Sample records for error prone pcr

  1. Thermostable DNA Ligase-Mediated PCR Production of Circular Plasmid (PPCP) and Its Application in Directed Evolution via In situ Error-Prone PCR

    PubMed Central

    Le, Yilin; Chen, Huayou; Zagursky, Robert; Wu, J.H. David; Shao, Weilan

    2013-01-01

    Polymerase chain reaction (PCR) is a powerful method to produce linear DNA fragments. Here we describe the Tma thermostable DNA ligase-mediated PCR production of circular plasmid (PPCP) and its application in directed evolution via in situ error-prone PCR. In this thermostable DNA ligase-mediated whole-plasmid amplification method, the resultant DNA nick between the 5? end of the PCR primer and the extended newly synthesized DNA 3? end of each PCR cycle is ligated by Tma DNA ligase, resulting in circular plasmid DNA product that can be directly transformed. The template plasmid DNA is eliminated by ‘selection marker swapping’ upon transformation. When performed under an error-prone condition with Taq DNA polymerase, PPCP allows one-step construction of mutagenesis libraries based on in situ error-prone PCR so that random mutations are introduced into the target gene without altering the expression vector plasmid. A significant difference between PPCP and previously published methods is that PPCP allows exponential amplification of circular DNA. We used this method to create random mutagenesis libraries of a xylanase gene and two cellulase genes. Screening of these libraries resulted in mutant proteins with desired properties, demonstrating the usefulness of in situ error-prone PPCP for creating random mutagenesis libraries for directed evolution. PMID:23633530

  2. Error-prone signalling.

    PubMed

    Johnstone, R A; Grafen, A

    1992-06-22

    The handicap principle of Zahavi is potentially of great importance to the study of biological communication. Existing models of the handicap principle, however, make the unrealistic assumption that communication is error free. It seems possible, therefore, that Zahavi's arguments do not apply to real signalling systems, in which some degree of error is inevitable. Here, we present a general evolutionarily stable strategy (ESS) model of the handicap principle which incorporates perceptual error. We show that, for a wide range of error functions, error-prone signalling systems must be honest at equilibrium. Perceptual error is thus unlikely to threaten the validity of the handicap principle. Our model represents a step towards greater realism, and also opens up new possibilities for biological signalling theory. Concurrent displays, direct perception of quality, and the evolution of 'amplifiers' and 'attenuators' are all probable features of real signalling systems, yet handicap models based on the assumption of error-free communication cannot accommodate these possibilities. PMID:1354361

  3. Error-prone pcr-based mutagenesis strategy for rapidly generating high-yield influenza vaccine candidates.

    PubMed

    Ye, Jianqiang; Wen, Feng; Xu, Yifei; Zhao, Nan; Long, Liping; Sun, Hailiang; Yang, Jialiang; Cooley, Jim; Todd Pharr, G; Webby, Richard; Wan, Xiu-Feng

    2015-08-01

    Vaccination is the primary strategy for the prevention and control of influenza outbreaks. However, the manufacture of influenza vaccine requires a high-yield seed strain, and the conventional methods for generating such strains are time consuming. In this study, we developed a novel method to rapidly generate high-yield candidate vaccine strains by integrating error-prone PCR, site-directed mutagenesis strategies, and reverse genetics. We used this method to generate seed strains for the influenza A(H1N1)pdm09 virus and produced six high-yield candidate strains. We used a mouse model to assess the efficacy of two of the six candidate strains as a vaccine seed virus: both strains provided complete protection in mice against lethal challenge, thus validating our method. Results confirmed that the efficacy of these candidate vaccine seed strains was not affected by the yield-optimization procedure. PMID:25899178

  4. Error-Prone Signalling

    Microsoft Academic Search

    Rufus A. Johnstone; Alan Grafen

    1992-01-01

    The handicap principle of Zahavi is potentially of great importance to the study of biological communication. Existing models of the handicap principle, however, make the unrealistic assumption that communication is error free. It seems possible, therefore, that Zahavi's arguments do not apply to real signalling systems, in which some degree of error is inevitable. Here, we present a general evolutionarily

  5. Stepwise error-prone PCR and DNA shuffling changed the pH activity range and product specificity of the cyclodextrin glucanotransferase from an alkaliphilic Bacillus sp.

    PubMed Central

    Melzer, Susanne; Sonnendecker, Christian; Föllner, Christina; Zimmermann, Wolfgang

    2015-01-01

    Cyclodextrin glucanotransferase (EC 2.4.1.19) from the alkaliphilic Bacillus sp. G-825-6 converts starch mainly to ?-cyclodextrin (CD8). A combination of error-prone PCR and DNA shuffling was used to obtain variants of this enzyme with higher product specificity for CD8 and a broad pH activity range. The variant S54 with seven amino acid substitutions showed a 1.2-fold increase in CD8-synthesizing activity and the product ratio of CD7:CD8 was shifted to 1:7 compared to 1:3 of the wild-type enzyme. Nine amino acid substitutions of the cyclodextrin glucanotransferase were performed to generate the variant S35 active in a pH range 4.0–10.0. Compared to the wild-type enzyme which is inactive below pH 6.0, S35 retained 70% of its CD8-synthesizing activity at pH 4.0.

  6. Data Broadcasting Algorithms on Error-Prone Wireless Channels

    E-print Network

    Pinotti, Maria Cristina

    . Keywords. Wireless communication, Data broadcasting, Multiple channels, Flat scheduling, Average expected In wireless asymmetric communications, data broadcasting is an efficient way of simul- taneously disseminatingData Broadcasting Algorithms on Error-Prone Wireless Channels Paolo BARSOCCHI a , Alan A. BERTOSSI

  7. Size and Shape Analysis of Error-Prone Shape Data

    PubMed Central

    Du, Jiejun; Dryden, Ian L.; Huang, Xianzheng

    2015-01-01

    We consider the problem of comparing sizes and shapes of objects when landmark data are prone to measurement error. We show that naive implementation of ordinary Procrustes analysis that ignores measurement error can compromise inference. To account for measurement error, we propose the conditional score method for matching configurations, which guarantees consistent inference under mild model assumptions. The effects of measurement error on inference from naive Procrustes analysis and the performance of the proposed method are illustrated via simulation and application in three real data examples. Supplementary materials for this article are available online. PMID:26109745

  8. Mismatch-mediated error prone repair at the immunoglobulin genes.

    PubMed

    Chahwan, Richard; Edelmann, Winfried; Scharff, Matthew D; Roa, Sergio

    2011-12-01

    The generation of effective antibodies depends upon somatic hypermutation (SHM) and class-switch recombination (CSR) of antibody genes by activation induced cytidine deaminase (AID) and the subsequent recruitment of error prone base excision and mismatch repair. While AID initiates and is required for SHM, more than half of the base changes that accumulate in V regions are not due to the direct deamination of dC to dU by AID, but rather arise through the recruitment of the mismatch repair complex (MMR) to the U:G mismatch created by AID and the subsequent perversion of mismatch repair from a high fidelity process to one that is very error prone. In addition, the generation of double-strand breaks (DSBs) is essential during CSR, and the resolution of AID-generated mismatches by MMR to promote such DSBs is critical for the efficiency of the process. While a great deal has been learned about how AID and MMR cause hypermutations and DSBs, it is still unclear how the error prone aspect of these processes is largely restricted to antibody genes. The use of knockout models and mice expressing mismatch repair proteins with separation-of-function point mutations have been decisive in gaining a better understanding of the roles of each of the major MMR proteins and providing further insight into how mutation and repair are coordinated. Here, we review the cascade of MMR factors and repair signals that are diverted from their canonical error free role and hijacked by B cells to promote genetic diversification of the Ig locus. This error prone process involves AID as the inducer of enzymatically-mediated DNA mismatches, and a plethora of downstream MMR factors acting as sensors, adaptors and effectors of a complex and tightly regulated process from much of which is not yet well understood. PMID:22100214

  9. Mismatch-mediated error prone repair at the Immunoglobulin genes

    PubMed Central

    Chahwan, Richard; Edelmann, Winfried; Scharff, Matthew D; Roa, Sergio

    2011-01-01

    The generation of effective antibodies depends upon somatic hypermutation (SHM) and class-switch recombination (CSR) of antibody genes by activation induced cytidine deaminase (AID) and the subsequent recruitment of error prone base excision and mismatch repair. While AID initiates and is required for SHM, more than half of the base changes that accumulate in V regions are not due to the direct deamination of dC to dU by AID, but rather arise through the recruitment of the mismatch repair complex (MMR) to the U:G mismatch created by AID and the subsequent perversion of mismatch repair from a high fidelity process to one that is very error prone. In addition, the generation of double-strand breaks (DSBs) is essential during CSR, and the resolution of AID-generated mismatches by MMR to promote such DSBs is critical for the efficiency of the process. While a great deal has been learned about how AID and MMR cause hypermutations and DSBs, it is still unclear how the error prone aspect of these processes is largely restricted to antibody genes. The use of knockout models and mice expressing mismatch repair proteins with separation-of-function point mutations have been decisive in gaining a better understanding of the roles of each of the major MMR proteins and providing further insight into how mutation and repair are coordinated. Here, we review the cascade of MMR factors and repair signals that are diverted from their canonical error free role and hijacked by B cells to promote genetic diversification of the Ig locus. This error prone process involves AID as the inducer of enzymatically-mediated DNA mismatches, and a plethora of downstream MMR factors acting as sensors, adaptors and effectors of a complex and tightly regulated process from much of which is not yet well understood. PMID:22100214

  10. Replicative mechanisms for CNV formation are error prone

    PubMed Central

    Carvalho, Claudia M. B.; Pehlivan, Davut; Ramocki, Melissa B.; Fang, Ping; Alleva, Benjamin; Franco, Luis M.; Belmont, John W.; Hastings, P. J.; Lupski, James R.

    2013-01-01

    Summary We investigated 67 breakpoint junctions of gene copy number gains (CNVs) in 31 unrelated subjects. We observed a strikingly high frequency of small deletions and insertions (29%) apparently originating from polymerase-slippage events, in addition to frameshifts and point mutations in homonucleotide runs (13%), at or flanking the breakpoint junctions of complex CNVs. These simple nucleotide variants (SNV) were generated concomitantly with the de novo complex genomic rearrangement (CGR) event. Our findings implicate a low fidelity error-prone DNA polymerase in synthesis associated with DNA repair mechanisms that leads to a local increase in point mutation burden associated with human CGR. PMID:24056715

  11. Mutagenesis of Neisseria gonorrhoeae: absence of error-prone repair

    SciTech Connect

    Campbell, L.A.; Yasbin, R.E.

    1984-10-01

    The lethal and mutagenic effects of various mutagens on Neisseria gonorrhoeae were investigated. Lethality studies demonstrated that N. gonorrhoeae was relatively sensitive to ethyl methanesulfonate, UV light, and methyl methanesulfonate. Although N. gonorrhoeae was readily mutated by ethyl methanesulfonate and N-methyl-n'-nitro-N-nitrosoguanidine for the three genetic markers assayed, no increase in the mutation frequency was observed for any of the selective markers after UV irradiation of methyl methanesulfonate treatment. These results suggest than N. gonorrhoeae lacks an error-prone repair mechanism.

  12. Error-prone rolling circle amplification greatly simplifies random mutagenesis.

    PubMed

    Fujii, Ryota; Kitaoka, Motomitsu; Hayashi, Kiyoshi

    2014-01-01

    We describe a simple and easy protocol to introduce random mutations into plasmid DNA: error-prone rolling circle amplification. A template plasmid is amplified via rolling circle amplification with decreased fidelity in the presence of MnCl2 and is used to transform a host strain resulting in a mutant library with several random point mutations per kilobase through the entire plasmid. The primary advantage of this method is its simplicity. This protocol does not require the design of specific primers or thermal cycling. The reaction mixture can be used for direct transformation of a host strain. This method allows rapid preparation of randomly mutated plasmid libraries, enabling wider application of random mutagenesis. PMID:25055768

  13. A study of errors, error-proneness, and error diagnosis in Cobol

    Microsoft Academic Search

    Charles R. Litecky; Gordon B. Davis

    1976-01-01

    This paper provides data on Cobol error frequency for correction of errors in student-oriented compilers, improvement of teaching, and changes in programming language. Cobol was studied because of economic importance, widespread usage, possible error-inducing design, and lack of research. The types of errors were identified in a pilot study; then, using the 132 error types found, 1,777 errors were classified

  14. Leaving an Unknown Maze Using an Error-Prone Tom Kamphans, Elmar Langetepe

    E-print Network

    Klein, Rolf

    Leaving an Unknown Maze Using an Error-Prone Compass Tom Kamphans, Elmar Langetepe University,langetep}@cs.uni-bonn.de Abstract Imagine you are trapped in a maze of caves. All you have is an old rusty compass and barely enough light to read it. How much inaccuracy can you allow to ensure that you can leave the maze? Or you

  15. A QUANTITATIVE MODEL OF ERROR ACCUMULATION DURING PCR AMPLIFICATION

    PubMed Central

    Pienaar, E; Theron, M; Nelson, M; Viljoen, HJ

    2006-01-01

    The amplification of target DNA by the polymerase chain reaction (PCR) produces copies which may contain errors. Two sources of errors are associated with the PCR process: (1) editing errors that occur during DNA polymerase-catalyzed enzymatic copying and (2) errors due to DNA thermal damage. In this study a quantitative model of error frequencies is proposed and the role of reaction conditions is investigated. The errors which are ascribed to the polymerase depend on the efficiency of its editing function as well as the reaction conditions; specifically the temperature and the dNTP pool composition. Thermally induced errors stem mostly from three sources: A+G depurination, oxidative damage of guanine to 8-oxoG and cytosine deamination to uracil. The post-PCR modifications of sequences are primarily due to exposure of nucleic acids to elevated temperatures, especially if the DNA is in a single-stranded form. The proposed quantitative model predicts the accumulation of errors over the course of a PCR cycle. Thermal damage contributes significantly to the total errors; therefore consideration must be given to thermal management of the PCR process. PMID:16412692

  16. Estimation via corrected scores in general semiparametric regression models with error-prone covariates

    PubMed Central

    Maity, Arnab; Apanasovich, Tatiyana V.

    2011-01-01

    This paper considers the problem of estimation in a general semiparametric regression model when error-prone covariates are modeled parametrically while covariates measured without error are modeled nonparametrically. To account for the effects of measurement error, we apply a correction to a criterion function. The specific form of the correction proposed allows Monte Carlo simulations in problems for which the direct calculation of a corrected criterion is difficult. Therefore, in contrast to methods that require solving integral equations of possibly multiple dimensions, as in the case of multiple error-prone covariates, we propose methodology which offers a simple implementation. The resulting methods are functional, they make no assumptions about the distribution of the mismeasured covariates. We utilize profile kernel and backfitting estimation methods and derive the asymptotic distribution of the resulting estimators. Through numerical studies we demonstrate the applicability of proposed methods to Poisson, logistic and multivariate Gaussian partially linear models. We show that the performance of our methods is similar to a computationally demanding alternative. Finally, we demonstrate the practical value of our methods when applied to Nevada Test Site (NTS) Thyroid Disease Study data. PMID:22773940

  17. Estimation via corrected scores in general semiparametric regression models with error-prone covariates.

    PubMed

    Maity, Arnab; Apanasovich, Tatiyana V

    2011-01-01

    This paper considers the problem of estimation in a general semiparametric regression model when error-prone covariates are modeled parametrically while covariates measured without error are modeled nonparametrically. To account for the effects of measurement error, we apply a correction to a criterion function. The specific form of the correction proposed allows Monte Carlo simulations in problems for which the direct calculation of a corrected criterion is difficult. Therefore, in contrast to methods that require solving integral equations of possibly multiple dimensions, as in the case of multiple error-prone covariates, we propose methodology which offers a simple implementation. The resulting methods are functional, they make no assumptions about the distribution of the mismeasured covariates. We utilize profile kernel and backfitting estimation methods and derive the asymptotic distribution of the resulting estimators. Through numerical studies we demonstrate the applicability of proposed methods to Poisson, logistic and multivariate Gaussian partially linear models. We show that the performance of our methods is similar to a computationally demanding alternative. Finally, we demonstrate the practical value of our methods when applied to Nevada Test Site (NTS) Thyroid Disease Study data. PMID:22773940

  18. DNA polymerases ? and Rev1 mediate error-prone bypass of non-B DNA structures

    PubMed Central

    Northam, Matthew R.; Moore, Elizabeth A.; Mertz, Tony M.; Binz, Sara K.; Stith, Carrie M.; Stepchenkova, Elena I.; Wendt, Kathern L.; Burgers, Peter M. J.; Shcherbakova, Polina V.

    2014-01-01

    DNA polymerase ? (Pol ?) and Rev1 are key players in translesion DNA synthesis. The error-prone Pol ? can also participate in replication of undamaged DNA when the normal replisome is impaired. Here we define the nature of the replication disturbances that trigger the recruitment of error-prone polymerases in the absence of DNA damage and describe the specific roles of Rev1 and Pol ? in handling these disturbances. We show that Pol ?/Rev1-dependent mutations occur at sites of replication stalling at short repeated sequences capable of forming hairpin structures. The Rev1 deoxycytidyl transferase can take over the stalled replicative polymerase and incorporate an additional ‘C’ at the hairpin base. Full hairpin bypass often involves template-switching DNA synthesis, subsequent realignment generating multiply mismatched primer termini and extension of these termini by Pol ?. The postreplicative pathway dependent on polyubiquitylation of proliferating cell nuclear antigen provides a backup mechanism for accurate bypass of these sequences that is primarily used when the Pol ?/Rev1-dependent pathway is inactive. The results emphasize the pivotal role of noncanonical DNA structures in mutagenesis and reveal the long-sought-after mechanism of complex mutations that represent a unique signature of Pol ?. PMID:24049079

  19. Is Non-Homologous End-Joining Really an Inherently Error-Prone Process?

    PubMed Central

    Bétermier, Mireille; Bertrand, Pascale; Lopez, Bernard S.

    2014-01-01

    DNA double-strand breaks (DSBs) are harmful lesions leading to genomic instability or diversity. Non-homologous end-joining (NHEJ) is a prominent DSB repair pathway, which has long been considered to be error-prone. However, recent data have pointed to the intrinsic precision of NHEJ. Three reasons can account for the apparent fallibility of NHEJ: 1) the existence of a highly error-prone alternative end-joining process; 2) the adaptability of canonical C-NHEJ (Ku- and Xrcc4/ligase IV–dependent) to imperfect complementary ends; and 3) the requirement to first process chemically incompatible DNA ends that cannot be ligated directly. Thus, C-NHEJ is conservative but adaptable, and the accuracy of the repair is dictated by the structure of the DNA ends rather than by the C-NHEJ machinery. We present data from different organisms that describe the conservative/versatile properties of C-NHEJ. The advantages of the adaptability/versatility of C-NHEJ are discussed for the development of the immune repertoire and the resistance to ionizing radiation, especially at low doses, and for targeted genome manipulation. PMID:24453986

  20. Making a task difficult: evidence that device-oriented steps are effortful and error-prone.

    PubMed

    Ament, Maartje G A; Cox, Anna L; Blandford, Ann; Brumby, Duncan P

    2013-09-01

    Errors in the execution of procedural tasks can have severe consequences. Attempts to ameliorate these slip errors through increased training and motivation have been shown to be ineffective. Instead, we identified the steps in a task procedure on which errors are most likely to occur, so that these might be designed out of the task procedure in the first place. Specifically, we considered whether device-oriented steps (i.e., steps in the task procedure that do not directly contribute to the achievement of the task goal) are more error-prone than task-oriented steps (i.e., steps that do directly contribute to the task goal). Two experiments are reported in which participants were trained to perform a novel procedural task. Across conditions, we manipulated the extent to which each step in the task procedure appeared to contribute to the achievement of the task goal (i.e., alternating the assignment of a task step between device- and task-oriented), while keeping the interface and underlying task procedure the same. Results show that participants made more errors and took longer to complete a task step when it played a device-oriented role rather than a task-orientated role. These effects were exacerbated by the introduction of a secondary task designed to increase working memory load, suggesting that when a task step plays a device-oriented role it is more weakly represented in memory. We conclude that device-oriented task steps are inherently problematic and should be avoided where possible in the design of task procedures. PMID:24059822

  1. Human oocytes. Error-prone chromosome-mediated spindle assembly favors chromosome segregation defects in human oocytes.

    PubMed

    Holubcová, Zuzana; Blayney, Martyn; Elder, Kay; Schuh, Melina

    2015-06-01

    Aneuploidy in human eggs is the leading cause of pregnancy loss and several genetic disorders such as Down syndrome. Most aneuploidy results from chromosome segregation errors during the meiotic divisions of an oocyte, the egg's progenitor cell. The basis for particularly error-prone chromosome segregation in human oocytes is not known. We analyzed meiosis in more than 100 live human oocytes and identified an error-prone chromosome-mediated spindle assembly mechanism as a major contributor to chromosome segregation defects. Human oocytes assembled a meiotic spindle independently of either centrosomes or other microtubule organizing centers. Instead, spindle assembly was mediated by chromosomes and the small guanosine triphosphatase Ran in a process requiring ~16 hours. This unusually long spindle assembly period was marked by intrinsic spindle instability and abnormal kinetochore-microtubule attachments, which favor chromosome segregation errors and provide a possible explanation for high rates of aneuploidy in human eggs. PMID:26045437

  2. Possible error-prone repair of neoplastic transformation induced by fission-spectrum neutrons.

    PubMed

    Hill, C K; Han, A; Elkind, M M

    1984-01-01

    We have examined the effect of fission-spectrum neutrons from the JANUS reactor at Argonne National Laboratory, delivered either as acute or protracted irradiation, on the incidence of neoplastic transformation in the C3H 10T1/2 mouse embryo cell line. Acute exposures were delivered at 10-38 cGy min-1, protracted exposures at 0.086 or 0.43 cGy min-1. The total doses for both ranged from 2.4 to 350 cGy. In the low dose region (2.4-80 cGy), there was a large enhancement in transformation frequency when the neutrons were delivered at the low dose rates compared with the high dose rates, but the survival of the cells was not significantly different between the two exposures conditions. Analysis of the initial parts of the curves shows that the regression line for protracted doses is about 9 times steeper than that for single acute exposures. Finally, the possibility is discussed that an "error-prone" repair process may be causing the enhanced transformation frequency by protracted neutron exposures. PMID:6582923

  3. Possible error-prone repair of neoplastic transformation induced by fission-spectrum neutrons

    SciTech Connect

    Hill, C.K.; Han, A.; Elkind, M.M.

    1983-07-18

    We have examined the effect of fission-spectrum neutrons from the JANUS reactor at Argonne National Laboratory, delivered either as acute or protracted irradiation, on the incidence of neoplastic transformation in the C3H 1OT1/2 mouse embryo cell line. Acute exposures were delivered at 10 to 38 rads/min, protracted exposures at 0.086 or 0.43 rad/min. The total doses for both ranged from 2.4 to 350 rads. In the low dose region (2.4 to 80 rads), there was a large enhancement in transformation frequency when the neutrons were delivered at the low dose rates compared with the high dose rates, but the survival of the cells was not significantly different between the two exposure conditions. Analysis of the initial parts of the curves shows that the regression line for protracted doses is about 9 times steeper than that for single acute exposures. Finally, the possibility is discussed that an error-prone repair process may be causing the enhanced transformation frequency by protracted neutron exposures. 12 references, 2 figures, 1 table.

  4. Improvement of cellulase activity using error-prone rolling circle amplification and site-directed mutagenesis.

    PubMed

    Vu, Van Hanh; Kim, Keun

    2012-05-01

    Improvement of endoglucanase activity was accomplished by utilizing error-prone rolling circle amplification, supplemented with 1.7 mM MnCl2. This procedure generated random mutations in the Bacillus amyloliquefaciens endoglucanase gene with a frequency of 10 mutations per kilobase. Six mutated endoglucanase genes, recovered from six colonies, possessed endoglucanase activity between 2.50- and 3.12-folds higher than wild type. We sequenced these mutants, and the different mutated sites of nucleotides were identified. The mutated endoglucanase sequences had five mutated amino acids: A15T, P24A, P26Q, G27A, and E289V. Among these five substitutions, E289V was determined to be responsible for the improved enzyme activity. This observation was confirmed with site-directed mutagenesis; the introduction of only one mutation (E289V) in the wild-type endoglucanase gene resulted in a 7.93-fold (5.55 U/mg protein) increase in its enzymatic activity compared with that (0.7 U/mg protein) of wild type. PMID:22561853

  5. Thermoadaptation-directed evolution of chloramphenicol acetyltransferase in an error-prone thermophile using improved procedures.

    PubMed

    Kobayashi, Jyumpei; Furukawa, Megumi; Ohshiro, Takashi; Suzuki, Hirokazu

    2015-07-01

    Enhancing the thermostability of thermolabile enzymes extends their practical utility. We previously demonstrated that an error-prone thermophile derived from Geobacillus kaustophilus HTA426 can generate mutant genes encoding enzyme variants that are more thermostable than the parent enzyme. Here, we used this approach, termed as thermoadaptation-directed enzyme evolution, to increase the thermostability of the chloramphenicol acetyltransferase (CAT) of Staphylococcus aureus and successfully generated a CAT variant with an A138T replacement (CAT(A138T)). This variant was heterologously produced, and its enzymatic properties were compared with those of the wild type. We found that CAT(A138T) had substantially higher thermostability than CAT but had comparable activities, showing that the A138T replacement enhanced protein thermostability without affecting the catalytic activity. Because variants CAT(A138S) and CAT(A138V), which were generated via in vitro site-directed mutagenesis, were more thermostable than CAT, the thermostability enhancement resulting from the A138T replacement can be attributed to both the presence of a hydroxyl group and the bulk of the threonine side chain. CAT(A138T) conferred chloramphenicol resistance to G. kaustophilus cells at high temperature more efficiently than CAT. Therefore, the gene encoding CAT(A138T) may be useful as a genetic marker in Geobacillus spp. Notably, CAT(A138T) generation was achieved only by implementing improved procedures (plasmid-based mutations on solid media); previous procedures (chromosome-based mutations in liquid media) were unsuccessful. This result suggests that this improved procedure is crucial for successful thermoadaptation-directed evolution in certain cases and increases the opportunities for generating thermostable enzymes. PMID:25783628

  6. Use of Damaged DNA and dNTP Substrates by the Error-Prone DNA Polymerase X from African Swine Fever Virus

    E-print Network

    Tsai, Ming-Daw

    Use of Damaged DNA and dNTP Substrates by the Error-Prone DNA Polymerase X from African Swine Fever a fitness advantage. The repair polymerase, Pol X, encoded by the African swine fever virus (ASFV) is one

  7. Human PrimPol is a highly error-prone polymerase regulated by single-stranded DNA binding proteins

    PubMed Central

    Guilliam, Thomas A.; Jozwiakowski, Stanislaw K.; Ehlinger, Aaron; Barnes, Ryan P.; Rudd, Sean G.; Bailey, Laura J.; Skehel, J. Mark; Eckert, Kristin A.; Chazin, Walter J.; Doherty, Aidan J.

    2015-01-01

    PrimPol is a recently identified polymerase involved in eukaryotic DNA damage tolerance, employed in both re-priming and translesion synthesis mechanisms to bypass nuclear and mitochondrial DNA lesions. In this report, we investigate how the enzymatic activities of human PrimPol are regulated. We show that, unlike other TLS polymerases, PrimPol is not stimulated by PCNA and does not interact with it in vivo. We identify that PrimPol interacts with both of the major single-strand binding proteins, RPA and mtSSB in vivo. Using NMR spectroscopy, we characterize the domains responsible for the PrimPol-RPA interaction, revealing that PrimPol binds directly to the N-terminal domain of RPA70. In contrast to the established role of SSBs in stimulating replicative polymerases, we find that SSBs significantly limit the primase and polymerase activities of PrimPol. To identify the requirement for this regulation, we employed two forward mutation assays to characterize PrimPol's replication fidelity. We find that PrimPol is a mutagenic polymerase, with a unique error specificity that is highly biased towards insertion-deletion errors. Given the error-prone disposition of PrimPol, we propose a mechanism whereby SSBs greatly restrict the contribution of this enzyme to DNA replication at stalled forks, thus reducing the mutagenic potential of PrimPol during genome replication. PMID:25550423

  8. A Nucleotide-Analogue-Induced Gain of Function Corrects the Error-Prone Nature of Human DNA Polymerase iota

    SciTech Connect

    Ketkar, Amit; Zafar, Maroof K.; Banerjee, Surajit; Marquez, Victor E.; Egli, Martin; Eoff, Robert L. (Cornell); (Vanderbilt); (NCI); (Arkansas)

    2012-10-25

    Y-family DNA polymerases participate in replication stress and DNA damage tolerance mechanisms. The properties that allow these enzymes to copy past bulky adducts or distorted template DNA can result in a greater propensity for them to make mistakes. Of the four human Y-family members, human DNA polymerase iota (hpol{iota}) is the most error-prone. In the current study, we elucidate the molecular basis for improving the fidelity of hpol{iota} through use of the fixed-conformation nucleotide North-methanocarba-2{prime}-deoxyadenosine triphosphate (N-MC-dATP). Three crystal structures were solved of hpol{iota} in complex with DNA containing a template 2{prime}-deoxythymidine (dT) paired with an incoming dNTP or modified nucleotide triphosphate. The ternary complex of hpol{iota} inserting N-MC-dATP opposite dT reveals that the adenine ring is stabilized in the anti orientation about the pseudo-glycosyl torsion angle, which mimics precisely the mutagenic arrangement of dGTP:dT normally preferred by hpol{iota}. The stabilized anti conformation occurs without notable contacts from the protein but likely results from constraints imposed by the bicyclo[3.1.0]hexane scaffold of the modified nucleotide. Unmodified dATP and South-MC-dATP each adopt syn glycosyl orientations to form Hoogsteen base pairs with dT. The Hoogsteen orientation exhibits weaker base-stacking interactions and is less catalytically favorable than anti N-MC-dATP. Thus, N-MC-dATP corrects the error-prone nature of hpol{iota} by preventing the Hoogsteen base-pairing mode normally observed for hpol{iota}-catalyzed insertion of dATP opposite dT. These results provide a previously unrecognized means of altering the efficiency and the fidelity of a human translesion DNA polymerase.

  9. The Saccharomyces cerevisiae RAD6 group is composed of an error-prone and two error-free postreplication repair pathways.

    PubMed Central

    Xiao, W; Chow, B L; Broomfield, S; Hanna, M

    2000-01-01

    The RAD6 postreplication repair and mutagenesis pathway is the only major radiation repair pathway yet to be extensively characterized. It has been previously speculated that the RAD6 pathway consists of two parallel subpathways, one error free and another error prone (mutagenic). Here we show that the RAD6 group genes can be exclusively divided into three rather than two independent subpathways represented by the RAD5, POL30, and REV3 genes; the REV3 pathway is largely mutagenic, whereas the RAD5 and the POL30 pathways are deemed error free. Mutants carrying characteristic mutations in each of the three subpathways are phenotypically indistinguishable from a single mutant such as rad18, which is defective in the entire RAD6 postreplication repair/tolerance pathway. Furthermore, the rad18 mutation is epistatic to all single or combined mutations in any of the above three subpathways. Our data also suggest that MMS2 and UBC13 play a key role in coordinating the response of the error-free subpathways; Mms2 and Ubc13 form a complex required for a novel polyubiquitin chain assembly, which probably serves as a signal transducer to promote both RAD5 and POL30 error-free postreplication repair pathways. The model established by this study will facilitate further research into the molecular mechanisms of postreplication repair and translesion DNA synthesis. In view of the high degree of sequence conservation of the RAD6 pathway genes among all eukaryotes, the model presented in this study may also apply to mammalian cells and predicts links to human diseases. PMID:10924462

  10. DNA polymerase ?-dependent lesion bypass in Saccharomyces cerevisiae is accompanied by error-prone copying of long stretches of adjacent DNA.

    PubMed

    Kochenova, Olga V; Daee, Danielle L; Mertz, Tony M; Shcherbakova, Polina V

    2015-03-01

    Translesion synthesis (TLS) helps cells to accomplish chromosomal replication in the presence of unrepaired DNA lesions. In eukaryotes, the bypass of most lesions involves a nucleotide insertion opposite the lesion by either a replicative or a specialized DNA polymerase, followed by extension of the resulting distorted primer terminus by DNA polymerase ? (Pol?). The subsequent events leading to disengagement of the error-prone Pol? from the primer terminus and its replacement with an accurate replicative DNA polymerase remain largely unknown. As a first step toward understanding these events, we aimed to determine the length of DNA stretches synthesized in an error-prone manner during the Pol?-dependent lesion bypass. We developed new in vivo assays to identify the products of mutagenic TLS through a plasmid-borne tetrahydrofuran lesion and a UV-induced chromosomal lesion. We then surveyed the region downstream of the lesion site (in respect to the direction of TLS) for the presence of mutations indicative of an error-prone polymerase activity. The bypass of both lesions was associated with an approximately 300,000-fold increase in the mutation rate in the adjacent DNA segment, in comparison to the mutation rate during normal replication. The hypermutated tract extended 200 bp from the lesion in the plasmid-based assay and as far as 1 kb from the lesion in the chromosome-based assay. The mutation rate in this region was similar to the rate of errors produced by purified Pol? during copying of undamaged DNA in vitro. Further, no mutations downstream of the lesion were observed in rare TLS products recovered from Pol?-deficient cells. This led us to conclude that error-prone Pol? synthesis continues for several hundred nucleotides after the lesion bypass is completed. These results provide insight into the late steps of TLS and show that error-prone TLS tracts span a substantially larger region than previously appreciated. PMID:25826305

  11. Quality Control Analysis of Selected Aspects of Programs Administered by the Bureau of Student Financial Assistance. Task 1 and Quality Control Sample; Error-Prone Modeling Analysis Plan.

    ERIC Educational Resources Information Center

    Saavedra, Pedro; And Others

    Parameters and procedures for developing an error-prone model (EPM) to predict financial aid applicants who are likely to misreport on Basic Educational Opportunity Grant (BEOG) applications are introduced. Specifications to adapt these general parameters to secondary data analysis of the Validation, Edits, and Applications Processing Systems…

  12. Rapid and apparently error-prone excision repair of nonreplicating UV-irradiated plasmids in Xenopus laevis oocytes.

    PubMed Central

    Hays, J B; Ackerman, E J; Pang, Q S

    1990-01-01

    Repair of UV-irradiated plasmid DNA microinjected into frog oocytes was measured by two techniques: transformation of repair-deficient (delta uvrB delta recA delta phr) bacteria, and removal of UV endonuclease-sensitive sites (ESS). Transformation efficiencies relative to unirradiated plasmids were used to estimate the number of lethal lesions; the latter were assumed to be Poisson distributed. These estimates were in good agreement with measurements of ESS. By both criteria, plasmid DNA was efficiently repaired, mostly during the first 2 h, when as many as 2 x 10(10) lethal lesions were removed per oocyte. This rate is about 10(6) times the average for removal of ESS from repair-proficient human cells. Repair was slower but still significant after 2 h, but some lethal lesions usually remained after overnight incubation. Most repair occurred in the absence of light, in marked contrast to differentiated frog cells, previously shown to possess photoreactivating but no excision repair activity. There was no increase in the resistance to DpnI restriction of plasmids (methylated in Escherichia coli at GATC sites) incubated in oocytes; this implies no increase in hemimethylated GATC sites, and hence no semiconservative DNA replication. Plasmid substrates capable of either intramolecular or intermolecular homologous recombination were not recombined, whether UV-irradiated or not. Repair of Lac+ plasmids was accompanied by a significant UV-dependent increase in the frequency of Lac- mutants, corresponding to a repair synthesis error frequency on the order of 10(-4) per nucleotide. PMID:2355915

  13. Quality Control Analysis of Selected Aspects of Programs Administered by the Bureau of Student Financial Assistance. Error-Prone Model Derived from 1978-1979 Quality Control Study. Data Report. [Task 3.

    ERIC Educational Resources Information Center

    Saavedra, Pedro; Kuchak, JoAnn

    An error-prone model (EPM) to predict financial aid applicants who are likely to misreport on Basic Educational Opportunity Grant (BEOG) applications was developed, based on interviews conducted with a quality control sample of 1,791 students during 1978-1979. The model was designed to identify corrective methods appropriate for different types of…

  14. The Werner syndrome protein limits the error-prone 8-oxo-dG lesion bypass activity of human DNA polymerase kappa

    PubMed Central

    Maddukuri, Leena; Ketkar, Amit; Eddy, Sarah; Zafar, Maroof K.; Eoff, Robert L.

    2014-01-01

    Human DNA polymerase kappa (hpol ?) is the only Y-family member to preferentially insert dAMP opposite 7,8-dihydro-8-oxo-2?-deoxyguanosine (8-oxo-dG) during translesion DNA synthesis. We have studied the mechanism of action by which hpol ? activity is modulated by the Werner syndrome protein (WRN), a RecQ helicase known to influence repair of 8-oxo-dG. Here we show that WRN stimulates the 8-oxo-dG bypass activity of hpol ? in vitro by enhancing the correct base insertion opposite the lesion, as well as extension from dC:8-oxo-dG base pairs. Steady-state kinetic analysis reveals that WRN improves hpol ?-catalyzed dCMP insertion opposite 8-oxo-dG ?10-fold and extension from dC:8-oxo-dG by 2.4-fold. Stimulation is primarily due to an increase in the rate constant for polymerization (kpol), as assessed by pre-steady-state kinetics, and it requires the RecQ C-terminal (RQC) domain. In support of the functional data, recombinant WRN and hpol ? were found to physically interact through the exo and RQC domains of WRN, and co-localization of WRN and hpol ? was observed in human cells treated with hydrogen peroxide. Thus, WRN limits the error-prone bypass of 8-oxo-dG by hpol ?, which could influence the sensitivity to oxidative damage that has previously been observed for Werner's syndrome cells. PMID:25294835

  15. Error-prone translesion synthesis past DNA-peptide cross-links conjugated to the major groove of DNA via C5 of thymidine.

    PubMed

    Wickramaratne, Susith; Boldry, Emily J; Buehler, Charles; Wang, Yen-Chih; Distefano, Mark D; Tretyakova, Natalia Y

    2015-01-01

    DNA-protein cross-links (DPCs) are exceptionally bulky, structurally diverse DNA adducts formed in cells upon exposure to endogenous and exogenous bis-electrophiles, reactive oxygen species, and ionizing radiation. If not repaired, DPCs can induce toxicity and mutations. It has been proposed that the protein component of a DPC is proteolytically degraded, giving rise to smaller DNA-peptide conjugates, which can be subject to nucleotide excision repair and replication bypass. In this study, polymerase bypass of model DNA-peptide conjugates structurally analogous to the lesions induced by reactive oxygen species and DNA methyltransferase inhibitors was examined. DNA oligomers containing site-specific DNA-peptide conjugates were generated by copper-catalyzed [3 + 2] Huisgen cyclo-addition between an alkyne-functionalized C5-thymidine in DNA and an azide-containing 10-mer peptide. The resulting DNA-peptide conjugates were subjected to steady-state kinetic experiments in the presence of recombinant human lesion bypass polymerases ? and ?, followed by PAGE-based assays to determine the catalytic efficiency and the misinsertion frequency opposite the lesion. We found that human polymerase ? and ? can incorporate A, G, C, or T opposite the C5-dT-conjugated DNA-peptide conjugates, whereas human polymerase ? preferentially inserts G opposite the lesion. Furthermore, HPLC-ESI(-)-MS/MS sequencing of the extension products has revealed that post-lesion synthesis was highly error-prone, resulting in mutations opposite the adducted site or at the +1 position from the adduct and multiple deletions. Collectively, our results indicate that replication bypass of peptides conjugated to the C5 position of thymine by human translesion synthesis polymerases leads to large numbers of base substitution and frameshift mutations. PMID:25391658

  16. Self-Regulated Exposure to Erotica, Recall Errors, and Subjective Reactions as a Function of Erotophobia and Type A Coronary-Prone Behavior

    Microsoft Academic Search

    Michael A. Becker; Donn Byrne

    1985-01-01

    Self-regulated exposure to erotic stimuli was investigated in the context of a controlled laboratory experiment. It was hypothesized that erotophiles spend more time viewing erotica and remember the content of the material more accurately than do erotophobes. It was also hypothesized that Type A coronary-prone individuals spend less time viewing erotica than Type Bs. Subjects were 36 male and 34

  17. Mean squared error of prediction (MSEP) estimates for principal component regression (PCR) and partial least squares regression (PLSR)

    Microsoft Academic Search

    2004-01-01

    Abstract The paper presents results from simulations based on real data, comparing several competing,mean,squared,error of prediction,(MSEP) estimators on principal compo- nents regression (PCR) and partial least squares regression (PLSR): leave-one-out cross- validation, K-fold and adjusted K-fold cross-validation, the ordinary bootstrap estimate, the bootstrap,smoothed,cross-validation (BCV) estimate,and the 0.632 bootstrap,esti- mate. The overall performance of the estimators is compared in terms of

  18. DNA double-strand–break complexity levels and their possible contributions to the probability for error-prone processing and repair pathway choice

    PubMed Central

    Schipler, Agnes; Iliakis, George

    2013-01-01

    Although the DNA double-strand break (DSB) is defined as a rupture in the double-stranded DNA molecule that can occur without chemical modification in any of the constituent building blocks, it is recognized that this form is restricted to enzyme-induced DSBs. DSBs generated by physical or chemical agents can include at the break site a spectrum of base alterations (lesions). The nature and number of such chemical alterations define the complexity of the DSB and are considered putative determinants for repair pathway choice and the probability that errors will occur during this processing. As the pathways engaged in DSB processing show distinct and frequently inherent propensities for errors, pathway choice also defines the error-levels cells opt to accept. Here, we present a classification of DSBs on the basis of increasing complexity and discuss how complexity may affect processing, as well as how it may cause lethal or carcinogenic processing errors. By critically analyzing the characteristics of DSB repair pathways, we suggest that all repair pathways can in principle remove lesions clustering at the DSB but are likely to fail when they encounter clusters of DSBs that cause a local form of chromothripsis. In the same framework, we also analyze the rational of DSB repair pathway choice. PMID:23804754

  19. The spectra of base substitutions induced by the impCAB, mucAB and umuDC error-prone DNA repair operons differ following exposure to methyl methanesulfonate.

    PubMed

    Doyle, N; Strike, P

    1995-06-25

    We have used the lacZ reversion assay to study the mutation spectra induced by the Escherichia coli chromosomal umuDC operon and of its two plasmid-borne analogues impCAB and mucAB following exposure of cells to UV light and methyl methanesulfonate (MMS). We have shown that the impCAB, mucAB and umuDC operons all produce a similar response to UV light which results almost exclusively in AT-->GC transitions. However, we found that the three operons produced different responses to alkylating agents. We found that with MMS the chromosomal umuDC operon produced almost exclusively AT-->GC transitions, whilst both mucAB and impCAB produced predominantly transversions. In the case of the impCAB operon the mutation spectrum contained more AT-->TA than GC-->TA transversions; this balance was reversed with mucAB. The effect of the copy number of the error-prone DNA repair operons upon the mutagenic spectra was also studied. The results obtained suggest that the copy number of the imp operon does not greatly affect the specificity of base substitutions observed. However, an increase in the copy number of the umuDC operon greatly affected the specificity of base substitution, such that virtually no transitions were produced and the spectrum was dominated by GC/AT-->TA transversions. It appears that the three error-prone DNA repair operons impCAB, mucAB and umuDC, despite showing strong structural and functional homologies, can display major differences in the spectrum of base changes induced during mutagenesis.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7616965

  20. The reverse transcriptase encoded by the non-LTR retrotransposon R2 is as error-prone as that encoded by HIV-1.

    PubMed

    Jamburuthugoda, Varuni K; Eickbush, Thomas H

    2011-04-15

    Reverse transcriptases (RTs) encoded by a wide range of mobile retroelements have had a major impact on the structure and function of genomes. Among the most abundant elements in eukaryotes are the non long terminal repeat (LTR) retrotransposons. Here we compare the dNTP concentration requirements and error rates of the RT encoded by the non-LTR retrotransposon R2 of Bombyx mori with the well-characterized RTs of retroviruses. Surprisingly, R2 was found to have properties more similar to those of lentiviral RTs, such as human immunodeficiency virus type 1 (HIV-1), than to those of oncoretroviral RTs, such as murine leukemia virus. Like HIV-1 RT, R2 RT was able to synthesize DNA at low dNTP concentrations, suggesting that R2 is able to retrotranspose in nondividing cells. R2 RT also showed levels of misincorporation in biased dNTP pools and replication error rates in M13 lacZ? forward mutation assays, similar to HIV-1 RT. Most of the R2 base substitutions in the forward mutation assay were caused by the misincorporation of dTMP. Analogous to HIV-1, the high error rate of R2 RT appears to be a result of its ability to extend mismatches once generated. We suggest that the low fidelity of R2 RT is a by-product of the flexibility of its active site/dNTP binding pocket required for the target-primed reverse transcription reaction used by R2 for retrotransposition. Finally, we discuss that in spite of the high R2 RT error rate, the long-term nucleotide substitution rate for R2 is not significantly above that associated with cellular DNA replication, based on the frequency of R2 retrotranspositions determined in natural populations. PMID:21320510

  1. Somatic microindels in human cancer: the insertions are highly error-prone and derive from nearby but not adjacent sense and antisense templates.

    PubMed

    Scaringe, William A; Li, Kai; Gu, Dongqing; Gonzalez, Kelly D; Chen, Zhenbin; Hill, Kathleen A; Sommer, Steve S

    2008-09-15

    Somatic microindels (microdeletions with microinsertions) have been studied in normal mouse tissues using the Big Blue lacI transgenic mutation detection system. Here we analyze microindels in human cancers using an endogenous and transcribed gene, the TP53 gene. Microindel frequency, the enhancement of 1-2 microindels and other features are generally similar to that observed in the non-transcribed lacI gene in normal mouse tissues. The current larger sample of somatic microindels reveals recurroids: mutations in which deletions are identical and the co-localized insertion is similar. The data reveal that the inserted sequences derive from nearby but not adjacent sequences in contrast to the slippage that characterizes the great majority of pure microinsertions. The microindel inserted sequences derive from a template on the sense or antisense strand with similar frequency. The estimated error rate of the insertion process of 13% per bp is by far the largest reported in vivo, with the possible exception of somatic hypermutation in the immunoglobulin gene. The data constrain possible mechanisms of microindels and raise the question of whether microindels are 'scars' from the bypass of large DNA adducts by a translesional polymerase, e.g. the 'Tarzan model' presented herein. PMID:18632684

  2. Mutational analysis of the C8-guanine adduct of the environmental carcinogen 3-nitrobenzanthrone in human cells: critical roles of DNA polymerases ? and ? and Rev1 in error-prone translesion synthesis.

    PubMed

    Pande, Paritosh; Malik, Chanchal K; Bose, Arindam; Jasti, Vijay P; Basu, Ashis K

    2014-08-19

    3-Nitrobenzanthrone (3-NBA), a potent mutagen and suspected human carcinogen, is a common environmental pollutant. The genotoxicity of 3-NBA has been associated with its ability to form DNA adducts, including N-(2'-deoxyguanosin-8-yl)-3-aminobenzanthrone (C8-dG-ABA). To investigate the molecular mechanism of C8-dG-ABA mutagenesis in human cells, we have replicated a plasmid containing a single C8-dG-ABA in human embryonic kidney 293T (HEK293T) cells, which yielded 14% mutant progeny. The major types of mutations induced by C8-dG-ABA were G?T>G?A>G?C. siRNA knockdown of the translesion synthesis (TLS) DNA polymerases (pols) in HEK293T cells indicated that pol ?, pol ?, pol ?, pol ?, and Rev1 each have a role in replication across this adduct. The extent of TLS was reduced with each pol knockdown, but the largest decrease (of ?55% reduction) in the level of TLS occurred in cells with knockdown of pol ?. Pol ? and pol ? were considered the major contributors of the mutagenic TLS, because the mutation frequency (MF) decreased by 70%, when these pols were simultaneously knocked down. Rev1 also is important for mutagenesis, as reflected by the 60% reduction in MF upon Rev1 knockdown, but it probably plays a noncatalytic role by physically interacting with the other two Y-family pols. In contrast, pol ? appeared to be involved in the error-free bypass of the lesion, because MF increased by 60% in pol ? knockdown cells. These results provide important mechanistic insight into the bypass of the C8-dG-ABA adduct. PMID:25080294

  3. Error processing in patients with Alzheimer's disease

    Microsoft Academic Search

    Junko Ito; Junko Kitagawa

    2005-01-01

    Patients with dementia are prone to make errors while they perform a task. To evaluate error detection and action monitoring in patients with dementia of the Alzheimer type (DAT) at a relatively early stage of the illness, error negativity (Ne) and error positivity (Pe) of event-related potentials (ERPs) obtained by averages time-locked to error response were studied using a lexical

  4. Vegetation fire proneness in Europe

    NASA Astrophysics Data System (ADS)

    Pereira, Mário; Aranha, José; Amraoui, Malik

    2015-04-01

    Fire selectivity has been studied for vegetation classes in terms of fire frequency and fire size in a few European regions. This analysis is often performed along with other landscape variables such as topography, distance to roads and towns. These studies aims to assess the landscape sensitivity to forest fires in peri-urban areas and land cover changes, to define landscape management guidelines and policies based on the relationships between landscape and fires in the Mediterranean region. Therefore, the objectives of this study includes the: (i) analysis of the spatial and temporal variability statistics within Europe; and, (ii) the identification and characterization of the vegetated land cover classes affected by fires; and, (iii) to propose a fire proneness index. The datasets used in the present study comprises: Corine Land Cover (CLC) maps for 2000 and 2006 (CLC2000, CLC2006) and burned area (BA) perimeters, from 2000 to 2013 in Europe, provided by the European Forest Fire Information System (EFFIS). The CLC is a part of the European Commission programme to COoRdinate INformation on the Environment (Corine) and it provides consistent, reliable and comparable information on land cover across Europe. Both the CLC and EFFIS datasets were combined using geostatistics and Geographical Information System (GIS) techniques to access the spatial and temporal evolution of the types of shrubs and forest affected by fires. Obtained results confirms the usefulness and efficiency of the land cover classification scheme and fire proneness index which allows to quantify and to compare the propensity of vegetation classes and countries to fire. As expected, differences between northern and southern Europe are notorious in what concern to land cover distribution, fire incidence and fire proneness of vegetation cover classes. This work was supported by national funds by FCT - Portuguese Foundation for Science and Technology, under the project PEst-OE/AGR/UI4033/2014 and by the project SUSTAINSYS: Environmental Sustainable Agro-Forestry Systems (NORTE-07-0124-FEDER-000044), financed by the North Portugal Regional Operational Programme (ON.2 - O Novo Norte), under the National Strategic Reference Framework (QREN), through the European Regional Development Fund (FEDER), as well as by National Funds (PIDDAC) through the Portuguese Foundation for Science and Technology (FCT/MEC).

  5. Fission Yeast Rad52 Phosphorylation Restrains Error Prone Recombination Pathways

    PubMed Central

    Bellini, Angela; Girard, Pierre-Marie; Tessier, Ludovic; Sage, Evelyne; Francesconi, Stefania

    2014-01-01

    Rad52 is a key protein in homologous recombination (HR), a DNA repair pathway dedicated to double strand breaks and recovery of blocked or collapsed replication forks. Rad52 allows Rad51 loading on single strand DNA, an event required for strand invasion and D-loop formation. In addition, Rad52 functions also in Rad51 independent pathways because of its ability to promote single strand annealing (SSA) that leads to loss of genetic material and to promote D-loops formation that are cleaved by Mus81 endonuclease. We have previously reported that fission yeast Rad52 is phosphorylated in a Sty1 dependent manner upon oxidative stress and in cells where the early step of HR is impaired because of lack of Rad51. Here we show that Rad52 is also constitutively phosphorylated in mus81 null cells and that Sty1 partially impinges on such phosphorylation. As upon oxidative stress, the Rad52 phosphorylation in rad51 and mus81 null cells appears to be independent of Tel1, Rad3 and Cdc2. Most importantly, we show that mutating serine 365 to glycine (S365G) in Rad52 leads to loss of the constitutive Rad52 phosphorylation observed in cells lacking Rad51 and to partial loss of Rad52 phosphorylation in cells lacking Mus81. Contrariwise, phosphorylation of Rad52-S365G protein is not affected upon oxidative stress. These results indicate that different Rad52 residues are phosphorylated in a Sty1 dependent manner in response to these distinct situations. Analysis of spontaneous HR at direct repeats shows that mutating serine 365 leads to an increase in spontaneous deletion-type recombinants issued from mitotic recombination that are Mus81 dependent. In addition, the recombination rate in the rad52-S365G mutant is further increased by hydroxyurea, a drug to which mutant cells are sensitive. PMID:24748152

  6. List of Error-Prone Abbreviations, Symbols, and Dose Designations

    MedlinePLUS

    ... unit dose (e.g., diltiazem 125 mg IV infusion “UD” misinterpreted as meaning to give the entire infusion as a unit [bolus] dose) Use “as directed” ... Drug NamesIntended Meaning Misinterpretation Correction “Nitro” drip nitroglycerin infusion Mistaken as sodium nitroprusside infusion Use complete drug ...

  7. Error-prone translesion synthesis mediates acquired chemoresistance

    E-print Network

    Xie, Kun

    The development of cancer drug resistance is a persistent clinical problem limiting the successful treatment of disseminated malignancies. However, the molecular mechanisms by which initially chemoresponsive tumors develop ...

  8. Fantasy Proneness: Hypnosis, Developmental Antecedents, and Psychopathology

    Microsoft Academic Search

    Steven Jay Lynn; Judith W. Rhue

    1988-01-01

    This article presents a summary of the findings of our ongoing research program on the fantasy-prone person. In seven studies, nearly 6,000 college students were screened in order to obtain five samples of 156 fantasy-prone subjects. Fantasy-prone subjects (fantasizers) were selected from the upper 2%–4% of the college population on a measure of imaginative involvement and contrasted with nonfantasizers (lower

  9. Operationalizing Proneness to Externalizing Psychopathology as a Multivariate Psychophysiological Phenotype

    PubMed Central

    Nelson, Lindsay D.; Patrick, Christopher J.; Bernat, Edward M.

    2010-01-01

    The externalizing dimension is viewed as a broad dispositional factor underlying risk for numerous disinhibitory disorders. Prior work has documented deficits in event-related brain potential (ERP) responses in individuals prone to externalizing problems. Here, we constructed a direct physiological index of externalizing vulnerability from three ERP indicators and evaluated its validity in relation to criterion measures in two distinct domains: psychometric and physiological. The index was derived from three ERP measures that covaried in their relations with externalizing proneness the error-related negativity and two variants of the P3. Scores on this ERP composite predicted psychometric criterion variables and accounted for externalizing-related variance in P3 response from a separate task. These findings illustrate how a diagnostic construct can be operationalized as a composite (multivariate) psychophysiological variable (phenotype). PMID:20573054

  10. Virtual PCR

    Microsoft Academic Search

    S N Gardner; D S Clague; J A Vandersall; G Hon; P L Williams

    2006-01-01

    The polymerase chain reaction (PCR) stands among the keystone technologies for analysis of biological sequence data. PCR is used to amplify DNA, to generate many copies from as little as a single template. This is essential, for example, in processing forensic DNA samples, pathogen detection in clinical or biothreat surveillance applications, and medical genotyping for diagnosis and treatment of disease.

  11. Digital PCR

    PubMed Central

    Vogelstein, Bert; Kinzler, Kenneth W.

    1999-01-01

    The identification of predefined mutations expected to be present in a minor fraction of a cell population is important for a variety of basic research and clinical applications. Here, we describe an approach for transforming the exponential, analog nature of the PCR into a linear, digital signal suitable for this purpose. Single molecules are isolated by dilution and individually amplified by PCR; each product is then analyzed separately for the presence of mutations by using fluorescent probes. The feasibility of the approach is demonstrated through the detection of a mutant ras oncogene in the stool of patients with colorectal cancer. The process provides a reliable and quantitative measure of the proportion of variant sequences within a DNA sample. PMID:10430926

  12. Ethnic and gender differences in boredom proneness

    SciTech Connect

    Gibson, G.S.; Morales,

    1996-02-01

    Although boredom may exhibit many shared elements, culturally specific attitudes have also been found to exist. The present paper investigated boredom proneness among African-American college students. Data from 120 participants on the Boredom Proneness (BP) Scale was analyzed and compared to cross-cultural participants. African-American females scored significantly higher than African-American males. Scores were presented from two other studies to show a comparative look at boredom proneness in five other ethnic groups. African-American females are the only female ethnic group to score higher on the BP Scale than their male counterparts. Additionally, overall African-Americans, were found to have higher BP scores than their Western counterparts.

  13. PCR thermocycler

    DOEpatents

    Benett, William J.; Richards, James B.

    2005-05-17

    A sleeve-type silicon polymerase chain reaction (PCR) chamber or thermocycler having improved thermal performance. The silicon sleeve reaction chamber is improved in thermal performance by etched features therein that reduce thermal mass and increase the surface area of the sleeve for cooling. This improved thermal performance of the thermocycler enables an increase in speed and efficiency of the reaction chamber. The improvement is accomplished by providing grooves in the faces of the sleeve and a series of grooves on the interior surfaces that connect with grooves on the faces of the sleeve. The grooves can be anisotropically etched in the silicon sleeve simultaneously with formation of the chamber.

  14. The Detection of Fault-Prone Programs

    Microsoft Academic Search

    John C. Munson; Taghi M. Khoshgoftaar

    1992-01-01

    The use of the statistical technique of discriminant analysis as a tool for the detection of fault-prone programs is explored. A principal-components procedure was employed to reduce simple multicollinear complexity metrics to uncorrelated measures on orthogonal complexity domains. These uncorrelated measures were then used to classify programs into alternate groups, depending on the metric values of the program. The criterion

  15. Interfraction and Intrafraction Setup Variability for Prone Breast Radiation Therapy

    SciTech Connect

    Mitchell, James; Formenti, Silvia C. [Department of Radiation Oncology, New York University School of Medicine, New York, NY (United States); DeWyngaert, J. Keith, E-mail: Keith.DeWyngaert@nyumc.or [Department of Radiation Oncology, New York University School of Medicine, New York, NY (United States)

    2010-04-15

    Purpose: To report the interfraction and intrafraction setup variation for prone breast radiotherapy and to determine an appropriate clinical tumor volume (CTV) to planning target volume (PTV) margin to account for motion and positional uncertainties. Methods and Materials: Ten consecutive patients were prospectively enrolled in a protocol of accelerated, hypofractionated prone breast irradiation. Portal images were acquired using an electronic portal imaging device in cine mode. Interfraction setup error was determined by comparing the first image from each fraction with the digitally reconstructed radiograph. The intrafraction motion was determined by evaluating every image acquired during each fraction and measuring the maximum displacement of an external fiducial and the breast surface. Mean values and 95% confidence intervals (CI) were calculated. Based on these results, a CTV to PTV expansion was derived using the equation M = 2.5SIGMA{sub tot} + 0.7sigma{sub tot.} Results: The mean interfraction setup variability for the fiducial was 0.08 cm (CI: 0.02-0.14) in the anterior to posterior (AP) direction and -0.04 cm (CI: -0.07-0.00) in the superior to inferior (SI) direction. The mean interfraction variability of the breast surface was -0.14 cm (CI: -0.24 to -0.04) in the AP direction. The mean intrafraction displacements of the fiducial and the breast surface were 0.13 cm (CI: 0.12-0.15) and 0.15 cm (CI: 0.14-0.17), respectively. Using the systematic and random errors for the external fiducial, the calculated CTV to PTV expansion was 1.4 cm. Conclusions: Acceptable interfraction and intrafraction variability were demonstrated. The findings resulted in a CTV to PTV expansion of 1.4 cm.

  16. Covariation bias in panic-prone individuals.

    PubMed

    Pauli, P; Montoya, P; Martz, G E

    1996-11-01

    Covariation estimates between fear-relevant (FR; emergency situations) or fear-irrelevant (FI; mushrooms and nudes) stimuli and an aversive outcome (electrical shock) were examined in 10 high-fear (panic-prone) and 10 low-fear respondents. When the relation between slide category and outcome was random (illusory correlation), only high-fear participants markedly overestimated the contingency between FR slides and shocks. However, when there was a high contingency of shocks following FR stimuli (83%) and a low contingency of shocks following FI stimuli (17%), the group difference vanished. Reversal of contingencies back to random induced a covariation bias for FR slides in high- and low-fear respondents. Results indicate that panic-prone respondents show a covariation bias for FR stimuli and that the experience of a high contingency between FR slides and aversive outcomes may foster such a covariation bias even in low-fear respondents. PMID:8952200

  17. Paranormal belief and proneness to dissociation.

    PubMed

    Irwin, H J

    1994-12-01

    The study investigated the relationship between scores on paranormal belief and proneness to dissociation in a sample of 100 Australian students of psychology. Scores on dissociation were positively correlated with those on global paranormal belief and with belief in psi, precognition, spiritualism, and extraordinary life-forms. It is suggested that in some instances paranormal beliefs may be a component of a complex defensive framework constructed in the face of the perceived uncontrollability of life. PMID:7892403

  18. Why is psychiatry prone to fads?

    PubMed

    Paris, Joel

    2013-10-01

    Psychiatry has long been prone to fads. The main reason is that mental illness is poorly understood and can be difficult to treat. Most diagnostic fads have involved the extension of well-known categories into broader spectra. The most prominent treatment fads have involved the overuse of pharmacological interventions and a proliferation of methods for psychotherapy. The best antidote to fads is a commitment to evidence-based psychiatry. PMID:24165102

  19. Digital PCR and Quantitation

    E-print Network

    Perkins, Richard A.

    Applied Genetics Digital PCR and Quantitation Ross Haynes Research Biologist, Applied Genetics Group Forensics@NIST 2012 Meeting Gaithersburg, MD November 28, 2012 #12;Applied Genetics Agenda · Why quantitate with qPCR? · How digital PCR Will Help Quantitation · Quantitative PCR versus Digital PCR

  20. New fire-prone areas in Europe

    NASA Astrophysics Data System (ADS)

    Thonicke, Kirsten; Knorr, Wolfgang; Wu, Minchao; Arneth, Almut

    2014-05-01

    With climate change, fire risk is projected to increase in many parts of Europe. Under severe climate change this could also lead to an increase of fire in ecosystems, which are not dominated by fires under current climate. In that case, fire risk would cause area and biomass burnt to increase, i.e. keep the linear relationship, and lead to an enormous increase in fire severity. We have developed an algorithm to map new fire-prone areas in Europe. It identifies grid points where large-scale fires, yet rare, are becoming the mean at the end of the 21st century. We applied this algorithm to simulation results from experiments where the dynamic vegetation-fire models LPJ-GUESS-SIMFIRE and LPJmL-SPITFIRE model were applied to scenarios of climate change and human population. Since both models simulate bi-directional feedbacks of vegetation dynamics and fire, simulated changes in fire regimes inherently reflect changes in fuel composition and fuel availability. Changes in future fire regimes and resulting new fire-prone areas as projected for the 21st century using CMIP5 climate scenarios (RCP8.5 vs. RPC2.6) will be presented. First results indicate that the new fire-prone areas would be found in eastern Europe. Depending on the climate scenario and vegetation-fire model used, it could also extend to central and south-eastern Europe. What this implies for vegetation composition and dynamics in the affected areas and how fire and climate change interact to lead to such changes will be shown.

  1. 44 CFR 60.24 - Planning considerations for flood-related erosion-prone areas.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ...Planning considerations for flood-related erosion-prone areas. 60.24 Section...Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.24 Planning considerations for flood-related erosion-prone areas. The planning...

  2. Characterization of genetic deletions in Becker muscular dystrophy using monoclonal antibodies against a deletion-prone region of dystrophin

    Microsoft Academic Search

    Le Thiet Thanh; Nguyen Thi Man; G. E. Morris; C. A. Sewry; V. Dubowitz

    1995-01-01

    We have produced a new panel of 20 monoclonal antibodies (mAbs) against a region of the dystrophin protein corresponding to a deletion-prone region of the Duchenne muscular dystrophy gene (exons 45-50). We show that immunohistochemistry or Western blotting with these {open_quotes}exon-specific{close_quotes} mAbs can provide a valuable addition to Southern blotting or PCR methods for the accurate identification of genetic deletions

  3. The cognitive underpinnings of coronary-prone behaviors

    Microsoft Academic Search

    Lynda H. Powell

    1992-01-01

    Research on the cognitive underpinnings of coronary-prone behaviors is important to the development of sophisticated transactional models to explain coronary-prone behaviors, and to the successful promotion of an enduring change in them. The cognitive literature has been organized around three central coronary-prone behaviors—hostility\\/competitiveness, low self-esteem, and low perceived control—and for each behavior, the literature on basic beliefs, attitudes, overt behaviors,

  4. Predicting Attack-prone Components with Internal Metrics

    Microsoft Academic Search

    Michael Gegick; Laurie Williams; Jason Osborne

    Extensive research has shown that reliability models based upon software metrics can be used to predict which components are fault- and\\/or failure-prone early in the development process. In this research, we seek to parallel failure-prone component prediction with security models to predict which components are attack-prone. Security experts can use these models to make informed risk management decisions and to

  5. The effect of shame-proneness, guilt-proneness, and internalizing tendencies on nonsuicidal self-injury.

    PubMed

    VanDerhei, Susan; Rojahn, Johannes; Stuewig, Jeffrey; McKnight, Patrick E

    2014-06-01

    Nonsuicidal self-injury is especially common in adolescents and young adults. Self-injury may be related to shame or guilt--two moral emotions--as these differentially predict other maladaptive behaviors. Using a college sample, we examined not only how shame-proneness, guilt-proneness, and internalizing emotional tendencies related to self-injury, but also whether these moral emotions moderate the relation between internalizing tendencies and self-injury. High shame-proneness was associated with higher frequencies of self-injury. High guilt-proneness was associated with less self-injury, although this effect was mitigated at higher levels of internalizing tendencies. These results suggest shame-proneness is a risk factor for self-injury, while guilt-proneness is protective. PMID:24313627

  6. The accident-prone and overuse-prone profiles of the young athlete.

    PubMed

    Lysens, R J; Ostyn, M S; Vanden Auweele, Y; Lefevre, J; Vuylsteke, M; Renson, L

    1989-01-01

    A 1 year prospective study was done to develop an accident-prone and overuse-prone profile of young athletes. A group of 185 freshman physical education students (118 males; 67 females of the same age (18.3 +/- 0.5 years) trained under the same conditions and were exposed to similar extrinsic risk factors. Using a descriptive statistical technique, an analysis of correspondence, the complex interrelation between the criterium variables (acute injuries and overuse injuries) and the predictor variables (intrinsic risk factors; physical characteristics--anthropometric data, physical fitness parameters, flexibility aspects and malalignment of the lower extremities; and psychological factors--16 personality traits) was estimated for males and females separately. Although dynamic strength seems to be an important risk factor in acute injuries, sports accidents must be seen in relation to psychological factors. However, the overuse-prone profile is mainly based on physical traits: a combination of muscle weakness, ligamentous laxity, and muscle tightness predisposes to stress injuries. In addition, these overuse effects are intensified by large body weight and length, a high explosive strength, and malalignment of the lower limbs. Nevertheless, it has to be kept in mind that psychosomatic factors play a role in how one experiences these overuse phenomena. PMID:2610274

  7. Examining the dimensionality of coupon proneness: a random coefficients approach

    Microsoft Academic Search

    Richard Colombo; Kapil Bawa; Srini S. Srinivasan

    2003-01-01

    Many previous studies have sought to measure consumers’ coupon proneness but have tended to assume that this trait is unidimensional in nature, i.e., an individual's coupon proneness is the same for all types of coupons. It is argued in this study that because consumers differ in the products they shop for and in the types of coupons they are exposed

  8. A Statistical Framework for the Prediction of Fault-Proneness

    Microsoft Academic Search

    Yan M; Lan Guo; Bojan Cukic

    Accurate prediction of fault prone modules in software development process enables eective discovery and identification of the defects. Such prediction models are espe- cially valuable for the large-scale systems, where verification experts need to focus their attention and resources to problem areas in the system under development. This pa- per presents a methodology for predicting fault prone modules using a

  9. The impact of covariate measurement error on risk prediction.

    PubMed

    Khudyakov, Polyna; Gorfine, Malka; Zucker, David; Spiegelman, Donna

    2015-07-10

    In the development of risk prediction models, predictors are often measured with error. In this paper, we investigate the impact of covariate measurement error on risk prediction. We compare the prediction performance using a costly variable measured without error, along with error-free covariates, to that of a model based on an inexpensive surrogate along with the error-free covariates. We consider continuous error-prone covariates with homoscedastic and heteroscedastic errors, and also a discrete misclassified covariate. Prediction performance is evaluated by the area under the receiver operating characteristic curve (AUC), the Brier score (BS), and the ratio of the observed to the expected number of events (calibration). In an extensive numerical study, we show that (i) the prediction model with the error-prone covariate is very well calibrated, even when it is mis-specified; (ii) using the error-prone covariate instead of the true covariate can reduce the AUC and increase the BS dramatically; (iii) adding an auxiliary variable, which is correlated with the error-prone covariate but conditionally independent of the outcome given all covariates in the true model, can improve the AUC and BS substantially. We conclude that reducing measurement error in covariates will improve the ensuing risk prediction, unless the association between the error-free and error-prone covariates is very high. Finally, we demonstrate how a validation study can be used to assess the effect of mismeasured covariates on risk prediction. These concepts are illustrated in a breast cancer risk prediction model developed in the Nurses' Health Study. Copyright © 2015?John Wiley & Sons, Ltd. PMID:25865315

  10. Pre-PCR processing

    Microsoft Academic Search

    Peter Rådström; Rickard Knutsson; Petra Wolffs; Maria Lövenklev; Charlotta Löfström

    2004-01-01

    Polymerase chain reaction (PCR) is recognized as a rapid, sensitive, and specific molecular diagnostic tool for the analysis\\u000a of nucleic acids. However, the sensitivity and kinetics of diagnostic PCR may be dramatically reduced when applied directly\\u000a to biological samples, such as blood and feces, owing to PCR-inhibitory components. As a result, pre-PCR processing procedures\\u000a have been developed to remove or

  11. Errors of Inference in Structural Equation Modeling

    ERIC Educational Resources Information Center

    McCoach, D. Betsy; Black, Anne C.; O'Connell, Ann A.

    2007-01-01

    Although structural equation modeling (SEM) is one of the most comprehensive and flexible approaches to data analysis currently available, it is nonetheless prone to researcher misuse and misconceptions. This article offers a brief overview of the unique capabilities of SEM and discusses common sources of user error in drawing conclusions from…

  12. Psychological performance of accident-prone automobile drivers in China: a case-control study.

    PubMed

    Jin, H Q; Araki, S; Wu, X K; Zhang, Y W; Yokoyama, K

    1991-03-01

    To evaluate the role of neurobehavioural factors in the aetiology of recurrent automobile accidents, we administered the Revised Wechsler Adult Intelligence Scale (WAIS-R), the Eysenck Personality Questionnaire (EPQ), and choice and simple reaction time tests to 31 accident-prone automobile drivers. These drivers who had caused three or more traffic accidents during the years 1980-1984, were selected from records of 2723 traffic accidents registered by Hefei Traffic Police Department during the years 1980-1984. The same tests were administered to an equal number of sex- and age-matched control drivers who had no reported involvement in automobile accidents. None of the subjects had suffered from any neuropsychiatric illness or head injury. Comparisons between the two groups indicated that for accident-prone drivers scores on picture completion and block design subtests of the WAIS-R were significantly lowered (p less than 0.05); scores for neurosis extrovert behaviour and psychosis (EPQ) were significantly higher (p less than 0.05); and the number of errors in the choice reaction time test was significantly higher (p less than 0.01). It is suggested that accident-prone drivers have lower psychological performance, poorer judgement and a higher tendency than safe drivers to be neurotic, extrovert and psychotic. PMID:2066226

  13. MRI Guidance for Accelerated Partial Breast Irradiation in Prone Position: Imaging Protocol Design and Evaluation

    SciTech Connect

    Ahn, Kang-Hyun [Department of Radiation Oncology, Stanford University, Stanford, CA (United States)], E-mail: ahn.2007@stanford.edu; Hargreaves, Brian A.; Alley, Marcus T. [Department of Radiology, Stanford University, Stanford, CA (United States); Horst, Kathleen C.; Luxton, Gary [Department of Radiation Oncology, Stanford University, Stanford, CA (United States); Daniel, Bruce L. [Department of Radiology, Stanford University, Stanford, CA (United States); Hristov, Dimitre [Department of Radiation Oncology, Stanford University, Stanford, CA (United States)

    2009-09-01

    Purpose: To design and evaluate a magnetic resonance imaging (MRI) protocol to be incorporated in the simulation process for external beam accelerated partial breast irradiation. Methods and Materials: An imaging protocol was developed based on an existing breast MRI technique with the patient in the prone position on a dedicated coil. Pulse sequences were customized to exploit T1 and T2 contrast mechanisms characteristic of lumpectomy cavities. A three-dimensional image warping algorithm was included to correct for geometric distortions related to nonlinearity of spatially encoding gradients. Respiratory motion, image distortions, and susceptibility artifacts of 3.5-mm titanium surgical clips were examined. Magnetic resonance images of volunteers were acquired repeatedly to analyze residual setup deviations resulting from breast tissue deformation. Results: The customized sequences generated high-resolution magnetic resonance images emphasizing lumpectomy cavity morphology. Respiratory motion was negligible with the subject in the prone position. The gradient-induced nonlinearity was reduced to less than 1 mm in a region 15 cm away from the isocenter of the magnet. Signal-void regions of surgical clips were 4 mm and 8 mm for spin echo and gradient echo images, respectively. Typical residual repositioning errors resulting from breast deformation were estimated to be 3 mm or less. Conclusions: MRI guidance for accelerated partial breast irradiation with the patient in the prone position with adequate contrast, spatial fidelity, and resolution is possible.

  14. Restraint in police use of force events: examining sudden in custody death for prone and not-prone positions.

    PubMed

    Hall, Christine; Votova, Kristine; Heyd, Christopher; Walker, Matthew; MacDonald, Scott; Eramian, Doug; Vilke, Gary M

    2015-04-01

    Little is understood about the incidence of sudden death, its underlying pathophysiology, or its actual relationship to subject positioning. We report data from 4828 consecutive use of force events (August 2006-March 2013) in 7 Canadian police agencies in Eastern and Western Canada. Consecutive subjects aged >18 years who were involved in a police use of force event were included regardless of outcome. Officers prospectively documented: final resting position of the subject (prone or non-prone), intoxicants and/or emotional distress, presence of features of excited delirium, and the use of all force modalities. Our outcome of interest was sudden in-custody death. Our study has 80% power to detect a difference of 0.5% in sudden death between the positions. In over 3.25 million consecutive police--public interactions; use of force occurred in 4,828 subjects (0.1% of police public interactions; 95% CI = 0.1%, 0.1%). Subjects were usually male (87.5%); median age 32 years; 81.5% exhibited alcohol and/or drug intoxication, and/or emotional distress at the scene. Significantly more subjects remained in a non-prone vs. prone position; but over 2000 subjects remained prone. One individual died suddenly and unexpectedly in the non-prone position with all 10 features of excited delirium. No subject died in the prone position. There was no significant difference in sudden in custody death, in a worst case scenario 99.8% of subjects would be expected to survive being in either the prone or non-prone position following police use of force. PMID:25735781

  15. Seborrhoea in Acne-Prone and Acne-Free Patients

    Microsoft Academic Search

    G. E. Piérard; C. Piérard-Franchimont; T. Lê

    1987-01-01

    We have studied the relationship between seborrhoea and acne by using the Lipometre® and Sebutape® films. Seborrhoea is more intense in acne-prone than in acne-free patients. For a given overall amount of sebum excreted, the individual activity of sebaceous follicles differs in the two groups of individuals tested. Seborrhoea in acne-prone patients is due to the presence of some highly

  16. Hemodynamic evaluation of the prone position by transesophageal echocardiography

    Microsoft Academic Search

    Shigeyoshi Toyota; Yoshikiyo Amaki

    1998-01-01

    Study Objective: To evaluate the hemodynamic response in the prone position in surgical patients by measuring the effects of prone positioning on cardiac function using transesophageal echocardiography (TEE).Design: Prospective study.Setting: Elective surgery at a university hospital.Patients: 15 adult ASA physical status I and II patients free of significant coexisting disease undergoing lumbar laminectomy.Interventions and Measurements: Approximately 15 minutes after the

  17. A PCR based protocol for detecting indel mutations induced by TALENs and CRISPR/Cas9 in zebrafish.

    PubMed

    Yu, Chuan; Zhang, Yaguang; Yao, Shaohua; Wei, Yuquan

    2014-01-01

    Genome editing techniques such as the zinc-finger nucleases (ZFNs), transcription activator-like effecter nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system Cas9 can induce efficient DNA double strand breaks (DSBs) at the target genomic sequence and result in indel mutations by the error-prone non-homologous end joining (NHEJ) DNA repair system. Several methods including sequence specific endonuclease assay, T7E1 assay and high resolution melting curve assay (HRM) etc have been developed to detect the efficiency of the induced mutations. However, these assays have some limitations in that they either require specific sequences in the target sites or are unable to generate sequencing-ready mutant DNA fragments or unable to distinguish induced mutations from natural nucleotide polymorphism. Here, we developed a simple PCR-based protocol for detecting indel mutations induced by TALEN and Cas9 in zebrafish. We designed 2 pairs of primers for each target locus, with one putative amplicon extending beyond the putative indel site and the other overlapping it. With these primers, we performed a qPCR assay to efficiently detect the frequencies of newly induced mutations, which was accompanied with a T-vector-based colony analysis to generate single-copy mutant fragment clones for subsequent DNA sequencing. Thus, our work has provided a very simple, efficient and fast assay for detecting induced mutations, which we anticipate will be widely used in the area of genome editing. PMID:24901507

  18. Perspective-taking abilities in the balance between autism tendencies and psychosis proneness.

    PubMed

    Abu-Akel, Ahmad M; Wood, Stephen J; Hansen, Peter C; Apperly, Ian A

    2015-06-01

    Difficulties with the ability to appreciate the perspective of others (mentalizing) is central to both autism and schizophrenia spectrum disorders. While the disorders are diagnostically independent, they can co-occur in the same individual. The effect of such co-morbidity is hypothesized to worsen mentalizing abilities. The recent influential 'diametric brain theory', however, suggests that the disorders are etiologically and phenotypically diametrical, predicting opposing effects on one's mentalizing abilities. To test these contrasting hypotheses, we evaluated the effect of psychosis and autism tendencies on the perspective-taking (PT) abilities of 201 neurotypical adults, on the assumption that autism tendencies and psychosis proneness are heritable dimensions of normal variation. We show that while both autism tendencies and psychosis proneness induce PT errors, their interaction reduced these errors. Our study is, to our knowledge, the first to observe that co-occurring autistic and psychotic traits can exert opposing influences on performance, producing a normalizing effect possibly by way of their diametrical effects on socio-cognitive abilities. This advances the notion that some individuals may, to some extent, be buffered against developing either illness or present fewer symptoms owing to a balanced expression of autistic and psychosis liability. PMID:25972469

  19. Sampling Error

    NSDL National Science Digital Library

    This one page article, created by Statistics Canada, describes the meaning behind random sampling error. It points our the relationship of the random sampling error with the sample size, population size, variability of the characteristic, sampling plan, and measuring sampling error. While brief, this provides valuable information and also links users to additional resources concerning statistics.

  20. [Real time quantitative PCR].

    PubMed

    Kim, D W

    2001-04-21

    So far, quantitative techniques, such as PCR and FISH, have been used to detect of DNA and RNA. However, it is difficult to measure and compare the exact amount of amplified products with the results of endpoint analysis in conventional PCR techniques. Theoretically, there is a quantitative relationship between amount of starting target sequence and amount of PCR product at any given cycle. The development of real-time quantitative PCR (RQ-PCR) has eliminated the variability associated with conventional quantitative PCR, thus allowing the routine and reliable quantitation of PCR products. Detection of fluorescence during the thermal cycling process can be performed using iCycler(Bio-Rad), the GeneAmp 5700 or 7700(ABI-PRISM), and Light-Cycler(Roche). Two fluorogenic probes are available for use on real time quantitation. The fluorogenic 5'-nuclease assay(Taqman method) uses a fluorogenic probe to enable the detection of a sequence specific PCR product. Fluorogenic probe is incorporated with the reporter dye on the 5' end and the quencher on the 3' end. The second method uses SYBR Green I dye which is a highly specific double-stranded DNA binding dye. Real-time PCR is able to be possible exact quantitation of DNA and RNA much more precise and reproducible because it is based on CT values acquired during the exponential phase of PCR rather than endpoint. In this review, the detail protocol of real time quantitative PCR technique will be introduced and our recently developed system for exact quantitation of BCR-ABL fusion gene in CML is going to be described. PMID:11708318

  1. DEM-based Approaches for the Identification of Flood Prone Areas

    NASA Astrophysics Data System (ADS)

    Samela, Caterina; Manfreda, Salvatore; Nardi, Fernando; Grimaldi, Salvatore; Roth, Giorgio; Sole, Aurelia

    2013-04-01

    The remarkable number of inundations that caused, in the last decades, thousands of deaths and huge economic losses, testifies the extreme vulnerability of many Countries to the flood hazard. As a matter of fact, human activities are often developed in the floodplains, creating conditions of extremely high risk. Terrain morphology plays an important role in understanding, modelling and analyzing the hydraulic behaviour of flood waves. Research during the last 10 years has shown that the delineation of flood prone areas can be carried out using fast methods that relay on basin geomorphologic features. In fact, the availability of new technologies to measure surface elevation (e.g., GPS, SAR, SAR interferometry, RADAR and LASER altimetry) has given a strong impulse to the development of Digital Elevation Models (DEMs) based approaches. The identification of the dominant topographic controls on the flood inundation process is a critical research question that we try to tackle with a comparative analysis of several techniques. We reviewed four different approaches for the morphological characterization of a river basin with the aim to provide a description of their performances and to identify their range of applicability. In particular, we explored the potential of the following tools. 1) The hydrogeomorphic method proposed by Nardi et al. (2006) which defines the flood prone areas according to the water level in the river network through the hydrogeomorphic theory. 2) The linear binary classifier proposed by Degiorgis et al. (2012) which allows distinguishing flood-prone areas using two features related to the location of the site under exam with respect to the nearest hazard source. The two features, proposed in the study, are the length of the path that hydrologically connects the location under exam to the nearest element of the drainage network and the difference in elevation between the cell under exam and the final point of the same path. 3) The method by Manfreda et al. (2011) that suggested a modified Topographic Index (TIm) for the identification of flood prone area. 4) The downslope index proposed by Hjerdt et al. (2004) that quantifies the topographic controls on hydrology by evaluating head differences following the (surface) flow path in the steepest direction. The method does not use the exit point at the stream as reference; instead, the algorithm looks at how far a parcel of water has to travel along its flow path to lose a given head potential, d [m]. This last index was not defined with the aim to describe flood prone areas; in fact it represents an interesting alternative descriptor of morphological features that deserve to be tested. Analyses have been carried out for some Italian catchments. The outcomes of the four methods are presented using, for calibration and validation purposes, flood inundation maps made available by River Basin Authorities. The aim is, therefore, to evaluate the reliability and the relative errors in the detection of the areas subject to the flooding hazard. These techniques should not be considered as an alternative of traditional procedures, but additional tool for the identification of flood-prone areas and hazard graduation over large regions or when a preliminary identification is needed. Reference Degiorgis M., G. Gnecco, S. Gorni, G. Roth, M. Sanguineti, A. C. Taramasso, Classifiers for the detection of flood-prone areas using remote sensed elevation data, J. Hydrol., 470-471, 302-315, 2012. Hjerdt, K. N., J. J. McDonnell, J. Seibert, A. Rodhe, A new topographic index to quantify downslope controls on local drainage, Water Resour. Res., 40, W05602, 2004. Manfreda, S., M. Di Leo, A. Sole, Detection of Flood Prone Areas using Digital Elevation Models, Journal of Hydrologic Engineering, Vol. 16, No. 10, 781-790, 2011. Nardi, F., E. R. Vivoni, S. Grimaldi, Investigating a floodplain scaling relation using a hydrogeomorphic delineation method, Water Resour. Res., 42, W09409, 2006.

  2. SyncChecker: Detecting Synchronization Errors between MPI Applications and Libraries

    E-print Network

    Qin, Feng

    SyncChecker: Detecting Synchronization Errors between MPI Applications and Libraries Zhezhe Chen the performance, nonblocking communication is prone to synchronization errors between MPI applications and the underlying MPI libraries. Such synchroniza- tion error occurs in the following way. After initiating nonblock

  3. Self-calibrating a Stereo Head: An Error Analysis in the Neighbourhood of Degenerate Configurations

    Microsoft Academic Search

    Lourdes De Agapito; D. Q. Huynh; Michael J. Brooks

    1998-01-01

    We show that the self-calibration of a stereo head corresponding points in an image pair is in certain circumstances prone to considerable error. A novel error analysis reveals that the automated determination of relative orientation and focal length is adversely affected when the cameras verge inwards a similar amount, and when the principal point locations have a horizontal error. This

  4. Pattern recognition of earthquake prone area in North China

    E-print Network

    Gu, Ji-Min

    1989-01-01

    PATTERN RECOGNITIOV OF EARTHQUAKE PRONE AREA IV NORTH CHINA A Thesis JI-XiiiV GU Submitted to the Office of Graduate Studies of Texas AkM University in partial fulfillment of the requirements for the degree of XIASTER OF SCIE'VCE August 1989... ( Xlember) J. E. Russell (lvtember) Joel S. Watkins (Head of Department) August 1989 ABSTRACT Pattern Recognition of Earthquake-Prone Areas in North China, ( August 1989) Ji-min Gu Shanghai University of Science and Technology, Shanghai, China Co...

  5. Reverse Transcription-PCR

    NSDL National Science Digital Library

    American Society For Microbiology

    2003-05-12

    This Flash animation shows how the method of reverse transcription-PCR is performed and some sample data are produced. It uses sound and mouse-over identification to help students learn more and retain the information.

  6. Quantitative PCR Protocol

    NSDL National Science Digital Library

    The Jackson Laboratory (The Jackson Laboratory)

    2012-01-06

    This protocol describes how to genotype mice using Quantitative Polymerase Chain Reaction (PCR). The protocol focuses specifically on Ts65Dn mice, but can be used as a basis for genotyping ohter strains.

  7. Automatic Error Correction of Java Programs

    NASA Astrophysics Data System (ADS)

    Kern, Christian; Esparza, Javier

    We present a technique for automatically detecting and correcting software bugs. The programmer is required to define a catalog of hotspots, syntactic constructs she considered to be error prone (e.g. i < N), together with suitable alternatives (e.g. i < (N + 1) and i < (N - 1)). Given a faulty program, search techniques are then applied to find a combination of alternatives yielding a correct program. The technique is implemented on top of the Java Pathfinder Framework.

  8. Complications associated with prone positioning in elective spinal surgery

    PubMed Central

    DePasse, J Mason; Palumbo, Mark A; Haque, Maahir; Eberson, Craig P; Daniels, Alan H

    2015-01-01

    Complications associated with prone surgical positioning during elective spine surgery have the potential to cause serious patient morbidity. Although many of these complications remain uncommon, the range of possible morbidities is wide and includes multiple organ systems. Perioperative visual loss (POVL) is a well described, but uncommon complication that may occur due to ischemia to the optic nerve, retina, or cerebral cortex. Closed-angle glaucoma and amaurosis have been reported as additional etiologies for vision loss following spinal surgery. Peripheral nerve injuries, such as those caused by prolonged traction to the brachial plexus, are more commonly encountered postoperative events. Myocutaneous complications including pressure ulcers and compartment syndrome may also occur after prone positioning, albeit rarely. Other uncommon positioning complications such as tongue swelling resulting in airway compromise, femoral artery ischemia, and avascular necrosis of the femoral head have also been reported. Many of these are well-understood and largely avoidable through thoughtful attention to detail. Other complications, such as POVL, remain incompletely understood and thus more difficult to predict or prevent. Here, the current literature on the complications of prone positioning for spine surgery is reviewed to increase awareness of the spectrum of potential complications and to inform spine surgeons of strategies to minimize the risk of prone patient morbidity. PMID:25893178

  9. Modifying the Type A coronary-prone behavior pattern

    Microsoft Academic Search

    Jeffrey C. Levenkron; Jerome D. Cohen; Hiltrud S. Mueller; E. B. Fisher

    1983-01-01

    Compared 3 treatments for modifying the Type A coronary-prone behavior pattern (TABP). Comprehensive behavior therapy (CBT), emphasizing self-control procedures, and group support (GS), encouraging change in TABP targets but without behavioral techniques, were contrasted to brief information (BI), a minimal treatment control simulating \\

  10. Virtual infrastructure for collision-prone wireless networks

    Microsoft Academic Search

    Gregory Chockler; Seth Gilbert; Nancy A. Lynch

    2008-01-01

    Wireless ad hoc networks pose several significant challenges: devices are unreliable; deployments are unpredictable; and communication is erratic. One proposed solution is Vir- tual Infrastructure, an abstraction in which unpredictable and unreliable devices are used to emulate reliable and pre- dictable infrastructure. In this paper, we present a new pro- tocol for emulating virtual infrastructure in collision-prone wireless networks. At

  11. The Development and Validation of the Health Proneness Questionnaire

    Microsoft Academic Search

    Deborah Erickson; Fiona Stapleton; Paul Erickson; Emmy Giannokopoulos; Clare Wilson

    2006-01-01

    This series of studies describes the development, validation and potential use of the Health Proneness Questionnaire (HPQ). Recent health, wellness and illness studies focus upon the dynamic interaction between psychological and physical well-being. This newly developed scale allows practitioners to quickly screen psychological characteristics related to health and a patient's perception of their quality of life. Participants were patients in

  12. Arthroscopic Subtalar Arthrodesis: The Posterior Approach in the Prone Position

    Microsoft Academic Search

    Luis Perez Carro; Pau Golanó; Jordi Vega

    2007-01-01

    Arthroscopic subtalar arthrodesis, as reported by Tasto, is done in the lateral decubitus position, and the portal sites are lateral. This report describes a new alternative method in which the patient is in the prone position and a posterior 2-portal approach is used, as described by van Dijk et al. The initial debridement and synovectomy are performed with 4- and

  13. Pathogenesis of A-beta+ ketosis-prone diabetes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A-beta+ ketosis-prone diabetes (KPD) is an emerging syndrome of obesity, unprovoked ketoacidosis, reversible beta-cell dysfunction, and near-normoglycemic remission. We combined metabolomics with targeted kinetic measurements to investigate its pathophysiology. Fasting plasma fatty acids, acylcarnit...

  14. Complications associated with prone positioning in elective spinal surgery.

    PubMed

    DePasse, J Mason; Palumbo, Mark A; Haque, Maahir; Eberson, Craig P; Daniels, Alan H

    2015-04-18

    Complications associated with prone surgical positioning during elective spine surgery have the potential to cause serious patient morbidity. Although many of these complications remain uncommon, the range of possible morbidities is wide and includes multiple organ systems. Perioperative visual loss (POVL) is a well described, but uncommon complication that may occur due to ischemia to the optic nerve, retina, or cerebral cortex. Closed-angle glaucoma and amaurosis have been reported as additional etiologies for vision loss following spinal surgery. Peripheral nerve injuries, such as those caused by prolonged traction to the brachial plexus, are more commonly encountered postoperative events. Myocutaneous complications including pressure ulcers and compartment syndrome may also occur after prone positioning, albeit rarely. Other uncommon positioning complications such as tongue swelling resulting in airway compromise, femoral artery ischemia, and avascular necrosis of the femoral head have also been reported. Many of these are well-understood and largely avoidable through thoughtful attention to detail. Other complications, such as POVL, remain incompletely understood and thus more difficult to predict or prevent. Here, the current literature on the complications of prone positioning for spine surgery is reviewed to increase awareness of the spectrum of potential complications and to inform spine surgeons of strategies to minimize the risk of prone patient morbidity. PMID:25893178

  15. Significance of prone positioning in planning treatment for esophageal cancer.

    PubMed

    Corn, B W; Coia, L R; Chu, J C; Hwang, C C; Stafford, P M; Hanks, G E

    1991-10-01

    The treatment of esophageal cancer is made difficult by the close proximity of the esophagus to the spinal cord and the requirement to treat the esophageal target volume to doses greater than or equal to 60 Gy while limiting the spinal cord dose to less than or equal to 46 Gy. By placing the patient in the prone position, the esophagus can be displaced away from the spinal cord. We explored the results of this commonly used technique on 16 patients who have undergone simulation in both supine and prone positions. Both AP and lateral orthogonal radiographs were obtained in both positions. The distance between contrast material in the esophagus and spinal cord was noted in at least four transverse planes through the thoracic esophagus on each of the 16 patients. These four transverse planes were located at 3 cm above the carina, at the carina, 3 cm below the carina and 6 cm below the carina. The mean displacement (+/- 1 SD) of the esophagus away from the spinal cord when the patient was in the prone position compared to supine at each of these levels was 1.3 (+/- 0.8) cm, 1.8 (+/- 0.9) cm, 1.8 (+/- 1.0) cm, and 1.9 (+/- 1.1) cm. The range of displacement for all 64 displacement determinations was 0 to 4.2 cm with a mean of 1.7 cm. To evaluate further the consequences of prone positioning on treatment planning and doses received to target volumes and critical structures, we performed 3-dimensional treatment planning with a patient in both prone and supine positions. The requirements were to achieve a tumor volume dose of 60 Gy while keeping the spinal cord dose below 46 Gy. Two types of conventional treatment plans were examined in prone and supine positions. A 6-field plan consisted of delivery of 40 Gy through a large 3-field beam arrangement followed by delivery of 20 Gy through a similar 3-field cone down. An 8-field plan involved the delivery of 30 Gy through AP/PA beams followed by a 3-field beam arrangement to 40 Gy and a subsequent 3-field cone-down for the final 20 Gy. Comparison of dose volume histograms revealed that the 6-field plan spared relatively more heart whereas the 8-field plan spared relatively more lung. Regarding the primary consideration of coverage of target volume with avoidance of spinal cord, prone positioning was superior to supine positioning whether 6- or 8-field arrangements were used. PMID:1938528

  16. Automated Forensic Animal Family Identification by Nested PCR and Melt Curve Analysis on an Off-the-Shelf Thermocycler Augmented with a Centrifugal Microfluidic Disk Segment

    PubMed Central

    Zengerle, Roland; von Stetten, Felix; Schmidt, Ulrike

    2015-01-01

    Nested PCR remains a labor-intensive and error-prone biomolecular analysis. Laboratory workflow automation by precise control of minute liquid volumes in centrifugal microfluidic Lab-on-a-Chip systems holds great potential for such applications. However, the majority of these systems require costly custom-made processing devices. Our idea is to augment a standard laboratory device, here a centrifugal real-time PCR thermocycler, with inbuilt liquid handling capabilities for automation. We have developed a microfluidic disk segment enabling an automated nested real-time PCR assay for identification of common European animal groups adapted to forensic standards. For the first time we utilize a novel combination of fluidic elements, including pre-storage of reagents, to automate the assay at constant rotational frequency of an off-the-shelf thermocycler. It provides a universal duplex pre-amplification of short fragments of the mitochondrial 12S rRNA and cytochrome b genes, animal-group-specific main-amplifications, and melting curve analysis for differentiation. The system was characterized with respect to assay sensitivity, specificity, risk of cross-contamination, and detection of minor components in mixtures. 92.2% of the performed tests were recognized as fluidically failure-free sample handling and used for evaluation. Altogether, augmentation of the standard real-time thermocycler with a self-contained centrifugal microfluidic disk segment resulted in an accelerated and automated analysis reducing hands-on time, and circumventing the risk of contamination associated with regular nested PCR protocols. PMID:26147196

  17. Medication Errors

    MedlinePLUS

    Medicines cure infectious diseases, prevent problems from chronic diseases, and ease pain. But medicines can also cause harmful reactions if not used ... You can help prevent errors by Knowing your medicines. Keep a list of the names of your ...

  18. Intralipid medication errors in the neonatal intensive care unit.

    PubMed

    Chuo, John; Lambert, George; Hicks, Rodney W

    2007-02-01

    These findings suggest that most intralipids errors occur during the administration phase. This complex process can generate high opportunities for error directly related to the use of IV pumps. Nursing staff members are prone to making dosing errors while accurately programming the infusion devices, especially during times of high workload. The evening hours around shift change appeared most vulnerable to such errors occurring. A further analysis to include error rates as a function of error opportunities is critical. The tracking and tallying of such opportunity for error can be accomplished using smart pump technology. A detailed analysis of the existing intralipid administration workflow process will guide the overall strategy of an error prevention plan. Understanding the nursing workload as a function of time of day and census is essential. These mission-critical tasks often require the hard work of a dedicated task force, the commitment of the hospital leadership, and cooperation from the health care providers. PMID:17370921

  19. Joint content authentication and error control for wireless multimedia communications

    Microsoft Academic Search

    Hong Heather Yu; Peng Yin; Xiaolong Yu

    2004-01-01

    Today, multimedia delivery through wireless networks is rapidly gaining popularity. Many cellular phones are already equipped with an extra large full-color display and various multimedia applications and devices. It is challenging to transmit and access multimedia data through wireless communications channels due to device mobility, power constraints, bandwidth limitations, and an error prone environment. We investigate multimedia services in wireless

  20. Software errors and complexity: an empirical investigation0

    Microsoft Academic Search

    Victor R. Basili; Barry T. Perricone

    1984-01-01

    An analysis of the distributions and relationships derived from the change data collected during development of a medium-scale software project produces some surprising insights into the factors influencing software development. Among these are the tradeoffs between modifying an existing module as opposed to creating a new one, and the relationship between module size and error proneness.

  1. QUALITY CONTROLS FOR PCR

    EPA Science Inventory

    The purpose of this presentation is to present an overview of the quality control (QC) sections of a draft EPA document entitled, "Quality Assurance/Quality Control Guidance for Laboratories Performing PCR Analyses on Environmental Samples." This document has been prepared by th...

  2. QUALITY ASSURANCE FOR PCR

    EPA Science Inventory

    The U.S. Environmental Protection Agency (EPA) held a workshop in January 2003 on the detection of viruses in water using polymerase chain reaction (PCR)-based methods. Speakers were asked to address a series of specific questions, including whether a single standard method coul...

  3. Performance of enhanced error concealment techniques in multi-view video coding systems

    Microsoft Academic Search

    Brian W. Micallef; Carl J. Debono; Reuben A. Farrugia

    2011-01-01

    Transmission of multi-view video encoded bit-streams over error-prone channels demands robust error concealment techniques. This paper studies the performance of solutions that exploit the neighbourhood spatial, temporal and inter-view information for this scope. Furthermore, different boundary distortion measurements, motion compensation refinement and temporal error concealment of Anchor frames were exploited to improve the results obtained by the basic error concealment

  4. Identification and estimation of nonlinear models using two samples with nonclassical measurement errors

    Microsoft Academic Search

    Raymond J. Carroll; Xiaohong Chen; Yingyao Hu

    2010-01-01

    This paper considers identification and estimation of a general nonlinear errors-in-variables (EIV) model using two samples. Both samples consist of a dependent variable, some error-free covariates, and an error-prone covariate, for which the measurement error has unknown distribution and could be arbitrarily correlated with the latent true values, and neither sample contains an accurate measurement of the corresponding true variable.

  5. Prone positioning in trauma patients: nursing roles and responsibilities.

    PubMed

    Chadwick, Jessica R

    2010-01-01

    One of the leading causes of mortality in the intensive care unit is Acute Respiratory Distress Syndrome (ARDS). Acute Respiratory Distress Syndrome can occur as a result from multiorgan dysfunction syndrome and sepsis. In the trauma population, ARDS accounts for an increase in mortality as well as morbidity and disability. Nurses have an essential role in the care of the trauma patients with ARDS or acute lung injury patients. Respiratory treatments such as airway pressure release ventilation and chest physiotherapy are utilized often for ARDS treatment. A lesser used therapy, intermittent prone positioning has also been found to be effective in increasing the pulmonary gas exchange in trauma patients. This article will explain the nursing roles and responsibilities in the initiation, continuation, and cessation of intermittent prone positioning. PMID:21157253

  6. Geophysical-geochemical investigation of fire-prone landfills

    Microsoft Academic Search

    Vladimir Frid; Dmitri Doudkinski; Gady Liskevich; Efim Shafran; Arie Averbakh; Nikolay Korostishevsky; Larisa Prihodko

    2010-01-01

    This paper deals with the integration of electrical resistivity tomography and geochemical methods for studying four different\\u000a fire-prone landfills. Landfill gas composition (CH4, H2S, O2, CO, CO2) and subsurface temperature were measured with the constant net 50 × 50 m from the depth 10–60 cm. 28 electrical resistivity\\u000a tomography lines were surveyed, while Wenner and Sclumberger electrode arrays were employed for all measurements. At

  7. A General Software Defect-Proneness Prediction Framework

    Microsoft Academic Search

    Qinbao Song; Zihan Jia; Martin J. Shepperd; Shi Ying; Jin Liu

    2011-01-01

    BACKGROUND—Predicting defect-prone software components is an economically important activity and so has received a good deal of attention. However, making sense of the many, and sometimes seemingly inconsistent, results is difficult. OBJECTIVE—We propose and evaluate a general framework for software defect prediction that supports 1) unbiased and 2) comprehensive comparison between competing prediction systems. METHOD—The framework is comprised of 1)

  8. Dynamic stability differences in fall-prone and healthy adults

    Microsoft Academic Search

    Kevin P. Granata; Thurmon E. Lockhart

    Abstract Typical stability assessments,characterize performance,in standing balance despite the fact that most falls occur during dynamic,activ- ities such as walking. The objective of this study was to identify dynamic stability differences between fall-prone elderly individuals, healthy age-matched adults, and young adults. Three-dimensional video-motion analysis kinematic data were recorded for 35 contiguous steps while subjects walked on a treadmill at three

  9. Dynamic stability differences in fall-prone and healthy adults

    Microsoft Academic Search

    Kevin P. Granata; Thurmon E. Lockhart

    2008-01-01

    Typical stability assessments characterize performance in standing balance despite the fact that most falls occur during dynamic activities such as walking. The objective of this study was to identify dynamic stability differences between fall-prone elderly individuals, healthy age-matched adults, and young adults. Three-dimensional video-motion analysis kinematic data were recorded for 35 contiguous steps while subjects walked on a treadmill at

  10. Breakdown-prone volume in terahertz wave beams

    NASA Astrophysics Data System (ADS)

    Nusinovich, G. S.; Qiao, F.; Kashyn, D. G.; Pu, R.; Dolin, L. S.

    2013-06-01

    This study was motivated by the recently proposed concept of remote detection of concealed radioactive materials by a focused terahertz (THz) radiation [V. L. Granatstein and G. S. Nusinovich, J. Appl. Phys. 108, 063304 (2010)]. According to this concept, a high-power THz radiation should be focused in a small spot where the field intensity exceeds the breakdown threshold. In the presence of free electrons in such a breakdown-prone volume, a THz discharge will occur there. However, this volume should be so small that in the absence of ionizing sources in its vicinity the probability to have there any free electrons is low. Then, the increased breakdown rate in a series of THz pulses would indicate the presence of hidden radioactive materials in the vicinity of the focused spot. For this concept, it is important to accurately determine the breakdown-prone volume created by a focused THz radiation. This problem is analyzed in this paper, first, for the case of a single wave beam and, then, for the case of crossing wave beams of different polarizations. The problem is studied first ignoring the diffraction spread of wave beams in the vicinity of the focal plane and, then, with the account for the diffraction spreading. Then, relations between the THz wave power, the range of such a system and the breakdown-prone volume are analyzed. Finally, the effect of the atmospheric turbulence on propagation and focusing of THz wave beams in air is considered.

  11. Thoracoscopic and laparoscopic radical esophagectomy with lateral-prone position

    PubMed Central

    Ma, Zheng; Niu, Huijun

    2014-01-01

    With 20 years of development, minimally-invasive treatment for esophageal cancer has been widely spread. However, surgeons have not reached consensus about the optimal minimally-invasive operation method, or whether the effect of radical lymph nodes dissection is comparable to the traditional open procedure. Thoracoscopic esophagectomy with lateral-prone position combines the advantages of both lateral position (allowing quick conversion to open procedure) and prone position (good visual area and complete lymphadenectomy). Together with laparoscopic abdominal lymphadenectomy, gastric tube formation and jejunostomy, this approach provides an easier way for minimally-invasive radical esophagectomy. In this article, approaches for thoracoscopic esophagectomy with lateral-prone position and total mediastinal lymphadenectomy, combined with totally laparoscopic gastric mobilization, abdominal lymphadenectomy, gastric tube formation and jejunostomy, will be presented by video instructions. All the procedures were under the rule of radical lymphadenectomy. Cervical lymph nodes dissection and esophago-gastrostomy were the same as those in open procedure, which will not be discussed here. PMID:24605231

  12. 44 CFR 60.24 - Planning considerations for flood-related erosion-prone areas.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...2010-10-01 false Planning considerations for flood-related erosion-prone areas. 60...INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT... Additional Considerations in Managing Flood-Prone, Mudslide (i.e.,...

  13. 44 CFR 60.24 - Planning considerations for flood-related erosion-prone areas.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ...2011-10-01 false Planning considerations for flood-related erosion-prone areas. 60...INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT... Additional Considerations in Managing Flood-Prone, Mudslide (i.e.,...

  14. 44 CFR 60.24 - Planning considerations for flood-related erosion-prone areas.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ...2013-10-01 false Planning considerations for flood-related erosion-prone areas. 60...INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT... Additional Considerations in Managing Flood-Prone, Mudslide (i.e.,...

  15. 44 CFR 60.24 - Planning considerations for flood-related erosion-prone areas.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ...2014-10-01 false Planning considerations for flood-related erosion-prone areas. 60...INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT... Additional Considerations in Managing Flood-Prone, Mudslide (i.e.,...

  16. Error Rate Comparison during Polymerase Chain Reaction by DNA Polymerase

    DOE PAGESBeta

    McInerney, Peter; Adams, Paul; Hadi, Masood Z.

    2014-01-01

    As larger-scale cloning projects become more prevalent, there is an increasing need for comparisons among high fidelity DNA polymerases used for PCR amplification. All polymerases marketed for PCR applications are tested for fidelity properties (i.e., error rate determination) by vendors, and numerous literature reports have addressed PCR enzyme fidelity. Nonetheless, it is often difficult to make direct comparisons among different enzymes due to numerous methodological and analytical differences from study to study. We have measured the error rates for 6 DNA polymerases commonly used in PCR applications, including 3 polymerases typically used for cloning applications requiring high fidelity. Error ratemore »measurement values reported here were obtained by direct sequencing of cloned PCR products. The strategy employed here allows interrogation of error rate across a very large DNA sequence space, since 94 unique DNA targets were used as templates for PCR cloning. The six enzymes included in the study,Taqpolymerase, AccuPrime-Taq High Fidelity, KOD Hot Start, clonedPfupolymerase, Phusion Hot Start, andPwopolymerase, we find the lowest error rates withPfu, Phusion, andPwopolymerases. Error rates are comparable for these 3 enzymes and are >10x lower than the error rate observed withTaqpolymerase. Mutation spectra are reported, with the 3 high fidelity enzymes displaying broadly similar types of mutations. For these enzymes, transition mutations predominate, with little bias observed for type of transition.« less

  17. Dissociative Experiences and Anger Proneness in Late Adolescent Females with Different Attachment Styles.

    ERIC Educational Resources Information Center

    Calamari, Elena; Pini, Mauro

    2003-01-01

    Study investigated the relationships between dissociative experiences, anger proneness, and attachment styles in a nonclinical sample of late adolescent females. Found a connection between anger proneness and dissociation. Insecurely attached females showed more anger proneness. Results confirm the importance of psychological intervention for…

  18. Dreaming to reduce fantasy? – Fantasy proneness, dissociation, and subjective sleep experiences

    Microsoft Academic Search

    Timo Giesbrecht; Harald Merckelbach

    2006-01-01

    Fantasy proneness refers to an extensive involvement in fantasy and daydreaming. Previous studies have shown that fantasy proneness overlaps with dissociative tendencies, as measured with the Dissociative Experiences Scale. We tested the hypothesis that deviant sleep experiences form the critical link between fantasy proneness and dissociation. Undergraduate students (N=205) completed the Creative Experiences Questionnaire, the Dissociative Experiences Scale, and the

  19. Pcr by Thermal Convection

    NASA Astrophysics Data System (ADS)

    Braun, Dieter

    The Polymerase Chain Reaction (PCR) allows for highly sensitive and specific amplification of DNA. It is the backbone of many genetic experiments and tests. Recently, three labs independently uncovered a novel and simple way to perform a PCR reaction. Instead of repetitive heating and cooling, a temperature gradient across the reaction vessel drives thermal convection. By convection, the reaction liquid circulates between hot and cold regions of the chamber. The convection triggers DNA amplification as the DNA melts into two single strands in the hot region and replicates into twice the amount in the cold region. The amplification progresses exponentially as the convection moves on. We review the characteristics of the different approaches and show the benefits and prospects of the method.

  20. ERROR RESILIENT VIDEO CODING TECHNIQUES USING SPARE PICTURES , Miska M. Hannuksela2

    E-print Network

    Gabbouj, Moncef

    ERROR RESILIENT VIDEO CODING TECHNIQUES USING SPARE PICTURES Dong Tian1 , Miska M. Hannuksela2 , Ye prone environments not all the picture data can be received correctly during video transmission. Error method, called spare pictures, is proposed to indicate the similarity between a reference picture

  1. Characterization of genetic deletions in Becker muscular dystrophy using monoclonal antibodies against a deletion-prone region of dystrophin

    SciTech Connect

    Thanh, L.T.; Man, Nguyen Thi; Morris, G.E. [Wales Institute, Clwyd (United Kingdom)] [and others

    1995-08-28

    We have produced a new panel of 20 monoclonal antibodies (mAbs) against a region of the dystrophin protein corresponding to a deletion-prone region of the Duchenne muscular dystrophy gene (exons 45-50). We show that immunohistochemistry or Western blotting with these {open_quotes}exon-specific{close_quotes} mAbs can provide a valuable addition to Southern blotting or PCR methods for the accurate identification of genetic deletions in Becker muscular dystrophy patients. The antibodies were mapped to the following exons: exon 45 (2 mAbs), exon 46 (6), exon 47 (1), exons 47/48 (4), exons 48-50 (6), and exon 50 (1). PCR amplification of single exons or groups of exons was used both to produce specific dystrophin immunogens and to map the mAbs obtained. PCR-mediated mutagenesis was also used to identify regions of dystrophin important for mAb binding. Because the mAbs can be used to characterize the dystrophin produced by individual muscle fibres, they will also be useful for studying {open_quotes}revertant{close_quotes} fibres in Duchenne muscle and for monitoring the results of myoblast therapy trials in MD patients with deletions in this region of the dystrophin gene. 27 refs., 7 figs., 3 tabs.

  2. Arginine vasopressin (AVP) expressional changes in the hypothalamic paraventricular and supraoptic nuclei of stroke-prone spontaneously hypertensive rats

    PubMed Central

    Yi, Sun Shin; Kim, Hyun-Jin; Do, Seon-Gil; Lee, Yoon-Bok; Ahn, Hee Jin; Hwang, In Koo

    2012-01-01

    Arginine vasopressin (AVP) is a neuropeptide with vasoconstrictive, antidiuretic, cardiovascular regulative and hepatic glycogenolysis effects, that also affects other behaviors including modulating learning. A number of studies on AVP regulation have been conducted in various metabolic diseases (disorders). In this study, the immunoreactivities of AVP in the paraventricular nucleus (PVN) and supraoptic nucleus (SON) and mRNA expressions in the hypothalamus were investigated by immunohistochemistry and quantitative real-time PCR (RT-qPCR) in stroke-prone spontaneously hypertensive rats at different ages (i.e., at postnatal months [PM] 1, 8, and 12). Blood glucose levels in the PM 8 group were higher than in the other groups. However, cresyl violet positive neurons were detected in the PVN and SON of all animals, and numbers of cresyl violet positive neurons were similar in all aged groups. In addition, AVP immunoreactivity was detected in the PVN and SON of all age groups, and AVP immunoreactivity and mRNA expression levels were found to be increased in proportion to age by immunohistochemistry and RT-qPCR. These results suggest that the diabetic condition is temporally generated after hypertension has developed. Furthermore, our findings suggest that increased AVP expressions in the hypothalamic PVN and SON are associated with hypertension by age. PMID:22822466

  3. [Reactance proneness, collectivism, uniqueness, and resistance to persuasion].

    PubMed

    Imajo, Shuzo

    2002-10-01

    This study examined the reliability and validity of Japanese psychological reactance scales. A total of 167 undergraduates completed a questionnaire of Therapeutic Reactance Scale (TRS), the Hong Reactance Scale (HRS), the Uniqueness Scale, and the Collectivism Scale. They also received messages involving three persuasion situations that were either high or low in terms of threat, and were asked to describe their reactions to them. The author categorized the reactions into three: acceptance, indirect resistance, and direct resistance. Reliabilities of the reactance scales were satisfactory. Their scores positively correlated with uniqueness scores, and negatively with collectivism scores. Those high on reactance proneness were less persuaded in two of the three situations. But in the third, an HRS by threat interaction was observed, indicating that only those who were high on reactance proneness under the high-threat condition showed resistance to persuasion. These results suggest that the Japanese versions of reactance scale were reliable and valid. However, the assertiveness aspect of TRS may not be appropriate for the definition of reactance. The influence of culture on psychological reactance was also discussed. PMID:12516187

  4. Human factors and medication errors: a case study.

    PubMed

    Gluyas, Heather; Morrison, Paul

    2014-12-15

    Human beings are error prone. A significant component of human error is flaws inherent in human cognitive processes, which are exacerbated by situations in which the individual making the error is distracted, stressed or overloaded, or does not have sufficient knowledge to undertake an action correctly. The scientific discipline of human factors deals with environmental, organisational and job factors, as well as human and individual characteristics, which influence behaviour at work in a way that potentially gives rise to human error. This article discusses how cognitive processing is related to medication errors. The case of a coronial inquest into the death of a nursing home resident is used to highlight the way people think and process information, and how such thinking and processing may lead to medication errors. PMID:25492790

  5. The Effect of Body Inclination During Prone Positioning on Intraocular Pressure in Awake Volunteers: A Comparison of Two Operating Tables

    Microsoft Academic Search

    Mehmet S. Ozcan; Claudia Praetel; M. Tariq Bhatti; Nikolaus Gravenstein; Michael E. Mahla; Christoph N. Seubert

    2004-01-01

    Visual loss is a rare, but catastrophic, complication of surgery in the prone position. The prone position in- creases intraocular pressure (IOP), which may lead to visual loss by decreasing perfusion of the anterior optic nerve. We tested whether the reverse Trendelenburg position ameliorates the increase in IOP caused by prone positioning. Furthermore, we compared two prone positioning setups. The

  6. Do guilt- and shame-proneness differentially predict prosocial, aggressive, and withdrawn behaviors during early adolescence?

    PubMed

    Roos, Sanna; Hodges, Ernest V E; Salmivalli, Christina

    2014-03-01

    In this short-term longitudinal study, we systematically examined the distinctiveness of guilt- and shame-proneness in early adolescents (N = 395, mean age = 11.8 years) in terms of differential relations with peer reported prosocial behavior, withdrawal, and aggression. Results from structural equation modeling indicated that guilt-proneness concurrently predicted more aggressive and less prosocial behavior as well as subsequent increases in prosocial behavior. Shame-proneness predicted subsequent decreases in prosocial behavior. Although girls reported a greater proneness to experience guilt and shame than boys, the associations between the two dispositional emotions and social behaviors were found to be similar across time and gender. PMID:23895166

  7. PCR amplification reactions in parasitology

    Microsoft Academic Search

    Henk L. Smits; Rudy A. Hartskeerl

    1995-01-01

    The development of PCR systems for the detection and identification of pathogenic human parasites has only recently started. Evaluation of most of these methods is still lacking. Most likely these methods will need considerable improvement before reliable diagnostic methods become available. Only for some parasitic diseases, such as cutaneous leishmaniasis, PCR has already proven to be of potential diagnostic value,

  8. Towards error-free profiling of immune repertoires.

    PubMed

    Shugay, Mikhail; Britanova, Olga V; Merzlyak, Ekaterina M; Turchaninova, Maria A; Mamedov, Ilgar Z; Tuganbaev, Timur R; Bolotin, Dmitriy A; Staroverov, Dmitry B; Putintseva, Ekaterina V; Plevova, Karla; Linnemann, Carsten; Shagin, Dmitriy; Pospisilova, Sarka; Lukyanov, Sergey; Schumacher, Ton N; Chudakov, Dmitriy M

    2014-06-01

    Deep profiling of antibody and T cell-receptor repertoires by means of high-throughput sequencing has become an attractive approach for adaptive immunity studies, but its power is substantially compromised by the accumulation of PCR and sequencing errors. Here we report MIGEC (molecular identifier groups-based error correction), a strategy for high-throughput sequencing data analysis. MIGEC allows for nearly absolute error correction while fully preserving the natural diversity of complex immune repertoires. PMID:24793455

  9. Rigorous bounding of position error estimates for aircraft surface movement

    Microsoft Academic Search

    K. O'Brien; J. Rife

    2010-01-01

    NextGen will require new navigation and surveillance capabilities to support safe and efficient surface operations based on tightly-coordinated 4D trajectories. In developing these new technologies, such as Automatic Dependent Surveillance-Broadcast (ADS-B) and the Ground Based Augmentation System (GBAS), it is essential to remember that all sensing technologies are prone to rare but potentially hazardous errors. Accordingly, the development of new

  10. The Prevalence of Boredom Proneness and Depression among Profoundly Deaf Residential School Adolescents.

    ERIC Educational Resources Information Center

    Watt, John D.; Davis, Faith E.

    1991-01-01

    Fifty profoundly deaf residential school adolescents were administered the Boredom Proneness scale and a modified version of the Beck Depression Inventory. Deaf students had a significantly higher incidence of depression and were more boredom prone than were hearing subjects. (Author/JDD)

  11. Internal organ motion in prostate cancer patients treated in prone and supine treatment position

    Microsoft Academic Search

    Joep C. Stroom; Peter C. M. Koper; Gert A. Korevaaar; Marjolein van Os; Marjolein Janssen; Hans C. J. de Boer; Peter C. Levendag; Ben J. M. Heijmen

    1999-01-01

    Background and Purpose: To compare supine and prone treatment positions for prostate cancer patients with respect to internal prostate motion and the required treatment planning margins.Materials and Methods: Fifteen patients were treated in supine and fifteen in prone position. For each patient, a planning computed tomography (CT) scan was used for treatment planning. Three repeat CT scans were made in

  12. A Comparison of Men Who Are Divorce Prone with Those Who Are Marriage Phobic.

    ERIC Educational Resources Information Center

    Counts, Robert M.; Reid, Kelly

    1986-01-01

    Compares two divorce prone men with two marriage phobic men. Marriage phobic men were fearful of getting married and used avoidance as a means of coping. Divorce prone were self-centered, hard driving, and reckless using acting out to manage conflict. Both groups were wary of the opposite sex and needed to be in control of relationships.…

  13. Critical Differences between the Type-A Prone and Type-A Personalitites.

    ERIC Educational Resources Information Center

    Cassel, Russell N.; Cassel, Susie L.

    1984-01-01

    Type-A Prone and Type-A personalities were assessed on the basis of the Cassel Type-A Personality Assessment Profile. Statistical data analysis indicated differences in positive lifestyle, blood pressure, and self-control and no differences in negative lifestyle, pulse rate, or peripheral temperature. Type-A Prone and Type-A norm profiles were…

  14. Coronary Prone Behavior Pattern in Women Preparing for Traditionally Male Professions.

    ERIC Educational Resources Information Center

    Gerdes, Eugenia Proctor; Sidler, John P.

    Although coronary prone, or Type A behavior, appears to predict coronary heart disease in women, as it does in men, little research has compared men and women in the same life circumstances. To determine if there is a coronary prone behavior pattern in women preparing for traditionally male professionals, two studies were conducted. In the first…

  15. Registration of prone and supine CT colonography scans based on correlation optimized warping and canonical correlation analysis.

    PubMed

    Wang, Shijun; Yao, Jianhua; Liu, Jiamin; Petrick, Nicholas; Summers, Ronald M

    2009-01-01

    In this paper, we propose an automated method for colon registration from supine and prone scans. Four anatomical salient points on the colon are distinguished first. Then correlation optimized warping (COW) method is applied to the segments defined by the anatomical landmarks to find better global registration based on local correlation of segments. To utilize more features along the colon centerline, we extended the COW method by embedding canonical correlation analysis into it for correlation calculation of colon segments. To verify the effectiveness of the proposed method, we tested the algorithm on a CTC dataset of 19 patients with 23 polyps. Experimental results show that by using our method, the estimation error of polyp location could be reduced 68.5% (from 41.6mm to 13.1mm on average) compared to a traditional dynamic warping algorithm. PMID:19964919

  16. Sun compass error model

    NASA Technical Reports Server (NTRS)

    Blucker, T. J.; Ferry, W. W.

    1971-01-01

    An error model is described for the Apollo 15 sun compass, a contingency navigational device. Field test data are presented along with significant results of the test. The errors reported include a random error resulting from tilt in leveling the sun compass, a random error because of observer sighting inaccuracies, a bias error because of mean tilt in compass leveling, a bias error in the sun compass itself, and a bias error because the device is leveled to the local terrain slope.

  17. Characterization of an alcohol addiction-prone phenotype in mice.

    PubMed

    Radwanska, Kasia; Kaczmarek, Leszek

    2012-05-01

    Human studies indicate that high impulsivity, novelty seeking and anxiety predispose individuals to alcohol abuse. Unclear, however, is whether the same phenotypes can be observed in laboratory animals prone to uncontrolled alcohol drinking. To characterize a novelty-seeking trait, anxiety, impulsivity, compulsivity and the motivation for natural rewards in mice, numerous tests were performed in the automated IntelliCage learning system. The same mice then had extended access to alcohol for 70 days, followed by the evaluation of addiction-like behaviors, including (1) the motivation for alcohol in a progressive-ratio schedule of reinforcement; (2) persistent and compulsive alcohol seeking and taking during signaled 'no alcohol' periods and (3) when subjected to punishment; and (4) the intensity of relapse after alcohol withdrawal. Our data suggest that high levels of anxiety-related traits (i.e. low novelty seeking, low resistance to punishment and a high level of compulsive behaviors) and high impulsivity predict addiction-like alcohol drinking in mice. Future studies are, however, warranted to create a valid model of alcohol addiction in mice in the IntelliCage system. PMID:22017485

  18. Neurobiological correlates of theory of mind in psychosis proneness.

    PubMed

    Modinos, Gemma; Renken, Remco; Shamay-Tsoory, Simone G; Ormel, Johan; Aleman, André

    2010-11-01

    Theory of mind (ToM) refers to the capacity to infer one's own and other persons' mental states. ToM abilities are compromised in schizophrenia, in association with dysfunctional activity in predominantly prefrontal brain regions. Prior behavioral studies have also suggested ToM deficits in healthy individuals with psychosis proneness (PP), although no study to date had investigated the associated neural mechanisms in such a sample. Here we used functional magnetic resonance imaging (fMRI) to compare brain activation of subjects with high versus low scores on positive-dimension PP and a ToM task. The ToM task involved first and second order attribution of cognitive and affective mental states to a cartoon character based on verbal and eye-gaze cues. No between-group differences were found on behavioral performance. fMRI analyses revealed a group interaction in anterior prefrontal cortex (BA 10), with the high PP group showing significantly more activity thereof, relative to the low PP, during second order mentalizing than during first order mentalizing. Further between-group differences were observed in dorsomedial and lateral prefrontal regions (BA 46/9), with the high PP group also showing greater activation during second order mentalizing. These results suggest that subjects with positive-dimension PP require more activation of prefrontal areas to adequately mentalize. Differences in the neural mechanisms underlying ToM might be associated with vulnerability to psychosis. PMID:20888847

  19. Preliminary Results on Setup Precision of Prone-Lateral Patient Positioning for Whole Breast Irradiation

    SciTech Connect

    Veldeman, Liv, E-mail: Liv.Veldeman@uzgent.b [Department of Radiotherapy, Ghent University Hospital, Ghent (Belgium); Speleers, Bruno; Bakker, Marlies; Jacobs, Filip; Coghe, Marc; De Gersem, Werner; Impens, Aline; Nechelput, Sarah; De Wagter, Carlos [Department of Radiotherapy, Ghent University Hospital, Ghent (Belgium)

    2010-09-01

    Purpose: The aim of this study was to develop a rapid and reproducible technique for prone positioning and to compare dose-volume indices in prone and supine positions. Methods and Materials: Eighteen patients underwent computed tomography imaging for radiotherapy planning in prone and supine position. Experience was gained in the first eight patients, which lead to modifications of the Horizon prone breast board (Civco Medical Solutions, Orange City, Iowa, USA) and the patient setup technique. A unilateral breast holder (U-BH) was developed (Van de Velde, Schellebelle, Belgium) to retract the contralateral breast away from the treated breast. The technique was then applied to an additional 10 patients. The setup precision was evaluated using daily cone-beam CT. Results: Modifications to the breast board were made to secure a prone-lateral rather then a pure prone position. We evolved from a classical setup using laser marks on the patients' body to a direct breast setup using marks on the breast only. The setup precision of the direct positioning procedure with the modified breast board and the U-BH is comparable to supine setup data in the literature. Dose-volume indices for heart and lung show significantly better results for prone than for supine position, and dose homogeneity within the treated breast did not differ according to the treatment position. Conclusions: The setup precision of our prone-lateral positioning technique is comparable to supine data in literature. Our data show the advantage of prone radiotherapy to spare the lung and heart. Further research is necessary to reduce the duration of prone setup.

  20. Unforced errors and error reduction in tennis

    PubMed Central

    Brody, H

    2006-01-01

    Only at the highest level of tennis is the number of winners comparable to the number of unforced errors. As the average player loses many more points due to unforced errors than due to winners by an opponent, if the rate of unforced errors can be reduced, it should lead to an increase in points won. This article shows how players can improve their game by understanding and applying the laws of physics to reduce the number of unforced errors. PMID:16632568

  1. When soft controls get slippery: User interfaces and human error

    SciTech Connect

    Stubler, W.F.; O`Hara, J.M.

    1998-12-01

    Many types of products and systems that have traditionally featured physical control devices are now being designed with soft controls--input formats appearing on computer-based display devices and operated by a variety of input devices. A review of complex human-machine systems found that soft controls are particularly prone to some types of errors and may affect overall system performance and safety. This paper discusses the application of design approaches for reducing the likelihood of these errors and for enhancing usability, user satisfaction, and system performance and safety.

  2. Cognitive Deficits Specific to Depression-Prone Smokers During Abstinence

    PubMed Central

    Ashare, Rebecca; Strasser, Andrew A.; Wileyto, E. Paul; Cuevas, Jocelyn; Audrain-McGovern, Janet

    2014-01-01

    Cigarette smoking is associated with a higher prevalence of depressive symptoms and individuals with elevated symptoms of depression have more difficulty quitting smoking. Depression is accompanied by cognitive deficits similar to those observed during nicotine withdrawal. Depressed smokers may smoke to alleviate these cognitive symptoms, which are exacerbated upon smoking abstinence. We hypothesized that following overnight abstinence, depression-prone smokers (DP+; past history and current depression symptoms; n = 34) would exhibit deficits in short-term and working memory, and experience greater attentional bias for affective stimuli, compared with smokers with no history or current symptoms of depression (DP?; n = 34). All participants underwent two laboratory sessions, once while smoking abstinent and once while smoking ad libitum (order counterbalanced, abstinence biochemically verified). Smokers completed measures of short-term memory (STM; word recognition task), working memory (N-back task), and attentional bias (Emotional Stroop task). The DP+ group showed declines in STM during abstinence compared with smoking, whereas the DP? group did not (interaction p = .02). There were small decrements in working memory accuracy during abstinence (p = .05), but this did not interact with depression status. During the Emotional Stroop task, the DP+ group showed an attentional bias toward positive versus neutral stimuli during abstinence compared with smoking (interaction p = .01). This study provides initial evidence that depressive symptoms may moderate abstinence-induced deficits in STM and shift attentional bias toward emotionally salient stimuli during abstinence. These cognitive changes may prompt relapse and may help identify novel targets for nicotine dependence treatment aimed at attenuating these deficits to improve cessation rates. PMID:24932895

  3. Body Investment, Depression, and Alcohol Use as Risk Factors for Suicide Proneness in College Students

    PubMed Central

    Lamis, Dorian A.; Malone, Patrick S.; Langhinrichsen-Rohling, Jennifer; Ellis, Thomas E.

    2009-01-01

    This study examined the relationships among three risk factors – body investment, depression, and alcohol use – and suicide proneness as measured by the Life Attitudes Schedule – Short Form (LAS-SF) in college students (n = 318). Path analysis was used to construct a causal model of suicide proneness. The Body Investment Scale (BIS) subscales were assumed to be causally prior to depression, which was in turn modeled as occurring prior to alcohol use, which was in turn modeled as prior to suicide proneness. Results revealed that, as expected suicide proneness was positively predicted by alcohol use, alcohol use was positively predicted by depression, and depression was negatively predicted by the body image component of the BIS. Additionally, the body image-suicide proneness link was significantly mediated by depression and its direct effect on suicide proneness as well as by the two-mediator path of body image on depression on drinking on suicide proneness. Implications are offered for the improved identification and treatment of young adults at risk for suicidal and health-diminishing behaviors. PMID:20573605

  4. Droplet-based micro oscillating-flow PCR chip

    NASA Astrophysics Data System (ADS)

    Wang, Wei; Li, Zhi-Xin; Luo, Rong; Lü, Shu-Hai; Xu, Ai-Dong; Yang, Yong-Jun

    2005-08-01

    Polymerase chain reactions (PCR), thermally activated chemical reactions which are widely used for nucleic acid amplification, have recently received much attention in microelectromechanical systems and micro total analysis systems because a wide variety of DNA/RNA molecules can be enriched by PCR for further analyses. In the present work, a droplet-based micro oscillating-flow PCR chip was designed and fabricated by the silicon microfabrication technique. Three different temperature zones, which were stable at denaturation, extension and annealing temperatures and isolated from each other by a thin-wall linkage, were integrated with a single, simple and straight microchannel to form the chip's basic functional structure. The PCR mixture was injected into the chip as a single droplet and flowed through the three temperature zones in the main microchannel in an oscillating manner to achieve the temperature maintenance and transitions. The chip's thermal performance was theoretically analyzed and numerically simulated. The results indicated that the time needed for the temperature of the droplet to change to the target value is less than 1 s, and the root mean square error of temperature is less than 0.2 °C. A droplet of 1 µl PCR mixture with standard HPV (Human Papilloma Virus)-DNA sample inside was amplified by the present chip and the results were analyzed by slab gel electrophoresis with separation of DNA markers in parallel. The electrophoresis results demonstrated that the micro oscillating-flow PCR chip successfully amplified the HPV-DNA, with a processing time of about 15 min which is significantly reduced compared to that for the conventional PCR instrument.

  5. Individual Positioning: A Comparative Study of Adjuvant Breast Radiotherapy in the Prone Versus Supine Position

    SciTech Connect

    Varga, Zoltan; Hideghety, Katalin; Mezo, Tamas; Nikolenyi, Aliz; Thurzo, Laszlo [Department of Oncotherapy, University of Szeged, Szeged (Hungary); Kahan, Zsuzsanna [Department of Oncotherapy, University of Szeged, Szeged (Hungary)], E-mail: kahan@onko.szote.u-szeged.hu

    2009-09-01

    Purpose: To study breast radiotherapy in the prone vs. supine positions through dosimetry and clinical implementation. Methods and Materials: Conformal radiotherapy plans in 61 patients requiring only breast irradiation were developed for both the prone and supine positions. After evaluation of the of the first 20 plan pairs, the patients were irradiated in the prone or supine position in a randomized fashion. These cases were analyzed for repositioning accuracy and skin reactions related to treatment position and patient characteristics. Results: The planning target volume covered with 47.5-53.5 Gy in the prone vs. the supine position was 85.1% {+-} 4.2% vs. 89.2 {+-} 2.2%, respectively (p < 0.0001). Radiation exposure of the ipsilateral lung, expressed in terms of the mean lung dose and the V{sub 20Gy}, was dramatically lower in the prone vs. supine position (p < 0.0001), but the doses to the heart did not differ. There was no difference in the need to correct positioning during radiotherapy, but the extent of displacement was significantly higher in the prone vs. supine position (p = 0.021). The repositioning accuracy in the prone position exhibited an improvement over time and did not depend on any patient-related parameters. Significantly more radiodermatitis of Grade 1-2 developed following prone vs. supine irradiation (p = 0.025). Conclusions: Conformal breast radiotherapy is feasible in the prone position. Its primary advantage is the substantially lower radiation dose to the ipsilateral lung. The higher dose inhomogeneity and increased rate of Grade 1-2 skin toxicity, however, may be of concern.

  6. Measurement Error Adjustment Using the SIMEX Method: An Application to Student Growth Percentiles

    ERIC Educational Resources Information Center

    Shang, Yi

    2012-01-01

    Growth models are used extensively in the context of educational accountability to evaluate student-, class-, and school-level growth. However, when error-prone test scores are used as independent variables or right-hand-side controls, the estimation of such growth models can be substantially biased. This article introduces a…

  7. Preserving non-programmers' motivation with error-prevention and debugging support tools

    Microsoft Academic Search

    Andrew Jensen Ko

    2003-01-01

    A significant challenge in teaching programming to disadvantaged populations is preserving learners' motivation and confidence. Because programming requires such a diverse set of skills and knowledge, the first steps in learning to program can be highly error- prone, and can quickly exhaust whatever attention learners are willing to give to a programming task. Our approach to preserving learners' motivation is

  8. Standing prone positioning in establishing causality between matched ventilation-perfusion defects and pleural effusion.

    PubMed

    Fotos, Joseph S; Tulchinsky, Mark

    2015-01-01

    Ventilation-perfusion scintigraphy is routinely performed in patients with suspected pulmonary thromboembolism. Pleural effusions in such patients are common and can cause matched ventilation-perfusion defects. This is especially true of the posterior projections in the supine patient. Prone positioning has been described as a useful technique to redistribute pleural fluid anteriorly, exposing perfusion in posterior lung fields; however, some patients have a concurrent condition that renders prone positioning difficult. This report discusses a modified technique that allows patients to be imaged in a standing prone position with excellent results. PMID:25247271

  9. Methods for detecting errors in numerically controlled machining of sculptured surfaces

    Microsoft Academic Search

    Robert B. Jerard; Robert L. Drysdale; Kenneth Hauck; Barry Schaudt; John Magewick

    1989-01-01

    The numerically controlled (NC) machining of sculptured surfaces is an error-prone process often requiring several attempts before an error-free NC program is produced. A technique designed to move the NC proof process into software is described. The system outputs a color-coded graphics display of the machined surface that shows out-of-tolerance areas. To gain efficiency, surface curvature and cutting-tool size are

  10. Skills, rules and knowledge in aircraft maintenance: errors in context

    NASA Technical Reports Server (NTRS)

    Hobbs, Alan; Williamson, Ann

    2002-01-01

    Automatic or skill-based behaviour is generally considered to be less prone to error than behaviour directed by conscious control. However, researchers who have applied Rasmussen's skill-rule-knowledge human error framework to accidents and incidents have sometimes found that skill-based errors appear in significant numbers. It is proposed that this is largely a reflection of the opportunities for error which workplaces present and does not indicate that skill-based behaviour is intrinsically unreliable. In the current study, 99 errors reported by 72 aircraft mechanics were examined in the light of a task analysis based on observations of the work of 25 aircraft mechanics. The task analysis identified the opportunities for error presented at various stages of maintenance work packages and by the job as a whole. Once the frequency of each error type was normalized in terms of the opportunities for error, it became apparent that skill-based performance is more reliable than rule-based performance, which is in turn more reliable than knowledge-based performance. The results reinforce the belief that industrial safety interventions designed to reduce errors would best be directed at those aspects of jobs that involve rule- and knowledge-based performance.

  11. Errors Affect Hypothetical Intertemporal Food Choice in Women

    PubMed Central

    Sellitto, Manuela; di Pellegrino, Giuseppe

    2014-01-01

    Growing evidence suggests that the ability to control behavior is enhanced in contexts in which errors are more frequent. Here we investigated whether pairing desirable food with errors could decrease impulsive choice during hypothetical temporal decisions about food. To this end, healthy women performed a Stop-signal task in which one food cue predicted high-error rate, and another food cue predicted low-error rate. Afterwards, we measured participants’ intertemporal preferences during decisions between smaller-immediate and larger-delayed amounts of food. We expected reduced sensitivity to smaller-immediate amounts of food associated with high-error rate. Moreover, taking into account that deprivational states affect sensitivity for food, we controlled for participants’ hunger. Results showed that pairing food with high-error likelihood decreased temporal discounting. This effect was modulated by hunger, indicating that, the lower the hunger level, the more participants showed reduced impulsive preference for the food previously associated with a high number of errors as compared with the other food. These findings reveal that errors, which are motivationally salient events that recruit cognitive control and drive avoidance learning against error-prone behavior, are effective in reducing impulsive choice for edible outcomes. PMID:25244534

  12. Gender Differences in Depression and Anxiety Among Victims of Intimate Partner Violence: The Moderating Effect of Shame Proneness

    Microsoft Academic Search

    Ryan C. Shorey; Amanda E. Sherman; Aaron J. Kivisto; Sara R. Elkins; Deborah L. Rhatigan; Todd M. Moore

    2011-01-01

    The current study examined the moderating role of shame proneness on the association between physical, psychological, and sexual intimate partner violence victimization and depressive and anxious symptoms among male and female college students (N = 967). Students completed self-report measures of dating violence, depression, anxiety, and shame proneness. Results showed that shame proneness moderated the association between all forms of

  13. Breast radiotherapy in the prone position primarily reduces the maximum out-of-field measured dose to the ipsilateral lung

    E-print Network

    Brenner, David Jonathan

    Breast radiotherapy in the prone position primarily reduces the maximum out-of-field measured dose advantages of prone position breast radiotherapy in terms of the radiation exposure to out-of-field organs) was to the treatment volume, the more dose spar- ing was seen for prone vs supine positioning. Breast radiotherapy

  14. Nanoliter high throughput quantitative PCR

    PubMed Central

    Morrison, Tom; Hurley, James; Garcia, Javier; Yoder, Karl; Katz, Arrin; Roberts, Douglas; Cho, Jamie; Kanigan, Tanya; Ilyin, Sergey E.; Horowitz, Daniel; Dixon, James M.; Brenan, Colin J.H.

    2006-01-01

    Understanding biological complexity arising from patterns of gene expression requires accurate and precise measurement of RNA levels across large numbers of genes simultaneously. Real time PCR (RT-PCR) in a microtiter plate is the preferred method for quantitative transcriptional analysis but scaling RT-PCR to higher throughputs in this fluidic format is intrinsically limited by cost and logistic considerations. Hybridization microarrays measure the transcription of many thousands of genes simultaneously yet are limited by low sensitivity, dynamic range, accuracy and sample throughput. The hybrid approach described here combines the superior accuracy, precision and dynamic range of RT-PCR with the parallelism of a microarray in an array of 3072 real time, 33 nl polymerase chain reactions (RT-PCRs) the size of a microscope slide. RT-PCR is demonstrated with an accuracy and precision equivalent to the same assay in a 384-well microplate but in a 64-fold smaller reaction volume, a 24-fold higher analytical throughput and a workflow compatible with standard microplate protocols. PMID:17000636

  15. An Improved Method of Gene Synthesis Based on DNA Works Software and Overlap Extension PCR

    Microsoft Academic Search

    Bingxue Dong; Runqian Mao; Baojian Li; Qiuyun Liu; Peilin Xu; Gang Li

    2007-01-01

    A bottleneck in recent gene synthesis technologies is the high cost of oligonucleotide synthesis and post-synthesis sequencing.\\u000a In this article, a simple and rapid method for low-cost gene synthesis technology was developed based on DNAWorks program\\u000a and an improved single-step overlap extension PCR (OE-PCR). This method enables any DNA sequence to be synthesized with few\\u000a errors, then any mutated sites

  16. Errors in autobiographical memory

    Microsoft Academic Search

    Ira E. Hyman; Elizabeth F. Loftus

    1998-01-01

    Memory is always constructive. People create the past based on the information that remains in memory, their general knowledge, and the social demands of the retrieval situation. Thus, memories will often contain some small errors and occasionally some large errors. In this article, we describe several different types of memory errors and consider how these errors may influence therapy.

  17. The discovery of error-prone DNA polymerase V and its unique regulation by RecA and ATP.

    PubMed

    Goodman, Myron F

    2014-09-26

    My career pathway has taken a circuitous route, beginning with a Ph.D. degree in electrical engineering from The Johns Hopkins University, followed by five postdoctoral years in biology at Hopkins and culminating in a faculty position in biological sciences at the University of Southern California. My startup package in 1973 consisted of $2,500, not to be spent all at once, plus an ancient Packard scintillation counter that had a series of rapidly flashing light bulbs to indicate a radioactive readout in counts/minute. My research pathway has been similarly circuitous. The discovery of Escherichia coli DNA polymerase V (pol V) began with an attempt to identify the mutagenic DNA polymerase responsible for copying damaged DNA as part of the well known SOS regulon. Although we succeeded in identifying a DNA polymerase, one that was induced as part of the SOS response, we actually rediscovered DNA polymerase II, albeit in a new role. A decade later, we discovered a new polymerase, pol V, whose activity turned out to be regulated by bound molecules of RecA protein and ATP. This Reflections article describes our research trajectory, includes a review of key features of DNA damage-induced SOS mutagenesis leading us to pol V, and reflects on some of the principal researchers who have made indispensable contributions to our efforts. PMID:25160630

  18. A Unified Mechanism for Multimedia Downlink Scheduling and Call Admission Control for Future Error-Prone Wireless Networks

    Microsoft Academic Search

    P. Koutsakis

    2005-01-01

    In this paper we design and evaluate the performance of a unified mechanism for downlink scheduling and call admission control of multimedia traffic in a high-capacity TDMA wireless channel. In our scheme, the Base Station interacts with the Call Admission Controller and incorporates predictions on the channel condition in its decision making. Our results show that, with the use of

  19. Up-Regulation of the Error-Prone DNA Polymerase K Promotes Pleiotropic Genetic Alterations and Tumorigenesis

    Microsoft Academic Search

    Clarisse Bavoux; Andreia Machado Leopoldino; Valerie Bergoglio; Jiyang O-Wang; Tomoo Ogi; Anne Bieth; Jean-Gabriel Judde; Marie-France Poupon; Thomas Helleday; Masatoshi Tagawa; CarlosRenato Machado; Jean-Sebastien Hoffmann; Christophe Cazaux

    2005-01-01

    It is currently widely accepted that genetic instability is key to cancer development. Many types of cancers arise as a consequence of a gradual accumulation of nucleotide aberra- tions, each mutation conferring growth and\\/or survival advantage. Genetic instability could also proceed in sudden bursts leading to a more drastic upheaval of structure and organization of the genome. Genetic instability, as

  20. 44 CFR 60.23 - Planning considerations for mudslide (i.e., mudflow)-prone areas.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ...Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF...MITIGATION National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Additional Considerations in Managing Flood-Prone, Mudslide...of rupture pose both health and site stability...

  1. 44 CFR 60.23 - Planning considerations for mudslide (i.e., mudflow)-prone areas.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF...MITIGATION National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Additional Considerations in Managing Flood-Prone, Mudslide...of rupture pose both health and site stability...

  2. Modeling interactions betweenspotted owl and barred owl populations in fire-prone forests

    EPA Science Inventory

    Background / Question / Methods Efforts to conserve northern spotted owls (Strix occidentalis caurina) in the eastern Cascades of Washington must merge the challenges of providing sufficient structurally complex forest habitat in a fire-prone landscape with the limitations impos...

  3. [Prone position: effect on gas exchange and functional capacity for exercise in patients with pulmonary hypertension].

    PubMed

    Bastidas-L, Andrea Carolina; Colina-Chourio, José A; Guevara, Jesnel M; Nunez, Alexis

    2015-03-01

    The objective of this investigation was to evaluate gas exchange and cardiopulmonary functional behavior in patients with pulmonary hypertension (PH) before, during and after the change to a prone position. Thirty patients with PH and alterations in gas exchange were included in the study. Gas exchange measurements were performed in four stages: at the baseline supine position and after 30, 120 and 240 minutes in prone position. Also, the patients were evaluated by the six minutes walking test (6MWT) after 30 days in prone position during night's sleep. After four hours in prone position, all patients showed an increase of PaO2 and arterial saturation of oxygen (SaO2), with a decrease of intrapulmonary shunts, improving the gas exchange and therefore the physiological demand imposed by exercise in patients with PH. PMID:25920183

  4. Errors in neurosurgery.

    PubMed

    Rolston, John D; Bernstein, Mark

    2015-04-01

    Medical errors are common and dangerous, estimated to cause over 400,000 deaths per year in the United States alone. The field of neurosurgery is not immune to these errors, and many studies have begun analyzing the frequency and types of errors that neurosurgical patients experience, along with their effects and causes. Fortunately, these data are guiding new innovations to reduce and prevent errors, like checklists, computerized order entry, and an increased appreciation for volume-outcome relationships. This article describes the epidemiology of errors, their classification, methods for identifying and discovering errors, and new strategies for error prevention. PMID:25771270

  5. Quantification Bias Caused by Plasmid DNA Conformation in Quantitative Real-Time PCR Assay

    PubMed Central

    Lin, Chih-Hui; Chen, Yu-Chieh; Pan, Tzu-Ming

    2011-01-01

    Quantitative real-time PCR (qPCR) is the gold standard for the quantification of specific nucleic acid sequences. However, a serious concern has been revealed in a recent report: supercoiled plasmid standards cause significant over-estimation in qPCR quantification. In this study, we investigated the effect of plasmid DNA conformation on the quantification of DNA and the efficiency of qPCR. Our results suggest that plasmid DNA conformation has significant impact on the accuracy of absolute quantification by qPCR. DNA standard curves shifted significantly among plasmid standards with different DNA conformations. Moreover, the choice of DNA measurement method and plasmid DNA conformation may also contribute to the measurement error of DNA standard curves. Due to the multiple effects of plasmid DNA conformation on the accuracy of qPCR, efforts should be made to assure the highest consistency of plasmid standards for qPCR. Thus, we suggest that the conformation, preparation, quantification, purification, handling, and storage of standard plasmid DNA should be described and defined in the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) to assure the reproducibility and accuracy of qPCR absolute quantification. PMID:22194997

  6. Long-term Clinical Outcomes of Whole-Breast Irradiation Delivered in the Prone Position

    Microsoft Academic Search

    Lauren D. Stegman; Katherine P. Beal; Margie A. Hunt; Monica N. Fornier; Beryl. McCormick

    2007-01-01

    Purpose: The aim of this study was to evaluate retrospectively the effectiveness and toxicity of post-lumpectomy whole-breast radiation therapy delivered with prone positioning. Methods and Materials: Between September 1992 and August 2004, 245 women with 248 early-stage invasive or in situ breast cancers were treated using a prone breast board. Photon fields treated the whole breast to 46 to 50.4

  7. BIOTECHNOLOGICALLY RELEVANT ENZYMES AND PROTEINS Protein engineering of hydrogenase 3 to enhance

    E-print Network

    Wood, Thomas K.

    BIOTECHNOLOGICALLY RELEVANT ENZYMES AND PROTEINS Protein engineering of hydrogenase 3 to enhance protein engineering of a hydrogenase. Keywords Protein engineering . Hydrogenase 3 . Error-prone PCR . DNA

  8. Reducing errors in radiology.

    PubMed

    Brusin, Joyce Helena

    2014-01-01

    Medical errors, even those that are relatively minor, can have serious consequences, such as misdiagnosis and longer and costlier hospital stays. Reducing errors requires all members of the health care clinical and administrative team to commit to the effort, and effective risk management addresses system-wide causes of errors. Errors often result from poor communication, inadequate training, chronic fatigue, and entrenched workplace hierarchies. Error reduction strategies support high-quality patient care, even in the most stressful and complex situations. PMID:25224086

  9. Children's proneness to shame and guilt predict risky and illegal behaviors in young adulthood.

    PubMed

    Stuewig, Jeffrey; Tangney, June P; Kendall, Stephanie; Folk, Johanna B; Meyer, Candace Reinsmith; Dearing, Ronda L

    2015-04-01

    Do shame and guilt help people avoid doing wrong? Although some research suggests that guilt-proneness is a protective factor while shame-proneness puts individuals at risk, most research is either cross-sectional or short-term. In this longitudinal study, 380 5th graders (ages 10-12) completed measures of proneness to shame and guilt. We re-interviewed 68 % of participants after they turned 18 years old (range 18-21). Guilt-proneness assessed in childhood predicted fewer sexual partners, less use of illegal drugs and alcohol, and less involvement with the criminal justice system. Shame-proneness, in contrast, was a risk factor for later deviant behavior. Shame-prone children were more likely to have unprotected sex and use illegal drugs in young adulthood. These results held when controlling for childhood SES and teachers' ratings of aggression. Children's moral emotional styles appear to be well established by at least middle childhood, with distinct downstream implications for risky behavior in early adulthood. PMID:24842762

  10. Design and Evaluation of a Stand-Up Motorized Prone Cart

    PubMed Central

    Harrow, Jeffrey J; Malassigné, Pascal; Nelson, Audrey L; Jensen, Robert P; Amato, Margaret; Palacios, Polly L

    2007-01-01

    Background/Objective: Prone carts are used for mobility by individuals with spinal cord injury in whom seated mobility (wheelchair) is contraindicated due to ischial or sacral pressure ulcers. Currently available prone carts are uncomfortable, subjecting the user to neck and shoulder strain, and make social interaction and performing activities of daily living difficult. A better design of prone carts is needed. In addition, standing devices have shown some medical benefits. The objective was to design and evaluate an improved prone cart that facilitates standing. Design: Engineering development project with user feedback through questionnaire. Users selected by convenience sampling. Methods: A marketing survey was performed of nurse managers of spinal cord injury units. Then 2 prototype carts were designed and built. These carts are able to tilt up to 45° and have a joystick-controlled motor for propulsion and other design features, including a workspace storage shelf and rearview mirrors. The carts were evaluated by both patients and caregivers at 2 Veteran's Administration hospitals. Outcome Measures: Questionnaire of subjects, both patients and caregivers, who used the cart. Findings: Both patients and caregivers liked the carts and the ability to assume a nonhorizontal body angle. The major complaint about the cart was that it seemed too long when it came to making turns. Conclusion: This prone cart design is an improvement over the standard, flat variety. However, further design changes will be necessary. This study provided valuable information that will be useful in the next-generation prone cart design project. PMID:17385270

  11. Delusion proneness in nonclinical individuals and cognitive insight: the contributions of rumination and reflection.

    PubMed

    Carse, Traci; Langdon, Robyn

    2013-08-01

    Although previous research demonstrates that clinical individuals with delusions score low on one of the facets of cognitive insight, self-reflection, and high on the other facet, self-certainty, analogous studies of delusion proneness in nonclinical individuals have found that delusion proneness in nonclinical individuals associates with higher levels of both self-certainty and self-reflection. The present study sought to reconcile these inconsistent results by examining the contributions of different facets of self-reflection, rumination and reflection, to delusion proneness. One hundred fifty-two individuals completed three questionnaires: the Beck Cognitive Insight Scale (BCIS), the Peters et al. Delusions Inventory (PDI), and the Rumination-Reflection Questionnaire (RRQ). The results showed that the individuals scoring higher on delusion proneness demonstrated higher levels of both self-certainty and self-reflection on the BCIS as well as higher levels of rumination and reflection on the RRQ. As predicted, the strength of the relationship between BCIS self-reflection and delusion proneness was diminished when rumination was controlled for. These findings suggest that the previously observed positive relation between BCIS self-reflection and nonclinical delusion proneness might be driven, in part, by the ruminative aspect of self-reflection. PMID:23896846

  12. Iterative design and evaluation of new prone carts for individuals with SCDs: a technical note.

    PubMed

    Malassigné, Pascal; Nelson, Audrey L; Cors, Mark W; Jensen, Robert P; Amato, Margaret; Schnurr, Emil Sam; Amerson, Thomas L

    2002-01-01

    This paper summarizes a series of projects funded since 1992 to address the compelling need to improve the quality of life for persons with spinal cord dysfunctions who use prone carts. Specifically, Veterans Services Organization, National Institute on Disability and Rehabilitation Research (NIDRR), and the VA Rehabilitation Research and Development funded studies to develop new consumer-driven designs for prone carts. Using an iterative approach, this team of clinicians and designers (1) evaluated existing prone carts; (2) designed a new manual prone cart; (3) designed a new motorized prone cart, including a standing model; and (4) are collaborating with manufacturers to market and commercialize the new prone carts. Prototypes were developed at the Milwaukee Institute of Art and Design with the assistance of Ortho-Kinetics, Inc., and Everest & Jennings and were clinically evaluated at two Veterans Affairs Medical Centers (Tampa and Milwaukee) with patients and caregivers and for compliance with applicable ISO (International Organization for Standardization) for electric wheelchair standards. PMID:11930905

  13. Whole-breast irradiation: a subgroup analysis of criteria to stratify for prone position treatment

    SciTech Connect

    Ramella, Sara, E-mail: s.ramella@unicampus.it [Radiation Oncology, Campus Bio-Medico University, Rome (Italy); Trodella, Lucio; Ippolito, Edy; Fiore, Michele; Cellini, Francesco; Stimato, Gerardina; Gaudino, Diego; Greco, Carlo [Radiation Oncology, Campus Bio-Medico University, Rome (Italy); Ramponi, Sara; Cammilluzzi, Eugenio; Cesarini, Claudio [Breast Unit, S. Pertini Hospital, Rome (Italy); Piermattei, Angelo [Department of Physics, Catholic University, Rome (Italy); Cesario, Alfredo [CdC San Raffaele Velletri (Italy); Department of Thoracic Surgery, Catholic University, Rome (Italy); D'Angelillo, Rolando Maria [Radiation Oncology, Campus Bio-Medico University, Rome (Italy)

    2012-07-01

    To select among breast cancer patients and according to breast volume size those who may benefit from 3D conformal radiotherapy after conservative surgery applied with prone-position technique. Thirty-eight patients with early-stage breast cancer were grouped according to the target volume (TV) measured in the supine position: small ({<=}400 mL), medium (400-700 mL), and large ({>=}700 ml). An ad-hoc designed and built device was used for prone set-up to displace the contralateral breast away from the tangential field borders. All patients underwent treatment planning computed tomography in both the supine and prone positions. Dosimetric data to explore dose distribution and volume of normal tissue irradiated were calculated for each patient in both positions. Homogeneity index, hot spot areas, the maximum dose, and the lung constraints were significantly reduced in the prone position (p < 0.05). The maximum heart distance and the V{sub 5Gy} did not vary consistently in the 2 positions (p = 0.06 and p = 0.7, respectively). The number of necessary monitor units was significantly higher in the supine position (312 vs. 232, p < 0.0001). The subgroups analysis pointed out the advantage in lung sparing in all TV groups (small, medium and large) for all the evaluated dosimetric constraints (central lung distance, maximum lung distance, and V{sub 5Gy}, p < 0.0001). In the small TV group, a dose reduction in nontarget areas of 22% in the prone position was detected (p = 0.056); in the medium and high TV groups, the difference was of about -10% (p = NS). The decrease in hot spot areas in nontarget tissues was 73%, 47%, and 80% for small, medium, and large TVs in the prone position, respectively. Although prone breast radiotherapy is normally proposed in patients with breasts of large dimensions, this study gives evidence of dosimetric benefit in all patient subgroups irrespective of breast volume size.

  14. Grammatical Errors Communication Breakdown.

    ERIC Educational Resources Information Center

    Tomiyana, Machiko

    1980-01-01

    Investigates to what extent ESL learners' syntactic errors in written communication cause comprehension breakdown. The variables considered are the omission, insertion, and wrong choice of articles and connectors. Results indicated that errors concerning connectors cause communication breakdown more often than do errors in article usage. (PMJ)

  15. Aggregate-prone desmin mutations impair mitochondrial calcium uptake in primary myotubes.

    PubMed

    Smolina, Natalia; Bruton, Joseph; Sjoberg, Gunnar; Kostareva, Anna; Sejersen, Thomas

    2014-10-01

    Desmin, being a major intermediate filament of mature muscle cell, interacts with mitochondria within the cell and participates in mitochondria proper localization. The goal of the present study was to assess the effect of aggregate-prone and non-aggregate-prone desmin mutations on mitochondrial calcium uptake. Primary murine satellite cells were transduced with lentiviruses carrying desmin in wild type or mutant form, and were induced to differentiate into myotubes. Four mutations resulting in different degree of desmin aggregates formation were analyzed. Tail domain mutation Asp399Tyr has the mildest impact on desmin filament polymerization, rod domain mutation Ala357Pro causes formation of large aggregates composed of filamentous material, and Leu345Pro and Leu370Pro are considered to be the most severest in their impact on desmin polymerization and structure. For mitochondrial calcium measurement cells were loaded with rhod 2-AM. We found that aggregate-prone mutations significantly decreased [Ca(2+)]mit, whereas non-aggregate-prone mutations did not decrease [Ca(2+)]mit. Moreover aggregate-prone desmin mutations resulted in increased resting cytosolic [Ca(2+)]. However this increase was not accompanied by any alterations in sarcoplasmic reticulum calcium release. We suggest that the observed decline in [Ca(2+)]mit was due to desmin aggregate accumulation resulting in the loss of desmin mitochondria interactions. PMID:25171807

  16. Relationship between childhood trauma, mindfulness, and dissociation in subjects with and without hallucination proneness.

    PubMed

    Perona-Garcelán, Salvador; García-Montes, José M; Rodríguez-Testal, Juan Francisco; López-Jiménez, Ana Ma; Ruiz-Veguilla, Miguel; Ductor-Recuerda, María Jesús; Benítez-Hernández, María del Mar; Arias-Velarde, Ma Ángeles; Gómez-Gómez, María Teresa; Pérez-Álvarez, Marino

    2014-01-01

    The purpose of this study was to examine the relationship between childhood traumas, mindfulness, and dissociation (more specifically, absorption and depersonalization) in healthy subjects with and without hallucination proneness. A sample of 318 subjects was given the Launay-Slade Hallucination Scale-Revised (R. P. Bentall & P. Slade, 1985). From this sample, 2 groups were formed: one with high and the other with low hallucination proneness. Furthermore, all participants were given the Tellegen Absorption Scale (A. Tellegen & G. Atkinson, 1974), the Cambridge Depersonalization Scale (M. Sierra & G. E. Berrios, 2000), the Southampton Mindfulness Questionnaire (P. D. J. Chadwick et al., 2008), and the Trauma Questionnaire (J. R. E. Davidson, D. Hughes, & D. G. Blazer, 1990). The results showed that in the group with high hallucination proneness, there were significantly more subjects with traumatic experiences than in the group with low predisposition, although no significant difference in the mean number of traumatic experiences undergone in childhood was found between the 2 groups, although there was a trend toward significance. A correlation analysis showed a significant negative association between mindfulness on the one hand and absorption and depersonalization on the other. A positive relationship was also found between childhood traumas and absorption and depersonalization. Finally, multiple mediation analysis showed that the absorption and depersonalization variables acted as mediators between childhood traumas and hallucination proneness. We discuss the importance of the relationship between the variables studied and hallucination proneness and suggest some approaches for their treatment. PMID:24377971

  17. Role of Disgust Proneness in Parkinson’s Disease: A Voxel-Based Morphometry Study

    PubMed Central

    Ille, Rottraut; Wabnegger, Albert; Schwingenschuh, Petra; Katschnig-Winter, Petra; Kögl-Wallner, Mariella; Wenzel, Karoline; Schienle, Anne

    2015-01-01

    The knowledge about personality traits in Parkinson’s disease (PD) is still limited. In particular, disgust proneness has not been investigated as well as its neuronal correlates. Although several morphometric studies demonstrated that PD is associated with gray matter volume (GMV) reduction in olfactory and gustatory regions involved in disgust processing, a possible correlation with disgust proneness has not been investigated. We conducted a voxel-based morphometry analysis to compare GMV between 16 cognitively normal male PD patients with mild to moderate symptoms and 24 matched control subjects. All participants had answered questionnaires for the assessment of disgust proneness, trait anger and trait anxiety. We correlated questionnaire scores with GMV in both groups. The clinical group reported selectively reduced disgust proneness toward olfactory stimuli associated with spoilage. Moreover, they showed GMV reduction in the central olfactory system [orbitofrontal cortex (OFC) and piriform cortex]. Disgust items referring to olfactory processing were positively correlated with OFC volume in PD patients. Our data suggest an association between PD-associated neurodegeneration and olfactory related facets of the personality trait disgust proneness. PMID:25908177

  18. Real-time PCR in virology

    Microsoft Academic Search

    Ian M. Mackay; Katherine E. Arden; Andreas Nitsche

    2002-01-01

    The use of the polymerase chain reaction (PCR) in molecular diagnostics has increased to the point where it is now accepted as the gold standard for detecting nucleic acids from a number of origins and it has become an essential tool in the research labora- tory. Real-time PCR has engendered wider acceptance of the PCR due to its improved rapidity,

  19. Real-Time PCR Dean Fraga,1

    E-print Network

    Jones, Michelle

    10 UNIT 10.3 Real-Time PCR Dean Fraga,1 Tea Meulia,2 and Steven Fenster3 1 College of Wooster, Ashland, Ohio OVERVIEW AND PRINCIPLES The real-time polymerase chain reaction (real-time PCR) is a recent since (Higuchi et al., 1992, 1993). Real-time PCR allows precise quantification of specific nucleic

  20. Detection of porcine teschoviruses and enteroviruses by LightCycler real-time PCR.

    PubMed

    Krumbholz, Andi; Wurm, Rüdiger; Scheck, Oliver; Birch-Hirschfeld, Eckard; Egerer, Renate; Henke, Andreas; Wutzler, Peter; Zell, Roland

    2003-10-01

    Porcine picornaviruses comprising at least 23 serotypes grouped into six species were described as causative agents of neurological disorders, reproductive failure, and aphthae-like dermal lesions of swine. Other viruses such as classical swine fever virus (CSFV), African swine fever virus, pseudorabies virus (PRV), vesicular stomatitis virus, vesicular exanthema virus, porcine respiratory and reproductive syndrome virus, and porcine parvovirus (PPV) may cause diseases with similar clinical symptoms. Therefore, rapid and reliable PCR detection of the most frequent porcine picornaviruses is of interest. A real-time RT-PCR protocol employing LightCycler technology to detect all known serotypes of the three porcine enterovirus (PEV) cytopathic effect (CPE) groups was established. It uses three sets of primer pairs and group-specific hybridisation probes. The primer pairs were designed to amplify highly conserved sequences of the 5'-non-translated region (5'-NTR) of the relevant virus species. The one-step real-time PCR based on the LightCycler technology is more rapid and less contamination-prone than the nested RT-PCR and allows the precise quantitation of the virus load in the tested specimens. All acknowledged serotypes of the three PEV CPE groups and all tested field strains isolated from clinical specimens were detectable. Viruses of the PEV CPE group III can be distinguished from the closely related swine vesicular disease virus (SVDV). PMID:14500127

  1. Boredom proneness--the development and correlates of a new scale.

    PubMed

    Farmer, R; Sundberg, N D

    1986-01-01

    This article reports the development, validation, and correlates of a self-report measure of boredom proneness. The 28-item Boredom Proneness (BP) Scale demonstrates satisfactory levels of internal consistency (coefficient alpha = .79) and test-retest reliability (r = .83) over a 1-week interval. Evidence of validity for the BP is supported by correlations with other boredom measures and from a set of studies evaluating interest and attention in the classroom. Other hypothesized relationships with boredom were tested, with significant positive associations found with depression, hopelessness, perceived effort, loneliness, and amotivational orientation. Additional findings indicate boredom proneness to be negatively related to life satisfaction and autonomy orientation. The relationship of boredom to other affective states is discussed, and directions for future research are outlined. PMID:3723312

  2. Deep vein thrombosis after spine operation in prone position with subclavian venous catheterization: a case report.

    PubMed

    Cho, Jae Kyung; Han, Jin Hee; Park, Sung Wook; Kim, Keon Sik

    2014-07-01

    We experienced a case of deep vein thrombosis after spine surgery in the prone position with a central venous catheter (CVC). Posterior lumbar interbody fusion was performed on a 73-year-old female patient who was diagnosed with spinal stenosis. Accordingly, in the operation room under general anesthesia, two-lumen CVC were inserted into the left subclavian vein. The surgery was performed in the prone position with a Wilson frame. On the next day, there was a sudden occurrence of severe edema in the patient's left arm. By ultrasonography and computed tomography scanning, extensive deep vein thrombosis was observed in the left subclavian vein. The existence of a factor affecting blood flow such as the prone position may increase the risk of thrombus formation. Therefore, careful perioperative evaluation should be implemented. PMID:25097742

  3. Medical errors in neurosurgery

    PubMed Central

    Rolston, John D.; Zygourakis, Corinna C.; Han, Seunggu J.; Lau, Catherine Y.; Berger, Mitchel S.; Parsa, Andrew T.

    2014-01-01

    Background: Medical errors cause nearly 100,000 deaths per year and cost billions of dollars annually. In order to rationally develop and institute programs to mitigate errors, the relative frequency and costs of different errors must be documented. This analysis will permit the judicious allocation of scarce healthcare resources to address the most costly errors as they are identified. Methods: Here, we provide a systematic review of the neurosurgical literature describing medical errors at the departmental level. Eligible articles were identified from the PubMed database, and restricted to reports of recognizable errors across neurosurgical practices. We limited this analysis to cross-sectional studies of errors in order to better match systems-level concerns, rather than reviewing the literature for individually selected errors like wrong-sided or wrong-level surgery. Results: Only a small number of articles met these criteria, highlighting the paucity of data on this topic. From these studies, errors were documented in anywhere from 12% to 88.7% of cases. These errors had many sources, of which only 23.7-27.8% were technical, related to the execution of the surgery itself, highlighting the importance of systems-level approaches to protecting patients and reducing errors. Conclusions: Overall, the magnitude of medical errors in neurosurgery and the lack of focused research emphasize the need for prospective categorization of morbidity with judicious attribution. Ultimately, we must raise awareness of the impact of medical errors in neurosurgery, reduce the occurrence of medical errors, and mitigate their detrimental effects. PMID:25371849

  4. Medication errors: analysis not blame.

    PubMed

    Horns, Kimberly M; Loper, Donna Lee

    2002-01-01

    This article summarizes current knowledge regarding neonatal medication errors and explicates the key concepts of human error and system error. A case report illustrates the sources of error. Medication error analysis must go beyond the blaming of individuals for active errors and explore the latent errors that exist in a complex health care environment. Using correct language to describe and define medication error may facilitate the development of a nonpunitive culture and enable effective evaluation of the causes of error. PMID:12033548

  5. Relationship between self-focused attention and mindfulness in people with and without hallucination proneness.

    PubMed

    Perona-Garcelán, Salvador; García-Montes, José M; López-Jiménez, Ana M; Rodríguez-Testal, Juan Francisco; Ruiz-Veguilla, Miguel; Ductor-Recuerda, María Jesús; Benítez-Hernández, María del Mar; Arias-Velarde, M Ángeles; Gómez-Gómez, María Teresa; Pérez-Álvarez, Marino

    2014-01-01

    The purpose of this work was to study the relationship between self-focused attention and mindfulness in participants prone to hallucinations and others who were not. A sample of 318 healthy participants, students at the universities of Sevilla and Almería, was given the Launay-Slade Hallucinations Scale-revised (LSHS-R, Bentall & Slade, 1985). Based on this sample, two groups were formed: participants with high (n = 55) and low proneness (n = 28) to hallucinations. Participants with a score higher than a standard deviation from the mean in the LSHS-R were included in the high proneness group, participants with a score lower than a standard deviation from the mean in the LSHR-R were included in the second one. All participants were also given the Self-Absorption Scale (SAS, McKenzie & Hoyle, 2008) and the Southampton Mindfulness Questionnaire (SMQ, Chadwick et al., 2008). The results showed that participants with high hallucination proneness had significantly higher levels of public (t(80) = 6.81, p < .001) and private (t(77) = 7.39, p < .001) self-focused attention and lower levels of mindfulness (t(81) = -4.56, p < .001) than participants in the group with low hallucination proneness. A correlational analysis showed a negative association between self-focused attention (private and public) and mindfulness (r = -0.23, p < .001; r = -0.38, p < .001 respectively). Finally, mindfulness was found to partly mediate between self-focused attention and hallucination proneness. The importance of self-focused attention and mindfulness in understanding the etiology of hallucinations discussed and suggest some approaches to their treatment. PMID:25012781

  6. PCR Template preparation Polymerase chain reaction (PCR) is a versatile tool for screening M. tuberculosis clones.

    E-print Network

    PCR Template preparation Polymerase chain reaction (PCR) is a versatile tool for screening M for each 100 µl PCR reaction. ALTERNATE PROTOCOL: 1. After Step 2 in main protocol, spin cells in microcentrifuge for 2 minutes then use 10 to 20 µL of the supernatant in a 100 µL PCR reaction. #12;

  7. Expected Estimating Equation using Calibration Data for Generalized Linear Models with a Mixture of Berkson and Classical Errors in Covariates

    PubMed Central

    de Dieu Tapsoba, Jean; Lee, Shen-Ming; Wang, Ching-Yun

    2013-01-01

    Data collected in many epidemiological or clinical research studies are often contaminated with measurement errors that may be of classical or Berkson error type. The measurement error may also be a combination of both classical and Berkson errors and failure to account for both errors could lead to unreliable inference in many situations. We consider regression analysis in generalized linear models when some covariates are prone to a mixture of Berkson and classical errors and calibration data are available only for some subjects in a subsample. We propose an expected estimating equation approach to accommodate both errors in generalized linear regression analyses. The proposed method can consistently estimate the classical and Berkson error variances based on the available data, without knowing the mixture percentage. Its finite-sample performance is investigated numerically. Our method is illustrated by an application to real data from an HIV vaccine study. PMID:24009099

  8. Expected estimating equation using calibration data for generalized linear models with a mixture of Berkson and classical errors in covariates.

    PubMed

    Tapsoba, Jean de Dieu; Lee, Shen-Ming; Wang, Ching-Yun

    2014-02-20

    Data collected in many epidemiological or clinical research studies are often contaminated with measurement errors that may be of classical or Berkson error type. The measurement error may also be a combination of both classical and Berkson errors and failure to account for both errors could lead to unreliable inference in many situations. We consider regression analysis in generalized linear models when some covariates are prone to a mixture of Berkson and classical errors, and calibration data are available only for some subjects in a subsample. We propose an expected estimating equation approach to accommodate both errors in generalized linear regression analyses. The proposed method can consistently estimate the classical and Berkson error variances based on the available data, without knowing the mixture percentage. We investigated its finite-sample performance numerically. Our method is illustrated by an application to real data from an HIV vaccine study. PMID:24009099

  9. hal-00164307,version1-20Jul2007 Application of probabilistic PCR5 Fusion Rule

    E-print Network

    Paris-Sud XI, Université de

    : Filtering, Robust estimation, non-Bayesian fu- sion rule, PCR5, Particle filtering. I. INTRODUCTION Bayesian. The non-linear distributed filter is implemented through a basic particles filtering technique filtering methods which are sufficiently robust against the bias at the initialization as well as error

  10. Predicting Fault Prone Modules by the Dempster-Shafer Belief Networks

    PubMed Central

    Guo, Lan; Cukic, Bojan; Singh, Harshinder

    2015-01-01

    This paper describes a novel methodology for predicting fault prone modules. The methodology is based on Dempster-Shafer (D-S) belief networks. Our approach consists of three steps: First, building the Dempster-Shafer network by the induction algorithm; Second, selecting the predictors (attributes) by the logistic procedure; Third, feeding the predictors describing the modules of the current project into the inducted Dempster-Shafer network and identifying fault prone modules. We applied this methodology to a NASA dataset. The prediction accuracy of our methodology is higher than that achieved by logistic regression or discriminant analysis on the same dataset.

  11. Flood-prone areas and waterways, Edwards Air Force Base, California

    USGS Publications Warehouse

    Meyer, Robert W.; Bowers, James C.

    2002-01-01

    Edwards Air Force Base (EAFB) is in the Mojave Desert region of southern California. Although the climate in the study area is arid, occasional intense storms result in flooding on the base, damaging roads and buildings. To plan for anticipated development at EAFB, the U.S. Department of the Air Force (USAF) and the U.S. Geological Survey (USGS) began a cooperative study to locate flood-prone areas on the base. This report describes flood hazards and shows flood-prone areas of the base.

  12. Principle and applications of digital PCR.

    PubMed

    Pohl, Gudrun; Shih, Ie-Ming

    2004-01-01

    Digital PCR represents an example of the power of PCR and provides unprecedented opportunities for molecular genetic analysis in cancer. The technique is to amplify a single DNA template from minimally diluted samples, therefore generating amplicons that are exclusively derived from one template and can be detected with different fluorophores or sequencing to discriminate different alleles (e.g., wild type vs. mutant or paternal vs. maternal alleles). Thus, digital PCR transforms the exponential, analog signals obtained from conventional PCR to linear, digital signals, allowing statistical analysis of the PCR product. Digital PCR has been applied in quantification of mutant alleles and detection of allelic imbalance in clinical specimens, providing a promising molecular diagnostic tool for cancer detection. The scope of this article is to review the principles of digital PCR and its practical applications in cancer research and in the molecular diagnosis of cancer. PMID:14711348

  13. Aircraft system modeling error and control error

    NASA Technical Reports Server (NTRS)

    Kulkarni, Nilesh V. (Inventor); Kaneshige, John T. (Inventor); Krishnakumar, Kalmanje S. (Inventor); Burken, John J. (Inventor)

    2012-01-01

    A method for modeling error-driven adaptive control of an aircraft. Normal aircraft plant dynamics is modeled, using an original plant description in which a controller responds to a tracking error e(k) to drive the component to a normal reference value according to an asymptote curve. Where the system senses that (1) at least one aircraft plant component is experiencing an excursion and (2) the return of this component value toward its reference value is not proceeding according to the expected controller characteristics, neural network (NN) modeling of aircraft plant operation may be changed. However, if (1) is satisfied but the error component is returning toward its reference value according to expected controller characteristics, the NN will continue to model operation of the aircraft plant according to an original description.

  14. Monte Carlo errors with less errors

    NASA Astrophysics Data System (ADS)

    Wolff, Ulli; Alpha Collaboration

    2004-01-01

    We explain in detail how to estimate mean values and assess statistical errors for arbitrary functions of elementary observables in Monte Carlo simulations. The method is to estimate and sum the relevant autocorrelation functions, which is argued to produce more certain error estimates than binning techniques and hence to help toward a better exploitation of expensive simulations. An effective integrated autocorrelation time is computed which is suitable to benchmark efficiencies of simulation algorithms with regard to specific observables of interest. A Matlab code is offered for download that implements the method. It can also combine independent runs (replica) allowing to judge their consistency.

  15. Error detection method

    DOEpatents

    Olson, Eric J.

    2013-06-11

    An apparatus, program product, and method that run an algorithm on a hardware based processor, generate a hardware error as a result of running the algorithm, generate an algorithm output for the algorithm, compare the algorithm output to another output for the algorithm, and detect the hardware error from the comparison. The algorithm is designed to cause the hardware based processor to heat to a degree that increases the likelihood of hardware errors to manifest, and the hardware error is observable in the algorithm output. As such, electronic components may be sufficiently heated and/or sufficiently stressed to create better conditions for generating hardware errors, and the output of the algorithm may be compared at the end of the run to detect a hardware error that occurred anywhere during the run that may otherwise not be detected by traditional methodologies (e.g., due to cooling, insufficient heat and/or stress, etc.).

  16. Science Shorts: Experimental Error

    NSDL National Science Digital Library

    Kimberly J. Davis

    2008-10-01

    One of the most challenging components of science inquiry is getting students to understand the fundamentally important concept of experimental error. While this concept can be tricky for children, there are straightforward lessons that can go a long way in getting students to think about and control for error. This month's activity leads students through a purposely flawed investigation of popcorn, allowing them to point out the potential sources of error.

  17. The importance of robust error control in data compression applications

    NASA Technical Reports Server (NTRS)

    Woolley, S. I.

    1993-01-01

    Data compression has become an increasingly popular option as advances in information technology have placed further demands on data storage capabilities. With compression ratios as high as 100:1 the benefits are clear; however, the inherent intolerance of many compression formats to error events should be given careful consideration. If we consider that efficiently compressed data will ideally contain no redundancy, then the introduction of a channel error must result in a change of understanding from that of the original source. While the prefix property of codes such as Huffman enables resynchronisation, this is not sufficient to arrest propagating errors in an adaptive environment. Arithmetic, Lempel-Ziv, discrete cosine transform (DCT) and fractal methods are similarly prone to error propagating behaviors. It is, therefore, essential that compression implementations provide sufficient combatant error control in order to maintain data integrity. Ideally, this control should be derived from a full understanding of the prevailing error mechanisms and their interaction with both the system configuration and the compression schemes in use.

  18. Error coding simulations

    NASA Technical Reports Server (NTRS)

    Noble, Viveca K.

    1993-01-01

    There are various elements such as radio frequency interference (RFI) which may induce errors in data being transmitted via a satellite communication link. When a transmission is affected by interference or other error-causing elements, the transmitted data becomes indecipherable. It becomes necessary to implement techniques to recover from these disturbances. The objective of this research is to develop software which simulates error control circuits and evaluate the performance of these modules in various bit error rate environments. The results of the evaluation provide the engineer with information which helps determine the optimal error control scheme. The Consultative Committee for Space Data Systems (CCSDS) recommends the use of Reed-Solomon (RS) and convolutional encoders and Viterbi and RS decoders for error correction. The use of forward error correction techniques greatly reduces the received signal to noise needed for a certain desired bit error rate. The use of concatenated coding, e.g. inner convolutional code and outer RS code, provides even greater coding gain. The 16-bit cyclic redundancy check (CRC) code is recommended by CCSDS for error detection.

  19. A Review of the Literature on the Early Identification of Delinquent-Prone Children.

    ERIC Educational Resources Information Center

    Wedge, Robert F.

    The paper reviews research on the early identification of delinquent-prone children and considers the role of prediction in developing effective delinqency prevention programs. Among issues addressed are definitions of delinquency, theories on causation, and the role of prediction in criminology. Pros and cons of prediction are examined. Among…

  20. Flood-prone area maps of three sites along the Trans-Alaska Pipeline, Alaska

    USGS Publications Warehouse

    Lamke, Robert D.; Jones, Stanley H.

    1980-01-01

    Flood-prone areas in Alaska are delineated on aerial photographs for the Sagavanirktok River near Pump Station 3, Middle Fork Koyukuk River at Coldfoot, and Jim River near Pump Station 5. An analysis of available flood data and a description of recent flood evidence and maximum evident flood marks are included. (Kosco-USGS)

  1. At Risk for Violence Test (ARFV). For Identifying Violence-Prone Teens and Adults. Manual.

    ERIC Educational Resources Information Center

    McConochie, William A.

    The At Risk for Violence Test (ARFV) is a test used to identify violence prone teens and adults. The ARFV, teen version, is designed for use in public and private schools, grades 6 through 12, as an annual screening early in the school year. Norms for girls and boys are used for scoring reports. The adult version may be used to screen job…

  2. An Empirical Study of the Fault-Proneness of Clone Mutation and Clone Migration

    E-print Network

    Zou, Ying

    An Empirical Study of the Fault-Proneness of Clone Mutation and Clone Migration Shuai Xie1, Foutse of code to reuse some existing code segments. This action creates code clones in the software system. The literature has documented different types of code clone (e.g., Type-1, Type-2, and Type-3). Once created

  3. Continuous gas monitoring for the assessment of outburst-proneness at a mining face

    Microsoft Academic Search

    B. B. Beamish

    1990-01-01

    Continuous gas monitoring has been performed in three development panels at No. 2 Mine, Collinsville, Queensland, Australia to assess seam gassiness at the mining face as an indication of outburst-proneness. The first panel monitored encountered two outbursts during mining of virgin conditions, and a third outburst occurred on the fringe of a gas-drained block, adjacent to a thrust fault. The

  4. Compartmental Analysis of Breathing in the Supine and Prone Positions by Optoelectronic Plethysmography

    Microsoft Academic Search

    Andrea Aliverti; Raffaele Dellacà; Paolo Pelosi; Davide Chiumello; Luciano Gattinoni; Antonio Pedotti

    2001-01-01

    Optoelectronic plethysmography (OEP) has been shown to be a reliable method for the analysis of chest wall kinematics partitioned into pulmonary rib cage, abdominal rib cage, abdomen, and right and left side in the seated and erect positions. In this paper, we extended the applicability of this method to the supine and prone positions, typically adopted in critically ill patients.

  5. [Methodic approaches to determining the level of occupational fitness in jobs prone to trauma].

    PubMed

    Iushkova, O I; Matiukhin, V V; Poroshenko, A S; Iampol'skaia, E G

    2006-01-01

    The article deals with main methods to evaluate functional state of various body systems and with the methods-based criteria of occupational fitness for miscellaneous activities. Examination of 11 types of jobs prone to trauma helped to specify integral parameter for occupational selection. PMID:16755758

  6. Dissociative symptoms and how they relate to fantasy proneness in women reporting repressed or recovered memories

    Microsoft Academic Search

    Elke Geraerts; Harald Merckelbach; Marko Jelicic; Elke Smeets; Jaap van Heerden

    2006-01-01

    Women with repressed or recovered memories have raised levels of dissociative symptoms. There are two interpretations of this. One emphasizes the defensive function of dissociation, while the other emphasizes the overlap between dissociation and fantasy proneness. This study aimed to investigate these two interpretations. Women with repressed (n=16), recovered (n=23), and continuous memories (n=55) of childhood sexual abuse (CSA), and

  7. Predicting Abuse-Prone Parental Attitudes and Discipline Practices in a Nationally Representative Sample.

    ERIC Educational Resources Information Center

    Jackson, Shelly; Thompson, Ross A.; Christiansen, Elaine H.; Colman, Rebecca A.; Wyatt, Jennifer; Buckendahl, Chad W.; Wilcox, Brian L.; Peterson, Reece

    1999-01-01

    A study involving 1,000 parents examined factors that place parents at risk of abusing their children. Results found that examining parental attitudes, history, and personality characteristics, as well as religion and ideology, were important in predicting abuse proneness. Child age was also an important predictor. (Author/CR)

  8. An Empirical Study on the Fault-Proneness of Clone Migration in Clone Genealogies

    E-print Network

    Zou, Ying

    An Empirical Study on the Fault-Proneness of Clone Migration in Clone Genealogies Shuai Xie1 genealogy. During the evolution of a clone group, developers may change the location of the code fragments the risk for faults in clone segments, clone groups, and clone genealogies from three long-lived software

  9. From Self-awareness to Shame-proneness: Evidence of Causal Sequence Among Women

    Microsoft Academic Search

    Jamie Arndt; Jamie L Goldenberg

    2004-01-01

    This article reports an experimental study designed to test the hypothesis that self-awareness plays a causal role in the experience of shame but not guilt. The effects of a self-focus manipulation on shame and guilt proneness were assessed by having male and female participants complete an internal vs. external focus of attention writing task and then complete the Test for

  10. Taurine accelerates the regression of hypercholesterolemia in stroke-prone spontaneously hypertensive rats

    Microsoft Academic Search

    Shigeru Murakami; Yasuo Nara; Yukio Yamori

    1996-01-01

    The effects of taurine on the regression of pre-established hypercholesterolemia were examined in stroke-prone spontaneously hypertensive rats (SHRSP). Hypercholesterolemia was induced by feeding a hypercholesterolemic diet to SHRSP for 30 days. Then, the diet was switched to normal chow with or without 3% taurine, and the effects were followed up for another 30 days. During regression serum cholesterol level was

  11. Hypolipidemic Effect of Taurine in Stroke-Prone Spontaneously Hypertensive Rats

    Microsoft Academic Search

    Shigeru Murakami; Izumi Yamagishi; Yumiko Asami; Yukiko Ohta; Yoshihisa Toda; Yasuo Nara; Yukio Yamori

    1996-01-01

    The hypolipidemic and antiatherosclerotic effects of taurine were investigated in genetically hypertensive rats: stroke-prone spontaneously hypertensive rats (SHRSP). SHRSP were fed a hypercholesterolemic (HC) diet supplemented with 3% taurine for 50 days, and serum cholesterol was monitored. Cholesterol content and enzymatic activity responsible for cholesterol synthesis and metabolism were also determined in the liver, aorta, and intestine. Taurine prevented increases

  12. Generators and Interpretors in a Performing Arts Population: Dissociation, Trauma, Fantasy Proneness, and Affective States

    Microsoft Academic Search

    Paula Thomson; E. B. Keehn; Thomas P. Gumpel

    2009-01-01

    An international sample of 130 working artists was divided into two domains: generators (writers, designers, choreographers, one composer) and interpreters (directors, actors, opera singers, dancers). The correlations between dissociation, trauma experiences, fantasy proneness, and affective states were examined, followed by a regression analysis to predict elevated levels of dissociation. Artists, regardless of creative domain, scored in the moderate range for

  13. API Change and Fault Proneness: A Threat to the Success of Android Apps

    E-print Network

    Poshyvanyk, Denys

    that developers use to build apps (i.e., Application Program- ming Interfaces - APIs). APIs encapsulateAPI Change and Fault Proneness: A Threat to the Success of Android Apps Mario Linares-Vásquez1@cs.wm.edu ABSTRACT During the recent years, the market of mobile software appli- cations (apps) has maintained

  14. "Deviance Proneness" and Adolescent Smoking 1980 versus 2001: Has There Been a "Hardening" of Adolescent Smoking?

    ERIC Educational Resources Information Center

    Chassin, Laurie; Presson, Clark; Morgan-Lopez, Antonio; Sherman, Steven J.

    2007-01-01

    In a midwestern community sample, we tested for evidence of "hardening" of adolescent cigarette smoking between 1980 and 2001 by comparing adolescent smokers and nonsmokers at these two times on measures indicative of "deviance proneness" in Jessor and Jessor's [Jessor, R., & Jessor, S. L. (1977). "Problem behavior and psychosocial development: A…

  15. The relationship between dysphoria and proneness to hallucination and delusions among young adults

    Microsoft Academic Search

    Matteo Cella; Andrew Cooper; Simon O. Dymond; Phil Reed

    2008-01-01

    Previous research suggests that measures of dysphoria relate to positive schizophrenic symptoms. These relationships have rarely been studied within the dimensionality of psychopathology framework. The present study examined the relationship between 3 distinct aspects of dysphoria (depression and state and trait anxiety) and delusion and hallucination proneness in a nonclinical sample of young adults. A total of 472 participants were

  16. Alexithymia, Emotional Instability, and Vulnerability to Stress Proneness in Patients Seeking Help for Hypersexual Behavior

    Microsoft Academic Search

    Rory C. Reid; Bruce N. Carpenter; Matthew Spackman; Debbie L. Willes

    2008-01-01

    This article reports the findings of a study investigating alexithymia, emotional instability, and vulnerability to stress proneness among individuals (N = 120) seeking help for hypersexual behavior. At the onset of treatment at an outpatient community clinic, subjects completed the Sexual Compulsivity Scale (SCS), the 20-item Toronto Alexithymia Scale (TAS-20), and the NEO Personality Inventory Revised (NEO-PI-R). The results of

  17. Characterization of the permeability and acoustic properties of an outburst-prone sandstone

    Microsoft Academic Search

    Stephen D. Butt; Paul K. Frempong; Chinmoy Mukherjee; James Upshall

    2005-01-01

    Two underground coal mines in the Sydney Coalfield, Nova Scotia, Canada have encountered gas outbursts from sandstone formations overlying the coal seams. These have consistently occurred while driving mine roadways into virgin ground at and below mining depths of 700 m. In this investigation, triaxial compression tests were conducted on samples of the outburst-prone sandstone from one of these mines,

  18. Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA

    PubMed Central

    2013-01-01

    Background 454 sequencing technology is a promising approach for characterizing HIV-1 populations and for identifying low frequency mutations. The utility of 454 technology for determining allele frequencies and linkage associations in HIV infected individuals has not been extensively investigated. We evaluated the performance of 454 sequencing for characterizing HIV populations with defined allele frequencies. Results We constructed two HIV-1 RT clones. Clone A was a wild type sequence. Clone B was identical to clone A except it contained 13 introduced drug resistant mutations. The clones were mixed at ratios ranging from 1% to 50% and were amplified by standard PCR conditions and by PCR conditions aimed at reducing PCR-based recombination. The products were sequenced using 454 pyrosequencing. Sequence analysis from standard PCR amplification revealed that 14% of all sequencing reads from a sample with a 50:50 mixture of wild type and mutant DNA were recombinants. The majority of the recombinants were the result of a single crossover event which can happen during PCR when the DNA polymerase terminates synthesis prematurely. The incompletely extended template then competes for primer sites in subsequent rounds of PCR. Although less often, a spectrum of other distinct crossover patterns was also detected. In addition, we observed point mutation errors ranging from 0.01% to 1.0% per base as well as indel (insertion and deletion) errors ranging from 0.02% to nearly 50%. The point errors (single nucleotide substitution errors) were mainly introduced during PCR while indels were the result of pyrosequencing. We then used new PCR conditions designed to reduce PCR-based recombination. Using these new conditions, the frequency of recombination was reduced 27-fold. The new conditions had no effect on point mutation errors. We found that 454 pyrosequencing was capable of identifying minority HIV-1 mutations at frequencies down to 0.1% at some nucleotide positions. Conclusion Standard PCR amplification results in a high frequency of PCR-introduced recombination precluding its use for linkage analysis of HIV populations using 454 pyrosequencing. We designed a new PCR protocol that resulted in a much lower recombination frequency and provided a powerful technique for linkage analysis and haplotype determination in HIV-1 populations. Our analyses of 454 sequencing results also demonstrated that at some specific HIV-1 drug resistant sites, mutations can reliably be detected at frequencies down to 0.1%. PMID:23402264

  19. Exploring the impact of forcing error characteristics on physically based snow simulations within a global sensitivity analysis framework

    NASA Astrophysics Data System (ADS)

    Raleigh, M. S.; Lundquist, J. D.; Clark, M. P.

    2014-12-01

    Physically based models provide insights into key hydrologic processes, but are associated with uncertainties due to deficiencies in forcing data, model parameters, and model structure. Forcing uncertainty is enhanced in snow-affected catchments, where weather stations are scarce and prone to measurement errors, and meteorological variables exhibit high variability. Hence, there is limited understanding of how forcing error characteristics affect simulations of cold region hydrology. Here we employ global sensitivity analysis to explore how different error types (i.e., bias, random errors), different error distributions, and different error magnitudes influence physically based simulations of four snow variables (snow water equivalent, ablation rates, snow disappearance, and sublimation). We use Sobol' global sensitivity analysis, which is typically used for model parameters, but adapted here for testing model sensitivity to co-existing errors in all forcings. We quantify the Utah Energy Balance model's sensitivity to forcing errors with 1 520 000 Monte Carlo simulations across four sites and four different scenarios. Model outputs were generally (1) more sensitive to forcing biases than random errors, (2) less sensitive to forcing error distributions, and (3) sensitive to different forcings depending on the relative magnitude of errors. For typical error magnitudes, precipitation bias was the most important factor for snow water equivalent, ablation rates, and snow disappearance timing, but other forcings had a significant impact depending on forcing error magnitudes. Additionally, the relative importance of forcing errors depended on the model output of interest. Sensitivity analysis can reveal which forcing error characteristics matter most for hydrologic modeling.

  20. Mattress and pillow for prone positioning for treatment of obstructive sleep apnoea

    PubMed Central

    Nilsson, Michael; Attia, John; Ejnell, Hasse

    2015-01-01

    Conclusion: The new mattress and pillow for prone positioning (MPP) is efficient in reducing the apnoea-hypopnoea index (AHI) and oxygen desaturation index (ODI) in most patients with obstructive sleep apnoea (OSA), with satisfactory compliance. Objective: The aim of the present study was to evaluate the effect of the prone body and head sleep position on severity of disease in patients with OSA after 4 weeks of adaptation to a mattress and pillow facilitating prone positioning. Methods: Fourteen patients with mild to severe OSA, 11 men and 3 women with a mean AHI of 26 (min, 6; max, 53) and mean ODI of 21 (min, 6; max, 51) were evaluated. Two polysomnographic (PSG) studies were performed. The first PSG study was without any treatment and the second was after 4 weeks of adaptation to the MPP for prone positioning of the body and the head. Results: Mean AHI and ODI decreased from 26 and 21 to 8 and 7, respectively (p < 0.001) with treatment. The mean time spent in the supine position was reduced from 128 to 10 min (p = 0.02) and the prone time increased from 42 to 174 min (p = 0.02) with the MPP. The mean total sleep time was 390 min during the first PSG study night without treatment and 370 min during the second night with the MPP (p = 0.7). Ten patients (71%) reduced their AHI by at least 50% and reached a value < 10 during treatment. All patients managed to sleep on the MPP for > 4 h per night during the 4-week study. PMID:25649886

  1. Refractive error blindness.

    PubMed Central

    Dandona, R.; Dandona, L.

    2001-01-01

    Recent data suggest that a large number of people are blind in different parts of the world due to high refractive error because they are not using appropriate refractive correction. Refractive error as a cause of blindness has been recognized only recently with the increasing use of presenting visual acuity for defining blindness. In addition to blindness due to naturally occurring high refractive error, inadequate refractive correction of aphakia after cataract surgery is also a significant cause of blindness in developing countries. Blindness due to refractive error in any population suggests that eye care services in general in that population are inadequate since treatment of refractive error is perhaps the simplest and most effective form of eye care. Strategies such as vision screening programmes need to be implemented on a large scale to detect individuals suffering from refractive error blindness. Sufficient numbers of personnel to perform reasonable quality refraction need to be trained in developing countries. Also adequate infrastructure has to be developed in underserved areas of the world to facilitate the logistics of providing affordable reasonable-quality spectacles to individuals suffering from refractive error blindness. Long-term success in reducing refractive error blindness worldwide will require attention to these issues within the context of comprehensive approaches to reduce all causes of avoidable blindness. PMID:11285669

  2. Everyday Scale Errors

    ERIC Educational Resources Information Center

    Ware, Elizabeth A.; Uttal, David H.; DeLoache, Judy S.

    2010-01-01

    Young children occasionally make "scale errors"--they attempt to fit their bodies into extremely small objects or attempt to fit a larger object into another, tiny, object. For example, a child might try to sit in a dollhouse-sized chair or try to stuff a large doll into it. Scale error research was originally motivated by parents' and…

  3. Preventing errors in laterality.

    PubMed

    Landau, Elliot; Hirschorn, David; Koutras, Iakovos; Malek, Alexander; Demissie, Seleshie

    2015-04-01

    An error in laterality is the reporting of a finding that is present on the right side as on the left or vice versa. While different medical and surgical specialties have implemented protocols to help prevent such errors, very few studies have been published that describe these errors in radiology reports and ways to prevent them. We devised a system that allows the radiologist to view reports in a separate window, displayed in a simple font and with all terms of laterality highlighted in separate colors. This allows the radiologist to correlate all detected laterality terms of the report with the images open in PACS and correct them before the report is finalized. The system is monitored every time an error in laterality was detected. The system detected 32 errors in laterality over a 7-month period (rate of 0.0007 %), with CT containing the highest error detection rate of all modalities. Significantly, more errors were detected in male patients compared with female patients. In conclusion, our study demonstrated that with our system, laterality errors can be detected and corrected prior to finalizing reports. PMID:25273506

  4. Absolute quantification by droplet digital PCR versus analog real-time PCR

    PubMed Central

    Hindson, Christopher M; Chevillet, John R; Briggs, Hilary A; Gallichotte, Emily N; Ruf, Ingrid K; Hindson, Benjamin J; Vessella, Robert L; Tewari, Muneesh

    2014-01-01

    Nanoliter-sized droplet technology paired with digital PCR (ddPCR) holds promise for highly precise, absolute nucleic acid quantification. Our comparison of microRNA quantification by ddPCR and real-time PCR revealed greater precision (coefficients of variation decreased by 37–86%) and improved day-to-day reproducibility (by a factor of seven) of ddPCR but with comparable sensitivity. When we applied ddPCR to serum microRNA biomarker analysis, this translated to superior diagnostic performance for identifying individuals with cancer. PMID:23995387

  5. PCR markers distinguish Plantago major subspecies

    Microsoft Academic Search

    K. Wolff; M. Morgan-Richards

    1998-01-01

    Plantago major plants from several Scottish and Dutch locations were surveyed for their genetic variation using PCR markers, namely RAPD\\u000a analysis, anchored inter-SSR PCR, and chloroplast PCR followed by RFLP analysis. The RAPD and inter-SSR markers showed a differentiation\\u000a between the two subspecies of P. major. These results are discussed in relation to earlier results using allozyme electrophoresis, DNA fingerprinting,

  6. Simple Fool's Guide GUIDE TO PCR

    E-print Network

    Palumbi, Stephen

    .F.G.........................................................................3 DNA Extraction For PCR ....................................................................4 General Extraction Protocol for Total DNA..........................................................4 Variations on the Extraction Protocol...................................................................5

  7. Direct free-form deformation of NC programs for surface reconstruction and form-error compensation

    Microsoft Academic Search

    Dirk Biermann; Alexei Sacharow; Tobias Surmann; Tobias Wagner

    2010-01-01

    In this paper a new approach for manufacturing modified workpieces by milling is presented. In course of product development,\\u000a several optimization iterations are often required, in which the shape of the workpiece is modified. Conventional method for\\u000a manufacturing modified workpieces includes a time-consuming and error-prone step of reverse engineering, where the new CAD\\/CAM\\u000a data is generated with respect to the

  8. Error in anatomic pathology.

    PubMed

    Foucar, E

    2001-12-01

    Error in anatomic pathology is a topic that is currently making the difficult transition from a problem peculiar to a subset of poorly trained or otherwise inadequate pathologists to a problem shared by the specialty of pathology. This transition will involve a number of difficult steps, including sorting error from both inherent diagnostic uncertainty andfrom variations in practice patterns from which no evidence-based best practice has emerged. Identification of error will require scientifically valid diagnostic gold standards, and in those areas of diagnosis without such a standard, the identification of and response to error will continue to be heavily influenced by hindsight bias and subjective opinion. The pathologist, like other physicians, has limited options to "make things right" following a significant error The silver lining is that many errors have the potential to prompt changes that will prevent future patient harm. Unfortunately, a dysfunctional legal system that values punishment and transfer of assets over future improvements in health care has wrung much of the positive potential out of error, leaving only the damaged patient and damaged pathologist. PMID:11993701

  9. Surprise beyond prediction error

    PubMed Central

    Chumbley, Justin R; Burke, Christopher J; Stephan, Klaas E; Friston, Karl J; Tobler, Philippe N; Fehr, Ernst

    2014-01-01

    Surprise drives learning. Various neural “prediction error” signals are believed to underpin surprise-based reinforcement learning. Here, we report a surprise signal that reflects reinforcement learning but is neither un/signed reward prediction error (RPE) nor un/signed state prediction error (SPE). To exclude these alternatives, we measured surprise responses in the absence of RPE and accounted for a host of potential SPE confounds. This new surprise signal was evident in ventral striatum, primary sensory cortex, frontal poles, and amygdala. We interpret these findings via a normative model of surprise. PMID:24700400

  10. Intraoperative visualization and assessment of electromagnetic tracking error

    NASA Astrophysics Data System (ADS)

    Harish, Vinyas; Ungi, Tamas; Lasso, Andras; MacDonald, Andrew; Nanji, Sulaiman; Fichtinger, Gabor

    2015-03-01

    Electromagnetic tracking allows for increased flexibility in designing image-guided interventions, however it is well understood that electromagnetic tracking is prone to error. Visualization and assessment of the tracking error should take place in the operating room with minimal interference with the clinical procedure. The goal was to achieve this ideal in an open-source software implementation in a plug and play manner, without requiring programming from the user. We use optical tracking as a ground truth. An electromagnetic sensor and optical markers are mounted onto a stylus device, pivot calibrated for both trackers. Electromagnetic tracking error is defined as difference of tool tip position between electromagnetic and optical readings. Multiple measurements are interpolated into the thin-plate B-spline transform visualized in real time using 3D Slicer. All tracked devices are used in a plug and play manner through the open-source SlicerIGT and PLUS extensions of the 3D Slicer platform. Tracking error was measured multiple times to assess reproducibility of the method, both with and without placing ferromagnetic objects in the workspace. Results from exhaustive grid sampling and freehand sampling were similar, indicating that a quick freehand sampling is sufficient to detect unexpected or excessive field distortion in the operating room. The software is available as a plug-in for the 3D Slicer platforms. Results demonstrate potential for visualizing electromagnetic tracking error in real time for intraoperative environments in feasibility clinical trials in image-guided interventions.

  11. Comparative analysis of conventional PCR and real-time PCR to diagnose shrimp WSD

    PubMed Central

    Leal, C.A.G.; Carvalho-Castro, G.A.; Cottorello, A.C.; Leite, R.C.; Figueiredo, H.C.P.

    2013-01-01

    The aims of this study were to standard and optimize a qPCR protocol with FAM-BHQ1 probe, and to compare its sensitivity against TaqMan qPCR and PCR methods to diagnose shrimp WSD. The FAM-BHQ1 qPCR presented higher clinical sensitivity and showed to be a robust alternative to detect WSSV in clinical samples. PMID:24516428

  12. Measurement Error Webinar Series

    Cancer.gov

    Concepts related to accounting for complex survey methods, estimating total intakes from diet and supplements, and the use of multiple dietary assessment instruments and self-report data along with biomarker data to reduce measurement error are also addressed.

  13. Help prevent hospital errors

    MedlinePLUS

    ... prevent medical errors when you are in the hospital. ... Share your health information with health care providers in the hospital. DO NOT think they already know it. Know what tests are being done. Ask what the test is for, ...

  14. Estimating Bias Error Distributions

    NASA Technical Reports Server (NTRS)

    Liu, Tian-Shu; Finley, Tom D.

    2001-01-01

    This paper formulates the general methodology for estimating the bias error distribution of a device in a measuring domain from less accurate measurements when a minimal number of standard values (typically two values) are available. A new perspective is that the bias error distribution can be found as a solution of an intrinsic functional equation in a domain. Based on this theory, the scaling- and translation-based methods for determining the bias error distribution arc developed. These methods are virtually applicable to any device as long as the bias error distribution of the device can be sufficiently described by a power series (a polynomial) or a Fourier series in a domain. These methods have been validated through computational simulations and laboratory calibration experiments for a number of different devices.

  15. PCR-based technology in veterinary parasitology

    Microsoft Academic Search

    Robin B. Gasser

    1999-01-01

    DNA technology is having a major impact in many areas of veterinary parasitology. In particular, the polymerase chain reaction (PCR) has found broad applicability because its sensitivity permits enzymatic amplification of gene fragments from minute quantities of nucleic acids derived from limited amounts of parasite material. This paper discusses some recent applications of PCR-based methods to parasites and highlights their

  16. Errata: Papers in Error Analysis.

    ERIC Educational Resources Information Center

    Svartvik, Jan, Ed.

    Papers presented at the symposium of error analysis in Lund, Sweden, in September 1972, approach error analysis specifically in its relation to foreign language teaching and second language learning. Error analysis is defined as having three major aspects: (1) the description of the errors, (2) the explanation of errors by means of contrastive…

  17. Prone decubitus: A solution to inferior wall attenuation in thallium-201 myocardial tomography

    SciTech Connect

    Esquerre, J.P.; Coca, F.J.; Martinez, S.J.; Guiraud, R.F.

    1989-03-01

    We propose an efficient method to suppress inferior wall attenuation in /sup 201/TI 180 degrees myocardial tomography. We systematically performed redistribution studies in both supine and prone decubitus, assuming that the latter should result in shifting with respect to each other's cardiac structures and diaphragm as well as subphrenic organs possibly responsible for attenuation. The comparison of both studies in 25 normal subjects by visual interpretation and circumferential profiles analysis showed a complete suppression of significant attenuation in the inferior wall in prone studies. In addition and consequently, the standard deviation of activity in this area was markedly reduced and became close to its value in anterior and lateral walls. This simple technique now routinely performed in over 400 patients drastically improves specificity in the evaluation of inferior wall abnormalities by suppressing attenuation artifacts and, incidently, the effect of high individual variability in left phrenic and subphrenic anatomic configuration.

  18. Improved PCR performance using mutant Tpa-S DNA polymerases from the hyperthermophilic archaeon Thermococcus pacificus.

    PubMed

    Ppyun, Hyewoo; Kim, Inhye; Cho, Sung Suk; Seo, Kang Jin; Yoon, Keejung; Kwon, Suk-Tae

    2012-12-15

    We previously reported that Tpa-S DNA polymerase (constructed via fusion of the Sso7d DNA binding protein to the C-terminus of Thermococcus pacificus (Tpa) DNA polymerase) is more efficient in long and rapid PCR than wild-type Tpa, Taq, or Pfu DNA polymerases. However, Tpa-S DNA polymerase had a low yield of PCR products compared with commercialized Taq or Pfu DNA polymerases. To improve the yield of PCR products, mutant Tpa-S DNA polymerases were created via site-directed mutagenesis. In this study, we have targeted the N213 residue in the Exo II motif and the K501 residue in the Pol III motif. The mutant Tpa-S DNA polymerases showed enhanced PCR yields compared to that of the Tpa-S DNA polymerase. Specifically, the double mutant Tpa-S N213D/K501R DNA polymerase had an approximately three-fold increase in the yield of 8-10kb PCR products over that of the Tpa-S DNA polymerase, and catalyzed amplification of a 12kb PCR product using a lambda template with an extension time of 30s. Even though the mutation is in the Exo II motif, the error rate of the double mutant Tpa-S N213D/K501R (2.79×10(-5)) was nearly the same as that seen in the Pfu DNA polymerase (2.70×10(-5)). PMID:23395617

  19. Effects of prone position on alveolar recruitment and oxygenation in acute lung injury

    Microsoft Academic Search

    C. Guerin; M. Badet; S. Rosselli; L. Heyer; J.-M. Sab; B. Langevin; F. Philit; G. Fournier; D. Robert

    1999-01-01

    Objective: To investigate the effects of prone position (PP) on alveolar recruitment and oxygenation in acute respiratory failure.¶Design: Prospective physiologic study.¶Setting: Medical ICU two in a university hospital.¶Patients: Twelve adult patients intubated and mechanically ventilated with medical primary acute lung injury\\/adult respiratory distress\\u000a syndrome (ALI\\/ARDS) in whom PP was indicated.¶Measurements and results: We constructed the static inflation volume-pressure curves (V-P)

  20. Diets containing blueberry extract lower blood pressure in spontaneously hypertensive stroke-prone rats

    Microsoft Academic Search

    Kevin S. Shaughnessy; Ian A. Boswall; Adam P. Scanlan; Katherine T. Gottschall-Pass; Marva I. Sweeney

    2009-01-01

    Oxidative stress in the vasculature and kidneys contributes to hypertension, a major risk factor for cardiovascular disease. Blueberries (BB) are rich in antioxidants, and so we hypothesized that feeding diets enriched with BB would slow the development of hypertension in spontaneously hypertensive stroke-prone rats (SHRSP). Eight-week-old normotensive rats and SHRSP were fed either a control diet (Con) or a diet

  1. Income and its variability in a drought-prone region: seasonality, location and household characteristics

    Microsoft Academic Search

    Susanne van Dillen

    2008-01-01

    This paper investigates three questions in a poor and drought-prone region of western Orissa, India. Is aggregate income stable? How do a household's characteristics and its local environment influence both the level of its income and its variability? Does a short-lived, common shock cause significant income variability? The study is based on an original, three-season panel data set of 240

  2. HCV Genotypes Are Differently Prone to the Development of Resistance to Linear and Macrocyclic Protease Inhibitors

    Microsoft Academic Search

    Valeria Cento; Carmen Mirabelli; Romina Salpini; Salvatore Dimonte; Anna Artese; Giosuè Costa; Fabio Mercurio; Valentina Svicher; Lucia Parrotta; Ada Bertoli; Marco Ciotti; Daniele Di Paolo; Cesare Sarrecchia; Massimo Andreoni; Stefano Alcaro; Mario Angelico; Carlo Federico Perno; Francesca Ceccherini-Silberstein

    2012-01-01

    BackgroundBecause of the extreme genetic variability of hepatitis C virus (HCV), we analyzed whether specific HCV-genotypes are differently prone to develop resistance to linear and macrocyclic protease-inhibitors (PIs).MethodsThe study includes 1568 NS3-protease sequences, isolated from PI-naive patients infected with HCV-genotypes 1a (N = 621), 1b (N = 474), 2 (N = 72), 3 (N = 268), 4 (N = 54)

  3. Self-Reflection and the Psychosis-Prone Brain: An fMRI Study

    Microsoft Academic Search

    Gemma Modinos; Remco Renken; Johan Ormel; André Aleman

    2011-01-01

    Objective: The Cortical Midline Structures (CMS) play a critical role in self-reflection, together with the insula. Abnormalities in self-referential processing and its neural underpinnings have been reported in schizophrenia and at-risk populations, suggesting they might be markers of psychotic vulnerability. Psychometric measures of schizotypal traits may be used to index psychosis proneness (PP) in nonclinical samples. It remains an unresolved

  4. Long-term Clinical Outcomes of Whole-Breast Irradiation Delivered in the Prone Position

    SciTech Connect

    Stegman, Lauren D. [Department of Radiation Oncology, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY (United States); Beal, Katherine P. [Department of Radiation Oncology, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY (United States); Hunt, Margie A. [Department of Medical Physics, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY (United States); Fornier, Monica N. [Department of Breast Cancer Medicine Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY (United States); McCormick, Beryl [Department of Radiation Oncology, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY (United States)]. E-mail: mccormib@mskcc.org

    2007-05-01

    Purpose: The aim of this study was to evaluate retrospectively the effectiveness and toxicity of post-lumpectomy whole-breast radiation therapy delivered with prone positioning. Methods and Materials: Between September 1992 and August 2004, 245 women with 248 early-stage invasive or in situ breast cancers were treated using a prone breast board. Photon fields treated the whole breast to 46 to 50.4 Gy with standard fractionation. The target volume was clinically palpable breast tissue; no attempt was made to irradiate chest wall lymphatics. Tumor bed boosts were delivered in 85% of cases. Adjuvant chemotherapy and hormonal therapy were administered to 42% and 62% of patients, respectively. Results: After a median follow-up of 4.9 years, the 5 year actuarial true local and elsewhere ipsilateral breast tumor recurrence rates were 4.8% and 1.3%, respectively. The 5-year actuarial rates of regional nodal recurrence and distant metastases were 1.6% and 7.4%. Actuarial disease-free, disease-specific, and overall survival rates at 5 years were 89.4%, 97.3%, and 93%, respectively. Treatment breaks were required by 2.4% of patients. Grade 3 acute dermatitis and edema were each limited to 2% of patients. Only 4.9% of patients complained of acute chest wall discomfort. Chronic Grade 2 to 3 skin and subcutaneous tissue toxicities were reported in 4.4% and 13.7% of patients, respectively. Conclusions: Prone position breast radiation results in similar long-term disease control with a favorable toxicity profile compared with standard supine tangents. The anatomic advantages of prone positioning may contribute to improving the therapeutic ratio of post-lumpectomy radiation by improving dose homogeneity and minimizing incidental cardiac and lung dose.

  5. Electromagnetic Tracking of Intrafraction Prostate Displacement in Patients Externally Immobilized in the Prone Position

    SciTech Connect

    Bittner, Nathan [Tacoma/Valley Radiation Oncology Centers, Tacoma, WA (United States); Butler, Wayne M.; Reed, Joshua L.; Murray, Brian C.; Kurko, Brian S. [Schiffler Cancer Center and Wheeling Jesuit University, Wheeling, WV (United States); Wallner, Kent E. [Puget Sound Health Care System, Department of Veterans Affairs, Seattle, WA (United States); Merrick, Gregory S., E-mail: gmerrick@urologicresearchinstitute.or [Schiffler Cancer Center and Wheeling Jesuit University, Wheeling, WV (United States)

    2010-06-01

    Purpose: To evaluate intrafraction prostate displacement among patients immobilized in the prone position using real-time monitoring of implanted radiofrequency transponders. Methods and Materials: The Calypso localization system was used to track prostate motion in patients receiving external beam radiation therapy (XRT) for prostate cancer. All patients were treated in the prone position and immobilized with a thermoplastic immobilization device. Real-time measurement of prostate displacement was recorded for each treatment fraction. These measurements were used to determine the duration and magnitude of displacement along the three directional axes. Results: The calculated centroid of the implanted transponders was offset from the treatment isocenter by >=2 mm, >=3 mm, and >=4 mm for 38.0%, 13.9%, and 4.5% of the time. In the lateral dimension, the centroid was offset from the treatment isocenter by >=2 mm, >=3 mm, and >=4 mm for 2.7%, 0.4%, and 0.06% of the time. In the superior-inferior dimension, the centroid was offset from the treatment isocenter by >=2 mm, >=3 mm, and >=4 mm for 16.1%, 4.7%, and 1.5% of the time, respectively. In the anterior-posterior dimension, the centroid was offset from the treatment isocenter by >=2 mm, >=3 mm, and >=4 mm for 13.4%, 3.0%, and 0.5% of the time. Conclusions: Intrafraction prostate displacement in the prone position is comparable to that in the supine position. For patients with large girth, in whom the supine position may preclude accurate detection of implanted radiofrequency transponders, treatment in the prone position is a suitable alternative.

  6. Prone breast radiotherapy in early-stage breast cancer: a preliminary analysis

    Microsoft Academic Search

    Alison Grann; Beryl McCormick; Elizabeth S Chabner; Smitha V Gollamudi; Karen D Schupak; Borys R Mychalczak; Alexandra S Heerdt; Thomas E Merchant; Margie A Hunt

    2000-01-01

    Purpose: Women with large breasts have marked dose inhomogeneity and often an inferior cosmetic outcome when treated with breast conservation compared to smaller-sized patients. We designed a prone breast board, which both minimizes breast separation and irradiated lung or heart volume. We report feasibility, cosmesis, and preliminary local control and survival for selected women with Stage 0–II breast cancer.Materials and

  7. Introducing the GASP Scale: A New Measure of Guilt and Shame Proneness

    Microsoft Academic Search

    Taya R. Cohen; Scott T. Wolf; A. T. Panter; Chester A. Insko

    2011-01-01

    Although scholars agree that moral emotions are critical for deterring unethical and antisocial behavior, there is disagreement about how 2 prototypical moral emotions—guilt and shame—should be defined, differentiated, and measured. We addressed these issues by developing a new assessment—the Guilt and Shame Proneness scale (GASP)—that measures individual differences in the propensity to experience guilt and shame across a range of

  8. Two-Kidney, Two Clip Renovascular Hypertensive Rats Can Be Used as Stroke-prone Rats

    Microsoft Academic Search

    Jinsheng Zeng; Yiqin Zhang; Jianwei Mo; Zhenpei Su; Ruxun Huang

    Background and Purpose—The cerebrovascular lesions in stroke-prone spontaneously hypertensive rats are not only dependent on high blood pressure but partly related to pressure-independent genetic factors. The aim of the present study was to observe whether spontaneous stroke occurred in renovascular hypertensive rats without a genetic deficiency. Methods—The 1-kidney, 1 clip (1k1c); 2-kidney, 1 clip (2k1c); and 2-kidney, 2 clip (2k2c)

  9. A Rulebase physiographic characterization of a drought prone watershed applying remote sensing and GIS

    Microsoft Academic Search

    P. S. Arun; R. Jana; M. S. Nathawat

    2005-01-01

    Efficient micro-watershed management needs characterization of it to optimize natural resources, which is especially important\\u000a in drought prone areas. In the present study micro-watersheds of Gandheshwari tributary in Chotta-Nagpur Plateau are characterized\\u000a based on physiographic properties towards agricultural potentiality. An algorithm interpolating elevation values using an\\u000a empirical formula is proposed to obtain an improved Digital Elevation Model (DEM). IRS LISS-Ill

  10. Insertion and use of the LMA Supreme in the prone position.

    PubMed

    López, A M; Valero, R; Brimacombe, J

    2010-02-01

    We investigated whether insertion of an LMA Supreme and its use for maintenance of anaesthesia is feasible in the prone position. Forty adult patients positioned themselves prone and were given propofol until the Bispectral Index was < 50. A size-4 LMA Supreme was inserted by experienced anaesthetists. Ease of insertion, ease of ventilation, efficacy of seal, ease of gastric tube insertion, blood staining, postoperative sore throat, and other complications were recorded. Insertion was successful at the first and second attempt in 37 (92.5%) and 3 (7.5%) patients, respectively. The mean (SD) insertion time was 21 (15) s. Oropharyngeal leak pressure was greater in females than males (29 (4) vs 25 (4) cmH(2)O, respectively, p = 0.01). Adequate ventilation was achieved in all patients. Gastric tube placement was successful in all patients. The frequency of blood staining and sore throat was 7.5% each. No other complications were noted. We conclude that use of the LMA Supreme in the prone position by experienced users is feasible. PMID:19930218

  11. Abortion-prone mating influences placental antioxidant status and adversely affects placental and foetal development.

    PubMed

    Al-Gubory, K H; Krawiec, A; Grange, S; Faure, P; Garrel, C

    2014-12-01

    Oxidative stress is associated with decreased female fertility and adversely affects prenatal development. Mammalian cells have developed a network of enzymatic and non-enzymatic antioxidant defence systems to prevent oxidative stress. Little attention has been paid to the antioxidative pathways in placentas of normal and disturbed pregnancies, leaving a gap in our knowledge about the role of antioxidants in the control of foeto-placental development. The challenges in studying early human pregnancy can partly be overcome by designing animal models of abnormal pregnancy. We aimed to determine whether the antioxidant status of placentas from the CBA/J × DBA/2 abortion-prone pregnant mice differed from that of normal pregnant mice. The foetal/placental weight ratio was lower in abortion-prone matings compared with that in non-abortion-prone matings. The increased placental malondialdehyde (MDA) content, the end products of lipid peroxidation, with concomitants alterations in placental antioxidants, namely copper-zinc containing superoxide dismutase (SOD1), manganese containing (SOD2), glutathione peroxidases (GPX), glutathione reductase (GR) and catalase (CAT) activities may be involved in placental and foetal growth restriction. We show that placental oxidative stress is linked with poor prenatal development and pregnancy losses in CBA/J × DBA/2 mice matings. This animal model may be useful in the evaluation of nutritional antioxidant therapies for oxidative stress and associated prenatal developmental disorders. PMID:25263566

  12. Factors associated with larval control practices in a dengue outbreak prone area.

    PubMed

    Mohamad, Mariam; Selamat, Mohamad Ikhsan; Ismail, Zaliha

    2014-01-01

    In order to reduce the risk of dengue outbreak recurrence in a dengue outbreak prone area, the members of the community need to sustain certain behavior to prevent mosquito from breeding. Our study aims to identify the factors associated with larval control practices in this particular community. A cross-sectional study involves 322 respondents living in a dengue outbreak prone area who were interviewed using a pretested questionnaire. The level of knowledge about Aedes mosquitoes, dengue transmission, its symptoms, and personal preventive measures ranges from fair to good. The level of attitude towards preventive measures was high. However, reported level of personal larval control practices was low (33.2%). Our multiple logistic regression analysis showed that only those with a good level of attitude towards personal preventive measure and frequent attendance to health campaigns were significantly associated with the good larval control practices. We conclude that, in a dengue outbreak prone area, having a good attitude towards preventive measures and frequent participation in health campaigns are important factors to sustain practices on larval control. PMID:25309602

  13. The Chapman psychosis-proneness scales: Consistency across culture and time.

    PubMed

    Chan, Raymond C K; Shi, Hai-Song; Geng, Fu-Lei; Liu, Wen-Hua; Yan, Chao; Wang, Yi; Gooding, Diane C

    2015-07-30

    The purpose of the present study was to examine the factor structure and the temporal stability of the Chapman psychosis-proneness scales in a representative sample of nonclinical Chinese young adults. The four psychosis-proneness scales evaluated were the Perceptual Aberration (PAS), Magical Ideation (MIS), revised Social Anhedonia (RSAS), and revised Physical Anhedonia (RPAS) scales. The sample consisted of 1724 young adults with a mean age of 18.8 years (S.D.=0.84). The results of the confirmatory factor analyses indicated that the best fitting model was a two-factor model with positive schizotypy (PER and MIS) scales and negative schizotypy (RSAS and RPAS) scales. The data add to the growing literature indicating that the measurement of schizotypal traits is consistent across cultures. In addition, the results support the measurement invariance of the Chapman psychosis-proneness scales across time, i.e., there was ample evidence of test-retest reliability over a test interval of 6 months. PMID:25962355

  14. Whole breast radiotherapy in prone and supine position: is there a place for multi-beam IMRT?

    PubMed Central

    2013-01-01

    Background Early stage breast cancer patients are long-term survivors and finding techniques that may lower acute and late radiotherapy-induced toxicity is crucial. We compared dosimetry of wedged tangential fields (W-TF), tangential field intensity-modulated radiotherapy (TF-IMRT) and multi-beam IMRT (MB-IMRT) in prone and supine positions for whole-breast irradiation (WBI). Methods MB-IMRT, TF-IMRT and W-TF treatment plans in prone and supine positions were generated for 18 unselected breast cancer patients. The median prescription dose to the optimized planning target volume (PTVoptim) was 50 Gy in 25 fractions. Dose-volume parameters and indices of conformity were calculated for the PTVoptim and organs-at-risk. Results Prone MB-IMRT achieved (p<0.01) the best dose homogeneity compared to WTF in the prone position and WTF and MB-IMRT in the supine position. Prone IMRT scored better for all dose indices. MB-IMRT lowered lung and heart dose (p<0.05) in supine position, however the lowest ipsilateral lung doses (p<0.001) were in prone position. In left-sided breast cancer patients population averages for heart sparing by radiation dose was better in prone position; though non-significant. For patients with a PTVoptim volume ?600 cc heart dose was consistently lower in prone position; while for patients with smaller breasts heart dose metrics were comparable or worse compared to supine MB-IMRT. Doses to the contralateral breast were similar regardless of position or technique. Dosimetry of prone MB-IMRT and prone TF-IMRT differed slightly. Conclusions MB-IMRT is the treatment of choice in supine position. Prone IMRT is superior to any supine treatment for right-sided breast cancer patients and left-sided breast cancer patients with larger breasts by obtaining better conformity indices, target dose distribution and sparing of the organs-at-risk. The influence of treatment techniques in prone position is less pronounced; moreover dosimetric differences between TF-IMRT and MB-IMRT are rather small. PMID:23800109

  15. Comparison of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation

    PubMed Central

    Whale, Alexandra S.; Huggett, Jim F.; Cowen, Simon; Speirs, Valerie; Shaw, Jacqui; Ellison, Stephen; Foy, Carole A.; Scott, Daniel J.

    2012-01-01

    One of the benefits of Digital PCR (dPCR) is the potential for unparalleled precision enabling smaller fold change measurements. An example of an assessment that could benefit from such improved precision is the measurement of tumour-associated copy number variation (CNV) in the cell free DNA (cfDNA) fraction of patient blood plasma. To investigate the potential precision of dPCR and compare it with the established technique of quantitative PCR (qPCR), we used breast cancer cell lines to investigate HER2 gene amplification and modelled a range of different CNVs. We showed that, with equal experimental replication, dPCR could measure a smaller CNV than qPCR. As dPCR precision is directly dependent upon both the number of replicate measurements and the template concentration, we also developed a method to assist the design of dPCR experiments for measuring CNV. Using an existing model (based on Poisson and binomial distributions) to derive an expression for the variance inherent in dPCR, we produced a power calculation to define the experimental size required to reliably detect a given fold change at a given template concentration. This work will facilitate any future translation of dPCR to key diagnostic applications, such as cancer diagnostics and analysis of cfDNA. PMID:22373922

  16. Error monitoring in musicians.

    PubMed

    Maidhof, Clemens

    2013-01-01

    To err is human, and hence even professional musicians make errors occasionally during their performances. This paper summarizes recent work investigating error monitoring in musicians, i.e., the processes and their neural correlates associated with the monitoring of ongoing actions and the detection of deviations from intended sounds. Electroencephalography (EEG) studies reported an early component of the event-related potential (ERP) occurring before the onsets of pitch errors. This component, which can be altered in musicians with focal dystonia, likely reflects processes of error detection and/or error compensation, i.e., attempts to cancel the undesired sensory consequence (a wrong tone) a musician is about to perceive. Thus, auditory feedback seems not to be a prerequisite for error detection, consistent with previous behavioral results. In contrast, when auditory feedback is externally manipulated and thus unexpected, motor performance can be severely distorted, although not all feedback alterations result in performance impairments. Recent studies investigating the neural correlates of feedback processing showed that unexpected feedback elicits an ERP component after note onsets, which shows larger amplitudes during music performance than during mere perception of the same musical sequences. Hence, these results stress the role of motor actions for the processing of auditory information. Furthermore, recent methodological advances like the combination of 3D motion capture techniques with EEG will be discussed. Such combinations of different measures can potentially help to disentangle the roles of different feedback types such as proprioceptive and auditory feedback, and in general to derive at a better understanding of the complex interactions between the motor and auditory domain during error monitoring. Finally, outstanding questions and future directions in this context will be discussed. PMID:23898255

  17. Analysis of Atmospheric Delays and Asymmetric Positioning Errors in GPS

    NASA Astrophysics Data System (ADS)

    Materna, K.; Herring, T.

    2014-12-01

    Error in accounting for atmospheric delay is one of the most significant limiting factors in the accuracy of GPS position determination. Delay due to tropospheric water vapor is especially difficult to model, as it depends in part on local atmospheric dynamics. Currently, the delay models used in GPS data analysis produce millimeter-level position estimates for most of the stations in the Plate Boundary Observatory (PBO) GPS network. However, certain stations in the network often show large position errors of 10 millimeters or more, and the key characteristic of these errors is that they occur in a particular direction. By analyzing the PBO network for these asymmetric outliers, we found that all affected stations are located in mountainous regions of the United States, and that many are located in the Sierra Nevada Mountains. Furthermore, we found that the direction in which the asymmetric outliers occur is related to the direction of local topographic increase, suggesting that topography plays a role in creating asymmetric outliers. We compared the GPS time series data with several forms of weather data, including radiosonde balloon measurements, numerical weather models, and MODIS satellite imagery. The results suggest that GPS position errors in the Sierra Nevada occur when there is strong atmospheric turbulence, including variations in pressure and humidity, downwind of the mountain crest. Specifically, when GPS position errors occur in the Sierra Nevada, lee waves are likely to be observed over the ridge; however, not all lee wave events produce position errors. Our results suggest that GPS measurements in mountainous regions may be more prone to systematic errors than previously thought due to the formation of lee waves.

  18. Situating Student Errors: Linguistic-to-Algebra Translation Errors

    ERIC Educational Resources Information Center

    Adu-Gyamfi, Kwaku; Bossé, Michael J.; Chandler, Kayla

    2015-01-01

    While it is well recognized that students are prone to difficulties when performing linguistic-to-algebra translations, the nature of students' difficulties remain an issue of contention. Moreover, the literature indicates that these difficulties are not easily remediated by domain-specific instruction. Some have opined that this is the case…

  19. Experimental Quantum Error Detection

    PubMed Central

    Jin, Xian-Min; Yi, Zhen-Huan; Yang, Bin; Zhou, Fei; Yang, Tao; Peng, Cheng-Zhi

    2012-01-01

    Faithful transmission of quantum information is a crucial ingredient in quantum communication networks. To overcome the unavoidable decoherence in a noisy channel, to date, many efforts have been made to transmit one state by consuming large numbers of time-synchronized ancilla states. However, such huge demands of quantum resources are hard to meet with current technology and this restricts practical applications. Here we experimentally demonstrate quantum error detection, an economical approach to reliably protecting a qubit against bit-flip errors. Arbitrary unknown polarization states of single photons and entangled photons are converted into time bins deterministically via a modified Franson interferometer. Noise arising in both 10?m and 0.8?km fiber, which induces associated errors on the reference frame of time bins, is filtered when photons are detected. The demonstrated resource efficiency and state independence make this protocol a promising candidate for implementing a real-world quantum communication network. PMID:22953047

  20. Estimating GPS Positional Error

    NSDL National Science Digital Library

    Bill Witte

    After instructing students on basic receiver operation, each student will make many (10-20) position estimates of 3 benchmarks over a week. The different benchmarks will have different views of the skies or vegetation cover. Each student will download their data into a spreadsheet and calculate horizontal and vertical errors which are collated into a class spreadsheet. The positions are sorted by error and plotted in a cumulative frequency plot. The students are encouraged to discuss the distribution, sources of error, and estimate confidence intervals. This exercise gives the students a gut feeling for confidence intervals and the accuracy of data. Students are asked to compare results from different types of data and benchmarks with different views of the sky. Uses online and/or real-time data Has minimal/no quantitative component
    Addresses student fear of quantitative aspect and/or inadequate quantitative skills Addresses student misconceptions

  1. Medication errors in anesthesia.

    PubMed

    Prabhakar, Amit; Malapero, Raymond J; Gabriel, Rodney A; Kaye, Alan David; Elhassan, Amir O; Nelson, Ehren R; Bates, David W; Urman, Richard D

    2015-01-01

    Medication errors represent one of the most common causes of morbidity and mortality in hospitalized patients. Anesthesia has specific medication-related risks; providers must administer many potent intravenous medications quickly, often with minimal to no supervision. Well-described reasons for medication administration errors in anesthesia include medication ampoules with similar appearance and packaging, clinician inattention, ineffective communication, fatigue, and haste. Technologies that are used widely in other parts of the hospital, such as barcoding, are a challenge to implement in anesthesia, and systemic approaches, including color-coding of syringe labels and barcoding technology of syringes, have been evaluated with mixed results. Emphasis should be placed on implementing forcing functions when possible, utilizing technology, standardization, and education about the need for awareness in specific situations. More studies need to be done to define the epidemiology of medication errors in anesthesia, and more importantly, to assess interventions for preventing them. PMID:26062316

  2. ASR Context-Sensitive Error Correction Based on Microsoft N-Gram Dataset

    E-print Network

    Bassil, Youssef

    2012-01-01

    At the present time, computers are employed to solve complex tasks and problems ranging from simple calculations to intensive digital image processing and intricate algorithmic optimization problems to computationally-demanding weather forecasting problems. ASR short for Automatic Speech Recognition is yet another type of computational problem whose purpose is to recognize human spoken speech and convert it into text that can be processed by a computer. Despite that ASR has many versatile and pervasive real-world applications,it is still relatively erroneous and not perfectly solved as it is prone to produce spelling errors in the recognized text, especially if the ASR system is operating in a noisy environment, its vocabulary size is limited, and its input speech is of bad or low quality. This paper proposes a post-editing ASR error correction method based on MicrosoftN-Gram dataset for detecting and correcting spelling errors generated by ASR systems. The proposed method comprises an error detection algorit...

  3. jPopGen Suite: population genetic analysis of DNA polymorphism from nucleotide sequences with errors.

    PubMed

    Liu, Xiaoming

    2012-08-01

    1. Next-generation sequencing (NGS) is being increasingly used in ecological and evolutionary studies. Though promising, NGS is known to be error-prone. Sequencing error can cause significant bias for population genetic analysis of a sequence sample.2. We present jPopGen Suite, an integrated tool for population genetic analysis of DNA polymorphisms from nucleotide sequences. It is specially designed for data with a non-negligible error rate, although it serves well for "error-free" data. It implements several methods for estimating the population mutation rate, population growth rate, and conducting neutrality tests.3. jPopGen Suite facilitates the population genetic analysis of NGS data in various applications, and is freely available for non-commercial users at http://sites.google.com/site/jpopgen/. PMID:22905315

  4. A water-vapor radiometer error model. [for ionosphere in geodetic microwave techniques

    NASA Technical Reports Server (NTRS)

    Beckman, B.

    1985-01-01

    The water-vapor radiometer (WVR) is used to calibrate unpredictable delays in the wet component of the troposphere in geodetic microwave techniques such as very-long-baseline interferometry (VLBI) and Global Positioning System (GPS) tracking. Based on experience with Jet Propulsion Laboratory (JPL) instruments, the current level of accuracy in wet-troposphere calibration limits the accuracy of local vertical measurements to 5-10 cm. The goal for the near future is 1-3 cm. Although the WVR is currently the best calibration method, many instruments are prone to systematic error. In this paper, a treatment of WVR data is proposed and evaluated. This treatment reduces the effect of WVR systematic errors by estimating parameters that specify an assumed functional form for the error. The assumed form of the treatment is evaluated by comparing the results of two similar WVR's operating near each other. Finally, the observability of the error parameters is estimated by covariance analysis.

  5. Challenge and Error: Critical Events and Attention-Related Errors

    ERIC Educational Resources Information Center

    Cheyne, James Allan; Carriere, Jonathan S. A.; Solman, Grayden J. F.; Smilek, Daniel

    2011-01-01

    Attention lapses resulting from reactivity to task challenges and their consequences constitute a pervasive factor affecting everyday performance errors and accidents. A bidirectional model of attention lapses (error [image omitted] attention-lapse: Cheyne, Solman, Carriere, & Smilek, 2009) argues that errors beget errors by generating attention…

  6. 44 CFR 60.5 - Flood plain management criteria for flood-related erosion-prone areas.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 1 2011-10-01 2011-10-01 false Flood plain management criteria for flood-related erosion-prone areas. 60.5 Section...SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND...

  7. 44 CFR 60.5 - Flood plain management criteria for flood-related erosion-prone areas.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Flood plain management criteria for flood-related erosion-prone... 60.5 Section 60.5 Emergency Management and Assistance FEDERAL...

  8. IPTV multicast with peer-assisted lossy error control

    NASA Astrophysics Data System (ADS)

    Li, Zhi; Zhu, Xiaoqing; Begen, Ali C.; Girod, Bernd

    2010-07-01

    Emerging IPTV technology uses source-specific IP multicast to deliver television programs to end-users. To provide reliable IPTV services over the error-prone DSL access networks, a combination of multicast forward error correction (FEC) and unicast retransmissions is employed to mitigate the impulse noises in DSL links. In existing systems, the retransmission function is provided by the Retransmission Servers sitting at the edge of the core network. In this work, we propose an alternative distributed solution where the burden of packet loss repair is partially shifted to the peer IP set-top boxes. Through Peer-Assisted Repair (PAR) protocol, we demonstrate how the packet repairs can be delivered in a timely, reliable and decentralized manner using the combination of server-peer coordination and redundancy of repairs. We also show that this distributed protocol can be seamlessly integrated with an application-layer source-aware error protection mechanism called forward and retransmitted Systematic Lossy Error Protection (SLEP/SLEPr). Simulations show that this joint PARSLEP/ SLEPr framework not only effectively mitigates the bottleneck experienced by the Retransmission Servers, thus greatly enhancing the scalability of the system, but also efficiently improves the resistance to the impulse noise.

  9. Comparison of droplet digital PCR and conventional quantitative PCR for measuring EGFR gene mutation

    PubMed Central

    ZHANG, BO; XU, CHUN-WEI; SHAO, YUN; WANG, HUAI-TAO; WU, YONG-FANG; SONG, YE-YING; LI, XIAO-BING; ZHANG, ZHE; WANG, WEN-JING; LI, LI-QIONG; CAI, CONG-LI

    2015-01-01

    Early detection of epidermal growth factor receptor (EGFR) mutation, particularly EGFR T790M mutation, is of clinical significance. The aim of the present study was to compare the performances of amplification refractory mutation system-based quantitative polymerase chain reaction (ARMS-qPCR) and droplet digital polymerase chain reaction (ddPCR) approaches in the detection of EGFR mutation and explore the feasibility of using ddPCR in the detection of samples with low mutation rates. EGFR gene mutations in plasmid samples with different T790M mutation rates (0.1–5%) and 10 clinical samples were detected using the ARMS-qPCR and ddPCR approaches. The results demonstrated that the ARMS-qPCR method stably detected the plasmid samples (6,000 copies) with 5 and 1% mutation rates, while the ddPCR approach reliably detected those with 5% (398 copies), 1% (57 copies), 0.5% (24 copies) and 0.1% (average 6 copies) mutation rates. For the 10 clinical samples, the results for nine samples by the ARMS-qPCR and ddPCR methods were consistent; however, the sample N006, indicated to be EGFR wild-type by ARMS-qPCR, was revealed to have a clear EGFR T790M mutation with seven copies of mutant alleles in a background of 6,000 wild-type copies using ddPCR technology. This study demonstrates the feasibility of applying the ddPCR system to detect EGFR mutation and identified the advantage of ddPCR in the detection of samples with a low EGFR mutation abundance, particularly the secondary EGFR T790M resistance mutation, which enables early diagnosis before acquired resistance to tyrosine kinase inhibitors becomes clinically detectable. PMID:25780439

  10. A Diet Producing a Low Diabetes Incidence Modifies Immune Abnormalities in Diabetes-Prone BB Rats123

    Microsoft Academic Search

    CATHERINE J. FIELD

    The effect of feeding a diet that produces a high or low incidence of diabetes on immune abnor malities proposed to contribute to the pathogenesis of autoimmune-mediated diabetes was investigated. Di abetes-prone (BBdp) and nondiabetes-prone (BBn) BB rats (21 d) were fed for 21 da non pur ¡fled (high inci dence) or purified (low diabetes incidence) diet. Com pared with

  11. Ontogenic changes in proglucagon mRNA in BB diabetes prone and normal rats weaned onto a chow diet

    Microsoft Academic Search

    R. A. Reimer; C. J. Field; M. I. McBurney

    1997-01-01

    Summary   Weaning onto chow diets causes the highest incidence of diabetes in the BB rat. Changes in gut development and absorption\\u000a of nutrients in the diabetes prone rat and the subsequent effect on pancreatic function may play a role in the ultimate development\\u000a of the disease. BB diabetes prone (dp) and BB normal (n) dams were fed chow diets. Pups

  12. Assessing Jail Inmates’ Proneness To Shame and GuiltFeeling Bad About the Behavior or the Self?

    Microsoft Academic Search

    June P. Tangney; Jeffrey Stuewig; Debra Mashek; Mark Hastings

    2011-01-01

    This study of 550 jail inmates (379 male and 171 female) held on felony charges examines the reliability and validity of the Test of Self Conscious Affect—Socially Deviant Version as a measure of offenders’ proneness to shame and proneness to guilt. Discriminant validity (e.g., vis-à-vis self-esteem, negative affect, social desirability\\/impression management) and convergent validity (e.g., vis-à-vis correlations with empathy; externalization

  13. Accurate Estimation of Nucleic Acids by Amplification Efficiency Dependent PCR

    PubMed Central

    Chatterjee, Nilanjana; Banerjee, Tanmay; Datta, Santanu

    2012-01-01

    Accurate estimation of template - DNA or RNA by real time PCR is dependent on the amplification efficiency (F) of the reaction. The analytical equation describing the kinetics of PCR that is influenced by template re-annealing is formulated. It predicts the gradual reduction of F - from its initial value of 2, leading to template saturation. From an experimental standpoint, due to the exponential nature of the reaction a minute change in F can lead to a large error in the estimation of the initial template concentration. On the basis of individual variation in the amplification efficiency we have formulated a simple mathematical model and an MS Excel based data analysis software that allows accurate and automated quantification of initial template concentration. This method which does not require any normalisation with housekeeping genes was validated by transcript profiling of the genes in the TCA/glyoxylate cycle of E. coli. Consistent with published reports, we observed a precise and specific induction of the glyoxylate shunt genes when the bacteria was shifted from a six carbon glucose media to a two carbon source like acetate. PMID:22912684

  14. Laboratory 0: Error Analysis

    NSDL National Science Digital Library

    Virtual Labs, Real Data (Cornell University)

    2011-01-19

    The collection of data is an important part of all laboratory work, and interpreting the data is the major part of a laboratory report. Laboratory 0 presents a brief overview of techniques and concepts needed to estimate and analyze the errors inherent in experimental work.

  15. Accelerated Intensity-Modulated Radiotherapy to Breast in Prone Position: Dosimetric Results

    SciTech Connect

    De Wyngaert, J. Keith [Department of Radiation Oncology, New York University School of Medicine, New York, NY (United States)]. E-mail: keith.dewyngaert@med.nyu.edu; Jozsef, Gabor [Department of Radiation Oncology, New York University School of Medicine, New York, NY (United States); Mitchell, James [Department of Radiation Oncology, New York University School of Medicine, New York, NY (United States); Rosenstein, Barry [Department of Radiation Oncology, New York University School of Medicine, New York, NY (United States); Formenti, Silvia C. [Department of Radiation Oncology, New York University School of Medicine, New York, NY (United States)

    2007-07-15

    Purpose: To report the physics and dosimetry results of a trial of accelerated intensity-modulated radiotherapy to the whole breast with a concomitant boost to the tumor bed in patients treated in the prone position. Methods and Materials: Patients underwent computed tomography planning and treatment in the prone position on a dedicated treatment platform. The platform has an open aperture on the side to allow for the index breast to fall away from the chest wall. Noncontrast computed tomography images were acquired at 2.5- or 3.75-mm-thick intervals, from the level of the mandible to below the diaphragm. A dose of 40.5 Gy was delivered to the entire breast at 2.7-Gy fractions in 15 fractions. An additional dose of 0.5 Gy was delivered as a concomitant boost to the lumpectomy site, with a 1-cm margin, using inverse planning, for a total dose of 48 Gy in 15 fractions. No more than 10% of the heart and lung volume was allowed to receive >18 and >20 Gy, respectively. Results: Between September 2003 and August 2005, 91 patients were enrolled in the study. The median volume of heart that received {>=}18 Gy was 0.5%, with a maximal value of 4.7%. The median volume of ipsilateral lung that received {>=}20 Gy was 0.8%, with a maximum of 7.2%. Conclusion: This technique for whole breast radiotherapy is feasible and enables an accelerated regimen in the prone position while sparing the lung and heart.

  16. Accumulation of oligomer-prone ?-synuclein exacerbates synaptic and neuronal degeneration in vivo

    PubMed Central

    Rockenstein, Edward; Nuber, Silke; Overk, Cassia R.; Ubhi, Kiren; Mante, Michael; Patrick, Christina; Adame, Anthony; Trejo-Morales, Margarita; Gerez, Juan; Picotti, Paola; Jensen, Poul H.; Campioni, Silvia; Riek, Roland; Winkler, Jürgen; Gage, Fred H.; Winner, Beate

    2014-01-01

    In Parkinson’s disease and dementia with Lewy bodies, ?-synuclein aggregates to form oligomers and fibrils; however, the precise nature of the toxic ?-synuclein species remains unclear. A number of synthetic ?-synuclein mutations were recently created (E57K and E35K) that produce species of ?-synuclein that preferentially form oligomers and increase ?-synuclein-mediated toxicity. We have shown that acute lentiviral expression of ?-synuclein E57K leads to the degeneration of dopaminergic neurons; however, the effects of chronic expression of oligomer-prone ?-synuclein in synapses throughout the brain have not been investigated. Such a study could provide insight into the possible mechanism(s) through which accumulation of ?-synuclein oligomers in the synapse leads to neurodegeneration. For this purpose, we compared the patterns of neurodegeneration and synaptic damage between a newly generated mThy-1 ?-synuclein E57K transgenic mouse model that is prone to forming oligomers and the mThy-1 ?-synuclein wild-type mouse model (Line 61), which accumulates various forms of ?-synuclein. Three lines of ?-synuclein E57K (Lines 9, 16 and 54) were generated and compared with the wild-type. The ?-synuclein E57K Lines 9 and 16 were higher expressings of ?-synuclein, similar to ?-synuclein wild-type Line 61, and Line 54 was a low expressing of ?-synuclein compared to Line 61. By immunoblot analysis, the higher-expressing ?-synuclein E57K transgenic mice showed abundant oligomeric, but not fibrillar, ?-synuclein whereas lower-expressing mice accumulated monomeric ?-synuclein. Monomers, oligomers, and fibrils were present in ?-synuclein wild-type Line 61. Immunohistochemical and ultrastructural analyses demonstrated that ?-synuclein accumulated in the synapses but not in the neuronal cells bodies, which was different from the ?-synuclein wild-type Line 61, which accumulates ?-synuclein in the soma. Compared to non-transgenic and lower-expressing mice, the higher-expressing ?-synuclein E57K mice displayed synaptic and dendritic loss, reduced levels of synapsin 1 and synaptic vesicles, and behavioural deficits. Similar alterations, but to a lesser extent, were seen in the ?-synuclein wild-type mice. Moreover, although the oligomer-prone ?-synuclein mice displayed neurodegeneration in the frontal cortex and hippocampus, the ?-synuclein wild-type only displayed neuronal loss in the hippocampus. These results support the hypothesis that accumulating oligomeric ?-synuclein may mediate early synaptic pathology in Parkinson’s disease and dementia with Lewy bodies by disrupting synaptic vesicles. This oligomer-prone model might be useful for evaluating therapies directed at oligomer reduction. PMID:24662516

  17. Supine versus prone position in percutaneous nephrolithotomy for kidney calculi: a meta-analysis

    Microsoft Academic Search

    Peng WuLi; Li Wang; Kunjie Wang

    2011-01-01

    Background  Supine position and prone position were the choice for percutaneous nephrolithotomy (PCNL). However, there is still no consensus\\u000a on the optimal position for PCNL.\\u000a \\u000a \\u000a \\u000a \\u000a Methods  A systematic literature review was performed, searching Pubmed, Embase, CENTRAL and reference lists for relevant studies.\\u000a Data from all selected articles were extracted independently by two reviewers and analyzed by RevMan 5 software.\\u000a \\u000a \\u000a \\u000a \\u000a Results  Four comparative studies

  18. Development of one novel multiple-target plasmid for duplex quantitative PCR analysis of roundup ready soybean.

    PubMed

    Zhang, Haibo; Yang, Litao; Guo, Jinchao; Li, Xiang; Jiang, Lingxi; Zhang, Dabing

    2008-07-23

    To enforce the labeling regulations of genetically modified organisms (GMOs), the application of reference molecules as calibrators is becoming essential for practical quantification of GMOs. However, the reported reference molecules with tandem marker multiple targets have been proved not suitable for duplex PCR analysis. In this study, we developed one unique plasmid molecule based on one pMD-18T vector with three exogenous target DNA fragments of Roundup Ready soybean GTS 40-3-2 (RRS), that is, CaMV35S, NOS, and RRS event fragments, plus one fragment of soybean endogenous Lectin gene. This Lectin gene fragment was separated from the three exogenous target DNA fragments of RRS by inserting one 2.6 kb DNA fragment with no relatedness to RRS detection targets in this resultant plasmid. Then, we proved that this design allows the quantification of RRS using the three duplex real-time PCR assays targeting CaMV35S, NOS, and RRS events employing this reference molecule as the calibrator. In these duplex PCR assays, the limits of detection (LOD) and quantification (LOQ) were 10 and 50 copies, respectively. For the quantitative analysis of practical RRS samples, the results of accuracy and precision were similar to those of simplex PCR assays, for instance, the quantitative results were at the 1% level, the mean bias of the simplex and duplex PCR were 4.0% and 4.6%, respectively, and the statistic analysis ( t-test) showed that the quantitative data from duplex and simplex PCR had no significant discrepancy for each soybean sample. Obviously, duplex PCR analysis has the advantages of saving the costs of PCR reaction and reducing the experimental errors in simplex PCR testing. The strategy reported in the present study will be helpful for the development of new reference molecules suitable for duplex PCR quantitative assays of GMOs. PMID:18570432

  19. Modular error embedding

    DOEpatents

    Sandford, II, Maxwell T. (Los Alamos, NM); Handel, Theodore G. (Los Alamos, NM); Ettinger, J. Mark (Los Alamos, NM)

    1999-01-01

    A method of embedding auxiliary information into the digital representation of host data containing noise in the low-order bits. The method applies to digital data representing analog signals, for example digital images. The method reduces the error introduced by other methods that replace the low-order bits with auxiliary information. By a substantially reverse process, the embedded auxiliary data can be retrieved easily by an authorized user through use of a digital key. The modular error embedding method includes a process to permute the order in which the host data values are processed. The method doubles the amount of auxiliary information that can be added to host data values, in comparison with bit-replacement methods for high bit-rate coding. The invention preserves human perception of the meaning and content of the host data, permitting the addition of auxiliary data in the amount of 50% or greater of the original host data.

  20. Genome-Wide Profiling of Yeast DNA:RNA Hybrid Prone Sites with DRIP-Chip

    PubMed Central

    Lu, Phoebe Y. T.; Luo, Zongli; Hamza, Akil; Kobor, Michael S.; Stirling, Peter C.; Hieter, Philip

    2014-01-01

    DNA:RNA hybrid formation is emerging as a significant cause of genome instability in biological systems ranging from bacteria to mammals. Here we describe the genome-wide distribution of DNA:RNA hybrid prone loci in Saccharomyces cerevisiae by DNA:RNA immunoprecipitation (DRIP) followed by hybridization on tiling microarray. These profiles show that DNA:RNA hybrids preferentially accumulated at rDNA, Ty1 and Ty2 transposons, telomeric repeat regions and a subset of open reading frames (ORFs). The latter are generally highly transcribed and have high GC content. Interestingly, significant DNA:RNA hybrid enrichment was also detected at genes associated with antisense transcripts. The expression of antisense-associated genes was also significantly altered upon overexpression of RNase H, which degrades the RNA in hybrids. Finally, we uncover mutant-specific differences in the DRIP profiles of a Sen1 helicase mutant, RNase H deletion mutant and Hpr1 THO complex mutant compared to wild type, suggesting different roles for these proteins in DNA:RNA hybrid biology. Our profiles of DNA:RNA hybrid prone loci provide a resource for understanding the properties of hybrid-forming regions in vivo, extend our knowledge of hybrid-mitigating enzymes, and contribute to models of antisense-mediated gene regulation. A summary of this paper was presented at the 26th International Conference on Yeast Genetics and Molecular Biology, August 2013. PMID:24743342

  1. Thoracoscopic long myotomy in the prone position to treat rapid esophageal contractions with normal latency.

    PubMed

    Nomura, Tsutomu; Iwakiri, Katsuhiko; Matsutani, Takeshi; Hagiwara, Nobutoshi; Fujita, Itsuro; Nakamura, Yoshiharu; Kawami, Noriyuki; Miyashita, Masao; Uchida, Eiji

    2015-04-01

    A 56-year-old woman with an 8-year history of dysphagia and chest pain received a diagnosis of diffuse esophageal spasm by esophageal high-resolution manometry (HRM). Approximately 2 years of medical therapy was ineffective, and the patient's symptoms were worsening. Therefore, surgery was considered to be the most optimal treatment for this patient. The right thoracoscopic approach was selected because a long myotomy from the distal to proximal level of the esophagus was needed based on the HRM findings. The operation was performed in the prone position with establishment of pneumothorax. The total length of the myotomy was 16 cm, and the operation was finished within 2 hours. After the operation, the symptoms were considerably improved and no contractions were detected by HRM. The HRM findings before the operation were classified as rapid contractions with normal latency based on the 2012 Chicago classification of esophageal motility. Treatment for patients with rapid esophageal contractions with normal latency has not been previously described; however, treatment for diffuse esophageal spasm was considered to be pertinent to this patient. In conclusion, right thoracoscopic esophageal long myotomy in the prone position with establishment of pneumothorax may be useful when a proximal-level esophagomyotomy is required based on preoperative mapping by HRM. PMID:24667594

  2. Safe Sedation and Hypnosis using Dexmedetomidine for Minimally Invasive Spine Surgery in a Prone Position.

    PubMed

    Kim, Kyung Hoon

    2014-10-01

    Dexmedetomidine, an imidazoline compound, is a highly selective ?2-adrenoceptor agonist with sympatholytic, sedative, amnestic, and analgesic properties. In order to minimize the patients' pain and anxiety during minimally invasive spine surgery (MISS) when compared to conventional surgery under general anesthesia, an adequate conscious sedation (CS) or monitored anesthetic care (MAC) should be provided. Commonly used intravenous sedatives and hypnotics, such as midazolam and propofol, are not suitable for operations in a prone position due to undesired respiratory depression. Dexmedetomidine converges on an endogenous non-rapid eye movement (NREM) sleep-promoting pathway to exert its sedative effects. The great merit of dexmedetomidine for CS or MAC is the ability of the operator to recognize nerve damage during percutaneous endoscopic lumbar discectomy, a representative MISS. However, there are 2 shortcomings for dexmedetomidine in MISS: hypotension/bradycardia and delayed emergence. Its hypotension/bradycardiac effects can be prevented by ketamine intraoperatively. Using atipamezole (an ?2-adrenoceptor antagonist) might allow doctors to control the rate of recovery from procedural sedation in the future. MAC, with other analgesics such as ketorolac and opioids, creates ideal conditions for MISS. In conclusion, dexmedetomidine provides a favorable surgical condition in patients receiving MISS in a prone position due to its unique properties of conscious sedation followed by unconscious hypnosis with analgesia. However, no respiratory depression occurs based on the dexmedetomidine-related endogenous sleep pathways involves the inhibition of the locus coeruleus in the pons, which facilitates VLPO firing in the anterior hypothalamus. PMID:25317279

  3. A Consensus Method for the Prediction of ‘Aggregation-Prone’ Peptides in Globular Proteins

    PubMed Central

    Tsolis, Antonios C.; Papandreou, Nikos C.; Iconomidou, Vassiliki A.; Hamodrakas, Stavros J.

    2013-01-01

    The purpose of this work was to construct a consensus prediction algorithm of ‘aggregation-prone’ peptides in globular proteins, combining existing tools. This allows comparison of the different algorithms and the production of more objective and accurate results. Eleven (11) individual methods are combined and produce AMYLPRED2, a publicly, freely available web tool to academic users (http://biophysics.biol.uoa.gr/AMYLPRED2), for the consensus prediction of amyloidogenic determinants/‘aggregation-prone’ peptides in proteins, from sequence alone. The performance of AMYLPRED2 indicates that it functions better than individual aggregation-prediction algorithms, as perhaps expected. AMYLPRED2 is a useful tool for identifying amyloid-forming regions in proteins that are associated with several conformational diseases, called amyloidoses, such as Altzheimer's, Parkinson's, prion diseases and type II diabetes. It may also be useful for understanding the properties of protein folding and misfolding and for helping to the control of protein aggregation/solubility in biotechnology (recombinant proteins forming bacterial inclusion bodies) and biotherapeutics (monoclonal antibodies and biopharmaceutical proteins). PMID:23326595

  4. Study of prone positioning to reduce ventilator-associated pneumonia in hypoxaemic patients.

    PubMed

    Mounier, R; Adrie, C; Français, A; Garrouste-Orgeas, M; Cheval, C; Allaouchiche, B; Jamali, S; Dinh-Xuan, A T; Goldgran-Toledano, D; Cohen, Y; Azoulay, E; Timsit, J-F; Ricard, J-D

    2010-04-01

    The aim of the present study was to examine whether prone positioning (PP) affects ventilator associated-pneumonia (VAP) and mortality in patients with acute lung injury/adult respiratory distress syndrome. 2,409 prospectively included patients were admitted over 9 yrs (2000-2008) to 12 French intensive care units (ICUs) (OUTCOMEREA). The patients required invasive mechanical ventilation (MV) and had arterial oxygen tension/inspiratory oxygen fraction ratios <300 during the first 48 h. Controls were matched to PP patients on the PP propensity score (+/-10%), MV duration longer than that in PP patients before the first turn prone, and centre. VAP incidence was similar in the PP and control groups (24 versus 13 episodes.1,000 patient-days MV(-1) respectively, p = 0.14). After adjustment, PP did not decrease VAP occurrence (HR 1.64 (95% CI 0.70-3.84); p = 0.25) but significantly delayed hospital mortality (HR 0.56 (95% CI 0.39-0.79); p = 0.001), without decreasing 28-day mortality (37% in both groups). Post hoc analyses indicated that PP did not protect against VAP but, when used for >1 day, might decrease mortality and benefit the sickest patients (Simplified Acute Physiology Score >50). In ICU patients with hypoxaemic acute respiratory failure, PP had no effect on the risk of VAP. PP delayed mortality without decreasing 28-day mortality. PP >1 day might decrease mortality, particularly in the sickest patients. PMID:19741030

  5. A Mechanistic Model of PCR for Accurate Quantification of Quantitative PCR Data

    PubMed Central

    Boggy, Gregory J.; Woolf, Peter J.

    2010-01-01

    Background Quantitative PCR (qPCR) is a workhorse laboratory technique for measuring the concentration of a target DNA sequence with high accuracy over a wide dynamic range. The gold standard method for estimating DNA concentrations via qPCR is quantification cycle () standard curve quantification, which requires the time- and labor-intensive construction of a standard curve. In theory, the shape of a qPCR data curve can be used to directly quantify DNA concentration by fitting a model to data; however, current empirical model-based quantification methods are not as reliable as standard curve quantification. Principal Findings We have developed a two-parameter mass action kinetic model of PCR (MAK2) that can be fitted to qPCR data in order to quantify target concentration from a single qPCR assay. To compare the accuracy of MAK2-fitting to other qPCR quantification methods, we have applied quantification methods to qPCR dilution series data generated in three independent laboratories using different target sequences. Quantification accuracy was assessed by analyzing the reliability of concentration predictions for targets at known concentrations. Our results indicate that quantification by MAK2-fitting is as reliable as standard curve quantification for a variety of DNA targets and a wide range of concentrations. Significance We anticipate that MAK2 quantification will have a profound effect on the way qPCR experiments are designed and analyzed. In particular, MAK2 enables accurate quantification of portable qPCR assays with limited sample throughput, where construction of a standard curve is impractical. PMID:20814578

  6. Direct chromatin PCR (DC-PCR): hypotonic conditions allow differentiation of chromatin states during thermal cycling.

    PubMed

    Vatolin, Sergei; Khan, Shahper N; Reu, Frederic J

    2012-01-01

    Current methods to study chromatin configuration are not well suited for high throughput drug screening since they require large cell numbers and multiple experimental steps that include centrifugation for isolation of nuclei or DNA. Here we show that site specific chromatin analysis can be achieved in one step by simply performing direct chromatin PCR (DC-PCR) on cells. The basic underlying observation was that standard hypotonic PCR buffers prevent global cellular chromatin solubilization during thermal cycling while more loosely organized chromatin can be amplified. Despite repeated heating to >90 °C, 41 of 61 tested 5' sequences of silenced genes (CDKN2A, PU.1, IRF4, FOSB, CD34) were not amplifiable while 47 could be amplified from expressing cells. Two gene regions (IRF4, FOSB) even required pre-heating of cells in isotonic media to allow this differentiation; otherwise none of 19 assayed sequences yielded PCR products. Cells with baseline expression or epigenetic reactivation gave similar DC-PCR results. Silencing during differentiation of CD34 positive cord blood cells closed respective chromatin while treatment of myeloma cells with an IRF4 transcriptional inhibitor opened a site to DC-PCR that was occupied by RNA polymerase II and NF?B as determined by ChIP. Translation into real-time PCR can not be achieved with commercial real-time PCR buffers which potently open chromatin, but even with simple ethidium bromide addition to standard PCR mastermix we were able to identify hits in small molecules screens that suppressed IRF4 expression or reactivated CDKN2A in myeloma cells using densitometry or visual inspection of PCR plates under UV light. While need in drug development inspired this work, application to genome-wide analysis appears feasible using phi29 for selective amplification of open cellular chromatin followed by library construction from supernatants since such supernatants yielded similar results as gene specific DC-PCR. PMID:22984542

  7. Two Position Supine/Prone Myocardial Perfusion SPECT (MPS) Imaging Improves Visual Inter-Observer Correlation and Agreement

    PubMed Central

    Arsanjani, Reza; Hayes, Sean W.; Fish, Mathews; Shalev, Aryeh; Nakanishi, Rine; Thomson, Louise EJ; Friedman, John D; Germano, Guido; Berman, Daniel S.; Slomka, Piotr

    2014-01-01

    Objectives We aimed to compare the inter-observer agreement between two experienced readers using supine versus combined supine/prone myocardial perfusion SPECT (MPS) in a large population. Methods 1181 consecutive patients without known coronary artery disease (CAD) undergoing rest 201Tl/stress 99mTc-sestamibi MPS studies were evaluated. Visual reads were performed in 2 consecutive steps, with readers scoring the stress supine perfusion images during step 1 and rescoring the images using both supine/prone data during step 2. Visual summed stress scores (SSS) of 2 readers including regional scores in different vascular territories were compared. Results The specificity for both readers improved using combined supine/prone imaging (Reader 1: 92% vs. 86% [P=0.0002], Reader 2: 88% vs. 72% [P<0.0001]. The inter-observer correlation for SSS (0.90 vs. 0.84, P<0.0001) and inter-observer agreement for combined supine/prone reading (bias = 1.0, 95% confidence interval (CI) 0.9-1.2 vs. 3.1, 95% CI 2.8-3.4, P<0.0001) were significantly better than for supine-only reading. The overall correlation between SSS scores for two readers improved with supine/prone imaging for both genders, as well as in the left anterior descending and right coronary territories. New Knowledge Gained Combined supine/prone imaging improves overall inter-observer agreement as well as based on gender and vascular territories. Conclusion The inter-observer correlation and agreement significantly improves using two-position supine/prone versus supine-only imaging. PMID:24807622

  8. Prone Positioning Causes the Heart To Be Displaced Anteriorly Within the Thorax: Implications for Breast Cancer Treatment

    SciTech Connect

    Chino, Junzo P. [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States)], E-mail: chino001@mc.duke.edu; Marks, Lawrence B. [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States)

    2008-03-01

    Introduction: Prone positioning has been suggested as an alternative to the conventional supine position for patients receiving breast radiotherapy, but few data exist on how this may alter heart location. We herein quantitatively compare the intrathoracic location of the heart in the prone and supine positions in patients treated for breast cancer. Methods and Materials: In 16 patients treated with tangent photons for breast cancer, the computed tomography planning images (obtained in the supine position) and diagnostic magnetic resonance images (obtained in the prone position) were studied. For each case, the distance between the anterior pericardium and the anterior chest wall was measured at nine specific points; three points at each of three axial levels. The differences in the measurements between the prone and supine positions were compared with the Wilcoxon signed-rank test. Results: There is a systematic displacement of the lateral and superior aspect of the heart closer to the chest wall in the prone vs. supine position (mean displacement 19 mm (95% confidence interval 13.7-25.1 mm, p < 0.001); the medial and inferior aspects remain fixed. There was also a reduction in volume of lung interposed between the heart and chest wall when prone (mean decrease of 22 mL, p < 0.001 for difference). Conclusions: The superior and lateral aspects of the heart typically move anteriorly during prone positioning compared with the supine position. This may have negative consequences in situations in which the high-risk target tissues include the chest wall or deep breast.

  9. Nature of Human Error

    PubMed Central

    Cuschieri, Alfred

    2006-01-01

    Background: As the attitude to adverse events has changed from the defensive “blame and shame culture” to an open and transparent healthcare delivery system, it is timely to examine the nature of human errors and their impact on the quality of surgical health care. Methods: The approach of the review is generic rather than specific, and the account is based on the published psychologic and medical literature on the subject. Conclusions: Rather than detailing the various “surgical errors,” the concept of error categories within the surgical setting committed by surgeons as front-line operators is discussed. The important components of safe surgical practice identified include organizational structure with strategic control of healthcare delivery, teamwork and leadership, evidence-based practice, proficiency, continued professional development of all staff, availability of wireless health information technology, and well-embedded incident reporting and adverse events disclosure systems. In our quest for the safest possible surgical health care, there is a need for prospective observational multidisciplinary (surgeons and human factors specialists) studies as distinct for retrospective reports of adverse events. There is also need for research to establish the ideal system architecture for anonymous reporting of near miss and no harm events in surgical practice. PMID:17060751

  10. Real time PCR quantification of viable Mycobacterium tuberculosis from sputum samples treated with propidium monoazide.

    PubMed

    de Assunção, Thiago Milech; Batista, Eraldo L; Deves, Candida; Villela, Anne Drumond; Pagnussatti, Vany Elisa; de Oliveira Dias, Ana Christina; Kritski, Afrânio; Rodrigues-Junior, Valnês; Basso, Luiz Augusto; Santos, Diógenes Santiago

    2014-07-01

    Diagnostic methods of TB, nowadays, are prone to delay in diagnosis, increased false negative results and are not sensitive to many forms of paucibacillary disease. The aims of this study were to implement a quantitative nucleic acid-based diagnostic test for paucibacillary tuberculosis, enabling the identification and quantification of viable Mycobacterium tuberculosis bacilli by quantitative Real-Time PCR (qRT-PCR). The intergenic region of the single-copy inhA-mabA gene was chosen as the target region for design of primers and probes conjugated with fluorophores. The construction of synthetic DNA flanking the target region served as standards for absolute quantification of nucleic acids. Using the intercaling dye, propidium monoazide, we were able to discriminate between viable and dead cells of M. tuberculosis. The diagnosis method showed a broad sensitivity (96.1%) when only compared to samples of smear-positive sputum and ROC analyses shows that our approach performed well and yielded a specificity of 84.6% and a sensitivity of 84.6% when compared to M. tuberculosis colony-forming units counting. PMID:24863654

  11. Seismic hazard assessment and pattern recognition of earthquake prone areas in the Po Plain (Italy)

    NASA Astrophysics Data System (ADS)

    Gorshkov, Alexander; Peresan, Antonella; Soloviev, Alexander; Panza, Giuliano F.

    2014-05-01

    A systematic and quantitative assessment, capable of providing first-order consistent information about the sites where large earthquakes may occur, is crucial for the knowledgeable seismic hazard evaluation. The methodology for the pattern recognition of areas prone to large earthquakes is based on the morphostructural zoning method (MSZ), which employs topographic data and present-day tectonic structures for the mapping of earthquake-controlling structures (i.e. the nodes formed around lineaments intersections) and does not require the knowledge about past seismicity. The nodes are assumed to be characterized by a uniform set of topographic, geologic, and geophysical parameters; on the basis of such parameters the pattern recognition algorithm defines a classification rule to discriminate seismogenic and non-seismogenic nodes. This methodology has been successfully applied since the early 1970s in a number of regions worldwide, including California, where it permitted the identification of areas that have been subsequently struck by strong events and that previously were not considered prone to strong earthquakes. Recent studies on the Iberian Peninsula and the Rhone Valley, have demonstrated the applicability of MSZ to flat basins, with a relatively flat topography. In this study, the analysis is applied to the Po Plain (Northern Italy), an area characterized by a flat topography, to allow for the systematic identification of the nodes prone to earthquakes with magnitude larger or equal to M=5.0. The MSZ method differs from the standard morphostructural analysis where the term "lineament" is used to define the complex of alignments detectable on topographic maps or on satellite images. According to that definition the lineament is locally defined and the existence of the lineament does not depend on the surrounding areas. In MSZ, the primary element is the block - a relatively homogeneous area - while the lineament is a secondary element of the morphostructure. The identified earthquake prone areas provide first-order systematic information that may significantly contribute to seismic hazard assessment in the Italian territory. The information about the possible location of strong earthquakes provided by the morphostructural analysis, in fact, can be naturally incorporated in the neo-deterministic procedure for seismic hazard assessment (NDSHA), so as to fill in possible gaps in known seismicity. Moreover, the space information about earthquake prone areas can be fruitfully combined with the space-time information provided by the quantitative analysis of the seismic flow, so as to identify the priority areas (with linear dimensions of few tens kilometers), where the probability of a strong earthquake is relatively high, for detailed local scale studies. The new indications about the seismogenic potential obtained from this study, although less accurate than detailed fault studies, have the advantage of being independent on past seismicity information, since they rely on the systematic and quantitative analysis of the available geological and morphostructural data. Thus, this analysis appears particularly useful in areas where historical information is scarce; special attention should be paid to seismogenic nodes that are not related with known active faults or past earthquakes.

  12. Real-time PCR in the microbiology laboratory

    Microsoft Academic Search

    I. M. Mackay

    2004-01-01

    Use of PCR in the field of molecular diagnostics has increased to the point where it is now accepted as the standard method for detecting nucleic acids from a number of sample and microbial types. However, conventional PCR was already an essential tool in the research laboratory. Real-time PCR has catalysed wider acceptance of PCR because it is more rapid,

  13. Analyzing Water Samples for Sources of Contamination using PCR and qPCR Berenise Rivera

    E-print Network

    Fay, Noah

    Analyzing Water Samples for Sources of Contamination using PCR and qPCR Berenise Rivera Advisor: Dr. Channah Rock Department of Soil, Water and Environmental Science College of Agriculture and Life Sciences of contamination is essential to effective management of water resources and public health in resource waters

  14. A real-time error correction system for spindle errors

    Microsoft Academic Search

    Ping Ping Dai; Robert D. Lorenz

    1990-01-01

    A methodology for machining of near-perfect bores on mild steel workpieces using an error correction system attached to a conventional, preloaded ball bearing machine tool spindle is described. The approach detects machine tool errors in real-time by using a laser-based sensor, models the errors as a background computation and uses the model to compensate, in real-time, for the deterministic errors.

  15. ProSeal laryngeal mask airway™ insertion in the prone position: Optimal utilization of operation theatre personnel and time?

    PubMed Central

    Sharma, Bimla; Sood, Jayashree; Sehgal, Raminder; Sahai, Chand; Gera, Anjali

    2014-01-01

    Background: Positioning an anesthetized patient prone is challenging with regard to manpower requirement, time to surgical readiness and airway management. The ProSeal laryngeal mask airway™ (PLMA) is emerging as a suitable alternative, both as a primary and a rescue airway device to the tracheal tube (TT) for patients undergoing surgery in the prone position. Materials and Methods: In this prospective randomized study, 70 patients scheduled to undergo pilonidal sinus excision in prone position were allocated to two groups of 35 patients each, depending on the position of the patient at induction and device placement: Group S (device placed while supine) and Group P (device placed while prone). We compared the manpower requirement, time to surgical readiness, efficacy and safety of the PLMA for airway management in the two groups. Results: The number of personnel [5 (4-6) vs. 3 (3-3); P < 0.001] required for positioning the patient and surgical readiness time (22.1 ± 3 vs. 5.9 ± 0.9 min; P < 0.001) was higher in group S. There was no difference between the two groups with regard to efficacy and safety of the PLMA. Incidence of blood on the PLMA cuff and sore throat was comparable in the two groups (P = 1.000). Conclusion: We conclude that induction and placing the PLMA in the prone position by experienced users require fewer personnel and reduces surgical readiness time. PMID:24803753

  16. DNA methylation errors in imprinting disorders and assisted reproductive technology.

    PubMed

    Chiba, Hatsune; Hiura, Hitoshi; Okae, Hiroaki; Miyauchi, Naoko; Sato, Fumi; Sato, Akiko; Arima, Takahiro

    2013-10-01

    There have been increased incident reports of rare imprinting disorders associated with assisted reproductive technology (ART). ART is an important treatment for infertile people of reproductive age and is increasingly common. The identification of epigenetic changes at imprinted loci in ART infants has led to the suggestion that the techniques themselves may predispose embryos to acquisition of imprinting errors and disease. It is still unknown, however, at what point(s) these imprinting errors arise, or the risk factors. In this review it was hypothesized that the particular steps of the ART process may be prone to induction of imprinting methylation errors during gametogenesis, fertilization and early embryonic development. In addition, imprinting diseases and their causes are explained. Moreover, using a Japanese nationwide epidemiological study of imprinting diseases, their association with ART is determined. Epigenetic studies are required to understand the pathogenesis of this association; the ART-related risk factor(s); and the precautions that can be taken to prevent the occurrence of these syndromes. It is hoped that the constitution of children born after ART will indicate the safest and most ethical approach to use, which will be invaluable for the future development of standard ART treatment. PMID:23919517

  17. Prospective issues for error detection.

    PubMed

    Blavier, Adélaïde; Rouy, Emmanuelle; Nyssen, Anne-Sophie; de Keyser, Véronique

    2005-06-10

    From the literature on error detection, the authors select several concepts relating error detection mechanisms and prospective memory features. They emphasize the central role of intention in the classification of the errors into slips/lapses/mistakes, in the error handling process and in the usual distinction between action-based and outcome-based detection. Intention is again a core concept in their investigation of prospective memory theory, where they point out the contribution of intention retrievals, intention persistence and output monitoring in the individual's possibilities for detecting their errors. The involvement of the frontal lobes in prospective memory and in error detection is also analysed. From the chronology of a prospective memory task, the authors finally suggest a model for error detection also accounting for neural mechanisms highlighted by studies on error-related brain activity. PMID:16076736

  18. Improved error-tradeoff and error-disturbance relations in terms of measurement error components

    NASA Astrophysics Data System (ADS)

    Lu, Xiao-Ming; Yu, Sixia; Fujikawa, Kazuo; Oh, C. H.

    2014-10-01

    Heisenberg's uncertainty principle is quantified by error-disturbance tradeoff relations, which have been tested experimentally in various scenarios. Here we shall report various error-disturbance tradeoff relations by decomposing the measurement errors and disturbance into two different components, namely, operator bias and fuzziness. Our uncertainty relations reveal the tradeoffs between these two components of errors, and imply various conditionally valid error-tradeoff relations for the unbiased and projective measurements. We also design a quantum circuit to measure the two components of the error and disturbance.

  19. Comparison of real-time PCR and MassTag PCR for the multiplex detection of highly pathogenic agents.

    PubMed

    Doellinger, Joerg; Schroeder, Kati; Witt, Natalie; Heunemann, Carolin; Nitsche, Andreas

    2012-10-01

    Multiplex PCR assays are a cost- as well as labour-effective way to analyse one sample for several pathogens simultaneously. Besides the mutual competition of the individual PCR reactions included in a multiplex PCR assay, their specific read-out displays a limiting factor for the total number of PCR reactions that can be multiplexed. In this study, two PCR systems with different read-out approaches are compared, using a pentaplex PCR assay for the detection of highly pathogenic agents. A pentaplex assay was used since five represents the current limit of real-time PCR multiplexing capacity due to the low resolution of fluorescence emission peaks of the current equipment. In contrast, MassTag PCR as a quite new technique offers the possibility to detect up to 20-30 target sequences from one reaction. After extensive and separate optimisation of the PCR protocol for both platforms, a comparative probit analysis showed good sensitivities for MassTag and real-time PCR detection. Nevertheless, the detection limits of MassTag PCR have been undercut by the real-time PCR for each target. We therefore conclude that MassTag PCR is a useful diagnostic technique for the sensitive screening for pathogens by highly multiplexed PCR assays, but cannot reach the sensitivity of real-time PCR for lower multiplexed PCR assays. PMID:22819946

  20. Identification of bacterial plant pathogens using multilocus PCR and electrospray ionization-mass spectrometry (PCR/ESI-MS)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    PCR/electrospray ionization-mass spectrometry (PCR/ESI-MS, previously known as “TIGER”) utilizes PCR with broad range primers to amplify products from wide array of organisms within a taxonomic group, followed by analysis of PCR amplicons using mass spectrometry. Computer analysis of precise masses ...

  1. Design risk assessment for burst-prone mines: Application in a Canadian mine

    NASA Astrophysics Data System (ADS)

    Cheung, David J.

    A proactive stance towards improving the effectiveness and consistency of risk assessments has been adopted recently by mining companies and industry. The next 10-20 years forecasts that ore deposits accessible using shallow mining techniques will diminish. The industry continues to strive for success in "deeper" mining projects in order to keep up with the continuing demand for raw materials. Although the returns are quite profitable, many projects have been sidelined due to high uncertainty and technical risk in the mining of the mineral deposit. Several hardrock mines have faced rockbursting and seismicity problems. Within those reported, mines in countries like South Africa, Australia and Canada have documented cases of severe rockburst conditions attributed to the mining depth. Severe rockburst conditions known as "burst-prone" can be effectively managed with design. Adopting a more robust design can ameliorate the exposure of workers and equipment to adverse conditions and minimize the economic consequences, which can hinder the bottom line of an operation. This thesis presents a methodology created for assessing the design risk in burst-prone mines. The methodology includes an evaluation of relative risk ratings for scenarios with options of risk reduction through several design principles. With rockbursts being a hazard of seismic events, the methodology is based on research in the area of mining seismicity factoring in rockmass failure mechanisms, which results from a combination of mining induced stress, geological structures, rockmass properties and mining influences. The methodology was applied to case studies at Craig Mine of Xstrata Nickel in Sudbury, Ontario, which is known to contain seismically active fault zones. A customized risk assessment was created and applied to rockburst case studies, evaluating the seismic vulnerability and consequence for each case. Application of the methodology to Craig Mine demonstrates that changes in the design can reduce both exposure risk (personnel and equipment), and economical risk (revenue and costs). Fatal and catastrophic consequences can be averted through robust planning and design. Two customized approaches were developed to conduct risk assessment of case studies at Craig Mine. Firstly, the Brownfield Approach utilizes the seismic database to determine the seismic hazard from a rating system that evaluates frequency-magnitude, event size, and event-blast relation. Secondly, the Greenfield Approach utilizes the seismic database, focusing on larger magnitude events, rocktype, and geological structure. The customized Greenfield Approach can also be applied in the evaluation of design risk in deep mines with the same setting and condition as Craig Mine. Other mines with different settings and conditions can apply the principles in the methodology to evaluate design alternatives and risk reduction strategies for burst-prone mines.

  2. Low error rate LDPC decoders

    Microsoft Academic Search

    Zhengya Zhang; Lara Dolecek; Pamela Lee; Venkat Anantharam; Martin J. Wainwright; Brian Richards; Borivoje Nikolic

    2009-01-01

    Low-density parity-check (LDPC) codes have been demonstrated to perform very close to the Shannon limit when decoded iteratively. However challenges persist in building practical high-throughput decoders due to the existence of error floors at low error rate levels. We apply high-throughput hardware emulation to capture errors and error-inducing noise realizations, which allow for in-depth analysis. This method enables the design

  3. Mitotic errors in chromosome 21 of human preimplantation embryos are associated with non-viability

    Microsoft Academic Search

    M. G. Katz-Jaffe; A. O. Trounson; D. S. Cram

    2004-01-01

    Fluorescent in situ hybridization (FISH) studies of human preimplantation embryos have demonstrated a high proportion of chromosomal mosaicism. To investigate the different timings and nature of chromosomal mosaicism, we developed single cell multiplex fluorescent (FL)-PCR to distinguish meiotic and mitotic cell division errors. Chromosome 21 was investigated as the model chromosome as trisomy 21 (Down's syndrome) represents the most common

  4. Variability in DNA polymerase efficiency: effects of random error, DNA extraction method, and isolate type

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using computer-generated data calculated with known amounts of random error (E = 1, 5 & 10%) associated with calculated qPCR cycle number (C ) at four jth 1:10 dilutions, we found that the “efficiency” (eff) associated with each population distribution of n = 10,000 measurements varied from 0.95 to ...

  5. MUST: A Scalable Approach to Runtime Error Detection in MPI Programs

    SciTech Connect

    Hilbrich, T; Schulz, M; de Supinski, B R; Muller, M

    2010-03-24

    The Message-Passing Interface (MPI) is large and complex. Therefore, programming MPI is error prone. Several MPI runtime correctness tools address classes of usage errors, such as deadlocks or nonportable constructs. To our knowledge none of these tools scales to more than about 100 processes. However, some of the current HPC systems use more than 100,000 cores and future systems are expected to use far more. Since errors often depend on the task count used, we need correctness tools that scale to the full system size. We present a novel framework for scalable MPI correctness tools to address this need. Our fine-grained, module-based approach supports rapid prototyping and allows correctness tools built upon it to adapt to different architectures and use cases. The design uses PnMPI to instantiate a tool from a set of individual modules. We present an overview of our design, along with first performance results for a proof of concept implementation.

  6. Uncertainty quantification and error analysis

    SciTech Connect

    Higdon, Dave M [Los Alamos National Laboratory; Anderson, Mark C [Los Alamos National Laboratory; Habib, Salman [Los Alamos National Laboratory; Klein, Richard [Los Alamos National Laboratory; Berliner, Mark [OHIO STATE UNIV.; Covey, Curt [LLNL; Ghattas, Omar [UNIV OF TEXAS; Graziani, Carlo [UNIV OF CHICAGO; Seager, Mark [LLNL; Sefcik, Joseph [LLNL; Stark, Philip [UC/BERKELEY; Stewart, James [SNL

    2010-01-01

    UQ studies all sources of error and uncertainty, including: systematic and stochastic measurement error; ignorance; limitations of theoretical models; limitations of numerical representations of those models; limitations on the accuracy and reliability of computations, approximations, and algorithms; and human error. A more precise definition for UQ is suggested below.

  7. Interactive Histogram with Error Graph

    NSDL National Science Digital Library

    Kyle Siegrist

    This resource consists of a Java applet and expository text. The applet allows the user to construct a histogram by clicking on a number line to generate the sample data. The graph of an error function is shown, either mean square error or mean absolute error.

  8. Error functions Nikolai G. Lehtinen

    E-print Network

    Lehtinen, Nikolai G.

    Error functions Nikolai G. Lehtinen April 23, 2010 1 Error function erf x and complementary er- ror function erfc x (Gauss) error function is erf x = 2 x 0 e-t2 dt (1) and has properties erf (-) = -1, erf (+) = 1 erf (-x) = -erf (x), erf (x ) = [erf (x)] where the asterisk denotes complex conjugation

  9. Quantum Zero-error Capacity

    E-print Network

    Rex A. C. Medeiros; Francisco M. De Assis

    2006-11-08

    We define here a new kind of quantum channel capacity by extending the concept of zero-error capacity for a noisy quantum channel. The necessary requirement for which a quantum channel has zero-error capacity greater than zero is given. Finally, we point out some directions on how to calculate the zero-error capacity of such channels.

  10. Data Entry Errors and Design for Model-Based Tight Glycemic Control in Critical Care

    PubMed Central

    Ward, Logan; Steel, James; Le Compte, Aaron; Evans, Alicia; Tan, Chia-Siong; Penning, Sophie; Shaw, Geoffrey M; Desaive, Thomas; Chase, J Geoffrey

    2012-01-01

    Introduction Tight glycemic control (TGC) has shown benefits but has been difficult to achieve consistently. Model-based methods and computerized protocols offer the opportunity to improve TGC quality but require human data entry, particularly of blood glucose (BG) values, which can be significantly prone to error. This study presents the design and optimization of data entry methods to minimize error for a computerized and model-based TGC method prior to pilot clinical trials. Method To minimize data entry error, two tests were carried out to optimize a method with errors less than the 5%-plus reported in other studies. Four initial methods were tested on 40 subjects in random order, and the best two were tested more rigorously on 34 subjects. The tests measured entry speed and accuracy. Errors were reported as corrected and uncorrected errors, with the sum comprising a total error rate. The first set of tests used randomly selected values, while the second set used the same values for all subjects to allow comparisons across users and direct assessment of the magnitude of errors. These research tests were approved by the University of Canterbury Ethics Committee. Results The final data entry method tested reduced errors to less than 1–2%, a 60–80% reduction from reported values. The magnitude of errors was clinically significant and was typically by 10.0 mmol/liter or an order of magnitude but only for extreme values of BG < 2.0 mmol/liter or BG > 15.0–20.0 mmol/liter, both of which could be easily corrected with automated checking of extreme values for safety. Conclusions The data entry method selected significantly reduced data entry errors in the limited design tests presented, and is in use on a clinical pilot TGC study. The overall approach and testing methods are easily performed and generalizable to other applications and protocols. PMID:22401331

  11. Period, epoch, and prediction errors of ephemerides from continuous sets of timing measurements

    NASA Astrophysics Data System (ADS)

    Deeg, H. J.

    2015-06-01

    Space missions such as Kepler and CoRoT have led to large numbers of eclipse or transit measurements in nearly continuous time series. This paper shows how to obtain the period error in such measurements from a basic linear least-squares fit, and how to correctly derive the timing error in the prediction of future transit or eclipse events. Assuming strict periodicity, a formula for the period error of these time series is derived, ?P = ?T (12 / (N3-N))1 / 2, where ?P is the period error, ?T the timing error of a single measurement, and N the number of measurements. Compared to the iterative method for period error estimation by Mighell & Plavchan (2013), this much simpler formula leads to smaller period errors, whose correctness has been verified through simulations. For the prediction of times of future periodic events, usual linear ephemeris were epoch errors are quoted for the first time measurement, are prone to an overestimation of the error of that prediction. This may be avoided by a correction for the duration of the time series. An alternative is the derivation of ephemerides whose reference epoch and epoch error are given for the centre of the time series. For long continuous or near-continuous time series whose acquisition is completed, such central epochs should be the preferred way for the quotation of linear ephemerides. While this work was motivated from the analysis of eclipse timing measures in space-based light curves, it should be applicable to any other problem with an uninterrupted sequence of discrete timings for which the determination of a zero point, of a constant period and of the associated errors is needed.

  12. Commission errors of active intentions: the roles of aging, cognitive load, and practice.

    PubMed

    Boywitt, C Dennis; Rummel, Jan; Meiser, Thorsten

    2015-09-01

    Performing an intended action when it needs to be withheld, for example, when temporarily prescribed medication is incompatible with the other medication, is referred to as commission errors of prospective memory (PM). While recent research indicates that older adults are especially prone to commission errors for finished intentions, there is a lack of research on the effects of aging on commission errors for still active intentions. The present research investigates conditions which might contribute to older adults' propensity to perform planned intentions under inappropriate conditions. Specifically, disproportionally higher rates of commission errors for still active intentions were observed in older than in younger adults with both salient (Experiment 1) and non-salient (Experiment 2) target cues. Practicing the PM task in Experiment 2, however, helped execution of the intended action in terms of higher PM performance at faster ongoing-task response times but did not increase the rate of commission errors. The results have important implications for the understanding of older adults' PM commission errors and the processes involved in these errors. PMID:25599267

  13. Mining Co-location Relationships among Bug Reports to Localize Fault-Prone Modules

    NASA Astrophysics Data System (ADS)

    Chen, Ing-Xiang; Li, Chien-Hung; Yang, Cheng-Zen

    Automated bug localization is an important issue in software engineering. In the last few decades, various proactive and reactive localization approaches have been proposed to predict the fault-prone software modules. However, most proactive or reactive approaches need source code information or software complexity metrics to perform localization. In this paper, we propose a reactive approach which considers only bug report information and historical revision logs. In our approach, the co-location relationships among bug reports are explored to improve the prediction accuracy of a state-of-the-art learning method. Studies on three open source projects reveal that the proposed scheme can consistently improve the prediction accuracy in all three software projects by nearly 11.6% on average.

  14. Simulating Turbulent Wind Fields for Offshore Turbines in Hurricane-Prone Regions (Poster)

    SciTech Connect

    Guo, Y.; Damiani, R.; Musial, W.

    2014-04-01

    Extreme wind load cases are one of the most important external conditions in the design of offshore wind turbines in hurricane prone regions. Furthermore, in these areas, the increase in load with storm return-period is higher than in extra-tropical regions. However, current standards have limited information on the appropriate models to simulate wind loads from hurricanes. This study investigates turbulent wind models for load analysis of offshore wind turbines subjected to hurricane conditions. Suggested extreme wind models in IEC 61400-3 and API/ABS (a widely-used standard in oil and gas industry) are investigated. The present study further examines the wind turbine response subjected to Hurricane wind loads. Three-dimensional wind simulator, TurbSim, is modified to include the API wind model. Wind fields simulated using IEC and API wind models are used for an offshore wind turbine model established in FAST to calculate turbine loads and response.

  15. A Method to Quantify Supine to Prone Thoracoabdominal Deformation and Organ Migration in a Set of Healthy Young Adults.

    PubMed

    Guleyupoglu, Berkan; Tan, Josh C; Hamilton, Craig A; Gayzik, F Scott

    2015-01-01

    Medical image data used for the development of computational human body models are often retrospectively acquired, and researchers are unlikely to encounter scans of healthy individuals in specific postures. We prospectively acquired scans in both prone and supine postures from 22 healthy young adults; M:F 1:1, with age, height, and weight of 28.8±7.0 years, 173.0±7.8 cm, and 70.6±10.9 kg. While prone, subjects? arms were superior to the head and supported by a foam insert at axilla. Breath held, T1-weighted MRI scans were acquired using a Siemen?s Skyra 3T with an in-plane resolution of 1.56 mm (TR: 4.10 ms, TE: 1.23 ms, thickness: 2 mm, matrix: 256x256, FOV: 400 mm). Gross thoraco-abdominal compression was considered as the change in perpendicular distance in the transverse plane measured from the anterior margin of L4/L5 to the table (for prone) or exterior body surface (for supine). Gross thoraco-abdominal, liver and spleen compression were found to be 8.5% (71.6±12.9 mm prone vs. 78.7±12.4 mm supine; p=0.0013), 17.7% (110.4±4.1 mm prone vs. 134.8±2.6 mm supine; p<0.0001), and 3.5% (53.8±1.9 mm prone vs. 57.3±2.9 mm supine) respectively. Gender and spleen compression differences were not noted. The liver and spleen migrated on average 8.3 mm posteriorly, 11.4 mm rightward, 15.1 mm superiorly and 4.1 mm anteriorly, 6.1 mm rightward, 1.7 mm superiorly respectively. The data obtained from this set may be of use in computational biomechanics, surgical simulation, and medical device design. PMID:25996713

  16. The Aggregation-Prone Intracellular Serpin SRP-2 Fails to Transit the ER in Caenorhabditis elegans.

    PubMed

    Silverman, Richard M; Cummings, Erin E; O'Reilly, Linda P; Miedel, Mark T; Silverman, Gary A; Luke, Cliff J; Perlmutter, David H; Pak, Stephen C

    2015-05-01

    Familial encephalopathy with neuroserpin inclusions bodies (FENIB) is a serpinopathy that induces a rare form of presenile dementia. Neuroserpin contains a classical signal peptide and like all extracellular serine proteinase inhibitors (serpins) is secreted via the endoplasmic reticulum (ER)-Golgi pathway. The disease phenotype is due to gain-of-function missense mutations that cause neuroserpin to misfold and aggregate within the ER. In a previous study, nematodes expressing a homologous mutation in the endogenous Caenorhabditis elegans serpin, srp-2, were reported to model the ER proteotoxicity induced by an allele of mutant neuroserpin. Our results suggest that SRP-2 lacks a classical N-terminal signal peptide and is a member of the intracellular serpin family. Using confocal imaging and an ER colocalization marker, we confirmed that GFP-tagged wild-type SRP-2 localized to the cytosol and not the ER. Similarly, the aggregation-prone SRP-2 mutant formed intracellular inclusions that localized to the cytosol. Interestingly, wild-type SRP-2, targeted to the ER by fusion to a cleavable N-terminal signal peptide, failed to be secreted and accumulated within the ER lumen. This ER retention phenotype is typical of other obligate intracellular serpins forced to translocate across the ER membrane. Neuroserpin is a secreted protein that inhibits trypsin-like proteinase. SRP-2 is a cytosolic serpin that inhibits lysosomal cysteine peptidases. We concluded that SRP-2 is neither an ortholog nor a functional homolog of neuroserpin. Furthermore, animals expressing an aggregation-prone mutation in SRP-2 do not model the ER proteotoxicity associated with FENIB. PMID:25786854

  17. The Effects of Overfeeding on Spontaneous Physical Activity in Obesity Prone and Obesity Resistant Humans

    PubMed Central

    Schmidt, Stacy L.; Harmon, Kristin A.; Sharp, Teresa A.; Kealey, Elizabeth H.; Bessesen, Daniel H.

    2013-01-01

    Despite living in an environment that promotes weight gain in many individuals, some individuals maintain a thin phenotype while self-reporting expending little or no effort to control their weight. When compared with obesity prone (OP) individuals, we wondered if obesity resistant (OR) individuals would have higher levels of spontaneous physical activity (SPA) or respond to short-term overfeeding by increasing their level of SPA in a manner that could potentially limit future weight gain. SPA was measured in 55 subjects (23 OP and 32 OR) using a novel physical activity monitoring system (PAMS) that measured body position and movement while subjects were awake for 6 days, either in a controlled eucaloric condition or during 3 days of overfeeding (1.4× basal energy) and for the subsequent 3 days (ad libitum recovery period). Pedometers were also used before and during use of the PAMS to provide an independent measure of SPA. SPA was quantified by the PAMS as fraction of recording time spent lying, sitting, or in an upright posture. Accelerometry, measured while subjects were in an upright posture, was used to categorize time spent in different levels of movement (standing, walking slowly, quickly, etc.). There were no differences in SPA between groups when examined across all study periods (P > 0.05). However, 3 days following overfeeding, OP subjects significantly decreased the amount of time they spent walking (?2.0% of time, P = 0.03), whereas OR subjects maintained their walking (+0.2%, P > 0.05). The principle findings of this study are that increased levels of SPA either during eucaloric feeding or following short term overfeeding likely do not significantly contribute to obesity resistance although a decrease in SPA following overfeeding may contribute to future weight gain in individuals prone to obesity. PMID:22522883

  18. Introducing the GASP scale: a new measure of guilt and shame proneness.

    PubMed

    Cohen, Taya R; Wolf, Scott T; Panter, A T; Insko, Chester A

    2011-05-01

    Although scholars agree that moral emotions are critical for deterring unethical and antisocial behavior, there is disagreement about how 2 prototypical moral emotions--guilt and shame--should be defined, differentiated, and measured. We addressed these issues by developing a new assessment--the Guilt and Shame Proneness scale (GASP)--that measures individual differences in the propensity to experience guilt and shame across a range of personal transgressions. The GASP contains 2 guilt subscales that assess negative behavior-evaluations and repair action tendencies following private transgressions and 2 shame subscales that assess negative self-evaluations (NSEs) and withdrawal action tendencies following publically exposed transgressions. Both guilt subscales were highly correlated with one another and negatively correlated with unethical decision making. Although both shame subscales were associated with relatively poor psychological functioning (e.g., neuroticism, personal distress, low self-esteem), they were only weakly correlated with one another, and their relationships with unethical decision making diverged. Whereas shame-NSE constrained unethical decision making, shame-withdraw did not. Our findings suggest that differentiating the tendency to make NSEs following publically exposed transgressions from the tendency to hide or withdraw from public view is critically important for understanding and measuring dispositional shame proneness. The GASP's ability to distinguish these 2 classes of responses represents an important advantage of the scale over existing assessments. Although further validation research is required, the present studies are promising in that they suggest the GASP has the potential to be an important measurement tool for detecting individuals susceptible to corruption and unethical behavior. PMID:21517196

  19. Efficacy of fixed daily 20 mg of isotretinoin in moderate to severe scar prone acne

    PubMed Central

    Rasi, Abbas; Behrangi, Elham; Rohaninasab, Masoumeh; Nahad, Zahra Mehr

    2014-01-01

    Background: Despite advances in acne therapy in recent years, treatment failure is common. Isotretinoin is the only drug that affects almost all factors in acne pathogenesis, but side-effects are common at the doses reported in published studies in the literature. The aim of this study was to investigate the efficacy of low daily dose isotretinoin in moderate to severe acne patients. The secondary objective was to measure the rate of relapse 5 years after the completion of therapy. Materials and Methods: In this retrospective, noncomparative study, 146 patients with moderate to severe scare prone acne. Treatment regimen consisted of isotretinoin, fixed 20 mg daily, and duration of treatment-based on the weight of patient, until total cumulative dose of 120 mg/kg of body weight is achieved. No topical or other systemic therapy was allowed during the trial. Liver function tests (serum glutamic-oxalocetic transaminase, serum glutamate pyruvate transaminase, direct and total bilirubin), and lipid profiles (total cholesterol, low-density lipoprotein, high-density lipoprotein, triglyceride) were evaluated for all patients, before the initiation of treatment and again after the 2nd month of treatment. All data analyzed by Microsoft Office Excel 2007; in descriptive statics frequency and SPSS.18 software. Results: At the end of treatment course, (96.4%) demonstrated complete clearing of their acne, defined as no acne or occasional isolated lesions. In 5-year follow-up, relapse accrued in 11 (7.9%) of patients. All adverse effects were mild, and discontinuation of treatment was not necessary. Conclusion: Low dose isotretinoin was found to be a safe and effective choice for patients with moderate to severe scar prone acne vulgaris. PMID:24804178

  20. Decomposition and humification of soil organic carbon after land use change on erosion prone slopes

    NASA Astrophysics Data System (ADS)

    Häring, Volker; Fischer, Holger; Cadisch, Georg; Stahr, Karl

    2014-05-01

    Soil organic carbon decline after land use change from forest to maize usually lead to soil degradation and elevated CO2 emissions. However, limited knowledge is available on the interactions between rates of SOC change and soil erosion and how SOC dynamics vary with soil depth and clay contents. The 13C isotope based CIDE approach (Carbon Input, Decomposition and Erosion) was developed to determine SOC dynamics on erosion prone slopes. The aims of the present study were: (1) to test the applicability of the CIDE approach to determine rates of decomposition and SOC input under particular considerations of concurrent erosion events on three soil types (Alisol, Luvisol, Vertisol), (2) to adapt the CIDE approach to deeper soil layers (10-20 and 20-30 cm) and (3) to determine the variation of decomposition and SOC input with soil depth and soil texture. SOC dynamics were determined for bulk soil and physically separated SOC fractions along three chronosequences after land use change from forest to maize (up to 21 years) in northwestern Vietnam. Consideration of the effects of soil erosion on SOC dynamics by the CIDE approach yielded a higher total SOC loss (6 to 32%), a lower decomposition (13 to 40%) and a lower SOC input (14 to 31%) relative to the values derived from a commonly applied 13C isotope based mass balance approach. Comparison of decomposition between depth layers revealed that tillage accelerated decomposition in the plough layer (0-10 cm), accounting for 3 to 34% of total decomposition. With increasing clay contents SOC input increased. In addition, decomposition increased with increasing clay contents, too, being attributed to decomposition of exposed labile SOC which was attached to clay particles in the sand sized stable aggregate fraction. This study suggests that in situ SOC dynamics on erosion prone slopes are commonly misrepresented by erosion unadjusted approaches.

  1. Social capital and disaster preparedness among low income Mexican Americans in a disaster prone area.

    PubMed

    Reininger, Belinda M; Rahbar, Mohammad H; Lee, Minjae; Chen, Zhongxue; Alam, Sartaj R; Pope, Jennifer; Adams, Barbara

    2013-04-01

    Examination of social capital and its relationship to disaster preparedness has grown in prominence partially due to world-wide need to effectively respond to terrorist attacks, viral epidemics, or natural disasters. Recent studies suggested that social capital may be related to a community's ability to plan for and respond to such disasters. Few studies, however, have examined social capital constructs among low income populations living in disaster prone areas and accounted for the influence of social capital at the individual and community level. We examined social capital as measured by perceived fairness, perceived civic trust, perceived reciprocity and group membership. We undertook a multistage random cluster survey in three coastal counties in Texas (U.S.) noted for their high levels of poverty. Individuals from 3088 households provided data on social capital, socioeconomic and demographic characteristics, and self-reported level of preparedness for a hurricane. We used multivariable logistic regression to test potential associations between social capital measures and disaster preparedness. After adjusting for age, gender, marital status, ethnicity, education, employment, household income, acculturation, self-reported health, special needs persons in household, household size, and distance to the shore we found a higher prevalence of preparedness among individuals who reported the highest perception of fairness [AOR = 3.12, 95% CI: (1.86, 5.21)] compared to those individuals who reported lowest perceptions of fairness. We also found a higher prevalence of preparedness [AOR = 2.06; 95% CI: (1.17, 3.62)] among individuals who reported highest perceptions of trust compared to individuals who reported lowest perceptions of trust. Perceived reciprocity and group membership were not associated with preparedness. These results extend previous findings on social capital and disaster preparedness and further characterize social capital's presence among a low income population living in a hurricane prone area. PMID:23465204

  2. PCR detection of potato cyst nematode.

    PubMed

    Reid, Alex

    2009-01-01

    Potato cyst nematode (PCN) is responsible for losses in potato production totalling millions of euros every year in the EC. It is important for growers to know which species is present in their land as this determines its subsequent use. The two species Globodera pallida and Globodera rostochiensis can be differentiated using an allele-specific PCR. PMID:19301763

  3. [Mutation detection by PCR-TGGE].

    PubMed

    Shirakawa, T; Nishiyama, K; Matsuo, M

    1995-07-01

    The variants in enterotoxigenic Escherichia coli (ETEC) heat-labile toxin (LT) gene were detected by temperature gradient gel electrophoresis (TGGE). 15 clinical strains isolated from patients and a wild type strain (B2C) were analyzed after the conventional PCR. Although all PCR products (707bp) corresponded to A-subunit of LT, three strains were the different electrophoretic patterns after silver staining as compared to the wild type. For further electrophoretic analyses, the 707bp region was divided into 4 parts. The different ones were localized in the downstream part (183bp), but each those DNA bands was not so clear than DNA bands in 707bp. The clearer patterns were obtained by using a primer attached GC-clamp. The hetero-duplex assays in TGGE were proceeded by a series of procedures in mixing with the equal quantity of PCR products derived from a variant and a wild type, heat-denaturation and then annealing. TGGE of those mixed samples had 4 bands that were 2 front bands as homo-duplex and 2 slower migration bands as hetero-duplex. To Confirm the site of the mutations, the nucleotide sequences in each 183bp PCR products were decided by dideoxynucleotide-fluorescent dye method. Indeed, two variants were recognized four one-base substitutions without deletions and the one was five. Thus, the difference of migration in TGGE depended on the number and the localization in mutation sites. PMID:7674540

  4. PCR and recombinant DNA Cristiano V. Bizarro

    E-print Network

    Ritort, Felix

    :Chloroform extraction Ethanol precipitationIsolated plasmid 4. 5. 6. #12;Recombinant DNA technology Source:Color Atlas Biosystems Lab Universitat de Barcelona #12;Topics to be covered Introduction (DNA isolation, modification enzymes) PCR DNA Electrophoresis Recombinant DNA technology Applications in single-molecule biophysics

  5. PCR and recombinant DNA Joan Camuas

    E-print Network

    Ritort, Felix

    precipitationIsolated plasmid 4. 5. 6. #12;Recombinant DNA technology Source:Color Atlas Of Biochemistry 2d ed de Barcelona #12;Topics to be covered Introduction (DNA isolation, modification enzymes) PCR DNA Electrophoresis Recombinant DNA technology Applications in single-molecule biophysics #12;Zooming in on cellular

  6. The Power of Real-Time PCR

    ERIC Educational Resources Information Center

    Valasek, Mark A.; Repa, Joyce J.

    2005-01-01

    In recent years, real-time polymerase chain reaction (PCR) has emerged as a robust and widely used methodology for biological investigation because it can detect and quantify very small amounts of specific nucleic acid sequences. As a research tool, a major application of this technology is the rapid and accurate assessment of changes in gene…

  7. Calibration Curves for Real-Time PCR

    Microsoft Academic Search

    K. Kay-Yin Lai; Linda Cook; Elizabeth M. Krantz; Lawrence Corey; Keith R. Jerome

    2005-01-01

    Background: Despite the increasing use of real-time PCR in the diagnosis and management of viral infec- tions, there are no published studies adequately ad- dressing the optimum number of calibrators, the num- ber of replicates of each calibrator, and the frequency with which calibration needs to be repeated. This study was designed to address these issues. Methods: Cycle threshold data

  8. Antigenic typing of canine parvovirus using differential PCR.

    PubMed

    Kaur, Gurpreet; Chandra, Mudit; Dwivedi, P N; Sharma, N S

    2014-12-01

    Canine parvovirus (CPV) is an enteric pathogen causing hemorrhagic enteritis in pups of 3-6 months of age and is mainly transmitted via feco-oral route. In the present study, a total of 85 animals rectal swabs suspected of CPV were tested using a PCR, nested PCR and a newly designed differential PCR. Using PCR 7 (8.23 %) animals were positive whereas 39 (45.88 %) were positive by using nested PCR and 40 (47.05 %) were positive for either one or more than one antigenic types of CPV using differential PCR. Using differential PCR it was found that CPV-2a and CPV-2b were the most prevailing antigenic types. Also it was found that dogs that were vaccinated too yielded positive CPV indicating a possible presence of additional CPV antigenic types. Thus, the primers used in differential PCR can be used in a single PCR reaction to detect various antigenic types of CPV. PMID:25674626

  9. Transcription Errors Observed in a Teaching Hospital

    Microsoft Academic Search

    Fanak Fahimi; Pharm D; Mohammad Abbasi; Nazari Pharm; Ramin Abrishami; Mohammad Sistanizad; Talya Mazidi; Toktam Faghihi; Rasoul Soltani; Shadi Baniasadi

    Medication errors are among the most common medical errors in the hospitals. Transcription error is a specific type of medication errors and is due to data entry error that is commonly made by the human operators. This study was designed to detect transcription errors in a teaching hospital in Tehran. Direct observational method was used in this study. Error was

  10. Beta systems error analysis

    NASA Technical Reports Server (NTRS)

    1984-01-01

    The atmospheric backscatter coefficient, beta, measured with an airborne CO Laser Doppler Velocimeter (LDV) system operating in a continuous wave, focussed model is discussed. The Single Particle Mode (SPM) algorithm, was developed from concept through analysis of an extensive amount of data obtained with the system on board a NASA aircraft. The SPM algorithm is intended to be employed in situations where one particle at a time appears in the sensitive volume of the LDV. In addition to giving the backscatter coefficient, the SPM algorithm also produces as intermediate results the aerosol density and the aerosol backscatter cross section distribution. A second method, which measures only the atmospheric backscatter coefficient, is called the Volume Mode (VM) and was simultaneously employed. The results of these two methods differed by slightly less than an order of magnitude. The measurement uncertainties or other errors in the results of the two methods are examined.

  11. Next-Generation Sequencing of HIV-1 RNA Genomes: Determination of Error Rates and Minimizing Artificial Recombination

    PubMed Central

    Duport, Yannick; Leemann, Christine; Joos, Beda; Künzli-Gontarczyk, Marzanna; Bruggmann, Rémy; Beerenwinkel, Niko; Günthard, Huldrych F.; Metzner, Karin J.

    2013-01-01

    Next-generation sequencing (NGS) is a valuable tool for the detection and quantification of HIV-1 variants in vivo. However, these technologies require detailed characterization and control of artificially induced errors to be applicable for accurate haplotype reconstruction. To investigate the occurrence of substitutions, insertions, and deletions at the individual steps of RT-PCR and NGS, 454 pyrosequencing was performed on amplified and non-amplified HIV-1 genomes. Artificial recombination was explored by mixing five different HIV-1 clonal strains (5-virus-mix) and applying different RT-PCR conditions followed by 454 pyrosequencing. Error rates ranged from 0.04–0.66% and were similar in amplified and non-amplified samples. Discrepancies were observed between forward and reverse reads, indicating that most errors were introduced during the pyrosequencing step. Using the 5-virus-mix, non-optimized, standard RT-PCR conditions introduced artificial recombinants in a fraction of at least 30% of the reads that subsequently led to an underestimation of true haplotype frequencies. We minimized the fraction of recombinants down to 0.9–2.6% by optimized, artifact-reducing RT-PCR conditions. This approach enabled correct haplotype reconstruction and frequency estimations consistent with reference data obtained by single genome amplification. RT-PCR conditions are crucial for correct frequency estimation and analysis of haplotypes in heterogeneous virus populations. We developed an RT-PCR procedure to generate NGS data useful for reliable haplotype reconstruction and quantification. PMID:24058534

  12. Equivalence of error diffusion and minimal average error algorithms

    NASA Astrophysics Data System (ADS)

    Fetthauer, F.; Weissbach, S.; Bryngdahl, O.

    1995-01-01

    Error diffusion and minimal average error are well known quantization algorithms which can be applied in electronic imaging and digital holography. It is shown that to each set of free parameters of any one of these methods a corresponding set of free parameters of the other algotithm exists resulting in the first algorithm. The significance of this equivalence is demonstrated with a stability criterion for the choice of error diffusion weights and a filter combination algorithm.

  13. Multibit Error Tolerant Caches Using Two-Dimensional Error Coding

    Microsoft Academic Search

    Jangwoo Kim; Nikos Hardavellas; Ken Mai; Babak Falsafi; James C. Hoe

    2007-01-01

    In deep sub-micron ICs, growing amounts of on- die memory and scaling effects make embedded memories increasingly vulnerable to reliability and yield problems. As scaling progresses, soft and hard errors in the memory system will increase and single error events are more likely to cause large-scale multi- bit errors. However, conventional memory protection techniques can neither detect nor correct large-scale

  14. Multibit Error Tolerant Caches Using Two-Dimensional Error Coding

    Microsoft Academic Search

    Jangwoo Kim; Nikos Hardavellas; Ken Mai; Babak Falsafi; James C. Hoe

    2007-01-01

    In deep sub-micron ICs, growing amounts of on-die memory and scaling effects make embedded memories increasingly vulnerable to reliability and yield problems. As scaling progresses, soft and hard errors in the memory system will increase and single error events are more likely to cause large-scale multi- bit errors. However, conventional memory protection techniques can neither detect nor correct large-scale multi-bit

  15. Error analysis in laparoscopic surgery

    NASA Astrophysics Data System (ADS)

    Gantert, Walter A.; Tendick, Frank; Bhoyrul, Sunil; Tyrrell, Dana; Fujino, Yukio; Rangel, Shawn; Patti, Marco G.; Way, Lawrence W.

    1998-06-01

    Iatrogenic complications in laparoscopic surgery, as in any field, stem from human error. In recent years, cognitive psychologists have developed theories for understanding and analyzing human error, and the application of these principles has decreased error rates in the aviation and nuclear power industries. The purpose of this study was to apply error analysis to laparoscopic surgery and evaluate its potential for preventing complications. Our approach is based on James Reason's framework using a classification of errors according to three performance levels: at the skill- based performance level, slips are caused by attention failures, and lapses result form memory failures. Rule-based mistakes constitute the second level. Knowledge-based mistakes occur at the highest performance level and are caused by shortcomings in conscious processing. These errors committed by the performer 'at the sharp end' occur in typical situations which often times are brought about by already built-in latent system failures. We present a series of case studies in laparoscopic surgery in which errors are classified and the influence of intrinsic failures and extrinsic system flaws are evaluated. Most serious technical errors in lap surgery stem from a rule-based or knowledge- based mistake triggered by cognitive underspecification due to incomplete or illusory visual input information. Error analysis in laparoscopic surgery should be able to improve human performance, and it should detect and help eliminate system flaws. Complication rates in laparoscopic surgery due to technical errors can thus be considerably reduced.

  16. Allelism of PSO4 and PRP19 links pre-mRNA processing with recombination and error-prone DNA repair in Saccharomyces cerevisiae.

    PubMed Central

    Grey, M; Düsterhöft, A; Henriques, J A; Brendel, M

    1996-01-01

    The radiation-sensitive mutant pso4-1 of Saccharomyces cerevisiae shows a pleiotropic phenotype, including sensitivity to DNA cross-linking agents, nearly blocked sporulation and reduced mutability. We have cloned the putative yeast DNA repair gene PSO4 from a genomic library by complementation of the blocked UV-induced mutagenesis and of sporulation in diploids homozygous for pso4-1. Sequence analysis revealed that gene PSO4 consists of 1512 bp located upstream of UBI4 on chromosome XII and encodes a putative protein of 56.7 kDa. PSO4 is allelic to PRP19, a gene encoding a spliceosome-associated protein, but shares no significant homology with other yeast genes. Gene disruption with a destroyed reading frame of our PSO4 clone resulted in death of haploid cells, confirming the finding that PSO4/PRP19 is an essential gene. Thus, PSO4 is the third essential DNA repair gene found in the yeast S.cerevisiae. PMID:8918805

  17. Rapid PCR thermocycling using microscale thermal convection.

    PubMed

    Muddu, Radha; Hassan, Yassin A; Ugaz, Victor M

    2011-01-01

    Many molecular biology assays depend in some way on the polymerase chain reaction (PCR) to amplify an initially dilute target DNA sample to a detectable concentration level. But the design of conventional PCR thermocycling hardware, predominantly based on massive metal heating blocks whose temperature is regulated by thermoelectric heaters, severely limits the achievable reaction speed(1). Considerable electrical power is also required to repeatedly heat and cool the reagent mixture, limiting the ability to deploy these instruments in a portable format. Thermal convection has emerged as a promising alternative thermocycling approach that has the potential to overcome these limitations(2-9). Convective flows are an everyday occurrence in a diverse array of settings ranging from the Earth's atmosphere, oceans, and interior, to decorative and colorful lava lamps. Fluid motion is initiated in the same way in each case: a buoyancy driven instability arises when a confined volume of fluid is subjected to a spatial temperature gradient. These same phenomena offer an attractive way to perform PCR thermocycling. By applying a static temperature gradient across an appropriately designed reactor geometry, a continuous circulatory flow can be established that will repeatedly transport PCR reagents through temperature zones associated with the denaturing, annealing, and extension stages of the reaction (Figure 1). Thermocycling can therefore be actuated in a pseudo-isothermal manner by simply holding two opposing surfaces at fixed temperatures, completely eliminating the need to repeatedly heat and cool the instrument. One of the main challenges facing design of convective thermocyclers is the need to precisely control the spatial velocity and temperature distributions within the reactor to ensure that the reagents sequentially occupy the correct temperature zones for a sufficient period of time(10,11). Here we describe results of our efforts to probe the full 3-D velocity and temperature distributions in microscale convective thermocyclers(12). Unexpectedly, we have discovered a subset of complex flow trajectories that are highly favorable for PCR due to a synergistic combination of (1) continuous exchange among flow paths that provides an enhanced opportunity for reagents to sample the full range of optimal temperature profiles, and (2) increased time spent within the extension temperature zone the rate limiting step of PCR. Extremely rapid DNA amplification times (under 10 min) are achievable in reactors designed to generate these flows. PMID:21403639

  18. Arginine vasopressin regulated ASCT1 expression in astrocytes from stroke-prone spontaneously hypertensive rats and congenic SHRpch1_18 rats.

    PubMed

    Yamagata, K; Yamamoto, M; Kawakami, K; Ohara, H; Nabika, T

    2014-05-16

    In stroke-prone spontaneously hypertensive rats (SHRSP/Izm), ischemia induces swelling of astrocytes, a process that subsequently leads to neuronal death. Following ischemic insult, arginine vasopressin (AVP) can induce edema and l-serine released by astrocytes supports the survival of neuronal cells. The purpose of this study was to examine whether AVP contributed to the regulation of l-serine production following ischemic stroke. Here, we used cultured astrocytes from SHRSP/Izm rats and Wistar Kyoto rats (WKY/Izm) to examine whether AVP changed the production of l-serine and/or altered gene expression levels of the neural amino acid transporter (Slc1a4), 3-phosphoglycerate dehydrogenase (Phgdh) and serine racemase (SRR). Furthermore, using astrocytes from the congenic rat SHRpch1_18 strain having quantitative trait loci (QTL) of stroke, we examined expression of those genes under conditions of hypoxia and reoxygenation (H/R). The expression levels of ASCT1 protein, the genes described above and l-serine levels were determined by Western blotting (WB), RT-PCR, real-time quantitative RT-PCR and HPLC. AVP increased the production of l-serine and the expression of Slc1a4 in WKY/Izm and SHRSP/Izm astrocytes. The production of l-serine and the expression of Slc1a4 were lower in SHRSP/Izm than in WKY/Izm cells. This difference was not seen with Phgdh. In the SHRpch1_18 strain, the expression of Slc1a4 and Phgdh significantly decreased after H/R. AVP-mediated enhanced expression of ASCT1 was blocked by the addition of bumetanide. These results suggest that the AVP-mediated attenuated expression of ASCT1 in astrocytes is associated with reduced l-serine production in SHRSP/Izm astrocytes. We hypothesize that reduction of gene expression by AVP might be related to the induction of stroke in the SHRpch1_18 rat strain. PMID:24613720

  19. The Contribution of Prone Sleeping Position to the Racial Disparity in Sudden Infant Death Syndrome: The Chicago Infant Mortality Study

    Microsoft Academic Search

    Fern R. Hauck; Cathryn Merrick Moore; Stanislaw M. Herman; Mark Donovan; Mitra Kalelkar; Katherine Kaufer Christoffel; Howard J. Hoffman; Diane Rowley

    2002-01-01

    Background. Rates of sudden infant death syndrome (SIDS) are over twice as high among African Americans compared with Caucasians. Little is known, however, about the relationship between prone sleeping, other sleep environment factors, and the risk of SIDS in the United States and how differences in risk factors may account for disparities in mortality. Objective. To assess the contribution of

  20. Effects of Early Motor Intervention in the Prone Position of Full-Term Infants through the First Year of Life.

    ERIC Educational Resources Information Center

    Douret, L.

    1993-01-01

    Full-term infants who had slept in the prone position since birth were followed to detect early postural abnormalities and differentiate potential peripheral abnormality from abnormalities of a central origin. Results showed that disappearance of initial signs of abnormality appeared to be muscular, and symptoms disappeared faster when a motor…

  1. Diesel Exhaust-Induced Cardiac Dysfunction Is Mediated by Sympathetic Dominance in Heart Failure-Prone Rats

    EPA Science Inventory

    Short-term exposure to vehicular emissions is associated with adverse cardiac events. Diesel exhaust (DE) may provoke cardiac events through defective co-ordination of the two main autonomic nervous system (ANS) branches. We exposed heart failure-prone rats once to DE (500 ¿g/m3 ...

  2. Fluoxetine Treatment in Poststroke Depression, Emotional Incontinence, and Anger Proneness A Double-Blind, Placebo-Controlled Study

    Microsoft Academic Search

    Smi Choi-Kwon; Sung W. Han; Sun U. Kwon; Dong-Wha Kang; Ji M. Choi; Jong S. Kim

    2010-01-01

    Background and Purpose—The efficacy and safety of the selective serotonin reuptake inhibitor fluoxetine have rarely been studied in the treatment of poststroke emotional disturbances. Methods—Stroke patients (152) who had poststroke depression (PSD), emotional incontinence (PSEI), or anger proneness (PSAP) were studied. PSD was evaluated by Beck Depression Inventory and Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, PSEI by

  3. Green water security for the food makers of tomorrow: windows of opportunity in drought-prone savannahs

    Microsoft Academic Search

    Johan Rockström

    The largest remaining biophysical water challenge is whether there is enough fresh water to sustain global food production and service natural ecosytems. Focussing on the drought-prone savannahs and small-scale farming, this paper argues that the crucial resource is vapour flow, not \\

  4. Borderline Personality Features and Implicit Shame-Prone Self-Concept in Middle Childhood and Early Adolescence

    ERIC Educational Resources Information Center

    Hawes, David J.; Helyer, Rebekah; Herlianto, Eugene C.; Willing, Jonah

    2013-01-01

    This study tested if children and adolescents with high levels of borderline personality features (BPF) exhibit the same shame-prone self-concept previously found to characterize adults with borderline personality disorder (Rusch et al., 2007). Self-concept was indexed using the Implicit Association Test, in a community sample of…

  5. When Passive Feels Active - Delusion-Proneness Alters Self-Recognition in the Moving Rubber Hand Illusion.

    PubMed

    Louzolo, Anaïs; Kalckert, Andreas; Petrovic, Predrag

    2015-01-01

    Psychotic patients have problems with bodily self-recognition such as the experience of self-produced actions (sense of agency) and the perception of the body as their own (sense of ownership). While it has been shown that such impairments in psychotic patients can be explained by hypersalient processing of external sensory input it has also been suggested that they lack normal efference copy in voluntary action. However, it is not known how problems with motor predictions like efference copy contribute to impaired sense of agency and ownership in psychosis or psychosis-related states. We used a rubber hand illusion based on finger movements and measured sense of agency and ownership to compute a bodily self-recognition score in delusion-proneness (indexed by Peters' Delusion Inventory - PDI). A group of healthy subjects (n=71) experienced active movements (involving motor predictions) or passive movements (lacking motor predictions). We observed a highly significant correlation between delusion-proneness and self-recognition in the passive conditions, while no such effect was observed in the active conditions. This was seen for both ownership and agency scores. The result suggests that delusion-proneness is associated with hypersalient external input in passive conditions, resulting in an abnormal experience of the illusion. We hypothesize that this effect is not present in the active condition because deficient motor predictions counteract hypersalience in psychosis proneness. PMID:26090797

  6. Delineation of flood-prone areas of the Rio Minho Watershed, Jamaica using topographic index and watershed physical parameters

    Microsoft Academic Search

    N. Tunkuda; A. M. Melesse

    2008-01-01

    The Rio Minho watershed is an active watershed system in the Clarendon parish of Jamaica which is characterized by a dynamic topography that extends from coastal alluvial plains along the Caribbean Sea, to a rugged mountainous region that borders the north. The watershed has historically been prone to flash flooding and flood hazards. In recent years, certain areas of the

  7. Black and Green Tea Polyphenols Attenuate Blood Pressure Increases in Stroke-Prone Spontaneously Hypertensive Rats1

    Microsoft Academic Search

    Hiroko Negishi; Jin-Wen Xu; Katsumi Ikeda; Marina Njelekela; Yasuo Nara; Yukio Yamori

    Oxidative stress was reported to be involved not only in cardiovascular diseases, but also in hypertension. Epidemiologic studies indicated that tea consumption slightly reduces blood pressure. We con- ducted two studies to determine whether black and green tea can lower blood pressure (BP) in stroke-prone spontaneously hypertensive rats (SHRSP). Male SHRSP (n 15) were allowed to recover for 2 wk

  8. AN URBAN ECONOMIC MODEL OF ILEGAL SETTLEMENTS IN FLOOD PRONE AREAS IN PALANGKARAYA CITY, INDONESIA -A PARTIAL EQUILIBRIUM ANALYSIS

    Microsoft Academic Search

    Indrawan PERMANA; Yuzuru MIYATA

    2012-01-01

    This paper presents a theoretical study regarding occupations of flood prone areas by illegal settlements in urban area of Palangkaraya city, Central Kalimantan province, Indonesia. Such unusual urban land use pattern has been observed in many urbanized cities particularly in developing countries. However, scientific explanations about the urban phenomena were not formulated yet as well as literatures on that topic

  9. Gender Differences in Depression and Anxiety among Victims of Intimate Partner Violence: The Moderating Effect of Shame Proneness

    ERIC Educational Resources Information Center

    Shorey, Ryan C.; Sherman, Amanda E.; Kivisto, Aaron J.; Elkins, Sara R.; Rhatigan, Deborah L.; Moore, Todd M.

    2011-01-01

    The current study examined the moderating role of shame proneness on the association between physical, psychological, and sexual intimate partner violence victimization and depressive and anxious symptoms among male and female college students (N = 967). Students completed self-report measures of dating violence, depression, anxiety, and shame…

  10. Possible Role of Nutritional Factors in the Incidence of Cerebral Lesions in Stroke-Prone Spontaneously Hypertensive Rats

    Microsoft Academic Search

    YUKIO YAMORI; RYOICHI HORIE; HISAO TANASE; KEIGO FUJIWARA; YASUO NARA; WALTER LOVENBERG

    SUMMARY The incidence of cerebral lesions in stroke-prone spontaneously hypertensive rats appears to depend on the severity of the hypertension and nutritional factors. Comparison of Ameri- can and Japanese commercial rat diets revealed a much higher incidence of stroke in rats receiving the Japanese diet (88% vs 30% by 9 months of age). Analyses of the diets indicate that perhaps

  11. Positioning a proned patient with cauda equina syndrome who presents at 15 weeks gestation: a case report

    PubMed Central

    Speirs, Elizabeth; Wiles, Matthew; Bacon, Andrew; Radley, Stephen

    2014-01-01

    Cauda equina syndrome is a neurosurgical emergency that requires prompt intervention to prevent irreversible spinal cord paralysis. This article describes how we managed a case of an obese pregnant patient who was placed in the prone position for surgery. We discuss the evidence behind the management options and choice of operating tables available. PMID:25110580

  12. When Passive Feels Active - Delusion-Proneness Alters Self-Recognition in the Moving Rubber Hand Illusion

    PubMed Central

    Louzolo, Anaïs; Kalckert, Andreas; Petrovic, Predrag

    2015-01-01

    Psychotic patients have problems with bodily self-recognition such as the experience of self-produced actions (sense of agency) and the perception of the body as their own (sense of ownership). While it has been shown that such impairments in psychotic patients can be explained by hypersalient processing of external sensory input it has also been suggested that they lack normal efference copy in voluntary action. However, it is not known how problems with motor predictions like efference copy contribute to impaired sense of agency and ownership in psychosis or psychosis-related states. We used a rubber hand illusion based on finger movements and measured sense of agency and ownership to compute a bodily self-recognition score in delusion-proneness (indexed by Peters’ Delusion Inventory - PDI). A group of healthy subjects (n=71) experienced active movements (involving motor predictions) or passive movements (lacking motor predictions). We observed a highly significant correlation between delusion-proneness and self-recognition in the passive conditions, while no such effect was observed in the active conditions. This was seen for both ownership and agency scores. The result suggests that delusion-proneness is associated with hypersalient external input in passive conditions, resulting in an abnormal experience of the illusion. We hypothesize that this effect is not present in the active condition because deficient motor predictions counteract hypersalience in psychosis proneness. PMID:26090797

  13. Breast tumor PDXs are genetically plastic and correspond to a subset of aggressive cancers prone to relapse.

    E-print Network

    Paris-Sud XI, Université de

    1 Breast tumor PDXs are genetically plastic and correspond to a subset of aggressive cancers prone for preclinical testing, as they reflect the patient's tumor biology more accurately than cancer cell lines. We cancers (70%), our collection comprised five ER+ cases (25%). Remarkably, the tumors that produced PDXs

  14. A simulation test of the effectiveness of several methods for error-checking non-invasive genetic data

    USGS Publications Warehouse

    Roon, D.A.; Waits, L.P.; Kendall, K.C.

    2005-01-01

    Non-invasive genetic sampling (NGS) is becoming a popular tool for population estimation. However, multiple NGS studies have demonstrated that polymerase chain reaction (PCR) genotyping errors can bias demographic estimates. These errors can be detected by comprehensive data filters such as the multiple-tubes approach, but this approach is expensive and time consuming as it requires three to eight PCR replicates per locus. Thus, researchers have attempted to correct PCR errors in NGS datasets using non-comprehensive error checking methods, but these approaches have not been evaluated for reliability. We simulated NGS studies with and without PCR error and 'filtered' datasets using non-comprehensive approaches derived from published studies and calculated mark-recapture estimates using CAPTURE. In the absence of data-filtering, simulated error resulted in serious inflations in CAPTURE estimates; some estimates exceeded N by ??? 200%. When data filters were used, CAPTURE estimate reliability varied with per-locus error (E??). At E?? = 0.01, CAPTURE estimates from filtered data displayed < 5% deviance from error-free estimates. When E?? was 0.05 or 0.09, some CAPTURE estimates from filtered data displayed biases in excess of 10%. Biases were positive at high sampling intensities; negative biases were observed at low sampling intensities. We caution researchers against using non-comprehensive data filters in NGS studies, unless they can achieve baseline per-locus error rates below 0.05 and, ideally, near 0.01. However, we suggest that data filters can be combined with careful technique and thoughtful NGS study design to yield accurate demographic information. ?? 2005 The Zoological Society of London.

  15. SINGLE-TUBE, HIGHLY PARALLEL MUTATION ENRICHMENT IN CANCER GENE PANELS USING TEMPERATURE-TOLERANT-COLD-PCR

    PubMed Central

    Castellanos-Rizaldos, E.; Richardson, K.; Lin, R.; Wu, G.; Makrigiorgos, G. M.

    2014-01-01

    BACKGROUND Multiplexed detection of low-level mutations presents a technical challenge for many technologies, including cancer gene panels used for targeted-re-sequencing. Analysis of mutations below ~2–5% abundance in tumors with heterogeneity, samples with stromal contamination, or biofluids, is problematic due to increased ‘noise’ from sequencing errors. Technologies that reduce noise via deep-sequencing unavoidably reduce throughput and increase cost. Here we provide proof-of-principle that COLD-PCR technology enables multiplex low-level mutation detection in cancer gene panels while retaining throughput. METHODS We have developed a multiplex temperature-tolerant-COLD-PCR (fast-TT-COLD-PCR) approach that uses cancer gene panels developed for massively parallel sequencing. Following a multiplex pre-amplification from genomic DNA we attach tails to all amplicons and perform fast-TT-COLD-PCR. This approach gradually increases denaturation temperatures in a step-wise fashion, such that all possible denaturation temperatures are encompassed. By introducing modified nucleotides, fast-COLD-PCR is adapted to enrich for Tm-increasing as well as Tm-decreasing mutations over all amplicons, in a single tube. RESULTS Using custom-made and commercial gene panels containing 8, 50, 190 or 16,000 amplicons we demonstrate that fast-TT-COLD-PCR enriches mutations on all examined targets simultaneously. Incorporation of dITP/dDTP in place of dGTP/dATP enables enrichment of Tm-increasing mutations. Serial dilution experiments demonstrate a limit-of-detection of ~ 0.01–0.1% mutation abundance using Ion-Torrent and 0.1–0.3% using Sanger sequencing. CONCLUSIONS Fast-TT-COLD-PCR improves the limit of detection of cancer gene panels by enabling mutation enrichment in multiplex, single tube reactions. This novel adaptation of COLD-PCR converts subclonal mutations to clonal, thereby facilitating detection and subsequent mutation sequencing. PMID:25297854

  16. Statistical errors in Monte Carlo estimates of systematic errors

    NASA Astrophysics Data System (ADS)

    Roe, Byron P.

    2007-01-01

    For estimating the effects of a number of systematic errors on a data sample, one can generate Monte Carlo (MC) runs with systematic parameters varied and examine the change in the desired observed result. Two methods are often used. In the unisim method, the systematic parameters are varied one at a time by one standard deviation, each parameter corresponding to a MC run. In the multisim method (see ), each MC run has all of the parameters varied; the amount of variation is chosen from the expected distribution of each systematic parameter, usually assumed to be a normal distribution. The variance of the overall systematic error determination is derived for each of the two methods and comparisons are made between them. If one focuses not on the error in the prediction of an individual systematic error, but on the overall error due to all systematic errors in the error matrix element in data bin m, the number of events needed is strongly reduced because of the averaging effect over all of the errors. For simple models presented here the multisim model was far better if the statistical error in the MC samples was larger than an individual systematic error, while for the reverse case, the unisim model was better. Exact formulas and formulas for the simple toy models are presented so that realistic calculations can be made. The calculations in the present note are valid if the errors are in a linear region. If that region extends sufficiently far, one can have the unisims or multisims correspond to k standard deviations instead of one. This reduces the number of events required by a factor of k2. The specific terms unisim and multisim were coined by Peter Meyers and Steve Brice, respectively, for the MiniBooNE experiment. However, the concepts have been developed over time and have been in general use for some time.

  17. Targeted chromosomal gene knockout using PCR fragments.

    PubMed

    Murphy, Kenan C

    2011-01-01

    The development of recombineering technology has converged to a point that virtually any type of genetic modification can be made in the Escherichia coli chromosome. The most straightforward -modification is a chromosomal gene knockout, which is done by electroporation of a PCR fragment that contains a selectable drug marker flanked by 50 bp of target DNA. The phage ? Red recombination system expressed in vivo from a plasmid promotes deletion of the gene of interest at high efficiency. The combination of this technology with site-specific recombination systems of Cre and Flp has enabled genetic engineers to construct a variety of marked and precise gene knockouts in a variety of microbial chromosomes. The basic protocols for designing PCR substrates for recombineering, generating -recombineering-proficient electrocompetent strains of E. coli, and for selection and verification of recombinant clones are described. PMID:21815084

  18. Assessment of Prone Positioning of Restrained, Seated Crewmembers in a Post Landing Stable 2 Orion Configuration

    NASA Technical Reports Server (NTRS)

    Barr, Yael; Fogarty, Jennifer

    2010-01-01

    During the Orion landing and recovery subsystem design review, June 2009, it was noted that the human system and various vehicle systems, the environmental control and life support (ECLSS) and guidance, navigation and control (GN&C) systems for example, are negatively affected by Orion assuming a stable 2 (upside down; Figure A) configuration post landing. The stable 2 configuration is predicted to occur about 50% of the time based on Apollo landing data and modeling of the current capsule. The stable 2 configuration will be countered by an active up-righting system (crew module up-righting system; CMUS). Post landing balloons will deploy and inflate causing the vehicle to assume or maintain the stable 1 (up-right; Figure B) configuration. During the design review it was proposed that the up-righting system could be capable of righting the vehicle within 60 seconds. However, this time limit posed a series of constraints on the design which made it less robust than desired. The landing and recovery subsystem team requested an analysis of Orion vehicle systems as well as the human system with regard to the effect of stable 2 in order to determine if an up-righting response time greater than 60 seconds could be tolerated. The following report focuses on the assessment of the human system in the posture assumed when Orion is in the stable 2 configuration. Stable 2 will place suited, seated, and restrained crewmembers in a prone (facedown), head-up position for a period of time dependent on the functionality of the up-righting systems, ability of the crew to release themselves from the seat and restraints, and/or time to arrival of rescue forces. Given that the Orion seat and restraint system design is not complete and therefore, not available for evaluation, Space Medicine assessed how long a healthy but deconditioned crewmember could stay in this prone, restrained position and the physiological consequences of this posture by researching terrestrial analogs and considered the known physiological alterations and deconditioning experienced by long duration crewmembers.

  19. Are transported soil aggregates prone to flocculation and/or disaggregation during a flood event?

    NASA Astrophysics Data System (ADS)

    Grangeon, Thomas; Droppo, Ian; Legout, Cédric; Esteves, Michel

    2013-04-01

    Particles eroded from hillslopes and exported to rivers are recognized to be composite particles of high internal complexity. Their structure and composition are known to influence their transport behaviour within the water column relative to discrete particles. However, to-date, hillslope erosion studies consider aggregates to be stable once they are detached from the soil matrix. Alternatively lowland rivers and estuaries studies often suggest that particle structure and dynamics are controlled by flocculation within the water column. These conceptualisations led to different modelling strategies. In order to improve the understanding of particles dynamics along the continuum from hillslopes to lowland rivers, soil particle behaviour was tested under controlled laboratory conditions. Seven flume erosion and deposition experiments, designed to simulate a natural erosive event, and five shear cell experiments were performed using three contrasting materials: two of them were ill-developed and as such cannot be considered as soils, whilst the third one was a calcareous brown soil. Particle size distributions were measured using a CILAS 930 laser sizer which allowed for the real-time assessment of aggregate breakdown dynamics. When applied to suspended particles sampled from the flume, it was found that soil aggregates were prone to flocculation. The combined used of an optical backscatter sensor, manual sampling and particle size measurement during the flume experiments also revealed that soil particles were prone to disaggregation. Flocculation and disaggregation were not previously demonstrated to be important for soil aggregates, and may have large consequences on suspended solids modelling. Moreover, large variations in particle size were found between soil types. Indeed, at the maximum applied bed shear stress, the median diameter was found to be three times higher for the well-developed soil than for the two others. Differences were smaller in the falling limb, suggesting that soil aggregates underwent structural changes during transport. However, characterization of particles strength parameters showed that these changes did not fully turn soil aggregates into flocs as defined in estuaries for instance, but rather into hybrid soil aggregates-flocs particles. While particle characteristics changed once introduced within the water column, there is still an underlying need to clearly define the way eroded soil aggregates may modify/integrate into riverine flocs during their transport.

  20. Reorganization of the flood-prone atmospheric patterns at the onset of the 20th century?

    NASA Astrophysics Data System (ADS)

    Wilhelm, Bruno; Vogel, Hendrik; Anselmetti, Flavio

    2015-04-01

    Frequency and intensity of heavy rainfalls, triggering floods and causing human and large economic losses, are expected to increase in the context of the global warming, due to the larger water carrying capacity of warmer air masses. However, the relationship between such events and climatic changes remains still poorly understood. In particular, the stability of the flood-prone atmospheric circulations under future climate changes is a key question for projections of extreme precipitation. This study aims at exploring this issue using flood reconstructions from the NW Mediterranean domain. We compiled existing historical records from the Southern Massif Central and lake-sediment records from the Eastern Pyrenees and the Southern French Alps. We completed this West-East transect by studying new lake sequences in the SE French Alps and the Western Italian Alps. For both of the new lake sediment sequences (Lake Foréant, Queyras massif, France and Lago Inferiore di Laurès, Aosta valley, Italy), several short cores were retrieved to understand the sedimentary processes. In the laboratory, high-resolution pictures, bulk density, geochemistry and grain size were measured. Dating was undertaken by short-lived radionuclides (EAWAG, Zürich) and radiocarbon (University of Bern) measurements. Lago Inferiore sequence covers the last 250 years and Lake Foréant sequence the last millennium. 232 turbidites were identified; 11 of which seem to be related to mass movements, whereas the other 221 were triggered by flood events. The reconstructed flood regimes were then compared to local flood activity based on historical data. The good agreement between the datasets supports the quality and sensitivity of flood reconstructions. In the NW Mediterranean domain, floods and related heavy rainfalls are mostly triggered by autumn humid air masses coming from the Mediterranean Sea. In detail, distinct atmospheric pathways transport these air masses and trigger floods in the different studied regions. Comparing all the flood reconstructions over the last 250 years aims at tracking these atmospheric pathways and their possible changes over time. Strong similarities in flood frequency are observed from 1750 to 1900 for the western part (Cévennes, Southern French Alps), while no convincing correlation appears between the other records. Around 1900, a drastic change appears with strong similarities between records of the eastern part (Southern Alps, SE French Alps and NW Italian Alps). In particular, the flood frequency largely increased in the Cévennes during the first part of the 20th century, while this period is one of the most 'quiet' in all other records. Hence, these results suggest a reorganization of the flood-prone atmospheric patterns at the onset of the 20th century.

  1. Microfluidic digital PCR enables rapid prenatal diagnosis of fetal aneuploidy

    E-print Network

    Quake, Stephen R.

    : Digital PCR accurately identified all cases of fetal trisomy (3 cases of trisomy 21, 3 cases of trisomy 18 and sixty PCR reactions were performed for each of the target chromosomes (X, Y, 13, 18, and 21

  2. Registration of central paths and colonic polyps between supine and prone scans in computed tomography colonography: Pilot study

    SciTech Connect

    Li Ping; Napel, Sandy; Acar, Burak; Paik, David S.; Jeffrey, R. Brooke Jr.; Beaulieu, Christopher F. [Department of Statistics, Stanford University, Stanford, California 94305 (United States); Department of Radiology, Stanford University, Stanford, California 94305 (United States); Electrical and Electronics Engineering Department, Bogazici University 34342 Bebek, Istanbul (Turkey); Department of Radiology, Stanford University, Stanford, California 94305 (United States); Department of Radiology, Stanford University, Stanford, California 94305 (United States); Department of Radiology, Stanford University, Stanford, California 94305 (United States)

    2004-10-01

    Computed tomography colonography (CTC) is a minimally invasive method that allows the evaluation of the colon wall from CT sections of the abdomen/pelvis. The primary goal of CTC is to detect colonic polyps, precursors to colorectal cancer. Because imperfect cleansing and distension can cause portions of the colon wall to be collapsed, covered with water, and/or covered with retained stool, patients are scanned in both prone and supine positions. We believe that both reading efficiency and computer aided detection (CAD) of CTC images can be improved by accurate registration of data from the supine and prone positions. We developed a two-stage approach that first registers the colonic central paths using a heuristic and automated algorithm and then matches polyps or polyp candidates (CAD hits) by a statistical approach. We evaluated the registration algorithm on 24 patient cases. After path registration, the mean misalignment distance between prone and supine identical anatomic landmarks was reduced from 47.08 to 12.66 mm, a 73% improvement. The polyp registration algorithm was specifically evaluated using eight patient cases for which radiologists identified polyps separately for both supine and prone data sets, and then manually registered corresponding pairs. The algorithm correctly matched 78% of these pairs without user input. The algorithm was also applied to the 30 highest-scoring CAD hits in the prone and supine scans and showed a success rate of 50% in automatically registering corresponding polyp pairs. Finally, we computed the average number of CAD hits that need to be manually compared in order to find the correct matches among the top 30 CAD hits. With polyp registration, the average number of comparisons was 1.78 per polyp, as opposed to 4.28 comparisons without polyp registration.

  3. Prospective Assessment of Optimal Individual Position (Prone Versus Supine) for Breast Radiotherapy: Volumetric and Dosimetric Correlations in 100 Patients

    SciTech Connect

    Lymberis, Stella C.; Wyngaert, John Keith de; Parhar, Preeti; Chhabra, Arpit M.; Fenton-Kerimian, Maria; Chang Jengwha [Department of Radiation Oncology, New York University School of Medicine and Langone Medical Center, New York, New York (United States)] [Department of Radiation Oncology, New York University School of Medicine and Langone Medical Center, New York, New York (United States); Hochman, Tsivia [Division of Biostatistics, New York University School of Medicine and Langone Medical Center, New York, New York (United States) [Division of Biostatistics, New York University School of Medicine and Langone Medical Center, New York, New York (United States); Department of Environmental Medicine, New York University School of Medicine and Langone Medical Center, New York, New York (United States); Guth, Amber; Roses, Daniel [Department of Surgery, New York University School of Medicine and Langone Medical Center, New York, New York (United States)] [Department of Surgery, New York University School of Medicine and Langone Medical Center, New York, New York (United States); Goldberg, Judith D. [Division of Biostatistics, New York University School of Medicine and Langone Medical Center, New York, New York (United States) [Division of Biostatistics, New York University School of Medicine and Langone Medical Center, New York, New York (United States); Department of Environmental Medicine, New York University School of Medicine and Langone Medical Center, New York, New York (United States); Formenti, Silvia C., E-mail: silvia.formenti@nyumc.org [Department of Radiation Oncology, New York University School of Medicine and Langone Medical Center, New York, New York (United States)

    2012-11-15

    Purpose: Damage to heart and lung from breast radiotherapy is associated with increased cardiovascular mortality and lung cancer development. We conducted a prospective study to evaluate which position is best to spare lung and heart from radiotherapy exposure. Methods and Materials: One hundred consecutive Stage 0-IIA breast cancer patients consented to participate in a research trial that required two computed tomography simulation scans for planning both supine and prone positions. The optimal position was defined as that which best covered the contoured breast and tumor bed while it minimized critical organ irradiation, as quantified by the in-field heart and lung volume. The trial was designed to plan the first 100 patients in each position to study correlations between in-field volumes of organs at risk and dose. Results: Fifty-three left and 47 right breast cancer patients were consecutively accrued to the trial. In all patients, the prone position was optimal for sparing lung volume compared to the supine setup (mean lung volume reduction was 93.5 cc for right and 103.6 cc for left breast cancer patients). In 46/53 (87%) left breast cancer patients best treated prone, in-field heart volume was reduced by a mean of 12 cc and by 1.8 cc for the other 7/53 (13%) patients best treated supine. As predicted, supine-prone differences in in-field volume and mean dose of heart and lung were highly correlated (Spearman's correlation coefficient for left breast cancer patients was 0.90 for heart and 0.94 for lung and 0.92 for right breast cancer patients for lung). Conclusions: Prone setup reduced the amount of irradiated lung in all patients and reduced the amount of heart volume irradiated in 87% of left breast cancer patients. In-field organ volume is a valid surrogate for predicting dose; the trial continued to the planned target of 400.

  4. Dopaminergic basis of the psychosis-prone personality investigated with functional magnetic resonance imaging of procedural learning

    PubMed Central

    Ettinger, Ulrich; Corr, Philip J.; Mofidi, Ardeshier; Williams, Steven C. R.; Kumari, Veena

    2013-01-01

    Previous evidence shows a reliable association between psychosis-prone (especially schizotypal) personality traits and performance on dopamine (DA)-sensitive tasks (e.g., prepulse inhibition and antisaccade). Here, we used blood oxygen level-dependent (BOLD) fMRI and an established procedural learning (PL) task to examine the dopaminergic basis of two aspects of psychosis-proneness (specific schizotypy and general psychoticism). Thirty healthy participants (final N = 26) underwent fMRI during a blocked, periodic sequence-learning task which, in previous studies, has been shown to reveal impaired performance in schizophrenia patients given drugs blocking the DA D2 receptor subtype (DRD2), and to correspond with manipulation of DA activity and elicit fronto-striatal-cerebellar activity in healthy people. Psychosis-proneness was indexed by the Psychoticism (P) scale of the Eysenck Personality Questionnaire-Revised (EPQ-R; 1991) and the Schizotypal Personality Scale (STA; 1984). EPQ-R Extraversion and Neuroticism scores were also examined to establish discriminant validity. We found a positive correlation between the two psychosis-proneness measures (r = 0.43), and a robust and unique positive association between EPQ-R P and BOLD signal in the putamen, caudate, thalamus, insula, and frontal regions. STA schizotypy score correlated positively with activity in the right middle temporal gyrus. As DA is a key transmitter in the basal ganglia, and the thalamus contains the highest levels of DRD2 receptors of all extrastriatal regions, our results support a dopaminergic basis of psychosis-proneness as measured by the EPQ-R Psychoticism. PMID:23596404

  5. TqPCR: A Touchdown qPCR Assay with Significantly Improved Detection Sensitivity and Amplification Efficiency of SYBR Green qPCR

    PubMed Central

    Zhang, Qian; Wang, Jing; Deng, Fang; Yan, Zhengjian; Xia, Yinglin; Wang, Zhongliang; Ye, Jixing; Deng, Youlin; Zhang, Zhonglin; Qiao, Min; Li, Ruifang; Denduluri, Sahitya K.; Wei, Qiang; Zhao, Lianggong; Lu, Shun; Wang, Xin; Tang, Shengli; Liu, Hao; Luu, Hue H.; Haydon, Rex C.; He, Tong-Chuan; Jiang, Li

    2015-01-01

    The advent of fluorescence-based quantitative real-time PCR (qPCR) has revolutionized the quantification of gene expression analysis in many fields, including life sciences, agriculture, forensic science, molecular diagnostics, and medicine. While SYBR Green-based qPCR is the most commonly-used platform due to its inexpensive nature and robust chemistry, quantifying the expression of genes with low abundance or RNA samples extracted from highly restricted or limited sources can be challenging because the detection sensitivity of SYBR Green-based qPCR is limited. Here, we develop a novel and effective touchdown qPCR (TqPCR) protocol by incorporating a 4-cycle touchdown stage prior to the quantification amplification stage. Using the same cDNA templates, we find that TqPCR can reduce the average Cq values for Gapdh, Rps13, and Hprt1 reference genes by 4.45, 5.47, and 4.94 cycles, respectively, when compared with conventional qPCR; the overall average Cq value reduction for the three reference genes together is 4.95. We further find that TqPCR can improve PCR amplification efficiency and thus increase detection sensitivity. When the quantification of Wnt3A-induced target gene expression in mesenchymal stem cells is analyzed, we find that, while both conventional qPCR and TqPCR can detect the up-regulation of the relatively abundant target Axin2, only TqPCR can detect the up-regulation of the lowly-expressed targets Oct4 and Gbx2. Finally, we demonstrate that the MRQ2 and MRQ3 primer pairs derived from mouse reference gene Tbp can be used to validate the RNA/cDNA integrity of qPCR samples. Taken together, our results strongly suggest that TqPCR may increase detection sensitivity and PCR amplification efficiency. Overall, TqPCR should be advantageous over conventional qPCR in expression quantification, especially when the transcripts of interest are lowly expressed, and/or the availability of total RNA is highly restricted or limited. PMID:26172450

  6. PCR microfluidic devices for DNA amplification

    Microsoft Academic Search

    Chunsun Zhang; Jinliang Xu; Wenli Ma; Wenling Zheng

    2006-01-01

    The miniaturization of biological and chemical analytical devices by micro-electro-mechanical-systems (MEMS) technology has posed a vital influence on such fields as medical diagnostics, microbial detection and other bio-analysis. Among many miniaturized analytical devices, the polymerase chain reaction (PCR) microchip\\/microdevices are studied extensively, and thus great progress has been made on aspects of on-chip micromachining (fabrication, bonding and sealing), choice of

  7. Salmonella real-time PCR-Nachweis

    Microsoft Academic Search

    B. Malorny; A. Anderson; I. Huber

    2007-01-01

    :  Salmonella belongs to the most important bacterial pathogens worldwide causing disease in humans and animals mainly by the oral uptake\\u000a of contaminated food. Consequently, detection methodologies for Salmonella from food items are meaningful for routine laboratories. Here, we describe two different real-time PCR based methods for\\u000a the detection of Salmonella in food. The procedure begins with a cultural pre-enrichment in

  8. A theory of human error

    NASA Technical Reports Server (NTRS)

    Mcruer, D. T.; Clement, W. F.; Allen, R. W.

    1980-01-01

    Human error, a significant contributing factor in a very high proportion of civil transport, general aviation, and rotorcraft accidents is investigated. Correction of the sources of human error requires that one attempt to reconstruct underlying and contributing causes of error from the circumstantial causes cited in official investigative reports. A validated analytical theory of the input-output behavior of human operators involving manual control, communication, supervisory, and monitoring tasks which are relevant to aviation operations is presented. This theory of behavior, both appropriate and inappropriate, provides an insightful basis for investigating, classifying, and quantifying the needed cause-effect relationships governing propagation of human error.

  9. Retransmission error control with memory

    NASA Technical Reports Server (NTRS)

    Sindhu, P. S.

    1977-01-01

    In this paper, an error control technique that is a basic improvement over automatic-repeat-request ARQ is presented. Erroneously received blocks in an ARQ system are used for error control. The technique is termed ARQ-with-memory (MRQ). The general MRQ system is described, and simple upper and lower bounds are derived on the throughput achievable by MRQ. The performance of MRQ with respect to throughput, message delay and probability of error is compared to that of ARQ by simulating both systems using error data from a VHF satellite channel being operated in the ALOHA packet broadcasting mode.

  10. Compensating For GPS Ephemeris Error

    NASA Technical Reports Server (NTRS)

    Wu, Jiun-Tsong

    1992-01-01

    Method of computing position of user station receiving signals from Global Positioning System (GPS) of navigational satellites compensates for most of GPS ephemeris error. Present method enables user station to reduce error in its computed position substantially. User station must have access to two or more reference stations at precisely known positions several hundred kilometers apart and must be in neighborhood of reference stations. Based on fact that when GPS data used to compute baseline between reference station and user station, vector error in computed baseline is proportional ephemeris error and length of baseline.

  11. Practical histological microdissection for PCR analysis.

    PubMed

    Going, J J; Lamb, R F

    1996-05-01

    Recovery of cells by histological microdissection is increasingly used for analysis by polymerase chain reaction (PCR) or microchemical techniques. This paper describes techniques of histological microdissection. Sections of archival formalin-fixed, paraffin-embedded tissue up to 15 years old were mounted on plain glass slides. Sections 6-7 microns in thickness stained with toluidine blue were dissected under proteinase K buffer solution, using an electrolytically sharpened tungsten needle in a bacteriological loop-holder and a Leitz mechanical micromanipulator (model M). Detached cell groups were recovered in a silicone-coated pipette tip for PCR analysis after digestion in 25-50 microliters of proteinase K (500/ml) in TRIS-HCl buffer (pH 8.3). Consistent amplification and analysis of microsatellite loci were obtained from 2 microliters of crude lysate using 28-30 cycles of PCR incorporating a 32P 5'-end-labelled primer, electrophoresis under denaturing conditions on 6 per cent polyacrylamide gels, and autoradiographic detection. PMID:8691336

  12. Learning Label Preferences: Ranking Error versus Position Error

    E-print Network

    Hüllermeier, Eyke

    Learning Label Preferences: Ranking Error versus Position Error Eyke H¨ullermeier1 and Johannes F consider the problem of learning a ranking function, that is a mapping from instances to rankings over a finite number of la- bels. Our learning method, referred to as ranking by pairwise comparison (RPC

  13. Data& Error Analysis 1 DATA and ERROR ANALYSIS

    E-print Network

    Mukasyan, Alexander

    Data& Error Analysis 1 DATA and ERROR ANALYSIS Performing the experiment and collecting data learned, you might get a better grade.) Data analysis should NOT be delayed until all of the data. This will help one avoid the problem of spending an entire class collecting bad data because of a mistake

  14. Confirmatory factor analysis of the Child Feeding Questionnaire: a measure of parental attitudes, beliefs and practices about child feeding and obesity proneness

    Microsoft Academic Search

    L. L Birch; J. O Fisher; K Grimm-Thomas; C. N Markey; R Sawyer; S. L Johnson

    2001-01-01

    The Child Feeding Questionnaire (CFQ) is a self-report measure to assess parental beliefs, attitudes, and practices regarding child feeding, with a focus on obesity proneness in children. Confirmatory factor analysis tested a 7-factor model, which included four factors measuring parental beliefs related to child's obesity proneness, and three factors measuring parental control practices and attitudes regarding child feeding. Using a

  15. Quantifying Potential Error in Painting Breast Excision Specimens

    PubMed Central

    Godden, Amy

    2013-01-01

    Aim. When excision margins are close or involved following breast conserving surgery, many surgeons will attempt to reexcise the corresponding cavity margin. Margins are ascribed to breast specimens such that six faces are identifiable to the pathologist, a process that may be prone to error at several stages. Methods. An experimental model was designed according to stated criteria in order to answer the research question. Computer software was used to measure the surface areas of experimental surfaces to compare human-painted surfaces with experimental controls. Results. The variability of the hand-painted surfaces was considerable. Thirty percent of hand-painted surfaces were 20% larger or smaller than controls. The mean area of the last surface painted was significantly larger than controls (mean 58996 pixels versus 50096 pixels, CI 1477–16324, P = 0.014). By chance, each of the six volunteers chose to paint the deep surface last. Conclusion. This study is the first to attempt to quantify the extent of human error in marking imaginary boundaries on a breast excision model and suggests that humans do not make these judgements well, raising questions about the safety of targeting single margins at reexcision. PMID:23762569

  16. Error studies for SNS Linac. Part 1: Transverse errors

    SciTech Connect

    Crandall, K.R. [TechSource, Inc. (United States)

    1998-12-31

    The SNS linac consist of a radio-frequency quadrupole (RFQ), a drift-tube linac (DTL), a coupled-cavity drift-tube linac (CCDTL) and a coupled-cavity linac (CCL). The RFQ and DTL are operated at 402.5 MHz; the CCDTL and CCL are operated at 805 MHz. Between the RFQ and DTL is a medium-energy beam-transport system (MEBT). This error study is concerned with the DTL, CCDTL and CCL, and each will be analyzed separately. In fact, the CCL is divided into two sections, and each of these will be analyzed separately. The types of errors considered here are those that affect the transverse characteristics of the beam. The errors that cause the beam center to be displaced from the linac axis are quad displacements and quad tilts. The errors that cause mismatches are quad gradient errors and quad rotations (roll).

  17. Error begat error: design error analysis and prevention in social infrastructure projects.

    PubMed

    Love, Peter E D; Lopez, Robert; Edwards, David J; Goh, Yang M

    2012-09-01

    Design errors contribute significantly to cost and schedule growth in social infrastructure projects and to engineering failures, which can result in accidents and loss of life. Despite considerable research that has addressed their error causation in construction projects they still remain prevalent. This paper identifies the underlying conditions that contribute to design errors in social infrastructure projects (e.g. hospitals, education, law and order type buildings). A systemic model of error causation is propagated and subsequently used to develop a learning framework for design error prevention. The research suggests that a multitude of strategies should be adopted in congruence to prevent design errors from occurring and so ensure that safety and project performance are ameliorated. PMID:22664673

  18. Real-time PCR for universal phytoplasma detection and quantification.

    PubMed

    Christensen, Nynne Meyn; Nyskjold, Henriette; Nicolaisen, Mogens

    2013-01-01

    Currently, the most efficient detection and precise quantification of phytoplasmas is by real-time PCR. Compared to nested PCR, this method is less sensitive to contamination and is less work intensive. Therefore, a universal real-time PCR method will be valuable in screening programs and in other setups in which large numbers of samples are tested. PMID:22987421

  19. Malaria real-time PCR: correlation with clinical presentation.

    PubMed

    Dormond, L; Jaton, K; de Vallière, S; Genton, B; Greub, G

    2015-05-01

    Among 112 patients infected only by Plasmodium falciparum, WHO criteria of severity were compared with parasite load assessed by microscopy and quantitative PCR. Clinical severity was significantly correlated with higher parasite load as determined by microscopy (p < 0.001) and by PCR (p < 0.001). Hence, quantitative PCR might be useful to predict outcome. PMID:25905022

  20. Error concealment based on directional interpolation

    Microsoft Academic Search

    Jae-Won Suh; Yo-Sung Ho

    1997-01-01

    Compressed bitstreams are, in general, very sensitive to channel errors. For instance, a single bit error in a coded video bitstream may cause severe degradation on picture quality. When bit errors occur during transmission and cannot be corrected by an error correction scheme, error concealment is needed to conceal the corrupted image at the receiver. Error concealment algorithms attempt to

  1. Error coding simulations in C

    NASA Technical Reports Server (NTRS)

    Noble, Viveca K.

    1994-01-01

    When data is transmitted through a noisy channel, errors are produced within the data rendering it indecipherable. Through the use of error control coding techniques, the bit error rate can be reduced to any desired level without sacrificing the transmission data rate. The Astrionics Laboratory at Marshall Space Flight Center has decided to use a modular, end-to-end telemetry data simulator to simulate the transmission of data from flight to ground and various methods of error control. The simulator includes modules for random data generation, data compression, Consultative Committee for Space Data Systems (CCSDS) transfer frame formation, error correction/detection, error generation and error statistics. The simulator utilizes a concatenated coding scheme which includes CCSDS standard (255,223) Reed-Solomon (RS) code over GF(2(exp 8)) with interleave depth of 5 as the outermost code, (7, 1/2) convolutional code as an inner code and CCSDS recommended (n, n-16) cyclic redundancy check (CRC) code as the innermost code, where n is the number of information bits plus 16 parity bits. The received signal-to-noise for a desired bit error rate is greatly reduced through the use of forward error correction techniques. Even greater coding gain is provided through the use of a concatenated coding scheme. Interleaving/deinterleaving is necessary to randomize burst errors which may appear at the input of the RS decoder. The burst correction capability length is increased in proportion to the interleave depth. The modular nature of the simulator allows for inclusion or exclusion of modules as needed. This paper describes the development and operation of the simulator, the verification of a C-language Reed-Solomon code, and the possibility of using Comdisco SPW(tm) as a tool for determining optimal error control schemes.

  2. Group VII ethylene response factor diversification and regulation in four species from flood-prone environments.

    PubMed

    van Veen, Hans; Akman, Melis; Jamar, Diaan C L; Vreugdenhil, Dick; Kooiker, Maarten; van Tienderen, Peter; Voesenek, Laurentius A C J; Schranz, M Eric; Sasidharan, Rashmi

    2014-10-01

    Flooding events negatively affect plant performance and survival. Flooding gradients thereby determine the dynamics in vegetation composition and species abundance. In adaptation to flooding, the group VII Ethylene Response Factor genes (ERF-VIIs) play pivotal roles in rice and Arabidopsis through regulation of anaerobic gene expression and antithetical survival strategies. We investigated if ERF-VIIs have a similar role in mediating survival strategies in eudicot species from flood-prone environments. Here, we studied the evolutionary origin and regulation of ERF-VII transcript abundance and the physiological responses in species from two genera of divergent taxonomic lineages (Rumex and Rorippa). Synteny analysis revealed that angiosperm ERF-VIIs arose from two ancestral loci and that subsequent diversification and duplication led to the present ERF-VII variation. We propose that subtle variation in the regulation of ERF-VII transcript abundance could explain variation in tolerance among Rorippa species. In Rumex, the main difference in flood tolerance correlated with the genetic variation in ERF-VII genes. Large transcriptional differences were found by comparing the two genera: darkness and dark submergence-induced Rumex?ERF-VIIs, whereas HRE2 expression was increased in submerged Rorippa roots. We conclude that the involvement of ERF-VIIs in flooding tolerance developed in a phylogenetic-dependent manner, with subtle variations within taxonomic clades. PMID:24548060

  3. Individual differences in gambling proneness among rats and common marmosets: an automated choice task.

    PubMed

    Zoratto, Francesca; Sinclair, Emma; Manciocco, Arianna; Vitale, Augusto; Laviola, Giovanni; Adriani, Walter

    2014-01-01

    Interest is rising for animal modeling of pathological gambling. Using the operant probabilistic-delivery task (PDT), gambling proneness can be evaluated in laboratory animals. Drawing a comparison with rats, this study evaluated the common marmoset (Callithrix jacchus) using a PDT. By nose- or hand-poking, subjects learnt to prefer a large (LLL, 5-6 pellets) over a small (SS, 1-2 pellets) reward and, subsequently, the probability of occurrence of large-reward delivery was decreased progressively to very low levels (from 100% to 17% and 14%). As probability decreased, subjects showed a great versus little shift in preference from LLL to SS reinforcer. Hence, two distinct subpopulations ("non-gambler" versus "gambler") were differentiated within each species. A proof of the model validity comes from marmosets' reaction to reward-delivery omission. Namely, depending on individual temperament ("gambler" versus "non-gambler"), they showed either persistence (i.e., inadequate pokes towards LLL) or restlessness (i.e., inadequate pokes towards SS), respectively. In conclusion, the marmoset could be a suitable model for preclinical gambling studies. Implementation of the PDT to species other than rats may be relevant for determining its external validity/generalizability and improving its face/construct validity. PMID:24971360

  4. Social Participation and Disaster Risk Reduction Behaviors in Tsunami Prone Areas.

    PubMed

    Witvorapong, Nopphol; Muttarak, Raya; Pothisiri, Wiraporn

    2015-01-01

    This paper examines the relationships between social participation and disaster risk reduction actions. A survey of 557 households in tsunami prone areas in Phang Nga, Thailand was conducted following the 2012 Indian Ocean earthquakes. We use a multivariate probit model to jointly estimate the likelihood of undertaking three responses to earthquake and tsunami hazards (namely, (1) following disaster-related news closely, (2) preparing emergency kits and/or having a family emergency plan, and (3) having an intention to migrate) and community participation. We find that those who experienced losses from the 2004 tsunami are more likely to participate in community activities and respond to earthquake hazards. Compared to men, women are more likely to prepare emergency kits and/or have an emergency plan and have a greater intention to migrate. Living in a community with a higher proportion of women with tertiary education increases the probability of engaging in community activities and carrying out disaster risk reduction measures. Individuals who participate in village-based activities are 5.2% more likely to undertake all three risk reduction actions compared to those not engaging in community activities. This implies that encouraging participation in community activities can have positive externalities in disaster mitigation. PMID:26153891

  5. Automated landform classification in a rockfall prone area, Gunung Kelir, Java

    NASA Astrophysics Data System (ADS)

    Samodra, G.; Chen, G.; Sartohadi, J.; Hadmoko, D. S.; Kasama, K.

    2014-01-01

    This paper presents an automated landform classification in a rockfall prone area. Digital Terrain Models (DTM) and geomorphological inventory of rockfall deposits were the basis of landform classification analysis. DTM pre-processing was applied to improve the quality of DTM-derived products. Several data layers produced merely from DTM were slope, plan curvature, stream power index, shape complexity index; whereas layers produced from DTM and rockfall modeling were velocity and energy. Unsupervised fuzzy k-means was applied to classify the generic landforms. It was classified into seven classes: interfluve, convex creep slope, fall face, transportational middle slope, colluvial foot slope, lower slope and channel bed. The classification result was analyzed by draping it over DTMs and performing probability distribution of rockfall volume. Cumulative probability density was adopted to estimate the probability density of rockfall volume in four generic landforms i.e. fall face, transportational middle slope, colluvial foot slope and lower slope. It shows negative power laws, with exponents 0.58, 0.73, 0.68, 0.64; for fall face, transportational middle slope, colluvial foot slope and lower slope, respectively. Different values of the scaling exponents in each landform reflect that geomorphometry influences the volume statistics of rockfall. The methodology introduced in this paper has possibility for preliminary rockfall risk analysis. It reveals that the potential high risk is located in the transportational middle slope and colluvial footslope. This is useful information to account for the prioritization action of countermeasures policy and design.

  6. Prophylactic effects of ajoene on cerebral injury in stroke-prone spontaneously hypertensive rats (SHRSP).

    PubMed

    Yamada, Norihiko; Hattori, Atsuhiko; Nishikawa, Tomoaki; Fukuda, Hiroyuki; Fujino, Tsuchiyoshi

    2006-04-01

    As part of a basic study on the prevention of cerebral injury, ajoene (0.5 mg/d) and oil-macerated garlic extract (OMGE, containing 0.5 mg ajoene/d) were administrated to stroke-prone spontaneously hypertensive rats (SHRSP) among 8 weeks from 9 weeks of age. In the control group, 3 of 10 rats died (30%), whereas all SHRSP treated by ajoene or OMGE survived. Our results suggested that ajoene and OMGE-treatment reduced the mortality and cerebral injury in SHRSP. The levels of thiobarbituric acid reactive substance (TBARS) and the enzymatic activities of glutathione peroxidase (GSH-Px), superoxide dismutase (SOD) and catalase (CAT) in the serum of stroke stage of SHRSP were measured. The results obtained were as follows; the TBARS level of the ajoene and OMGE-treated groups were lower than those of control groups. On the other hand, the GSH-Px and SOD activities of the ajoene and OMGE-treated groups were higher. Our results suggested that ajoene and OMGE were capable of having prophylactic effects on cerebral injury in SHRSP. PMID:16595890

  7. Investigation on the use of geomorphic approaches for the delineation of flood prone areas

    NASA Astrophysics Data System (ADS)

    Manfreda, Salvatore; Nardi, Fernando; Samela, Caterina; Grimaldi, Salvatore; Taramasso, Angela Celeste; Roth, Giorgio; Sole, Aurelia

    2014-09-01

    Three different geomorphic approaches to the identification of flood prone areas are investigated by means of a comparative analysis of the input parameters, the performances and the range of applicability. The selected algorithms are: the method proposed by Manfreda et al. (2011) based on a modified version of the Topographic Index (TIm); the linear binary classifier proposed by Degiorgis et al. (2012), which uses different geomorphic features related to the location of the site under exam with respect to the nearest hazard source; the hydro-geomorphic method by Nardi et al. (2006) simulating inundation flow depths along the river valley with the associated extent of surrounding inundated areas. Comparison has been carried out on two sub-catchments of the Tiber River in Central Italy. The simulated flooded areas, obtained using the selected three methods, are evaluated using as a reference the Tiber River Basin Authority standard flood maps. The aim of the research is to deepen our understanding on the potential of geomorphic algorithms and to define new strategies for prompt hydraulic risk mapping and preliminary flood hazard graduation. This is of foremost importance when detailed hydrologic and hydraulic studies are not available, e.g., over large regions and for ungauged basins.

  8. Social Participation and Disaster Risk Reduction Behaviors in Tsunami Prone Areas

    PubMed Central

    Witvorapong, Nopphol; Muttarak, Raya; Pothisiri, Wiraporn

    2015-01-01

    This paper examines the relationships between social participation and disaster risk reduction actions. A survey of 557 households in tsunami prone areas in Phang Nga, Thailand was conducted following the 2012 Indian Ocean earthquakes. We use a multivariate probit model to jointly estimate the likelihood of undertaking three responses to earthquake and tsunami hazards (namely, (1) following disaster-related news closely, (2) preparing emergency kits and/or having a family emergency plan, and (3) having an intention to migrate) and community participation. We find that those who experienced losses from the 2004 tsunami are more likely to participate in community activities and respond to earthquake hazards. Compared to men, women are more likely to prepare emergency kits and/or have an emergency plan and have a greater intention to migrate. Living in a community with a higher proportion of women with tertiary education increases the probability of engaging in community activities and carrying out disaster risk reduction measures. Individuals who participate in village-based activities are 5.2% more likely to undertake all three risk reduction actions compared to those not engaging in community activities. This implies that encouraging participation in community activities can have positive externalities in disaster mitigation. PMID:26153891

  9. Unaltered caffeine-induced relaxation in the aorta of stroke-prone spontaneously hypertensive rats (SHRSP).

    PubMed

    Sekiguchi, Fumiko; Miyake, Yoshimasa; Kashimoto, Takafumi; Sunano, Satoru

    2002-04-01

    Caffeine-induced relaxation was studied in aortic segments from Wistar Kyoto rats (WKY) and stroke-prone spontaneously hypertensive rats (SHRSP). Although acetylcholine-induced endothelium-dependent relaxation was impaired in preparations from SHRSP, the relaxation induced by caffeine was identical in both groups. In addition, caffeine-induced relaxation was not affected by removal of the endothelium in either group. The relaxation induced by N6,2'-O-dibutyryladenosine 3':5'-cyclic monophosphate (db-cAMP), a membrane-permeable analog of adenosine 3':5'-cyclic monophosphate (cAMP), was identical in both groups. No significant difference was observed in the increase in cAMP content induced by caffeine in the aortic smooth muscle between the groups, although the basal content was significantly higher in preparations from SHRSP. These results suggest that the relaxation induced by caffeine in these preparations is brought about by its direct effect on smooth muscle and that the response of the smooth muscle to caffeine, including cAMP production, is not altered in preparations from SHRSP compared with those from WKY. PMID:12199529

  10. O-arm failure traps patient prone on a Jackson table.

    PubMed

    Pisklakov, Sergey; Houten, John K; Echt, Murray; Kosse, Angelika; Abramowicz, Apolonia E

    2015-08-01

    The O-arm Surgical Imaging System (Medtronic Sofamor Danek, Memphis, TN, USA) is an increasingly popular tool for spinal surgical procedures that allows for intraoperative acquisition of multi-dimensional spinal imaging that can be used either to confirm placement of spinal instrumentation or to guide spinal screw placement in conjunction with a navigation system. The machine is typically placed open from the side of the patient positioned prone on the Jackson spinal table (Mizuho OSI, Union City, CA, USA) and then closed to complete a ring around the patient to acquire images. A failure of the O-arm opening mechanism can lead to a patient becoming effectively trapped within the device with limited physician access to the patient's body, a situation that may be remedied by using a manual opening procedure. This report highlights a patient safety issue encountered when a mechanical failure of the O-arm occurred and one of the two tools required for its manual opening was missing. We describe the improvised method employed to successfully open the device. PMID:25937572

  11. Index Cohesive Force Analysis Reveals That the US Market Became Prone to Systemic Collapses Since 2002

    PubMed Central

    Kenett, Dror Y.; Shapira, Yoash; Madi, Asaf; Bransburg-Zabary, Sharron; Gur-Gershgoren, Gitit; Ben-Jacob, Eshel

    2011-01-01

    Background The 2007–2009 financial crisis, and its fallout, has strongly emphasized the need to define new ways and measures to study and assess the stock market dynamics. Methodology/Principal Findings The S&P500 dynamics during 4/1999–4/2010 is investigated in terms of the index cohesive force (ICF - the balance between the stock correlations and the partial correlations after subtraction of the index contribution), and the Eigenvalue entropy of the stock correlation matrices. We found a rapid market transition at the end of 2001 from a flexible state of low ICF into a stiff (nonflexible) state of high ICF that is prone to market systemic collapses. The stiff state is also marked by strong effect of the market index on the stock-stock correlations as well as bursts of high stock correlations reminiscence of epileptic brain activity. Conclusions/Significance The market dynamical states, stability and transition between economic states was studies using new quantitative measures. Doing so shed new light on the origin and nature of the current crisis. The new approach is likely to be applicable to other classes of complex systems from gene networks to the human brain. PMID:21556323

  12. Breast Shape Change Associated with Aging: A Study Using Prone Breast Magnetic Resonance Imaging

    PubMed Central

    Nakadate, Masashi

    2015-01-01

    Background: Objective assessments of the shapes of various parts of the body can be made using images acquired with multidetector row computed tomography or magnetic resonance imaging. These images can be useful for understanding the changes in body shape that accompany aging. Methods: Data from our previous bilateral prone breast magnetic resonance imaging studies between March and August 2013 were analyzed. Breast size and volume were measured using these images. All the patients included in the study were divided into a younger group (54 years or younger) and an older group (55 years or older). The values were compared between the 2 groups using paired t tests. Regarding variables that were shown to have a significant difference between the 2 groups, the relationships between age and the values of the variables were evaluated using the Pearson correlation coefficient. Results: A total of 90 breasts, 45 breasts in the younger group and 45 breasts in the older group, were used for analysis. There was a significant correlation between age and craniocaudal nipple deviation (R = ?0.38; P < 0.001) and between age and the measured breast volume (R = 0.26; P < 0.05). There was also a significant correlation between the measured breast volume and the craniocaudal nipple deviation (R = ?0.48; P < 0.001). Conclusions: A caudal deviation of the nipple and an increase in volume were age-related changes in breast shape. These 2 variables were also correlated.

  13. Geophysical modeling of collapse-prone zones at Rumble III seamount, southern Pacific Ocean, New Zealand

    NASA Astrophysics Data System (ADS)

    Tontini, F. Caratori; Ronde, C. E. J.; Kinsey, J. C.; Soule, A.; Yoerger, D.; Cocchi, L.

    2013-10-01

    Catastrophic collapses of submarine volcanoes have the potential to generate major tsunami, threatening many coastal populations. Recognizing the difficulties surrounding anticipations of these events, quantitative assessment of collapse-prone regions based on detailed morphological, geological, and geophysical mapping can still provide important information about the hazards associated with these collapses. Rumble III is one of the shallowest, and largest, submarine volcanoes found along the Kermadec arc, and is both volcanically and hydrothermally active. Previous surveys have delineated major collapse features at Rumble III; based on time-lapse bathymetry, dramatic changes in the volcano morphology have been shown to have occurred over the interval 2007-2009. Furthermore, this volcano is located just ˜300 km from the east coast of the North Island of New Zealand. Here, we present a geophysical model for Rumble III that provides the locations and sizes of potential weak regions of this volcano. Shipborne and near-seafloor geological and geophysical data collected by the AUV Sentry are used to determine the subsurface distribution of weak and unstable volcanic rocks. The resulting model provides evidence for potentially unstable areas located in the Southeastern flank of this volcano which should be included in future hazard predictions.

  14. Repeated treatment with quinolones potentiates the seizures induced by aminophylline in genetically epilepsy-prone rats.

    PubMed

    De Sarro, A; Trimarchi, G R; Ammendola, D; De Sarro, G

    1992-09-01

    1. The effects of a chronic treatment with several quinolone derivatives on on the aminophylline-induced convulsions in the genetically epilepsy-prone rat have been investigated. 2. Two series of experiments have been performed: in the first one animals received the quinolone twice a day for 5 days, then were given aminophylline (80-140 mg.kg-1, i.p.); in the second series of experiments the rats were treated once a day with the quinolone plus 120 mg.kg-1 of aminophylline for 5 days. The changes induced by both treatment protocols on electrocortical activity and on the occurrance of seizures have been evaluated. 3. Enoxacin reduced the dose of aminophylline necessary for the induction of seizures in a higher degree with respect to the other quinolone derivatives. The derivatives which showed minor proconvulsant properties were ofloxacin, ciprofloxacin and cinoxacin. The potentiation of seizures induced by quinolones appeared a dose-dependent phenomenon which was more evident when high doses of quinolones were used. 4. The chronic treatment carried out daily with quinolones and aminophylline suggests that additive neurotoxic effects of both classes of drugs may contribute to the increase of severity of seizure scores. 5. The possible role of GABA-benzodiazepine, excitatory amino acid, purinergic mechanisms as well as the role of pharmacokynetic factors are discussed. PMID:1426928

  15. Explaining Errors in Children's Questions

    ERIC Educational Resources Information Center

    Rowland, Caroline F.

    2007-01-01

    The ability to explain the occurrence of errors in children's speech is an essential component of successful theories of language acquisition. The present study tested some generativist and constructivist predictions about error on the questions produced by ten English-learning children between 2 and 5 years of age. The analyses demonstrated that,…

  16. Human error in recreational boating

    Microsoft Academic Search

    A. James McKnight; Wayne W. Becker; Anthony J. Pettit; A. Scott McKnight

    2007-01-01

    Each year over 600 people die and more than 4000 are reported injured in recreational boating accidents. As with most other accidents, human error is the major contributor. U.S. Coast Guard reports of 3358 accidents were analyzed to identify errors in each of the boat types by which statistics are compiled: auxiliary (motor) sailboats, cabin motorboats, canoes and kayaks, house

  17. Dual Processing and Diagnostic Errors

    ERIC Educational Resources Information Center

    Norman, Geoff

    2009-01-01

    In this paper, I review evidence from two theories in psychology relevant to diagnosis and diagnostic errors. "Dual Process" theories of thinking, frequently mentioned with respect to diagnostic error, propose that categorization decisions can be made with either a fast, unconscious, contextual process called System 1 or a slow, analytical,…

  18. Correcting errors in shotgun sequences

    Microsoft Academic Search

    Martti T. Tammi; Erik Arner; Ellen Kindlund; Bjorn Andersson

    2003-01-01

    Sequencing errors in combination with repeated regions cause major problems in shotgun sequen- cing, mainly due to the failure of assembly pro- grams to distinguish single base differences between repeat copies from erroneous base calls. In this paper, a new strategy designed to correct errors in shotgun sequence data using defined nucleotide positions, DNPs, is presented. The method distin- guishes

  19. Error Symmetrization in Quantum Computers

    Microsoft Academic Search

    Asher Peres

    1999-01-01

    Errors in quantum computers are of two kinds:sudden perturbations to isolated qubits, and slow,random drifts of all the qubits. Isolated errors can becorrected by using quantum codewords that represent a logical qubit in a redundant way, by severalphysical qubits. On the other hand, slow drifts can bereduced, but not completely eliminated, by means ofsymmetrization, namely by using many replicas of

  20. Onorbit IMU alignment error budget

    NASA Technical Reports Server (NTRS)

    Corson, R. W.

    1980-01-01

    The Star Tracker, Crew Optical Alignment Sight (COAS), and Inertial Measurement Unit (IMU) from a complex navigation system with a multitude of error sources were combined. A complete list of the system errors is presented. The errors were combined in a rational way to yield an estimate of the IMU alignment accuracy for STS-1. The expected standard deviation in the IMU alignment error for STS-1 type alignments was determined to be 72 arc seconds per axis for star tracker alignments and 188 arc seconds per axis for COAS alignments. These estimates are based on current knowledge of the star tracker, COAS, IMU, and navigation base error specifications, and were partially verified by preliminary Monte Carlo analysis.

  1. A theory of human error

    NASA Technical Reports Server (NTRS)

    Mcruer, D. T.; Clement, W. F.; Allen, R. W.

    1981-01-01

    Human errors tend to be treated in terms of clinical and anecdotal descriptions, from which remedial measures are difficult to derive. Correction of the sources of human error requires an attempt to reconstruct underlying and contributing causes of error from the circumstantial causes cited in official investigative reports. A comprehensive analytical theory of the cause-effect relationships governing propagation of human error is indispensable to a reconstruction of the underlying and contributing causes. A validated analytical theory of the input-output behavior of human operators involving manual control, communication, supervisory, and monitoring tasks which are relevant to aviation, maritime, automotive, and process control operations is highlighted. This theory of behavior, both appropriate and inappropriate, provides an insightful basis for investigating, classifying, and quantifying the needed cause-effect relationships governing propagation of human error.

  2. Human error in recreational boating.

    PubMed

    McKnight, A James; Becker, Wayne W; Pettit, Anthony J; McKnight, A Scott

    2007-03-01

    Each year over 600 people die and more than 4000 are reported injured in recreational boating accidents. As with most other accidents, human error is the major contributor. U.S. Coast Guard reports of 3358 accidents were analyzed to identify errors in each of the boat types by which statistics are compiled: auxiliary (motor) sailboats, cabin motorboats, canoes and kayaks, house boats, personal watercraft, open motorboats, pontoon boats, row boats, sail-only boats. The individual errors were grouped into categories on the basis of similarities in the behavior involved. Those presented here are the categories accounting for at least 5% of all errors when summed across boat types. The most revealing and significant finding is the extent to which the errors vary across types. Since boating is carried out with one or two types of boats for long periods of time, effective accident prevention measures, including safety instruction, need to be geared to individual boat types. PMID:17049472

  3. DNA fingerprinting of medically important microorganisms by use of PCR.

    PubMed Central

    van Belkum, A

    1994-01-01

    Selected segments of any DNA molecule can be amplified exponentially by PCR. This technique provides a powerful tool to detect and identify minimal numbers of microorganisms. PCR is applicable both in diagnosis and in epidemiology. By amplification of hypervariable DNA domains, differences can be detected even among closely related strains. PCR fingerprinting is a valuable tool for medical microbiologists, epidemiologists, and microbial taxonomists. The current state of PCR-mediated genotyping is reviewed, and a comparison with conventional molecular typing methods is included. Because of its speed and versatility, PCR fingerprinting will play an important role in microbial genetics, epidemiology, and systematics. Images PMID:8055466

  4. Orthosis reduces breast pain and mechanical forces through natural and augmented breast tissue in women lying prone

    PubMed Central

    2014-01-01

    Background Breast implant displacement or rupture can cause aesthetic problems and serious medical complications. Activities with prone positioning and loading of the anterior chest wall, such as massage, chiropractic or osteopathic therapies may increase the risk of implant failure and can also cause discomfort in women with natural breast tissue. Here we test the effectiveness of a newly developed orthosis on pain, mechanical pressure and displacement of breast tissue in women with cosmetic augmentation, post-mastectomy reconstruction, lactating or natural breast tissue. Methods Thirty-two females volunteers, aged 25–56 years with augmented, reconstructed, natural or lactating breast tissue and cup sizes B-F, participated in this open-label clinical trial. We measured pain perception, peak pressure, maximum force, and breast tissue displacement using different sizes of the orthosis compared to no orthosis. Different densities of the orthosis were also tested in a subgroup of women (n?=?7). Pain perception was rated using a validated 11-point visual-analogue scale. Peak pressure and maximum force were assessed using a bilateral set of capacitance-pliance® sensor strips whilst participants were load bearing in a prone position, and breast displacement was measured by magnetic-resonance-imaging. Results The orthosis significantly reduced pain, breast displacement and mechanical pressures in women with natural and augmented breast tissue in prone position. Greater relief of pain and greater reduction in mechanical forces were found with increased size and density of the orthosis. Use of the orthosis improved overall comfort by 64-100%, lowered peak pressure by up to 85% and maximum force by up to 96%. Medio-lateral displacement of breast tissue was reduced by 16%, resulting in a 51% desirable increase of breast tissue height. Conclusion Our study demonstrated that the newly developed orthosis significantly reduced pain, mechanical pressure and breast tissue displacement in women with augmented and natural breast tissue when lying prone. Our findings are of clinical significance, potentially reducing the risk of complication from prone activities in women with breast augmentation or reconstruction, as well as improving comfort whilst undergoing prone procedures. Trial registration Australia and New Zealand Clinical Trials Register, ACTRN12613000541707. PMID:24410925

  5. An Efficient Multistrategy DNA Decontamination Procedure of PCR Reagents for Hypersensitive PCR Applications

    PubMed Central

    Pruvost, Mélanie; Bennett, E. Andrew; Grange, Thierry; Geigl, Eva-Maria

    2010-01-01

    Background PCR amplification of minute quantities of degraded DNA for ancient DNA research, forensic analyses, wildlife studies and ultrasensitive diagnostics is often hampered by contamination problems. The extent of these problems is inversely related to DNA concentration and target fragment size and concern (i) sample contamination, (ii) laboratory surface contamination, (iii) carry-over contamination, and (iv) contamination of reagents. Methodology/Principal Findings Here we performed a quantitative evaluation of current decontamination methods for these last three sources of contamination, and developed a new procedure to eliminate contaminating DNA contained in PCR reagents. We observed that most current decontamination methods are either not efficient enough to degrade short contaminating DNA molecules, rendered inefficient by the reagents themselves, or interfere with the PCR when used at doses high enough to eliminate these molecules. We also show that efficient reagent decontamination can be achieved by using a combination of treatments adapted to different reagent categories. Our procedure involves ?- and UV-irradiation and treatment with a mutant recombinant heat-labile double-strand specific DNase from the Antarctic shrimp Pandalus borealis. Optimal performance of these treatments is achieved in narrow experimental conditions that have been precisely analyzed and defined herein. Conclusions/Significance There is not a single decontamination method valid for all possible contamination sources occurring in PCR reagents and in the molecular biology laboratory and most common decontamination methods are not efficient enough to decontaminate short DNA fragments of low concentration. We developed a versatile multistrategy decontamination procedure for PCR reagents. We demonstrate that this procedure allows efficient reagent decontamination while preserving the efficiency of PCR amplification of minute quantities of DNA. PMID:20927390

  6. Automated PCR setup for forensic casework samples using the Normalization Wizard and PCR Setup robotic methods.

    PubMed

    Greenspoon, S A; Sykes, K L V; Ban, J D; Pollard, A; Baisden, M; Farr, M; Graham, N; Collins, B L; Green, M M; Christenson, C C

    2006-12-20

    Human genome, pharmaceutical and research laboratories have long enjoyed the application of robotics to performing repetitive laboratory tasks. However, the utilization of robotics in forensic laboratories for processing casework samples is relatively new and poses particular challenges. Since the quantity and quality (a mixture versus a single source sample, the level of degradation, the presence of PCR inhibitors) of the DNA contained within a casework sample is unknown, particular attention must be paid to procedural susceptibility to contamination, as well as DNA yield, especially as it pertains to samples with little biological material. The Virginia Department of Forensic Science (VDFS) has successfully automated forensic casework DNA extraction utilizing the DNA IQ(trade mark) System in conjunction with the Biomek 2000 Automation Workstation. Human DNA quantitation is also performed in a near complete automated fashion utilizing the AluQuant Human DNA Quantitation System and the Biomek 2000 Automation Workstation. Recently, the PCR setup for casework samples has been automated, employing the Biomek 2000 Automation Workstation and Normalization Wizard, Genetic Identity version, which utilizes the quantitation data, imported into the software, to create a customized automated method for DNA dilution, unique to that plate of DNA samples. The PCR Setup software method, used in conjunction with the Normalization Wizard method and written for the Biomek 2000, functions to mix the diluted DNA samples, transfer the PCR master mix, and transfer the diluted DNA samples to PCR amplification tubes. Once the process is complete, the DNA extracts, still on the deck of the robot in PCR amplification strip tubes, are transferred to pre-labeled 1.5 mL tubes for long-term storage using an automated method. The automation of these steps in the process of forensic DNA casework analysis has been accomplished by performing extensive optimization, validation and testing of the software methods. PMID:16542806

  7. Rapid and simple method of qPCR primer design.

    PubMed

    Thornton, Brenda; Basu, Chhandak

    2015-01-01

    Quantitative real-time polymerase chain reaction (qPCR) is a powerful tool for analysis and quantification of gene expression. It is advantageous compared to traditional gel-based method of PCR, as gene expression can be visualized "real-time" using a computer. In qPCR, a reporter dye system is used which intercalates with DNA's region of interest and detects DNA amplification. Some of the popular reporter systems used in qPCR are the following: Molecular Beacon(®), SYBR Green(®), and Taqman(®). However, success of qPCR depends on the optimal primers used. Some of the considerations for primer design are the following: GC content, primer self-dimer, or secondary structure formation. Freely available software could be used for ideal qPCR primer design. Here we have shown how to use some freely available web-based software programs (such as Primerquest(®), Unafold(®), and Beacon designer(®)) to design qPCR primers. PMID:25697660

  8. PCR-based diagnosis of human fungal infections

    PubMed Central

    Khot, Prasanna D; Fredricks, David N

    2010-01-01

    PCR is a very appealing technology for the detection of human pathogens, but the detection of fungal pathogens is particularly challenging. Fungi have cell walls that impede the efficient lysis of organisms and liberation of DNA, which can lead to false-negative PCR results. Conversely, some human pathogens are also ubiquitous environmental saprophytes that can contaminate PCR reagents and cause false-positive results. We examine the quality of PCR-based studies for fungal diagnostics using 42 variables within the Minimum Information for Publication of Quantitative Real-Time PCR Experiments guidelines. This review focuses on taxon-directed PCR assays for the diagnosis of invasive aspergillosis, candidiasis and Pneumocystis pneumonia. Finally, we evaluate broad-range fungal PCR assays capable of detecting a wide spectrum of human pathogens. PMID:19968513

  9. Why you can't program your VCR, or, predicting errors and performance with production system models of display-based action

    Microsoft Academic Search

    Wayne D. Gray; Haresh Sabnani

    1994-01-01

    We present a production rule model of display-based action for a humble yet error-prone task: programming a VCR. The system is data-driven in that the task goal is achieved in spite of partially specified plans by relying on changes in the display to trigger the creation of new goals. Knowledge in the system is partitioned into Task Knowledge, DisplayBased Knowledge,

  10. The efficacy and safety of prone positioning in adults patients with acute respiratory distress syndrome: a meta-analysis of randomized controlled trials

    PubMed Central

    Park, So Young; Kim, Hyun Jung; Yoo, Kwan Ha; Park, Yong Bum; Kim, Seo Woo; Lee, Seok Jeong; Kim, Eun Kyung; Kim, Jung Hyun; Kim, Yee Hyung; Moon, Ji-yong; Min, Kyung Hoon; Park, Sung Soo; Lee, Jinwoo; Lee, Chang-Hoon; Park, Jinkyeong; Byun, Min Kwang; Lee, Sei Won; Rlee, ChinKook; Jung, Ji Ye

    2015-01-01

    Background Prone positioning for acute respiratory distress syndrome (ARDS) has no impact on mortality despite significant improvements in oxygenation. However, a recent trial demonstrated reduced mortality rates in the prone position for severe ARDS. We evaluated effects of prone position duration and protective lung strategies on mortality rates in ARDS. Methods We extensively searched MEDLINE, EMBASE, and the Cochrane Central Register of Controlled Trials to identify randomized controlled trials (RCTs) reporting on prone positioning during acute respiratory failure in adults for inclusion in our meta-analysis. Results Eight trials met our inclusion criteria, Totals of 1,099 and 1,042 patients were randomized to the prone and supine ventilation positions. The mortality rates associated with the prone and supine positions were 41% and 47% [risk ratio (RR), 0.90; 95% confidence interval (CI), 0.82-0.98, P=0.02], but the heterogeneity was moderate (P=0.01, I2=61%). In a subgroup analysis, the mortality rates for lung protective ventilation (RR 0.73, 95% CI, 0.62-0.86, P=0.0002) and duration of prone positioning >12 h (RR 0.75, 95% CI, 0.65-0.87, P<0.0001) were reduced in the prone position. Prone positioning was not associated with an increased incidence of cardiac events (RR 1.01, 95% CI, 0.87-1.17) or ventilator associated pneumonia (RR 0.88, 95% CI, 0.71-1.09), but it was associated with an increased incidence of pressure sores (RR 1.23, 95% CI, 1.07-1.41) and endotracheal dislocation (RR 1.33, 95% CI, 1.02-1.74). Conclusions Prone positioning tends to reduce the mortality rates in ARDS patients, especially when used in conjunction with a lung protective strategy and longer prone position durations. Prone positioning for ARDS patients should be prioritized over other invasive procedures because related life-threatening complications are rare. However, further additional randomized controlled design to study are required for confirm benefit of prone position in ARDS. PMID:25922713

  11. Variation in pre-PCR processing of FFPE samples leads to discrepancies in BRAF and EGFR mutation detection: a diagnostic RING trial

    PubMed Central

    Kapp, Joshua R; Diss, Tim; Spicer, James; Gandy, Michael; Schrijver, Iris; Jennings, Lawrence J; Li, Marilyn M; Tsongalis, Gregory J; de Castro, David Gonzalez; Bridge, Julia A; Wallace, Andrew; Deignan, Joshua L; Hing, Sandra; Butler, Rachel; Verghese, Eldo; Latham, Gary J; Hamoudi, Rifat A

    2015-01-01

    Aims Mutation detection accuracy has been described extensively; however, it is surprising that pre-PCR processing of formalin-fixed paraffin-embedded (FFPE) samples has not been systematically assessed in clinical context. We designed a RING trial to (i) investigate pre-PCR variability, (ii) correlate pre-PCR variation with EGFR/BRAF mutation testing accuracy and (iii) investigate causes for observed variation. Methods 13 molecular pathology laboratories were recruited. 104 blinded FFPE curls including engineered FFPE curls, cell-negative FFPE curls and control FFPE tissue samples were distributed to participants for pre-PCR processing and mutation detection. Follow-up analysis was performed to assess sample purity, DNA integrity and DNA quantitation. Results Rate of mutation detection failure was 11.9%. Of these failures, 80% were attributed to pre-PCR error. Significant differences in DNA yields across all samples were seen using analysis of variance (p<0.0001), and yield variation from engineered samples was not significant (p=0.3782). Two laboratories failed DNA extraction from samples that may be attributed to operator error. DNA extraction protocols themselves were not found to contribute significant variation. 10/13 labs reported yields averaging 235.8?ng (95% CI 90.7 to 380.9) from cell-negative samples, which was attributed to issues with spectrophotometry. DNA measurements using Qubit Fluorometry demonstrated a median fivefold overestimation of DNA quantity by Nanodrop Spectrophotometry. DNA integrity and PCR inhibition were factors not found to contribute significant variation. Conclusions In this study, we provide evidence demonstrating that variation in pre-PCR steps is prevalent and may detrimentally affect the patient's ability to receive critical therapy. We provide recommendations for preanalytical workflow optimisation that may reduce errors in down-stream sequencing and for next-generation sequencing library generation. PMID:25430497

  12. Rapid micro-PCR system for hepatitis C virus amplification

    NASA Astrophysics Data System (ADS)

    Lin, Yu-Cheng; Huang, Ming-Yuan; Young, Kung-Chia; Chang, Ting-Tsung; Wu, Ching-Yi

    2000-08-01

    A rapid micro-polymerase chain reaction ((mu) -PCR) system was integrated to amplify the complementary DNA (cDNA) molecules of hepatitis C virus (HCV). This system consists of a rapid thermal cycling system and a (mu) PCR chip fabricated by MEMS fabrication techniques. This rapid (mu) PCR system is verified by using serum samples from patients with chronic hepatitis C. The HCV amplicon of the rapid (mu) PCR system was analyzed by slab gel electrophoresis with separation of DNA marker in parallel. The (mu) PCR chip was fabricated on silicon wafer and Pyrex glass using photolithography, wet etching, and anodic bonding methods. Using silicon material to fabricate the raction well improves the temperature uniformity of sample and helps to reach the desired temperature faster. The rapid close loop thermal cycling system comprises power supplies, a thermal generator, a computer control PID controller, and a data acquisition subsystem. The thermoelectric (T.E.) cooler is used to work as the thermal generator and a heat sink by controlling the polarity of supplied power. The (mu) PCR system was verified with traditional PCR equipment by loading the same PCR mixture with HCV cDNA and running the same cycle numbers, then comparing both HCV amplicon slab gel electrophoresis. The HCV amplicon from the (mu) PCR system shows a DNA fragment with an expected size of 145 base pairs. The background is lower with the (mu) PCR system than that with the tradional PCR equipment. Comparing the traditional PCR equipment which spends 5.5 hours for 30 cycles to gain the detectable amount of HCV amplicon in slab gel separation, this (mu) PCR system takes 30 minutes to finish the 30 thermal cycles. This work has demonstrated that this rapid (mu) PCR system can provide rapid heat generation and dissipation, improved temperature uniformity in DNA amplification.

  13. Bose's Method: A Logical Error

    NASA Astrophysics Data System (ADS)

    Kalanov, Temur Z.

    2006-04-01

    The critical analysis of Bose's method---starting-point of Dirac's method of secondary quantization---is proposed. It is proved that Bose's method for derivation of Planck's formula stated by S.N. Bose in the article ``Planck's law and light quanta hypothesis'' (1924) contains logical errors (i.e. errors in definition of concepts). The main logical error is as follows [1]: the method does not take into explicit consideration an interaction between radiation and substance, i.e. the subsystem ``photon gas'' (radiation) is defined as the isolated subsystem which does not interact with the subsystem ``molecule gas'' (substance). (Such definition of concept ``photon gas'' represents a logic error because presence of radiating substance is an essential condition of existence of temperature and thermal radiation). Conclusions: firstly, this error leads to the incorrect statement that photon gas (quantum gas) is characterized by temperature; secondly, this error puts obstacles in the way of correct definition of the important concepts ``phase cell'' and ``empty phase cell'' which concern substance; thirdly, this error enters into the starting-point of Dirac's method of secondary quantization and, hence, into the standard theory of physical vacuum (i.e. the theory of ``empty phase cell''). Ref.: T.Z. Kalanov, ``On statistics of photon gas'', Doklady Akademii Nauk SSSR (Russia), Vol. 316, No. 1 (1991), p. 100.

  14. Errors In Short Distance Photometry

    NASA Astrophysics Data System (ADS)

    Holmes, J. G.; Moermann, J. J. B.

    1982-02-01

    The errors involved in the short-distance photometry of projectors are evaluated and the same conclusions have been shown to apply to general purpose luminaires. The mathematical analysis from which the equations were derived has been published in Lighting Research and Technology (1981). The illuminance at a short distance from the projector does not follow the inverse square law; the errors depend on the angular subtense of the aperture of the projector relative to the divergence of the beam, and on the distribution of luminance across the aperture of the projector. At any particular distance, the errors are least in directions in which the curvature of the intensity distribution curve is least; the errors may therefore be greatest in the axial direction or in the direction of a shoulder on the curve, and they may change sign where the intensity distribution curve changes from convex to concave. In any particular direction, the error is greater if the outer zones of the projector have higher luminance or give a narrower relative spread; the worst case is a ring-shaped luminaire. If the relative error is less than 10 per cent, it is inversely proportional to the square of the distance of measurement. For general guidance, a nomogram relates the maximum likely percentage error to the beam divergence and to the relative distance of measurement; an empirical reference distance, to be known as the Beam Cross-over Distance, is suggested to replace the traditional 'cross-over distance' of a projector.

  15. Alpha-tocopherol in the brain tissue preservation of stroke-prone spontaneously hypertensive rats.

    PubMed

    Murad, Leonardo Borges; Guimarães, Marcela Rodrigues Moreira; Paganelli, Aline; de Oliveira, Carlos Alberto Basílio; Vianna, Lucia Marques

    2014-03-01

    Oxidative stress has an important role in neuronal damage during cerebral ischemia and can lead to cognitive and behavioral impairment. Alpha-tocopherol, a powerful antioxidant, may be able to preserve neuronal tissue and circumvent neurological deficits. Thus, this study aimed to investigate the influence of alpha-tocopherol in the preservation of brain tissue and the maintenance of memory formation in stroke-prone spontaneously hypertensive rats (SHRSP). To achieve this aim, twenty-four 15-week-old male SHRSP rats were separated into the following four groups (n?=?6 each) that received different treatments over a 4-week period: the alpha-tocopherol group, the control group, the L-NAME group, and the L-NAME?+?alpha-tocopherol group. We evaluated the physiological parameters (body weight, diuresis, and food and water intake), an oxidative stress marker (malondialdehyde levels), and neurological responses (the Morris Water Maze and Novel Objects Recognition tests). Afterwards, the brains were removed for histopathological analysis and quantification of the number of cells in the hippocampus. Statistically, the alpha-tocopherol group demonstrated better results when compared to all groups. The data indicated a reduction in oxidative stress and the preservation of neurological responses in groups treated with alpha-tocopherol. In contrast, the L-NAME group exhibited increased malondialdehyde levels, impairment of neurological responses, and several hippocampus tissue injuries. The others groups exhibited nerve tissue changes that were restricted to the glial nodes. No significant alterations were observed in the physiologic parameters. Based on these findings, we suggest that alpha-tocopherol can prevent stroke, preserve the structure of the hippocampus, and maintain both memory and cognition functions. PMID:23949732

  16. Comparative effects of plant oils on the cerebral hemorrhage in stroke-prone spontaneously hypertensive rats.

    PubMed

    Cai, Jingmei; Jang, Ja-Young; Kim, Jihyun; Shin, Kyungha; Kim, Kwang Sei; Park, Dongsun; Kim, Tae-Su; Lee, Sung-Pyo; Ahn, Byeongwoo; Choi, Ehn-Kyoung; Lee, Junsoo; Kim, Yun-Bae

    2014-05-26

    Objectives Since oils and fats can induce metabolic syndrome, leading to cardiovascular and cerebrovascular diseases, the present study was performed to find out whether the plant oils affect the cerebral hemorrhage in stroke-prone spontaneously hypertensive (SHR-SP) rats. Methods From 47 days of age, male SHR-SP rats were given drinking water containing 1% NaCl to induce hypertension, and simultaneously fed semi-purified diets containing 10% perilla oil, canola oil, or shortening. The onset time of convulsion following cerebral hemorrhage was recorded, and the areas of hemorrhage and infarction were analyzed in the stroke brains. Results In comparison with 58-day survival of SHR-SP rats during feeding NaCl alone, perilla oil extended the survival time to 68.5 days, whereas canola oil shortened it to 45.7 days. Feeding perilla oil greatly reduced the total volume of cerebral hemorrhage from 17.27% in the control group to 4.53%, while shortening increased the lesions to 21.23%. In a microscopic analysis, perilla oil also markedly decreased the hemorrhagic and infarction lesions to 1/10 of those in control rats, in contrast to an exacerbating effect of shortening. In blood analyses, perilla oil reduced blood total cholesterol and low-density lipoproteins which were increased in SHR-SP, but canola oil further increased them and markedly lowered platelet counts. Discussion Perilla oil delayed and attenuated cerebral hemorrhage by improving hyperlipidemia in hypertensive stroke animals, in contrast to the aggravating potential of canola oil and shortening. It is suggested that perilla oil should be the first choice oil for improving metabolic syndrome in hypertensive persons at risk of hemorrhagic stroke. PMID:24856006

  17. Convulsant effects of some xanthine derivatives in genetically epilepsy-prone rats.

    PubMed

    De Sarro, A; Grasso, S; Zappala, M; Nava, F; De Sarro, G

    1997-07-01

    The behavioural and electrocorticographic (ECoG) convulsant effects of several xanthine derivatives injected intraperitoneally (i.p.) were studied in genetically-epilepsy prone rats. The aim of the study was to evaluate the relationship among convulsant potency, molecular structure and lipophilicity of some xanthines. Animals were injected i.p. with various doses (250-1000 micromol/kg) and a different convulsant potency was observed among the various xanthines tested. IBMX (3-isobutyl-1-methylxanthine), theophylline (1,3-dimethylxanthine) and caffeine (1,3,7-trimethylxanthine) induced an epileptogenic pattern that consisted in an initial phase characterized by wet-dog shakes followed by head tremor, nodding, clonic convulsion and they appeared to be the most potent xanthines among those studied. During seizures, the electrocortical activity was usually characterized by single or multiple sharp- or spike-wave episodes followed by polyspike discharges. After the highest doses of IBMX, theophylline and caffeine, the animals react with falling down, transient tonic clonic seizures, escape response and generalized seizures followed by post-ictal period. Equimolar doses of 8-chlorotheophylline and theobromine (3,7-dimethylxanthine) produced less evident epileptic responses in comparison to previous compounds, whereas no epileptic signs were observed following the administration of enprofylline (3-propylxanthine), etofylline [7-(2-hydroxyethyl)theophylline], diprophylline [7-(2,3-dihydroxy-propyl)theophylline] and doxofylline [7-(1,3-dioxolan-2-ylmethyl) theophylline]. Lipophylicity of the compounds was determined, but no convincing correlations were found between the rank order of lipophilicities and the convulsant potencies of the compounds studied. On the other hand, structure-activity relationship was also investigated. We suggest that the substitution pattern on the xanthine nucleus may explain, in part, the different convulsant potency of the compounds studied. Furthermore, a selective antagonism of adenosine subtype receptors should be considered. PMID:9228189

  18. Cholinergic control over attention in rats prone to attribute incentive salience to reward cues

    PubMed Central

    Paolone, Giovanna; Angelakos, Christopher C.; Meyer, Paul J.; Robinson, Terry E.; Sarter, Martin

    2013-01-01

    Some rats (sign-trackers, ST) are especially prone to attribute incentive salience to reward cues, relative to others (goal-trackers, GT). Thus, reward cues are more likely to promote maladaptive reward-seeking behavior in ST than GT. Here, we asked whether ST and GT differ on another trait that can contribute to poor restraint over behavior evoked by reward cues. We report that, relative to GT, ST have poor control over attentional performance, due in part to insufficient cholinergic stimulation of cortical circuitry. We found that, relative to GT, ST showed poor performance on a sustained attention task (SAT). Furthermore, their performance fluctuated rapidly between periods of good to near-chance performance. This finding was reproduced using a separate cohort of rats. As demonstrated earlier, performance on the SAT was associated with increases in extracellular levels of cortical acetylcholine (ACh); however, SAT performance-associated increases in ACh levels were significantly attenuated in ST relative to GT. Consistent with the view that the modulatory effects of ACh involves stimulation of ?4?2* nicotinic acetylcholine receptors (nAChRs), systemic administration of the partial nAChR agonist ABT-089 improved SAT performance in ST and abolished the difference between SAT-associated ACh levels in ST and GT. Neither the nonselective nAChR agonist nicotine nor the psychostimulant amphetamine improved SAT performance. These findings suggest that individuals who have a propensity to attribute high incentive salience to reward cues also exhibit relatively poor attentional control. A combination of these traits may render individuals especially vulnerable to disorders such as obesity and addiction. PMID:23658172

  19. IgD in nasopharyngeal secretions and tonsils from otitis-prone children.

    PubMed Central

    Sørensen, C H; Larsen, P L

    1988-01-01

    Quantification of IgD was performed by ELISA in 180 plasma samples and 83 nasopharyngeal secretions (NPS) from children aged 2-162 months with varying degrees of recurrent otitis media. Furthermore, in 24 of the children the density of the IgD-immunocytes (IgD-cells) was calculated in immunoenzyme-stained cross-sections of their nasopharyngeal tonsils (NPT). Owing to a considerable variation of the IgD cell density throughout the NPT, a semi-quantitative counting system was applied. An irregular distribution of plasma IgD was observed during childhood and maximum levels were found between 48 and 72 months of age. However, an even distribution of plasma IgD was found among the four groups of children investigated. Based on calculations of the transudation of albumin from plasma to the NPS the amount of locally produced IgD in NPS (NPS-IgD (local] was estimated to 88% (range 41-99%). Significantly higher levels of NPS-IgD (local) were found in otitis-prone children than in the other groups. Moreover, a positive correlation was calculated between levels of NPS-IgD (local) and NPT-IgD cell density, indicating that NPT, being the local lymphoepithelial tissue, also functions as an important source of NPS-IgD. NPS-IgD was not found to be associated with secretory component, indicating a passive transfer of IgD through the mucosal membranes. Our results support the hypothesis of an association between the occurrence of IgD in the mucosa and secretions of the upper respiratory tract with localized inflammatory events. Images Fig. 1 PMID:3048811

  20. Rehabilitation of a debris-flow prone mountain stream in southwestern China - Strategies, effects and implications

    NASA Astrophysics Data System (ADS)

    Yu, Guo-an; Huang, He Qing; Wang, Zhaoyin; Brierley, Gary; Zhang, Kang

    2012-01-01

    SummaryRehabilitation of Shengou Creek, a small, steep mountain stream in southwestern China that is prone to debris flows, started more than 30 years ago through an integrated program of engineering applications (check dams and guiding dikes), biological measures (reforestation), and social measures (reducing human disturbance). Small and medium-sized check dams and guiding dikes were constructed on key upper and middle sections of the creek to stabilize hillslopes and channel bed. Meanwhile, Leucaena leucocephala, a drought-tolerant, fast-growing, and highly adaptive plant species, was introduced to promote vegetation recovery in the watershed. The collective community structure of tree, shrub, and herb assemblages in the artificial L. leucocephala forest, which developed after 7 years, enhanced soil structure and drastically reduced soil erosion on hillslopes. Cultivation of steep land was strictly controlled in the basin, and some inhabitants were encouraged to move from upstream areas to downstream towns to reduce disturbance. These integrated measures reduced sediment supply from both hillslopes and upstream channels, preventing sediment-related hazards. The development of natural streambed resistance structures (mainly step-pool systems) and luxuriant riparian vegetation aided channel stability, diversity of stream habitat, and ecological maintenance in the creek. These findings are compared with Jiangjia and Xiaobaini Ravines, two adjacent non-rehabilitated debris-flow streams which have climate and geomorphologic conditions similar to Shengou Creek. Habitat diversity indices, taxa richness, biodiversity, and bio-community indices are much higher in Shengou Creek relative to Jiangjia and Xiaobaini Ravines, attesting to the effectiveness of rehabilitation measures.

  1. Spatial task context makes short-latency reaches prone to induced Roelofs illusion

    PubMed Central

    Taghizadeh, Bahareh; Gail, Alexander

    2014-01-01

    The perceptual localization of an object is often more prone to illusions than an immediate visuomotor action towards that object. The induced Roelofs effect (IRE) probes the illusory influence of task-irrelevant visual contextual stimuli on the processing of task-relevant visuospatial instructions during movement preparation. In the IRE, the position of a task-irrelevant visual object induces a shift in the localization of a visual target when subjects indicate the position of the target by verbal response, key-presses or delayed pointing to the target (“perception” tasks), but not when immediately pointing or reaching towards it without instructed delay (“action” tasks). This discrepancy was taken as evidence for the dual-visual-stream or perception-action hypothesis, but was later explained by a phasic distortion of the egocentric spatial reference frame which is centered on subjective straight-ahead (SSA) and used for reach planning. Both explanations critically depend on delayed movements to explain the IRE for action tasks. Here we ask: first, if the IRE can be observed for short-latency reaches; second, if the IRE in fact depends on a distorted egocentric frame of reference. Human subjects were tested in new versions of the IRE task in which the reach goal had to be localized with respect to another object, i.e., in an allocentric reference frame. First, we found an IRE even for immediate reaches in our allocentric task, but not for an otherwise similar egocentric control task. Second, the IRE depended on the position of the task-irrelevant frame relative to the reference object, not relative to SSA. We conclude that the IRE for reaching does not mandatorily depend on prolonged response delays, nor does it depend on motor planning in an egocentric reference frame. Instead, allocentric encoding of a movement goal is sufficient to make immediate reaches susceptible to IRE, underlining the context dependence of visuomotor illusions. PMID:25221500

  2. Impaired motor function in senescence-accelerated mouse prone 1 (SAMP1).

    PubMed

    Aoyama, Yo; Kim, Tae Yeon; Yoshimoto, Takuro; Niimi, Kimie; Takahashi, Eiki; Itakura, Chitoshi

    2013-06-17

    Senescence-accelerated mouse prone (SAMP) strains of mice show early onset of senescence, whereas senescence-accelerated mouse resistant (SAMR) strains are resistant to early senescence and serve as controls. Although SAMP6 and SAMP8 are established models of central nervous system alterations, it is unclear whether SAMP1/Sku (SAMP1) is characterized by brain alterations and dysfunction related to behavioral functioning. In the present study, behavioral tests (i.e., locomotor activity, Y-maze, rotating rod, hind-limb extension, and traction), histochemistry, and Western blot analyses were employed to study this mouse model using 2- and 4-month-old SAMP1 and age-matched control SAMR1. Although 2-month-old SAMP1 and SAMR1 showed similar activity, 4-month-old SAMP1 exhibited less activity than age-matched SAMR1 in locomotor activity and Y-maze tests. In rotating rod test, 2- and 4-month-old SAMP1 showed motor-coordination dysfunction. An abnormal extension reflex in the hind-limb test was observed in 2- and 4-month-old SAMP1. There were no significant differences between SAMP1 and SAMR1 with respect to grip strength in the traction test or alternation behavior in the Y-maze test. Histochemistry and Western blot analyses exhibited that cerebellar Purkinje cells in 4-month-old SAMP1 mice persistently expressed tyrosine hydroxylase. These results suggest that SAMP1 is a useful model for examining mechanisms underlying motor dysfunction. PMID:23583482

  3. True colors - changing perceptions of hydrological processes at a hillslope prone to slide

    NASA Astrophysics Data System (ADS)

    Schneider, P.; Strouhal, L.; Pool, S.; Seibert, J.

    2013-06-01

    This study investigated runoff formation processes of a pre-alpine hillslope prone to slide. The experimental pasture plot (40 m × 60 m) is located in the northern front range of the Swiss Alps on a 30° steep hillslope (1180 m a.s.l., 1500+ mm annual precipitation). A gleysol (H-Go-Gr) overlies weathered marlstone and conglomerate of subalpine molasse. We conducted sprinkling experiments on a subplot (10 m × 10 m) with variable rainfall intensities. During both experiments fluorescein line-tracer injections into the topsoil, and sodium chloride (NaCl) injections into the sprinkling water were used to monitor flow velocities in the soil. The observed flow velocities for fluorescein in the soil were 1.2 and 1.4 × 10-3 m s-1. The NaCl breakthrough occurred almost simultaneously in all monitored discharge levels (0.05, 0.25 and 1 m depth), indicating a high infiltration capacity and efficient drainage of the soil. These initial observations suggested "transmissivity feedback", a form of subsurface stormflow, as the dominant runoff process. However, the results of a brilliant blue dye tracer experiment completely changed our perceptions of the hillslope's hydrological processes. Excavation of the dye-stained soils highlighted the dominance of "organic layer interflow", a form of shallow subsurface stormflow. The dye stained the entire H horizon, vertical soil fractures, and macropores (mostly worm burrows) up to 50 cm depth. Lateral drainage in the subsoil or at the soil-bedrock interface was not observed, and thus was limited to the organic topsoil. In the context of shallow landslides, the subsoil (Go/Gr) acted as an infiltration and exfiltration barrier, which produced significant lateral saturated drainage in the topsoil (H) and possibly a confined aquifer in the bedrock.

  4. True colors - experimental identification of hydrological processes at a hillslope prone to slide

    NASA Astrophysics Data System (ADS)

    Schneider, P.; Pool, S.; Strouhal, L.; Seibert, J.

    2014-02-01

    This study investigated runoff formation processes of a pre-alpine hillslope prone to slide. The experimental pasture plot (40 m × 60 m) is located in the northern front range of the Swiss Alps on a 30° steep hillslope (1180 m a.s.l., 1500 + mm annual precipitation). A gleysol (H-Go-Gr) overlies weathered marlstone and conglomerate of subalpine molasse. We conducted sprinkling experiments on a subplot (10 m × 10 m) with variable rainfall intensities. During both experiments fluorescein line-tracer injections into the topsoil, and sodium chloride (NaCl) injections into the sprinkling water were used to monitor flow velocities in the soil. The observed flow velocities for fluorescein in the soil were 1.2 and 1.4 × 10-3 m s-1. The NaCl breakthrough occurred almost simultaneously in all monitored discharge levels (0.05, 0.25 and 1.0 m depth), indicating a high-infiltration capacity and efficient drainage of the soil. These initial observations suggested "transmissivity feedback", a form of subsurface stormflow, as the dominant runoff process. However, the results of a brilliant blue dye tracer experiment completely changed our perceptions of the hillslope's hydrological processes. Excavation of the dye-stained soils highlighted the dominance of "organic layer interflow", a form of shallow subsurface stormflow. The dye stained the entire H horizon, vertical soil fractures, and macropores (mostly worm burrows) up to 0.5 m depth. Lateral drainage in the subsoil or at the soil-bedrock interface was not observed, and thus was limited to the organic topsoil. In the context of shallow landslides, the subsoil (Go/Gr) acted as an infiltration and exfiltration barrier, which produced significant lateral saturated drainage in the topsoil (H) and possibly a confined aquifer in the bedrock.

  5. Hydrologic Simulation in Mediterranean flood prone Watersheds using high-resolution quality data

    NASA Astrophysics Data System (ADS)

    Eirini Vozinaki, Anthi; Alexakis, Dimitrios; Pappa, Polixeni; Tsanis, Ioannis

    2015-04-01

    Flooding is a significant threat causing lots of inconveniencies in several societies, worldwide. The fact that the climatic change is already happening, increases the flooding risk, which is no longer a substantial menace to several societies and their economies. The improvement of spatial-resolution and accuracy of the topography and land use data due to remote sensing techniques could provide integrated flood inundation simulations. In this work hydrological analysis of several historic flood events in Mediterranean flood prone watersheds (island of Crete/Greece) takes place. Satellite images of high resolution are elaborated. A very high resolution (VHR) digital elevation model (DEM) is produced from a GeoEye-1 0.5-m-resolution satellite stereo pair and is used for floodplain management and mapping applications such as watershed delineation and river cross-section extraction. Sophisticated classification algorithms are implemented for improving Land Use/ Land Cover maps accuracy. In addition, soil maps are updated with means of Radar satellite images. The above high-resolution data are innovatively used to simulate and validate several historical flood events in Mediterranean watersheds, which have experienced severe flooding in the past. The hydrologic/hydraulic models used for flood inundation simulation in this work are HEC-HMS and HEC-RAS. The Natural Resource Conservation Service (NRCS) curve number (CN) approach is implemented to account for the effect of LULC and soil on the hydrologic response of the catchment. The use of high resolution data provides detailed validation results and results of high precision, accordingly. Furthermore, the meteorological forecasting data, which are also combined to the simulation model results, manage the development of an integrated flood forecasting and early warning system tool, which is capable of confronting or even preventing this imminent risk. The research reported in this paper was fully supported by the "ARISTEIA II" Action ("REINFORCE" program) of the "Operational Education and Life Long Learning programme" and is co-funded by the European Social Fund (ESF) and National Resources.

  6. Characterization of the permeability and acoustic properties of an outburst-prone sandstone

    NASA Astrophysics Data System (ADS)

    Butt, Stephen D.; Frempong, Paul K.; Mukherjee, Chinmoy; Upshall, James

    2005-08-01

    Two underground coal mines in the Sydney Coalfield, Nova Scotia, Canada have encountered gas outbursts from sandstone formations overlying the coal seams. These have consistently occurred while driving mine roadways into virgin ground at and below mining depths of 700 m. In this investigation, triaxial compression tests were conducted on samples of the outburst-prone sandstone from one of these mines, the Phalen Colliery, while simultaneously measuring gas permeability, acoustic emissions and ultrasonic P-wave velocity and attenuation. Experimental results characterized these sandstone properties over the full range of axial stresses up to compressive failure. These data were intended to assist with (i) evaluating the potential for degassing the sandstone and (ii) evaluating the results of in-seam seismic surveys, which were conducted to map the sandstone ahead of mining. At the estimated in situ conditions in virgin rock at 700 m depth, the sandstone permeability is expected to be in the 0.005 to 0.04 mD range, the P-wave velocity is approximately 4000 m/s and the attenuation quality factor in the 20 to 25 range. Near mine openings at 700 m depth, where the lateral confining pressures are reduced, the permeability can be several orders of magnitude higher in the 4 to 15 mD range, the P-wave velocity is 3800 m/s and the attenuation quality factor is in the 10 to 15 range. Experimental data suggests that microcracking in the sandstone prior to compressive failure does not significantly enhance permeability but there may be local pockets of higher permeability within the sandstone.

  7. Error compensation for thermally induced errors on a machine tool

    SciTech Connect

    Krulewich, D.A.

    1996-11-08

    Heat flow from internal and external sources and the environment create machine deformations, resulting in positioning errors between the tool and workpiece. There is no industrially accepted method for thermal error compensation. A simple model has been selected that linearly relates discrete temperature measurements to the deflection. The biggest problem is how to locate the temperature sensors and to determine the number of required temperature sensors. This research develops a method to determine the number and location of temperature measurements.

  8. Available at www.sciencedirect.com journal homepage: www.elsevier.com/locate/he

    E-print Network

    Wood, Thomas K.

    shuffling, error- prone PCR, and saturation mutagenesis; for example, epoxide hydrolase [1], amine oxidase lyase (FHL) system from formate [9]. The FHL system consists of hydrogenase 3 and formate dehydrogenase

  9. Stochastic Models of Human Errors

    NASA Technical Reports Server (NTRS)

    Elshamy, Maged; Elliott, Dawn M. (Technical Monitor)

    2002-01-01

    Humans play an important role in the overall reliability of engineering systems. More often accidents and systems failure are traced to human errors. Therefore, in order to have meaningful system risk analysis, the reliability of the human element must be taken into consideration. Describing the human error process by mathematical models is a key to analyzing contributing factors. Therefore, the objective of this research effort is to establish stochastic models substantiated by sound theoretic foundation to address the occurrence of human errors in the processing of the space shuttle.

  10. Synthetic aperture interferometry: error analysis.

    PubMed

    Biswas, Amiya; Coupland, Jeremy

    2010-07-10

    Synthetic aperture interferometry (SAI) is a novel way of testing aspherics and has a potential for in-process measurement of aspherics [Appl. Opt. 42, 701 (2003)]. A method to measure steep aspherics using the SAI technique has been previously reported [Appl. Opt. 47, 1705 (2008)]. Here we investigate the computation of surface form using the SAI technique in different configurations and discuss the computational errors. A two-pass measurement strategy is proposed to reduce the computational errors, and a detailed investigation is carried out to determine the effect of alignment errors on the measurement process. PMID:20648161

  11. DNA bending facilitates the error-free DNA damage tolerance pathway and upholds genome integrity.

    PubMed

    Gonzalez-Huici, Victor; Szakal, Barnabas; Urulangodi, Madhusoodanan; Psakhye, Ivan; Castellucci, Federica; Menolfi, Demis; Rajakumara, Eerappa; Fumasoni, Marco; Bermejo, Rodrigo; Jentsch, Stefan; Branzei, Dana

    2014-02-18

    DNA replication is sensitive to damage in the template. To bypass lesions and complete replication, cells activate recombination-mediated (error-free) and translesion synthesis-mediated (error-prone) DNA damage tolerance pathways. Crucial for error-free DNA damage tolerance is template switching, which depends on the formation and resolution of damage-bypass intermediates consisting of sister chromatid junctions. Here we show that a chromatin architectural pathway involving the high mobility group box protein Hmo1 channels replication-associated lesions into the error-free DNA damage tolerance pathway mediated by Rad5 and PCNA polyubiquitylation, while preventing mutagenic bypass and toxic recombination. In the process of template switching, Hmo1 also promotes sister chromatid junction formation predominantly during replication. Its C-terminal tail, implicated in chromatin bending, facilitates the formation of catenations/hemicatenations and mediates the roles of Hmo1 in DNA damage tolerance pathway choice and sister chromatid junction formation. Together, the results suggest that replication-associated topological changes involving the molecular DNA bender, Hmo1, set the stage for dedicated repair reactions that limit errors during replication and impact on genome stability. PMID:24473148

  12. Chronic stress reduces body fat content in both obesity-prone and obesity-resistant strains of mice

    Microsoft Academic Search

    C. Michel; M. Duclos; M. Cabanac; D. Richard

    2005-01-01

    Unpredictable stressors have been used to assess the effect of stress on energy metabolism in obesity-prone (C57BL6J) and obesity-resistant (AJ) mice. Mice were exposed for 25 days to a stress protocol. Both strains of mice were divided into groups of control and stressed mice, which had access to either a high-fat or a high-carbohydrate diet. Twenty-four hours after the last

  13. Cardiopulmonary Responses of Wistar Kyoto, Spontaneously Hypertensive, and Stroke-prone Spontaneously Hypertensive Rats to Particulate Matter (PM) Exposure

    Microsoft Academic Search

    J. Grace Wallenborn; Mette C. Schladweiler; Abraham Nyska; Jo Anne Johnson; Ronald Thomas; Richard H. Jaskot; Judy H. Richards; Allen D. Ledbetter; Urmila P. Kodavanti

    2007-01-01

    Humans with underlying cardiovascular disease, including stroke, are more susceptible to ambient particulate matter (PM)-induced morbidity and mortality. We hypothesized that stroke-prone spontaneously hypertensive rats (SHRSP) would be more susceptible than healthy Wistar Kyoto (WKY) rats to PM-induced cardiac oxidative stress and pulmonary injury. We further postulated that PM-induced injury would be greater in SHRSP than in spontaneously hypertensive rats

  14. Neuroprotective effects of icariin on memory impairment and neurochemical deficits in senescence-accelerated mouse prone 8 (SAMP8) mice

    Microsoft Academic Search

    Xiao-Li He; Wei-Qin Zhou; Ming-Gang Bi; Guan-Hua Du

    2010-01-01

    The senescence-accelerated mouse prone 8 (SAMP8) is a novel aging model characterized by early onset and rapid advancement of senescence. In the present study, 6-month-old male SAMP8 mice were orally administered icariin (75, 150mg\\/kg) for 15weeks. Mice were submitted to passageway water maze test and step-down passive avoidance test for evaluating cognitive impairments. The HPLC-EC technique was used to determine

  15. Reduction of diabetes incidence of BB Wistar rats by early prophylactic insulin treatment of diabetes-prone animals

    Microsoft Academic Search

    C. F. Gotfredsen; K. Buschard; E. K. Frandsen

    1985-01-01

    Summary  A group of 36 diabetes-prone BB Wistar rats were given prophylactic insulin treatment with heat-treated bovine ultralente insulin (15 IU · kg–1 · day–1) from 50 to 142 days of age. The incidence of Type 1 (insulin-dependent) diabetes at the end of the treatment period was compared to that of 36 control animals given insulin only from the first day

  16. Early hyperbaric oxygen therapy attenuates disease severity in lupus-prone autoimmune (NZB × NZW) F1 mice

    Microsoft Academic Search

    Shao-Yuan Chen; Yen-Chen Chen; Jehng-Kang Wang; Hsiao-Ping Hsu; Pey-Shen Ho; Yi-Chyan Chen; Huey-Kang Sytwu

    2003-01-01

    The effects of hyperbaric oxygen (HBO2) therapy on the immune system are reported including potential changes to the CD4\\/CD8 ratio and a decreased proliferation of lymphocytes during exposure. The immunosuppressive effect of HBO2 had been suggested to be applicable for the treatment of certain autoimmune diseases. (NZB × NZW) F1 hybrid mice, the unique lupus-prone mice, have been used for

  17. Prevention of hypercholesterolemia and atherosclerosis in the hyperlipidemia and atherosclerosis-prone Japanese (LAP) quail by taurine supplementation

    Microsoft Academic Search

    Shigeru Murakami; T. Sakurai; H. Tomoike; M. Sakono; T. Nasu; N. Fukuda

    2010-01-01

    The effects of taurine supplementation on the serum cholesterol levels and the progression of atherosclerosis were investigated\\u000a in the hyperlipidemia- and atherosclerosis-prone Japanese (LAP) quail. The ingestion of a high-cholesterol diet containing\\u000a 1% cholesterol by LAP quails for 60 days resulted in a marked elevation in serum non-HDL cholesterol and triglyceride, as\\u000a well as severe aortic lesions with lipid droplets. An

  18. Regulation of T cell-dependent autoantibody production by a ?? T cell line derived from lupus-prone mice

    Microsoft Academic Search

    Takao Fujii; Masato Okada; Joe Craft

    2002-01-01

    Lupus-prone (MRL×C57BL\\/6) F1 mice lacking ?? T cells show more severe lupus than their T cell-intact counterparts, suggesting that ?? T cells down-modulate murine lupus. To determine the mechanisms for this effect, we assessed the capacity of ?? T cell lines derived from spleens of ?? T cell-deficient MRL\\/Mp-Faslpr (MRL\\/Faslpr) mice to down-regulate anti-dsDNA production generated by CD4+?? T helper

  19. Influence of sources of dietary oils on the life span of stroke-prone spontaneously hypertensive rats

    Microsoft Academic Search

    W. M. N. Ratnayake; L. Plouffe; R. Hollywood; M. R. L'Abbé; N. Hidiroglou; G. Sarwar; R. Mueller

    2000-01-01

    In recent studies, the life span of stroke-prone spontaneously hypertensive (SHRSP) rats was altered by a variety of dietary\\u000a fats. It was relatively shorter in rats fed canola oil as the sole source of fat. The present study was performed to find\\u000a out whether the fatty acid profile and the high content of sulfur compounds in canola oil could modulate

  20. Novel application of red-light runner proneness theory within traffic microsimulation to an actual signal junction.

    PubMed

    Bell, Margaret Carol; Galatioto, Fabio; Giuffrè, Tullio; Tesoriere, Giovanni

    2012-05-01

    Building on previous research a conceptual framework, based on potential conflicts analysis, has provided a quantitative evaluation of 'proneness' to red-light running behaviour at urban signalised intersections of different geometric, flow and driver characteristics. The results provided evidence that commonly used violation rates could cause inappropriate evaluation of the extent of the red-light running phenomenon. Initially, an in-depth investigation of the functional form of the mathematical relationship between the potential and actual red-light runners was carried out. The application of the conceptual framework was tested on a signalised intersection in order to quantify the proneness to red-light running. For the particular junction studied proneness for daytime was found to be 0.17 north and 0.16 south for opposing main road approaches and 0.42 east and 0.59 west for the secondary approaches. Further investigations were carried out using a traffic microsimulation model, to explore those geometric features and traffic volumes (arrival patterns at the stop-line) that significantly affect red-light running. In this way the prediction capability of the proposed potential conflict model was improved. A degree of consistency in the measured and simulated red-light running was observed and the conceptual framework was tested through a sensitivity analysis applied to different stop-line positions and traffic volume variations. The microsimulation, although at its early stages of development, has shown promise in its ability to model unintentional red light running behaviour and following further work through application to other junctions, potentially provides a tool for evaluation of alternative junction designs on proneness. In brief, this paper proposes and applies a novel approach to model red-light running using a microsimulation and demonstrates consistency with the observed and theoretical results. PMID:22310040

  1. Sensitivity of PCR and real-time PCR for the diagnosis of human visceral leishmaniasis using peripheral blood

    PubMed Central

    da Costa Lima, Manoel Sebastião; Zorzenon, Denielly Christina Rodrigues; Dorval, Maria Elizabeth Cavalheiros; Pontes, Elenir Rose Jardim Cury; Oshiro, Elisa Teruya; Cunha, Rodrigo; Andreotti, Renato; Matos, Maria de Fatima Cepa

    2013-01-01

    Objective To evaluate the effectiveness of PCR and real-time PCR for the diagnosis of human visceral leishmaniasis using peripheral blood samples. Methods DNA extraction was performed using Promega Wizard® Genomic kits. PCR employing RV1/RV2 primers yielded 145-bp amplicons. Real-time PCR was performed with the same primers and SYBR Green ROX Plus mix. These techniques were used to analyze 100 peripheral blood samples from patients with clinical signs of the disease. Results The sensitivity and specificity levels were 91,3%% and 29,6%, respectively, for real-time PCR and 97.78% and 61.82%, respectively, for PCR. Conclusions Real-time PCR proved to be a satisfactory method for the diagnosis of human visceral leishmaniasis.

  2. Correction of errors in tandem mass spectrum extraction enhances phosphopeptide identification.

    PubMed

    Hao, Piliang; Ren, Yan; Tam, James P; Sze, Siu Kwan

    2013-12-01

    The tandem mass spectrum extraction of phosphopeptides is more difficult and error-prone than that of unmodified peptides due to their lower abundance, lower ionization efficiency, the cofragmentation with other high-abundance peptides, and the use of MS(3) on MS(2) fragments with neutral losses. However, there are still no established methods to evaluate its correctness. Here we propose to identify and correct these errors via the combinatorial use of multiple spectrum extraction tools. We evaluated five free and two commercial extraction tools using Mascot and phosphoproteomics raw data from LTQ FT Ultra, in which RawXtract 1.9.9.2 identified the highest number of unique phosphopeptides (peptide expectation value <0.05). Surprisingly, ProteoWizzard (v. 3.0.3476) extracted wrong precursor mass for most MS(3) spectra. Comparison of the top three free extraction tools showed that only 54% of the identified spectra were identified consistently from all three tools, indicating that some errors might happen during spectrum extraction. Manual check of 258 spectra not identified from all three tools revealed 405 errors of spectrum extraction with 7.4% in selecting wrong precursor charge, 50.6% in selecting wrong precursor mass, and 42.1% in exporting MS/MS fragments. We then corrected the errors by selecting the best extracted MGF file for each spectrum among the three tools for another database search. With the errors corrected, it results in the 22.4 and 12.2% increase in spectrum matches and unique peptide identification, respectively, compared with the best single method. Correction of errors in spectrum extraction improves both the sensitivity and confidence of phosphopeptide identification. Data analysis on nonphosphopeptide spectra indicates that this strategy applies to unmodified peptides as well. The identification of errors in spectrum extraction will promote the improvement of spectrum extraction tools in future. PMID:24147958

  3. An evaluation of direct PCR amplification

    PubMed Central

    Hall, Daniel E.; Roy, Reena

    2014-01-01

    Aim To generate complete DNA profiles from blood and saliva samples deposited on FTA® and non-FTA® paper substrates following a direct amplification protocol. Methods Saliva samples from living donors and blood samples from deceased individuals were deposited on ten different FTA® and non-FTA® substrates. These ten paper substrates containing body fluids were kept at room temperature for varying lengths of time ranging from one day to approximately one year. For all assays in this research, 1.2 mm punches were collected from each substrate containing one type of body fluid and amplified with reagents provided in the nine commercial polymerase chain reaction (PCR) amplification kits. The substrates were not subjected to purification reagent or extraction buffer prior to amplification. Results Success rates were calculated for all nine amplification kits and all ten substrates based on their ability to yield complete DNA profiles following a direct amplification protocol. Six out of the nine amplification kits, and four out of the ten paper substrates had the highest success rates overall. Conclusion The data show that it is possible to generate complete DNA profiles following a direct amplification protocol using both standard (non-direct) and direct PCR amplification kits. The generation of complete DNA profiles appears to depend more on the success of the amplification kit rather than the than the FTA®- or non-FTA®-based substrates. PMID:25559837

  4. False negative results from using common PCR reagents

    PubMed Central

    2011-01-01

    Background The sensitivity of the PCR reaction makes it ideal for use when identifying potentially novel viral infections in human disease. Unfortunately, this same sensitivity also leaves this popular technique open to potential contamination with previously amplified PCR products, or "carry-over" contamination. PCR product carry-over contamination can be prevented with uracil-DNA-glycosylase (UNG), and it is for this reason that it is commonly included in many commercial PCR master-mixes. While testing the sensitivity of PCR assays to detect murine DNA contamination in human tissue samples, we inadvertently discovered that the use of this common PCR reagent may lead to the production of false-negative PCR results. Findings We show here that contamination with minute quantities of UNG-digested PCR product or any negative control PCR reactions containing primer-dimers regardless of UNG presence can completely block amplification from as much as 60 ng of legitimate target DNA. Conclusions These findings could potentially explain discrepant results from laboratories attempting to amplify MLV-related viruses including XMRV from human samples, as none of the published reports used internal-tube controls for amplification. The potential for false negative results needs to be considered and carefully controlled in PCR experiments, especially when the target copy number may be low - just as the potential for false positive results already is. PMID:22032271

  5. Computer Laboratory Grammatical Error Detection

    E-print Network

    Narasayya, Vivek

    errors. 2. Tagging and parsing Parsing with RASP provides further information about the words adaptations RASP performs better on correct English; e.g., its grammatical rules does not allow a singular

  6. Human errors and measurement uncertainty

    NASA Astrophysics Data System (ADS)

    Kuselman, Ilya; Pennecchi, Francesca

    2015-04-01

    Evaluating the residual risk of human errors in a measurement and testing laboratory, remaining after the error reduction by the laboratory quality system, and quantifying the consequences of this risk for the quality of the measurement/test results are discussed based on expert judgments and Monte Carlo simulations. A procedure for evaluation of the contribution of the residual risk to the measurement uncertainty budget is proposed. Examples are provided using earlier published sets of expert judgments on human errors in pH measurement of groundwater, elemental analysis of geological samples by inductively coupled plasma mass spectrometry, and multi-residue analysis of pesticides in fruits and vegetables. The human error contribution to the measurement uncertainty budget in the examples was not negligible, yet also not dominant. This was assessed as a good risk management result.

  7. Dual processing and diagnostic errors

    Microsoft Academic Search

    Geoff Norman

    2009-01-01

    In this paper, I review evidence from two theories in psychology relevant to diagnosis and diagnostic errors. “Dual Process”\\u000a theories of thinking, frequently mentioned with respect to diagnostic error, propose that categorization decisions can be\\u000a made with either a fast, unconscious, contextual process called System 1 or a slow, analytical, conscious, and conceptual\\u000a process, called System 2. Exemplar theories of

  8. Analysis of ``Immersed'' Thermocouple Error

    Microsoft Academic Search

    J. E. Bauerle

    1961-01-01

    The error of an ``immersed'' thermocouple due to heat leaks through the thermocouple wires has been estimated by means of a simple model. The error is shown to decrease exponentially with quantity L1?l1, where L1 is the ``immersion'' depth of the thermocouple and l1 is a characteristic length depending on thermocouple parameters and the mode of heat transfer. It is

  9. Range from focus-error

    Microsoft Academic Search

    M. W. Siegel; M. L. Leary

    We derive theoretically and demonstrate experimentally an approach to range-from-focus with an important improvement over all previous methods. Previous methods rely on subjective measures of sharpness to focus a selected locale of the image. Our method uses measured physical features of the optical signal to generate an objective focus-error distance map. To compute range-from-focus-error distance it is not necessary to

  10. Interpolation Errors in Spectrum Analyzers

    NASA Technical Reports Server (NTRS)

    Martin, J. L.

    1996-01-01

    To obtain the proper measurement amplitude with a spectrum analyzer, the correct frequency-dependent transducer factor must be added to the voltage measured by the transducer. This report examines how entering transducer factors into a spectrum analyzer can cause significant errors in field amplitude due to the misunderstanding of the analyzer's interpolation methods. It also discusses how to reduce these errors to obtain a more accurate field amplitude reading.

  11. Quantum error correction for beginners.

    PubMed

    Devitt, Simon J; Munro, William J; Nemoto, Kae

    2013-07-01

    Quantum error correction (QEC) and fault-tolerant quantum computation represent one of the most vital theoretical aspects of quantum information processing. It was well known from the early developments of this exciting field that the fragility of coherent quantum systems would be a catastrophic obstacle to the development of large-scale quantum computers. The introduction of quantum error correction in 1995 showed that active techniques could be employed to mitigate this fatal problem. However, quantum error correction and fault-tolerant computation is now a much larger field and many new codes, techniques, and methodologies have been developed to implement error correction for large-scale quantum algorithms. In response, we have attempted to summarize the basic aspects of quantum error correction and fault-tolerance, not as a detailed guide, but rather as a basic introduction. The development in this area has been so pronounced that many in the field of quantum information, specifically researchers who are new to quantum information or people focused on the many other important issues in quantum computation, have found it difficult to keep up with the general formalisms and methodologies employed in this area. Rather than introducing these concepts from a rigorous mathematical and computer science framework, we instead examine error correction and fault-tolerance largely through detailed examples, which are more relevant to experimentalists today and in the near future. PMID:23787909

  12. The usability-error ontology.

    PubMed

    Elkin, Peter L; Beuscart-Zephir, Marie-Catherine; Pelayo, Sylvia; Patel, Vimla; Nøhr, Christian

    2013-01-01

    Clinical Systems have become standard partners with clinicians in the care of patients. As these systems become integral parts of the clinical workflow, they have the potential to help improve patient outcomes, however they have also in some cases have led to adverse events and has resulted in patients coming to harm. Often the root cause analysis of these adverse events can be traced back to Usability Errors in the Health Information Technology (HIT) or its interaction with users. Interoperability of the documentation of HIT related Usability Errors in a consistent fashion can improve our ability to do systematic reviews and meta-analyses. In an effort to support improved and more interoperable data capture regarding Usability Errors, we have created the Usability Error Ontology (UEO) as a classification method for representing knowledge regarding Usability Errors. We expect the UEO will grow over time to support an increasing number of HIT system types. In this manuscript, we present this Ontology of Usability Error Types and specifically address Computerized Physician Order Entry (CPOE), Electronic Health Records (EHR) and Revenue Cycle HIT systems. PMID:23941937

  13. Methods for producing partially digested restriction DNA fragments and for producing a partially modified PCR product

    Microsoft Academic Search

    2000-01-01

    The present invention is an improved method of making a partially modified PCR product from a DNA fragment with a polymerase chain reaction (PCR). In a standard PCR process, the DNA fragment is combined with starting deoxynucleoside triphosphates, a primer, a buffer and a DNA polymerase in a PCR mixture. The PCR mixture is then reacted in the PCR producing

  14. DNA polymerase preference determines PCR priming efficiency

    PubMed Central

    2014-01-01

    Background Polymerase chain reaction (PCR) is one of the most important developments in modern biotechnology. However, PCR is known to introduce biases, especially during multiplex reactions. Recent studies have implicated the DNA polymerase as the primary source of bias, particularly initiation of polymerization on the template strand. In our study, amplification from a synthetic library containing a 12 nucleotide random portion was used to provide an in-depth characterization of DNA polymerase priming bias. The synthetic library was amplified with three commercially available DNA polymerases using an anchored primer with a random 3’ hexamer end. After normalization, the next generation sequencing (NGS) results of the amplified libraries were directly compared to the unamplified synthetic library. Results Here, high throughput sequencing was used to systematically demonstrate and characterize DNA polymerase priming bias. We demonstrate that certain sequence motifs are preferred over others as primers where the six nucleotide sequences at the 3’ end of the primer, as well as the sequences four base pairs downstream of the priming site, may influence priming efficiencies. DNA polymerases in the same family from two different commercial vendors prefer similar motifs, while another commercially available enzyme from a different DNA polymerase family prefers different motifs. Furthermore, the preferred priming motifs are GC-rich. The DNA polymerase preference for certain sequence motifs was verified by amplification from single-primer templates. We incorporated the observed DNA polymerase preference into a primer-design program that guides the placement of the primer to an optimal location on the template. Conclusions DNA polymerase priming bias was characterized using a synthetic library amplification system and NGS. The characterization of DNA polymerase priming bias was then utilized to guide the primer-design process and demonstrate varying amplification efficiencies among three commercially available DNA polymerases. The results suggest that the interaction of the DNA polymerase with the primer:template junction during the initiation of DNA polymerization is very important in terms of overall amplification bias and has broader implications for both the primer design process and multiplex PCR. PMID:24479830

  15. Extreme value analysis in typhoon prone areas: case study of the Pearl River estuary

    NASA Astrophysics Data System (ADS)

    Moerman, E.; de Graaff, R.; Rego, J. L.

    2014-12-01

    Extreme events such as tropical storms and typhoons are often the determining factor for the extreme values of wind, wave and water level conditions. The storm track, its propagation speed, the air pressure drop and the wind speed intensity of a typhoon determine the maximum occurring wave heights, water levels and currents. The stochastic behaviour of typhoons and tropical storms, however, lead to uncertainty in the extreme value analysis, because a slight variation of the typhoon track, propagation speed or wind speed intensity can have a significant impact on these local extreme hydrodynamic conditions. To determine the significance of the stochastic behaviour of typhoons a model assessment is performed comparing standard extreme value analysis values of measured water levels (e.g. values of 1/10, 1/50, and 1/100 year return periods) against model results of artificial typhoons. In the model assessment, making use of Delft3D, various artificial typhoons are modelled in which the typhoon tracks, propagation speeds and wind speed intensities are varied within realistic ranges (based on observed historical typhoons). The study focusses on the Pearl River estuary (China) where typically about 5 to 10 tropical storms or typhoons are observed every year. Once every few years an extreme typhoon hits the area. By quantifying the potential impact of artificial typhoons the uncertainty in the extreme water level values in such a typhoon prone area are better assessed. The model is validated simulating several historic typhoons. Subsequently the typhoons tracks, their propagation speeds and wind speed intensities are varied. The extreme water level values (extreme surge height + mean high water value) that follow from the artificial typhoon modelling are compared against values from a standard extreme value analysis, making use of the central limit theorem for the extreme values in a sample. A Peaks over Threshold approach is applied and the extremes are fitted and extrapolated according to a Generalized Pareto Distribution. One of our main conclusions is that while the peak surge heights and related total water levels resulting from the historical and synthetic typhoon simulations can exceed the once per 100 year extreme total water level estimates, they are generally within the 95% confidence interval of the estimate.

  16. Sotagliflozin improves glycemic control in nonobese diabetes-prone mice with type 1 diabetes

    PubMed Central

    Powell, David R; Doree, Deon; Jeter-Jones, Sabrina; Ding, Zhi-Ming; Zambrowicz, Brian; Sands, Arthur

    2015-01-01

    Purpose Oral agents are needed that improve glycemic control without increasing hypoglycemic events in patients with type 1 diabetes (T1D). Sotagliflozin may meet this need, because this compound lowers blood glucose through the insulin-independent mechanisms of inhibiting kidney SGLT2 and intestinal SGLT1. We examined the effect of sotagliflozin on glycemic control and rate of hypoglycemia measurements in T1D mice maintained on a low daily insulin dose, and compared these results to those from mice maintained in better glycemic control with a higher daily insulin dose alone. Materials and methods Nonobese diabetes-prone mice with cyclophosphamide-induced T1D were randomized to receive one of four daily treatments: 0.2 U insulin/vehicle, 0.05 U insulin/vehicle, 0.05 U insulin/2 mg/kg sotagliflozin or 0.05 U insulin/30 mg/kg sotagliflozin. Insulin was delivered subcutaneously by micro-osmotic pump; the day after pump implantation, mice received their first of 22 once-daily oral doses of sotagliflozin or vehicle. Glycemic control was monitored by measuring fed blood glucose and hemoglobin A1c levels. Results Blood glucose levels decreased rapidly and comparably in the 0.05 U insulin/sotagliflozin-treated groups and the 0.2 U insulin/vehicle group compared to the 0.05 U insulin/vehicle group, which had significantly higher levels than the other three groups from day 2 through day 23. A1c levels were also significantly higher in the 0.05 U insulin/vehicle group compared to the other three groups on day 23. Importantly, the 0.2 U insulin/vehicle group had, out of 100 blood glucose measurements, 13 that were <70 mg/dL compared to one of 290 for the other three groups combined. Conclusion Sotagliflozin significantly improved glycemic control, without increasing the rate of hypoglycemia measurements, in diabetic mice maintained on a low insulin dose. This sotagliflozin-mediated improvement in glycemic control was comparable to that achieved by raising the insulin dose alone, but was not accompanied by the increased rate of hypoglycemia measurements observed with the higher insulin dose. PMID:25759591

  17. Monitoring human cytomegalovirus infection with nested PCR: comparison of positive rates in plasma and leukocytes and with quantitative PCR

    PubMed Central

    2010-01-01

    Background Human cytomegalovirus (HCMV) infection poses a significant health threat to immunocompromised individuals. Here we performed this study to set up a highly sensitive nested PCR method applicable for detecting HCMV infection in high-risk individuals. In this work, 106 blood specimens from 66 patients with potential HCMV infection were obtained. Total DNA was extracted separately from plasma and peripheral blood leukocytes (PBL) of each sample. HCMV DNA was detected in parallel by nested PCR and quantitative real-time PCR (qRT-PCR), and the results were compared. Results Serial dilution test revealed that the detection limit of nested PCR was 180 copies/ml. The nested PCR showed a higher positive rate than qRT-PCR (34.9% vs. 12.3%, p < 0.001). The positive rate of nested PCR based on PBL DNA was significantly higher than that based on plasma DNA (34.9% vs. 18.9%, p = 0.002). Of the 14 patients with serial samples, 11 were positive for HCMV DNA in PBL while only 7 were positive in plasma. Moreover, for each patient, nested PCR using PBL DNA also detected more positive samples than that using plasma DNA. Conclusion Combined use of nested PCR with PBL DNA is highly sensitive in defining HCMV infection. This assay is particularly useful in the case of quantification not essential. PMID:20398295

  18. Reverse Transcriptase (RT) Inhibition of PCR at Low Concentrations of Template and Its Implications for Quantitative RT-PCR

    PubMed Central

    Chandler, Darrell P.; Wagnon, Christina A.; Bolton, Harvey

    1998-01-01

    Numerous instances of reverse transcriptase (RT) inhibition of the PCR were observed while developing nonquantitative uncoupled RT-PCR techniques for detecting nitrogenase and ammonia monooxygenase gene expression in situ. The inhibitory effect of RT on the PCR was removed with increasing template concentrations beyond 105 to 106 copies. Including T4 gene 32 protein during the reverse transcription phase of the RT-PCR reaction increased the RT-PCR product yield by as much as 483%; if gene 32 protein was introduced after reverse transcription but prior to the PCR phase, no improvement in product yield was observed. Addition of 1 ?g of exogenous calf thymus DNA or yeast tRNA did little to relieve RT inhibition of the PCR on both genomic DNA and mRNA templates. These results suggest that RT inhibition of the PCR is mediated through direct interaction with the specific primer-template combination (DNA and RNA) and point to specific assay modifications for estimating the extent of RT inhibition and counteracting some of the inhibitory effect. Furthermore, the working hypothesis of RT inhibition below a 105 to 106 copy threshold has important implications for quantitative RT-PCR studies. In particular, competitive, quantitative RT-PCR systems will consistently underestimate the actual RNA concentration. Hence, enumerations of RNA templates below 105 to 106 copies will be relative to an internal standard and will not be an absolute measure of RNA abundance in situ. PMID:9464406

  19. Forensic implications of PCR inhibition--A review.

    PubMed

    Alaeddini, Reza

    2012-05-01

    Polymerase chain reaction (PCR) is currently the method of choice for the identification of human remains in forensic coursework. DNA samples from crime scenes often contain co-purified impurities which inhibit PCR. PCR inhibition is the most common cause of PCR failure when adequate copies of DNA are present. Inhibitors have been routinely reported in forensic investigations of DNA extracted from a variety of templates. Humic compounds, a series of substances produced during decay process have been considered as the materials contaminating DNA in soil, natural waters and recent sediments. Those compounds have been frequently assigned as PCR inhibitors. The current report reviews the characteristics of PCR inhibition, including the proposed mechanisms of inhibition, detection methods and the available technologies to remove or overcome the inhibitory activities. PMID:21917539

  20. Posttreatment Follow-Up of Brucellosis by PCR Assay

    PubMed Central

    Morata, Pilar; Queipo-Ortuño, María Isabel; Reguera, José María; García-Ordoñez, Miguel Angel; Pichardo, Cristina; Colmenero, Juan de Dios

    1999-01-01

    In order to evaluate the usefulness of a peripheral blood PCR assay in the posttreatment follow-up of brucellosis, a cohort of 30 patients was studied by means of blood cultures, rose Bengal, seroagglutination, Coombs' antibrucella tests, and PCR assay at the time of diagnosis, at the end of treatment, and 2, 4, and 6 months later. Of the 29 patients whose PCR assays were initially positive, 28 (96.5%) were negative at the conclusion of the treatment. PCR was positive for the two patients who had relapses and negative for another four who had suspected but unconfirmed relapses. PCR was negative for 98.3% of the follow-up samples from those patients who had a favorable evolution. In conclusion, PCR appears to be a very useful technique, not only for the initial diagnosis of the disease, but also for posttreatment follow-up and the early detection of relapses. PMID:10565954

  1. In most data recording systems and many data communication systems, some sequences are more prone to error than others. Thus, in order to reduce the likelihood of error, it

    E-print Network

    Roth, Ronny

    : combinatorial, algebraic and probabilistic. In the course of doing so, we show how to compute the capacity and computer science. The main prerequisites are elementary linear algebra and elementary probability for courses on Constrained Systems. One of these versions appeared as Chapter 20 of the Handbook of Coding

  2. Crowdsourcing Correction of Speech Recognition Captioning Errors

    E-print Network

    Southampton, University of

    Crowdsourcing Correction of Speech Recognition Captioning Errors M Wald, University of Southampton crowdsourcing correction of speech recognition captioning errors to provide a sustainable method of making using speech recognition technologies but this results in many recognition errors requiring manual

  3. Unequal error protection of subband coded bits 

    E-print Network

    Devalla, Badarinath

    1994-01-01

    Source coded data can be separated into different classes based on their susceptibility to channel errors. Errors in the Important bits cause greater distortion in the reconstructed signal. This thesis presents an Unequal Error Protection scheme...

  4. Lessons to Be Learned from Past Errors

    MedlinePLUS

    Lessons to Be Learned from Past Errors The following advice, based on real errors that have happened, ... medicines safely General Advice on Safe Medication Use Lessons to Be Learned from Past Errors Preventing Drug ...

  5. Two-Layer Error Control Codes Combining Rectangular and Hamming Product Codes for Cache Error

    E-print Network

    Zhang, Meilin

    We propose a novel two-layer error control code, combining error detection capability of rectangular codes and error correction capability of Hamming product codes in an efficient way, in order to increase cache error ...

  6. Ultrafast rotary PCR system for multiple influenza viral RNA detection.

    PubMed

    Jung, Jae Hwan; Choi, Seok Jin; Park, Byung Hyun; Choi, Young Ki; Seo, Tae Seok

    2012-05-01

    We presented a novel platform for an ultrafast PCR system, called the Rotary PCR Genetic Analyzer, which incorporates a thermal block and resistive temperature detector (RTD) for thermal cycling control, a disposable PCR microchip, and a stepper motor. The influenza viral RNAs from H3N2, H5N1, and H1N1 were simultaneously identified with high sensitivity and speed. PMID:22437437

  7. Detection of episomal banana streak badnavirus by IC-PCR

    Microsoft Academic Search

    Glyn Harper; Ganesh Dahal; George Thottappilly; R. Hull

    1999-01-01

    A polymerase chain reaction (PCR) based strategy to detect episomal banana streak badnavirus (BSV) in banana and plantain plants that carry integrated BSV sequences was developed. Antisera used in immuno-capture polymerase chain reaction (IC-PCR) are capable of binding a large number of BSV serotypes. The primers used for PCR are capable of annealing to and amplifying across the aspartic protease-reverse

  8. Highly Precise Measurement of HIV DNA by Droplet Digital PCR

    PubMed Central

    Strain, Matthew C.; Lada, Steven M.; Luong, Tiffany; Rought, Steffney E.; Gianella, Sara; Terry, Valeri H.; Spina, Celsa A.; Woelk, Christopher H.; Richman, Douglas D.

    2013-01-01

    Deoxyribonucleic acid (DNA) of the human immunodeficiency virus (HIV) provides the most sensitive measurement of residual infection in patients on effective combination antiretroviral therapy (cART). Droplet digital PCR (ddPCR) has recently been shown to provide highly accurate quantification of DNA copy number, but its application to quantification of HIV DNA, or other equally rare targets, has not been reported. This paper demonstrates and analyzes the application of ddPCR to measure the frequency of total HIV DNA (pol copies per million cells), and episomal 2-LTR (long terminal repeat) circles in cells isolated from infected patients. Analysis of over 300 clinical samples, including over 150 clinical samples assayed in triplicate by ddPCR and by real-time PCR (qPCR), demonstrates a significant increase in precision, with an average 5-fold decrease in the coefficient of variation of pol copy numbers and a >20-fold accuracy improvement for 2-LTR circles. Additional benefits of the ddPCR assay over qPCR include absolute quantification without reliance on an external standard and relative insensitivity to mismatches in primer and probe sequences. These features make digital PCR an attractive alternative for measurement of HIV DNA in clinical specimens. The improved sensitivity and precision of measurement of these rare events should facilitate measurements to characterize the latent HIV reservoir and interventions to eradicate it. PMID:23573183

  9. The inhibitory effect of pentobarbitone on reverse transcription-PCR.

    PubMed

    Hyun, Changbaig; Filippich, Lucio John; Hughes, Ian

    2005-01-31

    Pentobarbitone sodium (Sodium 5-ethyl-5[1-methylbutyl]-pentobarbitone) is a short-acting barbiturate that is commonly used to euthanase animals. As part of our studies into the molecular genetics of copper toxicosis in Bedlington terrier dogs, reverse-transcription (RT)-PCR was noted to always fail on RNA samples collected from livers of dogs sacrificed by pentobarbitone injection. When samples were collected without pentobarbitone, however, RT-PCR was always successful. We suspected the possible inhibition by pentobarbitone sodium of either reverse transcriptase or Taq polymerase. In vitro studies showed that pentobarbitone interference of PCR occurred at >4 microg/microl. To identify if pentobarbitone produced competitive inhibition, each components (Taq polymerase, MgCl(2), dNTP, etc.) of the PCR was individually altered. However, inhibition still persisted, suggesting that multiple PCR components may be affected. Also it was shown that pentobarbitone interference was not dependent on the PCR product size. Simple dilution of pentobarbitone contaminated DNA solutions, and the addition of bovine serum albumin (BSA) to the PCR mix overcame pentobarbitone interference. In vivo, PCR by pentobarbitone was found to be compounded by high DNA concentration and pentobarbitone contamination. In addition, both high DNA concentration and pentobarbitone contamination could be overcome through dilution and the addition of BSA. Further work is required to quantify pentobarbitone concentration in the liver-extracted DNA and RNA samples before this inhibition effect on PCR can be fully elucidated. PMID:15656944

  10. Comparison of the effect of robotic reinforced movement learning technology on the development of prone locomotion in infants with and without risk for cerebral

    E-print Network

    Fagg, Andrew H.

    of prone locomotion in infants with and without risk for cerebral palsy. Kolobe, Thubi H.A, PT, PhD1 , Fagg in infants with cerebral palsy (CP). Study Design: Repeated measures experimental design with 3 groups

  11. Error-associated behaviors and error rates for robotic geology

    NASA Technical Reports Server (NTRS)

    Anderson, Robert C.; Thomas, Geb; Wagner, Jacob; Glasgow, Justin

    2004-01-01

    This study explores human error as a function of the decision-making process. One of many models for human decision-making is Rasmussen's decision ladder [9]. The decision ladder identifies the multiple tasks and states of knowledge involved in decision-making. The tasks and states of knowledge can be classified by the level of cognitive effort required to make the decision, leading to the skill, rule, and knowledge taxonomy (Rasmussen, 1987). Skill based decisions require the least cognitive effort and knowledge based decisions require the greatest cognitive effort. Errors can occur at any of the cognitive levels.

  12. Unbounded Error Quantum Query Complexity

    E-print Network

    Ashley Montanaro; Harumichi Nishimura; Rudy Raymond

    2007-12-10

    This work studies the quantum query complexity of Boolean functions in a scenario where it is only required that the query algorithm succeeds with a probability strictly greater than 1/2. We show that, just as in the communication complexity model, the unbounded error quantum query complexity is exactly half of its classical counterpart for any (partial or total) Boolean function. Moreover, we show that the "black-box" approach to convert quantum query algorithms into communication protocols by Buhrman-Cleve-Wigderson [STOC'98] is optimal even in the unbounded error setting. We also study a setting related to the unbounded error model, called the weakly unbounded error setting, where the cost of a query algorithm is given by q+log(1/2(p-1/2)), where q is the number of queries made and p>1/2 is the success probability of the algorithm. In contrast to the case of communication complexity, we show a tight Theta(log n) separation between quantum and classical query complexity in the weakly unbounded error setting for a partial Boolean function. We also show the asymptotic equivalence between them for some well-studied total Boolean functions.

  13. Between-year variation in flowering and fruit set in frost-prone and frost-sheltered populations of dioecious Rubus chamaemorus

    Microsoft Academic Search

    Jon Ågren

    1988-01-01

    The flowering and fruiting patterns of the dioecious perennial herb Rubus chamaemorus L. were studied in frost-prone (open) and frost-sheltered (Shaded) habitats in northern Sweden over 6 years. The number of ramets with flower buds, the proportion of flower buds that opened, and fruit set varied markedly between years. In the frost-prone populations, the occurrence or absence of detrimental frosts

  14. Characterising the deal-proneness of consumers by analysis of price sensitivity and brand loyalty: an analysis in the retail environment

    Microsoft Academic Search

    Juan C. Gázquez-Abad; Manuel Sánchez-Pérez

    2009-01-01

    This study characterises the ‘deal-proneness’ of consumers by analysis of the consumer-level characteristics of price sensitivity and brand loyalty. The study first develops a multinomial logistic (MNL) latent class model suitable for use with universal product code (UPC) point-of-sale (hypermarket) scanner data. The model is then used to assess the deal-proneness of consumers with respect to monetary promotions (price reductions)

  15. Real-time PCR evaluation of Strongylus vulgaris in horses on farms in Denmark and Central Kentucky.

    PubMed

    Nielsen, M K; Olsen, S N; Lyons, E T; Monrad, J; Thamsborg, S M

    2012-12-21

    Strongyle parasites are ubiquitous in grazing horses, and the large strongyle Strongylus vulgaris is considered the most pathogenic helminth parasite of horses. Recent investigations have suggested an association between occurrence of this parasite and usage of selective therapy based on regular fecal egg counts. The established diagnostic method for S. vulgaris involves larval culture and subsequent morphological identification of third stage larvae under the microscope. Recently, a real-time PCR assay was developed and validated for the detection and semi-quantification of S. vulgaris eggs in equine fecal samples. The purposes of the present study were (a) to determine the presence of S. vulgaris by real-time PCR in Danish and American horses on farms using vastly different anthelmintic treatment regimens and (b) to evaluate the association between larval culture results and the PCR. A total of 991 horses representing 53 different horse farms in Denmark and Central Kentucky were studied. Fresh fecal samples were collected from all horses, and strongyle eggs retrieved for DNA extraction and subsequent real-time PCR analysis. Individual larval cultures were performed on the Danish part of the data set (663 horses on 42 farms). On the Danish farms, the S. vulgaris PCR prevalence was found to be 9.2% on farms not basing parasite control on fecal egg counts, and 14.1% on farms using selective therapy. No horses were PCR positive in the American part of the study (328 horses on 11 farms). Kappa-values indicated a moderate agreement between PCR and larval culture results, while McNemar tests revealed no statistical difference between the paired proportions. Significant associations were found between PCR cycle of threshold (Ct) value groups and larval culture counts. Results indicate that both diagnostic methods can be useful for determining the occurrence of S. vulgaris on horse farms, but that they both are affected by potential sources of error. The PCR results confirmed previous findings suggesting that S. vulgaris can reemerge under selective therapy regimens. PMID:22877828

  16. Constraint checking during error recovery

    NASA Technical Reports Server (NTRS)

    Lutz, Robyn R.; Wong, Johnny S. K.

    1993-01-01

    The system-level software onboard a spacecraft is responsible for recovery from communication, power, thermal, and computer-health anomalies that may occur. The recovery must occur without disrupting any critical scientific or engineering activity that is executing at the time of the error. Thus, the error-recovery software may have to execute concurrently with the ongoing acquisition of scientific data or with spacecraft maneuvers. This work provides a technique by which the rules that constrain the concurrent execution of these processes can be modeled in a graph. An algorithm is described that uses this model to validate that the constraints hold for all concurrent executions of the error-recovery software with the software that controls the science and engineering activities of the spacecraft. The results are applicable to a variety of control systems with critical constraints on the timing and ordering of the events they control.

  17. Cloned plasmid DNA fragments as calibrators for controlling GMOs: different real-time duplex quantitative PCR methods.

    PubMed

    Taverniers, Isabel; Van Bockstaele, Erik; De Loose, Marc

    2004-03-01

    Analytical real-time PCR technology is a powerful tool for implementation of the GMO labeling regulations enforced in the EU. The quality of analytical measurement data obtained by quantitative real-time PCR depends on the correct use of calibrator and reference materials (RMs). For GMO methods of analysis, the choice of appropriate RMs is currently under debate. So far, genomic DNA solutions from certified reference materials (CRMs) are most often used as calibrators for GMO quantification by means of real-time PCR. However, due to some intrinsic features of these CRMs, errors may be expected in the estimations of DNA sequence quantities. In this paper, two new real-time PCR methods are presented for Roundup Ready soybean, in which two types of plasmid DNA fragments are used as calibrators. Single-target plasmids (STPs) diluted in a background of genomic DNA were used in the first method. Multiple-target plasmids (MTPs) containing both sequences in one molecule were used as calibrators for the second method. Both methods simultaneously detect a promoter 35S sequence as GMO-specific target and a lectin gene sequence as endogenous reference target in a duplex PCR. For the estimation of relative GMO percentages both "delta C(T)" and "standard curve" approaches are tested. Delta C(T) methods are based on direct comparison of measured C(T) values of both the GMO-specific target and the endogenous target. Standard curve methods measure absolute amounts of target copies or haploid genome equivalents. A duplex delta C(T) method with STP calibrators performed at least as well as a similar method with genomic DNA calibrators from commercial CRMs. Besides this, high quality results were obtained with a standard curve method using MTP calibrators. This paper demonstrates that plasmid DNA molecules containing either one or multiple target sequences form perfect alternative calibrators for GMO quantification and are especially suitable for duplex PCR reactions. PMID:14689155

  18. Selection of reference genes for reverse transcription quantitative real-time PCR normalization in black rockfish (Sebastes schlegeli).

    PubMed

    Liman, Ma; Wenji, Wang; Conghui, Liu; Haiyang, Yu; Zhigang, Wang; Xubo, Wang; Jie, Qi; Quanqi, Zhang

    2013-09-01

    Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is a technique widely used for quantification of mRNA transcription. Data normalization is an indispensable process for RT-qPCR and reference genes are most commonly used to normalize RT-qPCR and to reduce possible errors generated in the quantification of genes among several proposed methods. To date, RT-qPCR has been used in terms of gene expression studies in black rockfish (Sebastes schlegeli) but the majority of published RT-qPCR studies still lack proper validation of the reference genes. In the present study, mRNA transcription profiles of eight putative reference genes (18S rRNA, ACTB, GAPDH, TUBA, RPL17, EF1A, HPRT, and B2M) were examined using RT-qPCR in different tissues and larvae developmental stages of black rockfish. Three common statistical algorithms (geNorm, NormFinder, and BestKeeper) were used to assess expression stability and select the most stable genes for gene normalization. Two reference genes, RPL17 and EF1A showed high stability in black rockfish tissue analysis, while GAPDH was the least stable gene. During larvae developmental stages, EF1A, RPL17 and ACTB were identified as the optimal reference genes for data normalization, whereas B2M appeared unsuitable as the reference gene. In summary, our results could provide a useful guideline for reference gene selection and enable more accurate normalization of gene expression data in gene expression studies of black rockfish. PMID:24007945

  19. Methods for delineating flood-prone areas in the Great Basin of Nevada and adjacent states

    USGS Publications Warehouse

    Burkham, D.E.

    1988-01-01

    The Great Basin is a region of about 210,000 square miles having no surface drainage to the ocean; it includes most of Nevada and parts of Utah, California, Oregon, Idaho, and Wyoming. The area is characterized by many parallel mountain ranges and valleys trending north-south. Stream channels usually are well defined and steep within the mountains, but on reaching the alluvial fan at the canyon mouth, they may diverge into numerous distributary channels, be discontinuous near the apex of the fan, or be deeply entrenched in the alluvial deposits. Larger rivers normally have well-defined channels to or across the valley floors, but all terminate at lakes or playas. Major floods occur in most parts of the Great Basin and result from snowmelt, frontal-storm rainfall, and localized convective rainfall. Snowmelt floods typically occur during April-June. Floods resulting from frontal rain and frontal rain on snow generally occur during November-March. Floods resulting from convective-type rainfall during localized thunderstorms occur most commonly during the summer months. Methods for delineating flood-prone areas are grouped into five general categories: Detailed, historical, analytical, physiographic, and reconnaissance. The detailed and historical methods are comprehensive methods; the analytical and physiographic are intermediate; and the reconnaissance method is only approximate. Other than the reconnaissance method, each method requires determination of a T-year discharge (the peak rate of flow during a flood with long-term average recurrence interval of T years) and T-year profile and the development of a flood-boundary map. The procedure is different, however, for each method. Appraisal of the applicability of each method included consideration of its technical soundness, limitations and uncertainties, ease of use, and costs in time and money. Of the five methods, the detailed method is probably the most accurate, though most expensive. It is applicable to hydraulic and topographic conditions found in many parts of the Great Basin. The historical method is also applicable over a wide range of conditions and is less expensive than the detailed method. However, it requires more historical flood data than are usually available, and experience and judgement are needed to obtain meaningful results. The analytical method is also less expensive than the detailed method and can be used over a wide range of conditions in which the T-year discharge can be determined directly. Experience, good judgement, and thorough knowledge of hydraulic principles are required to obtain adequate results, and the method has limited application in other than rigid-channel situations. The physiographic method is applicable to rigid-boundary channels and is less accurate than the detailed method. The reconnaissance method is relatively imprecise, but it may be the most rational method to use on alluvial fans or valley floors with discontinuous channels. In general, a comprehensive method is most suitable for use with rigid-bank streams in urban areas; only an approximate method seems justified in undeveloped areas.

  20. mtDNA and the origin of Caucasians: identification of ancient Caucasian-specific haplogroups, one of which is prone to a recurrent somatic duplication in the D-loop region.

    PubMed Central

    Torroni, A.; Lott, M. T.; Cabell, M. F.; Chen, Y. S.; Lavergne, L.; Wallace, D. C.

    1994-01-01

    mtDNA sequence variation was examined in 175 Caucasians from the United States and Canada by PCR amplification and high-resolution restriction-endonuclease analysis. The majority of the Caucasian mtDNAs were subsumed within four mtDNA lineages (haplogroups) defined by mutations that are rarely seen in Africans and Mongoloids. The sequence divergence of these haplogroups indicates that they arose early in Caucasian radiation and gave raise to modern European mtDNAs. Although ancient, none of these haplogroups is old enough to be compatible with a Neanderthal origin, suggesting that Homo sapiens sapiens displaced H. s. neanderthaliensis, rather than mixed with it. The mtDNAs of one of these haplogroups have a unique homoplasmic insertion between nucleotide pair (np) 573 and np 574, within the D-loop control region. This insertion makes these mtDNAs prone to a somatic mutation that duplicates a 270-bp portion of the D-loop region between np 309 and np 572. This finding suggests that certain nonpathogenic mtDNA mutations could predispose individuals to mtDNA rearrangements. Images Figure 3 Figure 4 PMID:7942855

  1. Statistical Reporting Errors and Collaboration on Statistical Analyses in Psychological Science

    PubMed Central

    Veldkamp, Coosje L. S.; Nuijten, Michèle B.; Dominguez-Alvarez, Linda; van Assen, Marcel A. L. M.; Wicherts, Jelte M.

    2014-01-01

    Statistical analysis is error prone. A best practice for researchers using statistics would therefore be to share data among co-authors, allowing double-checking of executed tasks just as co-pilots do in aviation. To document the extent to which this ‘co-piloting’ currently occurs in psychology, we surveyed the authors of 697 articles published in six top psychology journals and asked them whether they had collaborated on four aspects of analyzing data and reporting results, and whether the described data had been shared between the authors. We acquired responses for 49.6% of the articles and found that co-piloting on statistical analysis and reporting results is quite uncommon among psychologists, while data sharing among co-authors seems reasonably but not completely standard. We then used an automated procedure to study the prevalence of statistical reporting errors in the articles in our sample and examined the relationship between reporting errors and co-piloting. Overall, 63% of the articles contained at least one p-value that was inconsistent with the reported test statistic and the accompanying degrees of freedom, and 20% of the articles contained at least one p-value that was inconsistent to such a degree that it may have affected decisions about statistical significance. Overall, the probability that a given p-value was inconsistent was over 10%. Co-piloting was not found to be associated with reporting errors. PMID:25493918

  2. Perfect Quantum Error Correcting Code

    SciTech Connect

    Laflamme, R.; Miquel, C.; Paz, J.P.; Zurek, W.H. [Theoretical Astrophysics, T-6, MS B288, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)] [Theoretical Astrophysics, T-6, MS B288, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); [Departamento de Fisica, FCEyN, Pabellon 1, Ciudad Universitaria, 1428 Buenos Aires (Argentina)

    1996-07-01

    We present a quantum error correction code which protects a qubit of information against general one qubit errors. To accomplish this, we encode the original state by distributing quantum information over five qubits, the minimal number required for this task. We describe a circuit which takes the initial state with four extra qubits in the state {vert_bar}0{r_angle} to the encoded state. It can also be converted into a decoder by running it backward. The original state of the encoded qubit can then be restored by a simple unitary transformation. {copyright} {ital 1996 The American Physical Society.}

  3. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes

    PubMed Central

    Vandesompele, Jo; De Preter, Katleen; Pattyn, Filip; Poppe, Bruce; Van Roy, Nadine; De Paepe, Anne; Speleman, Frank

    2002-01-01

    Background Gene-expression analysis is increasingly important in biological research, with real-time reverse transcription PCR (RT-PCR) becoming the method of choice for high-throughput and accurate expression profiling of selected genes. Given the increased sensitivity, reproducibility and large dynamic range of this methodology, the requirements for a proper internal control gene for normalization have become increasingly stringent. Although housekeeping gene expression has been reported to vary considerably, no systematic survey has properly determined the errors related to the common practice of using only one control gene, nor presented an adequate way of working around this problem. Results We outline a robust and innovative strategy to identify the most stably expressed control genes in a given set of tissues, and to determine the minimum number of genes required to calculate a reliable normalization factor. We have evaluated ten housekeeping genes from different abundance and functional classes in various human tissues, and demonstrated that the conventional use of a single gene for normalization leads to relatively large errors in a significant proportion of samples tested. The geometric mean of multiple carefully selected housekeeping genes was validated as an accurate normalization factor by analyzing publicly available microarray data. Conclusions The normalization strategy presented here is a prerequisite for accurate RT-PCR expression profiling, which, among other things, opens up the possibility of studying the biological relevance of small expression differences. PMID:12184808

  4. Mapping flood prone areas in southern Brazil: a combination of frequency analysis, HAND algorithm and remote sensing methods

    NASA Astrophysics Data System (ADS)

    Fabris Goerl, Roberto; Borges Chaffe, Pedro Luiz; Marcel Pellerin, Joel Robert; Altamirano Flores, Juan Antonio; Josina Abreu, Janete; Speckhann, Gustavo Andrei; Mattos Sanchez, Gerly

    2015-04-01

    Floods disaster damages several people around the world. There is a worldwide increasing trend of natural disasters frequency and their negative impacts related to the population growth and high urbanization in natural hazards zones. In Santa Catarina state, such as almost all southern Brazilian territory, floods are a frequent hydrological disaster. In this context, flood prone areas map is a important tool to avoid the construction of new settlements in non-urbanizations areas. The present work aimed to map flood prone areas in Palhoça City, Southern Brazil combining high resolution digital elevations data, remote sensing information, frequency analysis and High Above Nearest Drainage (HAND) algorithm. We used 17 years of daily discharge and stage data to calculate flood probability and return period. Remote Sensing (RS) with CBERS HRC image with 2,7m resolution was used. This image was taken one day after one flood occurrence and a band difference was used to extract the flood extent. HAND using DEM to calculate the altimetric difference between channel pixel and adjacent terrain values. All morphometric attributes used in HAND were extracted directly from the high resolution DEM (1m). Through CBERS image areas where flood level was higher than 0.5m were mapped. There is some kind of uncertain in establish HAND classes, since only distance to the channel was take in account. Thus, using other hydrological or spatial information can reduce this uncertain. To elaborate the final flood prone map, all this methods were combined. This map was classified in three main classes based on return period. It was notices that there is a strong spatial correlation between high susceptibility flood areas and geomorphological features like floodplains and Holocene beach ridges, places where water table emerges frequently. The final map was classified using three different colors (red, yellow and green) related to high, medium an law susceptibility flood areas. This mapping technique can be applied on flood zonation to avoid urbanization without planning.

  5. The PRONE score: an algorithm for predicting doctors’ risks of formal patient complaints using routinely collected administrative data

    PubMed Central

    Spittal, Matthew J; Bismark, Marie M; Studdert, David M

    2015-01-01

    Background Medicolegal agencies—such as malpractice insurers, medical boards and complaints bodies—are mostly passive regulators; they react to episodes of substandard care, rather than intervening to prevent them. At least part of the explanation for this reactive role lies in the widely recognised difficulty of making robust predictions about medicolegal risk at the individual clinician level. We aimed to develop a simple, reliable scoring system for predicting Australian doctors’ risks of becoming the subject of repeated patient complaints. Methods Using routinely collected administrative data, we constructed a national sample of 13?849 formal complaints against 8424 doctors. The complaints were lodged by patients with state health service commissions in Australia over a 12-year period. We used multivariate logistic regression analysis to identify predictors of subsequent complaints, defined as another complaint occurring within 2?years of an index complaint. Model estimates were then used to derive a simple predictive algorithm, designed for application at the doctor level. Results The PRONE (Predicted Risk Of New Event) score is a 22-point scoring system that indicates a doctor's future complaint risk based on four variables: a doctor's specialty and sex, the number of previous complaints and the time since the last complaint. The PRONE score performed well in predicting subsequent complaints, exhibiting strong validity and reliability and reasonable goodness of fit (c-statistic=0.70). Conclusions The PRONE score appears to be a valid method for assessing individual doctors’ risks of attracting recurrent complaints. Regulators could harness such information to target quality improvement interventions, and prevent substandard care and patient dissatisfaction. The approach we describe should be replicable in other agencies that handle large numbers of patient complaints or malpractice claims. PMID:25855664

  6. Unusual effects of some vegetable oils on the survival time of stroke-prone spontaneously hypertensive rats

    Microsoft Academic Search

    Min-Zhao Huang; Shiro Watanabe; Tetsuyuki Kobayashi; Akito Nagatsu; Jinsaku Sakakibara; Harumi Okuyama

    1997-01-01

    Preliminary experiments have shown that a diet containing 10% rapeseed oil (low-erucic acid) markedly shortens the survival\\u000a time of stroke-prone spontaneously hypertensive (SHRSP) rats under 1% NaCl loading as compared with diets containing perilla\\u000a oil or soybean oil. High-oleate safflower oil and high-oleate sunflower oil were found to have survival time-shortening activities\\u000a comparable to that of rapeseed oil; olive oil

  7. General and scalable amide bond formation with epimerization-prone substrates using T3P and pyridine.

    PubMed

    Dunetz, Joshua R; Xiang, Yanqiao; Baldwin, Aaron; Ringling, Justin

    2011-10-01

    The mild combination of T3P (n-propanephosphonic acid anhydride) and pyridine has been developed for low-epimerization amide bond formation and implemented for the synthesis of a key intermediate to a glucokinase activator. This robust method is general for the coupling of various racemization-prone acid substrates and amines, including relatively non-nucleophilic anilines, and provides amides in high yields with very low epimerization. With easy reaction setup and product isolation, this protocol offers several practical and experimental benefits. PMID:21875100

  8. Genotyping errors in a calibrated DNA register: implications for identification of individuals

    PubMed Central

    2011-01-01

    Background The use of DNA methods for the identification and management of natural resources is gaining importance. In the future, it is likely that DNA registers will play an increasing role in this development. Microsatellite markers have been the primary tool in ecological, medical and forensic genetics for the past two decades. However, these markers are characterized by genotyping errors, and display challenges with calibration between laboratories and genotyping platforms. The Norwegian minke whale DNA register (NMDR) contains individual genetic profiles at ten microsatellite loci for 6737 individuals captured in the period 1997-2008. These analyses have been conducted in four separate laboratories for nearly a decade, and offer a unique opportunity to examine genotyping errors and their consequences in an individual based DNA register. We re-genotyped 240 samples, and, for the first time, applied a mixed regression model to look at potentially confounding effects on genotyping errors. Results The average genotyping error rate for the whole dataset was 0.013 per locus and 0.008 per allele. Errors were, however, not evenly distributed. A decreasing trend across time was apparent, along with a strong within-sample correlation, suggesting that error rates heavily depend on sample quality. In addition, some loci were more error prone than others. False allele size constituted 18 of 31 observed errors, and the remaining errors were ten false homozygotes (i.e., the true genotype was a heterozygote) and three false heterozygotes (i.e., the true genotype was a homozygote). Conclusions To our knowledge, this study represents the first investigation of genotyping error rates in a wildlife DNA register, and the first application of mixed models to examine multiple effects of different factors influencing the genotyping quality. It was demonstrated that DNA registers accumulating data over time have the ability to maintain calibration and genotyping consistency, despite analyses being conducted on different genotyping platforms and in different laboratories. Although errors were detected, it is demonstrated that if the re-genotyping of individual samples is possible, these will have a minimal effect on the database's primary purpose, i.e., to perform individual identification. PMID:21507252

  9. Diagnostic multiplex PCR for toxin genotyping of Clostridium perfringens isolates

    Microsoft Academic Search

    Christoph G Baums; Ulrich Schotte; Gunter Amtsberg; Ralph Goethe

    2004-01-01

    In this study we provide a protocol for genotyping Clostridium perfringens with a new multiplex PCR. This PCR enables reliable and specific detection of the toxin genes cpa, cpb, etx, iap, cpe and cpb2 from heat lysed bacterial suspensions. The efficiency of the protocol was demonstrated by typing C. perfringens reference strains and isolates from veterinary bacteriological routine diagnostic specimens.

  10. Diagnostic multiplex PCR for toxin genotyping of Clostridium perfringens isolates.

    PubMed

    Baums, Christoph G; Schotte, Ulrich; Amtsberg, Gunter; Goethe, Ralph

    2004-05-20

    In this study we provide a protocol for genotyping Clostridium perfringens with a new multiplex PCR. This PCR enables reliable and specific detection of the toxin genes cpa, cpb, etx, iap, cpe and cpb2 from heat lysed bacterial suspensions. The efficiency of the protocol was demonstrated by typing C. perfringens reference strains and isolates from veterinary bacteriological routine diagnostic specimens. PMID:15135508

  11. Multiplex PCR for the identification of white Tuber species

    Microsoft Academic Search

    Antonella Amicucci; Chiara Guidi; Alessandra Zambonelli; Lucia Potenza; Vilberto Stocchi

    2000-01-01

    Species-specific primers selected from the internal transcribed spacer region sequence were used to set up a multiplex polymerase chain reaction (PCR) able to simultaneously identify the white truffle species Tuber magnatum, Tuber borchii, Tuber maculatum and Tuber puberulum. Furthermore, a primer specific for the competitive fungus Sphaerosporella brunnea was designed and added to the multiplex PCR set, allowing the detection

  12. Bose 4/2004 Cloning PCR fragments into TOPO vectors

    E-print Network

    Doering, Tamara

    Bose 4/2004 Cloning PCR fragments into TOPO vectors Overview: This is to facilitate the cloning cloning kit has enough for 20 reactions. Each kit contains the following reagents: 20 µl vector, 100 µl as fragments that have been stored for a week or more may not clone well.] 2. Purify the PCR fragment

  13. Quantitative RT-PCR for measuring gene expression.

    PubMed

    Riedy, M C; Timm, E A; Stewart, C C

    1995-01-01

    Classical Northern blot analysis for measuring mRNA requires too many cells to be practical for cell sorting. Yet, measurement of gene expression in small subsets within a heterogeneous population of cells is often desired. The PCR in combination with prior reverse transcription (RT-PCR) of the mRNA of interest provides a means for measuring gene expression using as few as one cell. When RT-PCR is performed, the reliability of the data can be highly subjective due to the efficiency of both RT and PCR steps. This subjectivity can be eliminated by a technique for quantitating specific RNA molecules using an internal RNA competitive reference standard (RNA-CRS), which is identical to the sequence of interest except for a deletion of 80 bases. Here we illustrate a strategy for quantitative PCR using a RNA-CRS, synthesized solely using nonplasmid-based PCR techniques. The competitive reaction consists of a constant quantity of wild-type mRNA (from 100-1000 cells) added individually to tubes containing a serially decreasing amount of RNA-CRS. The RT-PCR is performed on these samples, then the resulting product is analyzed by gel electrophoresis and densitometry. The procedure for preparing the RNA-CRS and subsequent RT-PCR steps are described in detail. PMID:7702857

  14. Genetic relationships among strains of Xanthomonas fragariae based on random amplified polymorphic DNA PCR, repetitive extragenic palindromic PCR, and enterobacterial repetitive intergenic consensus PCR data and generation of multiplexed PCR primers useful for the identification of this phytopathogen.

    PubMed Central

    Pooler, M R; Ritchie, D F; Hartung, J S

    1996-01-01

    Genetic relationships among 25 isolates of Xanthomonas fragariae from diverse geographic regions were determined by three PCR methods that rely on different amplification priming strategies: random amplified polymorphic DNA (RAPD) PCR, repetitive extragenic palindromic (REP) PCR, and enterobacterial repetitive intergenic consensus (ERIC) PCR. The results of these assays are mutually consistent and indicate that pathogenic strains are very closely related to each other. RAPD, ERIC, and REP PCR assays identified nine, four, and two genotypes, respectively, within X. fragariae isolates. A single nonpathogenic isolate of X. fragariae was not distinguishable by these methods. The results of the PCR assays were also fully confirmed by physiological tests. There was no correlation between DNA amplification product patterns and geographic sites of isolation, suggesting that this bacterium has spread largely through exchange of infected plant germ plasm. Sequences identified through the RAPD assays were used to develop three primer pairs for standard PCR assays to identify X. fragariae. In addition, we developed a stringent multiplexed PCR assay to identify X. fragariae by simultaneously using the three independently derived sets of primers specific for pathogenic strains of the bacteria. PMID:8795198

  15. ANIMAL DNA IN PCR REAGENTS PLAGUES ANCIENT DNA RESEARCH

    EPA Science Inventory

    Ancient DNA analysis is becoming widespread. These studies use polymerase chain reaction (PCR) to amplify minute quantities of heavily damaged template. Unusual steps are taken to achieve the sensitivity necessary to detect ancient DNA, including high-cycle PCR amplification targ...

  16. Interlaboratory Comparison of Quantitative PCR Test Results for Dehalococcoides

    EPA Science Inventory

    Quantitative PCR (qPCR) techniques have been widely used to measure Dehalococcoides (Dhc) DNA in the groundwater at field sites for several years. Interpretation of these data may be complicated when different laboratories using alternate methods conduct the analysis. An...

  17. PCR as a diagnostic and quantitative technique in veterinary parasitology

    Microsoft Academic Search

    Dante S. Zarlenga; James Higgins

    2001-01-01

    Over the past 15 years, there has been a dramatic evolution in molecular approaches to study parasites and parasitic diseases. Many of these advancements have been brought about through the development of new applications of the polymerase chain reaction (PCR). Enhancements in sensitivity that can be achieved using PCR now permit scientists to investigate changes at the level of a

  18. Applications of Competitor RNA in Diagnostic Reverse Transcription-PCR

    Microsoft Academic Search

    Steven B. Kleiboeker

    2003-01-01

    Detection of RNA viruses by reverse transcription (RT)-PCR has proven to be a useful approach for the diagnosis of infections caused by many viral pathogens. However, adequate controls are required for each step of the RT-PCR protocol to ensure the accuracies of diagnostic test results. Heterologous competitor RNA can be used as a control for a number of different aspects

  19. PCR-based cost-effective sequencing Name: Changjun Wu

    E-print Network

    Krishnamoorthy, Bala

    1 PCR-based cost-effective sequencing Name: Changjun Wu WSU ID: 10949637 Course: Math 574 #12;2 1. Preliminary re- sults on five plastomes in the Solanaceae family demonstrate the high effectiveness of our and experimentally effective framework to enable the use of PCR technology for sequencing arbitrarily long DNA

  20. SENSITIVITY TO MOTOR ERROR IN CHILDREN WITH

    E-print Network

    Shadmehr, Reza

    SENSITIVITY TO MOTOR ERROR IN CHILDREN WITH AUTISM by Mollie Marko A dissertation submitted movements. How much the brain adapts to error is governed by its sensitivity. Computationally, sensitivity as an increased sensitivity to proprioceptive error and a decreased sensitivity to visual error. Further, we