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Sample records for review dna testing

  1. 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.

  2. 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 ...

  3. 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.

  4. Dna fingerprinting - review paper

    OpenAIRE

    Blundell, Renald

    2006-01-01

    Before the Polymerase Chain Reaction (PCR) was established, DNA fingerprinting technology has relied for years on Restriction Fragment Length Polymorphism (RFLP) and Variable Number of Tandom Repeats (VNTR) analysis, a very efficient technique but quite laborious and not suitable for high throughput mapping. Since its, development, PCR has provided a new and powerful tool for DNA fingerprinting.

  5. Aging and DNA repair capability. [Review

    Energy Technology Data Exchange (ETDEWEB)

    Tice, R R

    1977-01-01

    A review of the literature on DNA repair processes in relation to aging is presented under the following headings: DNA repair processes; age-related occurrence of unrepaired DNA lesions; DNA repair capability as a function of age; tissue-specific DNA repair capability; acceleration of the aging process by exposure to DNA damaging agents; human genetic syndromes; and longevity and DNA repair processes. (HLW)

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Forensic trace DNA: A review

    NARCIS (Netherlands)

    R.A.H. van Oorschot (Roland ); K. Ballantyne (Kaye); R.J. Mitchell (R. John)

    2010-01-01

    textabstractDNA analysis is frequently used to acquire information from biological material to aid enquiries associated with criminal offences, disaster victim identification and missing persons investigations. As the relevance and value of DNA profiling to forensic investigations has increased, so

  11. Nuclear Test Personnel Review

    Science.gov (United States)

    FOIA Electronic Reading Room Privacy Impact Assessment DTRA No Fear Act Reporting Nuclear Test Personnel Review NTPR Fact Sheets NTPR Radiation Dose Assessment Documents US Atmospheric Nuclear Test History Documents US Underground Nuclear Test History Reports NTPR Radiation Exposure Reports Enewetak

  12. Advances in forensic DNA quantification: a review.

    Science.gov (United States)

    Lee, Steven B; McCord, Bruce; Buel, Eric

    2014-11-01

    This review focuses upon a critical step in forensic biology: detection and quantification of human DNA from biological samples. Determination of the quantity and quality of human DNA extracted from biological evidence is important for several reasons. Firstly, depending on the source and extraction method, the quality (purity and length), and quantity of the resultant DNA extract can vary greatly. This affects the downstream method as the quantity of input DNA and its relative length can determine which genotyping procedure to use-standard short-tandem repeat (STR) typing, mini-STR typing or mitochondrial DNA sequencing. Secondly, because it is important in forensic analysis to preserve as much of the evidence as possible for retesting, it is important to determine the total DNA amount available prior to utilizing any destructive analytical method. Lastly, results from initial quantitative and qualitative evaluations permit a more informed interpretation of downstream analytical results. Newer quantitative techniques involving real-time PCR can reveal the presence of degraded DNA and PCR inhibitors, that provide potential reasons for poor genotyping results and may indicate methods to use for downstream typing success. In general, the more information available, the easier it is to interpret and process the sample resulting in a higher likelihood of successful DNA typing. The history of the development of quantitative methods has involved two main goals-improving precision of the analysis and increasing the information content of the result. This review covers advances in forensic DNA quantification methods and recent developments in RNA quantification. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Nanopores formed by DNA origami: a review.

    Science.gov (United States)

    Bell, Nicholas A W; Keyser, Ulrich F

    2014-10-01

    Nanopores have emerged over the past two decades to become an important technique in single molecule experimental physics and biomolecule sensing. Recently DNA nanotechnology, in particular DNA origami, has been used for the formation of nanopores in insulating materials. DNA origami is a very attractive technique for the formation of nanopores since it enables the construction of 3D shapes with precise control over geometry and surface functionality. DNA origami has been applied to nanopore research by forming hybrid architectures with solid state nanopores and by direct insertion into lipid bilayers. This review discusses recent experimental work in this area and provides an outlook for future avenues and challenges. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  14. 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.

  15. Innovative configurations of electrochemical DNA biosensors (a review)

    OpenAIRE

    Girousi, Stella; Karastogianni, Sofia; Serpi, Constantina

    2011-01-01

    In the field of electrochemical biosensing, transition metal complexes achieved a significant importance as hybridization indicators or electroactive markers of DNA. Their incorporation in electro-chemical DNA biosensors enables to offer a promising perspective in understanding of the biological activity of some chemical compounds. In this context, the development of innovative configurations of electrochemical DNA biosensors applied to life sciences during the last years were reviewed ...

  16. 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.

  17. Atomic force microscopy on chromosomes, chromatin and DNA: a review.

    Science.gov (United States)

    Kalle, Wouter; Strappe, Padraig

    2012-12-01

    The purpose of this review is to discuss the achievements and progress that has been made in the use of atomic force microscopy in DNA related research in the last 25 years. For this review DNA related research is split up in chromosomal-, chromatin- and DNA focused research to achieve a logical flow from large- to smaller structures. The focus of this review is not only on the AFM as imaging tool but also on the AFM as measuring tool using force spectroscopy, as therein lays its greatest advantage and future. The amazing technological and experimental progress that has been made during the last 25 years is too extensive to fully cover in this review but some key developments and experiments have been described to give an overview of the evolution of AFM use from 'imaging tool' to 'measurement tool' on chromosomes, chromatin and DNA. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

  18. Plant DNA banks for genetic resources conservation (review

    Directory of Open Access Journals (Sweden)

    Н. Е. Волкова

    2016-12-01

    Full Text Available Purpose. Literature review of DNA banks creation as the current strategy of plant genetic resources conservation. Results. The current state of plant genetic resources conservation was analyzed in the context of the threat of gene­tic erosion. The importance of DNA banks was shown which function is to store DNA samples and associated products and disseminate them for research purposes. The main DNA banks in the world were described, including the Republican DNA Bank of Human, Animals, Plants and Microorganisms at the Institute of Genetics and Cytology of the National Academy of Sciences of Belarus. Stages of DNA banking were considered: tissue sampling (usually from leaves, cell destruction, DNA extraction, DNA storage. Different methods of tissue sampling, extraction and DNA storage were compared. The need for Plant DNA Bank creation in Ukraine was highlighted. Conclusions. DNA collections is an important resource in the global effort to overcome the crisis in biodiversity, for managing world genetic resources and maximi­zing their potential.

  19. Role of fetal DNA in preeclampsia (review).

    Science.gov (United States)

    Konečná, Barbora; Vlková, Barbora; Celec, Peter

    2015-02-01

    Preeclampsia is an autoimmune disorder characterized by hypertension. It begins with abnormal cytotrophoblast apoptosis, which leads to inflammation and an increase in the levels of anti-angiogenic factors followed by the disruption of the angiogenic status. Increased levels of fetal DNA and RNA coming from the placenta, one of the most commonly affected organs in pregnancies complicated by preeclampsia, have been found in pregnant women with the condition. However, it remains unknown as to whether this is a cause or a consequence of preeclampsia. Few studies have been carried out on preeclampsia in which an animal model of preeclampsia was induced by an injection of different types of DNA that are mimic fetal DNA and provoke inflammation through Toll-like receptor 9 (TLR9) or cyclic guanosine monophosphate-adenosine monophosphate (cGAMP). The specific mechanisms involved in the development of preeclampsia are not yet fully understood. It is hypothesized that the presence of different fragments of fetal DNA in maternal plasma may cause for the development of preeclampsia. The function of DNase during preeclampsia also remains unresolved. Studies have suggested that its activity is decreased or the DNA is protected against its effects. Further research is required to uncover the pathogenesis of preeclampsia and focus more on the condition of patients with the condition.

  20. 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.

  1. 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

  2. Review of Autism Screening Tests

    Directory of Open Access Journals (Sweden)

    Farin Soleimani

    2014-10-01

    Full Text Available Background: Autism is a neurodevelopmental disorder that onset in the first 3 years of life and led to lifelong disability.Despite the early onset of symptoms, diagnosis of thissyndromedoes not happenuntil severalyears later, somany childrenlosethe opportunityfor earlyintervention.There arevarious toolsforscreening anddiagnosis, buttheirdesign, strengths and weaknesses aredifferent. The aim of this study was assess these tools from various aspects to provide a comprehensive view. Materials and methods: This study is a narrative literature review on screeningtoolsof autism. Comprehensive searches of the scientific literature were conducted in textbooks and 8 electronic databases(proquest,wiley,google scholar,SID,Scopus, Web of Science ،Science Direct ، and Medline and Pediatric book. language restriction (Persian and English was applied. The search strategy consisted of keywords and medical subject headings for autism and various screening tests. Result: In this study, 28 screening tests were identified from 1992 to 2014. CHAT is oldest test and the most recent test is CAST The minimum age that can perform the screening is six months that related to ITC. Minimum time of testing was 5 minutes  for CHAT and the maximum time was 90-120 minutes for ASIEP-3.RAADS-R test was the highest specificity and specificity (100% and the lowest specificity was 14% in ESAT test Conclusion: The results of this study indicate that any of the autism screening tools consider specific skill and various aspects of the disease, careful evaluation is need to choose proper test.

  3. Metaphors of DNA: a review of the popularisation processes

    Directory of Open Access Journals (Sweden)

    Sergi Cortiñas Rovira

    2008-03-01

    Full Text Available This article offers a 1953-present day review of the models that have popularised DNA, one of the fundamental molecules of biochemistry. DNA has become an iconic concept over the 20th century, overcoming the boundaries of science and spreading into literature, painting, sculpture or religion. This work analyses the reasons why DNA has penetrated society so effectively and examines some of the main metaphors used by the scientists and scientific popularisers. Furthermore, this article, taken from the author's PhD thesis, describes some recent popularisation models for this molecule.

  4. 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....

  5. 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...

  6. Test Review: TestDaF

    Science.gov (United States)

    Norris, John; Drackert, Anastasia

    2018-01-01

    The Test of German as a Foreign Language (TestDaF) plays a critical role as a standardized test of German language proficiency. Developed and administered by the Society for Academic Study Preparation and Test Development (g.a.s.t.), TestDaF was launched in 2001 and has experienced persistent annual growth, with more than 44,000 test takers in…

  7. A systematic review on sperm DNA fragmentation in male factor infertility: Laboratory assessment

    Directory of Open Access Journals (Sweden)

    Manesh Kumar Panner Selvam

    2018-03-01

    Full Text Available Objective: To review sperm DNA fragmentation (SDF testing as an important sperm function test in addition to conventional semen analysis. High SDF is negatively associated with semen quality, the fertilisation process, embryo quality, and pregnancy outcome. Over recent decades, different SDF assays have been developed and reviewed extensively to assess their applicability and accuracy as advanced sperm function tests. Amongst them, the standardisation of the terminal deoxynucleotidyl transferased UTP nick-end labelling (TUNEL assay with a bench top flow cytometer in clinical practice deserves special mention with a threshold value of 16.8% to differentiate infertile men with DNA damage from fertile men. Materials and methods: A systematic literature search was performed through the PubMed, Medline, and ScienceDirect databases using the keywords ‘sperm DNA fragmentation’ and ‘laboratory assessment’. Non-English articles were excluded and studies related to humans were only included. Results: Of the 618 identified, 87 studies (original research and reviews and in addition eight book chapters meeting the selection criteria were included in this review. In all, 366 articles were rejected in the preliminary screening and a further 165 articles related to non-human subjects were excluded. Conclusion: There are pros and cons to all the available SDF assays. TUNEL is a reliable technique with greater accuracy and as an additional diagnostic test in Andrology laboratories along with basic semen analysis can predict fertility outcome, and thus direct the choice of an assisted reproductive technology procedure for infertile couples. Also, the TUNEL assay can be used as a prognostic test and results are beneficial in deciding personalised treatment for infertile men. Keywords: Sperm DNA fragmentation (SDF, Terminal deoxynucleotidyl transferased UTP nick-end labelling (TUNEL, DNA damage, Sperm DNA fragmentation (SDF assay

  8. 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.

  9. 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...

  10. A Review of Circulating Tumor DNA in Hepatobiliary Malignancies

    Directory of Open Access Journals (Sweden)

    Kabir Mody

    2018-06-01

    Full Text Available Circulating tumor DNA (ctDNA is released into circulation (blood specifically from tumor cells undergoing metabolic secretion, apoptosis, or necrosis, carries tumor-specific genetic or epigenetic alterations. Technologies enabling clinical evaluation of ctDNA continue to advance rapidly and allow for the assessment of patient-specific tumoral genetic and epigenetic alterations. This holds great potential for earlier detection of disease, serial monitoring of tumor heterogeneity, identification of therapeutic targets, and evaluation of treatment response and mechanisms of resistance. Hepatobiliary malignancies are often diagnosed late, recur commonly, yield limited available tumor on biopsy, and harbor several genomic alterations with potential therapeutic impacts. Patients suffering from or at risk for these diseases thus stand to benefit immensely from this technology. Herein, we review the limited literature pertaining to the potential for ctDNA technologies in such patients. Patients with these cancers stand to benefit greatly from the application of ctDNA technologies, and concerted efforts at further investigation of such are ongoing and greatly needed.

  11. Residual DNA analysis in biologics development: review of measurement and quantitation technologies and future directions.

    Science.gov (United States)

    Wang, Xing; Morgan, Donna M; Wang, Gan; Mozier, Ned M

    2012-02-01

    Residual DNA (rDNA) is comprised of deoxyribonucleic acid (DNA) fragments and longer length molecules originating from the host organism that may be present in samples from recombinant biological processes. Although similar in basic structural base pair units, rDNA may exist in different sizes and physical forms. Interest in measuring rDNA in recombinant products is based primarily on demonstration of effective purification during manufacturing, but also on some hypothetical concerns that, in rare cases, depending on the host expression system, some DNA sequences may be potentially infectious or oncogenic (e.g., HIV virus and the Ras oncogene, respectively). Recent studies suggest that a sequence known as long interspersed nucleotide element-1 (LINE-1), widely distributed in the mammalian genome, is active as a retrotransposon that can be transcribed to RNA, reverse-transcribed into DNA and inserts into a new site in genome. This integration process could potentially disrupt critical gene functions or induce tumorigenesis in mammals. Genomic DNA from microbial sources, on the other hand, could add to risk of immunogenicity to the target recombinant protein being expressed, due to the high CpG content and unmethylated DNA sequence. For these and other reasons, it is necessary for manufacturers to show clearance of DNA throughout production processes and to confirm low levels in the final drug substance using an appropriately specific and quantitative analytical method. The heterogeneity of potential rDNA sequences that might be makes the testing of all potential analytes challenging. The most common methodology for rDNA quantitation used currently is real-time polymerase chain reaction (RT-PCR), a robust and proven technology. Like most rDNA quantitation methods, the specificity of RT-PCR is limited by the sequences to which the primers are directed. To address this, primase-based whole genome amplification is introduced herein. This paper will review the recent

  12. 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.

  13. Age Estimation with DNA: From Forensic DNA Fingerprinting to Forensic (Epi)Genomics: A Mini-Review.

    Science.gov (United States)

    Parson, Walther

    2018-01-23

    Forensic genetics developed from protein-based techniques a quarter of a century ago and became famous as "DNA fingerprinting," this being based on restriction fragment length polymorphisms (RFLPs) of high-molecular-weight DNA. The amplification of much smaller short tandem repeat (STR) sequences using the polymerase chain reaction soon replaced RFLP analysis and advanced to become the gold standard in genetic identification. Meanwhile, STR multiplexes have been developed and made commercially available which simultaneously amplify up to 30 STR loci from as little as 15 cells or fewer. The enormous information content that comes with the large variety of observed STR genotypes allows for genetic individualisation (with the exception of identical twins). Carefully selected core STR loci form the basis of intelligence-led DNA databases that provide investigative leads by linking unsolved crime scenes and criminals through their matched STR profiles. Nevertheless, the success of modern DNA fingerprinting depends on the availability of reference material from suspects. In order to provide new investigative leads in cases where such reference samples are absent, forensic scientists started to explore the prediction of phenotypic traits from the DNA of the evidentiary sample. This paradigm change now uses DNA and epigenetic markers to forecast characteristics that are useful to triage further investigative work. So far, the best investigated externally visible characteristics are eye, hair and skin colour, as well as geographic ancestry and age. Information on the chronological age of a stain donor (or any sample donor) is elemental for forensic investigations in a number of aspects and has, therefore, been explored by researchers in some detail. Among different methodological approaches tested to date, the methylation-sensitive analysis of carefully selected DNA markers (CpG sites) has brought the most promising results by providing prediction accuracies of ±3-4 years

  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. 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.

  16. 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...

  17. 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

  18. 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

  19. Systematic reviews of diagnostic test accuracy

    DEFF Research Database (Denmark)

    Leeflang, Mariska M G; Deeks, Jonathan J; Gatsonis, Constantine

    2008-01-01

    More and more systematic reviews of diagnostic test accuracy studies are being published, but they can be methodologically challenging. In this paper, the authors present some of the recent developments in the methodology for conducting systematic reviews of diagnostic test accuracy studies....... Restrictive electronic search filters are discouraged, as is the use of summary quality scores. Methods for meta-analysis should take into account the paired nature of the estimates and their dependence on threshold. Authors of these reviews are advised to use the hierarchical summary receiver...

  20. Effects of atmospheric pressure plasmas on isolated and cellular DNA-a review.

    Science.gov (United States)

    Arjunan, Krishna Priya; Sharma, Virender K; Ptasinska, Sylwia

    2015-01-29

    Atmospheric Pressure Plasma (APP) is being used widely in a variety of biomedical applications. Extensive research in the field of plasma medicine has shown the induction of DNA damage by APP in a dose-dependent manner in both prokaryotic and eukaryotic systems. Recent evidence suggests that APP-induced DNA damage shows potential benefits in many applications, such as sterilization and cancer therapy. However, in several other applications, such as wound healing and dentistry, DNA damage can be detrimental. This review reports on the extensive investigations devoted to APP interactions with DNA, with an emphasis on the critical role of reactive species in plasma-induced damage to DNA. The review consists of three main sections dedicated to fundamental knowledge of the interactions of reactive oxygen species (ROS)/reactive nitrogen species (RNS) with DNA and its components, as well as the effects of APP on isolated and cellular DNA in prokaryotes and eukaryotes.

  1. Effect of food processing on plant DNA degradation and PCR-based GMO analysis: a review.

    Science.gov (United States)

    Gryson, Nicolas

    2010-03-01

    The applicability of a DNA-based method for GMO detection and quantification depends on the quality and quantity of the DNA. Important food-processing conditions, for example temperature and pH, may lead to degradation of the DNA, rendering PCR analysis impossible or GMO quantification unreliable. This review discusses the effect of several food processes on DNA degradation and subsequent GMO detection and quantification. The data show that, although many of these processes do indeed lead to the fragmentation of DNA, amplification of the DNA may still be possible. Length and composition of the amplicon may, however, affect the result, as also may the method of extraction used. Also, many techniques are used to describe the behaviour of DNA in food processing, which occasionally makes it difficult to compare research results. Further research should be aimed at defining ingredients in terms of their DNA quality and PCR amplification ability, and elaboration of matrix-specific certified reference materials.

  2. Review of the clinical applications and technological advances of circulating tumor DNA in cancer monitoring.

    Science.gov (United States)

    Chang, Yi; Tolani, Bhairavi; Nie, Xiuhong; Zhi, Xiuyi; Hu, Mu; He, Biao

    2017-01-01

    Circulating cell-free DNA (cfDNA) released by tumor cells, termed ctDNA, closely reflects the heterogeneity of primary cancers and their metastases. As a noninvasive, real-time monitoring biomarker, ctDNA is a promising tool for detecting driver gene mutations, assessing tumor burden and acquired resistance, and early diagnosis. However, isolation and enrichment of cfDNA is a big challenge due to the high degree of DNA fragmentation and its relatively low abundance in the bloodstream. This review aims to provide insights into the recent technological advances in acquisition of optimal quality cfDNA, the use of preservatives, isolation methods, processing timelines, and detection techniques. It also describes clinical applications of ctDNA in cancer patient management.

  3. A review of bioinformatic methods for forensic DNA analyses.

    Science.gov (United States)

    Liu, Yao-Yuan; Harbison, SallyAnn

    2018-03-01

    Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial analyses are three classes of markers which will play an important role in the future of forensic DNA typing. The arrival of massively parallel sequencing platforms in forensic science reveals new information such as insights into the complexity and variability of the markers that were previously unseen, along with amounts of data too immense for analyses by manual means. Along with the sequencing chemistries employed, bioinformatic methods are required to process and interpret this new and extensive data. As more is learnt about the use of these new technologies for forensic applications, development and standardization of efficient, favourable tools for each stage of data processing is being carried out, and faster, more accurate methods that improve on the original approaches have been developed. As forensic laboratories search for the optimal pipeline of tools, sequencer manufacturers have incorporated pipelines into sequencer software to make analyses convenient. This review explores the current state of bioinformatic methods and tools used for the analyses of forensic markers sequenced on the massively parallel sequencing (MPS) platforms currently most widely used. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. 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…

  5. 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....

  6. Current developments in forensic interpretation of mixed DNA samples (Review)

    Science.gov (United States)

    HU, NA; CONG, BIN; LI, SHUJIN; MA, CHUNLING; FU, LIHONG; ZHANG, XIAOJING

    2014-01-01

    A number of recent improvements have provided contemporary forensic investigations with a variety of tools to improve the analysis of mixed DNA samples in criminal investigations, producing notable improvements in the analysis of complex trace samples in cases of sexual assult and homicide. Mixed DNA contains DNA from two or more contributors, compounding DNA analysis by combining DNA from one or more major contributors with small amounts of DNA from potentially numerous minor contributors. These samples are characterized by a high probability of drop-out or drop-in combined with elevated stutter, significantly increasing analysis complexity. At some loci, minor contributor alleles may be completely obscured due to amplification bias or over-amplification, creating the illusion of additional contributors. Thus, estimating the number of contributors and separating contributor genotypes at a given locus is significantly more difficult in mixed DNA samples, requiring the application of specialized protocols that have only recently been widely commercialized and standardized. Over the last decade, the accuracy and repeatability of mixed DNA analyses available to conventional forensic laboratories has greatly advanced in terms of laboratory technology, mathematical models and biostatistical software, generating more accurate, rapid and readily available data for legal proceedings and criminal cases. PMID:24748965

  7. Ancient DNA investigations: A review on their significance in ...

    African Journals Online (AJOL)

    However, its degradation and post-mortem chemical alteration make difficult its quantification and amplification. Moreover the study of aDNA is challenging due to the contamination by exogenous current DNA. Recently, the progress of molecular techniques and the use of sophisticated approaches greatly improved the ratio ...

  8. Energy and Technology Review: Unlocking the mysteries of DNA repair

    Energy Technology Data Exchange (ETDEWEB)

    Quirk, W.A.

    1993-04-01

    DNA, the genetic blueprint, has the remarkable property of encoding its own repair following diverse types of structural damage induced by external agents or normal metabolism. We are studying the interplay of DNA damaging agents, repair genes, and their protein products to decipher the complex biochemical pathways that mediate such repair. Our research focuses on repair processes that correct DNA damage produced by chemical mutagens and radiation, both ionizing and ultraviolet. The most important type of DNA repair in human cells is called excision repair. This multistep process removes damaged or inappropriate pieces of DNA -- often as a string of 29 nucleotides containing the damage -- and replaces them with intact ones. We have isolated, cloned, and mapped several human repair genes associated with the nucleotide excision repair pathway and involved in the repair of DNA damage after exposure to ultraviolet light or mutagens in cooked food. We have shown that a defect in one of these repair genes, ERCC2, is responsible for the repair deficiency in one of the groups of patients with the recessive genetic disorder xeroderma pigmentosum (XP group D). We are exploring ways to purify sufficient quantities (milligrams) of the protein products of these and other repair genes so that we can understand their functions. Our long-term goals are to link defective repair proteins to human DNA repair disorders that predispose to cancer, and to produce DNA-repair-deficient mice that can serve as models for the human disorders.

  9. 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.

  10. 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.

  11. Detection of human papillomavirus DNA in urine. A review of the literature.

    Science.gov (United States)

    Vorsters, A; Micalessi, I; Bilcke, J; Ieven, M; Bogers, J; Van Damme, P

    2012-05-01

    The detection of human papillomavirus (HPV) DNA in urine, a specimen easily obtained by a non-invasive self-sampling method, has been the subject of a considerable number of studies. This review provides an overview of 41 published studies; assesses how different methods and settings may contribute to the sometimes contradictory outcomes; and discusses the potential relevance of using urine samples in vaccine trials, disease surveillance, epidemiological studies, and specific settings of cervical cancer screening. Urine sampling, storage conditions, sample preparation, DNA extraction, and DNA amplification may all have an important impact on HPV DNA detection and the form of viral DNA that is detected. Possible trends in HPV DNA prevalence in urine could be inferred from the presence of risk factors or the diagnosis of cervical lesions. HPV DNA detection in urine is feasible and may become a useful tool but necessitates further improvement and standardization.

  12. A review of software project testing

    Directory of Open Access Journals (Sweden)

    Jose Calvo-Manzano Villalón

    2016-03-01

    Full Text Available In this article a review of software projects based on a taxonomy project is established, allowing the development team or testing personnel to identify the tests to which the project must be subjected for validation. The taxonomy is focused on identifying software projects according to their technology. To establish the taxonomy, a development method comprised of 5 phases was applied. The developed taxonomy is comprised of 10 categories and 35 subcategories and was validated by a group of information technology (IT managers and professionals in the field of IT through the use of a survey. The results obtained from the survey are subjected to the Mann-Whitney U test, which indicates that the taxonomy is validated. The taxonomy can be implemented in development organizations with or without a testing team that provides a classification for technology projects.

  13. Microfluidic Devices for Forensic DNA Analysis: A Review.

    Science.gov (United States)

    Bruijns, Brigitte; van Asten, Arian; Tiggelaar, Roald; Gardeniers, Han

    2016-08-05

    Microfluidic devices may offer various advantages for forensic DNA analysis, such as reduced risk of contamination, shorter analysis time and direct application at the crime scene. Microfluidic chip technology has already proven to be functional and effective within medical applications, such as for point-of-care use. In the forensic field, one may expect microfluidic technology to become particularly relevant for the analysis of biological traces containing human DNA. This would require a number of consecutive steps, including sample work up, DNA amplification and detection, as well as secure storage of the sample. This article provides an extensive overview of microfluidic devices for cell lysis, DNA extraction and purification, DNA amplification and detection and analysis techniques for DNA. Topics to be discussed are polymerase chain reaction (PCR) on-chip, digital PCR (dPCR), isothermal amplification on-chip, chip materials, integrated devices and commercially available techniques. A critical overview of the opportunities and challenges of the use of chips is discussed, and developments made in forensic DNA analysis over the past 10-20 years with microfluidic systems are described. Areas in which further research is needed are indicated in a future outlook.

  14. Environmental chemicals and DNA methylation in adults: a systematic review of the epidemiologic evidence

    Science.gov (United States)

    Current evidence supports the notion that environmental exposures are associated with DNA-methylation and expression changes that can impact human health. Our objective was to conduct a systematic review of epidemiologic studies evaluating the association between environmental chemicals with DNA met...

  15. 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.

  16. The role of DNA methylation and histone modifications in neurodegenerative diseases: A systematic review

    NARCIS (Netherlands)

    K.-X. Wen (Ke-Xin); J. Milic (Jelena); El-Khodor, B. (Bassem); K. Dhana (Klodian); J. Nano (Jana); Pulido, T. (Tammy); B. Kraja (Bledar); A. Zaciragic (Asija); W.M. Bramer (Wichor); J. Troup; R. Chowdhury (Rajiv); Arfam Ikram, M.; A. Dehghan (Abbas); T. Muka (Taulant); O.H. Franco (Oscar)

    2016-01-01

    textabstractImportance Epigenetic modifications of the genome, such as DNA methylation and histone modifications, have been reported to play a role in neurodegenerative diseases (ND) such as Alzheimer's disease (AD) and Parkinson's disease (PD). Objective To systematically review studies

  17. 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)

  18. 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.

  19. Review about hiperventilation test and Valsalva Maneuver

    Directory of Open Access Journals (Sweden)

    Eduardo Antonio MENA-DOMÍNGUEZ

    2018-04-01

    Full Text Available Introduction and objective: With this paper, we pretend to explain the characteristics and the field of application of two clinical explorations used in the patient with suspected vestibular pathology, the hyperventilation maneuver and the Valsalva maneuver. Methodology: Narrative review. Results: Through different neurophysiological mechanisms, hyperventilation can induce nystagmus in cases of vestibular asymmetry, both peripheral and central. The Valsalva maneuver may also trigger nystagmus and vertigo because of direct transmission of internal ear pressure in cases of perilymphatic fistula, anomalies of the cranio-cervical junction (Arnold-Chiari malformation, and other ossicles, oval window and saccule pathologies. Discussion and conclusions: Both the hyperventilation test and the Valsalva maneuver should be included in the battery of tests for patients with vestibular pathology to, depending on the results obtained, anatomically locate the site of the lesion and justify the use of imaging techniques.

  20. Review: Clinical aspects of hereditary DNA Mismatch repair gene mutations

    NARCIS (Netherlands)

    Sijmons, Rolf H.; Hofstra, Robert M. W.

    Inherited mutations of the DNA Mismatch repair genes MLH1, MSH2, MSH6 and PMS2 can result in two hereditary tumor syndromes: the adult-onset autosomal dominant Lynch syndrome, previously referred to as Hereditary Non-Polyposis Colorectal Cancer (HNPCC) and the childhood-onset autosomal recessive

  1. Testing the universality of biology: a review

    International Nuclear Information System (INIS)

    Chela-Flores, J.

    2007-08-01

    We discuss whether it is possible to test the universality of biology, a quest that is of paramount relevance for one of its most recent branches, namely astrobiology. We review this topic in terms of the relative roles played on the Earth biota by contingency and evolutionary convergence. Following the seminal contribution of Darwin, it is reasonable to assume that all forms of life known to us so far are not only terrestrial, but are descendants of a common ancestor that evolved on this planet at the end of a process of chemical evolution. We also raise the related question of whether the molecular events that were precursors to the origin of life on Earth are bound to occur elsewhere in the universe, wherever the environmental conditions are similar to the terrestrial ones. We refer to 'cosmic convergence' as the possible occurrence elsewhere in the universe of Earth-like environmental conditions. We argue that cosmic convergence is already suggested by observational data. The set of hypotheses for addressing the question of the universality of biology can be tested by future experiments that are feasible with current technology. We focus on landing on Europa and the broader implications of selecting the specific example of the right landing location. We had discussed earlier the corresponding miniaturized equipment that is already in existence. The significance of these crucial points needs to be put into a wider scientific perspective, which is one of the main objectives of this review. (author)

  2. Testing the universality of biology: a review

    International Nuclear Information System (INIS)

    Chela-Flores, J.

    2007-05-01

    We discuss whether it is possible to test the universality of biology, a quest that is of paramount relevance for one of its most recent branches, namely astrobiology. We review this topic in terms of the relative roles played on the Earth biota by contingency and evolutionary convergence. Following the seminal contribution of Darwin, it is reasonable to assume that all forms of life known to us so far are not only terrestrial, but are descendants of a common ancestor that evolved on this planet at the end of a process of chemical evolution. We also raise the related question of whether the molecular events that were precursors to the origin of life on Earth are bound to occur elsewhere in the universe, wherever the environmental conditions are similar to the terrestrial ones. We refer to 'cosmic convergence' as the possible occurrence elsewhere in the universe of Earth-like environmental conditions. We argue that cosmic convergence is already suggested by observational data. The set of hypotheses for addressing the question of the universality of biology can be tested by future experiments that are feasible with current technology. We focus on landing on Europe and the broader implications of selecting the specific example of the right landing location. We had discussed earlier the corresponding miniaturized equipment that is already in existence. The significance of these crucial points needs to be put into a wider scientific perspective, which is one of the main objectives of this review. (author)

  3. 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

  4. 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

  5. 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.

  6. 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

  7. Review of SKB's Code Documentation and Testing

    International Nuclear Information System (INIS)

    Hicks, T.W.

    2005-01-01

    SKB is in the process of developing the SR-Can safety assessment for a KBS 3 repository. The assessment will be based on quantitative analyses using a range of computational codes aimed at developing an understanding of how the repository system will evolve. Clear and comprehensive code documentation and testing will engender confidence in the results of the safety assessment calculations. This report presents the results of a review undertaken on behalf of SKI aimed at providing an understanding of how codes used in the SR 97 safety assessment and those planned for use in the SR-Can safety assessment have been documented and tested. Having identified the codes us ed by SKB, several codes were selected for review. Consideration was given to codes used directly in SKB's safety assessment calculations as well as to some of the less visible codes that are important in quantifying the different repository barrier safety functions. SKB's documentation and testing of the following codes were reviewed: COMP23 - a near-field radionuclide transport model developed by SKB for use in safety assessment calculations. FARF31 - a far-field radionuclide transport model developed by SKB for use in safety assessment calculations. PROPER - SKB's harness for executing probabilistic radionuclide transport calculations using COMP23 and FARF31. The integrated analytical radionuclide transport model that SKB has developed to run in parallel with COMP23 and FARF31. CONNECTFLOW - a discrete fracture network model/continuum model developed by Serco Assurance (based on the coupling of NAMMU and NAPSAC), which SKB is using to combine hydrogeological modelling on the site and regional scales in place of the HYDRASTAR code. DarcyTools - a discrete fracture network model coupled to a continuum model, recently developed by SKB for hydrogeological modelling, also in place of HYDRASTAR. ABAQUS - a finite element material model developed by ABAQUS, Inc, which is used by SKB to model repository buffer

  8. 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

  9. Metaphors of DNA: a review of the popularisation processes (Spanish original version

    Directory of Open Access Journals (Sweden)

    Sergi Cortiñas Rovira

    2008-03-01

    Full Text Available This article offers a 1953-present day review of the models that have popularised DNA, one of the fundamental molecules of biochemistry. DNA has become an iconic concept over the 20th century, overcoming the boundaries of science and spreading into literature, painting, sculpture or religion. This work analyses the reasons why DNA has penetrated society so effectively and examines some of the main metaphors used by the scientists and scientific popularisers. Furthermore, this article, taken from the author's PhD thesis, describes some recent popularisation models for this molecule.

  10. Alternatives to animal testing: A review.

    Science.gov (United States)

    Doke, Sonali K; Dhawale, Shashikant C

    2015-07-01

    The number of animals used in research has increased with the advancement of research and development in medical technology. Every year, millions of experimental animals are used all over the world. The pain, distress and death experienced by the animals during scientific experiments have been a debating issue for a long time. Besides the major concern of ethics, there are few more disadvantages of animal experimentation like requirement of skilled manpower, time consuming protocols and high cost. Various alternatives to animal testing were proposed to overcome the drawbacks associated with animal experiments and avoid the unethical procedures. A strategy of 3 Rs (i.e. reduction, refinement and replacement) is being applied for laboratory use of animals. Different methods and alternative organisms are applied to implement this strategy. These methods provide an alternative means for the drug and chemical testing, up to some levels. A brief account of these alternatives and advantages associated is discussed in this review with examples. An integrated application of these approaches would give an insight into minimum use of animals in scientific experiments.

  11. 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...

  12. Cell-Free DNA in Metastatic Colorectal Cancer: A Systematic Review and Meta-Analysis.

    Science.gov (United States)

    Spindler, Karen-Lise G; Boysen, Anders K; Pallisgård, Niels; Johansen, Julia S; Tabernero, Josep; Sørensen, Morten M; Jensen, Benny V; Hansen, Torben F; Sefrioui, David; Andersen, Rikke F; Brandslund, Ivan; Jakobsen, Anders

    2017-09-01

    Circulating DNA can be detected and quantified in the blood of cancer patients and used for detection of tumor-specific genetic alterations. The clinical utility has been intensively investigated for the past 10 years. The majority of reports focus on analyzing the clinical potential of tumor-specific mutations, whereas the use of total cell-free DNA (cfDNA) quantification is somehow controversial and sparsely described in the literature, but holds important clinical information in itself. The purpose of the present report was to present a systematic review and meta-analysis of the prognostic value of total cfDNA in patients with metastatic colorectal cancer (mCRC) treated with chemotherapy. In addition, we report on the overall performance of cfDNA as source for KRAS mutation detection. A systematic literature search of PubMed and Embase was performed by two independent investigators. Eligibility criteria were (a) total cfDNA analysis, (b) mCRC, and (c) prognostic value during palliative treatment. The preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines were followed, and meta-analysis applied on both aggregate data extraction and individual patients' data. Ten eligible cohorts were identified, including a total of 1,076 patients. Seven studies used quantitative polymerase chain reaction methods, two BEAMing [beads, emulsification, amplification, and magnetics] technology, and one study digital droplet polymerase chain reaction. The baseline levels of cfDNA was similar in the presented studies, and all studies reported a clear prognostic value in favor of patients with lowest levels of baseline cfDNA. A meta-analysis revealed a combined estimate of favorable overall survival hazard ratio (HR) in patients with levels below the median cfDNA (HR = 2.39, 95% confidence interval 2.03-2.82, p  meta-analysis. Reliable prognostic markers could help to guide patients and treating physicians regarding the relevance and choice of

  13. 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....

  14. 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...

  15. 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)

  16. 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.

  17. 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)

  18. 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.

  19. 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

  20. 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

  1. Tests in Print II: An Index to Tests, Test Reviews, and the Literature on Specific Tests.

    Science.gov (United States)

    Buros, Oscar K., Ed.

    Tests in Print II is a comprehensive, annotated bibliography of all in-print tests published as separates for use with English-speaking subjects. The 1,155 two-column pages list 2,467 tests in print as of early 1974; 16,574 references through 1971 on specific tests; a reprinting of the 1974 APA-AERA-NCME Standards for Educational andPsychological…

  2. 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.

  3. 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 ...

  4. 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

  5. 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

  6. Guardians of the mycobacterial genome: A review on DNA repair systems in Mycobacterium tuberculosis.

    Science.gov (United States)

    Singh, Amandeep

    2017-12-01

    The genomic integrity of Mycobacterium tuberculosis is continuously threatened by the harsh survival conditions inside host macrophages, due to immune and antibiotic stresses. Faithful genome maintenance and repair must be accomplished under stress for the bacillus to survive in the host, necessitating a robust DNA repair system. The importance of DNA repair systems in pathogenesis is well established. Previous examination of the M. tuberculosis genome revealed homologues of almost all the major DNA repair systems, i.e. nucleotide excision repair (NER), base excision repair (BER), homologous recombination (HR) and non-homologous end joining (NHEJ). However, recent developments in the field have pointed to the presence of novel proteins and pathways in mycobacteria. Homologues of archeal mismatch repair proteins were recently reported in mycobacteria, a pathway previously thought to be absent. RecBCD, the major nuclease-helicase enzymes involved in HR in E. coli, were implicated in the single-strand annealing (SSA) pathway. Novel roles of archeo-eukaryotic primase (AEP) polymerases, previously thought to be exclusive to NHEJ, have been reported in BER. Many new proteins with a probable role in DNA repair have also been discovered. It is now realized that the DNA repair systems in M. tuberculosis are highly evolved and have redundant backup mechanisms to mend the damage. This review is an attempt to summarize our current understanding of the DNA repair systems in M. tuberculosis.

  7. Some Effective Tight-Binding Models for Electrons in DNA Conduction: A Review

    International Nuclear Information System (INIS)

    Yamada, H.; Iguchi, K.

    2010-01-01

    Quantum transport for DNA conduction has been widely studied with interest in application as a candidate in making nanowires as well as interest in the scientific mechanism. In this paper, we review recent works concerning the electronic states and the conduction/transfer in DNA polymers. We have mainly investigated the energy-band structure and the correlation effects of localization property in the two- and three-chain systems (ladder model) with long-range correlation as a simple model for electronic property in a double strand of DNA by using the tight-bindingmodel. In addition, we investigated the localization properties of electronic states in several actual DNA sequences such as bacteriophages of Escherichia coli, human-chromosome 22, compared with those of the artificial disordered sequences with correlation. The charge-transfer properties for poly(dA)-poly(dT) and poly(dG)-poly(dC) DNA polymers are also presented in terms of localization lengths within the frameworks of the polaron models due to the coupling between the charge carriers and the lattice vibrations of the double strand of DNA

  8. Review of Test Theory and Methods.

    Science.gov (United States)

    1981-01-01

    literature, although some books , technical reports, and unpub- lished literature have been included where relevant. The focus of the review is on practical...1977) and Abu-Sayf (1977) developed new versions of formula scores, and Molenaar (1977) took a Bayesian approach to correcting for random guessing. The...Snow’s (1977) book on aptitude and instructional methods is a landmark review of the research on the interaction between instructional methods and

  9. 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.

  10. 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.

  11. 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

  12. Implicit Messages:A Review of "Bias in Mental Testing."

    Science.gov (United States)

    Scarr, Sandra

    1981-01-01

    Reviews Arthur Jensen's "Bias in Mental Testing" in terms of its implications for racial genetic inferiority, and offers alternate explanations for racial differences in testing based on data from studies on Black socialization and cultural differences in child rearing. (CM)

  13. 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.

  14. Testing Scientific Software: A Systematic Literature Review

    Science.gov (United States)

    Kanewala, Upulee; Bieman, James M.

    2014-01-01

    Context Scientific software plays an important role in critical decision making, for example making weather predictions based on climate models, and computation of evidence for research publications. Recently, scientists have had to retract publications due to errors caused by software faults. Systematic testing can identify such faults in code. Objective This study aims to identify specific challenges, proposed solutions, and unsolved problems faced when testing scientific software. Method We conducted a systematic literature survey to identify and analyze relevant literature. We identified 62 studies that provided relevant information about testing scientific software. Results We found that challenges faced when testing scientific software fall into two main categories: (1) testing challenges that occur due to characteristics of scientific software such as oracle problems and (2) testing challenges that occur due to cultural differences between scientists and the software engineering community such as viewing the code and the model that it implements as inseparable entities. In addition, we identified methods to potentially overcome these challenges and their limitations. Finally we describe unsolved challenges and how software engineering researchers and practitioners can help to overcome them. Conclusions Scientific software presents special challenges for testing. Specifically, cultural differences between scientist developers and software engineers, along with the characteristics of the scientific software make testing more difficult. Existing techniques such as code clone detection can help to improve the testing process. Software engineers should consider special challenges posed by scientific software such as oracle problems when developing testing techniques. PMID:25125798

  15. Testing Scientific Software: A Systematic Literature Review.

    Science.gov (United States)

    Kanewala, Upulee; Bieman, James M

    2014-10-01

    Scientific software plays an important role in critical decision making, for example making weather predictions based on climate models, and computation of evidence for research publications. Recently, scientists have had to retract publications due to errors caused by software faults. Systematic testing can identify such faults in code. This study aims to identify specific challenges, proposed solutions, and unsolved problems faced when testing scientific software. We conducted a systematic literature survey to identify and analyze relevant literature. We identified 62 studies that provided relevant information about testing scientific software. We found that challenges faced when testing scientific software fall into two main categories: (1) testing challenges that occur due to characteristics of scientific software such as oracle problems and (2) testing challenges that occur due to cultural differences between scientists and the software engineering community such as viewing the code and the model that it implements as inseparable entities. In addition, we identified methods to potentially overcome these challenges and their limitations. Finally we describe unsolved challenges and how software engineering researchers and practitioners can help to overcome them. Scientific software presents special challenges for testing. Specifically, cultural differences between scientist developers and software engineers, along with the characteristics of the scientific software make testing more difficult. Existing techniques such as code clone detection can help to improve the testing process. Software engineers should consider special challenges posed by scientific software such as oracle problems when developing testing techniques.

  16. Direct PCR amplification of forensic touch and other challenging DNA samples: A review.

    Science.gov (United States)

    Cavanaugh, Sarah E; Bathrick, Abigail S

    2018-01-01

    advantages of direct PCR of forensic evidentiary samples justify a re-examination of the factors that have delayed widespread implementation of this method and of the evidence supporting its use. In this review, the current and potential future uses of direct PCR in forensic DNA laboratories are summarized. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. 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

  18. 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

  19. 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

  20. Test Review: Autism Spectrum Rating Scales

    Science.gov (United States)

    Simek, Amber N.; Wahlberg, Andrea C.

    2011-01-01

    This article reviews Autism Spectrum Rating Scales (ASRS) which are designed to measure behaviors in children between the ages of 2 and 18 that are associated with disorders on the autism spectrum as rated by parents/caregivers and/or teachers. The rating scales include items related to behaviors associated with Autism, Asperger's Disorder, and…

  1. 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

  2. Interactions of DNA with graphene and sensing applications of graphene field-effect transistor devices: A review

    Energy Technology Data Exchange (ETDEWEB)

    Green, Nathaniel S.; Norton, Michael L., E-mail: norton@marshall.edu

    2015-01-01

    Highlights: • The interaction of DNA, including DNA nanostructures, and graphene is reviewed. • Comparison of DNA graphene field-effect transistor (GFET) with other detection methods. • Discussion of challenges present in the detection mechanism of GFETs. • Use of DNA aptamer GFET sensors for the detection of small molecules and proteins. - Abstract: Graphene field-effect transistors (GFET) have emerged as powerful detection platforms enabled by the advent of chemical vapor deposition (CVD) production of the unique atomically thin 2D material on a large scale. DNA aptamers, short target-specific oligonucleotides, are excellent sensor moieties for GFETs due to their strong affinity to graphene, relatively short chain-length, selectivity, and a high degree of analyte variability. However, the interaction between DNA and graphene is not fully understood, leading to questions about the structure of surface-bound DNA, including the morphology of DNA nanostructures and the nature of the electronic response seen from analyte binding. This review critically evaluates recent insights into the nature of the DNA graphene interaction and its affect on sensor viability for DNA, small molecules, and proteins with respect to previously established sensing methods. We first discuss the sorption of DNA to graphene to introduce the interactions and forces acting in DNA based GFET devices and how these forces can potentially affect the performance of increasingly popular DNA aptamers and even future DNA nanostructures as sensor substrates. Next, we discuss the novel use of GFETs to detect DNA and the underlying electronic phenomena that are typically used as benchmarks for characterizing the analyte response of these devices. Finally, we address the use of DNA aptamers to increase the selectivity of GFET sensors for small molecules and proteins and compare them with other, state of the art, detection methods.

  3. Phase 1: ISOCELL demonstration test performance review

    International Nuclear Information System (INIS)

    Chatwin, T.D.

    1991-04-01

    This document consolidates and organizes information available concerning cryogenic retrieval of hazardous, radioactive, and mixed wastes and is mainly derived from a report on the ISOCELL Demonstration Project prepared by Concept RKK, Ltd. ISOCELL cryogenic technology is designed to immobilize hazardous, radioactive, and mixed waste by creating a block of frozen waste and soil that can be safely retrieved, stored, transported, and treated with a minimum of dust. A test of the ISOCELL process was conducted in Carnation, Washington by Concept RKK, Ltd. Test conditions were compared to possible testing conditions at Idaho National Engineering Laboratory. Results indicate ISOCELL technology successfully froze wet soil into a soil block capable of being lifted. 5 refs., 6 figs., 1 tab

  4. 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

  5. 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.

  6. 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.

  7. Anaerobic exercise testing in rehabilitation : A systematic review of available tests and protocols

    NARCIS (Netherlands)

    Krops, Leonie A.; Albada, Trijntje; van der Woude, Lucas H. V.; Hijmans, Juha M.; Dekker, Rienk

    Objective: Anaerobic capacity assessment in rehabilitation has received increasing scientific attention in recent years. However, anaerobic capacity is not tested consistently in clinical rehabilitation practice. This study reviews tests and protocols for anaerobic capacity in adults with various

  8. Review of short-term screening tests for mutagens, toxigens, and carcinogens

    Energy Technology Data Exchange (ETDEWEB)

    Carney, H.J.; Hass, B.S.

    1979-07-01

    In order to test the thousands of man-made chemicals in the environment for carcinogenic and genetic hazards, a multitude of short-term screening tests has been developed to complement long-term mammalian bioassays and epidemiological studies. These tests cover a broad spectrum of organisms, and include the use of naked and viral nucleic acids, bacteria, fungi, higher plants, insects in vitro mammalian cell cultures (cell transformation, cell-mediated mutagenesis, DNA repair, and chromosome aberration tests) and live mammals. Assay end points include effects on nucleic acids, DNA repair synthesis, point or gene mutation, structural and numerical chromosome aberrations, cytological alterations, and in vitro cell transformation. The present review describes and compares these assays. In addition, it discusses their historical development, the problems and limitations associated with their use, and their implementation in comprehensive testing programs. It is intended to provide overview and specific information to the laboratory that is in the process of establishing genetic toxicological systems. (The literature is reviewed to January 1978.)

  9. Rapid Diagnostic Tests for Malaria: A Review

    Science.gov (United States)

    2005-06-01

    4.92% 0% 100% [25] France** 557 15.5% 1.3%*** 100% 14.3% 1.3%*** 100% [26] Kuwait** 240 0% - 75.4% - - - [27] Peru 72 - - - 7.7% 0% 100% [28...expression of aldolase isoenzymes in the rodent malaria parasite Plasmodium berghei. Mol. Biochem. Parasitol., 52, 15-27. [21] Cloonan, N., Fischer...R. L. (2003). Performance of an immunochromatography test for vivax malaria in the Amazon region, Brazil. Rev. Saude Publica, 37, 390-392. [69

  10. A Review of Multiple Hypothesis Testing in Otolaryngology Literature

    Science.gov (United States)

    Kirkham, Erin M.; Weaver, Edward M.

    2018-01-01

    Objective Multiple hypothesis testing (or multiple testing) refers to testing more than one hypothesis within a single analysis, and can inflate the Type I error rate (false positives) within a study. The aim of this review was to quantify multiple testing in recent large clinical studies in the otolaryngology literature and to discuss strategies to address this potential problem. Data sources Original clinical research articles with >100 subjects published in 2012 in the four general otolaryngology journals with the highest Journal Citation Reports 5-year impact factors. Review methods Articles were reviewed to determine whether the authors tested greater than five hypotheses in at least one family of inferences. For the articles meeting this criterion for multiple testing, Type I error rates were calculated and statistical correction was applied to the reported results. Results Of the 195 original clinical research articles reviewed, 72% met the criterion for multiple testing. Within these studies, there was a mean 41% chance of a Type I error and, on average, 18% of significant results were likely to be false positives. After the Bonferroni correction was applied, only 57% of significant results reported within the articles remained significant. Conclusion Multiple testing is common in recent large clinical studies in otolaryngology and deserves closer attention from researchers, reviewers and editors. Strategies for adjusting for multiple testing are discussed. PMID:25111574

  11. Test Marketing Exemption (TME) for New Chemical Review under TSCA

    Science.gov (United States)

    Under section 5 of TSCA, EPA established an exemption for certain chemicals that are manufactured (including imported) for test marketing. You can learn more here about the requirements of this exemption, along with the review and submission process.

  12. Metabolic activation of polycyclic and heterocyclic aromatic hydrocarbons and DNA damage: A review

    International Nuclear Information System (INIS)

    Xue Weiling; Warshawsky, David

    2005-01-01

    Polycyclic aromatic hydrocarbons (PAHs) and heterocyclic aromatic compounds (HACs) constitute a major class of chemical carcinogens present in the environment. These compounds require activation to electrophilic metabolites to exert their mutagenic or carcinogenic effects. There are three principal pathways currently proposed for metabolic activation of PAH and HAC: the pathway via bay region dihydrodiol epoxide by cytochrome P450 enzymes (CYPs), the pathway via radical cation by one-electron oxidation, and the ortho-quinone pathway by dihydrodiol dehydrogenase (DD). In addition to these major pathways, a brief description of a minor metabolic activation pathway, sulfonation, for PAHs that contain a primary benzylic alcoholic group or secondary hydroxyl group(s) is included in this review. The DNA damages caused through the reactive metabolites of PAH/HAC are described involving the DNA covalent binding to form stable or depurinating adducts, the formation of apurinic sites, and the oxidative damage. The review emphasizes the chemical/biochemical reactions involved in the metabolic processes and the chemical structures of metabolites and DNA adducts

  13. 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.

  14. 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...

  15. 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

  16. 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.

  17. 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.)

  18. 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.)

  19. 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.

  20. 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.

  1. Non-invasive prenatal testing for fetal chromosome abnormalities: review of clinical and ethical issues

    Directory of Open Access Journals (Sweden)

    Gekas J

    2016-02-01

    Full Text Available Jean Gekas,1,2 Sylvie Langlois,3 Vardit Ravitsky,4 François Audibert,5 David Gradus van den Berg,6 Hazar Haidar,4 François Rousseau2,7 1Prenatal Diagnosis Unit, Department of Medical Genetics and Pediatrics, Faculty of Medicine, Université Laval, Québec City, QC, Canada; 2Department of Medical Biology, CHU de Québec, Québec City, QC, Canada; 3Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; 4Bioethics Program, Department of Social and Preventive Medicine, School of Public Health, University of Montreal, Montreal, QC, Canada; 5Department of Obstetrics and Gynecology, Hospital Sainte-Justine, Montreal, QC, Canada; 6Department of Social and Preventive Medicine, Faculty of Medicine, Université Laval, Québec City, QC, Canada; 7Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Québec City, QC, Canada Abstract: Genomics-based non-invasive prenatal screening using cell-free DNA (cfDNA screening was proposed to reduce the number of invasive procedures in current prenatal diagnosis for fetal aneuploidies. We review here the clinical and ethical issues of cfDNA screening. To date, it is not clear how cfDNA screening is going to impact the performances of clinical prenatal diagnosis and how it could be incorporated in real life. The direct marketing to users may have facilitated the early introduction of cfDNA screening into clinical practice despite limited evidence-based independent research data supporting this rapid shift. There is a need to address the most important ethical, legal, and social issues before its implementation in a mass setting. Its introduction might worsen current tendencies to neglect the reproductive autonomy of pregnant women. Keywords: prenatal diagnosis, Down syndrome, non-invasive prenatal testing, cell-free fetal DNA, informed consent, reproductive autonomy

  2. 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.

  3. 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.

  4. 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.

  5. 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...

  6. 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.

  7. 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.

  8. Test methods for evaluating hot cracking: Review and perspective

    International Nuclear Information System (INIS)

    Goodwin, G.M.

    1990-01-01

    The phenomenon of hot cracking is described and discussed, and criteria for tests to assess hot cracking are elucidated. The historical development of hot cracking tests is traced from the 1930s to present, with categorization of tests into several types. It is noted that the number of tests developed continues to increase dramatically. The number of literature citations also increases with time, with few popular tests receiving a major share of interest. Predominant countries of origin of both tests and citations shift with time, and a few journals account for most of the published information. Reviews of hot cracking are reviewed, and it is predicted that modeling and other developing analytical techniques will contribute greatly to an increase in our understanding of hot cracking. 30 refs., 10 figs., 1 tab

  9. 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).

  10. Non-Invasive Prenatal Testing: Review of Ethical, Legal and Social Implications

    Directory of Open Access Journals (Sweden)

    Haidar, Hazar

    2016-02-01

    Full Text Available Non-invasive prenatal testing (NIPT using cell-free fetal DNA (cffDNA from maternal blood has recently entered clinical practice in many countries, including Canada. This test can be performed early during pregnancy to detect Down syndrome and other conditions. While NIPT promises numerous benefits, it also has challenging ethical, legal and social implications (ELSI. This paper reviews concerns currently found in the literature on the ELSI of NIPT. We make four observations. First, NIPT seems to exacerbate some of the already existing concerns raised by other prenatal tests (amniocentesis and maternal serum screening such as threats to women’s reproductive autonomy and the potential for discrimination and stigmatization of disabled individuals and their families. This may be due to the likely upcoming large scale implementation and routinization of NIPT. Second, the distinction between NIPT as a screening test (as it is currently recommended and as a diagnostic test (potentially in the future, has certain implications for the ELSI discussion. Third, we observed a progressive shift in the literature from initially including mostly conceptual analysis to an increasing number of empirical studies. This demonstrates the contribution of empirical bioethics approaches as the technology is being implemented into clinical use. Finally, we noted an increasing interest in equity and justice concerns regarding access to NIPT as it becomes more widely implemented.

  11. Review of Department of Energy HEPA filter test activities

    International Nuclear Information System (INIS)

    McIntyre, J.A.

    1993-01-01

    Filter Test Facilities (FTFs) and the FTF Technical Support Group (TSG) continue to provide services to the Department of Energy (DOE). Additional tasks relating to the HEPA filter cycle have been added to the TSG. The tasks include the quality assessment review for the in-place testing of HEPA filters at DOE sites and the formation of an in-place testing standards writing group. Summary of ongoing FTFs and TSG activities for FY 1990-FY 1992 including the technical input for implementation of the High Flow Alternative Test System (HFATS), update of the DOE Standards, the status of the quality assessment review and in-place testing standards writing group are discussed

  12. The Role of DNA Methylation and Histone Modifications in Neurodegenerative Diseases: A Systematic Review.

    Directory of Open Access Journals (Sweden)

    Ke-Xin Wen

    Full Text Available Epigenetic modifications of the genome, such as DNA methylation and histone modifications, have been reported to play a role in neurodegenerative diseases (ND such as Alzheimer's disease (AD and Parkinson's disease (PD.To systematically review studies investigating epigenetic marks in AD or PD.Eleven bibliographic databases (Embase.com, Medline (Ovid, Web-of-Science, Scopus, PubMed, Cinahl (EBSCOhost, Cochrane Central, ProQuest, Lilacs, Scielo and Google Scholar were searched until July 11th 2016 to identify relevant articles. We included all randomized controlled trials, cohort, case-control and cross-sectional studies in humans that examined associations between epigenetic marks and ND. Two independent reviewers, with a third reviewer available for disagreements, performed the abstract and full text selection. Data was extracted using a pre-designed data collection form.Of 6,927 searched references, 73 unique case-control studies met our inclusion criteria. Overall, 11,453 individuals were included in this systematic review (2,640 AD and 2,368 PD outcomes. There was no consistent association between global DNA methylation pattern and any ND. Studies reported epigenetic regulation of 31 genes (including cell communication, apoptosis, and neurogenesis genes in blood and brain tissue in relation to AD and PD. Methylation at the BDNF, SORBS3 and APP genes in AD were the most consistently reported associations. Methylation of α-synuclein gene (SNCA was also found to be associated with PD. Seven studies reported histone protein alterations in AD and PD.Many studies have investigated epigenetics and ND. Further research should include larger cohort or longitudinal studies, in order to identify clinically significant epigenetic changes. Identifying relevant epigenetic changes could lead to interventional strategies in ND.

  13. "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

    with the lowest zip code in each state, we took every fifth name from the directory, excluding providers who were retired, did not currently practice in the state in which they were listed, or were not involved in a prenatal specialty. After repeating this step twice and sending a total of 461 invitations, 37 providers expressed interest in participating, and we completed telephone interviews with 21 providers (4.6%). We developed a semi-structured interview guide including questions about providers' use of and attitudes toward cfDNA screening. A single interviewer conducted and audio-recorded all interviews by telephone, and the interviews lasted approximately 30 minutes each. We collaboratively developed a codebook through an iterative process of transcript review and code application, and a primary coder coded all transcripts. Prenatal care providers have varying perspectives on the advantages of cfDNA screening and express a range of concerns regarding the implementation of cfDNA screening in practice. While providers agreed on several advantages of cfDNA, including increased accuracy, earlier return of results, and decreased risk of complications, many expressed concern that there is not enough time to adequately counsel and educate patients on their prenatal screening and testing options. Providers also agreed that demand for cfDNA screening has increased and expressed a desire for more information from professional societies, labs, and publications. Providers disagreed about the healthcare implications and future of cfDNA screening. Some providers anticipated that cfDNA screening would decrease healthcare costs when implemented widely and expressed optimism for expanded cfDNA screening panels. Others were concerned that cfDNA screening would increase costs over time and questioned whether the expansion to include microdeletions could be done ethically. The perspectives and experiences of the providers in this study allow insight into the clinical benefit, burden

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. Test Review: Test of English as a Foreign Language[TM]--Internet-Based Test (TOEFL iBT[R])

    Science.gov (United States)

    Alderson, J. Charles

    2009-01-01

    In this article, the author reviews the TOEFL iBT which is the latest version of the TOEFL, whose history stretches back to 1961. The TOEFL iBT was introduced in the USA, Canada, France, Germany and Italy in late 2005. Currently the TOEFL test is offered in two testing formats: (1) Internet-based testing (iBT); and (2) paper-based testing (PBT).…

  2. A narrative review of manual muscle testing and implications for muscle testing research.

    Science.gov (United States)

    Conable, Katharine M; Rosner, Anthony L

    2011-09-01

    Manual muscle testing (MMT) is used for a variety of purposes in health care by medical, osteopathic, chiropractic, physical therapy, rehabilitation, and athletic training professionals. The purpose of this study is to provide a narrative review of variations in techniques, durations, and forces used in MMT putting applied kinesiology (AK) muscle testing in context and highlighting aspects of muscle testing important to report in MMT research. PubMed, the Collected Papers of the International College of Applied Kinesiology-USA, and related texts were searched on the subjects of MMT, maximum voluntary isometric contraction testing, and make/break testing. Force parameters (magnitude, duration, timing of application), testing variations of MMT, and normative data were collected and evaluated. "Break" tests aim to evaluate the muscle's ability to resist a gradually increasing pressure and may test different aspects of neuromuscular control than tests against fixed resistances. Applied kinesiologists use submaximal manual break tests and a binary grading scale to test short-term changes in muscle function in response to challenges. Many of the studies reviewed were not consistent in reporting parameters for testing. To increase the chances for replication, studies using MMT should specify parameters of the tests used, such as exact procedures and instrumentation, duration of test, peak force, and timing of application of force. Copyright © 2011 National University of Health Sciences. Published by Elsevier Inc. All rights reserved.

  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. Fuels for research and test reactors, status review: July 1982

    International Nuclear Information System (INIS)

    Stahl, D.

    1982-12-01

    A thorough review is provided on nuclear fuels for steady-state thermal research and test reactors. The review was conducted to provide a documented data base in support of recent advances in research and test reactor fuel development, manufacture, and demonstration in response to current US policy on availability of enriched uranium. The review covers current fabrication practice, fabrication development efforts, irradiation performance, and properties affecting fuel utilization, including thermal conductivity, specific heat, density, thermal expansion, corrosion, phase stability, mechanical properties, and fission-product release. The emphasis is on US activities, but major work in Europe and elsewhere is included. The standard fuel types discussed are the U-Al alloy, UZrH/sub x/, and UO 2 rod fuels. Among new fuels, those given major emphasis include H 3 Si-Al dispersion and UO 2 caramel plate fuels

  6. 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

  7. 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

  8. Review of tolerances at the Final Focus Test Beam

    International Nuclear Information System (INIS)

    Bulos, F.; Burke, D.; Helm, R.; Irwin, J.; Roy, G.; Yamamoto, N.

    1991-01-01

    The authors review the tolerances associated with the Final Focus Test Beam (FFTB). The authors have computed the acceptability window of the input beam for orbit jitter, emittance beta functions mismatch, incoming dispersion and coupling; tolerances on magnet alignment, strength and multipole content; and the initial tuneability capture of the line

  9. Review of tolerances at the Final Focus Test Beam

    International Nuclear Information System (INIS)

    Bulos, F.; Burke, D.; Helm, R.; Irwin, J.; Roy, G.; Yamamoto, N.

    1991-05-01

    We review the tolerances associated with the Final Focus Test Beam (FFTB). We have computed the acceptability window of the input beam for orbit jitter, emittance beta functions mismatch, incoming dispersion and coupling; tolerances on magnet alignment, strength and multipole content; and the initial tuneability capture of the line. 2 refs., 1 fig

  10. 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.

  11. 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.

  12. Test Anxiety among Foreign Language Learners: A Review of Literature

    Directory of Open Access Journals (Sweden)

    Selami Aydın

    2009-04-01

    Full Text Available The findings obtained from previous research indicate that test anxiety has significant effects on the foreign language learning process. Thus, this paper aims to present a synthesis of research results on the sources and effects of test anxiety among foreign language learners. The results of the studies reviewed in the paper were mainly categorized under two sub-sections: the sources and effects of test anxiety. It is expected that the study will not only contribute to the limited research on the subject in Turkey, but also help increase the awareness among target groups such as learners, teacher and examiners.

  13. 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

  14. Background review for diagnostic test development for Zika virus infection.

    Science.gov (United States)

    Charrel, Rémi N; Leparc-Goffart, Isabelle; Pas, Suzan; de Lamballerie, Xavier; Koopmans, Marion; Reusken, Chantal

    2016-08-01

    To review the state of knowledge about diagnostic testing for Zika virus infection and identify areas of research needed to address the current gaps in knowledge. We made a non-systematic review of the published literature about Zika virus and supplemented this with information from commercial diagnostic test kits and personal communications with researchers in European preparedness networks. The review covered current knowledge about the geographical spread, pathogen characteristics, life cycle and infection kinetics of the virus. The available molecular and serological tests and biosafety issues are described and discussed in the context of the current outbreak strain. We identified the following areas of research to address current knowledge gaps: (i) an urgent assessment of the laboratory capacity and capability of countries to detect Zika virus; (ii) rapid and extensive field validation of the available molecular and serological tests in areas with and without Zika virus transmission, with a focus on pregnant women; (iii) monitoring the genomic diversity of circulating Zika virus strains; (iv) prospective studies into the virus infection kinetics, focusing on diagnostic sampling (specimen types, combinations and timings); and (v) developing external quality assessments for molecular and serological testing, including differential diagnosis for similar viruses and symptom clusters. The availability of reagents for diagnostic development (virus strains and antigens, quantified viral ribonucleic acid) needs to be facilitated. An international laboratory response is needed, including preparation of protocols for prospective studies to address the most pressing information needs.

  15. DNA repair gene polymorphisms and risk of cutaneous melanoma: a systematic review and meta-analysis.

    Science.gov (United States)

    Mocellin, Simone; Verdi, Daunia; Nitti, Donato

    2009-10-01

    Polymorphisms of DNA repair-related genes might modulate cancer predisposition. We performed a systematic review and meta-analysis of the available evidence regarding the relationship between these polymorphisms and the risk of developing cutaneous melanoma. Relevant studies were searched using PubMed, Medline, Embase, Cancerlit, Cochrane and ISI Web of Knowledge databases. Data were gathered according to the Meta-analysis Of Observational Studies in Epidemiology (MOOSE) guidelines. The model-free approach was adopted to perform the meta-analysis of the retrieved data. We identified 20 original reports that describe the relationship between melanoma risk and the single-nucleotide polymorphisms (SNPs) of 16 genes (cases = 4195). For seven SNPs considered in at least two studies, the findings were heterogeneous. Data were suitable for meta-analysis only in the case of the XPD/ERCC2 SNP rs13181 (cases = 2308, controls = 3698) and demonstrated that the variant C allele is associated with increased melanoma risk (odds ratio = 1.12, 95% confidence interval = 1.03-1.21, P = 0.01; population attributable risk = 9.6%). This is the first meta-analysis suggesting that XPD/ERCC2 might represent a low-penetrance melanoma susceptibility gene. Much work is still to be done before definitive conclusions can be drawn on the role of DNA repair alterations in melanomagenesis since for the other genes involved in this highly complex process, the available information is scarce or null.

  16. Personal utility in genomic testing: a systematic literature review.

    Science.gov (United States)

    Kohler, Jennefer N; Turbitt, Erin; Biesecker, Barbara B

    2017-06-01

    Researchers and clinicians refer to outcomes of genomic testing that extend beyond clinical utility as 'personal utility'. No systematic delineation of personal utility exists, making it challenging to appreciate its scope. Identifying empirical elements of personal utility reported in the literature offers an inventory that can be subsequently ranked for its relative value by those who have undergone genomic testing. A systematic review was conducted of the peer-reviewed literature reporting non-health-related outcomes of genomic testing from 1 January 2003 to 5 August 2016. Inclusion criteria specified English language, date of publication, and presence of empirical evidence. Identified outcomes were iteratively coded into unique domains. The search returned 551 abstracts from which 31 studies met the inclusion criteria. Study populations and type of genomic testing varied. Coding resulted in 15 distinct elements of personal utility, organized into three domains related to personal outcomes: affective, cognitive, and behavioral; and one domain related to social outcomes. The domains of personal utility may inform pre-test counseling by helping patients anticipate potential value of test results beyond clinical utility. Identified elements may also inform investigations into the prevalence and importance of personal utility to future test users.

  17. Pharmacists performing quality spirometry testing: an evidence based review.

    Science.gov (United States)

    Cawley, Michael J; Warning, William J

    2015-10-01

    The scope of pharmacist services for patients with pulmonary disease has primarily focused on drug related outcomes; however pharmacists have the ability to broaden the scope of clinical services by performing diagnostic testing including quality spirometry testing. Studies have demonstrated that pharmacists can perform quality spirometry testing based upon international guidelines. The primary aim of this review was to assess the published evidence of pharmacists performing quality spirometry testing based upon American Thoracic Society/European Respiratory Society (ATS/ERS) guidelines. In order to accomplish this, the description of evidence and type of outcome from these services were reviewed. A literature search was conducted using five databases [PubMed (1946-January 2015), International Pharmaceutical Abstracts (1970 to January 2015), Cumulative Index of Nursing and Allied Health Literature, Cochrane Central Register of Controlled Trials and Cochrane Database of Systematic Reviews] with search terms including pharmacy, spirometry, pulmonary function, asthma or COPD was conducted. Searches were limited to publications in English and reported in humans. In addition, Uniform Resource Locators and Google Scholar searches were implemented to include any additional supplemental information. Eight studies (six prospective multi-center trials, two retrospective single center studies) were included. Pharmacists in all studies received specialized training in performing spirometry testing. Of the eight studies meeting inclusion and exclusion criteria, 8 (100%) demonstrated acceptable repeatability of spirometry testing based upon standards set by the ATS/ERS guidelines. Acceptable repeatability of seven studies ranged from 70 to 99% consistent with published data. Available evidence suggests that quality spirometry testing can be performed by pharmacists. More prospective studies are needed to add to the current evidence of quality spirometry testing performed by

  18. Applicability of the comet assay in evaluation of DNA damage in healthcare providers' working with antineoplastic drugs: a systematic review and meta-analysis.

    Science.gov (United States)

    Zare Sakhvidi, Mohammad Javad; Hajaghazadeh, Mohammad; Mostaghaci, Mehrdad; Mehrparvar, Amir Houshang; Zare Sakhvidi, Fariba; Naghshineh, Elham

    2016-01-01

    Unintended occupational exposure to antineoplastic drugs (ANDs) may occur in medical personnel. Some ANDs are known human carcinogens and exposure can be monitored by genotoxic biomarkers. To evaluate the obstacles to obtaining conclusive results from a comet assay test to determine DNA damage among AND exposed healthcare workers. We systematically reviewed studies that used alkaline comet assay to determine the magnitude and significance of DNA damage among health care workers with potential AND exposure. Fifteen studies were eligible for review and 14 studies were used in the meta-analysis. Under random effect assumption, the estimated standardized mean difference (SMD) in the DNA damage of health care workers was 1.93 (95% CI: 1.15-2.71, p comet moment, I2 test results, as a measure of heterogeneity, dropped to zero. Heterogeneity analysis showed that date of study publication was a possible source of heterogeneity (B = -0.14; p comet assay methodological variables, and exposure characteristics may be responsible for heterogenic data from comet assay studies and interfere with obtaining conclusive results. Lack of quantitative environmental exposure measures and variation in comet assay protocols across studies are important obstacles in generalization of results.

  19. Applicability of the comet assay in evaluation of DNA damage in healthcare providers’ working with antineoplastic drugs: a systematic review and meta-analysis

    Science.gov (United States)

    Zare Sakhvidi, Mohammad Javad; Hajaghazadeh, Mohammad; Mostaghaci, Mehrdad; Mehrparvar, Amir houshang; Zare Sakhvidi, Fariba; Naghshineh, Elham

    2016-01-01

    Background Unintended occupational exposure to antineoplastic drugs (ANDs) may occur in medical personnel. Some ANDs are known human carcinogens and exposure can be monitored by genotoxic biomarkers. Objective To evaluate the obstacles to obtaining conclusive results from a comet assay test to determine DNA damage among AND exposed healthcare workers. Methods We systematically reviewed studies that used alkaline comet assay to determine the magnitude and significance of DNA damage among health care workers with potential AND exposure. Fifteen studies were eligible for review and 14 studies were used in the meta-analysis. Results Under random effect assumption, the estimated standardized mean difference (SMD) in the DNA damage of health care workers was 1.93 (95% CI: 1.15–2.71, p comet moment, I2 test results, as a measure of heterogeneity, dropped to zero. Heterogeneity analysis showed that date of study publication was a possible source of heterogeneity (B = −0.14; p comet assay methodological variables, and exposure characteristics may be responsible for heterogenic data from comet assay studies and interfere with obtaining conclusive results. Lack of quantitative environmental exposure measures and variation in comet assay protocols across studies are important obstacles in generalization of results. PMID:27110842

  20. 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

  1. Effects of latent fingerprint development reagents on subsequent forensic DNA typing: a review.

    Science.gov (United States)

    Kumar, Parveen; Gupta, Ritika; Singh, Rajinder; Jasuja, Om Prakash

    2015-05-01

    Successful development of latent fingerprints can be helpful in solving the case but in case where fingerprints are smudged, distorted or overlapped, the question arises whether it is still possible to identify the person apart from dermatoglyphic features. Sweat residue present in the latent prints is supposed to have quite good quantity of cellular material which if analyzed properly can be used to generate forensic DNA profile of the individual and may answer the queries related to the effect of reagents used to develop the prints, as they may have a significant effect on the process of examination of this evidentiary material. In the present work an effort has been made to summarize the published review of literature on this aspect of personal identification. Copyright © 2015 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

  2. Stress, burnout and depression: A systematic review on DNA methylation mechanisms.

    Science.gov (United States)

    Bakusic, Jelena; Schaufeli, Wilmar; Claes, Stephan; Godderis, Lode

    2017-01-01

    Despite that burnout presents a serious burden for modern society, there are no diagnostic criteria. Additional difficulty is the differential diagnosis with depression. Consequently, there is a need to dispose of a burnout biomarker. Epigenetic studies suggest that DNA methylation is a possible mediator linking individual response to stress and psychopathology and could be considered as a potential biomarker of stress-related mental disorders. Thus, the aim of this review is to provide an overview of DNA methylation mechanisms in stress, burnout and depression. In addition to state-of-the-art overview, the goal of this review is to provide a scientific base for burnout biomarker research. We performed a systematic literature search and identified 25 pertinent articles. Among these, 15 focused on depression, 7 on chronic stress and only 3 on work stress/burnout. Three epigenome-wide studies were identified and the majority of studies used the candidate-gene approach, assessing 12 different genes. The glucocorticoid receptor gene (NR3C1) displayed different methylation patterns in chronic stress and depression. The serotonin transporter gene (SLC6A4) methylation was similarly affected in stress, depression and burnout. Work-related stress and depressive symptoms were associated with different methylation patterns of the brain derived neurotrophic factor gene (BDNF) in the same human sample. The tyrosine hydroxylase (TH) methylation was correlated with work stress in a single study. Additional, thoroughly designed longitudinal studies are necessary for revealing the cause-effect relationship of work stress, epigenetics and burnout, including its overlap with depression. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. 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

  4. Improving Molecular Genetic Test Utilization through Order Restriction, Test Review, and Guidance.

    Science.gov (United States)

    Riley, Jacquelyn D; Procop, Gary W; Kottke-Marchant, Kandice; Wyllie, Robert; Lacbawan, Felicitas L

    2015-05-01

    The ordering of molecular genetic tests by health providers not well trained in genetics may have a variety of untoward effects. These include the selection of inappropriate tests, the ordering of panels when the assessment of individual or fewer genes would be more appropriate, inaccurate result interpretation and inappropriate patient guidance, and significant unwarranted cost expenditure. We sought to improve the utilization of molecular genetic tests by requiring providers without specialty training in genetics to use genetic counselors and molecular genetic pathologists to assist in test selection. We used a genetic and genomic test review process wherein the laboratory-based genetic counselor performed the preanalytic assessment of test orders and test triage. Test indication and clinical findings were evaluated against the test panel composition, methods, and test limitations under the supervision of the molecular genetic pathologist. These test utilization management efforts resulted in a decrease in genetic test ordering and a gross cost savings of $1,531,913 since the inception of these programs in September 2011 through December 2013. The combination of limiting the availability of complex genetic tests and providing guidance regarding appropriate test strategies is an effective way to improve genetic tests, contributing to judicious use of limited health care resources. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  5. Genetic Testing in Psychiatry: A Review of Attitudes and Beliefs

    Science.gov (United States)

    Lawrence, Ryan E; Appelbaum, Paul S.

    2012-01-01

    The advent of genetic testing for psychiatric conditions raises difficult questions about when and how the tests should be used. Development of policies regarding these issues may be informed in a variety of ways by the views of key stakeholders: patients, family members, healthcare professionals, and the general public. Here we review empirical studies of attitudes towards genetic testing among these groups. Patients and family members show strong interest in diagnostic and predictive genetic testing, and to a considerable extent psychiatrists share their enthusiasm. Prenatal test utilization seems likely to depend both on parental views on abortion and the seriousness of the disorder. Parents show a surprising degree of interest in predictive testing of children, even when there are no preventive interventions available. Many persons report themselves ready to alter their lifestyles and plans for marriage and family in response to test results. Respondents also fear negative consequences, from discrimination to being unable to cope with knowledge of their “genetic fate.” Empirical studies of beliefs about genetic testing suggest tests are likely to be embraced widely, but the studies have methodologic limitations, reducing the certainty of their conclusions, and indicating a need for further research with more representative samples. PMID:22168293

  6. [Test Reviews in Child Psychology: Test Users Wish to Obtain Practical Information Relevant to their Respective Field of Work].

    Science.gov (United States)

    Renner, Gerolf; Irblich, Dieter

    2016-11-01

    Test Reviews in Child Psychology: Test Users Wish to Obtain Practical Information Relevant to their Respective Field of Work This study investigated to what extent diagnosticians use reviews of psychometric tests for children and adolescents, how they evaluate their quality, and what they expect concerning content. Test users (n = 323) from different areas of work (notably social pediatrics, early intervention, special education, speech and language therapy) rated test reviews as one of the most important sources of information. Readers of test reviews value practically oriented descriptions and evaluations of tests that are relevant to their respective field of work. They expect independent reviews that critically discuss opportunities and limits of the tests under scrutiny. The results show that authors of test reviews should not only have a background in test theory but should also be familiar with the practical application of tests in various settings.

  7. MPV17-related mitochondrial DNA maintenance defect: New cases and review of clinical, biochemical, and molecular aspects.

    Science.gov (United States)

    El-Hattab, Ayman W; Wang, Julia; Dai, Hongzheng; Almannai, Mohammed; Staufner, Christian; Alfadhel, Majid; Gambello, Michael J; Prasun, Pankaj; Raza, Saleem; Lyons, Hernando J; Afqi, Manal; Saleh, Mohammed A M; Faqeih, Eissa A; Alzaidan, Hamad I; Alshenqiti, Abduljabbar; Flore, Leigh Anne; Hertecant, Jozef; Sacharow, Stephanie; Barbouth, Deborah S; Murayama, Kei; Shah, Amit A; Lin, Henry C; Wong, Lee-Jun C

    2018-04-01

    Mitochondrial DNA (mtDNA) maintenance defects are a group of diseases caused by deficiency of proteins involved in mtDNA synthesis, mitochondrial nucleotide supply, or mitochondrial dynamics. One of the mtDNA maintenance proteins is MPV17, which is a mitochondrial inner membrane protein involved in importing deoxynucleotides into the mitochondria. In 2006, pathogenic variants in MPV17 were first reported to cause infantile-onset hepatocerebral mtDNA depletion syndrome and Navajo neurohepatopathy. To date, 75 individuals with MPV17-related mtDNA maintenance defect have been reported with 39 different MPV17 pathogenic variants. In this report, we present an additional 25 affected individuals with nine novel MPV17 pathogenic variants. We summarize the clinical features of all 100 affected individuals and review the total 48 MPV17 pathogenic variants. The vast majority of affected individuals presented with an early-onset encephalohepatopathic disease characterized by hepatic and neurological manifestations, failure to thrive, lactic acidemia, and mtDNA depletion detected mainly in liver tissue. Rarely, MPV17 deficiency can cause a late-onset neuromyopathic disease characterized by myopathy and peripheral neuropathy with no or minimal liver involvement. Approximately half of the MPV17 pathogenic variants are missense. A genotype with biallelic missense variants, in particular homozygous p.R50Q, p.P98L, and p.R41Q, can carry a relatively better prognosis. © 2017 Wiley Periodicals, Inc.

  8. 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...

  9. [SUCLA2-related encephalomyopathic mitochondrial DNA depletion syndrome: a case report and review of literature].

    Science.gov (United States)

    Liu, Zhimei; Fang, Fang; Ding, Changhong; Wu, Husheng; Lyu, Junlan; Wu, Yun

    2014-11-01

    To analyze the clinical characteristics of SUCLA2-related encephalomyopathic mitochondrial DNA depletion syndrome (MDS) in one patient, and review the latest clinical research reports. Clinical, laboratory and genetic data of one case of SUCLA2-related encephalomyopathic MDS diagnosed by department of Neurology, Beijing Children's Hospital in November, 2013 were reported, and through taking "SUCLA2" as key words to search at CNKI, Wanfang, PubMed and the Human Gene Mutation Database (HGMD) professional to date, the clinical characteristics of 24 reported cases of SUCLA2-related encephalomyopathic MDS in international literature in combination with our case were analyzed. (1) The patient was 5 years and 9 months old, born as a term small for gestational age infant whose birth weight was 2 400 g, and presented since birth with severe muscular hypotonia, feeding difficulties, failure to thrive, psychomotor retardation and hearing impairment. Until now, he still showed severe developmental retardation, together with muscular atrophy, thoracocyllosis and scoliosis, and facial features. The patient is the first born from consanguineous healthy parents, whose relationship is cousins. Laboratory tests showed urinary excretion of mild methylmalonic acid (MMA), elevated plasma lactate concentration, and increased C3-carnitine and C4-dicarboxylic-carnitine in plasma carnitine ester profiling. MRI showed brain atrophy-like and bilateral T2 hyperintensities in bilateral caudate nuclei and putamen. By Next-Generation Sequencing (NGS), we identified a novel homozygous missense mutation (c.970G > A) in the SUCLA2 in a highly conserved amino acid residue. (2) The total number was only 25 with a male to female ratio of 14: 11, and age of onset of 23 was 0-4 months. The most common clinical features in patients with SUCLA2 mutation were permanent hypotonia, muscle atrophy, psychomotor retardation and scoliosis or kyphosis. Frequent signs included hearing impairment, hyperkinesia

  10. 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.

  11. Theoretical frameworks for testing relativistic gravity: A review

    Science.gov (United States)

    Thorne, K. S.; Will, C. M.; Ni, W.

    1971-01-01

    Metric theories of gravity are presented, including the definition of metric theory, evidence for its existence, and response of matter to gravity with test body trajectories, gravitational red shift, and stressed matter responses. Parametrized post-Newtonian framework and interpretations are reviewed. Gamma, beta and gamma, and varied other parameters were measured. Deflection of electromagnetic waves, radar time delay, geodetic gyroscope precession, perihelion shifts, and periodic effects in orbits are among various studies carried out for metric theory experimentation.

  12. 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

  13. Review of Artificial Abrasion Test Methods for PV Module Technology

    Energy Technology Data Exchange (ETDEWEB)

    Miller, David C. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Muller, Matt T. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Simpson, Lin J. [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2016-08-01

    This review is intended to identify the method or methods--and the basic details of those methods--that might be used to develop an artificial abrasion test. Methods used in the PV literature were compared with their closest implementation in existing standards. Also, meetings of the International PV Quality Assurance Task Force Task Group 12-3 (TG12-3, which is concerned with coated glass) were used to identify established test methods. Feedback from the group, which included many of the authors from the PV literature, included insights not explored within the literature itself. The combined experience and examples from the literature are intended to provide an assessment of the present industry practices and an informed path forward. Recommendations toward artificial abrasion test methods are then identified based on the experiences in the literature and feedback from the PV community. The review here is strictly focused on abrasion. Assessment methods, including optical performance (e.g., transmittance or reflectance), surface energy, and verification of chemical composition were not examined. Methods of artificially soiling PV modules or other specimens were not examined. The weathering of artificial or naturally soiled specimens (which may ultimately include combined temperature and humidity, thermal cycling and ultraviolet light) were also not examined. A sense of the purpose or application of an abrasion test method within the PV industry should, however, be evident from the literature.

  14. 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

  15. 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

  16. 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

  17. Tritium Systems Test Assembly: design for major device fabrication review

    International Nuclear Information System (INIS)

    Anderson, J.L.; Sherman, R.H.

    1977-06-01

    This document has been prepared for the Major Device Fabrication Review for the Tritium Systems Test Assembly (TSTA). The TSTA is dedicated to the development, demonstration, and interfacing of technologies related to the deuterium-tritium fuel cycle for fusion reactor systems. The principal objectives for TSTA are: (a) demonstrate the fuel cycle for fusion reactor systems; (b) develop test and qualify equipment for tritium service in the fusion program; (c) develop and test environmental and personnel protective systems; (d) evaluate long-term reliability of components; (e) demonstrate long-term safe handling of tritium with no major releases or incidents; and (f) investigate and evaluate the response of the fuel cycle and environmental packages to normal, off-normal, and emergency situations. This document presents the current status of a conceptual design and cost estimate for TSTA. The total cost to design, construct, and operate TSTA through FY-1981 is estimated to be approximately $12.2 M

  18. Microgrids research: A review of experimental microgrids and test systems

    Energy Technology Data Exchange (ETDEWEB)

    Lidula, N.W.A.; Rajapakse, A.D. [Department of Electrical and Computer Engineering, 75A Chancellor' s Circle, University of Manitoba, Winnipeg, Manitoba R3T 5V6 (Canada)

    2011-01-15

    A microgrid is particularly a portion of the power distribution system that comprises distributed generation, energy storage and loads. To be capable of operating in parallel to the grid, as an autonomous power island and in transition modes, microgrids must be robust in controlling the local voltage and frequency, and protecting the network and equipment connected to the microgrid. It also needs to facilitate demand side management and resynchronization. This paper presents a review of existing microgrid test networks around the world (North America, Europe and Asia) and some significantly different microgrid simulation networks present in the literature. Paper is focused on the test systems and available microgrid control options. A summary table comparing and contrasting the existing test systems is presented. The paper is concluded highlighting the worthy findings and possible areas of research that would enhance practical use of microgrid facilities. (author)

  19. 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.

  20. Inner ear test battery in guinea pig models - a review.

    Science.gov (United States)

    Young, Yi-Ho

    2018-06-01

    This study reviewed the development of the inner ear test battery comprising auditory brainstem response (ABR), and caloric, ocular vestibular-evoked myogenic potential (oVEMP), and cervical vestibular-evoked myogenic potential (cVEMP) tests in guinea pig models at our laboratory over the last 20 years. Detailed description of the methodology for testing the small animals is also included. Inner ear disorders, i.e. ototoxicity, noise exposure, or perilymph fistula were established in guinea pig models first. One to four weeks after operation, each animal underwent ABR, oVEMP, cVEMP, and caloric tests. Then, animals were sacrificed for morphological study in the temporal bones. Inner ear endorgans can be comprehensively evaluated in guinea pig models via an inner ear test battery, which provides thorough information on the cochlea, saccule, utricle, and semicircular canal function of guinea pigs. Coupled with morphological study in the temporal bones of the animals may help elucidate the mechanism of inner ear disorders in humans. The inner ear test battery in guinea pig models may encourage young researchers to perform basic study in animals and stimulate the progress of experimental otology which is in evolution.

  1. 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...

  2. 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.

  3. 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).

  4. Acceptability of HIV self-testing: a systematic literature review.

    Science.gov (United States)

    Krause, Janne; Subklew-Sehume, Friederike; Kenyon, Chris; Colebunders, Robert

    2013-08-08

    The uptake of HIV testing and counselling services remains low in risk groups around the world. Fear of stigmatisation, discrimination and breach of confidentiality results in low service usage among risk groups. HIV self-testing (HST) is a confidential HIV testing option that enables people to find out their status in the privacy of their homes. We evaluated the acceptability of HST and the benefits and challenges linked to the introduction of HST. A literature review was conducted on the acceptability of HST in projects in which HST was offered to study participants. Besides acceptability rates of HST, accuracy rates of self-testing, referral rates of HIV-positive individuals into medical care, disclosure rates and rates of first-time testers were assessed. In addition, the utilisation rate of a telephone hotline for counselling issues and clients` attitudes towards HST were extracted. Eleven studies met the inclusion criteria (HST had been offered effectively to study participants and had been administered by participants themselves) and demonstrated universally high acceptability of HST among study populations. Studies included populations from resource poor settings (Kenya and Malawi) and from high-income countries (USA, Spain and Singapore). The majority of study participants were able to perform HST accurately with no or little support from trained staff. Participants appreciated the confidentiality and privacy but felt that the provision of adequate counselling services was inadequate. The review demonstrates that HST is an acceptable testing alternative for risk groups and can be performed accurately by the majority of self-testers. Clients especially value the privacy and confidentiality of HST. Linkage to counselling as well as to treatment and care services remain major challenges.

  5. 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...

  6. 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

    High-risk human papillomavirus (hrHPV) causes virtually all cervical cancers. Trans masculine (TM) people (those assigned female at birth who identify with a gender other than female) have low uptake of conventional cervical cancer screening. Self-collected hrHPV DNA testing has high levels of acceptability among cisgender (non-transgender) females and may support increased cervical cancer screening uptake in TM individuals. To assess the test performance and acceptability of self-collected vaginal specimens in comparison to provider-collected cervical swabs for hrHPV DNA detection in TM individuals ages 21-64 years. Between March 2015-September 2016, 150 TM participants with a cervix (mean age = 27.5 years; SD = 5.7) completed a one-time study visit comprised of a self-report survey, self-collected vaginal HPV DNA swab, clinician-administered cervical HPV swab, and brief interview on acceptability of clinical procedures. Participants were randomized to complete either self- or provider-collection first to minimize ordering effects. Self- and provider-collected samples were tested for 13 hrHPV DNA types using a DNA Hybridization Assay. The primary outcome variable was the concordance (kappa statistic) and performance (sensitivity, specificity) of self-collected vaginal HPV DNA specimens versus provider-collected cervical HPV swabs as the gold standard. Of the 131 participants completing both the self- and provider-collected HPV tests, 21 cases of hrHPV were detected by the provider cervical swab (gold standard; 16.0% hrHPV prevalence); 15 of these cases were accurately detected by the self-collected vaginal swab (71.4% concordance) (Kappa = 0.75, 95% Confidence Interval [CI]: 0.59, 0.92; p<0.001). Compared to the provider-collected cervical hrHPV DNA sample (gold standard), the self-collected vaginal hrHPV DNA test demonstrated a sensitivity of 71.4% (95% CI: 0.52, 0.91; p = 0.0495) and specificity of 98.2% (95% CI: 0.96, 1.00; p<0.0001). Over 90% of participants

  7. 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.

  8. Caffeine challenge test and panic disorder: a systematic literature review.

    Science.gov (United States)

    Vilarim, Marina Machado; Rocha Araujo, Daniele Marano; Nardi, Antonio Egidio

    2011-08-01

    This systematic review aimed to examine the results of studies that have investigated the induction of panic attacks and/or the anxiogenic effect of the caffeine challenge test in patients with panic disorder. The literature search was performed in PubMed, Biblioteca Virtual em Saúde and the ISI Web of Knowledge. The words used for the search were caffeine, caffeine challenge test, panic disorder, panic attacks and anxiety disorder. In total, we selected eight randomized, double-blind studies where caffeine was administered orally, and none of them controlled for confounding factors in the analysis. The percentage of loss during follow-up ranged between 14.3% and 73.1%. The eight studies all showed a positive association between caffeine and anxiogenic effects and/or panic disorder.

  9. Separation/extraction, detection, and interpretation of DNA mixtures in forensic science (review).

    Science.gov (United States)

    Tao, Ruiyang; Wang, Shouyu; Zhang, Jiashuo; Zhang, Jingyi; Yang, Zihao; Sheng, Xiang; Hou, Yiping; Zhang, Suhua; Li, Chengtao

    2018-05-25

    Interpreting mixed DNA samples containing material from multiple contributors has long been considered a major challenge in forensic casework, especially when encountering low-template DNA (LT-DNA) or high-order mixtures that may involve missing alleles (dropout) and unrelated alleles (drop-in), among others. In the last decades, extraordinary progress has been made in the analysis of mixed DNA samples, which has led to increasing attention to this research field. The advent of new methods for the separation and extraction of DNA from mixtures, novel or jointly applied genetic markers for detection and reliable interpretation approaches for estimating the weight of evidence, as well as the powerful massively parallel sequencing (MPS) technology, has greatly extended the range of mixed samples that can be correctly analyzed. Here, we summarized the investigative approaches and progress in the field of forensic DNA mixture analysis, hoping to provide some assistance to forensic practitioners and to promote further development involving this issue.

  10. Review: Diagnostic accuracy of PCR-based detection tests for Helicobacter Pylori in stool samples.

    Science.gov (United States)

    Khadangi, Fatemeh; Yassi, Maryam; Kerachian, Mohammad Amin

    2017-12-01

    Although different methods have been established to detect Helicobacter pylori (H. pylori) infection, identifying infected patients is an ongoing challenge. The aim of this meta-analysis was to provide pooled diagnostic accuracy measures for stool PCR test in the diagnosis of H. pylori infection. In this study, a systematic review and meta-analysis were carried out on various sources, including MEDLINE, Web of Sciences, and the Cochrane Library from April 1, 1999, to May 1, 2016. This meta-analysis adheres to the guidelines provided by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses report (PRISMA Statement). The clinical value of DNA stool PCR test was based on the pooled false positive, false negative, true positive, and true negative of different genes. Twenty-six of 328 studies identified met the eligibility criteria. Stool PCR test had a performance of 71% (95% CI: 68-73) sensitivity, 96% (95% CI: 94-97) specificity, and 65.6 (95% CI: 30.2-142.5) diagnostic odds ratio (DOR) in diagnosis of H. pylori. The DOR of genes which showed the highest performance of stool PCR tests was as follows: 23S rRNA 152.5 (95% CI: 55.5-418.9), 16S rRNA 67.9 (95%CI: 6.4-714.3), and glmM 68.1 (95%CI: 20.1-231.7). The sensitivity and specificity of stool PCR test are relatively in the same spectrum of other diagnostic methods for the detection of H. pylori infection. In descending order of significance, the most diagnostic candidate genes using PCR detection were 23S rRNA, 16S rRNA, and glmM. PCR for 23S rRNA gene which has the highest performance could be applicable to detect H. pylori infection. © 2017 John Wiley & Sons Ltd.

  11. 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

  12. DNA: The Strand that Connects Us All

    Energy Technology Data Exchange (ETDEWEB)

    Kaplan, Matt [Univ. of Arizona, Tucson, AZ (United States). Genetics Core Facility

    2011-03-29

    Learn how the methods and discoveries of human population genetics are applied for personal genealogical reconstruction and anthropological testing. Dr. Kaplan starts with a short general review of human genetics and the biology behind this form of DNA testing. He looks at how DNA testing is performed and how samples are processed in the University of Arizona laboratory. He also examines examples of personal genealogical results from Family Tree DNA and personal anthropological results from the Genographic Project. Finally, he describes the newest project in the UA laboratory, the DNA Shoah Project.

  13. A review on leakage rate tests for containment isolation systems

    International Nuclear Information System (INIS)

    Kim, In Goo; Kim, Hho Jung

    1992-01-01

    Wide experiences in operating containment isolation systems have been accumulated in Korea since 1978. Hence, it becomes necessary to review the operating data in order to confirm the integrity of containments with about 50 reactor-years of experience and to establish the future direction to the containment test program. The objectives of present work are to collect, consolidate and assess the leakage rate data, and then to find out dominant leakage paths and factors affecting integrated leakage rate test. General trends of overall leakage show that more careful surveillance during pre-operational test can reduce the containment leakage. Dominant leakage paths are found to be through air locks and large-sized valves, such as butterfly valves of purge lines, so that weighted surveillance and inspection on these dominant leakage paths can considerably reduce the containment leakage. The atmosphere stabilization are found to be the most important to obtain the reliable result. In order to get well stabilized atmosphere, temperature and flow rate of compressed air should be kept constant and it is preferable not to operate fan cooler during pressurizing the containment for test

  14. Non-invasive prenatal testing for fetal chromosome abnormalities: review of clinical and ethical issues.

    Science.gov (United States)

    Gekas, Jean; Langlois, Sylvie; Ravitsky, Vardit; Audibert, François; van den Berg, David Gradus; Haidar, Hazar; Rousseau, François

    2016-01-01

    Genomics-based non-invasive prenatal screening using cell-free DNA (cfDNA screening) was proposed to reduce the number of invasive procedures in current prenatal diagnosis for fetal aneuploidies. We review here the clinical and ethical issues of cfDNA screening. To date, it is not clear how cfDNA screening is going to impact the performances of clinical prenatal diagnosis and how it could be incorporated in real life. The direct marketing to users may have facilitated the early introduction of cfDNA screening into clinical practice despite limited evidence-based independent research data supporting this rapid shift. There is a need to address the most important ethical, legal, and social issues before its implementation in a mass setting. Its introduction might worsen current tendencies to neglect the reproductive autonomy of pregnant women.

  15. 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.

  16. Is DNA a worm-like chain in Couette flow? In search of persistence length, a critical review.

    Science.gov (United States)

    Rittman, Martyn; Gilroy, Emma; Koohya, Hashem; Rodger, Alison; Richards, Adair

    2009-01-01

    Persistence length is the foremost measure of DNA flexibility. Its origins lie in polymer theory which was adapted for DNA following the determination of BDNA structure in 1953. There is no single definition of persistence length used, and the links between published definitions are based on assumptions which may, or may not be, clearly stated. DNA flexibility is affected by local ionic strength, solvent environment, bound ligands and intrinsic sequence-dependent flexibility. This article is a review of persistence length providing a mathematical treatment of the relationships between four definitions of persistence length, including: correlation, Kuhn length, bending, and curvature. Persistence length has been measured using various microscopy, force extension and solution methods such as linear dichroism and transient electric birefringence. For each experimental method a model of DNA is required to interpret the data. The importance of understanding the underlying models, along with the assumptions required by each definition to determine a value of persistence length, is highlighted for linear dichroism data, where it transpires that no model is currently available for long DNA or medium to high shear rate experiments.

  17. 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.

  18. Dispersant field testing : a review of procedures and considerations

    International Nuclear Information System (INIS)

    Fingas, M.F.

    2004-01-01

    The effectiveness of a dispersant is defined by the amount of oil that the dispersant puts into the water column compared to the amount of oil that was initially spilled. Effectiveness is generally determined visually in plumes of dispersed oil that are visible from ships and aircraft. This paper describes 25 specific issues and technical concerns regarding field testing of dispersant effectiveness. Recent field tests were reviewed and literature that relates to testing procedures was sited. The 25 factors that are important for the appropriate outcome of dispersant field experiments include: mass balance; proper controls; analytical method; differential plume movement; time lag and length of time followed; mathematics of calculation and integration; lower and upper limits of analytical methods; use of remote sensing; thickness measurement; behaviour of oil with surfactant content; surfactant stripping; tracking surface oil and dispersed oil; recovering surface oil; visibility of oil from the surface; background levels of hydrocarbons; fluorescence of dispersant; herding; emulsion breaking; application success; heterogeneity of slick and plume; deposition measurements; true analytical standards; effect of wind on dispersant and slick; dispersant run-off; and weathering of the oil. It was concluded that the most important factors are the ability to determine mass balance, use proper controls, analytical methods and to avoid procedures that give incorrect results. 34 refs., 4 tabs., 1 fig

  19. The etiologies of sperm DNA abnormalities in male infertility: An assessment and review

    Directory of Open Access Journals (Sweden)

    Soheila Pourmasumi

    2017-07-01

    Full Text Available The sperm DNA damage may occur in testis, genital ducts, and also after ejaculation. Mechanisms altering chromatin remodeling are abortive apoptosis and oxidative stress resulting from reactive oxygen species. Three classifications of intratesticular, post-testicular, and external factors have been correlated with increased levels of sperm DNA damage which can affect the potential of fertility. Alcohol consumption may not increase the rate of sperm residual histones and protamine deficiency; however, it causes an increase in the percentage of spermatozoa with DNA fragmentation and apoptosis. In a medical problem as spinal cord injury, poor semen parameters and sperm DNA damage were reported. Infection induces reactive oxygen species production, decreases the total antioxidant capacity and sperm DNA fragmentation or antigen production that lead to sperm dysfunctions and DNA fragmentation. While reactive oxygen species generation increases with age, oxidative stress may be responsible for the age-dependent sperm DNA damage. The exposing of reproductive organs in older men to oxidative stress for a long time may produce more DNA-damaged spermatozoa than youngers. Examining the sperm chromatin quality in testicular cancer and Hodgkin’s lymphoma patients prior to chemotherapy demonstrated the high incidence of DNA damage and low compaction in spermatozoa at the time of diagnosis. In chemotherapy cycles with genotoxic agents in cancer patients, an increase in sperm DNA damage was shown after treatment. In overall, those factors occurring during the prenatal or the adult life alter the distribution of proteins associated with sperm chromatin induce changes in germ cells which can be detected in infertile patients.

  20. 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.

  1. A REVIEW OF SINGLE SPECIES TOXICITY TESTS: ARE THE TESTS RELIABLE PREDICTORS OF AQUATIC ECOSYSTEM COMMUNITY RESPONSES?

    Science.gov (United States)

    This document provides a comprehensive review to evaluate the reliability of indicator species toxicity test results in predicting aquatic ecosystem impacts, also called the ecological relevance of laboratory single species toxicity tests.

  2. 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.

  3. 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.

  4. 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.

  5. Review Paper: Review of Instrumentation for Irradiation Testing of Nuclear Fuels and Materials

    International Nuclear Information System (INIS)

    Kim, Bong Goo; Rempe, Joy L.; Villard, Jean-Francois; Solstadd, Steinar

    2011-01-01

    Over 50 years of nuclear fuels and materials irradiation testing has led to many countries developing significant improvements in instrumentation to monitor physical parameters and to control the test conditions in material test reactors (MTRs). Recently, there is increased interest to irradiate new materials and reactor fuels for advanced pressurized water reactors and Gen-IV reactor systems, such as sodium-cooled fast reactors, very high temperature reactors, supercritical water-cooled reactors, and gas-cooled fast reactors. This review paper documents the current state of instrumentation technologies in MTRs in the world and summarizes ongoing research efforts to deploy new sensors. As described in this paper, a wide range of sensors is available to measure key parameters of interest during fuels and materials irradiations in MTRs. Ongoing development efforts focus on providing MTR users a wider range of parameter measurements with smaller, higher accuracy sensors.

  6. Biomarker-Based Analysis for Contaminants in Sediments/Soil: Review of Cell-Based Assays and cDNA Arrays

    National Research Council Canada - National Science Library

    Inouye, Laura

    2000-01-01

    This technical note reviews the existing technology for cell-based biomarker assays and cDNA arrays and explores their potential as rapid, sensitive, and low-cost tools for sediment/soil toxicity screening...

  7. 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 ...

  8. The tokamak fusion test reactor tritium systems test contractor operational readiness review

    International Nuclear Information System (INIS)

    Gentile, C.A.; Levine, J.; Norris, M.; Rehill, F.; Such, C.

    1993-01-01

    In preparation for D-T operations at TFTR, the TFTR project has successfully completed the C-ORR process which has led to the introduction of 200 curies of tritium to the site. Preparations for the C-ORR began approximately 2 years ago. During July 1992 a one-week Site Assistance Review was conducted by the C-ORR , and C-ORR Team consisting of 12 persons, all of whom were outside experts, many of whom were from other facilities within the DOE complex. During the July 1992 Site Assistance Review 201 findings were documented which fell into one of three categories. All of the 109 category one findings which were generated were required to be resolved prior to the introduction of tritium to the TFTR site. On April 5, 1993, the TFTR Tritium System Test C-ORR commenced. The results of the C-ORR as documented in the final report by the C-ORR was that category 1 findings were resolved, and it was the recommendation of the C-ORR Team to the PPPL ES ampersand H Board that TFTR initiate the Tritium Systems Test. DOE (Chicago Operations, Princeton Area Office) concurred with the C-ORR final report and on April 29, 1993, at 12:15 pm tritium was introduced to the TFTR site

  9. 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

  10. Recommendations for reporting of systematic reviews and meta-analyses of diagnostic test accuracy: a systematic review

    NARCIS (Netherlands)

    McGrath, Trevor A.; Alabousi, Mostafa; Skidmore, Becky; Korevaar, Daniël A.; Bossuyt, Patrick M. M.; Moher, David; Thombs, Brett; McInnes, Matthew D. F.

    2017-01-01

    This study is to perform a systematic review of existing guidance on quality of reporting and methodology for systematic reviews of diagnostic test accuracy (DTA) in order to compile a list of potential items that might be included in a reporting guideline for such reviews: Preferred Reporting Items

  11. 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.

  12. 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.

  13. 10 CFR 707.13 - Medical review of results of tests for illegal drug use.

    Science.gov (United States)

    2010-01-01

    ... another test, performed by the gas chromatography/mass spectrometry method (GC/MS). This procedure is... 10 Energy 4 2010-01-01 2010-01-01 false Medical review of results of tests for illegal drug use... Procedures § 707.13 Medical review of results of tests for illegal drug use. (a) All test results shall be...

  14. Strength testing and training of rowers: a review.

    Science.gov (United States)

    Lawton, Trent W; Cronin, John B; McGuigan, Michael R

    2011-05-01

    In the quest to maximize average propulsive stroke impulses over 2000-m racing, testing and training of various strength parameters have been incorporated into the physical conditioning plans of rowers. Thus, the purpose of this review was 2-fold: to identify strength tests that were reliable and valid correlates (predictors) of rowing performance; and, to establish the benefits gained when strength training was integrated into the physical preparation plans of rowers. The reliability of maximal strength and power tests involving leg extension (e.g. leg pressing) and arm pulling (e.g. prone bench pull) was high (intra-class correlations 0.82-0.99), revealing that elite rowers were significantly stronger than their less competitive peers. The greater strength of elite rowers was in part attributed to the correlation between strength and greater lean body mass (r = 0.57-0.63). Dynamic lower body strength tests that determined the maximal external load for a one-repetition maximum (1RM) leg press (kg), isokinetic leg extension peak force (N) or leg press peak power (W) proved to be moderately to strongly associated with 2000-m ergometer times (r = -0.54 to -0.68; p training experience and muscle morphology, in that those individuals with greater training experience and/or proportions of slow twitch fibres performed more repetitions. Muscle balance ratios derived from strength data (e.g. hamstring-quadriceps ratio training may be counterproductive to strength development over the shorter term (i.e. training within the sequence of training units should be considered, particularly over the non-competition phase (e.g. 2-6 sets × 4-12 repetitions, three sessions a week). Maximal strength was sustained when infrequent (e.g. one or two sessions a week) but intense (e.g. 73-79% of maximum) strength training units were scheduled; however, it was unclear whether training adaptations should emphasize maximal strength, endurance or power in order to enhance

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. A Review of Microwave Thermography Nondestructive Testing and Evaluation

    Directory of Open Access Journals (Sweden)

    Hong Zhang

    2017-05-01

    Full Text Available Microwave thermography (MWT has many advantages including strong penetrability, selective heating, volumetric heating, significant energy savings, uniform heating, and good thermal efficiency. MWT has received growing interest due to its potential to overcome some of the limitations of microwave nondestructive testing (NDT and thermal NDT. Moreover, during the last few decades MWT has attracted growing interest in materials assessment. In this paper, a comprehensive review of MWT techniques for materials evaluation is conducted based on a detailed literature survey. First, the basic principles of MWT are described. Different types of MWT, including microwave pulsed thermography, microwave step thermography, microwave pulsed phase thermography, and microwave lock-in thermography are defined and introduced. Then, MWT case studies are discussed. Next, comparisons with other thermography and NDT methods are conducted. Finally, the trends in MWT research are outlined, including new theoretical studies, simulations and modelling, signal processing algorithms, internal properties characterization, automatic separation and inspection systems. This work provides a summary of MWT, which can be utilized for material failures prevention and quality control.

  1. A Review of Microwave Thermography Nondestructive Testing and Evaluation.

    Science.gov (United States)

    Zhang, Hong; Yang, Ruizhen; He, Yunze; Foudazi, Ali; Cheng, Liang; Tian, Guiyun

    2017-05-15

    Microwave thermography (MWT) has many advantages including strong penetrability, selective heating, volumetric heating, significant energy savings, uniform heating, and good thermal efficiency. MWT has received growing interest due to its potential to overcome some of the limitations of microwave nondestructive testing (NDT) and thermal NDT. Moreover, during the last few decades MWT has attracted growing interest in materials assessment. In this paper, a comprehensive review of MWT techniques for materials evaluation is conducted based on a detailed literature survey. First, the basic principles of MWT are described. Different types of MWT, including microwave pulsed thermography, microwave step thermography, microwave pulsed phase thermography, and microwave lock-in thermography are defined and introduced. Then, MWT case studies are discussed. Next, comparisons with other thermography and NDT methods are conducted. Finally, the trends in MWT research are outlined, including new theoretical studies, simulations and modelling, signal processing algorithms, internal properties characterization, automatic separation and inspection systems. This work provides a summary of MWT, which can be utilized for material failures prevention and quality control.

  2. The tear turnover and tear clearance tests - a review.

    Science.gov (United States)

    Garaszczuk, Izabela K; Montes Mico, Robert; Iskander, D Robert; Expósito, Alejandro Cerviño

    2018-03-01

    The aim is to provide a summary of methods available for the assessment of tear turnover and tear clearance rates. The review defines tear clearance and tear turnover and describes their implication for ocular surface health. Additionally, it describes main types of techniques for measuring tear turnover, including fluorescein tear clearance tests, techniques utilizing electromagnetic spectrum and tracer molecule and novel experimental techniques utilizing optical coherence tomography and fluorescein profilometry. Areas covered: Internet databases (PubMed, Science Direct, Google Scholar) and most frequently cited references were used as a principal resource of information on tear turnover rate and tear clearance rate, presenting methodologies and equipment, as well as their definition and implications for the anterior eye surface health and function. Keywords used for data-search were as follows: tear turnover, tear clearance, fluorescein clearance, scintigraphy, fluorophotometry, tear flow, drainage, tear meniscus dynamics, Krehbiel flow and lacrimal functional unit. Expert commentary: After decades, the topic of tear turnover assessment has been reintroduced. Recently, new techniques have been developed to propose less invasive, less time consuming and simpler methodologies for the assessment of tear dynamics that have the potential to be utilized in clinical practice.

  3. Standard review plan for the review and evaluation of emergency plans for research and test reactors

    International Nuclear Information System (INIS)

    1983-10-01

    This document provides a Standard Review Plan to assure that complete and uniform reviews are made of research and test reactor radiological emergency plans. The report is organized under ten planning standards which correspond to the guidance criteria in American National Standard ANSI/ANS 15.16 - 1982 as endorsed by Revision 1 to Regulatory Guide 2.6. The applicability of the items under each planning standard is indicated by subdivisions of the steady-state thermal power levels at which the reactors are licensed to operate. Standard emergency classes and example action levels for research and test reactors which should initiate these classes are given in an Appendix. The content of the emergency plan is as follows: the emergency plan addresses the necessary provisions for coping with radiological emergencies. Activation of the emergency plan is in response to the emergency action levels. In addition to addressing those severe emergencies that will fall within one of the standard emergency classes, the plan also discusses the necessary provisions to deal with radiological emergencies of lesser severity that can occur within the operations boundary. The emergency plan allows for emergency personnel to deviate from actions described in the plan for unusual or unanticipated conditions

  4. 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.

  5. Stress, burnout and depression : A systematic review on DNA methylation mechanisms

    NARCIS (Netherlands)

    Bakusic, Jelena; Schaufeli, Wilmar; Claes, Stephan; Godderis, Lode

    2017-01-01

    Despite that burnout presents a serious burden for modern society, there are no diagnostic criteria. Additional difficulty is the differential diagnosis with depression. Consequently, there is a need to dispose of a burnout biomarker. Epigenetic studies suggest that DNA methylation is a possible

  6. Forensic DNA databases–Ethical and legal standards: A global review

    Directory of Open Access Journals (Sweden)

    H.M. Wallace

    2014-09-01

    Conclusion: There is an ongoing need for greater public and policy debate as DNA databases expand around the world. Some safeguards are implemented at the national or regional level, but there is an ongoing lack of global standards and a need for more societal engagement and debate.

  7. Review and future prospects for DNA barcoding methods in forensic palynology.

    Science.gov (United States)

    Bell, Karen L; Burgess, Kevin S; Okamoto, Kazufusa C; Aranda, Roman; Brosi, Berry J

    2016-03-01

    Pollen can be a critical forensic marker in cases where determining geographic origin is important, including investigative leads, missing persons cases, and intelligence applications. However, its use has previously been limited by the need for a high level of specialization by expert palynologists, slow speeds of identification, and relatively poor taxonomic resolution (typically to the plant family or genus level). By contrast, identification of pollen through DNA barcoding has the potential to overcome all three of these limitations, and it may seem surprising that the method has not been widely implemented. Despite what might seem a straightforward application of DNA barcoding to pollen, there are technical issues that have delayed progress. However, recent developments of standard methods for DNA barcoding of pollen, along with improvements in high-throughput sequencing technology, have overcome most of these technical issues. Based on these recent methodological developments in pollen DNA barcoding, we believe that now is the time to start applying these techniques in forensic palynology. In this article, we discuss the potential for these methods, and outline directions for future research to further improve on the technology and increase its applicability to a broader range of situations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  8. Testing flow diversion in animal models: a systematic review.

    Science.gov (United States)

    Fahed, Robert; Raymond, Jean; Ducroux, Célina; Gentric, Jean-Christophe; Salazkin, Igor; Ziegler, Daniela; Gevry, Guylaine; Darsaut, Tim E

    2016-04-01

    Flow diversion (FD) is increasingly used to treat intracranial aneurysms. We sought to systematically review published studies to assess the quality of reporting and summarize the results of FD in various animal models. Databases were searched to retrieve all animal studies on FD from 2000 to 2015. Extracted data included species and aneurysm models, aneurysm and neck dimensions, type of flow diverter, occlusion rates, and complications. Articles were evaluated using a checklist derived from the Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines. Forty-two articles reporting the results of FD in nine different aneurysm models were included. The rabbit elastase-induced aneurysm model was the most commonly used, with 3-month occlusion rates of 73.5%, (95%CI [61.9-82.6%]). FD of surgical sidewall aneurysms, constructed in rabbits or canines, resulted in high occlusion rates (100% [65.5-100%]). FD resulted in modest occlusion rates (15.4% [8.9-25.1%]) when tested in six complex canine aneurysm models designed to reproduce more difficult clinical contexts (large necks, bifurcation, or fusiform aneurysms). Adverse events, including branch occlusion, were rarely reported. There were no hemorrhagic complications. Articles complied with 20.8 ± 3.9 of 41 ARRIVE items; only a small number used randomization (3/42 articles [7.1%]) or a control group (13/42 articles [30.9%]). Preclinical studies on FD have shown various results. Occlusion of elastase-induced aneurysms was common after FD. The model is not challenging but standardized in many laboratories. Failures of FD can be reproduced in less standardized but more challenging surgical canine constructions. The quality of reporting could be improved.

  9. 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...

  10. 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.

  11. Colposcopic triage methods for detecting cervical intraepithelial neoplasia grade 3 after cytopathological diagnosis of low-grade squamous intraepithelial lesion: a systematic review on diagnostic tests

    Directory of Open Access Journals (Sweden)

    Flávia de Miranda Corrêa

    Full Text Available CONTEXT AND OBJECTIVE: The age-stratified performance of the oncogenic HPV-DNA (human papillomavirus deoxyribonucleic acid test for triage of low-grade squamous intraepithelial lesions (LSIL requires investigation. The objective of this study was to evaluate and compare the age-stratified performance (cutoff point: 35 years of oncogenic HPV-DNA testing and repeated cytological tests, for detecting cervical intraepithelial neoplasia grade 3 (CIN3, in order to triage for LSIL. DESIGN AND SETTING: Systematic review. Studies were identified in nine electronic databases and in the reference lists of the articles retrieved. METHODS: The eligibility criteria consisted of initial cytological findings of LSIL; subsequent oncogenic HPV-DNA testing and repeated cytological tests; and CIN3 detection. The Quality Assessment of Diagnostic Accuracy Studies (QUADAS guidelines were used for quality assessment. Qualitative information synthesis was performed. RESULTS: Out of 7,776 studies, 284 were identified as pertinent and three fulfilled the eligibility criteria. The CIN3 prevalence ranged from 6% to 12%. The HPV-DNA positivity rate ranged from 64% to 83%; sensitivity for CIN3 detection ranged from 95.2% to 100%; and specificity was available in two studies (27% and 52%. The sensitivity of repeated cytological tests, in relation to the threshold for atypical squamous cells of undetermined significance (ASCUS, was available in two studies (33% and 90.8%; and specificity was available in one study (53%. CONCLUSIONS: Currently, there is no scientific evidence available that would prove that colposcopic triage using oncogenic HPV-DNA testing to detect CIN3 performs better than repeated cytological tests, among women with LSIL aged 35 years and over.

  12. Worldwide Test Reviewing at the Beginning of the Twenty-First Century

    Science.gov (United States)

    Geisinger, Kurt F.

    2012-01-01

    This article sets the stage for the description of a variety of approaches to test reviewing worldwide. It describes the importance of test reviewing as a protection of the public and of society and also the benefits of this activity for test users, who must choose measures to use in particular situations with particular clients at a particular…

  13. A Critical Review of the IELTS Writing Test

    Science.gov (United States)

    Uysal, Hacer Hande

    2010-01-01

    Administered at local centres in 120 countries throughout the world, IELTS (International English Language Testing System) is one of the most widely used large-scale ESL tests that also offers a direct writing test component. Because of its popularity and its use for making critical decisions about test takers, it is crucial to draw attention to…

  14. 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.

  15. 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...

  16. 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.

  17. Test Review: Prueba de Lectura y Lenguaje Escrito.

    Science.gov (United States)

    Crawford, Alan N.

    1984-01-01

    Describes the Prueba de Lectura y Lenguaje Escrito (PPLE--roughly translatable as the "Test of Early Language Development") that may meet the need for standardized and diagnostic tests of reading and written composition in Spanish. (HOD)

  18. Literature review : an analysis of laboratory fatigue tests.

    Science.gov (United States)

    1975-01-01

    This report discusses the various types of fatigue tests, grouped by the type of specimen (beam, plate, Marshall, etc.) used. The discussion under each type of specimen covers the test, and the analytical methods used in evaluating the data. The test...

  19. Review of antenatal-linked voluntary counseling and HIV testing in ...

    African Journals Online (AJOL)

    Review of antenatal-linked voluntary counseling and HIV testing in Sub-Saharan Africa: lessons and options for Ghana. ... Voluntary counselling and HIV testing has become an integral part of HIV prevention ... AJOL African Journals Online.

  20. Test Review: D. Wechsler "Wechsler Individual Achievement Test" (3rd ed.). San Antonio, Texas--Pearson, 2009

    Science.gov (United States)

    Vaughan-Jensen, Jessica; Adame, Cindy; McLean, Lauren; Gamez, Brenda

    2011-01-01

    This article reviews "Wechsler Individual Achievement Test-Third Edition" (WIAT-III), which is designed to assess students' skills in listening, speaking, reading, writing, and mathematics. The test can identify an individual's strengths and weaknesses, assist professionals who are determining whether a student is eligible for special…

  1. Test Reviews: Reynolds, C., & Voress, J. K. (2007). "Test of Memory and Learning: Second Edition." Austin, TX: PRO-ED

    Science.gov (United States)

    Schmitt, Ara J.; Decker, Scott L.

    2009-01-01

    This article reviews the Test of Memory and Learning: Second Edition (TOMAL-2), published by PRO-ED, which constitutes a recent revision of the Test of Memory and Learning (TOMAL; Reynolds & Bigler, 1994). Advertised as the "single most comprehensive memory battery available for the entire age range of 5 years through 59 years of age", the TOMAL-2…

  2. Fuel fragmentation data review and separate effects testing

    International Nuclear Information System (INIS)

    Yueh, Ken. H.; Snis, N.; Mitchell, D.; Munoz-Reja, C.

    2014-01-01

    A simple alternative test has been developed to study the fuel fragmentation process at loss of coolant accident (LOCA) temperatures. The new test heats a short section of fuel, approximately two pellets worth of material, in a tube furnace open to air. An axial slit is cut in the test sample cladding to reduce radial restraint and to simulate ballooned condition. The tube furnace allows the fuel fragmentation process be observed during the experiment. The test was developed as a simple alternative so large number of tests could be conducted quickly and efficiently to identify key variables that influence fuel fragmentation and to zeroing on the fuel fragmentation burn-up threshold. Several tests were conducted, using fuel materials from fuel rods that were used in earlier integral tests to benchmark and validate the test technique. High burn-up fuel materials known to be above the fragmentation threshold was used to evaluate the fragmentation process as a function of temperature. Even with an axial slit and both ends open, no significant fuel detachment/release was detected until above 750°C. Additional tests were conducted with fuel materials at burn-ups closer to the fuel fragmentation burn-up threshold. Results from these tests indicate a minor power history effect on the fuel fragmentation burn-up threshold. An evaluation of available literature and data generated from this work suggest a fuel fragmentation burn-up threshold between 70 and 75 GWd/MTU. (author)

  3. 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.

  4. Heavy Metal-Induced Oxidative DNA Damage in Earthworms: A Review

    Directory of Open Access Journals (Sweden)

    Takeshi Hirano

    2010-01-01

    Full Text Available Earthworms can be used as a bio-indicator of metal contamination in soil, Earlier reports claimed the bioaccumulation of heavy metals in earthworm tissues, while the metal-induced mutagenicity reared in contaminated soils for long duration. But we examined the metal-induced mutagenicity in earthworms reared in metal containing culture beddings. In this experiment we observed the generation of 8-oxoguanine (8-oxo-Gua in earthworms exposed to cadmium and nickel in soil. 8-oxo-Gua is a major premutagenic form of oxidative DNA damage that induces GC-to-TA point mutations, leading to carcinogenesis.

  5. A review on software testing approaches for cloud applications

    Directory of Open Access Journals (Sweden)

    Tamanna Siddiqui

    2016-09-01

    Full Text Available Cloud computing has actually been invented to be the latest computing standard that will work several distinctive research areas, such as software testing. Testing cloud applications will keep its unique characteristics that involve more recent testing techniques. Software testing helps to reduce the need for hardware and software services and also provide adaptable and valuable cloud platform. Testing within the cloud platform is easily manageable based on new test models and criteria. Prioritization approach is made responsive to build much better relationship between test cases. These test cases are clustered dependent on priority level. The resources can be used properly by applying load balancing algorithm. Cloud guarantees maximum usage of existing resources. But, security defined as a primary problem in cloud. At the present time, organizations are progressively moving excited about deploying and making use of ready-prepared business applications, with particular short-term to the marketplace. The possible lack of capital budgets for software planning and on principle deployments, along with the swift progression of cloud these are the reasons why one should make the interest on business application. However, these are the interests that help make the SaaS based business application on-demand. In this paper different approaches has been discussed that will help to extend the cloud environment. Also, the study of several well-known software testing approaches.

  6. 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.

  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. NRC review of passive reactor design certification testing programs: Overview, progress, and regulatory perspective

    Energy Technology Data Exchange (ETDEWEB)

    Levin, A.E.

    1995-09-01

    New reactor designs, employing passive safety systems, are currently under development by reactor vendors for certification under the U.S. Nuclear Regulatory Commission`s (NRC`s) design certification rule. The vendors have established testing programs to support the certification of the passive designs, to meet regulatory requirements for demonstration of passive safety system performance. The NRC has, therefore, developed a process for the review of the vendors` testing programs and for incorporation of the results of those reviews into the safety evaluations for the passive plants. This paper discusses progress in the test program reviews, and also addresses unique regulatory aspects of those reviews.

  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. Monophyly, review, six new species and DNA barcode of micropterous Afromontane Afropictinus (Heteroptera: Aradidae).

    Science.gov (United States)

    Heiss, Ernst; Grebennikov, Vasily

    2016-12-15

    The micropterous East African flat bug genus Afropictinus Heiss, 1986 (Heteroptera: Aradidae: Mezirinae) is revised. In addition to the type and only known species A. congoensis (Hoberlandt, 1956) from Rwanda, four new species from Tanzania (A. castor sp. nov., A. hylas sp. nov., A. idas sp. nov., A. nauplius sp. nov.), one new species from the Democratic Republic of the Congo (A. kahuzianus sp. nov.), and one new species from Ethiopia (A. nabu sp. nov.) are described and illustrated. An identification key is presented to all seven nominal species of Afropictinus. DNA barcodes of 28 individuals of Afropictinus species were newly generated and together with 12 sequences of other Aradidae were made publicly available at dx.doi.org/10.5883/DS-AFROPICT. These mtDNA sequences were analyzed phylogenetically using Maximum Likelihood approach with 500 bootstraps. Obtained topology reveals a monophyletic Afropictinus with high statistical support (84%), although its sister group remains elusive. Both specimens of non-Tanzanian Afropictinus species included in the study (A. kahuzianus and A. nabu) were nested among Tanzanian congeners. The internal clades within Afropictinus, except for those at species and population level, had lesser statistical support. Despite of intense sampling, no Afropictinus species was found in mountain forests of geologically young (Ngorongoro-Kilimanjaro Volcanic Belt, which suggest reduced dispersal capacities.

  11. A review of serological tests used in the diagnosis of Brucellosis ...

    African Journals Online (AJOL)

    Brucellosis is of serious economic importance in livestock and in humans. There are batteries of serological tests developed and in use for the diagnosis of brucellosis in human and livestock Brief history, merits and demerits of some of these test are enumerated in this review. The purpose of the review is to bring together in ...

  12. 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.

  13. 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.

  14. Test Review: Prueba del Desarrollo Inicial del Lenguaje.

    Science.gov (United States)

    Crawford, Alan N.

    1985-01-01

    Concludes that the PDIL (the Spanish version of the Test of Early Language Development) should be used with caution. Since its reliability and validity were determined with the English language version, the method used to translate test items may have some ambiguities, and some illustrations on picture cards may not be culturally appropriate for…

  15. International Test Comparisons: Reviewing Translation Error in Different Source Language-Target Language Combinations

    Science.gov (United States)

    Zhao, Xueyu; Solano-Flores, Guillermo; Qian, Ming

    2018-01-01

    This article addresses test translation review in international test comparisons. We investigated the applicability of the theory of test translation error--a theory of the multidimensionality and inevitability of test translation error--across source language-target language combinations in the translation of PISA (Programme of International…

  16. 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

  17. 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

  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. The recognition heuristic : A review of theory and tests

    OpenAIRE

    Pachur, T.; Todd, P.; Gigerenzer, G.; Schooler, L.; Goldstein, D.

    2011-01-01

    The recognition heuristic is a prime example of how, by exploiting a match between mind and environment, a simple mental strategy can lead to efficient decision making. The proposal of the heuristic initiated a debate about the processes underlying the use of recognition in decision making. We review research addressing four key aspects of the recognition heuristic: (a) that recognition is often an ecologically valid cue; (b) that people often follow recognition when making inferences; (c) th...

  20. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  1. DNA nanotechnology

    Science.gov (United States)

    Seeman, Nadrian C.; Sleiman, Hanadi F.

    2018-01-01

    DNA is the molecule that stores and transmits genetic information in biological systems. The field of DNA nanotechnology takes this molecule out of its biological context and uses its information to assemble structural motifs and then to connect them together. This field has had a remarkable impact on nanoscience and nanotechnology, and has been revolutionary in our ability to control molecular self-assembly. In this Review, we summarize the approaches used to assemble DNA nanostructures and examine their emerging applications in areas such as biophysics, diagnostics, nanoparticle and protein assembly, biomolecule structure determination, drug delivery and synthetic biology. The introduction of orthogonal interactions into DNA nanostructures is discussed, and finally, a perspective on the future directions of this field is presented.

  2. DNA Amplification Techniques for the Detection of Toxoplasma gondii Tissue Cysts in Meat Producing Animals: A Narrative Review Article

    Directory of Open Access Journals (Sweden)

    Farooq RIAZ

    2016-12-01

    Full Text Available Background: Toxoplasma gondii is an intracellular parasite, which infects one-third population of world. Humans and animals acquire infection by ingesting oocytes from feces of cats or by meat of other animals having cysts that may lead to congenital, ocular or cephalic toxoplasmosis. Either it is important to detect T. gondii from meat of food animals from retail shops or directly at slaughterhouses, which is meant for export.Methods: The current research was done without time limitation using such terms as follows: “Toxoplasma gondii”, “Meat”, “Tissue cyst”, “PCR”, “LAMP”, “Screening” and “Immunological assay” alone or in combination, in English language. The used electronic databases for searching included as follows: PubMed, Scopus, Google Scholar, Web of Science and Science Direct. The searches were limited to the published papers to English language.Results: Sensitivity of different molecular techniques for diagnosis of Toxoplasma is real-time PCR > LAMP > conventional PCR. In addition to these DNA analysis tools, bioassay in mice and cats is considered as “gold standard” to detect T. gondii. Conclusion: This review article will help the readers for grasping advantages and limitations of different diagnostic tools for screening meat samples for T. gondii. This review also makes bibliography about the type of meat sample to be processed for diagnosis and different primers or sequences to be targeted for T. gondii by number of researches for its detection from meat or tissue sample using DNA amplification techniques.

  3. The role of oxytocin receptor gene (OXTR) DNA methylation (DNAm) in human social and emotional functioning: a systematic narrative review.

    Science.gov (United States)

    Maud, Catherine; Ryan, Joanne; McIntosh, Jennifer E; Olsson, Craig A

    2018-05-29

    The neuropeptide Oxytocin (OXT) plays a central role in birthing, mother-infant bonding and a broad range of related social behaviours in mammals. More recently, interest has extended to epigenetic programming of genes involved in oxytocinergic neurotransmission. This review brings together early findings in a rapidly developing field of research, examining relationships between DNA methylation (DNAm) of the Oxytocin Receptor Gene (OXTR) and social and emotional behaviour in human populations. A systematic search across Web of Knowledge/Science, Scopus, Medline and EMBASE captured all published studies prior to June 2017 examining the association between OXTR DNAm and human social and emotional outcomes. Search terms included 'oxytocin gene' or 'oxytocin receptor gene' and 'epigenetics' or 'DNA methylation'. Any article with a focus on social and emotional functioning was then identified from this set by manual review. Nineteen studies met eligibility criteria. There was considerable heterogeneity of study populations, tissue samples, instrumentation, measurement, and OXTR site foci. Only three studies examined functional consequences of OXTR DNAm on gene expression and protein synthesis. Increases in OXTR DNAm were associated with callous-unemotional traits in youth, social cognitive deficits in Autistic Spectrum Disorder (ASD), rigid thinking in anorexia nervosa, affect regulation problems, and problems with facial and emotional recognition. In contrast, reductions in DNAm were associated with perinatal stress, postnatal depression, social anxiety and autism in children. Consistent with an emerging field of inquiry, there is not yet sufficient evidence to draw conclusions about the role of OXTR DNAm in human social and emotional behaviour. However, taken together, findings point to increased OXTR DNAm in general impairments in social, cognitive and emotional functioning, and decreased OXTR DNAm in specific patterns of impairment related to mood and anxiety

  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. Review of Nuclear Thermal Propulsion Ground Test Options

    Science.gov (United States)

    Coote, David J.; Power, Kevin P.; Gerrish, Harold P.; Doughty, Glen

    2015-01-01

    High efficiency rocket propulsion systems are essential for humanity to venture beyond the moon. Nuclear Thermal Propulsion (NTP) is a promising alternative to conventional chemical rockets with relatively high thrust and twice the efficiency of highest performing chemical propellant engines. NTP utilizes the coolant of a nuclear reactor to produce propulsive thrust. An NTP engine produces thrust by flowing hydrogen through a nuclear reactor to cool the reactor, heating the hydrogen and expelling it through a rocket nozzle. The hot gaseous hydrogen is nominally expected to be free of radioactive byproducts from the nuclear reactor; however, it has the potential to be contaminated due to off-nominal engine reactor performance. NTP ground testing is more difficult than chemical engine testing since current environmental regulations do not allow/permit open air testing of NTP as was done in the 1960's and 1970's for the Rover/NERVA program. A new and innovative approach to rocket engine ground test is required to mitigate the unique health and safety risks associated with the potential entrainment of radioactive waste from the NTP engine reactor core into the engine exhaust. Several studies have been conducted since the ROVER/NERVA program in the 1970's investigating NTP engine ground test options to understand the technical feasibility, identify technical challenges and associated risks and provide rough order of magnitude cost estimates for facility development and test operations. The options can be divided into two distinct schemes; (1) real-time filtering of the engine exhaust and its release to the environment or (2) capture and storage of engine exhaust for subsequent processing.

  6. A review of DOE HEPA filter component test activities

    Energy Technology Data Exchange (ETDEWEB)

    Slawski, J.W.; Bresson, J.F. [Informatics Corp., Inc., Albuquerque, NM (United States); Scripsick, R.C. [Los Alamos National Lab., NM (United States)

    1997-08-01

    All HEPA filters purchased for installation in DOE nuclear facilities are required to be tested at a Filter Test Facility (FTF) prior to installation. The number of HEPA filters purchased by DOE has been reduced so much that the Hanford FTF was closed. From Fiscal Year (FY) 1992 to 1994, funding was not provided to the FTF Technical Support Group (TSG) at the Los Alamos National Laboratory. As a consequence, Round Robin Tests (RRTs), performed twice each year by the FTFs to assess constituency of test results among the FTFs, were not performed in FY 1992 and FY 1993. The Annual Reports of FTF test activities were not prepared for FY 1992 - 1995. Technical support provided to the FTFs was minimal. There is talk of closing a second FTF, and ongoing discussions as to whether DOE will continue to fund operation of the FTFs. In FY 1994, DOE Defense Programs commenced funding the TSG. RRT data for FY 1994 and 1995 have been entered into the database; the FY 1994 RRT report has been issued; and the FY 1995 RRT report is in progress. Data from semiannual reports have been retrieved and entered into the database. Standards related to HEPA filter test and procurement activities are now scheduled for issuance by FY 1996. Continuation of these activities depends on whether DOE will continue to support the HEPA filter test program. The history and activities of the FTFs and the TSG at Los Alamos have been reported at previous Air Cleaning Conferences. Data from the FY 1991 Annual Report of FTF activities was presented at the 1992 Air Cleaning Conference. Preparation of the Annual Reports was temporarily suspended in 1992. However, all of the FTF Semiannual report data have been retrieved and entered into the data base. This paper focuses primarily on the results of HEPA filter tests conducted by FTFs during FY 1992 - FY 1995, and the possible effects of the DOE program uncertainties on the quality of HEPA filters for installation at the DOE sites. 15 refs., 13 tabs.

  7. Test Review: Wechsler Abbreviated Scale of Intelligence, Second Edition

    Science.gov (United States)

    Irby, Sarah M.; Floyd, Randy G.

    2013-01-01

    The Wechsler Abbreviated Scale of Intelligence, Second Edition (WASI-II; Wechsler, 2011) is a brief intelligence test designed for individuals aged 6 through 90 years. It is a revision of the Wechsler Abbreviated Scale of Intelligence (WASI; Wechsler, 1999). During revision, there were three goals: enhancing the link between the Wechsler…

  8. Neurocognitive mechanisms of the "testing effect" : A review

    NARCIS (Netherlands)

    van den Broek, Gesa; Takashima, Atsuko; Wiklund-Hörnqvist, Carola; Karlsson Wirebring, Linnea; Segers, Eliane; Verhoeven, Ludo; Nyberg, Lars

    2016-01-01

    Memory retrieval is an active process that can alter the content and accessibility of stored memories. Of potential relevance for educational practice are findings that memory retrieval fosters better retention than mere studying. This so-called testing effect has been demonstrated for different

  9. 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

  10. 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.

  11. Women and Educational Testing: A Selective Review of the Research Literature and Testing Practices.

    Science.gov (United States)

    Tittle, Carol Kehr; And Others

    This report provides an exploratory survey of several aspects of educational testing, with a view toward identifying discrimination against women. Two major ways in which discrimination can occur are examined in educational testing: reinforcement of sex-role stereotypes and restriction of individual choice. Major educational achievement tests are…

  12. Can trained lay providers perform HIV testing services? A review of national HIV testing policies.

    Science.gov (United States)

    Flynn, David E; Johnson, Cheryl; Sands, Anita; Wong, Vincent; Figueroa, Carmen; Baggaley, Rachel

    2017-01-04

    Only an estimated 54% of people living with HIV are aware of their status. Despite progress scaling up HIV testing services (HTS), a testing gap remains. Delivery of HTS by lay providers may help close this testing gap, while also increasing uptake and acceptability of HIV testing among key populations and other priority groups. 50 National HIV testing policies were collated from WHO country intelligence databases, contacts and testing program websites. Data regarding lay provider use for HTS was extracted and collated. Our search had no geographical or language restrictions. This data was then compared with reported data from the Global AIDS Response Progress Reporting (GARPR) from July 2015. Forty-two percent of countries permit lay providers to perform HIV testing and 56% permit lay providers to administer pre-and post-test counseling. Comparative analysis with GARPR found that less than half (46%) of reported data from countries were consistent with their corresponding national HIV testing policy. Given the low uptake of lay provider use globally and their proven use in increasing HIV testing, countries should consider revising policies to support lay provider testing using rapid diagnostic tests.

  13. A Review of Neuropathic Pain: From Diagnostic Tests to Mechanisms

    OpenAIRE

    Truini, Andrea

    2017-01-01

    Neuropathic pain develops when the somatosensory nervous system is affected by a lesion or disease. Diagnostic tests aimed at assessing somatosensory afferent pathway damage are therefore useful for diagnosing neuropathic pain. Neuropathic pain manifests with a range of different symptoms such as ongoing burning pain, squeezing or pressure pain, paroxysmal electric shock-like sensations, stabbing pain, or mechanical dynamic allodynia. The various types of neuropathic pain are associated with ...

  14. Review of benchmark tests on JENDL-2B library

    International Nuclear Information System (INIS)

    Kikuchi, Yasuyuki

    1982-01-01

    JENDL-2B is a mixed library consisting of JENDL-2 for the most important nuclides, i.e., 235 U, 238 U, 239 Pu, 240 Pu, 241 Pu, Cr, Fe and Ni and of JENDL-1 for other nuclides. Complete reevaluation work was made for these eight nuclides. The simultaneous evaluation method was adopted in the evaluation for the five heavy nuclides. The resonance structure was carefully studied for the structural materials in the unresolved resonance region up to several MeV. Benchmark tests have been made on JENDL-2B. Various core center characteristics were tested with one-dimensional model for total of 27 assemblies. Satisfactory results were obtained as a whole. The results of spectrum indices, however, suggested some inconsistent spectrum prediction. Moreover, the reactivity worths were overestimated for most of materials, and apparent C/E discrepancies were observed between the Pu and U cores. Applicability of JENDL-2B was further tested to more sophisticated problems for MOZART and ZPPR-3 assemblies. The reaction rate distributions were better predicted with JENDL-2B than with JENDL-1. The positive sodium void reactivity worth was much overestimated with JENDL-2B due to too large moderation components. The control rod worths were well predicted in MOZART, but were considerably underpredicted in ZPPR-3. (author)

  15. A Review of Standardized Tests of Nonverbal Oral and Speech Motor Performance in Children

    Science.gov (United States)

    McCauley, Rebecca J.; Strand, Edythe A.

    2008-01-01

    Purpose: To review the content and psychometric characteristics of 6 published tests currently available to aid in the study, diagnosis, and treatment of motor speech disorders in children. Method: We compared the content of the 6 tests and critically evaluated the degree to which important psychometric characteristics support the tests' use for…

  16. Testing of tubular goods - a critical review of past and actual testing procedures

    Energy Technology Data Exchange (ETDEWEB)

    Teodoriu, C. [Texas A and M Univ., Houston, TX (United States); Holzmann, J.; Klaws, M. [TU Clausthal (Germany). Inst. fuer Erdoel- und Erdgastechnik

    2007-09-13

    Testing of oil country tubular goods (OCTG) is based on standards and offers the user a comparison platform between products of different manufacturers. But, do the standard based testing procedures assume the real loads on OCTG? More likely, the existing standards or recommendations on tubular testing have been evolving together with the new demands on OCTG loading. Since nowadays the oil and gas industry is looking to develop extreme reservoir types (deep water, HP/HT), there is a need of a better understanding and continuous improvement of testing procedures. The following poster proposes an analysis of existing procedures to test tubular goods and then will focus on the future demands on OCTG testing. New loads, as casing fatigue, will be discussed and analyzed based on the authors experience gained during more than 8 years of testing tubular goods at the Clausthal University of Technology, Institute of Petroleum Engineering. (orig.)

  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. Test ban treaty verification with regional data: a review

    International Nuclear Information System (INIS)

    Pomeroy, P.W.; Best, W.J.; McEvilly, T.V.

    1982-01-01

    This paper summarizes the use of regional (Δ ≤ 30 0 ) seismic data in a test ban context for detecting, locating, identifying, and determining the yield of underground nuclear explosions. In many areas of the world (Eastern North America, Africa, Eastern USSR), Lg is the largest amplitude wave recorded on standard seismograph systems and thus is the most appropriate phase for monitoring small magnitude events. Excellent location capability for near-regional events has been demonstrated at the Norwegian small aperture array (NORESS) using Lg and P waves. Lg and other regional phases may contain information on source depth, but such information has not been exploited to date. Fifteen classes of regional discriminants are listed. Most have been tested only on limited data, usually from one geographic region and only one or two recording stations. No systematic analyses have been done to determine the best individual discriminant or combination of them. Preliminary evaluation of the use of Lg for yield determination suggests that regional waves hold promise in this application. Theoretical studies have contributed significantly to the understanding of propagation characteristics of regional waves but further studies are required emphasizing modeling for realistic anisotropic sources. The major conclusion of this study is that a systematic and comparative evaluation of all the proposed regional discriminants is now required, utilizing a common data base derived from all present-day test sites. This evaluation would suggest the optimal discrimination procedure using regional waves, and would also define areas of needed research. Without such an integrated evaluation, it is still possible to speculate, using existing results, on the most promising regional discriminants

  1. Test Review: D. Wechsler "Wechsler Individual Achievement Test-Third Edition." San Antonio, TX--NCS Pearson, 2009

    Science.gov (United States)

    McCrimmon, Adam W.; Climie, Emma A.

    2011-01-01

    This article reviews the "Wechsler Individual Achievement Test-Third Edition" (WIAT-III), a newly updated individual measure of academic achievement for students in Pre-Kindergarten through Grade 12 (age 4 years, 0 months to 19 years, 11 months). Suitable for use in educational, clinical, and research settings, the stated purposes of the WIAT-III…

  2. A review of experiments testing the shoving model

    DEFF Research Database (Denmark)

    Hecksher, Tina; Dyre, J. C.

    2015-01-01

    According to the shoving model the non-Arrhenius temperature dependence of supercooled liquids' relaxation time (or viscosity) derives from the fact that the high-frequency shear modulus is temperature dependent in the supercooled phase, often increasing a factor of three or four in the temperature...... interval over which the relaxation time increases by ten to fifteen decades. In this paper we have compiled all tests of the shoving model known to us. These involve rheological data obtained by different techniques, high-frequency sound-wave data, neutron scattering data for the vibrational mean...

  3. 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.

  4. The recognition heuristic: a review of theory and tests.

    Science.gov (United States)

    Pachur, Thorsten; Todd, Peter M; Gigerenzer, Gerd; Schooler, Lael J; Goldstein, Daniel G

    2011-01-01

    The recognition heuristic is a prime example of how, by exploiting a match between mind and environment, a simple mental strategy can lead to efficient decision making. The proposal of the heuristic initiated a debate about the processes underlying the use of recognition in decision making. We review research addressing four key aspects of the recognition heuristic: (a) that recognition is often an ecologically valid cue; (b) that people often follow recognition when making inferences; (c) that recognition supersedes further cue knowledge; (d) that its use can produce the less-is-more effect - the phenomenon that lesser states of recognition knowledge can lead to more accurate inferences than more complete states. After we contrast the recognition heuristic to other related concepts, including availability and fluency, we carve out, from the existing findings, some boundary conditions of the use of the recognition heuristic as well as key questions for future research. Moreover, we summarize developments concerning the connection of the recognition heuristic with memory models. We suggest that the recognition heuristic is used adaptively and that, compared to other cues, recognition seems to have a special status in decision making. Finally, we discuss how systematic ignorance is exploited in other cognitive mechanisms (e.g., estimation and preference).

  5. The Recognition Heuristic: A Review of Theory and Tests

    Directory of Open Access Journals (Sweden)

    Thorsten ePachur

    2011-07-01

    Full Text Available The recognition heuristic is a prime example of how, by exploiting a match between mind and environment, a simple mental strategy can lead to efficient decision making. The proposal of the heuristic initiated a debate about the processes underlying the use of recognition in decision making. We review research addressing four key aspects of the recognition heuristic: (a that recognition is often an ecologically valid cue; (b that people often follow recognition when making inferences; (c that recognition supersedes further cue knowledge; (d that its use can produce the less-is-more effect—the phenomenon that lesser states of recognition knowledge can lead to more accurate inferences than more complete states. After we contrast the recognition heuristic to other related concepts, including availability and fluency, we carve out, from the existing findings, some boundary conditions of the use of the recognition heuristic as well as key questions for future research. Moreover, we summarize developments concerning the connection of the recognition heuristic with memory models. We suggest that the recognition heuristic is used adaptively and that, compared to other cues, recognition seems to have a special status in decision making. Finally, we discuss how systematic ignorance is exploited in other cognitive mechanisms (e.g., estimation and preference.

  6. The Recognition Heuristic: A Review of Theory and Tests

    Science.gov (United States)

    Pachur, Thorsten; Todd, Peter M.; Gigerenzer, Gerd; Schooler, Lael J.; Goldstein, Daniel G.

    2011-01-01

    The recognition heuristic is a prime example of how, by exploiting a match between mind and environment, a simple mental strategy can lead to efficient decision making. The proposal of the heuristic initiated a debate about the processes underlying the use of recognition in decision making. We review research addressing four key aspects of the recognition heuristic: (a) that recognition is often an ecologically valid cue; (b) that people often follow recognition when making inferences; (c) that recognition supersedes further cue knowledge; (d) that its use can produce the less-is-more effect – the phenomenon that lesser states of recognition knowledge can lead to more accurate inferences than more complete states. After we contrast the recognition heuristic to other related concepts, including availability and fluency, we carve out, from the existing findings, some boundary conditions of the use of the recognition heuristic as well as key questions for future research. Moreover, we summarize developments concerning the connection of the recognition heuristic with memory models. We suggest that the recognition heuristic is used adaptively and that, compared to other cues, recognition seems to have a special status in decision making. Finally, we discuss how systematic ignorance is exploited in other cognitive mechanisms (e.g., estimation and preference). PMID:21779266

  7. Development and evaluation of a novel fast broad-range 16S ribosomal DNA PCR and sequencing assay for diagnosis of bacterial infective endocarditis: multi-year experience in a large Canadian healthcare zone and a literature review.

    Science.gov (United States)

    Miller, Robert J H; Chow, Barbara; Pillai, Dylan; Church, Deirdre

    2016-04-12

    The study aimed to explore the sensitivity and specificity of a novel fast 16S rDNA PCR and sequencing assay for the improved diagnosis of infective endocarditis (IE) in patients with suspected native or prosthetic heart valve (HV) infection over a multi-year period at our cardiovascular center. Sixty-eight patients were prospectively enrolled who underwent HV replacement for suspected or confirmed IE between February 1, 2009 and September 1, 2014. Patient demographics, medical co-morbidities, Duke's criteria, culture results, and antibiotic therapy were collected by detailed chart reviews. Dual-priming oligonucleotide primers targeted to 500 bps of the V1-V3 region of the 16S rRNA gene were used to perform fast broad-range 16S rDNA PCR and Sanger sequencing on ribosomal DNA extracted from HV tissues. The performance/diagnostic efficiency of the molecular test was evaluated against blood cultures and Gram stain and culture of HV tissue in patients' with definite IE according to Duke's criteria. Fifty patients (73.5%) had definite IE and another 8 (11.8%) had possible IE according to Duke's criteria. Cardiac surgery was delayed an average of 15.4 days from the time of the patient's last positive blood culture, and appropriate antibiotic therapy was given in the pre-operative period. While 44/50 (88%) patients had a positive blood culture, HV tissue culture was only positive in 23 (46%) of them. Molecular testing of all HV tissues had sensitivity, specificity, NPV and PPV of 92, 77.8, 77.8 and 92% compared to 44, 100, 39.1 and 100% respectively for culture for diagnosis of definite IE. For prosthetic HV tissue, 16S rDNA PCR had sensitivity of 93% and specificity of 83% compared to 35 and 100% respectively for culture. A literature review showed that the diagnostic accuracy of our novel fast broad-range 16S rDNA PCR assay was similar or better than that of previously published studies. This novel fast broad-range 16S rDNA PCR/sequencing test had superior sensitivity

  8. 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...

  9. 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)

  10. 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...

  11. A review of Studsvik's international power ramp test projects

    International Nuclear Information System (INIS)

    Mogard, H.; Kjaer-Pedersen, N.

    1985-11-01

    Since 1975 a series of internationally sponsored fuel irradiation research projects have been and are being conducted at Studsvik, Sweden, under the management of Studsvik Energiteknik AB. The sponsoring parties comprise fuel vendors, nuclear power utilities, national research organizations and, in some cases, safety authorities. Geographically the parties represent organizations in Europe, Japan, and the USA. The main research topic of the Studsvik projects is the Pellet Clad Interaction (PCI) induced Stress Corrosion Cracking (SCC) failure occurrence in LWR fuel under power ramping conditions. The research is conducted in the 50 MW R2 test reactor and the associated hot cell laboratory. Prior to the experiments the test fuel is base irradiated, normally in commercially operated light water reactors. Results have been published for the INTER-RAMP, OVER-RAMP, DEMO-RAMP I, DEMO-RAMP II and SUPER-RAMP projects. The release of the TRANS-RAMP I results is imminent. There are two ongoing projects, i.e. SUPER-RAMP EXTENSION and TRANS-RAMP II. The paper presents an overview of the objectives and main results of the various projects. An attempt is made to summarize the more important observations on PCI failure performance in the perspective of design parameters, fuel burnup levels, power histories, power ramp rates, etc. With 14 refs. (Author)

  12. SRNL Review And Assessment Of WTP UFP-02 Sparger Design And Testing

    Energy Technology Data Exchange (ETDEWEB)

    Poirier, M. R. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Duignan, M. R. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Fink, S. D. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Steimke, J. L. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2014-03-24

    During aerosol testing conducted by Parsons Constructors and Fabricators, Inc. (PCFI), air sparger plugging was observed in small-scale and medium-scale testing. Because of this observation, personnel identified a concern that the steam spargers in Pretreatment Facility vessel UFP-02 could plug during Waste Treatment and Immobilization Plant (WTP) operation. The U. S. Department of Energy (DOE) requested that Savannah River National Laboratory (SRNL) provide consultation on the evaluation of known WTP bubbler, and air and steam sparger issues. The authors used the following approach for this task: reviewed previous test reports (including smallscale testing, medium-scale testing, and Pretreatment Engineering Platform [PEP] testing), met with Bechtel National, Inc. (BNI) personnel to discuss sparger design, reviewed BNI documents supporting the sparger design, discussed sparger experience with Savannah River Site Defense Waste Processing Facility (DWPF) and Sellafield personnel, talked to sparger manufacturers about relevant operating experience and design issues, and reviewed UFP-02 vessel and sparger drawings.

  13. A Comparison of Eighth Grade Students' Testing Scores between the "Jeopardy" and "Seatwork" Types of Review.

    Science.gov (United States)

    Daft, Lee T.

    This study focused on the review process before social studies testing. The students involved in the study were 71 13 and 14-year olds and came from predominantly middle to upper class social status in a Knoxville, Tennessee suburb. The influence of an interactive review based on the quiz show "Jeopardy" was compared with that of a "seatwork"…

  14. The diagnostic value of circulating cell free DNA quantification in non-small cell lung cancer: A systematic review with meta-analysis.

    Science.gov (United States)

    Jiang, Tao; Zhai, Changyun; Su, Chunxia; Ren, Shengxiang; Zhou, Caicun

    2016-10-01

    The aim of the current study was to assess the diagnostic value of circulating cell free DNA (cfDNA) quantification in discriminating non-small cell lung cancer (NSCLC) from healthy individuals. An electronic search was conducted on PubMed, EMBASE, Web of Science, and Cochrane Library. Eligible studies regarding to examine the diagnostic value of cfDNA in the detection of NSCLC were extracted and analyzed. We identified 15 eligible studies with a total of 2125 patients. The pooled results for quantification of cfDNA in lung cancer screening in the included studies were as follows: sensitivity, 81% (95% confidence interval (CI), 76%-84%); specificity, 85% (95% CI, 77%-91%); diagnostic odds ratio, 23.87 (95% CI, 13.37-42.61); and areas under the summary receiver operating characteristic curves were 0.89 (95% CI, 0.86-0.92). Subgroup analyses according to the time of sample collection, sample materials, test method, reference gene and cutoff value did not improve sensitivity, but specificity could be significantly improved when we only included the studies using cfDNA sample before surgery or antitumor treatment and real-time PCR to detect cfDNA and human β-actin as a reference gene. Quantification of cfDNA was a promising and effective biomarker for discriminating NSCLC from healthy individuals. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  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. Specialist committee's review reports for experimental fast reactor JOYO' MK-III performance tests

    International Nuclear Information System (INIS)

    Yamashita, Kiyonobu; Okubo, Toshiyuki; Kamide, Hideki

    2004-02-01

    Performance tests (startup-physics tests and power elevation tests) were planed for experimental fast reactor 'JOYO' MK-III where irradiation performances were upgraded by power increase from 100 to 140 MW. The reactor safety committee of O-arai Engineering Center has established a specialist committee for 'JOYO' MK-III Performance Tests at the first meeting of 2003 on 23th. April 2003, to accomplish the tests successfully. Subjects of the specialist committee were reviews of following items covering a wide range. 1) Contents of modification works. 2) Reflections of functional test results to the plant and facilities. 3) Reflections of safety rule modification to instruction and manual for operation. 4) Quality assurances and pre-calculation for performance test. 5) Inspection plan and its results. 6) Adequacy of performance test plan. 7) Confirmation of performance test results. Before test-starts, the specialist committee has confirmed by reviewing the items from 1) to 6) based on explanations and documents of the Division of Experimental Reactor, that the test plan and pre-inspections are adequate. After the tests, the specialist committee had confirmed by reviewing the item 7) in the same way, that the each test result satisfies the corresponding criterion. The specialist committee has concluded from these review's results before and after the tests that the 'JOYO' MK-III Performance Tests were carried out appropriately. Besides, the first criticality of the JOYO MK-III was achieved on 2nd. July 2003, and the continuous full power operation was carried on 20th. Nov. 2003. Finally, all performance tests were completed by the pass of the last governmental pre-serviced inspection (dose rate measurement during the shut down condition). (author)

  17. Review of the Factory Acceptance Tests and Cold Tests of the W7-X Superconducting Magnets

    International Nuclear Information System (INIS)

    Ehmler, H.; Baldzuhn, J.; Genini, L.

    2006-01-01

    The W7-X magnet system consists of 50 non-planar coils of five different types and 20 planar coils of two different types. Factory acceptance tests of the non-planar coils are carried out at the manufacturer site of Babcock-Noell, Germany, and for the planar coils at Tesla Engineering, UK. They consist of electrical insulation checks, mass flow measurements and leak tests. In the test facility of CEA Saclay, France, each coil is cooled down to ∼ 6 K and operated at nominal current. At least one coil of each type is quenched by increasing the inlet temperature. The characteristic parameters of the quench tests (temperature, pressure, speed of normal-conducting zone, etc.) will be presented. Coils of the same type show a uniform behavior. The occurrences of leaks during cool-down on planar coils revealed quality problems with aluminum welds and stress corrosion of stainless steel tubes at the soldered connections with copper heat sinks. AC tests (impulse and impedance tests) were applied to detect short circuits during the fabrication of the winding packs. High voltage DC tests under vacuum and low gas pressure (Paschen-minimum conditions) revealed electrical insulation defects, which had not been found using standard high-voltage tests. These were mainly due to voids and cavities present in the winding pack after vacuum impregnation, insufficient glass-epoxy wrapped insulation and inappropriate design of the Kapton insulated quench detection cables. The mass flow measurements of the superconductor showed that the deviation between individual double layers of the coils is within acceptable limits. Two winding packs were given up by the supplier because of a superconductor blockage with resin and a short circuited winding, respectively. All other quality issues could be resolved by repair or changes in the components. The coil instrumentation with temperature sensors seems to be adequate. The strain gauges need improvements in temperature compensation and gluing

  18. Systematic reviews of diagnostic tests in endocrinology: an audit of methods, reporting, and performance.

    Science.gov (United States)

    Spencer-Bonilla, Gabriela; Singh Ospina, Naykky; Rodriguez-Gutierrez, Rene; Brito, Juan P; Iñiguez-Ariza, Nicole; Tamhane, Shrikant; Erwin, Patricia J; Murad, M Hassan; Montori, Victor M

    2017-07-01

    Systematic reviews provide clinicians and policymakers estimates of diagnostic test accuracy and their usefulness in clinical practice. We identified all available systematic reviews of diagnosis in endocrinology, summarized the diagnostic accuracy of the tests included, and assessed the credibility and clinical usefulness of the methods and reporting. We searched Ovid MEDLINE, EMBASE, and Cochrane CENTRAL from inception to December 2015 for systematic reviews and meta-analyses reporting accuracy measures of diagnostic tests in endocrinology. Experienced reviewers independently screened for eligible studies and collected data. We summarized the results, methods, and reporting of the reviews. We performed subgroup analyses to categorize diagnostic tests as most useful based on their accuracy. We identified 84 systematic reviews; half of the tests included were classified as helpful when positive, one-fourth as helpful when negative. Most authors adequately reported how studies were identified and selected and how their trustworthiness (risk of bias) was judged. Only one in three reviews, however, reported an overall judgment about trustworthiness and one in five reported using adequate meta-analytic methods. One in four reported contacting authors for further information and about half included only patients with diagnostic uncertainty. Up to half of the diagnostic endocrine tests in which the likelihood ratio was calculated or provided are likely to be helpful in practice when positive as are one-quarter when negative. Most diagnostic systematic reviews in endocrine lack methodological rigor, protection against bias, and offer limited credibility. Substantial efforts, therefore, seem necessary to improve the quality of diagnostic systematic reviews in endocrinology.

  19. A review of centrifugal testing of gasoline contamination and remediation.

    Science.gov (United States)

    Meegoda, Jay N; Hu, Liming

    2011-08-01

    Leaking underground storage tanks (USTs) containing gasoline represent a significant public health hazard. Virtually undetectable to the UST owner, gasoline leaks can contaminate groundwater supplies. In order to develop remediation plans one must know the extent of gasoline contamination. Centrifugal simulations showed that in silty and sandy soils gasoline moved due to the physical process of advection and was retained as a pool of free products above the water table. However, in clayey soils there was a limited leak with lateral spreading and without pooling of free products above the water table. Amount leaked depends on both the type of soil underneath the USTs and the amount of corrosion. The soil vapor extraction (SVE) technology seems to be an effective method to remove contaminants from above the water table in contaminated sites. In-situ air sparging (IAS) is a groundwater remediation technology for contamination below the water table, which involves the injection of air under pressure into a well installed into the saturated zone. However, current state of the art is not adequate to develop a design guide for site implementation. New information is being currently generated by both centrifugal tests as well as theoretical models to develop a design guide for IAS. The petroleum contaminated soils excavated from leaking UST sites can be used for construction of highway pavements, specifically as sub-base material or blended and used as hot or cold mix asphalt concrete. Cost analysis shows that 5% petroleum contaminated soils is included in hot or cold mix asphalt concrete can save US$5.00 production cost per ton of asphalt produced.

  20. A Review of Centrifugal Testing of Gasoline Contamination and Remediation

    Directory of Open Access Journals (Sweden)

    Jay N. Meegoda

    2011-08-01

    Full Text Available Leaking underground storage tanks (USTs containing gasoline represent a significant public health hazard. Virtually undetectable to the UST owner, gasoline leaks can contaminate groundwater supplies. In order to develop remediation plans one must know the extent of gasoline contamination. Centrifugal simulations showed that in silty and sandy soils gasoline moved due to the physical process of advection and was retained as a pool of free products above the water table. However, in clayey soils there was a limited leak with lateral spreading and without pooling of free products above the water table. Amount leaked depends on both the type of soil underneath the USTs and the amount of corrosion. The soil vapor extraction (SVE technology seems to be an effective method to remove contaminants from above the water table in contaminated sites. In-situ air sparging (IAS is a groundwater remediation technology for contamination below the water table, which involves the injection of air under pressure into a well installed into the saturated zone. However, current state of the art is not adequate to develop a design guide for site implementation. New information is being currently generated by both centrifugal tests as well as theoretical models to develop a design guide for IAS. The petroleum contaminated soils excavated from leaking UST sites can be used for construction of highway pavements, specifically as sub-base material or blended and used as hot or cold mix asphalt concrete. Cost analysis shows that 5% petroleum contaminated soils is included in hot or cold mix asphalt concrete can save US$5.00 production cost per ton of asphalt produced.

  1. Ecotoxicity of engineered nanoparticles to aquatic invertebrates: a brief review and recommendations for future toxicity testing

    DEFF Research Database (Denmark)

    Baun, Anders; Hartmann, Nanna Isabella Bloch; Grieger, Khara Deanne

    2008-01-01

    Based on a literature review and an overview of toxic effects of engineered nanoparticles in aquatic invertebrates, this paper proposes a number of recommendations for the developing field of nanoecotoxicology by highlighting the importance of invertebrates as sensitive and relevant test organisms...... through standardized short-term (lethality) tests with invertebrates as a basis for investigating behaviour and bioavailability of engineered nanoparticles in the aquatic environment. Based on this literature review, we further recommend that research is directed towards invertebrate tests employing long....... Results show that there is a pronounced lack of data in this field (less than 20 peer-reviewed papers are published so far), and the most frequently tested engineered nanoparticles in invertebrate tests are C-60, carbon nanotubes, and titanium dioxide. In addition, the majority of the studies have used...

  2. 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.

  3. 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.

  4. 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.

  5. Review of test methods used to determine the corrosion rate of metals in contact with treated wood

    Science.gov (United States)

    Samuel L. Zelinka; Douglas R. Rammer

    2005-01-01

    The purpose of this literature review is to give an overview of test methods previously used to evaluate the corrosion of metals in contact with wood. This article reviews the test methods used to evaluate the corrosion of metals in contact with wood by breaking the experiments into three groups: exposure tests, accelerated exposure tests, and electrochemical tests....

  6. 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

  7. Impact Strength of Natural Fibre Composites Measured by Different Test Methods: A Review

    Directory of Open Access Journals (Sweden)

    Navaranjan Namasivayam

    2017-01-01

    Full Text Available Different types of impact test methods have been used in recent years to measure the impact resistance of natural fibre composites (NFCs. After reviewing the literature, the impact resistance of flax, hemp, sisal, wood and jute fibre composites that were measured using different test methods have been compared and discussed. It has been learned that the test methods were selected for research interest, industry requirement or availability of test equipment. Each method had its own advantages and limitations. The result from a particular test could be compared but not with the result from other test methods. Most impact test methods were developed for testing ductile-brittle transition of metals. However, each NFC has a different morphology and cannot be comparable to metals in failure mode and energy absorption characteristic during an impact test. A post evaluation of morphology of an NFC sample after an impact test is important to characterise the material.

  8. A Psychometric Review of Norm-Referenced Tests Used to Assess Phonological Error Patterns

    Science.gov (United States)

    Kirk, Celia; Vigeland, Laura

    2014-01-01

    Purpose: The authors provide a review of the psychometric properties of 6 norm-referenced tests designed to measure children's phonological error patterns. Three aspects of the tests' psychometric adequacy were evaluated: the normative sample, reliability, and validity. Method: The specific criteria used for determining the psychometric…

  9. In-vitro orthodontic bond strength testing : A systematic review and meta-analysis

    NARCIS (Netherlands)

    Finnema, K.J.; Ozcan, M.; Post, W.J.; Ren, Y.J.; Dijkstra, P.U.

    INTRODUCTION: The aims of this study were to systematically review the available literature regarding in-vitro orthodontic shear bond strength testing and to analyze the influence of test conditions on bond strength. METHODS: Our data sources were Embase and Medline. Relevant studies were selected

  10. 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.

  11. HIV-1 tropism testing and clinical management of CCR5 antagonists: Quebec review and recommendations.

    Science.gov (United States)

    Tremblay, Cécile; Hardy, Isabelle; Lalonde, Richard; Trottier, Benoit; Tsarevsky, Irina; Vézina, Louis-Philippe; Roger, Michel; Wainberg, Mark; Baril, Jean-Guy

    2013-01-01

    HIV-1 tropism assays play a crucial role in determining the response to CCR5 receptor antagonists. Initially, phenotypic tests were used, but limited access to these tests prompted the development of alternative strategies. Recently, genotyping tropism has been validated using a Canadian technology in clinical trials investigating the use of maraviroc in both experienced and treatment-naive patients. The present guidelines review the evidence supporting the use of genotypic assays and provide recommendations regarding tropism testing in daily clinical management.

  12. Safety review on unit testing of safety system software of nuclear power plant

    International Nuclear Information System (INIS)

    Liu Le; Zhang Qi

    2013-01-01

    Software unit testing has an important place in the testing of safety system software of nuclear power plants, and in the wider scope of the verification and validation. It is a comprehensive, systematic process, and its documentation shall meet the related requirements. When reviewing software unit testing, attention should be paid to the coverage of software safety requirements, the coverage of software internal structure, and the independence of the work. (authors)

  13. Reliability of physical functioning tests in patients with low back pain: a systematic review.

    Science.gov (United States)

    Denteneer, Lenie; Van Daele, Ulrike; Truijen, Steven; De Hertogh, Willem; Meirte, Jill; Stassijns, Gaetane

    2018-01-01

    The aim of this study was to provide a comprehensive overview of physical functioning tests in patients with low back pain (LBP) and to investigate their reliability. A systematic computerized search was finalized in four different databases on June 24, 2017: PubMed, Web of Science, Embase, and MEDLINE. Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines were followed during all stages of this review. Clinical studies that investigate the reliability of physical functioning tests in patients with LBP were eligible. The methodological quality of the included studies was assessed with the use of the Consensus-based Standards for the selection of health Measurement Instruments (COSMIN) checklist. To come to final conclusions on the reliability of the identified clinical tests, the current review assessed three factors, namely, outcome assessment, methodological quality, and consistency of description. A total of 20 studies were found eligible and 38 clinical tests were identified. Good overall test-retest reliability was concluded for the extensor endurance test (intraclass correlation coefficient [ICC]=0.93-0.97), the flexor endurance test (ICC=0.90-0.97), the 5-minute walking test (ICC=0.89-0.99), the 50-ft walking test (ICC=0.76-0.96), the shuttle walk test (ICC=0.92-0.99), the sit-to-stand test (ICC=0.91-0.99), and the loaded forward reach test (ICC=0.74-0.98). For inter-rater reliability, only one test, namely, the Biering-Sörensen test (ICC=0.88-0.99), could be concluded to have an overall good inter-rater reliability. None of the identified clinical tests could be concluded to have a good intrarater reliability. Further investigation should focus on a better overall study methodology and the use of identical protocols for the description of clinical tests. The assessment of reliability is only a first step in the recommendation process for the use of clinical tests. In future research, the identified clinical tests in the

  14. 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

  15. Mechanisms for radiation damage in DNA

    International Nuclear Information System (INIS)

    Sevilla, M.D.

    1993-12-01

    In this project the author has proposed several mechanisms for radiation damage to DNA and its constituents, and has detailed a series of experiments utilizing electron spin resonance spectroscopy, HPLC, GC-mass spectroscopy and ab initio molecular orbital calculations to test the proposed mechanisms. In this years work he has completed several experiments on the role of hydration water on DNA radiation damage, continued the investigation of the localization of the initial charges and their reactions on DNA, investigated protonation reactions in DNA base anions, and employed ab initio molecular orbital theory to gain insight into the initial events of radiation damage to DNA. Ab initio calculations have provided an understanding of the energetics evolved in anion and cation formation, ion radical transfer in DNA as well as proton transfer with DNA base pair radical ions. This has been extended in this years work to a consideration of ionization energies of various components of the DNA deoxyribose backbone and resulting neutral sugar radicals. This information has aided the formation of new radiation models for the effect of radiation on DNA. During this fiscal year four articles have been published, four are in press, one is submitted and several more are in preparation. Four papers have been presented at scientific meetings. This years effort will include another review article on the open-quotes Electron Spin Resonance of Radiation Damage to DNAclose quotes

  16. Diagnostic accuracy of physical examination tests of the ankle/foot complex: a systematic review.

    Science.gov (United States)

    Schwieterman, Braun; Haas, Deniele; Columber, Kirby; Knupp, Darren; Cook, Chad

    2013-08-01

    Orthopedic special tests of the ankle/foot complex are routinely used during the physical examination process in order to help diagnose ankle/lower leg pathologies. The purpose of this systematic review was to investigate the diagnostic accuracy of ankle/lower leg special tests. A search of the current literature was conducted using PubMed, CINAHL, SPORTDiscus, ProQuest Nursing and Allied Health Sources, Scopus, and Cochrane Library. Studies were eligible if they included the following: 1) a diagnostic clinical test of musculoskeletal pathology in the ankle/foot complex, 2) description of the clinical test or tests, 3) a report of the diagnostic accuracy of the clinical test (e.g. sensitivity and specificity), and 4) an acceptable reference standard for comparison. The quality of included studies was determined by two independent reviewers using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) tool. Nine diagnostic accuracy studies met the inclusion criteria for this systematic review; analyzing a total of 16 special tests of the ankle/foot complex. After assessment using the QUADAS-2, only one study had low risk of bias and low concerns regarding applicability. Most ankle/lower leg orthopedic special tests are confirmatory in nature and are best utilized at the end of the physical examination. Most of the studies included in this systematic review demonstrate notable biases, which suggest that results and recommendations in this review should be taken as a guide rather than an outright standard. There is need for future research with more stringent study design criteria so that more accurate diagnostic power of ankle/lower leg special tests can be determined. 3a.

  17. Standard review plan for the review and evaluation of emergency plans for research and test reactors. Technical report

    International Nuclear Information System (INIS)

    Bates, E.F.; Grimes, B.K.; Ramos, S.L.

    1982-05-01

    This document provides a Standard Review Plan for the guidance of the NRC staff to assure that complete and uniform reviews are made of research and test reactor emergency plans. The report is organized under ten planning standards which correspond to the guidance criteria in Draft II of ANSI/ANS 15.16 as endorsed by Revision 1 to Regulatory Guide 2.6. The applicability of the items under each planning standard is indicated by subdivisions of the steady state thermal power levels at which the reactors are licensed to operate. Standard emergency classes and example action levels for research and test reactors which should initiate these classes are given in an Appendix

  18. 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.

  19. Review of Department of Energy HEPA filter test activities, FY 1990--FY 1992

    International Nuclear Information System (INIS)

    McIntyre, J.A.

    1992-01-01

    Filter Test Facilities (FTFs) and the FTF Technical Support Group (TSG) continue to provide services to the Department of Energy (DOE). Additional tasks relating to the HEPA filter cycle have been added to the TSG. The tasks include the quality assessment review for the in-place testing of HEPA filters at DOE sites and the formation of an in-place testing standards writing group. Summary of ongoing FTFs and TSG activities for FY 1990-FY 1992 including the technical input for implementation of the High Flow Alternative Test System (HFATS), update of the DOE Standards, the status of the quality assessment review and in-place testing standards writing group are discussed

  20. Review of Evidence of Environmental Impacts of Animal Research and Testing

    OpenAIRE

    Katherine Groff; Eric Bachli; Molly Lansdowne; Theodora Capaldo

    2014-01-01

    Millions of animals are used in research and toxicity testing, including in drug, medical device, chemical, cosmetic, personal care, household, and other product sectors, but the environmental consequences are yet to be adequately addressed. Evidence suggests that their use and disposal, and the associated use of chemicals and supplies, contribute to pollution as well as adverse impacts on biodiversity and public health. The objective of this review is to examine such evidence. The review in...

  1. Independent review of Oak Ridge HCTW test program and development of seismic evaluation criteria

    International Nuclear Information System (INIS)

    1995-05-01

    Many of the existing buildings at the Oak Ridge Y-12 Plant are steel frame construction with unreinforced hollow clay tile infill walls (HCTW). The HCTW infill provides some lateral seismic resistance to the design/evaluation basis earthquake; however acceptance criteria for this construction must be developed. The basis for the development of seismic criteria is the Oak Ridge HCTW testing and analysis program and the target performance goals of DOE 5480.28 and DOE-STD-1020-94. This report documents and independent review of the testing and analysis program and development of recommended acceptance criteria for Oak Ridge HCTW construction. The HCTW test program included ''macro'' wall in-plane and out-of-plane tests, full-scale wall in-plane and out-of-plane tests, in-situ out-of-plane test, shake table tests, and masonry component tests

  2. HIV Point-of-Care Testing in Canadian Settings: A Scoping Review.

    Science.gov (United States)

    Minichiello, Alexa; Swab, Michelle; Chongo, Meck; Marshall, Zack; Gahagan, Jacqueline; Maybank, Allison; Hot, Aurélie; Schwandt, Michael; Gaudry, Sonia; Hurley, Oliver; Asghari, Shabnam

    2017-01-01

    HIV point-of-care testing (POCT) was approved for use in Canada in 2005 and provides important public health benefits by providing rapid screening results rather than sending a blood sample to a laboratory and waiting on test results. Access to test results soon after testing (or during the same visit) is believed to increase the likelihood that individuals will receive their results and improve access to confirmatory testing and linkages to care. This paper reviews the literature on the utilization of HIV POCT across Canadian provinces. We searched OVID Medline, Embase, EBM Reviews, PsycINFO, CINAHL, and 20 electronic grey literature databases. All empirical studies investigating HIV POCT programs in Canada published in French or English were included. Searches of academic databases identified a total of 6,091 records. After removing duplicates and screening for eligibility, 27 records were included. Ten studies are peer-reviewed articles, and 17 are grey literature reports. HIV POCT in Canada is both feasible and accepted by Canadians. It is preferred to conventional HIV testing (ranging from 81.1 to 97%), and users are highly satisfied with the testing process (ranging between 96 and 100%). The majority of studies demonstrate that HIV POCT is feasible, preferred, and accepted by diverse populations in Canada. Losses to follow-up and linkage rates are also good. However, more research is needed to understand how best to scale up HIV POCT in contexts that currently have very limited or no access to testing.

  3. Review of Evidence of Environmental Impacts of Animal Research and Testing

    Directory of Open Access Journals (Sweden)

    Katherine Groff

    2014-06-01

    Full Text Available Millions of animals are used in research and toxicity testing, including in drug, medical device, chemical, cosmetic, personal care, household, and other product sectors, but the environmental consequences are yet to be adequately addressed. Evidence suggests that their use and disposal, and the associated use of chemicals and supplies, contribute to pollution as well as adverse impacts on biodiversity and public health. The objective of this review is to examine such evidence. The review includes examinations of (1 resources used in animal research; (2 waste production in laboratories; (3 sources of pollution; (4 impacts on laboratory workers’ health; and (5 biodiversity impacts. The clear conclusion from the review is that the environmental implications of animal testing must be acknowledged, reported, and taken into account as another factor in addition to ethical and scientific reasons weighing heavily in favor of moving away from allowing and requiring animal use in research and testing.

  4. A systematic review of the diagnostic performance of orthopedic physical examination tests of the hip.

    Science.gov (United States)

    Rahman, Labib Ataur; Adie, Sam; Naylor, Justine Maree; Mittal, Rajat; So, Sarah; Harris, Ian Andrew

    2013-08-30

    Previous reviews of the diagnostic performances of physical tests of the hip in orthopedics have drawn limited conclusions because of the low to moderate quality of primary studies published in the literature. This systematic review aims to build on these reviews by assessing a broad range of hip pathologies, and employing a more selective approach to the inclusion of studies in order to accurately gauge diagnostic performance for the purposes of making recommendations for clinical practice and future research. It specifically identifies tests which demonstrate strong and moderate diagnostic performance. A systematic search of Medline, Embase, Embase Classic and CINAHL was conducted to identify studies of hip tests. Our selection criteria included an analysis of internal and external validity. We reported diagnostic performance in terms of sensitivity, specificity, predictive values and likelihood ratios. Likelihood ratios were used to identify tests with strong and moderate diagnostic utility. Only a small proportion of tests reported in the literature have been assessed in methodologically valid primary studies. 16 studies were included in our review, producing 56 independent test-pathology combinations. Two tests demonstrated strong clinical utility, the patellar-pubic percussion test for excluding radiologically occult hip fractures (negative LR 0.05, 95% Confidence Interval [CI] 0.03-0.08) and the hip abduction sign for diagnosing sarcoglycanopathies in patients with known muscular dystrophies (positive LR 34.29, 95% CI 10.97-122.30). Fifteen tests demonstrated moderate diagnostic utility for diagnosing and/or excluding hip fractures, symptomatic osteoarthritis and loosening of components post-total hip arthroplasty. We have identified a number of tests demonstrating strong and moderate diagnostic performance. These findings must be viewed with caution as there are concerns over the methodological quality of the primary studies from which we have extracted our

  5. 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.

  6. Systematic review of studies on cost-effectiveness of cystic fibrosis carrier testing

    Directory of Open Access Journals (Sweden)

    Ernesto Andrade-Cerquera

    2016-10-01

    Full Text Available Introduction: Cystic fibrosis is considered the most common autosomal disease with multisystem complications in non-Hispanic white population. Objective: To review the available evidence on cost-effectiveness of the cystic fibrosis carrier testing compared to no intervention. Materials and methods: The databases of MEDLINE, Embase, NHS, EBM Reviews - Cochrane Database of Systematic Reviews, LILACS, Health Technology Assessment, Genetests.org, Genetsickkids.org and Web of Science were used to conduct a systematic review of the cost-effectiveness of performing the genetic test in cystic fibrosis patients. Cost-effectiveness studies were included without language or date of publication restrictions. Results: Only 13 studies were relevant for full review. Prenatal, preconception and mixed screening strategies were found. Health perspective was the most used; the discount rate applied was heterogeneous between 3.5% and 5%; the main analysis unit was the cost per detected carrier couple, followed by cost per averted birth with cystic fibrosis. It was evident that the most cost-effective strategy was preconception screening associated with prenatal test. Conclusions: A marked heterogeneity in the methodology was found, which led to incomparable results and to conclude that there are different approaches to this genetic test.

  7. Prediction of pre-eclampsia: a protocol for systematic reviews of test accuracy

    Directory of Open Access Journals (Sweden)

    Khan Khalid S

    2006-10-01

    Full Text Available Abstract Background Pre-eclampsia, a syndrome of hypertension and proteinuria, is a major cause of maternal and perinatal morbidity and mortality. Accurate prediction of pre-eclampsia is important, since high risk women could benefit from intensive monitoring and preventive treatment. However, decision making is currently hampered due to lack of precise and up to date comprehensive evidence summaries on estimates of risk of developing pre-eclampsia. Methods/Design A series of systematic reviews and meta-analyses will be undertaken to determine, among women in early pregnancy, the accuracy of various tests (history, examinations and investigations for predicting pre-eclampsia. We will search Medline, Embase, Cochrane Library, MEDION, citation lists of review articles and eligible primary articles and will contact experts in the field. Reviewers working independently will select studies, extract data, and assess study validity according to established criteria. Language restrictions will not be applied. Bivariate meta-analysis of sensitivity and specificity will be considered for tests whose studies allow generation of 2 × 2 tables. Discussion The results of the test accuracy reviews will be integrated with results of effectiveness reviews of preventive interventions to assess the impact of test-intervention combinations for prevention of pre-eclampsia.

  8. 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)

  9. Reviews of the Comprehensive Nuclear-Test-Ban Treaty and U.S. security

    Science.gov (United States)

    Jeanloz, Raymond

    2017-11-01

    Reviews of the Comprehensive Nuclear-Test-Ban Treaty (CTBT) by the National Academy of Sciences concluded that the United States has the technical expertise and physical means to i) maintain a safe, secure and reliable nuclear-weapons stockpile without nuclear-explosion testing, and ii) effectively monitor global compliance once the Treaty enters into force. Moreover, the CTBT is judged to help constrain proliferation of nuclear-weapons technology, so it is considered favorable to U.S. security. Review of developments since the studies were published, in 2002 and 2012, show that the study conclusions remain valid and that technical capabilities are better than anticipated.

  10. Methods Used in Economic Evaluations of Chronic Kidney Disease Testing — A Systematic Review

    Science.gov (United States)

    Sutton, Andrew J.; Breheny, Katie; Deeks, Jon; Khunti, Kamlesh; Sharpe, Claire; Ottridge, Ryan S.; Stevens, Paul E.; Cockwell, Paul; Kalra, Philp A.; Lamb, Edmund J.

    2015-01-01

    Background The prevalence of chronic kidney disease (CKD) is high in general populations around the world. Targeted testing and screening for CKD are often conducted to help identify individuals that may benefit from treatment to ameliorate or prevent their disease progression. Aims This systematic review examines the methods used in economic evaluations of testing and screening in CKD, with a particular focus on whether test accuracy has been considered, and how analysis has incorporated issues that may be important to the patient, such as the impact of testing on quality of life and the costs they incur. Methods Articles that described model-based economic evaluations of patient testing interventions focused on CKD were identified through the searching of electronic databases and the hand searching of the bibliographies of the included studies. Results The initial electronic searches identified 2,671 papers of which 21 were included in the final review. Eighteen studies focused on proteinuria, three evaluated glomerular filtration rate testing and one included both tests. The full impact of inaccurate test results was frequently not considered in economic evaluations in this setting as a societal perspective was rarely adopted. The impact of false positive tests on patients in terms of the costs incurred in re-attending for repeat testing, and the anxiety associated with a positive test was almost always overlooked. In one study where the impact of a false positive test on patient quality of life was examined in sensitivity analysis, it had a significant impact on the conclusions drawn from the model. Conclusion Future economic evaluations of kidney function testing should examine testing and monitoring pathways from the perspective of patients, to ensure that issues that are important to patients, such as the possibility of inaccurate test results, are properly considered in the analysis. PMID:26465773

  11. DNA multigene characterization of Fasciola hepatica and Lymnaea neotropica and its fascioliasis transmission capacity in Uruguay, with historical correlation, human report review and infection risk analysis.

    Science.gov (United States)

    Bargues, María Dolores; Gayo, Valeria; Sanchis, Jaime; Artigas, Patricio; Khoubbane, Messaoud; Birriel, Soledad; Mas-Coma, Santiago

    2017-02-01

    Fascioliasis is a pathogenic disease transmitted by lymnaeid snails and recently emerging in humans, in part due to effects of climate changes, anthropogenic environment modifications, import/export and movements of livestock. South America is the continent presenting more human fascioliasis hyperendemic areas and the highest prevalences and intensities known. These scenarios appear mainly linked to altitude areas in Andean countries, whereas lowland areas of non-Andean countries, such as Uruguay, only show sporadic human cases or outbreaks. A study including DNA marker sequencing of fasciolids and lymnaeids, an experimental study of the life cycle in Uruguay, and a review of human fascioliasis in Uruguay, are performed. The characterization of Fasciola hepatica from cattle and horses of Uruguay included the complete sequences of the ribosomal DNA ITS-2 and ITS-1 and mitochondrial DNA cox1 and nad1. ITS-2, ITS-1, partial cox1 and rDNA 16S gene of mtDNA were used for lymnaeids. Results indicated that vectors belong to Lymnaea neotropica instead of to Lymnaea viator, as always reported from Uruguay. The life cycle and transmission features of F. hepatica by L. neotropica of Uruguay were studied under standardized experimental conditions to enable a comparison with the transmission capacity of F. hepatica by Galba truncatula at very high altitude in Bolivia. On this baseline, we reviewed the 95 human fascioliasis cases reported in Uruguay and analyzed the risk of human infection in front of future climate change estimations. The correlation of fasciolid and lymnaeid haplotypes with historical data on the introduction and spread of livestock into Uruguay allowed to understand the molecular diversity detected. Although Uruguayan L. neotropica is a highly efficient vector, its transmission capacity is markedly lower than that of Bolivian G. truncatula. This allows to understand the transmission and epidemiological differences between Andean highlands and non

  12. 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.

  13. Critical Review of EU Nuclear Stress Tests in Bulgaria, Hungary, Romania and Ukraine

    International Nuclear Information System (INIS)

    Becker, O.; Lorenz, P.; Wallner, A.

    2012-01-01

    In March 2011, the core melt accidents at the Fukushima Daiichi 1 nuclear power plant (NPP) showed the world that the nuclear industry cannot prevent severe accidents from happening. The accidents in Japan proved that highly unlikely accidents cannot be excluded. The Fukushima accident confirmed the mistrust towards nuclear power among the Japanese but also European citizens. In reaction to the devastating nuclear disaster in Japan the European Council concluded in March 2011, that the safety of all EU nuclear plants should be reviewed on the basis of a comprehensive and transparent risk and safety assessment ('stress tests'). The EU Nuclear Safety Regulators Group – ENSREG took over the task to provide a “targeted reassessment of the safety margins of nuclear power plants”, thus examining whether the safety margins which were used in the licensing of NPPs are sufficient to cover unexpected events. It is important to understand that the stress tests could not take into account all key safety issues such as the capability to prevent accidents - the scope of the stress tests defined by ENSREG didn´t promise to deliver a comprehensive risk and safety assessment. According to some observers the stress tests were mainly set up to improve the confidence in the safety of European NPPs. Nevertheless, the stress tests provided some interesting findings concerning safety: This study assesses the safety of the nuclear power plants in Bulgaria, Hungary, Romania and the Ukraine. The introduction contains an overview of the content and procedure of the stress tests. This “Critical Review of the Stress Tests” is based on the national stress tests reports written by the national nuclear safety authorities and on the Peer review country reports attached to the Peer review report - Stress tests performed on European nuclear power plants written by the Peer review Teams, the Peer Review Board respectively, and endorsed by ENSREG [ENSREG 2012a, ENSREG 2012c]. It

  14. Critical Review of EU Nuclear Stress Tests in Bulgaria, Hungary, Romania and Ukraine

    Energy Technology Data Exchange (ETDEWEB)

    Becker, O.; Lorenz, P.; Wallner, A.

    2012-07-01

    In March 2011, the core melt accidents at the Fukushima Daiichi 1 nuclear power plant (NPP) showed the world that the nuclear industry cannot prevent severe accidents from happening. The accidents in Japan proved that highly unlikely accidents cannot be excluded. The Fukushima accident confirmed the mistrust towards nuclear power among the Japanese but also European citizens. In reaction to the devastating nuclear disaster in Japan the European Council concluded in March 2011, that the safety of all EU nuclear plants should be reviewed on the basis of a comprehensive and transparent risk and safety assessment ('stress tests'). The EU Nuclear Safety Regulators Group – ENSREG took over the task to provide a “targeted reassessment of the safety margins of nuclear power plants”, thus examining whether the safety margins which were used in the licensing of NPPs are sufficient to cover unexpected events. It is important to understand that the stress tests could not take into account all key safety issues such as the capability to prevent accidents - the scope of the stress tests defined by ENSREG didn´t promise to deliver a comprehensive risk and safety assessment. According to some observers the stress tests were mainly set up to improve the confidence in the safety of European NPPs. Nevertheless, the stress tests provided some interesting findings concerning safety: This study assesses the safety of the nuclear power plants in Bulgaria, Hungary, Romania and the Ukraine. The introduction contains an overview of the content and procedure of the stress tests. This “Critical Review of the Stress Tests” is based on the national stress tests reports written by the national nuclear safety authorities and on the Peer review country reports attached to the Peer review report - Stress tests performed on European nuclear power plants written by the Peer review Teams, the Peer Review Board respectively, and endorsed by ENSREG [ENSREG 2012a, ENSREG 2012c]. It continues

  15. Review of design criteria and safety analysis of safety class electric building for fuel test loop

    Energy Technology Data Exchange (ETDEWEB)

    Kim, J. Y.

    1998-02-01

    Steady state fuel test loop will be equipped in HANARO to obtain the development and betterment of advanced fuel and materials through the irradiation tests. HANARO fuel test loop was designed for CANDU and PWR fuel testing. Safety related system of Fuel Test Loop such as emergency cooling water system, component cooling water system, safety ventilation system, high energy line break mitigation system and remote control room was required 1E class electric supply to meet the safety operation in accordance with related code. Therefore, FTL electric building was designed to construction and install the related equipment based on seismic category I. The objective of this study is to review the design criteria and analysis the safety function of safety class electric building for fuel test loop, and this results will become guidance for the irradiation testing in future. (author). 10 refs., 6 tabs., 30 figs.

  16. Review of the acceptance tests of the W7-X superconducting magnets

    International Nuclear Information System (INIS)

    Ehmler, H.; Baldzuhn, J.; Genini, L.; Heyn, K.; Sborchia, C.; Schild, T.

    2007-01-01

    The W7-X magnet system consists of 50 non-planar coils of five different types and 20 planar coils of two different types. Factory tests of the non-planar coils are carried out at the manufacturer site of Babcock-Noell, Germany, and for the planar coils at Tesla Engineering, UK. They consist of electrical insulation checks, mass flow measurements, leak tests and sensor checks. In the test facility of CEA Saclay, France, each coil is cooled down to ∼5 K and operated at nominal current. At least one coil of each type is quenched by increasing the inlet temperature. Results of the mass flow measurements and the quench tests are presented. The manufacturing and testing progress is reviewed and the impact of technical failures is discussed. In conclusion, the scope of the tests allows a very strict quality control. This experience is highly beneficial for the construction and testing of similar components for future superconducting fusion experiments

  17. A review of HIV testing and counseling policies and practices in the Eastern Mediterranean Region.

    Science.gov (United States)

    Hermez, Joumana; Petrak, Jenny; Karkouri, Mehdi; Riedner, Gabriele

    2010-07-01

    To review HIV testing and counseling policies and practices in the World Health Organization's (WHO) Eastern Mediterranean Region. We reviewed gray and published literature on HIV testing policies and practices in the 22 countries of the Eastern Mediterranean Region, including surveillance, monitoring and evaluation reports. Missing or unclear information was clarified by telephone interviews of key informants. Field observations were conducted in four countries. Of reported diagnostic HIV tests conducted in the Eastern Mediterranean Region from 1995 to 2008, 59.3% were carried out on migrant workers. Only 4.0% were carried out on key populations at higher risk for HIV and 8.1% were conducted in sexually transmitted infection, tuberculosis and antenatal care services. The largest proportions of HIV-positive cases identified were among key populations at higher risk (23.4%) and in sexually transmitted infection, tuberculosis and antenatal care services (17.5%). Mandatory testing was the most common approach to identifying HIV-positive cases, yet most policy documents reviewed identified voluntary counseling and testing as a key intervention for prevention, care and treatment. Provider initiated testing and counseling was rarely considered. HIV testing strategies are cumbersome, as they require central laboratory-based Enzyme Linked Immuno-Sorbant Assay (ELISA) and/or Western Blot confirmation in most countries presenting barriers to receiving results. Although policies in the Eastern Mediterranean Region include a mix of mandatory and voluntary HIV testing, mandatory testing predominates, especially for migrant and foreign workers and key populations at higher risk of HIV. There is a paucity of programs providing voluntary testing. Strategies to enhance access to true voluntary HIV testing and counseling services are urgently needed, particularly targeting key populations at higher risk.

  18. Barriers to workplace HIV testing in South Africa: a systematic review of the literature.

    Science.gov (United States)

    Weihs, Martin; Meyer-Weitz, Anna

    2016-01-01

    Low workplace HIV testing uptake makes effective management of HIV and AIDS difficult for South African organisations. Identifying barriers to workplace HIV testing is therefore crucial to inform urgently needed interventions aimed at increasing workplace HIV testing. This study reviewed literature on workplace HIV testing barriers in South Africa. Pubmed, ScienceDirect, PsycInfo and SA Publications were systematically researched. Studies needed to include measures to assess perceived or real barriers to participate in HIV Counselling and Testing (HCT) at the workplace or discuss perceived or real barriers of HIV testing at the workplace based on collected data, provide qualitative or quantitative evidence related to the research topic and needed to refer to workplaces in South Africa. Barriers were defined as any factor on economic, social, personal, environmental or organisational level preventing employees from participating in workplace HIV testing. Four peer-reviewed studies were included, two with quantitative and two with qualitative study designs. The overarching barriers across the studies were fear of compromised confidentiality, being stigmatised or discriminated in the event of testing HIV positive or being observed participating in HIV testing, and a low personal risk perception. Furthermore, it appeared that an awareness of an HIV-positive status hindered HIV testing at the workplace. Further research evidence of South African workplace barriers to HIV testing will enhance related interventions. This systematic review only found very little and contextualised evidence about workplace HCT barriers in South Africa, making it difficult to generalise, and not really sufficient to inform new interventions aimed at increasing workplace HCT uptake.

  19. DNA damage and autophagy

    International Nuclear Information System (INIS)

    Rodriguez-Rocha, Humberto; Garcia-Garcia, Aracely; Panayiotidis, Mihalis I.; Franco, Rodrigo

    2011-01-01

    Both exogenous and endogenous agents are a threat to DNA integrity. Exogenous environmental agents such as ultraviolet (UV) and ionizing radiation, genotoxic chemicals and endogenous byproducts of metabolism including reactive oxygen species can cause alterations in DNA structure (DNA damage). Unrepaired DNA damage has been linked to a variety of human disorders including cancer and neurodegenerative disease. Thus, efficient mechanisms to detect DNA lesions, signal their presence and promote their repair have been evolved in cells. If DNA is effectively repaired, DNA damage response is inactivated and normal cell functioning resumes. In contrast, when DNA lesions cannot be removed, chronic DNA damage triggers specific cell responses such as cell death and senescence. Recently, DNA damage has been shown to induce autophagy, a cellular catabolic process that maintains a balance between synthesis, degradation, and recycling of cellular components. But the exact mechanisms by which DNA damage triggers autophagy are unclear. More importantly, the role of autophagy in the DNA damage response and cellular fate is unknown. In this review we analyze evidence that supports a role for autophagy as an integral part of the DNA damage response.

  20. Physical examination tests for the diagnosis of femoroacetabular impingement. A systematic review.

    Science.gov (United States)

    Pacheco-Carrillo, Aitana; Medina-Porqueres, Ivan

    2016-09-01

    Numerous clinical tests have been proposed to diagnose FAI, but little is known about their diagnostic accuracy. To summarize and evaluate research on the accuracy of physical examination tests for diagnosis of FAI. A search of the PubMed, SPORTDiscus and CINAHL databases was performed. Studies were considered eligible if they compared the results of physical examination tests to those of a reference standard. Methodological quality and internal validity assessment was performed by two independent reviewers using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS) tool. The systematic search strategy revealed 298 potential articles, five of which articles met the inclusion criteria. After assessment using the QUADAS score, four of the five articles were of high quality. Clinical tests included were Impingement sign, IROP test (Internal Rotation Over Pressure), FABER test (Flexion-Abduction-External Rotation), Stinchfield/RSRL (Resisted Straight Leg Raise) test, Scour test, Maximal squat test, and the Anterior Impingement test. IROP test, impingement sign, and FABER test showed the most sensitive values to identify FAI. The diagnostic accuracy of physical examination tests to assess FAI is limited due to its heterogenecity. There is a strong need for sound research of high methodological quality in this area. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Review of in-place HEPA filter testing at several DOE facilities

    Energy Technology Data Exchange (ETDEWEB)

    Mokler, B.V.; Scripsick, R.C. [Los Alamos National Laboratory, NM (United States)

    1995-02-01

    The Office of Nuclear Energy Self-Assessment recently sponsored reviews of HEPA filter systems at several DOE facilities. One aspect emphasized in these reviews was in-place filter testing practices. Although in-place testing was generally performed as required in facility specifications, we noted several areas in which improvements were possible. Examples of some common problems and approaches to their solution will be presented. Areas of suggested improvement include: (1) ensuring the validity of test results; (2) recognizing and quantifying the uncertainty in penetration measurements; (3) expanding the analysis and reporting of test results to provide more than pass/fail information; (4) addressing the special problems of multiple stage systems; and (5) increasing the technical support and training provided in-place testing personnel. Ensuring the validity of test results, for example, requires more careful attention to the operation of test equipment, checking test measurements and system operating parameters for internal consistency, and more attention to documentation of system geometry and operation. Some issues will require additional study before the results can be incorporated into decision making on filter bank testing requirements and performance specifications.

  2. Review of in-place HEPA filter testing at several DOE facilities

    International Nuclear Information System (INIS)

    Mokler, B.V.; Scripsick, R.C.

    1995-01-01

    The Office of Nuclear Energy Self-Assessment recently sponsored reviews of HEPA filter systems at several DOE facilities. One aspect emphasized in these reviews was in-place filter testing practices. Although in-place testing was generally performed as required in facility specifications, we noted several areas in which improvements were possible. Examples of some common problems and approaches to their solution will be presented. Areas of suggested improvement include: (1) ensuring the validity of test results; (2) recognizing and quantifying the uncertainty in penetration measurements; (3) expanding the analysis and reporting of test results to provide more than pass/fail information; (4) addressing the special problems of multiple stage systems; and (5) increasing the technical support and training provided in-place testing personnel. Ensuring the validity of test results, for example, requires more careful attention to the operation of test equipment, checking test measurements and system operating parameters for internal consistency, and more attention to documentation of system geometry and operation. Some issues will require additional study before the results can be incorporated into decision making on filter bank testing requirements and performance specifications

  3. Independent technical review of the Bin and Alcove test programs at the Waste Isolation Pilot Plant

    International Nuclear Information System (INIS)

    1993-12-01

    This Independent Technical Review (ITR) assessed the need for and technical validity of the proposed Bin and Alcove test programs using TRU-waste at the WIPP site. The ITR Team recommends that the planned Bin and Alcove tests be abandoned, and that new activities be initiated in support of the WIPP regulatory compliance processes. Recommendations in this report offer an alternate path for expeditiously attaining disposal certification and permitting

  4. Towards Point-of-Care Diagnosis of Pulmonary Tuberculosis and Drug Susceptibility Testing by Whole Genome Sequencing of DNA Isolated from Sputum

    Directory of Open Access Journals (Sweden)

    Kayzad S. Nilgiriwala

    2017-12-01

    Full Text Available Preliminary screening of pulmonary tuberculosis (TB in India still relies on sputum microscopy, which has low sensitivity leading to high rate of false negatives. Moreover, conventional phenotypic drug susceptibility testing (DST is conducted over a period of weeks leading to delays in correct treatment. Next generation sequencing technologies (Illumina and Oxford Nanopore have made it possible to sequence miniscule amount of DNA and generate enough data within a day for detecting specific microbes and their DST profile. Sputum samples from two pulmonary TB patients were processed by decontamination and DNA was isolated from the decontaminated sputum sediments. The isolated DNA was used for sequencing by Illumina and by MinION (Oxford Nanopore Technologies. The sequence data was used to diagnose TB and to determine the DST profiles for the first- and second-line drugs by Mykrobe Predictor. Validation was conducted by sequencing DNA (by Illumina isolated from pure growth culture from both the samples individually. DNA sequencing data (for both, Ilumina and MinION from one of the sputum samples indicated the presence of Mycobacterium tuberculosis (M. tb resistant to streptomycin, isoniazid, rifampicin and ethambutol and its lineage was predicted to be Beijing East Asia. The second sample indicated the presence of M. tb sensitive to the first- and second-line drugs by MinION and showed minor resistance call only to rifampicin by Illumina. Lineage of the second sample was predicted to be East Africa Indian Ocean, whereas Illumina data indicated it to be Delhi Central Asia. The two samples were correctly diagnosed for the presence of M. tb in the sputum DNA. Their DST profiles and lineage were also successfully determined from both the sequencing platforms (with minor discrepancies paving the way towards diagnosis and DST of TB from DNA isolated from sputum samples at point-of-care. Nanopore sequencing currently requires skilled personnel for DNA

  5. Implications of failure to achieve a result from prenatal maternal serum cell-free DNA testing: a historical cohort study.

    Science.gov (United States)

    Chan, N; Smet, M-E; Sandow, R; da Silva Costa, F; McLennan, A

    2017-11-01

    To investigate the pregnancy outcomes in a cohort of women who failed to obtain a result in non-invasive prenatal testing (NIPT). Historical cohort study. A multicentre private practice in Sydney, Australia. Women who failed to obtain a result from NIPT (n = 131). The maternal characteristics, antenatal investigations and pregnancy outcomes for these women were compared with those who obtained a result at the same practice and to the general Australian obstetric population. Antenatal investigations: pregnancy-associated plasma protein-A (PAPP-A), free β-human chorionic gonadotrophin (β-hCG), placental growth factor (PlGF), uterine artery pulsatility index (PI), mean arterial pressure (MAP). Pregnancy outcomes: chromosomal abnormality, pre-eclampsia, gestational diabetes, small-for-gestational-age (SGA), preterm delivery. Only 1.1% of NIPT samples failed to return a result. This cohort was significantly older and had significantly increased weight compared with the general Australian obstetric population. Pregnancy outcomes were available for 94% of the cohort. There were significantly higher rates of chromosomal aneuploidies (6.5% versus 0.2%, P < 0.0001), pre-eclampsia (11% versus 1.5%, P < 0.0001) and gestational diabetes (23% versus 7.5%, P < 0.0001) compared with the general obstetric population. Rates of preterm delivery and SGA were elevated but did not reach significance. Antenatal investigations demonstrated decreased PAPP-A MoM (0.75 versus 1.14, P < 0.0001), decreased free β-hCG (0.71 versus 1.01, P < 0.0001) and increased uterine artery PI (1.79 versus 1.65, P = 0.02). Women who fail to obtain a result from NIPT are at increased risk of adverse pregnancy outcomes, in particular chromosomal aneuploidy, gestational diabetes and pre-eclampsia. None received. Women who fail to obtain a result from cell-free DNA NIPT are at increased risk of adverse pregnancy outcomes. © 2017 Royal College of Obstetricians and Gynaecologists.

  6. Nuclear waste transportation package testing: A review of selected programs in the United States and abroad

    International Nuclear Information System (INIS)

    Snedeker, D.F.

    1990-12-01

    This report provides an overview of some recent nuclear waste transportation package development programs. This information is intended to aid the State of Nevada in its review of US Department of Energy (DOE) nuclear waste transportation programs. This report addresses cask testing programs in the United Kingdom and selected 1/4 and full scale testing in the US. Facilities that can provide cask testing services, both in the US and to a limited extent abroad, are identified. The costs for different type test programs are identified as a means to estimate costs for future test programs. Not addressed is the public impact such testing might have in providing an increased sense of safety or confidence. The British test program was apparently quite successful in demonstrating safety to the public at the time. There is no US test effort that is similar in scope for direct comparison. Also addressed are lessons learned from testing programs and areas that may merit possible future integrated examination. Areas that may require further examination are both technical and institutional. This report provides information which, when combined with other sources of information will enable the State of Nevada to assess the following areas: feasibility of full scale testing; costs of full scale tests; potential benefits of testing; limits that full scale testing impose; and disadvantages of emphasis on testing vs analytical solutions. This assessment will then allow the state to comment on DOE Office of Civilian Radioactive Waste Management (OCRWM) plans for the development and licensing of new shipping cask designs. These plans currently expect contractors to perform engineering testing for materials development, quarter scale model testing to validate analytical assessments and full scale prototype testing of operational features. DOE currently plans no full scale or extra-regulatory destructive testing to aid in cask licensing. 1 tab

  7. A systematic review investigating measurement properties of physiological tests in rugby.

    Science.gov (United States)

    Chiwaridzo, Matthew; Oorschot, Sander; Dambi, Jermaine M; Ferguson, Gillian D; Bonney, Emmanuel; Mudawarima, Tapfuma; Tadyanemhandu, Cathrine; Smits-Engelsman, Bouwien C M

    2017-01-01

    This systematic review was conducted with the first objective aimed at providing an overview of the physiological characteristics commonly evaluated in rugby and the corresponding tests used to measure each construct. Secondly, the measurement properties of all identified tests per physiological construct were evaluated with the ultimate purpose of identifying tests with strongest level of evidence per construct. The review was conducted in two stages. In all stages, electronic databases of EBSCOhost, Medline and Scopus were searched for full-text articles. Stage 1 included studies examining physiological characteristics in rugby. Stage 2 included studies evaluating measurement properties of all tests identified in Stage 1 either in rugby or related sports such as Australian Rules football and Soccer. Two independent reviewers screened relevant articles from titles and abstracts for both stages. Seventy studies met the inclusion criteria for Stage 1. The studies described 63 tests assessing speed (8), agility/change of direction speed (7), upper-body muscular endurance (8), upper-body muscular power (6), upper-body muscular strength (5), anaerobic endurance (4), maximal aerobic power (4), lower-body muscular power (3), prolonged high-intensity intermittent running ability/endurance (5), lower-body muscular strength (5), repeated high-intensity exercise performance (3), repeated-sprint ability (2), repeated-effort ability (1), maximal aerobic speed (1) and abdominal endurance (1). Stage 2 identified 20 studies describing measurement properties of 21 different tests. Only moderate evidence was found for the reliability of the 30-15 Intermittent Fitness. There was limited evidence found for the reliability and/or validity of 5 m, 10 m, 20 m speed tests, 505 test, modified 505 test, L run test, Sergeant Jump test and bench press repetitions-to-fatigue tests. There was no information from high-quality studies on the measurement properties of all the other tests

  8. Diagnostic accuracy of detection and quantification of HBV-DNA and HCV-RNA using dried blood spot (DBS) samples - a systematic review and meta-analysis.

    Science.gov (United States)

    Lange, Berit; Roberts, Teri; Cohn, Jennifer; Greenman, Jamie; Camp, Johannes; Ishizaki, Azumi; Messac, Luke; Tuaillon, Edouard; van de Perre, Philippe; Pichler, Christine; Denkinger, Claudia M; Easterbrook, Philippa

    2017-11-01

    The detection and quantification of hepatitis B (HBV) DNA and hepatitis C (HCV) RNA in whole blood collected on dried blood spots (DBS) may facilitate access to diagnosis and treatment of HBV and HCV infection in resource-poor settings. We evaluated the diagnostic performance of DBS compared to venous blood samples for detection and quantification of HBV-DNA and HCV-RNA in two systematic reviews and meta-analyses on the diagnostic accuracy of HBV DNA and HCV RNA from DBS compared to venous blood samples. We searched MEDLINE, Embase, Global Health, Web of Science, LILAC and Cochrane library for studies that assessed diagnostic accuracy with DBS. Heterogeneity was assessed and where appropriate pooled estimates of sensitivity and specificity were generated using bivariate analyses with maximum likelihood estimates and 95% confidence intervals. We also conducted a narrative review on the impact of varying storage conditions or different cut-offs for detection from studies that undertook this in a subset of samples. The QUADAS-2 tool was used to assess risk of bias. In the quantitative synthesis for diagnostic accuracy of HBV-DNA using DBS, 521 citations were identified, and 12 studies met the inclusion criteria. Overall quality of studies was rated as low. The pooled estimate of sensitivity and specificity for HBV-DNA was 95% (95% CI: 83-99) and 99% (95% CI: 53-100), respectively. In the two studies that reported on cut-offs and limit of detection (LoD) - one reported a sensitivity of 98% for a cut-off of ≥2000 IU/ml and another reported a LoD of 914 IU/ml using a commercial assay. Varying storage conditions for individual samples did not result in a significant variation of results. In the synthesis for diagnostic accuracy of HCV-RNA using DBS, 15 studies met the inclusion criteria, and this included six additional studies to a previously published review. The pooled sensitivity and specificity was 98% (95% CI:95-99) and 98% (95% CI:95-99.0), respectively

  9. Fundamental and assessment of concrete structure monitoring by using acoustic emission technique testing: A review

    Science.gov (United States)

    Desa, M. S. M.; Ibrahim, M. H. W.; Shahidan, S.; Ghadzali, N. S.; Misri, Z.

    2018-04-01

    Acoustic emission (AE) technique is one of the non-destructive (NDT) testing, where it can be used to determine the damage of concrete structures such as crack, corrosion, stability, sensitivity, as structure monitoring and energy formed within cracking opening growth in the concrete structure. This article gives a comprehensive review of the acoustic emission (AE) technique testing due to its application in concrete structure for structural health monitoring (SHM). Assessment of AE technique used for structural are reviewed to give the perception of its structural engineering such as dam, bridge and building, where the previous research has been reviewed based on AE application. The assessment of AE technique focusing on basic fundamental of parametric and signal waveform analysis during analysis process and its capability in structural monitoring. Moreover, the assessment and application of AE due to its function have been summarized and highlighted for future references

  10. Gender Differences among Children with ADHD on Continuous Performance Tests: A Meta-Analytic Review

    Science.gov (United States)

    Hasson, Ramzi; Fine, Jodene Goldenring

    2012-01-01

    Objective: Gender differences among children with ADHD are not well understood. The continuous performance test (CPT) is the most frequently used direct measure of inattention and impulsivity. This meta-analysis compared CPT performance between boys and girls with and without ADHD. Method: All peer-reviewed ADHD studies published between 1980 and…

  11. HIV Testing among Men Who Have Sex with Men (MSM): Systematic Review of Qualitative Evidence

    Science.gov (United States)

    Lorenc, Theo; Marrero-Guillamon, Isaac; Llewellyn, Alexis; Aggleton, Peter; Cooper, Chris; Lehmann, Angela; Lindsay, Catriona

    2011-01-01

    We conducted a systematic review of qualitative evidence relating to the views and attitudes of men who have sex with men (MSM) concerning testing for HIV. Studies conducted in high-income countries (Organisation for Economic Co-operation and Development members) since 1996 were included. Seventeen studies were identified, most of gay or bisexual…

  12. Accuracy of monofilament testing to diagnose peripheral neuropathy: a systematic review

    NARCIS (Netherlands)

    Dros, Jacquelien; Wewerinke, Astrid; Bindels, Patrick J.; van Weert, Henk C.

    2009-01-01

    We wanted to summarize evidence about the diagnostic accuracy of the 5.07/10-g monofilament test in peripheral neuropathy. We conducted a systematic review of studies in which the accuracy of the 5.07/10-g monofilament was evaluated to detect peripheral neuropathy of any cause using nerve conduction

  13. Accuracy of Monofilament Testing to Diagnose Peripheral Neuropathy: A Systematic Review

    NARCIS (Netherlands)

    Dros, J.; Wewerinke, A.; Bindels, P.J.; van Weert, H.C.

    2009-01-01

    PURPOSE We wanted to summarize evidence about the diagnostic accuracy of the 5.07/10-g monofilament test in peripheral neuropathy. METHODS We conducted a systematic review of studies in which the accuracy of the 5.07/10-g monofilament was evaluated to detect peripheral neuropathy of any cause using

  14. Clinical tests to diagnose lumbar spondylolysis and spondylolisthesis: A systematic review.

    Science.gov (United States)

    Alqarni, Abdullah M; Schneiders, Anthony G; Cook, Chad E; Hendrick, Paul A

    2015-08-01

    The aim of this paper was to systematically review the diagnostic ability of clinical tests to detect lumbar spondylolysis and spondylolisthesis. A systematic literature search of six databases, with no language restrictions, from 1950 to 2014 was concluded on February 1, 2014. Clinical tests were required to be compared against imaging reference standards and report, or allow computation, of common diagnostic values. The systematic search yielded a total of 5164 articles with 57 retained for full-text examination, from which 4 met the full inclusion criteria for the review. Study heterogeneity precluded a meta-analysis of included studies. Fifteen different clinical tests were evaluated for their ability to diagnose lumbar spondylolisthesis and one test for its ability to diagnose lumbar spondylolysis. The one-legged hyperextension test demonstrated low to moderate sensitivity (50%-73%) and low specificity (17%-32%) to diagnose lumbar spondylolysis, while the lumbar spinous process palpation test was the optimal diagnostic test for lumbar spondylolisthesis; returning high specificity (87%-100%) and moderate to high sensitivity (60-88) values. Lumbar spondylolysis and spondylolisthesis are identifiable causes of LBP in athletes. There appears to be utility to lumbar spinous process palpation for the diagnosis of lumbar spondylolisthesis, however the one-legged hyperextension test has virtually no value in diagnosing patients with spondylolysis. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Review of WWER fuel and material tests in the Halden reactor

    International Nuclear Information System (INIS)

    Volkov, B.; Kolstad, E.

    2006-01-01

    A review of the tests with WWER fuels and materials conducted in HBWR over the years of cooperation with Russia is presented. The first test with old generation WWER-440 fuel and PWR specification fuel was carried out from 1995 to 1998. Some differences between these fuels regarding irradiation induced densification and pellet design as well as similar fuel thermal behaviour, swelling and FGR were revealed during the test. The data from this test are reviewed and compared with PIE recently performed to confirm the in-pile measurements. The second test was started in March 1999 with the main objective to study different modified WWER fuels also in comparison with PWR fuel. The results indicated that all these modified WWER fuels exhibit improved densification properties relative to earlier tested fuel. In-pile data on fuel densification have been analysed with respect to as fabricated fuel microstructure and can be used for verification of fuel behaviour models. Corrosion and creep tests in the Halden reactor encompass WWER cladding alloys and some results are given. Prospective WWER fuel and material tests foreseen within the frame of the joint program of OECD HRP are also presented. (authors)

  16. Quantification of viral DNA during HIV-1 infection: A review of relevant clinical uses and laboratory methods.

    Science.gov (United States)

    Alidjinou, E K; Bocket, L; Hober, D

    2015-02-01

    Effective antiretroviral therapy usually leads to undetectable HIV-1 RNA in the plasma. However, the virus persists in some cells of infected patients as various DNA forms, both integrated and unintegrated. This reservoir represents the greatest challenge to the complete cure of HIV-1 infection and its characteristics highly impact the course of the disease. The quantification of HIV-1 DNA in blood samples constitutes currently the most practical approach to measure this residual infection. Real-time quantitative PCR (qPCR) is the most common method used for HIV-DNA quantification and many strategies have been developed to measure the different forms of HIV-1 DNA. In the literature, several "in-house" PCR methods have been used and there is a need for standardization to have comparable results. In addition, qPCR is limited for the precise quantification of low levels by background noise. Among new assays in development, digital PCR was shown to allow an accurate quantification of HIV-1 DNA. Total HIV-1 DNA is most commonly measured in clinical routine. The absolute quantification of proviruses and unintegrated forms is more often used for research purposes. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  17. Using DNA to test the utility of pellet-group counts as an index of deer counts

    Science.gov (United States)

    T. J. Brinkman; D. K. Person; W. Smith; F. Stuart Chapin; K. McCoy; M. Leonawicz; K. Hundertmark

    2013-01-01

    Despite widespread use of fecal pellet-group counts as an index of ungulate density, techniques used to convert pellet-group numbers to ungulate numbers rarely are based on counts of known individuals, seldom evaluated across spatial and temporal scales, and precision is infrequently quantified. Using DNA from fecal pellets to identify individual deer, we evaluated the...

  18. A test of the utility of DNA barcoding in the radiation of the freshwater stingray genus Potamotrygon (Potamotrygonidae, Myliobatiformes

    Directory of Open Access Journals (Sweden)

    Daniel Toffoli

    2008-01-01

    Full Text Available DNA barcoding is a recently proposed global standard in taxonomy based on DNA sequences. The two main goals of DNA barcoding methodology are assignment of specimens to a species and discovery of new species. There are two main underlying assumptions: i reciprocal monophyly of species, and ii intraspecific divergence is always less than interspecific divergence. Here we present a phylogenetic analysis of the family Potamotrygonidae based on mitochondrial cytochrome c oxidase I gene, sampling 10 out of the 18 to 20 valid species including two non-described species. Potamotrygonidae systematics is still not fully resolved with several still-to-be-described species while some other species are difficult to delimit due to overlap in morphological characters and because of sharing a complex color patterns. Our results suggest that the family passed through a process of rapid speciation and that the species Potamotrygon motoro, P. scobina, and P. orbignyi share haplotypes extensively. Our results suggest that systems of identification of specimens based on DNA sequences, together with morphological and/or ecological characters, can aid taxonomic studies, but delimitation of new species based on threshold values of genetic distances are overly simplistic and misleading.

  19. Should trained lay providers perform HIV testing? A systematic review to inform World Health Organization guidelines.

    Science.gov (United States)

    Kennedy, C E; Yeh, P T; Johnson, C; Baggaley, R

    2017-12-01

    New strategies for HIV testing services (HTS) are needed to achieve UN 90-90-90 targets, including diagnosis of 90% of people living with HIV. Task-sharing HTS to trained lay providers may alleviate health worker shortages and better reach target groups. We conducted a systematic review of studies evaluating HTS by lay providers using rapid diagnostic tests (RDTs). Peer-reviewed articles were included if they compared HTS using RDTs performed by trained lay providers to HTS by health professionals, or to no intervention. We also reviewed data on end-users' values and preferences around lay providers preforming HTS. Searching was conducted through 10 online databases, reviewing reference lists, and contacting experts. Screening and data abstraction were conducted in duplicate using systematic methods. Of 6113 unique citations identified, 5 studies were included in the effectiveness review and 6 in the values and preferences review. One US-based randomized trial found patients' uptake of HTS doubled with lay providers (57% vs. 27%, percent difference: 30, 95% confidence interval: 27-32, p lay providers. Studies from Cambodia, Malawi, and South Africa comparing testing quality between lay providers and laboratory staff found little discordance and high sensitivity and specificity (≥98%). Values and preferences studies generally found support for lay providers conducting HTS, particularly in non-hypothetical scenarios. Based on evidence supporting using trained lay providers, a WHO expert panel recommended lay providers be allowed to conduct HTS using HIV RDTs. Uptake of this recommendation could expand HIV testing to more people globally.

  20. Outcomes Definitions and Statistical Tests in Oncology Studies: A Systematic Review of the Reporting Consistency.

    Science.gov (United States)

    Rivoirard, Romain; Duplay, Vianney; Oriol, Mathieu; Tinquaut, Fabien; Chauvin, Franck; Magne, Nicolas; Bourmaud, Aurelie

    2016-01-01

    Quality of reporting for Randomized Clinical Trials (RCTs) in oncology was analyzed in several systematic reviews, but, in this setting, there is paucity of data for the outcomes definitions and consistency of reporting for statistical tests in RCTs and Observational Studies (OBS). The objective of this review was to describe those two reporting aspects, for OBS and RCTs in oncology. From a list of 19 medical journals, three were retained for analysis, after a random selection: British Medical Journal (BMJ), Annals of Oncology (AoO) and British Journal of Cancer (BJC). All original articles published between March 2009 and March 2014 were screened. Only studies whose main outcome was accompanied by a corresponding statistical test were included in the analysis. Studies based on censored data were excluded. Primary outcome was to assess quality of reporting for description of primary outcome measure in RCTs and of variables of interest in OBS. A logistic regression was performed to identify covariates of studies potentially associated with concordance of tests between Methods and Results parts. 826 studies were included in the review, and 698 were OBS. Variables were described in Methods section for all OBS studies and primary endpoint was clearly detailed in Methods section for 109 RCTs (85.2%). 295 OBS (42.2%) and 43 RCTs (33.6%) had perfect agreement for reported statistical test between Methods and Results parts. In multivariable analysis, variable "number of included patients in study" was associated with test consistency: aOR (adjusted Odds Ratio) for third group compared to first group was equal to: aOR Grp3 = 0.52 [0.31-0.89] (P value = 0.009). Variables in OBS and primary endpoint in RCTs are reported and described with a high frequency. However, statistical tests consistency between methods and Results sections of OBS is not always noted. Therefore, we encourage authors and peer reviewers to verify consistency of statistical tests in oncology studies.

  1. Eukaryotic DNA Replication Fork.

    Science.gov (United States)

    Burgers, Peter M J; Kunkel, Thomas A

    2017-06-20

    This review focuses on the biogenesis and composition of the eukaryotic DNA replication fork, with an emphasis on the enzymes that synthesize DNA and repair discontinuities on the lagging strand of the replication fork. Physical and genetic methodologies aimed at understanding these processes are discussed. The preponderance of evidence supports a model in which DNA polymerase ε (Pol ε) carries out the bulk of leading strand DNA synthesis at an undisturbed replication fork. DNA polymerases α and δ carry out the initiation of Okazaki fragment synthesis and its elongation and maturation, respectively. This review also discusses alternative proposals, including cellular processes during which alternative forks may be utilized, and new biochemical studies with purified proteins that are aimed at reconstituting leading and lagging strand DNA synthesis separately and as an integrated replication fork.

  2. Raising the standards of the calf-raise test: a systematic review.

    Science.gov (United States)

    Hébert-Losier, Kim; Newsham-West, Richard J; Schneiders, Anthony G; Sullivan, S John

    2009-11-01

    The calf-raise test is used by clinicians and researchers in sports medicine to assess properties of the calf muscle-tendon unit. The test generally involves repetitive concentric-eccentric muscle action of the plantar-flexors in unipedal stance and is quantified by the number of raises performed. Although the calf-raise test appears to have acceptable reliability and face validity, and is commonly used for medical assessment and rehabilitation of injuries, no universally acceptable test parameters have been published to date. A systematic review of the existing literature was conducted to investigate the consistency as well as universal acceptance of the evaluation purposes, test parameters, outcome measurements and psychometric properties of the calf-raise test. Nine electronic databases were searched during the period May 30th to September 21st 2008. Forty-nine articles met the inclusion criteria and were quality assessed. Information on study characteristics and calf-raise test parameters, as well as quantitative data, were extracted; tabulated; and statistically analysed. The average quality score of the reviewed articles was 70.4+/-12.2% (range 44-90%). Articles provided various test parameters; however, a consensus was not ascertained. Key testing parameters varied, were often unstated, and few studies reported reliability or validity values, including sensitivity and specificity. No definitive normative values could be established and the utility of the test in subjects with pathologies remained unclear. Although adapted for use in several disciplines and traditionally recommended for clinical assessment, there is no uniform description of the calf-raise test in the literature. Further investigation is recommended to ensure consistent use and interpretation of the test by researchers and clinicians.

  3. HIV-1 Tropism Testing and Clinical Management of CCR5 Antagonists: Quebec Review and Recommendations

    Directory of Open Access Journals (Sweden)

    Cécile Tremblay

    2013-01-01

    Full Text Available HIV-1 tropism assays play a crucial role in determining the response to CCR5 receptor antagonists. Initially, phenotypic tests were used, but limited access to these tests prompted the development of alternative strategies. Recently, genotyping tropism has been validated using a Canadian technology in clinical trials investigating the use of maraviroc in both experienced and treatment-naive patients. The present guidelines review the evidence supporting the use of genotypic assays and provide recommendations regarding tropism testing in daily clinical management.

  4. 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.

  5. Physical examination tests of the shoulder: a systematic review and meta-analysis of diagnostic test performance.

    Science.gov (United States)

    Gismervik, Sigmund Ø; Drogset, Jon O; Granviken, Fredrik; Rø, Magne; Leivseth, Gunnar

    2017-01-25

    settings, review the inclusion criteria of the included primary studies. We further propose that future studies on the validity of PETS use randomized research designs rather than the accuracy design relying less on well-established gold standard reference tests and efficient treatment options.

  6. User testing of an adaptation of fishbone diagrams to depict results of systematic reviews.

    Science.gov (United States)

    Gartlehner, Gerald; Schultes, Marie-Therese; Titscher, Viktoria; Morgan, Laura C; Bobashev, Georgiy V; Williams, Peyton; West, Suzanne L

    2017-12-12

    Summary of findings tables in systematic reviews are highly informative but require epidemiological training to be interpreted correctly. The usage of fishbone diagrams as graphical displays could offer researchers an effective approach to simplify content for readers with limited epidemiological training. In this paper we demonstrate how fishbone diagrams can be applied to systematic reviews and present the results of an initial user testing. Findings from two systematic reviews were graphically depicted in the form of the fishbone diagram. To test the utility of fishbone diagrams compared with summary of findings tables, we developed and pilot-tested an online survey using Qualtrics. Respondents were randomized to the fishbone diagram or a summary of findings table presenting the same body of evidence. They answered questions in both open-ended and closed-answer formats; all responses were anonymous. Measures of interest focused on first and second impressions, the ability to find and interpret critical information, as well as user experience with both displays. We asked respondents about the perceived utility of fishbone diagrams compared to summary of findings tables. We analyzed quantitative data by conducting t-tests and comparing descriptive statistics. Based on real world systematic reviews, we provide two different fishbone diagrams to show how they might be used to display complex information in a clear and succinct manner. User testing on 77 students with basic epidemiological training revealed that participants preferred summary of findings tables over fishbone diagrams. Significantly more participants liked the summary of findings table than the fishbone diagram (71.8% vs. 44.8%; p testing, however, did not support the utility of such graphical displays.

  7. Physical examination tests for the diagnosis of posterior cruciate ligament rupture: a systematic review.

    Science.gov (United States)

    Kopkow, Christian; Freiberg, Alice; Kirschner, Stephan; Seidler, Andreas; Schmitt, Jochen

    2013-11-01

    Systematic literature review. To summarize and evaluate research on the accuracy of physical examination tests for diagnosis of posterior cruciate ligament (PCL) tear. Rupture of the PCL is a severe knee injury that can lead to delayed rehabilitation, instability, or chronic knee pathologies. To our knowledge, there is currently no systematic review of studies on the diagnostic accuracy of clinical examination tests to evaluate the integrity of the PCL. A comprehensive systematic literature search was conducted in MEDLINE from 1946, Embase from 1974, and the Allied and Complementary Medicine Database from 1985 until April 30, 2012. Studies were considered eligible if they compared the results of physical examination tests performed in the context of a PCL physical examination to those of a reference standard (arthroscopy, arthrotomy, magnetic resonance imaging). Methodological quality assessment was performed by 2 independent reviewers using the revised version of the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. The search strategy revealed 1307 articles, of which 11 met the inclusion criteria for this review. In these studies, 11 different physical examination tests were identified. Due to differences in study types, different patient populations, and methodological quality, meta-analysis was not indicated. Presently, most physical examination tests have not been evaluated sufficiently enough to be confident in their ability to either confirm or rule out a PCL tear. The diagnostic accuracy of physical examination tests to assess the integrity of the PCL is largely unknown. There is a strong need for further research in this area. Level of Evidence Diagnosis, level 3a.

  8. Systematic Review of Health Economic Evaluations of Diagnostic Tests in Brazil: How accurate are the results?

    Science.gov (United States)

    Oliveira, Maria Regina Fernandes; Leandro, Roseli; Decimoni, Tassia Cristina; Rozman, Luciana Martins; Novaes, Hillegonda Maria Dutilh; De Soárez, Patrícia Coelho

    2017-08-01

    The aim of this study is to identify and characterize the health economic evaluations (HEEs) of diagnostic tests conducted in Brazil, in terms of their adherence to international guidelines for reporting economic studies and specific questions in test accuracy reports. We systematically searched multiple databases, selecting partial and full HEEs of diagnostic tests, published between 1980 and 2013. Two independent reviewers screened articles for relevance and extracted the data. We performed a qualitative narrative synthesis. Forty-three articles were reviewed. The most frequently studied diagnostic tests were laboratory tests (37.2%) and imaging tests (32.6%). Most were non-invasive tests (51.2%) and were performed in the adult population (48.8%). The intended purposes of the technologies evaluated were mostly diagnostic (69.8%), but diagnosis and treatment and screening, diagnosis, and treatment accounted for 25.6% and 4.7%, respectively. Of the reviewed studies, 12.5% described the methods used to estimate the quantities of resources, 33.3% reported the discount rate applied, and 29.2% listed the type of sensitivity analysis performed. Among the 12 cost-effectiveness analyses, only two studies (17%) referred to the application of formal methods to check the quality of the accuracy studies that provided support for the economic model. The existing Brazilian literature on the HEEs of diagnostic tests exhibited reasonably good performance. However, the following points still require improvement: 1) the methods used to estimate resource quantities and unit costs, 2) the discount rate, 3) descriptions of sensitivity analysis methods, 4) reporting of conflicts of interest, 5) evaluations of the quality of the accuracy studies considered in the cost-effectiveness models, and 6) the incorporation of accuracy measures into sensitivity analyses.

  9. European Union response to Fukushima. European stress tests and peer review

    Energy Technology Data Exchange (ETDEWEB)

    Jamet, Philippe [Autorite de Surete Nucleaire (ASN), Paris (France)

    2012-07-01

    Following the severe accidents which started in the Fukushima Dai-ichi NPP on 11 March 2011, the European Council requested that a comprehensive safety and risk assessment, in light of preliminary lessons learned, be performed on all EU nuclear plants. Therefore, stress tests and peer review assessing natural initiating events, the loss of safety systems and severe accident management have been performed in the 15 European Union countries with nuclear power plants as well as Switzerland and Ukraine. The final peer review report of the European Nuclear Safety Regulators Group (ENSREG) highlights four main areas for improvement to be explored across Europe: 1. Development by the Western European Nuclear Regulators' Association (WENRA), with the contribution of the best available EU expertise, of a European guidance on assessment of natural hazards and margins; 2. Importance of Periodic Safety Review to be underlined by ENSREG; 3. Expeditious implementation of the recognised measures to protect containment integrity; 4. Prevention of accidents resulting from natural hazards and limitation of their consequences. The peer review of the European stress tests was completed in April 2012. In their conclusive statement issued 26 April 2012, the national European regulators and the European Commission as European Nuclear Safety Regulators Group (ENSREG) required that follow-up would occur by way of an ENSREG action plan. Country specific action plans will be developed and peer review workshop will be organised to share lessons learned on the implementation of post-Fukushima safety improvements.

  10. European Union response to Fukushima. European stress tests and peer review

    International Nuclear Information System (INIS)

    Jamet, Philippe

    2012-01-01

    Following the severe accidents which started in the Fukushima Dai-ichi NPP on 11 March 2011, the European Council requested that a comprehensive safety and risk assessment, in light of preliminary lessons learned, be performed on all EU nuclear plants. Therefore, stress tests and peer review assessing natural initiating events, the loss of safety systems and severe accident management have been performed in the 15 European Union countries with nuclear power plants as well as Switzerland and Ukraine. The final peer review report of the European Nuclear Safety Regulators Group (ENSREG) highlights four main areas for improvement to be explored across Europe: 1. Development by the Western European Nuclear Regulators' Association (WENRA), with the contribution of the best available EU expertise, of a European guidance on assessment of natural hazards and margins; 2. Importance of Periodic Safety Review to be underlined by ENSREG; 3. Expeditious implementation of the recognised measures to protect containment integrity; 4. Prevention of accidents resulting from natural hazards and limitation of their consequences. The peer review of the European stress tests was completed in April 2012. In their conclusive statement issued 26 April 2012, the national European regulators and the European Commission as European Nuclear Safety Regulators Group (ENSREG) required that follow-up would occur by way of an ENSREG action plan. Country specific action plans will be developed and peer review workshop will be organised to share lessons learned on the implementation of post-Fukushima safety improvements.

  11. DNA fragmentation in spermatozoa

    DEFF Research Database (Denmark)

    Rex, A S; Aagaard, J.; Fedder, J

    2017-01-01

    Sperm DNA Fragmentation has been extensively studied for more than a decade. In the 1940s the uniqueness of the spermatozoa protein complex which stabilizes the DNA was discovered. In the fifties and sixties, the association between unstable chromatin structure and subfertility was investigated....... In the seventies, the impact of induced DNA damage was investigated. In the 1980s the concept of sperm DNA fragmentation as related to infertility was introduced as well as the first DNA fragmentation test: the Sperm Chromatin Structure Assay (SCSA). The terminal deoxynucleotidyl transferase nick end labelling...... (TUNEL) test followed by others was introduced in the nineties. The association between DNA fragmentation in spermatozoa and pregnancy loss has been extensively investigated spurring the need for a therapeutic tool for these patients. This gave rise to an increased interest in the aetiology of DNA damage...

  12. Development and pilot test of a process to identify research needs from a systematic review.

    Science.gov (United States)

    Saldanha, Ian J; Wilson, Lisa M; Bennett, Wendy L; Nicholson, Wanda K; Robinson, Karen A

    2013-05-01

    To ensure appropriate allocation of research funds, we need methods for identifying high-priority research needs. We developed and pilot tested a process to identify needs for primary clinical research using a systematic review in gestational diabetes mellitus. We conducted eight steps: abstract research gaps from a systematic review using the Population, Intervention, Comparison, Outcomes, and Settings (PICOS) framework; solicit feedback from the review authors; translate gaps into researchable questions using the PICOS framework; solicit feedback from multidisciplinary stakeholders at our institution; establish consensus among multidisciplinary external stakeholders on the importance of the research questions using the Delphi method; prioritize outcomes; develop conceptual models to highlight research needs; and evaluate the process. We identified 19 research questions. During the Delphi method, external stakeholders established consensus for 16 of these 19 questions (15 with "high" and 1 with "medium" clinical benefit/importance). We pilot tested an eight-step process to identify clinically important research needs. Before wider application of this process, it should be tested using systematic reviews of other diseases. Further evaluation should include assessment of the usefulness of the research needs generated using this process for primary researchers and funders. Copyright © 2013 Elsevier Inc. All rights reserved.

  13. Measurement properties of the craniocervical flexion test: a systematic review protocol.

    Science.gov (United States)

    Araujo, Francisco Xavier de; Ferreira, Giovanni Esteves; Scholl Schell, Maurício; Castro, Marcelo Peduzzi de; Silva, Marcelo Faria; Ribeiro, Daniel Cury

    2018-02-22

    Neck pain is the leading cause of years lived with disability worldwide and it accounts for high economic and societal burden. Altered activation of the neck muscles is a common musculoskeletal impairment presented by patients with neck pain. The craniocervical flexion test with pressure biofeedback unit has been widely used in clinical practice to assess function of deep neck flexor muscles. This systematic review will assess the measurement properties of the craniocervical flexion test for assessing deep cervical flexor muscles. This is a protocol for a systematic review that will follow the Preferred Reporting Items for Systematic Review and Meta-Analysis statement. MEDLINE (via PubMed), EMBASE, PEDro, Cochrane Central Register of Controlled Trials (CENTRAL), Scopus and Science Direct will be systematically searched from inception. Studies of any design that have investigated and reported at least one measurement property of the craniocervical flexion test for assessing the deep cervical flexor muscles will be included. All measurement properties will be considered as outcomes. Two reviewers will independently rate the risk of bias of individual studies using the updated COnsensus-based Standards for the selection of health Measurement Instruments risk of bias checklist. A structured narrative synthesis will be used for data analysis. Quantitative findings for each measurement property will be summarised. The overall rating for a measurement property will be classified as 'positive', 'indeterminate' or 'negative'. The overall rating will be accompanied with a level of evidence. Ethical approval and patient consent are not required since this is a systematic review based on published studies. Findings will be submitted to a peer-reviewed journal for publication. CRD42017062175. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  14. Annual banned-substance review: analytical approaches in human sports drug testing.

    Science.gov (United States)

    Thevis, Mario; Kuuranne, Tiia; Geyer, Hans; Schänzer, Wilhelm

    2017-01-01

    There has been an immense amount of visibility of doping issues on the international stage over the past 12 months with the complexity of doping controls reiterated on various occasions. Hence, analytical test methods continuously being updated, expanded, and improved to provide specific, sensitive, and comprehensive test results in line with the World Anti-Doping Agency's (WADA) 2016 Prohibited List represent one of several critical cornerstones of doping controls. This enterprise necessitates expediting the (combined) exploitation of newly generated information on novel and/or superior target analytes for sports drug testing assays, drug elimination profiles, alternative test matrices, and recent advances in instrumental developments. This paper is a continuation of the series of annual banned-substance reviews appraising the literature published between October 2015 and September 2016 concerning human sports drug testing in the context of WADA's 2016 Prohibited List. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  15. The PWR integrated leak rate test, a review of experiences and results

    International Nuclear Information System (INIS)

    Keogh, P.

    1985-01-01

    The paper reviews the Integrated Leak Rate Test (ILRT) as it has been carried out in the USA and as reported in papers in European countries. The test procedures are critically appraised and recommendations are given for modifications to them. The values used in a PWR are identified as a main source of leaks and possibilities for improvement are discussed. The use of a part pressure test and its limitations are considered. A part pressure test cannot give the same assurance as a full pressure test but may be useful for the identification of gross leaks. Secondary effects such as weather and the use of Van de Waals equations are considered and are found to be not important for concrete containments. (orig.)

  16. Evaluation of the 8th TNM classification on p16-positive oropharyngeal squamous cell carcinomas in the Netherlands, and the importance of additional HPV DNA-testing.

    Science.gov (United States)

    Nauta, I H; Rietbergen, M M; van Bokhoven, A A J D; Bloemena, E; Witte, B I; Heideman, D A M; Baatenburg de Jong, R J; Brakenhoff, R H; Leemans, C R

    2018-02-09

    Oropharyngeal squamous cell carcinomas (OPSCCs) are traditionally caused by smoking and excessive alcohol consumption. However, in the last decades high-risk human papillomavirus (HR-HPV) infections play an increasingly important role in tumorigenesis. HPV-driven OPSCCs are known to have a more favorable prognosis, which has led to important and marked changes in the recently released TNM-8. In this edition, OPSCCs are divided based on p16-immunostaining, with p16-overexpression as surrogate marker for the presence of HPV. The aims of this study are to evaluate TNM-8 on a Dutch consecutive cohort of patients with p16-positive OPSCC and to determine the relevance of additional HPV DNA-testing. All OPSCC patients without distant metastases at diagnosis and treated with curative intent at VU University Medical Center (2000-2015) and Erasmus Medical Center (2000-2006) were included (N = 1,204). HPV-status was established by p16-immunostaining followed by HPV DNA-PCR on the p16-immunopositive cases. We compared TNM-7 and TNM-8 using the Harrell's C index. In total, 388 of 1,204 (32.2%) patients were p16-immunopositive. In these patients, TNM-8 had a markedly better predictive prognostic power than TNM-7 (Harrell's C index 0.63 versus 0.53). Of the 388 p16-positive OPSCCs, 48 tumors (12.4%) were HPV DNA-negative. This subgroup had distinct demographic, clinical and morphologic characteristics and showed a significantly worse five-year overall survival compared to the HPV DNA-positive tumors (P HPV DNA-negative subgroup with distinct features and a worse overall survival, indicating the importance to perform additional HPV DNA-testing when predicting prognosis and particularly for selecting patients for de-intensified treatment regimens. © The Author 2018. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  17. DNA Damage Potential of Engine Emissions Measured In Vitro by Micronucleus Test in Human Bronchial Epithelial Cells

    Czech Academy of Sciences Publication Activity Database

    Červená, Tereza; Rössnerová, Andrea; Sikorová, Jitka; Beránek, V.; Vojtíšek-Lom, M.; Cigánek, M.; Topinka, Jan; Rössner ml., Pavel

    2017-01-01

    Roč. 121, SI (2017), s. 102-108 ISSN 1742-7835 R&D Projects: GA MŠk(CZ) LO1508; GA MŠk(CZ) LM2015073; GA ČR(CZ) GA13-01438S Institutional support: RVO:68378041 Keywords : saliva DNA * methylation patterns * cancer-patients Subject RIV: DN - Health Impact of the Environment Quality OBOR OECD: Public and environmental health Impact factor: 3.176, year: 2016

  18. Non-invasive prenatal testing: a review of international implementation and challenges

    Science.gov (United States)

    Allyse, Megan; Minear, Mollie A; Berson, Elisa; Sridhar, Shilpa; Rote, Margaret; Hung, Anthony; Chandrasekharan, Subhashini

    2015-01-01

    Noninvasive prenatal genetic testing (NIPT) is an advance in the detection of fetal chromosomal aneuploidies that analyzes cell-free fetal DNA in the blood of a pregnant woman. Since its introduction to clinical practice in Hong Kong in 2011, NIPT has quickly spread across the globe. While many professional societies currently recommend that NIPT be used as a screening method, not a diagnostic test, its high sensitivity (true positive rate) and specificity (true negative rate) make it an attractive alternative to the serum screens and invasive tests currently in use. Professional societies also recommend that NIPT be accompanied by genetic counseling so that families can make informed reproductive choices. If NIPT becomes more widely adopted, States will have to implement regulation and oversight to ensure it fits into existing legal frameworks, with particular attention to returning fetal sex information in areas where sex-based abortions are prevalent. Although there are additional challenges for NIPT uptake in the developing world, including the lack of health care professionals and infrastructure, the use of NIPT in low-resource settings could potentially reduce the need for skilled clinicians who perform invasive testing. Future advances in NIPT technology promise to expand the range of conditions that can be detected, including single gene disorders. With these advances come questions of how to handle incidental findings and variants of unknown significance. Moving forward, it is essential that all stakeholders have a voice in crafting policies to ensure the ethical and equitable use of NIPT across the world. PMID:25653560

  19. Interventions to Improve Follow-Up of Laboratory Test Results Pending at Discharge: A Systematic Review.

    Science.gov (United States)

    Whitehead, Nedra S; Williams, Laurina; Meleth, Sreelatha; Kennedy, Sara; Epner, Paul; Singh, Hardeep; Wooldridge, Kathleene; Dalal, Anuj K; Walz, Stacy E; Lorey, Tom; Graber, Mark L

    2018-02-28

    Failure to follow up test results pending at discharge (TPAD) from hospitals or emergency departments is a major patient safety concern. The purpose of this review is to systematically evaluate the effectiveness of interventions to improve follow-up of laboratory TPAD. We conducted literature searches in PubMed, CINAHL, Cochrane, and EMBASE using search terms for relevant health care settings, transition of patient care, laboratory tests, communication, and pending or missed tests. We solicited unpublished studies from the clinical laboratory community and excluded articles that did not address transitions between settings, did not include an intervention, or were not related to laboratory TPAD. We also excluded letters, editorials, commentaries, abstracts, case reports, and case series. Of the 9,592 abstracts retrieved, 8 met the inclusion criteria and reported the successful communication of TPAD. A team member abstracted predetermined data elements from each study, and a senior scientist reviewed the abstraction. Two experienced reviewers independently appraised the quality of each study using published LMBP™ A-6 scoring criteria. We assessed the body of evidence using the A-6 methodology, and the evidence suggested that electronic tools or one-on-one education increased documentation of pending tests in discharge summaries. We also found that automated notifications improved awareness of TPAD. The interventions were supported by suggestive evidence; this type of evidence is below the level of evidence required for LMBP™ recommendations. We encourage additional research into the impact of these interventions on key processes and health outcomes. © 2018 Society of Hospital Medicine.

  20. Physical examination tests for screening and diagnosis of cervicogenic headache: A systematic review.

    Science.gov (United States)

    Rubio-Ochoa, J; Benítez-Martínez, J; Lluch, E; Santacruz-Zaragozá, S; Gómez-Contreras, P; Cook, C E

    2016-02-01

    It has been suggested that differential diagnosis of headaches should consist of a robust subjective examination and a detailed physical examination of the cervical spine. Cervicogenic headache (CGH) is a form of headache that involves referred pain from the neck. To our knowledge, no studies have summarized the reliability and diagnostic accuracy of physical examination tests for CGH. The aim of this study was to summarize the reliability and diagnostic accuracy of physical examination tests used to diagnose CGH. A systematic review following PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines was performed in four electronic databases (MEDLINE, Web of Science, Embase and Scopus). Full text reports concerning physical tests for the diagnosis of CGH which reported the clinometric properties for assessment of CGH, were included and screened for methodological quality. Quality Appraisal for Reliability Studies (QAREL) and Quality Assessment of Studies of Diagnostic Accuracy (QUADAS-2) scores were completed to assess article quality. Eight articles were retrieved for quality assessment and data extraction. Studies investigating diagnostic reliability of physical examination tests for CGH scored poorer on methodological quality (higher risk of bias) than those of diagnostic accuracy. There is sufficient evidence showing high levels of reliability and diagnostic accuracy of the selected physical examination tests for the diagnosis of CGH. The cervical flexion-rotation test (CFRT) exhibited both the highest reliability and the strongest diagnostic accuracy for the diagnosis of CGH. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Triage of HR-HPV positive women with minor cytological abnormalities: a comparison of mRNA testing, HPV DNA testing, and repeat cytology using a 4-year follow-up of a population-based study.

    Science.gov (United States)

    Persson, Maria; Elfström, K Miriam; Brismar Wendel, Sophia; Weiderpass, Elisabete; Andersson, Sonia

    2014-01-01

    Expression of the viral E6/E7 oncogenes of high-risk human papillomaviruses (HR-HPV) is necessary for malignant conversion and maintenance in cervical tissue. In order to determine whether HR-HPV E6/E7 mRNA testing more effectively predicts precancerous lesions and invasive cervical cancer than HR-HPV DNA testing, we aimed to compare triage using HR-HPV E6/E7 mRNA testing by APTIMA HPV Assay (APTIMA) to HPV16 DNA testing, HPV16/18 DNA testing, and repeat cytology. Liquid-based (PreservCyt) cell samples were obtained from HR-HPV-positive women diagnosed with atypical squamous cells of undetermined significance (ASCUS) and low-grade squamous intraepithelial lesions (LSIL) within the framework of the population-based cervical cancer screening program in Stockholm, Sweden. Samples were tested for HR-HPV E6/E7 mRNA by APTIMA (Gene-Probe Inc., San Diego, CA, USA). Women were followed up for 4 years after the index cytology via medical and laboratory records, and the Stockholm Oncology Center. Nine of 25 (36%) women in the ASCUS group, and 64 of 180 (36%) women in the LSIL group developed cervical intraepithelial neoplasia (CIN) grade 2 or worse during 4 years of follow-up. 162 (74%) women were APTIMA-positive, and APTIMA had the highest sensitivity to predict CIN2 or worse and CIN3 or worse in the ASCUS (77.8% and 100%) and LSIL (78.1 and 75.8%) groups, although specificity was insufficient (cytology were more specific than APTIMA. The results of this population-based study with comprehensive follow-up support the use of APTIMA as a triage test for women with ASCUS. More focused investigation is required for women with LSIL.

  2. A Review on Key Issues and Challenges in Devices Level MEMS Testing

    Directory of Open Access Journals (Sweden)

    Muhammad Shoaib

    2016-01-01

    Full Text Available The present review provides information relevant to issues and challenges in MEMS testing techniques that are implemented to analyze the microelectromechanical systems (MEMS behavior for specific application and operating conditions. MEMS devices are more complex and extremely diverse due to the immersion of multidomains. Their failure modes are distinctive under different circumstances. Therefore, testing of these systems at device level as well as at mass production level, that is, parallel testing, is becoming very challenging as compared to the IC test, because MEMS respond to electrical, physical, chemical, and optical stimuli. Currently, test systems developed for MEMS devices have to be customized due to their nondeterministic behavior and complexity. The accurate measurement of test systems for MEMS is difficult to quantify in the production phase. The complexity of the device to be tested required maturity in the test technique which increases the cost of test development; this practice is directly imposed on the device cost. This factor causes a delay in time-to-market.

  3. A Systematic Review of Point of Care Testing for Chlamydia trachomatis, Neisseria gonorrhoeae, and Trichomonas vaginalis

    Directory of Open Access Journals (Sweden)

    Sasha Herbst de Cortina

    2016-01-01

    Full Text Available Objectives. Systematic review of point of care (POC diagnostic tests for sexually transmitted infections: Chlamydia trachomatis (CT, Neisseria gonorrhoeae (NG, and Trichomonas vaginalis (TV. Methods. Literature search on PubMed for articles from January 2010 to August 2015, including original research in English on POC diagnostics for sexually transmitted CT, NG, and/or TV. Results. We identified 33 publications with original research on POC diagnostics for CT, NG, and/or TV. Thirteen articles evaluated test performance, yielding at least one test for each infection with sensitivity and specificity ≥90%. Each infection also had currently available tests with sensitivities <60%. Three articles analyzed cost effectiveness, and five publications discussed acceptability and feasibility. POC testing was acceptable to both providers and patients and was also demonstrated to be cost effective. Fourteen proof of concept articles introduced new tests. Conclusions. Highly sensitive and specific POC tests are available for CT, NG, and TV, but improvement is possible. Future research should focus on acceptability, feasibility, and cost of POC testing. While pregnant women specifically have not been studied, the results available in nonpregnant populations are encouraging for the ability to test and treat women in antenatal care to prevent adverse pregnancy and neonatal outcomes.

  4. Performance Validity Testing in Neuropsychology: Scientific Basis and Clinical Application-A Brief Review.

    Science.gov (United States)

    Greher, Michael R; Wodushek, Thomas R

    2017-03-01

    Performance validity testing refers to neuropsychologists' methodology for determining whether neuropsychological test performances completed in the course of an evaluation are valid (ie, the results of true neurocognitive function) or invalid (ie, overly impacted by the patient's effort/engagement in testing). This determination relies upon the use of either standalone tests designed for this sole purpose, or specific scores/indicators embedded within traditional neuropsychological measures that have demonstrated this utility. In response to a greater appreciation for the critical role that performance validity issues play in neuropsychological testing and the need to measure this variable to the best of our ability, the scientific base for performance validity testing has expanded greatly over the last 20 to 30 years. As such, the majority of current day neuropsychologists in the United States use a variety of measures for the purpose of performance validity testing as part of everyday forensic and clinical practice and address this issue directly in their evaluations. The following is the first article of a 2-part series that will address the evolution of performance validity testing in the field of neuropsychology, both in terms of the science as well as the clinical application of this measurement technique. The second article of this series will review performance validity tests in terms of methods for development of these measures, and maximizing of diagnostic accuracy.

  5. Economic Evaluations of Pharmacogenetic and Pharmacogenomic Screening Tests: A Systematic Review. Second Update of the Literature.

    Directory of Open Access Journals (Sweden)

    Elizabeth J J Berm

    Full Text Available Due to extended application of pharmacogenetic and pharmacogenomic screening (PGx tests it is important to assess whether they provide good value for money. This review provides an update of the literature.A literature search was performed in PubMed and papers published between August 2010 and September 2014, investigating the cost-effectiveness of PGx screening tests, were included. Papers from 2000 until July 2010 were included via two previous systematic reviews. Studies' overall quality was assessed with the Quality of Health Economic Studies (QHES instrument.We found 38 studies, which combined with the previous 42 studies resulted in a total of 80 included studies. An average QHES score of 76 was found. Since 2010, more studies were funded by pharmaceutical companies. Most recent studies performed cost-utility analysis, univariate and probabilistic sensitivity analyses, and discussed limitations of their economic evaluations. Most studies indicated favorable cost-effectiveness. Majority of evaluations did not provide information regarding the intrinsic value of the PGx test. There were considerable differences in the costs for PGx testing. Reporting of the direction and magnitude of bias on the cost-effectiveness estimates as well as motivation for the chosen economic model and perspective were frequently missing.Application of PGx tests was mostly found to be a cost-effective or cost-saving strategy. We found that only the minority of recent pharmacoeconomic evaluations assessed the intrinsic value of the PGx tests. There was an increase in the number of studies and in the reporting of quality associated characteristics. To improve future evaluations, scenario analysis including a broad range of PGx tests costs and equal costs of comparator drugs to assess the intrinsic value of the PGx tests, are recommended. In addition, robust clinical evidence regarding PGx tests' efficacy remains of utmost importance.

  6. ERG and GRG review of the draft of ''preliminary test plan for in situ testing from an exploratory shaft in salt - October 1983''

    International Nuclear Information System (INIS)

    Kalia, H.N.

    1986-03-01

    The Engineering Review Group (ERG) and Geologic Review Group (GRG) were established by the Office of Nuclear Waste Isolation (ONWI) to help evaluate engineering- and geologic-related issues in the US Department of Energy's nuclear waste repository program. The January 1984 meeting of the ERG and GRG reviewed the In Situ Test Plan (ISTP) titled ''Preliminary Test Plan for In Situ Testing From an Exploratory Shaft in Salt - October 1983.'' This report documents the ERG's and GRG's comments and recommendations on this subject and the ONWI responses to the specific points raised by the ERG and GRG. 6 refs., 2 figs., 1 tab

  7. Book Review: Professional Penetration Testing: Creating and Learning in a Hacking Lab 2E

    Directory of Open Access Journals (Sweden)

    Joshua Bartolomie

    2013-09-01

    Full Text Available Wilhelm, T. (2013. Professional Penetration Testing: Creating and Learning in a Hacking Lab 2E. Waltham, MA: Syngress, 464 pages, ISBN-10: 1597499935; ISBN-13: 978-1597499934, US$79.99Reviewed by Joshua Bartolomie, CISSP, CEECS, CFCE, DFCP, CRISC, CSMOrganizations often strive for proactive information security programs in an effort to limit occurrence and impact of security breaches. However, traditional security programs run the risk of being unable to provide adequate insight and proactive awareness into real attack vectors that may exist within their organizations. With attack methods and efforts becoming increasingly aggressive, and effective, organizations must take equally assertive measures to protect their critical information and assets. Penetration testing is one of those tools that is often misunderstood, overlooked, and undervalued. A true adversary would not hesitate to exploit every potential to gain entry or cause a disruption to their target.(see PDF for full review

  8. Diagnostic accuracy of scapular physical examination tests for shoulder disorders: a systematic review.

    Science.gov (United States)

    Wright, Alexis A; Wassinger, Craig A; Frank, Mason; Michener, Lori A; Hegedus, Eric J

    2013-09-01

    To systematically review and critique the evidence regarding the diagnostic accuracy of physical examination tests for the scapula in patients with shoulder disorders. A systematic, computerised literature search of PubMED, EMBASE, CINAHL and the Cochrane Library databases (from database inception through January 2012) using keywords related to diagnostic accuracy of physical examination tests of the scapula. The Quality Assessment of Diagnostic Accuracy Studies tool was used to critique the quality of each paper. Eight articles met the inclusion criteria; three were considered to be of high quality. Of the three high-quality studies, two were in reference to a 'diagnosis' of shoulder pain. Only one high-quality article referenced specific shoulder pathology of acromioclavicular dislocation with reported sensitivity of 71% and 41% for the scapular dyskinesis and SICK scapula test, respectively. Overall, no physical examination test of the scapula was found to be useful in differentially diagnosing pathologies of the shoulder.

  9. Review of ultimate pressure capacity test of containment structure and scale model design techniques

    Energy Technology Data Exchange (ETDEWEB)

    Seo, Jeong Moon; Choi, In Kil [Korea Atomic Energy Research Institute, Taejeon (Korea)

    2000-03-01

    This study was performed to obtain the basic knowledge of the scaled model test through the review of experimental studies conducted in foreign countries. The results of this study will be used for the wall segment test planed in next year. It was concluded from the previous studies that the larger the model, the greater the trust of the community in the obtained results. It is recommended that a scale model 1/4 - 1/6 be suitable considering the characteristics of concrete, reinforcement, liner and tendon. Such a large scale model test require large amounts of time and budget. Because of these reasons, it is concluded that the containment wall segment test with analytical studies is efficient for the verification of the ultimate pressure capacity of the containment structures. 57 refs., 46 figs., 11 tabs. (Author)

  10. Sporadic colorectal cancer and individual susceptibility: A review of the association studies investigating the role of DNA repair genetic polymorphisms

    Czech Academy of Sciences Publication Activity Database

    Naccarati, Alessio; Pardini, B.; Hemminki, K.; Vodička, Pavel

    2007-01-01

    Roč. 635, 2-3(2007), s.118-145 ISSN 1383-5742 R&D Projects: GA MZd NR8563; GA ČR GA310/05/2626 Institutional research plan: CEZ:AV0Z50390512 Keywords : Sporadic colorectal cancer * Individual susceptibility * DNA repair Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.353, year: 2007

  11. 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.

  12. Identification of suicidal ideations with the help of projective tests: a review.

    Science.gov (United States)

    Kumar, Devvarta; Nizamie, S Haque; Abhishek, Priyadarshee; Prasanna, Lavanya Tumkur

    2014-12-01

    Identification of the presence of suicidal ideations in an individual is crucial for the timely intervention. However, these ideations may remain unidentified as an individual with serious intentions of self-harm may not express them explicitly. Various projective tests can provide crucial clues to clinicians about the presence of suicidal ideations in an individual's mind. The present review is intended to update clinicians working in the field of suicide prevention about salient findings on these tests which can serve as a ready reckoner for them. We also highlight the status of research in this domain. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Review of 2 kW grid connected LOPF tests in Nissum Bredning

    DEFF Research Database (Denmark)

    Margheritini, Lucia

    This report has been prepared by Per Resen and Aalborg University for the ForskVE project 10878: 2 kW grid connected LOPF test buoy. AAU has the role of reviewing and advise on the data analysis, besides compiling this report. The purpose of this project was to document the mechanical power...... production against a target power curve of a 2kW grid connected wave energy buoy in Nissum Bredning at Helligsø....

  14. Safety and efficacy of Regadenoson in myocardial perfusion imaging (MPI) stress tests: A review

    Science.gov (United States)

    Ahmed, Ambereen

    2018-02-01

    Myocardial perfusion imaging (MPI) tests are often used to help diagnose coronary heart disease (CAD). The tests usually involve applying stress, such as hard physical exercise together with administration of vasodilators, to the patients. To date, many of these tests use non-selective A2A adenosine receptor agonists which, however, can be associated with highly undesirable and life-threatening side effects such as chest pain, dyspnea, severe bronchoconstriction and atrioventricular conduction anomalies. Regadenoson is a relatively new, highly selective A2A adenosine receptor agonist, suitable for use in MPI tests which exhibits far fewer adverse side effects and, unlike others testing agents, can be used without the necessity of excessive concomitant exercise. Also, the dose of regadenoson required is not dependent upon patient weight or renal impairment, and it can be rapidly administered by i.v. Injection. Regadenoson use in MPI testing thus has the potential as a simplified, relatively safe, time-saving and cost-effective method for helping diagnose CAD. The present study was designed to review several articles on the safety, efficacy, and suitability of regadenoson in MPI testing for CAD. Overall, the combined studies demonstrated that use of regadenoson in conjunction with low-level exercise in MPI is a highly efficient and relatively safe test for CAD, especially for more severe health-compromised patients.

  15. Giant Magnetoresistance Sensors: A Review on Structures and Non-Destructive Eddy Current Testing Applications

    Directory of Open Access Journals (Sweden)

    Damhuji Rifai

    2016-02-01

    Full Text Available Non-destructive eddy current testing (ECT is widely used to examine structural defects in ferromagnetic pipe in the oil and gas industry. Implementation of giant magnetoresistance (GMR sensors as magnetic field sensors to detect the changes of magnetic field continuity have increased the sensitivity of eddy current techniques in detecting the material defect profile. However, not many researchers have described in detail the structure and issues of GMR sensors and their application in eddy current techniques for nondestructive testing. This paper will describe the implementation of GMR sensors in non-destructive testing eddy current testing. The first part of this paper will describe the structure and principles of GMR sensors. The second part outlines the principles and types of eddy current testing probe that have been studied and developed by previous researchers. The influence of various parameters on the GMR measurement and a factor affecting in eddy current testing will be described in detail in the third part of this paper. Finally, this paper will discuss the limitations of coil probe and compensation techniques that researchers have applied in eddy current testing probes. A comprehensive review of previous studies on the application of GMR sensors in non-destructive eddy current testing also be given at the end of this paper.

  16. Functional assessment of the ex vivo vocal folds through biomechanical testing: A review

    Science.gov (United States)

    Dion, Gregory R.; Jeswani, Seema; Roof, Scott; Fritz, Mark; Coelho, Paulo; Sobieraj, Michael; Amin, Milan R.; Branski, Ryan C.

    2016-01-01

    The human vocal folds are complex structures made up of distinct layers that vary in cellular and extracellular composition. The mechanical properties of vocal fold tissue are fundamental to the study of both the acoustics and biomechanics of voice production. To date, quantitative methods have been applied to characterize the vocal fold tissue in both normal and pathologic conditions. This review describes, summarizes, and discusses the most commonly employed methods for vocal fold biomechanical testing. Force-elongation, torsional parallel plate rheometry, simple-shear parallel plate rheometry, linear skin rheometry, and indentation are the most frequently employed biomechanical tests for vocal fold tissues and each provide material properties data that can be used to compare native tissue verses diseased for treated tissue. Force-elongation testing is clinically useful, as it allows for functional unit testing, while rheometry provides physiologically relevant shear data, and nanoindentation permits micrometer scale testing across different areas of the vocal fold as well as whole organ testing. Thoughtful selection of the testing technique during experimental design to evaluate a hypothesis is important to optimizing biomechanical testing of vocal fold tissues. PMID:27127075

  17. Giant Magnetoresistance Sensors: A Review on Structures and Non-Destructive Eddy Current Testing Applications

    Science.gov (United States)

    Rifai, Damhuji; Abdalla, Ahmed N.; Ali, Kharudin; Razali, Ramdan

    2016-01-01

    Non-destructive eddy current testing (ECT) is widely used to examine structural defects in ferromagnetic pipe in the oil and gas industry. Implementation of giant magnetoresistance (GMR) sensors as magnetic field sensors to detect the changes of magnetic field continuity have increased the sensitivity of eddy current techniques in detecting the material defect profile. However, not many researchers have described in detail the structure and issues of GMR sensors and their application in eddy current techniques for nondestructive testing. This paper will describe the implementation of GMR sensors in non-destructive testing eddy current testing. The first part of this paper will describe the structure and principles of GMR sensors. The second part outlines the principles and types of eddy current testing probe that have been studied and developed by previous researchers. The influence of various parameters on the GMR measurement and a factor affecting in eddy current testing will be described in detail in the third part of this paper. Finally, this paper will discuss the limitations of coil probe and compensation techniques that researchers have applied in eddy current testing probes. A comprehensive review of previous studies on the application of GMR sensors in non-destructive eddy current testing also be given at the end of this paper. PMID:26927123

  18. User testing of an adaptation of fishbone diagrams to depict results of systematic reviews

    Directory of Open Access Journals (Sweden)

    Gerald Gartlehner

    2017-12-01

    Full Text Available Abstract Background Summary of findings tables in systematic reviews are highly informative but require epidemiological training to be interpreted correctly. The usage of fishbone diagrams as graphical displays could offer researchers an effective approach to simplify content for readers with limited epidemiological training. In this paper we demonstrate how fishbone diagrams can be applied to systematic reviews and present the results of an initial user testing. Methods Findings from two systematic reviews were graphically depicted in the form of the fishbone diagram. To test the utility of fishbone diagrams compared with summary of findings tables, we developed and pilot-tested an online survey using Qualtrics. Respondents were randomized to the fishbone diagram or a summary of findings table presenting the same body of evidence. They answered questions in both open-ended and closed-answer formats; all responses were anonymous. Measures of interest focused on first and second impressions, the ability to find and interpret critical information, as well as user experience with both displays. We asked respondents about the perceived utility of fishbone diagrams compared to summary of findings tables. We analyzed quantitative data by conducting t-tests and comparing descriptive statistics. Results Based on real world systematic reviews, we provide two different fishbone diagrams to show how they might be used to display complex information in a clear and succinct manner. User testing on 77 students with basic epidemiological training revealed that participants preferred summary of findings tables over fishbone diagrams. Significantly more participants liked the summary of findings table than the fishbone diagram (71.8% vs. 44.8%; p < .01; significantly more participants found the fishbone diagram confusing (63.2% vs. 35.9%, p < .05 or indicated that it was difficult to find information (65.8% vs. 45%; p < .01. However, more than half

  19. Helicobacter pylori diagnostic tests in children: review of the literature from 1999 to 2009.

    Science.gov (United States)

    Guarner, Jeannette; Kalach, Nicolas; Elitsur, Yoram; Koletzko, Sibylle

    2010-01-01

    The array of tests that can be used for diagnosis of Helicobacter pylori infection is large, and it can be confusing to define which test to use particularly in children where results may not be comparable to those obtained in adult patients. Using PubMed, we reviewed the English literature from January 1999 to May 2009 to identify articles that determined sensitivity and specificity of H. pylori invasive and non-invasive diagnostic tests in children. We excluded articles that presented a review of the literature, abstracts, case reports, or series where children's results could not be separated from adult populations. Of the tissue based methods, rapid urease tests have better sensitivity than histology to detect presence of H. pylori; however, histology can detect the pathology associated with disease including gastritis, intestinal metaplasia, and other conditions that could be the cause of the child's symptoms. Culture of gastric tissues or stool has 100% specificity but sensitivity is low. Of the serologic tests, immunoblot has the best sensitivity. The urea breath tests have >75% sensitivity for detection of H. pylori before and after treatment. Immunoassays in stool using monoclonal antibodies have >95% sensitivity for detection of H. pylori before and after treatment. PCR testing can be performed in tissue and stool samples and can detect genes associated to antibiotic resistance. In summary, the current commercial non-invasive tests have adequate sensitivity and specificity for detecting the presence of H. pylori; however, endoscopy with histopathology is the only method that can detect H. pylori and lesions associated with the infection.

  20. A transcontinental challenge--a test of DNA barcode performance for 1,541 species of Canadian Noctuoidea (Lepidoptera.

    Directory of Open Access Journals (Sweden)

    Reza Zahiri

    Full Text Available This study provides a first, comprehensive, diagnostic use of DNA barcodes for the Canadian fauna of noctuoids or "owlet" moths (Lepidoptera: Noctuoidea based on vouchered records for 1,541 species (99.1% species coverage, and more than 30,000 sequences. When viewed from a Canada-wide perspective, DNA barcodes unambiguously discriminate 90% of the noctuoid species recognized through prior taxonomic study, and resolution reaches 95.6% when considered at a provincial scale. Barcode sharing is concentrated in certain lineages with 54% of the cases involving 1.8% of the genera. Deep intraspecific divergence exists in 7.7% of the species, but further studies are required to clarify whether these cases reflect an overlooked species complex or phylogeographic variation in a single species. Non-native species possess higher Nearest-Neighbour (NN distances than native taxa, whereas generalist feeders have lower NN distances than those with more specialized feeding habits. We found high concordance between taxonomic names and sequence clusters delineated by the Barcode Index Number (BIN system with 1,082 species (70% assigned to a unique BIN. The cases of discordance involve both BIN mergers and BIN splits with 38 species falling into both categories, most likely reflecting bidirectional introgression. One fifth of the species are involved in a BIN merger reflecting the presence of 158 species sharing their barcode sequence with at least one other taxon, and 189 species with low, but diagnostic COI divergence. A very few cases (13 involved species whose members fell into both categories. Most of the remaining 140 species show a split into two or three BINs per species, while Virbia ferruginosa was divided into 16. The overall results confirm that DNA barcodes are effective for the identification of Canadian noctuoids. This study also affirms that BINs are a strong proxy for species, providing a pathway for a rapid, accurate estimation of animal diversity.

  1. A systematic review of current immunological tests for the diagnosis of cattle brucellosis.

    Science.gov (United States)

    Ducrotoy, Marie J; Muñoz, Pilar M; Conde-Álvarez, Raquel; Blasco, José M; Moriyón, Ignacio

    2018-03-01

    Brucellosis is a worldwide extended zoonosis with a heavy economic and public health impact. Cattle, sheep and goats are infected by smooth Brucella abortus and Brucella melitensis, and represent a common source of the human disease. Brucellosis diagnosis in these animals is largely based on detection of a specific immunoresponse. We review here the immunological tests used for the diagnosis of cattle brucellosis. First, we discuss how the diagnostic sensitivity (DSe) and specificity (DSp), balance should be adjusted for brucellosis diagnosis, and the difficulties that brucellosis tests specifically present for the estimation of DSe/DSp in frequentistic (gold standard) and Bayesian analyses. Then, we present a systematic review (PubMed, GoogleScholar and CABdirect) of works (154 out of 991; years 1960-August 2017) identified (by title and Abstract content) as DSe and DSp studies of smooth lipopolysaccharide, O-polysaccharide-core, native hapten and protein diagnostic tests. We summarize data of gold standard studies (n = 23) complying with strict inclusion and exclusion criteria with regards to test methodology and definition of the animals studied (infected and S19 or RB51 vaccinated cattle, and Brucella-free cattle affected or not by false positive serological reactions). We also discuss some studies (smooth lipopolysaccharide tests, protein antibody and delayed type hypersensitivity [skin] tests) that do not meet the criteria and yet fill some of the gaps in information. We review Bayesian studies (n = 5) and report that in most cases priors and assumptions on conditional dependence/independence are not coherent with the variable serological picture of the disease in different epidemiological scenarios and the bases (antigen, isotype and immunoglobulin properties involved) of brucellosis tests, practical experience and the results of gold standard studies. We conclude that very useful lipopolysaccharide (buffered plate antigen and indirect ELISA) and

  2. Underground Test Area Activity Preemptive Review Guidance Nevada National Security Site, Nevada, Revision 0

    Energy Technology Data Exchange (ETDEWEB)

    Farnham, Irene [Navarro, Las Vegas, NV (United States); Rehfeldt, Kenneth [Navarro, Las Vegas, NV (United States)

    2016-10-01

    Preemptive reviews (PERs) of Underground Test Area (UGTA) Activity corrective action unit (CAU) studies are an important and long-maintained quality improvement process. The CAU-specific PER committees provide internal technical review of ongoing work throughout the CAU lifecycle. The reviews, identified in the UGTA Quality Assurance Plan (QAP) (Sections 1.3.5.1 and 3.2), assure work is comprehensive, accurate, in keeping with the state of the art, and consistent with CAU goals. PER committees review various products, including data, documents, software/codes, analyses, and models. PER committees may also review technical briefings including Federal Facility Agreement and Consent Order (FFACO)-required presentations to the Nevada Division of Environmental Protection (NDEP) and presentations supporting key technical decisions (e.g., investigation plans and approaches). PER committees provide technical recommendations to support regulatory decisions that are the responsibility of the U.S. Department of Energy (DOE), National Nuclear Security Administration Nevada Field Office (NNSA/NFO) and NDEP.

  3. Review: Accuracy of Salivary Lithium Testing in Treatment Monitoring in Mood Disorders

    Directory of Open Access Journals (Sweden)

    Abbas Ali Asadi

    2006-04-01

    Full Text Available Lithium preparations have been used in bipolar mood disorders since 19th Century. Lethal toxic effect of lithium due to it's narrow (therapeutic index had been known from several years ago and is the most problem when is prescribed. Serum level of lithium is accepted for monitoring of toxicity, but frequency of blood testing especially in stabilizing period is stressful for patients, also it is difficult in such psychiatric patients especially in children. Many researchers worked to find a less aggressive method. One of these methods is monitoring based on salivary lithium concentration, which is controversy according to this review articles. All papers from 1949 till now are reviewed in this article and revealed this controversy. According to this review article, three ways are being suggested to solve this problem 1- Stimulation of salivary – serum ratio of lithium based on tree separated paired tests 2- Improving methods and techniques of testing. 3- Modifying of this ratio based on natural markers.

  4. Radioactive waste isolation in salt: Peer review of the Golder Associates draft test plan for in situ testing in an exploratory shaft in salt

    International Nuclear Information System (INIS)

    Hambley, D.F.; Mraz, D.Z.; Unterberter, R.R.

    1987-01-01

    This report documents the peer review conducted by Argonne National Laboratory of a document entitled ''Draft Test Plan for In Situ Testing in an Exploratory Shaft in Salt,'' prepared for Battelle Memorial Institute's Office of Nuclear Waste Isolation by Golder Associates, Inc. In general, the peer review panelists found the test plan to be technically sound, although some deficiencies were identified. Recommendations for improving the test plan are presented in this review report. A microfiche copy of the following unpublished report is attached to the inside back cover of this report: ''Draft Test Plan for In Situ Testing in an Exploratory Shaft in Salt,'' prepared by Golder Associates, Inc., for Office of Nuclear Waste Isolation, Battelle Memorial Institute, Columbus, Ohio (March 1985)

  5. Cell-type specific role of the RNA-binding protein, NONO, in the DNA double-strand break response in the mouse testes.

    Science.gov (United States)

    Li, Shuyi; Shu, Feng-Jue; Li, Zhentian; Jaafar, Lahcen; Zhao, Shourong; Dynan, William S

    2017-03-01

    The tandem RNA recognition motif protein, NONO, was previously identified as a candidate DNA double-strand break (DSB) repair factor in a biochemical screen for proteins with end-joining stimulatory activity. Subsequent work showed that NONO and its binding partner, SFPQ, have many of the properties expected for bona fide repair factors in cell-based assays. Their contribution to the DNA damage response in intact tissue in vivo has not, however, been demonstrated. Here we compare DNA damage sensitivity in the testes of wild-type mice versus mice bearing a null allele of the NONO homologue (Nono gt ). In wild-type mice, NONO protein was present in Sertoli, peritubular myoid, and interstitial cells, with an increase in expression following induction of DNA damage. As expected for the product of an X-linked gene, NONO was not detected in germ cells. The Nono gt/0 mice had at most a mild testis developmental phenotype in the absence of genotoxic stress. However, following irradiation at sublethal, 2-4 Gy doses, Nono gt/0 mice displayed a number of indicators of radiosensitivity as compared to their wild-type counterparts. These included higher levels of persistent DSB repair foci, increased numbers of apoptotic cells in the seminiferous tubules, and partial degeneration of the blood-testis barrier. There was also an almost complete loss of germ cells at later times following irradiation, evidently arising as an indirect effect reflecting loss of stromal support. Results demonstrate a role for NONO protein in protection against direct and indirect biological effects of ionizing radiation in the whole animal. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. DNA multigene characterization of Fasciola hepatica and Lymnaea neotropica and its fascioliasis transmission capacity in Uruguay, with historical correlation, human report review and infection risk analysis

    Science.gov (United States)

    Gayo, Valeria; Sanchis, Jaime; Artigas, Patricio; Khoubbane, Messaoud; Birriel, Soledad; Mas-Coma, Santiago

    2017-01-01

    Background Fascioliasis is a pathogenic disease transmitted by lymnaeid snails and recently emerging in humans, in part due to effects of climate changes, anthropogenic environment modifications, import/export and movements of livestock. South America is the continent presenting more human fascioliasis hyperendemic areas and the highest prevalences and intensities known. These scenarios appear mainly linked to altitude areas in Andean countries, whereas lowland areas of non-Andean countries, such as Uruguay, only show sporadic human cases or outbreaks. A study including DNA marker sequencing of fasciolids and lymnaeids, an experimental study of the life cycle in Uruguay, and a review of human fascioliasis in Uruguay, are performed. Methodology/Principal findings The characterization of Fasciola hepatica from cattle and horses of Uruguay included the complete sequences of the ribosomal DNA ITS-2 and ITS-1 and mitochondrial DNA cox1 and nad1. ITS-2, ITS-1, partial cox1 and rDNA 16S gene of mtDNA were used for lymnaeids. Results indicated that vectors belong to Lymnaea neotropica instead of to Lymnaea viator, as always reported from Uruguay. The life cycle and transmission features of F. hepatica by L. neotropica of Uruguay were studied under standardized experimental conditions to enable a comparison with the transmission capacity of F. hepatica by Galba truncatula at very high altitude in Bolivia. On this baseline, we reviewed the 95 human fascioliasis cases reported in Uruguay and analyzed the risk of human infection in front of future climate change estimations. Conclusions/Significance The correlation of fasciolid and lymnaeid haplotypes with historical data on the introduction and spread of livestock into Uruguay allowed to understand the molecular diversity detected. Although Uruguayan L. neotropica is a highly efficient vector, its transmission capacity is markedly lower than that of Bolivian G. truncatula. This allows to understand the transmission and

  7. Evaluation of the efficacy of the four tests (p16 immunochemistry, PCR, DNA and RNA In situ Hybridization) to evaluate a Human Papillomavirus infection in head and neck cancers: a cohort of 348 French squamous cell carcinomas.

    Science.gov (United States)

    Augustin, Jérémy; Outh-Gauer, Sophie; Mandavit, Marion; Gasne, Cassandre; Grard, Ophélie; Denize, Thomas; Nervo, Marine; Mirghani, Haïtham; Laccourreye, Ollivier; Bonfils, Pierre; Bruneval, Patrick; Veyer, David; Péré, Hélène; Tartour, Eric; Badoual, Cécile

    2018-04-20

    It is now established that HPV plays a role in the development of a subset of head and neck squamous cell carcinomas (HNSCCs), notably oropharyngeal squamous cell carcinomas (SCCs). However, it is not clear which test one should use to detect HPV in oropharyngeal (OP) and non-OP SCCs. In this study, using 348 HNSCCs (126 OP SCCs and 222 non-OP SCCs), we evaluated diagnostic performances of different HPV tests in OP and non-OP SCCs: PCR, p16 immunostaining, in situ hybridization targeting DNA (DNA-CISH) and RNA (RNA-CISH), combined p16 + DNA-CISH, and combined p16 + RNA-CISH. HPV DNA (PCR) was detected in 26% of all tumors (44% of OP SCCs and 17% of non-OP SCCs). For OP SCCs, RNA-CISH was the most sensitive standalone test (88%), but p16 + RNA-CISH was even more sensitive (95%). Specificities were the same for RNA-CISH and DNA-CISH (97%) but it was better for p16 + RNA-CISH (100%). For non-OP SCCs, all tests had sensitivities below 50%, and RNA-CISH, DNA-CISH and p16 + DNA-CISH had respectively 100%, 97% and 99% specificities. As a standalone test, RNA-CISH is the most performant assay to detect HPV in OP SCCs, and combined p16 + RNA-CISH test slightly improves its performances. However, RNA-CISH has the advantage of being one single test. Like p16 and DNA-CISH, RNA-CISH performances are poor in non-OP SCCs to detect HPV, and combining tests does not improve performances. Copyright © 2018. Published by Elsevier Inc.

  8. Interfacing DNA nanodevices with biology

    DEFF Research Database (Denmark)

    Vinther, Mathias; Kjems, Jørgen

    2016-01-01

    in biology and biomedicine acting as a molecular ‘nanorobot’ or smart drug interacting with the cellular machinery. In this review, we will explore and examine the perspective of DNA nanotechnology for such use. We summarize which requirements DNA nanostructures must fulfil to function in cellular...... environments and inside living organisms. In addition, we highlight recent advances in interfacing DNA nanostructures with biology....

  9. Testing DNA barcode performance in 1000 species of European lepidoptera: large geographic distances have small genetic impacts.

    Science.gov (United States)

    Huemer, Peter; Mutanen, Marko; Sefc, Kristina M; Hebert, Paul D N

    2014-01-01

    This study examines the performance of DNA barcodes (mt cytochrome c oxidase 1 gene) in the identification of 1004 species of Lepidoptera shared by two localities (Finland, Austria) that are 1600 km apart. Maximum intraspecific distances for the pooled data were less than 2% for 880 species (87.6%), while deeper divergence was detected in 124 species. Despite such variation, the overall DNA barcode library possessed diagnostic COI sequences for 98.8% of the taxa. Because a reference library based on Finnish specimens was highly effective in identifying specimens from Austria, we conclude that barcode libraries based on regional sampling can often be effective for a much larger area. Moreover, dispersal ability (poor, good) and distribution patterns (disjunct, fragmented, continuous, migratory) had little impact on levels of intraspecific geographic divergence. Furthermore, the present study revealed that, despite the intensity of past taxonomic work on European Lepidoptera, nearly 20% of the species shared by Austria and Finland require further work to clarify their status. Particularly discordant BIN (Barcode Index Number) cases should be checked to ascertain possible explanatory factors such as incorrect taxonomy, hybridization, introgression, and Wolbachia infections.

  10. Testing DNA barcode performance in 1000 species of European lepidoptera: large geographic distances have small genetic impacts.

    Directory of Open Access Journals (Sweden)

    Peter Huemer

    Full Text Available This study examines the performance of DNA barcodes (mt cytochrome c oxidase 1 gene in the identification of 1004 species of Lepidoptera shared by two localities (Finland, Austria that are 1600 km apart. Maximum intraspecific distances for the pooled data were less than 2% for 880 species (87.6%, while deeper divergence was detected in 124 species. Despite such variation, the overall DNA barcode library possessed diagnostic COI sequences for 98.8% of the taxa. Because a reference library based on Finnish specimens was highly effective in identifying specimens from Austria, we conclude that barcode libraries based on regional sampling can often be effective for a much larger area. Moreover, dispersal ability (poor, good and distribution patterns (disjunct, fragmented, continuous, migratory had little impact on levels of intraspecific geographic divergence. Furthermore, the present study revealed that, despite the intensity of past taxonomic work on European Lepidoptera, nearly 20% of the species shared by Austria and Finland require further work to clarify their status. Particularly discordant BIN (Barcode Index Number cases should be checked to ascertain possible explanatory factors such as incorrect taxonomy, hybridization, introgression, and Wolbachia infections.

  11. Comparison of the clinical performances of the AdvanSure HPV Screening Real-Time PCR, the Abbott Real-Time High-Risk HPV Test, and the Hybrid Capture High-Risk HPV DNA Test for Cervical Cancer Screening.

    Science.gov (United States)

    Chung, Hae-Sun; Hahm, Chorong; Lee, Miae

    2014-09-01

    The clinical performance of three human papillomavirus (HPV) DNA commercial assays for cervical cancer screening was evaluated; the AdvanSure HPV Screening Real-Time PCR (AdvanSure PCR; LG Life Sciences) that was developed recently for the detection of both high-risk and low-risk genotypes, the Abbott RealTime High-Risk HPV Test (Abbott PCR; Abbott Molecular) and the Hybrid Capture High-Risk HPV DNA test (HC2; Qiagen). The three different HPV DNA tests were compared using cytology samples obtained from 619 women who underwent routine cervical cancer screening. The gold-standard assay was histopathological confirmation of cervical intraepithelial neoplasia of grade 2 or worse. The clinical sensitivities of the AdvanSure PCR, the Abbott PCR and the HC2 for the detection of cervical intraepithelial neoplasia of grade 2 or worse were 95.5%, 95.5% and 100%, respectively, while the clinical specificities were 61.6%, 86.4% and 83.3%, respectively. There were no significant differences in the clinical sensitivities of the Abbott PCR and the AdvanSure PCR compared to the HC2. The clinical specificities of the Abbott PCR and the AdvanSure PCR for the detection of HPV types 16/18 were 97.8% and 98.5%, respectively. For cervical cancer screening, all three tests showed relatively good clinical sensitivities, but the AdvanSure PCR had lower clinical specificity than the Abbott PCR and the HC2. The AdvanSure PCR and the Abbott PCR assays have the advantage of being automated and the ability to distinguish between HPV types 16/18 and other HPV types. The two real-time PCR assays could be useful tools in HPV testing for cervical cancer screening. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Transfer of test-enhanced learning: Meta-analytic review and synthesis.

    Science.gov (United States)

    Pan, Steven C; Rickard, Timothy C

    2018-05-07

    Attempting recall of information from memory, as occurs when taking a practice test, is one of the most potent training techniques known to learning science. However, does testing yield learning that transfers to different contexts? In the present article, we report the findings of the first comprehensive meta-analytic review into that question. Our review encompassed 192 transfer effect sizes extracted from 122 experiments and 67 published and unpublished articles (N = 10,382) that together comprise more than 40 years of research. A random-effects model revealed that testing can yield transferrable learning as measured relative to a nontesting reexposure control condition (d = 0.40, 95% CI [0.31, 0.50]). That transfer of learning is greatest across test formats, to application and inference questions, to problems involving medical diagnoses, and to mediator and related word cues; it is weakest to rearranged stimulus-response items, to untested materials seen during initial study, and to problems involving worked examples. Moderator analyses further indicated that response congruency and elaborated retrieval practice, as well as initial test performance, strongly influence the likelihood of positive transfer. In two assessments for publication bias using PET-PEESE and various selection methods, the moderator effect sizes were minimally affected. However, the intercept predictions were substantially reduced, often indicating no positive transfer when none of the aforementioned moderators are present. Overall, our results motivate a three-factor framework for transfer of test-enhanced learning and have practical implications for the effective use of practice testing in educational and other training contexts. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

  13. Impact of Enterovirus Testing on Resource Use in Febrile Young Infants: A Systematic Review.

    Science.gov (United States)

    Wallace, Sowdhamini S; Lopez, Michelle A; Caviness, A Chantal

    2017-02-01

    Enterovirus infection commonly causes fever in infants aged 0 to 90 days and, without testing, is difficult to differentiate from serious bacterial infection. To determine the cost savings of routine enterovirus testing and identify subgroups of infants with greater potential impact from testing among infants 0 to 90 days old with fever. Studies were identified systematically from published and unpublished literature by using Embase, Medline, the Cochrane database, and conference proceedings. Inclusion criteria were original studies, in any language, of enterovirus infection including the outcomes of interest in infants aged 0 to 90 days. Standardized instruments were used to appraise each study. The evidence quality was evaluated using Grading of Recommendations Assessment, Development, and Evaluation criteria. Two investigators independently searched the literature, screened and critically appraised the studies, extracted the data, and applied the Grading of Recommendations Assessment, Development, and Evaluation criteria. Of the 257 unique studies identified and screened, 32 were completely reviewed and 8 were included. Routine enterovirus testing was associated with reduced hospital length of stay and cost savings during peak enterovirus season. Cerebrospinal fluid pleocytosis was a poor predictor of enterovirus meningitis. The studies were all observational and the evidence was of low quality. Enterovirus polymerase chain reaction testing, independent of cerebrospinal fluid pleocytosis, can reduce length of stay and achieve cost savings, especially during times of high enterovirus prevalence. Additional study is needed to identify subgroups that may achieve greater cost savings from testing to additionally enhance the efficiency of testing. Copyright © 2017 by the American Academy of Pediatrics.

  14. Measurement properties of maximal cardiopulmonary exercise tests protocols in persons after stroke: A systematic review.

    Science.gov (United States)

    Wittink, Harriet; Verschuren, Olaf; Terwee, Caroline; de Groot, Janke; Kwakkel, Gert; van de Port, Ingrid

    2017-11-21

    To systematically review and critically appraise the literature on measurement properties of cardiopulmonary exercise test protocols for measuring aerobic capacity, VO2max, in persons after stroke. PubMed, Embase and Cinahl were searched from inception up to 15 June 2016. A total of 9 studies were identified reporting on 9 different cardiopulmonary exercise test protocols. VO2max measured with cardiopulmonary exercise test and open spirometry was the construct of interest. The target population was adult persons after stroke. We included all studies that evaluated reliability, measurement error, criterion validity, content validity, hypothesis testing and/or responsiveness of cardiopulmonary exercise test protocols. Two researchers independently screened the literature, assessed methodological quality using the COnsensus-based Standards for the selection of health Measurement INstruments checklist and extracted data on measurement properties of cardiopulmonary exercise test protocols. Most studies reported on only one measurement property. Best-evidence synthesis was derived taking into account the methodological quality of the studies, the results and the consistency of the results. No judgement could be made on which protocol is "best" for measuring VO2max in persons after stroke due to lack of high-quality studies on the measurement properties of the cardiopulmonary exercise test.

  15. Review of present groundwater monitoring programs at the Nevada Test Site

    International Nuclear Information System (INIS)

    Hershey, R.L.; Gillespie, D.

    1993-09-01

    Groundwater monitoring at the Nevada Test Site (NTS) is conducted to detect the presence of radionuclides produced by underground nuclear testing and to verify the quality and safety of groundwater supplies as required by the State of Nevada and federal regulations, and by U.S. Department of Energy (DOE) Orders. Groundwater is monitored at water-supply wells and at other boreholes and wells not specifically designed or located for traditional groundwater monitoring objectives. Different groundwater monitoring programs at the NTS are conducted by several DOE Nevada Operations Office (DOE/NV) contractors. Presently, these individual groundwater monitoring programs have not been assessed or administered under a comprehensive planning approach. Redundancy exists among the programs in both the sampling locations and the constituents analyzed. Also, sampling for certain radionuclides is conducted more frequently than required. The purpose of this report is to review the existing NTS groundwater monitoring programs and make recommendations for modifying the programs so a coordinated, streamlined, and comprehensive monitoring effort may be achieved by DOE/NV. This review will be accomplished in several steps. These include: summarizing the present knowledge of the hydrogeology of the NTS and the potential radionuclide source areas for groundwater contamination; reviewing the existing groundwater monitoring programs at the NTS; examining the rationale for monitoring and the constituents analyzed; reviewing the analytical methods used to quantify tritium activity; discussing monitoring network design criteria; and synthesizing the information presented and making recommendations based on the synthesis. This scope of work was requested by the DOE/NV Hydrologic Resources Management Program (HRMP) and satisfies the 1993 (fiscal year) HRMP Groundwater Monitoring Program Review task

  16. Economic Evaluations of Pathology Tests, 2010-2015: A Scoping Review.

    Science.gov (United States)

    Watts, Rory D; Li, Ian W; Geelhoed, Elizabeth A; Sanfilippo, Frank M; St John, Andrew

    2017-09-01

    Concerns about pathology testing such as the value provided by new tests and the potential for inappropriate utilization have led to a greater need to assess costs and benefits. Economic evaluations are a formal method of analyzing costs and benefits, yet for pathology tests, questions remain about the scope and quality of the economic evidence. To describe the extent and quality of published evidence provided by economic evaluations of pathology tests from 2010 to 2015. Economic evaluations relating to pathology tests from 2010 to 2015 were reviewed. Eight databases were searched for published studies, and details recorded for the country, clinical focus, type of testing, and consideration of sensitivity, specificity, and false test results. The reporting quality of studies was assessed using the Consolidated Health Economic Evaluation Reporting Standards checklist and cost-effectiveness ratios were analyzed for publication bias. We found 356 economic evaluations of pathology tests, most of which regarded developed countries. The most common economic evaluations were cost-utility analyses and the most common clinical focus was infectious diseases. More than half of the studies considered sensitivity and specificity, but few studies considered the impact of false test results. The average Consolidated Health Economic Evaluation Reporting Standards checklist score was 17 out of 24. Cost-utility ratios were commonly less than $10,000/quality-adjusted life-year or more than $200,000/quality-adjusted life-year. The number of economic evaluations of pathology tests has increased in recent years, but the rate of increase has plateaued. Furthermore, the quality of studies in the past 5 years was highly variable, and there is some question of publication bias in reporting cost-effectiveness ratios. Copyright © 2017 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

  17. The English Proficiency Test of the Iranian Ministry of Science, Research, and Technology: A Review

    Directory of Open Access Journals (Sweden)

    Mahdieh Noori

    2017-08-01

    Full Text Available One of the serious decisions which every administrator may need to make during his/her professional career is to select or reject applicants based on their general language skills or competence. These significant decisions, which may be of serious consequences not only for the individuals but also for the society in general, are occasionally made based on norm-referenced proficiency tests. Out of internationally available proficiency tests such as the TOEFL test, those which fit the specific local cultural and academic contexts seem of greater prominence. One such test, which has been specifically designed for the Iranian EFL context by the Ministry of Science, Research, and Technology, is the MSRT proficiency test. While a few studies have been conducted on the analysis of the reliability and validity of the mentioned test, no study has yet reviewed the test and its component parts. Therefore, the current study aimed at considering the strengths and weaknesses of the test in general and its component items in particular. The results implicated that the MSRT benefits from more efficient general reliability and validity, well planned language items, practicality, ease of administration, objective scoring, ease of accessibility, as well as reasonable fees, while it needs to be more substantiated in terms of the inclusion of the speaking skill assessment, the computerized adaptive assessment procedures, and the correction factor for guessing. In addition, the use of the individual-based listening apparatus for testing listening comprehension as well as the consideration of the integrative communicative tests for its concurrent validity purposes can contribute to more appropriate distinction of proficient and non-proficient applicants.

  18. 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.

  19. Close encounters with DNA

    Science.gov (United States)

    Maffeo, C.; Yoo, J.; Comer, J.; Wells, D. B.; Luan, B.; Aksimentiev, A.

    2014-01-01

    Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena and we review the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field. PMID:25238560

  20. A systematic review and meta-analysis of tests to predict wound healing in diabetic foot.

    Science.gov (United States)

    Wang, Zhen; Hasan, Rim; Firwana, Belal; Elraiyah, Tarig; Tsapas, Apostolos; Prokop, Larry; Mills, Joseph L; Murad, Mohammad Hassan

    2016-02-01

    This systematic review summarized the evidence on noninvasive screening tests for the prediction of wound healing and the risk of amputation in diabetic foot ulcers. We searched MEDLINE In-Process & Other Non-Indexed Citations, MEDLINE, Embase, Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials, and Scopus from database inception to October 2011. We pooled sensitivity, specificity, and diagnostic odds ratio (DOR) and compared test performance. Thirty-seven studies met the inclusion criteria. Eight tests were used to predict wound healing in this setting, including ankle-brachial index (ABI), ankle peak systolic velocity, transcutaneous oxygen measurement (TcPo2), toe-brachial index, toe systolic blood pressure, microvascular oxygen saturation, skin perfusion pressure, and hyperspectral imaging. For the TcPo2 test, the pooled DOR was 15.81 (95% confidence interval [CI], 3.36-74.45) for wound healing and 4.14 (95% CI, 2.98-5.76) for the risk of amputation. ABI was also predictive but to a lesser degree of the risk of amputations (DOR, 2.89; 95% CI, 1.65-5.05) but not of wound healing (DOR, 1.02; 95% CI, 0.40-2.64). It was not feasible to perform meta-analysis comparing the remaining tests. The overall quality of evidence was limited by the risk of bias and imprecision (wide CIs due to small sample size). Several tests may predict wound healing in the setting of diabetic foot ulcer; however, most of the available evidence evaluates only TcPo2 and ABI. The overall quality of the evidence is low, and further research is needed to provide higher quality comparative effectiveness evidence. Copyright © 2016 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

  1. Dynamic rock tests using split Hopkinson (Kolsky bar system – A review

    Directory of Open Access Journals (Sweden)

    Kaiwen Xia

    2015-02-01

    Full Text Available Dynamic properties of rocks are important in a variety of rock mechanics and rock engineering problems. Due to the transient nature of the loading, dynamic tests of rock materials are very different from and much more challenging than their static counterparts. Dynamic tests are usually conducted using the split Hopkinson bar or Kolsky bar systems, which include both split Hopkinson pressure bar (SHPB and split Hopkinson tension bar (SHTB systems. Significant progress has been made on the quantification of various rock dynamic properties, owing to the advances in the experimental techniques of SHPB system. This review aims to fully describe and critically assess the detailed procedures and principles of techniques for dynamic rock tests using split Hopkinson bars. The history and principles of SHPB are outlined, followed by the key loading techniques that are useful for dynamic rock tests with SHPB (i.e. pulse shaping, momentum-trap and multi-axial loading techniques. Various measurement techniques for rock tests in SHPB (i.e. X-ray micro computed tomography (CT, laser gap gauge (LGG, digital image correlation (DIC, Moiré method, caustics method, photoelastic coating method, dynamic infrared thermography are then discussed. As the main objective of the review, various dynamic measurement techniques for rocks using SHPB are described, including dynamic rock strength measurements (i.e. dynamic compression, tension, bending and shear tests, dynamic fracture measurements (i.e. dynamic imitation and propagation fracture toughness, dynamic fracture energy and fracture velocity, and dynamic techniques for studying the influences of temperature and pore water.

  2. Assessment of evidence for nanosized titanium dioxide-generated DNA strand breaks and oxidatively damaged DNA in cells and animal models

    DEFF Research Database (Denmark)

    Møller, Peter; Jensen, Ditte Marie; Wils, Regitze Sølling

    2017-01-01

    Nanosized titanium dioxide (TiO2) has been investigated in numerous studies on genotoxicity, including comet assay endpoints and oxidatively damaged DNA in cell cultures and animal models. The results have been surprisingly mixed, which might be attributed to physico-chemical differences...... culture studies also demonstrate increased levels of oxidatively damaged DNA after exposure to TiO2. There are relatively few studies on animal models where DNA strand breaks and oxidatively damaged DNA have been tested with reliable methods. Collectively, this review shows that exposure to nanosized TiO2...... of the tested TiO2. In the present review, we assess the role of certain methodological issues and publication bias. The analysis shows that studies on DNA strand breaks without proper assay controls or very low intra-group variation tend to show statistically significant effects. Levels of oxidatively damaged...

  3. Reliability of physical examination tests for the diagnosis of knee disorders: Evidence from a systematic review.

    Science.gov (United States)

    Décary, Simon; Ouellet, Philippe; Vendittoli, Pascal-André; Desmeules, François

    2016-12-01

    Clinicians often rely on physical examination tests to guide them in the diagnostic process of knee disorders. However, reliability of these tests is often overlooked and may influence the consistency of results and overall diagnostic validity. Therefore, the objective of this study was to systematically review evidence on the reliability of physical examination tests for the diagnosis of knee disorders. A structured literature search was conducted in databases up to January 2016. Included studies needed to report reliability measures of at least one physical test for any knee disorder. Methodological quality was evaluated using the QAREL checklist. A qualitative synthesis of the evidence was performed. Thirty-three studies were included with a mean QAREL score of 5.5 ± 0.5. Based on low to moderate quality evidence, the Thessaly test for meniscal injuries reached moderate inter-rater reliability (k = 0.54). Based on moderate to excellent quality evidence, the Lachman for anterior cruciate ligament injuries reached moderate to excellent inter-rater reliability (k = 0.42 to 0.81). Based on low to moderate quality evidence, the Tibiofemoral Crepitus, Joint Line and Patellofemoral Pain/Tenderness, Bony Enlargement and Joint Pain on Movement tests for knee osteoarthritis reached fair to excellent inter-rater reliability (k = 0.29 to 0.93). Based on low to moderate quality evidence, the Lateral Glide, Lateral Tilt, Lateral Pull and Quality of Movement tests for patellofemoral pain reached moderate to good inter-rater reliability (k = 0.49 to 0.73). Many physical tests appear to reach good inter-rater reliability, but this is based on low-quality and conflicting evidence. High-quality research is required to evaluate the reliability of knee physical examination tests. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Health-care providers' experiences with opt-out HIV testing: a systematic review.

    Science.gov (United States)

    Leidel, Stacy; Wilson, Sally; McConigley, Ruth; Boldy, Duncan; Girdler, Sonya

    2015-01-01

    HIV is now a manageable chronic disease with a good prognosis, but early detection and referral for treatment are vital. In opt-out HIV testing, patients are informed that they will be tested unless they decline. This qualitative systematic review explored the experiences, attitudes, barriers, and facilitators of opt-out HIV testing from a health-care provider (HCP) perspective. Four articles were included in the synthesis and reported on findings from approximately 70 participants, representing diverse geographical regions and a range of human development status and HIV prevalence. Two synthesized findings emerged: HCP attitudes and systems. The first synthesized finding encompassed HCP decision-making attitudes about who and when to test for HIV. It also included the assumptions the HCPs made about patient consequences. The second synthesized finding related to systems. System-related barriers to opt-out HIV testing included lack of time, resources, and adequate training. System-related facilitators included integration into standard practice, support of the medical setting, and electronic reminders. A common attitude among HCPs was the outdated notion that HIV is a terrible disease that equates to certain death. Some HCPs stated that offering the HIV test implied that the patient had engaged in immoral behaviour, which could lead to stigma or disengagement with health services. This paternalism diminished patient autonomy, because patients who were excluded from opt-out HIV testing could have benefited from it. One study highlighted the positive aspects of opt-out HIV testing, in which participants underscored the professional satisfaction that arose from making an HIV diagnosis, particularly when marginalized patients could be connected to treatment and social services. Recommendations for opt-out HIV testing should be disseminated to HCPs in a broad range of settings. Implementation of system-related factors such as electronic reminders and care coordination

  5. In Situ Estuarine and Marine Toxicity Testing: A Review, Including Recommendations for Future Use in Ecological Risk Assessment

    Science.gov (United States)

    2009-09-01

    field and microcosms than they do under laboratory test conditions. In the case of tributyltin ( TBT ) exposures in San Diego Bay, he found that...TECHNICAL REPORT 1986 September 2009 In Situ Estuarine and Marine Toxicity Testing A Review, Including Recommendations for Future Use in...Pacific TECHNICAL REPORT 1986 September 2009 In Situ Estuarine and Marine Toxicity Testing A Review, Including Recommendations for Future Use in

  6. Validation of a new test for Schistosoma haematobium based on detection of Dra1 DNA fragments in urine: evaluation through latent class analysis.

    Directory of Open Access Journals (Sweden)

    Olufunmilola Ibironke

    2012-01-01

    Full Text Available Diagnosis of urogenital schistosomiasis in chronically infected adults is challenging but important, especially because long term infection of the bladder and urinary tract can have dire consequences. We evaluated three tests for viable infection: detection of parasite specific DNA Dra1 fragments, haematuria and presence of parasite eggs for sensitivity (Se and specificity (Sp.Over 400 urine specimens collected from adult volunteers in an endemic area in Western Nigeria were assessed for haematuria then filtered in the field, the filter papers dried and later examined for eggs and DNA. The results were stratified according to sex and age and subjected to Latent Class analysis.Presence of Dra1 in males (Se=100%; Sp=100% exceeded haematuria (Se=87.6%: Sp=34.7% and detection of eggs (Se=70.1%; Sp=100%. In females presence of Dra1 was Se=100%: Sp=100%, exceeding haematuria (Se=86.7%: Sp=77.0% and eggs (Se=70.1%; Sp=100%. Dra1 became undetectable 2 weeks after praziquantel treatment. We conclude detection of Dra1 fragment is a definitive test for the presence of Schistosoma haematobium infection.

  7. The usefulness of DNA sequencing after extraction by Whatman FTA filter matrix technology and phenotypic tests for differentiation of Candida albicans and Candida dubliniensis.

    Science.gov (United States)

    Kiraz, Nuri; Oz, Yasemin; Aslan, Huseyin; Muslumanoglu, Hamza

    2014-02-01

    Since C. dubliniensis is similar to C. albicans phenotypically, it can be misidentified as C. albicans. We aimed to investigate the prevalence of C. dubliniensis among isolates previously identified as C. albicans in our stocks and to compare the phenotypic methods and DNA sequencing of D1/D2 region on the ribosomal large subunit (rLSU) gene. A total of 850 isolates included in this study. Phenotypic identification was performed based on germ tube formation, chlamydospore production, colony colors on chromogenic agar, inability of growth at 45 °C and growth on hypertonic Sabouraud dextrose agar. Eighty isolates compatible with C. dubliniensis by at least one phenotypic test were included in the sequence analysis. Nested PCR amplification of D1/D2 region of the rLSU gene was performed after the fungal DNA extraction by Whatman FTA filter paper technology. The sequencing analysis of PCR products carried out by an automated capillary gel electrophoresis device. The rate of C. dubliniensis was 2.35 % (n = 20) among isolates previously described as C. albicans. Consequently, none of the phenotypic tests provided satisfactory performance alone in our study, and molecular methods required special equipment and high cost. Thus, at least two phenotypic methods can be used for identification of C. dubliniensis, and molecular methods can be used for confirmation.

  8. Immunochemical faecal occult blood test for colorectal cancer screening: a systematic review.

    Science.gov (United States)

    Syful Azlie, M F; Hassan, M R; Junainah, S; Rugayah, B

    2015-02-01

    A systematic review on the effectiveness and costeffectiveness of Immunochemical faecal occult IFOBT for CRC screening was carried out. A total of 450 relevant titles were identified, 41 abstracts were screened and 18 articles were included in the results. There was fair level of retrievable evidence to suggest that the sensitivity and specificity of IFOBT varies with the cut-off point of haemoglobin, whereas the diagnostic accuracy performance was influenced by high temperature and haemoglobin stability. A screening programme using IFOBT can be effective for prevention of advanced CRC and reduced mortality. There was also evidence to suggest that IFOBT is cost-effective in comparison with no screening, whereby a two-day faecal collection method was found to be costeffective as a means of screening for CRC. Based on the review, quantitative IFOBT method can be used in Malaysia as a screening test for CRC. The use of fully automated IFOBT assay would be highly desirable.

  9. The Ins and Outs of DNA Fingerprinting the Infectious Fungi

    Science.gov (United States)

    Soll, David R.

    2000-01-01

    DNA fingerprinting methods have evolved as major tools in fungal epidemiology. However, no single method has emerged as the method of choice, and some methods perform better than others at different levels of resolution. In this review, requirements for an effective DNA fingerprinting method are proposed and procedures are described for testing the efficacy of a method. In light of the proposed requirements, the most common methods now being used to DNA fingerprint the infectious fungi are described and assessed. These methods include restriction fragment length polymorphisms (RFLP), RFLP with hybridization probes, randomly amplified polymorphic DNA and other PCR-based methods, electrophoretic karyotyping, and sequencing-based methods. Procedures for computing similarity coefficients, generating phylogenetic trees, and testing the stability of clusters are then described. To facilitate the analysis of DNA fingerprinting data, computer-assisted methods are described. Finally, the problems inherent in the collection of test and control isolates are considered, and DNA fingerprinting studies of strain maintenance during persistent or recurrent infections, microevolution in infecting strains, and the origin of nosocomial infections are assessed in light of the preceding discussion of the ins and outs of DNA fingerprinting. The intent of this review is to generate an awareness of the need to verify the efficacy of each DNA fingerprinting method for the level of genetic relatedness necessary to answer the epidemiological question posed, to use quantitative methods to analyze DNA fingerprint data, to use computer-assisted DNA fingerprint analysis systems to analyze data, and to file data in a form that can be used in the future for retrospective and comparative studies. PMID:10756003

  10. Molecular biological mechanisms I. DNA repair

    International Nuclear Information System (INIS)

    Friedl, A.A.

    2000-01-01

    Cells of all living systems possess a variety of mechanisms that allow to repair spontaneous and exogeneously induced DNA damage. DNA repair deficiencies may invoke enhanced sensitivity towards DNA-damaging agents such as ionizing radiation. They may also enhance the risk of cancer development, both spontaneously or after induction. This article reviews several DNA repair mechanisms, especially those dealing with DNA double-strand breaks, and describes hereditary diseases associated with DNA repair defects. (orig.) [de

  11. Mutation Detection in Patients With Advanced Cancer by Universal Sequencing of Cancer-Related Genes in Tumor and Normal DNA vs Guideline-Based Germline Testing.

    Science.gov (United States)

    Mandelker, Diana; Zhang, Liying; Kemel, Yelena; Stadler, Zsofia K; Joseph, Vijai; Zehir, Ahmet; Pradhan, Nisha; Arnold, Angela; Walsh, Michael F; Li, Yirong; Balakrishnan, Anoop R; Syed, Aijazuddin; Prasad, Meera; Nafa, Khedoudja; Carlo, Maria I; Cadoo, Karen A; Sheehan, Meg; Fleischut, Megan H; Salo-Mullen, Erin; Trottier, Magan; Lipkin, Steven M; Lincoln, Anne; Mukherjee, Semanti; Ravichandran, Vignesh; Cambria, Roy; Galle, Jesse; Abida, Wassim; Arcila, Marcia E; Benayed, Ryma; Shah, Ronak; Yu, Kenneth; Bajorin, Dean F; Coleman, Jonathan A; Leach, Steven D; Lowery, Maeve A; Garcia-Aguilar, Julio; Kantoff, Philip W; Sawyers, Charles L; Dickler, Maura N; Saltz, Leonard; Motzer, Robert J; O'Reilly, Eileen M; Scher, Howard I; Baselga, Jose; Klimstra, David S; Solit, David B; Hyman, David M; Berger, Michael F; Ladanyi, Marc; Robson, Mark E; Offit, Kenneth

    2017-09-05

    Guidelines for cancer genetic testing based on family history may miss clinically actionable genetic changes with established implications for cancer screening or prevention. To determine the proportion and potential clinical implications of inherited variants detected using simultaneous sequencing of the tumor and normal tissue ("tumor-normal sequencing") compared with genetic test results based on current guidelines. From January 2014 until May 2016 at Memorial Sloan Kettering Cancer Center, 10 336 patients consented to tumor DNA sequencing. Since May 2015, 1040 of these patients with advanced cancer were referred by their oncologists for germline analysis of 76 cancer predisposition genes. Patients with clinically actionable inherited mutations whose genetic test results would not have been predicted by published decision rules were identified. Follow-up for potential clinical implications of mutation detection was through May 2017. Tumor and germline sequencing compared with the predicted yield of targeted germline sequencing based on clinical guidelines. Proportion of clinically actionable germline mutations detected by universal tumor-normal sequencing that would not have been detected by guideline-directed testing. Of 1040 patients, the median age was 58 years (interquartile range, 50.5-66 years), 65.3% were male, and 81.3% had stage IV disease at the time of genomic analysis, with prostate, renal, pancreatic, breast, and colon cancer as the most common diagnoses. Of the 1040 patients, 182 (17.5%; 95% CI, 15.3%-19.9%) had clinically actionable mutations conferring cancer susceptibility, including 149 with moderate- to high-penetrance mutations; 101 patients tested (9.7%; 95% CI, 8.1%-11.7%) would not have had these mutations detected using clinical guidelines, including 65 with moderate- to high-penetrance mutations. Frequency of inherited mutations was related to case mix, stage, and founder mutations. Germline findings led to discussion or initiation of

  12. Commercial serological antibody detection tests for the diagnosis of pulmonary tuberculosis: a systematic review.

    Directory of Open Access Journals (Sweden)

    Karen R Steingart

    2007-06-01

    Full Text Available BACKGROUND: The global tuberculosis epidemic results in nearly 2 million deaths and 9 million new cases of the disease a year. The vast majority of tuberculosis patients live in developing countries, where the diagnosis of tuberculosis relies on the identification of acid-fast bacilli on unprocessed sputum smears using conventional light microscopy. Microscopy has high specificity in tuberculosis-endemic countries, but modest sensitivity which varies among laboratories (range 20% to 80%. Moreover, the sensitivity is poor for paucibacillary disease (e.g., pediatric and HIV-associated tuberculosis. Thus, the development of rapid and accurate new diagnostic tools is imperative. Immune-based tests are potentially suitable for use in low-income countries as some test formats can be performed at the point of care without laboratory equipment. Currently, dozens of distinct commercial antibody detection tests are sold in developing countries. The question is "do they work?" METHODS AND FINDINGS: We conducted a systematic review to assess the accuracy of commercial antibody detection tests for the diagnosis of pulmonary tuberculosis. Studies from all countries using culture and/or microscopy smear for confirmation of pulmonary tuberculosis were eligible. Studies with fewer than 50 participants (25 patients and 25 control participants were excluded. In a comprehensive search, we identified 68 studies. The results demonstrate that (1 overall, commercial tests vary widely in performance; (2 sensitivity is higher in smear-positive than smear-negative samples; (3 in studies of smear-positive patients, Anda-TB IgG by enzyme-linked immunosorbent assay shows limited sensitivity (range 63% to 85% and inconsistent specificity (range 73% to 100%; (4 specificity is higher in healthy volunteers than in patients in whom tuberculosis disease is initially suspected and subsequently ruled out; and (5 there are insufficient data to determine the accuracy of most

  13. Cholesterol Point-of-Care Testing for Community Pharmacies: A Review of the Current Literature.

    Science.gov (United States)

    Haggerty, Lauren; Tran, Deanna

    2017-08-01

    To summarize the literature on cholesterol point-of-care tests (POCTs). This article would serve as a resource to assist community pharmacists in developing cholesterol point-of-care (POC) pharmacy services. A literature search was performed in MEDLINE Ovid, PubMed, EMBASE, and Cochrane database using the following medical subject headings (MeSH) terms: point-of-care test, cholesterol, blood chemical analysis, rapid testing, collaborative practice, community pharmacy, and ambulatory care. Additional resources including device manufacturer web sites were summarized to supplement the current literature. All human research articles, review articles, meta-analyses, and abstracts published in English through September 1, 2014, were considered. A total of 36 articles were applicable for review. Information was divided into the following categories to be summarized: devices, pharmacists' impact, and operational cost for the pharmacy. The current literature suggests that POCTs in community pharmacies assist with patient outcomes by providing screenings and referring patients with dyslipidemia for further evaluation. The majority of studies on cholesterol POC devices focused on accuracy, revealing the need for further studies to develop best practices and practice models with successful reimbursement. Accuracy, device specifications, required supplies, and patient preference should be considered when selecting a POC device for purchase.

  14. Reviews of the In-situ Demonstration Test of the Engineered Barrier System in Many Countries

    International Nuclear Information System (INIS)

    Lee, Minsoo; Choi, Heui Joo

    2013-01-01

    Many nations considering the deep geologic disposal of HLW are now planning or executing in-situ demonstration experiments on their regional EBS (Engineering barrier system) at their deep underground research facilities. The main purpose of the in-situ EBS test is the experimental confirmation of its performance, and the prediction of its long-term evolution through the modeling of EBS based on the experimental data. Additionally, the engineering feasibility for the construction of an engineering barrier system can also be checked through full scale construction of an in-situ test. KAERI is currently preparing an in-situ test at a large 1/3 scale, called IN-DEBS (In-situ Demonstration of EBS) at KURT (KAERI Underground Research Tunnel) for the generic EBS suggested in A-KRS (Advanced KAERI Reference System), which was developed to treat the HLW from pyroprocessing. As the first step for the design of IN-DEBS, the foreign in-situ demonstrations of EBS were reviewed in this paper. The demonstration projects, which were completed or are still being executed in some countries such as Sweden, France, Finland, Canada, Belgium, Switzerland, Spain, and Japan, were surveyed and summarized. In particular, hardware constitutions such as the heating element or compact bentonite, and the experimental procedures, have focused more on reviews than on experimental results in this survey, since their hardware information is very important for the design of the IN-DEBS

  15. Reviews of the In-situ Demonstration Test of the Engineered Barrier System in Many Countries

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Minsoo; Choi, Heui Joo [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2013-10-15

    Many nations considering the deep geologic disposal of HLW are now planning or executing in-situ demonstration experiments on their regional EBS (Engineering barrier system) at their deep underground research facilities. The main purpose of the in-situ EBS test is the experimental confirmation of its performance, and the prediction of its long-term evolution through the modeling of EBS based on the experimental data. Additionally, the engineering feasibility for the construction of an engineering barrier system can also be checked through full scale construction of an in-situ test. KAERI is currently preparing an in-situ test at a large 1/3 scale, called IN-DEBS (In-situ Demonstration of EBS) at KURT (KAERI Underground Research Tunnel) for the generic EBS suggested in A-KRS (Advanced KAERI Reference System), which was developed to treat the HLW from pyroprocessing. As the first step for the design of IN-DEBS, the foreign in-situ demonstrations of EBS were reviewed in this paper. The demonstration projects, which were completed or are still being executed in some countries such as Sweden, France, Finland, Canada, Belgium, Switzerland, Spain, and Japan, were surveyed and summarized. In particular, hardware constitutions such as the heating element or compact bentonite, and the experimental procedures, have focused more on reviews than on experimental results in this survey, since their hardware information is very important for the design of the IN-DEBS.

  16. Clinical outcomes following inpatient penicillin allergy testing: A systematic review and meta-analysis.

    Science.gov (United States)

    Sacco, K A; Bates, A; Brigham, T J; Imam, J S; Burton, M C

    2017-09-01

    A documented penicillin allergy is associated with increased morbidity including length of hospital stay and an increased incidence of resistant infections attributed to use of broader-spectrum antibiotics. The aim of the systematic review was to identify whether inpatient penicillin allergy testing affected clinical outcomes during hospitalization. We performed an electronic search of Ovid MEDLINE/PubMed, Embase, Web of Science, Scopus, and the Cochrane Library over the past 20 years. Inpatients having a documented penicillin allergy that underwent penicillin allergy testing were included. Twenty-four studies met eligibility criteria. Study sample size was between 24 and 252 patients in exclusively inpatient cohorts. Penicillin skin testing (PST) with or without oral amoxicillin challenge was the main intervention described (18 studies). The population-weighted mean for a negative PST was 95.1% [CI 93.8-96.1]. Inpatient penicillin allergy testing led to a change in antibiotic selection that was greater in the intensive care unit (77.97% [CI 72.0-83.1] vs 54.73% [CI 51.2-58.2], Pallergy testing was associated with decreased healthcare cost in four studies. Inpatient penicillin allergy testing is safe and effective in ruling out penicillin allergy. The rate of negative tests is comparable to outpatient and perioperative data. Patients with a documented penicillin allergy who require penicillin should be tested during hospitalization given its benefit for individual patient outcomes and antibiotic stewardship. © 2017 EAACI and John Wiley and Sons A/S. Published by John Wiley and Sons Ltd.

  17. Non-invasive prenatal testing: a review of international implementation and challenges

    Directory of Open Access Journals (Sweden)

    Allyse M

    2015-01-01

    Full Text Available Megan Allyse,1 Mollie A Minear,2 Elisa Berson,3 Shilpa Sridhar,3 Margaret Rote,3 Anthony Hung,3 Subhashini Chandrasekharan4 1Institute for Health and Aging, University of California San Francisco, San Francisco, California, USA, 2Duke Science & Society, Duke University, Durham, NC, USA, 3Trinity College of Arts and Sciences, Duke University, Durham, NC, USA; 4Duke Global Health Institute, Duke University, Durham, NC, USA Abstract: Noninvasive prenatal genetic testing (NIPT is an advance in the detection of fetal chromosomal aneuploidies that analyzes cell-free fetal DNA in the blood of a pregnant woman. Since its introduction to clinical practice in Hong Kong in 2011, NIPT has quickly spread across the globe. While many professional societies currently recommend that NIPT be used as a screening method, not a diagnostic test, its high sensitivity (true positive rate and specificity (true negative rate make it an attractive alternative to the serum screens and invasive tests currently in use. Professional societies also recommend that NIPT be accompanied by genetic counseling so that families can make informed reproductive choices. If NIPT becomes more widely adopted, States will have to implement regulation and oversight to ensure it fits into existing legal frameworks, with particular attention to returning fetal sex information in areas where sex-based abortions are prevalent. Although there are additional challenges for NIPT uptake in the developing world, including the lack of health care professionals and infrastructure, the use of NIPT in low-resource settings could potentially reduce the need for skilled clinicians who perform invasive testing. Future advances in NIPT technology promise to expand the range of conditions that can be detected, including single gene disorders. With these advances come questions of how to handle incidental findings and variants of unknown significance. Moving forward, it is essential that all stakeholders have

  18. A systematic review of tests for lymph node status in primary endometrial cancer.

    Science.gov (United States)

    Selman, Tara J; Mann, Christopher H; Zamora, Javier; Khan, Khalid S

    2008-05-05

    The lymph node status of a patient is a key determinate in staging, prognosis and adjuvant treatment of endometrial cancer. Despite this, the potential additional morbidity associated with lymphadenectomy makes its role controversial. This study systematically reviews the accuracy literature on sentinel node biopsy; ultra sound scanning, magnetic resonance imaging (MRI) and computer tomography (CT) for determining lymph node status in endometrial cancer. Relevant articles were identified form MEDLINE (1966-2006), EMBASE (1980-2006), MEDION, the Cochrane library, hand searching of reference lists from primary articles and reviews, conference abstracts and contact with experts in the field. The review included 18 relevant primary studies (693 women). Data was extracted for study characteristics and quality. Bivariate random-effect model meta-analysis was used to estimate diagnostic accuracy of the various index tests. MRI (pooled positive LR 26.7, 95% CI 10.6 - 67.6 and negative LR 0.29 95% CI 0.17 - 0.49) and successful sentinel node biopsy (pooled positive LR 18.9 95% CI 6.7 - 53.2 and negative LR 0.22, 95% CI 0.1 - 0.48) were the most accurate tests. CT was not as accurate a test (pooled positive LR 3.8, 95% CI 2.0 - 7.3 and negative LR of 0.62, 95% CI 0.45 - 0.86. There was only one study that reported the use of ultrasound scanning. MRI and sentinel node biopsy have shown similar diagnostic accuracy in confirming lymph node status among women with primary endometrial cancer than CT scanning, although the comparisons made are indirect and hence subject to bias. MRI should be used in preference, in light of the ASTEC trial, because of its non invasive nature.

  19. A systematic review of tests for lymph node status in primary endometrial cancer

    Directory of Open Access Journals (Sweden)

    Zamora Javier

    2008-05-01

    Full Text Available Abstract Background The lymph node status of a patient is a key determinate in staging, prognosis and adjuvant treatment of endometrial cancer. Despite this, the potential additional morbidity associated with lymphadenectomy makes its role controversial. This study systematically reviews the accuracy literature on sentinel node biopsy; ultra sound scanning, magnetic resonance imaging (MRI and computer tomography (CT for determining lymph node status in endometrial cancer. Methods Relevant articles were identified form MEDLINE (1966–2006, EMBASE (1980–2006, MEDION, the Cochrane library, hand searching of reference lists from primary articles and reviews, conference abstracts and contact with experts in the field. The review included 18 relevant primary studies (693 women. Data was extracted for study characteristics and quality. Bivariate random-effect model meta-analysis was used to estimate diagnostic accuracy of the various index tests. Results MRI (pooled positive LR 26.7, 95% CI 10.6 – 67.6 and negative LR 0.29 95% CI 0.17 – 0.49 and successful sentinel node biopsy (pooled positive LR 18.9 95% CI 6.7 – 53.2 and negative LR 0.22, 95% CI 0.1 – 0.48 were the most accurate tests. CT was not as accurate a test (pooled positive LR 3.8, 95% CI 2.0 – 7.3 and negative LR of 0.62, 95% CI 0.45 – 0.86. There was only one study that reported the use of ultrasound scanning. Conclusion MRI and sentinel node biopsy have shown similar diagnostic accuracy in confirming lymph node status among women with primary endometrial cancer than CT scanning, although the comparisons made are indirect and hence subject to bias. MRI should be used in preference, in light of the ASTEC trial, because of its non invasive nature.

  20. [Contributions of cortisol suppression tests to understanding of psychiatric disorders: a narrative review of literature].

    Science.gov (United States)

    Tajima-Pozo, Kazuhiro; Montes-Montero, Ana; Güemes, Itziar; González-Vives, Sara; Díaz-Marsá, Marina; Carrasco, José Luis

    2013-01-01

    Activity of the hypothalamic-pituitary-adrenal axis had been studied for the past half century, when some researchers noted that some patients with Cushing's syndrome and severe mood disorders had high baseline cortisol levels, which resulted in an inhibited response in the 1mg dexamethasone suppression test. Altered dexamethasone suppression test results were subsequently found in many psychiatric diseases, including anorexia nervosa, obsessive-compulsive disorder, degenerative dementia, bipolar disorders, and schizophrenia. The relationship between high baseline cortisol levels and stress has also been studied. Some researches on the genesis of borderline personality disorder focused on traumatic childhood backgrounds. Other investigations aimed at elucidating the relationship between traumatic backgrounds and some psychiatric disorders noted that patients with post-traumatic stress disorder and borderline personality disorder showed an enhanced cortisol suppression with low cortisol doses (0.5 mg). Recent studies showed that use of an ultra-low dose of cortisol during the dexamethasone suppression test may be helpful for detecting disorders with hyperactivity of the hypothalamic-pituitary-adrenal axis. Recent advances in neuroimaging support the existence of hyperactivity of the hypothalamic-pituitary-adrenal axis in patients with borderline personality disorder, relating a decreased pituitary gland volume to major traumatic backgrounds and suicidal attempts. The purpose of this paper is to make a narrative review of research using dexamethasone suppression test in psychiatric disorders, in order to ascertain its value as a supplemental diagnostic test or as a prognostic marker. Copyright © 2012 SEEN. Published by Elsevier Espana. All rights reserved.

  1. Bovine paratuberculosis: a review of the advantages and disadvantages of different diagnostic tests.

    Science.gov (United States)

    Gilardoni, Liliana R; Paolicchi, Fernando A; Mundo, Silvia L

    2012-01-01

    Paratuberculosis (PTB), or Johne's disease, is a chronic infectious granulomatous enteritis of ruminants, caused by Mycobacterium avium subspecies paratuberculosis (Map). It is characterized by diarrhea and progressive cachexia, which may cause the death of the animal. Calves are the most susceptible to infection. Infected animals excrete Map mainly by the feces. PTB is endemic worldwide, with high prevalence levels, strong economic impact and public health relevance because of its possible association with Crohn's disease. Although the current reference diagnostic test is identification of Map in the bacterial culture, there are different diagnostic tests to identify infected individuals and/or herds. The sensitivity and specificity of these tests vary according to the stage of the disease in the animals to be evaluated. The correct choice and application of each of these diagnostic tests will ensure their success and may allow to establish a control program. The aim of this work is to review and discuss the different diagnostic tests used in the detection of Map-infected animals, focusing on their advantages and disadvantages.

  2. State-of-the-art review of nondestructive testing with computer-assisted tomography

    International Nuclear Information System (INIS)

    Bansal, A; Islam, M.R.

    1991-01-01

    Computer assisted tomography (CAT) has been a revolutionary technique in medical radiology. Recently, CAT scanners started to be used as non-destructive testing facilities in different industrial applications. Most of the application of the new technology are in the areas of petroleum engineering. Majority of this CAT scanner technology has been developed in the U.S.A. However, several Canadian companies have acquired CAT scanners and are using for novel commercial as well as research applications. This paper presents a comprehensive review of advances made in the areas of CAT scan technology as applied to the petroleum industry

  3. 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

  4. Internet-Based Direct-to-Consumer Genetic Testing: A Systematic Review.

    Science.gov (United States)

    Covolo, Loredana; Rubinelli, Sara; Ceretti, Elisabetta; Gelatti, Umberto

    2015-12-14

    Direct-to-consumer genetic tests (DTC-GT) are easily purchased through the Internet, independent of a physician referral or approval for testing, allowing the retrieval of genetic information outside the clinical context. There is a broad debate about the testing validity, their impact on individuals, and what people know and perceive about them. The aim of this review was to collect evidence on DTC-GT from a comprehensive perspective that unravels the complexity of the phenomenon. A systematic search was carried out through PubMed, Web of Knowledge, and Embase, in addition to Google Scholar according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) checklist with the key term "Direct-to-consumer genetic test." In the final sample, 118 articles were identified. Articles were summarized in five categories according to their focus on (1) knowledge of, attitude toward use of, and perception of DTC-GT (n=37), (2) the impact of genetic risk information on users (n=37), (3) the opinion of health professionals (n=20), (4) the content of websites selling DTC-GT (n=16), and (5) the scientific evidence and clinical utility of the tests (n=14). Most of the articles analyzed the attitude, knowledge, and perception of DTC-GT, highlighting an interest in using DTC-GT, along with the need for a health care professional to help interpret the results. The articles investigating the content analysis of the websites selling these tests are in agreement that the information provided by the companies about genetic testing is not completely comprehensive for the consumer. Given that risk information can modify consumers' health behavior, there are surprisingly few studies carried out on actual consumers and they do not confirm the overall concerns on the possible impact of DTC-GT. Data from studies that investigate the quality of the tests offered confirm that they are not informative, have little predictive power, and do not measure genetic risk

  5. Internet-Based Direct-to-Consumer Genetic Testing: A Systematic Review

    Science.gov (United States)

    Rubinelli, Sara; Ceretti, Elisabetta; Gelatti, Umberto

    2015-01-01

    Background Direct-to-consumer genetic tests (DTC-GT) are easily purchased through the Internet, independent of a physician referral or approval for testing, allowing the retrieval of genetic information outside the clinical context. There is a broad debate about the testing validity, their impact on individuals, and what people know and perceive about them. Objective The aim of this review was to collect evidence on DTC-GT from a comprehensive perspective that unravels the complexity of the phenomenon. Methods A systematic search was carried out through PubMed, Web of Knowledge, and Embase, in addition to Google Scholar according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) checklist with the key term “Direct-to-consumer genetic test.” Results In the final sample, 118 articles were identified. Articles were summarized in five categories according to their focus on (1) knowledge of, attitude toward use of, and perception of DTC-GT (n=37), (2) the impact of genetic risk information on users (n=37), (3) the opinion of health professionals (n=20), (4) the content of websites selling DTC-GT (n=16), and (5) the scientific evidence and clinical utility of the tests (n=14). Most of the articles analyzed the attitude, knowledge, and perception of DTC-GT, highlighting an interest in using DTC-GT, along with the need for a health care professional to help interpret the results. The articles investigating the content analysis of the websites selling these tests are in agreement that the information provided by the companies about genetic testing is not completely comprehensive for the consumer. Given that risk information can modify consumers’ health behavior, there are surprisingly few studies carried out on actual consumers and they do not confirm the overall concerns on the possible impact of DTC-GT. Data from studies that investigate the quality of the tests offered confirm that they are not informative, have little predictive

  6. Antimicrobial susceptibility determined by the E test, Löwenstein-Jensen proportion, and DNA sequencing methods among Mycobacterium tuberculosis isolates discrepancies, preliminary results

    Directory of Open Access Journals (Sweden)

    Maria Inês Moura Freixo

    2004-02-01

    Full Text Available Mycobacterium tuberculosis strains resistant to streptomycin (SM, isoniazid (INH, and/or rifampin (RIF as determined by the conventional Löwenstein-Jensen proportion method (LJPM were compared with the E test, a minimum inhibitory concentration susceptibility method. Discrepant isolates were further evaluated by BACTEC and by DNA sequence analyses for mutations in genes most often associated with resistance to these drugs (rpsL, katG, inhA, and rpoB. Preliminary discordant E test results were seen in 75% of isolates resistant to SM and in 11% to INH. Discordance improved for these two drugs (63% for SM and none for INH when isolates were re-tested but worsened for RIF (30%. Despite good agreement between phenotypic results and sequencing analyses, wild type profiles were detected on resistant strains mainly for SM and INH. It should be aware that susceptible isolates according to molecular methods might contain other mechanisms of resistance. Although reproducibility of the LJPM susceptibility method has been established, variable E test results for some M. tuberculosis isolates poses questions regarding its reproducibility particularly the impact of E test performance which may vary among laboratories despite adherence to recommended protocols. Further studies must be done to enlarge the evaluated samples and looked possible mutations outside of the hot spot sequenced gene among discrepant strains.

  7. Which physical examination tests provide clinicians with the most value when examining the shoulder? Update of a systematic review with meta-analysis of individual tests.

    Science.gov (United States)

    Hegedus, Eric J; Goode, Adam P; Cook, Chad E; Michener, Lori; Myer, Cortney A; Myer, Daniel M; Wright, Alexis A

    2012-11-01

    To update our previously published systematic review and meta-analysis by subjecting the literature on shoulder physical examination (ShPE) to careful analysis in order to determine each tests clinical utility. This review is an update of previous work, therefore the terms in the Medline and CINAHL search strategies remained the same with the exception that the search was confined to the dates November, 2006 through to February, 2012. The previous study dates were 1966 - October, 2006. Further, the original search was expanded, without date restrictions, to include two new databases: EMBASE and the Cochrane Library. The Quality Assessment of Diagnostic Accuracy Studies, version 2 (QUADAS 2) tool was used to critique the quality of each new paper. Where appropriate, data from the prior review and this review were combined to perform meta-analysis using the updated hierarchical summary receiver operating characteristic and bivariate models. Since the publication of the 2008 review, 32 additional studies were identified and critiqued. For subacromial impingement, the meta-analysis revealed that the pooled sensitivity and specificity for the Neer test was 72% and 60%, respectively, for the Hawkins-Kennedy test was 79% and 59%, respectively, and for the painful arc was 53% and 76%, respectively. Also from the meta-analysis, regarding superior labral anterior to posterior (SLAP) tears, the test with the best sensitivity (52%) was the relocation test; the test with the best specificity (95%) was Yergason's test; and the test with the best positive likelihood ratio (2.81) was the compression-rotation test. Regarding new (to this series of reviews) ShPE tests, where meta-analysis was not possible because of lack of sufficient studies or heterogeneity between studies, there are some individual tests that warrant further investigation. A highly specific test (specificity >80%, LR+ ≥ 5.0) from a low bias study is the passive distraction test for a SLAP lesion. This test may

  8. A review of statistical methods for testing genetic anticipation: looking for an answer in Lynch syndrome

    DEFF Research Database (Denmark)

    Boonstra, Philip S; Gruber, Stephen B; Raymond, Victoria M

    2010-01-01

    Anticipation, manifested through decreasing age of onset or increased severity in successive generations, has been noted in several genetic diseases. Statistical methods for genetic anticipation range from a simple use of the paired t-test for age of onset restricted to affected parent-child pairs......, and this right truncation effect is more pronounced in children than in parents. In this study, we first review different statistical methods for testing genetic anticipation in affected parent-child pairs that address the issue of bias due to right truncation. Using affected parent-child pair data, we compare...... the issue of multiplex ascertainment and its effect on the different methods. We then focus on exploring genetic anticipation in Lynch syndrome and analyze new data on the age of onset in affected parent-child pairs from families seen at the University of Michigan Cancer Genetics clinic with a mutation...

  9. Polymorphism of κ-Casein in Italian Goat Breeds: A New ACRS-PCR Designed DNA Test for Discrimination of A and B Alleles

    Directory of Open Access Journals (Sweden)

    Vlatka Cubric-Curik

    2002-01-01

    Full Text Available The objective of this study was to develop a DNA test for rapid characterisation of goat κ-casein (κ-CN A and B variants and to study this polymorphism in Italian goat breeds. Genetic polymorphism of κ-CN gene was, in addition to isoelectric focusing, analysed according to a new technique designated as amplification created restriction site. Two alleles that differ in one nucleotide mutation (G Ø A in exon 4 were characterised. The 167-bp PCR product surrounding the nucleotide mutation was amplified from genomic DNA and the PCR product was digested with MaeIII. After digestion the A allele gives three fragments of 77, 65 and 25 bp in comparison with the B allele which gives two fragments of 90 and 77 bp. The analysis of allele frequency distribution at κ-CN locus, based on 401 individual samples, revealed significant differences among three goat breeds from the north of Italy (Nera di Verzasca, Frontalasca and Alpine with frequency of κ-CN B allele around 0.3, versus two goat breeds from the south of Italy (Maltese and Sarda with frequency of κ-CN B allele around 0.5. While two goat breeds (Maltese and Nera di Verzasca did not show significant deviations from the Hardy-Weinberg equilibrium, a highly significant excess of heterozygote genotype (AB was observed in Alpine, Frontalasca and Sarda goats. Here the developed DNA method and observed relatively high frequency of κ-CN B allele give a prerequisite for the assessment of research related to the simultaneous estimation of the effects of composite αs1/κ-CN genotypes on milk production and cheese-making properties.

  10. Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass--Sequence Relationships with an Innovative Metabarcoding Protocol.

    Directory of Open Access Journals (Sweden)

    Vasco Elbrecht

    Full Text Available Metabarcoding is an emerging genetic tool to rapidly assess biodiversity in ecosystems. It involves high-throughput sequencing of a standard gene from an environmental sample and comparison to a reference database. However, no consensus has emerged regarding laboratory pipelines to screen species diversity and infer species abundances from environmental samples. In particular, the effect of primer bias and the detection limit for specimens with a low biomass has not been systematically examined, when processing samples in bulk. We developed and tested a DNA metabarcoding protocol that utilises the standard cytochrome c oxidase subunit I (COI barcoding fragment to detect freshwater macroinvertebrate taxa. DNA was extracted in bulk, amplified in a single PCR step, and purified, and the libraries were directly sequenced in two independent MiSeq runs (300-bp paired-end reads. Specifically, we assessed the influence of specimen biomass on sequence read abundance by sequencing 31 specimens of a stonefly species with known haplotypes spanning three orders of magnitude in biomass (experiment I. Then, we tested the recovery of 52 different freshwater invertebrate taxa of similar biomass using the same standard barcoding primers (experiment II. Each experiment was replicated ten times to maximise statistical power. The results of both experiments were consistent across replicates. We found a distinct positive correlation between species biomass and resulting numbers of MiSeq reads. Furthermore, we reliably recovered 83% of the 52 taxa used to test primer bias. However, sequence abundance varied by four orders of magnitudes between taxa despite the use of similar amounts of biomass. Our metabarcoding approach yielded reliable results for high-throughput assessments. However, the results indicated that primer efficiency is highly species-specific, which would prevent straightforward assessments of species abundance and biomass in a sample. Thus, PCR

  11. Annual banned-substance review: analytical approaches in human sports drug testing.

    Science.gov (United States)

    Thevis, Mario; Kuuranne, Tiia; Walpurgis, Katja; Geyer, Hans; Schänzer, Wilhelm

    2016-01-01

    The aim of improving anti-doping efforts is predicated on several different pillars, including, amongst others, optimized analytical methods. These commonly result from exploiting most recent developments in analytical instrumentation as well as research data on elite athletes' physiology in general, and pharmacology, metabolism, elimination, and downstream effects of prohibited substances and methods of doping, in particular. The need for frequent and adequate adaptations of sports drug testing procedures has been incessant, largely due to the uninterrupted emergence of new chemical entities but also due to the apparent use of established or even obsolete drugs for reasons other than therapeutic means, such as assumed beneficial effects on endurance, strength, and regeneration capacities. Continuing the series of annual banned-substance reviews, literature concerning human sports drug testing published between October 2014 and September 2015 is summarized and reviewed in reference to the content of the 2015 Prohibited List as issued by the World Anti-Doping Agency (WADA), with particular emphasis on analytical approaches and their contribution to enhanced doping controls. Copyright © 2016 John Wiley & Sons, Ltd.

  12. Review of waste package verification tests. Semiannual report, October 1984-March 1985

    International Nuclear Information System (INIS)

    Soo, P.

    1985-07-01

    The potential of WAPPA, a second-generation waste package system code, to meet the needs of the regulatory community is analyzed. The analysis includes an indepth review of WAPPA's individual process models and a review of WAPPA's operation. It is concluded that the code is of limited use to the NRC in the present form. Recommendations for future improvement, usage, and implementation of the code are given. This report also describes the results of a testing program undertaken to determine the chemical environment that will be present near a high-level waste package emplaced in a basalt repository. For this purpose, low carbon 1020 steel (a current BWIP reference container material), synthetic basaltic groundwater and a mixture of bentonite and basalt were exposed, in an autoclave, to expected conditions some period after repository sealing (150 0 C, approx. =10.4 MPa). Parameters measured include changes in gas pressure with time and gas composition, variation in dissolved oxygen (DO), pH and certain ionic concentrations of water in the packing material across an imposed thermal gradient, mineralogic alteration of the basalt/bentonite mixture, and carbon steel corrosion behavior. A second testing program was also initiated to check the likelihood of stress corrosion cracking of austenitic stainless steels and Incoloy 825 which are being considered for use as waste container materials in the tuff repository program. 82 refs., 70 figs., 27 tabs

  13. Comparison of Domestic Safety Review and European Union(EU) Stress Test After Nuclear Accident in Fukushima Daiichi NPPs

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Hwa Sung; Kim, Jin Weon [Chosun University, Gwangju (Korea, Republic of)

    2016-05-15

    The European Union(EU) nuclear regulators group established stress test criteria and procedures, and utilities performed a self-review in accordance with those criteria and procedures. For Wolsung nuclear unit-1,the stress test was additionally conducted for deciding the continued operation of NPP, even though the safety review had been conducted after Fukushima NPP accident. Thus, this study is to compares the process, criteria, and results of the safety review performed in domestic NPPs and EU stress test performed in Cernavoda NPP. From the comparisons, the effectiveness and necessity of the stress test to decide the continued operation of NPPs is discussed. and the improvement items for safety enhancement are derived. The comparison showed that the process and review criteria of EU stress test was more systematic and specific than those used in domestic NPPs. But it was indicated that the improvement items resulted from the safety review performed in domestic NPPs are more comprehensive and powerful than EU stress tests (Cernavoda NPP) results. EU stress test for Cernavoda NPP evaluated in 3 fieldsand derived 13 design change items. The 50 improvement items derived from domestic safety review were including the contents of these 13 items.

  14. Review of inservice inspection and nondestructive examination practices at DOE Category A test and research reactors

    International Nuclear Information System (INIS)

    Anderson, M.T.; Aldrich, D.A.

    1990-09-01

    In-service inspection (ISI) programs are used at commercial nuclear power plants for monitoring the pressure boundary integrity of various systems and components to ensure their continued safe operation. The Department of Energy (DOE) operates several test and research reactors. This report represents an evaluation of the ISI and nondestructive examination (NDE) practices at five DOE Category A (> 20 MW thermal) reactors as compared, where applicable, to the current ISI activities of commercial nuclear power facilities. The purpose of an inservice inspection (ISI) program is to establish regular surveillance of safety-related components to ensure their safe and reliable operation. The integrity of materials comprising these components is generally monitored by means of periodic nondestructive examinations (NDE), which, if appropriately performed, provide methods for identifying degradation that could render components unable to perform their intended safety functions. The reactors evaluated during this review were the Experimental Breeder Reactor 2 and the Fast Flux Test Facility (liquid-metal cooled plants), the Advanced Test Reactor and the High Flux Isotopes Reactor (light-water cooled reactors), and the High Flux Beam Reactor (a heavy-water cooled facility). Although these facilities are extremely diverse in design and operation, they all have less stored energy, smaller inventories of radionuclides, and generally, more remote locations than commercial reactors. However, all DOE test and research facilities contain components similar to those of commercial reactors for which continued integrity is important to maintain plant safety. 10 refs., 6 tabs

  15. Journal: A Review of Some Tracer-Test Design Equations for ...

    Science.gov (United States)

    Determination of necessary tracer mass, initial sample-collection time, and subsequent sample-collection frequency are the three most difficult aspects to estimate for a proposed tracer test prior to conducting the tracer test. To facilitate tracer-mass estimation, 33 mass-estimation equations are reviewed here, 32 of which were evaluated using previously published tracer-test design examination parameters. Comparison of the results produced a wide range of estimated tracer mass, but no means is available by which one equation may be reasonably selected over the others. Each equation produces a simple approximation for tracer mass. Most of the equations are based primarily on estimates or measurements of discharge, transport distance, and suspected transport times. Although the basic field parameters commonly employed are appropriate for estimating tracer mass, the 33 equations are problematic in that they were all probably based on the original developers' experience in a particular field area and not necessarily on measured hydraulic parameters or solute-transport theory. Suggested sampling frequencies are typically based primarily on probable transport distance, but with little regard to expected travel times. This too is problematic in that tends to result in false negatives or data aliasing. Simulations from the recently developed efficient hydrologic tracer-test design methodology (EHTD) were compared with those obtained from 32 of the 33 published tracer-

  16. Patch testing in Israeli children with suspected allergic contact dermatitis: A retrospective study and literature review.

    Science.gov (United States)

    Zafrir, Yaron; Trattner, Akiva; Hodak, Emmillia; Eldar, Oren; Lapidoth, Moshe; Ben Amitai, Dan

    2018-01-01

    Childhood allergic contact dermatitis is recognized as a significant clinical problem. The objective was to evaluate the rate of positive patch tests in Israeli children with clinically suspected allergic contact dermatitis, identify possible sex and age differences, compare results with those in Israeli adults, and review pediatric studies in the literature. The study sample included 343 children and adolescents (197 female, 146 male; 1-18 years of age, mean age 11.8 years) with clinically suspected allergic contact dermatitis who underwent patch testing with a standard pediatric series of 23 allergens at a tertiary medical center from 1999 to 2012. Data on clinical characteristics and test results were collected retrospectively from the medical files. Ninety-eight subjects (28.6%) (75 girls [38.1%], 23 boys [15.8%]) had at least one positive reaction. The most frequent reactions were to nickel sulfate, followed by potassium dichromate and cobalt chloride. Nickel sulfate sensitivity was more common in girls, especially those younger than 3 years and older than 12 years. The prevalence of contact sensitization was similar in subjects with and without atopic dermatitis (50% and 51%, respectively). Nickel is the most common allergen in Israeli children, especially girls. Patch testing should be performed in children with clinically suspected allergic contact dermatitis regardless of atopic background. © 2017 Wiley Periodicals, Inc.

  17. Months backward test: A review of its use in clinical studies.

    Science.gov (United States)

    Meagher, James; Leonard, Maeve; Donoghue, Laura; O'Regan, Niamh; Timmons, Suzanne; Exton, Chris; Cullen, Walter; Dunne, Colum; Adamis, Dimitrios; Maclullich, Alasdair J; Meagher, David

    2015-09-22

    To review the use of the Months Backwards Test (MBT) in clinical and research contexts. We conducted a systematic review of reports relating to the MBT based upon a search of PsychINFO and MEDLINE between January 1980 and December 2014. Only reports that specifically described findings pertaining to the MBT were included. Findings were considered in terms of rating procedures, testing performance, psychometric properties, neuropsychological studies and use in clinical populations. We identified 22 data reports. The MBT is administered and rated in a variety of ways with very little consistency across studies. It has been used to assess various cognitive functions including focused and sustained attention as well as central processing speed. Performance can be assessed in terms of the ability to accurately complete the test without errors ("MB accuracy"), and time taken to complete the test ("MB duration"). Completion time in cognitively intact subjects is usually upper limits of 60-90 s typically applied in studies. The majority of cognitively intact adults can complete the test without error such that any errors of omission are strongly suggestive of cognitive dysfunction. Coverage of clinical populations, including those with significant cognitive difficulties is high with the majority of subjects able to engage with MBT procedures. Performance correlates highly with other cognitive tests, especially of attention, including the digit span backwards, trailmaking test B, serial threes and sevens, tests of simple and complex choice reaction time, delayed story recall and standardized list learning measures. Test-retest and inter-rater reliability are high (both > 0.90). Functional magnetic resonance imaging studies comparing the months forward test and MBT indicate greater involvement of more complex networks (bilateral middle and inferior frontal gyri, the posterior parietal cortex and the left anterior cingulate gyrus) for backwards cognitive processing. The MBT

  18. Study of HIV-1 subtypes in serodiscordant couples attending an integrated counselling and testing centre in Mumbai using heteroduplex mobility analysis and DNA sequencing

    Directory of Open Access Journals (Sweden)

    Mehta P

    2010-01-01

    Full Text Available Aims: To determine the prevalent subtypes of HIV-1 in serodiscordant couples. Setting: Integrated Counselling and Testing Centre (ICTC, Department of Microbiology. Study Design: Prospective pilot study. Participants: Thirty HIV-1 serodiscordant couples. Inclusion Criteria: a Documentation of HIV-1 infection in one partner and seronegative status in the other, current history of continued unprotected sexual activity within the partnership, demonstration that they have been in a partnership for at least 1 year and are not currently on highly active antiretroviral therapy HAART; b willingness of both partners to provide written informed consent including consent to continued couple counselling for 3 months. Materials and Methods: HIV-1 subtyping was carried out by heteroduplex mobility analysis (HMA by amplifying env region; and DNA sequencing by amplifying gag region. Results: HIV-1 env gene was amplified successfully in 10/30 samples; gag gene, in 25/30 samples; and both env and gag gene were amplified successfully in 5/30 samples. HIV-1 subtype C was detected from 21 samples; subtype B, from 7; and subtype A, from 2. Sample from 1 positive partner was detected as subtype C by env HMA and subtype B by gag sequencing. Conclusion: HIV-1 subtype C was found to be the predominant subtype of HIV-1 in serodiscordant couples attending our ICTC, followed by HIV-1 subtype B and HIV-1 subtype A, respectively. DNA sequencing was found to be the most reliable method for determining the subtypes of HIV-1.

  19. Circulating Tumor Cells Versus Circulating Tumor DNA in Colorectal Cancer: Pros and Cons.

    Science.gov (United States)

    Tan, Carlyn Rose C; Zhou, Lanlan; El-Deiry, Wafik S

    2016-06-01

    Circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) are emerging noninvasive multifunctional biomarkers in liquid biopsy allowing for early diagnosis, accurate prognosis, therapeutic target selection, spatiotemporal monitoring of metastasis, as well as monitoring response and resistance to treatment. CTCs and ctDNA are released from different tumor types at different stages and contribute complementary information for clinical decision. Although big strides have been taken in technology development for detection, isolation and characterization of CTCs and sensitive and specific detection of ctDNA, CTC-, and ctDNA-based liquid biopsies may not be widely adopted for routine cancer patient care until the suitability, accuracy, and reliability of these tests are validated and more standardized protocols are corroborated in large, independent, prospectively designed trials. This review covers CTC- and ctDNA-related technologies and their application in colorectal cancer. The promise of CTC-and ctDNA-based liquid biopsies is envisioned.

  20. Rapid antigen group A streptococcus test to diagnose pharyngitis: a systematic review and meta-analysis.

    Directory of Open Access Journals (Sweden)

    Emily H Stewart

    Full Text Available BACKGROUND: Pharyngitis management guidelines include estimates of the test characteristics of rapid antigen streptococcus tests (RAST using a non-systematic approach. OBJECTIVE: To examine the sensitivity and specificity, and sources of variability, of RAST for diagnosing group A streptococcal (GAS pharyngitis. DATA SOURCES: MEDLINE, Cochrane Reviews, Centre for Reviews and Dissemination, Scopus, SciELO, CINAHL, guidelines, 2000-2012. STUDY SELECTION: Culture as reference standard, all languages. DATA EXTRACTION AND SYNTHESIS: Study characteristics, quality. MAIN OUTCOME(S AND MEASURE(S: Sensitivity, specificity. RESULTS: We included 59 studies encompassing 55,766 patients. Forty three studies (18,464 patients fulfilled the higher quality definition (at least 50 patients, prospective data collection, and no significant biases and 16 (35,634 patients did not. For the higher quality immunochromatographic methods in children (10,325 patients, heterogeneity was high for sensitivity (inconsistency [I(2] 88% and specificity (I(2 86%. For enzyme immunoassay in children (342 patients, the pooled sensitivity was 86% (95% CI, 79-92% and the pooled specificity was 92% (95% CI, 88-95%. For the higher quality immunochromatographic methods in the adult population (1,216 patients, the pooled sensitivity was 91% (95% CI, 87 to 94% and the pooled specificity was 93% (95% CI, 92 to 95%; however, heterogeneity was modest for sensitivity (I(2 61% and specificity (I(2 72%. For enzyme immunoassay in the adult population (333 patients, the pooled sensitivity was 86% (95% CI, 81-91% and the pooled specificity was 97% (95% CI, 96 to 99%; however, heterogeneity was high for sensitivity and specificity (both, I(2 88%. CONCLUSIONS: RAST immunochromatographic methods appear to be very sensitive and highly specific to diagnose group A streptococcal pharyngitis among adults but not in children. We could not identify sources of variability among higher quality studies. The

  1. Conectando famílias de construções genéticas: testes de DNA na reunificação da família somali na Finlândia Connecting genes-building families: DNA testing in somali family reunification in Finland

    Directory of Open Access Journals (Sweden)

    Petri Hautaniemi

    2007-12-01

    Full Text Available Os temas centrais desse artigo, reunificação familiar em geral e teste de DNA em particular, surgiram a partir de uma pesquisa em andamento acerca de jovens da Somália na Finlândia. Desde 1996, realizo uma pesquisa etnográfica - em escolas, clubes de jovens, ruas e cafés - com jovens da Somália que chegaram à Finlândia por volta de 1994 e que freqüentam escolas finlandesas nos subúrbios de Helsinki. Meu interesse geral nesta pesquisa longitudinal era conhecer as experiências de passagem para a vida adulta em contextos altamente diferenciados, não apenas do ponto de vista do país anfitrião, mas também cultural e transnacionalmente. O tema, testes de DNA, toca na questão central desta pesquisa de modo profundo. Aqui, crescer não é visto como uma simples questão biológica. É um processo social no qual as relações, como laços de parentesco, são constituídas, vivenciadas e contestadas. Essas relações são poderosas para a identificação individual e social. A testagem-DNA pode violar simbólica e fisicamente o processo social de identificações íntimas e de integridade pessoal.The central themes of this article, family reunification in general, and DNA testing in particular, came to the fore during a research project about young Somalians in Finland. Since 1996, I have been conducting ethnographic research - in schools, youth clubs, streets and cafés - with youngsters from Somalia who arrived in Finland around 1994, and who attend Finnish schools in the suburbs of Helsinki. My general interest in this longitudinal study was to learn about the experiences of coming of age in highly dispersed settings, not only in the vein of a local host country, but also culturally and transnationally. Here, growing up is seen not as a simple biological question. It is a social process in which relationships such as kinship ties are constituted, experienced, and contested. These are powerful relations for individual and social

  2. Empirical tests of natural selection-based evolutionary accounts of ADHD: a systematic review.

    Science.gov (United States)

    Thagaard, Marthe S; Faraone, Stephen V; Sonuga-Barke, Edmund J; Østergaard, Søren D

    2016-10-01

    ADHD is a prevalent and highly heritable mental disorder associated with significant impairment, morbidity and increased rates of mortality. This combination of high prevalence and high morbidity/mortality seen in ADHD and other mental disorders presents a challenge to natural selection-based models of human evolution. Several hypotheses have been proposed in an attempt to resolve this apparent paradox. The aim of this study was to review the evidence for these hypotheses. We conducted a systematic review of the literature on empirical investigations of natural selection-based evolutionary accounts for ADHD in adherence with the PRISMA guideline. The PubMed, Embase, and PsycINFO databases were screened for relevant publications, by combining search terms covering evolution/selection with search terms covering ADHD. The search identified 790 records. Of these, 15 full-text articles were assessed for eligibility, and three were included in the review. Two of these reported on the evolution of the seven-repeat allele of the ADHD-associated dopamine receptor D4 gene, and one reported on the results of a simulation study of the effect of suggested ADHD-traits on group survival. The authors of the three studies interpreted their findings as favouring the notion that ADHD-traits may have been associated with increased fitness during human evolution. However, we argue that none of the three studies really tap into the core symptoms of ADHD, and that their conclusions therefore lack validity for the disorder. This review indicates that the natural selection-based accounts of ADHD have not been subjected to empirical test and therefore remain hypothetical.

  3. A retrospective review of outcome and survival following surgery and adjuvant xenogeneic DNA vaccination in 32 dogs with oral malignant melanoma.

    Science.gov (United States)

    Treggiari, Elisabetta; Grant, Jessica Pauline; North, Susan Margaret

    2016-06-01

    A xenogeneic DNA vaccination has been licensed for use in dogs with locally controlled stage II and III oral malignant melanoma (OMM). At present, there are limited outcome data for dogs with OMM treated with surgery and immunotherapy. The aim of this study is to retrospectively review the outcome and survival of 32 dogs affected by OMM that were treated with a combination of surgery and the xenogeneic DNA vaccination (with the addition of radiotherapy in some cases) and to determine the influence of surgical margins and delay in receiving vaccination. The overall median survival time (MST) was 335 days (95% CI: 301-540 days), and the overall median progression-free survival (PFS) was 160 days (mean 182 days, 95% CI: 132-232 days). Stage, completeness of surgical margins and delay in administration of the vaccine did not appear to statistically influence survival or PFS, although these results may reflect the low statistical power of the study due to small numbers. Further studies are required to assess whether the addition of any adjuvant treatment to surgery, including immunotherapy, is able to significantly prolong survival in cases of canine oral melanoma.

  4. Close encounters with DNA.

    Science.gov (United States)

    Maffeo, C; Yoo, J; Comer, J; Wells, D B; Luan, B; Aksimentiev, A

    2014-10-15

    Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena. We also discuss the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field.

  5. Comprehensive analysis of sperm DNA fragmentation by five different assays: TUNEL assay, SCSA, SCD test and alkaline and neutral Comet assay.

    Science.gov (United States)

    Ribas-Maynou, J; García-Peiró, A; Fernández-Encinas, A; Abad, C; Amengual, M J; Prada, E; Navarro, J; Benet, J

    2013-09-01

    Sperm DNA fragmentation (SDF) is becoming an important test to assess male infertility. Several different tests are available, but no consensus has yet been reached as to which tests are most predictive of infertility. Few publications have reported a comprehensive analysis comparing these methods within the same population. The objective of this study was to analyze the differences between the five most common methodologies, to study their correlations and to establish their cut-off values, sensitivity and specificity in predicting male infertility. We found differences in SDF between fertile donors and infertile patients in TUNEL, SCSA, SCD and alkaline Comet assays, but none with the neutral Comet assay. The alkaline COMET assay was the best in predicting male infertility followed by TUNEL, SCD and SCSA, whereas the neutral COMET assay had no predictive power. For our patient population, threshold values for infertility were 20.05% for TUNEL assay, 18.90% for SCSA, 22.75% for the SCD test, 45.37% for alkaline Comet and 34.37% for neutral Comet. This work establishes in a comprehensive study that the all techniques except neutral Comet are useful to distinguish fertile and infertile men. © 2013 American Society of Andrology and European Academy of Andrology.

  6. NRC review of passive reactor design certification testing programs: Overview and regulatory perspective

    International Nuclear Information System (INIS)

    Levin, A.E.

    1993-01-01

    Reactor vendors are developing new designs for future deployment, including open-quotes passiveclose quotes light water reactors (LWRs), such as General Electric's (G.E.'s) simplified boiling water reactor (SBWR) and Westinghouse's AP600, which depend primarily on inherent processes, such as national convection and gravity feed, for safety injection and emergency core cooling. The U.S. Nuclear Regulatory Commission (NRC) has implemented a new process, certification of standardized reactor designs, for licensing these Plants. Part 52 of Title 10 of the Code of Federal Regulations (10CFR52) contains the requirements that vendors must meet for design certification. One important section, 10CFR52.47, reads open-quotes Certification of a standard design which . . . utilizes simplified, inherent, passive, or other innovative means to accomplish its safety functions will be granted only if: (1) The performance of each safety feature of the design has been demonstrated through either analysis, appropriate test programs, experience, or a combination thereof; (2) Interdependent effects among the safety features have been found acceptable by analysis, appropriate test programs, experience, or a combination thereof; and (3) Sufficient data exist on the safety features of the design to assess the analytical tools used for safety analyses. . . . The vendors have initiated programs to test innovative features of their designs and to develop data bases needed to validate their analytical codes, as required by the design certification rule. Accordingly, the NRC is reviewing and evaluating the vendors programs to ensure that they address adequately key issues concerning safety system performance. This paper provides an overview of the NRC's review process and regulatory perspective

  7. HCV Core Antigen Testing for Diagnosis of HCV Infection: A systematic review and meta-analysis

    Science.gov (United States)

    Freiman, J. Morgan; Tran, Trang M.; Schumacher, Samuel G; White, Laura F.; Ongarello, Stefano; Cohn, Jennifer; Easterbrook, Philippa J.; Linas, Benjamin P.; Denkinger, Claudia M.

    2017-01-01

    Background Diagnosis of chronic Hepatitis C Virus (HCV) infection requires both a positive HCV antibody screen and confirmatory nucleic acid test (NAT). HCV core antigen (HCVcAg) is a potential alternative to NAT. Purpose This systematic review evaluated the accuracy of diagnosis of active HCV infection among adults and children for five HCVcAg tests compared to NAT. Data Sources EMBASE, PubMed, Web of Science, Scopus, and Cochrane from 1990 through March 31, 2016. Study Selection Cohort, cross-sectional, and randomized controlled trials were included without language restriction Data Extraction Two independent reviewers extracted data and assessed quality using an adapted Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. Data Synthesis 44 studies evaluated 5 index tests. Studies for the ARCHITECT had the highest quality, while those for Ortho ELISA were the lowest. From bivariate analyses, the sensitivity and specificity with 95% CI were: ARCHITECT 93.4% (90.1, 96.4) and 98.8% (97.4, 99.5), Ortho ELISA 93.2% (81.6, 97.7) and 99.2% (87.9, 100), and Hunan Jynda 59.5% (46.0, 71.7) and 82.9% (58.6, 94.3). Insufficient data were available for a meta-analysis for Lumipulse and Lumispot. In three quantitative studies using ARCHITECT, HCVcAg correlated closely with HCV RNA above 3000 IU/mL. Limitations There was insufficient data on covariates such as HIV or HBV status for sub-group analyses. Few studies reported genotypes of isolates and there were scant data for genotypes 4, 5, and 6. Most studies were conducted in high resource settings within reference laboratories. Conclusions HCVcAg assays with signal amplification have high sensitivity, high specificity, and good correlation with HCV RNA above 3000 IU/mL. HCVcAg assays have the potential to replace NAT in high HCV prevalence settings. PMID:27322622

  8. Review of domestic and international experience on optimization of tests planning for safety related systems at NPP

    International Nuclear Information System (INIS)

    Skalozubov, V.I.; Komarov, Yu.A.; Kolykanov, V.N.; Kochneva, V.Yu.; Gablaya, T.V.

    2009-01-01

    There are represented the basic requirements of normative and operating documents on test periodicity of safety related systems at NPPs, sets out the theoretical methods of test optimization of the technical systems, and analyses foreign engineering methods for changing test periodicity of the NPP systems. Based on this review analyses further tasks are formulated for improvement of the methodical base of optimization of tests planning for safety related systems

  9. The utility of repeat enzyme immunoassay testing for the diagnosis of Clostridium difficile infection: A systematic review of the literature

    Directory of Open Access Journals (Sweden)

    P S Garimella

    2012-01-01

    Full Text Available Over the last 20 years, the prevalence of healthcare-associated Clostridium difficile (C. diff disease has increased. While multiple