjacent intron loss, 3'-side bias of intron loss, and germline expression of intron-lost genes also support the RT model. Compared with previous evidence, the correlation between the abundance of processed pseudogenes and intron loss frequency more directly supports the RT model of intron loss. Exploring such a correlation is a new strategy to test the RT model in organisms with abundant processed pseudogenes.

  18. Recombinase polymerase and enzyme-linked immunosorbent assay as a DNA amplification-detection strategy for food analysis

    Energy Technology Data Exchange (ETDEWEB)

    Santiago-Felipe, S.; Tortajada-Genaro, L.A.; Puchades, R.; Maquieira, A., E-mail: amaquieira@qim.upv.es

    2014-02-06

    Graphical abstract: -- Highlights: •Recombinase polymerase amplification is a powerful DNA method operating at 40 °C. •The combination RPA–ELISA gives excellent performances for high-throughput analysis. •Screening of food safety threats has been done using standard laboratory equipment. •Allergens, GMOs, bacteria, and fungi have been successfully determined. -- Abstract: Polymerase chain reaction in conjunction with enzyme-linked immunosorbent assay (PCR–ELISA) is a well-established technique that provides a suitable rapid, sensitive, and selective method for a broad range of applications. However, the need for precise rapid temperature cycling of PCR is an important drawback that can be overcome by employing isothermal amplification reactions such as recombinase polymerase amplification (RPA). The RPA–ELISA combination is proposed for amplification at a low, constant temperature (40 °C) in a short time (40 min), for the hybridisation of labelled products to specific 5′-biotinylated probes/streptavidin in coated microtiter plates at room temperature, and for detection by colorimetric immunoassay. RPA–ELISA was applied to screen common safety threats in foodstuffs, such as allergens (hazelnut, peanut, soybean, tomato, and maize), genetically modified organisms (P35S and TNOS), pathogenic bacteria (Salmonella sp. and Cronobacter sp.), and fungi (Fusarium sp.). Satisfactory sensitivity and reproducibility results were achieved for all the targets. The RPA–ELISA technique does away with thermocycling and provides a suitable sensitive, specific, and cost-effective method for routine applications, and proves particularly useful for resource-limited settings.

  19. Recombinase polymerase and enzyme-linked immunosorbent assay as a DNA amplification-detection strategy for food analysis

    International Nuclear Information System (INIS)

    Santiago-Felipe, S.; Tortajada-Genaro, L.A.; Puchades, R.; Maquieira, A.

    2014-01-01

    Graphical abstract: -- Highlights: •Recombinase polymerase amplification is a powerful DNA method operating at 40 °C. •The combination RPA–ELISA gives excellent performances for high-throughput analysis. •Screening of food safety threats has been done using standard laboratory equipment. •Allergens, GMOs, bacteria, and fungi have been successfully determined. -- Abstract: Polymerase chain reaction in conjunction with enzyme-linked immunosorbent assay (PCR–ELISA) is a well-established technique that provides a suitable rapid, sensitive, and selective method for a broad range of applications. However, the need for precise rapid temperature cycling of PCR is an important drawback that can be overcome by employing isothermal amplification reactions such as recombinase polymerase amplification (RPA). The RPA–ELISA combination is proposed for amplification at a low, constant temperature (40 °C) in a short time (40 min), for the hybridisation of labelled products to specific 5′-biotinylated probes/streptavidin in coated microtiter plates at room temperature, and for detection by colorimetric immunoassay. RPA–ELISA was applied to screen common safety threats in foodstuffs, such as allergens (hazelnut, peanut, soybean, tomato, and maize), genetically modified organisms (P35S and TNOS), pathogenic bacteria (Salmonella sp. and Cronobacter sp.), and fungi (Fusarium sp.). Satisfactory sensitivity and reproducibility results were achieved for all the targets. The RPA–ELISA technique does away with thermocycling and provides a suitable sensitive, specific, and cost-effective method for routine applications, and proves particularly useful for resource-limited settings

  20. Susceptibility Testing by Polymerase Chain Reaction DNA Quantitation: A Method to Measure Drug Resistance of Human Immunodeficiency Virus Type 1 Isolates

    Science.gov (United States)

    Eron, Joseph J.; Gorczyca, Paul; Kaplan, Joan C.; D'Aquila, Richard T.

    1992-04-01

    Polymerase chain reaction (PCR) DNA quantitation (PDQ) susceptibility testing rapidly and directly measures nucleoside sensitivity of human immunodeficiency virus type 1 (HIV-1) isolates. PCR is used to quantitate the amount of HIV-1 DNA synthesized after in vitro infection of peripheral blood mononuclear cells. The relative amounts of HIV-1 DNA in cell lysates from cultures maintained at different drug concentrations reflect drug inhibition of virus replication. The results of PDQ susceptibility testing of 2- or 3-day cultures are supported by assays measuring HIV-1 p24 antigen production in supernatants of 7- or 10-day cultures. DNA sequence analyses to identify mutations in the reverse transcriptase gene that cause resistance to 3'-azido-3'-deoxythymidine also support the PDQ results. With the PDQ method, both infectivity titration and susceptibility testing can be performed on supernatants from primary cultures of peripheral blood mononuclear cells. PDQ susceptibility testing should facilitate epidemiologic studies of the clinical significance of drug-resistant HIV-1 isolates.

  1. Determination of alkylation of bacterial DNA as a rapid test for toxicological evaluation of alkylating xenobiotic agents

    Energy Technology Data Exchange (ETDEWEB)

    Botzenhart, K.; Waldner-Sander, S.; Schweinsberg, F.

    1986-05-01

    Alkylated purine bases from hydrolized DNA can be separated by HPLC and quantified with a fluorescence detector. We applied this method to bacterial DNA. 7-methylguanine was detected after treatment of Serratia marcescens with iodoacetamide, dimethyl sulfate and with polluted air.

  2. Closure Strategy Nevada Test Site Area 5 Radioactive Waste Management Site

    Energy Technology Data Exchange (ETDEWEB)

    NSTec Environmental Management

    2007-03-01

    This paper presents an overview of the strategy for closure of part of the Area 5 Radioactive Waste Management Site (RWMS) at the Nevada Test Site (NTS), which is about 65 miles northwest of Las Vegas, Nevada (Figure 1). The Area 5 RWMS is in the northern part of Frenchman Flat, approximately 14 miles north of Mercury. The Area 5 RWMS encompasses 732 acres subdivided into quadrants, and is bounded by a 1,000-foot (ft)-wide buffer zone. The northwest and southwest quadrants have not been developed. The northeast and southeast quadrants have been used for disposal of unclassified low-level radioactive waste (LLW) and indefinite storage of classified materials. This paper focuses on closure of the 38 waste disposal and classified material storage units within the southeast quadrant of the Area 5 RWMS, called the ''92-Acre Area''. The U.S Department of Energy (DOE), National Nuclear Security Administration Nevada Site Office (NNSA/NSO) is currently planning to close the 92-Acre Area by 2011. Closure planning for this site must take into account the regulatory requirements for a diversity of waste streams, disposal and storage configurations, disposal history, and site conditions. For ease of discussion, the 92-Acre Area has been subdivided into six closure units defined by waste type, location, and similarity in regulatory requirements. Each of the closure units contains one or more waste disposal units; waste disposal units are also called waste disposal cells. The paper provides a brief background of the Area 5 RWMS, identifies key closure issues for the 92-Acre Area, recommends actions to address the issues, and provides the National Security Technologies, LLC (NSTec), schedule for closure.

  3. Use of expert judgment in the development and evaluation of risk-based inservice testing strategies for pumps and valves

    Energy Technology Data Exchange (ETDEWEB)

    McAllister, W.J.; Perdue, R.K.; Balkey, K.R.; Closky, N.B. [and others

    1996-12-01

    This paper describes a rigorous approach for quantitatively evaluating inservice testing effectiveness that evolved from two pilot plant studies. These studies prototyped methodologies for designing and selecting inservice testing (IST) strategies in a manner structured to insure that the targeted components will perform their required safety functions while minimizing life cycle inservice testing costs. The paper concentrates on the use of expert judgment in developing test effectiveness measures that move risk-based methods beyond ranking to optimization of plant IST programs. Selected results for check valves and pumps are shown to illustrate the practical significance of the approach.

  4. Use of expert judgment in the development and evaluation of risk-based inservice testing strategies for pumps and valves

    International Nuclear Information System (INIS)

    McAllister, W.J.; Perdue, R.K.; Balkey, K.R.; Closky, N.B.

    1996-01-01

    This paper describes a rigorous approach for quantitatively evaluating inservice testing effectiveness that evolved from two pilot plant studies. These studies prototyped methodologies for designing and selecting inservice testing (IST) strategies in a manner structured to insure that the targeted components will perform their required safety functions while minimizing life cycle inservice testing costs. The paper concentrates on the use of expert judgment in developing test effectiveness measures that move risk-based methods beyond ranking to optimization of plant IST programs. Selected results for check valves and pumps are shown to illustrate the practical significance of the approach

  5. Sex differences in DNA methylation and expression in zebrafish brain: a test of an extended 'male sex drive' hypothesis.

    Science.gov (United States)

    Chatterjee, Aniruddha; Lagisz, Malgorzata; Rodger, Euan J; Zhen, Li; Stockwell, Peter A; Duncan, Elizabeth J; Horsfield, Julia A; Jeyakani, Justin; Mathavan, Sinnakaruppan; Ozaki, Yuichi; Nakagawa, Shinichi

    2016-09-30

    The sex drive hypothesis predicts that stronger selection on male traits has resulted in masculinization of the genome. Here we test whether such masculinizing effects can be detected at the level of the transcriptome and methylome in the adult zebrafish brain. Although methylation is globally similar, we identified 914 specific differentially methylated CpGs (DMCs) between males and females (435 were hypermethylated and 479 were hypomethylated in males compared to females). These DMCs were prevalent in gene body, intergenic regions and CpG island shores. We also discovered 15 distinct CpG clusters with striking sex-specific DNA methylation differences. In contrast, at transcriptome level, more female-biased genes than male-biased genes were expressed, giving little support for the male sex drive hypothesis. Our study provides genome-wide methylome and transcriptome assessment and sheds light on sex-specific epigenetic patterns and in zebrafish for the first time. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Sex differences in strategy and performance on computerized neuropsychological tests as related to gender identity and age at puberty.

    Science.gov (United States)

    Meurling, A W; Tonning-Olsson, I; Levander, S

    2000-06-01

    Neuropsychological sex differences have since long been under debate. Support for the relation between behavioral differences and biological variables like hormone influence is, however, emerging. Sixteen men and sixteen women, all university students, were tested with computerized neuropsychological tests (APT), the Bem Sexual Role Inventory, and asked about pubertal age. The results were in line with earlier findings of sex differences in neuropsychological tests, men being faster and women more cautious. The assumption that women tend to use left-hemispheric, verbal/serial strategies also in spatial tasks was also partly supported. In women, late onset of puberty was related to better spatial performance, and there were also more intercorrelations between verbal and spatial tests in the female than in the male group, indicating that women use less specific strategies (more g-factor intelligence) in problem solving, or that aptitudes are less compartmentalized in women than in men.

  7. Workshop on acceleration of the validation and regulatory acceptance of alternative methods and implementation of testing strategies

    DEFF Research Database (Denmark)

    Piersma, A. H.; Burgdorf, T.; Louekari, K.

    2018-01-01

    concerning the regulatory acceptance and implementation of alternative test methods and testing strategies, with the aim to develop feasible solutions. Classical validation of alternative methods usually involves one to one comparison with the gold standard animal study. This approach suffers from...... the reductionist nature of an alternative test as compared to the animal study as well as from the animal study being considered as the gold standard. Modern approaches combine individual alternatives into testing strategies, for which integrated and defined approaches are emerging at OECD. Furthermore, progress......-focused hazard and risk assessment of chemicals requires an open mind towards stepping away from the animal study as the gold standard and defining human biologically based regulatory requirements for human hazard and risk assessment....

  8. Alpha test results for a Housing First eLearning strategy: the value of multiple qualitative methods for intervention design.

    Science.gov (United States)

    Ahonen, Emily Q; Watson, Dennis P; Adams, Erin L; McGuire, Alan

    2017-01-01

    Detailed descriptions of implementation strategies are lacking, and there is a corresponding dearth of information regarding methods employed in implementation strategy development. This paper describes methods and findings related to the alpha testing of eLearning modules developed as part of the Housing First Technical Assistance and Training (HFTAT) program's development. Alpha testing is an approach for improving the quality of a product prior to beta (i.e., real world) testing with potential applications for intervention development. Ten participants in two cities tested the modules. We collected data through (1) a structured log where participants were asked to record their experiences as they worked through the modules; (2) a brief online questionnaire delivered at the end of each module; and (3) focus groups. The alpha test provided useful data related to the acceptability and feasibility of eLearning as an implementation strategy, as well as identifying a number of technical issues and bugs. Each of the qualitative methods used provided unique and valuable information. In particular, logs were the most useful for identifying technical issues, and focus groups provided high quality data regarding how the intervention could best be used as an implementation strategy. Alpha testing was a valuable step in intervention development, providing us an understanding of issues that would have been more difficult to address at a later stage of the study. As a result, we were able to improve the modules prior to pilot testing of the entire HFTAT. Researchers wishing to alpha test interventions prior to piloting should balance the unique benefits of different data collection approaches with the need to minimize burdens for themselves and participants.

  9. Case study of the United States Marine Corps Advanced Amphibious Assault Vehicle (AAAV) program test and evaluation strategy

    OpenAIRE

    Buckles, Brian K.

    1999-01-01

    This thesis examined the evolution of the Direct Reporting Program Manager- Advanced Amphibious Assault's test and evaluation strategy from Milestone 0 to the present. The research effort involved reviewing the evolution of amphibious doctrine and amphibious vehicles, reviewing the DoD Acquisition Process and the role of T&E in that Acquisition Process, and analyzing three DRPM-AAA Test and Evaluation Master Plans. Interviews were conducted with personnel from the DRPM-AAA office and General ...

  10. Strategies for Solving Potential Problems Associated with Laboratory Diffusion and Batch Experiments - Part 1: An Overview of Conventional Test Methods

    International Nuclear Information System (INIS)

    Zhang, M.; Takeda, M.; Nakajima, H.

    2006-01-01

    Laboratory diffusion testing as well as batch experiments are well established and widely adopted techniques for characterizing the diffusive and adsorptive properties of geological, geotechnical, and synthetic materials in both scientific and applied fields, including geological disposal of radioactive waste. Although several types of diffusion test, such as the through- diffusion test, in-diffusion test, out-diffusion test, and column test, are currently available, different methods may have different advantages and disadvantages. In addition, traditional methods may have limitations, such as the need for relatively long test times, cumbersome test procedures, and the possibility of errors due to differences between analytical assumptions and actual test conditions. Furthermore, traditional batch experiments using mineral powders are known to overestimate the sorption coefficient. In part 1 of this report, we present a brief overview of laboratory diffusion and batch experiments. The advantages, disadvantages, limitations, and/or potential problems associated with individual tests were compared and summarized. This comprehensive report will provide practical references for reviewing the results obtained from relevant experiments, especially from the viewpoint of regulation. To solve and/or eliminate the potential problems associated with conventional methods, and to obtain the diffusion coefficient and rock capacity factor from a laboratory test both rapidly and accurately, part 2 of this study discusses possible strategies involving the development of rigorous solutions to some relevant test methods, and sensitivity analyses for the related tests that may be helpful to judge the accuracy of the two parameters to be determined from individual tests. (authors)

  11. Testing efficacy of distance and tree-based methods for DNA barcoding of grasses (Poaceae tribe Poeae) in Australia.

    Science.gov (United States)

    Birch, Joanne L; Walsh, Neville G; Cantrill, David J; Holmes, Gareth D; Murphy, Daniel J

    2017-01-01

    In Australia, Poaceae tribe Poeae are represented by 19 genera and 99 species, including economically and environmentally important native and introduced pasture grasses [e.g. Poa (Tussock-grasses) and Lolium (Ryegrasses)]. We used this tribe, which are well characterised in regards to morphological diversity and evolutionary relationships, to test the efficacy of DNA barcoding methods. A reference library was generated that included 93.9% of species in Australia (408 individuals, [Formula: see text] = 3.7 individuals per species). Molecular data were generated for official plant barcoding markers (rbcL, matK) and the nuclear ribosomal internal transcribed spacer (ITS) region. We investigated accuracy of specimen identifications using distance- (nearest neighbour, best-close match, and threshold identification) and tree-based (maximum likelihood, Bayesian inference) methods and applied species discovery methods (automatic barcode gap discovery, Poisson tree processes) based on molecular data to assess congruence with recognised species. Across all methods, success rate for specimen identification of genera was high (87.5-99.5%) and of species was low (25.6-44.6%). Distance- and tree-based methods were equally ineffective in providing accurate identifications for specimens to species rank (26.1-44.6% and 25.6-31.3%, respectively). The ITS marker achieved the highest success rate for specimen identification at both generic and species ranks across the majority of methods. For distance-based analyses the best-close match method provided the greatest accuracy for identification of individuals with a high percentage of "correct" (97.6%) and a low percentage of "incorrect" (0.3%) generic identifications, based on the ITS marker. For tribe Poeae, and likely for other grass lineages, sequence data in the standard DNA barcode markers are not variable enough for accurate identification of specimens to species rank. For recently diverged grass species similar challenges are

  12. Impact of Heterogeneity in Sexual Behavior on Effectiveness in Reducing HIV Transmission with Test-and-Treat Strategy

    NARCIS (Netherlands)

    Rozhnova, Ganna; Schim van der Loeff, Maarten F.; Heijne, Janneke C. M.; Kretzschmar, Mirjam E.

    2016-01-01

    The WHO's early-release guideline for antiretroviral treatment (ART) of HIV infection based on a recent trial conducted in 34 countries recommends starting treatment immediately upon an HIV diagnosis. Therefore, the test-and-treat strategy may become more widely used in an effort to scale up HIV

  13. Opportunities and Strategies for Testing and Infusion of ISRU in the Evolvable Mars Campaign

    Science.gov (United States)

    Mueller, Robert P.; Sibille, Laurent; Mantovani, James; Sanders, Gerald B.; Jones, Christopher A.

    2015-01-01

    HE Evolvable Mars Campaign (EMC) is developing the plans and systems needed for a robust, evolutionary strategy to explore cis-lunar space, the Mars sphere of influence (including the moons of Mars), and the surface of Mars. Recently, the emphasis of NASA's plans has changed to focus on the prolonged pioneering of space, rather than focusing on a single crewed mission as the ultimate goal. A sustainable, pioneering vision of space would include in-situ resource utilization (ISRU) in multiple forms and at multiple destinations: atmospheric capture of Mars CO2 and/or volatiles for consumables and propellants, regolith for bulk and refined materials, and in-situ manufacturing at the Moon, Mars, and other bodies. These resources would enable a reduction in the logistical needs from Earth for future missions, thus preparing the way for a sustained presence on Mars. Although the EMC initially relies only on propellant production for the Mars ascent vehicle via ISRU, one of its primary objectives is to prospect at every EMC destination to understand the potential for ISRU; this will permit true pioneering to be enabled after the first crew arrives at Mars. Recent and ongoing analysis has considered the possible prospecting measurements that can be performed at the asteroid returned to cis-lunar space by the Asteroid Robotic Redirect Mission (ARRM), at the lunar surface, at Phobos and Deimos, and on the surface of Mars to identify available resources for future use. These opportunities will be available on missions currently in the Evolvable Mars Campaign construct, and will also facilitate the testing and demonstration of resource acquisition, processing, storage, and useage technologies that can play a role in later missions. This analysis has also led to the identification of several objectives that should be targeted during the missions building up to and including the initial crewed missions. These objectives are mapped to strategies for incorporating ISRU to support

  14. DNA typing for personal identification of urine after long-term preservation for testing in doping control.

    Science.gov (United States)

    Aoki, Kimiko; Tanaka, Hiroyuki; Ueki, Makoto

    2017-08-01

    When the tampering of a urine sample is suspected in doping control, personal identification of the sample needs to be determined by short tandem repeat (STR) analysis using DNA. We established a method for extracting DNA from urine samples stored at -20 °C without using any additives or procedures, which is consistent with how samples are required to be managed for doping control. The method, using the Puregene® Blood Core kit followed by NucleoSpin® gDNA Clean-up or NucleoSpin® gDNA Clean-up XS kit, does not need any special instrument and can provide a purified extract with high-quality DNA from up to 40 mL of urine suitable for STR analysis using an AmpFlSTR® Identifiler® PCR amplification kit. Storing urine at -20 °C is detrimental to the stability of DNA. The DNA concentration of preserved urine could not be predicted by specific gravity or creatinine level at the time of urine collection. The DNA concentration of a purified extract (10 μL) was required to be >0.06 ng/μL to ensure a successful STR analysis. Thus, the required extraction volumes of urine preserved for 3-7 years at -20 °C were estimated to be 30 mL and 20 mL to succeed in at least 86% of men and 91% of women, respectively. Considering the long half-life of DNA during long-term preservation, our extraction method is applicable to urine samples stored even for 10 years, which is currently the storage duration allowed (increased from 8 years) before re-examination in doping control. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  15. Testing for strategy-structure fit and its importance for performance

    Directory of Open Access Journals (Sweden)

    Ana Aleksić

    2017-01-01

    Full Text Available Understanding different organizational elements, their mutual influence and creating congruence among them has been recognized as an important determinant of organizational performance. These complex interrelationships, and necessity of creating a fit between them, raises the question of how to align different organizational elements to contribute to overall organizational performance. In that sense, this paper addresses the issue of fit and, more specifically, analyses the presence and influence of strategy-structure fit on organizational performance. By using Miles and Snow typology, our goal was to capture and determine the pattern of relationships between strategy, structure, and strategy implementation processes and their influence on organizational performance. This paper presents results of a cross-sectional field research on a sample of 113 organizations in order to gain a better understanding of strategy-structure fit and its relation to performance. Results reinforce the existing literature and confirm the importance of fit among strategy, structure and strategy implementation process for higher levels of organizational performance.

  16. Targeting the PD-1/PD-L1 Immune Evasion Axis With DNA Aptamers as a Novel Therapeutic Strategy for the Treatment of Disseminated Cancers.

    Science.gov (United States)

    Prodeus, Aaron; Abdul-Wahid, Aws; Fischer, Nicholas W; Huang, Eric H-B; Cydzik, Marzena; Gariépy, Jean

    2015-04-28

    Blocking the immunoinhibitory PD-1:PD-L1 pathway using monoclonal antibodies has led to dramatic clinical responses by reversing tumor immune evasion and provoking robust and durable antitumor responses. Anti-PD-1 antibodies have now been approved for the treatment of melanoma, and are being clinically tested in a number of other tumor types as both a monotherapy and as part of combination regimens. Here, we report the development of DNA aptamers as synthetic, nonimmunogenic antibody mimics, which bind specifically to the murine extracellular domain of PD-1 and block the PD-1:PD-L1 interaction. One such aptamer, MP7, functionally inhibits the PD-L1-mediated suppression of IL-2 secretion in primary T-cells. A PEGylated form of MP7 retains the ability to block the PD-1:PD-L1 interaction, and significantly suppresses the growth of PD-L1+ colon carcinoma cells in vivo with a potency equivalent to an antagonistic anti-PD-1 antibody. Importantly, the anti-PD-1 DNA aptamer treatment was not associated with off-target TLR-9-related immune responses. Due to the inherent advantages of aptamers including their lack of immunogenicity, low cost, long shelf life, and ease of synthesis, PD-1 antagonistic aptamers may represent an attractive alternative over antibody-based anti PD-1 therapeutics.

  17. Targeting the PD-1/PD-L1 Immune Evasion Axis With DNA Aptamers as a Novel Therapeutic Strategy for the Treatment of Disseminated Cancers

    Directory of Open Access Journals (Sweden)

    Aaron Prodeus

    2015-01-01

    Full Text Available Blocking the immunoinhibitory PD-1:PD-L1 pathway using monoclonal antibodies has led to dramatic clinical responses by reversing tumor immune evasion and provoking robust and durable antitumor responses. Anti-PD-1 antibodies have now been approved for the treatment of melanoma, and are being clinically tested in a number of other tumor types as both a monotherapy and as part of combination regimens. Here, we report the development of DNA aptamers as synthetic, nonimmunogenic antibody mimics, which bind specifically to the murine extracellular domain of PD-1 and block the PD-1:PD-L1 interaction. One such aptamer, MP7, functionally inhibits the PD-L1-mediated suppression of IL-2 secretion in primary T-cells. A PEGylated form of MP7 retains the ability to block the PD-1:PD-L1 interaction, and significantly suppresses the growth of PD-L1+ colon carcinoma cells in vivo with a potency equivalent to an antagonistic anti-PD-1 antibody. Importantly, the anti-PD-1 DNA aptamer treatment was not associated with off-target TLR-9-related immune responses. Due to the inherent advantages of aptamers including their lack of immunogenicity, low cost, long shelf life, and ease of synthesis, PD-1 antagonistic aptamers may represent an attractive alternative over antibody-based anti PD-1 therapeutics.

  18. Testing the efficiency of rover science protocols for robotic sample selection: A GeoHeuristic Operational Strategies Test

    Science.gov (United States)

    Yingst, R. A.; Bartley, J. K.; Chidsey, T. C.; Cohen, B. A.; Gilleaudeau, G. J.; Hynek, B. M.; Kah, L. C.; Minitti, M. E.; Williams, R. M. E.; Black, S.; Gemperline, J.; Schaufler, R.; Thomas, R. J.

    2018-05-01

    The GHOST field tests are designed to isolate and test science-driven rover operations protocols, to determine best practices. During a recent field test at a potential Mars 2020 landing site analog, we tested two Mars Science Laboratory data-acquisition and decision-making methods to assess resulting science return and sample quality: a linear method, where sites of interest are studied in the order encountered, and a "walkabout-first" method, where sites of interest are examined remotely before down-selecting to a subset of sites that are interrogated with more resource-intensive instruments. The walkabout method cost less time and fewer resources, while increasing confidence in interpretations. Contextual data critical to evaluating site geology was acquired earlier than for the linear method, and given a higher priority, which resulted in development of more mature hypotheses earlier in the analysis process. Combined, this saved time and energy in the collection of data with more limited spatial coverage. Based on these results, we suggest that the walkabout method be used where doing so would provide early context and time for the science team to develop hypotheses-critical tests; and that in gathering context, coverage may be more important than higher resolution.

  19. A strategy for determination of test intervals of k-out-of-n multi-channel systems

    International Nuclear Information System (INIS)

    Cho, S.; Jiang, J.

    2007-01-01

    State space models for determination of the optimal test frequencies for k-out-of-n multi channel systems are developed in this paper. The analytic solutions for the optimal surveillance test frequencies are derived using the Markov process technique. The solutions show that an optimal test frequency which maximizes the target probability can be determined by decomposing the system states to 3 states based on the system configuration and success criteria. Examples of quantification of the state probabilities and the optimal test frequencies of a three-channel system and a four-channel system with different success criteria are presented. The strategy for finding the optimal test frequency developed in this paper can generally be applicable to any k-out-of-n multi-channel standby systems that involve complex testing schemes. (author)

  20. Damaging the Integrated HIV Proviral DNA with TALENs.

    Directory of Open Access Journals (Sweden)

    Christy L Strong

    Full Text Available HIV-1 integrates its proviral DNA genome into the host genome, presenting barriers for virus eradication. Several new gene-editing technologies have emerged that could potentially be used to damage integrated proviral DNA. In this study, we use transcription activator-like effector nucleases (TALENs to target a highly conserved sequence in the transactivation response element (TAR of the HIV-1 proviral DNA. We demonstrated that TALENs cleave a DNA template with the HIV-1 proviral target site in vitro. A GFP reporter, under control of HIV-1 TAR, was efficiently inactivated by mutations introduced by transfection of TALEN plasmids. When infected cells containing the full-length integrated HIV-1 proviral DNA were transfected with TALENs, the TAR region accumulated indels. When one of these mutants was tested, the mutated HIV-1 proviral DNA was incapable of producing detectable Gag expression. TALEN variants engineered for degenerate recognition of select nucleotide positions also cleaved proviral DNA in vitro and the full-length integrated proviral DNA genome in living cells. These results suggest a possible design strategy for the therapeutic considerations of incomplete target sequence conservation and acquired resistance mutations. We have established a new strategy for damaging integrated HIV proviral DNA that may have future potential for HIV-1 proviral DNA eradication.

  1. The use of novel DNA nanotracers to determine groundwater flow paths - a test study at the Grimsel Deep Underground Geothermal (DUG) Laboratory in Switzerland

    Science.gov (United States)

    Kittilä, Anniina; Evans, Keith; Puddu, Michela; Mikutis, Gediminas; Grass, Robert N.; Deuber, Claudia; Saar, Martin O.

    2016-04-01

    Groundwater flow in fractured media is heterogeneous and takes place in structures with complex geometry and scale effects, which make the characterization and modeling of the groundwater flow technically challenging. Surface geophysical surveys have limited resolution of permeable structures, and often provide ambiguous results, whereas the interpretation of borehole flow logs to infer hydraulic flow paths within fractured reservoirs is usually non-unique. Nonetheless, knowledge of the hydraulic properties of individual fractures and the role they play in determining the larger-scale flow within the fracture network (i.e. the overall flow conditions) is required in many hydrogeological and geo-engineering situations, such as in geothermal reservoir studies. Tracer tests can overcome some of the aforementioned limitations by providing strong constraints on the geometry and characteristics of flow paths linking boreholes within both porous media and fracture-dominated types of reservoirs. In the case of geothermal reservoirs, tracer tests are often used to provide estimates of the pore/fracture volume swept by flow between injection and production wells. This in turn places constraints on the swept surface area, a parameter that is key for estimating the commercial longevity of the geothermal system. A problem with conventional tracer tests is that the solute species used as the tracer tend to persist in detectable quantities within the reservoir for a long time, thereby impeding repeat tracer tests. DNA nanotracers do not suffer from this problem as they can be designed with a unique signature for each test. DNA nanotracers are environmentally friendly, sub-micron sized silica particles encapsulating small fragments of synthetic DNA which can be fabricated to have a specified, uniquely detectable configuration. For this reason, repeat tracer tests conducted with a differently-encoded DNA fragment to that used in the original will not suffer interference from the

  2. Advanced purification strategy for CueR, a cysteine containing copper(I) and DNA binding protein

    DEFF Research Database (Denmark)

    Balogh, Ria K.; Gyurcsik, Béla; Hunyadi-Gulyás, Éva

    2016-01-01

    . A detailed understanding of their function may be exploited in potential health, environmental and analytical applications. Members of the MerR protein family sense a broad range of mostly late transition and heavy metal ions through their cysteine thiolates. The air sensitivity of latter groups makes...... the expression and purification of such proteins challenging. Here we describe a method for the purification of the copper-regulatory CueR protein under optimized conditions. In order to avoid protein precipitation and/or eventual aggregation and to get rid of the co-purifying Escherichia coli elongation factor...... any affinity tag. Structure and functionality tests performed with mass spectrometry, circular dichroism spectroscopy and electrophoretic gel mobility shift assays approved the success of the purification procedure....

  3. Cervical human papilloma virus (HPV) DNA primary screening test: Results of a population-based screening programme in central Italy.

    Science.gov (United States)

    Passamonti, Basilio; Gustinucci, Daniela; Giorgi Rossi, Paolo; Cesarini, Elena; Bulletti, Simonetta; Carlani, Angela; Martinelli, Nadia; Broccolini, Massimo; D'Angelo, Valentina; D'Amico, Maria Rosaria; Di Dato, Eugenio; Galeazzi, Paola; Malaspina, Morena; Spita, Nicoletta; Tintori, Beatrice; Giaimo, Maria Donata

    2017-09-01

    Objective To present the results of the first and second round human papilloma virus (HPV)-based screening programme in the Umbria region after three years. Methods From August 2010 to November 2011, the entire female population aged 35-64 in a local health district was invited for HPV testing (HPV-DNA cobas4800 on a liquid-based cytology sample). HPV-negative women were re-invited after three years. For HPV-positive women, a slide was prepared and interpreted. Positive cytologies were referred to colposcopy; negatives were referred to repeat HPV after one year. If HPV was persistently positive, women were referred to colposcopy; if negative, to normal screening. Indicators of the first and second round are compared with those of cytology screening in the same area in the preceding three years. Results Participation was 56.5%, the same as cytology (56.6%). HPV-positivity was 6.4% (396/6272), cytology triage positivity was 35.6%; 251 cytology negative women were referred to one-year HPV retesting, 84.1% complied, and 55.5% were positive. Total colposcopy referral was 4.1%, and for cytology 1%. The detection rate for cervical intraepithelial neoplasia grade 2 or more severe was 10‰, compared with 3.7‰ using cytology. After three years, HPV-positivity was 3.4% (129/3831), overall colposcopy referral was 2.3% (most at one-year follow-up), and detection rate was 0.5/1000. Conclusions The first round detection rate was more than twice that of cytology screening, while colposcopy referral increased fourfold. At the second round, the detection rate decreased dramatically, showing that longer interval and more conservative protocols are needed.

  4. PRACCIS: a didactic strategy based on hermeneutic for knowledge circulation or about a pilot test

    International Nuclear Information System (INIS)

    Gonzalez Agudelo, Elvia Maria; Aguirre Ramirez, Nestor Jaime; Grisales Franco, Lina Maria; Giraldo Mejia, Gloria Eugenia; Villabona, Silvia Lucia; Uribe Rozo, Erika Gissell; Velasquez, Diana

    2012-01-01

    This article shows how to apply the teaching strategy called PRACCIS through an educational booklet entitled Zooplankton Ayapel Swamp and its role in the ecology of this ecosystem as a product of the research entitled Spatial and temporal dynamics of Zooplankton associated with macrophyte in the wetland complex Ayapel, Cordoba; Colombia. Implementation of this strategy was envelopment as a pilot where the information was collected through various texts, namely: two field journals, five cards completed applications, 52 surveys processed by the non-scientific community and a conversation with the coordinator the workshop. These texts are read from a hermeneutic perspective, where from prejudice, are reflected, analyzed, compared, understood and interpreted, the situations and the occurrences of the event participants to find meaning units on course to achieve unity sense, ie, to endorse the teaching strategy to facilitate the movement of scientific knowledge in non-scientific communities and be able to generate culture, in this case, around the object water

  5. Cost analysis of a novel HIV testing strategy in community pharmacies and retail clinics.

    Science.gov (United States)

    Lecher, Shirley Lee; Shrestha, Ram K; Botts, Linda W; Alvarez, Jorge; Moore, James H; Thomas, Vasavi; Weidle, Paul J

    2015-01-01

    To document the cost of implementing point-of-care (POC) human immunodeficiency virus (HIV) rapid testing in busy community pharmacies and retail clinics. Providing HIV testing services in community pharmacies and retail clinics is an innovative way to expand HIV testing. The cost of implementing POC HIV rapid testing in a busy retail environment needs to be documented to provide program and policy leaders with adequate information for planning and budgeting. Cost analysis from a pilot project that provided confidential POC HIV rapid testing services in community pharmacies and retail clinics. The pharmacy sites were operated under several different ownership structures (for-profit, nonprofit, sole proprietorship, corporation, public, and private) in urban and rural areas. We included data from the initial six sites that participated in the project. We collected the time spent by pharmacy and retail clinic staff for pretest and posttest counseling in an activity log for time-in-motion for each interaction. Pharmacists and retail clinic staff. HIV rapid testing. The total cost was calculated to include costs of test kits, control kits, shipping, test supplies, training, reporting, program administration, and advertising. The six sites trained 22 staff to implement HIV testing. A total of 939 HIV rapid tests were conducted over a median time of 12 months, of which 17 were reactive. Median pretest counseling time was 2 minutes. Median posttest counseling time was 2 minutes for clients with a nonreactive test and 10 minutes for clients with a reactive test. The average cost per person tested was an estimated $47.21. When we considered only recurrent costs, the average cost per person tested was $32.17. Providing POC HIV rapid testing services required a modest amount of staff time and costs that are comparable to other services offered in these settings. HIV testing in pharmacies and retail clinics can provide an additional alternative venue for increasing the

  6. A music quality rating test battery for cochlear implant users to compare the FSP and HDCIS strategies for music appreciation.

    Science.gov (United States)

    Looi, Valerie; Winter, Philip; Anderson, Ilona; Sucher, Catherine

    2011-08-01

    The purpose of this study was to develop a music quality rating test battery (MQRTB) and pilot test it by comparing appraisal ratings from cochlear implant (CI) recipients using the fine-structure processing (FSP) and high-definition continuous interleaved sampling (HDCIS) speech processing strategies. The development of the MQRTB involved three stages: (1) Selection of test items for the MQRTB; (2) Verification of its length and complexity with normally-hearing individuals; and (3) Pilot testing with CI recipients. Part 1 involved 65 adult listeners, Part 2 involved 10 normally-hearing adults, and Part 3 involved five adult MED-EL CI recipients. The MQRTB consisted of ten songs, with ratings made on scales assessing pleasantness, naturalness, richness, fullness, sharpness, and roughness. Results of the pilot study, which compared FSP and HDCIS for music, indicated that acclimatization to a strategy had a significant effect on ratings (p genre on ratings. Overall the results suggest that the use of FSP as the default strategy for MED-EL recipients would have a positive effect on music appreciation, and that the MQRTB is an effective tool for assessing music sound quality.

  7. LLNA variability: An essential ingredient for a comprehensive assessment of non-animal skin sensitization test methods and strategies.

    Science.gov (United States)

    Hoffmann, Sebastian

    2015-01-01

    The development of non-animal skin sensitization test methods and strategies is quickly progressing. Either individually or in combination, the predictive capacity is usually described in comparison to local lymph node assay (LLNA) results. In this process the important lesson from other endpoints, such as skin or eye irritation, to account for variability reference test results - here the LLNA - has not yet been fully acknowledged. In order to provide assessors as well as method and strategy developers with appropriate estimates, we investigated the variability of EC3 values from repeated substance testing using the publicly available NICEATM (NTP Interagency Center for the Evaluation of Alternative Toxicological Methods) LLNA database. Repeat experiments for more than 60 substances were analyzed - once taking the vehicle into account and once combining data over all vehicles. In general, variability was higher when different vehicles were used. In terms of skin sensitization potential, i.e., discriminating sensitizer from non-sensitizers, the false positive rate ranged from 14-20%, while the false negative rate was 4-5%. In terms of skin sensitization potency, the rate to assign a substance to the next higher or next lower potency class was approx.10-15%. In addition, general estimates for EC3 variability are provided that can be used for modelling purposes. With our analysis we stress the importance of considering the LLNA variability in the assessment of skin sensitization test methods and strategies and provide estimates thereof.

  8. Alkali content of fly ash : measuring and testing strategies for compliance : [tech transfer summary].

    Science.gov (United States)

    2015-04-01

    This study investigated the test methods used to determine the : alkali content of fly ash. It also evaluated if high-alkali fly ash : exacerbates alkali-silica reaction in laboratory tests and field : concrete.

  9. Acceptability of self-collection sampling for HPV-DNA testing in low-resource settings: a mixed methods approach.

    Science.gov (United States)

    Bansil, Pooja; Wittet, Scott; Lim, Jeanette L; Winkler, Jennifer L; Paul, Proma; Jeronimo, Jose

    2014-06-12

    Vaginal self-sampling with HPV-DNA tests is a promising primary screening method for cervical cancer. However, women's experiences, concerns and the acceptability of such tests in low-resource settings remain unknown. In India, Nicaragua, and Uganda, a mixed-method design was used to collect data from surveys (N = 3,863), qualitative interviews (N = 72; 20 providers and 52 women) and focus groups (N = 30 women) on women's and providers' experiences with self-sampling, women's opinions of sampling at home, and their future needs. Among surveyed women, 90% provided a self- collected sample. Of these, 75% reported it was easy, although 52% were initially concerned about hurting themselves and 24% were worried about not getting a good sample. Most surveyed women preferred self-sampling (78%). However it was not clear if they responded to the privacy of self-sampling or the convenience of avoiding a pelvic examination, or both. In follow-up interviews, most women reported that they didn't mind self-sampling, but many preferred to have a provider collect the vaginal sample. Most women also preferred clinic-based screening (as opposed to home-based self-sampling), because the sample could be collected by a provider, women could receive treatment if needed, and the clinic was sanitary and provided privacy. Self-sampling acceptability was higher when providers prepared women through education, allowed women to examine the collection brush, and were present during the self-collection process. Among survey respondents, aids that would facilitate self-sampling in the future were: staff help (53%), additional images in the illustrated instructions (31%), and a chance to practice beforehand with a doll/model (26%). Self-and vaginal-sampling are widely acceptable among women in low-resource settings. Providers have a unique opportunity to educate and prepare women for self-sampling and be flexible in accommodating women's preference for self-sampling.

  10. Counselor Hypothesis Testing Strategies: The Role of Initial Impressions and Self-Schema.

    Science.gov (United States)

    Strohmer, Douglas C.; Chiodo, Anthony L.

    1984-01-01

    Presents two experiments concerning confirmatory bias in the way counselors collect data to test their hypotheses. Counselors were asked either to develop their own clinical hypothesis or were given a hypothesis to test. Confirmatory bias in hypothesis testing was not supported in either experiment. (JAC)

  11. Is testing a more effective learning strategy than note-taking?

    Science.gov (United States)

    Rummer, Ralf; Schweppe, Judith; Gerst, Kathleen; Wagner, Simon

    2017-09-01

    The testing effect is both robust and generalizable. However, most of the underlying studies compare testing to a rather ineffective control condition: massed repeated reading. This article therefore compares testing with note-taking, which has been shown to be more effective than repeated reading. Experiment 1 is based on a 3 × 3 between-participants design with the factors learning condition (repeated reading vs. repeated testing vs. repeated note-taking) and final test delay (5 min vs. 1 week vs. 2 weeks). It shows that in the immediate condition, learning performance is best after note-taking. After 1 week, both the note-taking and the testing groups outperform the rereading group, and after 2 weeks, testing is superior to both note-taking and rereading. Since repeated notetaking may not be the most effective (and common) operationalization of note-taking, Experiment 2 contrasts repeated testing with 2 other note-taking conditions: note-taking plus note-reading and note-taking plus testing (with only a 2-week final test delay). Both conditions that include a testing phase result in better long-term learning than note-taking plus note-reading. In summary, our findings indicate that-in the long run-testing is a powerful learning tool both in isolation and in combination with note-taking. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  12. Implementation challenges for designing integrated in vitro testing strategies (ITS) aiming at reducing and replacing animal experimentation.

    Science.gov (United States)

    De Wever, Bart; Fuchs, Horst W; Gaca, Marianna; Krul, Cyrille; Mikulowski, Stan; Poth, Albrecht; Roggen, Erwin L; Vilà, Maya R

    2012-04-01

    At the IVTIP (in vitro testing industrial platform) meeting of November 26th 2009 entitled 'Toxicology in the 21st century ('21C')--working our way towards a visionary reality' all delegates endorsed the emerging concept of the '21C' vision as the way forward to enable a thorough, reliable and systematic approach to future toxicity testing without the use of animals. One of the emerging concepts focused on integrating a defined number of tests modelling in vivo-relevant and well-characterised toxicity pathways representing mechanistic endpoints. At this meeting the importance of Integrated Testing Strategies (ITS) as tools towards reduction and eventually replacement of the animals currently used for hazard identification and risk assessment was recognised. A follow-up IVTIP Spring 2010 meeting entitled 'Integrated In Vitro Testing Strategies (ITS)--Implementation Challenges' was organised to address pending questions about ITS. This report is not a review of the ITS literature, but a summary of the discussions triggered by presented examples on how to develop and implement ITS. Contrasts between pharmaceutical and chemical industry, as well as a list of general but practical aspects to be considered while developing an ITS emerged from the discussions. In addition, current recommendations on the validation of ITS were discussed. In conclusion, the outcome of this workshop improved the understanding of the participants of some important factors that may impact the design of an ITS in function of its purpose (e.g., screening, or early decision making versus regulatory), the context in which they need to be applied (e.g., ICH guidelines, REACH) and the status and quality of the available tools. A set of recommendations of best practices was established and the importance of the applicability of the individual tests as well as the testing strategy itself was highlighted. Copyright © 2012 Elsevier Ltd. All rights reserved.

  13. Free Recall Test Experience Potentiates Strategy-Driven Effects of Value on Memory

    Science.gov (United States)

    Cohen, Michael S.; Rissman, Jesse; Hovhannisyan, Mariam; Castel, Alan D.; Knowlton, Barbara J.

    2017-01-01

    People tend to show better memory for information that is deemed valuable or important. By one mechanism, individuals selectively engage deeper, semantic encoding strategies for high value items (Cohen, Rissman, Suthana, Castel, & Knowlton, 2014). By another mechanism, information paired with value or reward is automatically strengthened in…

  14. Strategies for Testing Statistical and Practical Significance in Detecting DIF with Logistic Regression Models

    Science.gov (United States)

    Fidalgo, Angel M.; Alavi, Seyed Mohammad; Amirian, Seyed Mohammad Reza

    2014-01-01

    This study examines three controversial aspects in differential item functioning (DIF) detection by logistic regression (LR) models: first, the relative effectiveness of different analytical strategies for detecting DIF; second, the suitability of the Wald statistic for determining the statistical significance of the parameters of interest; and…

  15. Thinking about U : Theorizing and testing U - and inverted U-shaped relationships in strategy research

    NARCIS (Netherlands)

    Haans, Richard; Pieters, Constant; He, Zilin

    U- and inverted U-shaped relationships are increasingly explored in strategy research, with 11 percent of all articles published in Strategic Management Journal (SMJ) in 2008–2012 investigating such quadratic relationships. Moreover, a movement towards introducing moderation to quadratic

  16. Maximising the clinical use of exercise gaseous exchange testing in children with repaired cyanotic congenital heart defects: the development of an appropriate test strategy.

    Science.gov (United States)

    McManus, A; Leung, M

    2000-04-01

    Implicit in deciding upon an exercise test strategy to elucidate cardiopulmonary function in children with congenital heart disease are appropriate application of gas exchange techniques and the significance of the data collected to the specific congenital heart disorder. Post-operative cardiopulmonary responses to exercise in cyanotic disorders are complex and, despite a large body of extant literature in paediatric patients, there has been much difficulty in achieving quality and consistency of data. Maximal oxygen uptake is widely recognised as the best single indicator of cardiopulmonary function and has therefore been the focus of most clinical exercise tests in children. Many children with various heart anomalies are able to exercise to maximum without adverse symptoms, and it is essential that test termination is based on the same criteria for these children. Choosing appropriate, valid indicators of maximum in children with congenital heart disease is beset by difficulties. Such maximal intensity exercise testing procedures have been challenged on the grounds that they do not give a good indication of cardiopulmonary function that is relevant to real life situations. Furthermore, they are prone to much interindividual variability and error in the definition of maximal exertion. Alternative strategies have been proposed which focus upon dynamic submaximal and kinetic cardiopulmonary responses, which are thought to be less dependent on maximal voluntary effort and more suited to the daily activity patterns of children. These methods are also not without problems. Variability in anaerobic threshold measurements and controversy regarding its physiological meaning have been debated. It is recommended that an appropriate cardiopulmonary exercise gas exchange test strategy, which provides clinically useful information for children with cyanotic congenital heart disease, should include both maximal and submaximal data. The inclusion of oxygen uptake kinetics and

  17. The DNA comet assay and the germination test in detection of food treated by ionizing radiation; Teste do cometa e teste de germinacao na deteccao do tratamento de alimentos com a radiacao ionizante

    Energy Technology Data Exchange (ETDEWEB)

    Huachaca, Nelida Simona Marin

    2002-07-01

    Two methods of irradiated food detection, one biochemical, the comet assay and, other biological, the germination test, were applied in bovine meat and fruit samples. The comet assay detects the damage on DNA caused by ionizing radiation. The germination test evaluates the sensitivity to radiation of seeds as for germination ability, shooting and, rooting. The samples were irradiated in gamma font and electron accelerator. For bovine meat samples, the doses were 0.0; 2.5; 4.5 e 7.0 kGy at chilled condition and, 0.0; 2.5; 4.5; 7.0 e 8.5 kGy at frozen conditions. For fruit samples such as melon, watermelon, apple, orange, papaya and, tomato, the doses were: 0.0; 0.5; 0.75; 1.0; 2.0 e 4.0 kGy. The differences between the gamma rays and the electron beam effects on extent of DNA migration and, on shooting and rooting, showed to be similar. The comet assay, under neutral conditions, permitted to discriminate between irradiated and unirradiated bovine meat samples, until one month of storage. Also, it was possible to distinguish, by the comet assay, the control sample with regard to irradiated fruit, at doses as low as 0,5 kGy. In the germination test, the root length was the best parameter to discriminate irradiated and unirradiated samples of melon, watermelon and tomato, while the germination percent was the best parameter for apple and orange. (author)

  18. Testing search strategies for systematic reviews in the Medline literature database through PubMed.

    Science.gov (United States)

    Volpato, Enilze S N; Betini, Marluci; El Dib, Regina

    2014-04-01

    A high-quality electronic search is essential in ensuring accuracy and completeness in retrieved records for the conducting of a systematic review. We analysed the available sample of search strategies to identify the best method for searching in Medline through PubMed, considering the use or not of parenthesis, double quotation marks, truncation and use of a simple search or search history. In our cross-sectional study of search strategies, we selected and analysed the available searches performed during evidence-based medicine classes and in systematic reviews conducted in the Botucatu Medical School, UNESP, Brazil. We analysed 120 search strategies. With regard to the use of phrase searches with parenthesis, there was no difference between the results with and without parenthesis and simple searches or search history tools in 100% of the sample analysed (P = 1.0). The number of results retrieved by the searches analysed was smaller using double quotations marks and using truncation compared with the standard strategy (P = 0.04 and P = 0.08, respectively). There is no need to use phrase-searching parenthesis to retrieve studies; however, we recommend the use of double quotation marks when an investigator attempts to retrieve articles in which a term appears to be exactly the same as what was proposed in the search form. Furthermore, we do not recommend the use of truncation in search strategies in the Medline via PubMed. Although the results of simple searches or search history tools were the same, we recommend using the latter.

  19. A simulation model to quantify the value of implementing whole-herd Bovine viral diarrhea virus testing strategies in beef cow-calf herds.

    Science.gov (United States)

    Nickell, Jason S; White, Brad J; Larson, Robert L; Renter, David G; Sanderson, Mike W

    2011-03-01

    Although numerous diagnostic tests are available to identify cattle persistently infected (PI) with Bovine viral diarrhea virus (BVDV) in cow-calf herds, data are sparse when evaluating the economic viability of individual tests or diagnostic strategies. Multiple factors influence BVDV testing in determining if testing should be performed and which strategy to use. A stochastic model was constructed to estimate the value of implementing various whole-herd BVDV cow-calf testing protocols. Three common BVDV tests (immunohistochemistry, antigen-capture enzyme-linked immunosorbent assay, and polymerase chain reaction) performed on skin tissue were evaluated as single- or two-test strategies. The estimated testing value was calculated for each strategy at 3 herd sizes that reflect typical farm sizes in the United States (50, 100, and 500 cows) and 3 probabilities of BVDV-positive herd status (0.077, 0.19, 0.47) based upon the literature. The economic value of testing was the difference in estimated gross revenue between simulated cow-calf herds that either did or did not apply the specific testing strategy. Beneficial economic outcomes were more frequently observed when the probability of a herd being BVDV positive was 0.47. Although the relative value ranking of many testing strategies varied by each scenario, the two-test strategy composed of immunohistochemistry had the highest estimated value in all but one herd size-herd prevalence permutation. These data indicate that the estimated value of applying BVDV whole-herd testing strategies is influenced by the selected strategy, herd size, and the probability of herd BVDV-positive status; therefore, these factors should be considered when designing optimum testing strategies for cow-calf herds.

  20. Multicenter evaluation of a commercial multiplex polymerase chain reaction test for screening plasma donations for parvovirus B19 DNA and hepatitis A virus RNA.

    Science.gov (United States)

    Koppelman, Marco H G M; Cuijpers, H Theo M; Wessberg, Susanna; Valkeajärvi, Anne; Pichl, Lutz; Schottstedt, Volkmar; Saldanha, John

    2012-07-01

    Three European laboratories evaluated the TaqScreen DPX test (DPX test), a multiplex nucleic acid test assay for the simultaneous detection and quantitation of parvovirus B19 (B19V) DNA and the detection of hepatitis A virus (HAV) RNA. The 95% limit of detection of the test for B19V and HAV was determined using the respective WHO International Standards. The reproducibility of the test was evaluated by testing replicate samples of B19V at log 4.0 and 40 IU/mL and HAV at 5 IU/mL. The accuracy of the DPX test for B19V was evaluated by replicate testing of B19V samples containing log 3.0, log 4.0, and log 5.0 IU/mL. Panels of B19V Genotypes 1, 2, and 3 and HAV genotypes were evaluated. Cross-contamination was evaluated. For comparison of the DPX test and the established tests, the sites tested plasma samples in pools of either 96 or 480 donations. The mean 95% lower limits of detection of the three laboratories for B19V and HAV were 20.30 and 1.85 IU/mL. The test showed good reproducibility with the major part of the variance of the test being attributed to intermediate assay variation. The test showed great accuracy for B19V, especially at log 4.0 IU/mL. Spiking of test pools of 480 donations and manufacturing pools with log 4.0 IU/mL B19 DNA and 4 IU/mL HAV RNA showed that the DPX assay was robust. The test was able to detect the three genotypes of B19V and HAV genotypes. No cross-contamination was seen. Test results of routine samples correlated well with those of the established tests. The DPX test is a robust and sensitive test for the detection of B19V and HAV in plasma samples. The quantitative B19V results obtained with the test are accurate, and the test is able to detect all the known genotypes of B19V and HAV and fulfills all the European Pharmacopoeia and Food and Drug Administration requirements for a B19V and HAV test for screening of plasma donations and samples from plasma pools for manufacture. © 2012 American Association of Blood Banks.

  1. Development and qualification of functional materials for the EU Test Blanket Modules: Strategy and R and D activities

    Energy Technology Data Exchange (ETDEWEB)

    Zmitko, M., E-mail: milan.zmitko@f4e.europa.eu [Fusion for Energy (F4E), 08019 Barcelona (Spain); Poitevin, Y. [Fusion for Energy (F4E), 08019 Barcelona (Spain); Boccaccini, L., E-mail: lorenzo.boccaccini@inr.fzk.de [Institut Fuer Neutronenphysik und Reaktortechnik, FZK, D-76021 Karlsruhe (Germany); Salavy, J.-F., E-mail: jfsalavy@cea.fr [CEA/Saclay, DEN/DM2S, F-91191 Gif-sur-Yvette (France); Knitter, R., E-mail: regina.knitter@imf.fzk.de [Institut Fuer Materialforschung III, FZK, D-76021 Karlsruhe (Germany); Moeslang, A., E-mail: anton.moeslang@imf.fzk.de [Institut Fuer Materialforschung I, FZK, D-76021 Karlsruhe (Germany); Magielsen, A.J., E-mail: magielsen@nrg.eu [NRG Petten, 1755 ZG Petten (Netherlands); Hegeman, J.B.J. [NRG Petten, 1755 ZG Petten (Netherlands); Laesser, R. [Fusion for Energy (F4E), 08019 Barcelona (Spain)

    2011-10-01

    Europe has developed two reference tritium breeder blankets concepts for a DEMO fusion reactor: the Helium-Cooled Lithium-Lead and the Helium-Cooled Pebble-Bed. Both will be tested in ITER under the form of Test Blanket Modules (TBMs). The paper reviews the current status of development and qualification of the EU TBMs functional materials; i.e. ceramic solid breeder materials, beryllium/beryllides multiplier materials and Lithium-Lead liquid metal breeder material Pb-15.7Li. For each functional material the main functional/performance requirements with key qualification issues, current status of the R and D activities and the EU development strategy are presented. In the development strategy major steps considered are listed pointing out importance of the 'Development/qualification/procurement plan', currently under elaboration, for definition of a roadmap of further activities aiming at delivery of qualified functional materials to be used in the European TBMs in ITER.

  2. Nuclear maintenance strategy and first steps for preliminary maintenance plan of the EU HCLL & HCPB Test Blanket Systems

    Energy Technology Data Exchange (ETDEWEB)

    Galabert, Jose, E-mail: jose.galabert@f4e.europa.eu [F4E Fusion for Energy, EU Domestic Agency, c/Josep Pla, 2. B3, 08019, Barcelona (Spain); Hopper, Dave [AMEC Foster Wheeler, Faraday Street, Birchwood Park, WA3 6GN (United Kingdom); Neviere, Jean-Cristophe [ITER Organization, Route de Vinon-sur-Verdon, CS 90046, 13067, St. Paul Lez Durance Cedex (France); Nodwell, David [CCFE, Culham Science Centre, Abingdon, OX14 3DB, Oxfordshire (United Kingdom); Pascal, Romain [ITER Organization, Route de Vinon-sur-Verdon, CS 90046, 13067, St. Paul Lez Durance Cedex (France); Poitevin, Yves; Ricapito, Italo [F4E Fusion for Energy, EU Domestic Agency, c/Josep Pla, 2. B3, 08019, Barcelona (Spain); White, Gareth [AMEC Foster Wheeler, Faraday Street, Birchwood Park, WA3 6GN (United Kingdom)

    2017-03-15

    Highlights: • Nuclear maintenance strategy for the two European (EU) Test Blanket Systems (TBS): i/. Helium Cooled Lead Lithium (HCLL) and ii/. Helium Cooled Pebble Bed (HCPB). • Preliminary identification of maintenance tasks for most relevant components of the EU HCLL & HCPB TBS. • Preliminary feasibility analysis for hands-on maintenance tasks of some relevant components of the European Test Blanket Systems. • Design recommendations for enhancement of the European Test Blanket Systems maintainability. - Abstract: This paper gives an overview of nuclear maintenance strategy to be followed for the European HCLL & HCPB Test Blanket Systems (TBS) to be installed in ITER. One of the several core documents to prepare in view of their licensing is their respective ‘Maintenance Plan’. This document is fundamental for ensuring sound performance and safety of the TBS during ITER’s operational phase and shall include, amongst others, relevant information on: maintenance organization, preventive and corrective maintenance task procedures, condition monitoring for key components, maintenance work planning, and a spare parts plan, just to mention some of the key topics. In compliance with the ITER Plant Maintenance policy, first steps have been taken aimed at defining nuclear maintenance strategy for some of the most relevant HCLL & HCPB TBS components, conducted by F4E in collaboration with industry. After a brief recall of maintenance strategy of the TBM Program (PBS-56), this paper analyses main features of EU HCLL & HCPB TBS maintainability and identifies, at their conceptual design phase, a preliminary list of maintenance tasks to be developed for their most representative components. In addition, the paper also presents the first nuclear maintenance studies conducted for replacement of the Q{sub 2} Getter Beds, identifying some design recommendations for their sound maintainability.

  3. Nuclear maintenance strategy and first steps for preliminary maintenance plan of the EU HCLL & HCPB Test Blanket Systems

    International Nuclear Information System (INIS)

    Galabert, Jose; Hopper, Dave; Neviere, Jean-Cristophe; Nodwell, David; Pascal, Romain; Poitevin, Yves; Ricapito, Italo; White, Gareth

    2017-01-01

    Highlights: • Nuclear maintenance strategy for the two European (EU) Test Blanket Systems (TBS): i/. Helium Cooled Lead Lithium (HCLL) and ii/. Helium Cooled Pebble Bed (HCPB). • Preliminary identification of maintenance tasks for most relevant components of the EU HCLL & HCPB TBS. • Preliminary feasibility analysis for hands-on maintenance tasks of some relevant components of the European Test Blanket Systems. • Design recommendations for enhancement of the European Test Blanket Systems maintainability. - Abstract: This paper gives an overview of nuclear maintenance strategy to be followed for the European HCLL & HCPB Test Blanket Systems (TBS) to be installed in ITER. One of the several core documents to prepare in view of their licensing is their respective ‘Maintenance Plan’. This document is fundamental for ensuring sound performance and safety of the TBS during ITER’s operational phase and shall include, amongst others, relevant information on: maintenance organization, preventive and corrective maintenance task procedures, condition monitoring for key components, maintenance work planning, and a spare parts plan, just to mention some of the key topics. In compliance with the ITER Plant Maintenance policy, first steps have been taken aimed at defining nuclear maintenance strategy for some of the most relevant HCLL & HCPB TBS components, conducted by F4E in collaboration with industry. After a brief recall of maintenance strategy of the TBM Program (PBS-56), this paper analyses main features of EU HCLL & HCPB TBS maintainability and identifies, at their conceptual design phase, a preliminary list of maintenance tasks to be developed for their most representative components. In addition, the paper also presents the first nuclear maintenance studies conducted for replacement of the Q_2 Getter Beds, identifying some design recommendations for their sound maintainability.

  4. Containment nuclear plant structures evaluation by non destructive testing: strategy and results

    OpenAIRE

    GARNIER, Vincent; HENAULT, Jean-Marie; HAFID, Hamid; VERDIER, Jérôme; CHAIX, Jean François; ABRAHAM, Odile; SBARTAÏ, Zoubir Medhi; BALAYSSAC, Jean Pierre; PIWAKOWSKI, Bogdan; VILLAIN, Géraldine; DEROBERT, Xavier; PAYAN, Cédric; RAKOTONARIVO, Sandrine; LAROSE, Eric; SOGBOSSI, Hognon

    2016-01-01

    Containment nuclear plants structures are an ultimate barrier in the event of an accident. Mechanical resistance and tightness are the two functions that they are expected to provide. To evaluate their capacity to perform them, destructive testing cannot be used to characterize the material. Non-Destructive Tests then represent a relevant solution to test concrete and the struc- ture. The article positions NDT within the context of containment structures supervision and maintenance, and prese...

  5. Identifying nurse staffing research in Medline: development and testing of empirically derived search strategies with the PubMed interface.

    Science.gov (United States)

    Simon, Michael; Hausner, Elke; Klaus, Susan F; Dunton, Nancy E

    2010-08-23

    The identification of health services research in databases such as PubMed/Medline is a cumbersome task. This task becomes even more difficult if the field of interest involves the use of diverse methods and data sources, as is the case with nurse staffing research. This type of research investigates the association between nurse staffing parameters and nursing and patient outcomes. A comprehensively developed search strategy may help identify nurse staffing research in PubMed/Medline. A set of relevant references in PubMed/Medline was identified by means of three systematic reviews. This development set was used to detect candidate free-text and MeSH terms. The frequency of these terms was compared to a random sample from PubMed/Medline in order to identify terms specific to nurse staffing research, which were then used to develop a sensitive, precise and balanced search strategy. To determine their precision, the newly developed search strategies were tested against a) the pool of relevant references extracted from the systematic reviews, b) a reference set identified from an electronic journal screening, and c) a sample from PubMed/Medline. Finally, all newly developed strategies were compared to PubMed's Health Services Research Queries (PubMed's HSR Queries). The sensitivities of the newly developed search strategies were almost 100% in all of the three test sets applied; precision ranged from 6.1% to 32.0%. PubMed's HSR queries were less sensitive (83.3% to 88.2%) than the new search strategies. Only minor differences in precision were found (5.0% to 32.0%). As with other literature on health services research, nurse staffing studies are difficult to identify in PubMed/Medline. Depending on the purpose of the search, researchers can choose between high sensitivity and retrieval of a large number of references or high precision, i.e. and an increased risk of missing relevant references, respectively. More standardized terminology (e.g. by consistent use of the

  6. Information access in a dual-task context: testing a model of optimal strategy selection

    Science.gov (United States)

    Wickens, C. D.; Seidler, K. S.

    1997-01-01

    Pilots were required to access information from a hierarchical aviation database by navigating under single-task conditions (Experiment 1) and when this task was time-shared with an altitude-monitoring task of varying bandwidth and priority (Experiment 2). In dual-task conditions, pilots had 2 viewports available, 1 always used for the information task and the other to be allocated to either task. Dual-task strategy, inferred from the decision of which task to allocate to the 2nd viewport, revealed that allocation was generally biased in favor of the monitoring task and was only partly sensitive to the difficulty of the 2 tasks and their relative priorities. Some dominant sources of navigational difficulties failed to adaptively influence selection strategy. The implications of the results are to pro